From wparker at mps.ohio-state.edu Tue Sep 1 01:24:19 2009 From: wparker at mps.ohio-state.edu (William Parker) Date: Mon, 31 Aug 2009 19:24:19 -0400 (EDT) Subject: [Pw_forum] cohesive energy In-Reply-To: References: Message-ID: Hi Udayaghiri, Please indicate your affiliation (and preferred name). My suggestions are: 1) Converge the k-point mesh better for the solid. V is a metal and probably needs more than 8x8x8. 2) Check the energy cutoff convergence on the pseudo-atom. I find that I need more plane waves to describe it than the solid for a given pseudopotential. --William ====================================================================== William Parker Tel : +1 (614) 292-2887 Graduate Research Associate Fax : +1 (614) 292-7557 Ohio State University Department of Physics 191 West Woodruff Avenue email: wparker at mps.ohio-state.edu Columbus, OH 43210-1117 http://www.physics.ohio-state.edu/~wparker U.S.A. Office: 2025 Physics Research Building ====================================================================== On Mon, 31 Aug 2009, udayagiri sai babu wrote: > Hi all > i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom > against an experimental value of 5.3 ev/atom which is almost 50% off can > anybody say what is going wrong with the calculation. the method i used is > calculate the total energy of a bcc crystal with 1 atom and deduct the > energy of isolated atom from it. the following input files are for finding > the total energy for isolated atom and the atom in the crystal. Please tell > me if my methodology is wrong. > > *cohesive energy=E per atom (in the crystal)-E per atom (isolated)* > > *input file for finding the total energy of an isolated atom* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=30, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > *input file for finding the total energy of the atom in the crystal* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > From w2agz at pacbell.net Tue Sep 1 06:14:41 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Mon, 31 Aug 2009 21:14:41 -0700 Subject: [Pw_forum] Generalized "Linhard-Like" Dielectric Function Message-ID: <000501ca2aba$bcc08e20$3641aa60$@net> I?m a frequent user of Andrea Banassi?s epsilon.x. However, the present version of the code addresses only epsilon(0, omega), whereas I need for a current project something like epsilon(q, omega + i eta). I?m in the process of recoding epsilon.f90 to accommodate q>0, but have noticed that the formalism (i.e. ?algebra?) is contained in Banassi?s thesis. So, has this recoding already been done by someone? Footnote when the eigenstates of a particular system are ?localized,? e.g., a PWscf calculation of a ?monolayer? where the 3D plane wave representation includes a large-real-space ?unit cell? in the ?perpendicular? direction, my na?ve assumption is that some sort of modification to epsilon according to Clausius-Mossott is in order have others in the PWscf community encountered this issue? Paul M. Grant, PhD Physicist and Science Writer Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/c2841e3f/attachment.htm From w2agz at pacbell.net Tue Sep 1 06:24:07 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Mon, 31 Aug 2009 21:24:07 -0700 Subject: [Pw_forum] Kirzhnits, Maximov, Khomskii Message-ID: <000a01ca2abc$0dad2630$29077290$@net> The Kirzhnits, Maximov, Khomskii formalism has long been recognized as a more viable alternative as a weak-coupling model for BCS superconductivity with respect to Eliashberg-McMillan in that it directly employs the overall charge density and eigenstates of a given extended quantum ensemble, rather than their second derivative. Has anyone in the community coded KMK as a post-processor for PWscf output? Paul M. Grant, PhD Physicist and Science Writer Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/e90dcb78/attachment.htm From elbuesta at icqmail.com Tue Sep 1 06:40:07 2009 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Tue, 01 Sep 2009 00:40:07 -0400 Subject: [Pw_forum] calculating cohesive energy In-Reply-To: References: Message-ID: <8CBF8D56AC51A51-1A80-2CD9B@webmail-d054.sysops.aol.com> I calculated some time ago some bulk properties of Vanadium using the same PP you used and I obtained the following: Isolated: -27.260Ry Bulk: -27.666Ry (a=5.675) Cohesive energy: 5.52eV/atom Predicted equilibrium lat. param.: 3.00angstrom (Experimental is 3.03, I think) The equilibrium values are well reproduced. I don't remember (I don't have the inputs with me) exactly all the details, but the difference is probably related to the fact that spin has to be included for the isolated atom, as already mentioned by other PW users. All best. P.S: Sorry for sending two e-mails. F?bio Negreiros Ribeiro PHd student - Departamento de F?sica - Universidade Federal de Minas Gerais Belo Horizonte - MG - Brazil -----Original Message----- From: udayagiri sai babu To: pw_forum at pwscf.org Sent: Mon, Aug 31, 2009 8:37 pm Subject: [Pw_forum] calculating cohesive energy Hi all i am claculating cohesive energy of V using pwscf but i got -8.15 ev/atom against an experimental value of 5.3 ev/atom which is almost 50% off can anybody say what is going wrong with the calculation. the method i used is calculate the total energy of a bcc crystal with 1 atom and deduct the energy of isolated atom from it. the following input files are for finding the total energy for isolated atom and the atom in the crystal. Please tell me if my methodology is wrong. cohesive energy=E per atom (in the crystal)-E per atom (isolated) inpu t file for finding the total energy of an isolated atom &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=1 celldm(1)=30, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', ? mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V? 50.9415? V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V?????? 0.00000000????? 0.00000000????? 0.00000000 K_POINTS {automatic} 1 1 1 0 0 0 input file for finding the total energy of the atom in the crystal &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='vanadium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=3 celldm(1)=5.654, nat=1, ntyp=1 ecutwfc=25, ecutrho=100, occupations='smearing', smearing='mv', degauss=0.010000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 / ATOMIC_SPECIES V? 50.9415? V.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) V?????? 0.00000000????? 0.00000000?????200.00000000 K_POINTS {aut omatic} 8 8 8 0 0 0_______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From udayagiri3 at gmail.com Tue Sep 1 07:41:19 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Tue, 1 Sep 2009 11:11:19 +0530 Subject: [Pw_forum] calculating cohesive energy In-Reply-To: <8CBF8D56AC51A51-1A80-2CD9B@webmail-d054.sysops.aol.com> References: <8CBF8D56AC51A51-1A80-2CD9B@webmail-d054.sysops.aol.com> Message-ID: Thanks guys ,i got the cohesive energy by including the spin in my input file. On Tue, Sep 1, 2009 at 10:10 AM, wrote: > I calculated some time ago some bulk properties of Vanadium using the > same PP you used and I obtained the following: > > Isolated: -27.260Ry > Bulk: -27.666Ry (a=5.675) > Cohesive energy: 5.52eV/atom > Predicted equilibrium lat. param.: 3.00angstrom (Experimental is 3.03, > I think) > > The equilibrium values are well reproduced. > I don't remember (I don't have the inputs with me) exactly all the > details, but the difference is probably related to the fact that spin > has to be included for the isolated atom, as already mentioned by other > PW users. > > All best. > > P.S: Sorry for sending two e-mails. > > F?bio Negreiros Ribeiro > PHd student - Departamento de F?sica - Universidade Federal de Minas > Gerais > Belo Horizonte - MG - Brazil > > -----Original Message----- > From: udayagiri sai babu > To: pw_forum at pwscf.org > Sent: Mon, Aug 31, 2009 8:37 pm > Subject: [Pw_forum] calculating cohesive energy > > Hi all > i am claculating cohesive energy of V using pwscf but i got > -8.15 ev/atom against an experimental value of 5.3 ev/atom which is > almost 50% off can anybody say what is going wrong with the > calculation. the method i used is calculate the total energy of a bcc > crystal with 1 atom and deduct the energy of isolated atom from it. the > following input files are for finding the total energy for isolated > atom and the atom in the crystal. Please tell me if my methodology is > wrong. > > > cohesive energy=E per atom (in the crystal)-E > per atom (isolated) > > inpu > t file for finding the total energy of an isolated atom > > &control > calculation = 'scf', > restart_mode='from_scratch', > > > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > > ibrav=1 > celldm(1)=30, > > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > > > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > input file for finding the total energy of the atom in the crystal > > > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > > > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > > > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 200.00000000 > > > K_POINTS {aut > omatic} > 8 8 8 0 0 0_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/19f541cf/attachment-0001.htm From sagarambavale at yahoo.co.in Tue Sep 1 08:05:10 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Tue, 1 Sep 2009 11:35:10 +0530 (IST) Subject: [Pw_forum] calculating cohesive energy In-Reply-To: References: Message-ID: <840336.21900.qm@web94602.mail.in2.yahoo.com> Hi, One more thing, use ecutrho= ecutwfc*(8or10) for ultrsoft pseudopotentials. Regards S.K. Ambavale Phd student M.S. Uni. of Baroda India > *input file for finding the total energy of an isolated atom* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=30, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 1 1 1 0 0 0 > > *input file for finding the total energy of the atom in the crystal* > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='vanadium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.654, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=100, > occupations='smearing', > smearing='mv', > degauss=0.010000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.3 > / > ATOMIC_SPECIES > V 50.9415 V.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > V 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 8 8 8 0 0 0 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090831/c2a9415e/attachment.htm ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 26, Issue 82 **************************************** See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/4512703a/attachment.htm From siyouber at yahoo.fr Tue Sep 1 10:18:36 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 1 Sep 2009 01:18:36 -0700 (PDT) Subject: [Pw_forum] Re : Re:Pseudopotential for Li Message-ID: <340630.63429.qm@web26507.mail.ukl.yahoo.com> Dear Lorenzo, Dear all I tried to regenerate the pseudopotential "Li.pw91-s-van_ak.UPF" using the human readable section in the head if the file. But I got the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from ld1_readin : error #???????? 1 ???? unbound states must be empty ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... I dont know more about the unbound state causing the problem. My input file, constructed using the information from the pseudo file is the following: &input ?? title ='AE for Li ion' ?? zed =3, ?? iswitch =3, ?? dft ='PW91' ?? prefix='Li' ?? config ='1s2.00 2s0.80 2p0.20' / &inputp pseudotype=3, rcloc=1.1000 file_pseudopw='Li.UPF' author='Sitamtze' / 3 1S? 1? 0? 2.00?? -3.84792392914?? 0.75000000000????? 1.10000000000???? 2S? 2? 0? 0.80?? -0.22057651078?? 0.75000000000????? 1.10000000000???? 2P? 2? 1? 0.20?? -0.08952793836?? 0.75000000000????? 1.10000000000???? Waiting for your help ************************ Bertrand SITAMTZE PhD student Department of physics University of Yaounde I-Cameroon ************************* --- En date de?: Jeu 27.8.09, Bertrand SITAMTZE a ?crit?: De: Bertrand SITAMTZE Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Jeudi 27 Ao?t 2009, 12h47 Dear Lorenzo, Thank very much for the hints --- En date de?: Jeu 27.8.09, Lorenzo Paulatto a ?crit?: De: Lorenzo Paulatto Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Jeudi 27 Ao?t 2009, 11h10 In data 27 agosto 2009 alle ore 10:33:06, Bertrand SITAMTZE? ha scritto: > I wanted to use the Li.pw91-s-van_ak.UPF. But, as we all know, this has? > to be tested. Normally pps from the quantum-espresso page have already been tested, and? often used in some published work. Yet, doing some extra testing is always? a good idea. > That is why I decided to generate a pseudopotential by myself. Do you? > know about this regeneration process? A good point to start to generate a new pp is an old one. At the begging? of the UPF file there is a short human-readable section where you can find? most of the parameters used to generate the file. The reference energy for? the second projector are actually missing, but you can usually find them? easily. > I used the default value From the manual: ???If not specified, the matching radius is determined ???by the condition:? rho_core(rcore) = 2*rho_valence(rcore) in you specific case it is probably too small. Furthermore, the pp you are trying to imitate includes the 1s electrons in? valence: it is practically an all-electron pseudopotential. Hence, it has? no core charge. Generating a pseudopotential for Lithium with only the 2s? electron in valence, using core-charge correction, can be quite difficult;? furthermore the result won't probably be very accurate. Nevertheless, it? will also be much softer (it requires a much lower cutoff). best regards -- Lorenzo Paulatto SISSA? &? DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www:???http://people.sissa.it/~paulatto/ ? ???*** save italian brains *** ? http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum start: 2008-09-03 end: 0000-00-00 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/85ff9d41/attachment.htm From paulatto at sissa.it Tue Sep 1 10:25:59 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 01 Sep 2009 10:25:59 +0200 Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: <340630.63429.qm@web26507.mail.ukl.yahoo.com> References: <340630.63429.qm@web26507.mail.ukl.yahoo.com> Message-ID: In data 01 settembre 2009 alle ore 10:18:36, Bertrand SITAMTZE ha scritto: > 1S 1 0 2.00 -3.84792392914 0.75000000000 1.10000000000 2S > 2 0 0.80 -0.22057651078 0.75000000000 1.10000000000 2P 2 > 1 0.20 -0.08952793836 0.75000000000 1.10000000000 Dear Betrand, if you want to use the eigenvalue energy for a reference orbital you don't have to copy it from the all-electron calculation: just use 0.00 instead and it will work. Also note that doing an ultrasoft pseudopotential you'll need at least two reference wavefunctions per value of l. In your specific case I would use 2 2s and 2 2p but only one 1s (it has the same l as 2s). best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From siyouber at yahoo.fr Tue Sep 1 12:11:33 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 1 Sep 2009 03:11:33 -0700 (PDT) Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: Message-ID: <2267.41597.qm@web26501.mail.ukl.yahoo.com> Hi Lorenzo, I ran the regeneration using the 0.00 energies and the error didn't occurs as expected. But I got one warning about the reference state: !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! ???? Message from routine ld1_readin: ???? US requires at least two energies per channel 2P ???? !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ???? --------------------------- All-electron run ---------------------------- Please, I would like you to help with the section concerning the 1 1S, 2 2S and 2 2P reference states. I mean, what should I put in the following section? / 3 1S? 1? 0? 2.00?? 0.00?? 0.75000000000????? 1.10000000000 2S? 2? 0? 0.80?? 0.00?? 0.75000000000????? 1.10000000000 2P? 2? 1? 0.20?? 0.00?? 0.75000000000????? 1.10000000000 Thanks one again for your help ********************************** Bertrand SITAMTZE PhD student Department of physics University of Yaound? I-Cameroon ********************************** --- En date de?: Mar 1.9.09, Lorenzo Paulatto a ?crit?: De: Lorenzo Paulatto Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Mardi 1 Septembre 2009, 10h25 In data 01 settembre 2009 alle ore 10:18:36, Bertrand SITAMTZE? ha scritto: > 1S? 1? 0? 2.00???-3.84792392914???0.75000000000? ? ? 1.10000000000???2S??? > 2? 0? 0.80???-0.22057651078???0.75000000000? ? ? 1.10000000000???2P? 2??? > 1? 0.20???-0.08952793836???0.75000000000? ? ? 1.10000000000 Dear Betrand, if you want to use the eigenvalue energy for a reference orbital you don't? have to copy it from the all-electron calculation: just use 0.00 instead? and it will work. Also note that doing an ultrasoft pseudopotential you'll need at least two? reference wavefunctions per value of l. In your specific case I would use? 2 2s and 2 2p but only one 1s (it has the same l as 2s). best regards -- Lorenzo Paulatto SISSA? &? DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www:???http://people.sissa.it/~paulatto/ ? ???*** save italian brains *** ? http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/13f4309e/attachment.htm From paulatto at sissa.it Tue Sep 1 12:16:56 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 01 Sep 2009 12:16:56 +0200 Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: <2267.41597.qm@web26501.mail.ukl.yahoo.com> References: <2267.41597.qm@web26501.mail.ukl.yahoo.com> Message-ID: In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE ha scritto: > Please, I would like you to help with the section concerning the 1 1S, 2 > 2S and 2 2P reference states. I mean, what should I put in the following > section? That's exactly what I told you in the other email: you need two reference wavefunction per value of l e.g. you could do something like this: 5 1S 1 0 2.00 0.00 0.75000000000 1.10000000000 2S 2 0 0.80 0.00 0.75000000000 1.10000000000 2S 2 0 0.00 0.10 0.75000000000 1.10000000000 2P 2 1 0.20 0.00 0.75000000000 1.10000000000 2P 2 1 0.00 0.10 0.75000000000 1.10000000000 for the second reference (that one that does not have the eigenvalue energy) occupation must be zero. The reference energy (in my example 0.10) has to be chosen by testing and error; it will likely be in the range -0.20 to 1.0 best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From siyouber at yahoo.fr Tue Sep 1 12:30:35 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 1 Sep 2009 03:30:35 -0700 (PDT) Subject: [Pw_forum] Re : Re:Pseudopotential for Li In-Reply-To: Message-ID: <631161.68256.qm@web26508.mail.ukl.yahoo.com> This time is OK despite the anomalous behavior of the 2P pseudo state. I hope the testing and error procedure will cure it. Best regards ********************************** Bertrand SITAMTZE PhD student Department of physics University of Yaound? I-Cameroon ********************************** --- En date de?: Mar 1.9.09, Lorenzo Paulatto a ?crit?: De: Lorenzo Paulatto Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Mardi 1 Septembre 2009, 12h16 In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE? ha scritto: > Please, I would like you to help with the section concerning the 1 1S, 2? > 2S and 2 2P reference states. I mean, what should I put in the following? > section? That's exactly what I told you in the other email: you need two reference? wavefunction per value of l e.g. you could do something like this: 5 1S? 1? 0? 2.00???0.00???0.75000000000? ? ? 1.10000000000 2S? 2? 0? 0.80???0.00???0.75000000000? ? ? 1.10000000000 2S? 2? 0? 0.00???0.10???0.75000000000? ? ? 1.10000000000 2P? 2? 1? 0.20???0.00???0.75000000000? ? ? 1.10000000000 2P? 2? 1? 0.00???0.10???0.75000000000? ? ? 1.10000000000 for the second reference (that one that does not have the eigenvalue? energy) occupation must be zero. The reference energy (in my example 0.10)? has to be chosen by testing and error; it will likely be in the range? -0.20 to 1.0 best regards -- Lorenzo Paulatto SISSA? &? DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www:???http://people.sissa.it/~paulatto/ ? ???*** save italian brains *** ? http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/f16106ec/attachment-0001.htm From paguado at gmail.com Tue Sep 1 12:38:18 2009 From: paguado at gmail.com (Pablo Aguado) Date: Tue, 1 Sep 2009 12:38:18 +0200 Subject: [Pw_forum] Relaxation doesn't converge Message-ID: Dear all, I'm doing some tests on the structural optimization with pw. I'm currently testing with the tetragonal structure of PbTiO3, using the following input: &control calculation = 'vc-relax' restart_mode = 'restart' pseudo_dir = '/****/espresso-4.1/pseudo/' outdir = '/***/tmp' forc_conv_thr = 1d-3 nstep = 50 / &system ibrav=6 celldm(1)=7.3699 celldm(3)=1.04 nat=5 ntyp=3 nbnd=28 ecutwfc=30.0 occupations = 'fixed' / &electrons conv_thr = 1d-12, mixing_beta=0.4, / &ions ion_dynamics = 'bfgs' bfgs_ndim = 5 / &cell cell_dynamics = 'damp-pr' press_conv_thr = 1.0d0 cell_dofree = 'z' / ATOMIC_SPECIES Pb 207.2 Pb.pz-d-van.UPF Ti 47.867 Ti.pz-sp-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS crystal Pb 0.000 0.000 0.040 0 0 1 Ti 0.500 0.500 0.520 0 0 1 O 0.000 0.500 0.500 0 0 1 O 0.500 0.500 0.000 0 0 1 O 0.500 0.000 0.500 0 0 1 K_POINTS automatic 6 6 6 1 1 1 The relaxation is taking forever so I've checked the output and I've found several steps where everything seems to be converged (notice I'm only relaxing out-of-plane lattice vector) but the code keeps running. An example: - Energy difference = 4e-7 - Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00085679 atom 2 type 2 force = 0.00000000 0.00000000 -0.00001779 atom 3 type 3 force = 0.00000000 0.00000000 -0.00024617 atom 4 type 3 force = 0.00000000 0.00000000 -0.00034665 atom 5 type 3 force = 0.00000000 0.00000000 -0.00024617 Total force = 0.000988 Total SCF correction = 0.000002 total stress (Ry/bohr**3) (kbar) P= -0.84 -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 Any idea of what's going on? Thank you very much Pablo From yccheng.nju at gmail.com Tue Sep 1 12:41:26 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Tue, 1 Sep 2009 18:41:26 +0800 Subject: [Pw_forum] What is the difference between total and absolute magnetization? Message-ID: Dear PWscf users, The example08 shows how to calculate the magnetic material. In the output file "ni.scf.out", I find that there are two different magnetization "total magnetization" and "absolute magnetization". What is the difference between them? Thank you in advance. -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/cf1fca99/attachment.htm From yccheng.nju at gmail.com Tue Sep 1 12:43:38 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Tue, 1 Sep 2009 18:43:38 +0800 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: Message-ID: You can try larger ecutwfc=80. 2009/9/1 Pablo Aguado > Dear all, > > I'm doing some tests on the structural optimization with pw. I'm > currently testing with the tetragonal structure of PbTiO3, using the > following input: > > &control > calculation = 'vc-relax' > restart_mode = 'restart' > pseudo_dir = '/****/espresso-4.1/pseudo/' > outdir = '/***/tmp' > forc_conv_thr = 1d-3 > nstep = 50 > / > &system > ibrav=6 > celldm(1)=7.3699 > celldm(3)=1.04 > nat=5 > ntyp=3 > nbnd=28 > ecutwfc=30.0 > occupations = 'fixed' > / > &electrons > conv_thr = 1d-12, > mixing_beta=0.4, > / > &ions > ion_dynamics = 'bfgs' > bfgs_ndim = 5 > / > &cell > cell_dynamics = 'damp-pr' > press_conv_thr = 1.0d0 > cell_dofree = 'z' > / > ATOMIC_SPECIES > Pb 207.2 Pb.pz-d-van.UPF > Ti 47.867 Ti.pz-sp-van_ak.UPF > O 15.9994 O.pz-van_ak.UPF > ATOMIC_POSITIONS crystal > Pb 0.000 0.000 0.040 0 0 1 > Ti 0.500 0.500 0.520 0 0 1 > O 0.000 0.500 0.500 0 0 1 > O 0.500 0.500 0.000 0 0 1 > O 0.500 0.000 0.500 0 0 1 > K_POINTS automatic > 6 6 6 1 1 1 > > The relaxation is taking forever so I've checked the output and I've > found several steps where everything seems to be converged (notice I'm > only relaxing out-of-plane lattice vector) but the code keeps running. > An example: > > - Energy difference = 4e-7 > - Forces acting on atoms (Ry/au): > > atom 1 type 1 force = 0.00000000 0.00000000 0.00085679 > atom 2 type 2 force = 0.00000000 0.00000000 -0.00001779 > atom 3 type 3 force = 0.00000000 0.00000000 -0.00024617 > atom 4 type 3 force = 0.00000000 0.00000000 -0.00034665 > atom 5 type 3 force = 0.00000000 0.00000000 -0.00024617 > > Total force = 0.000988 Total SCF correction = 0.000002 > > total stress (Ry/bohr**3) (kbar) P= > -0.84 > -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 > 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 > 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 > > Any idea of what's going on? > > Thank you very much > > Pablo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/c33f9db2/attachment.htm From giannozz at democritos.it Tue Sep 1 12:48:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 12:48:49 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: Message-ID: <4A9CFC11.1070805@democritos.it> ??? wrote: > You can try larger ecutwfc=80. not a good suggestion. The reason why relaxation doesn't stop has nothing to do with cutoff: no convergence criteria was ever implemented for the 'damp-pr' algorithm. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paguado at gmail.com Tue Sep 1 13:27:32 2009 From: paguado at gmail.com (Pablo Aguado) Date: Tue, 1 Sep 2009 13:27:32 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: <4A9CFC11.1070805@democritos.it> References: <4A9CFC11.1070805@democritos.it> Message-ID: Dear Paolo, > > not a good suggestion. The reason why relaxation doesn't stop > has nothing to do with cutoff: no convergence criteria was ever > implemented for the 'damp-pr' algorithm. > That's weird, I made a previous relaxation of cubic PbTiO3 with similar input and at the end I got entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 0.00 -0.00000001 0.00000000 0.00000000 0.00 0.00 0.00 0.00000000 -0.00000001 0.00000000 0.00 0.00 0.00 0.00000000 0.00000000 -0.00000001 0.00 0.00 0.00 Parrinello-Rahman Damped Dynamics: convergence achieved, Efinal= -333.75589821 How is that possible? Pablo -- ----------------------------------------------------------- Pablo Aguado Puente paguado at gmail.com ------------------------------------------------------------ From sclauzer at sissa.it Tue Sep 1 14:00:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 01 Sep 2009 14:00:45 +0200 Subject: [Pw_forum] What is the difference between total and absolute magnetization? In-Reply-To: References: Message-ID: <4A9D0CED.2050700@sissa.it> ??? wrote: > Dear PWscf users, > The example08 shows how to calculate the magnetic material. In > the output file "ni.scf.out", I find that there are two different > magnetization "total magnetization" and "absolute magnetization". What > is the difference between them? Thank you in advance. http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#What_is_the_difference_between_total_and_absolute_magnetization.3F regards, GS > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Tue Sep 1 14:44:28 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 14:44:28 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9CFC11.1070805@democritos.it> Message-ID: <4A9D172C.30609@democritos.it> Pablo Aguado wrote: > That's weird, I made a previous relaxation of cubic PbTiO3 with > similar input and at the end I got [...] > Parrinello-Rahman Damped Dynamics: convergence achieved nice, somebody has implemented convergence criteria. > How is that possible? likely you chose convergence criteria that were too strict. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Sep 1 15:35:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 15:35:48 +0200 Subject: [Pw_forum] matdyn file output In-Reply-To: References: Message-ID: <4A9D2334.9020705@democritos.it> Denny Jackson wrote: > Also, each column should add up to zero to preserve symmetry, > should it not? not necessarily. Acoustic modes at Gamma are rigid translations and do not add up to zero > For higher frequencies in this calculation the columns do indeed > add up to zero, but for lower frequencies (and negative frequencies) > this is not the case. see above: this is the expected behavior > Is there a resource for good documentation on the matdyn file no, but there are various utilities that read the force constants or dynamical matrix file, produce whatever you need. It is much easier to figure out what these codes do than to figure out the exact file format P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Sep 1 15:36:45 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 15:36:45 +0200 Subject: [Pw_forum] theory on Raman cross sections In-Reply-To: <36d476df0908261253y4042c013ie9226d200eb8145@mail.gmail.com> References: <36d476df0908261246w2d830f8fka32eee10164ddcd4@mail.gmail.com> <36d476df0908261253y4042c013ie9226d200eb8145@mail.gmail.com> Message-ID: <4A9D236D.1090005@democritos.it> shu xu wrote: > if you click the following [...] > you will find the link is invalid. it should be fixed now P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From rgonzalezh at unal.edu.co Tue Sep 1 16:42:00 2009 From: rgonzalezh at unal.edu.co (Rafael Julian Gonzalez Hernandez) Date: Tue, 01 Sep 2009 09:42:00 -0500 Subject: [Pw_forum] V - cohesive energy Message-ID: Hi, I am calculating cohesive energy for V in bcc structure. The electronic configuration for the V isolated atom is [Ar] 3d3 4s2. 1) I found for V isolated atom: ! total energy = -27.27735288 Ry total magnetization = 5.00 Bohr mag/cell and, cohesive energy = 5.28 (5.31 exp.) However, should I find a total magnetization = 3 in the isolated atom? 2) With the restriction (tot_magnetization=3) in my input file. I found: ! total energy = -27.22435471 Ry total magnetization = 3.00 Bohr mag/cell and, cohesive energy = 6.00 (5.31 exp.) why is this big difference in cohesive energy? Rafael J. Gonzalez ==================================================== Rafael Julian Gonzalez Tel:+57(1)3165000 Department of Physics Universidad Nacional de Colombia email: rgonzalezh at unal.edu.co ==================================================== From sylvian.cadars at cnrs-orleans.fr Tue Sep 1 17:25:19 2009 From: sylvian.cadars at cnrs-orleans.fr (Sylvian Cadars) Date: Tue, 01 Sep 2009 17:25:19 +0200 Subject: [Pw_forum] Temporary directory supposedly non existent or not writable Message-ID: <4A9D3CDF.9050009@cnrs-orleans.fr> Hi, I recently started to get the same systematic error on all calculations that I am running, whereas the exact same calcuation was running successfully before, and I can't figure out what happened in the meantime. The error is the following: The calculation crashes with error message (in a CRASH file) before anything can be written in the output file: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 12 from outdir: : error # 1 /work/scadars/espresso_tmp/jobID/ non existent or non writable %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% However the specified outdir directory, created with the environment variable ESPRESSO_TMPDIR actually DOES exist and IS writable (I even got the same error when forcing it to be writable for u,g,o, and a). The same error occurs if I define the outdir directory in the input file as: outdir = '/work/scadars/espresso_tmp/' and again, /work/scadars/espresso_tmp/ exists and is writable, since "ls -l /work/scadars/" gives: drwxrwxrwx 19 scadars dev 32768 sep 1 16:32 espresso_tmp On the other hand, the program runs successfully if I use the current directory as the temporary directory (by omitting definitions of outdir and ESPRESSO_TMPDIR) or if I use a temporary directory located in my home directory... Could you please help me figure out what is going wrong here? Thanks. Best regards. -- ------------------------------------------------------------------------ *Dr. Sylvian CADARS* CEMHTI-CNRS 1D, Av. de la Recherche Scientifique 45071 Orl?ans Cedex 2, France email: sylvian.cadars at cnrs-orleans.fr ------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/76fc5c9e/attachment.htm From giannozz at democritos.it Tue Sep 1 17:32:28 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 17:32:28 +0200 Subject: [Pw_forum] Temporary directory supposedly non existent or not writable In-Reply-To: <4A9D3CDF.9050009@cnrs-orleans.fr> References: <4A9D3CDF.9050009@cnrs-orleans.fr> Message-ID: <4A9D3E8C.1070807@democritos.it> Sylvian Cadars wrote: > However the specified outdir directory, created with the environment > variable ESPRESSO_TMPDIR actually DOES exist you are running in parallel. If your "outdir" is on a local filesystem, you have to create one for each processor. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From ttduyle at gmail.com Tue Sep 1 17:35:58 2009 From: ttduyle at gmail.com (Duy Le) Date: Tue, 1 Sep 2009 11:35:58 -0400 Subject: [Pw_forum] Temporary directory supposedly non existent or not writable In-Reply-To: <4A9D3CDF.9050009@cnrs-orleans.fr> References: <4A9D3CDF.9050009@cnrs-orleans.fr> Message-ID: <8974d3b20909010835j47b5572drbeada54a6220f5c0@mail.gmail.com> Hi, It seems like pw.x was looking for /work/scadars/espresso_tmp/jobID/, so make sure that you create this directory "jobID" If you are running parrallel, you also need to make sure this directory is reachable by all nodes. Best, On Tue, Sep 1, 2009 at 11:25 AM, Sylvian Cadars < sylvian.cadars at cnrs-orleans.fr> wrote: > Hi, > I recently started to get the same systematic error on all calculations > that I am running, whereas the exact same calcuation was running > successfully before, and I can't figure out what happened in the meantime. > The error is the following: > The calculation crashes with error message (in a CRASH file) before > anything can be written in the output file: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 12 > from outdir: : error # 1 > /work/scadars/espresso_tmp/jobID/ non existent or non writable > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > However the specified outdir directory, created with the environment > variable ESPRESSO_TMPDIR actually DOES exist and IS writable (I even got the > same error when forcing it to be writable for u,g,o, and a). > The same error occurs if I define the outdir directory in the input file > as: > outdir = '/work/scadars/espresso_tmp/' > and again, /work/scadars/espresso_tmp/ exists and is writable, since "ls > -l /work/scadars/" gives: > > drwxrwxrwx 19 scadars dev 32768 sep 1 16:32 espresso_tmp > > On the other hand, the program runs successfully if I use the current > directory as the temporary directory (by omitting definitions of outdir and > ESPRESSO_TMPDIR) or if I use a temporary directory located in my home > directory... > > Could you please help me figure out what is going wrong here? > Thanks. > Best regards. > > > > -- > ------------------------------ > *Dr. Sylvian CADARS* > CEMHTI-CNRS > 1D, Av. de la Recherche Scientifique > 45071 Orl?ans Cedex 2, France > email: sylvian.cadars at cnrs-orleans.fr > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/669276e0/attachment.htm From giannozz at democritos.it Tue Sep 1 17:42:31 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 17:42:31 +0200 Subject: [Pw_forum] V - cohesive energy In-Reply-To: References: Message-ID: <4A9D40E7.1070902@democritos.it> Rafael Julian Gonzalez Hernandez wrote: > 1) I found for V isolated atom: > > ! total energy = -27.27735288 Ry > total magnetization = 5.00 Bohr mag/cell > [...] > However, should I find a total magnetization = 3 in the isolated atom? calculations on isolated atoms with plane waves are tricky. Compare your results with what you get with the atomic code, in which you can fix occupancies at will Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From sh.shapt at gmail.com Tue Sep 1 18:33:30 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Tue, 1 Sep 2009 17:33:30 +0100 Subject: [Pw_forum] Calculating Projected density of states in Quantum espresso Message-ID: Hi there, I have already performed scff calculation in quantum espresso, now I would like to calculate projected density of states for my system, I serached it in PWscf manual however it did nto help me at all. Can anybody please tell me what will be the input file format for calculating PDOS. Thanks Shaptarishi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/c007bdc1/attachment.htm From giannozz at democritos.it Tue Sep 1 18:40:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 01 Sep 2009 18:40:44 +0200 Subject: [Pw_forum] Calculating Projected density of states in Quantum espresso In-Reply-To: References: Message-ID: <4A9D4E8C.8020007@democritos.it> Shaptrishi Sharma wrote: > I would like to calculate projected density of states for my system example08 -- Paolo Giannozzi, Democritos and University of Udine, Italy From siyouber at yahoo.fr Tue Sep 1 20:52:43 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Tue, 1 Sep 2009 11:52:43 -0700 (PDT) Subject: [Pw_forum] Xcrysden crashes! In-Reply-To: Message-ID: <61798.40361.qm@web26504.mail.ukl.yahoo.com> Dear all, I downloaded Xcrysden and installed it on one of our computer without any problem. But? I have not been able to do it with the other computer. The ./xcConfigure message does well, but running the executable xcryxden crashes with a message similar to this:/XCrySDen/xcrysden: line 163: 4240 Aborted (core dumped) ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPD DIR $XCRYSDEN_SCRATCH $ARGS > /dev/null I found that somebody got the same problem in 2007. See the link: http://www.democritos.it/pipermail/xcrysden/2007-December/000440.html I went through the forum and I didn't got any solution. Thanking for any help ************************ Bertrand SITAMTZE PhD student Department of Physics University of Yaounde I-Cameroon ************************* --- En date de?: Mar 1.9.09, Lorenzo Paulatto a ?crit?: De: Lorenzo Paulatto Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li ?: "PWSCF Forum" Date: Mardi 1 Septembre 2009, 12h16 In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE? ha scritto: > Please, I would like you to help with the section concerning the 1 1S, 2? > 2S and 2 2P reference states. I mean, what should I put in the following? > section? That's exactly what I told you in the other email: you need two reference? wavefunction per value of l e.g. you could do something like this: 5 1S? 1? 0? 2.00???0.00???0.75000000000? ? ? 1.10000000000 2S? 2? 0? 0.80???0.00???0.75000000000? ? ? 1.10000000000 2S? 2? 0? 0.00???0.10???0.75000000000? ? ? 1.10000000000 2P? 2? 1? 0.20???0.00???0.75000000000? ? ? 1.10000000000 2P? 2? 1? 0.00???0.10???0.75000000000? ? ? 1.10000000000 for the second reference (that one that does not have the eigenvalue? energy) occupation must be zero. The reference energy (in my example 0.10)? has to be chosen by testing and error; it will likely be in the range? -0.20 to 1.0 best regards -- Lorenzo Paulatto SISSA? &? DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www:???http://people.sissa.it/~paulatto/ ? ???*** save italian brains *** ? http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090901/98ae7736/attachment-0001.htm From liuyongduo at hotmail.com Wed Sep 2 07:48:33 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Wed, 2 Sep 2009 13:48:33 +0800 Subject: [Pw_forum] Temperature of Raman spectra Message-ID: Dear QE users: Anybody knows how to control the temperature of Raman spectra calculation? Is it 0 k by default? best Yongduo Liu University of California, Los Angeles MSE _________________________________________________________________ ????????????360??????? http://club.msn.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/8256f1e1/attachment.htm From baroni at sissa.it Wed Sep 2 08:34:44 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 2 Sep 2009 08:34:44 +0200 Subject: [Pw_forum] Quantum ESPRESSO reference paper Message-ID: <6600DB85-9310-4D1B-9B15-826EE8DC74E7@sissa.it> Dear all, it is my pleasure to announce that the reference paper on the Quantum ESPRESSO project has finally appeared and is available for FREE download from the IOP web site for the next 30 days at URL http://stacks.iop.org/0953-8984/21/395502 You are most warmly invited to cite this article whenever appropriate, and particularly in those papers reporting on results obtained using software from the Quantum ESPRESSO distribution. The correct way of citing the paper is: P. Giannozzi et al. J. Phys.: Condens. Matter 21, 395502 (2009), http://www.quantum-espresso.org . A BibTeX record follows: @article{QE-2009, Author = {Paolo Giannozzi and Stefano Baroni and Nicola Bonini and Matteo Calandra and Roberto Car and Carlo Cavazzoni and Davide Ceresoli and Guido L Chiarotti and Matteo Cococcioni and Ismaila Dabo and Andrea Dal Corso and Stefano de Gironcoli and Stefano Fabris and Guido Fratesi and Ralph Gebauer and Uwe Gerstmann and Christos Gougoussis and Anton Kokalj and Michele Lazzeri and Layla Martin-Samos and Nicola Marzari and Francesco Mauri and Riccardo Mazzarello and Stefano Paolini and Alfredo Pasquarello and Lorenzo Paulatto and Carlo Sbraccia and Sandro Scandolo and Gabriele Sclauzero and Ari P Seitsonen and Alexander Smogunov and Paolo Umari and Renata M Wentzcovitch}, Journal = {Journal of Physics: Condensed Matter}, Number = {39}, Pages = {395502 (19pp)}, Title = {QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials}, Url = {http://www.quantum-espresso.org}, Volume = {21}, Year = {2009}} I would like to thank all the developers of the Quantum ESPRESSO project, all the authors of the paper, and the entire Quantum ESPRESSO community from making all this possible. Happy Quantum BREWING, Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/f0ee8b25/attachment.htm From baroni at sissa.it Wed Sep 2 08:39:04 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 2 Sep 2009 08:39:04 +0200 Subject: [Pw_forum] Temperature of Raman spectra In-Reply-To: References: Message-ID: <1B8D3293-93F6-45B3-B79B-0263E32468EE@sissa.it> raman spectra depend on temperature through: 1) Bose occupation factors; 2) the dependence of frequencies on T; 3) the dependence of polarizabilities and their derivatives on T. I presume that (3) is very small, and I am not aware of any attempt to account of suche an effect; 2) is a standard anharmonic effect that can be approximately accounted for in a number of ways, such as e.g. the quasi-harmonic approximation; 1) is a trivial application of textbook formulas. HTE - Stefano B. On Sep 2, 2009, at 7:48 AM, ??? wrote: > Dear QE users: > > Anybody knows how to control the temperature of Raman > spectra calculation? Is it 0 k by default? > > best > > > Yongduo Liu > > University of California, Los Angeles > > MSE > > ??+??+?? ??????,??MSN????! ????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/554fb74f/attachment.htm From sclauzer at sissa.it Wed Sep 2 08:53:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Sep 2009 08:53:51 +0200 Subject: [Pw_forum] Xcrysden crashes! In-Reply-To: <61798.40361.qm@web26504.mail.ukl.yahoo.com> References: <61798.40361.qm@web26504.mail.ukl.yahoo.com> Message-ID: <4A9E167F.4030807@sissa.it> Dear Bertrand, Bertrand SITAMTZE wrote: > I found that somebody got the same problem in 2007. See the link: > > http://www..democritos.it/pipermail/xcrysden/2007-December/000440.html > > I went through the forum and I didn't got any solution. Did you mean that you already posted on the xcrysden users forum and got no solution? I think that the correct forum to search for a solution to your problem is the xcrysden mailing list, although many people from the QE community uses xcrysden. You can subscribe (and then post) to the xcrysden forum through this link: http://www.democritos.it/mailman/listinfo/xcrysden In order to help the troubleshooting you should give more details (version of the program, static binaries or compiled by yourself, on which HW/SW, ...). Regards, GS > > Thanking for any help > > > ************************ > Bertrand SITAMTZE > PhD student > Department of Physics > University of Yaounde > I-Cameroon > ************************* > > > > > > --- En date de : *Mar 1.9.09, Lorenzo Paulatto //* a > ?crit : > > > De: Lorenzo Paulatto > Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li > ?: "PWSCF Forum" > Date: Mardi 1 Septembre 2009, 12h16 > > In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE > > ha scritto: > > Please, I would like you to help with the section concerning the > 1 1S, 2 > > 2S and 2 2P reference states. I mean, what should I put in the > following > > section? > > That's exactly what I told you in the other email: you need two > reference > wavefunction per value of l > e.g. you could do something like this: > > 5 > 1S 1 0 2.00 0.00 0.75000000000 1.10000000000 > 2S 2 0 0.80 0.00 0.75000000000 1.10000000000 > 2S 2 0 0.00 0.10 0.75000000000 1.10000000000 > 2P 2 1 0.20 0.00 0.75000000000 1.10000000000 > 2P 2 1 0.00 0.10 0.75000000000 1.10000000000 > > for the second reference (that one that does not have the eigenvalue > energy) occupation must be zero. The reference energy (in my example > 0.10) > has to be chosen by testing and error; it will likely be in the range > -0.20 to 1.0 > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > start: 2008-09-03 end: 0000-00-00 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From yccheng.nju at gmail.com Wed Sep 2 08:39:29 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 2 Sep 2009 14:39:29 +0800 Subject: [Pw_forum] Temperature of Raman spectra In-Reply-To: References: Message-ID: As far as I know, there is no parameter to control temperature in Raman spectra calculation in PH package. However, the temperature effect in Raman spectra sometimes relates to the phonon lifetime. There are some papers (PRL_99_176802 and PRL_75_1819) refering to the temperature effect in Raman and phonon lifetime. The paper (PRL_99_176802) studied temperature effect in Raman spectra using Quantum-espresso. I have searched the examples directory and have no idea how to calculate phonon lifetime. Can someone give more advice ? 2009/9/2 ??? > Dear QE users: > > Anybody knows how to control the temperature of Raman spectra > calculation? Is it 0 k by default? > > best > > > Yongduo Liu > > University of California, Los Angeles > > MSE > > ------------------------------ > ??+??+?? ??????,??MSN????! ????? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/3ab13ba3/attachment.htm From liuyongduo at hotmail.com Wed Sep 2 09:20:13 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Wed, 2 Sep 2009 15:20:13 +0800 Subject: [Pw_forum] Temperature of Raman spectra (Stefano Baroni) In-Reply-To: References: Message-ID: Thanks, but my question is still not answered. I am asking, how to control the temperature when one use Quantum Espresso (by a tag or something?), what is the default setting of QE on Raman spectra calculation? best Yongduo Liu UCLA MSE > > Message: 3 > Date: Wed, 2 Sep 2009 08:39:04 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] Temperature of Raman spectra > To: PWSCF Forum > Message-ID: <1B8D3293-93F6-45B3-B79B-0263E32468EE at sissa.it> > Content-Type: text/plain; charset="gb2312" > > raman spectra depend on temperature through: 1) Bose occupation > factors; 2) the dependence of frequencies on T; 3) the dependence of > polarizabilities and their derivatives on T. I presume that (3) is > very small, and I am not aware of any attempt to account of suche an > effect; 2) is a standard anharmonic effect that can be approximately > accounted for in a number of ways, such as e.g. the quasi-harmonic > approximation; 1) is a trivial application of textbook formulas. HTE - > Stefano B. > > On Sep 2, 2009, at 7:48 AM, ??? wrote: > > > Dear QE users: > > > > Anybody knows how to control the temperature of Raman > > spectra calculation? Is it 0 k by default? > > > > best > > > > > > Yongduo Liu > > > > University of California, Los Angeles > > > > MSE > > > > ??+??+?? ??????,??MSN????! ????? > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/554fb74f/attachment-0001.htm > > ------------------------------ > _________________________________________________________________ MSN????????MSN??????????? http://10.msn.com.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/e1d8007b/attachment.htm From hqzhou at nju.edu.cn Wed Sep 2 09:45:32 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 2 Sep 2009 15:45:32 +0800 Subject: [Pw_forum] Relaxation doesn't converge References: Message-ID: Pablo, Usually, setting conv_thr = 1d-8 is sufficient, please make sure if you need such strict convergence criterion. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Pablo Aguado" To: Sent: Tuesday, September 01, 2009 6:38 PM Subject: [Pw_forum] Relaxation doesn't converge > Dear all, > > I'm doing some tests on the structural optimization with pw. I'm > currently testing with the tetragonal structure of PbTiO3, using the > following input: > > &control > calculation = 'vc-relax' > restart_mode = 'restart' > pseudo_dir = '/****/espresso-4.1/pseudo/' > outdir = '/***/tmp' > forc_conv_thr = 1d-3 > nstep = 50 > / > &system > ibrav=6 > celldm(1)=7.3699 > celldm(3)=1.04 > nat=5 > ntyp=3 > nbnd=28 > ecutwfc=30.0 > occupations = 'fixed' > / > &electrons > conv_thr = 1d-12, > mixing_beta=0.4, > / > &ions > ion_dynamics = 'bfgs' > bfgs_ndim = 5 > / > &cell > cell_dynamics = 'damp-pr' > press_conv_thr = 1.0d0 > cell_dofree = 'z' > / > ATOMIC_SPECIES > Pb 207.2 Pb.pz-d-van.UPF > Ti 47.867 Ti.pz-sp-van_ak.UPF > O 15.9994 O.pz-van_ak.UPF > ATOMIC_POSITIONS crystal > Pb 0.000 0.000 0.040 0 0 1 > Ti 0.500 0.500 0.520 0 0 1 > O 0.000 0.500 0.500 0 0 1 > O 0.500 0.500 0.000 0 0 1 > O 0.500 0.000 0.500 0 0 1 > K_POINTS automatic > 6 6 6 1 1 1 > > The relaxation is taking forever so I've checked the output and I've > found several steps where everything seems to be converged (notice I'm > only relaxing out-of-plane lattice vector) but the code keeps running. > An example: > > - Energy difference = 4e-7 > - Forces acting on atoms (Ry/au): > > atom 1 type 1 force = 0.00000000 0.00000000 0.00085679 > atom 2 type 2 force = 0.00000000 0.00000000 -0.00001779 > atom 3 type 3 force = 0.00000000 0.00000000 -0.00024617 > atom 4 type 3 force = 0.00000000 0.00000000 -0.00034665 > atom 5 type 3 force = 0.00000000 0.00000000 -0.00024617 > > Total force = 0.000988 Total SCF correction = 0.000002 > > total stress (Ry/bohr**3) (kbar) > P= -0.84 > -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 > 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 > 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 > > Any idea of what's going on? > > Thank you very much > > Pablo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Wed Sep 2 09:55:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 2 Sep 2009 09:55:48 +0200 (CEST) Subject: [Pw_forum] Xcrysden crashes! In-Reply-To: <61798.40361.qm@web26504.mail.ukl.yahoo.com> References: <61798.40361.qm@web26504.mail.ukl.yahoo.com> Message-ID: <40132.78.12.159.112.1251878148.squirrel@webmail.sissa.it> In data 01 settembre 2009 alle ore 20:52:43, Bertrand SITAMTZE ha scritto: > 4240 Aborted Dear Bertran, I found the solution to several months ago, but posted it in the xcrysden mailing list. Have a look here: http://www.democritos.it/pipermail/xcrysden/2009-February/000564.html cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From yccheng.nju at gmail.com Wed Sep 2 10:26:03 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 2 Sep 2009 16:26:03 +0800 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: Message-ID: In my opinion, the stricter the criterion, the more ecut and more K points sampling. 2009/9/2 Huiqun Zhou > Pablo, > > Usually, setting conv_thr = 1d-8 is sufficient, please make sure if you > need such strict convergence criterion. > > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > > ----- Original Message ----- > From: "Pablo Aguado" > To: > Sent: Tuesday, September 01, 2009 6:38 PM > Subject: [Pw_forum] Relaxation doesn't converge > > > > Dear all, > > > > I'm doing some tests on the structural optimization with pw. I'm > > currently testing with the tetragonal structure of PbTiO3, using the > > following input: > > > > &control > > calculation = 'vc-relax' > > restart_mode = 'restart' > > pseudo_dir = '/****/espresso-4.1/pseudo/' > > outdir = '/***/tmp' > > forc_conv_thr = 1d-3 > > nstep = 50 > > / > > &system > > ibrav=6 > > celldm(1)=7.3699 > > celldm(3)=1.04 > > nat=5 > > ntyp=3 > > nbnd=28 > > ecutwfc=30.0 > > occupations = 'fixed' > > / > > &electrons > > conv_thr = 1d-12, > > mixing_beta=0.4, > > / > > &ions > > ion_dynamics = 'bfgs' > > bfgs_ndim = 5 > > / > > &cell > > cell_dynamics = 'damp-pr' > > press_conv_thr = 1.0d0 > > cell_dofree = 'z' > > / > > ATOMIC_SPECIES > > Pb 207.2 Pb.pz-d-van.UPF > > Ti 47.867 Ti.pz-sp-van_ak.UPF > > O 15.9994 O.pz-van_ak.UPF > > ATOMIC_POSITIONS crystal > > Pb 0.000 0.000 0.040 0 0 1 > > Ti 0.500 0.500 0.520 0 0 1 > > O 0.000 0.500 0.500 0 0 1 > > O 0.500 0.500 0.000 0 0 1 > > O 0.500 0.000 0.500 0 0 1 > > K_POINTS automatic > > 6 6 6 1 1 1 > > > > The relaxation is taking forever so I've checked the output and I've > > found several steps where everything seems to be converged (notice I'm > > only relaxing out-of-plane lattice vector) but the code keeps running. > > An example: > > > > - Energy difference = 4e-7 > > - Forces acting on atoms (Ry/au): > > > > atom 1 type 1 force = 0.00000000 0.00000000 0.00085679 > > atom 2 type 2 force = 0.00000000 0.00000000 -0.00001779 > > atom 3 type 3 force = 0.00000000 0.00000000 -0.00024617 > > atom 4 type 3 force = 0.00000000 0.00000000 -0.00034665 > > atom 5 type 3 force = 0.00000000 0.00000000 -0.00024617 > > > > Total force = 0.000988 Total SCF correction = 0.000002 > > > > total stress (Ry/bohr**3) (kbar) > > P= -0.84 > > -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 > > 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 > > 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 > > > > Any idea of what's going on? > > > > Thank you very much > > > > Pablo > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/3bbdf3b9/attachment.htm From sh.shapt at gmail.com Wed Sep 2 10:49:39 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 2 Sep 2009 09:49:39 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 5 In-Reply-To: References: Message-ID: Hi Paolo, exmaple08?? What is that? I cannot understand what you are implying to me. Can you please explain it in details? I want to calculate the projected density of states. Thanks Shaptarishi On 9/1/09, pw_forum-request at pwscf.org wrote: > > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. V - cohesive energy (Rafael Julian Gonzalez Hernandez) > 2. Temporary directory supposedly non existent or not writable > (Sylvian Cadars) > 3. Re: Temporary directory supposedly non existent or not > writable (Paolo Giannozzi) > 4. Re: Temporary directory supposedly non existent or not > writable (Duy Le) > 5. Re: V - cohesive energy (Paolo Giannozzi) > 6. Calculating Projected density of states in Quantum espresso > (Shaptrishi Sharma) > 7. Re: Calculating Projected density of states in Quantum > espresso (Paolo Giannozzi) > 8. Xcrysden crashes! (Bertrand SITAMTZE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 01 Sep 2009 09:42:00 -0500 > From: Rafael Julian Gonzalez Hernandez > Subject: [Pw_forum] V - cohesive energy > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > I am calculating cohesive energy for V in bcc structure. The electronic > configuration for the V isolated atom is [Ar] 3d3 4s2. > > 1) I found for V isolated atom: > > ! total energy = -27.27735288 Ry > total magnetization = 5.00 Bohr mag/cell > and, > cohesive energy = 5.28 (5.31 exp.) > > However, should I find a total magnetization = 3 in the isolated atom? > > 2) With the restriction (tot_magnetization=3) in my input file. I found: > > ! total energy = -27.22435471 Ry > total magnetization = 3.00 Bohr mag/cell > and, > cohesive energy = 6.00 (5.31 exp.) > > why is this big difference in cohesive energy? > > Rafael J. Gonzalez > > ==================================================== > Rafael Julian Gonzalez Tel:+57(1)3165000 > Department of Physics > Universidad Nacional de Colombia > email: rgonzalezh at unal.edu.co > ==================================================== > > > > ------------------------------ > > Message: 2 > Date: Tue, 01 Sep 2009 17:25:19 +0200 > From: Sylvian Cadars > Subject: [Pw_forum] Temporary directory supposedly non existent or not > writable > To: pw_forum at pwscf.org > Message-ID: <4A9D3CDF.9050009 at cnrs-orleans.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > I recently started to get the same systematic error on all calculations > that I am running, whereas the exact same calcuation was running > successfully before, and I can't figure out what happened in the > meantime. The error is the following: > The calculation crashes with error message (in a CRASH file) before > anything can be written in the output file: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 12 > from outdir: : error # 1 > /work/scadars/espresso_tmp/jobID/ non existent or non writable > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > However the specified outdir directory, created with the environment > variable ESPRESSO_TMPDIR actually DOES exist and IS writable (I even got > the same error when forcing it to be writable for u,g,o, and a). > The same error occurs if I define the outdir directory in the input file > as: > outdir = '/work/scadars/espresso_tmp/' > and again, /work/scadars/espresso_tmp/ exists and is writable, since > "ls -l /work/scadars/" gives: > > drwxrwxrwx 19 scadars dev 32768 sep 1 16:32 espresso_tmp > > On the other hand, the program runs successfully if I use the current > directory as the temporary directory (by omitting definitions of outdir > and ESPRESSO_TMPDIR) or if I use a temporary directory located in my > home directory... > > Could you please help me figure out what is going wrong here? > Thanks. > Best regards. > > > > -- > ------------------------------------------------------------------------ > *Dr. Sylvian CADARS* > CEMHTI-CNRS > 1D, Av. de la Recherche Scientifique > 45071 Orl?ans Cedex 2, France > email: sylvian.cadars at cnrs-orleans.fr > ------------------------------------------------------------------------ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090901/76fc5c9e/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Tue, 01 Sep 2009 17:32:28 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Temporary directory supposedly non existent or > not writable > To: PWSCF Forum > Message-ID: <4A9D3E8C.1070807 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Sylvian Cadars wrote: > > > However the specified outdir directory, created with the environment > > variable ESPRESSO_TMPDIR actually DOES exist > > you are running in parallel. If your "outdir" is on a local > filesystem, you have to create one for each processor. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 4 > Date: Tue, 1 Sep 2009 11:35:58 -0400 > From: Duy Le > Subject: Re: [Pw_forum] Temporary directory supposedly non existent or > not writable > To: PWSCF Forum > Message-ID: > <8974d3b20909010835j47b5572drbeada54a6220f5c0 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > It seems like pw.x was looking for /work/scadars/espresso_tmp/jobID/, so > make sure that you create this directory "jobID" > If you are running parrallel, you also need to make sure this directory is > reachable by all nodes. > Best, > > > On Tue, Sep 1, 2009 at 11:25 AM, Sylvian Cadars < > sylvian.cadars at cnrs-orleans.fr> wrote: > > > Hi, > > I recently started to get the same systematic error on all calculations > > that I am running, whereas the exact same calcuation was running > > successfully before, and I can't figure out what happened in the > meantime. > > The error is the following: > > The calculation crashes with error message (in a CRASH file) before > > anything can be written in the output file: > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > task # 12 > > from outdir: : error # 1 > > /work/scadars/espresso_tmp/jobID/ non existent or non writable > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > However the specified outdir directory, created with the environment > > variable ESPRESSO_TMPDIR actually DOES exist and IS writable (I even got > the > > same error when forcing it to be writable for u,g,o, and a). > > The same error occurs if I define the outdir directory in the input file > > as: > > outdir = '/work/scadars/espresso_tmp/' > > and again, /work/scadars/espresso_tmp/ exists and is writable, since "ls > > -l /work/scadars/" gives: > > > > drwxrwxrwx 19 scadars dev 32768 sep 1 16:32 espresso_tmp > > > > On the other hand, the program runs successfully if I use the current > > directory as the temporary directory (by omitting definitions of outdir > and > > ESPRESSO_TMPDIR) or if I use a temporary directory located in my home > > directory... > > > > Could you please help me figure out what is going wrong here? > > Thanks. > > Best regards. > > > > > > > > -- > > ------------------------------ > > *Dr. Sylvian CADARS* > > CEMHTI-CNRS > > 1D, Av. de la Recherche Scientifique > > 45071 Orl?ans Cedex 2, France > > email: sylvian.cadars at cnrs-orleans.fr > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090901/669276e0/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Tue, 01 Sep 2009 17:42:31 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] V - cohesive energy > To: PWSCF Forum > Message-ID: <4A9D40E7.1070902 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Rafael Julian Gonzalez Hernandez wrote: > > > 1) I found for V isolated atom: > > > > ! total energy = -27.27735288 Ry > > total magnetization = 5.00 Bohr mag/cell > > [...] > > However, should I find a total magnetization = 3 in the isolated atom? > > calculations on isolated atoms with plane waves are tricky. > Compare your results with what you get with the atomic code, > in which you can fix occupancies at will > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 6 > Date: Tue, 1 Sep 2009 17:33:30 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] Calculating Projected density of states in Quantum > espresso > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi there, > > I have already performed scff calculation in quantum espresso, now I would > like to calculate projected density of states for my system, I serached it > in PWscf manual however it did nto help me at all. Can anybody please tell > me what will be the input file format for calculating PDOS. > > Thanks > Shaptarishi. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090901/c007bdc1/attachment-0001.htm > > ------------------------------ > > Message: 7 > Date: Tue, 01 Sep 2009 18:40:44 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Calculating Projected density of states in > Quantum espresso > To: PWSCF Forum > Message-ID: <4A9D4E8C.8020007 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Shaptrishi Sharma wrote: > > > I would like to calculate projected density of states for my system > > example08 > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 8 > Date: Tue, 1 Sep 2009 11:52:43 -0700 (PDT) > From: Bertrand SITAMTZE > Subject: [Pw_forum] Xcrysden crashes! > To: PWSCF Forum > Message-ID: <61798.40361.qm at web26504.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > Dear all, > > I downloaded Xcrysden and installed it on one of our computer without any > problem. But? I have not been able to do it with the other computer. The > ./xcConfigure message does well, but running the executable xcryxden crashes > with a message similar to this:/XCrySDen/xcrysden: line 163: 4240 Aborted > (core dumped) ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPD > DIR $XCRYSDEN_SCRATCH $ARGS > /dev/null > > I found that somebody got the same problem in 2007. See the link: > > http://www.democritos.it/pipermail/xcrysden/2007-December/000440.html > > I went through the forum and I didn't got any solution. > > Thanking for any help > > > ************************ > Bertrand SITAMTZE > PhD student > Department of Physics > University of Yaounde I-Cameroon > ************************* > > > > > --- En date de?: Mar 1.9.09, Lorenzo Paulatto a > ?crit?: > > De: Lorenzo Paulatto > Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li > ?: "PWSCF Forum" > Date: Mardi 1 Septembre 2009, 12h16 > > In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE? > ha scritto: > > Please, I would like you to help with the section concerning the 1 1S, 2? > > 2S and 2 2P reference states. I mean, what should I put in the following? > > section? > > That's exactly what I told you in the other email: you need two reference? > wavefunction per value of l > e.g. you could do something like this: > > 5 > 1S? 1? 0? 2.00???0.00???0.75000000000? ? ? 1.10000000000 > 2S? 2? 0? 0.80???0.00???0.75000000000? ? ? 1.10000000000 > 2S? 2? 0? 0.00???0.10???0.75000000000? ? ? 1.10000000000 > 2P? 2? 1? 0.20???0.00???0.75000000000? ? ? 1.10000000000 > 2P? 2? 1? 0.00???0.10???0.75000000000? ? ? 1.10000000000 > > for the second reference (that one that does not have the eigenvalue? > energy) occupation must be zero. The reference energy (in my example 0.10)? > has to be chosen by testing and error; it will likely be in the range? > -0.20 to 1.0 > > best regards > > -- > Lorenzo Paulatto > SISSA? &? DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www:???http://people.sissa.it/~paulatto/ > > ? ???*** save italian brains *** > ? http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090901/98ae7736/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 5 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/2d74c0d1/attachment-0001.htm From giannozz at democritos.it Wed Sep 2 10:52:25 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 10:52:25 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 5 In-Reply-To: References: Message-ID: <4A9E3249.5000701@democritos.it> Shaptrishi Sharma wrote: > exmaple08?? "example08", not "exmaple08". Look into the examples/ directory, subdirectory example08/ -- Paolo Giannozzi, Democritos and University of Udine, Italy From paguado at gmail.com Wed Sep 2 11:35:58 2009 From: paguado at gmail.com (Pablo Aguado) Date: Wed, 2 Sep 2009 11:35:58 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: Message-ID: Well, conv_thr is the convergence criterion for electronic self-consistency and seemingly my problem is with dynamics convergence. In fact the calculation achieves self-consistency in every dynamics step, so setting conv_thr = 8 shouldn't change anything. As I pointed out in my first mail, my problem is that all convergence criteria are satisfied but calculation doesn't stop. Regards, Pablo On Wed, Sep 2, 2009 at 10:26 AM, ??? wrote: > In my opinion, the stricter the criterion, the more ecut and more K points > sampling. > > 2009/9/2 Huiqun Zhou >> >> Pablo, >> >> Usually, setting conv_thr = 1d-8 is sufficient, please make sure if you >> need such strict convergence criterion. >> >> >> Huiqun Zhou >> @Earth Sciences, Nanjing University, China >> >> >> ----- Original Message ----- >> From: "Pablo Aguado" >> To: >> Sent: Tuesday, September 01, 2009 6:38 PM >> Subject: [Pw_forum] Relaxation doesn't converge >> >> >> > Dear all, >> > >> > I'm doing some tests on the structural optimization with pw. I'm >> > currently testing with the tetragonal structure of PbTiO3, using the >> > following input: >> > >> > &control >> > calculation = 'vc-relax' >> > restart_mode = 'restart' >> > pseudo_dir = '/****/espresso-4.1/pseudo/' >> > outdir = '/***/tmp' >> > forc_conv_thr = 1d-3 >> > nstep = 50 >> > / >> > &system >> > ibrav=6 >> > celldm(1)=7.3699 >> > celldm(3)=1.04 >> > nat=5 >> > ntyp=3 >> > nbnd=28 >> > ecutwfc=30.0 >> > occupations = 'fixed' >> > / >> > &electrons >> > conv_thr = 1d-12, >> > mixing_beta=0.4, >> > / >> > &ions >> > ion_dynamics = 'bfgs' >> > bfgs_ndim = 5 >> > / >> > &cell >> > cell_dynamics = 'damp-pr' >> > press_conv_thr = 1.0d0 >> > cell_dofree = 'z' >> > / >> > ATOMIC_SPECIES >> > Pb 207.2 Pb.pz-d-van.UPF >> > Ti 47.867 Ti.pz-sp-van_ak.UPF >> > O 15.9994 O.pz-van_ak.UPF >> > ATOMIC_POSITIONS crystal >> > Pb 0.000 0.000 0.040 0 0 1 >> > Ti 0.500 0.500 0.520 0 0 1 >> > O 0.000 0.500 0.500 0 0 1 >> > O 0.500 0.500 0.000 0 0 1 >> > O 0.500 0.000 0.500 0 0 1 >> > K_POINTS automatic >> > 6 6 6 1 1 1 >> > >> > The relaxation is taking forever so I've checked the output and I've >> > found several steps where everything seems to be converged (notice I'm >> > only relaxing out-of-plane lattice vector) but the code keeps running. >> > An example: >> > >> > - Energy difference = 4e-7 >> > - Forces acting on atoms (Ry/au): >> > >> > atom 1 type 1 force = 0.00000000 0.00000000 >> > 0.00085679 >> > atom 2 type 2 force = 0.00000000 0.00000000 >> > -0.00001779 >> > atom 3 type 3 force = 0.00000000 0.00000000 >> > -0.00024617 >> > atom 4 type 3 force = 0.00000000 0.00000000 >> > -0.00034665 >> > atom 5 type 3 force = 0.00000000 0.00000000 >> > -0.00024617 >> > >> > Total force = 0.000988 Total SCF correction = 0.000002 >> > >> > total stress (Ry/bohr**3) (kbar) >> > P= -0.84 >> > -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 >> > 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 >> > 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 >> > >> > Any idea of what's going on? >> > >> > Thank you very much >> > >> > Pablo >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ----------------------------------------------------------- Pablo Aguado Puente paguado at gmail.com ------------------------------------------------------------ From giannozz at democritos.it Wed Sep 2 11:49:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 11:49:08 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: Message-ID: <4A9E3F94.70607@democritos.it> Pablo Aguado wrote: > As I pointed out in my first mail, my problem is that all > convergence criteria are satisfied but calculation doesn't stop. are you really sure that all convergence criteria are satisfied? -- Paolo Giannozzi, Democritos and University of Udine, Italy From marzari at MIT.EDU Wed Sep 2 11:53:28 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 02 Sep 2009 05:53:28 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 5 In-Reply-To: References: Message-ID: <4A9E4098.1010506@mit.edu> Shaptrishi Sharma wrote: > Hi Paolo, > > exmaple08?? What is that? I cannot understand what you are implying to > me. Can you please explain it in details? > I want to calculate the projected density of states. > > Thanks > Shaptarishi Dear Shaptarishi, Paolo has become saintly in his replies, lately, and I'd love for him to remain so, but 1) if someone tells you example08, you could at a minimum look around in the code or read some documentation before asking again, and, 2) not eply attaching two dozen other emails to your reply, unrelated to the thread. Peace, nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From padmaja_patnaik at yahoo.co.uk Wed Sep 2 12:10:07 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 2 Sep 2009 03:10:07 -0700 (PDT) Subject: [Pw_forum] occupancy number Message-ID: <883291.69976.qm@web26103.mail.ukl.yahoo.com> Dear all, ?Can anybody tell me how to know whether a sate is fully or partially filled from the calculations using PWSCF. Also, how to know what is the number of occupancy in a state and the spin of the electrons in? a particular state. Thanks in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/a227f756/attachment.htm From baroni at sissa.it Wed Sep 2 12:26:06 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 2 Sep 2009 12:26:06 +0200 Subject: [Pw_forum] Temperature of Raman spectra (Stefano Baroni) In-Reply-To: References: Message-ID: <23239881-5A2C-4BB1-B5BB-5F14A2885F10@sissa.it> Phonon calculations always assume T=0 in QE (as it should be clear from the theory that is implemented in the codes, which I assume should be known to those who use the code). Unless, you are aiming at calculating the raman spectrum of a liquid, but in this case, I would beg you to be more specific in your question. Stefano B On Sep 2, 2009, at 9:20 AM, ??? wrote: > Thanks, but my question is still not answered. > I am asking, how to control the temperature when one use Quantum > Espresso (by a tag or something?), what is the default setting of QE > on Raman spectra calculation? > > best > > Yongduo Liu > > UCLA > MSE > > > > > > Message: 3 > > Date: Wed, 2 Sep 2009 08:39:04 +0200 > > From: Stefano Baroni > > Subject: Re: [Pw_forum] Temperature of Raman spectra > > To: PWSCF Forum > > Message-ID: <1B8D3293-93F6-45B3-B79B-0263E32468EE at sissa.it> > > Content-Type: text/plain; charset="gb2312" > > > > raman spectra depend on temperature through: 1) Bose occupation > > factors; 2) the dependence of frequencies on T; 3) the dependence of > > polarizabilities and their derivatives on T. I presume that (3) is > > very small, and I am not aware of any attempt to account of suche an > > effect; 2) is a standard anha rmonic effect that can be > approximately > > accounted for in a number of ways, such as e.g. the quasi-harmonic > > approximation; 1) is a trivial application of textbook formulas. > HTE - > > Stefano B. > > > > On Sep 2, 2009, at 7:48 AM, ??? wrote: > > > > > Dear QE users: > > > > > > Anybody knows how to control the temperature of Raman > > > spectra calculation? Is it 0 k by default? > > > > > > best > > > > > > > > > Yongduo Liu > > > > > > University of California, Los Angeles > > > > > > MSE > > > > > > ??+??+?? ??????,??MSN????! ????? > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > > Trieste > > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > > stefanobaroni (skype) > > > > La morale est une logique de l'action comme la logique est une > morale > > de la pens?e - Jean Piaget > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/554fb74f/attachment-0001.htm > > > > ------------------------------ > > > > > Messenger???2.0???????Messenger??? ?????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/762970d2/attachment-0001.htm From paguado at gmail.com Wed Sep 2 12:41:39 2009 From: paguado at gmail.com (Pablo Aguado) Date: Wed, 2 Sep 2009 12:41:39 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: <4A9E3F94.70607@democritos.it> References: <4A9E3F94.70607@democritos.it> Message-ID: Dear Paolo, > > are you really sure that all convergence criteria are satisfied? > All I can say is that it seems to be converged. My criteria are: etot_conv_thr = 1.0D-4 (default) forc_conv_thr = 1.0d-3 press_conv_thr = 1.0d0 cell_dofree = 'z' And at a given dynamic step get: Energy difference with respect to the previous step = 4e-7 Ry Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00085679 atom 2 type 2 force = 0.00000000 0.00000000 -0.00001779 atom 3 type 3 force = 0.00000000 0.00000000 -0.00024617 atom 4 type 3 force = 0.00000000 0.00000000 -0.00034665 atom 5 type 3 force = 0.00000000 0.00000000 -0.00024617 Total force = 0.000988 Total SCF correction = 0.000002 total stress (Ry/bohr**3) (kbar) P= -0.84 -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 And the code keeps running. Pablo -- Pablo Aguado-Puente Universidad de Cantabria Spain From sagarambavale at yahoo.co.in Wed Sep 2 12:41:51 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Wed, 2 Sep 2009 16:11:51 +0530 (IST) Subject: [Pw_forum] Calculating Projected density of states in Quantum espresso In-Reply-To: References: Message-ID: <477601.67269.qm@web94614.mail.in2.yahoo.com> Dear Saptarshi, Please remove unnecessary part and change the subject line according to thread before replying. There is example directory in espresso home directory where there are examples regarding different calculations implemented in espresso. Example 08 explains the PDOS calculation. Regards Sagar Ambavale M.S. University of Baroda India *********** See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/756b04c7/attachment.htm From giannozz at democritos.it Wed Sep 2 13:03:32 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 13:03:32 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> Message-ID: <4A9E5104.8030600@democritos.it> Pablo Aguado wrote: > All I can say is that it seems to be converged "it seems" /= "it is" > press_conv_thr = 1.0d0 this is internally called "epsp" > total stress (Ry/bohr**3) (kbar) P= -0.84 > -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 > 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 > 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 and this is where the convergence is checked: PW/vcsmd.f90, line 212 and following: DO i = 1, 3 ! conv_ions = conv_ions .AND. & ( ABS( sigma(i,i) - press) * uakbar < epsp ) ! DO j = ( i + 1 ), 3 conv_ions = conv_ions .AND. & ( ABS( sigma(i,j) ) * uakbar < epsp ) END DO ! END DO press=external pressure, sigma=stress tensor, uakbar=atomic units to KBar conversion factor. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From i_camps at yahoo.com.br Wed Sep 2 13:18:12 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Wed, 2 Sep 2009 08:18:12 -0300 Subject: [Pw_forum] << Surface calculations setup >> Message-ID: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> Dear PWscf users, I am new to QE and to PWscf. I would like to know how to set up surface calculations (I read the on-line manual, FAQs, examples, etc.). My questions: 1-) Is there a formal definition to a surface (in the same way I define a crystal with Bravais lattice, space group, etc.) or I have to use a bunch of atoms representing the surface? 2-) How do I select from the crystal which atoms correspond to a given surface? I will be very grateful if you can indicate me any resource in order to learn this. []s, Camps ___ Joan Crawford - "I, Joan Crawford, I believe in the dollar. Everything I earn, I spend." -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/506bc47c/attachment.htm From sh.shapt at gmail.com Wed Sep 2 13:27:06 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Wed, 2 Sep 2009 12:27:06 +0100 Subject: [Pw_forum] Calculation of projected density of states Message-ID: Hi there, well, I would like to know how do we choose the value of Emin and Emax while calculating the projected density fo states Thanks S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/fc86b40b/attachment.htm From baroni at sissa.it Wed Sep 2 13:42:05 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 2 Sep 2009 13:42:05 +0200 Subject: [Pw_forum] Calculation of projected density of states In-Reply-To: References: Message-ID: Nobody better than you can judge ... I presume that Emin and Emax are the minimum/maximum energies at which YOU want the pdos to be tabulated .?... SB On Sep 2, 2009, at 1:27 PM, Shaptrishi Sharma wrote: > Hi there, > well, I would like to know how do we choose the value of Emin and > Emax while calculating the projected density fo states > > Thanks > S > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/243fd4be/attachment.htm From sclauzer at sissa.it Wed Sep 2 13:44:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Sep 2009 13:44:39 +0200 Subject: [Pw_forum] occupancy number In-Reply-To: <883291.69976.qm@web26103.mail.ukl.yahoo.com> References: <883291.69976.qm@web26103.mail.ukl.yahoo.com> Message-ID: <4A9E5AA7.7080900@sissa.it> Dear Padmaja, Padmaja Patnaik wrote: > Dear all, > Can anybody tell me how to know whether a sate is fully or partially > filled from the calculations using PWSCF. Also, how to know what is the simply specify verbosity = 'high' in the &CONTROL namelist and at the end of the self-consistent cycle the occupation factors for each KS eigenstate will be printed on output. The occupations will be listed after the eigenvalues in a format which matches the way eigenvalues are listed (i.e. k-point tag, followed by real numbers, each of them corresponding to a band, ordered according to their energy). > number of occupancy in a state and the spin of the electrons in a > particular state. When you perform spin-polarized calculations the code distinguished between "SPIN UP" and "SPIN DOWN" states when listing their corresponding eigenvalues (I believe it will do the same for occupations). Regards, Gabriele > > Thanks in advance, > regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From nkxirainbow at gmail.com Wed Sep 2 13:39:49 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 2 Sep 2009 19:39:49 +0800 Subject: [Pw_forum] Calculation of projected density of states In-Reply-To: References: Message-ID: <21fbc4790909020439u7e1c1b3eo6795ba6fdc209026@mail.gmail.com> Dear Shaptrishi Sharma: *After scf or band calculation, you can check the Emin and Emax value in output file. * Or, you can plot the band structure first. Then you will easily get the Emin and Emax from the figure of electron band. *You can use the above values for pdos calculation. * On Wed, Sep 2, 2009 at 7:27 PM, Shaptrishi Sharma wrote: > Hi there, > well, I would like to know how do we choose the value of Emin and Emax > while calculating the projected density fo states > > Thanks > S > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/b4d5c5d4/attachment-0001.htm From degironc at sissa.it Wed Sep 2 13:51:25 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 02 Sep 2009 13:51:25 +0200 Subject: [Pw_forum] Calculation of projected density of states In-Reply-To: References: Message-ID: <4A9E5C3D.90505@sissa.it> Shaptrishi Sharma wrote: > Hi there, > well, I would like to know how do we choose the value of Emin and Emax > while calculating the projected density fo states > you decide what range of energy you are interested in. stefano > Thanks > S > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ttduyle at gmail.com Wed Sep 2 13:51:40 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 2 Sep 2009 07:51:40 -0400 Subject: [Pw_forum] Calculation of projected density of states In-Reply-To: References: Message-ID: <8974d3b20909020451n34b2045fle96d7344fb570e76@mail.gmail.com> Hi,Just plot once with randomly chosen Emin Emax. By looking at this plot, you will have a idea to chose the new Emin, Emax for your final plot. On Wed, Sep 2, 2009 at 7:42 AM, Stefano Baroni wrote: > Nobody better than you can judge ... I presume that Emin and Emax are the > minimum/maximum energies at which YOU want the pdos to be tabulated .?... SB > On Sep 2, 2009, at 1:27 PM, Shaptrishi Sharma wrote: > > Hi there, > well, I would like to know how do we choose the value of Emin and Emax > while calculating the projected density fo states > > Thanks > S > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/ee1a2ce7/attachment.htm From sclauzer at sissa.it Wed Sep 2 13:53:07 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Sep 2009 13:53:07 +0200 Subject: [Pw_forum] Calculation of projected density of states In-Reply-To: References: Message-ID: <4A9E5CA3.6050905@sissa.it> Stefano is right. From the Doc/INPUT_PROJWFC.txt input description: +-------------------------------------------------------------------- Variables: Emin, Emax Type: REAL Default: (band extrema) Description: min & max energy (eV) for DOS plot +-------------------------------------------------------------------- You don't even need to specify them, as the code computes by default the PDOS for all the energies from the bottom of the valence band to the eigenavlue of the highest energy state included in the pw.x calculation. You can later chose the desired plotting range with your favorite plotting program. Gabriele Stefano Baroni wrote: > Nobody better than you can judge ... I presume that Emin and Emax are > the minimum/maximum energies at which YOU want the pdos to be tabulated > .?... SB > > On Sep 2, 2009, at 1:27 PM, Shaptrishi Sharma wrote: > >> Hi there, >> well, I would like to know how do we choose the value of Emin and Emax >> while calculating the projected density fo states >> >> Thanks >> S >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ttduyle at gmail.com Wed Sep 2 13:46:32 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 2 Sep 2009 07:46:32 -0400 Subject: [Pw_forum] << Surface calculations setup >> In-Reply-To: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> References: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> Message-ID: <8974d3b20909020446h403e82a8s9efa5d153dd7da1@mail.gmail.com> Hi,1. If you cut crystal along (hkl) plan you will have (hkl) surface 2. I don't know if there is such document. Here is how I learned: start with simple cubic crystal, then from (100) surface, (110) then (111) surface. Good luck, D. On Wed, Sep 2, 2009 at 7:18 AM, I. Camps wrote: > Dear PWscf users, > > I am new to QE and to PWscf. > > I would like to know how to set up surface calculations (I read the on-line > manual, FAQs, examples, etc.). > > My questions: > > 1-) Is there a formal definition to a surface (in the same way I define a > crystal with Bravais lattice, space group, etc.) or I have to use a bunch of > atoms representing the surface? > 2-) How do I select from the crystal which atoms correspond to a given > surface? > > I will be very grateful if you can indicate me any resource in order to > learn this. > > []s, > > Camps > ___ > Joan Crawford - "I, Joan Crawford, I believe in the dollar. Everything I earn, I spend." > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/88115d4c/attachment.htm From paguado at gmail.com Wed Sep 2 13:57:25 2009 From: paguado at gmail.com (Pablo Aguado) Date: Wed, 2 Sep 2009 13:57:25 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: <4A9E5104.8030600@democritos.it> References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> Message-ID: I'm sorry, but I still can't see the problem ... forc_conv_thr = 1.0d-3 is satisfied ==> conv_ions = true Only z is allowed to relax (cell_dofree = 'z') so: sigma_xx & sigma_yy should be set to 0 at some point sigma = 0.87 Kbar press_conv_thr = epsp = 1.0 Kbar press = 0.0 so conv_ions.AND.(ABS( sigma(i,i) - press) * uakbar < epsp) is true, unless the program is still considering stress_xx and stress_yy (cell_dofree is not being taken into account) Pablo On Wed, Sep 2, 2009 at 1:03 PM, Paolo Giannozzi wrote: > Pablo Aguado wrote: > >> All I can say is that it seems to be converged > > "it seems" /= "it is" > >> press_conv_thr = 1.0d0 > > this is internally called "epsp" > >> total stress (Ry/bohr**3) (kbar) P= -0.84 >> -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 >> 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 >> 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 > > and this is where the convergence is checked: PW/vcsmd.f90, line 212 > and following: > > DO i = 1, 3 > ! > conv_ions = conv_ions .AND. & > ( ABS( sigma(i,i) - press) * uakbar < epsp ) > ! > DO j = ( i + 1 ), 3 > conv_ions = conv_ions .AND. & > ( ABS( sigma(i,j) ) * uakbar < epsp ) > END DO > ! > END DO > > press=external pressure, sigma=stress tensor, > uakbar=atomic units to KBar conversion factor. > From degironc at sissa.it Wed Sep 2 14:03:52 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 02 Sep 2009 14:03:52 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> Message-ID: <4A9E5F28.8010506@sissa.it> Dear Pablo, the convergence check on stress tests EACH component against the threshold your stress tensor is not yet converged. sigma_xx and sigma_yy are NOT converged HTH stefano de Gironcoli Pablo Aguado wrote: > I'm sorry, but I still can't see the problem ... > > forc_conv_thr = 1.0d-3 is satisfied ==> conv_ions = true > > Only z is allowed to relax (cell_dofree = 'z') so: > sigma_xx & sigma_yy should be set to 0 at some point > sigma = 0.87 Kbar > press_conv_thr = epsp = 1.0 Kbar > press = 0.0 > > so conv_ions.AND.(ABS( sigma(i,i) - press) * uakbar < epsp) is true, > unless the program is still considering stress_xx and stress_yy > (cell_dofree is not being taken into account) > > Pablo > > > On Wed, Sep 2, 2009 at 1:03 PM, Paolo Giannozzi wrote: > >> Pablo Aguado wrote: >> >> >>> All I can say is that it seems to be converged >>> >> "it seems" /= "it is" >> >> >>> press_conv_thr = 1.0d0 >>> >> this is internally called "epsp" >> >> >>> total stress (Ry/bohr**3) (kbar) P= -0.84 >>> -0.00001150 0.00000000 0.00000000 -1.69 0.00 0.00 >>> 0.00000000 -0.00001150 0.00000000 0.00 -1.69 0.00 >>> 0.00000000 0.00000000 0.00000591 0.00 0.00 0.87 >>> >> and this is where the convergence is checked: PW/vcsmd.f90, line 212 >> and following: >> >> DO i = 1, 3 >> ! >> conv_ions = conv_ions .AND. & >> ( ABS( sigma(i,i) - press) * uakbar < epsp ) >> ! >> DO j = ( i + 1 ), 3 >> conv_ions = conv_ions .AND. & >> ( ABS( sigma(i,j) ) * uakbar < epsp ) >> END DO >> ! >> END DO >> >> press=external pressure, sigma=stress tensor, >> uakbar=atomic units to KBar conversion factor. >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Wed Sep 2 14:23:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Sep 2009 14:23:25 +0200 Subject: [Pw_forum] << Surface calculations setup >> In-Reply-To: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> References: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> Message-ID: <4A9E63BD.8080801@sissa.it> I. Camps wrote: > Dear PWscf users, > > I am new to QE and to PWscf. > > I would like to know how to set up surface calculations (I read the > on-line manual, FAQs, examples, etc.). Like in any other 3D-periodic electronic structure code. You use a slab geometry, made of bulk layers, which are atomic planes perpendicular to the surface normal. You have to chose a direction (typically the z axis) on which you "remove" the periodicity by adding a vacuum region, while your periodicity in the xy plane depends on the Miller indexes of the surface (and on the coverage of adsorbed molecules, if any). > > My questions: > > 1-) Is there a formal definition to a surface (in the same way I define > a crystal with Bravais lattice, space group, etc.) or I have to use a > bunch of atoms representing the surface? You have to chose one of the 14 Bravais lattices used for bulk calculations, depending on the symmetry of the surface and stack atomic layers along a direction. For instance the FCC (100) surface has square symmetry and I would use a tetragonal lattice (ibrav=6), while the (110) has rectangular symmetry and I would use orthorhombic lattice. For (111), which has hexagonal symmetry, I would an use orthorhombic cell with 3-fold symmetry, since the ABC stacking of layers lowers the symmetry. > 2-) How do I select from the crystal which atoms correspond to a given > surface? > > I will be very grateful if you can indicate me any resource in order to > learn this. There is something in the examples: example03: This example shows how to use pw.x to compute the equilibrium geometry of a simple molecule, CO, and of an Al (001) slab. In the latter case the relaxation is performed in two ways: 1) using the quasi-Newton BFGS algorithm 2) using a damped dynamics algorithm. WorkFct_example: This example shows how to use pw.x, pp.x, and average.x to compute the work function of a metal using the slab-supercell approximation. This example is of a 4 layer unrelaxed Al(100) slab with 5 equivalent layers of vacuum between the surfaces. regards, GS > > []s, > > Camps > ___ > Joan Crawford > - "I, > Joan Crawford, I believe in the dollar. Everything I earn, I spend." > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Wed Sep 2 14:25:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 02 Sep 2009 14:25:08 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> Message-ID: In data 02 settembre 2009 alle ore 13:57:25, Pablo Aguado ha scritto: > Only z is allowed to relax (cell_dofree = 'z') so: > sigma_xx & sigma_yy should be set to 0 at some point > sigma = 0.87 Kbar press_conv_thr = epsp = 1.0 Kbar > press = 0.0 I can understand your concern: you would expect that if only z can move the pressure along x and y would not be considered for convergence. I think you are right, and it should be implemented that way. In order to do that you can modify PW/vcsmd.f90 in the following way: diff -r1.36 vcsmd.f90 215c215 < ( ABS( sigma(i,i) - press) * uakbar < epsp ) --- > ( ABS( sigma(i,i) - press) * uakbar * iforceh(i,i) < > epsp ) 219c219 < ( ABS( sigma(i,j) ) * uakbar < epsp ) --- > ( ABS( sigma(i,j) ) * uakbar * iforceh(i,j) < > epsp ) i.e. adding iforceh(*,*) where necessary. Could you please test this patch? best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Wed Sep 2 14:25:43 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 2 Sep 2009 20:25:43 +0800 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> Message-ID: <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> Dear Pablo: > Only z is allowed to relax (cell_dofree = 'z') so: > You choose bfgs parameter to do cell_dofree. However, cell_dofree is not applied to "bfgs" You can find the following content easily in pwscf_forum >> I'm playing around with the cell_dofree variable and I don't manage to >> make it work. Currently I'm trying to relax only the c lattice vector >> of a tetragonal cell together with the atomic coordinates, so I use >> the following: >As far as I know it works with damped dynamics, but not with bfgs. I've >started to implement it some time ago, but than dropped for lack of time >and interest. ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/495fc7cd/attachment.htm From paulatto at sissa.it Wed Sep 2 14:28:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 02 Sep 2009 14:28:16 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> Message-ID: In data 02 settembre 2009 alle ore 14:25:43, xirainbow ha scritto: > You choose bfgs parameter to do cell_dofree. > However, cell_dofree is not applied to "bfgs" > You can find the following content easily in pwscf_forum He is actually using damped Parrinello-Rahman dynamics for the cell, hence there is no problem with cell_dofree. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nkxirainbow at gmail.com Wed Sep 2 14:29:23 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 2 Sep 2009 20:29:23 +0800 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> Message-ID: <21fbc4790909020529l68cf8702o8e2bafe8fcee423@mail.gmail.com> sorry, I am wrong;) On Wed, Sep 2, 2009 at 8:28 PM, Lorenzo Paulatto wrote: > In data 02 settembre 2009 alle ore 14:25:43, xirainbow > ha scritto: > > You choose bfgs parameter to do cell_dofree. > > However, cell_dofree is not applied to "bfgs" > > You can find the following content easily in pwscf_forum > > He is actually using damped Parrinello-Rahman dynamics for the cell, hence > there is no problem with cell_dofree. > > regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/d01c8971/attachment.htm From giannozz at democritos.it Wed Sep 2 14:47:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 14:47:01 +0200 Subject: [Pw_forum] << Surface calculations setup >> In-Reply-To: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> References: <612c95fa0909020418s53e823fbk535dd3cfc5eb85a2@mail.gmail.com> Message-ID: <4A9E6945.7030106@democritos.it> I. Camps wrote: > 1-) Is there a formal definition to a surface Miller planes, described in any solid-state textbook; they will not help you in producing the input, though P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From siyouber at yahoo.fr Wed Sep 2 16:06:15 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Wed, 2 Sep 2009 07:06:15 -0700 (PDT) Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <4A9E5104.8030600@democritos.it> Message-ID: <676184.81166.qm@web26506.mail.ukl.yahoo.com> Dear all, Titanium belongs to the hexagonal P63/mmc (n? 194) space group. I would like somebody to confirm that my attached input section concerning the bravais lattice and specially the atomic positions are good. &SYSTEM ibrav=4 celldm(1)=5.576203 celldm(3)=1.587874 nat=2 ntyp=1 ecutwfc=40.0 / &ELECTRONS diagonalization='cg' / ATOMIC_SPECIES Ti 47.867 Ti.pw91-nsp-van.UPF ATOMIC_POSITIONS Ti 0.3333? 0.6666? 0.2500 Ti 0.6666? 0.3333? 0.7500 K_POINTS automatic 8 8 4 0 0 0 Best regards ********************* Bertrand SITAMTZE PhD student Department of Physics University of Yaound? I-Cameroon *********************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/27aeb988/attachment.htm From giannozz at democritos.it Wed Sep 2 16:30:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 16:30:15 +0200 Subject: [Pw_forum] Correlated wave-function in real space In-Reply-To: <4A9B8E6A.5090103@fu-berlin.de> References: <4A980700.8050002@fu-berlin.de> <4A9833EC.2050107@umn.edu> <4A9B8E6A.5090103@fu-berlin.de> Message-ID: <4A9E8177.7040301@democritos.it> Andreas Linscheid wrote: > Is it correct that > 1. The 3D real space vector R in lattice coordinates, that corresponds > to ir, where > ir = k + (j-1)*nrx3s +(i-1)*nrx3s*nrx2s ir = i + (j-1)*nrx1s+(k-1)*nrx1s*nrx2s > is > R(1) = DBLE(i)/DBLE(nrx1s) > R(2) = DBLE(j)/DBLE(nrx2s) > R(3) = DBLE(k)/DBLE(nrx3s) R(1)= DBLE(i-1)/DBLE(nr1s) R(2)= DBLE(j-1)/DBLE(nr2s) R(3)= DBLE(k-1)/DBLE(nr3s) > ? (I am using nrx1s instead of nr1s on purpose!) me too > 2. Is it correct, that the 3D vector to the same index ir in karthesian > coordinates is > R(:) = DBLE(i)/DBLE(nrx1s)*at(:,1) + DBLE(j)/DBLE(nrx2s)*at(:,2) + > DBLE(k)/DBLE(nrx3s)*at(:,3) > ? (I think in FAQ, this is described with nr3s,) R(:) = DBLE(i-1)/DBLE(nr1s)*at(:,1) + DBLE(j-1)/DBLE(nr2s)*at(:,2) + DBLE(k-1)/DBLE(nr3s)*at(:,3) > 3. Can I take this vector (for example in lattice coords) and add > R(:) = R(:) + S(:) only if S(:) connects points of the real-space grid. If not, the translation must be done in reciprocal space. > map back to first unit cell > R(:) = R(:)-nint(R(:)) > and map it back onto the real space FFT grid point (i_n,j_n,k_n): > i_n =nint(nrx1s*R(1)) + 1 > j_n =nint(nrx2s*R(2)) + 1 > k_n =nint(nrx3s*R(3)) + 1 i_n =nint(nr1s*R(1)) + 1 j_n =nint(nr2s*R(2)) + 1 k_n =nint(nr3s*R(3)) + 1 > What then has the the 1D index: > ir_n = k_n + (j_n-1)*nrx3s +(i_n-1)*nrx3s*nrx2s ir_n = i_n + (j_n-1)*nrx1s+(k_n-1)*nrx1s*nrx2s P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From hande at newton.physics.metu.edu.tr Wed Sep 2 16:46:52 2009 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Wed, 2 Sep 2009 17:46:52 +0300 (EEST) Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <676184.81166.qm@web26506.mail.ukl.yahoo.com> Message-ID: Dear Bertrand, Your atomic positions are rather off with a large gap between rumpled Ti layers. Perhaps you should double-check that your definition of the hcp unit cell matches that for ibrav=4 in the code. You can find this information in the Doc directory in your copy of espresso. Besides, you should be able to check your structure for yourself using xcrysden (--pwi option). Best wishes, Hande On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > > Dear all, > > Titanium belongs to the hexagonal P63/mmc > (n? 194) space group. I would like somebody to confirm that my attached > input section concerning the bravais lattice and specially the atomic positions are good. > > &SYSTEM > ibrav=4 > celldm(1)=5.576203 > celldm(3)=1.587874 > nat=2 > ntyp=1 > ecutwfc=40.0 > / > &ELECTRONS > diagonalization='cg' > / > ATOMIC_SPECIES > Ti 47.867 Ti.pw91-nsp-van.UPF > ATOMIC_POSITIONS > Ti 0.3333? 0.6666? 0.2500 > Ti 0.6666? 0.3333? 0.7500 > K_POINTS automatic > 8 8 4 0 0 0 > > > Best regards > > ********************* > Bertrand SITAMTZE > PhD student > Department of Physics > University of Yaound? I-Cameroon > *********************** > > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From Giovanni.Cantele at na.infn.it Wed Sep 2 16:48:55 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Wed, 02 Sep 2009 16:48:55 +0200 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: References: Message-ID: <4A9E85D7.9080503@na.infn.it> Beside the check of the hcp unit cell, which is crucial, I also guess that you gave the input positions in "crystal" units, didn't you? If it is the case, I think that you should add the "{ crystal }" string after ATOMIC_POSITIONS. Indeed, the default is "alat" units, I think, namely, cartesian coordinates in celldm(1) units. Also do not forget to check the convergence of your results with respect to ecutrho. The default value (4*ecutwfc) must be usually increased (6 to 12 times ecutwfc) if, as in you case, ultrasoft pseudopotentials are used. Giovanni Hande Ustunel wrote: > Dear Bertrand, > > Your atomic positions are rather off with a large gap between rumpled Ti > layers. Perhaps you should double-check that your definition of the hcp > unit cell matches that for ibrav=4 in the code. You can find this > information in the Doc directory in your copy of espresso. > > Besides, you should be able to check your structure for yourself using > xcrysden (--pwi option). > > Best wishes, > Hande > > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > > >> Dear all, >> >> Titanium belongs to the hexagonal P63/mmc >> (n? 194) space group. I would like somebody to confirm that my attached >> input section concerning the bravais lattice and specially the atomic positions are good. >> >> &SYSTEM >> ibrav=4 >> celldm(1)=5.576203 >> celldm(3)=1.587874 >> nat=2 >> ntyp=1 >> ecutwfc=40.0 >> / >> &ELECTRONS >> diagonalization='cg' >> / >> ATOMIC_SPECIES >> Ti 47.867 Ti.pw91-nsp-van.UPF >> ATOMIC_POSITIONS >> Ti 0.3333 0.6666 0.2500 >> Ti 0.6666 0.3333 0.7500 >> K_POINTS automatic >> 8 8 4 0 0 0 >> >> >> Best regards >> >> ********************* >> Bertrand SITAMTZE >> PhD student >> Department of Physics >> University of Yaound? I-Cameroon >> *********************** >> >> >> > > > > > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From sclauzer at sissa.it Wed Sep 2 17:23:08 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 02 Sep 2009 17:23:08 +0200 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <4A9E85D7.9080503@na.infn.it> References: <4A9E85D7.9080503@na.infn.it> Message-ID: <4A9E8DDC.8040202@sissa.it> >>> &SYSTEM >>> ibrav=4 >>> celldm(1)=5.576203 >>> celldm(3)=1.587874 >>> nat=2 >>> ntyp=1 >>> ecutwfc=40.0 >>> / >>> &ELECTRONS >>> diagonalization='cg' >>> / >>> ATOMIC_SPECIES >>> Ti 47.867 Ti.pw91-nsp-van.UPF >>> ATOMIC_POSITIONS >>> Ti 0.3333 0.6666 0.2500 >>> Ti 0.6666 0.3333 0.7500 Another suggestion: if 0.3333 is an approximation to 1/3, you need to use more significant digits in order for the symmetry checking subroutine to recognize all symmetry operations (at least 6 digits, I guess. See PW/eqvect.f90). GS >>> K_POINTS automatic >>> 8 8 4 0 0 0 >>> >>> >>> Best regards >>> >>> ********************* >>> Bertrand SITAMTZE >>> PhD student >>> Department of Physics >>> University of Yaound? I-Cameroon >>> *********************** >>> >>> >>> >> >> >> >> > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Wed Sep 2 17:27:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 02 Sep 2009 17:27:40 +0200 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <4A9E8DDC.8040202@sissa.it> References: <4A9E85D7.9080503@na.infn.it> <4A9E8DDC.8040202@sissa.it> Message-ID: <4A9E8EEC.9090007@democritos.it> Gabriele Sclauzero wrote: > Another suggestion: if 0.3333 is an approximation to 1/3, you need to use more significant > digits in order for the symmetry checking subroutine to recognize all symmetry operations or to write 1/3: it should be accepted (only for atomic positions! a poor-man's parser is included in PWscf) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From siyouber at yahoo.fr Wed Sep 2 17:50:29 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Wed, 2 Sep 2009 08:50:29 -0700 (PDT) Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <4A9E85D7.9080503@na.infn.it> Message-ID: <559538.73297.qm@web26505.mail.ukl.yahoo.com> Dear Giovanni, My coordinates are those taken from 2c position of the crystallographic space group? table. I though these correspond to the default (alat) in quantum espresso, in which case mentioning is not mandatory. Isn't it? Thanks once more --- En date de?: Mer 2.9.09, Giovanni Cantele a ?crit?: De: Giovanni Cantele Objet: Re: [Pw_forum] Titanium atomic positions ?: "PWSCF Forum" Date: Mercredi 2 Septembre 2009, 16h48 Beside the check of the hcp unit cell, which is crucial, I also guess that you gave the input positions in "crystal" units, didn't you? If it is the case, I think that you should add the "{ crystal }" string after ATOMIC_POSITIONS. Indeed, the default is "alat" units, I think, namely, cartesian coordinates in celldm(1) units. Also do not forget to check the convergence of your results with respect to ecutrho. The default value (4*ecutwfc) must be usually increased (6 to 12 times ecutwfc) if, as in you case, ultrasoft pseudopotentials are used. Giovanni Hande Ustunel wrote: > Dear Bertrand, > > Your atomic positions are rather off with a large gap between rumpled Ti > layers. Perhaps you should double-check that your definition of the hcp > unit cell matches that for ibrav=4 in the code. You can find this > information in the Doc directory in your copy of espresso. > > Besides, you should be able to check your structure for yourself using > xcrysden (--pwi option). > > Best wishes, > Hande > > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > >??? >> Dear all, >> >> Titanium belongs to the ??? hexagonal P63/mmc >> (n? 194) space group. I would like somebody to confirm that my attached >> input section concerning the bravais lattice and specially the atomic positions are good. >> >> &SYSTEM >> ibrav=4 >> celldm(1)=5.576203 >> celldm(3)=1.587874 >> nat=2 >> ntyp=1 >> ecutwfc=40.0 >> / >> &ELECTRONS >> diagonalization='cg' >> / >> ATOMIC_SPECIES >> Ti 47.867 Ti.pw91-nsp-van.UPF >> ATOMIC_POSITIONS >> Ti 0.3333? 0.6666? 0.2500 >> Ti 0.6666? 0.3333? 0.7500 >> K_POINTS automatic >> 8 8 4 0 0 0 >> >> >> Best regards ?********************* Bertrand SITAMTZE PhD student Department of Physics University of Yaound? I-Cameroon ?*********************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/612f9c97/attachment.htm From Giovanni.Cantele at na.infn.it Wed Sep 2 17:58:19 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Wed, 02 Sep 2009 17:58:19 +0200 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <559538.73297.qm@web26505.mail.ukl.yahoo.com> References: <559538.73297.qm@web26505.mail.ukl.yahoo.com> Message-ID: <4A9E961B.5040706@na.infn.it> Bertrand SITAMTZE wrote: > Dear Giovanni, > > My coordinates are those taken from 2c position of > the crystallographic space group table. I though these correspond to > the default (alat) in quantum espresso, > in which case mentioning is not mandatory. Isn't it? > > Thanks once more > It is not mandatory to specify the default, but I'm not very sure that your coordinates are in alat units. From http://cst-www.nrl.navy.mil/lattice/struk/a3.html I understand that (1/3,2/3,1/4) and (2/3,1/3,3/4) are in terms of the A1, A2 and A3 vectors rather than the x, y z axes versors. alat positions are cartesian coordinates (in unit of celldm(1)), which are the same as crystal coordinates only for a simple cubic lattice. If I'm not wrong, as pointed out by someone else, you should check that the A1, A2, A3 choice shown in the above link is the same as in Quantum-ESPRESSO (for the latter please have a look to Doc/INPUT_PW* ). If not, you may specify your own lattice vectors by using the CELL_PARAMETERS card. Giovanni > > --- En date de : *Mer 2.9.09, Giovanni Cantele > //* a ?crit : > > > De: Giovanni Cantele > Objet: Re: [Pw_forum] Titanium atomic positions > ?: "PWSCF Forum" > Date: Mercredi 2 Septembre 2009, 16h48 > > Beside the check of the hcp unit cell, which is crucial, I also guess > that you gave the input positions > in "crystal" units, didn't you? If it is the case, I think that you > should add the "{ crystal }" string after ATOMIC_POSITIONS. > Indeed, the > default is "alat" units, I think, namely, cartesian coordinates in > celldm(1) units. > > Also do not forget to check the convergence of your results with > respect > to ecutrho. The default value (4*ecutwfc) must be usually > increased (6 > to 12 times ecutwfc) if, as in you case, ultrasoft > pseudopotentials are > used. > > Giovanni > > > Hande Ustunel wrote: > > Dear Bertrand, > > > > Your atomic positions are rather off with a large gap between > rumpled Ti > > layers. Perhaps you should double-check that your definition of > the hcp > > unit cell matches that for ibrav=4 in the code. You can find this > > information in the Doc directory in your copy of espresso. > > > > Besides, you should be able to check your structure for yourself > using > > xcrysden (--pwi option). > > > > Best wishes, > > Hande > > > > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > > > > > >> Dear all, > >> > >> Titanium belongs to the hexagonal P63/mmc > >> (n? 194) space group. I would like somebody to confirm that my > attached > >> input section concerning the bravais lattice and specially the > atomic positions are good. > >> > >> &SYSTEM > >> ibrav=4 > >> celldm(1)=5.576203 > >> celldm(3)=1.587874 > >> nat=2 > >> ntyp=1 > >> ecutwfc=40.0 > >> / > >> &ELECTRONS > >> diagonalization='cg' > >> / > >> ATOMIC_SPECIES > >> Ti 47.867 Ti.pw91-nsp-van.UPF > >> ATOMIC_POSITIONS > >> Ti 0.3333 0..6666 0.2500 > >> Ti 0.6666 0.3333 0.7500 > >> K_POINTS automatic > >> 8 8 4 0 0 0 > >> > >> > >> Best regards > > ********************* > Bertrand SITAMTZE > PhD student > Department of Physics > University of Yaound? I-Cameroon > *********************** > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From paguado at gmail.com Wed Sep 2 20:02:36 2009 From: paguado at gmail.com (Pablo Aguado) Date: Wed, 2 Sep 2009 20:02:36 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: <21fbc4790909020529l68cf8702o8e2bafe8fcee423@mail.gmail.com> References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> <21fbc4790909020529l68cf8702o8e2bafe8fcee423@mail.gmail.com> Message-ID: Hi Lorenzo, You were right, that was the problem and the changes you proposed fix it. Thank you, Pablo -- Pablo Aguado Universidad de Cantabria Spain From giannozz at democritos.it Wed Sep 2 20:39:00 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 2 Sep 2009 20:39:00 +0200 Subject: [Pw_forum] Relaxation doesn't converge In-Reply-To: References: <4A9E3F94.70607@democritos.it> <4A9E5104.8030600@democritos.it> <21fbc4790909020525u7520ab3ya5d73eb6d7ebcdd5@mail.gmail.com> <21fbc4790909020529l68cf8702o8e2bafe8fcee423@mail.gmail.com> Message-ID: <77CD8E9A-51D5-4244-B37A-3D08F4DBDF50@democritos.it> On Sep 2, 2009, at 20:02 , Pablo Aguado wrote: > You were right, that was the problem and the changes you proposed > fix it. ok, thank you, the fix it will be included in the next release. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From udayagiri3 at gmail.com Wed Sep 2 20:48:50 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Thu, 3 Sep 2009 00:18:50 +0530 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <4A9E961B.5040706@na.infn.it> References: <559538.73297.qm@web26505.mail.ukl.yahoo.com> <4A9E961B.5040706@na.infn.it> Message-ID: for the ATOMIC_POSITIONS if you choose "crystal" your lattice coordinates are correct Ti 0.3333 0.6666 0.2500 Ti 0.6666 0.3333 0.7500 or else you can represent same as ATOMIC_POSITIONS (crystal) Ti 0 0.2500 Ti 0.6666 0.3333 0.7500 On Wed, Sep 2, 2009 at 9:28 PM, Giovanni Cantele < Giovanni.Cantele at na.infn.it> wrote: > Bertrand SITAMTZE wrote: > > Dear Giovanni, > > > > My coordinates are those taken from 2c position of > > the crystallographic space group table. I though these correspond to > > the default (alat) in quantum espresso, > > in which case mentioning is not mandatory. Isn't it? > > > > Thanks once more > > > > It is not mandatory to specify the default, but I'm not very sure that > your coordinates are in alat units. From > http://cst-www.nrl.navy.mil/lattice/struk/a3.html > I understand that (1/3,2/3,1/4) and (2/3,1/3,3/4) are in terms of the > A1, A2 and A3 vectors rather than > the x, y z axes versors. alat positions are cartesian coordinates (in > unit of celldm(1)), which are the same as crystal coordinates only for a > simple cubic lattice. > > If I'm not wrong, as pointed out by someone else, you should check that > the A1, A2, A3 choice shown in the > above link is the same as in Quantum-ESPRESSO (for the latter please > have a look to Doc/INPUT_PW* ). If not, you may specify your own lattice > vectors by using the CELL_PARAMETERS card. > > Giovanni > > > > > > --- En date de : *Mer 2.9.09, Giovanni Cantele > > //* a ?crit : > > > > > > De: Giovanni Cantele > > Objet: Re: [Pw_forum] Titanium atomic positions > > ?: "PWSCF Forum" > > Date: Mercredi 2 Septembre 2009, 16h48 > > > > Beside the check of the hcp unit cell, which is crucial, I also guess > > that you gave the input positions > > in "crystal" units, didn't you? If it is the case, I think that you > > should add the "{ crystal }" string after ATOMIC_POSITIONS. > > Indeed, the > > default is "alat" units, I think, namely, cartesian coordinates in > > celldm(1) units. > > > > Also do not forget to check the convergence of your results with > > respect > > to ecutrho. The default value (4*ecutwfc) must be usually > > increased (6 > > to 12 times ecutwfc) if, as in you case, ultrasoft > > pseudopotentials are > > used. > > > > Giovanni > > > > > > Hande Ustunel wrote: > > > Dear Bertrand, > > > > > > Your atomic positions are rather off with a large gap between > > rumpled Ti > > > layers. Perhaps you should double-check that your definition of > > the hcp > > > unit cell matches that for ibrav=4 in the code. You can find this > > > information in the Doc directory in your copy of espresso. > > > > > > Besides, you should be able to check your structure for yourself > > using > > > xcrysden (--pwi option). > > > > > > Best wishes, > > > Hande > > > > > > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > > > > > > > > >> Dear all, > > >> > > >> Titanium belongs to the hexagonal P63/mmc > > >> (n? 194) space group. I would like somebody to confirm that my > > attached > > >> input section concerning the bravais lattice and specially the > > atomic positions are good. > > >> > > >> &SYSTEM > > >> ibrav=4 > > >> celldm(1)=5.576203 > > >> celldm(3)=1.587874 > > >> nat=2 > > >> ntyp=1 > > >> ecutwfc=40.0 > > >> / > > >> &ELECTRONS > > >> diagonalization='cg' > > >> / > > >> ATOMIC_SPECIES > > >> Ti 47.867 Ti.pw91-nsp-van.UPF > > >> ATOMIC_POSITIONS > > >> Ti 0.3333 0..6666 0.2500 > > >> Ti 0.6666 0.3333 0.7500 > > >> K_POINTS automatic > > >> 8 8 4 0 0 0 > > >> > > >> > > >> Best regards > > > > ********************* > > Bertrand SITAMTZE > > PhD student > > Department of Physics > > University of Yaound? I-Cameroon > > *********************** > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > Skype contact: giocan74 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/f4c632e2/attachment-0001.htm From udayagiri3 at gmail.com Wed Sep 2 20:52:29 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Thu, 3 Sep 2009 00:22:29 +0530 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: References: <559538.73297.qm@web26505.mail.ukl.yahoo.com> <4A9E961B.5040706@na.infn.it> Message-ID: i am sorry for the previous message which i could not type completely.T his is what i mean for the ATOMIC_POSITIONS if you choose "crystal" your lattice coordinates are correct Ti 0.3333 0.6666 0.2500 Ti 0.6666 0.3333 0.7500 or else you can represent same as ATOMIC_POSITIONS (crystal) Ti 0 0 0 Ti 0.333333 0.666666 0.500000 both are same except they are displaced by (1/3,2/3,1/4) On Thu, Sep 3, 2009 at 12:18 AM, udayagiri sai babu wrote: > for the ATOMIC_POSITIONS if you choose "crystal" your lattice coordinates > are correct > Ti 0.3333 0.6666 0.2500 > Ti 0.6666 0.3333 0.7500 > > or else you can represent same as > ATOMIC_POSITIONS (crystal) > Ti 0 0.2500 > Ti 0.6666 0.3333 0.7500 > > On Wed, Sep 2, 2009 at 9:28 PM, Giovanni Cantele < > Giovanni.Cantele at na.infn.it> wrote: > >> Bertrand SITAMTZE wrote: >> > Dear Giovanni, >> > >> > My coordinates are those taken from 2c position of >> > the crystallographic space group table. I though these correspond to >> > the default (alat) in quantum espresso, >> > in which case mentioning is not mandatory. Isn't it? >> > >> > Thanks once more >> > >> >> It is not mandatory to specify the default, but I'm not very sure that >> your coordinates are in alat units. From >> http://cst-www.nrl.navy.mil/lattice/struk/a3.html >> I understand that (1/3,2/3,1/4) and (2/3,1/3,3/4) are in terms of the >> A1, A2 and A3 vectors rather than >> the x, y z axes versors. alat positions are cartesian coordinates (in >> unit of celldm(1)), which are the same as crystal coordinates only for a >> simple cubic lattice. >> >> If I'm not wrong, as pointed out by someone else, you should check that >> the A1, A2, A3 choice shown in the >> above link is the same as in Quantum-ESPRESSO (for the latter please >> have a look to Doc/INPUT_PW* ). If not, you may specify your own lattice >> vectors by using the CELL_PARAMETERS card. >> >> Giovanni >> >> >> > >> > --- En date de : *Mer 2.9.09, Giovanni Cantele >> > //* a ?crit : >> > >> > >> > De: Giovanni Cantele >> > Objet: Re: [Pw_forum] Titanium atomic positions >> > ?: "PWSCF Forum" >> > Date: Mercredi 2 Septembre 2009, 16h48 >> > >> > Beside the check of the hcp unit cell, which is crucial, I also >> guess >> > that you gave the input positions >> > in "crystal" units, didn't you? If it is the case, I think that you >> > should add the "{ crystal }" string after ATOMIC_POSITIONS. >> > Indeed, the >> > default is "alat" units, I think, namely, cartesian coordinates in >> > celldm(1) units. >> > >> > Also do not forget to check the convergence of your results with >> > respect >> > to ecutrho. The default value (4*ecutwfc) must be usually >> > increased (6 >> > to 12 times ecutwfc) if, as in you case, ultrasoft >> > pseudopotentials are >> > used. >> > >> > Giovanni >> > >> > >> > Hande Ustunel wrote: >> > > Dear Bertrand, >> > > >> > > Your atomic positions are rather off with a large gap between >> > rumpled Ti >> > > layers. Perhaps you should double-check that your definition of >> > the hcp >> > > unit cell matches that for ibrav=4 in the code. You can find this >> > > information in the Doc directory in your copy of espresso. >> > > >> > > Besides, you should be able to check your structure for yourself >> > using >> > > xcrysden (--pwi option). >> > > >> > > Best wishes, >> > > Hande >> > > >> > > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: >> > > >> > > >> > >> Dear all, >> > >> >> > >> Titanium belongs to the hexagonal P63/mmc >> > >> (n? 194) space group. I would like somebody to confirm that my >> > attached >> > >> input section concerning the bravais lattice and specially the >> > atomic positions are good. >> > >> >> > >> &SYSTEM >> > >> ibrav=4 >> > >> celldm(1)=5.576203 >> > >> celldm(3)=1.587874 >> > >> nat=2 >> > >> ntyp=1 >> > >> ecutwfc=40.0 >> > >> / >> > >> &ELECTRONS >> > >> diagonalization='cg' >> > >> / >> > >> ATOMIC_SPECIES >> > >> Ti 47.867 Ti.pw91-nsp-van.UPF >> > >> ATOMIC_POSITIONS >> > >> Ti 0.3333 0..6666 0.2500 >> > >> Ti 0.6666 0.3333 0.7500 >> > >> K_POINTS automatic >> > >> 8 8 4 0 0 0 >> > >> >> > >> >> > >> Best regards >> > >> > ********************* >> > Bertrand SITAMTZE >> > PhD student >> > Department of Physics >> > University of Yaound? I-Cameroon >> > *********************** >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> -- >> >> >> >> Dr. Giovanni Cantele >> Coherentia CNR-INFM and Dipartimento di Scienze Fisiche >> Universita' di Napoli "Federico II" >> Complesso Universitario di Monte S. Angelo - Ed. 6 >> Via Cintia, I-80126, Napoli, Italy >> Phone: +39 081 676910 >> Fax: +39 081 676346 >> E-mail: giovanni.cantele at cnr.it >> giovanni.cantele at na.infn.it >> Web: http://people.na.infn.it/~cantele >> Research Group: http://www.nanomat.unina.it >> Skype contact: giocan74 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/4fd0ffe6/attachment.htm From padmaja_patnaik at yahoo.co.uk Wed Sep 2 22:59:47 2009 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 2 Sep 2009 13:59:47 -0700 (PDT) Subject: [Pw_forum] occupancy number Message-ID: <291827.86577.qm@web26108.mail.ukl.yahoo.com> Dear all, ?Can anybody tell me how to know whether a state is fully or partially filled from the calculations using PWSCF. Also, how to know what is the number of occupancy in a state and the spin of the electrons in? a particular state. Thanks in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/83497154/attachment.htm From ttduyle at gmail.com Wed Sep 2 23:46:26 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 2 Sep 2009 17:46:26 -0400 Subject: [Pw_forum] occupancy number In-Reply-To: <291827.86577.qm@web26108.mail.ukl.yahoo.com> References: <291827.86577.qm@web26108.mail.ukl.yahoo.com> Message-ID: <8974d3b20909021446p7acbebb6v9ffd34c39eead9da@mail.gmail.com> Hi, Someone has answered your question yesterday. On Wed, Sep 2, 2009 at 4:59 PM, Padmaja Patnaik wrote: > Dear all, > Can anybody tell me how to know whether a state is fully or partially > filled from the calculations using PWSCF. Also, how to know what is the > number of occupancy in a state and the spin of the electrons in a > particular state. > > Thanks in advance, > regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090902/7d7f230e/attachment.htm From decboy9 at gmail.com Thu Sep 3 09:02:30 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 3 Sep 2009 12:32:30 +0530 Subject: [Pw_forum] problem in DOS caluclattion Message-ID: Hi 2 All, I have calculated the band structure of my system with occupancy =fixed as it is insulator. Then i tried to calculated LDOS and PDOS of the system using projwfc.x. But when i am plotting my total DOS i.e. the file "prefix.pdos_tot" , i am getting the DOS only corresponding to valance band. The conduction band peaks are missing. Means i am getting the # E (eV) dos(E) pdos(E) -15.000 0.916E-07 0.915E-07 / / 7.210 0.585E-04 0.582E-04 i.e. the energy range is Emin=-15 to Emax=7 ev, whereas my input file for projwfc is listed below, where i have given my Emax=15, &INPUTPP prefix='yvo', outdir='/home/physics/work/yvo/temp', ngauss=0, degauss=0.02, DeltaE=0.01, Emin=-15, Emax=15, / Please help. Thankful to all of you. Dev Sharma, University of delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/532fa66a/attachment.htm From lanhaiping at gmail.com Thu Sep 3 09:17:47 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 3 Sep 2009 15:17:47 +0800 Subject: [Pw_forum] problem in DOS caluclattion In-Reply-To: References: Message-ID: Hi, You need specify the number of bands when you adopt 'fixed' scheme for insulators. Hope it helps Regards Hai-Ping On Thu, Sep 3, 2009 at 3:02 PM, dev sharma wrote: > Hi 2 All, > > I have calculated the band structure of my system with occupancy =fixed > as it is insulator. Then i tried to calculated LDOS and PDOS of the system > using projwfc.x. But when i am plotting my total DOS i.e. the file > "prefix.pdos_tot" , i am getting the DOS only corresponding to valance > band. The conduction band peaks are missing. Means i am getting the > # E (eV) dos(E) pdos(E) > -15.000 0.916E-07 0.915E-07 > / > / > 7.210 0.585E-04 0.582E-04 > > i.e. the energy range is Emin=-15 to Emax=7 ev, whereas my input file for > projwfc is listed below, where i have given my Emax=15, > &INPUTPP > prefix='yvo', > outdir='/home/physics/work/yvo/temp', > ngauss=0, > degauss=0.02, > DeltaE=0.01, > Emin=-15, > Emax=15, > / > > Please help. Thankful to all of you. > > Dev Sharma, > University of delhi > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/3cb8b9cf/attachment.htm From sclauzer at sissa.it Thu Sep 3 09:25:12 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Sep 2009 09:25:12 +0200 Subject: [Pw_forum] problem in DOS caluclattion In-Reply-To: References: Message-ID: <4A9F6F58.8070509@sissa.it> That's right. More precisely, when you use fixed occupations, by default pw.x selects nbnd=nelec/2. In this way you don't know the eigenvalues for the empty states above the gap, so the projwfc.x code cannot compute pdos for energies higher than the top of the valence band. You have to increase nbnd higher than half the number of (valence) electrons and repeat the pdos calculation. HTH GS lan haiping wrote: > Hi, > You need specify the number of bands when you adopt 'fixed' scheme for > insulators. > > Hope it helps > Regards > > Hai-Ping > > On Thu, Sep 3, 2009 at 3:02 PM, dev sharma > wrote: > > Hi 2 All, > > I have calculated the band structure of my system with occupancy > =fixed as it is insulator. Then i tried to calculated LDOS and PDOS > of the system using projwfc.x. But when i am plotting my total DOS > i.e. the file "prefix.pdos_tot" , i am getting the DOS only > corresponding to valance band. The conduction band peaks are > missing. Means i am getting the > # E (eV) dos(E) pdos(E) > -15.000 0.916E-07 0.915E-07 > / > / > 7.210 0.585E-04 0.582E-04 > > i.e. the energy range is Emin=-15 to Emax=7 ev, whereas my input > file for projwfc is listed below, where i have given my Emax=15, > &INPUTPP > prefix='yvo', > outdir='/home/physics/work/yvo/temp', > ngauss=0, > degauss=0.02, > DeltaE=0.01, > Emin=-15, > Emax=15, > / > > Please help. Thankful to all of you. > > Dev Sharma, > University of delhi > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From degironc at sissa.it Thu Sep 3 09:41:33 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 03 Sep 2009 09:41:33 +0200 Subject: [Pw_forum] problem in DOS caluclattion In-Reply-To: References: Message-ID: <4A9F732D.7030603@sissa.it> Have you calculated enough bands ? You can use nbnd variable in system namelist in order to change the default value. Stefano de Gironcoli - SISSA and DEMOCRITOS dev sharma wrote: > Hi 2 All, > > I have calculated the band structure of my system with occupancy > =fixed as it is insulator. Then i tried to calculated LDOS and PDOS > of the system using projwfc.x. But when i am plotting my total DOS > i.e. the file "prefix.pdos_tot" , i am getting the DOS only > corresponding to valance band. The conduction band peaks are missing. > Means i am getting the > # E (eV) dos(E) pdos(E) > -15.000 0.916E-07 0.915E-07 > / > / > 7.210 0.585E-04 0.582E-04 > > i.e. the energy range is Emin=-15 to Emax=7 ev, whereas my input file > for projwfc is listed below, where i have given my Emax=15, > &INPUTPP > prefix='yvo', > outdir='/home/physics/work/yvo/temp', > ngauss=0, > degauss=0.02, > DeltaE=0.01, > Emin=-15, > Emax=15, > / > > Please help. Thankful to all of you. > > Dev Sharma, > University of delhi > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From siyouber at yahoo.fr Thu Sep 3 09:57:16 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Thu, 3 Sep 2009 00:57:16 -0700 (PDT) Subject: [Pw_forum] Titanium atomic positions In-Reply-To: Message-ID: <520777.84249.qm@web26505.mail.ukl.yahoo.com> Dear udayagiri, Thank very much for this clear answer. I will do it with ATOMIC_POSITIONS crystal Ti 0.3333? 0.6666? 0.2500 Ti 0.6666? 0.3333? 0.7500 Many thanks once again ********************* Bertrand SITAMTZE PhD student Department of Physics University of Yaound? I-Cameroon *********************** --- En date de?: Mer 2.9.09, udayagiri sai babu a ?crit?: De: udayagiri sai babu Objet: Re: [Pw_forum] Titanium atomic positions ?: Giovanni.Cantele at na.infn.it, "PWSCF Forum" Date: Mercredi 2 Septembre 2009, 20h52 i am sorry for the previous message which i could not type completely.T his is what i mean for the ATOMIC_POSITIONS if you choose "crystal" your lattice coordinates are correct Ti 0.3333? 0.6666? 0.2500 Ti 0.6666? 0.3333? 0.7500 or else you can represent same as ATOMIC_POSITIONS (crystal) Ti 0 0 0 Ti 0.333333? 0.666666? 0.500000 both are same except they are displaced by (1/3,2/3,1/4) On Thu, Sep 3, 2009 at 12:18 AM, udayagiri sai babu wrote: for the ATOMIC_POSITIONS if you choose "crystal" your lattice coordinates are correct Ti 0.3333? 0.6666? 0.2500 Ti 0.6666? 0.3333? 0.7500 or else you can represent same as ATOMIC_POSITIONS (crystal) Ti 0? 0.2500 Ti 0.6666? 0.3333? 0.7500 On Wed, Sep 2, 2009 at 9:28 PM, Giovanni Cantele wrote: Bertrand SITAMTZE wrote: > Dear Giovanni, > > My coordinates are those taken from 2c position of > the crystallographic space group ?table. I though these correspond to > the default (alat) in quantum espresso, > in which case mentioning is not mandatory. Isn't it? > > Thanks once more > It is not mandatory to specify the default, but I'm not very sure that your coordinates are in alat units. From http://cst-www.nrl.navy.mil/lattice/struk/a3.html I understand that (1/3,2/3,1/4) and (2/3,1/3,3/4) are in terms of the A1, A2 and A3 vectors rather than the x, y z axes versors. alat positions are cartesian coordinates (in unit of celldm(1)), which are the same as crystal coordinates only for a simple cubic lattice. If I'm not wrong, as pointed out by someone else, you should check that the A1, A2, A3 choice shown in the above link is the same as in Quantum-ESPRESSO (for the latter please have a look to Doc/INPUT_PW* ). If not, you may specify your own lattice vectors by using the CELL_PARAMETERS card. Giovanni > > --- En date de : *Mer 2.9.09, Giovanni Cantele > //* a ?crit : > > > ? ? De: Giovanni Cantele > ? ? Objet: Re: [Pw_forum] Titanium atomic positions > ? ? ?: "PWSCF Forum" > ? ? Date: Mercredi 2 Septembre 2009, 16h48 > > ? ? Beside the check of the hcp unit cell, which is crucial, I also guess > ? ? that you gave the input positions > ? ? in "crystal" units, didn't you? If it is the case, I think that you > ? ? should add the "{ crystal }" string after ATOMIC_POSITIONS. > ? ? Indeed, the > ? ? default is "alat" units, I think, namely, cartesian coordinates in > ? ? celldm(1) units. > > ? ? Also do not forget to check the convergence of your results with > ? ? respect > ? ? to ecutrho. The default value (4*ecutwfc) must be usually > ? ? increased (6 > ? ? to 12 times ecutwfc) if, as in you case, ultrasoft > ? ? pseudopotentials are > ? ? used. > > ? ? Giovanni > > > ? ? Hande Ustunel wrote: > ? ? > Dear Bertrand, > ? ? > > ? ? > Your atomic positions are rather off with a large gap between > ? ? rumpled Ti > ? ? > layers. Perhaps you should double-check that your definition of > ? ? the hcp > ? ? > unit cell matches that for ibrav=4 in the code. You can find this > ? ? > information in the Doc directory in your copy of espresso. > ? ? > > ? ? > Besides, you should be able to check your structure for yourself > ? ? using > ? ? > xcrysden (--pwi option). > ? ? > > ? ? > Best wishes, > ? ? > Hande > ? ? > > ? ? > On Wed, 2 Sep 2009, Bertrand SITAMTZE wrote: > ? ? > > ? ? > > ? ? >> Dear all, > ? ? >> > ? ? >> Titanium belongs to the ? ? hexagonal P63/mmc > ? ? >> (n? 194) space group. I would like somebody to confirm that my > ? ? attached > ? ? >> input section concerning the bravais lattice and specially the > ? ? atomic positions are good. > ? ? >> > ? ? >> &SYSTEM > ? ? >> ibrav=4 > ? ? >> celldm(1)=5.576203 > ? ? >> celldm(3)=1.587874 > ? ? >> nat=2 > ? ? >> ntyp=1 > ? ? >> ecutwfc=40.0 > ? ? >> / > ? ? >> &ELECTRONS > ? ? >> diagonalization='cg' > ? ? >> / > ? ? >> ATOMIC_SPECIES > ? ? >> Ti 47.867 Ti.pw91-nsp-van.UPF > ? ? >> ATOMIC_POSITIONS > ? ? >> Ti 0.3333 ?0..6666 ?0.2500 > ? ? >> Ti 0.6666 ?0.3333 ?0.7500 > ? ? >> K_POINTS automatic > ? ? >> 8 8 4 0 0 0 > ? ? >> > ? ? >> > ? ? >> Best regards > ********************* > ? ? Bertrand SITAMTZE > ? ? PhD student > ? ? Department of Physics > ? ? University of Yaound? I-Cameroon > ? ? ?*********************** > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: ? +39 081 676346 E-mail: giovanni.cantele at cnr.it ? ? ? ?giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/ade0a51c/attachment-0001.htm From sh.shapt at gmail.com Thu Sep 3 11:00:25 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Thu, 3 Sep 2009 10:00:25 +0100 Subject: [Pw_forum] Calculation of projected denstiy of states Message-ID: Hi there, I would like to know about the script file for calculating the projectedd ensity of state. As previously in my script file I gave written projwfc.x, however the programm was not accepted, thus I rename it to pw.x. Now my programm is in queu.So I donot know whether this time it will be accpeted or not. Will it work for pw.x in the script file for calculating the projected density of states? Thanks S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/fe134a8a/attachment.htm From decboy9 at gmail.com Thu Sep 3 10:31:09 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 3 Sep 2009 14:01:09 +0530 Subject: [Pw_forum] problem in DOS caluclattion In-Reply-To: <4A9F732D.7030603@sissa.it> References: <4A9F732D.7030603@sissa.it> Message-ID: Dear sir, In my structure , number of electrons= 192.00 and in my calculations =bands, I have already given nbnd= 115, which is greater then nelect/2 i.e. 96 but for the band structure. I want to know that for PDOS whether , i have to give nbnd in scf /nscf file ??? Thanks in advance, Dev Sharma On Thu, Sep 3, 2009 at 1:11 PM, Stefano de Gironcoli wrote: > Have you calculated enough bands ? > You can use nbnd variable in system namelist in order to change the > default value. > Stefano de Gironcoli - SISSA and DEMOCRITOS > > dev sharma wrote: > > Hi 2 All, > > > > I have calculated the band structure of my system with occupancy > > =fixed as it is insulator. Then i tried to calculated LDOS and PDOS > > of the system using projwfc.x. But when i am plotting my total DOS > > i.e. the file "prefix.pdos_tot" , i am getting the DOS only > > corresponding to valance band. The conduction band peaks are missing. > > Means i am getting the > > # E (eV) dos(E) pdos(E) > > -15.000 0.916E-07 0.915E-07 > > / > > / > > 7.210 0.585E-04 0.582E-04 > > > > i.e. the energy range is Emin=-15 to Emax=7 ev, whereas my input file > > for projwfc is listed below, where i have given my Emax=15, > > &INPUTPP > > prefix='yvo', > > outdir='/home/physics/work/yvo/temp', > > ngauss=0, > > degauss=0.02, > > DeltaE=0.01, > > Emin=-15, > > Emax=15, > > / > > > > Please help. Thankful to all of you. > > > > Dev Sharma, > > University of delhi > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/48249f27/attachment.htm From paulatto at sissa.it Thu Sep 3 11:19:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 03 Sep 2009 11:19:10 +0200 Subject: [Pw_forum] problem in DOS caluclattion In-Reply-To: References: <4A9F732D.7030603@sissa.it> Message-ID: In data 03 settembre 2009 alle ore 10:31:09, dev sharma ha scritto: > i > have to give nbnd in scf /nscf file ??? > Thanks in advance, I you have already computed the scf calculation you can just do an nscf one with increased number of bands. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Thu Sep 3 11:24:36 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 03 Sep 2009 11:24:36 +0200 Subject: [Pw_forum] Calculation of projected denstiy of states In-Reply-To: References: Message-ID: <4A9F8B54.1020008@sissa.it> Shaptrishi Sharma wrote: > Hi there, > I would like to know about the script file for calculating the > projectedd ensity of state. As previously in my script file I gave > written projwfc.x, however the programm was not accepted, thus I rename Was does it mean "not accepted" precisely??? Please report some error message! > it to pw.x. Now my programm is in queu.So I donot know whether this time > it will be accpeted or not. Have you compiled the postprocessing programs? Type 'make' to see the available targets, or 'make all' if you want to compile all the packages in the quantum-espresso suite. > > Will it work for pw.x in the script file for calculating the projected > density of states? No, pw.x does not compute DOS/PDOS. > > Thanks > > S Please supply your affiliation. Thanks! GS > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From eminekb at yahoo.com Thu Sep 3 11:46:32 2009 From: eminekb at yahoo.com (e kb) Date: Thu, 3 Sep 2009 02:46:32 -0700 (PDT) Subject: [Pw_forum] Calculation of projected denstiy of states In-Reply-To: Message-ID: <428017.67090.qm@web112617.mail.gq1.yahoo.com> Dear?Shaptrishi,I would like to help you out with your problem but I really cannot follow you.. What do you mean by ?your script of?projwfc.x was not accepted? projwfc.x was giving errors? are you able to successfully reproduce example08 reference results?I am totally lost about renaming projwfc.x to pw.x part of your issue.Please try to be more clear. Input& output files and errors can help us to understand what is going wrong.And instead of opening a new thread with the same title in every mail, you can simply reply so ppl can follow the thread easier later in the archive.cheers,emine kucukbenli,SISSA, Italy --- On Thu, 9/3/09, Shaptrishi Sharma wrote: From: Shaptrishi Sharma Subject: [Pw_forum] Calculation of projected denstiy of states To: pw_forum at pwscf.org Date: Thursday, September 3, 2009, 12:00 PM Hi there, I would like to know about the script file for calculating the projectedd ensity of state. As previously in my script file I gave written projwfc.x, however the programm was not accepted, thus I rename it to pw.x. Now my programm is in queu.So I donot know whether this time it will be accpeted or not. Will it work for pw.x in the script file for calculating the projected density of states? Thanks S -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/17c0da3d/attachment.htm From Silvia.Bakalova-Hadjikrasteva at bristol.ac.uk Thu Sep 3 15:52:06 2009 From: Silvia.Bakalova-Hadjikrasteva at bristol.ac.uk (Dr Silvia Bakalova) Date: Thu, 03 Sep 2009 14:52:06 +0100 Subject: [Pw_forum] Symmetry of the band states Message-ID: Hi, I have obtained the band structure, PDOS and dielectric function of B12As2 with QE (pw.x/projwfc.x/epsilon.x). I need some advice in how to determine the symmetry of the band states (classes of symmetry at high-symmetry points and for every band). So far: - I can determine which orbitals contribute to which band form the projections (s, pz, px? etc of As and B) - I printed the character table (indeed it is D_3d) Should I visualize the wfs and see their symmetry (symmetry under inversion / under reflection from vertical plane associated with the Laporte selection rule)? Thanks in advance, Silvia ---------------------- Dr. Silvia Bakalova, Post Doctoral Researcher, HH Wills Physics Laboratory, Bristol, BS8 1TL, UK http://spectra.phy.bris.ac.uk/ From yccheng.nju at gmail.com Thu Sep 3 16:20:37 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Thu, 3 Sep 2009 22:20:37 +0800 Subject: [Pw_forum] Symmetry of the band states In-Reply-To: References: Message-ID: I think bands.x is what you needs. You can find it in the QE package. 2009/9/3 Dr Silvia Bakalova > Hi, > I have obtained the band structure, PDOS and dielectric function of B12As2 > with QE (pw.x/projwfc.x/epsilon.x). > I need some advice in how to determine the symmetry of the band states > (classes of symmetry at high-symmetry points and for every band). So far: > - I can determine which orbitals contribute to which band form the > projections (s, pz, px? etc of As and B) > - I printed the character table (indeed it is D_3d) > Should I visualize the wfs and see their symmetry (symmetry under inversion > / under reflection from vertical plane associated with the Laporte > selection rule)? > Thanks in advance, > Silvia > > > ---------------------- > Dr. Silvia Bakalova, > Post Doctoral Researcher, > HH Wills Physics Laboratory, > Bristol, BS8 1TL, UK > http://spectra.phy.bris.ac.uk/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/1e0e7c5a/attachment.htm From nkxirainbow at gmail.com Thu Sep 3 16:21:40 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 3 Sep 2009 22:21:40 +0800 Subject: [Pw_forum] Symmetry of the band states In-Reply-To: References: Message-ID: <21fbc4790909030721n40598a92k5bc04061101667e6@mail.gmail.com> Dear Dr Silvia Bakalova: You can determine the symmetry of the band states by adding "lsym = true" in your xxx.bands.in file For example: &INPUTPP outdir = '/home/' , filband = 'xxxbands.dat' , lsym = .true. , / ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/108e6a85/attachment-0001.htm From kazempoor2000 at yahoo.com Thu Sep 3 17:25:36 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 3 Sep 2009 08:25:36 -0700 (PDT) Subject: [Pw_forum] GWW-band Message-ID: <372235.36792.qm@web112509.mail.gq1.yahoo.com> Hi all I am trying to use implemented approach GWW in espresso to obtain quasiparticle state for bulk TiO2 ,but I didn,t succeed to get true band gap by GW density of state. I used 10 10 12 kmesh for k sampling but I don't know which file and which rows contains dielectric constant. when I grep E_HEAD ,the last lines is E_HEAD : 58 (-0.288322417972075195E-19,-0.347622164532722579E-06) E_HEAD : 59 (0.136048521030191330E-19,-0.268035068560476896E-06) E_HEAD : 60 (-0.562749703002366818E-20,-0.199037475630983443E-06) E_HEAD : 61 (-0.246456835447587453E-19,-0.139320684851361126E-06) E_HEAD : 62 (-0.140385361912330342E-20,-0.874710056217020343E-07) E_HEAD : 63 (-0.136889611087276274E-19,-0.425462567302966249E-07) E_HEAD : 64 (0.768141330640736074E-21,-0.345502880250938209E-08) E_HEAD : 65 (0.107544342599385735E-20,0.304924298030858145E-07) E_HEAD : 66 (-0.671894800358640115E-21,0.599998026878208404E-07) E_HEAD : 67 (-0.375064376440559633E-20,0.856803318704701437E-07) E_HEAD : 68 (0.129039143800604427E-20,0.107981120709046864E-06) E_HEAD : 69 (-0.152241559615558039E-19,0.127297350596598846E-06) E_HEAD : 70 (-0.244342562407378874E-20,0.144032713772979207E-06) E_HEAD : 71 (0.198849485733610600E-19,0.158423408825083901E-06) E_HEAD : 72 (0.219404232386768220E-20,0.170765538857496266E-06) E_HEAD : 73 (0.813380241001557854E-20,0.181265846697849958E-06) E_HEAD : 74 (-0.509064059105312810E-20,0.190124058103262224E-06) E_HEAD : 75 (-0.107771697951803568E-19,0.197507480698692005E-06) E_HEAD : 76 (-0.755628381457475164E-20,0.203488676149189520E-06) E_HEAD : 77 (0.371877756929380836E-21,0.208211859121554605E-06) E_HEAD : 78 (-0.250163334688176281E-19,0.211741944281895265E-06) E_HEAD : 79 (-0.450176577358151232E-20,0.214163773837653336E-06) E_HEAD : 80 (0.111342594432056654E-20,0.215490995789092124E-06) what is these two columns? where do I look for dielectric constant? also when I grep the energy in exchange file I see X energy 1 -3.13056306094735648 X energy 2 -3.13125888267243768 X energy 3 -2.56505488760584210 X energy 4 -2.56505496437444780 X energy 5 -2.56683481217169884 X energy 6 -2.56683439322773843 X energy 7 -2.57403536452406989 X energy 8 -2.57295775811234151 X energy 9 -2.29952361470927169 X energy 10 -2.36757500687829703 X energy 11 -2.37632661585543126 X energy 12 -2.37632650375416299 X energy 13 -1.72370046221945539 X energy 14 -1.77636454255141807 X energy 15 -1.60170507625502379 X energy 16 -1.81076344235177400 X energy 17 -1.81076344671808909 X energy 18 -1.76589211249002198 X energy 19 -1.76589206392332332 X energy 20 -1.82208492695257473 X energy 21 -1.85042251355195186 X energy 22 -1.82815140295191192 X energy 23 -1.82815105271344058 X energy 24 -1.82718632043692120 X energy 25 -0.890395593964818821 X energy 26 -0.887974129642995047 X energy 27 -0.900839858974197383 X energy 28 -0.902277881230984180 X energy 29 -0.902276970932468392 X energy 30 -1.04934158998102989 X energy 31 -0.962865050316516147 X energy 32 -1.11061163384487793 X energy 33 -1.11061206732082796 X energy 34 -1.06420854530274700 X energy 35 -0.523436808399921905 X energy 36 -0.406604087930116875 X energy 37 -0.406604162637408506 X energy 38 -0.453038499132750461 X energy 39 -0.368261805733013314 X energy 40 -0.350145281021921162 X energy 41 -0.575993591072415878 X energy 42 -0.419593201827778928 X energy 43 -0.419593052276878598 X energy 44 -0.234200550211784625 X energy 45 -0.391296377238919968 X energy 46 -0.320118869687510410 X energy 47 -0.274223229681573089 X energy 48 -0.274223174645249645 X energy 49 -0.203773634312640867 X energy 50 -0.201021532629956590 and it seems to be converged. so what is the problem that I get very wide gap(about 10 eV)? I attach my script for this material. Please say how can I do that? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/50e2253c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: run_example Type: application/octet-stream Size: 9506 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090903/50e2253c/attachment.obj From decboy9 at gmail.com Thu Sep 3 17:54:36 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 3 Sep 2009 21:24:36 +0530 Subject: [Pw_forum] Titanium atomic positions In-Reply-To: <676184.81166.qm@web26506.mail.ukl.yahoo.com> References: <4A9E5104.8030600@democritos.it> <676184.81166.qm@web26506.mail.ukl.yahoo.com> Message-ID: hi , If your problem is solved then it is good, otherwise use the following co-ordinates coordinates --> atmoic positions{bohr} Ti 0.00000000000000 3.21920458635140 2.21041264840500 Ti 2.78791295220304 1.60960229317570 6.63123794521501 and if you want cell vectors also then these are, cell vectors 5.57582590440609 0.00000000000000 0.00000000000000 -2.78791295220304 4.82880688029501 0.00000000000000 0.00000000000000 0.00000000000000 8.84165059362001 Gud luck, Dev Sharma On Wed, Sep 2, 2009 at 7:36 PM, Bertrand SITAMTZE wrote: > > Dear all, > > Titanium belongs to the hexagonal P63/mmc (n? 194) space group. I would > like somebody to confirm that my attached > input section concerning the bravais lattice and specially the atomic > positions are good. > > &SYSTEM > ibrav=4 > celldm(1)=5.576203 > celldm(3)=1.587874 > nat=2 > ntyp=1 > ecutwfc=40.0 > / > &ELECTRONS > diagonalization='cg' > / > ATOMIC_SPECIES > Ti 47.867 Ti.pw91-nsp-van.UPF > ATOMIC_POSITIONS > Ti 0.3333 0.6666 0.2500 > Ti 0.6666 0.3333 0.7500 > K_POINTS automatic > 8 8 4 0 0 0 > > > Best regards > > ********************* > Bertrand SITAMTZE > PhD student > Department of Physics > University of Yaound? I-Cameroon > *********************** > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090903/9d92f99c/attachment-0001.htm From iori at theory.polytechnique.fr Thu Sep 3 17:55:00 2009 From: iori at theory.polytechnique.fr (iori at theory.polytechnique.fr) Date: Thu, 3 Sep 2009 17:55:00 +0200 (CEST) Subject: [Pw_forum] GWW-band In-Reply-To: <372235.36792.qm@web112509.mail.gq1.yahoo.com> References: <372235.36792.qm@web112509.mail.gq1.yahoo.com> Message-ID: <45181.155.185.13.41.1251993300.squirrel@theory.polytechnique.fr> hi. a very small comment: 1) keep in mind that for this kind of materials if you want to perform a nice GW calculation is bettter to use pseudopotential with semicore states inside. 2) are yiou sure to be converged with the kpoint ? 3) and in particular with the nunmber of G vectors? i think also the others with hands-on-gw in pwscf can tell you more about. ciao. federico iori. Dr. Federico Iori, PhD! Laboratoire des Solides Irradi?s, Ecole Polytechnique - CEA/DSM, CNRS 91128 Palaiseau, France www.etsf.polytechnique.fr phone: +33 (0) 1 69 33 44 85 emails: federico.iori @ polytechnique.edu iori.federico @ unimore.it http://www.pdmodena.it/ http://www.comune.mo.it > Hi all > > > I am trying to use implemented approach GWW in espresso to obtain > quasiparticle state for bulk TiO2 ,but I didn,t succeed to get true band > gap by GW density of state. > I used 10 10 12 kmesh for k sampling but I don't know which file and which > rows contains dielectric constant. when I grep E_HEAD ,the last lines is > E_HEAD : 58 (-0.288322417972075195E-19,-0.347622164532722579E-06) > E_HEAD : 59 (0.136048521030191330E-19,-0.268035068560476896E-06) > E_HEAD : 60 (-0.562749703002366818E-20,-0.199037475630983443E-06) > E_HEAD : 61 (-0.246456835447587453E-19,-0.139320684851361126E-06) > E_HEAD : 62 (-0.140385361912330342E-20,-0.874710056217020343E-07) > E_HEAD : 63 (-0.136889611087276274E-19,-0.425462567302966249E-07) > E_HEAD : 64 (0.768141330640736074E-21,-0.345502880250938209E-08) > E_HEAD : 65 (0.107544342599385735E-20,0.304924298030858145E-07) > E_HEAD : 66 (-0.671894800358640115E-21,0.599998026878208404E-07) > E_HEAD : 67 (-0.375064376440559633E-20,0.856803318704701437E-07) > E_HEAD : 68 (0.129039143800604427E-20,0.107981120709046864E-06) > E_HEAD : 69 (-0.152241559615558039E-19,0.127297350596598846E-06) > E_HEAD : 70 (-0.244342562407378874E-20,0.144032713772979207E-06) > E_HEAD : 71 (0.198849485733610600E-19,0.158423408825083901E-06) > E_HEAD : 72 (0.219404232386768220E-20,0.170765538857496266E-06) > E_HEAD : 73 (0.813380241001557854E-20,0.181265846697849958E-06) > E_HEAD : 74 (-0.509064059105312810E-20,0.190124058103262224E-06) > E_HEAD : 75 (-0.107771697951803568E-19,0.197507480698692005E-06) > E_HEAD : 76 (-0.755628381457475164E-20,0.203488676149189520E-06) > E_HEAD : 77 (0.371877756929380836E-21,0.208211859121554605E-06) > E_HEAD : 78 (-0.250163334688176281E-19,0.211741944281895265E-06) > E_HEAD : 79 (-0.450176577358151232E-20,0.214163773837653336E-06) > E_HEAD : 80 (0.111342594432056654E-20,0.215490995789092124E-06) > > > what is these two columns? where do I look for dielectric constant? > also when I grep the energy in exchange file I see > X energy 1 -3.13056306094735648 > X energy 2 -3.13125888267243768 > X energy 3 -2.56505488760584210 > X energy 4 -2.56505496437444780 > X energy 5 -2.56683481217169884 > X energy 6 -2.56683439322773843 > X energy 7 -2.57403536452406989 > X energy 8 -2.57295775811234151 > X energy 9 -2.29952361470927169 > X energy 10 -2.36757500687829703 > X energy 11 -2.37632661585543126 > X energy 12 -2.37632650375416299 > X energy 13 -1.72370046221945539 > X energy 14 -1.77636454255141807 > X energy 15 -1.60170507625502379 > X energy 16 -1.81076344235177400 > X energy 17 -1.81076344671808909 > X energy 18 -1.76589211249002198 > X energy 19 -1.76589206392332332 > X energy 20 -1.82208492695257473 > X energy 21 -1.85042251355195186 > X energy 22 -1.82815140295191192 > X energy 23 -1.82815105271344058 > X energy 24 -1.82718632043692120 > X energy 25 -0.890395593964818821 > X energy 26 -0.887974129642995047 > X energy 27 -0.900839858974197383 > X energy 28 -0.902277881230984180 > X energy 29 -0.902276970932468392 > X energy 30 -1.04934158998102989 > X energy 31 -0.962865050316516147 > X energy 32 -1.11061163384487793 > X energy 33 -1.11061206732082796 > X energy 34 -1.06420854530274700 > X energy 35 -0.523436808399921905 > X energy 36 -0.406604087930116875 > X energy 37 -0.406604162637408506 > X energy 38 -0.453038499132750461 > X energy 39 -0.368261805733013314 > X energy 40 -0.350145281021921162 > X energy 41 -0.575993591072415878 > X energy 42 -0.419593201827778928 > X energy 43 -0.419593052276878598 > X energy 44 -0.234200550211784625 > X energy 45 -0.391296377238919968 > X energy 46 -0.320118869687510410 > X energy 47 -0.274223229681573089 > X energy 48 -0.274223174645249645 > X energy 49 -0.203773634312640867 > X energy 50 -0.201021532629956590 > and it seems to be converged. > > > > so what is the problem that I get very wide gap(about 10 eV)? > I attach my script for this material. Please say how can I do that? > thanks a lot > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From colonel.sreekar at gmail.com Thu Sep 3 22:04:14 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Fri, 4 Sep 2009 01:34:14 +0530 Subject: [Pw_forum] references for philosophy of parallel execution Message-ID: hello QE users, i would be grateful if u could provide me with any references for the principles involved in parallel execution like how the grids are divided among processors which, should supposedly enhance perfomance, etc. because i performed a parallel execution and the CPU time taken is more than that in the serial case thnks in advance -- Sreekar Guddeti Physics Department IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/03b37fcb/attachment.htm From ferretti at MIT.EDU Thu Sep 3 22:17:14 2009 From: ferretti at MIT.EDU (Andrea Ferretti) Date: Thu, 3 Sep 2009 16:17:14 -0400 (EDT) Subject: [Pw_forum] references for philosophy of parallel execution In-Reply-To: Message-ID: Hi Sreekar, you can have a look at the QE user-guide, which comes along with the distribution in ~espresso/Doc . There you can find more than one sections devoted to parallelism in QE. Regards Andrea > hello QE users, > i would be grateful if u could provide me with any references for the > principles involved in parallel execution like how the grids are divided > among processors which, should supposedly enhance perfomance, etc. because i > performed a parallel execution and the CPU time taken is more than that in > the serial case > > thnks in advance > > > -- Andrea Ferretti MIT, Dept Material Science & Engineering bldg 13-4078, 77, Massachusetts Ave, Cambridge, MA Tel: +1 617-452-2455; Skype: andrea_ferretti URL: http://quasiamore.mit.edu Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From marc at fq.edu.uy Fri Sep 4 01:22:25 2009 From: marc at fq.edu.uy (Marc Segovia) Date: Thu, 03 Sep 2009 20:22:25 -0300 Subject: [Pw_forum] parallel matrix problem Message-ID: <4AA04FB1.8020007@fq.edu.uy> Dear all Up to now we are using espresso-4.0.4 serial 32 bit, a few days ago, we install espresso-4.1 parallel 64 bit, we made smalls tests with pw.x which runs well, now I try to do some cp.x, but an error appear likes below. from cyc2blk_redist : error # 1 inconsistent block dim nb I track the subroutine, error statement and variable definition, but still is unclear which is wrong, my guess is that some problem with parallel libraries , can someone guide me a bit. Thanking in advance your help Marc SUBROUTINE cyc2blk_redist( n, a, lda, nca, b, ldb, ncb, desc ) ! ! Parallel square matrix redistribution. ! A (input) is cyclically distributed by rows across processors ! B (output) is distributed by block across 2D processors grid ! ALLOCATE( sndbuf( nb/nproc+2, nb ) ) ALLOCATE( rcvbuf( nb/nproc+2, nb, nproc ) ) DO ip = 0, nproc - 1 ! IF( ip_desc( nlax_ , ip + 1 ) /= nb ) & CALL errore( ' cyc2blk_redist ', ' inconsistent block dim nb ', 1 ) np = desc( la_npr_ ) ! dimension of the processor mesh nb = desc( nlax_ ) ! leading dimension of the local matrix block me = desc( la_me_ ) ! my processor id (starting from 0) comm_a = desc( la_comm_ ) nproc = desc( la_npr_ ) * desc( la_npc_ ) -- ------------------------------------------------------------- Marc E. Segovia Becker, PhD,Ch.Eng Computational Chemistry and Biology Group, Detema Facultad de Quimica Universidad de la Republica CC 1157A 11800 Montevideo Uruguay www.ccbg.fq.edu.uy -------------------------------------------------------------- Models are not reality. Nao se afobe nao, que nada ? pra ja. Chico If things seem under control, you're just not going fast enough.Andretti Soy jardinero de mis dilemas.Drexler From marzari at MIT.EDU Fri Sep 4 03:52:10 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 03 Sep 2009 21:52:10 -0400 Subject: [Pw_forum] references for philosophy of parallel execution In-Reply-To: References: Message-ID: <4AA072CA.6030808@mit.edu> sreekar guddeti wrote: > hello QE users, > i would be grateful if u could provide me with any references for the > principles involved in parallel execution like how the grids are > divided among processors which, should supposedly enhance perfomance, > etc. because i performed a parallel execution and the CPU time taken > is more than that in the serial case > > thnks in advance > > Dear Sreekar, you could start with the QE reference paper (Stefano Baroni just posted its reference, freely accessible in the next 30 days on J Phys Cond Matt) and (I would guess) ref 167 and 168 there. If I remember correctly, a detailed explanation of parallelization in G space is in L. J. Clarke, I. Stich and M. C. Payne Large-scale ab initio total energy calculations on parallel computers Comput. Phys. Commun. 72 14 (1992) M. C. Payne, L. J. Clarke and I. Stich Role of parallel architectures in periodic boudnary calculations Phil Trans. Roy. Soc. A341 211 (1992) (the first ever electronic-structure calculations on parallel machines were done on the 7x7 Takanayagi Si(111) surface, by the group of Mike Payne in Cambridge, and separately John Joannopoulos at MIT) I think the G space parallelization of Espresso follows the same philosophy. Note that other parallelization schemes (read the QE article) such as those on the k-points, involve very little communications, and so they should be very efficient. More concise info on your system size you studied, and your parallelization strategy, could allow others to give you specific advice. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at democritos.it Fri Sep 4 08:45:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Sep 2009 08:45:40 +0200 Subject: [Pw_forum] parallel matrix problem In-Reply-To: <4AA04FB1.8020007@fq.edu.uy> References: <4AA04FB1.8020007@fq.edu.uy> Message-ID: <38C24D57-9E1B-450E-A1FF-3168C3E38B1B@democritos.it> On Sep 4, 2009, at 1:22 , Marc Segovia wrote: > from cyc2blk_redist : error # 1 > inconsistent block dim nb please provide a test job (or, better, file a bug report on qe-forge) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Fri Sep 4 09:44:26 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 04 Sep 2009 09:44:26 +0200 Subject: [Pw_forum] references for philosophy of parallel execution In-Reply-To: References: Message-ID: <4AA0C55A.30300@sissa.it> Dear Sreekar Guddeti, in addition to reading the documentation you have been pointed to, please take into account the hardware (cpu and communication network) you have at hand. R and G parallelization is memory efficient but involves large and frequent communications hence it will not be efficient unless your communication network is very good. For massively parallel machines (such as blue gene etc) one needs to introduce further divide and conquer tricks (see the discussion in our recently appeared "reference paper") Other types of parallelization (k-point, neb-images) involve much less communication and can be of help even if the network is not very good. In any case at the end of PWscf output there is some timing report that should tell you how much are you spending in computing and how much in communicating ... this should give you an idea whether increasing the number of cpus can help or actually worsen the performance Hope this helps, stefano de Gironcoli sreekar guddeti wrote: > hello QE users, > i would be grateful if u could provide me with any references for the > principles involved in parallel execution like how the grids are > divided among processors which, should supposedly enhance perfomance, > etc. because i performed a parallel execution and the CPU time taken > is more than that in the serial case > > thnks in advance > > > -- > Sreekar Guddeti > Physics Department > IIT Bombay > India > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From umari at democritos.it Fri Sep 4 11:10:27 2009 From: umari at democritos.it (umari at democritos.it) Date: Fri, 04 Sep 2009 11:10:27 +0200 Subject: [Pw_forum] GWW-band (P. Umari) Message-ID: <20090904111027.hyr4720hs00csosk@mail.democritos.it> Dear Ali, First of all, note that the GWW is implemented only at the gamma point, so it requires large supercells, (or better it is appropriate for non-crystalline systems). However the long-range parts of the symmetric dielectric matrix and of the screened-interaction can be calculated using k-points. With the code ph.x you are calculating the head and the wings of the symmetric dielectric matrix. E_HEAD are the head terms of the symmetric dielectric matrix calculated on the imaginary frequency axis (e.g. "E_HEAD : 58" is relative to the 58th frequency step). These terms together with the wings are calculated using linear response. Then, also the long range part (element G=0,G=0) of the screened interaction can also be calculated using a k-points grid. The calculated elements are <\Psi_i|G(i \tau)v|\Psi_i>, where \Psi_i are the KS states G(i\tau) is the KS Green function in imaginary time and v is the bare Coulomb interaction. The term "X energy 1" is the exchange energy relative to the 1st KS state. > I am trying to use implemented approach GWW in espresso to obtain > quasiparticle state for bulk TiO2 ,but I didn,t succeed to get true band > gap by GW density of state. > I used 10 10 12 kmesh for k sampling but I don't know which file and which > rows contains dielectric constant. when I grep E_HEAD ,the last lines is > E_HEAD : 58 (-0.288322417972075195E-19,-0.347622164532722579E-06) > E_HEAD : 59 (0.136048521030191330E-19,-0.268035068560476896E-06) ..... ..... > what is these two columns? where do I look for dielectric constant? > also when I grep the energy in exchange file I see > X energy 1 -3.13056306094735648 > X energy 2 -3.13125888267243768 Best regards, P. Umari (Democritos) ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From manoj at phys.ufl.edu Fri Sep 4 15:54:38 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 4 Sep 2009 09:54:38 -0400 (EDT) Subject: [Pw_forum] How to figure out machine accuracy In-Reply-To: <4AA04FB1.8020007@fq.edu.uy> Message-ID: Dear PWSCF users and developers, I am wondering how can one find machine accuracy? I am having some symmetry problem, and for that I want to solve eigen value problem with the best accuracy. In the lapack library it says- ABSTOL (input) DOUBLE PRECISION * The absolute error tolerance for the eigenvalues. * An approximate eigenvalue is accepted as converged * when it is determined to lie in an interval [a,b] * of width less than or equal to * * ABSTOL + EPS * max( |a|,|b| ) , * * where EPS is the machine precision. If ABSTOL is less than * or equal to zero, then EPS*|T| will be used in its place, * where |T| is the 1-norm of the tridiagonal matrix obtained * by reducing A to tridiagonal form. * * Eigenvalues will be computed most accurately when ABSTOL is * set to twice the underflow threshold 2*DLAMCH('S'), not zero. * If this routine returns with INFO>0, indicating that some * eigenvectors did not converge, try setting ABSTOL to * 2*DLAMCH('S'). the last paragraph is useful. so i looked up DLAMCH- DOUBLE PRECISION FUNCTION DLAMCH( CMACH ) The input is CMACH, I can specify various input variables for 'CMACH' to get output, but what variable is returned as output, as there is only one in this subroutine? Would you mind having a look at this- its in espresso4.0.4/flib/dlamch.f espresso4.0.4 can be replaced by whatever version you are using. Regards, Manoj Srivastava University of Florida Gainesville, USA From paulatto at sissa.it Fri Sep 4 16:15:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 04 Sep 2009 16:15:13 +0200 Subject: [Pw_forum] How to figure out machine accuracy In-Reply-To: References: Message-ID: In data 04 settembre 2009 alle ore 15:54:38, Manoj Srivastava ha scritto: > The input is CMACH, I can specify various input variables for 'CMACH' to > get output, but what variable is returned as output, as there is only one > in this subroutine? Would you mind having a look at this- its in > espresso4.0.4/flib/dlamch.f Dear Manoj, QE does not use simple LAPACK routines for most of its algebra. Hamiltonian diagonalization is computed using a custom implementation of the iterative Davidson (or conjugate-gradient) algorithm that only uses LAPACK to diagonalize a reduced hamiltonian during each iteration. Said that, you can control the accuracy to which eigenvalues are computed cannot be controlled directly by the user (without modifying the code) and is decreased automatically as the self-consistency approaches convergence. The formula used is the following: ethr = MIN( ethr, 0.1D0*dr2 / MAX( 1.D0, nelec ) ) where dr2 is the estimated scf accuracy. As you can see you can increase the accuracy (at convergence) of eigenvalues and eigenvectors by increasing the convergence threshold. In a more general frame, I think you could disclose some more information on your "symmetry problem"; personally I doubt it is caused by insufficient diagonalization accuracy. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From manoj at phys.ufl.edu Fri Sep 4 16:41:56 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 4 Sep 2009 10:41:56 -0400 (EDT) Subject: [Pw_forum] How to figure out machine accuracy In-Reply-To: Message-ID: Dear Lorenzo, Thank you for your reply. I figured out my problem. You are right, it is not coming from lapack routine. Regards, Manoj On Fri, 4 Sep 2009, Lorenzo Paulatto wrote: > In data 04 settembre 2009 alle ore 15:54:38, Manoj Srivastava > ha scritto: > > The input is CMACH, I can specify various input variables for 'CMACH' to > > get output, but what variable is returned as output, as there is only one > > in this subroutine? Would you mind having a look at this- its in > > espresso4.0.4/flib/dlamch.f > > > Dear Manoj, > QE does not use simple LAPACK routines for most of its algebra. > Hamiltonian diagonalization is computed using a custom implementation of > the iterative Davidson (or conjugate-gradient) algorithm that only uses > LAPACK to diagonalize a reduced hamiltonian during each iteration. > > Said that, you can control the accuracy to which eigenvalues are computed > cannot be controlled directly by the user (without modifying the code) and > is decreased automatically as the self-consistency approaches convergence. > > The formula used is the following: > ethr = MIN( ethr, 0.1D0*dr2 / MAX( 1.D0, nelec ) ) > where dr2 is the estimated scf accuracy. > As you can see you can increase the accuracy (at convergence) of > eigenvalues and eigenvectors by increasing the convergence threshold. > > > In a more general frame, I think you could disclose some more information > on your "symmetry problem"; personally I doubt it is caused by > insufficient diagonalization accuracy. > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From neelphysics at yahoo.in Fri Sep 4 18:14:16 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Fri, 4 Sep 2009 21:44:16 +0530 (IST) Subject: [Pw_forum] Help in using xcrysden for making structures Message-ID: <172991.32602.qm@web95007.mail.in2.yahoo.com> hi, I need some help in drawing crystal using xcrysden. Sir/Madam, let us take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that how can i draw my unit cell with giving positions of all the atoms without using the symmetries by xcrysden??. Means like if i specifiy, & system ibrav=2, celldm(1)=9.00, nat=1,...... ATOMIC POSITIONS{angstrom} A? 0? 4.5 0 now if we visualise this type of structure with Xcrysden, we found a number of atoms genrated due to symmetry. If i make a file like ?& system ibrav=2, celldm(1)=9.00, nat=18,...... ATOMIC POSITIONS{angstrom} A? 0? 4.5 0 / 18 times we have specified the co-ordinates / / A? 4.5 0 0 Xcrysden will give warning like atom 10 and 90 are very close like that. Sir i want to know is there any way so that i can make my PWSCF input file with angstrom/bohr postions such that with one atomic postion Xcrysden will show only one atom?? Means i will give 18 atomic postions and xcrysden will produce 18 atom unit cell without using symmatries. Thanks for your help, Neel Singh, Univeristy of Delhi, India See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/e7c0711c/attachment.htm From marzari at MIT.EDU Fri Sep 4 13:17:58 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 04 Sep 2009 07:17:58 -0400 Subject: [Pw_forum] Use of wannier90.x for the calculation of Born Effective Charge In-Reply-To: References: Message-ID: <4AA0F766.3000505@mit.edu> Dear Yukihiro, not sure if you got an answer (btw, this question might be more suited to the wannier mailing list) - but wouldn't it just require the calculation with the undisplaced Ti to be done with the exact same mesh of the displaced Ti ? A quick and dirty approach would be moving the Ti by a tiny amount, that essentially does not change the results for the cubic system, but is recognized by the code as off axis. Try 0.50001 and 0.500001. Note that BaTiO3 cubic has zero polarization, although that is not always the case (there is a 2007 review paper by Resta and Vanderbilt on this - e.g. from Vanderbilt's web site). nicola > If we set nosym in the input file of non-SCF calculation with k-points is > same as > > BaTiO3.win file., the symmetry of the results of wannier center > > broken, so the calculated Born Effective Charges are wrong. > > How should treat the k-points inconsistent when we calculate the Born > effective > > charge in displacing the atom. > > Here is my input file for BaTiO3.win. > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From ttduyle at gmail.com Fri Sep 4 20:08:25 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 4 Sep 2009 14:08:25 -0400 Subject: [Pw_forum] Help in using xcrysden for making structures In-Reply-To: <172991.32602.qm@web95007.mail.in2.yahoo.com> References: <172991.32602.qm@web95007.mail.in2.yahoo.com> Message-ID: <8974d3b20909041108m29d027a6k9abb46b80df0fb68@mail.gmail.com> If 1. you know there are 18 atoms in a unit cell 2. AND if you know their Cartesian coordinates 3. AND if you don't want to use the Bravais-lattice index, you could use 1. ibrav=0 2. AND define your unit cell (using CELL_PARAMETERS): nothing more than the 3 "primitive" lattice vectors 3. AND ATOMIC_POSITIONS: I suggest that you should use crystal coordinates instead of using Cartesian coordinates. You can find description in http://www.quantum-espresso.org/input-syntax/INPUT_PW.html :) On Fri, Sep 4, 2009 at 12:14 PM, Neel Singh wrote: > hi, > I need some help in drawing crystal using xcrysden. Sir/Madam, let us take > the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i > have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z} > of each atom in angstrom/bhor. I want to know that how can i draw my unit > cell with giving positions of all the atoms without using the symmetries by > xcrysden??. Means like if i specifiy, > & system > ibrav=2, celldm(1)=9.00, nat=1,...... > ATOMIC POSITIONS{angstrom} > A 0 4.5 0 > > now if we visualise this type of structure with Xcrysden, we found a number > of atoms genrated due to symmetry. If i make a file like > & system > ibrav=2, celldm(1)=9.00, nat=18,...... > ATOMIC POSITIONS{angstrom} > A 0 4.5 0 > / > 18 times we have specified the co-ordinates > / > / > A 4.5 0 0 > Xcrysden will give warning like atom 10 and 90 are very close like that. > Sir i want to know is there any way so that i can make my PWSCF input file > with angstrom/bohr postions such that with one atomic postion Xcrysden will > show only one atom?? > Means i will give 18 atomic postions and xcrysden will produce 18 atom unit > cell without using symmatries. > > Thanks for your help, > Neel Singh, > Univeristy of Delhi, > India > > ------------------------------ > See the Web's breaking stories, chosen by people like you. Check out Yahoo! > Buzz . > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/79ef42d9/attachment-0001.htm From mambom1902 at yahoo.com Sat Sep 5 03:59:30 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Fri, 4 Sep 2009 18:59:30 -0700 (PDT) Subject: [Pw_forum] Lowdin charge problem Message-ID: <845801.47719.qm@web38802.mail.mud.yahoo.com> Dear QE users, I try to analysis the atomic charge. I found that Lowdin charge analysis can be implemeted by QE. I dod a test with NO2. I get the the result as following: Lowdin Charges: ???? Atom #?? 1: total charge =?? 4.5377, s =? 1.2595, p =? 3.2782, ???????????????? spin up????? =?? 2.4718, s =? 0.7016, p =? 1.7701, ???????????????? spin down??? =?? 2.0659, s =? 0.5578, p =? 1.5081, ???????????????? polarization =?? 0.4058, s =? 0.1438, p =? 0.2620, ???? Atom #?? 2: total charge =?? 6.1075, s =? 1.7256, p =? 4.3818, ???????????????? spin up????? =?? 3.1926, s =? 0.8642, p =? 2.3284, ???????????????? spin down??? =?? 2.9149, s =? 0.8614, p =? 2.0534, ???????????????? polarization =?? 0.2777, s =? 0.0027, p =? 0.2749, ???? Atom #?? 3: total charge =?? 6.1113, s =? 1.7254, p =? 4.3859, ???????????????? spin up????? =?? 3.1939, s =? 0.8641, p =? 2.3298, ???????????????? spin down??? =?? 2.9174, s =? 0.8613, p =? 2.0561, ???????????????? polarization =?? 0.2765, s =? 0.0028, p =? 0.2737, The strange thing is that the total charge of all atom is ~16.7 instead of 17 in NO2 molecules. Can you give me some instructions or explanation to fix this problem? I great appreciate your help. Sincerely,?----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu From ttduyle at gmail.com Sat Sep 5 04:31:06 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 4 Sep 2009 22:31:06 -0400 Subject: [Pw_forum] Lowdin charge problem In-Reply-To: <845801.47719.qm@web38802.mail.mud.yahoo.com> References: <845801.47719.qm@web38802.mail.mud.yahoo.com> Message-ID: <8974d3b20909041931s1212c7b6xe4b739de25a4a40a@mail.gmail.com> Hi,I don't think you can get 17e for not only Lowdin charge but also others. This estimated charge does not follow the sum rule. I believe the "error" comes from the delocolized charge which can not be well estimated or taken in to account. D. On Fri, Sep 4, 2009 at 9:59 PM, loc duong ding wrote: > Dear QE users, > > I try to analysis the atomic charge. I found that Lowdin charge analysis > can be implemeted by QE. I dod a test with NO2. I get the the result as > following: > > Lowdin Charges: > Atom # 1: total charge = 4.5377, s = 1.2595, p = 3.2782, > spin up = 2.4718, s = 0.7016, p = 1.7701, > spin down = 2.0659, s = 0.5578, p = 1.5081, > polarization = 0.4058, s = 0.1438, p = 0.2620, > Atom # 2: total charge = 6.1075, s = 1.7256, p = 4.3818, > spin up = 3.1926, s = 0.8642, p = 2.3284, > spin down = 2.9149, s = 0.8614, p = 2.0534, > polarization = 0.2777, s = 0.0027, p = 0.2749, > Atom # 3: total charge = 6.1113, s = 1.7254, p = 4.3859, > spin up = 3.1939, s = 0.8641, p = 2.3298, > spin down = 2.9174, s = 0.8613, p = 2.0561, > polarization = 0.2765, s = 0.0028, p = 0.2737, > > The strange thing is that the total charge of all atom is ~16.7 instead of > 17 in NO2 molecules. > > Can you give me some instructions or explanation to fix this problem? > > I great appreciate your help. > > Sincerely, ----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/48e51ed7/attachment.htm From huilinhe at 126.com Sat Sep 5 10:35:33 2009 From: huilinhe at 126.com (huilinhe) Date: Sat, 5 Sep 2009 16:35:33 +0800 (CST) Subject: [Pw_forum] A question from He Lin In-Reply-To: References: Message-ID: <24151671.174831252139733379.JavaMail.coremail@bj126app32.126.com> Dear: I used ev.f90 ( in pwtools) to fit the equation of sates, and I am so confused. Does the program only deal with cubic or hexagonal systems? Can it deal with other systems? Such as Orthorhombic or Monoclinic system. Thank you1 He Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090905/f13f8a07/attachment.htm From siyouber at yahoo.fr Sat Sep 5 16:18:34 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Sat, 5 Sep 2009 07:18:34 -0700 (PDT) Subject: [Pw_forum] O.pw91-van_ak.UPF oxygen pseudopotential In-Reply-To: <24151671.174831252139733379.JavaMail.coremail@bj126app32.126.com> Message-ID: <999314.60572.qm@web26503.mail.ukl.yahoo.com> Dear all, ?I wanted to use the pseudopotential "O.pw91-van_ak.UPF" downloaded from the QE espresso web site. But there is something strange: In the human-readable section ?of the file, there are two unusual things: 1) The Rcut is set to 10.0000000. Is it not too high? According to me, this number should be between 0.90 and 1.20 2) The pricipal quantum number of the 2S state is set to 2, ?? and I think? it should be 1. I would like you to shed more light on this issue. A comment from somebody who has already use this pseudopotential is welcomed. Also, I would like you to confirm, as Lorenzo wrote some days ago, that a pseudowavefunction with opposite sign of that of all electron wavefunction is still valid Thanks for your reaction ******************** Bertrand SITAMTZE PhD Student Department of physics University of Yaound? I-Cameroon ************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090905/1f7990ff/attachment.htm From lfhuang at theory.issp.ac.cn Sat Sep 5 16:21:35 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Sat, 05 Sep 2009 22:21:35 +0800 Subject: [Pw_forum] =?utf-8?q?Lowdin_charge_problem?= Message-ID: <20090905142135.25526.qmail@ms.hfcas.ac.cn> Dear L. D. Ding: In my opinion, this kind of thing also can be understood from group theory for quantum mechanics: the "carrier space" of the eigen-function of bulk materials are not consistent with the one of the atomic wavefunctions, although both of them form orthogonal and complete basis sets. So the projection operation between the two spaces will miss some information. To some extent, this is the same as Duy Le's comment. Best Regards L. F. Huang Institute of Solid State Physics of China > 1. Lowdin charge problem (loc duong ding) > 2. Re: Lowdin charge problem (Duy Le) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 Sep 2009 18:59:30 -0700 (PDT) > From: loc duong ding > Subject: [Pw_forum] Lowdin charge problem > To: PWscf forum > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Dear QE users, > > I try to analysis the atomic charge. I found that Lowdin charge analysis can be implemeted by QE. I dod a test with NO2. I get the the result as following: > > Lowdin Charges: > ???? Atom #?? 1: total charge =?? 4.5377, s =? 1.2595, p =? 3.2782, > ???????????????? spin up????? =?? 2.4718, s =? 0.7016, p =? 1.7701, > ???????????????? spin down??? =?? 2.0659, s =? 0.5578, p =? 1.5081, > ???????????????? polarization =?? 0.4058, s =? 0.1438, p =? 0.2620, > ???? Atom #?? 2: total charge =?? 6.1075, s =? 1.7256, p =? 4.3818, > ???????????????? spin up????? =?? 3.1926, s =? 0.8642, p =? 2.3284, > ???????????????? spin down??? =?? 2.9149, s =? 0.8614, p =? 2.0534, > ???????????????? polarization =?? 0.2777, s =? 0.0027, p =? 0.2749, > ???? Atom #?? 3: total charge =?? 6.1113, s =? 1.7254, p =? 4.3859, > ???????????????? spin up????? =?? 3.1939, s =? 0.8641, p =? 2.3298, > ???????????????? spin down??? =?? 2.9174, s =? 0.8613, p =? 2.0561, > ???????????????? polarization =?? 0.2765, s =? 0.0028, p =? 0.2737, > > The strange thing is that the total charge of all atom is ~16.7 instead of 17 in NO2 molecules. > > Can you give me some instructions or explanation to fix this problem? > > I great appreciate your help. > > Sincerely,?----------------------------------------------- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 4 Sep 2009 22:31:06 -0400 > From: Duy Le > Subject: Re: [Pw_forum] Lowdin charge problem > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi,I don't think you can get 17e for not only Lowdin charge but also others. > This estimated charge does not follow the sum rule. I believe the "error" > comes from the delocolized charge which can not be well estimated or taken > in to account. > > D. > > On Fri, Sep 4, 2009 at 9:59 PM, loc duong ding wrote: > > > Dear QE users, > > > > I try to analysis the atomic charge. I found that Lowdin charge analysis > > can be implemeted by QE. I dod a test with NO2. I get the the result as > > following: > > > > Lowdin Charges: > > Atom # 1: total charge = 4.5377, s = 1.2595, p = 3.2782, > > spin up = 2.4718, s = 0.7016, p = 1.7701, > > spin down = 2.0659, s = 0.5578, p = 1.5081, > > polarization = 0.4058, s = 0.1438, p = 0.2620, > > Atom # 2: total charge = 6.1075, s = 1.7256, p = 4.3818, > > spin up = 3.1926, s = 0.8642, p = 2.3284, > > spin down = 2.9149, s = 0.8614, p = 2.0534, > > polarization = 0.2777, s = 0.0027, p = 0.2749, > > Atom # 3: total charge = 6.1113, s = 1.7254, p = 4.3859, > > spin up = 3.1939, s = 0.8641, p = 2.3298, > > spin down = 2.9174, s = 0.8613, p = 2.0561, > > polarization = 0.2765, s = 0.0028, p = 0.2737, > > > > The strange thing is that the total charge of all atom is ~16.7 instead of > > 17 in NO2 molecules. > > > > Can you give me some instructions or explanation to fix this problem? > > > > I great appreciate your help. > > > > Sincerely, ----------------------------------------------- > > Loc Duong Dinh > > Ms-Ph.D Student > > Sungkyunkwan Advanced Institute of Nanotechnology, > > Sungkyunkwan University, > > Suwon, 440-746, Korea > > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/48e51ed7/attachment.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 20 > **************************************** > ------ ====================================================================== L.F.Huang(???) ph.D candidate ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090905/4658f55f/attachment-0001.htm From marzari at MIT.EDU Sat Sep 5 16:35:51 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 05 Sep 2009 10:35:51 -0400 Subject: [Pw_forum] O.pw91-van_ak.UPF oxygen pseudopotential In-Reply-To: <999314.60572.qm@web26503.mail.ukl.yahoo.com> References: <999314.60572.qm@web26503.mail.ukl.yahoo.com> Message-ID: <4AA27747.9050909@mit.edu> Dear Bertran, others more conversant with the UPF format might answer better (http://www.quantum-espresso.org/wiki/index.php/Unified_pseudopotential_format) but I suspect that a large Rcut means just that the ultrasoft pseudo was not generated starting from a norm-conserving pseudo, but directly from an all-electron calculation, and the principal quantum number is exactly what it says - i.e. the principal quantum number (of the all electron calculation). Note that we found some oddities with the oxygen pseudopotential generated from David Vanderbilt's published table - we put a comment in the PBE version of it: http://quantum-espresso.org/pseudo/upfdetails.php?upf=O.pbe-van_bm.UPF The Bernd Meyer version above seems to have a smaller cutoff radius than the version converted by Axel (ak); still, I would be extra careful before using this, and consider instead the rrkj PBE pseudo of Andrea Dal Corso. I'd actually suggest to remove the O.pbe-van_bm.UPF from the pseudo table, alhough not sure what to do on the pw91-van_ak . nicola Bertrand SITAMTZE wrote: > Dear all, > > I wanted to use the pseudopotential "O.pw91-van_ak.UPF" downloaded > from the QE espresso web site.. But there is something strange: In the > human-readable section > of the file, there are two unusual things: > > 1) The Rcut is set to 10.0000000. Is it not too high? According to me, > this number should be between 0..90 and 1.20 > 2) The pricipal quantum number of the 2S state is set to 2, > and I think it should be 1. > > I would like you to shed more light on this issue. > A comment from somebody who has already use this pseudopotential is > welcomed. > > Also, I would like you to confirm, as Lorenzo > wrote some days ago, that a pseudowavefunction with > opposite sign of that of all electron wavefunction is still > valid > > Thanks for your reaction > > > ******************** > Bertrand SITAMTZE > PhD Student > Department of physics > University of Yaound? I-Cameroon > ************************ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at democritos.it Sat Sep 5 16:55:00 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 5 Sep 2009 16:55:00 +0200 Subject: [Pw_forum] O.pw91-van_ak.UPF oxygen pseudopotential In-Reply-To: <999314.60572.qm@web26503.mail.ukl.yahoo.com> References: <999314.60572.qm@web26503.mail.ukl.yahoo.com> Message-ID: <394A8A5B-7C70-4486-9BE2-FAF3C3CBDB6A@democritos.it> On Sep 5, 2009, at 16:18 , Bertrand SITAMTZE wrote: > 1) The Rcut is set to 10.0000000. Is it not too high? Rcut = radius for norm conserving pseudization > Rcutus=radius for ultrasoft pseudization For ultrasoft pseudopotentials generated using the Vanderbilt code, only the latter is significant. > 2) The pricipal quantum number of the 2S state is set to 2, > and I think it should be 1. it should be 1 when you generate the pseudopotential. > Also, I would like you to confirm, as Lorenzo wrote some days ago, > that a pseudowavefunction with opposite sign of that of all electron > wavefunction is still valid don't you trust Lorenzo on this issue? the overall sign of a radial wavefunction is arbitrary (it depends on how the integration algorithm starts the integration) P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Sat Sep 5 22:32:09 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 5 Sep 2009 22:32:09 +0200 Subject: [Pw_forum] O.pw91-van_ak.UPF oxygen pseudopotential In-Reply-To: <394A8A5B-7C70-4486-9BE2-FAF3C3CBDB6A@democritos.it> References: <999314.60572.qm@web26503.mail.ukl.yahoo.com> <394A8A5B-7C70-4486-9BE2-FAF3C3CBDB6A@democritos.it> Message-ID: <704995C7-1F3F-42AF-9BF6-EE275E52BA4B@sissa.it> On Sep 5, 2009, at 4:55 PM, Paolo Giannozzi wrote: >> Also, I would like you to confirm, as Lorenzo wrote some days ago, >> that a pseudowavefunction with opposite sign of that of all electron >> wavefunction is still valid > > don't you trust Lorenzo on this issue? the overall sign of a radial > wavefunction is arbitrary (it depends on how the integration > algorithm starts the integration) what Paolo justly says is a fundamental property of (linear and homogeneous) differential equations, which is also a fundamental property (or an axiom, if you prefer) of quantum mechanics: any wavefunction defines a quantum state modulo an arbitrary phase (or sign, if you restrict yourself to real wavefunctions) ... S. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090905/19c80c86/attachment.htm From colonel.sreekar at gmail.com Sun Sep 6 01:20:45 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sun, 6 Sep 2009 04:50:45 +0530 Subject: [Pw_forum] error loading shared libraries on parallel execution Message-ID: i know this issuehas been addressed and documented in troubleshooting section of the users guide. but i giveup in despair trying for a whole day to figure this problem i run my jobs on rocks cluster by using SGE's facility of submitting batch jobs http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html what i 'apparently' observe(or doubtfully infer) is that i can successfully run a single parallel job, but on submitting a second job i get the error ____________________________________________ /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory ____________________________________________ i find out the path for the library and added to the LD_LIBRARY_PATH by writing _______________________________________ #set the library path to include gfortran libraries export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib $ECHO $ECHO "$LD_LIBRARY_PATH" $ECHO _______________________________________ in the file which acts as script for qsub ($qsub -pe orte 4 dosroutine.qsub) which is dosroutine.qsub ----------------------------------------------------------------- #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash # #extract the info about no of processors involved from command line arguments of 'qsub' PROCESSORS=$NSLOTS #heuristically assign the no of processors per pool NPR NPR=4 #as a result no of pools are give by NPK=`expr $PROCESSORS / $NPR` #!/bin/bash # # #Script for performing a dos calculation on a parallel processor WORKINGDIR=`pwd` ECHO="echo" #set the library path to include gfortran libraries export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib $ECHO $ECHO "$LD_LIBRARY_PATH" $ECHO # set the needed environment variables PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` $ECHO $PREFIX BIN_DIR=$PREFIX/bin PSEUDO_DIR=$PREFIX/pseudo TMP_DIR=$HOME/tmp PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" PARA_POSTFIX="-npool $NPK" # required executables and pseudopotentials $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" #create results directory for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $WORKINGDIR/results # variables to represent programs PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" # DOS calculation for 0Ni0 cat > 0ni0.dos.in << EOF &control calculation='nscf' restart_mode='from_scratch', prefix='0ni0', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, nspin = 2, starting_magnetization(1)=0.7, ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, occupations='tetrahedra' / &electrons conv_thr = 1.0e-10 mixing_beta = 0.7 / ATOMIC_SPECIES Ni 58.69 NiUS.RRKJ3.UPF ATOMIC_POSITIONS Ni 0.0 0.0 0.0 K_POINTS {automatic} !special points generated by tetrahedra method 12 12 12 0 0 0 EOF $ECHO " running DOS calculation for 0Ni0 ...\c" $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out $ECHO $ECHO " done" ------------------------------------------------------------- the output i get is ************************************************ :/usr/lib64:/usr/lib /home3/colonel/espresso-4.0.5 executables directory: /home3/colonel/espresso-4.0.5/bin pseudo directory: /home3/colonel/espresso-4.0.5/pseudo temporary directory: /home3/colonel/tmp running DOS calculation for 0Ni0 ...\c /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory done ************************************************* plz suggest solutions which donot require root permissions , as i dont have thanks in advance -- Sreekar Guddeti Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/2e064769/attachment-0001.htm From ttduyle at gmail.com Sun Sep 6 01:39:17 2009 From: ttduyle at gmail.com (Duy Le) Date: Sat, 5 Sep 2009 19:39:17 -0400 Subject: [Pw_forum] error loading shared libraries on parallel execution In-Reply-To: References: Message-ID: <8974d3b20909051639u575aed19xdf474c53f9a7d877@mail.gmail.com> Hi,I am not sure if this help. Could you please try to add #$ -V in your submitting script. Like this: #!/bin/bash # #$ -V #$ -cwd #$ -j y #$ -S /bin/bash # Good luck. D. On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti wrote: > i know this issuehas been addressed and documented in troubleshooting > section of the users guide. > but i giveup in despair trying for a whole day to figure this problem > i run my jobs on rocks cluster by using SGE's facility of submitting batch > jobs > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > what i 'apparently' observe(or doubtfully infer) is that i can successfully > run a single parallel job, but on submitting a second job i get the error > ____________________________________________ > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > ____________________________________________ > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > writing > _______________________________________ > #set the library path to include gfortran libraries > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > $ECHO > $ECHO "$LD_LIBRARY_PATH" > $ECHO > _______________________________________ > > in the file which acts as script for qsub ($qsub -pe orte 4 > dosroutine.qsub) which is > > dosroutine.qsub > ----------------------------------------------------------------- > > #!/bin/bash > # > #$ -cwd > #$ -j y > #$ -S /bin/bash > # > > #extract the info about no of processors involved from command line > arguments of 'qsub' > PROCESSORS=$NSLOTS > > #heuristically assign the no of processors per pool NPR > NPR=4 > #as a result no of pools are give by > NPK=`expr $PROCESSORS / $NPR` > > #!/bin/bash > # > # > #Script for performing a dos calculation on a parallel processor > WORKINGDIR=`pwd` > ECHO="echo" > > #set the library path to include gfortran libraries > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > $ECHO > $ECHO "$LD_LIBRARY_PATH" > $ECHO > > # set the needed environment variables > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > $ECHO $PREFIX > BIN_DIR=$PREFIX/bin > PSEUDO_DIR=$PREFIX/pseudo > TMP_DIR=$HOME/tmp > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > PARA_POSTFIX="-npool $NPK" > > # required executables and pseudopotentials > $ECHO > $ECHO " executables directory: $BIN_DIR" > $ECHO " pseudo directory: $PSEUDO_DIR" > $ECHO " temporary directory: $TMP_DIR" > > #create results directory > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > if test ! -d $DIR ; then > mkdir $DIR > fi > done > cd $WORKINGDIR/results > > > # variables to represent programs > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > # DOS calculation for 0Ni0 > cat > 0ni0.dos.in << EOF > &control > calculation='nscf' > restart_mode='from_scratch', > prefix='0ni0', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > nspin = 2, starting_magnetization(1)=0.7, > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > occupations='tetrahedra' > / > &electrons > conv_thr = 1.0e-10 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > K_POINTS {automatic} !special points generated by tetrahedra method > 12 12 12 0 0 0 > EOF > > $ECHO " running DOS calculation for 0Ni0 ...\c" > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > $ECHO > $ECHO " done" > > ------------------------------------------------------------- > > the output i get is > > ************************************************ > :/usr/lib64:/usr/lib > > /home3/colonel/espresso-4.0.5 > > executables directory: /home3/colonel/espresso-4.0.5/bin > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > temporary directory: /home3/colonel/tmp > running DOS calculation for 0Ni0 ...\c > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > > done > ************************************************* > plz suggest solutions which donot require root permissions , as i dont have > thanks in advance > -- > Sreekar Guddeti > Department of Physics > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment.htm From wangqj1 at 126.com Sun Sep 6 02:33:25 2009 From: wangqj1 at 126.com (wangqj1) Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) Subject: [Pw_forum] pw.x running but nothing happens Message-ID: <25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com> Dear pwscf users When I run vc-relax on the computing cluster use one node which has 8 CPUs. The output file is as following: Program PWSCF v.4.0.1 starts ... Today is 6Sep2009 at 7:49:30 Parallel version (MPI) Number of processors in use: 8 R & G space division: proc/pool = 8 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW ..................................................................... Initial potential from superposition of free atoms starting charge 435.99565, renormalised to 436.00000 Starting wfc are 254 atomic + 8 random wfc After one day ,it still like this and no iteration has completed ,there is also no error was turn up .There is no error in the input file because I have test it on anthoer computer which has 4 CPUs and it runs well . I can't find the reason about this ,any help will be appreciated . Best Regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment.htm From bipulrr at gmail.com Sun Sep 6 08:58:49 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sun, 6 Sep 2009 07:58:49 +0100 Subject: [Pw_forum] error loading shared libraries on parallel execution In-Reply-To: References: Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5@mail.gmail.com> hi, Just from root user type yum install libgfortran.so.3 then it will install this files which is not present in your machine On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti wrote: > i know this issuehas been addressed and documented in troubleshooting > section of the users guide. > but i giveup in despair trying for a whole day to figure this problem > i run my jobs on rocks cluster by using SGE's facility of submitting batch > jobs > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > what i 'apparently' observe(or doubtfully infer) is that i can successfully > run a single parallel job, but on submitting a second job i get the error > ____________________________________________ > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > ____________________________________________ > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > writing > _______________________________________ > #set the library path to include gfortran libraries > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > $ECHO > $ECHO "$LD_LIBRARY_PATH" > $ECHO > _______________________________________ > > in the file which acts as script for qsub ($qsub -pe orte 4 > dosroutine.qsub) which is > > dosroutine.qsub > ----------------------------------------------------------------- > > #!/bin/bash > # > #$ -cwd > #$ -j y > #$ -S /bin/bash > # > > #extract the info about no of processors involved from command line > arguments of 'qsub' > PROCESSORS=$NSLOTS > > #heuristically assign the no of processors per pool NPR > NPR=4 > #as a result no of pools are give by > NPK=`expr $PROCESSORS / $NPR` > > #!/bin/bash > # > # > #Script for performing a dos calculation on a parallel processor > WORKINGDIR=`pwd` > ECHO="echo" > > #set the library path to include gfortran libraries > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > $ECHO > $ECHO "$LD_LIBRARY_PATH" > $ECHO > > # set the needed environment variables > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > $ECHO $PREFIX > BIN_DIR=$PREFIX/bin > PSEUDO_DIR=$PREFIX/pseudo > TMP_DIR=$HOME/tmp > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > PARA_POSTFIX="-npool $NPK" > > # required executables and pseudopotentials > $ECHO > $ECHO " executables directory: $BIN_DIR" > $ECHO " pseudo directory: $PSEUDO_DIR" > $ECHO " temporary directory: $TMP_DIR" > > #create results directory > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > if test ! -d $DIR ; then > mkdir $DIR > fi > done > cd $WORKINGDIR/results > > > # variables to represent programs > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > # DOS calculation for 0Ni0 > cat > 0ni0.dos.in << EOF > &control > calculation='nscf' > restart_mode='from_scratch', > prefix='0ni0', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > nspin = 2, starting_magnetization(1)=0.7, > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > occupations='tetrahedra' > / > &electrons > conv_thr = 1.0e-10 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > K_POINTS {automatic} !special points generated by tetrahedra method > 12 12 12 0 0 0 > EOF > > $ECHO " running DOS calculation for 0Ni0 ...\c" > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > $ECHO > $ECHO " done" > > ------------------------------------------------------------- > > the output i get is > > ************************************************ > :/usr/lib64:/usr/lib > > /home3/colonel/espresso-4.0.5 > > executables directory: /home3/colonel/espresso-4.0.5/bin > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > temporary directory: /home3/colonel/tmp > running DOS calculation for 0Ni0 ...\c > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > libraries: libgfortran.so.3: cannot open shared object file: No such > file or directory > > done > ************************************************* > plz suggest solutions which donot require root permissions , as i dont have > thanks in advance > -- > Sreekar Guddeti > Department of Physics > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment-0001.htm From bipulrr at gmail.com Sun Sep 6 09:03:29 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sun, 6 Sep 2009 08:03:29 +0100 Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: <25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com> References: <25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com> Message-ID: <3a749910909060003k38e7f62fn4aa040900b71b42c@mail.gmail.com> Dear Wangqj, The same thing happens to me. since you are using large no. of wfc, although it shows the job is running in 8 procs, but sometimes if the installation is not proper, it is running in 1 procs only. So better you check the parallel installation using a small job, with different no. of procs and see whether its taking lesser time as no. of procs increases or not? cheers 2009/9/6 wangqj1 > > Dear pwscf users > When I run vc-relax on the computing cluster use one node which has 8 > CPUs. > The output file is as following: > > Program PWSCF v.4.0.1 starts ... > Today is 6Sep2009 at 7:49:30 > Parallel version (MPI) > Number of processors in use: 8 > R & G space division: proc/pool = 8 > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > ..................................................................... > Initial potential from superposition of free atoms > starting charge 435.99565, renormalised to 436.00000 > Starting wfc are 254 atomic + 8 random wfc > > After one day ,it still like this and no iteration has completed ,there is > also no error was turn up .There is no error in the input file because I > have test it on anthoer computer which has 4 CPUs and it runs well . > I can't find the reason about this ,any help will be appreciated . > Best Regards > Q.J.Wang > XiangTan University > > > > ------------------------------ > ???????????,www.yeah.net > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment.htm From mansourehp at gmail.com Sun Sep 6 09:55:06 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sun, 6 Sep 2009 11:25:06 +0330 Subject: [Pw_forum] pseudo potential Message-ID: Dear all how can I plot these pseudo potentials? how can I discribe the properties of pseudo potentials? *Fe.pbe-nd-rrkjus.UPF* ( *details*) Perdew-Burke-Ernzerhof (PBE) exch-corr nonlinear core-correction semicore state d in valence Rabe Rappe Kaxiras Joannopoulos (ultrasoft) and *H.pbe-rrkjus.UPF* (*details* ) Perdew-Burke-Ernzerhof (PBE) exch-corr Rabe Rappe Kaxiras Joannopoulos (ultrasoft) and *O.pbe-rrkjus.UPF* (*details* ) Perdew-Burke-Ernzerhof (PBE) exch-corr Rabe Rappe Kaxiras Joannopoulos (ultrasoft) Thanks Mansoureh Pashangpour Ph.D student Islami Azad university science & reaserch branch Tehran, IRAN -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment.htm From giannozz at democritos.it Sun Sep 6 10:24:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 6 Sep 2009 10:24:48 +0200 Subject: [Pw_forum] error loading shared libraries on parallel execution In-Reply-To: References: Message-ID: On Sep 6, 2009, at 1:20 , sreekar guddeti wrote: > plz suggest solutions which donot require root permissions , > as i dont have somebody must have it. Report the problem and the solution (i.e. install gfortran on ALL processors) to whoever has root access. As an alternative, try static link (add -static to LDFLAGS in make.sys). --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From paulatto at sissa.it Sun Sep 6 12:20:40 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST) Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: <25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com> References: <25470012.218281252197205181.JavaMail.coremail@bj126app52.126.com> Message-ID: <46134.78.12.159.112.1252232440.squirrel@webmail.sissa.it> On Sun, September 6, 2009 02:33, wangqj1 wrote: > After one day ,it still like this and no iteration has completed ,there > is > also no error was turn up .There is no error in the input file because I > have test it on anthoer computer which has 4 CPUs and it runs well . > I can't find the reason about this ,any help will be appreciated . Dear QJ, this is strange. But we would need more information on your hardwre configuration in order to help you. In the mean while you can check the behaviour of te pw.x processes with "top". E.g. if they are all runing at 100% CPU, how much memory they are taking and so on. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From colonel.sreekar at gmail.com Sun Sep 6 20:05:26 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sun, 6 Sep 2009 23:35:26 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23 In-Reply-To: References: Message-ID: @duy lee i inserted the line #$ -V in my qsub script and the env variable $LD_LIBRARY_PATH is being set from script... thanks for that but still problem persists. @rakshit ----------------------------- $find /usr/lib -name libgfortran* ----------------------------- and output is _______________________ /usr/lib/libgfortran.so.1.0.0 /usr/lib/libgfortran.so.1 /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so _______________________ whereas on doing ----------------------------- $find /usr/lib64 -name libgfortran* ----------------------------- ouput is _________________ /usr/lib64/libgfortran.so.3.0.0 /usr/lib64/libgfortran.so.1.0.0 /usr/lib64/libgfortran.so.1 find: /usr/lib64/audit: Permission denied */usr/lib64/libgfortran.so.3* _________________ it means my OS has the required library, i guess i installed the QE on the head node This cluster is a Rocks cluster with # of nodes: 10 (1 head node + 9 compute nodes) # of processors/node: 8 # Total # of processors: 10X8 = 80 i tested the sample program for submitting batch jobs using SGE utility and it is working fine( http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html) sincerely, sreekar guddeti Dept. Physics IIT Bombay India On Sun, Sep 6, 2009 at 12:28 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: error loading shared libraries on parallel execution (Duy Le) > 2. pw.x running but nothing happens (wangqj1) > 3. Re: error loading shared libraries on parallel execution > (Bipul Rakshit) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 5 Sep 2009 19:39:17 -0400 > From: Duy Le > Subject: Re: [Pw_forum] error loading shared libraries on parallel > execution > To: PWSCF Forum > Message-ID: > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi,I am not sure if this help. Could you please try to add > #$ -V in your submitting script. Like this: > > #!/bin/bash > # > #$ -V > #$ -cwd > #$ -j y > #$ -S /bin/bash > # > > Good luck. > D. > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti > wrote: > > > i know this issuehas been addressed and documented in troubleshooting > > section of the users guide. > > but i giveup in despair trying for a whole day to figure this problem > > i run my jobs on rocks cluster by using SGE's facility of submitting > batch > > jobs > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > what i 'apparently' observe(or doubtfully infer) is that i can > successfully > > run a single parallel job, but on submitting a second job i get the error > > ____________________________________________ > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > ____________________________________________ > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > > writing > > _______________________________________ > > #set the library path to include gfortran libraries > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > $ECHO > > $ECHO "$LD_LIBRARY_PATH" > > $ECHO > > _______________________________________ > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > dosroutine.qsub) which is > > > > dosroutine.qsub > > ----------------------------------------------------------------- > > > > #!/bin/bash > > # > > #$ -cwd > > #$ -j y > > #$ -S /bin/bash > > # > > > > #extract the info about no of processors involved from command line > > arguments of 'qsub' > > PROCESSORS=$NSLOTS > > > > #heuristically assign the no of processors per pool NPR > > NPR=4 > > #as a result no of pools are give by > > NPK=`expr $PROCESSORS / $NPR` > > > > #!/bin/bash > > # > > # > > #Script for performing a dos calculation on a parallel processor > > WORKINGDIR=`pwd` > > ECHO="echo" > > > > #set the library path to include gfortran libraries > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > $ECHO > > $ECHO "$LD_LIBRARY_PATH" > > $ECHO > > > > # set the needed environment variables > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > $ECHO $PREFIX > > BIN_DIR=$PREFIX/bin > > PSEUDO_DIR=$PREFIX/pseudo > > TMP_DIR=$HOME/tmp > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > PARA_POSTFIX="-npool $NPK" > > > > # required executables and pseudopotentials > > $ECHO > > $ECHO " executables directory: $BIN_DIR" > > $ECHO " pseudo directory: $PSEUDO_DIR" > > $ECHO " temporary directory: $TMP_DIR" > > > > #create results directory > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > if test ! -d $DIR ; then > > mkdir $DIR > > fi > > done > > cd $WORKINGDIR/results > > > > > > # variables to represent programs > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > # DOS calculation for 0Ni0 > > cat > 0ni0.dos.in << EOF > > &control > > calculation='nscf' > > restart_mode='from_scratch', > > prefix='0ni0', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > / > > &system > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > nspin = 2, starting_magnetization(1)=0.7, > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > occupations='tetrahedra' > > / > > &electrons > > conv_thr = 1.0e-10 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Ni 58.69 NiUS.RRKJ3.UPF > > ATOMIC_POSITIONS > > Ni 0.0 0.0 0.0 > > K_POINTS {automatic} !special points generated by tetrahedra > method > > 12 12 12 0 0 0 > > EOF > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > $ECHO > > $ECHO " done" > > > > ------------------------------------------------------------- > > > > the output i get is > > > > ************************************************ > > :/usr/lib64:/usr/lib > > > > /home3/colonel/espresso-4.0.5 > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > temporary directory: /home3/colonel/tmp > > running DOS calculation for 0Ni0 ...\c > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > > > done > > ************************************************* > > plz suggest solutions which donot require root permissions , as i dont > have > > thanks in advance > > -- > > Sreekar Guddeti > > Department of Physics > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > From: wangqj1 > Subject: [Pw_forum] pw.x running but nothing happens > To: pw_forum > Message-ID: > <25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com> > Content-Type: text/plain; charset="gbk" > > > Dear pwscf users > When I run vc-relax on the computing cluster use one node which has 8 > CPUs. > The output file is as following: > > Program PWSCF v.4.0.1 starts ... > Today is 6Sep2009 at 7:49:30 > Parallel version (MPI) > Number of processors in use: 8 > R & G space division: proc/pool = 8 > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > ..................................................................... > Initial potential from superposition of free atoms > starting charge 435.99565, renormalised to 436.00000 > Starting wfc are 254 atomic + 8 random wfc > > After one day ,it still like this and no iteration has completed ,there is > also no error was turn up .There is no error in the input file because I > have test it on anthoer computer which has 4 CPUs and it runs well . > I can't find the reason about this ,any help will be appreciated . > Best Regards > Q.J.Wang > XiangTan University > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sun, 6 Sep 2009 07:58:49 +0100 > From: Bipul Rakshit > Subject: Re: [Pw_forum] error loading shared libraries on parallel > execution > To: PWSCF Forum > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hi, > Just from root user type > yum install libgfortran.so.3 > > then it will install this files which is not present in your machine > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti > wrote: > > > i know this issuehas been addressed and documented in troubleshooting > > section of the users guide. > > but i giveup in despair trying for a whole day to figure this problem > > i run my jobs on rocks cluster by using SGE's facility of submitting > batch > > jobs > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > what i 'apparently' observe(or doubtfully infer) is that i can > successfully > > run a single parallel job, but on submitting a second job i get the error > > ____________________________________________ > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > ____________________________________________ > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > > writing > > _______________________________________ > > #set the library path to include gfortran libraries > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > $ECHO > > $ECHO "$LD_LIBRARY_PATH" > > $ECHO > > _______________________________________ > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > dosroutine.qsub) which is > > > > dosroutine.qsub > > ----------------------------------------------------------------- > > > > #!/bin/bash > > # > > #$ -cwd > > #$ -j y > > #$ -S /bin/bash > > # > > > > #extract the info about no of processors involved from command line > > arguments of 'qsub' > > PROCESSORS=$NSLOTS > > > > #heuristically assign the no of processors per pool NPR > > NPR=4 > > #as a result no of pools are give by > > NPK=`expr $PROCESSORS / $NPR` > > > > #!/bin/bash > > # > > # > > #Script for performing a dos calculation on a parallel processor > > WORKINGDIR=`pwd` > > ECHO="echo" > > > > #set the library path to include gfortran libraries > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > $ECHO > > $ECHO "$LD_LIBRARY_PATH" > > $ECHO > > > > # set the needed environment variables > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > $ECHO $PREFIX > > BIN_DIR=$PREFIX/bin > > PSEUDO_DIR=$PREFIX/pseudo > > TMP_DIR=$HOME/tmp > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > PARA_POSTFIX="-npool $NPK" > > > > # required executables and pseudopotentials > > $ECHO > > $ECHO " executables directory: $BIN_DIR" > > $ECHO " pseudo directory: $PSEUDO_DIR" > > $ECHO " temporary directory: $TMP_DIR" > > > > #create results directory > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > if test ! -d $DIR ; then > > mkdir $DIR > > fi > > done > > cd $WORKINGDIR/results > > > > > > # variables to represent programs > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > # DOS calculation for 0Ni0 > > cat > 0ni0.dos.in << EOF > > &control > > calculation='nscf' > > restart_mode='from_scratch', > > prefix='0ni0', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > / > > &system > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > nspin = 2, starting_magnetization(1)=0.7, > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > occupations='tetrahedra' > > / > > &electrons > > conv_thr = 1.0e-10 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Ni 58.69 NiUS.RRKJ3.UPF > > ATOMIC_POSITIONS > > Ni 0.0 0.0 0.0 > > K_POINTS {automatic} !special points generated by tetrahedra > method > > 12 12 12 0 0 0 > > EOF > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > $ECHO > > $ECHO " done" > > > > ------------------------------------------------------------- > > > > the output i get is > > > > ************************************************ > > :/usr/lib64:/usr/lib > > > > /home3/colonel/espresso-4.0.5 > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > temporary directory: /home3/colonel/tmp > > running DOS calculation for 0Ni0 ...\c > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > libraries: libgfortran.so.3: cannot open shared object file: No such > > file or directory > > > > done > > ************************************************* > > plz suggest solutions which donot require root permissions , as i dont > have > > thanks in advance > > -- > > Sreekar Guddeti > > Department of Physics > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 23 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment-0001.htm From colonel.sreekar at gmail.com Mon Sep 7 01:53:12 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 7 Sep 2009 05:23:12 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 24 In-Reply-To: References: Message-ID: i have set variable LD_FLAGS = static in make.sys file and on $make all i get error ---------------------------------------- libiotk.a mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -c iotk_print_kinds.f90 make loclib_only make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src' make[3]: Nothing to be done for `loclib_only'. make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a /opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open': (.text+0x123): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /opt/openmpi/lib/libopen-rte.a(sys_info.o): In function `orte_sys_info': (.text+0x16f): warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname': (.text+0x780): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `__malloc_check_init': (.text+0x1060): multiple definition of `__malloc_check_init' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first defined here /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 144 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_free': (.text+0x2230): multiple definition of `_int_free' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first defined here /usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_malloc': (.text+0x2a50): multiple definition of `_int_malloc' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first defined here /usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_memalign': (.text+0x3900): multiple definition of `_int_memalign' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first defined here /usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_valloc': (.text+0x3c30): multiple definition of `_int_valloc' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first defined here /usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `_int_realloc': (.text+0x3d80): multiple definition of `_int_realloc' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first defined here /usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `free': (.text+0x5f20): multiple definition of `free' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first defined here /usr/bin/ld: Warning: size of symbol `free' changed from 256 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `malloc': (.text+0x4690): multiple definition of `malloc' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first defined here /usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): In function `realloc': (.text+0x60f0): multiple definition of `realloc' /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first defined here /usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) collect2: ld returned 1 exit status make[2]: *** [iotk_print_kinds.x] Error 1 make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' make[1]: *** [lib+util] Error 2 make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk' make: *** [libiotk] Error 2 --------------------------------------------- sincerely On Sun, Sep 6, 2009 at 11:35 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: pw.x running but nothing happens (Bipul Rakshit) > 2. pseudo potential (Mansoureh Pashangpour) > 3. Re: error loading shared libraries on parallel execution > (Paolo Giannozzi) > 4. Re: pw.x running but nothing happens (Lorenzo Paulatto) > 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 6 Sep 2009 08:03:29 +0100 > From: Bipul Rakshit > Subject: Re: [Pw_forum] pw.x running but nothing happens > To: PWSCF Forum > Message-ID: > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> > Content-Type: text/plain; charset="gb2312" > > Dear Wangqj, > The same thing happens to me. > since you are using large no. of wfc, although it shows the job is running > in 8 procs, but sometimes if the installation is not proper, it is running > in 1 procs only. > > So better you check the parallel installation using a small job, with > different no. of procs and see whether its taking lesser time as no. of > procs increases or not? > > cheers > > 2009/9/6 wangqj1 > > > > > Dear pwscf users > > When I run vc-relax on the computing cluster use one node which has > 8 > > CPUs. > > The output file is as following: > > > > Program PWSCF v.4.0.1 starts ... > > Today is 6Sep2009 at 7:49:30 > > Parallel version (MPI) > > Number of processors in use: 8 > > R & G space division: proc/pool = 8 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > PAW > > ..................................................................... > > Initial potential from superposition of free atoms > > starting charge 435.99565, renormalised to 436.00000 > > Starting wfc are 254 atomic + 8 random wfc > > > > After one day ,it still like this and no iteration has completed ,there > is > > also no error was turn up .There is no error in the input file because I > > have test it on anthoer computer which has 4 CPUs and it runs well . > > I can't find the reason about this ,any help will be appreciated . > > Best Regards > > Q.J.Wang > > XiangTan University > > > > > > > > ------------------------------ > > ???????????,www.yeah.net > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Dr. Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Sun, 6 Sep 2009 11:25:06 +0330 > From: Mansoureh Pashangpour > Subject: [Pw_forum] pseudo potential > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > how can I plot these pseudo potentials? how can I discribe the properties > of pseudo potentials? > > *Fe.pbe-nd-rrkjus.UPF*< > http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF> > ( > *details*< > http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF>) > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > nonlinear core-correction > semicore state d in valence > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > and > > *H.pbe-rrkjus.UPF* > (*details* < > http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>) > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > and > > *O.pbe-rrkjus.UPF* > (*details* > ) > > Perdew-Burke-Ernzerhof (PBE) exch-corr > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > Thanks > Mansoureh Pashangpour > Ph.D student > Islami Azad university > science & reaserch branch > Tehran, IRAN > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sun, 6 Sep 2009 10:24:48 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] error loading shared libraries on parallel > execution > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Sep 6, 2009, at 1:20 , sreekar guddeti wrote: > > > plz suggest solutions which donot require root permissions , > > as i dont have > > somebody must have it. Report the problem and the > solution (i.e. install gfortran on ALL processors) to > whoever has root access. As an alternative, try static > link (add -static to LDFLAGS in make.sys). > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 4 > Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST) > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] pw.x running but nothing happens > To: "PWSCF Forum" > Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it> > Content-Type: text/plain;charset=iso-8859-1 > > > On Sun, September 6, 2009 02:33, wangqj1 wrote: > > After one day ,it still like this and no iteration has completed ,there > > is > > also no error was turn up .There is no error in the input file because I > > have test it on anthoer computer which has 4 CPUs and it runs well . > > I can't find the reason about this ,any help will be appreciated . > > > Dear QJ, > this is strange. But we would need more information on your hardwre > configuration in order to help you. In the mean while you can check the > behaviour of te pw.x processes with "top". E.g. if they are all runing at > 100% CPU, how much memory they are taking and so on. > > regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > > > ------------------------------ > > Message: 5 > Date: Sun, 6 Sep 2009 23:35:26 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23 > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > @duy lee > i inserted the line #$ -V in my qsub script and the env variable > $LD_LIBRARY_PATH is being set from script... thanks for that but still > problem persists. > > @rakshit > > ----------------------------- > $find /usr/lib -name libgfortran* > ----------------------------- > and output is > _______________________ > /usr/lib/libgfortran.so.1.0.0 > /usr/lib/libgfortran.so.1 > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so > _______________________ > whereas on doing > ----------------------------- > $find /usr/lib64 -name libgfortran* > ----------------------------- > ouput is > _________________ > /usr/lib64/libgfortran.so.3.0.0 > /usr/lib64/libgfortran.so.1.0.0 > /usr/lib64/libgfortran.so.1 > find: /usr/lib64/audit: Permission denied > */usr/lib64/libgfortran.so.3* > _________________ > > it means my OS has the required library, i guess > > i installed the QE on the head node > This cluster is a Rocks cluster with > > # of nodes: 10 (1 head node + 9 compute nodes) > # of processors/node: 8 > # Total # of processors: 10X8 = 80 > > i tested the sample program for submitting batch jobs using SGE utility and > it is working fine( > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > ) > > sincerely, > sreekar guddeti > Dept. Physics > IIT Bombay > India > > > On Sun, Sep 6, 2009 at 12:28 PM, wrote: > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: error loading shared libraries on parallel execution (Duy Le) > > 2. pw.x running but nothing happens (wangqj1) > > 3. Re: error loading shared libraries on parallel execution > > (Bipul Rakshit) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 5 Sep 2009 19:39:17 -0400 > > From: Duy Le > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > execution > > To: PWSCF Forum > > Message-ID: > > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi,I am not sure if this help. Could you please try to add > > #$ -V in your submitting script. Like this: > > > > #!/bin/bash > > # > > #$ -V > > #$ -cwd > > #$ -j y > > #$ -S /bin/bash > > # > > > > Good luck. > > D. > > > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti > > wrote: > > > > > i know this issuehas been addressed and documented in troubleshooting > > > section of the users guide. > > > but i giveup in despair trying for a whole day to figure this problem > > > i run my jobs on rocks cluster by using SGE's facility of submitting > > batch > > > jobs > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > successfully > > > run a single parallel job, but on submitting a second job i get the > error > > > ____________________________________________ > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > ____________________________________________ > > > > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > > > writing > > > _______________________________________ > > > #set the library path to include gfortran libraries > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > $ECHO > > > $ECHO "$LD_LIBRARY_PATH" > > > $ECHO > > > _______________________________________ > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > dosroutine.qsub) which is > > > > > > dosroutine.qsub > > > ----------------------------------------------------------------- > > > > > > #!/bin/bash > > > # > > > #$ -cwd > > > #$ -j y > > > #$ -S /bin/bash > > > # > > > > > > #extract the info about no of processors involved from command line > > > arguments of 'qsub' > > > PROCESSORS=$NSLOTS > > > > > > #heuristically assign the no of processors per pool NPR > > > NPR=4 > > > #as a result no of pools are give by > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > #!/bin/bash > > > # > > > # > > > #Script for performing a dos calculation on a parallel processor > > > WORKINGDIR=`pwd` > > > ECHO="echo" > > > > > > #set the library path to include gfortran libraries > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > $ECHO > > > $ECHO "$LD_LIBRARY_PATH" > > > $ECHO > > > > > > # set the needed environment variables > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > $ECHO $PREFIX > > > BIN_DIR=$PREFIX/bin > > > PSEUDO_DIR=$PREFIX/pseudo > > > TMP_DIR=$HOME/tmp > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > PARA_POSTFIX="-npool $NPK" > > > > > > # required executables and pseudopotentials > > > $ECHO > > > $ECHO " executables directory: $BIN_DIR" > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > #create results directory > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > if test ! -d $DIR ; then > > > mkdir $DIR > > > fi > > > done > > > cd $WORKINGDIR/results > > > > > > > > > # variables to represent programs > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > # DOS calculation for 0Ni0 > > > cat > 0ni0.dos.in << EOF > > > &control > > > calculation='nscf' > > > restart_mode='from_scratch', > > > prefix='0ni0', > > > pseudo_dir = '$PSEUDO_DIR/', > > > outdir='$TMP_DIR/' > > > / > > > &system > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > nspin = 2, starting_magnetization(1)=0.7, > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > occupations='tetrahedra' > > > / > > > &electrons > > > conv_thr = 1.0e-10 > > > mixing_beta = 0.7 > > > / > > > ATOMIC_SPECIES > > > Ni 58.69 NiUS.RRKJ3.UPF > > > ATOMIC_POSITIONS > > > Ni 0.0 0.0 0.0 > > > K_POINTS {automatic} !special points generated by tetrahedra > > method > > > 12 12 12 0 0 0 > > > EOF > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > $ECHO > > > $ECHO " done" > > > > > > ------------------------------------------------------------- > > > > > > the output i get is > > > > > > ************************************************ > > > :/usr/lib64:/usr/lib > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > temporary directory: /home3/colonel/tmp > > > running DOS calculation for 0Ni0 ...\c > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > > > > done > > > ************************************************* > > > plz suggest solutions which donot require root permissions , as i dont > > have > > > thanks in advance > > > -- > > > Sreekar Guddeti > > > Department of Physics > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > -------------------------------------------------- > > Duy Le > > PhD Student > > Department of Physics > > University of Central Florida. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > > From: wangqj1 > > Subject: [Pw_forum] pw.x running but nothing happens > > To: pw_forum > > Message-ID: > > <25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com > > > > Content-Type: text/plain; charset="gbk" > > > > > > Dear pwscf users > > When I run vc-relax on the computing cluster use one node which has 8 > > CPUs. > > The output file is as following: > > > > Program PWSCF v.4.0.1 starts ... > > Today is 6Sep2009 at 7:49:30 > > Parallel version (MPI) > > Number of processors in use: 8 > > R & G space division: proc/pool = 8 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > ..................................................................... > > Initial potential from superposition of free atoms > > starting charge 435.99565, renormalised to 436.00000 > > Starting wfc are 254 atomic + 8 random wfc > > > > After one day ,it still like this and no iteration has completed ,there > is > > also no error was turn up .There is no error in the input file because I > > have test it on anthoer computer which has 4 CPUs and it runs well . > > I can't find the reason about this ,any help will be appreciated . > > Best Regards > > Q.J.Wang > > XiangTan University > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > > > ------------------------------ > > > > Message: 3 > > Date: Sun, 6 Sep 2009 07:58:49 +0100 > > From: Bipul Rakshit > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > execution > > To: PWSCF Forum > > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > hi, > > Just from root user type > > yum install libgfortran.so.3 > > > > then it will install this files which is not present in your machine > > > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti > > wrote: > > > > > i know this issuehas been addressed and documented in troubleshooting > > > section of the users guide. > > > but i giveup in despair trying for a whole day to figure this problem > > > i run my jobs on rocks cluster by using SGE's facility of submitting > > batch > > > jobs > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > successfully > > > run a single parallel job, but on submitting a second job i get the > error > > > ____________________________________________ > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > ____________________________________________ > > > > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH by > > > writing > > > _______________________________________ > > > #set the library path to include gfortran libraries > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > $ECHO > > > $ECHO "$LD_LIBRARY_PATH" > > > $ECHO > > > _______________________________________ > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > dosroutine.qsub) which is > > > > > > dosroutine.qsub > > > ----------------------------------------------------------------- > > > > > > #!/bin/bash > > > # > > > #$ -cwd > > > #$ -j y > > > #$ -S /bin/bash > > > # > > > > > > #extract the info about no of processors involved from command line > > > arguments of 'qsub' > > > PROCESSORS=$NSLOTS > > > > > > #heuristically assign the no of processors per pool NPR > > > NPR=4 > > > #as a result no of pools are give by > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > #!/bin/bash > > > # > > > # > > > #Script for performing a dos calculation on a parallel processor > > > WORKINGDIR=`pwd` > > > ECHO="echo" > > > > > > #set the library path to include gfortran libraries > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > $ECHO > > > $ECHO "$LD_LIBRARY_PATH" > > > $ECHO > > > > > > # set the needed environment variables > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > $ECHO $PREFIX > > > BIN_DIR=$PREFIX/bin > > > PSEUDO_DIR=$PREFIX/pseudo > > > TMP_DIR=$HOME/tmp > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > PARA_POSTFIX="-npool $NPK" > > > > > > # required executables and pseudopotentials > > > $ECHO > > > $ECHO " executables directory: $BIN_DIR" > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > #create results directory > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > if test ! -d $DIR ; then > > > mkdir $DIR > > > fi > > > done > > > cd $WORKINGDIR/results > > > > > > > > > # variables to represent programs > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > # DOS calculation for 0Ni0 > > > cat > 0ni0.dos.in << EOF > > > &control > > > calculation='nscf' > > > restart_mode='from_scratch', > > > prefix='0ni0', > > > pseudo_dir = '$PSEUDO_DIR/', > > > outdir='$TMP_DIR/' > > > / > > > &system > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > nspin = 2, starting_magnetization(1)=0.7, > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > occupations='tetrahedra' > > > / > > > &electrons > > > conv_thr = 1.0e-10 > > > mixing_beta = 0.7 > > > / > > > ATOMIC_SPECIES > > > Ni 58.69 NiUS.RRKJ3.UPF > > > ATOMIC_POSITIONS > > > Ni 0.0 0.0 0.0 > > > K_POINTS {automatic} !special points generated by tetrahedra > > method > > > 12 12 12 0 0 0 > > > EOF > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > $ECHO > > > $ECHO " done" > > > > > > ------------------------------------------------------------- > > > > > > the output i get is > > > > > > ************************************************ > > > :/usr/lib64:/usr/lib > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > temporary directory: /home3/colonel/tmp > > > running DOS calculation for 0Ni0 ...\c > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > file or directory > > > > > > done > > > ************************************************* > > > plz suggest solutions which donot require root permissions , as i dont > > have > > > thanks in advance > > > -- > > > Sreekar Guddeti > > > Department of Physics > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > Dr. Bipul Rakshit > > Research Associate, > > S N Bose Centre for Basic Sciences, > > Salt Lake, > > Kolkata 700 098 > > India > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 27, Issue 23 > > **************************************** > > > > > > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 24 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f9410638/attachment-0001.htm From colonel.sreekar at gmail.com Mon Sep 7 03:06:10 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 7 Sep 2009 06:36:10 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 25 In-Reply-To: References: Message-ID: > As an alternative, try static > link (add -static to LDFLAGS in make.sys). The other thing that i tried was $make clean $./configure --enable-parallel --disable-shared --host=x86_64 output is ___________________________________________ configure: WARNING: If you wanted to set the --build type, don't use --host. If a cross compiler is detected then cross compile mode will be used. checking build system type... x86_64-unknown-linux-gnu configure: WARNING: incorrect host name ? checking architecture... configure: WARNING: unsupported architecture? checking for x86_64-g95... no checking for x86_64-gfortran... no checking for x86_64-f90... no checking for g95... no checking for gfortran... gfortran checking for Fortran 77 compiler default output file name... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking for x86_64-mpif90... no checking for x86_64-gfortran... no checking for mpif90... mpif90 checking whether we are using the GNU Fortran 77 compiler... yes checking whether mpif90 accepts -g... yes setting F90... gfortran setting MPIF90... mpif90 checking for x86_64-cc... no checking for x86_64-gcc... no checking for cc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed setting CC... gcc checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int *... yes checking size of int *... 8 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes checking for x86_64-gfortran... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes setting F77... gfortran using F90... gfortran setting FFLAGS... -O3 setting F90FLAGS... $(FFLAGS) -x f95-cpp-input setting FFLAGS_NOOPT... -O0 setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... mpif90 setting LDFLAGS... -static setting AR... ar setting ARFLAGS... ruv setting ARFLAGS_DYNAMIC...ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... no checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2 -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/intel/Compiler/11.1/046/lib/intel64 -L/opt/intel/Compiler/11.1/046/ipp/em64t/lib -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t -L/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../.. -lgfortranbegin -lgfortran -lm -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: checking for library containing dgemm... no in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... no in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... no checking for library containing dgemm... no in /usr/local/lib: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library containing dgemm... no in /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: checking for library containing dgemm... no in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... no in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... no checking for library containing zggev... no in /usr/local/lib: checking for library containing zggev... no in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing zggev... no in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library containing zggev... no in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library containing zggev... no in /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: checking for library containing zggev... no in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev... no in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev... no setting BLAS_LIBS... ../flib/blas.a setting LAPACK_LIBS... ../flib/lapack.a checking for library containing fftwnd... no in /usr/local/lib: checking for library containing fftwnd... no in /cineca/prod/gnu/lib: checking for library containing fftwnd... no in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library containing fftwnd... no in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library containing fftwnd... no in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library containing fftwnd... no in /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: checking for library containing fftwnd... no in /opt/gridengine/lib/lx26-amd64: checking for library containing fftwnd... no in /opt/gridengine/lib/lx26-amd64: checking for library containing fftwnd... no setting FFT_LIBS... checking for library containing fftwnd... (cached) no setting MASS_LIBS... checking for library containing mpi_init... no setting MPI_LIBS... checking for library containing mpi_init... (cached) no setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) setting RANLIB... echo configure: creating ./config.status config.status: creating include/fft_defs.h config.status: creating make.sys config.status: creating configure.msg config.status: creating include/c_defs.h config.status: include/c_defs.h is unchanged -------------------------------------------------------------------- ESPRESSO can take advantage of several optimized numerical libraries (essl, fftw, mkl...). This configure script attempts to find them, but may fail if they have been installed in non-standard locations. If a required library is not found, the local copy will be compiled. The following libraries have been found: BLAS_LIBS=../flib/blas.a LAPACK_LIBS=../flib/lapack.a FFT_LIBS= Please check if this is what you expect. If any libraries are missing, you may specify a list of directories to search and retry, as follows: ./configure LIBDIRS="list of directories, separated by spaces" Parallel environment not detected (is this a parallel machine?). Configured for compilation of serial executables. For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). -------------------------------------------------------------------- configure: success ______________________________________________ but parallel version is not getting compiled sincerely, Sreekar Guddeti Dept. Physics IIT Bombay India On Mon, Sep 7, 2009 at 5:23 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 27, Issue 24 (sreekar guddeti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Sep 2009 05:23:12 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 24 > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > i have set variable LD_FLAGS = static in make.sys file > > and on $make all > > i get error > ---------------------------------------- > libiotk.a > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW > -I../PH -c iotk_print_kinds.f90 > make loclib_only > make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src' > make[3]: Nothing to be done for `loclib_only'. > make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a > /opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open': > (.text+0x123): warning: Using 'dlopen' in statically linked applications > requires at runtime the shared libraries from the glibc version used for > linking > /opt/openmpi/lib/libopen-rte.a(sys_info.o): In function `orte_sys_info': > (.text+0x16f): warning: Using 'getpwuid' in statically linked applications > requires at runtime the shared libraries from the glibc version used for > linking > /opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname': > (.text+0x780): warning: Using 'gethostbyname' in statically linked > applications requires at runtime the shared libraries from the glibc > version > used for linking > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `__malloc_check_init': > (.text+0x1060): multiple definition of `__malloc_check_init' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first defined > here > /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 144 > in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `_int_free': > (.text+0x2230): multiple definition of `_int_free' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first defined > here > /usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `_int_malloc': > (.text+0x2a50): multiple definition of `_int_malloc' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first defined > here > /usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `_int_memalign': > (.text+0x3900): multiple definition of `_int_memalign' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first defined > here > /usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `_int_valloc': > (.text+0x3c30): multiple definition of `_int_valloc' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first defined > here > /usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `_int_realloc': > (.text+0x3d80): multiple definition of `_int_realloc' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first defined > here > /usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `free': > (.text+0x5f20): multiple definition of `free' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first defined > here > /usr/bin/ld: Warning: size of symbol `free' changed from 256 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `malloc': > (.text+0x4690): multiple definition of `malloc' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first defined > here > /usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > In function `realloc': > (.text+0x60f0): multiple definition of `realloc' > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first defined > here > /usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > collect2: ld returned 1 exit status > make[2]: *** [iotk_print_kinds.x] Error 1 > make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > make[1]: *** [lib+util] Error 2 > make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk' > make: *** [libiotk] Error 2 > > --------------------------------------------- > > sincerely > > > On Sun, Sep 6, 2009 at 11:35 PM, wrote: > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: pw.x running but nothing happens (Bipul Rakshit) > > 2. pseudo potential (Mansoureh Pashangpour) > > 3. Re: error loading shared libraries on parallel execution > > (Paolo Giannozzi) > > 4. Re: pw.x running but nothing happens (Lorenzo Paulatto) > > 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 6 Sep 2009 08:03:29 +0100 > > From: Bipul Rakshit > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > To: PWSCF Forum > > Message-ID: > > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> > > Content-Type: text/plain; charset="gb2312" > > > > Dear Wangqj, > > The same thing happens to me. > > since you are using large no. of wfc, although it shows the job is > running > > in 8 procs, but sometimes if the installation is not proper, it is > running > > in 1 procs only. > > > > So better you check the parallel installation using a small job, with > > different no. of procs and see whether its taking lesser time as no. of > > procs increases or not? > > > > cheers > > > > 2009/9/6 wangqj1 > > > > > > > > Dear pwscf users > > > When I run vc-relax on the computing cluster use one node which > has > > 8 > > > CPUs. > > > The output file is as following: > > > > > > Program PWSCF v.4.0.1 starts ... > > > Today is 6Sep2009 at 7:49:30 > > > Parallel version (MPI) > > > Number of processors in use: 8 > > > R & G space division: proc/pool = 8 > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > > PAW > > > ..................................................................... > > > Initial potential from superposition of free atoms > > > starting charge 435.99565, renormalised to 436.00000 > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > After one day ,it still like this and no iteration has completed ,there > > is > > > also no error was turn up .There is no error in the input file because > I > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > I can't find the reason about this ,any help will be appreciated . > > > Best Regards > > > Q.J.Wang > > > XiangTan University > > > > > > > > > > > > ------------------------------ > > > ???????????,www.yeah.net > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > Dr. Bipul Rakshit > > Research Associate, > > S N Bose Centre for Basic Sciences, > > Salt Lake, > > Kolkata 700 098 > > India > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 6 Sep 2009 11:25:06 +0330 > > From: Mansoureh Pashangpour > > Subject: [Pw_forum] pseudo potential > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all > > how can I plot these pseudo potentials? how can I discribe the > properties > > of pseudo potentials? > > > > *Fe.pbe-nd-rrkjus.UPF*< > > http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF> > > ( > > *details*< > > http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF>) > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > nonlinear core-correction > > semicore state d in valence > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > and > > > > *H.pbe-rrkjus.UPF* > > > (*details* < > > http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>) > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > and > > > > *O.pbe-rrkjus.UPF* > > (*details* > > ) > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > Thanks > > Mansoureh Pashangpour > > Ph.D student > > Islami Azad university > > science & reaserch branch > > Tehran, IRAN > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm > > > > ------------------------------ > > > > Message: 3 > > Date: Sun, 6 Sep 2009 10:24:48 +0200 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > execution > > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > > On Sep 6, 2009, at 1:20 , sreekar guddeti wrote: > > > > > plz suggest solutions which donot require root permissions , > > > as i dont have > > > > somebody must have it. Report the problem and the > > solution (i.e. install gfortran on ALL processors) to > > whoever has root access. As an alternative, try static > > link (add -static to LDFLAGS in make.sys). > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST) > > From: "Lorenzo Paulatto" > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > To: "PWSCF Forum" > > Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it> > > Content-Type: text/plain;charset=iso-8859-1 > > > > > > On Sun, September 6, 2009 02:33, wangqj1 wrote: > > > After one day ,it still like this and no iteration has completed > ,there > > > is > > > also no error was turn up .There is no error in the input file because > I > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > I can't find the reason about this ,any help will be appreciated . > > > > > > Dear QJ, > > this is strange. But we would need more information on your hardwre > > configuration in order to help you. In the mean while you can check the > > behaviour of te pw.x processes with "top". E.g. if they are all runing at > > 100% CPU, how much memory they are taking and so on. > > > > regards > > > > > > -- > > Lorenzo Paulatto > > SISSA & DEMOCRITOS (Trieste) > > phone: +39 040 3787 511 > > skype: paulatz > > www: http://people.sissa.it/~paulatto/ > > > > > > > > > ---------------------------------------------------------------- > > SISSA Webmail https://webmail.sissa.it/ > > Powered by SquirrelMail http://www.squirrelmail.org/ > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Sun, 6 Sep 2009 23:35:26 +0530 > > From: sreekar guddeti > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23 > > To: pw_forum at pwscf.org > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > @duy lee > > i inserted the line #$ -V in my qsub script and the env variable > > $LD_LIBRARY_PATH is being set from script... thanks for that but still > > problem persists. > > > > @rakshit > > > > ----------------------------- > > $find /usr/lib -name libgfortran* > > ----------------------------- > > and output is > > _______________________ > > /usr/lib/libgfortran.so.1.0.0 > > /usr/lib/libgfortran.so.1 > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so > > _______________________ > > whereas on doing > > ----------------------------- > > $find /usr/lib64 -name libgfortran* > > ----------------------------- > > ouput is > > _________________ > > /usr/lib64/libgfortran.so.3.0.0 > > /usr/lib64/libgfortran.so.1.0.0 > > /usr/lib64/libgfortran.so.1 > > find: /usr/lib64/audit: Permission denied > > */usr/lib64/libgfortran.so.3* > > _________________ > > > > it means my OS has the required library, i guess > > > > i installed the QE on the head node > > This cluster is a Rocks cluster with > > > > # of nodes: 10 (1 head node + 9 compute nodes) > > # of processors/node: 8 > > # Total # of processors: 10X8 = 80 > > > > i tested the sample program for submitting batch jobs using SGE utility > and > > it is working fine( > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > ) > > > > sincerely, > > sreekar guddeti > > Dept. Physics > > IIT Bombay > > India > > > > > > On Sun, Sep 6, 2009 at 12:28 PM, wrote: > > > > > Send Pw_forum mailing list submissions to > > > pw_forum at pwscf.org > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > or, via email, send a message with subject or body 'help' to > > > pw_forum-request at pwscf.org > > > > > > You can reach the person managing the list at > > > pw_forum-owner at pwscf.org > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of Pw_forum digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Re: error loading shared libraries on parallel execution (Duy Le) > > > 2. pw.x running but nothing happens (wangqj1) > > > 3. Re: error loading shared libraries on parallel execution > > > (Bipul Rakshit) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Sat, 5 Sep 2009 19:39:17 -0400 > > > From: Duy Le > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > execution > > > To: PWSCF Forum > > > Message-ID: > > > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi,I am not sure if this help. Could you please try to add > > > #$ -V in your submitting script. Like this: > > > > > > #!/bin/bash > > > # > > > #$ -V > > > #$ -cwd > > > #$ -j y > > > #$ -S /bin/bash > > > # > > > > > > Good luck. > > > D. > > > > > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti > > > wrote: > > > > > > > i know this issuehas been addressed and documented in troubleshooting > > > > section of the users guide. > > > > but i giveup in despair trying for a whole day to figure this problem > > > > i run my jobs on rocks cluster by using SGE's facility of submitting > > > batch > > > > jobs > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > successfully > > > > run a single parallel job, but on submitting a second job i get the > > error > > > > ____________________________________________ > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > ____________________________________________ > > > > > > > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH > by > > > > writing > > > > _______________________________________ > > > > #set the library path to include gfortran libraries > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > $ECHO > > > > $ECHO "$LD_LIBRARY_PATH" > > > > $ECHO > > > > _______________________________________ > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > dosroutine.qsub) which is > > > > > > > > dosroutine.qsub > > > > ----------------------------------------------------------------- > > > > > > > > #!/bin/bash > > > > # > > > > #$ -cwd > > > > #$ -j y > > > > #$ -S /bin/bash > > > > # > > > > > > > > #extract the info about no of processors involved from command line > > > > arguments of 'qsub' > > > > PROCESSORS=$NSLOTS > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > NPR=4 > > > > #as a result no of pools are give by > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > #!/bin/bash > > > > # > > > > # > > > > #Script for performing a dos calculation on a parallel processor > > > > WORKINGDIR=`pwd` > > > > ECHO="echo" > > > > > > > > #set the library path to include gfortran libraries > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > $ECHO > > > > $ECHO "$LD_LIBRARY_PATH" > > > > $ECHO > > > > > > > > # set the needed environment variables > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > $ECHO $PREFIX > > > > BIN_DIR=$PREFIX/bin > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > TMP_DIR=$HOME/tmp > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > # required executables and pseudopotentials > > > > $ECHO > > > > $ECHO " executables directory: $BIN_DIR" > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > #create results directory > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > if test ! -d $DIR ; then > > > > mkdir $DIR > > > > fi > > > > done > > > > cd $WORKINGDIR/results > > > > > > > > > > > > # variables to represent programs > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > cat > 0ni0.dos.in << EOF > > > > &control > > > > calculation='nscf' > > > > restart_mode='from_scratch', > > > > prefix='0ni0', > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > outdir='$TMP_DIR/' > > > > / > > > > &system > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > occupations='tetrahedra' > > > > / > > > > &electrons > > > > conv_thr = 1.0e-10 > > > > mixing_beta = 0.7 > > > > / > > > > ATOMIC_SPECIES > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > ATOMIC_POSITIONS > > > > Ni 0.0 0.0 0.0 > > > > K_POINTS {automatic} !special points generated by tetrahedra > > > method > > > > 12 12 12 0 0 0 > > > > EOF > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > $ECHO > > > > $ECHO " done" > > > > > > > > ------------------------------------------------------------- > > > > > > > > the output i get is > > > > > > > > ************************************************ > > > > :/usr/lib64:/usr/lib > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > temporary directory: /home3/colonel/tmp > > > > running DOS calculation for 0Ni0 ...\c > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > > > > > done > > > > ************************************************* > > > > plz suggest solutions which donot require root permissions , as i > dont > > > have > > > > thanks in advance > > > > -- > > > > Sreekar Guddeti > > > > Department of Physics > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > -- > > > -------------------------------------------------- > > > Duy Le > > > PhD Student > > > Department of Physics > > > University of Central Florida. > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > > > From: wangqj1 > > > Subject: [Pw_forum] pw.x running but nothing happens > > > To: pw_forum > > > Message-ID: > > > < > 25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com > > > > > > Content-Type: text/plain; charset="gbk" > > > > > > > > > Dear pwscf users > > > When I run vc-relax on the computing cluster use one node which has > 8 > > > CPUs. > > > The output file is as following: > > > > > > Program PWSCF v.4.0.1 starts ... > > > Today is 6Sep2009 at 7:49:30 > > > Parallel version (MPI) > > > Number of processors in use: 8 > > > R & G space division: proc/pool = 8 > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > PAW > > > ..................................................................... > > > Initial potential from superposition of free atoms > > > starting charge 435.99565, renormalised to 436.00000 > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > After one day ,it still like this and no iteration has completed ,there > > is > > > also no error was turn up .There is no error in the input file because > I > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > I can't find the reason about this ,any help will be appreciated . > > > Best Regards > > > Q.J.Wang > > > XiangTan University > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Sun, 6 Sep 2009 07:58:49 +0100 > > > From: Bipul Rakshit > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > execution > > > To: PWSCF Forum > > > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > hi, > > > Just from root user type > > > yum install libgfortran.so.3 > > > > > > then it will install this files which is not present in your machine > > > > > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti > > > wrote: > > > > > > > i know this issuehas been addressed and documented in troubleshooting > > > > section of the users guide. > > > > but i giveup in despair trying for a whole day to figure this problem > > > > i run my jobs on rocks cluster by using SGE's facility of submitting > > > batch > > > > jobs > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > successfully > > > > run a single parallel job, but on submitting a second job i get the > > error > > > > ____________________________________________ > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > ____________________________________________ > > > > > > > > > > > > i find out the path for the library and added to the LD_LIBRARY_PATH > by > > > > writing > > > > _______________________________________ > > > > #set the library path to include gfortran libraries > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > $ECHO > > > > $ECHO "$LD_LIBRARY_PATH" > > > > $ECHO > > > > _______________________________________ > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > dosroutine.qsub) which is > > > > > > > > dosroutine.qsub > > > > ----------------------------------------------------------------- > > > > > > > > #!/bin/bash > > > > # > > > > #$ -cwd > > > > #$ -j y > > > > #$ -S /bin/bash > > > > # > > > > > > > > #extract the info about no of processors involved from command line > > > > arguments of 'qsub' > > > > PROCESSORS=$NSLOTS > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > NPR=4 > > > > #as a result no of pools are give by > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > #!/bin/bash > > > > # > > > > # > > > > #Script for performing a dos calculation on a parallel processor > > > > WORKINGDIR=`pwd` > > > > ECHO="echo" > > > > > > > > #set the library path to include gfortran libraries > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > $ECHO > > > > $ECHO "$LD_LIBRARY_PATH" > > > > $ECHO > > > > > > > > # set the needed environment variables > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > $ECHO $PREFIX > > > > BIN_DIR=$PREFIX/bin > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > TMP_DIR=$HOME/tmp > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > # required executables and pseudopotentials > > > > $ECHO > > > > $ECHO " executables directory: $BIN_DIR" > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > #create results directory > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > if test ! -d $DIR ; then > > > > mkdir $DIR > > > > fi > > > > done > > > > cd $WORKINGDIR/results > > > > > > > > > > > > # variables to represent programs > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > cat > 0ni0.dos.in << EOF > > > > &control > > > > calculation='nscf' > > > > restart_mode='from_scratch', > > > > prefix='0ni0', > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > outdir='$TMP_DIR/' > > > > / > > > > &system > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > occupations='tetrahedra' > > > > / > > > > &electrons > > > > conv_thr = 1.0e-10 > > > > mixing_beta = 0.7 > > > > / > > > > ATOMIC_SPECIES > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > ATOMIC_POSITIONS > > > > Ni 0.0 0.0 0.0 > > > > K_POINTS {automatic} !special points generated by tetrahedra > > > method > > > > 12 12 12 0 0 0 > > > > EOF > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > $ECHO > > > > $ECHO " done" > > > > > > > > ------------------------------------------------------------- > > > > > > > > the output i get is > > > > > > > > ************************************************ > > > > :/usr/lib64:/usr/lib > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > temporary directory: /home3/colonel/tmp > > > > running DOS calculation for 0Ni0 ...\c > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > libraries: libgfortran.so.3: cannot open shared object file: No such > > > > file or directory > > > > > > > > done > > > > ************************************************* > > > > plz suggest solutions which donot require root permissions , as i > dont > > > have > > > > thanks in advance > > > > -- > > > > Sreekar Guddeti > > > > Department of Physics > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > -- > > > Dr. Bipul Rakshit > > > Research Associate, > > > S N Bose Centre for Basic Sciences, > > > Salt Lake, > > > Kolkata 700 098 > > > India > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > End of Pw_forum Digest, Vol 27, Issue 23 > > > **************************************** > > > > > > > > > > > -- > > Sreekar Guddeti > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 27, Issue 24 > > **************************************** > > > > > > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f9410638/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 25 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/9fbce729/attachment-0001.htm From wangqj1 at 126.com Mon Sep 7 03:21:25 2009 From: wangqj1 at 126.com (wangqj1) Date: Mon, 7 Sep 2009 09:21:25 +0800 (CST) Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: References: Message-ID: <19823194.60101252286485077.JavaMail.coremail@bj126app26.126.com> According to your advice ,I check the parallel installation using a small job, and it runs well in the same node ,but when I run the big job ,it still turn up the same question . Thank you for your advice . Best regards ?2009-09-07?02:05:35?pw_forum-request at pwscf.org???? >Subject:?Re:?[Pw_forum]?pw.x?running?but?nothing?happens >To:?PWSCF?Forum? >Message-ID: > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> >Content-Type:?text/plain;?charset="gb2312" > >Dear?Wangqj, >The?same?thing?happens?to?me. >since?you?are?using?large?no.?of?wfc,?although?it?shows?the?job?is?running >in?8?procs,?but?sometimes?if?the?installation?is?not?proper,?it?is?running >in?1?procs?only. > >So?better?you?check?the?parallel?installation?using?a?small?job,?with >different?no.?of?procs?and?see?whether?its?taking?lesser?time?as??no.?of >procs?increases?or?not? > >cheers > >2009/9/6?wangqj1? > >> >>?Dear?pwscf?users >>??????When?I?run?vc-relax?on?the?computing?cluster?use?one?node?which?has?8 >>?CPUs. >>?The?output?file?is?as?following: >> >>?Program?PWSCF?????v.4.0.1??starts?... >>??????Today?is??6Sep2009?at??7:49:30 >>??????Parallel?version?(MPI) >>??????Number?of?processors?in?use:???????8 >>??????R?&?G?space?division:??proc/pool?=????8 >>??????For?Norm-Conserving?or?Ultrasoft?(Vanderbilt)?Pseudopotentials?or?PAW >>?..................................................................... >>??????Initial?potential?from?superposition?of?free?atoms >>??????starting?charge??435.99565,?renormalised?to??436.00000 >>??????Starting?wfc?are??254?atomic?+????8?random?wfc >> >>?After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there?is >>?also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I >>?have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?. >>?I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?. >>?Best?Regards >>?Q.J.Wang >>?XiangTan?University >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/1805733c/attachment.htm From colonel.sreekar at gmail.com Mon Sep 7 04:25:49 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 7 Sep 2009 07:55:49 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 26 In-Reply-To: References: Message-ID: sorry for making repeated posts but on $./configure --enable-parallel --host=x86_64 configuration is successful for parallel version on $make all in the compilation report i get the following warnings related to libgfortran.so.3 and no other warnings /usr/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/libmpi_f90.so, may conflict with libgfortran.so.3 ( 8 times) /usr/bin/ld: warning: libgfortran.so.1, needed by /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../liblapack.a, may conflict with libgfortran.so.3 (many times) hope this information is useful for suggesting a solution to the problem sincerely, sreekar guddeti Dept.Physics IIT Bombay India On Mon, Sep 7, 2009 at 6:36 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 27, Issue 25 (sreekar guddeti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Sep 2009 06:36:10 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 25 > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > As an alternative, try static > > link (add -static to LDFLAGS in make.sys). > > The other thing that i tried was > $make clean > $./configure --enable-parallel --disable-shared --host=x86_64 > > output is > ___________________________________________ > configure: WARNING: If you wanted to set the --build type, don't use > --host. > If a cross compiler is detected then cross compile mode will be used. > checking build system type... x86_64-unknown-linux-gnu > configure: WARNING: incorrect host name ? > checking architecture... > configure: WARNING: unsupported architecture? > checking for x86_64-g95... no > checking for x86_64-gfortran... no > checking for x86_64-f90... no > checking for g95... no > checking for gfortran... gfortran > checking for Fortran 77 compiler default output file name... a.out > checking whether the Fortran 77 compiler works... yes > checking whether we are cross compiling... yes > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > checking for x86_64-mpif90... no > checking for x86_64-gfortran... no > checking for mpif90... mpif90 > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether mpif90 accepts -g... yes > setting F90... gfortran > setting MPIF90... mpif90 > checking for x86_64-cc... no > checking for x86_64-gcc... no > checking for cc... no > checking for gcc... gcc > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > setting CC... gcc > checking how to run the C preprocessor... gcc -E > checking for egrep... grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for int *... yes > checking size of int *... 8 > checking malloc.h usability... yes > checking malloc.h presence... yes > checking for malloc.h... yes > checking for struct mallinfo.arena... yes > checking for x86_64-gfortran... no > checking for gfortran... gfortran > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > setting F77... gfortran > using F90... gfortran > setting FFLAGS... -O3 > setting F90FLAGS... $(FFLAGS) -x f95-cpp-input > setting FFLAGS_NOOPT... -O0 > setting CFLAGS... -O3 > setting CPP... cpp > setting CPPFLAGS... -P -traditional > setting LD... mpif90 > setting LDFLAGS... -static > setting AR... ar > setting ARFLAGS... ruv > setting ARFLAGS_DYNAMIC...ruv > checking whether make sets $(MAKE)... yes > checking whether Fortran files must be preprocessed... no > checking how to get verbose linking output from gfortran... -v > checking for Fortran libraries of gfortran... > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2 > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64 > -L/lib/../lib64 > -L/usr/lib/../lib64 -L/opt/intel/Compiler/11.1/046/lib/intel64 > -L/opt/intel/Compiler/11.1/046/ipp/em64t/lib > -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t > > -L/opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../.. -lgfortranbegin > -lgfortran -lm -lgcc_s > checking for dummy main to link with Fortran libraries... none > checking for Fortran name-mangling scheme... lower case, underscore, no > extra underscore > checking for library containing dgemm... no > in /usr/local/lib: checking for library containing dgemm... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > dgemm... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library > containing dgemm... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing dgemm... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing dgemm... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... > no > checking for library containing dgemm... no > in /usr/local/lib: checking for library containing dgemm... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > dgemm... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library > containing dgemm... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing dgemm... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing dgemm... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing dgemm... > no > checking for library containing zggev... no > in /usr/local/lib: checking for library containing zggev... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > zggev... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library > containing zggev... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing zggev... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing zggev... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing zggev... > no > setting BLAS_LIBS... ../flib/blas.a > setting LAPACK_LIBS... ../flib/lapack.a > checking for library containing fftwnd... no > in /usr/local/lib: checking for library containing fftwnd... no > in /cineca/prod/gnu/lib: checking for library containing fftwnd... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > fftwnd... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for library > containing fftwnd... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing fftwnd... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing fftwnd... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > fftwnd... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > fftwnd... > no > setting FFT_LIBS... > checking for library containing fftwnd... (cached) no > setting MASS_LIBS... > checking for library containing mpi_init... no > setting MPI_LIBS... > checking for library containing mpi_init... (cached) no > setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > setting IFLAGS... -I../include > setting FDFLAGS... $(DFLAGS) > setting RANLIB... echo > configure: creating ./config.status > config.status: creating include/fft_defs.h > config.status: creating make.sys > config.status: creating configure.msg > config.status: creating include/c_defs.h > config.status: include/c_defs.h is unchanged > -------------------------------------------------------------------- > ESPRESSO can take advantage of several optimized numerical libraries > (essl, fftw, mkl...). This configure script attempts to find them, > but may fail if they have been installed in non-standard locations. > If a required library is not found, the local copy will be compiled. > > The following libraries have been found: > BLAS_LIBS=../flib/blas.a > LAPACK_LIBS=../flib/lapack.a > FFT_LIBS= > Please check if this is what you expect. > > If any libraries are missing, you may specify a list of directories > to search and retry, as follows: > ./configure LIBDIRS="list of directories, separated by spaces" > > Parallel environment not detected (is this a parallel machine?). > Configured for compilation of serial executables. > > For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). > -------------------------------------------------------------------- > configure: success > ______________________________________________ > > but parallel version is not getting compiled > > > sincerely, > Sreekar Guddeti > Dept. Physics > IIT Bombay > India > > > > > On Mon, Sep 7, 2009 at 5:23 AM, wrote: > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: Pw_forum Digest, Vol 27, Issue 24 (sreekar guddeti) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 7 Sep 2009 05:23:12 +0530 > > From: sreekar guddeti > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 24 > > To: pw_forum at pwscf.org > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > i have set variable LD_FLAGS = static in make.sys file > > > > and on $make all > > > > i get error > > ---------------------------------------- > > libiotk.a > > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > > -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW > > -I../PH -c iotk_print_kinds.f90 > > make loclib_only > > make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src' > > make[3]: Nothing to be done for `loclib_only'. > > make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > > mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a > > /opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open': > > (.text+0x123): warning: Using 'dlopen' in statically linked applications > > requires at runtime the shared libraries from the glibc version used for > > linking > > /opt/openmpi/lib/libopen-rte.a(sys_info.o): In function `orte_sys_info': > > (.text+0x16f): warning: Using 'getpwuid' in statically linked > applications > > requires at runtime the shared libraries from the glibc version used for > > linking > > /opt/openmpi/lib/libopen-pal.a(if.o): In function `opal_ifaddrtoname': > > (.text+0x780): warning: Using 'gethostbyname' in statically linked > > applications requires at runtime the shared libraries from the glibc > > version > > used for linking > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `__malloc_check_init': > > (.text+0x1060): multiple definition of `__malloc_check_init' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first defined > > here > > /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from > 144 > > in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `_int_free': > > (.text+0x2230): multiple definition of `_int_free' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `_int_malloc': > > (.text+0x2a50): multiple definition of `_int_malloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 3916 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `_int_memalign': > > (.text+0x3900): multiple definition of `_int_memalign' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 577 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `_int_valloc': > > (.text+0x3c30): multiple definition of `_int_valloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 378 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `_int_realloc': > > (.text+0x3d80): multiple definition of `_int_realloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 875 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `free': > > (.text+0x5f20): multiple definition of `free' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `free' changed from 256 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `malloc': > > (.text+0x4690): multiple definition of `malloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o): > > In function `realloc': > > (.text+0x60f0): multiple definition of `realloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/libc.a(malloc.o) > > collect2: ld returned 1 exit status > > make[2]: *** [iotk_print_kinds.x] Error 1 > > make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > > make[1]: *** [lib+util] Error 2 > > make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk' > > make: *** [libiotk] Error 2 > > > > --------------------------------------------- > > > > sincerely > > > > > > On Sun, Sep 6, 2009 at 11:35 PM, wrote: > > > > > Send Pw_forum mailing list submissions to > > > pw_forum at pwscf.org > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > or, via email, send a message with subject or body 'help' to > > > pw_forum-request at pwscf.org > > > > > > You can reach the person managing the list at > > > pw_forum-owner at pwscf.org > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of Pw_forum digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Re: pw.x running but nothing happens (Bipul Rakshit) > > > 2. pseudo potential (Mansoureh Pashangpour) > > > 3. Re: error loading shared libraries on parallel execution > > > (Paolo Giannozzi) > > > 4. Re: pw.x running but nothing happens (Lorenzo Paulatto) > > > 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Sun, 6 Sep 2009 08:03:29 +0100 > > > From: Bipul Rakshit > > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > > To: PWSCF Forum > > > Message-ID: > > > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> > > > Content-Type: text/plain; charset="gb2312" > > > > > > Dear Wangqj, > > > The same thing happens to me. > > > since you are using large no. of wfc, although it shows the job is > > running > > > in 8 procs, but sometimes if the installation is not proper, it is > > running > > > in 1 procs only. > > > > > > So better you check the parallel installation using a small job, with > > > different no. of procs and see whether its taking lesser time as no. > of > > > procs increases or not? > > > > > > cheers > > > > > > 2009/9/6 wangqj1 > > > > > > > > > > > Dear pwscf users > > > > When I run vc-relax on the computing cluster use one node which > > has > > > 8 > > > > CPUs. > > > > The output file is as following: > > > > > > > > Program PWSCF v.4.0.1 starts ... > > > > Today is 6Sep2009 at 7:49:30 > > > > Parallel version (MPI) > > > > Number of processors in use: 8 > > > > R & G space division: proc/pool = 8 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials > or > > > PAW > > > > ..................................................................... > > > > Initial potential from superposition of free atoms > > > > starting charge 435.99565, renormalised to 436.00000 > > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > > > After one day ,it still like this and no iteration has completed > ,there > > > is > > > > also no error was turn up .There is no error in the input file > because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > > I can't find the reason about this ,any help will be appreciated . > > > > Best Regards > > > > Q.J.Wang > > > > XiangTan University > > > > > > > > > > > > > > > > ------------------------------ > > > > ???????????,www.yeah.net > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > -- > > > Dr. Bipul Rakshit > > > Research Associate, > > > S N Bose Centre for Basic Sciences, > > > Salt Lake, > > > Kolkata 700 098 > > > India > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Sun, 6 Sep 2009 11:25:06 +0330 > > > From: Mansoureh Pashangpour > > > Subject: [Pw_forum] pseudo potential > > > To: PWSCF Forum > > > Message-ID: > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear all > > > how can I plot these pseudo potentials? how can I discribe the > > properties > > > of pseudo potentials? > > > > > > *Fe.pbe-nd-rrkjus.UPF*< > > > http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF> > > > ( > > > *details*< > > > http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF>) > > > > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > nonlinear core-correction > > > semicore state d in valence > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > and > > > > > > *H.pbe-rrkjus.UPF* < > http://www.pwscf.org/pseudo/1.3/UPF/H.pbe-rrkjus.UPF > > > > > > (*details* < > > > http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>) > > > > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > > > > and > > > > > > *O.pbe-rrkjus.UPF* > > > (*details* > > > ) > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > > > > Thanks > > > Mansoureh Pashangpour > > > Ph.D student > > > Islami Azad university > > > science & reaserch branch > > > Tehran, IRAN > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Sun, 6 Sep 2009 10:24:48 +0200 > > > From: Paolo Giannozzi > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > execution > > > To: PWSCF Forum > > > Message-ID: > > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > > > > > On Sep 6, 2009, at 1:20 , sreekar guddeti wrote: > > > > > > > plz suggest solutions which donot require root permissions , > > > > as i dont have > > > > > > somebody must have it. Report the problem and the > > > solution (i.e. install gfortran on ALL processors) to > > > whoever has root access. As an alternative, try static > > > link (add -static to LDFLAGS in make.sys). > > > --- > > > Paolo Giannozzi, Dept of Physics, University of Udine > > > via delle Scienze 208, 33100 Udine, Italy > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST) > > > From: "Lorenzo Paulatto" > > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > > To: "PWSCF Forum" > > > Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it> > > > Content-Type: text/plain;charset=iso-8859-1 > > > > > > > > > On Sun, September 6, 2009 02:33, wangqj1 wrote: > > > > After one day ,it still like this and no iteration has completed > > ,there > > > > is > > > > also no error was turn up .There is no error in the input file > because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > > I can't find the reason about this ,any help will be appreciated . > > > > > > > > > Dear QJ, > > > this is strange. But we would need more information on your hardwre > > > configuration in order to help you. In the mean while you can check the > > > behaviour of te pw.x processes with "top". E.g. if they are all runing > at > > > 100% CPU, how much memory they are taking and so on. > > > > > > regards > > > > > > > > > -- > > > Lorenzo Paulatto > > > SISSA & DEMOCRITOS (Trieste) > > > phone: +39 040 3787 511 > > > skype: paulatz > > > www: http://people.sissa.it/~paulatto/ > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > > SISSA Webmail https://webmail.sissa.it/ > > > Powered by SquirrelMail http://www.squirrelmail.org/ > > > > > > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Sun, 6 Sep 2009 23:35:26 +0530 > > > From: sreekar guddeti > > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23 > > > To: pw_forum at pwscf.org > > > Message-ID: > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > @duy lee > > > i inserted the line #$ -V in my qsub script and the env variable > > > $LD_LIBRARY_PATH is being set from script... thanks for that but still > > > problem persists. > > > > > > @rakshit > > > > > > ----------------------------- > > > $find /usr/lib -name libgfortran* > > > ----------------------------- > > > and output is > > > _______________________ > > > /usr/lib/libgfortran.so.1.0.0 > > > /usr/lib/libgfortran.so.1 > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so > > > _______________________ > > > whereas on doing > > > ----------------------------- > > > $find /usr/lib64 -name libgfortran* > > > ----------------------------- > > > ouput is > > > _________________ > > > /usr/lib64/libgfortran.so.3.0.0 > > > /usr/lib64/libgfortran.so.1.0.0 > > > /usr/lib64/libgfortran.so.1 > > > find: /usr/lib64/audit: Permission denied > > > */usr/lib64/libgfortran.so.3* > > > _________________ > > > > > > it means my OS has the required library, i guess > > > > > > i installed the QE on the head node > > > This cluster is a Rocks cluster with > > > > > > # of nodes: 10 (1 head node + 9 compute nodes) > > > # of processors/node: 8 > > > # Total # of processors: 10X8 = 80 > > > > > > i tested the sample program for submitting batch jobs using SGE utility > > and > > > it is working fine( > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > ) > > > > > > sincerely, > > > sreekar guddeti > > > Dept. Physics > > > IIT Bombay > > > India > > > > > > > > > On Sun, Sep 6, 2009 at 12:28 PM, wrote: > > > > > > > Send Pw_forum mailing list submissions to > > > > pw_forum at pwscf.org > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > or, via email, send a message with subject or body 'help' to > > > > pw_forum-request at pwscf.org > > > > > > > > You can reach the person managing the list at > > > > pw_forum-owner at pwscf.org > > > > > > > > When replying, please edit your Subject line so it is more specific > > > > than "Re: Contents of Pw_forum digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Re: error loading shared libraries on parallel execution (Duy > Le) > > > > 2. pw.x running but nothing happens (wangqj1) > > > > 3. Re: error loading shared libraries on parallel execution > > > > (Bipul Rakshit) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Sat, 5 Sep 2009 19:39:17 -0400 > > > > From: Duy Le > > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > > execution > > > > To: PWSCF Forum > > > > Message-ID: > > > > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Hi,I am not sure if this help. Could you please try to add > > > > #$ -V in your submitting script. Like this: > > > > > > > > #!/bin/bash > > > > # > > > > #$ -V > > > > #$ -cwd > > > > #$ -j y > > > > #$ -S /bin/bash > > > > # > > > > > > > > Good luck. > > > > D. > > > > > > > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti > > > > wrote: > > > > > > > > > i know this issuehas been addressed and documented in > troubleshooting > > > > > section of the users guide. > > > > > but i giveup in despair trying for a whole day to figure this > problem > > > > > i run my jobs on rocks cluster by using SGE's facility of > submitting > > > > batch > > > > > jobs > > > > > > > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > > successfully > > > > > run a single parallel job, but on submitting a second job i get the > > > error > > > > > ____________________________________________ > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > ____________________________________________ > > > > > > > > > > > > > > > i find out the path for the library and added to the > LD_LIBRARY_PATH > > by > > > > > writing > > > > > _______________________________________ > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > _______________________________________ > > > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > > dosroutine.qsub) which is > > > > > > > > > > dosroutine.qsub > > > > > ----------------------------------------------------------------- > > > > > > > > > > #!/bin/bash > > > > > # > > > > > #$ -cwd > > > > > #$ -j y > > > > > #$ -S /bin/bash > > > > > # > > > > > > > > > > #extract the info about no of processors involved from command line > > > > > arguments of 'qsub' > > > > > PROCESSORS=$NSLOTS > > > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > > NPR=4 > > > > > #as a result no of pools are give by > > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > > > #!/bin/bash > > > > > # > > > > > # > > > > > #Script for performing a dos calculation on a parallel processor > > > > > WORKINGDIR=`pwd` > > > > > ECHO="echo" > > > > > > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > > > > > > # set the needed environment variables > > > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > > $ECHO $PREFIX > > > > > BIN_DIR=$PREFIX/bin > > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > > TMP_DIR=$HOME/tmp > > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > > > # required executables and pseudopotentials > > > > > $ECHO > > > > > $ECHO " executables directory: $BIN_DIR" > > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > > > #create results directory > > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > > if test ! -d $DIR ; then > > > > > mkdir $DIR > > > > > fi > > > > > done > > > > > cd $WORKINGDIR/results > > > > > > > > > > > > > > > # variables to represent programs > > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > > cat > 0ni0.dos.in << EOF > > > > > &control > > > > > calculation='nscf' > > > > > restart_mode='from_scratch', > > > > > prefix='0ni0', > > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > > outdir='$TMP_DIR/' > > > > > / > > > > > &system > > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > > occupations='tetrahedra' > > > > > / > > > > > &electrons > > > > > conv_thr = 1.0e-10 > > > > > mixing_beta = 0.7 > > > > > / > > > > > ATOMIC_SPECIES > > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > > ATOMIC_POSITIONS > > > > > Ni 0.0 0.0 0.0 > > > > > K_POINTS {automatic} !special points generated by tetrahedra > > > > method > > > > > 12 12 12 0 0 0 > > > > > EOF > > > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > > $ECHO > > > > > $ECHO " done" > > > > > > > > > > ------------------------------------------------------------- > > > > > > > > > > the output i get is > > > > > > > > > > ************************************************ > > > > > :/usr/lib64:/usr/lib > > > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > > temporary directory: /home3/colonel/tmp > > > > > running DOS calculation for 0Ni0 ...\c > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > > > > > > done > > > > > ************************************************* > > > > > plz suggest solutions which donot require root permissions , as i > > dont > > > > have > > > > > thanks in advance > > > > > -- > > > > > Sreekar Guddeti > > > > > Department of Physics > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > > > > > > -- > > > > -------------------------------------------------- > > > > Duy Le > > > > PhD Student > > > > Department of Physics > > > > University of Central Florida. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > > > > From: wangqj1 > > > > Subject: [Pw_forum] pw.x running but nothing happens > > > > To: pw_forum > > > > Message-ID: > > > > < > > 25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com > > > > > > > > Content-Type: text/plain; charset="gbk" > > > > > > > > > > > > Dear pwscf users > > > > When I run vc-relax on the computing cluster use one node which > has > > 8 > > > > CPUs. > > > > The output file is as following: > > > > > > > > Program PWSCF v.4.0.1 starts ... > > > > Today is 6Sep2009 at 7:49:30 > > > > Parallel version (MPI) > > > > Number of processors in use: 8 > > > > R & G space division: proc/pool = 8 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > > PAW > > > > ..................................................................... > > > > Initial potential from superposition of free atoms > > > > starting charge 435.99565, renormalised to 436.00000 > > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > > > After one day ,it still like this and no iteration has completed > ,there > > > is > > > > also no error was turn up .There is no error in the input file > because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs well . > > > > I can't find the reason about this ,any help will be appreciated . > > > > Best Regards > > > > Q.J.Wang > > > > XiangTan University > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Sun, 6 Sep 2009 07:58:49 +0100 > > > > From: Bipul Rakshit > > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > > execution > > > > To: PWSCF Forum > > > > Message-ID: < > 3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > hi, > > > > Just from root user type > > > > yum install libgfortran.so.3 > > > > > > > > then it will install this files which is not present in your machine > > > > > > > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti > > > > wrote: > > > > > > > > > i know this issuehas been addressed and documented in > troubleshooting > > > > > section of the users guide. > > > > > but i giveup in despair trying for a whole day to figure this > problem > > > > > i run my jobs on rocks cluster by using SGE's facility of > submitting > > > > batch > > > > > jobs > > > > > > > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > > successfully > > > > > run a single parallel job, but on submitting a second job i get the > > > error > > > > > ____________________________________________ > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > ____________________________________________ > > > > > > > > > > > > > > > i find out the path for the library and added to the > LD_LIBRARY_PATH > > by > > > > > writing > > > > > _______________________________________ > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > _______________________________________ > > > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > > dosroutine.qsub) which is > > > > > > > > > > dosroutine.qsub > > > > > ----------------------------------------------------------------- > > > > > > > > > > #!/bin/bash > > > > > # > > > > > #$ -cwd > > > > > #$ -j y > > > > > #$ -S /bin/bash > > > > > # > > > > > > > > > > #extract the info about no of processors involved from command line > > > > > arguments of 'qsub' > > > > > PROCESSORS=$NSLOTS > > > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > > NPR=4 > > > > > #as a result no of pools are give by > > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > > > #!/bin/bash > > > > > # > > > > > # > > > > > #Script for performing a dos calculation on a parallel processor > > > > > WORKINGDIR=`pwd` > > > > > ECHO="echo" > > > > > > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > > > > > > # set the needed environment variables > > > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > > $ECHO $PREFIX > > > > > BIN_DIR=$PREFIX/bin > > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > > TMP_DIR=$HOME/tmp > > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > > > # required executables and pseudopotentials > > > > > $ECHO > > > > > $ECHO " executables directory: $BIN_DIR" > > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > > > #create results directory > > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > > if test ! -d $DIR ; then > > > > > mkdir $DIR > > > > > fi > > > > > done > > > > > cd $WORKINGDIR/results > > > > > > > > > > > > > > > # variables to represent programs > > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX" > > > > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > > cat > 0ni0.dos.in << EOF > > > > > &control > > > > > calculation='nscf' > > > > > restart_mode='from_scratch', > > > > > prefix='0ni0', > > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > > outdir='$TMP_DIR/' > > > > > / > > > > > &system > > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > > occupations='tetrahedra' > > > > > / > > > > > &electrons > > > > > conv_thr = 1.0e-10 > > > > > mixing_beta = 0.7 > > > > > / > > > > > ATOMIC_SPECIES > > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > > ATOMIC_POSITIONS > > > > > Ni 0.0 0.0 0.0 > > > > > K_POINTS {automatic} !special points generated by tetrahedra > > > > method > > > > > 12 12 12 0 0 0 > > > > > EOF > > > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > > $ECHO > > > > > $ECHO " done" > > > > > > > > > > ------------------------------------------------------------- > > > > > > > > > > the output i get is > > > > > > > > > > ************************************************ > > > > > :/usr/lib64:/usr/lib > > > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > > temporary directory: /home3/colonel/tmp > > > > > running DOS calculation for 0Ni0 ...\c > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: No > such > > > > > file or directory > > > > > > > > > > done > > > > > ************************************************* > > > > > plz suggest solutions which donot require root permissions , as i > > dont > > > > have > > > > > thanks in advance > > > > > -- > > > > > Sreekar Guddeti > > > > > Department of Physics > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > > > > > > -- > > > > Dr. Bipul Rakshit > > > > Research Associate, > > > > S N Bose Centre for Basic Sciences, > > > > Salt Lake, > > > > Kolkata 700 098 > > > > India > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > End of Pw_forum Digest, Vol 27, Issue 23 > > > > **************************************** > > > > > > > > > > > > > > > > -- > > > Sreekar Guddeti > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > End of Pw_forum Digest, Vol 27, Issue 24 > > > **************************************** > > > > > > > > > > > -- > > Sreekar Guddeti > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f9410638/attachment.htm > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 27, Issue 25 > > **************************************** > > > > > > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090907/9fbce729/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 26 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/6761f51c/attachment-0001.htm From udayagiri3 at gmail.com Mon Sep 7 08:35:44 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Mon, 7 Sep 2009 12:05:44 +0530 Subject: [Pw_forum] choosing degauss value Message-ID: Dear all can somebody tell me how to choose a correct degauss value for an SCF calculation and also the physics behind it. -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/9d8a7005/attachment.htm From baroni at sissa.it Mon Sep 7 08:42:40 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 7 Sep 2009 08:42:40 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 26 In-Reply-To: References: Message-ID: <0024107C-0FCE-4043-9E86-732ACE3D088F@sissa.it> please, in order to make the life of those who may want to help you easier: 1) always indicate the subject of your post in the "subject" field. the more accurate the short description of your problem, the easier it will be that somebody will pick your post up 2) group all the questions related to a same problem in a same post. the time that each of us devotes voluntarily to this community activity is limited. the easier it is to go through the forum, the highest are the chances that some relevant questions are answered. 3) strip unrelated material from the post. I understand that composing a regular mail massege may take 2-3 seconds more than just hitting "reply", but I think that this time is worth avoiding cluttering our mail boxes with garbage. this being said, I am not the most appropriate person to pick up your answers. I wish somebody else will ... best wishes - Stefano Baroni On Sep 7, 2009, at 4:25 AM, sreekar guddeti wrote: > sorry for making repeated posts but on > $./configure --enable-parallel --host=x86_64 > configuration is successful for parallel version > on $make all > in the compilation report i get the following warnings related to > libgfortran.so.3 and no other warnings > > /usr/bin/ld: warning: libgfortran.so.1, needed by /opt/openmpi/lib/ > libmpi_f90.so, may conflict with libgfortran.so.3 ( 8 times) > > /usr/bin/ld: warning: libgfortran.so.1, needed by /usr/lib/gcc/ > x86_64-redhat-linux6E/4.3.2/../../../liblapack.a, may conflict with > libgfortran.so.3 (many times) > > hope this information is useful for suggesting a solution to the > problem > sincerely, > sreekar guddeti > Dept.Physics > IIT Bombay > India > > On Mon, Sep 7, 2009 at 6:36 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 27, Issue 25 (sreekar guddeti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Sep 2009 06:36:10 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 25 > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > As an alternative, try static > > link (add -static to LDFLAGS in make.sys). > > The other thing that i tried was > $make clean > $./configure --enable-parallel --disable-shared --host=x86_64 > > output is > ___________________________________________ > configure: WARNING: If you wanted to set the --build type, don't use > --host. > If a cross compiler is detected then cross compile mode will be > used. > checking build system type... x86_64-unknown-linux-gnu > configure: WARNING: incorrect host name ? > checking architecture... > configure: WARNING: unsupported architecture? > checking for x86_64-g95... no > checking for x86_64-gfortran... no > checking for x86_64-f90... no > checking for g95... no > checking for gfortran... gfortran > checking for Fortran 77 compiler default output file name... a.out > checking whether the Fortran 77 compiler works... yes > checking whether we are cross compiling... yes > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > checking for x86_64-mpif90... no > checking for x86_64-gfortran... no > checking for mpif90... mpif90 > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether mpif90 accepts -g... yes > setting F90... gfortran > setting MPIF90... mpif90 > checking for x86_64-cc... no > checking for x86_64-gcc... no > checking for cc... no > checking for gcc... gcc > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > setting CC... gcc > checking how to run the C preprocessor... gcc -E > checking for egrep... grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for int *... yes > checking size of int *... 8 > checking malloc.h usability... yes > checking malloc.h presence... yes > checking for malloc.h... yes > checking for struct mallinfo.arena... yes > checking for x86_64-gfortran... no > checking for gfortran... gfortran > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > setting F77... gfortran > using F90... gfortran > setting FFLAGS... -O3 > setting F90FLAGS... $(FFLAGS) -x f95-cpp-input > setting FFLAGS_NOOPT... -O0 > setting CFLAGS... -O3 > setting CPP... cpp > setting CPPFLAGS... -P -traditional > setting LD... mpif90 > setting LDFLAGS... -static > setting AR... ar > setting ARFLAGS... ruv > setting ARFLAGS_DYNAMIC...ruv > checking whether make sets $(MAKE)... yes > checking whether Fortran files must be preprocessed... no > checking how to get verbose linking output from gfortran... -v > checking for Fortran libraries of gfortran... > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2 > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64 -L/ > lib/../lib64 > -L/usr/lib/../lib64 -L/opt/intel/Compiler/11.1/046/lib/intel64 > -L/opt/intel/Compiler/11.1/046/ipp/em64t/lib > -L/opt/intel/Compiler/11.1/046/mkl/lib/em64t > -L/opt/intel/Compiler/11.1/046/tbb/em64t/ > cc4.1.0_libc2.4_kernel2.6.16.21/lib > -L/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../.. -lgfortranbegin > -lgfortran -lm -lgcc_s > checking for dummy main to link with Fortran libraries... none > checking for Fortran name-mangling scheme... lower case, underscore, > no > extra underscore > checking for library containing dgemm... no > in /usr/local/lib: checking for library containing dgemm... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > dgemm... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for > library > containing dgemm... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing dgemm... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/ > cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing dgemm... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > dgemm... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > dgemm... > no > checking for library containing dgemm... no > in /usr/local/lib: checking for library containing dgemm... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > dgemm... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for > library > containing dgemm... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing dgemm... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/ > cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing dgemm... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > dgemm... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > dgemm... > no > checking for library containing zggev... no > in /usr/local/lib: checking for library containing zggev... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > zggev... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for > library > containing zggev... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing zggev... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/ > cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing zggev... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > zggev... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > zggev... > no > setting BLAS_LIBS... ../flib/blas.a > setting LAPACK_LIBS... ../flib/lapack.a > checking for library containing fftwnd... no > in /usr/local/lib: checking for library containing fftwnd... no > in /cineca/prod/gnu/lib: checking for library containing fftwnd... no > in /opt/intel/Compiler/11.1/046/lib/intel64: checking for library > containing > fftwnd... no > in /opt/intel/Compiler/11.1/046/ipp/em64t/sharedlib: checking for > library > containing fftwnd... no > in /opt/intel/Compiler/11.1/046/mkl/lib/em64t: checking for library > containing fftwnd... no > in > /opt/intel/Compiler/11.1/046/tbb/em64t/ > cc4.1.0_libc2.4_kernel2.6.16.21/lib: > checking for library containing fftwnd... no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > fftwnd... > no > in /opt/gridengine/lib/lx26-amd64: checking for library containing > fftwnd... > no > setting FFT_LIBS... > checking for library containing fftwnd... (cached) no > setting MASS_LIBS... > checking for library containing mpi_init... no > setting MPI_LIBS... > checking for library containing mpi_init... (cached) no > setting DFLAGS... -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > setting IFLAGS... -I../include > setting FDFLAGS... $(DFLAGS) > setting RANLIB... echo > configure: creating ./config.status > config.status: creating include/fft_defs.h > config.status: creating make.sys > config.status: creating configure.msg > config.status: creating include/c_defs.h > config.status: include/c_defs.h is unchanged > -------------------------------------------------------------------- > ESPRESSO can take advantage of several optimized numerical libraries > (essl, fftw, mkl...). This configure script attempts to find them, > but may fail if they have been installed in non-standard locations. > If a required library is not found, the local copy will be compiled. > > The following libraries have been found: > BLAS_LIBS=../flib/blas.a > LAPACK_LIBS=../flib/lapack.a > FFT_LIBS= > Please check if this is what you expect. > > If any libraries are missing, you may specify a list of directories > to search and retry, as follows: > ./configure LIBDIRS="list of directories, separated by spaces" > > Parallel environment not detected (is this a parallel machine?). > Configured for compilation of serial executables. > > For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). > -------------------------------------------------------------------- > configure: success > ______________________________________________ > > but parallel version is not getting compiled > > > sincerely, > Sreekar Guddeti > Dept. Physics > IIT Bombay > India > > > > > On Mon, Sep 7, 2009 at 5:23 AM, wrote: > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. Re: Pw_forum Digest, Vol 27, Issue 24 (sreekar guddeti) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 7 Sep 2009 05:23:12 +0530 > > From: sreekar guddeti > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 24 > > To: pw_forum at pwscf.org > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > i have set variable LD_FLAGS = static in make.sys file > > > > and on $make all > > > > i get error > > ---------------------------------------- > > libiotk.a > > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW - > D__USE_INTERNAL_FFTW > > -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src - > I../PW > > -I../PH -c iotk_print_kinds.f90 > > make loclib_only > > make[3]: Entering directory `/home3/colonel/espresso-4.0.5/iotk/src' > > make[3]: Nothing to be done for `loclib_only'. > > make[3]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > > mpif90 -static -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a > > /opt/openmpi/lib/libopen-pal.a(dlopen.o): In function `vm_open': > > (.text+0x123): warning: Using 'dlopen' in statically linked > applications > > requires at runtime the shared libraries from the glibc version > used for > > linking > > /opt/openmpi/lib/libopen-rte.a(sys_info.o): In function > `orte_sys_info': > > (.text+0x16f): warning: Using 'getpwuid' in statically linked > applications > > requires at runtime the shared libraries from the glibc version > used for > > linking > > /opt/openmpi/lib/libopen-pal.a(if.o): In function > `opal_ifaddrtoname': > > (.text+0x780): warning: Using 'gethostbyname' in statically linked > > applications requires at runtime the shared libraries from the glibc > > version > > used for linking > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `__malloc_check_init': > > (.text+0x1060): multiple definition of `__malloc_check_init' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3a0): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed > from 144 > > in /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 105 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `_int_free': > > (.text+0x2230): multiple definition of `_int_free' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1030): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_free' changed from 1219 > in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 2080 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `_int_malloc': > > (.text+0x2a50): multiple definition of `_int_malloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x18c0): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_malloc' changed from > 3916 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 3754 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `_int_memalign': > > (.text+0x3900): multiple definition of `_int_memalign' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2d40): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_memalign' changed from > 577 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 550 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `_int_valloc': > > (.text+0x3c30): multiple definition of `_int_valloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x2f90): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_valloc' changed from > 378 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 62 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `_int_realloc': > > (.text+0x3d80): multiple definition of `_int_realloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3180): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `_int_realloc' changed from > 875 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1411 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `free': > > (.text+0x5f20): multiple definition of `free' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x1500): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `free' changed from 256 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 454 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `malloc': > > (.text+0x4690): multiple definition of `malloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3830): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `malloc' changed from 363 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 466 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o): > > In function `realloc': > > (.text+0x60f0): multiple definition of `realloc' > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o):(.text+0x3bc0): first > defined > > here > > /usr/bin/ld: Warning: size of symbol `realloc' changed from 490 in > > /opt/openmpi/lib/libopen-pal.a(lt1-malloc.o) to 1184 in > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/../../../../lib64/ > libc.a(malloc.o) > > collect2: ld returned 1 exit status > > make[2]: *** [iotk_print_kinds.x] Error 1 > > make[2]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk/src' > > make[1]: *** [lib+util] Error 2 > > make[1]: Leaving directory `/home3/colonel/espresso-4.0.5/iotk' > > make: *** [libiotk] Error 2 > > > > --------------------------------------------- > > > > sincerely > > > > > > On Sun, Sep 6, 2009 at 11:35 PM, wrote: > > > > > Send Pw_forum mailing list submissions to > > > pw_forum at pwscf.org > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > or, via email, send a message with subject or body 'help' to > > > pw_forum-request at pwscf.org > > > > > > You can reach the person managing the list at > > > pw_forum-owner at pwscf.org > > > > > > When replying, please edit your Subject line so it is more > specific > > > than "Re: Contents of Pw_forum digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Re: pw.x running but nothing happens (Bipul Rakshit) > > > 2. pseudo potential (Mansoureh Pashangpour) > > > 3. Re: error loading shared libraries on parallel execution > > > (Paolo Giannozzi) > > > 4. Re: pw.x running but nothing happens (Lorenzo Paulatto) > > > 5. Re: Pw_forum Digest, Vol 27, Issue 23 (sreekar guddeti) > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Sun, 6 Sep 2009 08:03:29 +0100 > > > From: Bipul Rakshit > > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > > To: PWSCF Forum > > > Message-ID: > > > > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> > > > Content-Type: text/plain; charset="gb2312" > > > > > > Dear Wangqj, > > > The same thing happens to me. > > > since you are using large no. of wfc, although it shows the job is > > running > > > in 8 procs, but sometimes if the installation is not proper, it is > > running > > > in 1 procs only. > > > > > > So better you check the parallel installation using a small job, > with > > > different no. of procs and see whether its taking lesser time > as no. of > > > procs increases or not? > > > > > > cheers > > > > > > 2009/9/6 wangqj1 > > > > > > > > > > > Dear pwscf users > > > > When I run vc-relax on the computing cluster use one node > which > > has > > > 8 > > > > CPUs. > > > > The output file is as following: > > > > > > > > Program PWSCF v.4.0.1 starts ... > > > > Today is 6Sep2009 at 7:49:30 > > > > Parallel version (MPI) > > > > Number of processors in use: 8 > > > > R & G space division: proc/pool = 8 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) > Pseudopotentials or > > > PAW > > > > > > ..................................................................... > > > > Initial potential from superposition of free atoms > > > > starting charge 435.99565, renormalised to 436.00000 > > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > > > After one day ,it still like this and no iteration has > completed ,there > > > is > > > > also no error was turn up .There is no error in the input file > because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs > well . > > > > I can't find the reason about this ,any help will be > appreciated . > > > > Best Regards > > > > Q.J.Wang > > > > XiangTan University > > > > > > > > > > > > > > > > ------------------------------ > > > > ???????????,www.yeah.net > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > -- > > > Dr. Bipul Rakshit > > > Research Associate, > > > S N Bose Centre for Basic Sciences, > > > Salt Lake, > > > Kolkata 700 098 > > > India > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 2 > > > Date: Sun, 6 Sep 2009 11:25:06 +0330 > > > From: Mansoureh Pashangpour > > > Subject: [Pw_forum] pseudo potential > > > To: PWSCF Forum > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Dear all > > > how can I plot these pseudo potentials? how can I discribe the > > properties > > > of pseudo potentials? > > > > > > *Fe.pbe-nd-rrkjus.UPF*< > > > http://www.pwscf.org/pseudo/1.3/UPF/Fe.pbe-nd-rrkjus.UPF> > > > ( > > > *details*< > > > http://www.pwscf.org/pseudo/upfdetails.php?upf=Fe.pbe-nd-rrkjus.UPF > >) > > > > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > nonlinear core-correction > > > semicore state d in valence > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > and > > > > > > *H.pbe-rrkjus.UPF* > > > > > (*details* < > > > http://www.pwscf.org/pseudo/upfdetails.php?upf=H.pbe-rrkjus.UPF>) > > > > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > > > > and > > > > > > *O.pbe-rrkjus.UPF* > > > > (*details* > > > ) > > > > > > Perdew-Burke-Ernzerhof (PBE) exch-corr > > > Rabe Rappe Kaxiras Joannopoulos (ultrasoft) > > > > > > > > > Thanks > > > Mansoureh Pashangpour > > > Ph.D student > > > Islami Azad university > > > science & reaserch branch > > > Tehran, IRAN > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Sun, 6 Sep 2009 10:24:48 +0200 > > > From: Paolo Giannozzi > > > Subject: Re: [Pw_forum] error loading shared libraries on parallel > > > execution > > > To: PWSCF Forum > > > Message-ID: > > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > > > > > > On Sep 6, 2009, at 1:20 , sreekar guddeti wrote: > > > > > > > plz suggest solutions which donot require root permissions , > > > > as i dont have > > > > > > somebody must have it. Report the problem and the > > > solution (i.e. install gfortran on ALL processors) to > > > whoever has root access. As an alternative, try static > > > link (add -static to LDFLAGS in make.sys). > > > --- > > > Paolo Giannozzi, Dept of Physics, University of Udine > > > via delle Scienze 208, 33100 Udine, Italy > > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Sun, 6 Sep 2009 12:20:40 +0200 (CEST) > > > From: "Lorenzo Paulatto" > > > Subject: Re: [Pw_forum] pw.x running but nothing happens > > > To: "PWSCF Forum" > > > Message-ID: <46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it > > > > > Content-Type: text/plain;charset=iso-8859-1 > > > > > > > > > On Sun, September 6, 2009 02:33, wangqj1 wrote: > > > > After one day ,it still like this and no iteration has > completed > > ,there > > > > is > > > > also no error was turn up .There is no error in the input > file because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs > well . > > > > I can't find the reason about this ,any help will be > appreciated . > > > > > > > > > Dear QJ, > > > this is strange. But we would need more information on your > hardwre > > > configuration in order to help you. In the mean while you can > check the > > > behaviour of te pw.x processes with "top". E.g. if they are all > runing at > > > 100% CPU, how much memory they are taking and so on. > > > > > > regards > > > > > > > > > -- > > > Lorenzo Paulatto > > > SISSA & DEMOCRITOS (Trieste) > > > phone: +39 040 3787 511 > > > skype: paulatz > > > www: http://people.sissa.it/~paulatto/ > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > > SISSA Webmail https://webmail.sissa.it/ > > > Powered by SquirrelMail http://www.squirrelmail.org/ > > > > > > > > > > > > ------------------------------ > > > > > > Message: 5 > > > Date: Sun, 6 Sep 2009 23:35:26 +0530 > > > From: sreekar guddeti > > > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 23 > > > To: pw_forum at pwscf.org > > > Message-ID: > > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > @duy lee > > > i inserted the line #$ -V in my qsub script and the env variable > > > $LD_LIBRARY_PATH is being set from script... thanks for that but > still > > > problem persists. > > > > > > @rakshit > > > > > > ----------------------------- > > > $find /usr/lib -name libgfortran* > > > ----------------------------- > > > and output is > > > _______________________ > > > /usr/lib/libgfortran.so.1.0.0 > > > /usr/lib/libgfortran.so.1 > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a > > > /usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so > > > _______________________ > > > whereas on doing > > > ----------------------------- > > > $find /usr/lib64 -name libgfortran* > > > ----------------------------- > > > ouput is > > > _________________ > > > /usr/lib64/libgfortran.so.3.0.0 > > > /usr/lib64/libgfortran.so.1.0.0 > > > /usr/lib64/libgfortran.so.1 > > > find: /usr/lib64/audit: Permission denied > > > */usr/lib64/libgfortran.so.3* > > > _________________ > > > > > > it means my OS has the required library, i guess > > > > > > i installed the QE on the head node > > > This cluster is a Rocks cluster with > > > > > > # of nodes: 10 (1 head node + 9 compute nodes) > > > # of processors/node: 8 > > > # Total # of processors: 10X8 = 80 > > > > > > i tested the sample program for submitting batch jobs using SGE > utility > > and > > > it is working fine( > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > ) > > > > > > sincerely, > > > sreekar guddeti > > > Dept. Physics > > > IIT Bombay > > > India > > > > > > > > > On Sun, Sep 6, 2009 at 12:28 PM, > wrote: > > > > > > > Send Pw_forum mailing list submissions to > > > > pw_forum at pwscf.org > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > or, via email, send a message with subject or body 'help' to > > > > pw_forum-request at pwscf.org > > > > > > > > You can reach the person managing the list at > > > > pw_forum-owner at pwscf.org > > > > > > > > When replying, please edit your Subject line so it is more > specific > > > > than "Re: Contents of Pw_forum digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. Re: error loading shared libraries on parallel execution > (Duy Le) > > > > 2. pw.x running but nothing happens (wangqj1) > > > > 3. Re: error loading shared libraries on parallel execution > > > > (Bipul Rakshit) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Sat, 5 Sep 2009 19:39:17 -0400 > > > > From: Duy Le > > > > Subject: Re: [Pw_forum] error loading shared libraries on > parallel > > > > execution > > > > To: PWSCF Forum > > > > Message-ID: > > > > <8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Hi,I am not sure if this help. Could you please try to add > > > > #$ -V in your submitting script. Like this: > > > > > > > > #!/bin/bash > > > > # > > > > #$ -V > > > > #$ -cwd > > > > #$ -j y > > > > #$ -S /bin/bash > > > > # > > > > > > > > Good luck. > > > > D. > > > > > > > > On Sat, Sep 5, 2009 at 7:20 PM, sreekar guddeti > > > > wrote: > > > > > > > > > i know this issuehas been addressed and documented in > troubleshooting > > > > > section of the users guide. > > > > > but i giveup in despair trying for a whole day to figure > this problem > > > > > i run my jobs on rocks cluster by using SGE's facility of > submitting > > > > batch > > > > > jobs > > > > > > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > > successfully > > > > > run a single parallel job, but on submitting a second job i > get the > > > error > > > > > ____________________________________________ > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > ____________________________________________ > > > > > > > > > > > > > > > i find out the path for the library and added to the > LD_LIBRARY_PATH > > by > > > > > writing > > > > > _______________________________________ > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > _______________________________________ > > > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > > dosroutine.qsub) which is > > > > > > > > > > dosroutine.qsub > > > > > > ----------------------------------------------------------------- > > > > > > > > > > #!/bin/bash > > > > > # > > > > > #$ -cwd > > > > > #$ -j y > > > > > #$ -S /bin/bash > > > > > # > > > > > > > > > > #extract the info about no of processors involved from > command line > > > > > arguments of 'qsub' > > > > > PROCESSORS=$NSLOTS > > > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > > NPR=4 > > > > > #as a result no of pools are give by > > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > > > #!/bin/bash > > > > > # > > > > > # > > > > > #Script for performing a dos calculation on a parallel > processor > > > > > WORKINGDIR=`pwd` > > > > > ECHO="echo" > > > > > > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > > > > > > # set the needed environment variables > > > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > > $ECHO $PREFIX > > > > > BIN_DIR=$PREFIX/bin > > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > > TMP_DIR=$HOME/tmp > > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > > > # required executables and pseudopotentials > > > > > $ECHO > > > > > $ECHO " executables directory: $BIN_DIR" > > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > > > #create results directory > > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > > if test ! -d $DIR ; then > > > > > mkdir $DIR > > > > > fi > > > > > done > > > > > cd $WORKINGDIR/results > > > > > > > > > > > > > > > # variables to represent programs > > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x > $PARA_POSTFIX" > > > > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > > cat > 0ni0.dos.in << EOF > > > > > &control > > > > > calculation='nscf' > > > > > restart_mode='from_scratch', > > > > > prefix='0ni0', > > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > > outdir='$TMP_DIR/' > > > > > / > > > > > &system > > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > > occupations='tetrahedra' > > > > > / > > > > > &electrons > > > > > conv_thr = 1.0e-10 > > > > > mixing_beta = 0.7 > > > > > / > > > > > ATOMIC_SPECIES > > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > > ATOMIC_POSITIONS > > > > > Ni 0.0 0.0 0.0 > > > > > K_POINTS {automatic} !special points generated by > tetrahedra > > > > method > > > > > 12 12 12 0 0 0 > > > > > EOF > > > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > > $ECHO > > > > > $ECHO " done" > > > > > > > > > > ------------------------------------------------------------- > > > > > > > > > > the output i get is > > > > > > > > > > ************************************************ > > > > > :/usr/lib64:/usr/lib > > > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > > temporary directory: /home3/colonel/tmp > > > > > running DOS calculation for 0Ni0 ...\c > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > > > > > > done > > > > > ************************************************* > > > > > plz suggest solutions which donot require root permissions , > as i > > dont > > > > have > > > > > thanks in advance > > > > > -- > > > > > Sreekar Guddeti > > > > > Department of Physics > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > > > > > > -- > > > > -------------------------------------------------- > > > > Duy Le > > > > PhD Student > > > > Department of Physics > > > > University of Central Florida. > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm > > > > > > > > ------------------------------ > > > > > > > > Message: 2 > > > > Date: Sun, 6 Sep 2009 08:33:25 +0800 (CST) > > > > From: wangqj1 > > > > Subject: [Pw_forum] pw.x running but nothing happens > > > > To: pw_forum > > > > Message-ID: > > > > < > > 25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com > > > > > > > > Content-Type: text/plain; charset="gbk" > > > > > > > > > > > > Dear pwscf users > > > > When I run vc-relax on the computing cluster use one node > which has > > 8 > > > > CPUs. > > > > The output file is as following: > > > > > > > > Program PWSCF v.4.0.1 starts ... > > > > Today is 6Sep2009 at 7:49:30 > > > > Parallel version (MPI) > > > > Number of processors in use: 8 > > > > R & G space division: proc/pool = 8 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) > Pseudopotentials or > > PAW > > > > > > ..................................................................... > > > > Initial potential from superposition of free atoms > > > > starting charge 435.99565, renormalised to 436.00000 > > > > Starting wfc are 254 atomic + 8 random wfc > > > > > > > > After one day ,it still like this and no iteration has > completed ,there > > > is > > > > also no error was turn up .There is no error in the input file > because > > I > > > > have test it on anthoer computer which has 4 CPUs and it runs > well . > > > > I can't find the reason about this ,any help will be > appreciated . > > > > Best Regards > > > > Q.J.Wang > > > > XiangTan University > > > > > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm > > > > > > > > ------------------------------ > > > > > > > > Message: 3 > > > > Date: Sun, 6 Sep 2009 07:58:49 +0100 > > > > From: Bipul Rakshit > > > > Subject: Re: [Pw_forum] error loading shared libraries on > parallel > > > > execution > > > > To: PWSCF Forum > > > > Message-ID: <3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > hi, > > > > Just from root user type > > > > yum install libgfortran.so.3 > > > > > > > > then it will install this files which is not present in your > machine > > > > > > > > On Sun, Sep 6, 2009 at 12:20 AM, sreekar guddeti > > > > wrote: > > > > > > > > > i know this issuehas been addressed and documented in > troubleshooting > > > > > section of the users guide. > > > > > but i giveup in despair trying for a whole day to figure > this problem > > > > > i run my jobs on rocks cluster by using SGE's facility of > submitting > > > > batch > > > > > jobs > > > > > > > > > > > > > > > > > > > http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html > > > > > > > > > > what i 'apparently' observe(or doubtfully infer) is that i can > > > > successfully > > > > > run a single parallel job, but on submitting a second job i > get the > > > error > > > > > ____________________________________________ > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > ____________________________________________ > > > > > > > > > > > > > > > i find out the path for the library and added to the > LD_LIBRARY_PATH > > by > > > > > writing > > > > > _______________________________________ > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > _______________________________________ > > > > > > > > > > in the file which acts as script for qsub ($qsub -pe orte 4 > > > > > dosroutine.qsub) which is > > > > > > > > > > dosroutine.qsub > > > > > > ----------------------------------------------------------------- > > > > > > > > > > #!/bin/bash > > > > > # > > > > > #$ -cwd > > > > > #$ -j y > > > > > #$ -S /bin/bash > > > > > # > > > > > > > > > > #extract the info about no of processors involved from > command line > > > > > arguments of 'qsub' > > > > > PROCESSORS=$NSLOTS > > > > > > > > > > #heuristically assign the no of processors per pool NPR > > > > > NPR=4 > > > > > #as a result no of pools are give by > > > > > NPK=`expr $PROCESSORS / $NPR` > > > > > > > > > > #!/bin/bash > > > > > # > > > > > # > > > > > #Script for performing a dos calculation on a parallel > processor > > > > > WORKINGDIR=`pwd` > > > > > ECHO="echo" > > > > > > > > > > #set the library path to include gfortran libraries > > > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib > > > > > > > > > > > > > > > $ECHO > > > > > $ECHO "$LD_LIBRARY_PATH" > > > > > $ECHO > > > > > > > > > > # set the needed environment variables > > > > > > > > > > PREFIX=`cd /home3/colonel/espresso-4.0.5 ; pwd` > > > > > $ECHO $PREFIX > > > > > BIN_DIR=$PREFIX/bin > > > > > PSEUDO_DIR=$PREFIX/pseudo > > > > > TMP_DIR=$HOME/tmp > > > > > PARA_PREFIX="/opt/openmpi/bin/mpirun -np $PROCESSORS" > > > > > PARA_POSTFIX="-npool $NPK" > > > > > > > > > > # required executables and pseudopotentials > > > > > $ECHO > > > > > $ECHO " executables directory: $BIN_DIR" > > > > > $ECHO " pseudo directory: $PSEUDO_DIR" > > > > > $ECHO " temporary directory: $TMP_DIR" > > > > > > > > > > #create results directory > > > > > for DIR in "$TMP_DIR" "$WORKINGDIR/results" ; do > > > > > if test ! -d $DIR ; then > > > > > mkdir $DIR > > > > > fi > > > > > done > > > > > cd $WORKINGDIR/results > > > > > > > > > > > > > > > # variables to represent programs > > > > > PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" > > > > > DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX" > > > > > PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x > $PARA_POSTFIX" > > > > > > > > > > > > > > > # DOS calculation for 0Ni0 > > > > > cat > 0ni0.dos.in << EOF > > > > > &control > > > > > calculation='nscf' > > > > > restart_mode='from_scratch', > > > > > prefix='0ni0', > > > > > pseudo_dir = '$PSEUDO_DIR/', > > > > > outdir='$TMP_DIR/' > > > > > / > > > > > &system > > > > > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > > > > > nspin = 2, starting_magnetization(1)=0.7, > > > > > ecutwfc = 24.0, ecutrho = 288.0, nbnd=8, > > > > > occupations='tetrahedra' > > > > > / > > > > > &electrons > > > > > conv_thr = 1.0e-10 > > > > > mixing_beta = 0.7 > > > > > / > > > > > ATOMIC_SPECIES > > > > > Ni 58.69 NiUS.RRKJ3.UPF > > > > > ATOMIC_POSITIONS > > > > > Ni 0.0 0.0 0.0 > > > > > K_POINTS {automatic} !special points generated by > tetrahedra > > > > method > > > > > 12 12 12 0 0 0 > > > > > EOF > > > > > > > > > > $ECHO " running DOS calculation for 0Ni0 ...\c" > > > > > $PW_COMMAND < 0ni0.dos.in > 0ni0.dos.out > > > > > $ECHO > > > > > $ECHO " done" > > > > > > > > > > ------------------------------------------------------------- > > > > > > > > > > the output i get is > > > > > > > > > > ************************************************ > > > > > :/usr/lib64:/usr/lib > > > > > > > > > > /home3/colonel/espresso-4.0.5 > > > > > > > > > > executables directory: /home3/colonel/espresso-4.0.5/bin > > > > > pseudo directory: /home3/colonel/espresso-4.0.5/pseudo > > > > > temporary directory: /home3/colonel/tmp > > > > > running DOS calculation for 0Ni0 ...\c > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > /home3/colonel/espresso-4.0.5/bin/pw.x: error while loading > shared > > > > > libraries: libgfortran.so.3: cannot open shared object file: > No such > > > > > file or directory > > > > > > > > > > done > > > > > ************************************************* > > > > > plz suggest solutions which donot require root permissions , > as i > > dont > > > > have > > > > > thanks in advance > > > > > -- > > > > > Sreekar Guddeti > > > > > Department of Physics > > > > > > > > > > _______________________________________________ > > > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > > > > > > > > -- > > > > Dr. Bipul Rakshit > > > > Research Associate, > > > > S N Bose Centre for Basic Sciences, > > > > Salt Lake, > > > > Kolkata 700 098 > > > > India > > > > -------------- next part -------------- > > > > An HTML attachment was scrubbed... > > > > URL: > > > > > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > End of Pw_forum Digest, Vol 27, Issue 23 > > > > **************************************** > > > > > > > > > > > > > > > > -- > > > Sreekar Guddeti > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: > > > > > http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > End of Pw_forum Digest, Vol 27, Issue 24 > > > **************************************** > > > > > > > > > > > -- > > Sreekar Guddeti > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f9410638/attachment.htm > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 27, Issue 25 > > **************************************** > > > > > > -- > Sreekar Guddeti > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/9fbce729/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 26 > **************************************** --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/c55700ba/attachment-0001.htm From wangqj1 at 126.com Mon Sep 7 08:55:30 2009 From: wangqj1 at 126.com (wangqj1) Date: Mon, 7 Sep 2009 14:55:30 +0800 (CST) Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: References: Message-ID: <12336594.312101252306530738.JavaMail.coremail@bj126app103.126.com> Dear Lorenzo I now use 16 CPUs(2 nodes) to run the task ,the job runs but very slower than use 4 CPUs in my personal computer ,I use top to look CPU information,it as following: Tasks: 176 total, 1 running, 175 sleeping, 0 stopped, 0 zombie Cpu0 : 0.4%us, 0.4%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu1 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu3 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu5 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu6 : 0.7%us, 0.0%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 8048812k total, 5537848k used, 2510964k free, 315448k buffers Swap: 4192956k total, 0k used, 4192956k free, 5022856k cached Why only display 8 CPUs information and the usage of CPU is so small ? Best regards Q.J.Wang XiangTan University ?2009-09-07?02:05:35?pw_forum-request at pwscf.org???? >Send?Pw_forum?mailing?list?submissions?to > pw_forum at pwscf.org > >To?subscribe?or?unsubscribe?via?the?World?Wide?Web,?visit > http://www.democritos.it/mailman/listinfo/pw_forum >or,?via?email,?send?a?message?with?subject?or?body?'help'?to > pw_forum-request at pwscf.org > >You?can?reach?the?person?managing?the?list?at > pw_forum-owner at pwscf.org > >When?replying,?please?edit?your?Subject?line?so?it?is?more?specific >than?"Re:?Contents?of?Pw_forum?digest..." > > >Today's?Topics: > >???1.?Re:?pw.x?running?but?nothing?happens?(Bipul?Rakshit) >???2.?pseudo?potential?(Mansoureh?Pashangpour) >???3.?Re:?error?loading?shared?libraries?on?parallel?execution >??????(Paolo?Giannozzi) >???4.?Re:?pw.x?running?but?nothing?happens?(Lorenzo?Paulatto) >???5.?Re:?Pw_forum?Digest,?Vol?27,?Issue?23?(sreekar?guddeti) > > >---------------------------------------------------------------------- > >Message:?1 >Date:?Sun,?6?Sep?2009?08:03:29?+0100 >From:?Bipul?Rakshit? >Subject:?Re:?[Pw_forum]?pw.x?running?but?nothing?happens >To:?PWSCF?Forum? >Message-ID: > <3a749910909060003k38e7f62fn4aa040900b71b42c at mail.gmail.com> >Content-Type:?text/plain;?charset="gb2312" > >Dear?Wangqj, >The?same?thing?happens?to?me. >since?you?are?using?large?no.?of?wfc,?although?it?shows?the?job?is?running >in?8?procs,?but?sometimes?if?the?installation?is?not?proper,?it?is?running >in?1?procs?only. > >So?better?you?check?the?parallel?installation?using?a?small?job,?with >different?no.?of?procs?and?see?whether?its?taking?lesser?time?as??no.?of >procs?increases?or?not? > >cheers > >2009/9/6?wangqj1? > >> >>?Dear?pwscf?users >>??????When?I?run?vc-relax?on?the?computing?cluster?use?one?node?which?has?8 >>?CPUs. >>?The?output?file?is?as?following: >> >>?Program?PWSCF?????v.4.0.1??starts?... >>??????Today?is??6Sep2009?at??7:49:30 >>??????Parallel?version?(MPI) >>??????Number?of?processors?in?use:???????8 >>??????R?&?G?space?division:??proc/pool?=????8 >>??????For?Norm-Conserving?or?Ultrasoft?(Vanderbilt)?Pseudopotentials?or?PAW >>?..................................................................... >>??????Initial?potential?from?superposition?of?free?atoms >>??????starting?charge??435.99565,?renormalised?to??436.00000 >>??????Starting?wfc?are??254?atomic?+????8?random?wfc >> >>?After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there?is >>?also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I >>?have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?. >>?I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?. >>?Best?Regards >>?Q.J.Wang >>?XiangTan?University >> >> >> >>?------------------------------ >>????????????,www.yeah.net? >>?_______________________________________________ >>?Pw_forum?mailing?list >>?Pw_forum at pwscf.org >>?http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > >--? >Dr.?Bipul?Rakshit >Research?Associate, >S?N?Bose?Centre?for?Basic?Sciences, >Salt?Lake, >Kolkata?700?098 >India >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/197c5bd6/attachment-0001.htm? > >------------------------------ > >Message:?2 >Date:?Sun,?6?Sep?2009?11:25:06?+0330 >From:?Mansoureh?Pashangpour? >Subject:?[Pw_forum]?pseudo?potential >To:?PWSCF?Forum? >Message-ID: > >Content-Type:?text/plain;?charset="iso-8859-1" > >Dear?all >how?can?I??plot?these?pseudo?potentials??how?can?I?discribe?the?properties >of?pseudo?potentials? > >*Fe.pbe-nd-rrkjus.UPF* >?( >*details*) > > > ?Perdew-Burke-Ernzerhof?(PBE)?exch-corr > ?nonlinear?core-correction > ?semicore?state?d?in?valence > ?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft) > >and > >*H.pbe-rrkjus.UPF*? >(*details*?) > > > ?Perdew-Burke-Ernzerhof?(PBE)?exch-corr > ?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft) > > >and > >*O.pbe-rrkjus.UPF* >???(*details* >) > > ?Perdew-Burke-Ernzerhof?(PBE)?exch-corr > ?Rabe?Rappe?Kaxiras?Joannopoulos?(ultrasoft) > > >Thanks >Mansoureh?Pashangpour >Ph.D?student >Islami?Azad?university >science?&?reaserch?branch >Tehran,?IRAN >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/3efcd6f0/attachment-0001.htm? > >------------------------------ > >Message:?3 >Date:?Sun,?6?Sep?2009?10:24:48?+0200 >From:?Paolo?Giannozzi? >Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel > execution >To:?PWSCF?Forum? >Message-ID:? >Content-Type:?text/plain;?charset=US-ASCII;?format=flowed > > >On?Sep?6,?2009,?at?1:20?,?sreekar?guddeti?wrote: > >>?plz?suggest?solutions?which?donot?require?root?permissions?, >>?as?i?dont?have > >somebody?must?have?it.?Report?the?problem?and?the >solution??(i.e.?install?gfortran?on?ALL?processors)?to >whoever?has?root?access.?As?an?alternative,?try?static >link?(add?-static?to?LDFLAGS?in?make.sys). >--- >Paolo?Giannozzi,?Dept?of?Physics,?University?of?Udine >via?delle?Scienze?208,?33100?Udine,?Italy >Phone?+39-0432-558216,?fax?+39-0432-558222 > > > > > >------------------------------ > >Message:?4 >Date:?Sun,?6?Sep?2009?12:20:40?+0200?(CEST) >From:?"Lorenzo?Paulatto"? >Subject:?Re:?[Pw_forum]?pw.x?running?but?nothing?happens >To:?"PWSCF?Forum"? >Message-ID:?<46134.78.12.159.112.1252232440.squirrel at webmail.sissa.it> >Content-Type:?text/plain;charset=iso-8859-1 > > >On?Sun,?September?6,?2009?02:33,?wangqj1?wrote: >>??After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there >>??is >>??also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I >>??have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?. >>??I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?. > > >Dear?QJ, >this?is?strange.?But?we?would?need?more?information?on?your?hardwre >configuration?in?order?to?help?you.?In?the?mean?while?you?can?check?the >behaviour?of?te?pw.x?processes?with?"top".?E.g.?if?they?are?all?runing?at >100%?CPU,?how?much?memory?they?are?taking?and?so?on. > >regards > > >--? >Lorenzo?Paulatto >SISSA??&??DEMOCRITOS?(Trieste) >phone:?+39?040?3787?511 >skype:?paulatz >www:???http://people.sissa.it/~paulatto/ > > > >---------------------------------------------------------------- >??SISSA?Webmail?https://webmail.sissa.it/ >??Powered?by?SquirrelMail?http://www.squirrelmail.org/ > > > >------------------------------ > >Message:?5 >Date:?Sun,?6?Sep?2009?23:35:26?+0530 >From:?sreekar?guddeti? >Subject:?Re:?[Pw_forum]?Pw_forum?Digest,?Vol?27,?Issue?23 >To:?pw_forum at pwscf.org >Message-ID: > >Content-Type:?text/plain;?charset="iso-8859-1" > >@duy?lee >i?inserted?the?line?#$?-V?in?my?qsub?script?and?the?env?variable >$LD_LIBRARY_PATH?is?being?set?from?script...?thanks?for?that?but?still >problem?persists. > >@rakshit > >----------------------------- >$find?/usr/lib?-name?libgfortran* >----------------------------- >and?output?is >_______________________ >/usr/lib/libgfortran.so.1.0.0 >/usr/lib/libgfortran.so.1 >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.a >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortranbegin.a >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/libgfortran.so >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.a >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortranbegin.a >/usr/lib/gcc/x86_64-redhat-linux6E/4.3.2/32/libgfortran.so >_______________________ >whereas?on?doing >----------------------------- >$find?/usr/lib64?-name?libgfortran* >----------------------------- >ouput?is >_________________ >/usr/lib64/libgfortran.so.3.0.0 >/usr/lib64/libgfortran.so.1.0.0 >/usr/lib64/libgfortran.so.1 >find:?/usr/lib64/audit:?Permission?denied >*/usr/lib64/libgfortran.so.3* >_________________ > >it?means?my?OS?has?the?required?library,?i?guess > >i?installed?the?QE?on?the?head?node >This?cluster?is?a?Rocks?cluster?with > >???#?of?nodes:?10?(1?head?node?+?9?compute?nodes) >???#?of?processors/node:?8 >???#?Total?#?of?processors:?10X8?=?80 > >i?tested?the?sample?program?for?submitting?batch?jobs?using?SGE?utility?and >it?is?working?fine( >http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html) > >sincerely, >sreekar?guddeti >Dept.?Physics >IIT?Bombay >India > > >On?Sun,?Sep?6,?2009?at?12:28?PM,??wrote: > >>?Send?Pw_forum?mailing?list?submissions?to >>????????pw_forum at pwscf.org >> >>?To?subscribe?or?unsubscribe?via?the?World?Wide?Web,?visit >>????????http://www.democritos.it/mailman/listinfo/pw_forum >>?or,?via?email,?send?a?message?with?subject?or?body?'help'?to >>????????pw_forum-request at pwscf.org >> >>?You?can?reach?the?person?managing?the?list?at >>????????pw_forum-owner at pwscf.org >> >>?When?replying,?please?edit?your?Subject?line?so?it?is?more?specific >>?than?"Re:?Contents?of?Pw_forum?digest..." >> >> >>?Today's?Topics: >> >>???1.?Re:?error?loading?shared?libraries?on?parallel?execution?(Duy?Le) >>???2.?pw.x?running?but?nothing?happens?(wangqj1) >>???3.?Re:?error?loading?shared?libraries?on?parallel?execution >>??????(Bipul?Rakshit) >> >> >>?---------------------------------------------------------------------- >> >>?Message:?1 >>?Date:?Sat,?5?Sep?2009?19:39:17?-0400 >>?From:?Duy?Le? >>?Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel >>????????execution >>?To:?PWSCF?Forum? >>?Message-ID: >>????????<8974d3b20909051639u575aed19xdf474c53f9a7d877 at mail.gmail.com> >>?Content-Type:?text/plain;?charset="iso-8859-1" >> >>?Hi,I?am?not?sure?if?this?help.?Could?you?please?try?to?add >>?#$?-V?in?your?submitting?script.?Like?this: >> >>?#!/bin/bash >>?# >>?#$?-V >>?#$?-cwd >>?#$?-j?y >>?#$?-S?/bin/bash >>?# >> >>?Good?luck. >>?D. >> >>?On?Sat,?Sep?5,?2009?at?7:20?PM,?sreekar?guddeti >>?wrote: >> >>?>?i?know?this?issuehas?been?addressed?and?documented?in?troubleshooting >>?>?section?of?the?users?guide. >>?>?but?i?giveup?in?despair?trying?for?a?whole?day?to?figure?this?problem >>?>?i?run?my?jobs?on?rocks?cluster?by?using?SGE's?facility?of?submitting >>?batch >>?>?jobs >>?> >>?> >>?http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html >>?> >>?>?what?i?'apparently'?observe(or?doubtfully?infer)?is?that?i?can >>?successfully >>?>?run?a?single?parallel?job,?but?on?submitting?a?second?job?i?get?the?error >>?>?____________________________________________ >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?____________________________________________ >>?> >>?> >>?>?i?find?out?the?path?for?the?library?and?added?to?the?LD_LIBRARY_PATH?by >>?>?writing >>?>?_______________________________________ >>?>?#set?the?library?path?to?include?gfortran?libraries >>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib >>?> >>?> >>?>?$ECHO >>?>?$ECHO?"$LD_LIBRARY_PATH" >>?>?$ECHO >>?>?_______________________________________ >>?> >>?>?in?the?file?which?acts?as?script?for?qsub?($qsub?-pe?orte?4 >>?>?dosroutine.qsub)?which?is >>?> >>?>?dosroutine.qsub >>?>?----------------------------------------------------------------- >>?> >>?>?#!/bin/bash >>?>?# >>?>?#$?-cwd >>?>?#$?-j?y >>?>?#$?-S?/bin/bash >>?>?# >>?> >>?>?#extract?the?info?about?no?of?processors?involved?from?command?line >>?>?arguments?of?'qsub' >>?>?PROCESSORS=$NSLOTS >>?> >>?>?#heuristically?assign?the?no?of?processors?per?pool?NPR >>?>?NPR=4 >>?>?#as?a?result?no?of?pools?are?give?by >>?>?NPK=`expr?$PROCESSORS?/?$NPR` >>?> >>?>?#!/bin/bash >>?>?# >>?>?# >>?>?#Script?for?performing?a?dos?calculation?on?a?parallel?processor >>?>?WORKINGDIR=`pwd` >>?>?ECHO="echo" >>?> >>?>?#set?the?library?path?to?include?gfortran?libraries >>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib >>?> >>?> >>?>?$ECHO >>?>?$ECHO?"$LD_LIBRARY_PATH" >>?>?$ECHO >>?> >>?>?#?set?the?needed?environment?variables >>?> >>?>?PREFIX=`cd?/home3/colonel/espresso-4.0.5?;?pwd` >>?>?$ECHO?$PREFIX >>?>?BIN_DIR=$PREFIX/bin >>?>?PSEUDO_DIR=$PREFIX/pseudo >>?>?TMP_DIR=$HOME/tmp >>?>?PARA_PREFIX="/opt/openmpi/bin/mpirun?-np?$PROCESSORS" >>?>?PARA_POSTFIX="-npool?$NPK" >>?> >>?>?#?required?executables?and?pseudopotentials >>?>?$ECHO >>?>?$ECHO?"??executables?directory:?$BIN_DIR" >>?>?$ECHO?"??pseudo?directory:??????$PSEUDO_DIR" >>?>?$ECHO?"??temporary?directory:???$TMP_DIR" >>?> >>?>?#create?results?directory >>?>?for?DIR?in?"$TMP_DIR"?"$WORKINGDIR/results"?;?do >>?>?????if?test?!?-d?$DIR?;?then >>?>?????????mkdir?$DIR >>?>?????fi >>?>?done >>?>?cd?$WORKINGDIR/results >>?> >>?> >>?>?#?variables?to?represent?programs >>?>?PW_COMMAND="$PARA_PREFIX?$BIN_DIR/pw.x?$PARA_POSTFIX" >>?>?DOS_COMMAND="$PARA_PREFIX?$BIN_DIR/dos.x?$PARA_POSTFIX" >>?>?PROJWFC_COMMAND="$PARA_PREFIX?$BIN_DIR/projwfc.x?$PARA_POSTFIX" >>?> >>?> >>?>?#?DOS?calculation?for?0Ni0 >>?>?cat?>?0ni0.dos.in?<>?>??&control >>?>?????calculation='nscf' >>?>?????restart_mode='from_scratch', >>?>?????prefix='0ni0', >>?>?????pseudo_dir?=?'$PSEUDO_DIR/', >>?>?????outdir='$TMP_DIR/' >>?>??/ >>?>??&system >>?>?????ibrav=2,?celldm(1)?=6.48,?nat=1,?ntyp=1, >>?>?????nspin?=?2,??starting_magnetization(1)=0.7, >>?>?????ecutwfc?=?24.0,?ecutrho?=?288.0,?nbnd=8, >>?>?????occupations='tetrahedra' >>?>??/ >>?>??&electrons >>?>?????conv_thr?=?1.0e-10 >>?>?????mixing_beta?=?0.7 >>?>??/ >>?>?ATOMIC_SPECIES >>?>??Ni?58.69?NiUS.RRKJ3.UPF >>?>?ATOMIC_POSITIONS >>?>??Ni?0.0?0.0?0.0 >>?>?K_POINTS?{automatic}????????!special?points?generated?by?tetrahedra >>?method >>?>??12?12?12?0?0?0 >>?>?EOF >>?> >>?>?$ECHO?"??running?DOS?calculation?for?0Ni0?...\c" >>?>?$PW_COMMAND??0ni0.dos.out >>?>?$ECHO >>?>?$ECHO?"???done" >>?> >>?>?------------------------------------------------------------- >>?> >>?>?the?output?i?get?is >>?> >>?>?************************************************ >>?>?:/usr/lib64:/usr/lib >>?> >>?>?/home3/colonel/espresso-4.0.5 >>?> >>?>???executables?directory:?/home3/colonel/espresso-4.0.5/bin >>?>???pseudo?directory:?????/home3/colonel/espresso-4.0.5/pseudo >>?>???temporary?directory:???/home3/colonel/tmp >>?>???running?DOS?calculation?for?0Ni0?...\c >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?> >>?>????done >>?>?************************************************* >>?>?plz?suggest?solutions?which?donot?require?root?permissions?,?as?i?dont >>?have >>?>?thanks?in?advance >>?>?-- >>?>?Sreekar?Guddeti >>?>?Department?of?Physics >>?> >>?>?_______________________________________________ >>?>?Pw_forum?mailing?list >>?>?Pw_forum at pwscf.org >>?>?http://www.democritos.it/mailman/listinfo/pw_forum >>?> >>?> >> >> >>?-- >>?-------------------------------------------------- >>?Duy?Le >>?PhD?Student >>?Department?of?Physics >>?University?of?Central?Florida. >>?--------------?next?part?-------------- >>?An?HTML?attachment?was?scrubbed... >>?URL: >>?http://www.democritos.it/pipermail/pw_forum/attachments/20090905/010fb1e3/attachment-0001.htm >> >>?------------------------------ >> >>?Message:?2 >>?Date:?Sun,?6?Sep?2009?08:33:25?+0800?(CST) >>?From:?wangqj1? >>?Subject:?[Pw_forum]?pw.x?running?but?nothing?happens >>?To:?pw_forum? >>?Message-ID: >>????????<25470012.218281252197205181.JavaMail.coremail at bj126app52.126.com> >>?Content-Type:?text/plain;?charset="gbk" >> >> >>?Dear?pwscf?users >>?????When?I?run?vc-relax?on?the?computing?cluster?use?one?node?which?has?8 >>?CPUs. >>?The?output?file?is?as?following: >> >>?Program?PWSCF?????v.4.0.1??starts?... >>?????Today?is??6Sep2009?at??7:49:30 >>?????Parallel?version?(MPI) >>?????Number?of?processors?in?use:???????8 >>?????R?&?G?space?division:??proc/pool?=????8 >>?????For?Norm-Conserving?or?Ultrasoft?(Vanderbilt)?Pseudopotentials?or?PAW >>?..................................................................... >>?????Initial?potential?from?superposition?of?free?atoms >>?????starting?charge??435.99565,?renormalised?to??436.00000 >>?????Starting?wfc?are??254?atomic?+????8?random?wfc >> >>?After?one?day?,it?still?like?this?and?no?iteration?has?completed?,there?is >>?also?no?error?was?turn?up?.There?is?no?error?in?the?input?file?because?I >>?have?test?it?on?anthoer?computer?which?has?4?CPUs?and?it?runs?well?. >>?I?can't?find?the?reason?about?this?,any?help?will?be?appreciated?. >>?Best?Regards >>?Q.J.Wang >>?XiangTan?University >> >>?--------------?next?part?-------------- >>?An?HTML?attachment?was?scrubbed... >>?URL: >>?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/a4269bb4/attachment-0001.htm >> >>?------------------------------ >> >>?Message:?3 >>?Date:?Sun,?6?Sep?2009?07:58:49?+0100 >>?From:?Bipul?Rakshit? >>?Subject:?Re:?[Pw_forum]?error?loading?shared?libraries?on?parallel >>????????execution >>?To:?PWSCF?Forum? >>?Message-ID:?<3a749910909052358m6f23c3sf5bdbba1b595d8d5 at mail.gmail.com> >>?Content-Type:?text/plain;?charset="iso-8859-1" >> >>?hi, >>?Just?from?root?user?type >>?yum?install?libgfortran.so.3 >> >>?then?it?will?install?this?files?which?is?not?present?in?your?machine >> >>?On?Sun,?Sep?6,?2009?at?12:20?AM,?sreekar?guddeti >>?wrote: >> >>?>?i?know?this?issuehas?been?addressed?and?documented?in?troubleshooting >>?>?section?of?the?users?guide. >>?>?but?i?giveup?in?despair?trying?for?a?whole?day?to?figure?this?problem >>?>?i?run?my?jobs?on?rocks?cluster?by?using?SGE's?facility?of?submitting >>?batch >>?>?jobs >>?> >>?> >>?http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html >>?> >>?>?what?i?'apparently'?observe(or?doubtfully?infer)?is?that?i?can >>?successfully >>?>?run?a?single?parallel?job,?but?on?submitting?a?second?job?i?get?the?error >>?>?____________________________________________ >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?____________________________________________ >>?> >>?> >>?>?i?find?out?the?path?for?the?library?and?added?to?the?LD_LIBRARY_PATH?by >>?>?writing >>?>?_______________________________________ >>?>?#set?the?library?path?to?include?gfortran?libraries >>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib >>?> >>?> >>?>?$ECHO >>?>?$ECHO?"$LD_LIBRARY_PATH" >>?>?$ECHO >>?>?_______________________________________ >>?> >>?>?in?the?file?which?acts?as?script?for?qsub?($qsub?-pe?orte?4 >>?>?dosroutine.qsub)?which?is >>?> >>?>?dosroutine.qsub >>?>?----------------------------------------------------------------- >>?> >>?>?#!/bin/bash >>?>?# >>?>?#$?-cwd >>?>?#$?-j?y >>?>?#$?-S?/bin/bash >>?>?# >>?> >>?>?#extract?the?info?about?no?of?processors?involved?from?command?line >>?>?arguments?of?'qsub' >>?>?PROCESSORS=$NSLOTS >>?> >>?>?#heuristically?assign?the?no?of?processors?per?pool?NPR >>?>?NPR=4 >>?>?#as?a?result?no?of?pools?are?give?by >>?>?NPK=`expr?$PROCESSORS?/?$NPR` >>?> >>?>?#!/bin/bash >>?>?# >>?>?# >>?>?#Script?for?performing?a?dos?calculation?on?a?parallel?processor >>?>?WORKINGDIR=`pwd` >>?>?ECHO="echo" >>?> >>?>?#set?the?library?path?to?include?gfortran?libraries >>?>?export?LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/usr/lib >>?> >>?> >>?>?$ECHO >>?>?$ECHO?"$LD_LIBRARY_PATH" >>?>?$ECHO >>?> >>?>?#?set?the?needed?environment?variables >>?> >>?>?PREFIX=`cd?/home3/colonel/espresso-4.0.5?;?pwd` >>?>?$ECHO?$PREFIX >>?>?BIN_DIR=$PREFIX/bin >>?>?PSEUDO_DIR=$PREFIX/pseudo >>?>?TMP_DIR=$HOME/tmp >>?>?PARA_PREFIX="/opt/openmpi/bin/mpirun?-np?$PROCESSORS" >>?>?PARA_POSTFIX="-npool?$NPK" >>?> >>?>?#?required?executables?and?pseudopotentials >>?>?$ECHO >>?>?$ECHO?"??executables?directory:?$BIN_DIR" >>?>?$ECHO?"??pseudo?directory:??????$PSEUDO_DIR" >>?>?$ECHO?"??temporary?directory:???$TMP_DIR" >>?> >>?>?#create?results?directory >>?>?for?DIR?in?"$TMP_DIR"?"$WORKINGDIR/results"?;?do >>?>?????if?test?!?-d?$DIR?;?then >>?>?????????mkdir?$DIR >>?>?????fi >>?>?done >>?>?cd?$WORKINGDIR/results >>?> >>?> >>?>?#?variables?to?represent?programs >>?>?PW_COMMAND="$PARA_PREFIX?$BIN_DIR/pw.x?$PARA_POSTFIX" >>?>?DOS_COMMAND="$PARA_PREFIX?$BIN_DIR/dos.x?$PARA_POSTFIX" >>?>?PROJWFC_COMMAND="$PARA_PREFIX?$BIN_DIR/projwfc.x?$PARA_POSTFIX" >>?> >>?> >>?>?#?DOS?calculation?for?0Ni0 >>?>?cat?>?0ni0.dos.in?<>?>??&control >>?>?????calculation='nscf' >>?>?????restart_mode='from_scratch', >>?>?????prefix='0ni0', >>?>?????pseudo_dir?=?'$PSEUDO_DIR/', >>?>?????outdir='$TMP_DIR/' >>?>??/ >>?>??&system >>?>?????ibrav=2,?celldm(1)?=6.48,?nat=1,?ntyp=1, >>?>?????nspin?=?2,??starting_magnetization(1)=0.7, >>?>?????ecutwfc?=?24.0,?ecutrho?=?288.0,?nbnd=8, >>?>?????occupations='tetrahedra' >>?>??/ >>?>??&electrons >>?>?????conv_thr?=?1.0e-10 >>?>?????mixing_beta?=?0.7 >>?>??/ >>?>?ATOMIC_SPECIES >>?>??Ni?58.69?NiUS.RRKJ3.UPF >>?>?ATOMIC_POSITIONS >>?>??Ni?0.0?0.0?0.0 >>?>?K_POINTS?{automatic}????????!special?points?generated?by?tetrahedra >>?method >>?>??12?12?12?0?0?0 >>?>?EOF >>?> >>?>?$ECHO?"??running?DOS?calculation?for?0Ni0?...\c" >>?>?$PW_COMMAND??0ni0.dos.out >>?>?$ECHO >>?>?$ECHO?"???done" >>?> >>?>?------------------------------------------------------------- >>?> >>?>?the?output?i?get?is >>?> >>?>?************************************************ >>?>?:/usr/lib64:/usr/lib >>?> >>?>?/home3/colonel/espresso-4.0.5 >>?> >>?>???executables?directory:?/home3/colonel/espresso-4.0.5/bin >>?>???pseudo?directory:?????/home3/colonel/espresso-4.0.5/pseudo >>?>???temporary?directory:???/home3/colonel/tmp >>?>???running?DOS?calculation?for?0Ni0?...\c >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?>?/home3/colonel/espresso-4.0.5/bin/pw.x:?error?while?loading?shared >>?>?libraries:?libgfortran.so.3:?cannot?open?shared?object?file:?No?such >>?>?file?or?directory >>?> >>?>????done >>?>?************************************************* >>?>?plz?suggest?solutions?which?donot?require?root?permissions?,?as?i?dont >>?have >>?>?thanks?in?advance >>?>?-- >>?>?Sreekar?Guddeti >>?>?Department?of?Physics >>?> >>?>?_______________________________________________ >>?>?Pw_forum?mailing?list >>?>?Pw_forum at pwscf.org >>?>?http://www.democritos.it/mailman/listinfo/pw_forum >>?> >>?> >> >> >>?-- >>?Dr.?Bipul?Rakshit >>?Research?Associate, >>?S?N?Bose?Centre?for?Basic?Sciences, >>?Salt?Lake, >>?Kolkata?700?098 >>?India >>?--------------?next?part?-------------- >>?An?HTML?attachment?was?scrubbed... >>?URL: >>?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/d919f229/attachment.htm >> >>?------------------------------ >> >>?_______________________________________________ >>?Pw_forum?mailing?list >>?Pw_forum at pwscf.org >>?http://www.democritos.it/mailman/listinfo/pw_forum >> >> >>?End?of?Pw_forum?Digest,?Vol?27,?Issue?23 >>?**************************************** >> > > > >--? >Sreekar?Guddeti >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090906/b1909ffa/attachment.htm? > >------------------------------ > >_______________________________________________ >Pw_forum?mailing?list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End?of?Pw_forum?Digest,?Vol?27,?Issue?24 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/3f73ada9/attachment-0001.htm From baroni at sissa.it Mon Sep 7 08:59:21 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 7 Sep 2009 08:59:21 +0200 Subject: [Pw_forum] choosing degauss value In-Reply-To: References: Message-ID: Dear Salbadu: I am sure this has been explained many, many time on this forum, and I would like to invite you to search old posts. In a nutshell, mathematically allows to turn the integration of a discontinuous function (the T=0 Fermi distribution) into that of a continuous function; physically, degauss can be seen as a kind of fictitious temperature (the Fermi distribution is continuous at T=/= 0), and some of the tricks that are used in conjuction with Gaussian spearing (e.g. for the calculation of Hellmann-Feynman forces) actually take advantage from this physical analogy. If you want to know/understand more _after_ your browse the past posts in this form and read some of the relevant literature, please revert to us. Stefano Baroni On Sep 7, 2009, at 8:35 AM, udayagiri sai babu wrote: > Dear all > can somebody tell me how to choose a correct degauss value for an > SCF calculation and also the physics behind it. > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/6a8e4c48/attachment.htm From giannozz at democritos.it Mon Sep 7 09:03:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Sep 2009 09:03:57 +0200 Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: <12336594.312101252306530738.JavaMail.coremail@bj126app103.126.com> References: <12336594.312101252306530738.JavaMail.coremail@bj126app103.126.com> Message-ID: <092ABDEA-38CE-4A14-92D1-1D0AF52FCBBC@democritos.it> On Sep 7, 2009, at 8:55 , wangqj1 wrote: > I now use 16 CPUs(2 nodes) to run the task ,the job runs but very > slower than use 4 CPUs in my personal computer ,I use top to look > CPU information,it as following: > > Tasks: 176 total, 1 running, 175 sleeping, 0 stopped, 0 zombie > Cpu0 : 0.4%us, 0.4%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu1 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu3 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu5 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu6 : 0.7%us, 0.0%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Mem: 8048812k total, 5537848k used, 2510964k free, 315448k > buffers > Swap: 4192956k total, 0k used, 4192956k free, 5022856k > cached > > Why only display 8 CPUs information because only the CPUs of one node are shown > and the usage of CPU is so small ? because the code is not running. Maybe it is just waiting for input. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Sep 7 09:06:09 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Sep 2009 09:06:09 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 26 In-Reply-To: <0024107C-0FCE-4043-9E86-732ACE3D088F@sissa.it> References: <0024107C-0FCE-4043-9E86-732ACE3D088F@sissa.it> Message-ID: On Sep 7, 2009, at 8:42 , Stefano Baroni wrote: > this being said, I am not the most appropriate > person to pick up your answers. nor is this the most appropriate place where to find answers to software/library/installation problems of parallel machines. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From siyouber at yahoo.fr Mon Sep 7 09:26:35 2009 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Mon, 7 Sep 2009 00:26:35 -0700 (PDT) Subject: [Pw_forum] O.pw91-van_ak.UPF oxygen pseudopotential In-Reply-To: <394A8A5B-7C70-4486-9BE2-FAF3C3CBDB6A@democritos.it> Message-ID: <822837.34194.qm@web26502.mail.ukl.yahoo.com> Dear all, Thanks very much for your explanations *********************** Bertrand SITAMTZE PhD student Departmant of Physics University of Yaound? I-Cameroon ************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f5b926c1/attachment.htm From sclauzer at sissa.it Mon Sep 7 09:55:54 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 07 Sep 2009 09:55:54 +0200 Subject: [Pw_forum] pseudo potential In-Reply-To: References: Message-ID: <4AA4BC8A.1020603@sissa.it> Dear Mansoureh, Mansoureh Pashangpour wrote: > Dear all > how can I plot these pseudo potentials? how can I discribe the > properties of pseudo potentials? > Please follow this thread in the forum archives: http://www.democritos.it/pipermail/pw_forum/2009-February/011724.html Regards, GS o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Sep 7 10:13:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 07 Sep 2009 10:13:45 +0200 Subject: [Pw_forum] Help in using xcrysden for making structures In-Reply-To: <172991.32602.qm@web95007.mail.in2.yahoo.com> References: <172991.32602.qm@web95007.mail.in2.yahoo.com> Message-ID: <4AA4C0B9.3030709@sissa.it> Dear Neel, Neel Singh wrote: > hi, > I need some help in drawing crystal using xcrysden. Sir/Madam, let us > take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i > know that i have 18 atoms in my unit cell and i know the Cartesian > co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that > how can i draw my unit cell with giving positions of all the atoms > without using the symmetries by xcrysden??. Means like if i specifiy, I think that Xcrysden does not use rotational symmetries to visualize atoms (Tone, correct me if I'm wrong). What it can do is to repeat periodically the atomic basis (i.e. the minimal set of atoms which, repeat periodically with translations by lattice vectors, give you the full infinite crystal) to show a nicely cut unit cell, which sometimes includes translationally equivalent atoms. In the ATOMIC_POSITIONS list you should include ONLY non-equivalent atoms. > & system > ibrav=2, celldm(1)=9.00, nat=1,...... > ATOMIC POSITIONS{angstrom} > A 0 4.5 0 > > now if we visualise this type of structure with Xcrysden, we found a > number of atoms genrated due to symmetry. If i make a file like > & system > ibrav=2, celldm(1)=9.00, nat=18,...... > ATOMIC POSITIONS{angstrom} > A 0 4.5 0 > / > 18 times we have specified the co-ordinates > / > / > A 4.5 0 0 > Xcrysden will give warning like atom 10 and 90 are very close like that. It means that either you specified wrong positions for one or more atoms, or maybe you included translationally equivalent atoms in the list (i.e. at least a couple of atoms which have positions which differ by a lattice vector). BTW, you said that you have 18 atoms, not 90... > Sir i want to know is there any way so that i can make my PWSCF input > file with angstrom/bohr postions such that with one atomic postion > Xcrysden will show only one atom?? You have to specify the correct list of atomic positions. That's up to you, XCrysden cannot be used to build input files at the moment. When you have the correct atomic positions, you can switch between the 2 visualizations modes (atomic basis only, or "nicely cut unit cell" with some replicas of the atoms in the basis) using the menu bar on the bottom. If you want more help, please post a complete input file, otherwise we cannot understand what mistakes you made in building it. Regards, GS > Means i will give 18 atomic postions and xcrysden will produce 18 atom > unit cell without using symmatries. > > Thanks for your help, > Neel Singh, > Univeristy of Delhi, > India > > > ------------------------------------------------------------------------ > See the Web's breaking stories, chosen by people like you. Check out > Yahoo! Buzz > . > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From decboy9 at gmail.com Mon Sep 7 10:26:46 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 7 Sep 2009 13:56:46 +0530 Subject: [Pw_forum] problem with monoclinic cell with ibrav=0 Message-ID: hi 2 all, I was trying to draw the monoclinic structure of KY(PO3)4, potassium yttrium polyphosphate, with ibrav=0 and i have made it almost. The problem in my structure is that it is making an extra bond b/w Potassium and Yttrium instead of that bond between Potassium and oxygen . All the atoms are at their positions but only two bond are swapped. Means both the bonds should be in b/w Potassium and oxygen instead of Potassium and Yttrium. Please help or give advice. The Details are as follows. Thanks A lot in advance, Crystal data KY(PO3)4 Mr = 443.89 Monoclinic, P21 a = 7.2244 (3) A b = 8.2825 (3) A c = 7.854 (4) A beta = 91.735 (3) V = 469.7 (2) A3 My Input file is &control / / &system ibrav=0 nat=36 ntyp=4 ecutwfc=35.0 ecutrho=200.0, occupations = 'fixed' / &electrons / / ATOMIC_SPECIES / ATOMIC_POSITIONS {crystal} K 0.270300 0.456600 0.718800 K 0.729700 0.956600 0.281200 Y 0.237040 0.758970 0.242450 Y 0.762960 0.258970 0.757550 P 0.4367 0.3830 0.0947 P 0.5633 0.8830 0.9053 P 0.0994 0.1755 0.0978 P 0.9006 0.6755 0.9022 P 0.9982 0.4085 0.3809 P 0.0018 0.9085 0.6191 P 0.6161 0.5114 0.3992 P 0.3839 0.0114 0.6008 O 0.3212 0.5292 0.0721 O 0.6788 0.0292 0.9279 O 0.5736 0.3558 0.9613 O 0.4264 0.8558 0.0387 O 0.3126 0.2261 0.1093 O 0.6874 0.7261 0.8907 O 0.5360 0.3706 0.2789 O 0.4640 0.8706 0.7211 O 0.0239 0.2062 0.9224 O 0.9761 0.7062 0.0776 O 0.0880 0.0105 0.1732 O 0.9120 0.5105 0.8268 O 0.9924 0.2991 0.2159 O 0.0076 0.7991 0.7841 O 0.1660 0.5100 0.3846 O 0.8340 0.0100 0.6154 O 0.9663 0.3109 0.5348 O 0.0337 0.8109 0.4652 O 0.8245 0.5225 0.3407 O 0.1755 0.0225 0.6593 O 0.5258 0.6648 0.3514 O 0.4742 0.1648 0.6486 O 0.6118 0.4535 0.5773 O 0.3882 0.9535 0.4227 K_POINTS {automatic} 4 5 4 1 1 1 CELL_PARAMETERS 13.65213741740369 0.00000000000000 0.00000000000000 0.00000000000000 15.65165663025941 0.00000000000000 -0.44936602772498 0.00000000000000 14.83510473548868 With regards, Dev Sharma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/4e7748dd/attachment-0001.htm From shobhana at jncasr.ac.in Mon Sep 7 11:17:04 2009 From: shobhana at jncasr.ac.in (shobhana at jncasr.ac.in) Date: Mon, 7 Sep 2009 14:47:04 +0530 (IST) Subject: [Pw_forum] how to pick degauss In-Reply-To: References: Message-ID: <45115.172.16.1.1.1252315024.squirrel@172.16.1.1> Dear U. Saibabu, To get answers to your questions about smearing, I can suggest a few things: 1) Read Chapter 4 of Nicola Marzari's PhD thesis, available at http://quasiamore.mit.edu/phd 2) Read previous forum postings, e.g., by Nicola Marzari on Jan 17 2008. 3) Look at my lecture slides, posted on http://www.quantum-espresso.org/wiki/index.php/QESB09 click on the slides for lecture 2 on the first day. 4) Travel the 10 km from IISc to JNC (you can take the JNC bus, timetable available on web) and come and ask one of my students to explain it to you! (Notice that I am wickedly volunteering their time, not mine....) Shobhana > Message: 1 > Date: Mon, 7 Sep 2009 12:05:44 +0530 > From: udayagiri sai babu > Subject: [Pw_forum] choosing degauss value > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > can somebody tell me how to choose a correct degauss value for an SCF > calculation and also the physics behind it. > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > From udayagiri3 at gmail.com Mon Sep 7 11:26:19 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Mon, 7 Sep 2009 14:56:19 +0530 Subject: [Pw_forum] how to pick degauss In-Reply-To: <45115.172.16.1.1.1252315024.squirrel@172.16.1.1> References: <45115.172.16.1.1.1252315024.squirrel@172.16.1.1> Message-ID: Thank you madam i will look into the references you provided still if i have doubts i will meet one of your students. On Mon, Sep 7, 2009 at 2:47 PM, wrote: > Dear U. Saibabu, > > To get answers to your questions about smearing, I can suggest a few > things: > > 1) Read Chapter 4 of Nicola Marzari's PhD thesis, available at > http://quasiamore.mit.edu/phd > > 2) Read previous forum postings, e.g., by Nicola Marzari on Jan 17 2008. > > 3) Look at my lecture slides, posted on > http://www.quantum-espresso.org/wiki/index.php/QESB09 > click on the slides for lecture 2 on the first day. > > 4) Travel the 10 km from IISc to JNC (you can take the JNC bus, timetable > available on web) and come and ask one of my students to explain it to > you! > (Notice that I am wickedly volunteering their time, not mine....) > > Shobhana > > > Message: 1 > > Date: Mon, 7 Sep 2009 12:05:44 +0530 > > From: udayagiri sai babu > > Subject: [Pw_forum] choosing degauss value > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all > > can somebody tell me how to choose a correct degauss value for an SCF > > calculation and also the physics behind it. > > > > -- > > U.Saibabu > > PhD student, > > Deformation mechanisms modeling group, > > Materials engineering department, > > IISc Bangalore, > > India. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/1452f028/attachment.htm From samirmeher at gmail.com Mon Sep 7 12:13:15 2009 From: samirmeher at gmail.com (Samir Ranjan Meher) Date: Mon, 7 Sep 2009 15:43:15 +0530 Subject: [Pw_forum] Arbitrary k-points Message-ID: <8a4c6de60909070313i207f3d96ofd22fdc99cfb597a@mail.gmail.com> Dear all, I am trying to do some scf calculations for GaN. But, I am getting a set of arbitrary k-points in my output file (some of which are -ve also). Can anybody help me in this regard? The input file is as follows:- &control calculation = 'scf' restart_mode='from_scratch', prefix='test1', tstress = .true. tprnfor = .true. pseudo_dir = '/home/samirmeher/espresso-4.0.5/pseudo/', outdir='/home/samirmeher/tmp/' / &system ibrav= 4, celldm(1) =6.1037, celldm(3) =1.63, nat= 4, ntyp= 2, ecutwfc = 40.0, ecutrho = 200.0, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-7 / ATOMIC_SPECIES Ga 69.723 Ga.rel.TM.UPF N 14.007 N.rel.TM.UPF ATOMIC_POSITIONS crystal Ga 0.000000000 0.000000000 0.000000000 Ga 0.333000000 0.666000000 0.500000000 N 0.000000000 0.000000000 0.375000000 N 0.666000000 0.333000000 0.875000000 K_POINTS 60 0.0625000 0.0625000 0.0625000 1.00 0.0625000 0.0625000 0.1875000 3.00 0.0625000 0.0625000 0.3125000 3.00 0.0625000 0.0625000 0.4375000 3.00 0.0625000 0.0625000 0.5625000 3.00 0.0625000 0.0625000 0.6875000 3.00 0.0625000 0.0625000 0.8125000 3.00 0.0625000 0.0625000 0.9375000 3.00 0.0625000 0.1875000 0.1875000 3.00 0.0625000 0.1875000 0.3125000 6.00 0.0625000 0.1875000 0.4375000 6.00 0.0625000 0.1875000 0.5625000 6.00 0.0625000 0.1875000 0.6875000 6.00 0.0625000 0.1875000 0.8125000 6.00 0.0625000 0.1875000 0.9375000 6.00 0.0625000 0.3125000 0.3125000 3.00 0.0625000 0.3125000 0.4375000 6.00 0.0625000 0.3125000 0.5625000 6.00 0.0625000 0.3125000 0.6875000 6.00 0.0625000 0.3125000 0.8125000 6.00 0.0625000 0.3125000 0.9375000 6.00 0.0625000 0.4375000 0.4375000 3.00 0.0625000 0.4375000 0.5625000 6.00 0.0625000 0.4375000 0.6875000 6.00 0.0625000 0.4375000 0.8125000 6.00 0.0625000 0.4375000 0.9375000 6.00 0.0625000 0.5625000 0.5625000 3.00 0.0625000 0.5625000 0.6875000 6.00 0.0625000 0.5625000 0.8125000 6.00 0.0625000 0.6875000 0.6875000 3.00 0.0625000 0.6875000 0.8125000 6.00 0.0625000 0.8125000 0.8125000 3.00 0.1875000 0.1875000 0.1875000 1.00 0.1875000 0.1875000 0.3125000 3.00 0.1875000 0.1875000 0.4375000 3.00 0.1875000 0.1875000 0.5625000 3.00 0.1875000 0.1875000 0.6875000 3.00 0.1875000 0.1875000 0.8125000 3.00 0.1875000 0.3125000 0.3125000 3.00 0.1875000 0.3125000 0.4375000 6.00 0.1875000 0.3125000 0.5625000 6.00 0.1875000 0.3125000 0.6875000 6.00 0.1875000 0.3125000 0.8125000 6.00 0.1875000 0.4375000 0.4375000 3.00 0.1875000 0.4375000 0.5625000 6.00 0.1875000 0.4375000 0.6875000 6.00 0.1875000 0.4375000 0.8125000 6.00 0.1875000 0.5625000 0.5625000 3.00 0.1875000 0.5625000 0.6875000 6.00 0.1875000 0.6875000 0.6875000 3.00 0.3125000 0.3125000 0.3125000 1.00 0.3125000 0.3125000 0.4375000 3.00 0.3125000 0.3125000 0.5625000 3.00 0.3125000 0.3125000 0.6875000 3.00 0.3125000 0.4375000 0.4375000 3.00 0.3125000 0.4375000 0.5625000 6.00 0.3125000 0.4375000 0.6875000 6.00 0.3125000 0.5625000 0.5625000 3.00 0.4375000 0.4375000 0.4375000 1.00 0.4375000 0.4375000 0.5625000 3.00 Thanks in advance, Samir Ranjan Meher, IIT Madras, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f816e492/attachment.htm From wangqj1 at 126.com Mon Sep 7 13:27:31 2009 From: wangqj1 at 126.com (wangqj1) Date: Mon, 7 Sep 2009 19:27:31 +0800 (CST) Subject: [Pw_forum] pw.x running but nothing happens Message-ID: <24143877.519381252322851343.JavaMail.coremail@bj126app103.126.com> Dear Paolo Thank you very much for your advice . I still have some questions that need your help . I don't know why only display 8 CPUs while I use 2 nodes (16 CPUs) ? Untill now the job only has 2 iterations form 2:00 PM today ,it is so slowly . How can I solve this problem ? Best regards On Sep 7, 2009, at 8:55 , wangqj1 wrote: > I now use 16 CPUs(2 nodes) to run the task ,the job runs but very > slower than use 4 CPUs in my personal computer ,I use top to look > CPU information,it as following: > > Tasks: 176 total, 1 running, 175 sleeping, 0 stopped, 0 zombie > Cpu0 : 0.4%us, 0.4%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu1 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu3 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu5 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu6 : 0.7%us, 0.0%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0% > si, 0.0%st > Mem: 8048812k total, 5537848k used, 2510964k free, 315448k > buffers > Swap: 4192956k total, 0k used, 4192956k free, 5022856k > cached > > Why only display 8 CPUs information because only the CPUs of one node are shown > and the usage of CPU is so small ? because the code is not running. Maybe it is just waiting for input -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/c60520ec/attachment.htm From raamesh123 at rediffmail.com Mon Sep 7 13:36:36 2009 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 7 Sep 2009 11:36:36 -0000 Subject: [Pw_forum] to Neel singh Message-ID: <20090907113636.59174.qmail@f6mail-145-191.rediffmail.com> Neel Singh wrote: > hi, > I need some help in drawing crystal using xcrysden. Sir/Madam, let us > take the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i > know that i have 18 atoms in my unit cell and i know the Cartesian > co-ordinates{x,y,z} of each atom in angstrom/bhor. I want to know that > how can i draw my unit cell with giving positions of all the atoms > without using the symmetries by xcrysden??. Means like if i specifiy, Dear Neal singh....i hope u want to draw supercell with out using the symmetry ...it means using the p1 space group and manually placing all the atoms....in any case...please try using crystal maker demo version here is the link....please mind that the copying the figure is prohibited in the demo version http://www.crystalmaker.com/crystalmaker/download.html With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f52109d0/attachment-0001.htm From sclauzer at sissa.it Mon Sep 7 14:06:55 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 07 Sep 2009 14:06:55 +0200 Subject: [Pw_forum] Arbitrary k-points In-Reply-To: <8a4c6de60909070313i207f3d96ofd22fdc99cfb597a@mail.gmail.com> References: <8a4c6de60909070313i207f3d96ofd22fdc99cfb597a@mail.gmail.com> Message-ID: <4AA4F75F.7060802@sissa.it> Dear Samir, Samir Ranjan Meher wrote: > Dear all, > I am trying to do some scf calculations for GaN. But, I am getting a set > of arbitrary k-points in my output file (some of which are -ve also). If you look carefully in your output, you should find this warning: No symmetry! it means that pw.x is not able to find any rotational symmetry for your system, hence the reduced k-point grid you gave on input is not of the correct symmetry and the program enlarges it to include non-equivalent k-point not in the list. > Can anybody help me in this regard? The input file is as follows:- > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='test1', > tstress = .true. > tprnfor = .true. > pseudo_dir = '/home/samirmeher/espresso-4.0.5/pseudo/', > outdir='/home/samirmeher/tmp/' > / > &system > ibrav= 4, celldm(1) =6.1037, celldm(3) =1.63, nat= 4, ntyp= 2, I suspect that celldm(3) has not enough significant digits, or you gave wrong atomic coordinates. Please check. Regards, GS > ecutwfc = 40.0, > ecutrho = 200.0, > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-7 > / > ATOMIC_SPECIES > Ga 69.723 Ga.rel.TM.UPF > N 14.007 N.rel.TM.UPF > ATOMIC_POSITIONS crystal > Ga 0.000000000 0.000000000 0.000000000 > Ga 0.333000000 0.666000000 0.500000000 > N 0.000000000 0.000000000 0.375000000 > N 0.666000000 0.333000000 0.875000000 > K_POINTS > 60 > 0.0625000 0.0625000 0.0625000 1.00 > 0.0625000 0.0625000 0.1875000 3.00 > 0.0625000 0.0625000 0.3125000 3.00 > 0.0625000 0.0625000 0.4375000 3.00 > 0.0625000 0.0625000 0.5625000 3.00 > 0.0625000 0.0625000 0.6875000 3.00 > 0.0625000 0.0625000 0.8125000 3.00 > 0.0625000 0.0625000 0.9375000 3.00 > 0.0625000 0.1875000 0.1875000 3.00 > 0.0625000 0.1875000 0.3125000 6.00 > 0.0625000 0.1875000 0.4375000 6.00 > 0.0625000 0.1875000 0.5625000 6.00 > 0.0625000 0.1875000 0.6875000 6.00 > 0.0625000 0.1875000 0.8125000 6.00 > 0.0625000 0.1875000 0.9375000 6.00 > 0.0625000 0.3125000 0.3125000 3.00 > 0.0625000 0.3125000 0.4375000 6.00 > 0.0625000 0.3125000 0.5625000 6.00 > 0.0625000 0.3125000 0.6875000 6.00 > 0.0625000 0.3125000 0.8125000 6.00 > 0.0625000 0.3125000 0.9375000 6.00 > 0.0625000 0.4375000 0.4375000 3.00 > 0.0625000 0.4375000 0.5625000 6.00 > 0.0625000 0.4375000 0.6875000 6.00 > 0.0625000 0.4375000 0.8125000 6.00 > 0.0625000 0.4375000 0.9375000 6.00 > 0.0625000 0.5625000 0.5625000 3.00 > 0.0625000 0.5625000 0.6875000 6.00 > 0.0625000 0.5625000 0.8125000 6.00 > 0.0625000 0.6875000 0.6875000 3.00 > 0.0625000 0.6875000 0.8125000 6.00 > 0.0625000 0.8125000 0.8125000 3.00 > 0.1875000 0.1875000 0.1875000 1.00 > 0.1875000 0.1875000 0.3125000 3.00 > 0.1875000 0.1875000 0.4375000 3.00 > 0.1875000 0.1875000 0.5625000 3.00 > 0.1875000 0.1875000 0.6875000 3.00 > 0.1875000 0.1875000 0.8125000 3.00 > 0.1875000 0.3125000 0.3125000 3.00 > 0.1875000 0.3125000 0.4375000 6.00 > 0.1875000 0.3125000 0.5625000 6.00 > 0.1875000 0.3125000 0.6875000 6.00 > 0.1875000 0.3125000 0.8125000 6.00 > 0.1875000 0.4375000 0.4375000 3.00 > 0.1875000 0.4375000 0.5625000 6.00 > 0.1875000 0.4375000 0.6875000 6.00 > 0.1875000 0.4375000 0.8125000 6.00 > 0.1875000 0.5625000 0.5625000 3.00 > 0.1875000 0.5625000 0.6875000 6.00 > 0.1875000 0.6875000 0.6875000 3.00 > 0.3125000 0.3125000 0.3125000 1.00 > 0.3125000 0.3125000 0.4375000 3.00 > 0.3125000 0.3125000 0.5625000 3.00 > 0.3125000 0.3125000 0.6875000 3.00 > 0.3125000 0.4375000 0.4375000 3.00 > 0.3125000 0.4375000 0.5625000 6.00 > 0.3125000 0.4375000 0.6875000 6.00 > 0.3125000 0.5625000 0.5625000 3.00 > 0.4375000 0.4375000 0.4375000 1.00 > 0.4375000 0.4375000 0.5625000 3.00 > > Thanks in advance, > Samir Ranjan Meher, > IIT Madras, India. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Mon Sep 7 15:24:32 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 07 Sep 2009 15:24:32 +0200 Subject: [Pw_forum] pw.x running but nothing happens In-Reply-To: <24143877.519381252322851343.JavaMail.coremail@bj126app103.126.com> References: <24143877.519381252322851343.JavaMail.coremail@bj126app103.126.com> Message-ID: In data 07 settembre 2009 alle ore 13:27:31, wangqj1 ha scritto: > I don't know why only display 8 CPUs while I use 2 nodes (16 CPUs) top only displays process on the node it's running. > Untill now the job only has 2 iterations form 2:00 PM today ,it is so > slowly . How can I solve this problem ? Probably the network connection is slow, use k-point parallelisation (pools) among different nodes, it is not as efficient as g-space parallelization, but it requires much less communication. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From dimpy.sharma at tyndall.ie Mon Sep 7 15:42:54 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 7 Sep 2009 14:42:54 +0100 Subject: [Pw_forum] Band structure calculation Message-ID: Hi Quantum espresso user, I have been trying to perfom a band structute calculation in my system which is running in 32 processors, it is still running, however in the output I got the following information. Band Structure Calculation CG style diagonalization c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalues not converged I used 15 k points for my calculations. Can anybody give any suggesstion ? Thanks Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/8509c051/attachment.htm From paulatto at sissa.it Mon Sep 7 15:46:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 07 Sep 2009 15:46:08 +0200 Subject: [Pw_forum] Band structure calculation In-Reply-To: References: Message-ID: In data 07 settembre 2009 alle ore 15:42:54, Dimpy Sharma ha scritto: > I used 15 k points for my calculations. Can anybody give any > suggesstion ? Dear Dimpy, it has discussed uncountable times. Please have a look at the manual: (or < http://tr.im/y5mw>) best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mansourehp at gmail.com Mon Sep 7 15:47:54 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Mon, 7 Sep 2009 17:17:54 +0330 Subject: [Pw_forum] pseudo potential In-Reply-To: <4AA4BC8A.1020603@sissa.it> References: <4AA4BC8A.1020603@sissa.it> Message-ID: Dear Gabriele I have used the pseudo poteintials form PWscf pseudo potentials and I haven't used ld1.x to find them. as you said I can plot psedopotentials just I make with this way. Regards Pashangpour Ph.D student of IAU, Tehran, IRAN On Mon, Sep 7, 2009 at 11:25 AM, Gabriele Sclauzero wrote: > Dear Mansoureh, > > Mansoureh Pashangpour wrote: > > Dear all > > how can I plot these pseudo potentials? how can I discribe the > > properties of pseudo potentials? > > > > Please follow this thread in the forum archives: > > http://www.democritos.it/pipermail/pw_forum/2009-February/011724.html > > Regards, > > GS > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/f3331ad7/attachment.htm From eyvaz_isaev at yahoo.com Mon Sep 7 16:31:10 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 7 Sep 2009 07:31:10 -0700 (PDT) Subject: [Pw_forum] Arbitrary k-points In-Reply-To: <4AA4F75F.7060802@sissa.it> Message-ID: <430424.70646.qm@web65709.mail.ac4.yahoo.com> Hi, > ATOMIC_POSITIONS crystal >?Ga? ? ? 0.000000000? 0.000000000 0.000000000??? > Ga? ? ? 0.333000000? 0.666000000 0.500000000??? >??N? ? ? 0.000000000? ? 0.000000000 0.375000000??? >??N? ? ? 0.666000000? ? 0.333000000 0.875000000 Atomic positions you used are incorrect. Please have a look at http://cst-www.nrl.navy.mil/lattice/struk/b4.html Besides, you used insufficient number of significant digits for atomic positions which is 6 by default. Even with those correct atomic postitions but using 0.333 etc. instead of 0.333333 one gets only 2 symmetry opertions and warning messages (you can play around this isssue and try understand why and how to solve it, you can search in the forum archive, sure). With the correct positions one gets 12 symmetry operations, as it should be for B4 structure. With correct structure number of k-points is exactly the same as you expected. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From udayagiri3 at gmail.com Mon Sep 7 19:25:22 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Mon, 7 Sep 2009 22:55:22 +0530 Subject: [Pw_forum] All electron calculations for Cr and Ti Message-ID: Dear all I am looking for values of lattice parameter and bulk modulus values calculated from all electron calculation to compare my pseudo potentials. If somebody has the reference can you please let me know. -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/28725a6a/attachment.htm From baroni at sissa.it Mon Sep 7 21:32:09 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 7 Sep 2009 21:32:09 +0200 Subject: [Pw_forum] All electron calculations for Cr and Ti In-Reply-To: References: Message-ID: <288BDFCF-11C2-4207-935D-A08146C015CF@sissa.it> for which system? have you tried google? SB On Sep 7, 2009, at 7:25 PM, udayagiri sai babu wrote: > Dear all > I am looking for values of lattice parameter and bulk modulus values > calculated from all electron calculation to compare my pseudo > potentials. If somebody has the reference can you please let me know. > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090907/c2549368/attachment-0001.htm From wangqj1 at 126.com Tue Sep 8 03:38:44 2009 From: wangqj1 at 126.com (wangqj1) Date: Tue, 8 Sep 2009 09:38:44 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 32 In-Reply-To: References: Message-ID: <33091669.710241252373924112.JavaMail.coremail@bj126app21.126.com> Dear Lorenzo Thanks for your help, but what shoul I do to solve the problem ? Can you tell the specific course ? Message: 2 >Date: Mon, 07 Sep 2009 15:24:32 +0200 >From: "Lorenzo Paulatto" >Subject: Re: [Pw_forum] pw.x running but nothing happens >To: "PWSCF Forum" >Message-ID: >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > >In data 07 settembre 2009 alle ore 13:27:31, wangqj1 ha >scritto: >> I don't know why only display 8 CPUs while I use 2 nodes (16 CPUs) > >top only displays process on the node it's running. > >> Untill now the job only has 2 iterations form 2:00 PM today ,it is so >> slowly . How can I solve this problem ? > > >Probably the network connection is slow, use k-point parallelisation >(pools) among different nodes, it is not as efficient as g-space >parallelization, but it requires much less communication. > > >regards > > >-- >Lorenzo Paulatto >SISSA & DEMOCRITOS (Trieste) >phone: +39 040 3787 511 >skype: paulatz >www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/414a22d2/attachment.htm From udayagiri3 at gmail.com Tue Sep 8 07:44:45 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Tue, 8 Sep 2009 11:14:45 +0530 Subject: [Pw_forum] All electron calculations for Cr and Ti In-Reply-To: <288BDFCF-11C2-4207-935D-A08146C015CF@sissa.it> References: <288BDFCF-11C2-4207-935D-A08146C015CF@sissa.it> Message-ID: i tried google but could not found i am looking at V-Cr-Ti alloy On Tue, Sep 8, 2009 at 1:02 AM, Stefano Baroni wrote: > for which system? have you tried google? SB > On Sep 7, 2009, at 7:25 PM, udayagiri sai babu wrote: > > Dear all > I am looking for values of lattice parameter and bulk modulus values > calculated from all electron calculation to compare my pseudo potentials. If > somebody has the reference can you please let me know. > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/eda0bb30/attachment.htm From paulatto at sissa.it Tue Sep 8 09:03:23 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 8 Sep 2009 09:03:23 +0200 (CEST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 32 In-Reply-To: <33091669.710241252373924112.JavaMail.coremail@bj126app21.126.com> References: <33091669.710241252373924112.JavaMail.coremail@bj126app21.126.com> Message-ID: <51040.78.12.159.112.1252393403.squirrel@webmail.sissa.it> On Mar, Settembre 8, 2009 03:38, wangqj1 wrote: > Dear Lorenzo > Thanks for your help, but what shoul I do to solve the problem ? Can > you tell the specific course ? Please have a look at the user guide: http://www.quantum-espresso.org/user_guide/node14.html (and its subsections!) Don't be afraid to ask if you have some problem. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From njuxuyuehua at gmail.com Tue Sep 8 16:39:10 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 8 Sep 2009 22:39:10 +0800 Subject: [Pw_forum] is there PAW PP for cabon Message-ID: hello: i am now doing pp test for Carbon nanotube, i am wondering is there PAW pp for cabon atoms. thank you very much! cheers. -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/6162c55d/attachment.htm From yccheng.nju at gmail.com Tue Sep 8 17:02:22 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Tue, 8 Sep 2009 23:02:22 +0800 Subject: [Pw_forum] is there PAW PP for cabon In-Reply-To: References: Message-ID: You can use c.in in the /atomic_doc/paw_library/input/ directory. The ld1.x code can generate the PAW pp. 2009/9/8 xu yuehua > hello: > > i am now doing pp test for Carbon nanotube, i am wondering is there PAW pp > for cabon atoms. > > > thank you very much! > > > cheers. > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/f7ec9fbf/attachment.htm From udayagiri3 at gmail.com Tue Sep 8 21:04:01 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 9 Sep 2009 00:34:01 +0530 Subject: [Pw_forum] using ev.x Message-ID: hi all i am using ev.x file given in the pw_tools directory to calculate bulk modulus and lattice parameter values of chromium. i used murnaghan equation of state to fit my data i got bulk modulus of 256 gpa where as my experimental value is 160 gpa but when i used keane equation of state to fit the same data i got 148 gpa bulk modulus why is this much variation? which equation of state should i use for cr? because for vanadium and Ti murnagan euation of state has given reasonable (<20% error) values of bulk modulus but not for Cr please give some suggestions -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/73cee3c1/attachment.htm From baroni at sissa.it Tue Sep 8 21:33:00 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 8 Sep 2009 21:33:00 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: References: Message-ID: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> How about trying to fit a very accurate set of data around the minimum with a parabola and calculate thus the bulk modulus? Have you tries to plot the resulting fitted curves? which one fits best the raw data? Udaygiri: in Science (as well as in Life) there is no free lunch ... Enjoy Science, no less than Life. SB On Sep 8, 2009, at 9:04 PM, udayagiri sai babu wrote: > > hi all > i am using ev.x file given in the pw_tools directory to calculate > bulk modulus and lattice parameter values of chromium. i used > murnaghan equation of state to fit my data i got bulk modulus of 256 > gpa where as my experimental value is 160 gpa but when i used keane > equation of state to fit the same data i got 148 gpa bulk modulus > > why is this much variation? which equation of state should i use for > cr? because for vanadium and Ti murnagan euation of state has given > reasonable (<20% error) values of bulk modulus but not for Cr > > please give some suggestions > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/a28a6cfb/attachment.htm From udayagiri3 at gmail.com Tue Sep 8 22:09:08 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 9 Sep 2009 01:39:08 +0530 Subject: [Pw_forum] using ev.x In-Reply-To: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> Message-ID: Dear stefano baroni I tried that as well i am getting the same value (255gpa). This is the data i am using 5.35 -174.156857800 5.36 -174.156934850 5.37 -174.156989300 5.38 -174.156990580 5.39 -174.156955990 5.4 -174.156869280 this is one of the input file &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='chromium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=3 celldm(1)=5.350000, nat=1, ntyp=1 ecutwfc=30, ecutrho=300, occupations='smearing', smearing='mv', degauss=0.012000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.7 / ATOMIC_SPECIES Cr 51.9961 Cr.pw91-sp-van.UPF ATOMIC_POSITIONS (crystal) Cr 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 12 12 12 0 0 0 can you suggest me anything On Wed, Sep 9, 2009 at 1:03 AM, Stefano Baroni wrote: > How about trying to fit a very accurate set of data around the minimum with > a parabola and calculate thus the bulk modulus? Have you tries to plot the > resulting fitted curves? which one fits best the raw data? Udaygiri: in > Science (as well as in Life) there is no free lunch ... Enjoy Science, no > less than Life. SB > On Sep 8, 2009, at 9:04 PM, udayagiri sai babu wrote: > > > hi all > i am using ev.x file given in the pw_tools directory to calculate bulk > modulus and lattice parameter values of chromium. i used murnaghan equation > of state to fit my data i got bulk modulus of 256 gpa where as my > experimental value is 160 gpa but when i used keane equation of state to > fit the same data i got 148 gpa bulk modulus > > why is this much variation? which equation of state should i use for cr? > because for vanadium and Ti murnagan euation of state has given reasonable > (<20% error) values of bulk modulus but not for Cr > > please give some suggestions > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/1b745092/attachment-0001.htm From baroni at sissa.it Tue Sep 8 22:22:36 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 8 Sep 2009 22:22:36 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> Message-ID: look at the two fitted equations of state (draw pictures) and see which one fits best the raw data SB On Sep 8, 2009, at 10:09 PM, udayagiri sai babu wrote: > Dear stefano baroni > I tried that as well i am getting the same value (255gpa). This is > the data i am using > > 5.35 -174.156857800 > 5.36 -174.156934850 > 5.37 -174.156989300 > 5.38 -174.156990580 > 5.39 -174.156955990 > 5.4 -174.156869280 > > this is one of the input file > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='chromium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.350000, > nat=1, > ntyp=1 > ecutwfc=30, > ecutrho=300, > occupations='smearing', > smearing='mv', > degauss=0.012000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7 > / > ATOMIC_SPECIES > Cr 51.9961 Cr.pw91-sp-van.UPF > ATOMIC_POSITIONS (crystal) > Cr 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 12 12 12 0 0 0 > > can you suggest me anything > > On Wed, Sep 9, 2009 at 1:03 AM, Stefano Baroni > wrote: > How about trying to fit a very accurate set of data around the > minimum with a parabola and calculate thus the bulk modulus? Have > you tries to plot the resulting fitted curves? which one fits best > the raw data? Udaygiri: in Science (as well as in Life) there is no > free lunch ... Enjoy Science, no less than Life. SB > > On Sep 8, 2009, at 9:04 PM, udayagiri sai babu wrote: > >> >> hi all >> i am using ev.x file given in the pw_tools directory to calculate >> bulk modulus and lattice parameter values of chromium. i used >> murnaghan equation of state to fit my data i got bulk modulus of >> 256 gpa where as my experimental value is 160 gpa but when i used >> keane equation of state to fit the same data i got 148 gpa bulk >> modulus >> >> why is this much variation? which equation of state should i use >> for cr? because for vanadium and Ti murnagan euation of state has >> given reasonable (<20% error) values of bulk modulus but not for Cr >> >> please give some suggestions >> -- >> U.Saibabu >> PhD student, >> Deformation mechanisms modeling group, >> Materials engineering department, >> IISc Bangalore, >> India. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090908/52deb274/attachment.htm From giannozz at democritos.it Tue Sep 8 22:33:03 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 8 Sep 2009 22:33:03 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: References: Message-ID: <4A8D4466-5B5A-4918-895E-13A6354613B5@democritos.it> On Sep 8, 2009, at 21:04 , udayagiri sai babu wrote: > which equation of state should i use for cr? because for vanadium > and Ti > murnagan equation of state has given reasonable (<20% error) values of > bulk modulus but not for Cr you are not, for sure, the first one trying to find the ground state of Cr (which, if I remember correctly, is antiferromagnetic). Have you looked for previous theoretical work? P. -- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mozaharphysics25 at yahoo.com Wed Sep 9 09:20:24 2009 From: mozaharphysics25 at yahoo.com (Mozahar Ali) Date: Wed, 9 Sep 2009 00:20:24 -0700 (PDT) Subject: [Pw_forum] About missing q-points in q2r.in Message-ID: <664520.80709.qm@web58505.mail.re3.yahoo.com> Dear all users,I have run elph.out successfully but while i am going to run q2r.in an error messege is found i.e? from init : error # 1 > > missing q-point(s)! > > stopping ... Does anyone could tell me how to avoid this error ? Thanks in advance Here my input files under yours consideration. scf input&control ? prefix='BC3' ? restart_mode='from_scratch', ? calculation = 'scf' ? pseudo_dir = '/home/nahid/espresso-4.0.4/pseudo/' ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' ? tprnfor=.true. ? tstress = .true. ?/ ?&system ? ? ibrav= 6, a=3.530109, c=3.895778, nat=8, ntyp= 2, ? ecutwfc =50.0, ecutrho =400.0, ? occupations='smearing', smearing='m-v',degauss =0.02, ?/ ?&electrons ? diagonalization= 'cg' , ? mixing_mode = 'plain' ? mixing_beta = 0.7 ? conv_thr = 1.0d-8 ?/ ATOMIC_SPECIES B 10.81000 B.pw91-n-van_ak.UPF? C 12.0107 C.pw91-van_ak.UPF ATOMIC_POSITIONS {crystal} ? B 0.50000000 0.0000000 0.5000000 ? ? B 0.00000000 -0.5000000 -0.5000000 ? ? C 0.00000000 0.0000000 0.0000000 ? C 0.25000000 0.2500000 0.2290000 ? C -0.25000000 -0.2500000 0.2290000 ? C 0.25000000 -0.2500000 -0.2290000 ? C -0.25000000 0.2500000 -0.2290000 ? C 0.50000000 0.5000000 0.0000000? K_POINTS automatic? 6 6 6 0 0 0 scf.fit input &control ? calculation ='scf' ? restart_mode='from_scratch', ? prefix='BC3' ? pseudo_dir = '/home/nahid/espresso-4.0.4/pseudo/' ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' ?/ ?&system ? ? ibrav= 6, a=3.530109, c=3.895778, nat=8, ntyp= 2, ? ecutwfc =50.0, ecutrho =400.0, ? occupations='smearing', smearing='m-v',degauss =0.02, ? la2F = .true.,? ?/ ?&electrons ? mixing_beta = 0.7 ? conv_thr = 1.0d-8 ?/ ATOMIC_SPECIES B 10.81000 B.pw91-n-van_ak.UPF? C 12.0107 C.pw91-van_ak.UPF ATOMIC_POSITIONS {crystal} ? B 0.50000000 0.0000000 0.5000000 ? ? B 0.00000000 -0.5000000 -0.5000000 ? ? C 0.00000000 0.0000000 0.0000000 ? C 0.25000000 0.2500000 0.2290000 ? C -0.25000000 -0.2500000 0.2290000 ? C 0.25000000 -0.2500000 -0.2290000 ? C -0.25000000 0.2500000 -0.2290000 ? C 0.50000000 0.5000000 0.0000000 K_POINTS automatic? 12 12 12 0 0 0 elph.input ?Electron-phonon coefficients for BC3 ?&inputph ? tr2_ph=1.0d-14, ? prefix='BC3', ? fildvscf='BC3dv', ? amass(1)=10.810, ? amass(2)=12.0107 ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' ? fildyn='BC3.dyn', ? recover=.false., ? elph=.true., ? trans=.true., ? ldisp=.true. ? nq1=3, nq2=3, nq3=3, Mozahar Department of physics,Rajshahi University, Rajshahi Bangladesh. New Email names for you! Get the Email name you've always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/a59db376/attachment-0001.htm From bipulrr at gmail.com Wed Sep 9 09:30:37 2009 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 9 Sep 2009 13:00:37 +0530 Subject: [Pw_forum] About missing q-points in q2r.in In-Reply-To: <664520.80709.qm@web58505.mail.re3.yahoo.com> References: <664520.80709.qm@web58505.mail.re3.yahoo.com> Message-ID: <3a749910909090030n462ccee9n37a4c77a9891565@mail.gmail.com> HI Mozahar, Depending upon your structure and your nq's values, while running ph.x , it will show you, how many dynamical matrix it going to form. (see *.dyn0) If the programme get intrupt in the middle, and if it didnt form the required no. of dynamical matrix and after that if you run q2r.x then it shows these types of error. Just see your *.dyn0 file, and see how many point it contain (e.g. if it contain 8 points), then you must get *.dyn1, *.dyn2 .... *.dyn8 cheers On 9/9/09, Mozahar Ali wrote: > Dear all users,I have run elph.out successfully but while i am going to run > q2r.in an error messege is found i.e? from init : error # 1 >> > missing q-point(s)! >> > stopping ... > Does anyone could tell me how to avoid this error ? > > Thanks in advance > Here my input files under yours consideration. > scf input&control > ? prefix='BC3' > ? restart_mode='from_scratch', > ? calculation = 'scf' > ? pseudo_dir = '/home/nahid/espresso-4.0.4/pseudo/' > ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' > ? tprnfor=.true. > ? tstress = .true. > ?/ > ?&system > ? ibrav= 6, a=3.530109, c=3.895778, nat=8, ntyp= 2, > ? ecutwfc =50.0, ecutrho =400.0, > ? occupations='smearing', smearing='m-v',degauss =0.02, > ?/ > ?&electrons > ? diagonalization= 'cg' , > ? mixing_mode = 'plain' > ? mixing_beta = 0.7 > ? conv_thr = 1.0d-8 > ?/ > ATOMIC_SPECIES > B 10.81000 B.pw91-n-van_ak.UPF > C 12.0107 C.pw91-van_ak.UPF > ATOMIC_POSITIONS {crystal} > ? B 0.50000000 0.0000000 0.5000000 > ? B 0.00000000 -0.5000000 -0.5000000 > ? C 0.00000000 0.0000000 0.0000000 > ? C 0.25000000 0.2500000 0.2290000 > ? C -0.25000000 -0.2500000 0.2290000 > ? C 0.25000000 -0.2500000 -0.2290000 > ? C -0.25000000 0.2500000 -0.2290000 > ? C 0.50000000 0.5000000 0.0000000 > K_POINTS automatic > 6 6 6 0 0 0 > scf.fit input > &control > ? calculation ='scf' > ? restart_mode='from_scratch', > ? prefix='BC3' > ? pseudo_dir = '/home/nahid/espresso-4.0.4/pseudo/' > ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' > ?/ > ?&system > ? ibrav= 6, a=3.530109, c=3.895778, nat=8, ntyp= 2, > ? ecutwfc =50.0, ecutrho =400.0, > ? occupations='smearing', smearing='m-v',degauss =0.02, > ? la2F = .true., > ?/ > ?&electrons > ? mixing_beta = 0.7 > ? conv_thr = 1.0d-8 > ?/ > ATOMIC_SPECIES > B 10.81000 B.pw91-n-van_ak.UPF > C 12.0107 C.pw91-van_ak.UPF > ATOMIC_POSITIONS {crystal} > ? B 0.50000000 0.0000000 0.5000000 > ? B 0.00000000 -0.5000000 -0.5000000 > ? C 0.00000000 0.0000000 0.0000000 > ? C 0.25000000 0.2500000 0.2290000 > ? C -0.25000000 -0.2500000 0.2290000 > ? C 0.25000000 -0.2500000 -0.2290000 > ? C -0.25000000 0.2500000 -0.2290000 > ? C 0.50000000 0.5000000 0.0000000 > K_POINTS automatic > 12 12 12 0 0 0 > elph.input > ?Electron-phonon coefficients for BC3 > ?&inputph > ? tr2_ph=1.0d-14, > ? prefix='BC3', > ? fildvscf='BC3dv', > ? amass(1)=10.810, > ? amass(2)=12.0107 > ? outdir='/home/nahid/Mozahar/bc3ph/tmp/' > ? fildyn='BC3.dyn', > ? recover=.false., > ? elph=.true., > ? trans=.true., > ? ldisp=.true. > ? nq1=3, nq2=3, nq3=3, > Mozahar > Department of physics,Rajshahi University, Rajshahi Bangladesh. > > > New Email names for you! > Get the Email name you've always wanted on the new @ymail and > @rocketmail. > Hurry before someone else does! > http://mail.promotions.yahoo.com/newdomains/aa/ -- Dr. Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From degironc at sissa.it Wed Sep 9 09:39:35 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 09 Sep 2009 09:39:35 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> Message-ID: <4AA75BB7.9070201@sissa.it> Dear Saibabu, using your data with ev.x I obtain very similar results using birch 1 & 2 and murnaghan EoS while very different when using keane EoS... this indicates that keane EoS has met some problem (at least with your data...) I notice that your data points span less than 1% around the equilibrium geometry. Usually one takes a larger range (let's say 5-10 %) which reduces the signal/noise ratio. hope this helps stefano de Gironcoli - SISSA and DEMOCRITOS udayagiri sai babu wrote: > Dear stefano baroni > I tried that as well i am getting the same value (255gpa). This is the > data i am using > > 5.35 -174.156857800 > 5.36 -174.156934850 > 5.37 -174.156989300 > 5.38 -174.156990580 > 5.39 -174.156955990 > 5.4 -174.156869280 > > this is one of the input file > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='chromium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=3 > celldm(1)=5.350000, > nat=1, > ntyp=1 > ecutwfc=30, > ecutrho=300, > occupations='smearing', > smearing='mv', > degauss=0.012000 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7 > / > ATOMIC_SPECIES > Cr 51.9961 Cr.pw91-sp-van.UPF > ATOMIC_POSITIONS (crystal) > Cr 0.00000000 0.00000000 0.00000000 > K_POINTS {automatic} > 12 12 12 0 0 0 > > can you suggest me anything > > On Wed, Sep 9, 2009 at 1:03 AM, Stefano Baroni > wrote: > > How about trying to fit a very accurate set of data around the > minimum with a parabola and calculate thus the bulk modulus? Have > you tries to plot the resulting fitted curves? which one fits best > the raw data? Udaygiri: in Science (as well as in Life) there is > no free lunch ... Enjoy Science, no less than Life. SB > > On Sep 8, 2009, at 9:04 PM, udayagiri sai babu wrote: > >> >> hi all >> i am using ev.x file given in the pw_tools directory to calculate >> bulk modulus and lattice parameter values of chromium. i used >> murnaghan equation of state to fit my data i got bulk modulus of >> 256 gpa where as my experimental value is 160 gpa but when i >> used keane equation of state to fit the same data i got 148 gpa >> bulk modulus >> >> why is this much variation? which equation of state should i use >> for cr? because for vanadium and Ti murnagan euation of state has >> given reasonable (<20% error) values of bulk modulus but not for Cr >> >> please give some suggestions >> -- >> U.Saibabu >> PhD student, >> Deformation mechanisms modeling group, >> Materials engineering department, >> IISc Bangalore, >> India. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Wed Sep 9 09:47:16 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 09 Sep 2009 09:47:16 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: <4AA75BB7.9070201@sissa.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> <4AA75BB7.9070201@sissa.it> Message-ID: <4AA75D84.8000101@sissa.it> Stefano de Gironcoli wrote: > ... Usually one takes a larger range (let's say 5-10 > %) which reduces the signal/noise ratio. > actually it increases the ratio... which is what one wants. stefano From giannozz at democritos.it Wed Sep 9 09:51:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 09 Sep 2009 09:51:50 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: <4AA75BB7.9070201@sissa.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> <4AA75BB7.9070201@sissa.it> Message-ID: <4AA75E96.4020504@democritos.it> Stefano de Gironcoli wrote: > using your data with ev.x I obtain very similar results using birch 1 > & 2 and murnaghan EoS while very different when using keane EoS... this > indicates that keane EoS has met some problem (at least with your data...) the Keane equation of state always gives results that are rather different from those of the three other equations of state (which instead invariably give very close results). I am quite sure that it is correctly implemented, but I wouldn't use it. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Wed Sep 9 10:14:21 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 9 Sep 2009 10:14:21 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: <4AA75E96.4020504@democritos.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> <4AA75BB7.9070201@sissa.it> <4AA75E96.4020504@democritos.it> Message-ID: Thank you, Stefano & Paolo. I still maintain that before complaining because of "wrong" (i.e. unexpected) numerical results, one should make the effort to "stare numbers into the face". Plotting (which used to be routine work for students when I was one) is a very good way of doing so. Stefano B On Sep 9, 2009, at 9:51 AM, Paolo Giannozzi wrote: > Stefano de Gironcoli wrote: > >> using your data with ev.x I obtain very similar results using >> birch 1 >> & 2 and murnaghan EoS while very different when using keane EoS... >> this >> indicates that keane EoS has met some problem (at least with your >> data...) > > the Keane equation of state always gives results that are rather > different from those of the three other equations of state (which > instead invariably give very close results). I am quite sure > that it is correctly implemented, but I wouldn't use it. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/5910c6b9/attachment.htm From stenuit at sissa.it Wed Sep 9 10:19:12 2009 From: stenuit at sissa.it (Geoffrey Stenuit) Date: Wed, 9 Sep 2009 10:19:12 +0200 Subject: [Pw_forum] GWW-band (P. Umari) In-Reply-To: <20090904111027.hyr4720hs00csosk@mail.democritos.it> References: <20090904111027.hyr4720hs00csosk@mail.democritos.it> Message-ID: <20090909101912.otnxz18uqsskssgs@webmail.sissa.it> Dear Ali, Just a few additional words: The symmetric dielectric matrix is given in the output file generated by the binary head.x (based on the ph.x phonon code as Paolo said). In particular, it is also given by the second number on the line starting by "HEAD:" . In other words, if you do a "grep HEAD: output_file_name", you will obtain a list with three columns. The first will be "HEAD:", the second column will give the imaginary frequency at which the symmetric dielect. constant has been calculated, and the third will give the dielect constant. You should have n_gauss+1 lines. The convergence of these values should be checked as a function of the k-point sampling. Good luck, Joe Quoting umari at democritos.it: > Dear Ali, > > First of all, note that the GWW is implemented only at the gamma point, > so it requires large supercells, (or better it is appropriate for > non-crystalline systems). > However the long-range parts of the symmetric dielectric matrix > and of the screened-interaction can be calculated using k-points. > With the code ph.x you are calculating the head and the wings of > the symmetric dielectric matrix. > E_HEAD are the head terms of the symmetric dielectric matrix > calculated on the imaginary frequency axis (e.g. "E_HEAD : 58" > is relative to the 58th frequency step). These terms together with > the wings are calculated using linear response. > Then, also the long range part (element G=0,G=0) > of the screened interaction can also be calculated using a k-points grid. > The calculated elements are <\Psi_i|G(i \tau)v|\Psi_i>, > where \Psi_i are the KS states G(i\tau) is the KS Green function > in imaginary time and v is the bare Coulomb interaction. > The term "X energy 1" is the exchange energy relative to the 1st KS state. > >> I am trying to use implemented approach GWW in espresso to obtain >> quasiparticle state for bulk TiO2 ,but I didn,t succeed to get true band >> gap by GW density of state. >> I used 10 10 12 kmesh for k sampling but I don't know which file and which >> rows contains dielectric constant. when I grep E_HEAD ,the last lines is >> E_HEAD : 58 (-0.288322417972075195E-19,-0.347622164532722579E-06) >> E_HEAD : 59 (0.136048521030191330E-19,-0.268035068560476896E-06) > ..... ..... >> what is these two columns? where do I look for dielectric constant? >> also when I grep the energy in exchange file I see >> X energy 1 -3.13056306094735648 >> X energy 2 -3.13125888267243768 > > Best regards, > > P. Umari (Democritos) > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From xomiakk at gmail.com Wed Sep 9 11:53:48 2009 From: xomiakk at gmail.com (Olga Sedelnikova) Date: Wed, 9 Sep 2009 16:53:48 +0700 Subject: [Pw_forum] vdw Message-ID: Dear all, I cannot find any documentation about vdw code. Please describe basic approaches used for polarizability calculations. Examples 33 and 34 illustrates how to use ph.x and vdw.x to calculate polarizability of methane molecules. But results do not agree esecially for static value. Which method is better? Thank you, Olga -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/d5c7ba32/attachment.htm From eminekb at yahoo.com Wed Sep 9 12:10:22 2009 From: eminekb at yahoo.com (e kb) Date: Wed, 9 Sep 2009 03:10:22 -0700 (PDT) Subject: [Pw_forum] vdw In-Reply-To: Message-ID: <951200.10317.qm@web112614.mail.gq1.yahoo.com> Dear Olga,There are README files inside example directories to help you understand what is happening:In vdw example.."The Thomas-Fermi and von Weizsacker approximation is usedto simplify the full calculation done in ph.x. It is expectedthat this simplified calculation gives results deviatingabout 20% comparing to that of the full one(checked formethane and benzene)."cheers,emine kucukbenli, SISSA, Italy ? ? --- On Wed, 9/9/09, Olga Sedelnikova wrote: From: Olga Sedelnikova Subject: [Pw_forum] vdw To: pw_forum at pwscf.org Date: Wednesday, September 9, 2009, 12:53 PM Dear all, I cannot find any documentation about vdw code. Please describe basic approaches used for polarizability calculations. Examples 33 and 34 illustrates how to use ph.x and vdw.x to calculate polarizability of methane molecules. But results do not agree esecially for static value. Which method is better? Thank you, Olga -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/82acdf2c/attachment.htm From sclauzer at sissa.it Wed Sep 9 12:27:17 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 09 Sep 2009 12:27:17 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: <4AA75D84.8000101@sissa.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> <4AA75BB7.9070201@sissa.it> <4AA75D84.8000101@sissa.it> Message-ID: <4AA78305.8030104@sissa.it> Stefano de Gironcoli wrote: > Stefano de Gironcoli wrote: >> ... Usually one takes a larger range (let's say 5-10 >> %) which reduces the signal/noise ratio. >> > actually it increases the ratio... which is what one wants. On the other hand, I think that if one uses a range that is too large then the bulk modulus comes out worse from the fit because the fitting model is not as good as near the minimum (you need more fitting parameters to describe properly the curve on a larger range). Anyway, in my tests on a simple metal (bulk gold), the bulk modulus is not very sensitive to the fitting range. The "goodness" of the fit (chisq) seems to decrease with the range span (at fixed number of points), but the program does not give an estimate of the error on the fitting parameters. I think that a good estimate of the bulk modulus can be obtained also with a small range (if your data is not too noisy and well centered around the minimum), but other paraters need a larger range. From the data below you can see that k0 (the bulk modulus) is very stable from a range span of 1% up to 5%, but in order to estimate dk0 you need at least 2%. Maybe in other system this behaviour changes. HTH, Gabriele ==> Au.ev.1perc <== # equation of state: murnaghan. chisq = 0.7465D-12 # a0 = 7.67 a.u., k0 = 1923 kbar, dk0 = 1.76 d2k0 = 0.000 emin = -66.84630 # a0 = 4.058 A, V0 =112.706 (a.u.)^3, V0 = 16.701 A^3 ==> Au.ev.2perc <== # equation of state: murnaghan. chisq = 0.1161D-11 # a0 = 7.67 a.u., k0 = 1927 kbar, dk0 = 5.32 d2k0 = 0.000 emin = -66.84630 # a0 = 4.057 A, V0 =112.696 (a.u.)^3, V0 = 16.700 A^3 ==> Au.ev.3perc <== # equation of state: murnaghan. chisq = 0.1454D-11 # a0 = 7.67 a.u., k0 = 1925 kbar, dk0 = 5.51 d2k0 = 0.000 emin = -66.84630 # a0 = 4.057 A, V0 =112.693 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.4perc <== # equation of state: murnaghan. chisq = 0.1438D-11 # a0 = 7.67 a.u., k0 = 1926 kbar, dk0 = 5.57 d2k0 = 0.000 emin = -66.84630 # a0 = 4.057 A, V0 =112.692 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.5perc <== # equation of state: murnaghan. chisq = 0.1006D-10 # a0 = 7.67 a.u., k0 = 1922 kbar, dk0 = 5.61 d2k0 = 0.000 emin = -66.84630 # a0 = 4.057 A, V0 =112.692 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.6perc <== # equation of state: murnaghan. chisq = 0.3205D-10 # a0 = 7.67 a.u., k0 = 1916 kbar, dk0 = 5.68 d2k0 = 0.000 emin = -66.84630 # a0 = 4.057 A, V0 =112.688 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.7perc <== # equation of state: murnaghan. chisq = 0.1013D-09 # a0 = 7.67 a.u., k0 = 1909 kbar, dk0 = 5.70 d2k0 = 0.000 emin = -66.84629 # a0 = 4.057 A, V0 =112.689 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.8perc <== # equation of state: murnaghan. chisq = 0.2887D-09 # a0 = 7.67 a.u., k0 = 1903 kbar, dk0 = 5.71 d2k0 = 0.000 emin = -66.84629 # a0 = 4.057 A, V0 =112.691 (a.u.)^3, V0 = 16.699 A^3 ==> Au.ev.9perc <== # equation of state: murnaghan. chisq = 0.7385D-09 # a0 = 7.67 a.u., k0 = 1894 kbar, dk0 = 5.70 d2k0 = 0.000 emin = -66.84627 # a0 = 4.058 A, V0 =112.697 (a.u.)^3, V0 = 16.700 A^3 -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Wed Sep 9 13:02:55 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 09 Sep 2009 13:02:55 +0200 Subject: [Pw_forum] using ev.x In-Reply-To: <4AA75D84.8000101@sissa.it> References: <141F93D5-E4B3-49BB-B1C9-F5AB28077851@sissa.it> <4AA75BB7.9070201@sissa.it> <4AA75D84.8000101@sissa.it> Message-ID: <1252494175.8283.351.camel@walk.ijs.si> Let me just add one more item about bulk modulus. >From time to time I see the bulk modulus written with too many significant digits, e.g. 179.3 GPa. Due to the fact that it is a second derivative calculated numerically and due to a signal/noise that Stefano mentioned, it is a sensitive quantity. E.g. adding a few additional data point(s) (or expanding/shrinking the range) may easily change the last two digits above. Here is an example (silver-bulk) of how bulk modulus changes with the number of data points (the range of scan is from -4% to +4%, and the fits are performed for several subsets of so-obtained data points): Bulk Modulus, B0 (in kbar units):: ------------+------------+------------+------------+----------- # points | MURNAGHAN | BIRCH O(1) | BIRCH O(2) | KEANE ------------+------------+------------+------------+----------- 15: 1--15 | 896 | 905 | 905 | 610 14: 1--14 | 898 | 905 | 904 | 755 13: 2--14 | 898 | 905 | 903 | 638 12: 2--13 | 900 | 904 | 903 | 748 11: 3--13 | 900 | 904 | 904 | 645 10: 3--12 | 901 | 904 | 905 | 599 9: 4--12 | 901 | 904 | 910 | 665 8: 4--11 | 906 | 907 | 909 | 602 7: 5--11 | 905 | 907 | 906 | 672 ------------+------------+------------+------------+----------- (the meaning of the first column is "number-of-points: first-point -- last-point") To add to the Murnaghan vs Keane discussion, it is evident that the Keane column above displays the largest fluctuations (and also different result compared to others). Regards, Tone P.S.: for those interested: the above table was produced by the PWTK (http://qe-forge.org/projects/pwtk/) which can calculate lattice parameter and bulk modulus automatically. For more info see: Tutorial: http://pwtk.qe-forge.org/tutorial.html Examples: http://pwtk.qe-forge.org/documentation_tclPWTK2F32E20Examples.html -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From eminekb at yahoo.com Wed Sep 9 14:54:43 2009 From: eminekb at yahoo.com (e kb) Date: Wed, 9 Sep 2009 05:54:43 -0700 (PDT) Subject: [Pw_forum] using ev.x In-Reply-To: <1252494175.8283.351.camel@walk.ijs.si> Message-ID: <966261.94768.qm@web112619.mail.gq1.yahoo.com> Just a small note to be fair to Keane EOS after recently posted examples:As far as I know, Keane EOS is based on an assumption at high pressure.(B' is a?monotonicly decreasing function of pressure, and reaches to a limiting value as pressure goes to infinity) Therefore it works best when both low pressure and high pressure input is supplied and intermediate pressure values are found (like when we interpolate between acoustic lab data and shock wave data) So the deviations are not weird when only 5% compression is considered. ?cheers,?emine kucubenli, SISSA, Italy --- On Wed, 9/9/09, Tone Kokalj wrote: From: Tone Kokalj Subject: Re: [Pw_forum] using ev.x To: "PWSCF Forum" Date: Wednesday, September 9, 2009, 2:02 PM Let me just add one more item about bulk modulus. >From time to time I see the bulk modulus written with too many significant digits, e.g. 179.3 GPa. Due to the fact that it is a second derivative calculated numerically and due to a signal/noise that Stefano mentioned, it is a sensitive quantity. E.g. adding a few additional data point(s) (or expanding/shrinking the range) may easily change the last two digits above. Here is an example (silver-bulk) of how bulk modulus changes with the number of data points (the range of scan is from -4% to +4%, and the fits are performed for several subsets of so-obtained data points): Bulk Modulus, B0 (in kbar units):: ------------+------------+------------+------------+----------- ? # points???| MURNAGHAN? | BIRCH O(1) | BIRCH O(2) |? ? KEANE? ------------+------------+------------+------------+----------- ? 15:? 1--15 |? ???896? ? |? ???905? ? |? ???905? ? |? ???610 ? 14:? 1--14 |? ???898? ? |? ???905? ? |? ???904? ? |? ???755 ? 13:? 2--14 |? ???898? ? |? ???905? ? |? ???903? ? |? ???638 ? 12:? 2--13 |? ???900? ? |? ???904? ? |? ???903? ? |? ???748 ? 11:? 3--13 |? ???900? ? |? ???904? ? |? ???904? ? |? ???645 ? 10:? 3--12 |? ???901? ? |? ???904? ? |? ???905? ? |? ???599 ???9:? 4--12 |? ???901? ? |? ???904? ? |? ???910? ? |? ???665 ???8:? 4--11 |? ???906? ? |? ???907? ? |? ???909? ? |? ???602 ???7:? 5--11 |? ???905? ? |? ???907? ? |? ???906? ? |? ???672 ------------+------------+------------+------------+----------- (the meaning of the first column is "number-of-points: first-point -- last-point") To add to the Murnaghan vs Keane discussion, it is evident that the Keane column above displays the largest fluctuations (and also different result compared to others). Regards, Tone P.S.: for those interested: the above table was produced by the PWTK (http://qe-forge.org/projects/pwtk/) which can calculate lattice parameter and bulk modulus automatically. For more info see: Tutorial: http://pwtk.qe-forge.org/tutorial.html Examples: http://pwtk.qe-forge.org/documentation_tclPWTK2F32E20Examples.html -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See:? http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/d95e8f1c/attachment.htm From dalcorso at sissa.it Wed Sep 9 15:22:37 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 09 Sep 2009 15:22:37 +0200 Subject: [Pw_forum] vdw In-Reply-To: References: Message-ID: <1252502557.3250.13.camel@dhpc-5-36.sissa.it> On Wed, 2009-09-09 at 16:53 +0700, Olga Sedelnikova wrote: > Dear all, > > I cannot find any documentation about vdw code. Please describe basic > approaches used for polarizability calculations. > Examples 33 and 34 illustrates how to use ph.x and vdw.x to calculate > polarizability of methane molecules. But results do not agree > esecially for static value. Which method is better? The two results should agree in the limit of large boxes. The reason is that the results of vdw.x use the Clausius-Mossotti correction to speed up the convergence of the calculated polarizability with the box size. In the current 4.1 version, neither ph.x nor phcg.x apply the correction. This has been modified in cvs version of ph.x that now gives a polarizability that agrees with the frequency dependent result at w=0. HTH, Andrea See also Jour. of Chem. Phys. 120, 9934 (2004) for more details. > > Thank you, > > Olga > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34151 Trieste (Italy) e-mail: dalcorso at sissa.it From colonel.sreekar at gmail.com Thu Sep 10 00:59:55 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Thu, 10 Sep 2009 04:29:55 +0530 Subject: [Pw_forum] sorry for posting message in wrong format Message-ID: >Mr. Stefano Baroni wrote > >please, in order to make the life of those who may want to help you >easier: > >1) always indicate the subject of your post in the "subject" field. >the more accurate the short description of your problem, the easier it >will be that somebody will pick your post up >2) group all the questions related to a same problem in a same post. >he time that each of us devotes voluntarily to this community >activity is limited. the easier it is to go through the forum, the >highest are the chances that some relevant questions are answered. >3) strip unrelated material from the post. I understand that composing >a regular mail massege may take 2-3 seconds more than just hitting >reply", but I think that this time is worth avoiding cluttering our >mail boxes with garbage. > >this being said, I am not the most appropriate person to pick up your >answers. I wish somebody else will ... > >best wishes - Stefano Baroni sir Stefano Baroni and all, i m extremely sorry for posting messages in the wrong format. I will never do the mistake again. sincerely, Sreekar Guddeti Dual Degree(BTech+MTech) Dept Physics IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/af3a5216/attachment.htm From shypirate at gmail.com Thu Sep 10 05:03:47 2009 From: shypirate at gmail.com (shypirate) Date: Thu, 10 Sep 2009 11:03:47 +0800 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' Message-ID: <200909101103463595955@gmail.com> Dear all: When I use pw.x, I find that performance of different occupations are different. If I set occupation='smearing', it takes about 6 minutes for one diagonalization step, but 24 minutes for occupation='fixed'. I have set the same "nbnd" and "K_POINTS" for both. My question is, why is the performance difference? Best Wishes, Y.P.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/85f2e1b5/attachment.htm From nkxirainbow at gmail.com Thu Sep 10 05:12:10 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 10 Sep 2009 03:12:10 +0000 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' In-Reply-To: <200909101103463595955@gmail.com> References: <200909101103463595955@gmail.com> Message-ID: <21fbc4790909092012r2545e4anbe65ab8da314ae7f@mail.gmail.com> Dear Wang? Smearing is used to accelerate scf convergence when you deal with metal material. But the convergence of smearing must be checked carelfully:) -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/030b95ca/attachment.htm From meghdad_saeedian at yahoo.com Thu Sep 10 08:07:18 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Wed, 9 Sep 2009 23:07:18 -0700 (PDT) Subject: [Pw_forum] Phonon with Norm - Conserving pseudopotential Message-ID: <96088.70053.qm@web31404.mail.mud.yahoo.com> Dear all I calculated Dispersion curve of TiO2 with ultrasoft pseudopotential.? But? the experimental? data for checking? gamma point is not enough . I want to know, How much my data will change, if I use Norm - Conserving pseudopotential? Thanks in advance Meghdad saeedian M.Sc student , University of tehran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090909/9003d187/attachment-0001.htm From shypirate at gmail.com Thu Sep 10 08:31:48 2009 From: shypirate at gmail.com (shypirate) Date: Thu, 10 Sep 2009 14:31:48 +0800 Subject: [Pw_forum] performance of occupation='fixed' and Message-ID: <200909101431467813287@gmail.com> Dear xirainbow: I know that. But I think the amount of calculation is the same if 'nbnd' and 'K_POINTS' are set the same values. What I donot understand is the difference of performance. Best Wishes, Yunpeng Wang -------------------------------------------------------------------------- Date: Thu, 10 Sep 2009 03:12:10 +0000 From: xirainbow Subject: Re: [Pw_forum] performance of occupation='fixed' and ='smearing' To: PWSCF Forum Message-ID: <21fbc4790909092012r2545e4anbe65ab8da314ae7f at mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Wang? Smearing is used to accelerate scf convergence when you deal with metal material. But the convergence of smearing must be checked carelfully:) 2009-09-10 shypirate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/08e2cc42/attachment.htm From giannozz at democritos.it Thu Sep 10 08:46:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Sep 2009 08:46:29 +0200 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' In-Reply-To: <200909101103463595955@gmail.com> References: <200909101103463595955@gmail.com> Message-ID: On Sep 10, 2009, at 5:03 , shypirate wrote: > If I set occupation='smearing', it takes about 6 minutes for > one diagonalization step, but 24 minutes for occupation='fixed'. > I have set the same "nbnd" and "K_POINTS" for both. > My question is, why is the performance difference? make a "diff" between the two outputs and you will see why. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From shypirate at gmail.com Thu Sep 10 09:02:26 2009 From: shypirate at gmail.com (shypirate) Date: Thu, 10 Sep 2009 15:02:26 +0800 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' References: <200909101103463595955@gmail.com> Message-ID: <200909101502251717383@gmail.com> Thank you for your replying. But after I make a "diff", I still have trouble to find out the difference resulting in performance difference. For example, the data in "G cutoff" and "Largest allocated arrays" and "Largest temporary arrays" sections take exactly the same values. So, which parameter do you suggest is candidate for performance difference? Hope for your suggestions, Best Wishes, Y.P.Wang 2009-09-10 shypirate ???? Paolo Giannozzi ????? 2009-09-10 14:47:16 ???? PWSCF Forum ??? ??? Re: [Pw_forum] performance of occupation='fixed' and ='smearing' On Sep 10, 2009, at 5:03 , shypirate wrote: > If I set occupation='smearing', it takes about 6 minutes for > one diagonalization step, but 24 minutes for occupation='fixed'. > I have set the same "nbnd" and "K_POINTS" for both. > My question is, why is the performance difference? make a "diff" between the two outputs and you will see why. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/e534b058/attachment.htm From baroni at sissa.it Thu Sep 10 09:09:03 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 10 Sep 2009 09:09:03 +0200 Subject: [Pw_forum] Phonon with Norm - Conserving pseudopotential In-Reply-To: <96088.70053.qm@web31404.mail.mud.yahoo.com> References: <96088.70053.qm@web31404.mail.mud.yahoo.com> Message-ID: <5030F5F3-CDC0-44A0-A085-863C0B6AA8C4@sissa.it> just try and let us know SB On Sep 10, 2009, at 8:07 AM, meghdad saeedian wrote: > > Dear all > > I calculated Dispersion curve of TiO2 with ultrasoft > pseudopotential. But the experimental data for checking gamma > point is not enough . I want to know, How much my data will change, > if I use Norm - Conserving pseudopotential? > > Thanks in advance > > Meghdad saeedian > M.Sc student , University of tehran > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/3daf80aa/attachment.htm From giannozz at democritos.it Thu Sep 10 09:17:34 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Sep 2009 09:17:34 +0200 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' In-Reply-To: <200909101502251717383@gmail.com> References: <200909101103463595955@gmail.com> <200909101502251717383@gmail.com> Message-ID: <87F440FD-2063-42CE-87AD-895E6A43DB0A@democritos.it> On Sep 10, 2009, at 9:02 , shypirate wrote: > So, which parameter do you suggest is candidate for performance > difference? I suggest that there is no performance difference between a single scf iteration with occupation='fixed' and with occupation='smearing' if you use the same number of bands and of k-points. The self-consistency cycle may be very different, though. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Thu Sep 10 09:23:37 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Sep 2009 09:23:37 +0200 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' In-Reply-To: <200909101103463595955@gmail.com> References: <200909101103463595955@gmail.com> Message-ID: <4AA8A979.5030000@sissa.it> shypirate wrote: > Dear all: > When I use pw.x, I find that performance of different occupations are > different. If I set occupation='smearing', it takes about 6 minutes for > one diagonalization step, but 24 minutes for occupation='fixed'. I have > set the same "nbnd" and "K_POINTS" for both. My question is, why is the > performance difference? If it's like you say, the only possible difference that comes to my mind is in the number of iterations used in the Davidson algorithm for diagonalization (though I never thought it could depend on the occupations method). Please check for the keyword "iterations" (which is printed together with the number of iterations after each diagonalization step): > grep iterations yourfile and let me know the output. GS > Best Wishes, > Y.P.Wang > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From shypirate at gmail.com Thu Sep 10 09:36:35 2009 From: shypirate at gmail.com (shypirate) Date: Thu, 10 Sep 2009 15:36:35 +0800 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' References: <200909101103463595955@gmail.com>, <4AA8A979.5030000@sissa.it> Message-ID: <200909101536323900766@gmail.com> I am using CG style diagonalization, in fact. 2009-09-10 shypirate ???? Gabriele Sclauzero ????? 2009-09-10 15:23:48 ???? PWSCF Forum ??? ??? Re: [Pw_forum] performance of occupation='fixed' and ='smearing' shypirate wrote: > Dear all: > When I use pw.x, I find that performance of different occupations are > different. If I set occupation='smearing', it takes about 6 minutes for > one diagonalization step, but 24 minutes for occupation='fixed'. I have > set the same "nbnd" and "K_POINTS" for both. My question is, why is the > performance difference? If it's like you say, the only possible difference that comes to my mind is in the number of iterations used in the Davidson algorithm for diagonalization (though I never thought it could depend on the occupations method). Please check for the keyword "iterations" (which is printed together with the number of iterations after each diagonalization step): > grep iterations yourfile and let me know the output. GS > Best Wishes, > Y.P.Wang > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/3b271bb5/attachment-0001.htm From paulatto at sissa.it Thu Sep 10 10:23:49 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 10 Sep 2009 10:23:49 +0200 Subject: [Pw_forum] performance of occupation='fixed' and ='smearing' In-Reply-To: <200909101103463595955@gmail.com> References: <200909101103463595955@gmail.com> Message-ID: In data 10 settembre 2009 alle ore 05:03:47, shypirate ha scritto: > When I use pw.x, I find that performance of different occupations are > different. If I set occupation='smearing', it takes about 6 minutes for > one diagonalization step, but 24 minutes for occupation='fixed'. I have > set the same "nbnd" and "K_POINTS" for both. Dear Y.P.Wang, could you please specify better what you mean by "diagonalization step"? best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sh.shapt at gmail.com Thu Sep 10 12:25:19 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Thu, 10 Sep 2009 11:25:19 +0100 Subject: [Pw_forum] Spin polarisation for odd number of electrons Message-ID: Hi QE user, My question has not been answered. I asked earlier once that how shall I perform spin polarisation in my system , as I have odd number of electrons in my system . Can anybody give any suggetions? Thanks SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/9f9b72e7/attachment.htm From sclauzer at sissa.it Thu Sep 10 12:29:42 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Sep 2009 12:29:42 +0200 Subject: [Pw_forum] Spin polarisation for odd number of electrons In-Reply-To: References: Message-ID: <4AA8D516.3010304@sissa.it> Shaptrishi Sharma wrote: > Hi QE user, > My question has not been answered. I asked earlier once that how shall I > perform spin polarisation in my system , as I have odd number of > electrons > in my system . Can anybody give any suggetions? Use nspin=2 in &control namelist, as written in the user guide, and also in the Doc/INPUT_PW input description. Regards GS > Thanks > SS > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Thu Sep 10 12:29:43 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 10 Sep 2009 12:29:43 +0200 Subject: [Pw_forum] Spin polarisation for odd number of electrons In-Reply-To: References: Message-ID: In data 10 settembre 2009 alle ore 12:25:19, Shaptrishi Sharma ha scritto: > My question has not been answered. I asked earlier once that how > shall I perform spin polarisation in my system , as I have odd number of > electrons in my system . Can anybody give any suggetions? Dear Shaptrishi, just set nspin=2 in the &system namelist, you will also have to use smearing in order to improve convergence. Have a look at the manual for details. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From meghdad_saeedian at yahoo.com Thu Sep 10 14:07:34 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Thu, 10 Sep 2009 05:07:34 -0700 (PDT) Subject: [Pw_forum] Phonon with Norm - Conserving pseudopotential In-Reply-To: <5030F5F3-CDC0-44A0-A085-863C0B6AA8C4@sissa.it> Message-ID: <227190.52728.qm@web31404.mail.mud.yahoo.com> Dear all, I couldn't find the Ti norm-conserving LDA pseudopotential. Would you please some one provide me with it? Thanks in advance. Yours, Meghdad Saeedian --- On Thu, 9/10/09, Stefano Baroni wrote: From: Stefano Baroni Subject: Re: [Pw_forum] Phonon with Norm - Conserving pseudopotential To: "PWSCF Forum" Date: Thursday, September 10, 2009, 11:39 AM just try and let us knowSB On Sep 10, 2009, at 8:07 AM, meghdad saeedian wrote: Dear all I calculated Dispersion curve of TiO2 with ultrasoft pseudopotential.? But? the experimental? data for checking? gamma point is not enough . I want to know, How much my data will change, if I use Norm - Conserving pseudopotential? Thanks in advance Meghdad saeedian M.Sc student , University of tehran _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ---Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Triestehttp://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't??send me MS Word or PowerPoint attachmentsWhy? See:??http://www.gnu.org/philosophy/no-word-attachments.html -----Inline Attachment Follows----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/d892519d/attachment.htm From sh.shapt at gmail.com Thu Sep 10 15:12:46 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Thu, 10 Sep 2009 14:12:46 +0100 Subject: [Pw_forum] nelup and neldw in Qespresso Message-ID: Hi there, I have 21 Hydrogen atoms in my system, which means my nuber of electrons will be 21*1 - 21 electrons, thus the number of electrons are odd. Thus I shall need to mention nspin as well as nelup and neldw. Thus I mention nspin = 2 nelup = 21 neldw =21, However the program has been crashed and in the output it is showing as follows : task # 22 from system_checkin : error # 1 nelup out of range Can anybody give me any suggestions? Thanks SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/87553c9a/attachment.htm From paulatto at sissa.it Thu Sep 10 15:18:32 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 10 Sep 2009 15:18:32 +0200 Subject: [Pw_forum] nelup and neldw in Qespresso In-Reply-To: References: Message-ID: In data 10 settembre 2009 alle ore 15:12:46, Shaptrishi Sharma ha scritto: > will be 21*1 - 21 electrons, thus the number of electrons are odd. Thus I > shall need to mention nspin as well as nelup and neldw. Thus I mention > nspin = 2 > nelup = 21 > neldw =21, Dear Shaptrishi, if you have 21 electrons in total you cannot put 21 up and 21 down; this would make 42 total. A sensible choice is 11 up and 10 down. best regards P.S. please provide your affiliation when writing to this mailing list -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From ttduyle at gmail.com Thu Sep 10 22:14:50 2009 From: ttduyle at gmail.com (Duy Le) Date: Thu, 10 Sep 2009 16:14:50 -0400 Subject: [Pw_forum] Phonon with Norm - Conserving pseudopotential In-Reply-To: <227190.52728.qm@web31404.mail.mud.yahoo.com> References: <5030F5F3-CDC0-44A0-A085-863C0B6AA8C4@sissa.it> <227190.52728.qm@web31404.mail.mud.yahoo.com> Message-ID: <8974d3b20909101314s56f064cbp46eb60b384286c84@mail.gmail.com> Hi Meghdad, You could use ld1 code for generating norm-conserving pot. for Ti. http://www.quantum-espresso.org/input-syntax/INPUT_LD1.html Or you can also use opium to generate it (input is already available at its website). http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html#Ti1 :-) On Thu, Sep 10, 2009 at 8:07 AM, meghdad saeedian < meghdad_saeedian at yahoo.com> wrote: > Dear all, > > I couldn't find the Ti norm-conserving LDA pseudopotential. > Would you please some one provide me with it? > > Thanks in advance. > > Yours, > Meghdad Saeedian > > > --- On *Thu, 9/10/09, Stefano Baroni * wrote: > > > > From: Stefano Baroni > Subject: Re: [Pw_forum] Phonon with Norm - Conserving pseudopotential > To: "PWSCF Forum" > Date: Thursday, September 10, 2009, 11:39 AM > > > just try and let us know SB > > On Sep 10, 2009, at 8:07 AM, meghdad saeedian wrote: > > > Dear all > > I calculated Dispersion curve of TiO2 with ultrasoft pseudopotential. But > the experimental data for checking gamma point is not enough . I want to > know, How much my data will change, if I use Norm - Conserving > pseudopotential? > > Thanks in advance > > Meghdad saeedian > M.Sc student , University of tehran > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090910/b4101585/attachment-0001.htm From udayagiri3 at gmail.com Fri Sep 11 07:32:14 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Fri, 11 Sep 2009 11:02:14 +0530 Subject: [Pw_forum] input file for isolated atom Message-ID: Hi everybody I want to calculate the cohesive energy of Titanium for that i need to calculate the energy of an isolated atom previously in the forum somebody has suggested me to do spin polarisation calculation for the isolated atom. I have written an input file accordingly some one can see and tell me if my input script is true. I have read the forum archives on this topic but they are not exactly answering my question. Can somebody please help me. * Input file for isolated atom * &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/temp', prefix='titanium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', tstress = .TRUE., tprnfor = .TRUE., / &system ibrav=1 celldm(1)=20, nat=1, ntyp=1 ecutwfc=25, ecutrho=250, occupations='smearing', smearing='mv', degauss=0.010000 nspin=2 starting_magnetization(1)=0.2 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.7, / ATOMIC_SPECIES Ti 47.867 Ti.pbe-sp-van_ak.UPF ATOMIC_POSITIONS (crystal) Ti 0.00000000 0.00000000 0.00000000 K_POINTS GAMMA -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/2fcb49ec/attachment.htm From decboy9 at gmail.com Fri Sep 11 10:06:45 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 11 Sep 2009 13:36:45 +0530 Subject: [Pw_forum] problem with charge density with xcrysden Message-ID: hi 2 all, I am trying to plot the charge density with the XCrysden, but when i am opening's XSF(file--> open structure--> open XSF(xcryden structure file)) file , generated by my calculations, it is showing the structure of my system. And i am not getting the option tools--> DATA GRID as ready. Please help or advice ?? Thankful to all of you. What i did is listed below. I run my input file with command /home/physics/espresso-4.0.2/bin/pp.x density.xsf and inputs of density.in are &inputpp prefix = 'yvo' outdir = '/home/physics/work/yvo/temp/', filplot = 'yvocharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'yvocharge' weight(1) = 1.0 iflag = 3 output_format = 5, / with regards, Dev Sharma, University of Delhi, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/7f3604e4/attachment.htm From prasenjit.jnc at gmail.com Fri Sep 11 10:36:29 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 11 Sep 2009 10:36:29 +0200 Subject: [Pw_forum] input file for isolated atom In-Reply-To: References: Message-ID: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> Dear Udayagiri, First of all it's not clear whether you have any question other than whether your input file is correct. Now some comments about your input file: (a) while doing calculations for any zero dimensions you should always set nosym =.true. (b) Your value of degauss is too high.....you should use some value around 0.001 Ry. According to my experience, doing cal. for a single atom is tricky, specially when you are using a smearing. Even that doesn't confirm you will get the correct ground state for the atom. So what you should do is at the end of the calculation check the values of the total magnetization, absolute magnetization and the smearing contribution. The last term should be exactly zero. (c) You don't need to set tstress and tprnfor true. (c) mixing_beta= 0.7 too large.....I would put something smaller....0.3 (d) I hope you have checked the convergence of ecut rho & ecutwfc. Prasenjit. 2009/9/11 udayagiri sai babu > Hi everybody > I want to calculate the cohesive energy of Titanium for that i need to > calculate the energy of an isolated atom previously in the forum somebody > has suggested me to do spin polarisation calculation for the isolated atom. > I have written an input file accordingly some one can see and tell me if my > input script is true. I have read the forum archives on this topic but they > are not exactly answering my question. Can somebody please help me. > * > Input file for isolated atom * > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='titanium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=20, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=250, > occupations='smearing', > smearing='mv', > degauss=0.010000 > nspin=2 > starting_magnetization(1)=0.2 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7, > / > ATOMIC_SPECIES > Ti 47.867 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Ti 0.00000000 0.00000000 0.00000000 > K_POINTS GAMMA > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/87b3b7b8/attachment.htm From sclauzer at sissa.it Fri Sep 11 10:44:32 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 11 Sep 2009 10:44:32 +0200 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: References: Message-ID: <4AAA0DF0.5090702@sissa.it> Dear Dev, dev sharma wrote: > hi 2 all, > I am trying to plot the charge density with the XCrysden, but when i am > opening's XSF(file--> open structure--> open XSF(xcryden structure > file)) file , generated by my calculations, it is showing the structure > of my system. And i am not getting the option tools--> DATA GRID as > ready. Please help or advice ?? Thankful to all of you. What i did is > listed below. Have you had a look inside your .xsf file? How does it look? Does it actually contain the DATAGRID block? Is it complete? Please supply more information! Regards, GS > I run my input file with command > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > and inputs of density.in are > &inputpp > prefix = 'yvo' > outdir = '/home/physics/work/yvo/temp/', > filplot = 'yvocharge' > plot_num= 0 > / > &plot > nfile = 1 > filepp(1) = 'yvocharge' > weight(1) = 1.0 > iflag = 3 > output_format = 5, > / > > with regards, > Dev Sharma, > University of Delhi, > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From udayagiri3 at gmail.com Fri Sep 11 10:49:31 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Fri, 11 Sep 2009 14:19:31 +0530 Subject: [Pw_forum] input file for isolated atom In-Reply-To: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> References: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> Message-ID: Dear prasenajit this is the part of my output for the posted input file. (smearing contribution is there! though it is small ) is the degauss value too high for isolated atom or it is high for bulk calculation also? because i use around 0.01 Ry value for all my calculations. Does the mixing beta value effect the energy of the system? one-electron contribution = -155.91791626 Ry hartree contribution = 74.49216944 Ry xc contribution = -14.37611953 Ry ewald contribution = -20.42854186 Ry smearing contrib. (-TS) = -0.00972779 Ry total magnetization = 3.24 Bohr mag/cell absolute magnetization = 3.24 Bohr mag/cell convergence has been achieved in 34 iterations On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh wrote: > Dear Udayagiri, > > First of all it's not clear whether you have any question other than > whether your input file is correct. > > Now some comments about your input file: > > (a) while doing calculations for any zero dimensions you should always set > nosym =.true. > (b) Your value of degauss is too high.....you should use some value around > 0.001 Ry. According to my experience, doing cal. for a single atom is > tricky, specially when you are using a smearing. Even that doesn't confirm > you will get the correct ground state for the atom. So what you should do is > at the end of the calculation check the values of the total magnetization, > absolute magnetization and the smearing contribution. The last term should > be exactly zero. > (c) You don't need to set tstress and tprnfor true. > (c) mixing_beta= 0.7 too large.....I would put something smaller....0.3 > (d) I hope you have checked the convergence of ecut rho & ecutwfc. > > Prasenjit. > > 2009/9/11 udayagiri sai babu > >> Hi everybody >> I want to calculate the cohesive energy of Titanium for that i need to >> calculate the energy of an isolated atom previously in the forum somebody >> has suggested me to do spin polarisation calculation for the isolated atom. >> I have written an input file accordingly some one can see and tell me if my >> input script is true. I have read the forum archives on this topic but they >> are not exactly answering my question. Can somebody please help me. >> * >> Input file for isolated atom * >> >> &control >> calculation = 'scf', >> restart_mode='from_scratch', >> outdir='/home/sai/temp', >> prefix='titanium' >> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', >> tstress = .TRUE., >> tprnfor = .TRUE., >> / >> &system >> ibrav=1 >> celldm(1)=20, >> nat=1, >> ntyp=1 >> ecutwfc=25, >> ecutrho=250, >> occupations='smearing', >> smearing='mv', >> degauss=0.010000 >> nspin=2 >> starting_magnetization(1)=0.2 >> / >> &electrons >> conv_thr=1.D-8, >> diagonalization='david', >> mixing_mode='plain', >> mixing_beta= 0.7, >> / >> ATOMIC_SPECIES >> Ti 47.867 Ti.pbe-sp-van_ak.UPF >> ATOMIC_POSITIONS (crystal) >> Ti 0.00000000 0.00000000 0.00000000 >> K_POINTS GAMMA >> >> -- >> U.Saibabu >> PhD student, >> Deformation mechanisms modeling group, >> Materials engineering department, >> IISc Bangalore, >> India. >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/70352d34/attachment.htm From decboy9 at gmail.com Fri Sep 11 10:53:17 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 11 Sep 2009 14:23:17 +0530 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: <4AAA0DF0.5090702@sissa.it> References: <4AAA0DF0.5090702@sissa.it> Message-ID: Dear sir, my.xsf file is below Program POST-PROC v.4.0.2 starts ... Today is 11Sep2009 at 12:54:29 Check: negative/imaginary core charge= -0.000009 0.000000 negative rho (up, down): 0.188E+00 0.000E+00 Calling punch_plot, plot_num = 0 Writing data to file yvocharge Reading data from file yvocharge CRYSTAL PRIMVEC 7.118300514 0.000000000 0.000000000 0.000000000 7.118300514 0.000000000 0.000000000 0.000000000 6.289300454 PRIMCOORD 24 1 Y 0.000000000 5.338725356 0.786162553 / / O 1.311190868 5.338725356 2.835216639 BEGIN_BLOCK_DATAGRID_3D 3D_PWSCF DATAGRID_3D_UNKNOWN 61 61 49 0.000000 0.000000 0.000000 7.118301 0.000000 0.000000 0.000000 7.118301 0.000000 0.000000 0.000000 6.289300 0.19131E-01 0.18756E-01 0.17478E-01 0.15613E-01 0.13484E-01 0.11234E-01 / / 0.93736E-02 0.11234E-01 0.13484E-01 0.15613E-01 0.17478E-01 0.18756E-01 0.19131E-01 END_DATAGRID_3D END_BLOCK_DATAGRID_3D Plot Type: 3D Output format: XCrySDen thanks. On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero wrote: > Dear Dev, > > dev sharma wrote: > > hi 2 all, > > I am trying to plot the charge density with the XCrysden, but when i am > > opening's XSF(file--> open structure--> open XSF(xcryden structure > > file)) file , generated by my calculations, it is showing the structure > > of my system. And i am not getting the option tools--> DATA GRID as > > ready. Please help or advice ?? Thankful to all of you. What i did is > > listed below. > > Have you had a look inside your .xsf file? How does it look? Does it > actually contain the > DATAGRID block? Is it complete? Please supply more information! > > Regards, > > GS > > > > I run my input file with command > > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > > and inputs of density.in are > > &inputpp > > prefix = 'yvo' > > outdir = '/home/physics/work/yvo/temp/', > > filplot = 'yvocharge' > > plot_num= 0 > > / > > &plot > > nfile = 1 > > filepp(1) = 'yvocharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5, > > / > > > > with regards, > > Dev Sharma, > > University of Delhi, > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/c53a057b/attachment-0001.htm From shypirate at gmail.com Fri Sep 11 10:59:04 2009 From: shypirate at gmail.com (=?utf-8?B?c2h5cGlyYXRl?=) Date: Fri, 11 Sep 2009 16:59:04 +0800 Subject: [Pw_forum] =?utf-8?q?problem_with_charge_density_with_xcrysden?= References: , <4AAA0DF0.5090702@sissa.it>, Message-ID: <200909111659026090286@gmail.com> it definitely can not be used as input file for xcrysden. try to use the data included in "BLOCK_DATAGRID_3D" section 2009-09-11 shypirate ???? dev sharma ????? 2009-09-11 16:53:38 ???? PWSCF Forum ??? ??? Re: [Pw_forum] problem with charge density with xcrysden Dear sir, my.xsf file is below Program POST-PROC v.4.0.2 starts ... Today is 11Sep2009 at 12:54:29 Check: negative/imaginary core charge= -0.000009 0.000000 negative rho (up, down): 0.188E+00 0.000E+00 Calling punch_plot, plot_num = 0 Writing data to file yvocharge Reading data from file yvocharge CRYSTAL PRIMVEC 7.118300514 0.000000000 0.000000000 0.000000000 7.118300514 0.000000000 0.000000000 0.000000000 6.289300454 PRIMCOORD 24 1 Y 0.000000000 5.338725356 0.786162553 / / O 1.311190868 5.338725356 2.835216639 BEGIN_BLOCK_DATAGRID_3D 3D_PWSCF DATAGRID_3D_UNKNOWN 61 61 49 0.000000 0.000000 0.000000 7.118301 0.000000 0.000000 0.000000 7.118301 0.000000 0.000000 0.000000 6.289300 0.19131E-01 0.18756E-01 0.17478E-01 0.15613E-01 0.13484E-01 0.11234E-01 / / 0.93736E-02 0.11234E-01 0.13484E-01 0.15613E-01 0.17478E-01 0.18756E-01 0.19131E-01 END_DATAGRID_3D END_BLOCK_DATAGRID_3D Plot Type: 3D Output format: XCrySDen thanks. On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero wrote: Dear Dev, dev sharma wrote: > hi 2 all, > I am trying to plot the charge density with the XCrysden, but when i am > opening's XSF(file--> open structure--> open XSF(xcryden structure > file)) file , generated by my calculations, it is showing the structure > of my system. And i am not getting the option tools--> DATA GRID as > ready. Please help or advice ?? Thankful to all of you. What i did is > listed below. Have you had a look inside your .xsf file? How does it look? Does it actually contain the DATAGRID block? Is it complete? Please supply more information! Regards, GS > I run my input file with command > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > and inputs of density.in are > &inputpp > prefix = 'yvo' > outdir = '/home/physics/work/yvo/temp/', > filplot = 'yvocharge' > plot_num= 0 > / > &plot > nfile = 1 > filepp(1) = 'yvocharge' > weight(1) = 1.0 > iflag = 3 > output_format = 5, > / > > with regards, > Dev Sharma, > University of Delhi, > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/6ca7ece2/attachment.htm From prasenjit.jnc at gmail.com Fri Sep 11 11:02:59 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 11 Sep 2009 11:02:59 +0200 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: <200909111659026090286@gmail.com> References: <4AAA0DF0.5090702@sissa.it> <200909111659026090286@gmail.com> Message-ID: <627e0ffa0909110202l6ab17b9bo9234232802026d76@mail.gmail.com> You remove the following lines & try seeing it in xcrysden: Program POST-PROC v.4.0.2 starts ... Today is 11Sep2009 at 12:54:29 Check: negative/imaginary core charge= -0.000009 0.000000 negative rho (up, down): 0.188E+00 0.000E+00 Calling punch_plot, plot_num = 0 Writing data to file yvocharge Reading data from file yvocharge 2009/9/11 shypirate > it definitely can not be used as input file for xcrysden. > try to use the data included in "BLOCK_DATAGRID_3D" section > > > 2009-09-11 > ------------------------------ > shypirate > ------------------------------ > *????* dev sharma > *?????* 2009-09-11 16:53:38 > *????* PWSCF Forum > *???* > *???* Re: [Pw_forum] problem with charge density with xcrysden > Dear sir, my.xsf file is below > > Program POST-PROC v.4.0.2 starts ... > Today is 11Sep2009 at 12:54:29 > > Check: negative/imaginary core charge= -0.000009 0.000000 > > negative rho (up, down): 0.188E+00 0.000E+00 > > Calling punch_plot, plot_num = 0 > Writing data to file yvocharge > Reading data from file yvocharge > CRYSTAL > PRIMVEC > 7.118300514 0.000000000 0.000000000 > 0.000000000 7.118300514 0.000000000 > 0.000000000 0.000000000 6.289300454 > PRIMCOORD > 24 1 > Y 0.000000000 5.338725356 0.786162553 > / > / > O 1.311190868 5.338725356 2.835216639 > BEGIN_BLOCK_DATAGRID_3D > 3D_PWSCF > DATAGRID_3D_UNKNOWN > 61 61 49 > 0.000000 0.000000 0.000000 > 7.118301 0.000000 0.000000 > 0.000000 7.118301 0.000000 > 0.000000 0.000000 6.289300 > 0.19131E-01 0.18756E-01 0.17478E-01 0.15613E-01 0.13484E-01 > 0.11234E-01 > / > / > 0.93736E-02 0.11234E-01 0.13484E-01 0.15613E-01 0.17478E-01 > 0.18756E-01 > 0.19131E-01 > END_DATAGRID_3D > END_BLOCK_DATAGRID_3D > Plot Type: 3D Output format: XCrySDen > > thanks. > > On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero wrote: > >> Dear Dev, >> >> dev sharma wrote: >> > hi 2 all, >> > I am trying to plot the charge density with the XCrysden, but when i am >> > opening's XSF(file--> open structure--> open XSF(xcryden structure >> > file)) file , generated by my calculations, it is showing the structure >> > of my system. And i am not getting the option tools--> DATA GRID as >> > ready. Please help or advice ?? Thankful to all of you. What i did is >> > listed below. >> >> Have you had a look inside your .xsf file? How does it look? Does it >> actually contain the >> DATAGRID block? Is it complete? Please supply more information! >> >> Regards, >> >> GS >> >> >> > I run my input file with command >> > /home/physics/espresso-4.0.2/bin/pp.x density.xsf >> > and inputs of density.in are >> > &inputpp >> > prefix = 'yvo' >> > outdir = '/home/physics/work/yvo/temp/', >> > filplot = 'yvocharge' >> > plot_num= 0 >> > / >> > &plot >> > nfile = 1 >> > filepp(1) = 'yvocharge' >> > weight(1) = 1.0 >> > iflag = 3 >> > output_format = 5, >> > / >> > >> > with regards, >> > Dev Sharma, >> > University of Delhi, >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/1b541f08/attachment-0001.htm From prasenjit.jnc at gmail.com Fri Sep 11 11:13:29 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 11 Sep 2009 11:13:29 +0200 Subject: [Pw_forum] input file for isolated atom In-Reply-To: References: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> Message-ID: <627e0ffa0909110213k38e615abk7a759acd7ba60467@mail.gmail.com> For Ti atom, the electronic configuration is [*Ar*].*3d*2.*4s*2. So the magnetization should be 2.0 Bohr magneton due to the two electrons in the d-orbital, which is not what you are getting from your calculation. Also your smearing contribution is -0.00972779 Ry (about 0.1 eV), which I would say very high. If you would have find the correct magnetic ground state, then this should have been 0.0 Ry. As far as the bulk system is concerned, I'm not sure. It depends how Ti bulk behaves. You can search in the literature to find out what values of degauss other people have used. Mixing beta doesn't effect the energy of the system. It just helps you in convergence. Prasenjit. 2009/9/11 udayagiri sai babu > Dear prasenajit this is the part of my output for the posted input file. > (smearing contribution is there! though it is small ) is the degauss value > too high for isolated atom or it is high for bulk calculation also? because > i use around 0.01 Ry value for all my calculations. Does the mixing beta > value effect the energy of the system? > > one-electron contribution = -155.91791626 Ry > hartree contribution = 74.49216944 Ry > xc contribution = -14.37611953 Ry > ewald contribution = -20.42854186 Ry > smearing contrib. (-TS) = -0.00972779 Ry > > total magnetization = 3.24 Bohr mag/cell > absolute magnetization = 3.24 Bohr mag/cell > > convergence has been achieved in 34 iterations > > > On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh wrote: > >> Dear Udayagiri, >> >> First of all it's not clear whether you have any question other than >> whether your input file is correct. >> >> Now some comments about your input file: >> >> (a) while doing calculations for any zero dimensions you should always set >> nosym =.true. >> (b) Your value of degauss is too high.....you should use some value around >> 0.001 Ry. According to my experience, doing cal. for a single atom is >> tricky, specially when you are using a smearing. Even that doesn't confirm >> you will get the correct ground state for the atom. So what you should do is >> at the end of the calculation check the values of the total magnetization, >> absolute magnetization and the smearing contribution. The last term should >> be exactly zero. >> (c) You don't need to set tstress and tprnfor true. >> (c) mixing_beta= 0.7 too large.....I would put something smaller....0.3 >> (d) I hope you have checked the convergence of ecut rho & ecutwfc. >> >> Prasenjit. >> >> 2009/9/11 udayagiri sai babu >> >>> Hi everybody >>> I want to calculate the cohesive energy of Titanium for that i need to >>> calculate the energy of an isolated atom previously in the forum somebody >>> has suggested me to do spin polarisation calculation for the isolated atom. >>> I have written an input file accordingly some one can see and tell me if my >>> input script is true. I have read the forum archives on this topic but they >>> are not exactly answering my question. Can somebody please help me. >>> * >>> Input file for isolated atom * >>> >>> &control >>> calculation = 'scf', >>> restart_mode='from_scratch', >>> outdir='/home/sai/temp', >>> prefix='titanium' >>> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', >>> tstress = .TRUE., >>> tprnfor = .TRUE., >>> / >>> &system >>> ibrav=1 >>> celldm(1)=20, >>> nat=1, >>> ntyp=1 >>> ecutwfc=25, >>> ecutrho=250, >>> occupations='smearing', >>> smearing='mv', >>> degauss=0.010000 >>> nspin=2 >>> starting_magnetization(1)=0.2 >>> / >>> &electrons >>> conv_thr=1.D-8, >>> diagonalization='david', >>> mixing_mode='plain', >>> mixing_beta= 0.7, >>> / >>> ATOMIC_SPECIES >>> Ti 47.867 Ti.pbe-sp-van_ak.UPF >>> ATOMIC_POSITIONS (crystal) >>> Ti 0.00000000 0.00000000 0.00000000 >>> K_POINTS GAMMA >>> >>> -- >>> U.Saibabu >>> PhD student, >>> Deformation mechanisms modeling group, >>> Materials engineering department, >>> IISc Bangalore, >>> India. >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> PRASENJIT GHOSH, >> POST-DOC, >> ROOM NO: 265, MAIN BUILDING, >> CM SECTION, ICTP, >> STRADA COSTERIA 11, >> TRIESTE, 34104, >> ITALY >> PHONE: +39 040 2240 369 (O) >> +39 3807528672 (M) >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/4132494e/attachment.htm From sclauzer at sissa.it Fri Sep 11 11:14:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 11 Sep 2009 11:14:25 +0200 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: <627e0ffa0909110202l6ab17b9bo9234232802026d76@mail.gmail.com> References: <4AAA0DF0.5090702@sissa.it> <200909111659026090286@gmail.com> <627e0ffa0909110202l6ab17b9bo9234232802026d76@mail.gmail.com> Message-ID: <4AAA14F1.8060000@sissa.it> Prasenjit Ghosh wrote: > You remove the following lines & try seeing it in xcrysden: > > Program POST-PROC v.4.0.2 starts ... > Today is 11Sep2009 at 12:54:29 > > Check: negative/imaginary core charge= -0.000009 0.000000 > > negative rho (up, down): 0.188E+00 0.000E+00 > > Calling punch_plot, plot_num = 0 > Writing data to file yvocharge > Reading data from file yvocharge I think these lines are not the problem. In my version of Xcrysden (1.5.17) I could read successfully an XSF file including the pp.x information shown here above. I could also visualize the 3D data contained in a file produced with the same options of Dev, > > &plot > > nfile = 1 > > filepp(1) = 'yvocharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5, > > / so I think he has a problem with his installation of pw.x or xcrysden. GS > > 2009/9/11 shypirate > > > it definitely can not be used as input file for xcrysden. > try to use the data included in "BLOCK_DATAGRID_3D" section > > > 2009-09-11 > ------------------------------------------------------------------------ > shypirate > ------------------------------------------------------------------------ > *????* dev sharma > *?????* 2009-09-11 16:53:38 > *????* PWSCF Forum > *???* > *???* Re: [Pw_forum] problem with charge density with xcrysden > Dear sir, my.xsf file is below > > Program POST-PROC v.4.0.2 starts ... > Today is 11Sep2009 at 12:54:29 > > Check: negative/imaginary core charge= -0.000009 0.000000 > > negative rho (up, down): 0.188E+00 0.000E+00 > > Calling punch_plot, plot_num = 0 > Writing data to file yvocharge > Reading data from file yvocharge > CRYSTAL > PRIMVEC > 7.118300514 0.000000000 0.000000000 > 0.000000000 7.118300514 0.000000000 > 0.000000000 0.000000000 6.289300454 > PRIMCOORD > 24 1 > Y 0.000000000 5.338725356 0.786162553 > / > / > O 1.311190868 5.338725356 2.835216639 > BEGIN_BLOCK_DATAGRID_3D > 3D_PWSCF > DATAGRID_3D_UNKNOWN > 61 61 49 > 0.000000 0.000000 0.000000 > 7.118301 0.000000 0.000000 > 0.000000 7.118301 0.000000 > 0.000000 0.000000 6.289300 > 0.19131E-01 0.18756E-01 0.17478E-01 0.15613E-01 0.13484E-01 > 0.11234E-01 > / > / > 0.93736E-02 0.11234E-01 0.13484E-01 0.15613E-01 0.17478E-01 > 0.18756E-01 > 0.19131E-01 > END_DATAGRID_3D > END_BLOCK_DATAGRID_3D > Plot Type: 3D Output format: XCrySDen > > thanks. > > On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero > > wrote: > > Dear Dev, > > dev sharma wrote: > > hi 2 all, > > I am trying to plot the charge density with the XCrysden, > but when i am > > opening's XSF(file--> open structure--> open XSF(xcryden > structure > > file)) file , generated by my calculations, it is showing the > structure > > of my system. And i am not getting the option tools--> DATA > GRID as > > ready. Please help or advice ?? Thankful to all of you. What > i did is > > listed below. > > Have you had a look inside your .xsf file? How does it look? > Does it actually contain the > DATAGRID block? Is it complete? Please supply more information! > > Regards, > > GS > > > > I run my input file with command > > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > > and inputs of density.in > are > > &inputpp > > prefix = 'yvo' > > outdir = '/home/physics/work/yvo/temp/', > > filplot = 'yvocharge' > > plot_num= 0 > > / > > &plot > > nfile = 1 > > filepp(1) = 'yvocharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5, > > / > > > > with regards, > > Dev Sharma, > > University of Delhi, > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From udayagiri3 at gmail.com Fri Sep 11 11:17:57 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Fri, 11 Sep 2009 14:47:57 +0530 Subject: [Pw_forum] input file for isolated atom In-Reply-To: <627e0ffa0909110213k38e615abk7a759acd7ba60467@mail.gmail.com> References: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> <627e0ffa0909110213k38e615abk7a759acd7ba60467@mail.gmail.com> Message-ID: Dear prasenajit thank you for your valuable inputs On Fri, Sep 11, 2009 at 2:43 PM, Prasenjit Ghosh wrote: > For Ti atom, the electronic configuration is [*Ar*].*3d*2.*4s*2. So the > magnetization should be 2.0 Bohr magneton due to the two electrons in the > d-orbital, which is not what you are getting from your calculation. > > Also your smearing contribution is -0.00972779 Ry (about 0.1 eV), which I > would say very high. If you would have find the correct magnetic ground > state, then this should have been 0.0 Ry. > > As far as the bulk system is concerned, I'm not sure. It depends how Ti > bulk behaves. You can search in the literature to find out what values of > degauss other people have used. > > Mixing beta doesn't effect the energy of the system. It just helps you in > convergence. > > > Prasenjit. > > 2009/9/11 udayagiri sai babu > >> Dear prasenajit this is the part of my output for the posted input file. >> (smearing contribution is there! though it is small ) is the degauss value >> too high for isolated atom or it is high for bulk calculation also? because >> i use around 0.01 Ry value for all my calculations. Does the mixing beta >> value effect the energy of the system? >> >> one-electron contribution = -155.91791626 Ry >> hartree contribution = 74.49216944 Ry >> xc contribution = -14.37611953 Ry >> ewald contribution = -20.42854186 Ry >> smearing contrib. (-TS) = -0.00972779 Ry >> >> total magnetization = 3.24 Bohr mag/cell >> absolute magnetization = 3.24 Bohr mag/cell >> >> convergence has been achieved in 34 iterations >> >> >> On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh > > wrote: >> >>> Dear Udayagiri, >>> >>> First of all it's not clear whether you have any question other than >>> whether your input file is correct. >>> >>> Now some comments about your input file: >>> >>> (a) while doing calculations for any zero dimensions you should always >>> set nosym =.true. >>> (b) Your value of degauss is too high.....you should use some value >>> around 0.001 Ry. According to my experience, doing cal. for a single atom is >>> tricky, specially when you are using a smearing. Even that doesn't confirm >>> you will get the correct ground state for the atom. So what you should do is >>> at the end of the calculation check the values of the total magnetization, >>> absolute magnetization and the smearing contribution. The last term should >>> be exactly zero. >>> (c) You don't need to set tstress and tprnfor true. >>> (c) mixing_beta= 0.7 too large.....I would put something smaller....0.3 >>> (d) I hope you have checked the convergence of ecut rho & ecutwfc. >>> >>> Prasenjit. >>> >>> 2009/9/11 udayagiri sai babu >>> >>>> Hi everybody >>>> I want to calculate the cohesive energy of Titanium for that i need to >>>> calculate the energy of an isolated atom previously in the forum somebody >>>> has suggested me to do spin polarisation calculation for the isolated atom. >>>> I have written an input file accordingly some one can see and tell me if my >>>> input script is true. I have read the forum archives on this topic but they >>>> are not exactly answering my question. Can somebody please help me. >>>> * >>>> Input file for isolated atom * >>>> >>>> &control >>>> calculation = 'scf', >>>> restart_mode='from_scratch', >>>> outdir='/home/sai/temp', >>>> prefix='titanium' >>>> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', >>>> tstress = .TRUE., >>>> tprnfor = .TRUE., >>>> / >>>> &system >>>> ibrav=1 >>>> celldm(1)=20, >>>> nat=1, >>>> ntyp=1 >>>> ecutwfc=25, >>>> ecutrho=250, >>>> occupations='smearing', >>>> smearing='mv', >>>> degauss=0.010000 >>>> nspin=2 >>>> starting_magnetization(1)=0.2 >>>> / >>>> &electrons >>>> conv_thr=1.D-8, >>>> diagonalization='david', >>>> mixing_mode='plain', >>>> mixing_beta= 0.7, >>>> / >>>> ATOMIC_SPECIES >>>> Ti 47.867 Ti.pbe-sp-van_ak.UPF >>>> ATOMIC_POSITIONS (crystal) >>>> Ti 0.00000000 0.00000000 0.00000000 >>>> K_POINTS GAMMA >>>> >>>> -- >>>> U.Saibabu >>>> PhD student, >>>> Deformation mechanisms modeling group, >>>> Materials engineering department, >>>> IISc Bangalore, >>>> India. >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> PRASENJIT GHOSH, >>> POST-DOC, >>> ROOM NO: 265, MAIN BUILDING, >>> CM SECTION, ICTP, >>> STRADA COSTERIA 11, >>> TRIESTE, 34104, >>> ITALY >>> PHONE: +39 040 2240 369 (O) >>> +39 3807528672 (M) >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> U.Saibabu >> PhD student, >> Deformation mechanisms modeling group, >> Materials engineering department, >> IISc Bangalore, >> India. >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/4d9d0324/attachment-0001.htm From decboy9 at gmail.com Fri Sep 11 11:27:29 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 11 Sep 2009 14:57:29 +0530 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: <4AAA14F1.8060000@sissa.it> References: <4AAA0DF0.5090702@sissa.it> <200909111659026090286@gmail.com> <627e0ffa0909110202l6ab17b9bo9234232802026d76@mail.gmail.com> <4AAA14F1.8060000@sissa.it> Message-ID: Dear Sir, as suggested by Prasenjit Sir, when i removed the lies from Program POST-PROC v.4.0.2 starts ... Today is 11Sep2009 at 12:54:29 not upto Reading data from file yvocharge but upto BEGIN_BLOCK_DATAGRID_3D. and then open with XCrysden, the Data grid option is ok. and i can visualize iso surface. and one more doubt sir, the xcrysden terminal on import of .xsf file is showing the mssg . Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Is it ok ??? Thanks a lot 2 all of you. Dev sharma, On Fri, Sep 11, 2009 at 2:44 PM, Gabriele Sclauzero wrote: > > Prasenjit Ghosh wrote: > > You remove the following lines & try seeing it in xcrysden: > > > > Program POST-PROC v.4.0.2 starts ... > > Today is 11Sep2009 at 12:54:29 > > > > Check: negative/imaginary core charge= -0.000009 0.000000 > > > > negative rho (up, down): 0.188E+00 0.000E+00 > > > > Calling punch_plot, plot_num = 0 > > Writing data to file yvocharge > > Reading data from file yvocharge > > I think these lines are not the problem. In my version of Xcrysden (1.5.17) > I could read > successfully an XSF file including the pp.x information shown here above. > I could also visualize the 3D data contained in a file produced with the > same options of Dev, > > > &plot > > > nfile = 1 > > > filepp(1) = 'yvocharge' > > > weight(1) = 1.0 > > > iflag = 3 > > > output_format = 5, > > > / > > so I think he has a problem with his installation of pw.x or xcrysden. > > GS > > > > > > 2009/9/11 shypirate > > > > > it definitely can not be used as input file for xcrysden. > > try to use the data included in "BLOCK_DATAGRID_3D" section > > > > > > 2009-09-11 > > > ------------------------------------------------------------------------ > > shypirate > > > ------------------------------------------------------------------------ > > *????* dev sharma > > *?????* 2009-09-11 16:53:38 > > *????* PWSCF Forum > > *???* > > *???* Re: [Pw_forum] problem with charge density with xcrysden > > Dear sir, my.xsf file is below > > > > Program POST-PROC v.4.0.2 starts ... > > Today is 11Sep2009 at 12:54:29 > > > > Check: negative/imaginary core charge= -0.000009 0.000000 > > > > negative rho (up, down): 0.188E+00 0.000E+00 > > > > Calling punch_plot, plot_num = 0 > > Writing data to file yvocharge > > Reading data from file yvocharge > > CRYSTAL > > PRIMVEC > > 7.118300514 0.000000000 0.000000000 > > 0.000000000 7.118300514 0.000000000 > > 0.000000000 0.000000000 6.289300454 > > PRIMCOORD > > 24 1 > > Y 0.000000000 5.338725356 0.786162553 > > / > > / > > O 1.311190868 5.338725356 2.835216639 > > BEGIN_BLOCK_DATAGRID_3D > > 3D_PWSCF > > DATAGRID_3D_UNKNOWN > > 61 61 49 > > 0.000000 0.000000 0.000000 > > 7.118301 0.000000 0.000000 > > 0.000000 7.118301 0.000000 > > 0.000000 0.000000 6.289300 > > 0.19131E-01 0.18756E-01 0.17478E-01 0.15613E-01 0.13484E-01 > > 0.11234E-01 > > / > > / > > 0.93736E-02 0.11234E-01 0.13484E-01 0.15613E-01 0.17478E-01 > > 0.18756E-01 > > 0.19131E-01 > > END_DATAGRID_3D > > END_BLOCK_DATAGRID_3D > > Plot Type: 3D Output format: XCrySDen > > > > thanks. > > > > On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero > > > wrote: > > > > Dear Dev, > > > > dev sharma wrote: > > > hi 2 all, > > > I am trying to plot the charge density with the XCrysden, > > but when i am > > > opening's XSF(file--> open structure--> open XSF(xcryden > > structure > > > file)) file , generated by my calculations, it is showing the > > structure > > > of my system. And i am not getting the option tools--> DATA > > GRID as > > > ready. Please help or advice ?? Thankful to all of you. What > > i did is > > > listed below. > > > > Have you had a look inside your .xsf file? How does it look? > > Does it actually contain the > > DATAGRID block? Is it complete? Please supply more information! > > > > Regards, > > > > GS > > > > > > > I run my input file with command > > > /home/physics/espresso-4.0.2/bin/pp.x > density.xsf > > > and inputs of density.in > > are > > > &inputpp > > > prefix = 'yvo' > > > outdir = '/home/physics/work/yvo/temp/', > > > filplot = 'yvocharge' > > > plot_num= 0 > > > / > > > &plot > > > nfile = 1 > > > filepp(1) = 'yvocharge' > > > weight(1) = 1.0 > > > iflag = 3 > > > output_format = 5, > > > / > > > > > > with regards, > > > Dev Sharma, > > > University of Delhi, > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it > > | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > PRASENJIT GHOSH, > > POST-DOC, > > ROOM NO: 265, MAIN BUILDING, > > CM SECTION, ICTP, > > STRADA COSTERIA 11, > > TRIESTE, 34104, > > ITALY > > PHONE: +39 040 2240 369 (O) > > +39 3807528672 (M) > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/dc362375/attachment.htm From sclauzer at sissa.it Fri Sep 11 11:34:22 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 11 Sep 2009 11:34:22 +0200 Subject: [Pw_forum] input file for isolated atom In-Reply-To: References: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> <627e0ffa0909110213k38e615abk7a759acd7ba60467@mail.gmail.com> Message-ID: <4AAA199E.5000906@sissa.it> udayagiri sai babu wrote: > Dear prasenajit > thank you for your valuable inputs > > On Fri, Sep 11, 2009 at 2:43 PM, Prasenjit Ghosh > > wrote: > > For Ti atom, the electronic configuration is [*Ar*].*3d*^2 .*4s*^2 > . So the magnetization should be 2.0 Bohr magneton due to the two > electrons in the d-orbital, which is not what you are getting from > your calculation. > > Also your smearing contribution is -0.00972779 Ry (about 0.1 eV), > which I would say very high. If you would have find the correct > magnetic ground state, then this should have been 0.0 Ry. > > As far as the bulk system is concerned, I'm not sure. It depends how > Ti bulk behaves. You can search in the literature to find out what > values of degauss other people have used. If you want to obtain the correct ground state and magnetization for the isolated Ti atom, I suggest you to use either occupations=fixed and tot_magnetization=2 (but this calculation will not converge, probably), or better to use occupations='from_input' and use the OCCUPATIONS card to specify the correct electronic configuration. Another solution could be to use smearing and the constrained-magnetization method, though I never used it for isolated atoms. HTH GS > > Mixing beta doesn't effect the energy of the system. It just helps > you in convergence. > > > Prasenjit. > > 2009/9/11 udayagiri sai babu > > > Dear prasenajit this is the part of my output for the posted > input file. (smearing contribution is there! though it is small > ) is the degauss value too high for isolated atom or it is high > for bulk calculation also? because i use around 0.01 Ry value > for all my calculations. Does the mixing beta value effect the > energy of the system? > > one-electron contribution = -155.91791626 Ry > hartree contribution = 74.49216944 Ry > xc contribution = -14.37611953 Ry > ewald contribution = -20.42854186 Ry > smearing contrib. (-TS) = -0.00972779 Ry > > total magnetization = 3.24 Bohr mag/cell > absolute magnetization = 3.24 Bohr mag/cell > > convergence has been achieved in 34 iterations > > > On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh > > wrote: > > Dear Udayagiri, > > First of all it's not clear whether you have any question > other than whether your input file is correct. > > Now some comments about your input file: > > (a) while doing calculations for any zero dimensions you > should always set nosym =.true. > (b) Your value of degauss is too high.....you should use > some value around 0.001 Ry. According to my experience, > doing cal. for a single atom is tricky, specially when you > are using a smearing. Even that doesn't confirm you will get > the correct ground state for the atom. So what you should do > is at the end of the calculation check the values of the > total magnetization, absolute magnetization and the smearing > contribution. The last term should be exactly zero. > (c) You don't need to set tstress and tprnfor true. > (c) mixing_beta= 0.7 too large.....I would put something > smaller....0.3 > (d) I hope you have checked the convergence of ecut rho & > ecutwfc. > > Prasenjit. > > 2009/9/11 udayagiri sai babu > > > Hi everybody > I want to calculate the cohesive energy of Titanium for > that i need to calculate the energy of an isolated atom > previously in the forum somebody has suggested me to do > spin polarisation calculation for the isolated atom. I > have written an input file accordingly some one can see > and tell me if my input script is true. I have read the > forum archives on this topic but they are not exactly > answering my question. Can somebody please help me. > * > Input file for isolated atom * > > &control > calculation = 'scf', > restart_mode='from_scratch', > outdir='/home/sai/temp', > prefix='titanium' > pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', > tstress = .TRUE., > tprnfor = .TRUE., > / > &system > ibrav=1 > celldm(1)=20, > nat=1, > ntyp=1 > ecutwfc=25, > ecutrho=250, > occupations='smearing', > smearing='mv', > degauss=0.010000 > nspin=2 > starting_magnetization(1)=0.2 > / > &electrons > conv_thr=1.D-8, > diagonalization='david', > mixing_mode='plain', > mixing_beta= 0.7, > / > ATOMIC_SPECIES > Ti 47.867 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Ti 0.00000000 0.00000000 0.00000000 > K_POINTS GAMMA > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From degironc at sissa.it Fri Sep 11 11:57:37 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 11 Sep 2009 11:57:37 +0200 Subject: [Pw_forum] problem with charge density with xcrysden In-Reply-To: References: Message-ID: <4AAA1F11.3000805@sissa.it> dear Dev Sharma the xsf file with the DATAGRID field IS NOT the output of pp.x! Rather its name needs to be specified in variable fileout in the &plot namelist of your density.in input Please read the documentation of pp.x code for the meaning of the other variables. HTH Stefano de Gironcoli - SISSA and DEMOCRITOS dev sharma wrote: > hi 2 all, > I am trying to plot the charge density with the XCrysden, but when i > am opening's XSF(file--> open structure--> open XSF(xcryden structure > file)) file , generated by my calculations, it is showing the > structure of my system. And i am not getting the option tools--> > DATA GRID as ready. Please help or advice ?? Thankful to all of you. > What i did is listed below. > I run my input file with command > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > and inputs of density.in are > &inputpp > prefix = 'yvo' > outdir = '/home/physics/work/yvo/temp/', > filplot = 'yvocharge' > plot_num= 0 > / > &plot > nfile = 1 > filepp(1) = 'yvocharge' > weight(1) = 1.0 > iflag = 3 > output_format = 5, > / > > with regards, > Dev Sharma, > University of Delhi, > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Fri Sep 11 13:42:19 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 11 Sep 2009 13:42:19 +0200 Subject: [Pw_forum] [Fwd: Re: problem with charge density with xcrysden] Message-ID: <4AAA379B.4070804@sissa.it> Forwarding e-mail from Emine. So I guess it may be a compatibility issue. GS -------- Original Message -------- Subject: Re: [Pw_forum] problem with charge density with xcrysden Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT) From: e kb To: sclauzer at sissa.it The old version of xcrysden that i had didnt work with this line : > DATAGRID_3D_UNKNOWN but with this one: > BEGIN_DATAGRID_3D_UNKNOWN I am not up to date on this but you can check it. emine kucukbenli, SISSA, Italy -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Fri Sep 11 13:44:13 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 Sep 2009 13:44:13 +0200 Subject: [Pw_forum] input file for isolated atom In-Reply-To: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> References: <627e0ffa0909110136u6e7757degdf16043a57a769de@mail.gmail.com> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649@democritos.it> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote: > (a) while doing calculations for any zero dimensions > you should always set nosym =.true. for Gamma-point calculations it shouldn't make any difference P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sh.shapt at gmail.com Fri Sep 11 13:45:43 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Fri, 11 Sep 2009 12:45:43 +0100 Subject: [Pw_forum] K Points and Band structures Message-ID: Hi QEs users, Can anybody please help me in understanding what are the k points ?? I have read books a lot but its difficult to understand. And also how do we choose k points while performing a band structure calculation in quantum espresso when we are having 330 atoms. Thanks S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment.htm From paulatto at sissa.it Fri Sep 11 13:58:19 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 11 Sep 2009 13:58:19 +0200 Subject: [Pw_forum] K Points and Band structures In-Reply-To: References: Message-ID: In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma ha scritto: > Can anybody please help me in understanding what are the k points ?? I > have read books a lot but its difficult to understand. They are eigenvalues of the translation operator, T(R) where R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3 integer numbers. The eigenvectors are, of course, the Bloch wavefunctions. Because the hamiltonian is periodic it commutes with the translation operator, you can diagonalize both the hamiltonian and the translation operator at the same time. As a consequence each Bloch wavefunction has a well-defined energy (hamiltonian's eigenvalue) and k-point (translation eigenvalue). Using both eigenvalues you can classify the states without ambiguity, except where the bands cross. > And also how do we choose k points while performing a band structure > calculation in quantum espresso when we are having 330 atoms. It does not depend on the number of atoms. You have to test the convergence at fixed smearing. E.g. you choose a smearing that's small enough for you, than you increase the number of k-points until total energy converges. You may then try again for a smaller/larger smearing and see if the results are consistent. I would advise starting with a smaller system, it would take ages to do it on 330 atoms. Keep in mind that the number of k-points needed for an accurate sampling is directly proportional to the size of the Brillouin zone, hence inversely proportional to the size of the cell. E.g. if you estimate that 6x6x6 k-points converge a certain calculation than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly the same level. Best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From degironc at sissa.it Fri Sep 11 13:59:05 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 11 Sep 2009 13:59:05 +0200 Subject: [Pw_forum] K Points and Band structures In-Reply-To: References: Message-ID: <4AAA3B89.9020002@sissa.it> Shaptrishi Sharma wrote: > Hi QEs users, > > Can anybody please help me in understanding what are the k points ?? I > have read books a lot but its difficult to understand. Please ask to any solid state physicist nearby. > And also how do we choose k points while performing a band structure > calculation in quantum espresso when we are having 330 atoms. If you still have QE specific doubts after you have understood Bloch theorem, Real and Reciprocal Space lattices, Brilloun Zone and the like please formulate them again, trying to be specific. > Thanks > S Please provide your affilaition. Best regards, Stefano de Gironcoli - SISSA and DEMOCRITOS > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sh.shapt at gmail.com Fri Sep 11 14:04:08 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Fri, 11 Sep 2009 13:04:08 +0100 Subject: [Pw_forum] Problem in spin polarisation Message-ID: Hi QE users, In one of my previous mail, I have asked about the spin polarisation in a sytem having odd number of electrons , (I have 21 hydrogen atoms in my system ). As suggested I used nelup =11 and neldw = 10, however, it is showing me the same error, as nelp out of range. so what shall I do now?? Thanks SS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/3cbc0c0c/attachment.htm From degironc at sissa.it Fri Sep 11 14:05:20 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 11 Sep 2009 14:05:20 +0200 Subject: [Pw_forum] Problem in spin polarisation In-Reply-To: References: Message-ID: <4AAA3D00.6020106@sissa.it> what is your value for nbnd ? stefano Shaptrishi Sharma wrote: > Hi QE users, > > In one of my previous mail, I have asked about the spin polarisation > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > in my system ). > > As suggested I used nelup =11 and neldw = 10, however, it is showing > me the same error, as > > nelp out of range. > so what shall I do now?? > > Thanks > > SS > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ttduyle at gmail.com Fri Sep 11 14:16:52 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 11 Sep 2009 08:16:52 -0400 Subject: [Pw_forum] Problem in spin polarisation In-Reply-To: <4AAA3D00.6020106@sissa.it> References: <4AAA3D00.6020106@sissa.it> Message-ID: <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7@mail.gmail.com> Add nelec to input Please just reply instead of creating a new email starting with "In one of my previous mail" so that all your emails and communications are ordered in the same thread. :-) On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli wrote: > what is your value for nbnd ? > stefano > > Shaptrishi Sharma wrote: > > Hi QE users, > > > > In one of my previous mail, I have asked about the spin polarisation > > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > > in my system ). > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > me the same error, as > > > > nelp out of range. > > so what shall I do now?? > > > > Thanks > > > > SS > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0d71a230/attachment.htm From degironc at sissa.it Fri Sep 11 14:24:18 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 11 Sep 2009 14:24:18 +0200 Subject: [Pw_forum] Problem in spin polarisation In-Reply-To: References: Message-ID: <4AAA4172.7020306@sissa.it> I think that in this case you need to explicitly specify also the value for nelec because a test that 0<=nelup< =nelec is performed before the default for nelec is calculated. It should be fixed but it is not so straightforward as the default value is presently defined much later. stefano Shaptrishi Sharma wrote: > Hi QE users, > > In one of my previous mail, I have asked about the spin polarisation > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > in my system ). > > As suggested I used nelup =11 and neldw = 10, however, it is showing > me the same error, as > > nelp out of range. > so what shall I do now?? > > Thanks > > SS > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Fri Sep 11 14:35:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 Sep 2009 14:35:30 +0200 Subject: [Pw_forum] Problem in spin polarisation In-Reply-To: <4AAA4172.7020306@sissa.it> References: <4AAA4172.7020306@sissa.it> Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719@democritos.it> On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote: > It should be fixed or even better, removed, since there are alternative and simpler methods to specify occupancies P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wangqj1 at 126.com Fri Sep 11 14:29:34 2009 From: wangqj1 at 126.com (wangqj1) Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST) Subject: [Pw_forum] The low usage of CUPs Message-ID: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> Dear pwscf users I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as like: Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm-simple-gree 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0 The ifort ,MKL,and mpi I used is : INTFC=/opt/intel/Compiler/11.0/081 INTMKL=/opt/intel/mkl/10.1.1.019 /opt/mpich2/bin/mpd My machine model is as following : processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 23 model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz stepping : 10 cpu MHz : 2327.489 cache size : 6144 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est tm2 ssse3 cx 16 xtpr dca sse4_1 lahf_lm bogomips : 4654.97 ............... The pwscf version is espresso-4.0.3 . So , I want to know why the usage is so slow ? How can I solve this problem ? Anybody who meet the same problem ? Your kind help will be appreciated ! Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/e349a164/attachment-0001.htm From paulatto at sissa.it Fri Sep 11 15:17:31 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 11 Sep 2009 15:17:31 +0200 Subject: [Pw_forum] The low usage of CUPs In-Reply-To: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> References: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> Message-ID: In data 11 settembre 2009 alle ore 14:29:34, wangqj1 ha scritto: > So , I want to know why the usage is so slow ? Dear Q.J. it is the same issue you were asking the last time. As you have not provided any further detail (network connection speed, details on the job and on how you're running it) my answer is the same as the last time. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From Giovanni.Cantele at na.infn.it Fri Sep 11 15:18:11 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Fri, 11 Sep 2009 15:18:11 +0200 Subject: [Pw_forum] The low usage of CUPs In-Reply-To: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> References: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> Message-ID: <4AAA4E13.9060205@na.infn.it> wangqj1 wrote: > Dear pwscf users > I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as like: > Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie > Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st > Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers > Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd > 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald > 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X > 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd > 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd > 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm-simple-gree > 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init > 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd > 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0 > 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0 > > The ifort ,MKL,and mpi I used is : > INTFC=/opt/intel/Compiler/11.0/081 > INTMKL=/opt/intel/mkl/10.1.1.019 > /opt/mpich2/bin/mpd > My machine model is as following : > processor : 0 > vendor_id : GenuineIntel > cpu family : 6 > model : 23 > model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz > stepping : 10 > cpu MHz : 2327.489 > cache size : 6144 KB > physical id : 0 > siblings : 4 > core id : 0 > cpu cores : 4 > apicid : 0 > initial apicid : 0 > fpu : yes > fpu_exception : yes > cpuid level : 13 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov > pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx > lm constant > _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est > tm2 ssse3 cx > 16 xtpr dca sse4_1 lahf_lm > bogomips : 4654.97 > ............... > The pwscf version is espresso-4.0.3 . > So , I want to know why the usage is so slow ? > How can I solve this problem ? Anybody who meet the same problem ? > Your kind help will be appreciated ! > Best regards > Q.J.Wang > XiangTan University > Some possibilities are: 1) http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F 2) you are running a job over a very slow network (interconnecting the different nodes) 3) you are trying to force a node to write on a disk which is local to other nodes and connected to it through a very-low performance network 4) your job requests much more resources than you have, e.g. RAM memory (causing a node to swap). From your data it seems you are using all the 8Gb mem, actually the same test should be done on every node. How are distributed the 16 CPU? Over more than one node? Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From sh.shapt at gmail.com Fri Sep 11 15:23:39 2009 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Fri, 11 Sep 2009 14:23:39 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: References: Message-ID: Hi Stefano, My nband value is 122 as my total number of atoms are 66 .of which 21 Hydrogen.And if I remove the option nelup and neldw, I got it as "too many bands are not converged" thus I increased my vaccum, however it still remains the same. Thanks S On 9/11/09, pw_forum-request at pwscf.org wrote: > > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: problem with charge density with xcrysden > (Stefano de Gironcoli) > 2. [Fwd: Re: problem with charge density with xcrysden] > (Gabriele Sclauzero) > 3. Re: input file for isolated atom (Paolo Giannozzi) > 4. K Points and Band structures (Shaptrishi Sharma) > 5. Re: K Points and Band structures (Lorenzo Paulatto) > 6. Re: K Points and Band structures (Stefano de Gironcoli) > 7. Problem in spin polarisation (Shaptrishi Sharma) > 8. Re: Problem in spin polarisation (Stefano de Gironcoli) > 9. Re: Problem in spin polarisation (Duy Le) > 10. Re: Problem in spin polarisation (Stefano de Gironcoli) > 11. Re: Problem in spin polarisation (Paolo Giannozzi) > 12. The low usage of CUPs (wangqj1) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Sep 2009 11:57:37 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] problem with charge density with xcrysden > To: PWSCF Forum > Message-ID: <4AAA1F11.3000805 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > dear Dev Sharma > the xsf file with the DATAGRID field IS NOT the output of pp.x! > Rather its name needs to be specified in variable fileout in the &plot > namelist of your density.in input > Please read the documentation of pp.x code for the meaning of the > other variables. > HTH > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > dev sharma wrote: > > hi 2 all, > > I am trying to plot the charge density with the XCrysden, but when i > > am opening's XSF(file--> open structure--> open XSF(xcryden structure > > file)) file , generated by my calculations, it is showing the > > structure of my system. And i am not getting the option tools--> > > DATA GRID as ready. Please help or advice ?? Thankful to all of you. > > What i did is listed below. > > I run my input file with command > > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > > and inputs of density.in are > > &inputpp > > prefix = 'yvo' > > outdir = '/home/physics/work/yvo/temp/', > > filplot = 'yvocharge' > > plot_num= 0 > > / > > &plot > > nfile = 1 > > filepp(1) = 'yvocharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5, > > / > > > > with regards, > > Dev Sharma, > > University of Delhi, > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Sep 2009 13:42:19 +0200 > From: Gabriele Sclauzero > Subject: [Pw_forum] [Fwd: Re: problem with charge density with > xcrysden] > To: PWscf Mailing List > Message-ID: <4AAA379B.4070804 at sissa.it> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > Forwarding e-mail from Emine. So I guess it may be a compatibility issue. > > GS > > -------- Original Message -------- > Subject: Re: [Pw_forum] problem with charge density with xcrysden > Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT) > From: e kb > To: sclauzer at sissa.it > > > > > The old version of xcrysden that i had didnt work with this line : > > DATAGRID_3D_UNKNOWN > but with this one: > > BEGIN_DATAGRID_3D_UNKNOWN > > I am not up to date on this but you can check it. > emine kucukbenli, SISSA, Italy > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 3 > Date: Fri, 11 Sep 2009 13:44:13 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] input file for isolated atom > To: PWSCF Forum > Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote: > > > (a) while doing calculations for any zero dimensions > > you should always set nosym =.true. > > for Gamma-point calculations it shouldn't make any > difference > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 11 Sep 2009 12:45:43 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] K Points and Band structures > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi QEs users, > > Can anybody please help me in understanding what are the k points ?? I have > read books a lot but its difficult to understand. > > And also how do we choose k points while performing a band structure > calculation in quantum espresso when we are having 330 atoms. > > Thanks > > S > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Fri, 11 Sep 2009 13:58:19 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] K Points and Band structures > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma > ha scritto: > > > Can anybody please help me in understanding what are the k points ?? I > > have read books a lot but its difficult to understand. > > They are eigenvalues of the translation operator, T(R) where > R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3 > integer numbers. The eigenvectors are, of course, the Bloch wavefunctions. > > Because the hamiltonian is periodic it commutes with the translation > operator, you can diagonalize both the hamiltonian and the translation > operator at the same time. As a consequence each Bloch wavefunction has a > well-defined energy (hamiltonian's eigenvalue) and k-point (translation > eigenvalue). Using both eigenvalues you can classify the states without > ambiguity, except where the bands cross. > > > And also how do we choose k points while performing a band structure > > calculation in quantum espresso when we are having 330 atoms. > > It does not depend on the number of atoms. > > You have to test the convergence at fixed smearing. E.g. you choose a > smearing that's small enough for you, than you increase the number of > k-points until total energy converges. You may then try again for a > smaller/larger smearing and see if the results are consistent. > > I would advise starting with a smaller system, it would take ages to do it > on 330 atoms. Keep in mind that the number of k-points needed for an > accurate sampling is directly proportional to the size of the Brillouin > zone, hence inversely proportional to the size of the cell. > > E.g. if you estimate that 6x6x6 k-points converge a certain calculation > than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly the same > level. > > Best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Fri, 11 Sep 2009 13:59:05 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] K Points and Band structures > To: PWSCF Forum > Message-ID: <4AAA3B89.9020002 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Shaptrishi Sharma wrote: > > Hi QEs users, > > > > Can anybody please help me in understanding what are the k points ?? I > > have read books a lot but its difficult to understand. > Please ask to any solid state physicist nearby. > > > And also how do we choose k points while performing a band structure > > calculation in quantum espresso when we are having 330 atoms. > If you still have QE specific doubts after you have understood Bloch > theorem, Real and Reciprocal Space lattices, Brilloun Zone and the like > please formulate them again, trying to be specific. > > Thanks > > S > Please provide your affilaition. > > Best regards, > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 7 > Date: Fri, 11 Sep 2009 13:04:08 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] Problem in spin polarisation > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi QE users, > > In one of my previous mail, I have asked about the spin polarisation in a > sytem having odd number of electrons , (I have 21 hydrogen atoms in my > system ). > > As suggested I used nelup =11 and neldw = 10, however, it is showing me the > same error, as > > nelp out of range. > so what shall I do now?? > > Thanks > > SS > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090911/3cbc0c0c/attachment-0001.htm > > ------------------------------ > > Message: 8 > Date: Fri, 11 Sep 2009 14:05:20 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <4AAA3D00.6020106 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > what is your value for nbnd ? > stefano > > Shaptrishi Sharma wrote: > > Hi QE users, > > > > In one of my previous mail, I have asked about the spin polarisation > > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > > in my system ). > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > me the same error, as > > > > nelp out of range. > > so what shall I do now?? > > > > Thanks > > > > SS > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 9 > Date: Fri, 11 Sep 2009 08:16:52 -0400 > From: Duy Le > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: > <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Add nelec to input > Please just reply instead of creating a new email starting with "In one of > my previous mail" so that all your emails and communications are ordered in > the same thread. > > :-) > > On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli >wrote: > > > what is your value for nbnd ? > > stefano > > > > Shaptrishi Sharma wrote: > > > Hi QE users, > > > > > > In one of my previous mail, I have asked about the spin polarisation > > > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > > > in my system ). > > > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > > me the same error, as > > > > > > nelp out of range. > > > so what shall I do now?? > > > > > > Thanks > > > > > > SS > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0d71a230/attachment-0001.htm > > ------------------------------ > > Message: 10 > Date: Fri, 11 Sep 2009 14:24:18 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <4AAA4172.7020306 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I think that in this case you need to explicitly specify also the value > for nelec because a test that 0<=nelup< =nelec > is performed before the default for nelec is calculated. > It should be fixed but it is not so straightforward as the default value > is presently defined much later. > stefano > > Shaptrishi Sharma wrote: > > Hi QE users, > > > > In one of my previous mail, I have asked about the spin polarisation > > in a sytem having odd number of electrons , (I have 21 hydrogen atoms > > in my system ). > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > me the same error, as > > > > nelp out of range. > > so what shall I do now?? > > > > Thanks > > > > SS > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 11 > Date: Fri, 11 Sep 2009 14:35:30 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote: > > > It should be fixed > > or even better, removed, since there are alternative > and simpler methods to specify occupancies > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 12 > Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST) > From: wangqj1 > Subject: [Pw_forum] The low usage of CUPs > To: pw_forum > Message-ID: > <29861561.516411252672174463.JavaMail.coremail at bj126app106.126.com > > > Content-Type: text/plain; charset="gbk" > > Dear pwscf users > I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as > like: > > Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie > Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, > 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st > Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, > 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st > > Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, > 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st > > Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, > 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > > Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > > Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers > Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd > 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald > 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X > 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd > 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd > 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 > gdm-simple-gree > 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init > 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd > 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0 > 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0 > > The ifort ,MKL,and mpi I used is : > INTFC=/opt/intel/Compiler/11.0/081 > INTMKL=/opt/intel/mkl/10.1.1.019 > /opt/mpich2/bin/mpd > My machine model is as following : > processor : 0 > vendor_id : GenuineIntel > cpu family : 6 > model : 23 > model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz > stepping : 10 > cpu MHz : 2327.489 > cache size : 6144 KB > physical id : 0 > siblings : 4 > core id : 0 > cpu cores : 4 > apicid : 0 > initial apicid : 0 > fpu : yes > fpu_exception : yes > cpuid level : 13 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca > cmov > pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm > constant > _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est tm2 > ssse3 cx > 16 xtpr dca sse4_1 lahf_lm > bogomips : 4654.97 > ............... > The pwscf version is espresso-4.0.3 . > > So , I want to know why the usage is so slow ? > How can I solve this problem ? Anybody who meet the same problem ? > Your kind help will be appreciated ! > Best regards > Q.J.Wang > XiangTan University > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20090911/e349a164/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 47 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/7192d67a/attachment-0001.htm From paulatto at sissa.it Fri Sep 11 15:30:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 11 Sep 2009 15:30:08 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: References: Message-ID: In data 11 settembre 2009 alle ore 15:23:39, Shaptrishi Sharma ha scritto: > My nband value is 122 as my total number of atoms are 66 .of which 21 > Hydrogen.And if I remove the option nelup and neldw, I got it as "too > many bands are not converged" thus I increased my vaccum, however it > still > remains the same. Dear Shaptrishi, from the file Doc/INPUT_PW.txt Variable: nelec Type: REAL Default: the same as ionic charge (neutral cell) Description: number of electron in the unit cell (may be noninteger if you wish) as you see, nelec is the total number of electrons, not only the ones from hydrogen. Accordingly, a few lines later you should have found: Variables: nelup, neldw Type: REAL Description: number of spin-up and spin-down electrons, respectively Note that this fixes the final value of the magnetization. The sum must yield nelec that must also be specified explicitly in this case. Not valid for spin-unpolarized or noncollinear calculations, only for LSDA. Obsolescent: use multiplicity or tot_magnetization instead. it says quite clearly that nelec=nelup+neldw, again nelec is the total number of electrons. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From degironc at sissa.it Fri Sep 11 15:50:41 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 11 Sep 2009 15:50:41 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: References: Message-ID: <4AAA55B1.4070501@sissa.it> Dear Shaptrishi Sharma, I'm a bit confused... How many electrons your system has ? not 21 for sure since you have 66 atoms... so why are you focusing on the 21 Hydrogen atoms ? If you forget about spin polarization and perform a simple non-magnetic calculation...does it converge? try to face one difficulty at a time... Have you checked that your structure is reasonable ? if some of your atoms end up to be unrealistically close to each other the diagonalization routine gets crazy but the calculation would be useless anyway. check your structure by xcrysden. stefano Shaptrishi Sharma wrote: > Hi Stefano, > > My nband value is 122 as my total number of atoms are 66 .of which 21 > Hydrogen.And if I remove the option nelup and neldw, I got it as "too > many bands are not converged" thus I increased my vaccum, however it > still remains the same. > > Thanks > S From ttduyle at gmail.com Fri Sep 11 16:38:11 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 11 Sep 2009 10:38:11 -0400 Subject: [Pw_forum] The low usage of CUPs In-Reply-To: <4AAA4E13.9060205@na.infn.it> References: <29861561.516411252672174463.JavaMail.coremail@bj126app106.126.com> <4AAA4E13.9060205@na.infn.it> Message-ID: <8974d3b20909110738r41b126d0s22132002424b7fbe@mail.gmail.com> It seems that you provided wrong information: 1. You shown only 8 CPUs. Where are the other 8 as you were talking about 16 CPUs job. 2. There is only one task actually running ( PID 4404, run as root) 3. There's absolutely no other thing running in this node. My guess is that you took those information from wrong node, probably from head node. :) 2009/9/11 Giovanni Cantele > wangqj1 wrote: > >> Dear pwscf users >> I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as like: >> Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie >> Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st >> Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers >> Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd >> 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald >> 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X >> 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd >> 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd >> 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm-simple-gree >> 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init >> 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd >> 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0 >> 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0 >> >> The ifort ,MKL,and mpi I used is : >> INTFC=/opt/intel/Compiler/11.0/081 >> INTMKL=/opt/intel/mkl/10.1.1.019 >> /opt/mpich2/bin/mpd >> My machine model is as following : >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 6 >> model : 23 >> model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz >> stepping : 10 >> cpu MHz : 2327.489 >> cache size : 6144 KB >> physical id : 0 >> siblings : 4 >> core id : 0 >> cpu cores : 4 >> apicid : 0 >> initial apicid : 0 >> fpu : yes >> fpu_exception : yes >> cpuid level : 13 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov >> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm >> constant >> _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est tm2 >> ssse3 cx >> 16 xtpr dca sse4_1 lahf_lm >> bogomips : 4654.97 >> ............... >> The pwscf version is espresso-4.0.3 . >> So , I want to know why the usage is so slow ? >> How can I solve this problem ? Anybody who meet the same problem ? >> Your kind help will be appreciated ! >> Best regards >> Q.J.Wang >> XiangTan University >> >> Some possibilities are: > > 1) > http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F > 2) you are running a job over a very slow network (interconnecting the > different nodes) > 3) you are trying to force a node to write on a disk which is local to > other nodes and connected to it > through a very-low performance network > 4) your job requests much more resources than you have, e.g. RAM memory > (causing a node to swap). From > your data it seems you are using all the 8Gb mem, actually the same test > should be done on every node. > > > How are distributed the 16 CPU? Over more than one node? > > Giovanni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > Skype contact: giocan74 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/da0c9790/attachment.htm From nkxirainbow at gmail.com Fri Sep 11 18:01:30 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 11 Sep 2009 16:01:30 +0000 Subject: [Pw_forum] =?utf-8?q?How_to_control_number_of_slabs_in_pwcond_cal?= =?utf-8?b?Y3VsYXRpb27vvJ8=?= Message-ID: <21fbc4790909110901j480d415bx87a8eaed51f4cb15@mail.gmail.com> Dear all: I find the following content at "/espresso-4.0.4/examples/example12/results/al.cond.out" file. *" nrz = 21* *.........* * k slab z(k) z(k+1) crossing(iorb=1,norb)* * 1 0.0000 0.0673 0.0673 111100000000* *.........* * 20 1.2793 1.3467 0.0673 000001111111* * 21 1.3467 1.4140 0.0673 000000001111 "* I want to know, at *.cond.in input file, how to control the number of slabs along z direction in left, right lead and scattering region, respectively. By the way, what is the meaning of "crossing(iorb=1,norb)"? Thanks in advance ?? ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/d976d60f/attachment.htm From manoj at phys.ufl.edu Fri Sep 11 20:23:18 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 11 Sep 2009 14:23:18 -0400 (EDT) Subject: [Pw_forum] =?utf-8?q?How_to_control_number_of_slabs_in_pwcond_cal?= =?utf-8?b?Y3VsYXRpb27vvJ8=?= In-Reply-To: <21fbc4790909110901j480d415bx87a8eaed51f4cb15@mail.gmail.com> Message-ID: Dear Hui Wang, I dont think there is a straight forward way of doing this, at least not that I know of. (Community members are most welcome to correct me on this).changing the number of slabs along z direction is determined using the unit cell length along z direction. Here is what I found upon some grep. I tried to show here only when we have only one region present, lets say left lead. from cond_out.f90 do k=1, nrzl write(stdout,'(2x,i3,2x,3f7.4,3x,80i1)') & k,zl(k),zl(k+1),zl(k+1)-zl(k),(crosl(iorb,k),iorb=1,norbl) enddo so if you wish to change the number of slabs along z direction, you need to change nrzl and so on from init_cond.f90 line 211 nrzl = nrzreg(1) line 86 nrz1=0.0 do iz = 2, 5 naux=(dwid(iz)+dz1*0.5d0)/dz1-nrz1 nrzreg(iz-1) = naux ... .... we have two options, dz1 and dwid(2) line 44 nrztot = nr3s if(nrztot/2*2.eq.nrztot) nrztot = nrztot+1 zlen = at(3,3) dz1 = zlen/nrztot zlen=z component of a_3 lattice vector. nr3s= smooth fft dimension in z direction, so if you could change nr3s, you might be able to change nrzl. now, dwid(2)- line 80 dwid(2) = bd2 line 60 if(flag.eq.'l') then bd2 = bdl from the input file description - bdl: right boundary of the left lead (left one is supposed to be at 0) I dont know how one can change smooth fft dimesion in z direction. I believe its done in SCF part not in PWCOND. Regards, Manoj On Fri, 11 Sep 2009, xirainbow wrote: > Dear all: I find the following content at > "/espresso-4.0.4/examples/example12/results/al.cond.out" file. > *" nrz = 21* > *.........* > * k slab z(k) z(k+1) crossing(iorb=1,norb)* > * 1 0.0000 0.0673 0.0673 111100000000* > *.........* > * 20 1.2793 1.3467 0.0673 000001111111* > * 21 1.3467 1.4140 0.0673 000000001111 "* > > I want to know, at *.cond.in input file, how to control the number of > slabs along z direction in left, right lead and scattering region, > respectively. > By the way, what is the meaning of "crossing(iorb=1,norb)"? > > Thanks in advance ?????? > > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > From decboy9 at gmail.com Fri Sep 11 20:52:23 2009 From: decboy9 at gmail.com (dev sharma) Date: Sat, 12 Sep 2009 00:22:23 +0530 Subject: [Pw_forum] K Points and Band structures In-Reply-To: <4AAA3B89.9020002@sissa.it> References: <4AAA3B89.9020002@sissa.it> Message-ID: Dear Shaptrishi Sharma, I am also a student like you and what i have understood, what is K points, is as follows. We know that charge density is given by ?(r) = ?i=1 Ne/2 |?i(r)|2 with the Bloch theorem we can write as ?= ?n=1 Ne/cell ? d3k|?kn(r)|2 but since the integration is a continuous quantity, we choose the K point mesh in the Brillouin Zone and we have ?= ?n=1 Nb (2?)3/V ? (k ? mesh in BZ) d3k|?kn(r)|2 Where ?kn(r)= eik.r ?(G=reciprocal Lattice vector) Ckn[eiG.r/V(1/2)] And the term in bracket is the plane wave basis and for visualization, what u can do, make any structure, open with Xcrysden ,and go to tools --> K-path selection, there the BZ of your structure will be displayed, with some high symmetry K points (dots). Dear Shaptrishi Sharma, also a lot of times they have asked you to provide your full affilation. Please Do it. To all my guides, in the forum, I may be wrong at any point above, if so please correct me as my group is totally experimental and its my own understanding. Dev Sharma, University of Delhi On Fri, Sep 11, 2009 at 5:29 PM, Stefano de Gironcoli wrote: > Shaptrishi Sharma wrote: > > Hi QEs users, > > > > Can anybody please help me in understanding what are the k points ?? I > > have read books a lot but its difficult to understand. > Please ask to any solid state physicist nearby. > > > And also how do we choose k points while performing a band structure > > calculation in quantum espresso when we are having 330 atoms. > If you still have QE specific doubts after you have understood Bloch > theorem, Real and Reciprocal Space lattices, Brilloun Zone and the like > please formulate them again, trying to be specific. > > Thanks > > S > Please provide your affilaition. > > Best regards, > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/35361561/attachment-0001.htm From decboy9 at gmail.com Fri Sep 11 21:00:19 2009 From: decboy9 at gmail.com (dev sharma) Date: Sat, 12 Sep 2009 00:30:19 +0530 Subject: [Pw_forum] K Points and Band structures In-Reply-To: References: Message-ID: And also Dear, recently, Summer school on *Materials modeling from first principles: theory and practice*, ICMR, University of California at Santa Barbara, July 19-31, 2009 was held for Quantum Espresso, and the slides and video lectures are given at link http://www.quantum-espresso.org/wiki/index.php/QESB09 My advise is that please have a look on the slides, as they are very useful. Take Care. On Fri, Sep 11, 2009 at 5:15 PM, Shaptrishi Sharma wrote: > Hi QEs users, > > Can anybody please help me in understanding what are the k points ?? I have > read books a lot but its difficult to understand. > > And also how do we choose k points while performing a band structure > calculation in quantum espresso when we are having 330 atoms. > > Thanks > > S > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/539f7cd6/attachment.htm From baroni at sissa.it Fri Sep 11 21:10:36 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 11 Sep 2009 21:10:36 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: References: Message-ID: <95C24868-103C-4E60-A9F4-6C517FBE8070@sissa.it> please, stop hitting "reply" to digest dispatches of forum posts. this practice results in the forum members' mailboxes to be cluttered with garbage, and also decreases YOUR chance to get meaningul and prompt responses to your posts (people tend to throw into the wastebasket messages with generic subjects such as " Pw_forum Digest, Vol 27, Issue 47") SB causes nuisances to the mempers of the forum who have their mailboxes cluttered with gar On Sep 11, 2009, at 3:23 PM, Shaptrishi Sharma wrote: > Hi Stefano, > > My nband value is 122 as my total number of atoms are 66 .of which > 21 Hydrogen.And if I remove the option nelup and neldw, I got it as > "too many bands are not converged" thus I increased my vaccum, > however it still remains the same. > > Thanks > S > > On 9/11/09, pw_forum-request at pwscf.org > wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: problem with charge density with xcrysden > (Stefano de Gironcoli) > 2. [Fwd: Re: problem with charge density with xcrysden] > (Gabriele Sclauzero) > 3. Re: input file for isolated atom (Paolo Giannozzi) > 4. K Points and Band structures (Shaptrishi Sharma) > 5. Re: K Points and Band structures (Lorenzo Paulatto) > 6. Re: K Points and Band structures (Stefano de Gironcoli) > 7. Problem in spin polarisation (Shaptrishi Sharma) > 8. Re: Problem in spin polarisation (Stefano de Gironcoli) > 9. Re: Problem in spin polarisation (Duy Le) > 10. Re: Problem in spin polarisation (Stefano de Gironcoli) > 11. Re: Problem in spin polarisation (Paolo Giannozzi) > 12. The low usage of CUPs (wangqj1) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Sep 2009 11:57:37 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] problem with charge density with xcrysden > To: PWSCF Forum > Message-ID: <4AAA1F11.3000805 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > dear Dev Sharma > the xsf file with the DATAGRID field IS NOT the output of pp.x! > Rather its name needs to be specified in variable fileout in the &plot > namelist of your density.in input > Please read the documentation of pp.x code for the meaning of the > other variables. > HTH > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > dev sharma wrote: > > hi 2 all, > > I am trying to plot the charge density with the XCrysden, but > when i > > am opening's XSF(file--> open structure--> open XSF(xcryden > structure > > file)) file , generated by my calculations, it is showing the > > structure of my system. And i am not getting the option tools--> > > DATA GRID as ready. Please help or advice ?? Thankful to all of you. > > What i did is listed below. > > I run my input file with command > > /home/physics/espresso-4.0.2/bin/pp.x density.xsf > > and inputs of density.in are > > &inputpp > > prefix = 'yvo' > > outdir = '/home/physics/work/yvo/temp/', > > filplot = 'yvocharge' > > plot_num= 0 > > / > > &plot > > nfile = 1 > > filepp(1) = 'yvocharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5, > > / > > > > with regards, > > Dev Sharma, > > University of Delhi, > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Sep 2009 13:42:19 +0200 > From: Gabriele Sclauzero > Subject: [Pw_forum] [Fwd: Re: problem with charge density with > xcrysden] > To: PWscf Mailing List > Message-ID: <4AAA379B.4070804 at sissa.it> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > Forwarding e-mail from Emine. So I guess it may be a compatibility > issue. > > GS > > -------- Original Message -------- > Subject: Re: [Pw_forum] problem with charge density with > xcrysden > Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT) > From: e kb > To: sclauzer at sissa.it > > > > > The old version of xcrysden that i had didnt work with this line : > > DATAGRID_3D_UNKNOWN > but with this one: > > BEGIN_DATAGRID_3D_UNKNOWN > > I am not up to date on this but you can check it. > emine kucukbenli, SISSA, Italy > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > > > ------------------------------ > > Message: 3 > Date: Fri, 11 Sep 2009 13:44:13 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] input file for isolated atom > To: PWSCF Forum > Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote: > > > (a) while doing calculations for any zero dimensions > > you should always set nosym =.true. > > for Gamma-point calculations it shouldn't make any > difference > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 11 Sep 2009 12:45:43 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] K Points and Band structures > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi QEs users, > > Can anybody please help me in understanding what are the k points ?? > I have > read books a lot but its difficult to understand. > > And also how do we choose k points while performing a band structure > calculation in quantum espresso when we are having 330 atoms. > > Thanks > > S > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Fri, 11 Sep 2009 13:58:19 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] K Points and Band structures > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma > ha scritto: > > > Can anybody please help me in understanding what are the k > points ?? I > > have read books a lot but its difficult to understand. > > They are eigenvalues of the translation operator, T(R) where > R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3 > integer numbers. The eigenvectors are, of course, the Bloch > wavefunctions. > > Because the hamiltonian is periodic it commutes with the translation > operator, you can diagonalize both the hamiltonian and the translation > operator at the same time. As a consequence each Bloch wavefunction > has a > well-defined energy (hamiltonian's eigenvalue) and k-point > (translation > eigenvalue). Using both eigenvalues you can classify the states > without > ambiguity, except where the bands cross. > > > And also how do we choose k points while performing a band > structure > > calculation in quantum espresso when we are having 330 atoms. > > It does not depend on the number of atoms. > > You have to test the convergence at fixed smearing. E.g. you choose a > smearing that's small enough for you, than you increase the number of > k-points until total energy converges. You may then try again for a > smaller/larger smearing and see if the results are consistent. > > I would advise starting with a smaller system, it would take ages to > do it > on 330 atoms. Keep in mind that the number of k-points needed for an > accurate sampling is directly proportional to the size of the > Brillouin > zone, hence inversely proportional to the size of the cell. > > E.g. if you estimate that 6x6x6 k-points converge a certain > calculation > than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly > the same > level. > > Best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > > > ------------------------------ > > Message: 6 > Date: Fri, 11 Sep 2009 13:59:05 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] K Points and Band structures > To: PWSCF Forum > Message-ID: <4AAA3B89.9020002 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Shaptrishi Sharma wrote: > > Hi QEs users, > > > > Can anybody please help me in understanding what are the k > points ?? I > > have read books a lot but its difficult to understand. > Please ask to any solid state physicist nearby. > > > And also how do we choose k points while performing a band > structure > > calculation in quantum espresso when we are having 330 atoms. > If you still have QE specific doubts after you have understood Bloch > theorem, Real and Reciprocal Space lattices, Brilloun Zone and the > like > please formulate them again, trying to be specific. > > Thanks > > S > Please provide your affilaition. > > Best regards, > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 7 > Date: Fri, 11 Sep 2009 13:04:08 +0100 > From: Shaptrishi Sharma > Subject: [Pw_forum] Problem in spin polarisation > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi QE users, > > In one of my previous mail, I have asked about the spin polarisation > in a > sytem having odd number of electrons , (I have 21 hydrogen atoms in my > system ). > > As suggested I used nelup =11 and neldw = 10, however, it is showing > me the > same error, as > > nelp out of range. > so what shall I do now?? > > Thanks > > SS > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/3cbc0c0c/attachment-0001.htm > > ------------------------------ > > Message: 8 > Date: Fri, 11 Sep 2009 14:05:20 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <4AAA3D00.6020106 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > what is your value for nbnd ? > stefano > > Shaptrishi Sharma wrote: > > Hi QE users, > > > > In one of my previous mail, I have asked about the spin polarisation > > in a sytem having odd number of electrons , (I have 21 hydrogen > atoms > > in my system ). > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > me the same error, as > > > > nelp out of range. > > so what shall I do now?? > > > > Thanks > > > > SS > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 9 > Date: Fri, 11 Sep 2009 08:16:52 -0400 > From: Duy Le > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: > <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Add nelec to input > Please just reply instead of creating a new email starting with "In > one of > my previous mail" so that all your emails and communications are > ordered in > the same thread. > > :-) > > On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli >wrote: > > > what is your value for nbnd ? > > stefano > > > > Shaptrishi Sharma wrote: > > > Hi QE users, > > > > > > In one of my previous mail, I have asked about the spin > polarisation > > > in a sytem having odd number of electrons , (I have 21 hydrogen > atoms > > > in my system ). > > > > > > As suggested I used nelup =11 and neldw = 10, however, it is > showing > > > me the same error, as > > > > > > nelp out of range. > > > so what shall I do now?? > > > > > > Thanks > > > > > > SS > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0d71a230/attachment-0001.htm > > ------------------------------ > > Message: 10 > Date: Fri, 11 Sep 2009 14:24:18 +0200 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <4AAA4172.7020306 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I think that in this case you need to explicitly specify also the > value > for nelec because a test that 0<=nelup< =nelec > is performed before the default for nelec is calculated. > It should be fixed but it is not so straightforward as the default > value > is presently defined much later. > stefano > > Shaptrishi Sharma wrote: > > Hi QE users, > > > > In one of my previous mail, I have asked about the spin polarisation > > in a sytem having odd number of electrons , (I have 21 hydrogen > atoms > > in my system ). > > > > As suggested I used nelup =11 and neldw = 10, however, it is showing > > me the same error, as > > > > nelp out of range. > > so what shall I do now?? > > > > Thanks > > > > SS > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 11 > Date: Fri, 11 Sep 2009 14:35:30 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Problem in spin polarisation > To: PWSCF Forum > Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote: > > > It should be fixed > > or even better, removed, since there are alternative > and simpler methods to specify occupancies > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ------------------------------ > > Message: 12 > Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST) > From: wangqj1 > Subject: [Pw_forum] The low usage of CUPs > To: pw_forum > Message-ID: > <29861561.516411252672174463.JavaMail.coremail at bj126app106.126.com > > > Content-Type: text/plain; charset="gbk" > > Dear pwscf users > I use 16 CPUs to run a job,but the usage of CPUs is very > slow ,it as like: > > Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie > Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, > 4.5%si, 0.0%st > Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, > 0.0%si, 0.0%st > Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, > 0.0%si, 0.0%st > Mem: 8048812k total, 7995856k used, 52956k free, 283692k > buffers > Swap: 4192956k total, 124k used, 4192832k free, 7492420k > cached > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd > 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 > kjournald > 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X > 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd > 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd > 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm- > simple-gree > 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init > 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd > 3 root RT -5 0 0 0 S 0 0.0 0:00.00 > migration/0 > 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 > ksoftirqd/0 > > The ifort ,MKL,and mpi I used is : > INTFC=/opt/intel/Compiler/11.0/081 > INTMKL=/opt/intel/mkl/10.1.1.019 > /opt/mpich2/bin/mpd > My machine model is as following : > processor : 0 > vendor_id : GenuineIntel > cpu family : 6 > model : 23 > model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz > stepping : 10 > cpu MHz : 2327.489 > cache size : 6144 KB > physical id : 0 > siblings : 4 > core id : 0 > cpu cores : 4 > apicid : 0 > initial apicid : 0 > fpu : yes > fpu_exception : yes > cpuid level : 13 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr > pge mca cmov > pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx > lm constant > _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est > tm2 ssse3 cx > 16 xtpr dca sse4_1 lahf_lm > bogomips : 4654.97 > ............... > The pwscf version is espresso-4.0.3 . > > So , I want to know why the usage is so slow ? > How can I solve this problem ? Anybody who meet the same problem ? > Your kind help will be appreciated ! > Best regards > Q.J.Wang > XiangTan University > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/e349a164/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 27, Issue 47 > **************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0c034152/attachment-0001.htm From baroni at sissa.it Fri Sep 11 21:17:01 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 11 Sep 2009 21:17:01 +0200 Subject: [Pw_forum] K Points and Band structures In-Reply-To: References: Message-ID: On Sep 11, 2009, at 9:00 PM, dev sharma wrote: > And also Dear, recently, Summer school on Materials modeling from > first principles: theory and practice, ICMR, University of > California at Santa Barbara, July 19-31, 2009 was held for Quantum > Espresso, and the slides and video lectures are given at link > http://www.quantum-espresso.org/wiki/index.php/QESB09 > > My advise is that please have a look on the slides, as they are very > useful. thank you, Dev Sharma ;-) also, Davatri Sharma, do not forget textbooks I know ... they are hard to study, but this is only to teach you that "life is hard" (if it was not, it would not be as interesting) > Take Care. Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/364ad8b6/attachment.htm From ttduyle at gmail.com Fri Sep 11 21:36:01 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 11 Sep 2009 15:36:01 -0400 Subject: [Pw_forum] resp_mat.f90 Message-ID: <8974d3b20909111236h3c441260m9e78c34b9b5f07d5@mail.gmail.com> Dear Matteo and all, I am trying to calculated the U with resp_mat.f90 code for colbalt. The primitive cell has 16 Co. The code extrapolated to 2x2x2, 3x3x3 super cell successfully. However, when it came to 4x4x4 super cell, the code was initially doing pretty fine, and in the end it gave an U1, but the code did not finish normally. Then error came (see below). The worse thing is that the value of U1 given in 4x4x4 extrapolation is nonsense. 16 3.30938654705739 128 3.59144217433734 432 3.61280367128581 1024 -0.703549684908895 I did a quick search and found that you have mentioned the error of resp_mat.f90 code with hexagonal lattice (which my system is). Are the error you was talking about and the error I am facing with identical? Do you have the resp_mat.f90 fixed? Thank you. *-----------------------------------ERROR----------------------------* forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libpthread.so.0 000000397480DE80 Unknown Unknown Unknown libc.so.6 0000003973C71083 Unknown Unknown Unknown libc.so.6 0000003973C74CCC Unknown Unknown Unknown r.x 00000000006496CD Unknown Unknown Unknown r.x 000000000041111C Unknown Unknown Unknown r.x 00000000004065C2 Unknown Unknown Unknown libc.so.6 0000003973C1D8B4 Unknown Unknown Unknown r.x 00000000004064E9 Unknown Unknown Unknown *-----------------------------------OLD MESSAGE---------------------------- Matteo Cococcioni* matteo at umn.edu *Fri Dec 5 16:56:00 CET 2008* - Previous message: [Pw_forum] Strange things when calculating bands using pw.x - Next message: [Pw_forum] Scf can converge, But Band can not converge - *Messages sorted by:* [ date ] [ thread ] [ subject ] [ author ] ------------------------------ Dear all, I have recently realized that the code resp_mat.f90, contained in some tutorials on LDA+U calculations (e.g., from http://vlab.msi.umn.edu/events/lecture.shtml) and used to compute U, has some problems and doesn't work as expected. I have realized this on a hexagonal system but I'm not sure yet if the problem manifests itself also with other crystal structures. Hoping that not many people were using it I apologize for the inconvenient. I also hope to provide a fix in short time. regards, Matteo -------------- next part -------------- A non-text attachment was scrubbed... Name: matteo.vcf Type: text/x-vcard Size: 294 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20081205/7359fd01/attachment.vcf -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/5b7ce5fb/attachment.htm From ttduyle at gmail.com Fri Sep 11 21:43:18 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 11 Sep 2009 15:43:18 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: <95C24868-103C-4E60-A9F4-6C517FBE8070@sissa.it> References: <95C24868-103C-4E60-A9F4-6C517FBE8070@sissa.it> Message-ID: <8974d3b20909111243i1a720ccbn2140ce6101630bdb@mail.gmail.com> Sorry, I think it was my fault. Last time I suggested someone to hit "reply" instead of creating a new email starting with "in my last email". I did not expect he/she used Digest Mode. Duy On Fri, Sep 11, 2009 at 3:10 PM, Stefano Baroni wrote: > please, stop hitting "reply" to digest dispatches of forum posts.this > practice results in the forum members' mailboxes to be cluttered with > garbage, and also decreases YOUR chance to get meaningul and prompt > responses to your posts (people tend to throw into the wastebasket messages > with generic subjects such as " Pw_forum Digest, Vol 27, Issue 47") > SB > > causes nuisances to the mempers of the forum who have their mailboxes > cluttered with gar > > On Sep 11, 2009, at 3:23 PM, Shaptrishi Sharma wrote: > > Hi Stefano, > > My nband value is 122 as my total number of atoms are 66 .of which 21 > Hydrogen.And if I remove the option nelup and neldw, I got it as "too many > bands are not converged" thus I increased my vaccum, however it still > remains the same. > > Thanks > S > > On 9/11/09, pw_forum-request at pwscf.org wrote: >> >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. Re: problem with charge density with xcrysden >> (Stefano de Gironcoli) >> 2. [Fwd: Re: problem with charge density with xcrysden] >> (Gabriele Sclauzero) >> 3. Re: input file for isolated atom (Paolo Giannozzi) >> 4. K Points and Band structures (Shaptrishi Sharma) >> 5. Re: K Points and Band structures (Lorenzo Paulatto) >> 6. Re: K Points and Band structures (Stefano de Gironcoli) >> 7. Problem in spin polarisation (Shaptrishi Sharma) >> 8. Re: Problem in spin polarisation (Stefano de Gironcoli) >> 9. Re: Problem in spin polarisation (Duy Le) >> 10. Re: Problem in spin polarisation (Stefano de Gironcoli) >> 11. Re: Problem in spin polarisation (Paolo Giannozzi) >> 12. The low usage of CUPs (wangqj1) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 11 Sep 2009 11:57:37 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] problem with charge density with xcrysden >> To: PWSCF Forum >> Message-ID: <4AAA1F11.3000805 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> dear Dev Sharma >> the xsf file with the DATAGRID field IS NOT the output of pp.x! >> Rather its name needs to be specified in variable fileout in the &plot >> namelist of your density.in input >> Please read the documentation of pp.x code for the meaning of the >> other variables. >> HTH >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> dev sharma wrote: >> > hi 2 all, >> > I am trying to plot the charge density with the XCrysden, but when i >> > am opening's XSF(file--> open structure--> open XSF(xcryden structure >> > file)) file , generated by my calculations, it is showing the >> > structure of my system. And i am not getting the option tools--> >> > DATA GRID as ready. Please help or advice ?? Thankful to all of you. >> > What i did is listed below. >> > I run my input file with command >> > /home/physics/espresso-4.0.2/bin/pp.x density.xsf >> > and inputs of density.in are >> > &inputpp >> > prefix = 'yvo' >> > outdir = '/home/physics/work/yvo/temp/', >> > filplot = 'yvocharge' >> > plot_num= 0 >> > / >> > &plot >> > nfile = 1 >> > filepp(1) = 'yvocharge' >> > weight(1) = 1.0 >> > iflag = 3 >> > output_format = 5, >> > / >> > >> > with regards, >> > Dev Sharma, >> > University of Delhi, >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 11 Sep 2009 13:42:19 +0200 >> From: Gabriele Sclauzero >> Subject: [Pw_forum] [Fwd: Re: problem with charge density with >> xcrysden] >> To: PWscf Mailing List >> Message-ID: <4AAA379B.4070804 at sissa.it> >> Content-Type: text/plain; charset=iso-8859-1; format=flowed >> >> Forwarding e-mail from Emine. So I guess it may be a compatibility issue. >> >> GS >> >> -------- Original Message -------- >> Subject: Re: [Pw_forum] problem with charge density with xcrysden >> Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT) >> From: e kb >> To: sclauzer at sissa.it >> >> >> >> >> The old version of xcrysden that i had didnt work with this line : >> > DATAGRID_3D_UNKNOWN >> but with this one: >> > BEGIN_DATAGRID_3D_UNKNOWN >> >> I am not up to date on this but you can check it. >> emine kucukbenli, SISSA, Italy >> >> >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 11 Sep 2009 13:44:13 +0200 >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] input file for isolated atom >> To: PWSCF Forum >> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it> >> Content-Type: text/plain; charset=US-ASCII; format=flowed >> >> >> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote: >> >> > (a) while doing calculations for any zero dimensions >> > you should always set nosym =.true. >> >> for Gamma-point calculations it shouldn't make any >> difference >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 11 Sep 2009 12:45:43 +0100 >> From: Shaptrishi Sharma >> Subject: [Pw_forum] K Points and Band structures >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi QEs users, >> >> Can anybody please help me in understanding what are the k points ?? I >> have >> read books a lot but its difficult to understand. >> >> And also how do we choose k points while performing a band structure >> calculation in quantum espresso when we are having 330 atoms. >> >> Thanks >> >> S >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm >> >> ------------------------------ >> >> Message: 5 >> Date: Fri, 11 Sep 2009 13:58:19 +0200 >> From: "Lorenzo Paulatto" >> Subject: Re: [Pw_forum] K Points and Band structures >> To: "PWSCF Forum" >> Message-ID: >> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes >> >> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma >> ha scritto: >> >> > Can anybody please help me in understanding what are the k points ?? I >> > have read books a lot but its difficult to understand. >> >> They are eigenvalues of the translation operator, T(R) where >> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3 >> integer numbers. The eigenvectors are, of course, the Bloch wavefunctions. >> >> Because the hamiltonian is periodic it commutes with the translation >> operator, you can diagonalize both the hamiltonian and the translation >> operator at the same time. As a consequence each Bloch wavefunction has a >> well-defined energy (hamiltonian's eigenvalue) and k-point (translation >> eigenvalue). Using both eigenvalues you can classify the states without >> ambiguity, except where the bands cross. >> >> > And also how do we choose k points while performing a band structure >> > calculation in quantum espresso when we are having 330 atoms. >> >> It does not depend on the number of atoms. >> >> You have to test the convergence at fixed smearing. E.g. you choose a >> smearing that's small enough for you, than you increase the number of >> k-points until total energy converges. You may then try again for a >> smaller/larger smearing and see if the results are consistent. >> >> I would advise starting with a smaller system, it would take ages to do it >> on 330 atoms. Keep in mind that the number of k-points needed for an >> accurate sampling is directly proportional to the size of the Brillouin >> zone, hence inversely proportional to the size of the cell. >> >> E.g. if you estimate that 6x6x6 k-points converge a certain calculation >> than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly the same >> level. >> >> Best regards >> >> >> -- >> Lorenzo Paulatto >> SISSA & DEMOCRITOS (Trieste) >> phone: +39 040 3787 511 >> skype: paulatz >> www: http://people.sissa.it/~paulatto/ >> >> *** save italian brains *** >> http://saveitalianbrains.wordpress.com/ >> >> >> ------------------------------ >> >> Message: 6 >> Date: Fri, 11 Sep 2009 13:59:05 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] K Points and Band structures >> To: PWSCF Forum >> Message-ID: <4AAA3B89.9020002 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Shaptrishi Sharma wrote: >> > Hi QEs users, >> > >> > Can anybody please help me in understanding what are the k points ?? I >> > have read books a lot but its difficult to understand. >> Please ask to any solid state physicist nearby. >> >> > And also how do we choose k points while performing a band structure >> > calculation in quantum espresso when we are having 330 atoms. >> If you still have QE specific doubts after you have understood Bloch >> theorem, Real and Reciprocal Space lattices, Brilloun Zone and the like >> please formulate them again, trying to be specific. >> > Thanks >> > S >> Please provide your affilaition. >> >> Best regards, >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 7 >> Date: Fri, 11 Sep 2009 13:04:08 +0100 >> From: Shaptrishi Sharma >> Subject: [Pw_forum] Problem in spin polarisation >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi QE users, >> >> In one of my previous mail, I have asked about the spin polarisation in a >> sytem having odd number of electrons , (I have 21 hydrogen atoms in my >> system ). >> >> As suggested I used nelup =11 and neldw = 10, however, it is showing me >> the >> same error, as >> >> nelp out of range. >> so what shall I do now?? >> >> Thanks >> >> SS >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/3cbc0c0c/attachment-0001.htm >> >> ------------------------------ >> >> Message: 8 >> Date: Fri, 11 Sep 2009 14:05:20 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <4AAA3D00.6020106 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> what is your value for nbnd ? >> stefano >> >> Shaptrishi Sharma wrote: >> > Hi QE users, >> > >> > In one of my previous mail, I have asked about the spin polarisation >> > in a sytem having odd number of electrons , (I have 21 hydrogen atoms >> > in my system ). >> > >> > As suggested I used nelup =11 and neldw = 10, however, it is showing >> > me the same error, as >> > >> > nelp out of range. >> > so what shall I do now?? >> > >> > Thanks >> > >> > SS >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 9 >> Date: Fri, 11 Sep 2009 08:16:52 -0400 >> From: Duy Le >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: >> <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7 at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Add nelec to input >> Please just reply instead of creating a new email starting with "In one of >> my previous mail" so that all your emails and communications are ordered >> in >> the same thread. >> >> :-) >> >> On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli > >wrote: >> >> > what is your value for nbnd ? >> > stefano >> > >> > Shaptrishi Sharma wrote: >> > > Hi QE users, >> > > >> > > In one of my previous mail, I have asked about the spin polarisation >> > > in a sytem having odd number of electrons , (I have 21 hydrogen atoms >> > > in my system ). >> > > >> > > As suggested I used nelup =11 and neldw = 10, however, it is showing >> > > me the same error, as >> > > >> > > nelp out of range. >> > > so what shall I do now?? >> > > >> > > Thanks >> > > >> > > SS >> > > >> > > >> > > >> ------------------------------------------------------------------------ >> > > >> > > _______________________________________________ >> > > Pw_forum mailing list >> > > Pw_forum at pwscf.org >> > > http://www.democritos.it/mailman/listinfo/pw_forum >> > > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> -------------------------------------------------- >> Duy Le >> PhD Student >> Department of Physics >> University of Central Florida. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0d71a230/attachment-0001.htm >> >> ------------------------------ >> >> Message: 10 >> Date: Fri, 11 Sep 2009 14:24:18 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <4AAA4172.7020306 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> I think that in this case you need to explicitly specify also the value >> for nelec because a test that 0<=nelup< =nelec >> is performed before the default for nelec is calculated. >> It should be fixed but it is not so straightforward as the default value >> is presently defined much later. >> stefano >> >> Shaptrishi Sharma wrote: >> > Hi QE users, >> > >> > In one of my previous mail, I have asked about the spin polarisation >> > in a sytem having odd number of electrons , (I have 21 hydrogen atoms >> > in my system ). >> > >> > As suggested I used nelup =11 and neldw = 10, however, it is showing >> > me the same error, as >> > >> > nelp out of range. >> > so what shall I do now?? >> > >> > Thanks >> > >> > SS >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 11 >> Date: Fri, 11 Sep 2009 14:35:30 +0200 >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719 at democritos.it> >> Content-Type: text/plain; charset=US-ASCII; format=flowed >> >> >> On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote: >> >> > It should be fixed >> >> or even better, removed, since there are alternative >> and simpler methods to specify occupancies >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> >> ------------------------------ >> >> Message: 12 >> Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST) >> From: wangqj1 >> Subject: [Pw_forum] The low usage of CUPs >> To: pw_forum >> Message-ID: >> < >> 29861561.516411252672174463.JavaMail.coremail at bj126app106.126.com> >> Content-Type: text/plain; charset="gbk" >> >> Dear pwscf users >> I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as >> like: >> >> Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie >> Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, >> 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st >> Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, >> 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st >> >> Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, >> 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st >> >> Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, >> 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> >> Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> >> Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >> Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers >> Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd >> 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald >> 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X >> 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd >> 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd >> 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 >> gdm-simple-gree >> 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init >> 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd >> 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0 >> 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0 >> >> The ifort ,MKL,and mpi I used is : >> INTFC=/opt/intel/Compiler/11.0/081 >> INTMKL=/opt/intel/mkl/10.1.1.019 >> /opt/mpich2/bin/mpd >> My machine model is as following : >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 6 >> model : 23 >> model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz >> stepping : 10 >> cpu MHz : 2327.489 >> cache size : 6144 KB >> physical id : 0 >> siblings : 4 >> core id : 0 >> cpu cores : 4 >> apicid : 0 >> initial apicid : 0 >> fpu : yes >> fpu_exception : yes >> cpuid level : 13 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca >> cmov >> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm >> constant >> _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est tm2 >> ssse3 cx >> 16 xtpr dca sse4_1 lahf_lm >> bogomips : 4654.97 >> ............... >> The pwscf version is espresso-4.0.3 . >> >> So , I want to know why the usage is so slow ? >> How can I solve this problem ? Anybody who meet the same problem ? >> Your kind help will be appreciated ! >> Best regards >> Q.J.Wang >> XiangTan University >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/e349a164/attachment.htm >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 27, Issue 47 >> **************************************** >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/d84b6039/attachment-0001.htm From baroni at sissa.it Fri Sep 11 21:54:10 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 11 Sep 2009 21:54:10 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 47 In-Reply-To: <8974d3b20909111243i1a720ccbn2140ce6101630bdb@mail.gmail.com> References: <95C24868-103C-4E60-A9F4-6C517FBE8070@sissa.it> <8974d3b20909111243i1a720ccbn2140ce6101630bdb@mail.gmail.com> Message-ID: No problem. It is always difficult to imagine what others can do/think/ say ... Thank you for being with us (and for caring). SB --- Stefano Baroni - SISSA, Trieste - swift text written and sent on the go On 11/set/2009, at 21.43, Duy Le wrote: > Sorry, I think it was my fault. Last time I suggested someone to hit > "reply" instead of creating a new email starting with "in my last > email". I did not expect he/she used Digest Mode. > > Duy > > On Fri, Sep 11, 2009 at 3:10 PM, Stefano Baroni > wrote: > please, stop hitting "reply" to digest dispatches of forum posts. > this practice results in the forum members' mailboxes to be > cluttered with garbage, and also decreases YOUR chance to get > meaningul and prompt responses to your posts (people tend to throw > into the wastebasket messages with generic subjects such as " > Pw_forum Digest, Vol 27, Issue 47") > SB > > causes nuisances to the mempers of the forum who have their > mailboxes cluttered with gar > > On Sep 11, 2009, at 3:23 PM, Shaptrishi Sharma wrote: > >> Hi Stefano, >> >> My nband value is 122 as my total number of atoms are 66 .of which >> 21 Hydrogen.And if I remove the option nelup and neldw, I got it as >> "too many bands are not converged" thus I increased my vaccum, >> however it still remains the same. >> >> Thanks >> S >> >> On 9/11/09, pw_forum-request at pwscf.org >> wrote: >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. Re: problem with charge density with xcrysden >> (Stefano de Gironcoli) >> 2. [Fwd: Re: problem with charge density with xcrysden] >> (Gabriele Sclauzero) >> 3. Re: input file for isolated atom (Paolo Giannozzi) >> 4. K Points and Band structures (Shaptrishi Sharma) >> 5. Re: K Points and Band structures (Lorenzo Paulatto) >> 6. Re: K Points and Band structures (Stefano de Gironcoli) >> 7. Problem in spin polarisation (Shaptrishi Sharma) >> 8. Re: Problem in spin polarisation (Stefano de Gironcoli) >> 9. Re: Problem in spin polarisation (Duy Le) >> 10. Re: Problem in spin polarisation (Stefano de Gironcoli) >> 11. Re: Problem in spin polarisation (Paolo Giannozzi) >> 12. The low usage of CUPs (wangqj1) >> >> >> --- >> ------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 11 Sep 2009 11:57:37 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] problem with charge density with xcrysden >> To: PWSCF Forum >> Message-ID: <4AAA1F11.3000805 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> dear Dev Sharma >> the xsf file with the DATAGRID field IS NOT the output of pp.x! >> Rather its name needs to be specified in variable fileout in the >> &plot >> namelist of your density.in input >> Please read the documentation of pp.x code for the meaning of the >> other variables. >> HTH >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> dev sharma wrote: >> > hi 2 all, >> > I am trying to plot the charge density with the XCrysden, but >> when i >> > am opening's XSF(file--> open structure--> open XSF(xcryden >> structure >> > file)) file , generated by my calculations, it is showing the >> > structure of my system. And i am not getting the option tools--> >> > DATA GRID as ready. Please help or advice ?? Thankful to all of >> you. >> > What i did is listed below. >> > I run my input file with command >> > /home/physics/espresso-4.0.2/bin/pp.x density.xsf >> > and inputs of density.in are >> > &inputpp >> > prefix = 'yvo' >> > outdir = '/home/physics/work/yvo/temp/', >> > filplot = 'yvocharge' >> > plot_num= 0 >> > / >> > &plot >> > nfile = 1 >> > filepp(1) = 'yvocharge' >> > weight(1) = 1.0 >> > iflag = 3 >> > output_format = 5, >> > / >> > >> > with regards, >> > Dev Sharma, >> > University of Delhi, >> > >> --- >> --------------------------------------------------------------------- >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 11 Sep 2009 13:42:19 +0200 >> From: Gabriele Sclauzero >> Subject: [Pw_forum] [Fwd: Re: problem with charge density with >> xcrysden] >> To: PWscf Mailing List >> Message-ID: <4AAA379B.4070804 at sissa.it> >> Content-Type: text/plain; charset=iso-8859-1; format=flowed >> >> Forwarding e-mail from Emine. So I guess it may be a compatibility >> issue. >> >> GS >> >> -------- Original Message -------- >> Subject: Re: [Pw_forum] problem with charge density with >> xcrysden >> Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT) >> From: e kb >> To: sclauzer at sissa.it >> >> >> >> >> The old version of xcrysden that i had didnt work with this line : >> > DATAGRID_3D_UNKNOWN >> but with this one: >> > BEGIN_DATAGRID_3D_UNKNOWN >> >> I am not up to date on this but you can check it. >> emine kucukbenli, SISSA, Italy >> >> >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 11 Sep 2009 13:44:13 +0200 >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] input file for isolated atom >> To: PWSCF Forum >> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it> >> Content-Type: text/plain; charset=US-ASCII; format=flowed >> >> >> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote: >> >> > (a) while doing calculations for any zero dimensions >> > you should always set nosym =.true. >> >> for Gamma-point calculations it shouldn't make any >> difference >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 11 Sep 2009 12:45:43 +0100 >> From: Shaptrishi Sharma >> Subject: [Pw_forum] K Points and Band structures >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi QEs users, >> >> Can anybody please help me in understanding what are the k >> points ?? I have >> read books a lot but its difficult to understand. >> >> And also how do we choose k points while performing a band structure >> calculation in quantum espresso when we are having 330 atoms. >> >> Thanks >> >> S >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm >> >> ------------------------------ >> >> Message: 5 >> Date: Fri, 11 Sep 2009 13:58:19 +0200 >> From: "Lorenzo Paulatto" >> Subject: Re: [Pw_forum] K Points and Band structures >> To: "PWSCF Forum" >> Message-ID: >> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes >> >> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma >> ha scritto: >> >> > Can anybody please help me in understanding what are the k >> points ?? I >> > have read books a lot but its difficult to understand. >> >> They are eigenvalues of the translation operator, T(R) where >> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3 >> integer numbers. The eigenvectors are, of course, the Bloch >> wavefunctions. >> >> Because the hamiltonian is periodic it commutes with the translation >> operator, you can diagonalize both the hamiltonian and the >> translation >> operator at the same time. As a consequence each Bloch wavefunction >> has a >> well-defined energy (hamiltonian's eigenvalue) and k-point >> (translation >> eigenvalue). Using both eigenvalues you can classify the states >> without >> ambiguity, except where the bands cross. >> >> > And also how do we choose k points while performing a band >> structure >> > calculation in quantum espresso when we are having 330 atoms. >> >> It does not depend on the number of atoms. >> >> You have to test the convergence at fixed smearing. E.g. you choose a >> smearing that's small enough for you, than you increase the number of >> k-points until total energy converges. You may then try again for a >> smaller/larger smearing and see if the results are consistent. >> >> I would advise starting with a smaller system, it would take ages >> to do it >> on 330 atoms. Keep in mind that the number of k-points needed for an >> accurate sampling is directly proportional to the size of the >> Brillouin >> zone, hence inversely proportional to the size of the cell. >> >> E.g. if you estimate that 6x6x6 k-points converge a certain >> calculation >> than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly >> the same >> level. >> >> Best regards >> >> >> -- >> Lorenzo Paulatto >> SISSA & DEMOCRITOS (Trieste) >> phone: +39 040 3787 511 >> skype: paulatz >> www: http://people.sissa.it/~paulatto/ >> >> *** save italian brains *** >> http://saveitalianbrains.wordpress.com/ >> >> >> ------------------------------ >> >> Message: 6 >> Date: Fri, 11 Sep 2009 13:59:05 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] K Points and Band structures >> To: PWSCF Forum >> Message-ID: <4AAA3B89.9020002 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Shaptrishi Sharma wrote: >> > Hi QEs users, >> > >> > Can anybody please help me in understanding what are the k >> points ?? I >> > have read books a lot but its difficult to understand. >> Please ask to any solid state physicist nearby. >> >> > And also how do we choose k points while performing a band >> structure >> > calculation in quantum espresso when we are having 330 atoms. >> If you still have QE specific doubts after you have understood Bloch >> theorem, Real and Reciprocal Space lattices, Brilloun Zone and the >> like >> please formulate them again, trying to be specific. >> > Thanks >> > S >> Please provide your affilaition. >> >> Best regards, >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> > >> --- >> --------------------------------------------------------------------- >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 7 >> Date: Fri, 11 Sep 2009 13:04:08 +0100 >> From: Shaptrishi Sharma >> Subject: [Pw_forum] Problem in spin polarisation >> To: pw_forum at pwscf.org >> Message-ID: >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi QE users, >> >> In one of my previous mail, I have asked about the spin >> polarisation in a >> sytem having odd number of electrons , (I have 21 hydrogen atoms in >> my >> system ). >> >> As suggested I used nelup =11 and neldw = 10, however, it is >> showing me the >> same error, as >> >> nelp out of range. >> so what shall I do now?? >> >> Thanks >> >> SS >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/3cbc0c0c/attachment-0001.htm >> >> ------------------------------ >> >> Message: 8 >> Date: Fri, 11 Sep 2009 14:05:20 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <4AAA3D00.6020106 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> what is your value for nbnd ? >> stefano >> >> Shaptrishi Sharma wrote: >> > Hi QE users, >> > >> > In one of my previous mail, I have asked about the spin >> polarisation >> > in a sytem having odd number of electrons , (I have 21 hydrogen >> atoms >> > in my system ). >> > >> > As suggested I used nelup =11 and neldw = 10, however, it is >> showing >> > me the same error, as >> > >> > nelp out of range. >> > so what shall I do now?? >> > >> > Thanks >> > >> > SS >> > >> > >> > >> --- >> --------------------------------------------------------------------- >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 9 >> Date: Fri, 11 Sep 2009 08:16:52 -0400 >> From: Duy Le >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: >> <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7 at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Add nelec to input >> Please just reply instead of creating a new email starting with "In >> one of >> my previous mail" so that all your emails and communications are >> ordered in >> the same thread. >> >> :-) >> >> On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli > >wrote: >> >> > what is your value for nbnd ? >> > stefano >> > >> > Shaptrishi Sharma wrote: >> > > Hi QE users, >> > > >> > > In one of my previous mail, I have asked about the spin >> polarisation >> > > in a sytem having odd number of electrons , (I have 21 hydrogen >> atoms >> > > in my system ). >> > > >> > > As suggested I used nelup =11 and neldw = 10, however, it is >> showing >> > > me the same error, as >> > > >> > > nelp out of range. >> > > so what shall I do now?? >> > > >> > > Thanks >> > > >> > > SS >> > > >> > > >> > > >> --- >> --------------------------------------------------------------------- >> > > >> > > _______________________________________________ >> > > Pw_forum mailing list >> > > Pw_forum at pwscf.org >> > > http://www.democritos.it/mailman/listinfo/pw_forum >> > > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> -------------------------------------------------- >> Duy Le >> PhD Student >> Department of Physics >> University of Central Florida. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/0d71a230/attachment-0001.htm >> >> ------------------------------ >> >> Message: 10 >> Date: Fri, 11 Sep 2009 14:24:18 +0200 >> From: Stefano de Gironcoli >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <4AAA4172.7020306 at sissa.it> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> I think that in this case you need to explicitly specify also the >> value >> for nelec because a test that 0<=nelup< =nelec >> is performed before the default for nelec is calculated. >> It should be fixed but it is not so straightforward as the default >> value >> is presently defined much later. >> stefano >> >> Shaptrishi Sharma wrote: >> > Hi QE users, >> > >> > In one of my previous mail, I have asked about the spin >> polarisation >> > in a sytem having odd number of electrons , (I have 21 hydrogen >> atoms >> > in my system ). >> > >> > As suggested I used nelup =11 and neldw = 10, however, it is >> showing >> > me the same error, as >> > >> > nelp out of range. >> > so what shall I do now?? >> > >> > Thanks >> > >> > SS >> > >> > >> > >> --- >> --------------------------------------------------------------------- >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> ------------------------------ >> >> Message: 11 >> Date: Fri, 11 Sep 2009 14:35:30 +0200 >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] Problem in spin polarisation >> To: PWSCF Forum >> Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719 at democritos.it> >> Content-Type: text/plain; charset=US-ASCII; format=flowed >> >> >> On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote: >> >> > It should be fixed >> >> or even better, removed, since there are alternative >> and simpler methods to specify occupancies >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> >> ------------------------------ >> >> Message: 12 >> Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST) >> From: wangqj1 >> Subject: [Pw_forum] The low usage of CUPs >> To: pw_forum >> Message-ID: >> <29861561.516411252672174463.JavaMail.coremail at bj126app106.126.com >> > >> Content-Type: text/plain; charset="gbk" >> >> Dear pwscf users >> I use 16 CPUs to run a job,but the usage of CPUs is very >> slow ,it as like: >> >> Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie >> Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, >> 4.5%si, 0.0%st >> Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, >> 0.0%si, 0.0%st >> Mem: 8048812k total, 7995856k used, 52956k free, 283692k >> buffers >> Swap: 4192956k total, 124k used, 4192832k free, 7492420k >> cached >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd >> 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 >> kjournald >> 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X >> 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd >> 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd >> 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm- >> simple-gree >> 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init >> 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd >> 3 root RT -5 0 0 0 S 0 0.0 0:00.00 >> migration/0 >> 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 >> ksoftirqd/0 >> >> The ifort ,MKL,and mpi I used is : >> INTFC=/opt/intel/Compiler/11.0/081 >> INTMKL=/opt/intel/mkl/10.1.1.019 >> /opt/mpich2/bin/mpd >> My machine model is as following : >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 6 >> model : 23 >> model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz >> stepping : 10 >> cpu MHz : 2327.489 >> cache size : 6144 KB >> physical id : 0 >> siblings : 4 >> core id : 0 >> cpu cores : 4 >> apicid : 0 >> initial apicid : 0 >> fpu : yes >> fpu_exception : yes >> cpuid level : 13 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr >> pge mca cmov >> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall >> nx lm constant >> _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est >> tm2 ssse3 cx >> 16 xtpr dca sse4_1 lahf_lm >> bogomips : 4654.97 >> ............... >> The pwscf version is espresso-4.0.3 . >> >> So , I want to know why the usage is so slow ? >> How can I solve this problem ? Anybody who meet the same >> problem ? >> Your kind help will be appreciated ! >> Best regards >> Q.J.Wang >> XiangTan University >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/e349a164/attachment.htm >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 27, Issue 47 >> **************************************** >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090911/51e82436/attachment-0001.htm From matteo at umn.edu Fri Sep 11 23:06:24 2009 From: matteo at umn.edu (Matteo Cococcioni) Date: Fri, 11 Sep 2009 16:06:24 -0500 Subject: [Pw_forum] resp_mat.f90 In-Reply-To: <8974d3b20909111236h3c441260m9e78c34b9b5f07d5@mail.gmail.com> References: <8974d3b20909111236h3c441260m9e78c34b9b5f07d5@mail.gmail.com> Message-ID: <4AAABBD0.3010604@umn.edu> Dear Duy, I have no experience with hexagonal systems. but the first three results seem reasonable. maybe some array is not big enough to contain your system? in my experience it's usually a problem of this kind causing errors. Matteo Duy Le wrote: > Dear Matteo and all, > > I am trying to calculated the U with resp_mat.f90 code for colbalt. > > The primitive cell has 16 Co. > The code extrapolated to 2x2x2, 3x3x3 super cell successfully. > > However, when it came to 4x4x4 super cell, the code was initially > doing pretty fine, and in the end it gave an U1, but the code did not > finish normally. Then error came (see below). > > The worse thing is that the value of U1 given in 4x4x4 extrapolation > is nonsense. > > 16 3.30938654705739 > 128 3.59144217433734 > 432 3.61280367128581 > 1024 -0.703549684908895 > > I did a quick search and found that you have mentioned the error of > resp_mat.f90 code with hexagonal lattice (which my system is). Are the > error you was talking about and the error I am facing with identical? > Do you have the resp_mat.f90 fixed? > > Thank you. > > *-----------------------------------ERROR----------------------------* > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line > Source > libpthread.so.0 000000397480DE80 Unknown Unknown > Unknown > libc.so.6 0000003973C71083 Unknown Unknown > Unknown > libc.so.6 0000003973C74CCC Unknown Unknown > Unknown > r.x 00000000006496CD Unknown Unknown > Unknown > r.x 000000000041111C Unknown Unknown > Unknown > r.x 00000000004065C2 Unknown Unknown > Unknown > libc.so.6 0000003973C1D8B4 Unknown Unknown > Unknown > r.x 00000000004064E9 Unknown Unknown > Unknown > > > *-----------------------------------OLD > MESSAGE---------------------------- > Matteo Cococcioni* matteo at umn.edu > > /Fri Dec 5 16:56:00 CET 2008/ > > * Previous message: [Pw_forum] Strange things when calculating > bands using pw.x > > * Next message: [Pw_forum] Scf can converge, But Band can not > converge > > * *Messages sorted by:* [ date ] > > [ thread ] > > [ subject ] > > [ author ] > > > > Dear all, > > I have recently realized that the code resp_mat.f90, contained in some > tutorials on LDA+U calculations (e.g., > from http://vlab.msi.umn.edu/events/lecture.shtml) and used to compute > > > U, has some problems and doesn't work as expected. > I have realized this on a hexagonal system but I'm not sure yet if the > problem manifests itself also with other crystal structures. > > Hoping that not many people were using it I apologize for the > > > inconvenient. I also hope to provide a fix in short time. > > regards, > > Matteo > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: matteo.vcf > Type: text/x-vcard > Size: 294 bytes > > > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20081205/7359fd01/attachment.vcf > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From nkxirainbow at gmail.com Sat Sep 12 05:06:25 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 12 Sep 2009 03:06:25 +0000 Subject: [Pw_forum] =?utf-8?q?How_to_control_number_of_slabs_in_pwcond_cal?= =?utf-8?b?Y3VsYXRpb27vvJ8=?= In-Reply-To: References: <21fbc4790909110901j480d415bx87a8eaed51f4cb15@mail.gmail.com> Message-ID: <21fbc4790909112006w249e09e8m310fc487a1ea0f25@mail.gmail.com> Dear* *Manoj Srivastava: * Thanks very much for your reply ??* * As I am not familiar with fortran, it is not a good idea for me to change the script ??* * I collect the distance between neighboring slabs?* * 4.57*0.0566=0.259 (ni.cond.out) 12*0.025=0.3 (Alwireal.cond.out) 5.3*0.0673=0.357 (al.cond.out) 12*0.025=0.3(for lead) 12*0.0257=0.308(for scattering) (AlwireH.cond.out) I think the default value for neighboring-slab distance is around 0.3 a.u. Thanks again ?? *____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/a1f53635/attachment.htm From udayagiri3 at gmail.com Sat Sep 12 08:15:40 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Sat, 12 Sep 2009 11:45:40 +0530 Subject: [Pw_forum] occupations from input Message-ID: Dear all Can somebody clearly tell me how to define occupations from input. I cant find much about that in this forum. The card "occupations" described in the example 11 for Al is not at all clear to me. What are those values mean. Looking forward to your help.... -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/c83c7222/attachment.htm From nkxirainbow at gmail.com Sat Sep 12 08:29:12 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 12 Sep 2009 06:29:12 +0000 Subject: [Pw_forum] occupations from input In-Reply-To: References: Message-ID: <21fbc4790909112329h3826ff3cq9af6fe8a4104fcc2@mail.gmail.com> Dear udayagiri sai babu? *If you deal with non-metal, you can choose "fixed".* In metal, band structure will cross fermi level. This may result into non-convergence of scf calculation. *Therefore,if you deal with metal, the occupation can accelerate the convergence.* *But you much check the convergence of the occupation value.* http://blog.sina.com.cn/s/blog_5f15ead20100d1ki.html There are some convergence test result. I hope it will give you some help?? * * On Sat, Sep 12, 2009 at 6:15 AM, udayagiri sai babu wrote: > Dear all > Can somebody clearly tell me how to define occupations from input. I cant > find much about that in this forum. The card "occupations" described in the > example 11 for Al is not at all clear to me. What are those values mean. > Looking forward to your help.... > > > -- > U.Saibabu > PhD student, > Deformation mechanisms modeling group, > Materials engineering department, > IISc Bangalore, > India. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/b1f44092/attachment.htm From udayagiri3 at gmail.com Sat Sep 12 08:52:51 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Sat, 12 Sep 2009 12:22:51 +0530 Subject: [Pw_forum] occupations from input In-Reply-To: <21fbc4790909112329h3826ff3cq9af6fe8a4104fcc2@mail.gmail.com> References: <21fbc4790909112329h3826ff3cq9af6fe8a4104fcc2@mail.gmail.com> Message-ID: Dear Xirainbow If i have to write occupations from input for say for Cr (nbnd=12) how does my occupations card look like On Sat, Sep 12, 2009 at 11:59 AM, xirainbow wrote: > Dear udayagiri sai babu? *If you deal with non-metal, you can choose > "fixed".* > In metal, band structure will cross fermi level. This may result into > non-convergence of scf calculation. > *Therefore,if you deal with metal, the occupation can accelerate the > convergence.* > *But you much check the convergence of the occupation value.* > > http://blog.sina.com.cn/s/blog_5f15ead20100d1ki.html > There are some convergence test result. I hope it will give you some help?? > * > * > On Sat, Sep 12, 2009 at 6:15 AM, udayagiri sai babu wrote: > >> Dear all >> Can somebody clearly tell me how to define occupations from input. I cant >> find much about that in this forum. The card "occupations" described in the >> example 11 for Al is not at all clear to me. What are those values mean. >> Looking forward to your help.... >> >> >> -- >> U.Saibabu >> PhD student, >> Deformation mechanisms modeling group, >> Materials engineering department, >> IISc Bangalore, >> India. >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/28dfa5c7/attachment.htm From nkxirainbow at gmail.com Sat Sep 12 09:43:43 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 12 Sep 2009 07:43:43 +0000 Subject: [Pw_forum] occupations from input In-Reply-To: References: <21fbc4790909112329h3826ff3cq9af6fe8a4104fcc2@mail.gmail.com> Message-ID: <21fbc4790909120043k705274b5lcc41250355bdbd71@mail.gmail.com> Dear udayagiri sai babu?*Sorry, I am not fully understand what you want??* *You can find how to set occupation at example directory.* For example: &system occupation = 'smearing' smearing = 'gaussian' degauss=0.001 / Or you can use PWgui for convenience?? On Sat, Sep 12, 2009 at 6:52 AM, udayagiri sai babu wrote: > Dear Xirainbow > If i have to write occupations from input for say for Cr (nbnd=12) how does > my occupations card look like > ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/c7b89c14/attachment.htm From paulatto at sissa.it Sat Sep 12 10:15:01 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 12 Sep 2009 10:15:01 +0200 (CEST) Subject: [Pw_forum] occupations from input In-Reply-To: References: Message-ID: <48776.78.12.168.158.1252743301.squirrel@webmail.sissa.it> On Sat, September 12, 2009 08:15, udayagiri sai babu wrote: > Dear all > Can somebody clearly tell me how to define occupations from input. I cant > find much about that in this forum. The card "occupations" described in > the > example 11 for Al is not at all clear to me. What are those values mean. > Looking forward to your help.... It's quite easy, actually, there are only a couple of points you have to keep in mind: 1. if nspin=1 occupations can go from 0 to 2, you have to specify the occupation from the lower to the highest band and the sum of the occupations will have to be the number of electrons; 2. if nspin=2 occupations go from 0 to 1, you specify the occupation for spin up first, then for spin down (always on a newline); Let's say you want to reproduce the calculation of the Cr isolated atom, with semicore states in valence: 3s2 3p6 4s1 3d5 4p0 first with nspin=1 and spherical (as it is done in ld1.x): OCCUPATIONS 2 2 2 2 1 1 1 1 1 1 0 0 0 !3s2 3p6 4s1 3d5 4p0 then spin polarized (nspin=2), according to Hund's rule you have to maximize the total angular momentum: OCCUPATIONS 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 !3s2 3p6 4s1 3d5 4p0 Chrome is a lucky case, as it has a spherical ground state. As a last example let's take an oxygen atom (2s2 2p4) and set the occupations to reproduce the ld1.x calculation: OCCUPATIONS 2 4/3 4/3 4/3 or, equivalently: OCCUPATIONS 2 1.333333 1.333333 1.333334 I hope it helps, best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From udayagiri3 at gmail.com Sat Sep 12 10:34:13 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Sat, 12 Sep 2009 14:04:13 +0530 Subject: [Pw_forum] occupations from input In-Reply-To: <48776.78.12.168.158.1252743301.squirrel@webmail.sissa.it> References: <48776.78.12.168.158.1252743301.squirrel@webmail.sissa.it> Message-ID: dear Lorenzo PaulattoThank you for you clear explanation i understood it now. previously i was not clear how these fractions are coming but now it is clear. Thank you very much for your explanation On Sat, Sep 12, 2009 at 1:45 PM, Lorenzo Paulatto wrote: > > On Sat, September 12, 2009 08:15, udayagiri sai babu wrote: > > Dear all > > Can somebody clearly tell me how to define occupations from input. I > cant > > find much about that in this forum. The card "occupations" described in > > the > > example 11 for Al is not at all clear to me. What are those values mean. > > Looking forward to your help.... > > > It's quite easy, actually, there are only a couple of points you have to > keep in mind: > > 1. if nspin=1 occupations can go from 0 to 2, you have to specify the > occupation from the lower to the highest band and the sum of the > occupations will have to be the number of electrons; > > 2. if nspin=2 occupations go from 0 to 1, you specify the occupation for > spin up first, then for spin down (always on a newline); > > Let's say you want to reproduce the calculation of the Cr isolated atom, > with semicore states in valence: 3s2 3p6 4s1 3d5 4p0 > > first with nspin=1 and spherical (as it is done in ld1.x): > OCCUPATIONS > 2 2 2 2 1 1 1 1 1 1 0 0 0 > !3s2 3p6 4s1 3d5 4p0 > > then spin polarized (nspin=2), according to Hund's rule you have to > maximize the total angular momentum: > OCCUPATIONS > 1 1 1 1 1 1 1 1 1 1 0 0 0 > 1 1 1 1 0 0 0 0 0 0 0 0 0 > !3s2 3p6 4s1 3d5 4p0 > > Chrome is a lucky case, as it has a spherical ground state. As a last > example let's take an oxygen atom (2s2 2p4) and set the occupations to > reproduce the ld1.x calculation: > OCCUPATIONS > 2 4/3 4/3 4/3 > > or, equivalently: > OCCUPATIONS > 2 1.333333 1.333333 1.333334 > > > I hope it helps, best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/f14a56e7/attachment.htm From smogunov at sissa.it Sat Sep 12 18:11:19 2009 From: smogunov at sissa.it (Alexandre Smogunov) Date: Sat, 12 Sep 2009 18:11:19 +0200 Subject: [Pw_forum] How to control number of slabs in pwcond calculation? In-Reply-To: <21fbc4790909110901j480d415bx87a8eaed51f4cb15@mail.gmail.com> References: <21fbc4790909110901j480d415bx87a8eaed51f4cb15@mail.gmail.com> Message-ID: <20090912181119.ot0dd8ev4w0sg848@webmail.sissa.it> Dear Hui Wang. There is no simple way to control the number of slabs. By default it is equal to nr3s, the number of smooth mesh points in the z direction (direction of transport), as defined in PW and which is controlled by the cut-off energy for pseudo wave functions. Anyway, I do not think there is any reason to change nrz by hands (not by changing the cut-off energy) ... Quoting xirainbow : > Dear all: I find the following content at > "/espresso-4.0.4/examples/example12/results/al.cond.out" file. > *" nrz = 21* > *.........* > * k slab z(k) z(k+1) crossing(iorb=1,norb)* > * 1 0.0000 0.0673 0.0673 111100000000* > *.........* > * 20 1.2793 1.3467 0.0673 000001111111* > * 21 1.3467 1.4140 0.0673 000000001111 "* > > I want to know, at *.cond.in input file, how to control the number of > slabs along z direction in left, right lead and scattering region, > respectively. > By the way, what is the meaning of "crossing(iorb=1,norb)"? it is 1 (or 0) if the nonlocal orbital iorb intersects (or not) the corresponding slab. Regards, Alexander > > Thanks in advance :) > > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From asafis at yahoo.com.br Sat Sep 12 23:35:27 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Sat, 12 Sep 2009 14:35:27 -0700 (PDT) Subject: [Pw_forum] tetrahedron method Message-ID: <991254.75993.qm@web52311.mail.re2.yahoo.com> If a calculation is done using the tetrahedron method, how to get the LDOS and PDOS ? Regards, ?lvaro Santos Alves Universidade Federal Fluminense Niter?i, Rio de Janeiro, Brasil ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090912/1229c236/attachment.htm From jibiaoli at gmail.com Sun Sep 13 08:18:41 2009 From: jibiaoli at gmail.com (Clark Lee) Date: Sun, 13 Sep 2009 08:18:41 +0200 Subject: [Pw_forum] tetrahedron method In-Reply-To: <991254.75993.qm@web52311.mail.re2.yahoo.com> References: <991254.75993.qm@web52311.mail.re2.yahoo.com> Message-ID: Please use projwfc.x to get LDOS and PDOS. Detailed information for input parameters is included in /doc/INPUT_PROJWFC 2009/9/12 ?lvaro Alves > If a calculation is done using the tetrahedron method, how to get the LDOS > and PDOS ? > > Regards, > > ?lvaro Santos Alves > Universidade Federal Fluminense > Niter?i, Rio de Janeiro, Brasil > > > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jibiao Li AlbaNova University Center, Sweden State Key Lab of Corrosion and Protection (SKLCP) Institute of Metal Research (IMR) Chinese Academy of Sciences (CAS), China Phone: 024-23971339 Email: jibiaoli at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/3f57f452/attachment.htm From ihsanas at yahoo.com Sun Sep 13 14:04:12 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 13 Sep 2009 05:04:12 -0700 (PDT) Subject: [Pw_forum] Fortran runtime error Message-ID: <747225.26279.qm@web52307.mail.re2.yahoo.com> Hi when I put job for 2x2 surface the cluster work very well but when I put the job for 4x2 surface it give me this error Fortran runtime error: ALLOCATE: Out of memory. on the shell and this is the error in the output file ?number of k points=??? 8? gaussian broad. (Ry)=? 0.0150???? ngauss =?? 1 ?????????????????????? cart. coord. in units 2pi/a_0 ??????? k(??? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 2) = (?? 0.0000000?? 0.3333333?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 3) = (?? 0.0000000?? 0.6666667?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 4) = (?? 0.0000000? -1.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 5) = (?? 0.3333333?? 0.0000000?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 6) = (?? 0.3333333?? 0.3333333?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 7) = (?? 0.3333333?? 0.6666667?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 8) = (?? 0.3333333? -1.0000000?? 0.0000000), wk =?? 0.2222222 ???? G cutoff = 5499.5703? (2391129 G-vectors)???? FFT grid: (150, 75,432) ???? G cutoff = 2199.8281? ( 605201 G-vectors)? smooth grid: ( 96, 48,270) rank 7 in job 1? alpha_50605?? caused collective abort of all ranks ? exit status of rank 7: return code 2 please tell me what is the meaning of this error and how can I fixed it. best regards Ihsan Erikat Jordan university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/6bd812c7/attachment.htm From yccheng.nju at gmail.com Sun Sep 13 14:10:21 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sun, 13 Sep 2009 20:10:21 +0800 Subject: [Pw_forum] Fortran runtime error In-Reply-To: <747225.26279.qm@web52307.mail.re2.yahoo.com> References: <747225.26279.qm@web52307.mail.re2.yahoo.com> Message-ID: Out of memory. on the shell ? Please check the memory in your cluster. 2009/9/13 Ihsan Erikat > Hi > when I put job for 2x2 surface the cluster work very well but when I put > the job for 4x2 surface it give me this error > Fortran runtime error: ALLOCATE: Out of memory. on the shell > > and this is the error in the output file > > > number of k points= 8 gaussian broad. (Ry)= 0.0150 ngauss = 1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.1111111 > k( 2) = ( 0.0000000 0.3333333 0.0000000), wk = 0.2222222 > k( 3) = ( 0.0000000 0.6666667 0.0000000), wk = 0.2222222 > k( 4) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.1111111 > k( 5) = ( 0.3333333 0.0000000 0.0000000), wk = 0.2222222 > k( 6) = ( 0.3333333 0.3333333 0.0000000), wk = 0.4444444 > k( 7) = ( 0.3333333 0.6666667 0.0000000), wk = 0.4444444 > k( 8) = ( 0.3333333 -1.0000000 0.0000000), wk = 0.2222222 > > G cutoff = 5499.5703 (2391129 G-vectors) FFT grid: (150, 75,432) > G cutoff = 2199.8281 ( 605201 G-vectors) smooth grid: ( 96, 48,270) > rank 7 in job 1 alpha_50605 caused collective abort of all ranks > exit status of rank 7: return code 2 > > > please tell me what is the meaning of this error and how can I fixed it. > best regards > Ihsan Erikat > Jordan university > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/06735987/attachment.htm From ihsanas at yahoo.com Sun Sep 13 14:12:52 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 13 Sep 2009 05:12:52 -0700 (PDT) Subject: [Pw_forum] Fortran runtime error: ALLOCATE: Message-ID: <549224.51506.qm@web52306.mail.re2.yahoo.com> Hi when I put job for 2x2 surface the cluster work very well but when I put the job for 4x2 surface it give me this error Fortran runtime error: ALLOCATE: Out of memory. on the shell and this is the error in the output file ?number of k points=??? 8? gaussian broad. (Ry)=? 0.0150???? ngauss =?? 1 ?????????????????????? cart. coord. in units 2pi/a_0 ??????? k(??? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 2) = (?? 0.0000000?? 0.3333333?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 3) = (?? 0.0000000?? 0.6666667?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 4) = (?? 0.0000000? -1.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 5) = (?? 0.3333333?? 0.0000000?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 6) = (?? 0.3333333?? 0.3333333?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 7) = (?? 0.3333333?? 0.6666667?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 8) = (?? 0.3333333? -1.0000000?? 0.0000000), wk =?? 0.2222222 ???? G cutoff = 5499.5703? (2391129 G-vectors)???? FFT grid: (150, 75,432) ???? G cutoff = 2199.8281? ( 605201 G-vectors)? smooth grid: ( 96, 48,270) rank 7 in job 1? alpha_50605?? caused collective abort of all ranks ? exit status of rank 7: return code 2 please tell me what is the meaning of this error and how can I fixed it. best regards Ihsan Erikat Jordan university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/8647ea97/attachment.htm From asafis at yahoo.com.br Sun Sep 13 14:13:57 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Sun, 13 Sep 2009 05:13:57 -0700 (PDT) Subject: [Pw_forum] Res: tetrahedron method In-Reply-To: References: <991254.75993.qm@web52311.mail.re2.yahoo.com> Message-ID: <158586.23394.qm@web52302.mail.re2.yahoo.com> I asked the question because in the PROJWFC documentation is written as follows: The tetrahedron method is presently not implemented. Regards, ?lvaro Santos Alves Universidade Federal Fluminense Niter?i, Rio de Janeiro, Brasil ________________________________ De: Clark Lee Para: PWSCF Forum Enviadas: Domingo, 13 de Setembro de 2009 3:18:41 Assunto: Re: [Pw_forum] tetrahedron method Please use projwfc.x to get LDOS and PDOS. Detailed information for input parameters is included in /doc/INPUT_PROJWFC 2009/9/12 ?lvaro Alves If a calculation is done using the tetrahedron method, how to get the LDOS and PDOS ? > > Regards, > >?lvaro Santos Alves >Universidade Federal Fluminense >Niter?i, Rio de Janeiro, Brasil > > > > > >________________________________ Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes >_______________________________________________ >>Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jibiao Li AlbaNova University Center, Sweden State Key Lab of Corrosion and Protection (SKLCP) Institute of Metal Research (IMR) Chinese Academy of Sciences (CAS), China Phone: 024-23971339 Email: jibiaoli at gmail.com ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/1a1ac138/attachment.htm From ihsanas at yahoo.com Sun Sep 13 14:17:44 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 13 Sep 2009 05:17:44 -0700 (PDT) Subject: [Pw_forum] Fortran runtime error: ALLOCATE: Message-ID: <641781.98544.qm@web52309.mail.re2.yahoo.com> Hi when I put job for 2x2 surface the cluster work very well but when I put the job for 4x2 surface it give me this error Fortran runtime error: ALLOCATE: Out of memory. on the shell and this is the error in the output file ?number of k points=??? 8? gaussian broad. (Ry)=? 0.0150???? ngauss =?? 1 ?????????????????????? cart. coord. in units 2pi/a_0 ??????? k(??? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 2) = (?? 0.0000000?? 0.3333333?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 3) = (?? 0.0000000?? 0.6666667?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 4) = (?? 0.0000000? -1.0000000?? 0.0000000), wk =?? 0.1111111 ??????? k(??? 5) = (?? 0.3333333?? 0.0000000?? 0.0000000), wk =?? 0.2222222 ??????? k(??? 6) = (?? 0.3333333?? 0.3333333?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 7) = (?? 0.3333333?? 0.6666667?? 0.0000000), wk =?? 0.4444444 ??????? k(??? 8) = (?? 0.3333333? -1.0000000?? 0.0000000), wk =?? 0.2222222 ???? G cutoff = 5499.5703? (2391129 G-vectors)???? FFT grid: (150, 75,432) ???? G cutoff = 2199.8281? ( 605201 G-vectors)? smooth grid: ( 96, 48,270) rank 7 in job 1? alpha_50605?? caused collective abort of all ranks ? exit status of rank 7: return code 2 please tell me what is the meaning of this error and how can I fixed it. best regards Ihsan Erikat Jordan university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/b4663a42/attachment-0001.htm From yccheng.nju at gmail.com Sun Sep 13 14:20:05 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sun, 13 Sep 2009 20:20:05 +0800 Subject: [Pw_forum] Fortran runtime error: ALLOCATE: In-Reply-To: <641781.98544.qm@web52309.mail.re2.yahoo.com> References: <641781.98544.qm@web52309.mail.re2.yahoo.com> Message-ID: Why do you ask your question again and again? 2009/9/13 Ihsan Erikat > > > > Hi > when I put job for 2x2 surface the cluster work very well but when I put > the job for 4x2 surface it give me this error > Fortran runtime error: ALLOCATE: Out of memory. on the shell > > and this is the error in the output file > > > number of k points= 8 gaussian broad. (Ry)= 0.0150 ngauss = 1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.1111111 > k( 2) = ( 0.0000000 0.3333333 0.0000000), wk = 0.2222222 > k( 3) = ( 0.0000000 0.6666667 0.0000000), wk = 0.2222222 > k( 4) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.1111111 > k( 5) = ( 0.3333333 0.0000000 0.0000000), wk = 0.2222222 > k( 6) = ( 0.3333333 0.3333333 0.0000000), wk = 0.4444444 > k( 7) = ( 0.3333333 0.6666667 0.0000000), wk = 0.4444444 > k( 8) = ( 0.3333333 -1.0000000 0.0000000), wk = 0.2222222 > > G cutoff = 5499.5703 (2391129 G-vectors) FFT grid: (150, 75,432) > G cutoff = 2199.8281 ( 605201 G-vectors) smooth grid: ( 96, 48,270) > rank 7 in job 1 alpha_50605 caused collective abort of all ranks > exit status of rank 7: return code 2 > > > please tell me what is the meaning of this error and how can I fixed it. > best regards > Ihsan Erikat > Jordan university > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/1b4f3c98/attachment.htm From paulatto at sissa.it Sun Sep 13 14:29:59 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 13 Sep 2009 14:29:59 +0200 (CEST) Subject: [Pw_forum] Fortran runtime error In-Reply-To: <747225.26279.qm@web52307.mail.re2.yahoo.com> References: <747225.26279.qm@web52307.mail.re2.yahoo.com> Message-ID: <34163.78.12.168.158.1252844999.squirrel@webmail.sissa.it> On Sun, September 13, 2009 14:04, Ihsan Erikat wrote: > when I put job for 2x2 surface the cluster work very well but when I put > the job for 4x2 surface it give me this error > Fortran runtime error: ALLOCATE: Out of memory. on the shell Dear Ihsan, the error message is quite clear: your hardware does not have enough memory for the calculation you are trying to do! There are a few measures you can take to reduce the memory usage: 1. if you are using pools, reduce the number of pools, it requires more communication between nodes, but reduces the memory usage. 2. if you are using norm-conserving pseudopotentials try ultrasoft or PAW instead; more in general try to do more accurate test on convergence with respect to wfc and rho cutoff 3. if you have a slab geometry you may still have good results reducing the amount of vacuum (you'll have to test the convergence wrt the amount of vacuum) 4. if you are using a computation cluster, run the code on more processors 5. if you are using a PC, buy more RAM 6. us cg instead of david diagonalization, but only as a last measure best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From paulatto at sissa.it Sun Sep 13 14:38:54 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 13 Sep 2009 14:38:54 +0200 (CEST) Subject: [Pw_forum] Res: tetrahedron method In-Reply-To: <158586.23394.qm@web52302.mail.re2.yahoo.com> References: <991254.75993.qm@web52311.mail.re2.yahoo.com> <158586.23394.qm@web52302.mail.re2.yahoo.com> Message-ID: <50681.78.12.168.158.1252845534.squirrel@webmail.sissa.it> On Sun, September 13, 2009 14:13, ?lvaro Alves wrote: > I asked the question because in the PROJWFC documentation is written as > follows: The tetrahedron method is presently not implemented. Dear Alvaro, I think you can specify the kind of smearing you want to use with the parameter ngauss, independently from what you've used for the scf calculation. Incidentally, I hope you have not uses the tetrahedra method for structure optimization: it is explicitly deprecated in the input manual. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From colonel.sreekar at gmail.com Sun Sep 13 16:06:07 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sun, 13 Sep 2009 19:36:07 +0530 Subject: [Pw_forum] calculation of 'local' moments in a scf calculation Message-ID: Dear QE users, i performed a scf caculation under LSDA of a supercell containing 32 atoms. One cationic site of GaAs host matrix is replaced by Mn. i want to calculate the 'local' moment on Mn atom. sincerely, Sreekar Guddeti B.Tech+M.Tech Engineering Physics IIT Bombay India -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/4dbd589f/attachment.htm From paulatto at sissa.it Sun Sep 13 16:17:17 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sun, 13 Sep 2009 16:17:17 +0200 (CEST) Subject: [Pw_forum] calculation of 'local' moments in a scf calculation In-Reply-To: References: Message-ID: <59444.78.12.168.158.1252851437.squirrel@webmail.sissa.it> On Sun, September 13, 2009 16:06, sreekar guddeti wrote: > Dear QE users, > i performed a scf caculation under LSDA of a supercell containing 32 > atoms. > One cationic site of GaAs host matrix is replaced by Mn. i want to > calculate > the 'local' moment on Mn atom. Dear Sreekan, I think the simplest way to do this kind of analysis is using projwfc.x to compute projected density of states. It also computes overlaps projection of crystal wavefunctions on atomic ones, from that you can deduce how much the spin up and spin down atomic wavefunctions are occupied. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From yccheng.nju at gmail.com Sun Sep 13 16:23:05 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sun, 13 Sep 2009 22:23:05 +0800 Subject: [Pw_forum] calculation of 'local' moments in a scf calculation In-Reply-To: References: Message-ID: You can search of the forum using the key words "local moment". This has been discussed in detail before. Hope it helps. 2009/9/13 sreekar guddeti > Dear QE users, > i performed a scf caculation under LSDA of a supercell containing 32 atoms. > One cationic site of GaAs host matrix is replaced by Mn. i want to calculate > the 'local' moment on Mn atom. > > sincerely, > Sreekar Guddeti > B.Tech+M.Tech > Engineering Physics > IIT Bombay > India > > -- > Sreekar Guddeti > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/c5a4afd3/attachment.htm From ihsanas at yahoo.com Sun Sep 13 16:35:12 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Sun, 13 Sep 2009 07:35:12 -0700 (PDT) Subject: [Pw_forum] fortran error Message-ID: <739410.35937.qm@web52305.mail.re2.yahoo.com> Thank you and sorry for sending the same email three times, this is becouse I recieved MAILER-DAEMON at mail.sdu.edu.cn failar notice from yahoo email... for the three times I sent the same email for you. Ihsan Erikat Jordan university ? ? ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/a3af0314/attachment.htm From giannozz at democritos.it Sun Sep 13 17:38:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 13 Sep 2009 17:38:52 +0200 Subject: [Pw_forum] Res: tetrahedron method In-Reply-To: <158586.23394.qm@web52302.mail.re2.yahoo.com> References: <991254.75993.qm@web52311.mail.re2.yahoo.com> <158586.23394.qm@web52302.mail.re2.yahoo.com> Message-ID: On Sep 13, 2009, at 14:13 , ?lvaro Alves wrote: > in the PROJWFC documentation is written as follows: > The tetrahedron method is presently not implemented. and it isn't right now. If you are willing to implement it, I can send you the needed formulae. P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Sep 13 17:54:33 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 13 Sep 2009 17:54:33 +0200 Subject: [Pw_forum] Fortran runtime error In-Reply-To: <747225.26279.qm@web52307.mail.re2.yahoo.com> References: <747225.26279.qm@web52307.mail.re2.yahoo.com> Message-ID: <1BCF79C2-004A-4EB1-B151-DE380635B450@democritos.it> On Sep 13, 2009, at 14:04 , Ihsan Erikat wrote: > Fortran runtime error: ALLOCATE: Out of memory > G cutoff = 5499.5703 (2391129 G-vectors) FFT grid: (150, > 75,432) if you want to perform calculations on large systems, you need to have an idea of how much time and memory you need. From the above data, you can easily calculate 2391129*3*8/1024/1024 = 55Mb just for the list of G vectors; 150*75*432*8/1024/1024= 39Mb for each real, 2*39Mb for each complex array on the FFT grid (charge, potential, etc). These are not even the largest arrays. As a rule of thimb, if you increase the size of the unit cell by a factor N, the required memory increases as N^2 P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From meghdad_saeedian at yahoo.com Mon Sep 14 08:23:56 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Sun, 13 Sep 2009 23:23:56 -0700 (PDT) Subject: [Pw_forum] convert pseudopotential from Castep format to Pwscf format Message-ID: <501243.55436.qm@web31406.mail.mud.yahoo.com> Dear all, I want to convert the pseudopotential from CASTEP format into PWSCF format. I was wondering if there was any utility that I can use? Thanks in advance. Meghdad Saeedian, M.Sc student University of Tehran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090913/e6c96fb4/attachment-0001.htm From paulatto at sissa.it Mon Sep 14 08:48:33 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 08:48:33 +0200 (CEST) Subject: [Pw_forum] convert pseudopotential from Castep format to Pwscf format In-Reply-To: <501243.55436.qm@web31406.mail.mud.yahoo.com> References: <501243.55436.qm@web31406.mail.mud.yahoo.com> Message-ID: <33816.78.12.168.158.1252910913.squirrel@webmail.sissa.it> On Mon, September 14, 2009 08:23, meghdad saeedian wrote: > I want to convert the pseudopotential from CASTEP format into PWSCF > format. I was wondering if there was any utility that I can use? Dear Meghdad, as far as I know, if the pseudopotential you wish to use is ultrasoft than you can use it directly, without any conversion or converting it with uspp2upf.x from the upftools directory. On the other hand, the pseuso is normconserving I know of no tool that could do the conversion. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From colonel.sreekar at gmail.com Mon Sep 14 12:55:38 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 14 Sep 2009 16:25:38 +0530 Subject: [Pw_forum] occupations from input Message-ID: Dear Sir Paulatto, is it necessary to generate a new pseudopotential corresponding to the new occupations because the example doesnt do so. it uses Al pseudopotential corresponding to occupations nl l occ 3S 0 2.00 3P 1 1.00 3D 2 0.00 whereas the occupations card reads OCCUPATIONS 1.0 1.0 1.0 1.0 0.0 0.0 1.0 1/3 1/3 1/3 sincerely, Sreekar Guddeti BTech + MTech Engineering Physics IIT Bombay India > > Can somebody clearly tell me how to define occupations from input. I > cant ... .... > It's quite easy, actually, there are only a couple of points you have to > keep in mind: > > 1. if nspin=1 occupations can go from 0 to 2, you have to specify the > occupation from the lower to the highest band and the sum of the > occupations will have to be the number of electrons; > > 2. if nspin=2 occupations go from 0 to 1, you specify the occupation for > spin up first, then for spin down (always on a newline); > > Let's say you want to reproduce the calculation of the Cr isolated atom, > with semicore states in valence: 3s2 3p6 4s1 3d5 4p0 > > first with nspin=1 and spherical (as it is done in ld1.x): > OCCUPATIONS > 2 2 2 2 1 1 1 1 1 1 0 0 0 > !3s2 3p6 4s1 3d5 4p0 > > then spin polarized (nspin=2), according to Hund's rule you have to > maximize the total angular momentum: > OCCUPATIONS > 1 1 1 1 1 1 1 1 1 1 0 0 0 > 1 1 1 1 0 0 0 0 0 0 0 0 0 > !3s2 3p6 4s1 3d5 4p0 > .... -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/b6c13c72/attachment.htm From paulatto at sissa.it Mon Sep 14 13:21:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 13:21:10 +0200 Subject: [Pw_forum] occupations from input In-Reply-To: References: Message-ID: In data 14 settembre 2009 alle ore 12:55:38, sreekar guddeti ha scritto: > is it necessary to generate a new pseudopotential corresponding to the > new occupations because the example doesnt do so. Hi Srekar, which example are you talking about? > it uses Al pseudopotential > corresponding to occupations > nl l occ > 3S 0 2.00 > 3P 1 1.00 > 3D 2 0.00 that's correct > > whereas the occupations card reads > OCCUPATIONS > 1.0 1.0 1.0 1.0 0.0 0.0 > 1.0 1/3 1/3 1/3 There is some error here: the upper line specify 6 occupations (6 spin-up bands) while the lower one only specifies 4 bands, but the number of spin-up and spin-down bands must be equal! Furthermore you have a total of 6 electrons, which is twice as much as the Al atom. If you don't specify nbnd you'll have 2 bands, and you'll have to specify 2 occupations for spin-up and 2 for spin-down. If you have manually set nbnd to any other number (I would use at least 4), you'll have to specify that many occupations (of course the higher ones will be zero). Best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From neelphysics at yahoo.in Mon Sep 14 14:11:34 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Mon, 14 Sep 2009 17:41:34 +0530 (IST) Subject: [Pw_forum] problem with projwfc.x Message-ID: <557105.31190.qm@web95010.mail.in2.yahoo.com> hi, ?To calculate, LDOS we run the scf then nscf and the Projwfc.x. and to anyalysis that which band is due to which states of corresponding atoms. I have caluclated DOS of BaTiO3, and i got files like, BaTiO3.pdos_atm#2(Ti)_wfc#1(s) BaTiO3.pdos_atm#2(Ti)_wfc#2(p) BaTiO3.pdos_atm#2(Ti)_wfc#3(s) BaTiO3.pdos_atm#2(Ti)_wfc#4(d) take the last one, it means it is DOS of Ti atom 4d states. and i have used Ba Perdew-Wang 91 gradient-corrected functional , in which the valance states are 3S 3 0 2.00 3P 3 1 6.00 3D 3 2 2.00 4S 4 0 2.00 4P 4 1 0.00 i have a question that how we are getting 1s and 2p states as we have used the pseudo potentials. And the second one that Ti has 22 electrons, how we can get Ti4d as the configuration is 4s2 3d2. thanks , Neel Physics, Univeristy of Delhi. ? Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/484cedd4/attachment.htm From nedward at MIT.EDU Mon Sep 14 14:38:32 2009 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Mon, 14 Sep 2009 08:38:32 -0400 (EDT) Subject: [Pw_forum] problem with projwfc.x In-Reply-To: <557105.31190.qm@web95010.mail.in2.yahoo.com> References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: Hi Neel, I think the numbers 1-4 here are an index that runs over the number of atomic wave functions found in the pseudopotential file (i.e. they are not the shell quantum number). from projwfc.f90 ! ! In the collinear case and the non-collinear, non spin-orbit case ! projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), ! where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f ! (one file per atomic wavefunction found in the pseudopotential file) ! - The format for the collinear, spin-unpolarized case is ! E LDOS(E) PDOS_1(E) ... PDOS_2l+1(E) ! where LDOS = \sum m=1,2l+1 PDOS_m(E) ! and PDOS_m(E) = projected DOS on atomic wfc with component m ! - The format for the collinear, spin-polarized case and the ! non-collinear, non spin-orbit case is as above with ! two components for both LDOS(E) and PDOS_m(E) regards, Nicholas > BaTiO3.pdos_atm#2(Ti)_wfc#1(s) > BaTiO3.pdos_atm#2(Ti)_wfc#2(p) > BaTiO3.pdos_atm#2(Ti)_wfc#3(s) > BaTiO3.pdos_atm#2(Ti)_wfc#4(d) > take the last one, it means it is DOS of Ti atom 4d states. and i have used Ba Perdew-Wang 91 gradient-corrected functional , in which the valance states are > 3S 3 0 2.00 > 3P 3 1 6.00 > 3D 3 2 2.00 > 4S 4 0 2.00 > 4P 4 1 0.00 > i have a question that how we are getting 1s and 2p states as we have used the pseudo potentials. And the second one that Ti has 22 electrons, how we can get Ti4d as the > configuration is 4s2 3d2. > ***************************************** Nicholas E. Singh-Miller Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From paulatto at sissa.it Mon Sep 14 14:40:32 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 14:40:32 +0200 Subject: [Pw_forum] problem with projwfc.x In-Reply-To: <557105.31190.qm@web95010.mail.in2.yahoo.com> References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: In data 14 settembre 2009 alle ore 14:11:34, Neel Singh ha scritto: Dear Neel, > in which the valance states are > 3S 3 0 2.00 > 3P 3 1 6.00 > 3D 3 2 2.00 > 4S 4 0 2.00 > 4P 4 1 0.00 > i have a question that how we are getting 1s and 2p states as we have > used the pseudo potentials. You cannot, but you don't need to either. The pseudopotential approximation uses the froze-core approximation: the occupation of core states is exactly the same as in the isolated atoms. > And the second one that Ti has 22 electrons, It has only 12 electrons in valence, and only if you consider 3s and 3p to be valence. Pseudopotential calculations only use valence electrons. > how we can get Ti4d as the > configuration is 4s2 3d2. You cannot, because there is no 4d wavefunction in the pseudopotential file the code has no way to project the crystal wavefunctions on it. You can add a projector for the 4d wavefunction while generating the pseudo, but you would get a much slower pseudopotential. You could also modify the code to read additional projectors from somewhere and use them in projwfc, but you would have to do it yourself. The GIPAW may do something like this internally, but I don't know the details. But are you sure you do want it? The 4d electron in Titanium, in the DFT framework, has an energy higher than 5s 5p 6s and 6p; actually it is not even a bound state! best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From meghdad_saeedian at yahoo.com Mon Sep 14 16:15:21 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Mon, 14 Sep 2009 07:15:21 -0700 (PDT) Subject: [Pw_forum] convert ABINIT pseudopotential to UPF format Message-ID: <7184.46444.qm@web31406.mail.mud.yahoo.com> Dear all, ? Would you please tell me if it is possible to convert?Teter "extended norm-conserving"?pseudopotential from?ABINIT?to PWSCF format. ? Thanks in advance. ? Meghdad Saeedian, M.Sc. student, University of Tehran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/30d5dfb0/attachment.htm From decboy9 at gmail.com Mon Sep 14 16:19:53 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 14 Sep 2009 19:49:53 +0530 Subject: [Pw_forum] problem with projwfc.x In-Reply-To: References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: Nicholas E. Singh-Miller and Lorenzo Paulatto sir, I am confused in 1 in the BaTiO3.pdos_atm#2(Ti)_wfc#1(s), if this 1 in the wfc#1(s), is not the shell quantum number and it is an index that runs over the number of atomic wave functions , that means what i understood is that since i have 3S 3 0 2.00 > 3P 3 1 6.00 > 3D 3 2 2.00 > 4S 4 0 2.00 > 4P 4 1 0.00 in my pseudo potential of Ti the BaTiO3.pdos_atm#2(Ti)_wfc#1(s)--> giving 3s states contribuition > BaTiO3.pdos_atm#2(Ti)_wfc#2(p)--> giving 3p states contribution, > BaTiO3.pdos_atm#2(Ti)_wfc#3(s)--> giving 4s states contribution > BaTiO3.pdos_atm#2(Ti)_wfc#4(d)--> giving 3d states contribution and my 4p states contribution has been not calculted beacuse my energies( may be excited depending upon the structure) are not upto those level. Am i correct???? Please help Thanks. On Mon, Sep 14, 2009 at 6:10 PM, Lorenzo Paulatto wrote: > In data 14 settembre 2009 alle ore 14:11:34, Neel Singh > ha scritto: > > Dear Neel, > > > > in which the valance states are > > 3S 3 0 2.00 > > 3P 3 1 6.00 > > 3D 3 2 2.00 > > 4S 4 0 2.00 > > 4P 4 1 0.00 > > > i have a question that how we are getting 1s and 2p states as we have > > used the pseudo potentials. > > You cannot, but you don't need to either. The pseudopotential > approximation uses the froze-core approximation: the occupation of core > states is exactly the same as in the isolated atoms. > > > And the second one that Ti has 22 electrons, > > It has only 12 electrons in valence, and only if you consider 3s and 3p to > be valence. Pseudopotential calculations only use valence electrons. > > > how we can get Ti4d as the > > configuration is 4s2 3d2. > > You cannot, because there is no 4d wavefunction in the pseudopotential > file the code has no way to project the crystal wavefunctions on it. You > can add a projector for the 4d wavefunction while generating the pseudo, > but you would get a much slower pseudopotential. You could also modify the > code to read additional projectors from somewhere and use them in projwfc, > but you would have to do it yourself. The GIPAW may do something like this > internally, but I don't know the details. > > But are you sure you do want it? The 4d electron in Titanium, in the DFT > framework, has an energy higher than 5s 5p 6s and 6p; actually it is not > even a bound state! > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/e73c0b5b/attachment-0001.htm From giannozz at democritos.it Mon Sep 14 16:23:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Sep 2009 16:23:08 +0200 Subject: [Pw_forum] convert ABINIT pseudopotential to UPF format In-Reply-To: <7184.46444.qm@web31406.mail.mud.yahoo.com> References: <7184.46444.qm@web31406.mail.mud.yahoo.com> Message-ID: <4AAE51CC.3050605@democritos.it> meghdad saeedian wrote: > Would you please tell me if it is possible to convert Teter "extended > norm-conserving" pseudopotential from ABINIT to PWSCF format. it is definitely possible, but the current converters support only the "Fritz-Haber" format among those used by ABINIT P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Mon Sep 14 16:44:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 16:44:42 +0200 Subject: [Pw_forum] problem with projwfc.x In-Reply-To: References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: In data 14 settembre 2009 alle ore 16:19:53, dev sharma ha scritto: > and my 4p states contribution has been not calculted beacuse my energies( > may be excited depending upon the structure) are not upto those level. Not really, the 4P wavefunction has been used to generate the local potential, hence it does not have an associated projector. You can find more details on what the local potential is and why it does not have projectors in the pseudo-gen guide from Paolo Giannozzi, which you can find (the guide, not Paolo) in the atomic_doc directory of the QE distribution. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From decboy9 at gmail.com Mon Sep 14 17:38:29 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 14 Sep 2009 21:08:29 +0530 Subject: [Pw_forum] problem with projwfc.x In-Reply-To: References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: Dear Sir, hi BaTiO3.pdos_atm#2(Ti)_wfc#1(s)--> giving 3s states contribuition BaTiO3.pdos_atm#2(Ti)_wfc#2(p)--> giving 3p states contribution, / / and is this understanding right ??? Dev On Mon, Sep 14, 2009 at 8:14 PM, Lorenzo Paulatto wrote: > In data 14 settembre 2009 alle ore 16:19:53, dev sharma > ha scritto: > > and my 4p states contribution has been not calculted beacuse my energies( > > may be excited depending upon the structure) are not upto those level. > > Not really, the 4P wavefunction has been used to generate the local > potential, hence it does not have an associated projector. > > You can find more details on what the local potential is and why it does > not have projectors in the pseudo-gen guide from Paolo Giannozzi, which > you can find (the guide, not Paolo) in the atomic_doc directory of the QE > distribution. > > regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/6e7e22ab/attachment.htm From paulatto at sissa.it Mon Sep 14 17:39:31 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 17:39:31 +0200 Subject: [Pw_forum] problem with projwfc.x In-Reply-To: References: <557105.31190.qm@web95010.mail.in2.yahoo.com> Message-ID: In data 14 settembre 2009 alle ore 17:38:29, dev sharma ha scritto: > and is this understanding right ??? yes, it is -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From dimpy.sharma at tyndall.ie Mon Sep 14 17:42:47 2009 From: dimpy.sharma at tyndall.ie (Dimpy Sharma) Date: Mon, 14 Sep 2009 16:42:47 +0100 Subject: [Pw_forum] Energy convergence in a scf calculation Message-ID: Hello there, One of my scf calculation is running ( not yet finished), it has completed almost 10 iterations, however what I have found is in iteration #8, it is showing me as CG style diagonalization c_bands: 3 eigenvalues not converged c_bands: 5 eigenvalues not converged ethr = 1.00E-02, avg # of iterations = 8.6 After that it is still running and moved to iteration #10. Also I have seen that in some of the iteration steps the energy is either increasing or decreasing in the successive steps;i.e it is not converging .My thresold values are as follows etot_thr= 1.D-8 forc_thr values =1.D-8Ry conv_thr = 1.0D-8Ry . ecutwfc=35Ry ecutrho=120Ry So can anybody tell me why is it happening so? Thanks Dimpy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/ebb42a7f/attachment.htm From paulatto at sissa.it Mon Sep 14 17:46:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 17:46:48 +0200 Subject: [Pw_forum] Energy convergence in a scf calculation In-Reply-To: References: Message-ID: In data 14 settembre 2009 alle ore 17:42:47, Dimpy Sharma ha scritto: > ecutwfc=35Ry > ecutrho=120Ry > So can anybody tell me why is it happening so? Dear Dimpy, your ecutrho is far too low! It should be at least 4 times ecutwfc (this is the default) and often much more (8-12 times) for ultrasoft calculations. From the documentation: +-------------------------------------------------------------------- Variable: ecutrho Type: REAL Default: 4 * ecutwfc Description: kinetic energy cutoff (Ry) for charge density and potential If there are ultrasoft PP, a larger value than the default is often desirable (ecutrho = 8 to 12 times ecutwfc, typically). If all PP are norm-conserving, you should stick to the default; you may reduce it to spare time, but not by a large amount. +-------------------------------------------------------------------- best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Mon Sep 14 17:51:38 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 14 Sep 2009 17:51:38 +0200 Subject: [Pw_forum] Energy convergence in a scf calculation In-Reply-To: References: Message-ID: In data 14 settembre 2009 alle ore 17:42:47, Dimpy Sharma ha scritto: > forc_thr values =1.D-8Ry I forgot one point: the force is not in Ry but in Ry/bohr, and the same is valid for its convergence threshold. Furthermore the value you have choosen is far too low and will probably never converge, unless forces are zero by symmetry. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From i_camps at yahoo.com.br Mon Sep 14 19:01:17 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Mon, 14 Sep 2009 14:01:17 -0300 Subject: [Pw_forum] << Importing atomic coordinates in PWgui >> Message-ID: <612c95fa0909141001i24514e5al4d5a694e21bc2065@mail.gmail.com> Hello all, This could be a silly question, I searched in the forum archive and did not find anything related. Well, my questions is: which is the format for the file with the atomic coordinates to be imported in PWgui? I tried the following formats without success: (the file name was Si.xyz) -) Si -0.69570 3.71840 3.71840 0 0 0 Si -1.51140 0.69570 1.51140 0 0 0 -) Si -0.69570 3.71840 3.71840 Si -1.51140 0.69570 1.51140 -) Si, -0.69570, 3.71840, 3.71840 0, 0, 0 Si, -1.51140, 0.69570, 1.51140 0, 0, 0 -) Si, -0.69570, 3.71840, 3.71840 Si, -1.51140, 0.69570, 1.51140 Note: I let the nat and ntyp variables with zero and defined before importing the files, too. []'s, Camps ___ Joan Crawford - "I, Joan Crawford, I believe in the dollar. Everything I earn, I spend." -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090914/f112473c/attachment.htm From colonel.sreekar at gmail.com Tue Sep 15 04:13:08 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Tue, 15 Sep 2009 07:43:08 +0530 Subject: [Pw_forum] occupations from input Message-ID: >Hi Srekar, Hello Sir Paulatto, >which example are you talking about? in example 11 , scf calculation of isolated neutral Al is performed. suppose i want to do similar calculation for isolated Al+ ion, i gave input parameters as nelec=2, OCCUPATIONS 2.0 0.0 0.0 0.0 0.0 0.0 is this correct? is it necessary to generate a new Al+ pseudopotential with occupations card reading as nl l occ 3S 0 2.00 3P 1 0.00 3D 2 0.00 sincerely, Sreekar Guddeti BTech+MTech E.Physics IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090915/9046339a/attachment.htm From paulatto at sissa.it Tue Sep 15 08:29:45 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 15 Sep 2009 08:29:45 +0200 (CEST) Subject: [Pw_forum] occupations from input In-Reply-To: References: Message-ID: <50753.78.12.168.158.1252996185.squirrel@webmail.sissa.it> On Tue, September 15, 2009 04:13, sreekar guddeti wrote: > nelec=2, > OCCUPATIONS > 2.0 0.0 0.0 0.0 0.0 0.0 > > is this correct? Yes it is. > is it necessary to generate a new Al+ pseudopotential with occupations > card reading as > nl l occ > 3S 0 2.00 > 3P 1 0.00 > 3D 2 0.00 Not at all. But keep in mind that a calculation for a charged system is a bit difficult to converge, especially with respect to the cell size. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From sunshoutian168 at yahoo.com.cn Tue Sep 15 09:17:15 2009 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Tue, 15 Sep 2009 00:17:15 -0700 (PDT) Subject: [Pw_forum] compile QE Message-ID: <738829.33522.qm@web15308.mail.cnb.yahoo.com> >Dear all, >I have a problem when I compile QE in our cluster with ifort. The error is as follows: > >fortcom: Severe: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it >occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error. > >compilation aborted for realus.f90 (code 3) >make[1]: *** [realus.o] Error 3 >make[1]: Leaving directory `/ds13/zfliu/stsun/espresso-4.1/PW' >make: *** [pw] Error 2 > >Could anyone help me, thanks a lot. >Sun Shoutian Chemistry, The Chinese University of Hong Kong. ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090915/611a7c22/attachment.htm From paulatto at sissa.it Tue Sep 15 09:22:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 15 Sep 2009 09:22:34 +0200 Subject: [Pw_forum] compile QE In-Reply-To: <738829.33522.qm@web15308.mail.cnb.yahoo.com> References: <738829.33522.qm@web15308.mail.cnb.yahoo.com> Message-ID: In data 15 settembre 2009 alle ore 09:17:15, shoutian sun ha scritto: >> fortcom: Severe: **Internal compiler error: segmentation violation >> signal raised** Please report this error along with the circumstances >> in which it >occurred in a Software Problem Report. Note: File and >> line given may not be explicit cause of this error. Dear Shoutian Sun, The error says that you have to report to the compiler producers, not to us. It is a compiler bug, that we have no power to solve... >> Could anyone help me, thanks a lot. Nevertheless, if you compile that specific file with lower optimization (you can do it by hand, copying the compilation line displayed by make but replacing -O2 or -O3 with -O0) it will probably work. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Tue Sep 15 09:53:08 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 15 Sep 2009 09:53:08 +0200 Subject: [Pw_forum] << Importing atomic coordinates in PWgui >> In-Reply-To: <612c95fa0909141001i24514e5al4d5a694e21bc2065@mail.gmail.com> References: <612c95fa0909141001i24514e5al4d5a694e21bc2065@mail.gmail.com> Message-ID: In data 14 settembre 2009 alle ore 19:01:17, I. Camps ha scritto: > Well, my questions is: which is the format for the file with the atomic > coordinates to be imported in PWgui? Dear I., after a couple of tries I could have it load the coordinates from another pw input file. I don't know if it's the only option. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Tue Sep 15 10:05:50 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 15 Sep 2009 10:05:50 +0200 Subject: [Pw_forum] << Importing atomic coordinates in PWgui >> In-Reply-To: References: <612c95fa0909141001i24514e5al4d5a694e21bc2065@mail.gmail.com> Message-ID: <1253001950.23037.6.camel@walk.ijs.si> On Tue, 2009-09-15 at 09:53 +0200, Lorenzo Paulatto wrote: > In data 14 settembre 2009 alle ore 19:01:17, I. Camps > ha scritto: > > Well, my questions is: which is the format for the file with the atomic > > coordinates to be imported in PWgui? > > > Dear I., > after a couple of tries I could have it load the coordinates from another > pw input file. I don't know if it's the only option. Correct! Looking into the source files, one finds: ------------------------------------------------------------------------ # ::pwscf::pwLoadAtomCoord -- # # This function loads atomic coordinates from file. It supposes the # PWSCF syntax, i.e., searches for ATOMIC_POSTIONS keyword. This means # that atomic coordinates can be extracted from PWSCF's input file. # ------------------------------------------------------------------------ This simply means that the XYZ --> PWgui conversion is very easy: strip the first two lines from XYZ file, and decorate the so obtained coordinates with "ATOMIC_POSITIONS angstroms". Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sivaramakrishnaj at gmail.com Tue Sep 15 12:09:21 2009 From: sivaramakrishnaj at gmail.com (siva rama krishna) Date: Tue, 15 Sep 2009 15:39:21 +0530 Subject: [Pw_forum] Are Lowdin charge populations reliable ? In-Reply-To: References: Message-ID: Dear users, I am working on a surface catalyzed reaction problem in which I have to analyze the first elementary step of adsorption. I am performing a projected density of states (PDOS) analysis for a reactant molecule adsorbing on a metal surface. Could some one please tell me if the Lowdin charge populations that arise out of a PDOS analaysis are reliable ? To what extent can they be used to draw inferences on charge donation and acceptance patterns between metal substrate and reactant molecule. Thanks in advance and Good luck for your work ! Best regards, Siva Rama Krishna J Member of Technical staff Computational Research Laboratories Limited India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090915/b1d5bb66/attachment.htm From i_camps at yahoo.com.br Tue Sep 15 12:23:57 2009 From: i_camps at yahoo.com.br (I. Camps) Date: Tue, 15 Sep 2009 07:23:57 -0300 Subject: [Pw_forum] << Importing atomic coordinates in PWgui >> In-Reply-To: <1253001950.23037.6.camel@walk.ijs.si> References: <612c95fa0909141001i24514e5al4d5a694e21bc2065@mail.gmail.com> <1253001950.23037.6.camel@walk.ijs.si> Message-ID: <612c95fa0909150323i7ed8f3e5g96b0aa124b7ed9d3@mail.gmail.com> Thank you! This input works: ATOMIC_POSITIONS angstroms ATOMIC_POSITIONS angstroms Si -0.69570 3.71840 3.71840 Si -1.51140 0.69570 1.51140 Si -3.71840 1.51140 2.90270 Si -2.90270 2.90270 0.69570 Si -2.81310 3.80800 2.81310 Si -3.80800 0.60610 0.60610 Si -1.60100 1.60100 3.80800 Si -0.60610 2.81310 1.60100 []'s, Camps ___ Samuel Goldwyn - "I'm willing to admit that I may not always be right, but I am never wrong." On Tue, Sep 15, 2009 at 5:05 AM, Tone Kokalj wrote: > On Tue, 2009-09-15 at 09:53 +0200, Lorenzo Paulatto wrote: > > In data 14 settembre 2009 alle ore 19:01:17, I. Camps > > ha scritto: > > > Well, my questions is: which is the format for the file with the atomic > > > coordinates to be imported in PWgui? > > > > > > Dear I., > > after a couple of tries I could have it load the coordinates from another > > pw input file. I don't know if it's the only option. > > > Correct! > > Looking into the source files, one finds: > > > ------------------------------------------------------------------------ > # ::pwscf::pwLoadAtomCoord -- > # > # This function loads atomic coordinates from file. It supposes the > # PWSCF syntax, i.e., searches for ATOMIC_POSTIONS keyword. This means > # that atomic coordinates can be extracted from PWSCF's input file. > # > ------------------------------------------------------------------------ > > This simply means that the XYZ --> PWgui conversion is very easy: strip > the first two lines from XYZ file, and decorate the so obtained > coordinates with "ATOMIC_POSITIONS angstroms". > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090915/bdf016a2/attachment.htm From degironc at sissa.it Tue Sep 15 13:33:08 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Sep 2009 13:33:08 +0200 Subject: [Pw_forum] Are Lowdin charge populations reliable ? In-Reply-To: References: Message-ID: <4AAF7B74.1060404@sissa.it> As any atom-in-solid charge partitioning Lowdin method is somehow arbitrary, and gives only semi-quantitative trends. Variations of just fractions of % are insignificant while variations of several % are more reliable.. just apply common sense and do not over-emphasizes small details. Notice also that due to incompleteness of the atomic-orbital basis-set used in the decomposition the number of electrons in the PDOS does not equals exactly the total number of electrons in the system. Hope this helps, stefano de Gironcoli - SISSA and DEMOCRITOS siva rama krishna wrote: > Dear users, > > I am working on a surface catalyzed reaction problem in which I have > to analyze the first elementary step of adsorption. > I am performing a projected density of states (PDOS) analysis for a > reactant molecule adsorbing on a metal surface. > Could some one please tell me if the Lowdin charge populations that > arise out of a PDOS analaysis are reliable ? > To what extent can they be used to draw inferences on charge donation > and acceptance patterns between metal substrate and reactant molecule. > > Thanks in advance and Good luck for your work ! > > Best regards, > > Siva Rama Krishna J > Member of Technical staff > Computational Research Laboratories Limited > India > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sunshoutian168 at yahoo.com.cn Tue Sep 15 14:16:24 2009 From: sunshoutian168 at yahoo.com.cn (shoutian sun) Date: Tue, 15 Sep 2009 05:16:24 -0700 (PDT) Subject: [Pw_forum] error Message-ID: <287350.83250.qm@web15304.mail.cnb.yahoo.com> >Dear all, >I have a problem when I compile QE in our cluster with ifort. The error is as follows: > >fortcom: Severe: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it >occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error. > >compilation aborted for realus.f90 (code 3) >make[1]: *** [realus.o] Error 3 >make[1]: Leaving directory `/ds13/zfliu/stsun/espresso-4.1/PW' >make: *** [pw] Error 2 > >Could anyone help me, thanks a lot. >Sun Shoutian Chemistry, The Chinese University of Hong Kong. ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090915/5ea3e981/attachment.htm From degironc at sissa.it Tue Sep 15 14:20:51 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Sep 2009 14:20:51 +0200 Subject: [Pw_forum] error In-Reply-To: <287350.83250.qm@web15304.mail.cnb.yahoo.com> References: <287350.83250.qm@web15304.mail.cnb.yahoo.com> Message-ID: <4AAF86A3.1070109@sissa.it> shoutian sun wrote: > > >fortcom: Severe: **Internal compiler error: segmentation violation > signal raised** Please report this error along with the circumstances > in which it >occurred in a Software Problem Report. Note: File and > line given may not be explicit cause of this error. Internal compiler error means that this is a problem of the compiler not of QE ... stefano From jjr19 at zips.uakron.edu Tue Sep 15 14:27:42 2009 From: jjr19 at zips.uakron.edu (James J Ramsey) Date: Tue, 15 Sep 2009 08:27:42 -0400 Subject: [Pw_forum] compile QE In-Reply-To: <738829.33522.qm@web15308.mail.cnb.yahoo.com> References: <738829.33522.qm@web15308.mail.cnb.yahoo.com> Message-ID: <46e014700909150527w639364e9s36f524b3a40be2fd@mail.gmail.com> 2009/9/15 shoutian sun > > >Dear all, > >I have a problem when I compile QE in our cluster with ifort. The error is as follows: > > > >fortcom: Severe: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it >occurred in a Software Problem Report.? Note: File and line given may not be explicit cause of this error. > > > >compilation aborted for realus.f90 (code 3) > >make[1]: *** [realus.o] Error 3 > >make[1]: Leaving directory `/ds13/zfliu/stsun/espresso-4.1/PW' > >make: *** [pw] Error 2 > > > >Could anyone help me, thanks a lot. It would help to know which version of ifort that you are using. From yccheng.nju at gmail.com Wed Sep 16 03:53:28 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 16 Sep 2009 09:53:28 +0800 Subject: [Pw_forum] workfunction and efield Message-ID: Dear pwscf users, The PWscf can calculate the workfunction in slab model and the electronic structure under external efield. I am concerning that whether it it correct to calculate the workfunction of a certain materials under external efield? Thank you in advance. -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/18ae1a9f/attachment.htm From colonel.sreekar at gmail.com Wed Sep 16 08:14:06 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Wed, 16 Sep 2009 11:44:06 +0530 Subject: [Pw_forum] occupations from input Message-ID: >> is it necessary to generate a new Al+ pseudopotential with occupations >> card reading as >> nl l occ >> 3S 0 2.00 >> 3P 1 0.00 >> 3D 2 0.00 >Not at all >But keep in mind that a calculation for a charged system is a bit >difficult to converge, especially with respect to the cell size. Sir Paulatto, Thank you very much for your invaluable help. I got to understand that it is to do with transferability of pseudopotentials, but sir i would like to ask one last question regarding this occupations issue. Suppose i have a single Mn atom in a GaAs supercell. The hole(spin dw) associated with Mn sits in one of the Mn d states (as i inferred from spin resolved local moments on Mn atom (~5up + ~1dw )). I want to delocalize the hole by setting the d spindown occupations to ~zero. is there a way to specify this as i dont know the band number of hole apriorily sincerely -- Sreekar Guddeti BTech + MTech IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/9a1cae87/attachment.htm From udayagiri3 at gmail.com Wed Sep 16 08:19:07 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 16 Sep 2009 11:49:07 +0530 Subject: [Pw_forum] Acceptable error in cohesive energy Message-ID: Dear PWSCF users I calculated the cohesive energy for aluminium using GGA potential, which came out to be 3.59 ev/atom. When i compared this value with that of given in Kittel (3.34ev/atom) the error is 7.5%. Here i would like to know how much error in cohesive energy is acceptable and also if somebody can comment on error tolerance in lattice parameter and Bulk modulus (for GGA as well as LDA) as well it would be nice. Thanks in advance -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/48f0cee1/attachment.htm From giannozz at democritos.it Wed Sep 16 08:24:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Sep 2009 08:24:16 +0200 Subject: [Pw_forum] occupations from input In-Reply-To: References: Message-ID: On Sep 16, 2009, at 8:14 , sreekar guddeti wrote: > > Suppose i have a single Mn atom in a GaAs supercell. > The hole(spin dw) associated with Mn sits in one of the > Mn d states (...). I want to delocalize the hole by setting > the d spindown occupations to ~zero. is there a way to > specify this no --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Wed Sep 16 08:56:47 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 16 Sep 2009 08:56:47 +0200 Subject: [Pw_forum] workfunction and efield In-Reply-To: References: Message-ID: <553E9976-8B8B-456B-AEDA-E34805760F0F@sissa.it> Hi. before calculating anything, I think it is important to define and understand what one is going to calculate. Would you please give us a definition of "work function under an external field" and compare/ contrast it to the accepted definition of "workfunction at zero field"? Thanks - SB On Sep 16, 2009, at 3:53 AM, ??? wrote: > Dear pwscf users, > The PWscf can calculate the workfunction in slab model and > the electronic structure under external efield. I am concerning > that whether it it correct to calculate the workfunction of a > certain materials under external efield? Thank you in advance. > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/0e391337/attachment.htm From phylyh at nus.edu.sg Wed Sep 16 09:55:56 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Wed, 16 Sep 2009 15:55:56 +0800 Subject: [Pw_forum] Is the constrain card avaible? In-Reply-To: Message-ID: <000f01ca36a3$1f2a1060$71a213ac@nusa0bcf64b485> I set the constrains card in input file to constrain the distance between two atoms in relaxation, but the it does not work at all. I am not sure what's wrong. Is there anyone can help me? Thanks! The input file is included as follows: &CONTROL title = 'CO_O2' , calculation = 'relax' , prefix='CO_O2-con', restart_mode = 'from_scratch' , outdir = '/home/phylyh/00-Au-catalysis/CO_O2-constrain/tmp' , pseudo_dir = '/home/phylyh/pseudo_dir' , disk_io = 'none', etot_conv_thr = 1.0D-5, forc_conv_thr = 1.0D-4, / &SYSTEM ibrav = 0, nat = 76, ntyp = 3, ecutwfc = 30 , ecutrho = 300 , nosym = .false. , nspin = 2, starting_magnetization(2) = 0.7 , starting_magnetization(3) = 0.7 , occupations='smearing', smearing='gauss', degauss=0.01, / &ELECTRONS conv_thr = 1.D-6, mixing_mode = 'local-TF', mixing_beta = 0.8D0, mixing_ndim = 8, diagonalization = 'david' , electron_maxstep = 500 / &IONS ion_dynamics = 'bfgs', upscale = 18.0, bfgs_ndim = 1, trust_radius_max = 0.8D0, trust_radius_min = 1.D-3, trust_radius_ini = 0.5D0, w_1 = 0.01D0, w_2 = 0.5D0, pot_extrapolation = "second_order", / CELL_PARAMETERS cubic 24.18234040895346130 -13.96168074474439 0.000000000000000 0.000000000000000 27.9233614894888667 0.000000000000000 0.000000000000000 0.000000000000000 37.7945232712218137894 ATOMIC_SPECIES C 1.00000 C.pbe-rrkjus.UPF O 1.00000 O.pbe-rrkjus.UPF Au 1.00000 Au.pbe-nd-van.UPF ATOMIC_POSITIONS crystal C 0.0011800000211225 0.0029599999543280 0.3677699863910680 C 0.1123699992895130 0.0584199987351895 0.3688299953937530 C 0.1679899990558620 0.0030400000978262 0.3671199977397920 .... .... C 0.9457899928092950 0.8917999863624572 0.3670699894428250 C 0.5544400215148930 0.6150699853897090 0.5497099757194520 O 0.4347901741294347 0.4590097156291522 0.5539600253105161 O 0.5039499998092650 0.4248099923133851 0.5561699867248540 O 0.5783299803733830 0.6644200086593630 0.5974799990653990 Au 0.4996399879455560 0.5032899975776670 0.4675300121307370 K_POINTS gamma CONSTRAINTS 1 1.D-8 distance 72 73 From phylyh at nus.edu.sg Wed Sep 16 11:20:24 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Wed, 16 Sep 2009 17:20:24 +0800 Subject: [Pw_forum] Is the constrain card avaible? In-Reply-To: Message-ID: <000401ca36ae$ec115a10$71a213ac@nusa0bcf64b485> I set the constrains card in input file to constrain the distance between two atoms in relaxation, but the it does not work at all. I am not sure what's wrong. Is there anyone can help me? Thanks! The input file is included as follows: &CONTROL title = 'CO_O2' , calculation = 'relax' , prefix='CO_O2-con', restart_mode = 'from_scratch' , outdir = '/home/phylyh/00-Au-catalysis/CO_O2-constrain/tmp' , pseudo_dir = '/home/phylyh/pseudo_dir' , disk_io = 'none', etot_conv_thr = 1.0D-5, forc_conv_thr = 1.0D-4, / &SYSTEM ibrav = 0, nat = 76, ntyp = 3, ecutwfc = 30 , ecutrho = 300 , nosym = .false. , nspin = 2, starting_magnetization(2) = 0.7 , starting_magnetization(3) = 0.7 , occupations='smearing', smearing='gauss', degauss=0.01, / &ELECTRONS conv_thr = 1.D-6, mixing_mode = 'local-TF', mixing_beta = 0.8D0, mixing_ndim = 8, diagonalization = 'david' , electron_maxstep = 500 / &IONS ion_dynamics = 'bfgs', upscale = 18.0, bfgs_ndim = 1, trust_radius_max = 0.8D0, trust_radius_min = 1.D-3, trust_radius_ini = 0.5D0, w_1 = 0.01D0, w_2 = 0.5D0, pot_extrapolation = "second_order", / CELL_PARAMETERS cubic 24.18234040895346130 -13.96168074474439 0.000000000000000 0.000000000000000 27.9233614894888667 0.000000000000000 0.000000000000000 0.000000000000000 37.7945232712218137894 ATOMIC_SPECIES C 1.00000 C.pbe-rrkjus.UPF O 1.00000 O.pbe-rrkjus.UPF Au 1.00000 Au.pbe-nd-van.UPF ATOMIC_POSITIONS crystal C 0.0011800000211225 0.0029599999543280 0.3677699863910680 C 0.1123699992895130 0.0584199987351895 0.3688299953937530 C 0.1679899990558620 0.0030400000978262 0.3671199977397920 .... .... C 0.9457899928092950 0.8917999863624572 0.3670699894428250 C 0.5544400215148930 0.6150699853897090 0.5497099757194520 O 0.4347901741294347 0.4590097156291522 0.5539600253105161 O 0.5039499998092650 0.4248099923133851 0.5561699867248540 O 0.5783299803733830 0.6644200086593630 0.5974799990653990 Au 0.4996399879455560 0.5032899975776670 0.4675300121307370 K_POINTS gamma CONSTRAINTS 1 1.D-8 distance 72 73 Sincerely yours, Yunhao NUS phylyh at nus.edu.sg From paulatto at sissa.it Wed Sep 16 11:23:19 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 16 Sep 2009 11:23:19 +0200 Subject: [Pw_forum] Is the constrain card avaible? In-Reply-To: <000f01ca36a3$1f2a1060$71a213ac@nusa0bcf64b485> References: <000f01ca36a3$1f2a1060$71a213ac@nusa0bcf64b485> Message-ID: In data 16 settembre 2009 alle ore 09:55:56, Lu Yunhao ha scritto: > I set the constrains card in input file to constrain the distance between > two atoms in relaxation, but the it does not work at all. I am not sure > what's wrong. Is there anyone can help me? Thanks! > ... > ion_dynamics = 'bfgs', > CONSTRAINTS Dear Lu Yunhao, unluckily constraints are not implemented with bfgs, they are just ignored. I have an experimental version of the code that enforces them, but has some problems (constraints can break symmetry, causing the code to stop). If you want I can give you the experimental version for you to try, or you can use damped dynamics instead of bfgs. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yccheng.nju at gmail.com Wed Sep 16 15:17:45 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Wed, 16 Sep 2009 21:17:45 +0800 Subject: [Pw_forum] workfunction and efield In-Reply-To: <553E9976-8B8B-456B-AEDA-E34805760F0F@sissa.it> References: <553E9976-8B8B-456B-AEDA-E34805760F0F@sissa.it> Message-ID: Thank you for your reply. Recently I have read a paper published in Nano letters titled "Tuning the Graphene work function by electric field effect"( http://pubs.acs.org/doi/pdf/10.1021/nl901572a). The main conclusion is that the work function of graphene can be adjusted as the gate voltage tunes the Fermi level across the charge neutrality point. The tunable work function makes graphene an attractive material for low contact barrier electrodes. Motivated by this attractive application, I tried to calculate the work function under external electric field. Before the calculation, I firstly tried to understand the definition of the work function and how it is calculated in Pwscf package. The literature (J. Phys.: condens. Matter 11(1999) 2689-2696) mentioned in the description of the workFct_example directory shows the macroscopic-average method to the calculation of work functions. The work function is the minimum energy required to extract one electron to an infinite distance form the surface and its value is equivalent to the mean electrostatic potential energy across the metal surface minus the Fermi energy. And thus the question whether electric field can reflect the Fermi level of a certain material surface arises. The example31 shows how to perform electronic structure calculations using pwscf package for a system undergoing the presence of a static homogeneous finite electric field. As a test, I firstly calculated the work function of graphene at zero external electric field and the calculated value is consistent with the previous published paper(PRL_94_236602) and the experimental result. Secondly, I calculated the work function at finit external electric field, and then I use the pp.x and average.x to get the work function as at the zero external efield. It seems that the calculated work function value is different from that under zero external efield. But I don't know whether the calculated work function value is reasonable. My questions are as follows: 1) Whether the work function would be changed under a finite external efield? 2) Can I use the method calculating work function under zero efield to calculate work function under finite efield? 3) Can the plot number 11 in pp.x package deal with the potential under finite efield? Any suggestion or comment is appreciated. Thank you in advance. sincerely, 2009/9/16 Stefano Baroni > Hi. before calculating anything, I think it is important to define and > understand what one is going to calculate. Would you please give us a > definition of "work function under an external field" and compare/contrast > it to the accepted definition of "workfunction at zero field"? Thanks - SB > On Sep 16, 2009, at 3:53 AM, ??? wrote: > > Dear pwscf users, > The PWscf can calculate the workfunction in slab model and the > electronic structure under external efield. I am concerning that whether it > it correct to calculate the workfunction of a certain materials under > external efield? Thank you in advance. > > -- > Y. C. Cheng > Department of Physics > Nanjing University > Nanjing 210093 > P. R. China > Tel: 86-25-83592907 > Email: yccheng.nju at gmail.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de > la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/be8074ad/attachment-0001.htm From ditommas at googlemail.com Wed Sep 16 15:22:36 2009 From: ditommas at googlemail.com (Devis Di Tommaso) Date: Wed, 16 Sep 2009 14:22:36 +0100 Subject: [Pw_forum] Density functional for Van der Walls interactions Message-ID: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> Dear users, we are conducting simulations on organic molecular crystals using Quantum Espresso (cp code). I am writing to you regarding the last version of Quantum Espresso (4.1). Is it true that it contains a new functional (DFT-D?) with a correction for taking into account the Van der Waals interactions. If yes, where can I get more information on how to use this functional in the CP and PWSCF codes. Thank you very much, Devis Di Tommaso Department of Chemistry University College London From paulatto at sissa.it Wed Sep 16 15:30:34 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 16 Sep 2009 15:30:34 +0200 Subject: [Pw_forum] Density functional for Van der Walls interactions In-Reply-To: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> References: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> Message-ID: In data 16 settembre 2009 alle ore 15:22:36, Devis Di Tommaso ha scritto: > If yes, where can I get more information on how to use this functional > in the CP and PWSCF codes. Dear Devis, as far as I know for pw.x it is as easy as setting the following variables in the &system namelist: london = .true. london_s6 = 0.75 ! this is the default london_rcut = 200.00 ! this is the default the meaning of s6 and rcut should be accordingly to V. Barone et al. J. Comp. Chem., 30, 934 (2009). I don't know if it is implemented in cp.x too. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Wed Sep 16 15:33:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Sep 2009 15:33:15 +0200 Subject: [Pw_forum] Density functional for Van der Walls interactions In-Reply-To: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> References: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> Message-ID: <4AB0E91B.2020904@democritos.it> Devis Di Tommaso wrote: > we are conducting simulations on organic molecular crystals using > Quantum Espresso (cp code) [...] the last version of Quantum Espresso > (4.1) [...] contains a new functional (DFT-D?) with a correction > for taking into account the Van der Waals interactions it does (yes, DFT-D) but it is not yet implemented in CP. It shouldn't be that difficult, though. Example in tests/vdw.*, documentation for input variables in Doc/INPUT_PW.*, code in Modules/mm_dispersion.f90 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Wed Sep 16 15:41:33 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 16 Sep 2009 15:41:33 +0200 Subject: [Pw_forum] workfunction and efield In-Reply-To: References: <553E9976-8B8B-456B-AEDA-E34805760F0F@sissa.it> Message-ID: <4927FAFF-2A76-479B-A4E9-9E96CC1179F1@sissa.it> On Sep 16, 2009, at 3:17 PM, ??? wrote: > Thank you for your reply. > Recently I have read a paper published in Nano letters titled > "Tuning the Graphene work function by electric field effect"(http://pubs.acs.org/doi/pdf/10.1021/nl901572a > ). The main conclusion is that the work function of graphene can be > adjusted as the gate voltage tunes the Fermi level across the charge > neutrality point. The tunable work function makes graphene an > attractive material for low contact barrier electrodes. Motivated > by this attractive application, I tried to calculate the work > function under external electric field. > > Before the calculation, I firstly tried to understand the definition > of the work function and how it is calculated in Pwscf package. The > literature (J. Phys.: condens. Matter 11(1999) 2689-2696) mentioned > in the description of the workFct_example directory shows the > macroscopic-average method to the calculation of work functions. > The work function is the minimum energy required to extract one > electron to an infinite distance form the surface which equals plus or minus infinity, in the presence of an applied electric field ... > and its value is equivalent to the mean electrostatic potential > energy across the metal surface minus the Fermi energy. Efermi - average potential far from the surgace the average potential far from the surface does not approach a constant in the presence of an electric field, so you have to understand exactly what the experimentalists measure, when you are done, I would be pleased to learn that ... > And thus the question whether electric field can reflect the Fermi > level of a certain material surface arises. the above statement is beyond my understanding capabilities ... > > The example31 shows how to perform electronic structure calculations > using pwscf package for a system undergoing the presence of a static > homogeneous finite electric field. As a test, I firstly calculated > the work function of graphene at zero external electric field and > the calculated value is consistent with the previous published > paper(PRL_94_236602) and the experimental result. Secondly, I > calculated the work function at finit external electric field, and > then I use the pp.x and average.x to get the work function as at the > zero external efield. It seems that the calculated work function > value is different from that under zero external efield. But I > don't know whether the calculated work function value is reasonable. > > My questions are as follows: > 1) Whether the work function would be changed under a finite > external efield? this question does not have an answer until one understand what is meant by "work function in a finite field" (the usual definition does not apply) > 2) Can I use the method calculating work function under zero efield > to calculate work function under finite efield? NO, because of the above: the electrostatic potential does not tend to a cosnatant far from the surface > 3) Can the plot number 11 in pp.x package deal with the potential > under finite efield? no idea whatsoever SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/39255da2/attachment.htm From ditommas at googlemail.com Wed Sep 16 15:45:47 2009 From: ditommas at googlemail.com (Devis Di Tommaso) Date: Wed, 16 Sep 2009 14:45:47 +0100 Subject: [Pw_forum] Density functional for Van der Walls interactions In-Reply-To: <27fac710909160635l74505636iafb4ae6efa980edd@mail.gmail.com> References: <27fac710909160622p16b97fc6x3adfd6fe6b7ecefe@mail.gmail.com> <4AB0E91B.2020904@democritos.it> <27fac710909160635l74505636iafb4ae6efa980edd@mail.gmail.com> Message-ID: <27fac710909160645l50329364v258aac6591740129@mail.gmail.com> Dear Lorenzo and Paolo, thanks a lot for your response. Devis On Wed, Sep 16, 2009 at 2:35 PM, Devis Di Tommaso wrote: > > > Forwarded conversation > Subject: Density functional for Van der Walls interactions > ------------------------ > > From: Devis Di Tommaso > Date: Wed, Sep 16, 2009 at 2:22 PM > To: pw_forum at pwscf.org > > > Dear users, > > we are conducting simulations on organic molecular crystals using > Quantum Espresso (cp code). > > I am writing to you regarding the last version of Quantum Espresso > (4.1). Is it true that it contains a new functional (DFT-D?) with a > correction > for taking into account the Van der Waals interactions. > > If yes, where can I get more information on how to use this functional > in the CP and PWSCF codes. > > Thank you very much, > > Devis Di Tommaso > Department of Chemistry > University College London > > ---------- > From: Lorenzo Paulatto > Date: Wed, Sep 16, 2009 at 2:30 PM > To: PWSCF Forum > > > In data 16 settembre 2009 alle ore 15:22:36, Devis Di Tommaso > ha scritto: > Dear Devis, > as far as I know for pw.x it is as easy as setting the following variables > in the &system namelist: > ? ? ? ?london ? ? ?= .true. > ? ? ? ?london_s6 ? = 0.75 ? ?! this is the default > ? ? ? ?london_rcut = 200.00 ?! this is the default > the meaning of s6 and rcut should be accordingly to V. Barone et al. J. > Comp. Chem., 30, 934 (2009). > > I don't know if it is implemented in cp.x too. > > best regards > > > -- > Lorenzo Paulatto > SISSA ?& ?DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: ? http://people.sissa.it/~paulatto/ > > ? ? *** save italian brains *** > ?http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > ---------- > From: Paolo Giannozzi > Date: Wed, Sep 16, 2009 at 2:33 PM > To: PWSCF Forum > > >> Quantum Espresso (cp code) [...] the last version of Quantum Espresso >> (4.1) [...] contains a new functional (DFT-D?) with a correction > it does (yes, DFT-D) but it is not yet implemented in CP. It shouldn't > be that difficult, though. Example in tests/vdw.*, documentation for > input variables in Doc/INPUT_PW.*, code in Modules/mm_dispersion.f90 > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > From phylyh at nus.edu.sg Wed Sep 16 16:16:15 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Wed, 16 Sep 2009 22:16:15 +0800 Subject: [Pw_forum] Is the constrain card avaible? In-Reply-To: Message-ID: <000301ca36d8$40677bc0$71a213ac@nusa0bcf64b485> Message: 4 Date: Wed, 16 Sep 2009 11:23:19 +0200 From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] Is the constrain card avaible? To: "PWSCF Forum" Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes In data 16 settembre 2009 alle ore 09:55:56, Lu Yunhao ha scritto: > I set the constrains card in input file to constrain the distance between > two atoms in relaxation, but the it does not work at all. I am not sure > what's wrong. Is there anyone can help me? Thanks! > ... > ion_dynamics = 'bfgs', > CONSTRAINTS >Dear Lu Yunhao, >unluckily constraints are not implemented with bfgs, they are just >ignored. I have an experimental version of the code that enforces them, >but has some problems (constraints can break symmetry, causing the code to >stop). >If you want I can give you the experimental version for you to try, or you >can use damped dynamics instead of bfgs. > >best regards Dear Lorenzo Paulatto Great! Would you please send the code to me by Email ( phylyh at nus.edu.sg)? Thanks for your help! Best wishes, Yunhao NUS From decboy9 at gmail.com Wed Sep 16 19:34:26 2009 From: decboy9 at gmail.com (dev sharma) Date: Wed, 16 Sep 2009 23:04:26 +0530 Subject: [Pw_forum] thin film construction Message-ID: hi 2 all, I am somewhat confused about construction of a film. like whenever we calculate the band gap of a unit cell of any system and 2*2*2 supercell of that system we get the same value whereas when one moves from nano regime to larger scale the band gap should decrease. It means that the unit cell is treated as crystal.So, if i construct a film , by taking it as 2*2*1 supercell, it will again consider it as sum of crystals and will yield the same results ????? Hope so that my question is clear .. How to make a structure of film ??? Thanks in advance. With regards, Dev Sharma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/0784ce00/attachment.htm From baroni at sissa.it Wed Sep 16 19:52:37 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 16 Sep 2009 19:52:37 +0200 Subject: [Pw_forum] thin film construction In-Reply-To: References: Message-ID: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> On Sep 16, 2009, at 7:34 PM, dev sharma wrote: > hi 2 all, > > I am somewhat confused about construction of a film. like whenever > we calculate the band gap of a unit cell of any system and 2*2*2 > supercell of that system we get the same value whereas when one > moves from nano regime to larger scale the band gap should decrease. > It means that the unit cell is treated as crystal.So, if i construct > a film , by taking it as 2*2*1 supercell, it will again consider it > as sum of crystals and will yield the same results ????? Hope so > that my question is clear .. Not to me ... > How to make a structure of film ??? using supercells "intercalated" with vacuum, the same way you would to simulate a surface. Only, in this case the thickness of the slab is not an artifact of the model, but corresponds to the physical thickness of the film (if the film is thin enough to be simulated with a supercell) SB > Thanks in advance. > With regards, > Dev Sharma > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/925be666/attachment.htm From ttduyle at gmail.com Wed Sep 16 20:05:07 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 16 Sep 2009 14:05:07 -0400 Subject: [Pw_forum] thin film construction In-Reply-To: References: Message-ID: <8974d3b20909161105p4307941uf2d5ecbb2c043e02@mail.gmail.com> maybe you did not include the vacuum and maybe you did calculate from un-relaxed film. Best, On Wed, Sep 16, 2009 at 1:34 PM, dev sharma wrote: > hi 2 all, > > I am somewhat confused about construction of a film. like whenever we > calculate the band gap of a unit cell of any system and 2*2*2 supercell of > that system we get the same value whereas when one moves from nano regime to > larger scale the band gap should decrease. It means that the unit cell is > treated as crystal.So, if i construct a film , by taking it as 2*2*1 > supercell, it will again consider it as sum of crystals and will yield the > same results ????? Hope so that my question is clear .. How to make a > structure of film ??? Thanks in advance. > With regards, > Dev Sharma > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090916/17ecde5e/attachment.htm From decboy9 at gmail.com Thu Sep 17 19:45:40 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 17 Sep 2009 23:15:40 +0530 Subject: [Pw_forum] thin film construction In-Reply-To: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> References: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> Message-ID: Dear Sir, Like i want to make films of ZnO, then should i make a 2*2*2 supercell of ZnO and put vacuum in between two layers ??? It means we are using two mono layers seprated by vacuum ??? and Sir, how we will put vaccum between two layers means which inputs to study ? Sir ZnO is ibrav=4, and if i will put vacuum between supercell will the ibrav=4 not change ??? Is there any example/material to study related or any such problem in forum ?? Thanks , With regards, Dev Sharma, Univeristy of Delhi On Wed, Sep 16, 2009 at 11:22 PM, Stefano Baroni wrote: > > On Sep 16, 2009, at 7:34 PM, dev sharma wrote: > > hi 2 all, > > I am somewhat confused about construction of a film. like whenever we > calculate the band gap of a unit cell of any system and 2*2*2 supercell of > that system we get the same value whereas when one moves from nano regime to > larger scale the band gap should decrease. It means that the unit cell is > treated as crystal.So, if i construct a film , by taking it as 2*2*1 > supercell, it will again consider it as sum of crystals and will yield the > same results ????? Hope so that my question is clear .. > > > Not to me ... > > How to make a structure of film ??? > > > using supercells "intercalated" with vacuum, the same way you would to > simulate a surface. Only, in this case the thickness of the slab is not an > artifact of the model, but corresponds to the physical thickness of the film > (if the film is thin enough to be simulated with a supercell) > > SB > > Thanks in advance. > With regards, > Dev Sharma > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/989029f3/attachment.htm From nkxirainbow at gmail.com Fri Sep 18 04:26:05 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Sep 2009 02:26:05 +0000 Subject: [Pw_forum] thin film construction In-Reply-To: References: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> Message-ID: <21fbc4790909171926r11390cedu307df332f88855e7@mail.gmail.com> Dear dev sharma? The following is a example about monolayer graphene with a vacuum about 10 Angstrom. You can find that there is a large distance between neighboring layer with Xcrystden, which is the vacuum. For more information about this graphene example, you can visit http://blog.sina.com.cn/s/blog_5f15ead20100c9fu.html "*&CONTROL ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** calculation = 'scf' , ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** restart_mode = 'from_scratch' , ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** outdir = '/root/tmp' , ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** pseudo_dir = '/home/raman/espresso-4.0.4/pseudo' ,* / *&SYSTEM ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ibrav = 4, ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** celldm(1) = 4.608737, ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** celldm(3) = 4.536666, ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** nat = 2, ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ntyp = 1, ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ecutwfc = 60.D0 , **/ **&ELECTRONS ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** conv_thr = 1.D-8 , ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** mixing_beta = 0.3D0 , **/ ATOMIC_SPECIES ** ** ** C ** ** 12.00000 ** C.pz-rrkjus.UPF ATOMIC_POSITIONS crystal ** ** ** C ** ** ** ** ** 0.000000000 ** ** ** 0.000000000 ** ** ** 0.000000000 ** ** ** 1 ** 1 ** 1 ** ** ** C ** ** ** ** ** 0.333330000 ** ** -0.333330000 ** ** ** 0.000000000 ** ** ** 1 ** 1 ** 1 K_POINTS automatic ** 22 22 1 ** ** 0 0 0*"* * On Thu, Sep 17, 2009 at 5:45 PM, dev sharma wrote: > Dear Sir, > Like i want to make films of ZnO, then should i make a 2*2*2 supercell of > ZnO and put vacuum in between two layers ??? It means we are using two mono > layers seprated by vacuum ??? and Sir, how we will put vaccum between two > layers means which inputs to study ? Sir ZnO is ibrav=4, and if i will > put vacuum between supercell will the ibrav=4 not change ??? Is there any > example/material to study related or any such problem in forum ?? > Thanks , > With regards, > Dev Sharma, > Univeristy of Delhi > > ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/9b8bd29d/attachment.htm From yccheng.nju at gmail.com Fri Sep 18 05:18:02 2009 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 18 Sep 2009 11:18:02 +0800 Subject: [Pw_forum] workfunction and efield In-Reply-To: <4927FAFF-2A76-479B-A4E9-9E96CC1179F1@sissa.it> References: <553E9976-8B8B-456B-AEDA-E34805760F0F@sissa.it> <4927FAFF-2A76-479B-A4E9-9E96CC1179F1@sissa.it> Message-ID: > Efermi - average potential far from the surgace > the average potential far from the surface does not approach a constant in > the presence of an electric field, so you have to understand exactly what > the experimentalists measure, > when you are done, I would be pleased to learn that ... > In the experiment, they apply scanning kelvin probe microscope(SKPM) techniques to demonstrate that the work function can be controlled over a wide range by electric field effect (EFE). SKPM is an atomic force microscope (AFM) based experimental technique can map the surface potential variation of a sample surface relative to that of a metallic tip. The relative surface contact potential difference measured can be related to the difference in work function between the metallic tip and graphene sample surface. The work function of the metallic tip is insensitive to the gate voltage due to the large density of states near the Fermi level. So the variation of relative surface contact potential difference reflects the EFE modulation of work function of graphene sample. The authors conclude that the behavior of EFE tuned work function of graphene sample can be explained by the change of Efermi in graphene sample. Now I understand that in the experiment the local surface potential is measured. The local surface potential corresponds to the work function difference between the metal tip and the graphene surface . The general definition of work function is : average potential far from the surface - Efermi. Though the average potential far from the surface does not approach a constant in the presence of an electric field, the difference of the average potential between the metal tip and graphene equal zero. So local surface potential is : Efermi(metal tip) - Efermi(graphene). So I think that the title of the paper published in Nano letters "Tuning the graphene work function by EFE" means "Tuning the Fermi energy level of graphene by EFE". Thank Prof. Stefano Baroni very much. -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/c9dbdc3e/attachment-0001.htm From haoweipeng at gmail.com Fri Sep 18 06:19:11 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Thu, 17 Sep 2009 23:19:11 -0500 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". Message-ID: <7559eb240909172119m6f8f02efr6c62a559dce1b701@mail.gmail.com> Hi, all, I am running a scf calclation, but it fails several times due to the same reason. However, the relax calculation using similar parameters and input file goes well. the input file looks: &control calculation='scf' restart_mode='from_scratch', nstep=50, pseudo_dir = '/home/haowei/tools/pwscf/pseudo/', outdir='./results/' prefix='pwscf' etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav = 0, celldm(1) = 6.501000, nspin = 1 nat = 28, ntyp = 3, ecutwfc = 25, ecutrho = 200, occupations='smearing', smearing='gauss', degauss=0.001, lda_plus_u=.false. Hubbard_U(1)=1.d-8 / &electrons mixing_mode = 'plain' mixing_beta = 0.3 conv_thr = 1.0d-8 / ..... and this is the crash file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 4 from cdiaghg : error # 608 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% thanks a lot Best, -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/a36f0026/attachment.htm From haoweipeng at gmail.com Fri Sep 18 06:21:05 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Thu, 17 Sep 2009 23:21:05 -0500 Subject: [Pw_forum] How can I search the mail list archive? Message-ID: <7559eb240909172121p7eb8ff15x5a82a3a8228a21a0@mail.gmail.com> sorry for this problem..but i fail to find the website thanks a lot... -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/2f8a06dd/attachment.htm From haoweipeng at gmail.com Fri Sep 18 06:24:11 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Thu, 17 Sep 2009 23:24:11 -0500 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". Message-ID: <7559eb240909172124j59d28be1hfffe862e54fa46bb@mail.gmail.com> Hi, all, I am running a scf calclation, but it fails several times due to the same reason. However, the relax calculation using similar parameters and input file goes well. the input file looks: &control calculation='scf' restart_mode='from_scratch', nstep=50, pseudo_dir = '/home/haowei/tools/pwscf/pseudo/', outdir='./results/' prefix='pwscf' etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav = 0, celldm(1) = 6.501000, nspin = 1 nat = 28, ntyp = 3, ecutwfc = 25, ecutrho = 200, occupations='smearing', smearing='gauss', degauss=0.001, lda_plus_u=.false. Hubbard_U(1)=1.d-8 / &electrons mixing_mode = 'plain' mixing_beta = 0.3 conv_thr = 1.0d-8 / ..... and this is the crash file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 4 from cdiaghg : error # 608 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% thanks a lot Best, -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/48c77fe2/attachment.htm From haoweipeng at gmail.com Fri Sep 18 06:24:50 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Thu, 17 Sep 2009 23:24:50 -0500 Subject: [Pw_forum] How can I search the mail list archive? Message-ID: <7559eb240909172124o14284e08xd40deba2c5a6e689@mail.gmail.com> sorry for this problem..but i fail to find the website thanks a lot... -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/01bc61c9/attachment.htm From haoweipeng at gmail.com Fri Sep 18 06:37:50 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Thu, 17 Sep 2009 23:37:50 -0500 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". Message-ID: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> Hi, all, I am running a scf calclation, but it fails several times due to the same reason. However, the relax calculation using similar parameters and input file goes well. the input file looks: &control calculation='scf' restart_mode='from_scratch', nstep=50, pseudo_dir = '/home/haowei/tools/pwscf/pseudo/', outdir='./results/' prefix='pwscf' etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav = 0, celldm(1) = 6.501000, nspin = 1 nat = 28, ntyp = 3, ecutwfc = 25, ecutrho = 200, occupations='smearing', smearing='gauss', degauss=0.001, lda_plus_u=.false. Hubbard_U(1)=1.d-8 / &electrons mixing_mode = 'plain' mixing_beta = 0.3 conv_thr = 1.0d-8 / ..... and this is the crash file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 4 from cdiaghg : error # 608 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% thanks a lot btw, how can i search the mail list archive? Best, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090917/a840be18/attachment.htm From Michael at ihpc.a-star.edu.sg Fri Sep 18 06:34:18 2009 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Fri, 18 Sep 2009 12:34:18 +0800 Subject: [Pw_forum] How can I search the mail list archive? In-Reply-To: <7559eb240909172121p7eb8ff15x5a82a3a8228a21a0@mail.gmail.com> References: <7559eb240909172121p7eb8ff15x5a82a3a8228a21a0@mail.gmail.com> Message-ID: Haowei: I usually just use Google and start the search with pwscf and whatever I want to search on. If you want, you can also start your search with pw_forum site:democritos.it For example you could put this into Google: site:democritos.it diagonalization failed -OR- pwscf diagonalization failed Hope that helps. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Haowei Peng Sent: Friday, September 18, 2009 12:21 PM To: pw_forum at pwscf.org Subject: [Pw_forum] How can I search the mail list archive? sorry for this problem..but i fail to find the website thanks a lot... -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From decboy9 at gmail.com Fri Sep 18 07:20:18 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 18 Sep 2009 10:50:18 +0530 Subject: [Pw_forum] How can I search the mail list archive? In-Reply-To: <7559eb240909172121p7eb8ff15x5a82a3a8228a21a0@mail.gmail.com> References: <7559eb240909172121p7eb8ff15x5a82a3a8228a21a0@mail.gmail.com> Message-ID: hi dear here is the link http://www.democritos.it/cgi-bin/htsearch?restrict=;exclude=;method=and;format=builtin-long;sort=score;words=from%20cdiaghg%20%3A%20error%20%23%20%20%20%20%20%20%20363;page=1 whatever you want to search , type that in refine search and press search button. Take Care Dev Sharma, Univereity of Delhi On Fri, Sep 18, 2009 at 9:51 AM, Haowei Peng wrote: > sorry for this problem..but i fail to find the website > thanks a lot... > > > -- > Haowei Peng > Northwestern University > Department of Physics & Astronomy > 2145 Sheridan Rd. > Evanston, IL 60208-3112 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/b39d17b7/attachment.htm From nkxirainbow at gmail.com Fri Sep 18 07:22:07 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Sep 2009 05:22:07 +0000 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". In-Reply-To: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> References: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> Message-ID: <21fbc4790909172222i78cbf0ffy219541038d953978@mail.gmail.com> > > btw, how can i search the mail list archive? > > If you want to search "scf", you can try at www.google.cn: "scf site:http://www.democritos.it/pipermail/pw_forum/ " ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/794cde1b/attachment.htm From paulatto at sissa.it Fri Sep 18 08:12:27 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 18 Sep 2009 08:12:27 +0200 (CEST) Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". In-Reply-To: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> References: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> Message-ID: <52552.78.12.164.34.1253254347.squirrel@webmail.sissa.it> On Fri, September 18, 2009 06:37, Haowei Peng wrote: > However, the relax calculation using similar parameters and input file > goes well. Dear Haowei Peng, your input looks ok, apart that you may have missed to set lda_plus_U to true (or you just wanted to try the calculation without the U) > lda_plus_u=.false. Hubbard_U(1)=1.d-8 > diagonalization (ZHEGV*) failed I'm having this error a lot on a specific hardware with a specific version of ifort+acml libraries. On the same hardware, with mkl I can't even finish the first iteration because of those diagonalization errors. I know it's not a great advice, but I would try a different version of the compiler, just to be sure. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From decboy9 at gmail.com Fri Sep 18 08:21:43 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 18 Sep 2009 11:51:43 +0530 Subject: [Pw_forum] thin film construction In-Reply-To: <21fbc4790909171926r11390cedu307df332f88855e7@mail.gmail.com> References: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> <21fbc4790909171926r11390cedu307df332f88855e7@mail.gmail.com> Message-ID: Dear SIr, is XCRYSDEN have any option like we can cut 100 or 110 plane and add vaccum to it to build a slab-vacuum system ??? Dev Sharma, University of Delhi On Fri, Sep 18, 2009 at 7:56 AM, xirainbow wrote: > Dear dev sharma? > The following is a example about monolayer graphene with a vacuum about 10 > Angstrom. > You can find that there is a large distance between neighboring layer with > Xcrystden, which is the vacuum. > For more information about this graphene example, you can visit > http://blog.sina.com.cn/s/blog_5f15ead20100c9fu.html > > "*&CONTROL > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** calculation = 'scf' , > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** restart_mode = > 'from_scratch' , > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** outdir = > '/root/tmp' , > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** pseudo_dir = > '/home/raman/espresso-4.0.4/pseudo' ,* > / > *&SYSTEM > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ibrav = > 4, > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** celldm(1) = > 4.608737, > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** celldm(3) = > 4.536666, > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** nat > = 2, > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ntyp > = 1, > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ecutwfc = > 60.D0 , > **/ > **&ELECTRONS > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** conv_thr = 1.D-8 > , > ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** mixing_beta = 0.3D0 , > **/ > ATOMIC_SPECIES > ** ** ** C ** ** 12.00000 ** C.pz-rrkjus.UPF > ATOMIC_POSITIONS crystal > ** ** ** C ** ** ** ** ** 0.000000000 ** ** ** 0.000000000 ** ** ** > 0.000000000 ** ** ** 1 ** 1 ** 1 > ** ** ** C ** ** ** ** ** 0.333330000 ** ** -0.333330000 ** ** ** > 0.000000000 ** ** ** 1 ** 1 ** 1 > K_POINTS automatic > ** 22 22 1 ** ** 0 0 0*"* > > > > > * > > On Thu, Sep 17, 2009 at 5:45 PM, dev sharma wrote: > >> Dear Sir, >> Like i want to make films of ZnO, then should i make a 2*2*2 supercell of >> ZnO and put vacuum in between two layers ??? It means we are using two mono >> layers seprated by vacuum ??? and Sir, how we will put vaccum between two >> layers means which inputs to study ? Sir ZnO is ibrav=4, and if i will >> put vacuum between supercell will the ibrav=4 not change ??? Is there any >> example/material to study related or any such problem in forum ?? >> Thanks , >> With regards, >> Dev Sharma, >> Univeristy of Delhi >> >> > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/ac00dfa9/attachment.htm From nkxirainbow at gmail.com Fri Sep 18 08:30:58 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Sep 2009 14:30:58 +0800 Subject: [Pw_forum] thin film construction In-Reply-To: References: <4B3F085C-44B2-4F84-AE9E-E0EC075EBDB1@sissa.it> <21fbc4790909171926r11390cedu307df332f88855e7@mail.gmail.com> Message-ID: <21fbc4790909172330j10a67063x8471ba64d9493f2e@mail.gmail.com> Dear dev sharma : > is XCRYSDEN have any option like we can cut 100 or 110 plane and add > vaccum to it to build a slab-vacuum system ??? > I do not think so. ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/11f3e35f/attachment.htm From bobjohn.lzu at gmail.com Fri Sep 18 08:55:10 2009 From: bobjohn.lzu at gmail.com (john Bob) Date: Fri, 18 Sep 2009 14:55:10 +0800 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". In-Reply-To: <52552.78.12.164.34.1253254347.squirrel@webmail.sissa.it> References: <7559eb240909172137q11f7dd8draaecb4178ed9138f@mail.gmail.com> <52552.78.12.164.34.1253254347.squirrel@webmail.sissa.it> Message-ID: <401230aa0909172355p45c74249v2f1236007328e137@mail.gmail.com> Maybe, increase nbnd can solve this problem. 2009/9/18 Lorenzo Paulatto > > On Fri, September 18, 2009 06:37, Haowei Peng wrote: > > However, the relax calculation using similar parameters and input file > > goes well. > > Dear Haowei Peng, > your input looks ok, apart that you may have missed to set lda_plus_U to > true (or you just wanted to try the calculation without the U) > > lda_plus_u=.false. Hubbard_U(1)=1.d-8 > > > diagonalization (ZHEGV*) failed > > I'm having this error a lot on a specific hardware with a specific version > of ifort+acml libraries. On the same hardware, with mkl I can't even > finish the first iteration because of those diagonalization errors. > > I know it's not a great advice, but I would try a different version of the > compiler, just to be sure. > > best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/90e814c5/attachment.htm From sclauzer at sissa.it Fri Sep 18 09:28:35 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 18 Sep 2009 09:28:35 +0200 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". In-Reply-To: <7559eb240909172119m6f8f02efr6c62a559dce1b701@mail.gmail.com> References: <7559eb240909172119m6f8f02efr6c62a559dce1b701@mail.gmail.com> Message-ID: <4AB336A3.4060607@sissa.it> Dear Haowei Peng, in my experience this error may happen with GGA functionals when you push the scf threshold very low (let's say conv_thr below 10^(-10) ). Since you're hiding some relevant information of your input file (such as PP files, atomic coordinates and k-points) I cannot be sure if this is causing the problem. In your case conv_thr = 1.0d-8, which is not that low, so there may be other problems, such as a wrong set of coordinates on input, a bad pseudopotential, ... Maybe, you can try to increase the cutoffs. HTH GS Haowei Peng wrote: > Hi, all, > > I am running a scf calclation, but it fails several times due to the > same reason. > However, the relax calculation using similar parameters and input file > goes well. > the input file looks: > > &control > calculation='scf' > restart_mode='from_scratch', > nstep=50, > pseudo_dir = '/home/haowei/tools/pwscf/pseudo/', > outdir='./results/' > prefix='pwscf' > etot_conv_thr = 1.0d-5, > forc_conv_thr = 1.0d-4, > / > &system > ibrav = 0, > celldm(1) = 6.501000, > nspin = 1 > nat = 28, > ntyp = 3, > ecutwfc = 25, > ecutrho = 200, > occupations='smearing', smearing='gauss', degauss=0.001, > lda_plus_u=.false. Hubbard_U(1)=1.d-8 > / > &electrons > mixing_mode = 'plain' > mixing_beta = 0.3 > conv_thr = 1.0d-8 > / > ..... > > and this is the crash file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 4 > from cdiaghg : error # 608 > diagonalization (ZHEGV*) failed > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > thanks a lot > > Best, > -- > Haowei Peng > Northwestern University > Department of Physics & Astronomy > 2145 Sheridan Rd. > Evanston, IL 60208-3112 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From kazempoor2000 at yahoo.com Fri Sep 18 14:32:30 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Fri, 18 Sep 2009 05:32:30 -0700 (PDT) Subject: [Pw_forum] Fw: defect formation energy Message-ID: <4803.66276.qm@web112501.mail.gq1.yahoo.com> Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 --- On Fri, 9/18/09, ali kazempour wrote: From: ali kazempour Subject: defect formation energy To: forum at democritos.it Date: Friday, September 18, 2009, 5:31 AM Hi for study of point defect ,? i do relax calculation and obtain positive defect formation energy while by vc-relax i gain negative. ? what is the difference between positive and negative formation energy? waht is the physical reasons? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/a3e254da/attachment.htm From marsamos at democritos.it Fri Sep 18 14:39:44 2009 From: marsamos at democritos.it (marsamos at democritos.it) Date: Fri, 18 Sep 2009 14:39:44 +0200 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <4803.66276.qm@web112501.mail.gq1.yahoo.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> Message-ID: <20090918143944.snv2vhjj4kc0koow@mail.democritos.it> Dear Ali, a positive formation energy means that it cost energy to create the defect. A negative one means that the system lower its energy by forming defects --> it will spontaneously form defects. layla Quoting ali kazempour : > > > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On Fri, 9/18/09, ali kazempour wrote: > > From: ali kazempour > Subject: defect formation energy > To: forum at democritos.it > Date: Friday, September 18, 2009, 5:31 AM > > > Hi > for study of point defect ,? i do relax calculation and obtain > positive defect formation energy while by vc-relax i gain negative. ? > what is the difference between positive and negative formation > energy? waht is the physical reasons? > thanks a lot > Ali Kazempour > > Physics department, Isfahan University of Technology > > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From nkxirainbow at gmail.com Fri Sep 18 14:43:41 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 18 Sep 2009 12:43:41 +0000 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <4803.66276.qm@web112501.mail.gq1.yahoo.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> Message-ID: <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> Dear: When you calculate without vc-relax, you deal with a point defect. When you use vc-relax, you change the crystal parameters. That is to say, you deal with a new kind of crystal, not a point defect. It is just my own point of view ?? > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Fri, 9/18/09, ali kazempour * wrote: > > > From: ali kazempour > Subject: defect formation energy > To: forum at democritos.it > Date: Friday, September 18, 2009, 5:31 AM > > > Hi > for study of point defect , i do relax calculation and obtain positive > defect formation energy while by vc-relax i gain negative. ? > what is the difference between positive and negative formation energy? waht > is the physical reasons? > thanks a lot > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/bf9d6c74/attachment.htm From ttduyle at gmail.com Fri Sep 18 14:47:17 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 18 Sep 2009 08:47:17 -0400 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> Message-ID: <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> if the defect concentration is too hight, when you do vc-relax the lattice parameter will be re-optimized. In reality, the defect concentration is about zero. On Fri, Sep 18, 2009 at 8:43 AM, xirainbow wrote: > Dear: > > When you calculate without vc-relax, you deal with a point defect. > When you use vc-relax, you change the crystal parameters. That is to say, > you deal with a new kind of crystal, not a point defect. > It is just my own point of view ?? > > > >> >> Ali Kazempour >> Physics department, Isfahan University of Technology >> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >> >> --- On *Fri, 9/18/09, ali kazempour * wrote: >> >> >> From: ali kazempour >> Subject: defect formation energy >> To: forum at democritos.it >> Date: Friday, September 18, 2009, 5:31 AM >> >> >> Hi >> for study of point defect , i do relax calculation and obtain positive >> defect formation energy while by vc-relax i gain negative. ? >> what is the difference between positive and negative formation energy? >> waht is the physical reasons? >> thanks a lot >> Ali Kazempour >> Physics department, Isfahan University of Technology >> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >> >> > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/7e6b8cca/attachment.htm From sclauzer at sissa.it Fri Sep 18 15:04:05 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 18 Sep 2009 15:04:05 +0200 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> Message-ID: <4AB38545.7040600@sissa.it> Duy Le wrote: > if the defect concentration is too hight, when you do vc-relax the > lattice parameter will be re-optimized. In reality, the defect > concentration is about zero. I must admit that I have no experience in computing defects, but I agree with the above comment. If you want to study very low concentrations you should take care of converging your results with the supercell size (keeping lattice parameters "freezed", i.e. not reoptimizing them after defect formation) and add Makov-Payne-like corrections if you are dealing with charged defects. If you really want to study very high concentrations and take into account changes in the volume of the crystal, you should maybe consider formation enthalpy, not simply formation energy. HTH GS > > On Fri, Sep 18, 2009 at 8:43 AM, xirainbow > wrote: > > Dear: > > When you calculate without vc-relax, you deal with a point defect. > When you use vc-relax, you change the crystal parameters. That is to > say, you deal with a new kind of crystal, not a point defect. > It is just my own point of view ?? > > > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > --- On *Fri, 9/18/09, ali kazempour / >/* wrote: > > > From: ali kazempour > > Subject: defect formation energy > To: forum at democritos.it > Date: Friday, September 18, 2009, 5:31 AM > > > Hi > for study of point defect , i do relax calculation and > obtain positive defect formation energy while by vc-relax i > gain negative. ? > what is the difference between positive and negative > formation energy? waht is the physical reasons? > thanks a lot > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sandabotis at gmail.com Fri Sep 18 15:05:40 2009 From: sandabotis at gmail.com (Sanda Botis) Date: Fri, 18 Sep 2009 09:05:40 -0400 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> Message-ID: <98e923e50909180605g4e93ff9bya33991f6b2ace213@mail.gmail.com> I agree that is probably an effect of the supercell size. How big is the supercell that you are using? Cheers, Sanda On Fri, Sep 18, 2009 at 8:47 AM, Duy Le wrote: > if the defect concentration is too hight, when you do vc-relax the lattice > parameter will be re-optimized. In reality, the defect concentration is > about zero. > > On Fri, Sep 18, 2009 at 8:43 AM, xirainbow wrote: > >> Dear: >> >> When you calculate without vc-relax, you deal with a point defect. >> When you use vc-relax, you change the crystal parameters. That is to say, >> you deal with a new kind of crystal, not a point defect. >> It is just my own point of view ?? >> >> >> >>> >>> Ali Kazempour >>> Physics department, Isfahan University of Technology >>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >>> >>> --- On *Fri, 9/18/09, ali kazempour * wrote: >>> >>> >>> From: ali kazempour >>> Subject: defect formation energy >>> To: forum at democritos.it >>> Date: Friday, September 18, 2009, 5:31 AM >>> >>> >>> Hi >>> for study of point defect , i do relax calculation and obtain positive >>> defect formation energy while by vc-relax i gain negative. ? >>> what is the difference between positive and negative formation energy? >>> waht is the physical reasons? >>> thanks a lot >>> Ali Kazempour >>> Physics department, Isfahan University of Technology >>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >>> >>> >> >> >> -- >> ____________________________________ >> Hui Wang >> School of physics, Nankai University, Tianjin, China >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/fb5aa81f/attachment.htm From marsamos at democritos.it Fri Sep 18 15:11:01 2009 From: marsamos at democritos.it (marsamos at democritos.it) Date: Fri, 18 Sep 2009 15:11:01 +0200 Subject: [Pw_forum] Fw: defect formation energy In-Reply-To: <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> References: <4803.66276.qm@web112501.mail.gq1.yahoo.com> <21fbc4790909180543g14ffe3d3v22739aa7659b4ba6@mail.gmail.com> <8974d3b20909180547v63c6ae4au8b9e99d3f57465a9@mail.gmail.com> Message-ID: <20090918151101.izrf9xuggs800c0s@mail.democritos.it> I think that calculations relaxing the volume should give defect formation enthalpy. But I always saw people fixing the defective cell to its original volume, as in general one is interested in low defect concentration and the elastic field created by the defect is larger than the simulation cell --> giving rise to a too large variation in the volume. Quoting Duy Le : > if the defect concentration is too hight, when you do vc-relax the lattice > parameter will be re-optimized. In reality, the defect concentration is > about zero. > > On Fri, Sep 18, 2009 at 8:43 AM, xirainbow wrote: > >> Dear: >> >> When you calculate without vc-relax, you deal with a point defect. >> When you use vc-relax, you change the crystal parameters. That is to say, >> you deal with a new kind of crystal, not a point defect. >> It is just my own point of view ?? >> >> >> >>> >>> Ali Kazempour >>> Physics department, Isfahan University of Technology >>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >>> >>> --- On *Fri, 9/18/09, ali kazempour * wrote: >>> >>> >>> From: ali kazempour >>> Subject: defect formation energy >>> To: forum at democritos.it >>> Date: Friday, September 18, 2009, 5:31 AM >>> >>> >>> Hi >>> for study of point defect , i do relax calculation and obtain positive >>> defect formation energy while by vc-relax i gain negative. ? >>> what is the difference between positive and negative formation energy? >>> waht is the physical reasons? >>> thanks a lot >>> Ali Kazempour >>> Physics department, Isfahan University of Technology >>> 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 >>> Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 >>> >>> >> >> >> -- >> ____________________________________ >> Hui Wang >> School of physics, Nankai University, Tianjin, China >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ttduyle at gmail.com Fri Sep 18 15:45:25 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 18 Sep 2009 09:45:25 -0400 Subject: [Pw_forum] Acceptable error in cohesive energy In-Reply-To: References: Message-ID: <8974d3b20909180645v5c60294bs33dc109e7d56084@mail.gmail.com> From haoweipeng at gmail.com Fri Sep 18 16:25:42 2009 From: haoweipeng at gmail.com (Haowei Peng) Date: Fri, 18 Sep 2009 09:25:42 -0500 Subject: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". Message-ID: <7559eb240909180725p58db9849y86077e64f54b3476@mail.gmail.com> Thanks all.. and sorry for my sending the mail repeatedly (I kept receiving mails which told me that my mail was not delivered successfully...) finally I set the calculation restart mode to "restart"...and it give a result which seems right, at least the total energy but I have to check the other information. -- Haowei Peng Northwestern University Department of Physics & Astronomy 2145 Sheridan Rd. Evanston, IL 60208-3112 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090918/3be3c622/attachment.htm From colonel.sreekar at gmail.com Sun Sep 20 08:00:37 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sun, 20 Sep 2009 11:30:37 +0530 Subject: [Pw_forum] Acceptable error in cohesive energy Message-ID: >DFT-Cohesive energy is decided by the functional and the >pseudo-potential. >If the pseudo-potential and the functional predict correctly the >ground >state of isolated atom and the bulk, we usually get less than >10% error. @udai thanks for posting the question @duy thanks for giving an insight into the issue. my question is what are the other parameters/tests other from cohesive energy calculations that can be used to estimate the validity of a pseudopotential as i want to generate one for Gadolinium sincerely, sreekar guddeti BTech + MTech Dept. Physics IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090920/58a97aa7/attachment.htm From decboy9 at gmail.com Mon Sep 21 12:49:47 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 21 Sep 2009 16:19:47 +0530 Subject: [Pw_forum] MO DIAGRAM & DOS ANALYSIS Message-ID: hi 2 all, Hope so that all of you will be fine. First of all i want to know that can we calculate the molecular orbital diagram of VO4( 3-) by PWSCF. Secondly regrading the analysis, of DOS, like my valance band consist of 0-2p, V-3d and conduction band of V3d orbitals. Sir, how can we find that in valance band in p-d hybridization which orbitals are bonding/ non bonding means means out of 3 p orbitals and 5 d orbitals which orbitals (like 2px and 3dxy or 2pz and 3xy) have undergone hybridization ??? Can some body also suggest some ideas/ notes or books where it is described that weather the transitions like from O 2px (valance band with)--> V 3 d x2-y2 (conduction band ) is allowed or not and with how much probability so that we can explain absorption spectra also from the DOS analysis ?? Thanks in advance, Dev Sharma , Univeristy of Delhi, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090921/d3fd3bab/attachment.htm From guntherjegert at mytum.de Mon Sep 21 14:56:48 2009 From: guntherjegert at mytum.de (Gunther Jegert) Date: Mon, 21 Sep 2009 14:56:48 +0200 Subject: [Pw_forum] Geometry optimization does not converge Message-ID: <000001ca3aba$fb7705d0$f2651170$@de> Dear all, I am quite new to the PWscf community and currently I am trying to do a geometry relaxation for a SiO2-slab with 84 atoms, where I introduced an Oxygen vacancy. Things went pretty well for the neutral slab with vacancy. However, when I try to charge the vacancy by removing an electron, I run into problems. Starting from the relaxed geometry of the neutral vacancy, the BFGS algorithm does not converge anymore. I end up with the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% from bfgs : error # 1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% stopping ... This error has been discussed several times in the forum (f. i. (http://www.democritos.it/pipermail/pw_forum/2007-January/005834.html))and I, of course, checked the archives for propositions how to solve the problem. Following Stefano?s (http://www.democritos.it/pipermail/pw_forum/2007-January/005840.html) and Axel?s (http://www.democritos.it/pipermail/pw_forum/2007-January/005843.html) suggestions, I varied the energy cutoff between 40 ? 60 Ry and kept the density ten times higher. I added some additional unoccupied states and a smearing. I also increased the conv_thr for the electrons up to 1D-11. I even tried different starting geometries. However, I always end up with a too high force in the order of 1D-2 (forc_conv_thr = default). Might I still have problems with too noisy energies due to insufficient scf-convergence or inaccurate forces or do I just have a stupid beginner?s mistake in my input? Below, I have added an exemplary input file. I would be grateful, if you could have a look on it and check it. Any suggestion of you is very, very welcome! &CONTROL calculation = 'relax' , restart_mode = 'restart' , outdir = '/home/PWscf/SiO2_84_Ovacp1_relax/output//' , pseudo_dir = '/home/PWscf/pseudo//' , nstep = 200 , / &SYSTEM ibrav = 0, nat = 83, ntyp = 3, ecutwfc = 60 , ecutrho = 600 , nelec = 409 , nbnd = 220, occupations = 'smearing' , degauss = 0.05 , smearing = 'methfessel-paxton' , nspin = 2 , / &ELECTRONS conv_thr = 1.D-9 , mixing_beta = 0.1 , mixing_mode = 'local-TF' , mixing_ndim = 10 , / &IONS ion_dynamics = 'bfgs' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , / CELL_PARAMETERS hexagonal 17.414330330 6.200601079 0.000000000 0.000000000 13.777142870 0.000000000 0.000000000 0.000000000 42.588738040 ATOMIC_SPECIES O 15.99900 O.pbe-van_bm.UPF Si 28.08600 Si.pbe-n-van.UPF H 1.00794 H.pbe-van_bm.UPF ATOMIC_POSITIONS crystal H 0.442138619 0.127580299 0.242115140 H 0.896137968 0.169119175 0.231615489 H 0.145279030 0.729466154 0.185318477 H 0.568527920 0.766728712 0.198838355 H 0.457668337 0.648606147 0.882235439 H 0.943934588 0.667149402 0.882893664 H 0.230323559 0.332247876 0.847403349 H 0.718571406 0.319187862 0.839952063 O 0.364677524 0.489280841 0.306670494 O 0.867635321 0.478867163 0.284064758 O 0.147367650 0.236115994 0.598026320 O 0.649640819 0.240794516 0.584731050 O 0.006278921 0.852123145 0.451026193 O 0.505597281 0.853373705 0.451280302 O 0.272809908 0.659725422 0.767916947 O 0.779049125 0.652527075 0.765357869 O 0.012328673 0.412490052 0.389290845 O 0.531224781 0.403102299 0.404465186 O 0.301626474 0.205319075 0.698724798 O 0.781065101 0.224772715 0.689991966 O 0.399409099 0.024956692 0.247297497 O 0.872257458 0.051528049 0.239846197 O 0.165316856 0.807508121 0.552180617 O 0.674267803 0.814813814 0.545851753 O 0.371769306 0.230668120 0.470840104 O 0.874075269 0.237128242 0.461296955 O 0.140604238 0.045485854 0.762585096 O 0.636783689 0.032316531 0.746475796 O 0.227654885 0.869784726 0.305080065 O 0.732727431 0.858504650 0.301584259 O 0.016547404 0.618236231 0.612079200 O 0.499871866 0.635111488 0.584920922 O 0.352145267 0.087370571 0.364285089 O 0.869168592 0.063942036 0.358940555 O 0.147949565 0.833154474 0.667584191 O 0.651280724 0.772724044 0.662149348 O 0.227434967 0.645403363 0.208182128 O 0.662565566 0.668667284 0.208416304 O 1.017204746 0.453226494 0.506583053 O 0.136606701 0.247643881 0.288287407 O 0.625203555 0.236268317 0.300390560 O 0.422870566 0.005178966 0.601178945 O 0.910961373 -0.002707092 0.599445140 O 0.049445293 0.422821214 0.745842272 O 0.533616582 0.415059161 0.741837098 O 0.279059613 0.620877043 0.456332047 O 0.772220558 0.616326195 0.445880739 O 0.077686441 0.628262425 0.307134784 O 0.592714281 0.614412248 0.320651893 O 0.355511589 0.386483961 0.603007628 O 0.861212384 0.386623507 0.596590250 O 0.217865803 0.001430950 0.458554135 O 0.719084261 0.003380876 0.451700786 O -0.012841619 0.805524587 0.760936012 O 0.491588382 0.790461355 0.759417041 O 0.491159178 0.549730308 0.851262651 O 0.986487073 0.567079624 0.852990171 O 0.287151091 0.251418691 0.815141144 O 0.774113742 0.233345538 0.808313178 Si 0.022946405 0.442457010 0.317456331 Si 0.529681143 0.438905148 0.330234749 Si 0.304976291 0.200078045 0.627530596 Si 0.808520928 0.210558149 0.619785676 Si 0.161464516 0.828055173 0.481008952 Si 0.671356418 0.820865731 0.473400870 Si 0.445482049 0.605073868 0.781879032 Si 0.948636471 0.613116893 0.782529738 Si 0.279447583 0.058249921 0.300110703 Si 0.777972225 0.052171461 0.299130437 Si 0.059696263 0.813964553 0.608786133 Si 0.566523466 0.812843443 0.600031241 Si 0.193805384 0.233036488 0.756882342 Si 0.681560751 0.226501789 0.748830087 Si 0.408990216 0.420762023 0.452805513 Si 0.920407319 0.429512363 0.449897638 Si 0.222030251 0.663241013 0.280168453 Si 0.713290716 0.659481955 0.277387702 Si 0.010118971 0.426126379 0.578196606 Si 0.500224259 0.418800498 0.580296470 Si 0.362955019 0.035259574 0.433753945 Si 0.867091171 0.039993888 0.429863970 Si 0.137475224 0.836500083 0.740406223 Si 0.640529374 0.813508387 0.734302882 K_POINTS 2 0.2500000000000000 0.2500000000000000 0.0000000000000000 0.500000000000000 0.2500000000000000 -0.2500000000000000 0.0000000000000000 0.500000000000000 Best wishes Gunther _________________________________ Dipl.-Phys. Gunther Jegert Lehrstuhl f?r Nanoelektronik Technische Universit?t M?nchen Geb?ude N8, Raum 1820 Theresienstra?e 90 80333 M?nchen Phone: +49 89 289 25370 Mail: guntherjegert at mytum.de Web: http://www.nano.ei.tum.de _________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090921/4f54be13/attachment-0001.htm From ismotochi at gmail.com Mon Sep 21 19:43:38 2009 From: ismotochi at gmail.com (isaac motochi) Date: Mon, 21 Sep 2009 20:43:38 +0300 Subject: [Pw_forum] slab/cluster calculation for silicate Message-ID: <9d6ea92e0909211043s38d10897ra11fad3ee0fd5b75@mail.gmail.com> Hi great people in the forum. Am interested in calculating some structural properties of an extended material of silica. Can anybody sent me an input scf script to start with . Cheers Motochi Isaac Moi university- kenya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090921/7313c49f/attachment.htm From ttduyle at gmail.com Mon Sep 21 20:06:31 2009 From: ttduyle at gmail.com (Duy Le) Date: Mon, 21 Sep 2009 14:06:31 -0400 Subject: [Pw_forum] slab/cluster calculation for silicate In-Reply-To: <9d6ea92e0909211043s38d10897ra11fad3ee0fd5b75@mail.gmail.com> References: <9d6ea92e0909211043s38d10897ra11fad3ee0fd5b75@mail.gmail.com> Message-ID: <8974d3b20909211106q4932ab8ds7ec5faa3288c22a1@mail.gmail.com> You can find tutorial here http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples and examples: http://www.quantum-espresso.org/download.php :-) On Mon, Sep 21, 2009 at 1:43 PM, isaac motochi wrote: > Hi great people in the forum. Am interested in calculating some structural > properties of an extended material of silica. Can anybody sent me an input > scf script to start with . > > Cheers > Motochi Isaac > Moi university- kenya > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090921/649b4990/attachment.htm From paulatto at sissa.it Tue Sep 22 10:33:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 22 Sep 2009 10:33:16 +0200 Subject: [Pw_forum] Geometry optimization does not converge In-Reply-To: <000001ca3aba$fb7705d0$f2651170$@de> References: <000001ca3aba$fb7705d0$f2651170$@de> Message-ID: In data 21 settembre 2009 alle ore 14:56:48, Gunther Jegert ha scritto: > I varied the energy cutoff between 40 ? 60 Ry and kept the > density ten times higher. I added some additional unoccupied states and a > smearing. I also increased the conv_thr for the electrons up to 1D-11. I > even tried different starting geometries. However, I always end up with a > too high force in the order of 1D-2 (forc_conv_thr = default). Dear Gunther, your input looks ok to me, there are only a couple of point you could improve: 1. the values you've choosen for nbnd is lower than the default one, it may be too low 2. I'm not sure pot_extrapolation is supposed to work with bfgs 3. wfc_extrapolation is not implemented with ultrasoft pseudopotentials, it should be harmless though 4. you could increase upscale from 10 to 1.d+4 or even more, this would allow the code to tighten the convergence threshold if necessary 5. you can always try the damp algorithm instead of bfgs... I hope it helps, best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From ismotochi at gmail.com Tue Sep 22 20:00:41 2009 From: ismotochi at gmail.com (isaac motochi) Date: Tue, 22 Sep 2009 21:00:41 +0300 Subject: [Pw_forum] slab/cluster calculation for silicate In-Reply-To: <8974d3b20909211106q4932ab8ds7ec5faa3288c22a1@mail.gmail.com> References: <9d6ea92e0909211043s38d10897ra11fad3ee0fd5b75@mail.gmail.com> <8974d3b20909211106q4932ab8ds7ec5faa3288c22a1@mail.gmail.com> Message-ID: <9d6ea92e0909221100q3354e369h3f026166ad0edb8e@mail.gmail.com> Thanks Duy Lee for you smart and prompt response. Regards Motochi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090922/c9011ea2/attachment.htm From giannozz at democritos.it Tue Sep 22 21:39:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Sep 2009 21:39:23 +0200 Subject: [Pw_forum] Geometry optimization does not converge In-Reply-To: References: <000001ca3aba$fb7705d0$f2651170$@de> Message-ID: On Sep 22, 2009, at 10:33 , Lorenzo Paulatto wrote: > 2. I'm not sure pot_extrapolation is supposed to work with bfgs it works, but extrapolation doesn't give any advantage for structural optimization > 3. wfc_extrapolation is not implemented with ultrasoft > pseudopotentials, it is implemented, but again, it gives no advantage in structural optimization P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From quantumdft at gmail.com Wed Sep 23 09:32:07 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 23 Sep 2009 15:32:07 +0800 Subject: [Pw_forum] =?windows-1252?q?Six-Core_AMD_Opteron=99_Processor_V?= =?windows-1252?q?=2ES=2E_Intel_XEON_5500_series?= Message-ID: <412f6c680909230032x189acb73qa25e2b61f8e4369c@mail.gmail.com> Dear all, Dear all, We will launch a big program to set up a computer center for Q-E and CPMD. We wonder whether AMD Six-Core AMD Opteron? Processor or Intel XEON 5500 series will give us a more efficient performance. Of course, the infiniband is included in the program. and we design 3G DDR3-1333MHz for each Core (not each CPU). any suggestion will be appreciated. thank you for reading vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/1653be21/attachment.htm From wangqj1 at 126.com Wed Sep 23 10:05:46 2009 From: wangqj1 at 126.com (wangqj1) Date: Wed, 23 Sep 2009 16:05:46 +0800 (CST) Subject: [Pw_forum] how to improve the calculation speed ? Message-ID: <21870763.369701253693146938.JavaMail.coremail@bj126app103.126.com> Dear PWSCF users When I use R and G parallelization to run job ,it as if wait for the input . According peoples advice ,I use k-point parallelization ,it runs well . But it runs too slow .The information I can offerred as following: (1) : CUP usage of one node is as Tasks: 143 total, 10 running, 133 sleeping, 0 stopped, 0 zombie Cpu0 : 99.7%us, 0.3%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu1 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu2 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu3 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu4 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu5 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu6 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Cpu7 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 8044120k total, 6683720k used, 1360400k free, 1632k buffers Swap: 4192956k total, 2096476k used, 2096480k free, 1253712k cached (2) The input file of PBS #!/bin/sh #PBS -j oe #PBS -N pw #PBS -l nodes=1:ppn=8 #PBS -q small cd $PBS_O_WORKDIR hostname /usr/local/bin/mpirun -np 8 -machinefile $PBS_NODEFILE /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out (3) wang at node22:~> netstat -s Ip: 1894215181 total packets received 0 forwarded 0 incoming packets discarded 1894215181 incoming packets delivered 979205769 requests sent out 30 fragments received ok 60 fragments created Icmp: 2 ICMP messages received 1 input ICMP message failed. ICMP input histogram: destination unreachable: 2 2 ICMP messages sent 0 ICMP messages failed ICMP output histogram: destination unreachable: 2 IcmpMsg: InType3: 2 OutType3: 2 Tcp: 5662 active connections openings 9037 passive connection openings 68 failed connection attempts 1 connection resets received 18 connections established 1894049565 segments received 979043182 segments send out 284 segments retransmited 0 bad segments received. 55 resets sent Udp: 165614 packets received 0 packets to unknown port received. 0 packet receive errors 162301 packets sent RcvbufErrors: 0 SndbufErrors: 0 UdpLite: InDatagrams: 0 NoPorts: 0 InErrors: 0 OutDatagrams: 0 RcvbufErrors: 0 SndbufErrors: 0 TcpExt: 10 resets received for embryonic SYN_RECV sockets ArpFilter: 0 5691 TCP sockets finished time wait in fast timer 25 time wait sockets recycled by time stamp 17369935 delayed acks sent 1700 delayed acks further delayed because of locked socket 18 packets directly queued to recvmsg prequeue. 8140 packets directly received from backlog 1422037027 packets header predicted 7 packets header predicted and directly queued to user TCPPureAcks: 2794058 TCPHPAcks: 517887764 TCPRenoRecovery: 0 TCPSackRecovery: 56 TCPSACKReneging: 0 TCPFACKReorder: 0 TCPSACKReorder: 0 TCPRenoReorder: 0 TCPTSReorder: 0 TCPFullUndo: 0 TCPPartialUndo: 0 TCPDSACKUndo: 0 TCPLossUndo: 1 TCPLoss: 357 TCPLostRetransmit: 6 TCPRenoFailures: 0 TCPSackFailures: 0 TCPLossFailures: 0 TCPFastRetrans: 235 TCPForwardRetrans: 46 TCPSlowStartRetrans: 0 TCPTimeouts: 3 TCPRenoRecoveryFail: 0 TCPSackRecoveryFail: 0 TCPSchedulerFailed: 0 TCPRcvCollapsed: 0 TCPDSACKOldSent: 0 TCPDSACKOfoSent: 0 TCPDSACKRecv: 2 TCPDSACKOfoRecv: 0 TCPAbortOnSyn: 0 TCPAbortOnData: 0 TCPAbortOnClose: 0 TCPAbortOnMemory: 0 TCPAbortOnTimeout: 0 TCPAbortOnLinger: 0 TCPAbortFailed: 0 TCPMemoryPressures: 0 TCPSACKDiscard: 0 TCPDSACKIgnoredOld: 1 TCPDSACKIgnoredNoUndo: 0 TCPSpuriousRTOs: 0 TCPMD5NotFound: 0 TCPMD5Unexpected: 0 IpExt: InNoRoutes: 0 InTruncatedPkts: 0 InMcastPkts: 0 OutMcastPkts: 0 InBcastPkts: 0 OutBcastPkts: 0 when I install the PWSCF ,I only use the command line : ./configure make all . And it install successful . I don't know why it run so slow ,how to solve this problem ? Any advice will be appreciated ! Best regard Q . J. Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/f82797a3/attachment.htm From Giovanni.Cantele at na.infn.it Wed Sep 23 10:45:51 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Wed, 23 Sep 2009 10:45:51 +0200 Subject: [Pw_forum] how to improve the calculation speed ? In-Reply-To: <21870763.369701253693146938.JavaMail.coremail@bj126app103.126.com> References: <21870763.369701253693146938.JavaMail.coremail@bj126app103.126.com> Message-ID: <4AB9E03F.7080600@na.infn.it> wangqj1 wrote: > > Dear PWSCF users > When I use R and G parallelization to run job ,it as if wait for the > input . What does it mean? Does it print the output header or the output up to some point or nothing happens? > According peoples advice ,I use k-point parallelization ,it runs well > . But it runs too slow .The information I can offerred as following: > (1) : CUP usage of one node is as > Tasks: 143 total, 10 running, 133 sleeping, 0 stopped, 0 zombie > Cpu0 : 99.7%us, 0.3%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu1 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu2 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu3 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu4 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu5 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu6 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Cpu7 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st > Mem: 8044120k total, 6683720k used, 1360400k free, 1632k buffers > Swap: 4192956k total, 2096476k used, 2096480k free, 1253712k cached I'm not very expert about reading such information, but it seams that your node is making swap, maybe because the job is requiring too much memory with respect to the available one. This usually induces a huge performance degradation. In choosing the optimal number of nodes, processes per node, etc., several factors should be taken into account: memory requirements, communication hardware, etc. You might want have a look to this page from the user guide: http://www.quantum-espresso.org/user_guide/node33.html Also, consider that, at least for not very very recent CPU generation, using too many cores per CPU (e.g. if your cluster configuration is with quad-core processors), might not improve (maybe also make worse) the code performances (this is also reported in previous threads in this forum, you can make a search). Also this can be of interest for you: http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F > I don't know why it run so slow ,how to solve this problem ? Any > advice will be appreciated ! Apart from better suggestions coming from more expert people, it would be important to see what kind of job you are trying to run. For example: did you start directly with a "production run" (many k-points and/or large unit cells and/or large cut-off)? Did pw.x ever run on your cluster with simple jobs, like bulk silicon or any other (see the examples directory)? Another possibility would be starting with the serial executable (disabling parallel at configure time) and then switch to parallel once you check that everything is working OK. Unfortunately, in many cases the computation requires lot of work to correctly set-up and optimize compilation, performances, etc. (not to speak about results convergence issues!!!!). The only way is trying to isolate problems and solve one by one. Yet, I would say that in this respect quantum-espresso is one of the best choices, being the code made to properly work in as many cases as possible, rather then implementing all the human knowledge but just for those who wrote it!!! ;-) Good luck, Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From paulatto at sissa.it Wed Sep 23 10:50:48 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 23 Sep 2009 10:50:48 +0200 Subject: [Pw_forum] how to improve the calculation speed ? In-Reply-To: <4AB9E03F.7080600@na.infn.it> References: <21870763.369701253693146938.JavaMail.coremail@bj126app103.126.com> <4AB9E03F.7080600@na.infn.it> Message-ID: In data 23 settembre 2009 alle ore 10:45:51, Giovanni Cantele ha scritto: > I'm not very expert about reading such information, but it seams that > your node is making swap, maybe because the job is requiring too much > memory with respect to the available one. This usually induces a huge > performance degradation. If this is the case, reducing the number of pools will reduce the amount of memory required per node. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Wed Sep 23 12:13:18 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 23 Sep 2009 03:13:18 -0700 (PDT) Subject: [Pw_forum] write occupancy Message-ID: <432077.46189.qm@web112513.mail.gq1.yahoo.com> Hi How do we can force the code to print the occupancy in simple scf run? I know partial dos calculation , but I don't know wheather another way also exist or not? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/97a9ee58/attachment.htm From prasenjit.jnc at gmail.com Wed Sep 23 12:46:45 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 23 Sep 2009 12:46:45 +0200 Subject: [Pw_forum] write occupancy In-Reply-To: <432077.46189.qm@web112513.mail.gq1.yahoo.com> References: <432077.46189.qm@web112513.mail.gq1.yahoo.com> Message-ID: <627e0ffa0909230346wbdf3399i1b2a48f4edfa9c65@mail.gmail.com> use verbosity='high' Prasenjit. 2009/9/23 ali kazempour > Hi > How do we can force the code to print the occupancy in simple scf run? > I know partial dos calculation , but I don't know wheather another way also > exist or not? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/bc129707/attachment-0001.htm From kazempoor2000 at yahoo.com Wed Sep 23 14:17:23 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 23 Sep 2009 05:17:23 -0700 (PDT) Subject: [Pw_forum] Fw: isolated atom Message-ID: <40509.61396.qm@web112502.mail.gq1.yahoo.com> Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 ----- Forwarded Message ---- From: ali kazempour To: pw Sent: Wednesday, September 23, 2009 2:03:36 PM Subject: isolated atom Hi I want to get binding energy of O2 mulecule .For this I need the correct value for isolated atom energy. But when I change(reduce) the smearing ,the value of energy increase. So I DONT know which smearing should I use? the larger or the smaller? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/71a833e8/attachment.htm From wangqj1 at 126.com Wed Sep 23 14:12:53 2009 From: wangqj1 at 126.com (wangqj1) Date: Wed, 23 Sep 2009 20:12:53 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74 In-Reply-To: References: Message-ID: <28965552.516181253707973044.JavaMail.coremail@bj126app82.126.com> ?009-09-23 18:46:48?pw_forum-request at pwscf.org ??? >Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum >or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > >You can reach the person managing the list at > pw_forum-owner at pwscf.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Pw_forum digest..." > > >Today's Topics: > > 1. how to improve the calculation speed ? (wangqj1) > 2. Re: how to improve the calculation speed ? (Giovanni Cantele) > 3. Re: how to improve the calculation speed ? (Lorenzo Paulatto) > 4. write occupancy (ali kazempour) > 5. Re: write occupancy (Prasenjit Ghosh) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 23 Sep 2009 16:05:46 +0800 (CST) >From: wangqj1 >Subject: [Pw_forum] how to improve the calculation speed ? >To: pw_forum >Message-ID: > <21870763.369701253693146938.JavaMail.coremail at bj126app103.126.com> >Content-Type: text/plain; charset="gbk" > > >Dear PWSCF users > When I use R and G parallelization to run job ,it as if wait for the input . According peoples advice ,I use k-point parallelization ,it runs well . But it runs too slow .The information I can offerred as following: >(1) : CUP usage of one node is as >Tasks: 143 total, 10 running, 133 sleeping, 0 stopped, 0 zombie >Cpu0 : 99.7%us, 0.3%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu1 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu2 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu3 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu4 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu5 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu6 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Cpu7 :100.0%us, 0.0%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st >Mem: 8044120k total, 6683720k used, 1360400k free, 1632k buffers >Swap: 4192956k total, 2096476k used, 2096480k free, 1253712k cached > >(2) The input file of PBS >#!/bin/sh >#PBS -j oe >#PBS -N pw >#PBS -l nodes=1:ppn=8 >#PBS -q small >cd $PBS_O_WORKDIR >hostname >/usr/local/bin/mpirun -np 8 -machinefile $PBS_NODEFILE /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out >(3) >wang at node22:~> netstat -s >Ip: > 1894215181 total packets received > 0 forwarded > 0 incoming packets discarded > 1894215181 incoming packets delivered > 979205769 requests sent out > 30 fragments received ok > 60 fragments created >Icmp: > 2 ICMP messages received > 1 input ICMP message failed. > ICMP input histogram: > destination unreachable: 2 > 2 ICMP messages sent > 0 ICMP messages failed > ICMP output histogram: > destination unreachable: 2 >IcmpMsg: > InType3: 2 > OutType3: 2 >Tcp: > 5662 active connections openings > 9037 passive connection openings > 68 failed connection attempts > 1 connection resets received > 18 connections established > 1894049565 segments received > 979043182 segments send out > 284 segments retransmited > 0 bad segments received. > 55 resets sent >Udp: > 165614 packets received > 0 packets to unknown port received. > 0 packet receive errors > 162301 packets sent > RcvbufErrors: 0 > SndbufErrors: 0 >UdpLite: > InDatagrams: 0 > NoPorts: 0 > InErrors: 0 > OutDatagrams: 0 > RcvbufErrors: 0 > SndbufErrors: 0 >TcpExt: > 10 resets received for embryonic SYN_RECV sockets > ArpFilter: 0 > 5691 TCP sockets finished time wait in fast timer > 25 time wait sockets recycled by time stamp > 17369935 delayed acks sent > 1700 delayed acks further delayed because of locked socket > 18 packets directly queued to recvmsg prequeue. > 8140 packets directly received from backlog > 1422037027 packets header predicted > 7 packets header predicted and directly queued to user > TCPPureAcks: 2794058 > TCPHPAcks: 517887764 > TCPRenoRecovery: 0 > TCPSackRecovery: 56 > TCPSACKReneging: 0 > TCPFACKReorder: 0 > TCPSACKReorder: 0 > TCPRenoReorder: 0 > TCPTSReorder: 0 > TCPFullUndo: 0 > TCPPartialUndo: 0 > TCPDSACKUndo: 0 > TCPLossUndo: 1 > TCPLoss: 357 > TCPLostRetransmit: 6 > TCPRenoFailures: 0 > TCPSackFailures: 0 > TCPLossFailures: 0 > TCPFastRetrans: 235 > TCPForwardRetrans: 46 > TCPSlowStartRetrans: 0 > TCPTimeouts: 3 > TCPRenoRecoveryFail: 0 > TCPSackRecoveryFail: 0 > TCPSchedulerFailed: 0 > TCPRcvCollapsed: 0 > TCPDSACKOldSent: 0 > TCPDSACKOfoSent: 0 > TCPDSACKRecv: 2 > TCPDSACKOfoRecv: 0 > TCPAbortOnSyn: 0 > TCPAbortOnData: 0 > TCPAbortOnClose: 0 > TCPAbortOnMemory: 0 > TCPAbortOnTimeout: 0 > TCPAbortOnLinger: 0 > TCPAbortFailed: 0 > TCPMemoryPressures: 0 > TCPSACKDiscard: 0 > TCPDSACKIgnoredOld: 1 > TCPDSACKIgnoredNoUndo: 0 > TCPSpuriousRTOs: 0 > TCPMD5NotFound: 0 > TCPMD5Unexpected: 0 >IpExt: > InNoRoutes: 0 > InTruncatedPkts: 0 > InMcastPkts: 0 > OutMcastPkts: 0 > InBcastPkts: 0 > OutBcastPkts: 0 >when I install the PWSCF ,I only use the command line : >./configure >make all . >And it install successful . > >I don't know why it run so slow ,how to solve this problem ? Any advice will be appreciated ! > >Best regard >Q . J. Wang >XiangTan University > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/f82797a3/attachment-0001.htm > >------------------------------ > >Message: 2 >Date: Wed, 23 Sep 2009 10:45:51 +0200 >From: Giovanni Cantele >Subject: Re: [Pw_forum] how to improve the calculation speed ? >To: PWSCF Forum >Message-ID: <4AB9E03F.7080600 at na.infn.it> >Content-Type: text/plain; charset=x-gbk; format=flowed > >wangqj1 wrote: >> >> Dear PWSCF users >> When I use R and G parallelization to run job ,it as if wait for the >> input . > >What does it mean? Does it print the output header or the output up to >some point or nothing happens? It only print the output heander and not have iteration . > >>?According?peoples?advice?,I?use?k-point?parallelization?,it?runs?well? >>?.?But?it?runs?too?slow?.The?information?I?can?offerred?as?following: >>?(1)?:?CUP?usage?of?one?node?is?as >>?Tasks:?143?total,?10?running,?133?sleeping,?0?stopped,?0?zombie >>?Cpu0?:?99.7%us,?0.3%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu1?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu2?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu3?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu4?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu5?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu6?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Cpu7?:100.0%us,?0.0%sy,?0.0%ni,?0.0%id,?0.0%wa,?0.0%hi,?0.0%si,?0.0%st >>?Mem:?8044120k?total,?6683720k?used,?1360400k?free,?1632k?buffers >>?Swap:?4192956k?total,?2096476k?used,?2096480k?free,?1253712k?cached >I'm?not?very?expert?about?reading?such?information,?but?it?seams?that? >your?node?is?making?swap,?maybe?because?the?job?is?requiring?too?much? >memory?with?respect?to?the?available?one.?This?usually?induces?a?huge? >performance?degradation. > >In?choosing?the?optimal?number?of?nodes,?processes?per?node,?etc.,? >several?factors?should?be?taken?into?account:?memory?requirements,? >communication?hardware,?etc.?You?might?want?have?a?look?to?this?page? >from?the?user?guide:?http://www.quantum-espresso.org/user_guide/node33.html 8 processes per node in our cluster, model name????? : Intel(R) Xeon(R) CPU??? E5410? @ 2.33GHz stepping??????? : 10 cpu MHz???????? : 2327.489 cache size????? : 6144 KB >Also,?consider?that,?at?least?for?not?very?very?recent?CPU?generation,? >using too many cores per CPU (e.g. if your cluster configuration is with >quad-core processors), might not improve (maybe also make worse) the >code performances (this is also reported in previous threads in this >forum, you can make a search).> >Also this can be of interest for you: >http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F I am not the supperuser,I don't know how to Set the environment variable OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ? > >>?I?don't?know?why?it?run?so?slow?,how?to?solve?this?problem???Any? >>?advice?will?be?appreciated?! >Apart?from?better?suggestions?coming?from?more?expert?people,?it?would? >be?important?to?see?what?kind?of?job?you?are?trying?to?run.?For?example:? >did?you?start?directly?with?a?"production?run"?(many?k-points?and/or? >large?unit?cells?and/or?large?cut-off)??Did?pw.x?ever?run?on?your? >cluster?with?simple?jobs,?like?bulk?silicon?or?any?other?(see?the? >examples?directory)? The input file I had run on my single computer(4 CPUs).It runs well . > >Another?possibility?would?be?starting?with?the?serial?executable? >(disabling?parallel?at?configure?time)?and?then?switch?to?parallel?once? >you?check?that?everything?is?working?OK. > > > >Unfortunately,?in?many?cases?the?computation?requires?lot?of?work?to? >correctly?set-up?and?optimize?compilation,?performances,?etc.?(not?to? >speak?about?results?convergence?issues!!!!). >The?only?way?is?trying?to?isolate?problems?and?solve?one?by?one.?Yet,?I? >would?say?that?in?this?respect?quantum-espresso?is?one?of?the?best? >choices,?being?the?code?made?to?properly?work?in?as?many?cases?as? >possible,?rather?then?implementing?all?the?human?knowledge?but?just?for? >those?who?wrote?it!!! >;-) > >Good?luck, > >Giovanni > > >--? > > > >Dr.?Giovanni?Cantele >Coherentia?CNR-INFM?and?Dipartimento?di?Scienze?Fisiche >Universita'?di?Napoli?"Federico?II" >Complesso?Universitario?di?Monte?S.?Angelo?-?Ed.?6 >Via?Cintia,?I-80126,?Napoli,?Italy >Phone:?+39?081?676910 >Fax:???+39?081?676346 >E-mail:?giovanni.cantele at cnr.it >????????giovanni.cantele at na.infn.it >Web:?http://people.na.infn.it/~cantele >Research?Group:?http://www.nanomat.unina.it >Skype?contact:?giocan74 > > > >------------------------------ > >Message:?3 >Date:?Wed,?23?Sep?2009?10:50:48?+0200 >From:?"Lorenzo?Paulatto"? >Subject:?Re:?[Pw_forum]?how?to?improve?the?calculation?speed?? >To:?Giovanni.Cantele at na.infn.it,?"PWSCF?Forum"? >Message-ID:? >Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes > >In?data?23?settembre?2009?alle?ore?10:45:51,?Giovanni?Cantele?? >?ha?scritto: >>?I'm?not?very?expert?about?reading?such?information,?but?it?seams?that >>?your?node?is?making?swap,?maybe?because?the?job?is?requiring?too?much >>?memory?with?respect?to?the?available?one.?This?usually?induces?a?huge >>?performance?degradation. > >If?this?is?the?case,?reducing?the?number?of?pools?will?reduce?the?amount?? >of?memory?required?per?node. > >cheers > > >--? >Lorenzo?Paulatto >SISSA??&??DEMOCRITOS?(Trieste) >phone:?+39?040?3787?511 >skype:?paulatz >www:???http://people.sissa.it/~paulatto/ > >?????***?save?italian?brains?*** >??http://saveitalianbrains.wordpress.com/ > > >------------------------------ > >Message:?4 >Date:?Wed,?23?Sep?2009?03:13:18?-0700?(PDT) >From:?ali?kazempour? >Subject:?[Pw_forum]?write?occupancy >To:?pw? >Message-ID:?<432077.46189.qm at web112513.mail.gq1.yahoo.com> >Content-Type:?text/plain;?charset="us-ascii" > >Hi >How?do?we?can?force?the?code?to?print?the?occupancy?in?simple?scf?run? >I?know?partial?dos?calculation?,?but?I?don't?know?wheather?another?way?also?exist?or?not? >thanks?a?lot > >?Ali?Kazempour >Physics?department,?Isfahan?University?of?Technology >84156?Isfahan,?Iran.????????????Tel-1:??+98?311?391?3733 >Fax:?+98?311?391?2376??????Tel-2:??+98?311?391?2375 > > > >?????? >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090923/97a9ee58/attachment-0001.htm? > >------------------------------ > >Message:?5 >Date:?Wed,?23?Sep?2009?12:46:45?+0200 >From:?Prasenjit?Ghosh? >Subject:?Re:?[Pw_forum]?write?occupancy >To:?PWSCF?Forum? >Message-ID: > <627e0ffa0909230346wbdf3399i1b2a48f4edfa9c65 at mail.gmail.com> >Content-Type:?text/plain;?charset="iso-8859-1" > >use?verbosity='high' > >Prasenjit. > >2009/9/23?ali?kazempour? > >>?Hi >>?How?do?we?can?force?the?code?to?print?the?occupancy?in?simple?scf?run? >>?I?know?partial?dos?calculation?,?but?I?don't?know?wheather?another?way?also >>?exist?or?not? >>?thanks?a?lot >> >>?Ali?Kazempour >>?Physics?department,?Isfahan?University?of?Technology >>?84156?Isfahan,?Iran.?Tel-1:?+98?311?391?3733 >>?Fax:?+98?311?391?2376?Tel-2:?+98?311?391?2375 >> >> >>?_______________________________________________ >>?Pw_forum?mailing?list >>?Pw_forum at pwscf.org >>?http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > >--? >PRASENJIT?GHOSH, >POST-DOC, >ROOM?NO:?265,?MAIN?BUILDING, >CM?SECTION,?ICTP, >STRADA?COSTERIA?11, >TRIESTE,?34104, >ITALY >PHONE:?+39?040?2240?369?(O) >?????????????+39?3807528672?(M) >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090923/bc129707/attachment.htm? > >------------------------------ > >_______________________________________________ >Pw_forum?mailing?list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End?of?Pw_forum?Digest,?Vol?27,?Issue?74 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/1a72ca25/attachment-0001.htm From degironc at sissa.it Wed Sep 23 14:57:22 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 23 Sep 2009 14:57:22 +0200 Subject: [Pw_forum] Fw: isolated atom In-Reply-To: <40509.61396.qm@web112502.mail.gq1.yahoo.com> References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> Message-ID: <4ABA1B32.5050507@sissa.it> use nosym=.true. and tot_magnetization=2 with fixed occupations stefano ali kazempour wrote: > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ----- Forwarded Message ---- > *From:* ali kazempour > *To:* pw > *Sent:* Wednesday, September 23, 2009 2:03:36 PM > *Subject:* isolated atom > > > Hi > I want to get binding energy of O2 mulecule .For this I need the > correct value for isolated atom energy. But when I change(reduce) the > smearing ,the value of energy increase. So I DONT know which smearing > should I use? the larger or the smaller? > thanks > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Wed Sep 23 15:06:07 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 23 Sep 2009 15:06:07 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74 In-Reply-To: <28965552.516181253707973044.JavaMail.coremail@bj126app82.126.com> References: <28965552.516181253707973044.JavaMail.coremail@bj126app82.126.com> Message-ID: In data 23 settembre 2009 alle ore 14:12:53, wangqj1 ha scritto: >> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out > It only print the output heander and not have iteration . Maybe it's not reading the input at all! You should specify the full path to you input file, e.g. mpirun ... bin/pw.x -in /where/is/is/ZnO.pw.inp just to be sure. > I am not the supperuser,I don't know how to Set the environment variable > OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ? You don't need to be super-user (nor supper-user ;-) to set an environment variable, you only have to add export OMP_NUM_THREADS=1 in your PBS script, before calling mpirun. To be sure it's propagated to all the processors add the option -x OMP_NUM_THREAD to mpirun arguments (BEFORE pw.x). cheers P.S. when answering to a daily digest, please remove the irrelevant parts, and set the discussion title to whatever it was before; this make it easier for other people to follow the discussion! -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From kazempoor2000 at yahoo.com Wed Sep 23 14:03:36 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 23 Sep 2009 05:03:36 -0700 (PDT) Subject: [Pw_forum] isolated atom Message-ID: <331008.74684.qm@web112514.mail.gq1.yahoo.com> Hi I want to get binding energy of O2 mulecule .For this I need the correct value for isolated atom energy. But when I change(reduce) the smearing ,the value of energy increase. So I DONT know which smearing should I use? the larger or the smaller? thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/959fbd49/attachment.htm From marzari at MIT.EDU Wed Sep 23 15:31:20 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 23 Sep 2009 09:31:20 -0400 Subject: [Pw_forum] isolated atom In-Reply-To: <331008.74684.qm@web112514.mail.gq1.yahoo.com> References: <331008.74684.qm@web112514.mail.gq1.yahoo.com> Message-ID: <4ABA2328.5070609@mit.edu> ali kazempour wrote: > > Hi > I want to get binding energy of O2 mulecule .For this I need the > correct value for isolated atom energy. But when I change(reduce) the > smearing ,the value of energy increase. So I DONT know which smearing > should I use? the larger or the smaller? > thanks Smearing is used primarily to smooth the fermi discontinuity in metals, allowing to use coarser meshes of k-points. From this point of view, for an atom you'll have gamma sampling and no k-points issues. A secondary effect of smearing is that it helps reach selfconsistency - especially in atoms or molecules where the HOMO and LUMO are close and could swap order during selfconsistency. What you want is to use a smearing that is quite a bit smaller than the converged HOMO-LUMO gap - when that happens, the HOMO is full, the LUMO is empty, and the energy E or the free energy E-TS do not change as you vary the fictitious smearing temperature T. If you have trouble reaching self-consistency in this case, use a larger smearing, and then restart from your converged results with the smaller one. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From marzari at MIT.EDU Wed Sep 23 15:35:02 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 23 Sep 2009 09:35:02 -0400 Subject: [Pw_forum] =?windows-1252?q?Six-Core_AMD_Opteron=99_Processor_V?= =?windows-1252?q?=2ES=2E_Intel_XEON_5500_series?= In-Reply-To: <412f6c680909230032x189acb73qa25e2b61f8e4369c@mail.gmail.com> References: <412f6c680909230032x189acb73qa25e2b61f8e4369c@mail.gmail.com> Message-ID: <4ABA2406.60706@mit.edu> vega lew wrote: > Dear all, > > Dear all, > > We will launch a big program to set up a computer center for Q-E and > CPMD. We wonder whether AMD Six-Core AMD Opteron? Processor or Intel > XEON 5500 series will give us a more efficient performance. Of course, > the infiniband is included in the program. and we design 3G > DDR3-1333MHz for each Core (not each CPU). > > any suggestion will be appreciated. > > thank you for reading > > vega Dear Vega, *great* news ! And congratulations... We are also debating right now a Opteron vs Intel (small) purchase, especially for large memory jobs - so if anyone had any information on perfromance, or scalability with Infiniband, that would be greatly appreciated. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From kazempoor2000 at yahoo.com Wed Sep 23 15:40:55 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 23 Sep 2009 06:40:55 -0700 (PDT) Subject: [Pw_forum] Fw: isolated atom In-Reply-To: <4ABA1B32.5050507@sissa.it> References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> Message-ID: <603824.13177.qm@web112513.mail.gq1.yahoo.com> Dear Stefano But esspresso don't allow fixed occupation for spin-polarized thanks Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 ________________________________ From: Stefano de Gironcoli To: PWSCF Forum Sent: Wednesday, September 23, 2009 2:57:22 PM Subject: Re: [Pw_forum] Fw: isolated atom use nosym=.true. and tot_magnetization=2 with fixed occupations stefano ali kazempour wrote: > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ----- Forwarded Message ---- > *From:* ali kazempour > *To:* pw > *Sent:* Wednesday, September 23, 2009 2:03:36 PM > *Subject:* isolated atom > > > Hi > I want to get binding energy of O2 mulecule .For this I need the > correct value for isolated atom energy. But when I change(reduce) the > smearing ,the value of energy increase. So I DONT know which smearing > should I use? the larger or the smaller? > thanks > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090923/7e7fbcb8/attachment.htm From paulatto at sissa.it Wed Sep 23 16:47:56 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 23 Sep 2009 16:47:56 +0200 Subject: [Pw_forum] Fw: isolated atom In-Reply-To: <603824.13177.qm@web112513.mail.gq1.yahoo.com> References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> <603824.13177.qm@web112513.mail.gq1.yahoo.com> Message-ID: In data 23 settembre 2009 alle ore 15:40:55, ali kazempour ha scritto: > But esspresso don't allow fixed occupation for spin-polarized Dear Ali, it does! You have to specify the occupations for spin up then, on a new line, for spin down. that's all cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From manoj at phys.ufl.edu Wed Sep 23 23:50:22 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Wed, 23 Sep 2009 17:50:22 -0400 (EDT) Subject: [Pw_forum] relaxating only z coordinate? Message-ID: Dear PWSCF users, This might have been answered previously, but I was unable to find it. How can one relax only z coordinate of atoms inside unit cell using PW? In other words how can I constrain x and y coordinates of atoms during relaxation? Regards, Manoj Srivastava University of Florida Gainesville, FL From lanhaiping at gmail.com Thu Sep 24 00:29:11 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 24 Sep 2009 06:29:11 +0800 Subject: [Pw_forum] relaxating only z coordinate? In-Reply-To: References: Message-ID: Hi, Please check INPUT_PW document, you will find below description: if_pos(1), if_pos(2), if_pos(3) INTEGER *Default:* 1 component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in meta-dynamics, neb, smd, MD dynamics or structural optimization run. If you want to fix some atom or some direction , just set if_pos(i) =0 . Regards, Hai-Ping On Thu, Sep 24, 2009 at 5:50 AM, Manoj Srivastava wrote: > Dear PWSCF users, > This might have been answered previously, but I was unable to find > it. How can one relax only z coordinate of atoms inside unit cell using > PW? In other words how can I constrain x and y coordinates of atoms during > relaxation? > > > Regards, > Manoj Srivastava > University of Florida > Gainesville, FL > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/ac5c3cb0/attachment-0001.htm From wangqj1 at 126.com Thu Sep 24 03:27:31 2009 From: wangqj1 at 126.com (wangqj1) Date: Thu, 24 Sep 2009 09:27:31 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 76 In-Reply-To: References: Message-ID: <8435040.672811253755651762.JavaMail.coremail@bj126app21.126.com> >Message: 2 >Date: Wed, 23 Sep 2009 15:06:07 +0200 >From: "Lorenzo Paulatto" >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74 >To: "PWSCF Forum" >Message-ID: >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > >In data 23 settembre 2009 alle ore 14:12:53, wangqj1 ha >scritto: >>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out >> It only print the output heander and not have iteration . >Maybe?it's?not?reading?the?input?at?all!?You?should?specify?the?full?path?? >to?you?input?file,?e.g. >???mpirun?...?bin/pw.x?-in?/where/is/is/ZnO.pw.inp >just?to?be?sure. The output file is as following: Program PWSCF v.4.0.1 starts ... Today is 24Sep2009 at 8:49:30 Parallel version (MPI) Number of processors in use: 8 R & G space division: proc/pool = 8 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW ..................................................................... Initial potential from superposition of free atoms starting charge 435.99565, renormalised to 436.00000 Starting wfc are 254 atomic + 8 random wfc It seems that it had read the input file .When use K-point parallel ,it runs well. > >>?I?am?not?the?supperuser,I?don't?know?how?to?Set?the?environment?variable?? >>?OPEN_MP_THREADS?to?1,I?can't?find?where?is?OPEN_MP_THREADS?? > >You?don't?need?to?be?super-user?(nor?supper-user?;-)?to?set?an?environment?? >variable,?you?only?have?to?add >??export?OMP_NUM_THREADS=1 >in?your?PBS?script,?before?calling?mpirun.?To?be?sure?it's?propagated?to?? >all?the?processors?add?the?option >??-x?OMP_NUM_THREAD >to?mpirun?arguments?(BEFORE?pw.x). I want to know whether it is necessary to set environment?variable OPEN_MP_THREADS?(I installed MPICH2 not OPENMPI) ? Thanks very much for your help ! Best regards ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/2f43cad8/attachment.htm From manoj at phys.ufl.edu Thu Sep 24 05:37:22 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Wed, 23 Sep 2009 23:37:22 -0400 (EDT) Subject: [Pw_forum] relaxating only z coordinate? In-Reply-To: Message-ID: Thanks Hai-Ping! -Manoj On Thu, 24 Sep 2009, lan haiping wrote: > Hi, Please check INPUT_PW document, you will find below description: > if_pos(1), if_pos(2), if_pos(3) INTEGER *Default:* 1 > > component i of the force for this atom is multiplied by if_pos(i), > which must be either 0 or 1. Used to keep selected atoms and/or > selected components fixed in meta-dynamics, neb, smd, MD dynamics or > structural optimization run. > > If you want to fix some atom or some direction , just set if_pos(i) =0 . > > Regards, > > Hai-Ping > > On Thu, Sep 24, 2009 at 5:50 AM, Manoj Srivastava wrote: > > > Dear PWSCF users, > > This might have been answered previously, but I was unable to find > > it. How can one relax only z coordinate of atoms inside unit cell using > > PW? In other words how can I constrain x and y coordinates of atoms during > > relaxation? > > > > > > Regards, > > Manoj Srivastava > > University of Florida > > Gainesville, FL > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > From neelphysics at yahoo.in Thu Sep 24 06:29:35 2009 From: neelphysics at yahoo.in (Neel Singh) Date: Thu, 24 Sep 2009 09:59:35 +0530 (IST) Subject: [Pw_forum] from electrons : error # 1 charge is wrong Message-ID: <496521.84073.qm@web95007.mail.in2.yahoo.com> Hi, ?i am trying to relax a structure but after two iteration i am getting this error, Please help or advice, My input file is listed below. Thanks in advance ?iteration #? 1???? ecut=??? 40.00 Ry???? beta=0.20 ???? Davidson diagonalization with overlap ???? ethr =? 1.00E-02,? avg # of iterations =? 1.0 ???? total cpu time spent up to now is??? 252.18 secs ???? WARNING: integrated charge=?? 286.80000000, expected=?? 287.00000000 ???? total energy????????????? = -2892.51662082 Ry ???? Harris-Foulkes estimate?? = -2894.39255945 Ry ???? estimated scf accuracy??? In the forum I have seen the statement like doing scf calculation for an isolated atom is tricky. Can somebody explain me why is this so? and then while testing a pseudo potential is it a good idea to calculate cohesive energies (which involves isolated atom) and compare as we do for lattice parameter and bulk modulus. -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/a3dc3f3a/attachment.htm From sagarambavale at yahoo.co.in Thu Sep 24 07:37:15 2009 From: sagarambavale at yahoo.co.in (ambavale sagar) Date: Thu, 24 Sep 2009 11:07:15 +0530 (IST) Subject: [Pw_forum] relaxating only z coordinate In-Reply-To: References: Message-ID: <351720.19931.qm@web94616.mail.in2.yahoo.com> Dear Manoj i.e now in your input file the atomic position card will look like: ATOMIC POSITIONS Si 0 0 0 0 0 1 Si 0.5 0.5 0.5 0 0 1 Si 0.7 0.7 0.7 1 0 0 This atomic position card allow you to displace first two atoms in z direction while the third Si in x direction. Regards Sagar Ambavale The M. S. University of Baroda India =============================== Message: 8 Date: Wed, 23 Sep 2009 17:50:22 -0400 (EDT) From: Manoj Srivastava Subject: [Pw_forum] relaxating only z coordinate? To: PWSCF Forum Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear PWSCF users, This might have been answered previously, but I was unable to find it. How can one relax only z coordinate of atoms inside unit cell using PW? In other words how can I constrain x and y coordinates of atoms during relaxation? Regards, Manoj Srivastava University of Florida Gainesville, FL ------------------------------ Message: 9 Date: Thu, 24 Sep 2009 06:29:11 +0800 From: lan haiping Subject: Re: [Pw_forum] relaxating only z coordinate? To: PWSCF Forum Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, Please check INPUT_PW document, you will find below description: if_pos(1), if_pos(2), if_pos(3) INTEGER *Default:* 1 component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in meta-dynamics, neb, smd, MD dynamics or structural optimization run. If you want to fix some atom or some direction , just set if_pos(i) =0 . Regards, Hai-Ping From cricket scores to your friends. Try the Yahoo! India Homepage! http://in.yahoo.com/trynew -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/cd3a1dde/attachment-0001.htm From colonel.sreekar at gmail.com Thu Sep 24 08:17:46 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Thu, 24 Sep 2009 11:47:46 +0530 Subject: [Pw_forum] from electrons : error # 1 charge is wrong Message-ID: >Hi, Hi Neel >?i am trying to relax a structure but after two iteration i am getting this error, ???? from electrons : error #???????? 1 ???? charge is wrong have a look at this http://www.democritos.it/pipermail/pw_forum/2008-April/008784.html occupations = 'fixed' is for insulators and # of bands computed = nelec/2 mostly during iteration electrons are crossing over to higher bands. hence the underestimation of integrated charge. u can always dig in through the archives which has a wealth of helpful information and we all would be grateful if u could specify your affiliation. it gives a good estimate of the extent of the spread of our community, a community which adheres to the philosophy of using, distributing and writing free software. sincerely, Sreekar Guddeti B.Tech + M.Tech Physics Dept IIT Bombay India -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/0203126e/attachment.htm From sclauzer at sissa.it Thu Sep 24 08:40:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 24 Sep 2009 08:40:28 +0200 Subject: [Pw_forum] Fw: isolated atom In-Reply-To: References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> <603824.13177.qm@web112513.mail.gq1.yahoo.com> Message-ID: <4ABB145C.4000803@sissa.it> Maybe there is a bit of misunderstanding: I think that Stefano was referring to fixed occupations, while Lorenzo to occupations given from input. I just want to point out that these are two different options to the occupations keyword in the &system namelist (Ali, please read carefully the documentation in Doc/INPUT_PW). Anyway they are both allowed with spin-polarized calculations and should be both viable to get the desired GS of the molecule. Cheers GS Lorenzo Paulatto wrote: > In data 23 settembre 2009 alle ore 15:40:55, ali kazempour > ha scritto: >> But esspresso don't allow fixed occupation for spin-polarized > > Dear Ali, > it does! You have to specify the occupations for spin up then, on a new > line, for spin down. > > that's all > > cheers > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Sep 24 08:52:09 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 24 Sep 2009 08:52:09 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 76 In-Reply-To: <8435040.672811253755651762.JavaMail.coremail@bj126app21.126.com> References: <8435040.672811253755651762.JavaMail.coremail@bj126app21.126.com> Message-ID: <4ABB1719.7090605@sissa.it> wangqj1 wrote: > >Message: 2 > >Date: Wed, 23 Sep 2009 15:06:07 +0200 > >From: "Lorenzo Paulatto" > >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74 > >To: "PWSCF Forum" > >Message-ID: > >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > > >In data 23 settembre 2009 alle ore 14:12:53, wangqj1 ha > >scritto: > >>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out > >> It only print the output heander and not have iteration . > >>Maybe it's not reading the input at all! You should specify the full path >>to you input file, e.g. >> mpirun ... bin/pw.x -in /where/is/is/ZnO.pw.inp >>just to be sure. > > The output file is as following: > Program PWSCF v.4.0.1 starts ... > > Today is 24Sep2009 at 8:49:30 > Parallel version (MPI) > Number of processors in use: 8 > R & G space division: proc/pool = 8 > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > ..................................................................... > Initial potential from superposition of free atoms > starting charge 435.99565, renormalised to 436.00000 > Starting wfc are 254 atomic + 8 random wfc > > It seems that it had read the input file . I think so. Maybe you have problems with lack of memory or very slow disk access (as already pointed by previous responses). Have you tried running with smaller system, or increasing the number of processors, or using local scratch file system,...? > When use K-point parallel ,it runs well. Can you specify better the conditions on which it runs well? What does it mean that you use "K-point parallel"? > >> >>> I am not the supperuser,I don't know how to Set the environment variable >>> OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ? >> >>You don't need to be super-user (nor supper-user ;-) to set an environment >>variable, you only have to add >> export OMP_NUM_THREADS=1 >>in your PBS script, before calling mpirun. To be sure it's propagated to >>all the processors add the option >> -x OMP_NUM_THREAD >>to mpirun arguments (BEFORE pw.x). > I want to know whether it is necessary to set environment variable OPEN_MP_THREADS (I installed MPICH2 not OPENMPI) ? > In case of doubt (like yours), always specify it. It makes no harm, and it ensures that you're not running into troubles because of unwanted threads proliferation. HTH GS P.S.:Please, always sign your mails and put affiliation. It is not difficult to let it be done automatically by your (web)mail program. Personally, I don't even like seeing mail which use the username as display name in the mail header, instead of the full (real) name... but that's my opinion. -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Sep 24 09:00:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 24 Sep 2009 09:00:28 +0200 Subject: [Pw_forum] from electrons : error # 1 charge is wrong In-Reply-To: <496521.84073.qm@web95007.mail.in2.yahoo.com> References: <496521.84073.qm@web95007.mail.in2.yahoo.com> Message-ID: <4ABB190C.9010807@sissa.it> This question as been asked n! times... please first check forum archives at http://www.democritos.it/pipermail/pw_forum/ troubleshooting section of user guide, http://www.quantum-espresso.org/user_guide/user_guide.html FAQs, http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions ... Posting an incomplete input file does not allow anyone to check if your structure is correct. Anyway you can do it by yourself using xcrysden, if you haven't yet. Please, make an effort to put your name and affiliation at the bottom of your next mails. Thanks! Regards, Gabriele Neel Singh wrote: > Hi, > > i am trying to relax a structure but after two iteration i am getting > this error, Please help or advice, My input file is listed below. > Thanks in advance > > iteration # 1 ecut= 40.00 Ry beta=0.20 > Davidson diagonalization with overlap > ethr = 1.00E-02, avg # of iterations = 1.0 > > total cpu time spent up to now is 252.18 secs > > WARNING: integrated charge= 286.80000000, expected= 287.00000000 > > total energy = -2892.51662082 Ry > Harris-Foulkes estimate = -2894.39255945 Ry > estimated scf accuracy < 6.18305675 Ry > > iteration # 2 ecut= 40.00 Ry beta=0.20 > Davidson diagonalization with overlap > ethr = 2.15E-03, avg # of iterations = 2.0 > > total cpu time spent up to now is 438.77 secs > > WARNING: integrated charge= 286.60793701, expected= 287..00000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from electrons : error # 1 > charge is wrong > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > rank 2 in job 1 localhost.localdomain_55326 caused collective abort > of all ranks > exit status of rank 2: killed by signal 9 > ======================================== > > Relax input file > ==============================] > > &control > calculation='relax', > restart_mode='from_scratch', > prefix='ZnO' > wf_collect=.true. > pseudo_dir = '/home/sushil/pseudo/', > outdir='/home/sushil/kajal/dopedZnO/temp' > tprnfor = ..true. , > > / > &system > ibrav = 4, nat= 32, ntyp=3,celldm(1)=12.280421, > celldm(3) =1.60203 ,ecutwfc = 40.0,occupations='fixed', > > / > &electrons > mixing_beta = 0.2 > conv_thr = 1.0e-6 > startingpot = 'atomic' , > startingwfc = 'atomic' , > diagonalization = 'david', > > / > &ions > ion_dynamics='damp', > pot_extrapolation = "second_order", > / > > ATOMIC_SPECIES > Zn 65.39 Zn.pw91-n-van.UPF > O 15.9994 O.pw91-van_ak.UPF > N 14.00674 N.pw91-van_ak.UPF > > ATOMIC_POSITIONS {crystal} > Zn 0.1666665 0.3333335 0.0000000 > / > / > Zn 0.8333335 0.6666665 0.7500000 > > K_POINTS {automatic} > 4 4 2 0 0 0 > > > ------------------------------------------------------------------------ > From cricket scores to your friends. Try the Yahoo! India Homepage! > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From guntherjegert at mytum.de Thu Sep 24 09:54:55 2009 From: guntherjegert at mytum.de (Gunther Jegert) Date: Thu, 24 Sep 2009 09:54:55 +0200 Subject: [Pw_forum] Geometry optimization does not converge Message-ID: <001b01ca3cec$4e3f4c40$eabde4c0$@de> Thanks for your support. I will follow your suggestions and keep you informed. Best wishes Gunther _________________________________ Dipl.-Phys. Gunther Jegert Lehrstuhl f?r Nanoelektronik Technische Universit?t M?nchen Geb?ude N8, Raum 1820 Theresienstra?e 90 80333 M?nchen Phone: +49 89 289 25370 Mail: guntherjegert at mytum.de Web: http://www.nano.ei.tum.de _________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/f7047d8b/attachment.htm From paulatto at sissa.it Thu Sep 24 10:11:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 24 Sep 2009 10:11:10 +0200 Subject: [Pw_forum] from electrons : error # 1 charge is wrong In-Reply-To: <496521.84073.qm@web95007.mail.in2.yahoo.com> References: <496521.84073.qm@web95007.mail.in2.yahoo.com> Message-ID: Dear Neel, I only wish to add one remark to what has been already said by Sreekar and Gabriele. > ecutwfc = 40.0 you have specified ecutwfc, but not ecutrho, which will be set to 4*ecutwfc=160Ry. Nevertheless, as you are using ultrasoft pseudopotential your choice is not very wise; you can probably decrease ecutwfc a bit (like 25-30%), but your definitely should increase ecutrho consistently (about 8-12 times ecutwfc). best regards. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Thu Sep 24 10:20:17 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 24 Sep 2009 10:20:17 +0200 Subject: [Pw_forum] why SCF calculation for isolated atom is tricky In-Reply-To: References: Message-ID: In data 24 settembre 2009 alle ore 06:53:06, udayagiri sai babu ha scritto: > In the forum I have seen the statement like doing scf calculation for an > isolated atom is tricky. Can somebody explain me why is this so? Because finding the ground-state of an isolated atom often involves breaking the symmetry, which requires reading the manual (hint: nosym=.true. and specify a starting magnetization). The most serious problem is that the ground state is usually degenerate, e.g. Boron can put it's higher-energy electron in p_x, p_y or p_z or any linear combination of three and still get exactly the same energy. As a consequence Self-consistency cycle can start to oscillate between degenerate ground-states and never converge. That's why an abundant number of bands and a small smearing is usually a good idea. Other people prefer to break symmetry by hand, e.g. specifying a non-cubic unit cell, but I personally find it to be not very effective. > and then > while testing a pseudo potential is it a good idea to calculate cohesive > energies (which involves isolated atom) and compare as we do for lattice > parameter and bulk modulus. Yes, it is good idea. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From zl.liu.caep at gmail.com Thu Sep 24 11:44:28 2009 From: zl.liu.caep at gmail.com (Zhong-Li Liu) Date: Thu, 24 Sep 2009 17:44:28 +0800 Subject: [Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations Message-ID: <8cdd828c0909240244p2f9dbf61ha570120f3e241df7@mail.gmail.com> Dear all, Recently, I am doing the phonon dispersion calculations with lmto linear-response code and pwscf code. Using the lmto code, I can only obtain one of the matrices of the equivalent q-points in each set. For example, bcc Ta (one atom in unit cell) at q = ( -0.125000000 -0.125000000 0.500000000 ) in 8x8x8 q mesh, the matrix is 0.16975011 0.00000000 0.01325182 0.00000000 -0.03964828 0.00000000 0.01325182 0.00000000 0.16975011 0.00000000 -0.03964828 0.00000000 -0.03964828 0.00000000 -0.03964828 0.00000000 0.24323635 0.00000000 How can I transform the existed matrix to obtain the matrices of the others' equivalent q-points( because the others' matrices in the same set of equivalent q-points are needed by the q2r.x and matdyn.x code), such as q = ( 0.125000000 0.125000000 0.500000000 ) q = ( 0.125000000 -0.125000000 -0.500000000 ) . . . . . . q = ( -0.500000000 -0.125000000 0.125000000 ) ? Any information is appreciated very much! Best wishes, z.liu -- Dr. Liu, Luoyang Normal University, Luoyang, China E-mail: zl.liu.caep at gmail.com From decboy9 at gmail.com Thu Sep 24 12:03:02 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 24 Sep 2009 15:33:02 +0530 Subject: [Pw_forum] from electrons : error # 1 charge is wrong In-Reply-To: References: <496521.84073.qm@web95007.mail.in2.yahoo.com> Message-ID: Dear Sir, what i was find in my output file , is that the structure is metallic and asking for smearing and nosym see output below. I am doing calculation on ZnO doped with N, with one Zn replaced by N. Sir any comment or suggestion on this as ZnO is a insulator with band gap 3.32 eV approx. And when i am giving the smearing and set nosym=.true., the error is removed and positions are being releaxed. Program PWSCF v.4.0.2 starts ... Today is 24Sep2009 at 15:13:53 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Message from routine setup: the system is metallic, specify occupations Message from routine setup: Dynamics, you should have no symmetries Thanks In Advance, Neel Singh , University of Delhi, India On Thu, Sep 24, 2009 at 1:41 PM, Lorenzo Paulatto wrote: > Dear Neel, > I only wish to add one remark to what has been already said by Sreekar and > Gabriele. > > > ecutwfc = 40.0 > > you have specified ecutwfc, but not ecutrho, which will be set to > 4*ecutwfc=160Ry. Nevertheless, as you are using ultrasoft pseudopotential > your choice is not very wise; you can probably decrease ecutwfc a bit > (like 25-30%), but your definitely should increase ecutrho consistently > (about 8-12 times ecutwfc). > > best regards. > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/90a64b37/attachment.htm From paulatto at sissa.it Thu Sep 24 12:15:25 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 24 Sep 2009 12:15:25 +0200 Subject: [Pw_forum] from electrons : error # 1 charge is wrong In-Reply-To: References: <496521.84073.qm@web95007.mail.in2.yahoo.com> Message-ID: In data 24 settembre 2009 alle ore 12:03:02, dev sharma ha scritto: > Dear Sir, > what i was find in my output file , is that the structure is > metallic and asking for smearing and nosym see output below. I am doing > calculation on ZnO doped with N, with one Zn replaced by N. Sir any > comment or > suggestion on this as ZnO is a insulator with band gap 3.32 eV approx. > And when i am giving the smearing and set nosym=.true., the error is > removed and positions are being releaxed. I'm not sure I've understood your problem correctly, but in general, if you replace an atom with another there is no guarantee that the resulting crystal will still be insulator! In particular, by replacing a Zn (12 electrons in valence) with a Nitrogen (5 electrons in valence) you will change the parity of the total number of electrons in the cell: if before you had an even number of electrons than it will become odd, i.e. if before you had an insulator than you will have a conductor. Keep in mind that you're not just replacing *one* atom, you're replacing one atom *per unit cell*. best regards P.S. I'm confused... are you Neel Sing? -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From decboy9 at gmail.com Thu Sep 24 12:32:26 2009 From: decboy9 at gmail.com (dev sharma) Date: Thu, 24 Sep 2009 16:02:26 +0530 Subject: [Pw_forum] from electrons : error # 1 charge is wrong In-Reply-To: References: <496521.84073.qm@web95007.mail.in2.yahoo.com> Message-ID: Thanks Sir, Its neel here but i use my friend Dev Sharma's email Id also because gmail shows all reply in one window :):) thank you very much sir, Neel, University of Delhi On Thu, Sep 24, 2009 at 3:45 PM, Lorenzo Paulatto wrote: > In data 24 settembre 2009 alle ore 12:03:02, dev sharma > ha scritto: > > > Dear Sir, > > what i was find in my output file , is that the structure is > > metallic and asking for smearing and nosym see output below. I am doing > > calculation on ZnO doped with N, with one Zn replaced by N. Sir any > > comment or > > suggestion on this as ZnO is a insulator with band gap 3.32 eV approx. > > And when i am giving the smearing and set nosym=.true., the error is > > removed and positions are being releaxed. > > I'm not sure I've understood your problem correctly, but in general, if > you replace an atom with another there is no guarantee that the resulting > crystal will still be insulator! > > In particular, by replacing a Zn (12 electrons in valence) with a Nitrogen > (5 electrons in valence) you will change the parity of the total number of > electrons in the cell: if before you had an even number of electrons than > it will become odd, i.e. if before you had an insulator than you will have > a conductor. Keep in mind that you're not just replacing *one* atom, > you're replacing one atom *per unit cell*. > > best regards > > P.S. I'm confused... are you Neel Sing? > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/afb83d99/attachment-0001.htm From kazempoor2000 at yahoo.com Thu Sep 24 13:06:27 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Thu, 24 Sep 2009 04:06:27 -0700 (PDT) Subject: [Pw_forum] Fw: isolated atom In-Reply-To: References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> <603824.13177.qm@web112513.mail.gq1.yahoo.com> Message-ID: <946758.9392.qm@web112509.mail.gq1.yahoo.com> Dear Lorenzo I tried with this but I have error from system_checkin : error # 1 neldw out of range my input file is: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/kazempou/tmp/' , pseudo_dir = './' , prefix = 'iso-gga' , etot_conv_thr = 0.0000001 , forc_conv_thr = 0.001 , / &SYSTEM ibrav = 1, celldm(1) =30 nat = 1, ntyp = 1, ecutwfc = 60, ecutrho = 400 , nspin=2 occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2, / &ELECTRONS conv_thr = 1.0D-7 , / ATOMIC_SPECIES O 16 o.optgga1.fhi.UPF ATOMIC_POSITIONS crystal O 0.5 0.5 0.5 K_POINTS gamma would you tell me where did I do mistake? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 ________________________________ From: Lorenzo Paulatto To: PWSCF Forum Sent: Wednesday, September 23, 2009 4:47:56 PM Subject: Re: [Pw_forum] Fw: isolated atom In data 23 settembre 2009 alle ore 15:40:55, ali kazempour ha scritto: > But esspresso don't allow fixed occupation for spin-polarized Dear Ali, it does! You have to specify the occupations for spin up then, on a new line, for spin down. that's all cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/bd1778c2/attachment.htm From nkxirainbow at gmail.com Thu Sep 24 13:26:11 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 24 Sep 2009 11:26:11 +0000 Subject: [Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations In-Reply-To: <8cdd828c0909240244p2f9dbf61ha570120f3e241df7@mail.gmail.com> References: <8cdd828c0909240244p2f9dbf61ha570120f3e241df7@mail.gmail.com> Message-ID: <21fbc4790909240426i4c13f711s48cc36f5f8e8a923@mail.gmail.com> Dear Liu: If you just want to perform q2r calculation, I do not think you have to get daynamic matrix manually. You can follow example 06 to fulfill your calculation ?? ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/7660328e/attachment.htm From ttduyle at gmail.com Thu Sep 24 13:33:24 2009 From: ttduyle at gmail.com (Duy Le) Date: Thu, 24 Sep 2009 07:33:24 -0400 Subject: [Pw_forum] Fw: isolated atom In-Reply-To: <946758.9392.qm@web112509.mail.gq1.yahoo.com> References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> <603824.13177.qm@web112513.mail.gq1.yahoo.com> <946758.9392.qm@web112509.mail.gq1.yahoo.com> Message-ID: <8974d3b20909240433u1fac655bj29cb6ae428bd8e03@mail.gmail.com> nelec in &SYSTEM will solve this problem. This has been discussed many time in this forum. :) On Thu, Sep 24, 2009 at 7:06 AM, ali kazempour wrote: > Dear Lorenzo > I tried with this but I have error > from system_checkin : error # 1 > neldw out of range > my input file is: > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/kazempou/tmp/' , > pseudo_dir = './' , > prefix = 'iso-gga' , > etot_conv_thr = 0.0000001 , > forc_conv_thr = 0.001 , > / > &SYSTEM > ibrav = 1, > celldm(1) =30 > nat = 1, > ntyp = 1, > ecutwfc = 60, > ecutrho = 400 , > nspin=2 > occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2, > / > &ELECTRONS > conv_thr = 1.0D-7 , > / > ATOMIC_SPECIES > O 16 o.optgga1.fhi.UPF > ATOMIC_POSITIONS crystal > O 0.5 0.5 0.5 > K_POINTS gamma > would you tell me where did I do mistake? > thanks a lot > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > ------------------------------ > *From:* Lorenzo Paulatto > *To:* PWSCF Forum > *Sent:* Wednesday, September 23, 2009 4:47:56 PM > *Subject:* Re: [Pw_forum] Fw: isolated atom > > In data 23 settembre 2009 alle ore 15:40:55, ali kazempour > ha scritto: > > But esspresso don't allow fixed occupation for spin-polarized > > Dear Ali, > it does! You have to specify the occupations for spin up then, on a new > line, for spin down. > > that's all > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/17395584/attachment.htm From zl.liu.caep at gmail.com Thu Sep 24 14:41:00 2009 From: zl.liu.caep at gmail.com (Zhong-Li Liu) Date: Thu, 24 Sep 2009 20:41:00 +0800 Subject: [Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations In-Reply-To: <21fbc4790909240426i4c13f711s48cc36f5f8e8a923@mail.gmail.com> References: <8cdd828c0909240244p2f9dbf61ha570120f3e241df7@mail.gmail.com> <21fbc4790909240426i4c13f711s48cc36f5f8e8a923@mail.gmail.com> Message-ID: <8cdd828c0909240541m539a5ad7m776f365706bb237b@mail.gmail.com> Dear Wang, Thank you for the quick reply. You are right, just as the normal method that we usually use to calculate the phonon dispersion curve with ph.x, q2r.x and matdyn.x, we can obtain the dispersion curve. However, I am trying another way that the dynamical matrices are calculated using other methods such as lmto linear-reponse code. The code just provide one of the dynamical matrices of the same set of equivalent q-points, so I need reduce the known dynamical matrices to get the others' probably according to the symmetry operations of q-points. Best wishes, Z.Liu On 24/09/2009, xirainbow wrote: > Dear Liu: > If you just want to perform q2r calculation, I do not think you have to get > daynamic matrix manually. > You can follow example 06 to fulfill your calculation ?? > > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > -- Dr. Liu, Luoyang Normal University, Luoyang, China E-mail: zl.liu.caep at gmail.com From wangqj1 at 126.com Thu Sep 24 14:24:33 2009 From: wangqj1 at 126.com (wangqj1) Date: Thu, 24 Sep 2009 20:24:33 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 78 In-Reply-To: References: Message-ID: <17255719.1117491253795073426.JavaMail.coremail@bj126app104.126.com> >Message: 3 >Date: Thu, 24 Sep 2009 08:52:09 +0200 >From: Gabriele Sclauzero >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 76 >To: PWSCF Forum >Message-ID: <4ABB1719.7090605 at sissa.it> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >wangqj1 wrote: >> >Message: 2 >> >Date: Wed, 23 Sep 2009 15:06:07 +0200 >> >From: "Lorenzo Paulatto" >> >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74 >> >To: "PWSCF Forum" >> >Message-ID: >> >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes >> > >> >In data 23 settembre 2009 alle ore 14:12:53, wangqj1 ha >> >scritto: >> >>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out >> >> It only print the output heander and not have iteration . >> >>>Maybe it's not reading the input at all! You should specify the full path >>>to you input file, e.g. >>> mpirun ... bin/pw.x -in /where/is/is/ZnO.pw.inp >>>just to be sure. >> >> The output file is as following: >> Program PWSCF v.4.0.1 starts ... >> >> Today is 24Sep2009 at 8:49:30 >> Parallel version (MPI) >> Number of processors in use: 8 >> R & G space division: proc/pool = 8 >> For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW >> ..................................................................... >> Initial potential from superposition of free atoms >> starting charge 435.99565, renormalised to 436.00000 >> Starting wfc are 254 atomic + 8 random wfc >> >> It seems that it had read the input file . > >I think so. Maybe you have problems with lack of memory or very slow disk access (as >already pointed by previous responses). Have you tried running with smaller system, or >increasing the number of processors, or using local scratch file system,...? I had running with smaller system use R & G space division,it runs quickly and soon finished the task .When I run bigger system (48 atoms),it turns up the phenomena as I said last letter. >> When use K-point parallel ,it runs well. > >Can you specify better the conditions on which it runs well? What does it mean that you >use "K-point parallel"? I mean only I use K-points division,the big system can runs ,but very slow. > >> >>> >>>> I am not the supperuser,I don't know how to Set the environment variable >>>> OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ? >>> >>>You don't need to be super-user (nor supper-user ;-) to set an environment >>>variable, you only have to add >>> export OMP_NUM_THREADS=1 >>>in your PBS script, before calling mpirun. To be sure it's propagated to >>>all the processors add the option >>> -x OMP_NUM_THREAD >>>to mpirun arguments (BEFORE pw.x). >> I want to know whether it is necessary to set environment variable OPEN_MP_THREADS (I installed MPICH2 not OPENMPI) ? >> > >In case of doubt (like yours), always specify it. It makes no harm, and it ensures that >you're not running into troubles because of unwanted threads proliferation. > >HTH > >GS > > >P.S.:Please, always sign your mails and put affiliation. It is not difficult to let it be >done automatically by your (web)mail program. >Personally, I don't even like seeing mail which use the username as display name in the >mail header, instead of the full (real) name... but that's my opinion. > Thank you ! Best regard -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090924/765882c4/attachment-0001.htm From sclauzer at sissa.it Thu Sep 24 15:15:59 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 24 Sep 2009 15:15:59 +0200 Subject: [Pw_forum] Fw: isolated atom In-Reply-To: <8974d3b20909240433u1fac655bj29cb6ae428bd8e03@mail.gmail.com> References: <40509.61396.qm@web112502.mail.gq1.yahoo.com> <4ABA1B32.5050507@sissa.it> <603824.13177.qm@web112513.mail.gq1.yahoo.com> <946758.9392.qm@web112509.mail.gq1.yahoo.com> <8974d3b20909240433u1fac655bj29cb6ae428bd8e03@mail.gmail.com> Message-ID: <4ABB710F.2080806@sissa.it> No need to specify nelup and neldw, because specifying tot_magnetization (or, equivalently, multiplicity) is enough. Moreover the nelup and neldw are deprecated keywords and will be no more available in future versions of QE. Regards, GS Duy Le wrote: > nelec in &SYSTEM will solve this problem. This has been discussed many > time in this forum. > > :) > > On Thu, Sep 24, 2009 at 7:06 AM, ali kazempour > wrote: > > Dear Lorenzo > I tried with this but I have error > from system_checkin : error # 1 > neldw out of range > my input file is: > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/kazempou/tmp/' , > pseudo_dir = './' , > prefix = 'iso-gga' , > etot_conv_thr = 0.0000001 , > forc_conv_thr = 0.001 , > / > &SYSTEM > ibrav = 1, > celldm(1) =30 > nat = 1, > ntyp = 1, > ecutwfc = 60, > ecutrho = 400 , > nspin=2 > occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2, > / > &ELECTRONS > conv_thr = 1.0D-7 , > / > ATOMIC_SPECIES > O 16 o.optgga1.fhi.UPF > ATOMIC_POSITIONS crystal > O 0.5 0.5 0.5 > K_POINTS gamma > would you tell me where did I do mistake? > thanks a lot > > > Ali Kazempour > Physics department, Isfahan University of Technology > 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 > Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 > > > ------------------------------------------------------------------------ > *From:* Lorenzo Paulatto > > > *To:* PWSCF Forum > > *Sent:* Wednesday, September 23, 2009 4:47:56 PM > > *Subject:* Re: [Pw_forum] Fw: isolated atom > > In data 23 settembre 2009 alle ore 15:40:55, ali kazempour > > ha scritto: > > But esspresso don't allow fixed occupation for spin-polarized > > Dear Ali, > it does! You have to specify the occupations for spin up then, on a > new > line, for spin down. > > that's all > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From manoj at phys.ufl.edu Thu Sep 24 15:17:12 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Thu, 24 Sep 2009 09:17:12 -0400 (EDT) Subject: [Pw_forum] relaxating only z coordinate In-Reply-To: <351720.19931.qm@web94616.mail.in2.yahoo.com> Message-ID: Thanks Sagar! On Thu, 24 Sep 2009, ambavale sagar wrote: > Dear Manoj i.e now in your input file the atomic position card will look like: ATOMIC POSITIONS Si 0 0 0 0 0 1 Si 0.5 0.5 0.5 0 0 1 Si 0.7 0.7 0.7 1 0 0 This atomic position card allow you to displace first two atoms in z direction while the third Si in x direction. Regards Sagar Ambavale The M. S. University of Baroda India =============================== Message: 8 Date: Wed, 23 Sep 2009 17:50:22 -0400 (EDT) From: Manoj Srivastava Subject: [Pw_forum] relaxating only z coordinate? To: PWSCF Forum Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear PWSCF users, This might have been answered previously, but I was unable to find it. How can one relax only z coordinate of atoms inside unit cell using PW? In other words how can I constrain x and y coordinates of atoms during relaxation? Regards, Manoj Srivastava University of Florida Gainesville, FL ------------------------------ Message: 9 Date: Thu, 24 Sep 2009 06:29:11 +0800 From: lan haiping Subject: Re: [Pw_forum] relaxating only z coordinate? To: PWSCF Forum Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, Please check INPUT_PW document, you will find below description: if_pos(1), if_pos(2), if_pos(3) INTEGER *Default:* 1 component i of the force for this atom is multiplied by if_pos(i), which must be either 0 or 1. Used to keep selected atoms and/or selected components fixed in meta-dynamics, neb, smd, MD dynamics or structural optimization run. If you want to fix some atom or some direction , just set if_pos(i) =0 . Regards, Hai-Ping From cricket scores to your friends. Try the Yahoo! India Homepage! http://in.yahoo.com/trynew From decboy9 at gmail.com Fri Sep 25 07:33:21 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 25 Sep 2009 11:03:21 +0530 Subject: [Pw_forum] problem in phonon in prallel Message-ID: hi 2 all, i have done scf , phonon and the running ph.x in parallel for some optical properties. my programme stops without giving any error in the ph.out file and without any CRASH. My input file is listed below. Please help. Thanks in advance. phonons at gamma &inputph tr2_ph=1.0e-10, prefix='yvo', fpol=.true., trans=.false., epsil=.true., elop=.true., amass(1)= 44.995, amass(2)= 50.9415, amass(3)=15.9994, outdir = '/home/devsharma/work/newscvo/temp', fildyn='yvo.dyn1', / 0.0 0.0 0.0 FREQUENCIES 65 7.889e+14 / / 4.389e+14 and mssg in terminal is coming [devsharma at headnode newscvo]$ [headnode.du.ac.in:6309] *** An error occurred in MPI_Allreduce [headnode.du.ac.in:6309] *** on communicator MPI COMMUNICATOR 28 SPLIT FROM 4 [headnode.du.ac.in:6309] *** MPI_ERR_TRUNCATE: message truncated [headnode.du.ac.in:6309] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -------------------------------------------------------------------------- mpirun has exited due to process rank 1 with PID 6309 on node headnode.du.ac.in exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). ---------------------------------------------------------- and the output file runs upto Representation 52 1 modes - To be done PHONON : 0m41.95s CPU time, 2m31.11s wall time Alpha used in Ewald sum = 1.0000 Frequency Dependent Polarizability Calculation and after here it stops. Please help, sincerly, Dev Sharma, Univeristy of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/906a6c50/attachment.htm From decboy9 at gmail.com Fri Sep 25 10:16:44 2009 From: decboy9 at gmail.com (dev sharma) Date: Fri, 25 Sep 2009 13:46:44 +0530 Subject: [Pw_forum] problem in phonon in prallel In-Reply-To: References: Message-ID: Hi, when i am running the same file with the following inputs , it is running well phonons at gamma &inputph tr2_ph=1.0e-10, prefix='yvo', trans=.false., epsil=.true., amass(1)= 44.995, amass(2)= 50.9415, amass(3)=15.9994, outdir = '/home/devsharma/work/newscvo/temp', fildyn='yvo.dyn1', / 0.0 0.0 0.0 means there is some problem in inputs. Any comment on the extra parameters i gave in previous file i.e. fpol and elop. Thanks sincerly, Dev Sharma, University of Delhi, ~ ~ On Fri, Sep 25, 2009 at 11:03 AM, dev sharma wrote: > hi 2 all, > i have done scf , phonon and the running ph.x in parallel for some > optical properties. my programme stops without giving any error in the > ph.out file and without any CRASH. My input file is listed below. Please > help. > Thanks in advance. > phonons at gamma > &inputph > tr2_ph=1.0e-10, > prefix='yvo', > fpol=.true., > trans=.false., > epsil=.true., > elop=.true., > amass(1)= 44.995, > amass(2)= 50.9415, > amass(3)=15.9994, > outdir = '/home/devsharma/work/newscvo/temp', > fildyn='yvo.dyn1', > / > 0.0 0.0 0.0 > > FREQUENCIES > 65 > 7.889e+14 > / > / > 4.389e+14 > > and mssg in terminal is coming > > [devsharma at headnode newscvo]$ [headnode.du.ac.in:6309] *** An error > occurred in MPI_Allreduce > [headnode.du.ac.in:6309] *** on communicator MPI COMMUNICATOR 28 SPLIT > FROM 4 > [headnode.du.ac.in:6309] *** MPI_ERR_TRUNCATE: message truncated > [headnode.du.ac.in:6309] *** MPI_ERRORS_ARE_FATAL (your MPI job will now > abort) > -------------------------------------------------------------------------- > mpirun has exited due to process rank 1 with PID 6309 on > node headnode.du.ac.in exiting without calling "finalize". This may > have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > > ---------------------------------------------------------- > and the output file runs upto > > > Representation 52 1 modes - To be done > PHONON : 0m41.95s CPU time, 2m31.11s wall time > > > Alpha used in Ewald sum = 1.0000 > > Frequency Dependent Polarizability Calculation > > and after here it stops. > > > Please help, > > sincerly, > Dev Sharma, > Univeristy of Delhi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/270ab22b/attachment.htm From giannozz at democritos.it Fri Sep 25 10:18:39 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 Sep 2009 10:18:39 +0200 Subject: [Pw_forum] problem in phonon in prallel In-Reply-To: References: Message-ID: <4ABC7CDF.2050209@democritos.it> dev sharma wrote: > Any comment on the extra > parameters i gave in previous file i.e. fpol and elop. don't give any extra parameters unless you know what they do, and unless you need them P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From wangqj1 at 126.com Fri Sep 25 15:02:50 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Fri, 25 Sep 2009 21:02:50 +0800 (CST) Subject: [Pw_forum] Running on cluster often turn up Message-ID: <10083410.509721253883770555.JavaMail.coremail@bj126app104.126.com> Dear all When I running on cluster ,it often turn up some bizarre errors ,which not turn up ong single computer .I don't know why .Whether is it because the computing environment settings ? I don' know how to do .Plese help me . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/9b5d0c9e/attachment.htm From Giovanni.Cantele at na.infn.it Fri Sep 25 15:08:14 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Fri, 25 Sep 2009 15:08:14 +0200 Subject: [Pw_forum] Running on cluster often turn up In-Reply-To: <10083410.509721253883770555.JavaMail.coremail@bj126app104.126.com> References: <10083410.509721253883770555.JavaMail.coremail@bj126app104.126.com> Message-ID: <4ABCC0BE.40302@na.infn.it> Q.J.Wang wrote: > Dear all > When I running on cluster ,it often turn up some bizarre errors ,which > not turn up ong single computer .I don't know why .Whether is it > because the computing environment settings ? I don' know how to do > .Plese help me . > Well, I think that it will be rather difficult for anybody to answer unless you provide much more extensive information than you did. Which kind of errors? Parallel or serial runs? Some issues might be related to your cluster configuration / hardware / software rather than to the Quantum-ESPRESSO. You can also try to search the forum to find if some of these errors have been ever discussed before. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it Skype contact: giocan74 From wangqj1 at 126.com Fri Sep 25 15:41:03 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Fri, 25 Sep 2009 21:41:03 +0800 (CST) Subject: [Pw_forum] about OMP_NUM_THREADS Message-ID: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> Dear all According to the advice of the forum,I added OMP_NUM_THREADS=1 in my PBS script .But I can only run a task on the cluster .When one was running ,I run another task ,and one of them will turn up error and stop . -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/1089ca3e/attachment.htm From paulatto at sissa.it Fri Sep 25 15:45:13 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 25 Sep 2009 15:45:13 +0200 Subject: [Pw_forum] about OMP_NUM_THREADS In-Reply-To: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> References: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> Message-ID: In data 25 settembre 2009 alle ore 15:41:03, Q.J.Wang ha scritto: > According to the advice of the forum,I added OMP_NUM_THREADS=1 in > my PBS script .But I can only run a task on the cluster .When one was > running ,I run another task ,and one of them will turn up error and stop Dear Q.J. Wang, as usual, you MUST provide the error message and as many details as possible on how you run the job, there is very little we can say about you problem with any information. To begin you should check that the jobs do not have the same prefix and outdir, if it is the case they will crash after a while. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Fri Sep 25 15:45:54 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 25 Sep 2009 15:45:54 +0200 Subject: [Pw_forum] about OMP_NUM_THREADS In-Reply-To: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> References: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> Message-ID: <4ABCC992.30009@sissa.it> Q.J.Wang wrote: > Dear all > According to the advice of the forum,I added OMP_NUM_THREADS=1 in > my PBS script .But I can only run a task on the cluster .When one was > running ,I run another task ,and one of them will turn up error and stop . Have you specified different outdir and/or prefix for the two tasks? Have you checked that you have enough memory on a node to run two pw.x runs? ...? GS > > > -- > Best regards > > Q.J.Wang > > XiangTan University > > > ------------------------------------------------------------------------ > "????",????60??? > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From nkxirainbow at gmail.com Fri Sep 25 16:25:37 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 25 Sep 2009 14:25:37 +0000 Subject: [Pw_forum] About example 22 Message-ID: <21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com> Dear developers: There are three trivial slip of example22. In the "README" file of example22: ONE: "2) make a band structure calculation for Pt (input=pt.band.in, output=pt.band.out)." should be "(input=pt.nscf.in, output=pt.nscf.out)." TWO:"9) make a self-consistent calculation for Pt in a tetragonal cell with 4 atoms (input=pt.tet4.in, output=pt.tet4.out)." should be " (input=pt4.in, output=pt4.out)." THREE: When I try to open "pt.nscf_ph.in" with PWgui, I get the follow error"syntax error in the input file:expecting keyword ATOMIC SPECIES, but read PHONON instead" I use espresso4.0.4. But I notice that in espresso4.1, there is not " pt.nscf_ph.in" file any more. The "pt.nscf_ph.in" is given below: "Pt Pt &control calculation = 'phonon' restart_mode='from_scratch', prefix='Pt', pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/', outdir='/home/raman/tmp/' / &system ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, lspinorb=.true., noncolin=.true., starting_magnetization=0.0, occupations='smearing', degauss=0.02, smearing='mp', ecutwfc =30.0, ecutrho =250.0, / &electrons mixing_beta = 0.7, conv_thr = 1.0d-8 / &phonon xqq(1)=1.d0, xqq(2)=0.d0, xqq(3)=0.d0, / ATOMIC_SPECIES Pt 79.90 Ptrel.RRKJ3.UPF ATOMIC_POSITIONS Pt 0.0000000 0.00000000 0.0 K_POINTS AUTOMATIC 2 2 2 1 1 1" -- ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/642bd62b/attachment-0001.htm From jmlarkin at andrew.cmu.edu Fri Sep 25 16:06:16 2009 From: jmlarkin at andrew.cmu.edu (Jason Larkin) Date: Fri, 25 Sep 2009 10:06:16 -0400 Subject: [Pw_forum] about OMP_NUM_THREADS In-Reply-To: <4ABCC992.30009@sissa.it> References: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> <4ABCC992.30009@sissa.it> Message-ID: <4ABCCE58.1040308@andrew.cmu.edu> Hello Forum, First, thanks very much for the great software package. Here is my issue, one which is probably due to my own ignorance about QE/quantum physics in general: I'm trying to run a varaible cell relaxation on the compound GeTe. Below is my input file: &control calculation = 'vc-relax' prefix='gt', pseudo_dir = '$HOME/pseudo/', outdir='$HOME/QE/GST/GeTe/out/' forc_conv_thr = 1.0d-5, etot_conv_thr = 1.0d-5, nstep=300, / &system ibrav = 4, celldm(1)=7.993540933, celldm(3)=2.581560284 nat = 18, ntyp= 2, ecutwfc = 100, ecutrho = 800, / &electrons mixing_beta = 0.7 conv_thr = 1.0d-6, / &ions upscale = 100.d0, / &cell cell_dynamics='damp-w' / ATOMIC_SPECIES Te 1.0 Te.pz-bhs.UPF Ge 1.0 Ge.pz-bhs.UPF ATOMIC_POSITIONS {crystal} Te 0 0 0 Ge 0.666666 0.333333 0.055555556 Te 0.33333 0.666666 0.111111111 Ge 0 0 0.166666667 Te 0.6666666 0.3333333 0.222222222 Ge 0.3333333 0.6666666 0.277777778 Te 0 0 0.333333333 Ge 0.6666666 0.3333333 0.388888889 Te 0.3333333 0.6666666 0.444444444 Ge 0 0 0.5 Te 0.6666666 0.3333333 0.555555556 Ge 0.3333333 0.6666666 0.611111111 Te 0 0 0.666666667 Ge 0.6666666 0.3333333 0.722222222 Te 0.3333333 0.6666666 0.777777778 Ge 0 0 0.833333333 Te 0.6666666 0.3333333 0.888888889 Ge 0.3333333 0.6666666 0.944444444 K_POINTS {automatic} 12 12 2 0 0 0 My problem (issue) is this; the simulation continues to time out before completing the relaxation. As such, I've been coninuously increasing the amount of time and processors that I am requesting to perform this calculation. However, it has reached a point (32 processors and 3:30 hours) where I'm almost certain that I am doing something wrong. I was able to find one forum posting where a user was running a relaxation and the calculation was not stopping even though the Energy and Force calculation error thresh holds where being satisfied. It appears that my energy does indeed converge. Let me attach part of my output: ********************************************************************* ! total energy = -203.60367909 Ry Harris-Foulkes estimate = -203.60367961 Ry estimated scf accuracy < 0.00000054 Ry convergence has been achieved in 9 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 atom 2 type 2 force = 0.00000000 0.00000000 0.00052582 atom 3 type 1 force = 0.00000000 0.00000000 -0.00108418 atom 4 type 2 force = 0.00000000 0.00000000 -0.00111021 atom 5 type 1 force = 0.00000000 0.00000000 -0.00066898 atom 6 type 2 force = 0.00000000 0.00000000 0.00030722 atom 7 type 1 force = 0.00000000 0.00000000 -0.00150570 atom 8 type 2 force = 0.00000000 0.00000000 -0.00163780 atom 9 type 1 force = 0.00000000 0.00000000 0.00177984 atom 10 type 2 force = 0.00000000 0.00000000 0.00000000 atom 11 type 1 force = 0.00000000 0.00000000 -0.00177984 atom 12 type 2 force = 0.00000000 0.00000000 0.00163780 atom 13 type 1 force = 0.00000000 0.00000000 0.00150570 atom 14 type 2 force = 0.00000000 0.00000000 -0.00030722 atom 15 type 1 force = 0.00000000 0.00000000 0.00066898 atom 16 type 2 force = 0.00000000 0.00000000 0.00111021 atom 17 type 1 force = 0.00000000 0.00000000 0.00108418 atom 18 type 2 force = 0.00000000 0.00000000 -0.00052582 Total force = 0.004763 Total SCF correction = 0.002516 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 5650.32 0.02322957 0.00000000 0.00000000 3417.19 0.00 0.00 0.00000000 0.02322957 0.00000000 0.00 3417.19 0.00 0.00000000 0.00000000 0.06877108 0.00 0.00 10116.57 Wentzcovitch Damped Cell-Dynamics Minimization convergence thresholds: EPSE = 0.10E-04 EPSF = 0.10E-04 EPSP = 0.50E+00 Entering Dynamics; it = 1 time = 0.00000 pico-seconds ********************************************************************* The simulation goes through 23 complete Self-consistent Calculations. Here is the last self-consistent run (before the 24th run timed out): ********************************************************************* ! total energy = -216.83428802 Ry Harris-Foulkes estimate = -216.83428838 Ry estimated scf accuracy < 0.00000036 Ry convergence has been achieved in 10 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 atom 2 type 2 force = 0.00000000 0.00000000 -0.00120296 atom 3 type 1 force = 0.00000000 0.00000000 -0.00028879 atom 4 type 2 force = 0.00000000 0.00000000 0.00057200 atom 5 type 1 force = 0.00000000 0.00000000 0.00115400 atom 6 type 2 force = 0.00000000 0.00000000 -0.00030438 atom 7 type 1 force = 0.00000000 0.00000000 -0.00064802 atom 8 type 2 force = 0.00000000 0.00000000 -0.00012442 atom 9 type 1 force = 0.00000000 0.00000000 0.00095840 atom 10 type 2 force = 0.00000000 0.00000000 0.00000000 atom 11 type 1 force = 0.00000000 0.00000000 -0.00095840 atom 12 type 2 force = 0.00000000 0.00000000 0.00012442 atom 13 type 1 force = 0.00000000 0.00000000 0.00064802 atom 14 type 2 force = 0.00000000 0.00000000 0.00030438 atom 15 type 1 force = 0.00000000 0.00000000 -0.00115400 atom 16 type 2 force = 0.00000000 0.00000000 -0.00057200 atom 17 type 1 force = 0.00000000 0.00000000 0.00028879 atom 18 type 2 force = 0.00000000 0.00000000 0.00120296 Total force = 0.003045 Total SCF correction = 0.001829 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 1021.47 0.00437252 0.00000000 0.00000000 643.22 0.00 0.00 0.00000000 0.00437252 0.00000000 0.00 643.22 0.00 0.00000000 0.00000000 0.01208629 0.00 0.00 1777.95 Entering Dynamics; it = 24 time = 0.02226 pico-seconds ********************************************************************* It appears that my force(s) are not consistent with the force threshold that I set. I'm guessing this is because my initial guess at the structure is quite far from the relaxed structure. So, would it be reasonable to take the unit cell coordinates from the last completed self-consistent calcualtion and use those as starting coordinates for a brand new vc-relax run? This would be an effort to continue the calculation, but not lose the 3:30 of run time I've already used. Also, how would I handle a restart in this situation? Forgive me if this question is too basic. Thanks for the help Jason Larkin, PhD Student Carnegie Mellon University From dalcorso at sissa.it Fri Sep 25 16:39:31 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 25 Sep 2009 16:39:31 +0200 Subject: [Pw_forum] About example 22 In-Reply-To: <21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com> References: <21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com> Message-ID: <1253889571.3266.43.camel@dhpc-5-36.sissa.it> On Fri, 2009-09-25 at 14:25 +0000, xirainbow wrote: > Dear developers: > > There are three trivial slip of example22. > > > In the "README" file of example22: > ONE: "2) make a band structure calculation for Pt (input=pt.band.in, > output=pt.band.out)." > should be "(input=pt.nscf.in, output=pt.nscf.out)." > TWO:"9) make a self-consistent calculation for Pt in a tetragonal cell > with 4 atoms (input=pt.tet4.in, output=pt.tet4.out)." > should be " (input=pt4.in, output=pt4.out)." > Thank you. I will correct in the cvs version. > > THREE: When I try to open "pt.nscf_ph.in" with PWgui, I get the follow > error"syntax error in the input file:expecting keyword ATOMIC SPECIES, > but read PHONON instead" > I use espresso4.0.4. But I notice that in espresso4.1, there is > not "pt.nscf_ph.in" file any more. > The "pt.nscf_ph.in" is given below: > "Pt > Pt > &control > calculation = 'phonon' > restart_mode='from_scratch', > prefix='Pt', > pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/', > outdir='/home/raman/tmp/' > / > &system > ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, > lspinorb=.true., > noncolin=.true., > starting_magnetization=0.0, > occupations='smearing', > degauss=0.02, > smearing='mp', > ecutwfc =30.0, > ecutrho =250.0, > / > &electrons > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > &phonon > xqq(1)=1.d0, > xqq(2)=0.d0, > xqq(3)=0.d0, > / > ATOMIC_SPECIES > Pt 79.90 Ptrel.RRKJ3.UPF > ATOMIC_POSITIONS > Pt 0.0000000 0.00000000 0.0 > K_POINTS AUTOMATIC > 2 2 2 1 1 1" > > The option 'phonon' is no more available in the pw.x input. The band structure calculation is done by ph.x if needed. Andrea > > > -- > ____________________________________ > Hui Wang > School of physics, Nankai University, Tianjin, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34151 Trieste (Italy) e-mail: dalcorso at sissa.it From paulatto at sissa.it Fri Sep 25 16:51:39 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 25 Sep 2009 16:51:39 +0200 Subject: [Pw_forum] about OMP_NUM_THREADS In-Reply-To: <4ABCCE58.1040308@andrew.cmu.edu> References: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> <4ABCC992.30009@sissa.it> <4ABCCE58.1040308@andrew.cmu.edu> Message-ID: In data 25 settembre 2009 alle ore 16:06:16, Jason Larkin ha scritto: > First, thanks very much for the great software package. Welcome Jason, and thank you for providing all the necessary information from the beginning. There are indeed a couple of issues with your input, let's have a look. > forc_conv_thr = 1.0d-5, > etot_conv_thr = 1.0d-5, force and energy are not in the same unit of measure, I don't know if this is a sensible choice, but it looks like the force threshold is too strict compared to the energy: you are requesting the total energy to change less that 1mRy if you move one atom by one hundredth of bohr... > ecutwfc = 100, ecutrho = 800, These thresholds are very high: in QE cutoffs are specified in Rydberg units (some less-free DFT-base software uses eV). You are using norm-conserving pseudopotential, I think 50-60Ry should be enough (you convergence should test for a small system), for the same reason you can use the default value of ecutrho (=4*ecutwfc). > My problem (issue) is this; the simulation continues to time out before > completing the relaxation. You can always restart a simulation from the point you've left it (as long the new run has access to outdir), just set restart_mode='restart' in the control namelist. > As such, I've been coninuously increasing > the amount of time and processors that I am requesting to perform this > calculation. However, it has reached a point (32 processors and 3:30 > hours) where I'm almost certain that I am doing something wrong. You have about 100 electrons in your system, with such a high cutoff it won't be able to do many iterations, furthermore the very strict threshold for force convergence could cause problems (all criteria has to be satisfied!). > It appears that my force(s) are not consistent with the force threshold > that I set. I'm guessing this is because my initial guess at the > structure is quite far from the relaxed structure. So, would it be > reasonable to take the unit cell coordinates from the last completed > self-consistent calcualtion and use those as starting coordinates for a > brand new vc-relax run? Yes, or you can just use the restart feature, which will also recover the partially-completed scf cycle. > This would be an effort to continue the > calculation, but not lose the 3:30 of run time I've already used. If you want to be sure that you job is not killed when it's saving the restart data (which requires a boring manual restart) you can use the max_seconds variables. Be careful because setting it to close to the time limit will likely cause the effect it's meant to prevent! Finally, you cannot use the restart feature if you change the cutoff, you'll have to do a manual restart by copying the last atomic position. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From wangqj1 at 126.com Fri Sep 25 17:01:28 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Fri, 25 Sep 2009 23:01:28 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 82 In-Reply-To: References: Message-ID: <30627758.545641253890888918.JavaMail.coremail@bj126app104.126.com> Thank you very much Lorenzo Paulatto and Gabriele Sclauzero . The problem was solved ,because I specified same prefix for the two tasks . But another problem turn up . When I use R & G space division run the task ,it was interrupted at the 2 iteration of 18 time of vc-relax and turns up as following : forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source pw.x 40000000005D8710 Unknown Unknown Unknown pw.x 40000000005D8BF0 Unknown Unknown Unknown pw.x 40000000005F4A40 Unknown Unknown Unknown pw.x 400000000003C740 Unknown Unknown I use 1 node(8 CPUs) on the cluster . I am puzzled by the phenomena ,please give me some advice about this problem ,thank you . -- Best regards Q.J.Wang XiangTan University ?2009-09-25?22:26:04?pw_forum-request at pwscf.org???? >Send?Pw_forum?mailing?list?submissions?to > pw_forum at pwscf.org > >To?subscribe?or?unsubscribe?via?the?World?Wide?Web,?visit > http://www.democritos.it/mailman/listinfo/pw_forum >or,?via?email,?send?a?message?with?subject?or?body?'help'?to > pw_forum-request at pwscf.org > >You?can?reach?the?person?managing?the?list?at > pw_forum-owner at pwscf.org > >When?replying,?please?edit?your?Subject?line?so?it?is?more?specific >than?"Re:?Contents?of?Pw_forum?digest..." > > >Today's?Topics: > >???1.?Re:?problem?in?phonon?in?prallel?(dev?sharma) >???2.?Re:?problem?in?phonon?in?prallel?(Paolo?Giannozzi) >???3.?Running?on?cluster?often?turn?up?(Q.J.Wang) >???4.?Re:?Running?on?cluster?often?turn?up?(Giovanni?Cantele) >???5.?about?OMP_NUM_THREADS?(Q.J.Wang) >???6.?Re:?about?OMP_NUM_THREADS?(Lorenzo?Paulatto) >???7.?Re:?about?OMP_NUM_THREADS?(Gabriele?Sclauzero) >???8.?About?example?22?(xirainbow) > > >---------------------------------------------------------------------- > >Message:?1 >Date:?Fri,?25?Sep?2009?13:46:44?+0530 >From:?dev?sharma? >Subject:?Re:?[Pw_forum]?problem?in?phonon?in?prallel >To:?PWSCF?Forum? >Message-ID: > >Content-Type:?text/plain;?charset="iso-8859-1" > >Hi, > >?when?i?am?running?the?same?file?with?the?following?inputs?,?it?is?running >well > >phonons?at?gamma >?&inputph >??tr2_ph=1.0e-10, >??prefix='yvo', >??trans=.false., >??epsil=.true., >??amass(1)=?44.995, >??amass(2)=?50.9415, >??amass(3)=15.9994, >??outdir?=?'/home/devsharma/work/newscvo/temp', >??fildyn='yvo.dyn1', >?/ >0.0?0.0?0.0 > >means?there?is?some?problem?in?inputs.?Any?comment?on?the?extra?parameters?i >gave?in?previous?file?i.e.?fpol?and?elop. > >Thanks >sincerly, >Dev?Sharma, >University??of?Delhi, >~ > > >~ >On?Fri,?Sep?25,?2009?at?11:03?AM,?dev?sharma??wrote: > >>?hi?2?all, >>??i?have?done?scf?,?phonon??and?the?running?ph.x?in?parallel?for?some >>?optical?properties.?my?programme?stops?without?giving?any?error?in?the >>?ph.out?file?and?without?any?CRASH.?My?input?file?is?listed?below.?Please >>?help. >>?Thanks?in?advance. >>?phonons?at?gamma >>??&inputph >>???tr2_ph=1.0e-10, >>???prefix='yvo', >>????fpol=.true., >>????trans=.false., >>???epsil=.true., >>???elop=.true., >>???amass(1)=?44.995, >>???amass(2)=?50.9415, >>???amass(3)=15.9994, >>???outdir?=?'/home/devsharma/work/newscvo/temp', >>???fildyn='yvo.dyn1', >>??/ >>?0.0?0.0?0.0 >> >>?FREQUENCIES >>?65 >>?7.889e+14 >>?/ >>?/ >>?4.389e+14 >> >>?and?mssg?in?terminal?is?coming >> >>?[devsharma at headnode?newscvo]$?[headnode.du.ac.in:6309]?***?An?error >>?occurred?in?MPI_Allreduce >>?[headnode.du.ac.in:6309]?***?on?communicator?MPI?COMMUNICATOR?28?SPLIT >>?FROM?4 >>?[headnode.du.ac.in:6309]?***?MPI_ERR_TRUNCATE:?message?truncated >>?[headnode.du.ac.in:6309]?***?MPI_ERRORS_ARE_FATAL?(your?MPI?job?will?now >>?abort) >>?-------------------------------------------------------------------------- >>?mpirun?has?exited?due?to?process?rank?1?with?PID?6309?on >>?node?headnode.du.ac.in?exiting?without?calling?"finalize".?This?may >>?have?caused?other?processes?in?the?application?to?be >>?terminated?by?signals?sent?by?mpirun?(as?reported?here). >> >>?---------------------------------------------------------- >>?and?the?output?file?runs?upto >> >> >>??Representation????52??????1?modes?-?To?be?done >>??????PHONON???????:??0m41.95s?CPU?time,?????2m31.11s?wall?time >> >> >>??????Alpha?used?in?Ewald?sum?=???1.0000 >> >>??????Frequency?Dependent?Polarizability?Calculation >> >>?and?after?here?it?stops. >> >> >>?Please?help, >> >>?sincerly, >>?Dev?Sharma, >>?Univeristy?of?Delhi >> >> >> >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090925/270ab22b/attachment-0001.htm? > >------------------------------ > >Message:?2 >Date:?Fri,?25?Sep?2009?10:18:39?+0200 >From:?Paolo?Giannozzi? >Subject:?Re:?[Pw_forum]?problem?in?phonon?in?prallel >To:?PWSCF?Forum? >Message-ID:?<4ABC7CDF.2050209 at democritos.it> >Content-Type:?text/plain;?charset=ISO-8859-1;?format=flowed > >dev?sharma?wrote: > >>?Any?comment?on?the?extra? >>?parameters?i?gave?in?previous?file?i.e.?fpol?and?elop. > >don't?give?any?extra?parameters?unless?you?know?what?they?do, >and?unless?you?need?them > >P. >--? >Paolo?Giannozzi,?Democritos?and?University?of?Udine,?Italy > > >------------------------------ > >Message:?3 >Date:?Fri,?25?Sep?2009?21:02:50?+0800?(CST) >From:?"Q.J.Wang"? >Subject:?[Pw_forum]?Running?on?cluster?often?turn?up >To:?pw_forum? >Message-ID: > <10083410.509721253883770555.JavaMail.coremail at bj126app104.126.com> >Content-Type:?text/plain;?charset="gbk" > >Dear?all >?????When?I?running?on?cluster?,it?often?turn?up?some?bizarre?errors?,which?not?turn?up?ong?single?computer?.I?don't?know?why?.Whether?is?it?because?the?computing?environment?settings???I?don'?know?how?to?do?.Plese?help?me?. > >-- > >Best?regards >? >Q.J.Wang >? >XiangTan?University? >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090925/9b5d0c9e/attachment-0001.htm? > >------------------------------ > >Message:?4 >Date:?Fri,?25?Sep?2009?15:08:14?+0200 >From:?Giovanni?Cantele? >Subject:?Re:?[Pw_forum]?Running?on?cluster?often?turn?up >To:?PWSCF?Forum? >Message-ID:?<4ABCC0BE.40302 at na.infn.it> >Content-Type:?text/plain;?charset=x-gbk;?format=flowed > >Q.J.Wang?wrote: >>?Dear?all >>?When?I?running?on?cluster?,it?often?turn?up?some?bizarre?errors?,which? >>?not?turn?up?ong?single?computer?.I?don't?know?why?.Whether?is?it? >>?because?the?computing?environment?settings???I?don'?know?how?to?do? >>?.Plese?help?me?. >> >Well,?I?think?that?it?will?be?rather?difficult?for?anybody?to?answer? >unless?you?provide?much?more >extensive?information?than?you?did. > >Which?kind?of?errors??Parallel?or?serial?runs? > >Some?issues?might?be?related?to?your?cluster?configuration?/?hardware?/? >software?rather?than?to?the?Quantum-ESPRESSO. > >You?can?also?try?to?search?the?forum?to?find?if?some?of?these?errors? >have?been?ever?discussed?before. > >Giovanni > >--? > > > >Dr.?Giovanni?Cantele >Coherentia?CNR-INFM?and?Dipartimento?di?Scienze?Fisiche >Universita'?di?Napoli?"Federico?II" >Complesso?Universitario?di?Monte?S.?Angelo?-?Ed.?6 >Via?Cintia,?I-80126,?Napoli,?Italy >Phone:?+39?081?676910 >Fax:???+39?081?676346 >E-mail:?giovanni.cantele at cnr.it >????????giovanni.cantele at na.infn.it >Web:?http://people.na.infn.it/~cantele >Research?Group:?http://www.nanomat.unina.it >Skype?contact:?giocan74 > > > >------------------------------ > >Message:?5 >Date:?Fri,?25?Sep?2009?21:41:03?+0800?(CST) >From:?"Q.J.Wang"? >Subject:?[Pw_forum]?about?OMP_NUM_THREADS >To:?pw_forum? >Message-ID: > <12872053.521841253886063499.JavaMail.coremail at bj126app104.126.com> >Content-Type:?text/plain;?charset="gbk" > >Dear?all >?????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop?. > > > >-- > >Best?regards >? >Q.J.Wang >? >XiangTan?University? >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090925/1089ca3e/attachment-0001.htm? > >------------------------------ > >Message:?6 >Date:?Fri,?25?Sep?2009?15:45:13?+0200 >From:?"Lorenzo?Paulatto"? >Subject:?Re:?[Pw_forum]?about?OMP_NUM_THREADS >To:?"PWSCF?Forum"? >Message-ID:? >Content-Type:?text/plain;?charset=utf-8;?format=flowed;?delsp=yes > >In?data?25?settembre?2009?alle?ore?15:41:03,?Q.J.Wang??ha?? >scritto: >>??????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in?? >>?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was?? >>?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop > >Dear?Q.J.?Wang, >as?usual,?you?MUST?provide?the?error?message?and?as?many?details?as?? >possible?on?how?you?run?the?job,?there?is?very?little?we?can?say?about?you?? >problem?with?any?information. > >To?begin?you?should?check?that?the?jobs?do?not?have?the?same?prefix?and?? >outdir,?if?it?is?the?case?they?will?crash?after?a?while. > >best?regards > > >--? >Lorenzo?Paulatto >SISSA??&??DEMOCRITOS?(Trieste) >phone:?+39?040?3787?511 >skype:?paulatz >www:???http://people.sissa.it/~paulatto/ > >?????***?save?italian?brains?*** >??http://saveitalianbrains.wordpress.com/ > > >------------------------------ > >Message:?7 >Date:?Fri,?25?Sep?2009?15:45:54?+0200 >From:?Gabriele?Sclauzero? >Subject:?Re:?[Pw_forum]?about?OMP_NUM_THREADS >To:?PWSCF?Forum? >Message-ID:?<4ABCC992.30009 at sissa.it> >Content-Type:?text/plain;?charset=UTF-8;?format=flowed > >Q.J.Wang?wrote: >>?Dear?all >>??????According?to?the?advice?of?the?forum,I?added?OMP_NUM_THREADS=1?in? >>?my?PBS?script?.But?I?can?only?run?a?task?on?the?cluster?.When?one?was? >>?running?,I?run?another?task?,and?one?of?them?will?turn?up?error?and?stop?. > >Have?you?specified?different?outdir?and/or?prefix?for?the?two?tasks? >Have?you?checked?that?you?have?enough?memory?on?a?node?to?run?two?pw.x?runs? >...? > >GS > > >>? >>? >>?-- >>?Best?regards >>?? >>?Q.J.Wang >>?? >>?XiangTan?University >>? >>? >>?------------------------------------------------------------------------ >>?"????",????60???? >>? >>? >>? >>?------------------------------------------------------------------------ >>? >>?_______________________________________________ >>?Pw_forum?mailing?list >>?Pw_forum at pwscf.org >>?http://www.democritos.it/mailman/listinfo/pw_forum > >--? > > >o?------------------------------------------------?o >|?Gabriele?Sclauzero,?PhD?Student??????????????????| >|?c/o:???SISSA?&?CNR-INFM?Democritos,??????????????| >|????????via?Beirut?2-4,?34014?Trieste?(Italy)?????| >|?email:?sclauzer at sissa.it?????????????????????????| >|?phone:?+39?040?3787?511??????????????????????????| >|?skype:?gurlonotturno?????????????????????????????| >o?------------------------------------------------?o > > >------------------------------ > >Message:?8 >Date:?Fri,?25?Sep?2009?14:25:37?+0000 >From:?xirainbow? >Subject:?[Pw_forum]?About?example?22 >To:?pw_forum at pwscf.org >Message-ID: > <21fbc4790909250725r70d71cc3i3d271a58c4e382d2 at mail.gmail.com> >Content-Type:?text/plain;?charset="iso-8859-1" > >Dear?developers: >There?are?three?trivial?slip?of?example22. > >In?the?"README"?file?of?example22: >ONE:?"2)?make?a?band?structure?calculation?for?Pt?(input=pt.band.in, >output=pt.band.out)." >should?be?"(input=pt.nscf.in,???output=pt.nscf.out)." >TWO:"9)?make?a?self-consistent?calculation?for?Pt?in?a?tetragonal?cell?with >4?atoms??(input=pt.tet4.in,?output=pt.tet4.out)." >should?be?"?(input=pt4.in,?output=pt4.out)." > >THREE:?When?I?try?to?open?"pt.nscf_ph.in"?with?PWgui,?I?get?the?follow >error"syntax?error?in?the?input?file:expecting?keyword?ATOMIC?SPECIES,?but >read?PHONON?instead" >I?use?espresso4.0.4.?But?I?notice?that?in?espresso4.1,?there?is?not?" >pt.nscf_ph.in"?file?any?more. >The?"pt.nscf_ph.in"?is?given?below: >"Pt >Pt >?&control >????calculation?=?'phonon' >????restart_mode='from_scratch', >????prefix='Pt', >????pseudo_dir?=?'/home/raman/espresso-4.0.4/pseudo/', >????outdir='/home/raman/tmp/' >?/ >?&system >????ibrav=??2,?celldm(1)?=7.42,?nat=??1,?ntyp=?1, >????lspinorb=.true., >????noncolin=.true., >????starting_magnetization=0.0, >????occupations='smearing', >????degauss=0.02, >????smearing='mp', >????ecutwfc?=30.0, >????ecutrho?=250.0, >?/ >?&electrons >????mixing_beta?=?0.7, >????conv_thr?=??1.0d-8 >?/ >?&phonon >?xqq(1)=1.d0, >?xqq(2)=0.d0, >?xqq(3)=0.d0, >?/ >ATOMIC_SPECIES >Pt??79.90????Ptrel.RRKJ3.UPF >ATOMIC_POSITIONS >Pt??0.0000000???0.00000000???0.0 >K_POINTS?AUTOMATIC >2?2?2?1?1?1" > > >--? >____________________________________ >Hui?Wang >School?of?physics,?Nankai?University,?Tianjin,?China >--------------?next?part?-------------- >An?HTML?attachment?was?scrubbed... >URL:?http://www.democritos.it/pipermail/pw_forum/attachments/20090925/642bd62b/attachment.htm? > >------------------------------ > >_______________________________________________ >Pw_forum?mailing?list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End?of?Pw_forum?Digest,?Vol?27,?Issue?82 >**************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/b4828f51/attachment-0001.htm From ttduyle at gmail.com Fri Sep 25 17:51:37 2009 From: ttduyle at gmail.com (Duy Le) Date: Fri, 25 Sep 2009 11:51:37 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 82 In-Reply-To: <30627758.545641253890888918.JavaMail.coremail@bj126app104.126.com> References: <30627758.545641253890888918.JavaMail.coremail@bj126app104.126.com> Message-ID: <8974d3b20909250851y597fe1b4mf6bdeaf148cf03ab@mail.gmail.com> Hi Wang, 1. Good to hear that your problem was solved. 2. It seems to be memory problem. Please make sure that your cluster can afford the calculation and make sure the memory is in good condition :) 3. http://www.democritos.it/pipermail/pw_forum/2009-September/014269.html http://www.democritos.it/pipermail/pw_forum/2009-September/014389.html 2009/9/25 Q.J.Wang > Thank you very much Lorenzo Paulatto and Gabriele Sclauzero . > > The problem was solved ,because I specified same prefix for the two tasks > . > But another problem turn up . When I use R & G space division run the task > ,it was interrupted at the 2 iteration of 18 time of vc-relax and turns up > as following : > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line > Source > > pw.x 40000000005D8710 Unknown Unknown > Unknown > pw.x 40000000005D8BF0 Unknown Unknown > Unknown > pw.x 40000000005F4A40 Unknown Unknown > Unknown > pw.x 400000000003C740 Unknown Unknown > > I use 1 node(8 CPUs) on the cluster . I am puzzled by the phenomena ,please > give me some advice about this problem ,thank you . > > -- > Best regards > > Q.J.Wang > > XiangTan University > > ?2009-09-25 22:26:04?pw_forum-request at pwscf.org ??? > >Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > >To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > >or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > >You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > >When replying, please edit your Subject line so it is more specific > >than "Re: Contents of Pw_forum digest..." > > > > > >Today's Topics: > > > > 1. Re: problem in phonon in prallel (dev sharma) > > 2. Re: problem in phonon in prallel (Paolo Giannozzi) > > 3. Running on cluster often turn up (Q.J.Wang) > > 4. Re: Running on cluster often turn up (Giovanni Cantele) > > 5. about OMP_NUM_THREADS (Q.J.Wang) > > 6. Re: about OMP_NUM_THREADS (Lorenzo Paulatto) > > 7. Re: about OMP_NUM_THREADS (Gabriele Sclauzero) > > 8. About example 22 (xirainbow) > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Fri, 25 Sep 2009 13:46:44 +0530 > >From: dev sharma > >Subject: Re: [Pw_forum] problem in phonon in prallel > >To: PWSCF Forum > >Message-ID: > > > >Content-Type: text/plain; charset="iso-8859-1" > > > >Hi, > > > > when i am running the same file with the following inputs , it is running > >well > > > >phonons at gamma > > &inputph > > tr2_ph=1.0e-10, > > prefix='yvo', > > trans=.false., > > epsil=.true., > > amass(1)= 44.995, > > amass(2)= 50.9415, > > amass(3)=15.9994, > > outdir = '/home/devsharma/work/newscvo/temp', > > fildyn='yvo.dyn1', > > / > >0.0 0.0 0.0 > > > >means there is some problem in inputs. Any comment on the extra parameters i > >gave in previous file i.e. fpol and elop. > > > >Thanks > >sincerly, > >Dev Sharma, > >University of Delhi, > >~ > > > > > >~ > >On Fri, Sep 25, 2009 at 11:03 AM, dev sharma wrote: > > > >> hi 2 all, > >> i have done scf , phonon and the running ph.x in parallel for some > >> optical properties. my programme stops without giving any error in the > >> ph.out file and without any CRASH. My input file is listed below. Please > >> help. > >> Thanks in advance. > >> phonons at gamma > >> &inputph > >> tr2_ph=1.0e-10, > >> prefix='yvo', > >> fpol=.true., > >> trans=.false., > >> epsil=.true., > >> elop=.true., > >> amass(1)= 44.995, > >> amass(2)= 50.9415, > >> amass(3)=15.9994, > >> outdir = '/home/devsharma/work/newscvo/temp', > >> fildyn='yvo.dyn1', > >> / > >> 0.0 0.0 0.0 > >> > >> FREQUENCIES > >> 65 > >> 7.889e+14 > >> / > >> / > >> 4.389e+14 > >> > >> and mssg in terminal is coming > >> > >> [devsharma at headnode newscvo]$ [headnode.du.ac.in:6309] *** An error > >> occurred in MPI_Allreduce > >> [headnode.du.ac.in:6309] *** on communicator MPI COMMUNICATOR 28 SPLIT > >> FROM 4 > >> [headnode.du.ac.in:6309] *** MPI_ERR_TRUNCATE: message truncated > >> [headnode.du.ac.in:6309] *** MPI_ERRORS_ARE_FATAL (your MPI job will now > >> abort) > >> -------------------------------------------------------------------------- > >> mpirun has exited due to process rank 1 with PID 6309 on > >> node headnode.du.ac.in exiting without calling "finalize". This may > >> have caused other processes in the application to be > >> terminated by signals sent by mpirun (as reported here). > >> > >> ---------------------------------------------------------- > >> and the output file runs upto > >> > >> > >> Representation 52 1 modes - To be done > >> PHONON : 0m41.95s CPU time, 2m31.11s wall time > >> > >> > >> Alpha used in Ewald sum = 1.0000 > >> > >> Frequency Dependent Polarizability Calculation > >> > >> and after here it stops. > >> > >> > >> Please help, > >> > >> sincerly, > >> Dev Sharma, > >> Univeristy of Delhi > >> > >> > >> > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/270ab22b/attachment-0001.htm > > > >------------------------------ > > > >Message: 2 > >Date: Fri, 25 Sep 2009 10:18:39 +0200 > >From: Paolo Giannozzi > >Subject: Re: [Pw_forum] problem in phonon in prallel > >To: PWSCF Forum > >Message-ID: <4ABC7CDF.2050209 at democritos.it> > >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >dev sharma wrote: > > > >> Any comment on the extra > >> parameters i gave in previous file i.e. fpol and elop. > > > >don't give any extra parameters unless you know what they do, > >and unless you need them > > > >P. > >-- > >Paolo Giannozzi, Democritos and University of Udine, Italy > > > > > >------------------------------ > > > >Message: 3 > >Date: Fri, 25 Sep 2009 21:02:50 +0800 (CST) > >From: "Q.J.Wang" > >Subject: [Pw_forum] Running on cluster often turn up > >To: pw_forum > >Message-ID: > > <10083410.509721253883770555.JavaMail.coremail at bj126app104.126.com> > >Content-Type: text/plain; charset="gbk" > > > >Dear all > > When I running on cluster ,it often turn up some bizarre errors ,which not turn up ong single computer .I don't know why .Whether is it because the computing environment settings ? I don' know how to do .Plese help me . > > > >-- > > > >Best regards > > > >Q.J.Wang > > > >XiangTan University > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/9b5d0c9e/attachment-0001.htm > > > >------------------------------ > > > >Message: 4 > >Date: Fri, 25 Sep 2009 15:08:14 +0200 > >From: Giovanni Cantele > >Subject: Re: [Pw_forum] Running on cluster often turn up > >To: PWSCF Forum > >Message-ID: <4ABCC0BE.40302 at na.infn.it> > >Content-Type: text/plain; charset=x-gbk; format=flowed > > > >Q.J.Wang wrote: > >> Dear all > >> When I running on cluster ,it often turn up some bizarre errors ,which > >> not turn up ong single computer .I don't know why .Whether is it > >> because the computing environment settings ? I don' know how to do > >> .Plese help me . > >> > >Well, I think that it will be rather difficult for anybody to answer > >unless you provide much more > >extensive information than you did. > > > >Which kind of errors? Parallel or serial runs? > > > >Some issues might be related to your cluster configuration / hardware / > >software rather than to the Quantum-ESPRESSO. > > > >You can also try to search the forum to find if some of these errors > >have been ever discussed before. > > > >Giovanni > > > >-- > > > > > > > >Dr. Giovanni Cantele > >Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > >Universita' di Napoli "Federico II" > >Complesso Universitario di Monte S. Angelo - Ed. 6 > >Via Cintia, I-80126, Napoli, Italy > >Phone: +39 081 676910 > >Fax: +39 081 676346 > >E-mail: giovanni.cantele at cnr.it > > giovanni.cantele at na.infn.it > >Web: http://people.na.infn.it/~cantele > >Research Group: http://www.nanomat.unina.it > >Skype contact: giocan74 > > > > > > > >------------------------------ > > > >Message: 5 > >Date: Fri, 25 Sep 2009 21:41:03 +0800 (CST) > >From: "Q.J.Wang" > >Subject: [Pw_forum] about OMP_NUM_THREADS > >To: pw_forum > >Message-ID: > > <12872053.521841253886063499.JavaMail.coremail at bj126app104.126.com> > >Content-Type: text/plain; charset="gbk" > > > >Dear all > > According to the advice of the forum,I added OMP_NUM_THREADS=1 in my PBS script .But I can only run a task on the cluster .When one was running ,I run another task ,and one of them will turn up error and stop . > > > > > > > >-- > > > >Best regards > > > >Q.J.Wang > > > >XiangTan University > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/1089ca3e/attachment-0001.htm > > > >------------------------------ > > > >Message: 6 > >Date: Fri, 25 Sep 2009 15:45:13 +0200 > >From: "Lorenzo Paulatto" > >Subject: Re: [Pw_forum] about OMP_NUM_THREADS > >To: "PWSCF Forum" > >Message-ID: > >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > > >In data 25 settembre 2009 alle ore 15:41:03, Q.J.Wang ha > >scritto: > >> According to the advice of the forum,I added OMP_NUM_THREADS=1 in > >> my PBS script .But I can only run a task on the cluster .When one was > >> running ,I run another task ,and one of them will turn up error and stop > > > >Dear Q.J. Wang, > >as usual, you MUST provide the error message and as many details as > >possible on how you run the job, there is very little we can say about you > >problem with any information. > > > >To begin you should check that the jobs do not have the same prefix and > >outdir, if it is the case they will crash after a while. > > > >best regards > > > > > >-- > >Lorenzo Paulatto > >SISSA & DEMOCRITOS (Trieste) > >phone: +39 040 3787 511 > >skype: paulatz > >www: http://people.sissa.it/~paulatto/ > > > > *** save italian brains *** > > http://saveitalianbrains.wordpress.com/ > > > > > >------------------------------ > > > >Message: 7 > >Date: Fri, 25 Sep 2009 15:45:54 +0200 > >From: Gabriele Sclauzero > >Subject: Re: [Pw_forum] about OMP_NUM_THREADS > >To: PWSCF Forum > >Message-ID: <4ABCC992.30009 at sissa.it> > >Content-Type: text/plain; charset=UTF-8; format=flowed > > > >Q.J.Wang wrote: > >> Dear all > >> According to the advice of the forum,I added OMP_NUM_THREADS=1 in > >> my PBS script .But I can only run a task on the cluster .When one was > >> running ,I run another task ,and one of them will turn up error and stop . > > > >Have you specified different outdir and/or prefix for the two tasks? > >Have you checked that you have enough memory on a node to run two pw.x runs? > >...? > > > >GS > > > > > >> > >> > >> -- > >> Best regards > >> > >> Q.J.Wang > >> > >> XiangTan University > >> > >> > >> ------------------------------------------------------------------------ > >> "????",????60??? > >> > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > >-- > > > > > >o ------------------------------------------------ o > >| Gabriele Sclauzero, PhD Student | > >| c/o: SISSA & CNR-INFM Democritos, | > >| via Beirut 2-4, 34014 Trieste (Italy) | > >| email: sclauzer at sissa.it | > >| phone: +39 040 3787 511 | > >| skype: gurlonotturno | > >o ------------------------------------------------ o > > > > > >------------------------------ > > > >Message: 8 > >Date: Fri, 25 Sep 2009 14:25:37 +0000 > >From: xirainbow > >Subject: [Pw_forum] About example 22 > >To: pw_forum at pwscf.org > >Message-ID: > > <21fbc4790909250725r70d71cc3i3d271a58c4e382d2 at mail.gmail.com> > >Content-Type: text/plain; charset="iso-8859-1" > > > >Dear developers: > >There are three trivial slip of example22. > > > >In the "README" file of example22: > >ONE: "2) make a band structure calculation for Pt (input=pt.band.in, > >output=pt.band.out)." > >should be "(input=pt.nscf.in, output=pt.nscf.out)." > >TWO:"9) make a self-consistent calculation for Pt in a tetragonal cell with > >4 atoms (input=pt.tet4.in, output=pt.tet4.out)." > >should be " (input=pt4.in, output=pt4.out)." > > > >THREE: When I try to open "pt.nscf_ph.in" with PWgui, I get the follow > >error"syntax error in the input file:expecting keyword ATOMIC SPECIES, but > >read PHONON instead" > >I use espresso4.0.4. But I notice that in espresso4.1, there is not " > >pt.nscf_ph.in" file any more. > >The "pt.nscf_ph.in" is given below: > >"Pt > >Pt > > &control > > calculation = 'phonon' > > restart_mode='from_scratch', > > prefix='Pt', > > pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/', > > outdir='/home/raman/tmp/' > > / > > &system > > ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, > > lspinorb=.true., > > noncolin=.true., > > starting_magnetization=0.0, > > occupations='smearing', > > degauss=0.02, > > smearing='mp', > > ecutwfc =30.0, > > ecutrho =250.0, > > / > > &electrons > > mixing_beta = 0.7, > > conv_thr = 1.0d-8 > > / > > &phonon > > xqq(1)=1.d0, > > xqq(2)=0.d0, > > xqq(3)=0.d0, > > / > >ATOMIC_SPECIES > >Pt 79.90 Ptrel.RRKJ3.UPF > >ATOMIC_POSITIONS > >Pt 0.0000000 0.00000000 0.0 > >K_POINTS AUTOMATIC > >2 2 2 1 1 1" > > > > > >-- > >____________________________________ > >Hui Wang > >School of physics, Nankai University, Tianjin, China > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/642bd62b/attachment.htm > > > >------------------------------ > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > >End of Pw_forum Digest, Vol 27, Issue 82 > >**************************************** > > > > ------------------------------ > ?????????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/c2c77f12/attachment-0001.htm From giannozz at democritos.it Fri Sep 25 17:53:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 Sep 2009 17:53:41 +0200 Subject: [Pw_forum] about OMP_NUM_THREADS In-Reply-To: References: <12872053.521841253886063499.JavaMail.coremail@bj126app104.126.com> <4ABCC992.30009@sissa.it> <4ABCCE58.1040308@andrew.cmu.edu> Message-ID: <4ABCE785.7090903@democritos.it> Lorenzo Paulatto wrote: > Welcome Jason, and thank you for providing all the necessary > information from the beginning. ... with the exception of an appropriate subject :-) > You are using > norm-conserving pseudopotential, I think 50-60Ry should be enough for Ge and T, I think it is more than enough. One may spare time by making first a quick-and-dirty structural optimization, then refining it with higher cutoff and more k-points. I would start with a much lower cutoff (25Ry for instance) and the Gamma point only (maybe with a few more bands and small smearing: if the system is close to a metallic state, it is easy to run into trouble otherwise). For damped MD, a good choice of the time step is important. I personally prefer BFGS to damped MD. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From lanhaiping at gmail.com Fri Sep 25 22:03:56 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 26 Sep 2009 04:03:56 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 27, Issue 82 In-Reply-To: <30627758.545641253890888918.JavaMail.coremail@bj126app104.126.com> References: <30627758.545641253890888918.JavaMail.coremail@bj126app104.126.com> Message-ID: Hi, Q.J Wang. I just notice several times that you always break the thread of the mail-list. Please donot start a new-thread for an old topic , or reply a digest. Regards 2009/9/25 Q.J.Wang > Thank you very much Lorenzo Paulatto and Gabriele Sclauzero . > > The problem was solved ,because I specified same prefix for the two tasks > . > But another problem turn up . When I use R & G space division run the task > ,it was interrupted at the 2 iteration of 18 time of vc-relax and turns up > as following : > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line > Source > > pw.x 40000000005D8710 Unknown Unknown > Unknown > pw.x 40000000005D8BF0 Unknown Unknown > Unknown > pw.x 40000000005F4A40 Unknown Unknown > Unknown > pw.x 400000000003C740 Unknown Unknown > > I use 1 node(8 CPUs) on the cluster . I am puzzled by the phenomena ,please > give me some advice about this problem ,thank you . > > -- > Best regards > > Q.J.Wang > > XiangTan University > > ?2009-09-25 22:26:04?pw_forum-request at pwscf.org ??? > >Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > >To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > >or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > >You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > >When replying, please edit your Subject line so it is more specific > >than "Re: Contents of Pw_forum digest..." > > > > > >Today's Topics: > > > > 1. Re: problem in phonon in prallel (dev sharma) > > 2. Re: problem in phonon in prallel (Paolo Giannozzi) > > 3. Running on cluster often turn up (Q.J.Wang) > > 4. Re: Running on cluster often turn up (Giovanni Cantele) > > 5. about OMP_NUM_THREADS (Q.J.Wang) > > 6. Re: about OMP_NUM_THREADS (Lorenzo Paulatto) > > 7. Re: about OMP_NUM_THREADS (Gabriele Sclauzero) > > 8. About example 22 (xirainbow) > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Fri, 25 Sep 2009 13:46:44 +0530 > >From: dev sharma > >Subject: Re: [Pw_forum] problem in phonon in prallel > >To: PWSCF Forum > >Message-ID: > > > >Content-Type: text/plain; charset="iso-8859-1" > > > >Hi, > > > > when i am running the same file with the following inputs , it is running > >well > > > >phonons at gamma > > &inputph > > tr2_ph=1.0e-10, > > prefix='yvo', > > trans=.false., > > epsil=.true., > > amass(1)= 44.995, > > amass(2)= 50.9415, > > amass(3)=15.9994, > > outdir = '/home/devsharma/work/newscvo/temp', > > fildyn='yvo.dyn1', > > / > >0.0 0.0 0.0 > > > >means there is some problem in inputs. Any comment on the extra parameters i > >gave in previous file i.e. fpol and elop. > > > >Thanks > >sincerly, > >Dev Sharma, > >University of Delhi, > >~ > > > > > >~ > >On Fri, Sep 25, 2009 at 11:03 AM, dev sharma wrote: > > > >> hi 2 all, > >> i have done scf , phonon and the running ph.x in parallel for some > >> optical properties. my programme stops without giving any error in the > >> ph.out file and without any CRASH. My input file is listed below. Please > >> help. > >> Thanks in advance. > >> phonons at gamma > >> &inputph > >> tr2_ph=1.0e-10, > >> prefix='yvo', > >> fpol=.true., > >> trans=.false., > >> epsil=.true., > >> elop=.true., > >> amass(1)= 44.995, > >> amass(2)= 50.9415, > >> amass(3)=15.9994, > >> outdir = '/home/devsharma/work/newscvo/temp', > >> fildyn='yvo.dyn1', > >> / > >> 0.0 0.0 0.0 > >> > >> FREQUENCIES > >> 65 > >> 7.889e+14 > >> / > >> / > >> 4.389e+14 > >> > >> and mssg in terminal is coming > >> > >> [devsharma at headnode newscvo]$ [headnode.du.ac.in:6309] *** An error > >> occurred in MPI_Allreduce > >> [headnode.du.ac.in:6309] *** on communicator MPI COMMUNICATOR 28 SPLIT > >> FROM 4 > >> [headnode.du.ac.in:6309] *** MPI_ERR_TRUNCATE: message truncated > >> [headnode.du.ac.in:6309] *** MPI_ERRORS_ARE_FATAL (your MPI job will now > >> abort) > >> -------------------------------------------------------------------------- > >> mpirun has exited due to process rank 1 with PID 6309 on > >> node headnode.du.ac.in exiting without calling "finalize". This may > >> have caused other processes in the application to be > >> terminated by signals sent by mpirun (as reported here). > >> > >> ---------------------------------------------------------- > >> and the output file runs upto > >> > >> > >> Representation 52 1 modes - To be done > >> PHONON : 0m41.95s CPU time, 2m31.11s wall time > >> > >> > >> Alpha used in Ewald sum = 1.0000 > >> > >> Frequency Dependent Polarizability Calculation > >> > >> and after here it stops. > >> > >> > >> Please help, > >> > >> sincerly, > >> Dev Sharma, > >> Univeristy of Delhi > >> > >> > >> > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/270ab22b/attachment-0001.htm > > > >------------------------------ > > > >Message: 2 > >Date: Fri, 25 Sep 2009 10:18:39 +0200 > >From: Paolo Giannozzi > >Subject: Re: [Pw_forum] problem in phonon in prallel > >To: PWSCF Forum > >Message-ID: <4ABC7CDF.2050209 at democritos.it> > >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >dev sharma wrote: > > > >> Any comment on the extra > >> parameters i gave in previous file i.e. fpol and elop. > > > >don't give any extra parameters unless you know what they do, > >and unless you need them > > > >P. > >-- > >Paolo Giannozzi, Democritos and University of Udine, Italy > > > > > >------------------------------ > > > >Message: 3 > >Date: Fri, 25 Sep 2009 21:02:50 +0800 (CST) > >From: "Q.J.Wang" > >Subject: [Pw_forum] Running on cluster often turn up > >To: pw_forum > >Message-ID: > > <10083410.509721253883770555.JavaMail.coremail at bj126app104.126.com> > >Content-Type: text/plain; charset="gbk" > > > >Dear all > > When I running on cluster ,it often turn up some bizarre errors ,which not turn up ong single computer .I don't know why .Whether is it because the computing environment settings ? I don' know how to do .Plese help me . > > > >-- > > > >Best regards > > > >Q.J.Wang > > > >XiangTan University > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/9b5d0c9e/attachment-0001.htm > > > >------------------------------ > > > >Message: 4 > >Date: Fri, 25 Sep 2009 15:08:14 +0200 > >From: Giovanni Cantele > >Subject: Re: [Pw_forum] Running on cluster often turn up > >To: PWSCF Forum > >Message-ID: <4ABCC0BE.40302 at na.infn.it> > >Content-Type: text/plain; charset=x-gbk; format=flowed > > > >Q.J.Wang wrote: > >> Dear all > >> When I running on cluster ,it often turn up some bizarre errors ,which > >> not turn up ong single computer .I don't know why .Whether is it > >> because the computing environment settings ? I don' know how to do > >> .Plese help me . > >> > >Well, I think that it will be rather difficult for anybody to answer > >unless you provide much more > >extensive information than you did. > > > >Which kind of errors? Parallel or serial runs? > > > >Some issues might be related to your cluster configuration / hardware / > >software rather than to the Quantum-ESPRESSO. > > > >You can also try to search the forum to find if some of these errors > >have been ever discussed before. > > > >Giovanni > > > >-- > > > > > > > >Dr. Giovanni Cantele > >Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > >Universita' di Napoli "Federico II" > >Complesso Universitario di Monte S. Angelo - Ed. 6 > >Via Cintia, I-80126, Napoli, Italy > >Phone: +39 081 676910 > >Fax: +39 081 676346 > >E-mail: giovanni.cantele at cnr.it > > giovanni.cantele at na.infn.it > >Web: http://people.na.infn.it/~cantele > >Research Group: http://www.nanomat.unina.it > >Skype contact: giocan74 > > > > > > > >------------------------------ > > > >Message: 5 > >Date: Fri, 25 Sep 2009 21:41:03 +0800 (CST) > >From: "Q.J.Wang" > >Subject: [Pw_forum] about OMP_NUM_THREADS > >To: pw_forum > >Message-ID: > > <12872053.521841253886063499.JavaMail.coremail at bj126app104.126.com> > >Content-Type: text/plain; charset="gbk" > > > >Dear all > > According to the advice of the forum,I added OMP_NUM_THREADS=1 in my PBS script .But I can only run a task on the cluster .When one was running ,I run another task ,and one of them will turn up error and stop . > > > > > > > >-- > > > >Best regards > > > >Q.J.Wang > > > >XiangTan University > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/1089ca3e/attachment-0001.htm > > > >------------------------------ > > > >Message: 6 > >Date: Fri, 25 Sep 2009 15:45:13 +0200 > >From: "Lorenzo Paulatto" > >Subject: Re: [Pw_forum] about OMP_NUM_THREADS > >To: "PWSCF Forum" > >Message-ID: > >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > > >In data 25 settembre 2009 alle ore 15:41:03, Q.J.Wang ha > >scritto: > >> According to the advice of the forum,I added OMP_NUM_THREADS=1 in > >> my PBS script .But I can only run a task on the cluster .When one was > >> running ,I run another task ,and one of them will turn up error and stop > > > >Dear Q.J. Wang, > >as usual, you MUST provide the error message and as many details as > >possible on how you run the job, there is very little we can say about you > >problem with any information. > > > >To begin you should check that the jobs do not have the same prefix and > >outdir, if it is the case they will crash after a while. > > > >best regards > > > > > >-- > >Lorenzo Paulatto > >SISSA & DEMOCRITOS (Trieste) > >phone: +39 040 3787 511 > >skype: paulatz > >www: http://people.sissa.it/~paulatto/ > > > > *** save italian brains *** > > http://saveitalianbrains.wordpress.com/ > > > > > >------------------------------ > > > >Message: 7 > >Date: Fri, 25 Sep 2009 15:45:54 +0200 > >From: Gabriele Sclauzero > >Subject: Re: [Pw_forum] about OMP_NUM_THREADS > >To: PWSCF Forum > >Message-ID: <4ABCC992.30009 at sissa.it> > >Content-Type: text/plain; charset=UTF-8; format=flowed > > > >Q.J.Wang wrote: > >> Dear all > >> According to the advice of the forum,I added OMP_NUM_THREADS=1 in > >> my PBS script .But I can only run a task on the cluster .When one was > >> running ,I run another task ,and one of them will turn up error and stop . > > > >Have you specified different outdir and/or prefix for the two tasks? > >Have you checked that you have enough memory on a node to run two pw.x runs? > >...? > > > >GS > > > > > >> > >> > >> -- > >> Best regards > >> > >> Q.J.Wang > >> > >> XiangTan University > >> > >> > >> ------------------------------------------------------------------------ > >> "????",????60??? > >> > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > >-- > > > > > >o ------------------------------------------------ o > >| Gabriele Sclauzero, PhD Student | > >| c/o: SISSA & CNR-INFM Democritos, | > >| via Beirut 2-4, 34014 Trieste (Italy) | > >| email: sclauzer at sissa.it | > >| phone: +39 040 3787 511 | > >| skype: gurlonotturno | > >o ------------------------------------------------ o > > > > > >------------------------------ > > > >Message: 8 > >Date: Fri, 25 Sep 2009 14:25:37 +0000 > >From: xirainbow > >Subject: [Pw_forum] About example 22 > >To: pw_forum at pwscf.org > >Message-ID: > > <21fbc4790909250725r70d71cc3i3d271a58c4e382d2 at mail.gmail.com> > >Content-Type: text/plain; charset="iso-8859-1" > > > >Dear developers: > >There are three trivial slip of example22. > > > >In the "README" file of example22: > >ONE: "2) make a band structure calculation for Pt (input=pt.band.in, > >output=pt.band.out)." > >should be "(input=pt.nscf.in, output=pt.nscf.out)." > >TWO:"9) make a self-consistent calculation for Pt in a tetragonal cell with > >4 atoms (input=pt.tet4.in, output=pt.tet4.out)." > >should be " (input=pt4.in, output=pt4.out)." > > > >THREE: When I try to open "pt.nscf_ph.in" with PWgui, I get the follow > >error"syntax error in the input file:expecting keyword ATOMIC SPECIES, but > >read PHONON instead" > >I use espresso4.0.4. But I notice that in espresso4.1, there is not " > >pt.nscf_ph.in" file any more. > >The "pt.nscf_ph.in" is given below: > >"Pt > >Pt > > &control > > calculation = 'phonon' > > restart_mode='from_scratch', > > prefix='Pt', > > pseudo_dir = '/home/raman/espresso-4.0.4/pseudo/', > > outdir='/home/raman/tmp/' > > / > > &system > > ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, > > lspinorb=.true., > > noncolin=.true., > > starting_magnetization=0.0, > > occupations='smearing', > > degauss=0.02, > > smearing='mp', > > ecutwfc =30.0, > > ecutrho =250.0, > > / > > &electrons > > mixing_beta = 0.7, > > conv_thr = 1.0d-8 > > / > > &phonon > > xqq(1)=1.d0, > > xqq(2)=0.d0, > > xqq(3)=0.d0, > > / > >ATOMIC_SPECIES > >Pt 79.90 Ptrel.RRKJ3.UPF > >ATOMIC_POSITIONS > >Pt 0.0000000 0.00000000 0.0 > >K_POINTS AUTOMATIC > >2 2 2 1 1 1" > > > > > >-- > >____________________________________ > >Hui Wang > >School of physics, Nankai University, Tianjin, China > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090925/642bd62b/attachment.htm > > > >------------------------------ > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > >End of Pw_forum Digest, Vol 27, Issue 82 > >**************************************** > > > > ------------------------------ > ?????????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/f8aa4836/attachment-0001.htm From wangqj1 at 126.com Sat Sep 26 02:20:44 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sat, 26 Sep 2009 08:20:44 +0800 (CST) Subject: [Pw_forum] forrtl: severe (174): SIGSEGV, segmentation fault occurred Message-ID: <9331209.580201253924444324.JavaMail.coremail@bj126app104.126.com> Dear all According to people's advice ,I had checked it ,the reason of memory was ruled out .I task I run is a small system .With K-points division it can finish the task ,while with R G division, it can't. and turns up : node1 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source mca_pml_ob1.so 00007F34DE43BB56 Unknown Unknown Unknown mca_pml_ob1.so 00007F34DE43C268 Unknown Unknown Unknown mca_btl_sm.so 00007F34DDC2102D Unknown Unknown Unknown libopen-pal.so.0 00007F34E25ECFC9 Unknown Unknown Unknown mca_pml_ob1.so 00007F34DE43803C Unknown Unknown Unknown libmpi.so.0 00007F34E2B306E0 Unknown Unknown Unknown libmpi_f77.so.0 00007F34E2DCFB94 Unknown Unknown Unknown pw.x 000000000051F1BA Unknown Unknown Unknown pw.x 000000000067389F Unknown Unknown Unknown pw.x 0000000000663521 Unknown Unknown Unknown pw.x 0000000000664647 Unknown Unknown Unknown pw.x 0000000000595B60 Unknown Unknown Unknown pw.x 00000000004629DB Unknown Unknown Unknown pw.x 00000000004627CC Unknown Unknown Unknown libc.so.6 00007F34E180C586 Unknown Unknown Unknown pw.x 00000000004626C9 Unknown Unknown Unknown -------------------------------------------------------------------------- mpirun has exited due to process rank 4 with PID 6302 on node node1 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). Any advice will be appreciated ! -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/0a55e1bd/attachment.htm From jjr19 at zips.uakron.edu Sat Sep 26 03:33:11 2009 From: jjr19 at zips.uakron.edu (James J Ramsey) Date: Fri, 25 Sep 2009 21:33:11 -0400 Subject: [Pw_forum] forrtl: severe (174): SIGSEGV, segmentation fault occurred In-Reply-To: <9331209.580201253924444324.JavaMail.coremail@bj126app104.126.com> References: <9331209.580201253924444324.JavaMail.coremail@bj126app104.126.com> Message-ID: <46e014700909251833o548c29c5p93e8e1988f1c4a8@mail.gmail.com> 2009/9/25 Q.J.Wang : > Dear all > According to people's advice ,I had checked it ,the reason of memory was > ruled out .I task I run is a small system .With K-points division it can > finish the task ,while with R G division, it can't. and turns up : > > node1 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image????????????? PC??????????????? Routine??????????? Line > Source > mca_pml_ob1.so???? 00007F34DE43BB56? Unknown?????????????? Unknown? Unknown > mca_pml_ob1.so???? 00007F34DE43C268? Unknown?????????????? Unknown? Unknown > mca_btl_sm.so????? 00007F34DDC2102D? Unknown?????????????? Unknown? Unknown > libopen-pal.so.0?? 00007F34E25ECFC9? Unknown?????????????? Unknown? Unknown > mca_pml_ob1.so???? 00007F34DE43803C? Unknown?????????????? Unknown? Unknown > libmpi.so.0??????? 00007F34E2B306E0? Unknown?????????????? Unknown? Unknown > libmpi_f77.so.0??? 00007F34E2DCFB94? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 000000000051F1BA? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 000000000067389F? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 0000000000663521? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 0000000000664647? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 0000000000595B60? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 00000000004629DB? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 00000000004627CC? Unknown?????????????? Unknown? Unknown > libc.so.6????????? 00007F34E180C586? Unknown?????????????? Unknown? Unknown > pw.x?????????????? 00000000004626C9? Unknown?????????????? Unknown? Unknown > -------------------------------------------------------------------------- > mpirun has exited due to process rank 4 with PID 6302 on > node node1 exiting without calling "finalize". This may > have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > > Any advice will be appreciated ! What implementation of MPI are you using, and what version? For example, are you using MPICH 1.2.7 or OpenMPI 1.3? From kajalmh18 at gmail.com Sat Sep 26 08:51:28 2009 From: kajalmh18 at gmail.com (kajal jindal) Date: Sat, 26 Sep 2009 12:21:28 +0530 Subject: [Pw_forum] tot_magnetization value Message-ID: Hi, I am new to PWScf and i am working on ZnO doped with Nitrogen .I have replaced 1 Oxygen by 1 Nitrogen per unit cell and have used 2*2*2 ZnO supercell i.e 8*(ZnO)-O+N=143 total no. of electrons .It means our system has an odd no. of electrons and i have given ispin=2 but i m confused how to specify the tot-magnetization value. secondly ,I want to know whether one should use spin polarized calculation for geometry optimizations/relaxation for the above system.If needed, should I paste my input file also? sincerely, Miss Kajal (UTA)(University of Delhi) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/b29598a6/attachment.htm From nkxirainbow at gmail.com Sat Sep 26 09:01:52 2009 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 26 Sep 2009 07:01:52 +0000 Subject: [Pw_forum] tot_magnetization value In-Reply-To: References: Message-ID: <21fbc4790909260001p3af54cbcm606ac37b7da5cfca@mail.gmail.com> Dear kajal jindal: > > secondly ,I want to know whether one should use spin polarized calculation > for geometry optimizations/relaxation for the above system.If needed, should > I paste my input file also? > > For you second question, you need to use *spin polarize* for your optimization. ____________________________________ Hui Wang School of physics, Nankai University, Tianjin, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/5e9f5b63/attachment.htm From decboy9 at gmail.com Sat Sep 26 09:14:25 2009 From: decboy9 at gmail.com (dev sharma) Date: Sat, 26 Sep 2009 12:44:25 +0530 Subject: [Pw_forum] epsilon.x Message-ID: Hi 2 all, Is there any way that we can run epsilon.x if we dont have norm conserving pseudo-potential. I want to run epsilon.x for YVO4 and i dont know how to use ld1.x to make a pseudo potential. Please help or advice. Thanks in advance, Dev Sharma, University of Delhi, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/d7e5e71e/attachment.htm From wangqj1 at 126.com Sat Sep 26 09:42:37 2009 From: wangqj1 at 126.com (Q.J.Wang) Date: Sat, 26 Sep 2009 15:42:37 +0800 (CST) Subject: [Pw_forum] forrtl: severe (174): SIGSEGV, segmentation fault occurred (James J Ramsey) In-Reply-To: References: Message-ID: <21958824.765981253950957403.JavaMail.coremail@bj126app21.126.com> >Message: 2 >Date: Fri, 25 Sep 2009 21:33:11 -0400 >From: James J Ramsey >Subject: Re: [Pw_forum] forrtl: severe (174): SIGSEGV, segmentation > fault occurred >To: PWSCF Forum >Message-ID: > <46e014700909251833o548c29c5p93e8e1988f1c4a8 at mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >2009/9/25 Q.J.Wang : >> Dear all >> According to people's advice ,I had checked it ,the reason of memory was >> ruled out .I task I run is a small system .With K-points division it can >> finish the task ,while with R G division, it can't. and turns up : >> >> node1 >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> Image????????????? PC??????????????? Routine??????????? Line >> Source >> mca_pml_ob1.so???? 00007F34DE43BB56? Unknown?????????????? Unknown? Unknown >> mca_pml_ob1.so???? 00007F34DE43C268? Unknown?????????????? Unknown? Unknown >> mca_btl_sm.so????? 00007F34DDC2102D? Unknown?????????????? Unknown? Unknown >> libopen-pal.so.0?? 00007F34E25ECFC9? Unknown?????????????? Unknown? Unknown >> mca_pml_ob1.so???? 00007F34DE43803C? Unknown?????????????? Unknown? Unknown >> libmpi.so.0??????? 00007F34E2B306E0? Unknown?????????????? Unknown? Unknown >> libmpi_f77.so.0??? 00007F34E2DCFB94? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 000000000051F1BA? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 000000000067389F? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 0000000000663521? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 0000000000664647? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 0000000000595B60? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 00000000004629DB? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 00000000004627CC? Unknown?????????????? Unknown? Unknown >> libc.so.6????????? 00007F34E180C586? Unknown?????????????? Unknown? Unknown >> pw.x?????????????? 00000000004626C9? Unknown?????????????? Unknown? Unknown >> -------------------------------------------------------------------------- >> mpirun has exited due to process rank 4 with PID 6302 on >> node node1 exiting without calling "finalize". This may >> have caused other processes in the application to be >> terminated by signals sent by mpirun (as reported here). >> >> Any advice will be appreciated ! > >What implementation of MPI are you using, and what version? For >example, are you using MPICH 1.2.7 or OpenMPI 1.3? I use mpich2-1.0.6 version .SUSE 11 LINUX system. mkl version is l_mkl_p_10.1.1.019 ,Compiler version is l_cproc_p_11.0.083_intel64. Thank you ! -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/10d75cee/attachment.htm From giannozz at democritos.it Sat Sep 26 10:58:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Sep 2009 10:58:52 +0200 Subject: [Pw_forum] forrtl: severe (174): SIGSEGV, segmentation fault occurred In-Reply-To: <9331209.580201253924444324.JavaMail.coremail@bj126app104.126.com> References: <9331209.580201253924444324.JavaMail.coremail@bj126app104.126.com> Message-ID: <5FBBF1EC-74BD-4C2A-8098-F51F94D053E1@democritos.it> On Sep 26, 2009, at 2:20 , Q.J.Wang wrote: > forrtl: severe (174): SIGSEGV, segmentation fault occurred please have a look at the "troubleshooting" section of the user guide. If you cannot reproduce it on another machine, it is very likely that the problem is not in QE. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From kajalmh18 at gmail.com Sat Sep 26 12:02:36 2009 From: kajalmh18 at gmail.com (kajal jindal) Date: Sat, 26 Sep 2009 15:32:36 +0530 Subject: [Pw_forum] tot _magnetization value Message-ID: Hi, Sir, I am not getting any reply from your forum on my gmail account. I am just getting pw_forum digest messages(i.e volume 82, 83 etc msgs)...But I have checked my friend's gmail account and he is getting the reply to the current problems pasted on the forum. Sincerely, Miss kajal (UTA) University of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/b4dbc21f/attachment.htm From paulatto at sissa.it Sat Sep 26 12:15:14 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 26 Sep 2009 12:15:14 +0200 (CEST) Subject: [Pw_forum] tot _magnetization value In-Reply-To: References: Message-ID: <48261.78.12.158.197.1253960114.squirrel@webmail.sissa.it> On Sat, September 26, 2009 12:02, kajal jindal wrote: > Hi, > Sir, I am not getting any reply from your forum on my gmail account. I am > just getting pw_forum digest messages(i.e volume 82, 83 etc msgs)...But I > have checked my friend's gmail account and he is getting the reply to the > current problems pasted on the forum. Dear Kajal, getting the daily digests depends on the option you've selected when subscribing to the mailing list, not on your email address. You can change it at any time on this page: . Just eneter your email address in the box at the bottom of the page and click [Unsubscribe or edit options]; you will be prompted for the password, if you don't remember it (or didin't choose one when subscribing) you can click [remind] to hav it sent to your email address (it takes a few minute). Once you have logged in you can Set Digest Mode to Off to have the messages delivered as soon as they are posted. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From degironc at sissa.it Sat Sep 26 12:15:23 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 26 Sep 2009 12:15:23 +0200 Subject: [Pw_forum] tot_magnetization value In-Reply-To: References: Message-ID: <4ABDE9BB.9090701@sissa.it> Dear kajal jindal, you CAN specify total_magnetization (in your case total_magnetizatio=1 is probably what you may want) but you DO NOT NEED to do that and leave the code searching for a magnetic solution. In this case you need to specify a value for starting_magnetization for at least one atomic species (say for N in your case). NB: total_magneticzation is the tota unbalance between spin_up and spin_dw electrons while starting_magnetization is the initial guess for the atomic magnetization defined as zeta = (rho_up-rho_dw)/(rho_up+rho_dw) YES: if your system is magnetic you should relax it using nspin=2 Stefano de Gironcoli - SISSA and DEMOCRITOS kajal jindal wrote: > Hi, > > I am new to PWScf and i am working on ZnO doped with Nitrogen .I have > replaced 1 Oxygen by 1 Nitrogen per unit cell and have used 2*2*2 ZnO > supercell i.e 8*(ZnO)-O+N=143 total no. of electrons .It means our > system has an odd no. of electrons and i have given ispin=2 but i m > confused how to specify the tot-magnetization value. > > secondly ,I want to know whether one should use spin polarized > calculation for geometry optimizations/relaxation for the above > system.If needed, should I paste my input file also? > > sincerely, > Miss Kajal > (UTA)(University of Delhi) > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From yuminqian at gmail.com Sat Sep 26 14:32:02 2009 From: yuminqian at gmail.com (yumin qian) Date: Sat, 26 Sep 2009 20:32:02 +0800 Subject: [Pw_forum] spin orbital structure in crystal Message-ID: My dear friends Since the interplay of spin ,orbital ,charge and lattice is a important topic in strongly correlated system. spin ordering and orbital ordering is prevalent in transitional metal compounds , to illustrate these ordering by figures give us a vivid understanding or the ordering parameter . Is there anyone konw how to draw a picture of spin or d orbit orientation on a crystal lattice . Is there any tool that can be used. Many thanks . -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/f2aa6940/attachment-0001.htm From ttduyle at gmail.com Sat Sep 26 22:05:08 2009 From: ttduyle at gmail.com (Duy Le) Date: Sat, 26 Sep 2009 16:05:08 -0400 Subject: [Pw_forum] epsilon.x In-Reply-To: References: Message-ID: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> Hi >Is there any way that we can run epsilon.x if we dont have norm conserving pseudo-potential. I did not do any epsilon.x calculation before, and I don't understand what's wrong with non-norm conserving potential? To calculate dielectric constants, one needs energy and wavefunction of all states. PWscf provides those (Kohn-Sham eigenvalues and eigen wavefunctions), and epsilon.x will do it jobs as a post-processing. It would be nice if you or someone can explain the problem to me. Thank you. >I want to run epsilon.x for YVO4 and i dont know how to use ld1.x to make a pseudo potential. Please help or advice. http://www.quantum-espresso.org/wiki/index.php/QESB09, (Saturday 25) has tutorial and lectrure for generating pseudo potential (video available too). Give it a try if you really need to generate pseudo potental. Best, On Sat, Sep 26, 2009 at 3:14 AM, dev sharma wrote: > Hi 2 all, > > Is there any way that we can run epsilon.x if we dont have norm conserving > pseudo-potential. I want to run epsilon.x for YVO4 and i dont know how to > use ld1.x to make a pseudo potential. Please help or advice. > > Thanks in advance, > Dev Sharma, > University of Delhi, > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090926/43826df9/attachment.htm From decboy9 at gmail.com Sun Sep 27 11:42:28 2009 From: decboy9 at gmail.com (dev sharma) Date: Sun, 27 Sep 2009 15:12:28 +0530 Subject: [Pw_forum] epsilon.x In-Reply-To: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> Message-ID: Sir, Problem is that it gives the error with mssg that USPPs are not implement. What to do in that case. Earlier to one of the answer Lorenzo Paulatto sir write The error means that the calculation you are trying to do is not implemented for USPP (ultra-soft pseudo-potential). Either use norm-conserving only, or develop it for ultrasoft. I didnt get how to develop it for ultrasoft PPs. Thanks Dev Sharma, Univeristy of Delhi On Sun, Sep 27, 2009 at 1:35 AM, Duy Le wrote: > Hi > >Is there any way that we can run epsilon.x if we dont have norm > conserving pseudo-potential. > I did not do any epsilon.x calculation before, and I don't understand > what's wrong with non-norm conserving potential? To calculate dielectric > constants, one needs energy and wavefunction of all states. PWscf provides > those (Kohn-Sham eigenvalues and eigen wavefunctions), and epsilon.x will do > it jobs as a post-processing. It would be nice if you or someone can explain > the problem to me. Thank you. > > >I want to run epsilon.x for YVO4 and i dont know how to use ld1.x to make > a pseudo potential. Please help or advice. > http://www.quantum-espresso.org/wiki/index.php/QESB09, (Saturday 25) has > tutorial and lectrure for generating pseudo potential (video available too). > Give it a try if you really need to generate pseudo potental. > > Best, > > On Sat, Sep 26, 2009 at 3:14 AM, dev sharma wrote: > >> Hi 2 all, >> >> Is there any way that we can run epsilon.x if we dont have norm >> conserving pseudo-potential. I want to run epsilon.x for YVO4 and i dont >> know how to use ld1.x to make a pseudo potential. Please help or advice. >> >> Thanks in advance, >> Dev Sharma, >> University of Delhi, >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090927/c819a9bc/attachment.htm From colonel.sreekar at gmail.com Sun Sep 27 13:27:36 2009 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sun, 27 Sep 2009 16:57:36 +0530 Subject: [Pw_forum] equilibrium lattice constant determination Message-ID: Dear QE users, i performed 'vc-relax' on GaAs to find out zero temperature lattice constant. i performed similar calculation of energy vs lattice const(a). If we consider energy to be stored in the field (which is present in the volume of the cell) then minimum of Energy/Vol vs 'a' should give the result. But instead the minimum of E vs 'a' is giving a result(the earlier graph isnt giving a minimum at all) in accordance with that given by vc-relax. I would be grateful to be clarified of the understanding of the physics of this situation. sincerely, -- Sreekar Guddeti IIT Bombay BTech + MTech Physics Dept IIT Bombay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090927/445802d3/attachment.htm From kucukben at sissa.it Sun Sep 27 14:59:45 2009 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 27 Sep 2009 14:59:45 +0200 Subject: [Pw_forum] equilibrium lattice constant determination Message-ID: <20090927145945.ypz2ibupwgskg84s@webmail.sissa.it> Dear Sreekar, Could you please clarify why, in your opinion, energy/(unit cell volume) vs (unit cell volume) should give the minimum but not energy vs (unit cell volume)? Since you are trying to find the gs lattice constant, I am assuming you consider harmonic approximation around gs lattice parameter. So You'll expect to see a parabola in energy vs volume graph, as energy is proportional to (vol-v0)^2 around equilibrium(v0). In principle if you draw energy/vol vs vol, you should see energy/vol proportional to vol+v0^2/vol, which I think should still have a minimum.But why would you do that, since you are looking for the configuration with minimum energy? If this doesnt satisfy you, you can always use an equation of state fitting. Thats is my understanding of the issue, I'd be more than glad if somebody corrects me. emine kucukbenli, Sissa, Italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From kucukben at sissa.it Sun Sep 27 21:41:13 2009 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 27 Sep 2009 21:41:13 +0200 Subject: [Pw_forum] epsilon.x In-Reply-To: References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> Message-ID: <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> Dear Dev, I also have never used this feature of the code but Doc directory has useful documents when you need answers: Doc/eps_man.tex It is clearly stated there that "the non-local contribution due to the pseudopotential is neglected. Actually the correction to the matrix element that take into account the non-local part of the Hamiltonian is not implemented." So to develop the code for USPP you need to find a way to calculate & add these corrections, I guess. You can check epsilon.f90 to learn more.. emine kucukbenli, Sissa, Italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From chenhanghuipwscf at gmail.com Mon Sep 28 00:18:16 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Sun, 27 Sep 2009 18:18:16 -0400 Subject: [Pw_forum] tefield and LSDA Message-ID: <22ae3ca40909271518u1d1917f2rdf17c97937ecf3fa@mail.gmail.com> Dear PWSCF developers, I found that when I turn on an external electric field (tefield = .true.), I can not do spin-polarized calculation (LSDA = .false.). I am just curious whether there is any fundamental difficulties to do spin-polarized calculation in the presence of an external electric field or it is just that this function is not implemented in QE. Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090927/a09bbf63/attachment.htm From chenhanghuipwscf at gmail.com Mon Sep 28 03:26:41 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Sun, 27 Sep 2009 21:26:41 -0400 Subject: [Pw_forum] tefield and LSDA II Message-ID: <22ae3ca40909271826r110b87d7w3249dc2832d543bf@mail.gmail.com> Dear PWSCF developers, I just want to follow my previous email. After reading the code more carefully, I found in the subroutine input.f90 that if tefield = .true. and nspin > 2, then we have the error message that "LSDA not available with electric field". However, nspin > 2 or more precisely speaking nspin = 4 means non-collinear spin-polarized calculation. nspin = 2 is the standard spin-polarized calculation with magnetization along z direction. My question is when tefield = .true., can I do spin-polarized calculation with magnetization along z direction? The error message "LSDA not available with electric field" seems a little bit confusing to me. Thank you very much. Hanghui -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090927/4dd889af/attachment.htm From decboy9 at gmail.com Mon Sep 28 08:57:07 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 28 Sep 2009 12:27:07 +0530 Subject: [Pw_forum] epsilon.x In-Reply-To: <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> Message-ID: Dear sir, Thank you very much sir. The dielectric constant we can even found by phonon also. I want to know that can we calculate the dielectric constant , electro-optic coefficient as a function of external electric field. Like if i want to increase electric field in Z direction gradually , what is change in dielectric constant , electro optic properties and non linear optical properties???? which parameters to apply ?? which inputs to be added ??? Thanks, Take care, Dev Sharma, University of Delhi, India On Mon, Sep 28, 2009 at 1:11 AM, Emine Kucukbenli wrote: > Dear Dev, > I also have never used this feature of the code but Doc directory has > useful documents when you need answers: Doc/eps_man.tex > It is clearly stated there that "the non-local contribution due to the > pseudopotential is neglected. Actually the correction to the matrix > element that take into account the non-local part of the Hamiltonian > is not implemented." > So to develop the code for USPP you need to find a way to calculate & > add these corrections, I guess. You can check epsilon.f90 to learn > more.. > emine kucukbenli, Sissa, Italy > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/2d54ac8b/attachment.htm From sclauzer at sissa.it Mon Sep 28 09:06:15 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Sep 2009 09:06:15 +0200 Subject: [Pw_forum] tefield and LSDA II In-Reply-To: <22ae3ca40909271826r110b87d7w3249dc2832d543bf@mail.gmail.com> References: <22ae3ca40909271826r110b87d7w3249dc2832d543bf@mail.gmail.com> Message-ID: <4AC06067.7050708@sissa.it> Dear Hanghui Chen, hanghui chen wrote: > Dear PWSCF developers, > I just want to follow my previous email. After reading the code > more carefully, I found in the subroutine input.f90 that if tefield = > .true. and nspin > 2, then we have the error message that "LSDA not > available with electric field". However, nspin > 2 or more precisely > speaking nspin = 4 means non-collinear spin-polarized calculation. nspin > = 2 is the standard spin-polarized calculation with magnetization along > z direction. I think you're right, the error message should be rather: "Noncollinear calculation not available with electric field", but how could you get that message if you wanted to perform spin-polarized, collinear calculations (which corresponds to lsda=.TRUE., internally in the code; why did you write lsda=.FALSE. in your previous mail?) ??? It should show up only when you specify noncolin=.TRUE. > My question is when tefield = .true., can I do spin-polarized > calculation with magnetization along z direction? The error message > "LSDA not available with electric field" seems a little bit confusing to me. If actually it was only a wrong string for the error message (as I think: please someone of the developers which know that part of the code confirm) and the code doesn't stop and complain when you specify tefield=.TRUE. together with nspin=2, I think you can safely use that feature of QE. Regards GS > Thank you very much. > > > Hanghui > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Sep 28 09:08:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Sep 2009 09:08:51 +0200 Subject: [Pw_forum] tefield and LSDA II In-Reply-To: <22ae3ca40909271826r110b87d7w3249dc2832d543bf@mail.gmail.com> References: <22ae3ca40909271826r110b87d7w3249dc2832d543bf@mail.gmail.com> Message-ID: <4AC06103.1000904@sissa.it> hanghui chen wrote: > Dear PWSCF developers, > I just want to follow my previous email. After reading the code Just an advice to all those posting in the forum. I think that if you want to add something to you post, even when you haven't yet received any reply, it's much better if you simply reply to your own post coming from the forum address, DO NOT start a new thread! Thanks, GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Sep 28 09:19:17 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Sep 2009 09:19:17 +0200 Subject: [Pw_forum] spin orbital structure in crystal In-Reply-To: References: Message-ID: <4AC06375.4090307@sissa.it> yumin qian wrote: > Is there anyone konw how to draw a picture of spin or d orbit > orientation on a crystal lattice . The spin orientation can be plotted via pp.x using plot_num=6 for collinear LSDA, or plot_num=13 for noncollinear calculations. For orbital ordering you can devise something to visualize in a way that you like the information given by projwfc.x, which projects KS eigenstates onto atomic wave-functions (including the 5 d orbitals on the atoms which have those orbitals in valence). HTH GS > Is there any tool that can be used. > Many thanks . > > -- > Sincerely Y. M. Qian > Lab.of Condensed Matter Theory and Materials Computation > Institute of Physics > Chinese Academy of Sciences > Tel: + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603 Beijing 100190 > China > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Mon Sep 28 10:00:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Sep 2009 10:00:50 +0200 Subject: [Pw_forum] epsilon.x In-Reply-To: <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> Message-ID: <4AC06D32.90909@democritos.it> Emine Kucukbenli wrote: > It is clearly stated there that "the non-local contribution due to the > pseudopotential is neglected. Actually the correction to the matrix > element that take into account the non-local part of the Hamiltonian > is not implemented." > So to develop the code for USPP you need to find a way to calculate & > add these corrections, I guess. it is not sufficient. For norm-conserving PP, there is a nonlocal contribution to the matrix elements <\psi_i| r | \psi_j> (i /= j) that is not accounted for in epsilon.x . This is the meaning of the above statement. For USPP, additional terms have to be added, since only the smooth term of |\psi_i> (the one expanded into plane waves) is available. The correct calculation of matrix elements is actually performed in the phonon code and could be in principle imported into epsilon.f90. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From decboy9 at gmail.com Mon Sep 28 12:53:03 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 28 Sep 2009 16:23:03 +0530 Subject: [Pw_forum] epsilon.x In-Reply-To: <4AC06D32.90909@democritos.it> References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> <4AC06D32.90909@democritos.it> Message-ID: Dear sir, and the possibility about calculation of electro-optic properties with electric filed in phonon code ????? Please advice. Thanks Dev On Mon, Sep 28, 2009 at 1:30 PM, Paolo Giannozzi wrote: > Emine Kucukbenli wrote: > > > It is clearly stated there that "the non-local contribution due to the > > pseudopotential is neglected. Actually the correction to the matrix > > element that take into account the non-local part of the Hamiltonian > > is not implemented." > > So to develop the code for USPP you need to find a way to calculate & > > add these corrections, I guess. > > it is not sufficient. For norm-conserving PP, there is a nonlocal > contribution to the matrix elements <\psi_i| r | \psi_j> (i /= j) > that is not accounted for in epsilon.x . This is the meaning of > the above statement. > > For USPP, additional terms have to be added, since only the smooth > term of |\psi_i> (the one expanded into plane waves) is available. > > The correct calculation of matrix elements is actually performed > in the phonon code and could be in principle imported into > epsilon.f90. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/52d55cac/attachment.htm From marsamos at democritos.it Mon Sep 28 12:56:49 2009 From: marsamos at democritos.it (marsamos at democritos.it) Date: Mon, 28 Sep 2009 12:56:49 +0200 Subject: [Pw_forum] epsilon.x In-Reply-To: <4AC06D32.90909@democritos.it> References: <8974d3b20909261305n62b738dejf2bec1d1eb9fc294@mail.gmail.com> <20090927214113.vi8i814y8s8w400w@webmail.sissa.it> <4AC06D32.90909@democritos.it> Message-ID: <20090928125649.2r9vrflz1twkww4s@mail.democritos.it> epsilon.x calculate the dielectric function within the RPA approximation (no excitonic effects) without including local field effects and without including the commutator of H with r (contribution from the nonlocal part of the pseudo). more complete calculation of dielectric functions, can be made using SaX or yambo, or almost all the GW package available around. The equations on how to "implement", non-local fields or the inclusion of the non-local part of the pseudo can be found in old GW papers (REv. Mod. Phys. Onida, Reining ...). Quoting Paolo Giannozzi : > Emine Kucukbenli wrote: > >> It is clearly stated there that "the non-local contribution due to the >> pseudopotential is neglected. Actually the correction to the matrix >> element that take into account the non-local part of the Hamiltonian >> is not implemented." >> So to develop the code for USPP you need to find a way to calculate & >> add these corrections, I guess. > > it is not sufficient. For norm-conserving PP, there is a nonlocal > contribution to the matrix elements <\psi_i| r | \psi_j> (i /= j) > that is not accounted for in epsilon.x . This is the meaning of > the above statement. > > For USPP, additional terms have to be added, since only the smooth > term of |\psi_i> (the one expanded into plane waves) is available. > > The correct calculation of matrix elements is actually performed > in the phonon code and could be in principle imported into > epsilon.f90. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From carlo.nervi at unito.it Mon Sep 28 13:51:36 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Mon, 28 Sep 2009 13:51:36 +0200 Subject: [Pw_forum] About example 22 In-Reply-To: <1253889571.3266.43.camel@dhpc-5-36.sissa.it> References: <21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com> <1253889571.3266.43.camel@dhpc-5-36.sissa.it> Message-ID: <4AC0A348.9020205@unito.it> Hello, I found also that example21 in the CVS version of 25-09-09 returns "from read_namelists : error # 1 fpmd calculation no more supported, use cp instead" Hope this helps, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From yirigui321 at 126.com Mon Sep 28 14:39:55 2009 From: yirigui321 at 126.com (yirigui321) Date: Mon, 28 Sep 2009 20:39:55 +0800 (CST) Subject: [Pw_forum] error in scf calculation Message-ID: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> when I calculate scf,the error "inconsistent DFT read " appear how to solve this problem? thank for your request! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/f0cdaa1f/attachment.htm From paulatto at sissa.it Mon Sep 28 15:20:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 28 Sep 2009 15:20:35 +0200 Subject: [Pw_forum] error in scf calculation In-Reply-To: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> References: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> Message-ID: In data 28 settembre 2009 alle ore 14:39:55, yirigui321 ha scritto: > when I calculate scf,the error "inconsistent DFT read " appear > how to solve this problem? Dear yirigui321, the error message means that you have used pseudopotentials generated with different kind of density functionals, e.g. LDA, PBE, B3LYP... In order to have a consistent calculation all pseudopotentials must be generated with the same functional. The easier solution is to download other pseudopotentials from the web page, taking care that the choice functional matches. A few additional notes: 1. this problem has been discussed many times in this mailing list, please do a search of the archive: 2. please provide you affiliation when writing to this mailing list, we like to know who we are dealing with :-) 3. please spend some time reading the documentation, it will save you a lot of time in the future; e.g. you issue is described in detail in the troubleshooting section: best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Mon Sep 28 15:29:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Sep 2009 15:29:55 +0200 Subject: [Pw_forum] About example 22 In-Reply-To: <4AC0A348.9020205@unito.it> References: <21fbc4790909250725r70d71cc3i3d271a58c4e382d2@mail.gmail.com> <1253889571.3266.43.camel@dhpc-5-36.sissa.it> <4AC0A348.9020205@unito.it> Message-ID: <4AC0BA53.4090101@democritos.it> Carlo Nervi wrote: > I found also that example21 in the CVS version of 25-09-09 returns > "from read_namelists : error # 1 > fpmd calculation no more supported, use cp instead" same for example19. The 'fpmd' keyword, that was used for backward compatibility, has been removed. Examples will be fixed soon(er or later). Thank you Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From luchhi at 126.com Mon Sep 28 15:44:26 2009 From: luchhi at 126.com (=?gbk?B?wr20urqj?=) Date: Mon, 28 Sep 2009 21:44:26 +0800 (CST) Subject: [Pw_forum] =?gbk?b?wLTX1MK9tLq6o7XE08q8/g==?= In-Reply-To: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> References: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> Message-ID: <23456168.741401254145466406.JavaMail.coremail@bj126app16.126.com> Checking your input or optimazing geometry again. -- Associate Prof., Dr. Chunhai LU Tel: +86 816 3626738 E-mail: luchhi at 126.com ?2009-09-28 20:39:55?yirigui321 ??? when I calculate scf,the error "inconsistent DFT read " appear how to solve this problem? thank for your request! ?????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/c6333981/attachment.htm From cyc99 at postech.ac.kr Mon Sep 28 16:06:55 2009 From: cyc99 at postech.ac.kr (=?ks_c_5601-1987?B?w9a/tcO2?=) Date: Mon, 28 Sep 2009 23:06:55 +0900 Subject: [Pw_forum] Can I calculate the NMR shift for metallic system?? Message-ID: <001901ca4044$efca0b30$cf5e2190$@ac.kr> 1) Can I calculate the NMR shift for metallic system using PWSCF? 2) If yes, is the Knight shift also included in the calculations? 3) If the Knight shift is not included, is it meaningful to calculate the NMR shift for the metallic systems? Thank you for the answers. Regards, Choi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/58204084/attachment-0001.htm From giannozz at democritos.it Mon Sep 28 16:24:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Sep 2009 16:24:17 +0200 Subject: [Pw_forum] error in scf calculation In-Reply-To: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> References: <12727573.578661254141595950.JavaMail.coremail@bj126app52.126.com> Message-ID: <4AC0C711.9090405@democritos.it> yirigui321 wrote: > when I calculate scf,the error "inconsistent DFT read " appear http://www.quantum-espresso.org/user_guide/node40.html -- Paolo Giannozzi, Democritos and University of Udine, Italy From decboy9 at gmail.com Mon Sep 28 19:55:32 2009 From: decboy9 at gmail.com (dev sharma) Date: Mon, 28 Sep 2009 23:25:32 +0530 Subject: [Pw_forum] electro-optic properties Message-ID: Hi 2 All, I want to know that can we calculate the dielectric constant , electro-optic coefficient as a function of external electric field. Like if i want to increase electric field in Z direction gradually , what is change in dielectric constant , electro optic properties and non linear optical properties???? which parameters to apply ?? which inputs to be added ??? Sir what i thaink, i have to do the following things 1) Scf with these extra parameters tefield=.true., edir = 3 (Z dierection) emaxpos= 0.5D0,(it means that electric field is maximum at c/2 where c is the lattice constant along z axis) eopreg=0.1D0 (I dident get the Zone meaning) eamp= 1.9 *(10 raise to power -15) V/m,( only this electric field i have to vary and calculate optical properties at diffrent values) 2) pw.x with calculation =phonon with above same parameters 3) Ph.x (phonon at gamma) Please advice, Thanks, Take care Dev Sharma, Univeristy of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090928/9044d23c/attachment.htm From ceresoli at MIT.EDU Tue Sep 29 00:02:26 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Mon, 28 Sep 2009 18:02:26 -0400 (EDT) Subject: [Pw_forum] Can I calculate the NMR shift for metallic system?? In-Reply-To: <001901ca4044$efca0b30$cf5e2190$@ac.kr> References: <001901ca4044$efca0b30$cf5e2190$@ac.kr> Message-ID: On Mon, 28 Sep 2009, ??? wrote: > > 1) Can I calculate the NMR shift for metallic system using PWSCF? > > 2) If yes, is the Knight shift also included in the calculations? > > 3) If the Knight shift is not included, is it meaningful to calculate the NMR shift for the metallic systems? > Dear Choi, the answer to 1..3 is: no, not yet. But it doesn't take too much to implement. Are you volunteering? the implementation is explained in PRB 76, 165122. Davide +----------------------------------------------------------+ Davide Ceresoli DMSE 13-4084 Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, MA 02139-4307 Phone: (617) 253-6026 Mobile: +39-347-1001570 Skype: dceresoli +----------------------------------------------------------+ From cyc99 at postech.ac.kr Tue Sep 29 01:39:06 2009 From: cyc99 at postech.ac.kr (Young Cheol Choi) Date: Tue, 29 Sep 2009 08:39:06 +0900 (KST) Subject: [Pw_forum] About NMR calculations for metallic system. Message-ID: <1929911.1254181146242.JavaMail.root@mail1.postech.ac.kr> .Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Thank you Mr. Ceresoli for your fast reply. I'm so sorry for not being able to calculate the NMR shift for metallic system using PWSCF. But, I found your paper (Int. J. Quant. Chem. 2009, 109, 3336.),  where you calculated the NMR shift for the metallic system like graphene or graphite, and you didn't include the Knight shift. 1) so, I thought that it is possible to calculate the NMR shift for metallic systems using PWSCF,     though it is not considering the Knight shift. Am I right?     (cf. in the case of the Castep code where the same theory (GIPAW) is implemented,     I could not perform such calculations for the system with fractional occupation number     ,that is to say, metallic systems.) 2) If I'm right, is it meaningful to calculate the NMR shift for metallic system without the Knight shift?     I'm asking this question cause, as far as I know, the Knight shift is much larger than chemical shift. 3) lastly, Is it possible to calculate the NMR shift for the paramagnetic system using PWSCF?     (maybe, spin-polarized calculations for the NMR shift.)   Sorry for too many questions. And thank you very much, Mr. Ceresoli. Best regards, Choi. =========================================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/ab82a952/attachment.htm From gregor.mali at ki.si Tue Sep 29 08:21:18 2009 From: gregor.mali at ki.si (Gregor Mali) Date: Tue, 29 Sep 2009 08:21:18 +0200 Subject: [Pw_forum] Hyperfine interaction in Li-Mn compounds? In-Reply-To: References: <001901ca4044$efca0b30$cf5e2190$@ac.kr> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256012E52AE@postar.ki.si> Dear PWscf/GIPAW users. I am studying lithium-manganese oxides and lithium-manganese silicates. Isotropic shifts of 6Li MAS NMR signals in these compounds are predominantly determined by the contact hyperfine interaction (Fermi shifts), i.e. by the interaction between 6Li nuclei and unpaired electronic spins. Is it possible to calculate these hyperfine shifts or the magnitude of hyperfine interaction by the PWsfc/GIPAW module using job = 'hyperfine'. I also wonder if the corresponding GIPAW input file requires any additional input parameters. The option 'hyperfine' is, namely, not documented in the INPUT_GIPAW.html file. Best regards. Gregor Mali Gregor Mali Kemijski institut/National Institute of Chemistry Hajdrihova 19 SI-1001 Ljubljana tel. +386 1 47 60 412 fax +386 1 47 60 300 From marcello.rosini at unimore.it Tue Sep 29 10:53:55 2009 From: marcello.rosini at unimore.it (Marcello Rosini) Date: Tue, 29 Sep 2009 10:53:55 +0200 Subject: [Pw_forum] vc_relax problem Message-ID: <4AC1CB23.5080803@unimore.it> Hallo everybody I am performing a variable cell relaxaion with pw.x 4.1. In particular I put the keyword cell_dofree='z', since I want to relax only the z axis (there is vacuum along the other two directions). It seems to me that the program does not care for this constraint and relaxes all the cell parameters. Moreover, at the end the end the job exits with this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from scale_h : error # 1 Not enough space allocated for radial FFT: try restarting with a larger cell_factor. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Am I wrong in setting up the calculation or is it a problem with pw.x? any help is greatly appreciated. You can find my input and output here: http://cdm.unimo.it/home/fisica/rosini.marcello/relax_inout.txt Many thanks in advance, Marcello -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dipartimento di Fisica, Universit? di Modena e Reggio Emilia and S3 National Research Centre of CNR-INFM via campi 213/a - 41125 Modena - Italy tel: +39 059.205.5067 email: marcello.rosini at unimore.it www.nanomodelling.unimore.it ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From giannozz at democritos.it Tue Sep 29 11:22:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Sep 2009 11:22:49 +0200 Subject: [Pw_forum] vc_relax problem In-Reply-To: <4AC1CB23.5080803@unimore.it> References: <4AC1CB23.5080803@unimore.it> Message-ID: <737C33E9-0FC0-4706-98ED-3F2AD9BDC419@democritos.it> On Sep 29, 2009, at 10:53 , Marcello Rosini wrote: > I am performing a variable cell relaxaion with pw.x 4.1. In > particular I > put the keyword cell_dofree='z' [...] It seems to me that the program > does not care for this constraint and relaxes all the cell parameters. it seems to other people as well: http://www.democritos.it/pipermail/pw_forum/2009-August/013979.html > from scale_h : error # 1 > Not enough space allocated for radial FFT: try restarting with > a larger cell_factor. do what it suggests, or else restart from an initial cell (the one you provide in input) that is closer to what you found during relaxation. Plane waves and G-vectors are calculated for the input cell, rescaled for the new cell as the cell changes. The maximum value of |G| thus changes during optimization/molecular dynamics. If it exceeds the maximum allowed value, the code will stop. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ceresoli at MIT.EDU Tue Sep 29 14:48:07 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Tue, 29 Sep 2009 08:48:07 -0400 Subject: [Pw_forum] About NMR calculations for metallic system. In-Reply-To: <1929911.1254181146242.JavaMail.root@mail1.postech.ac.kr> References: <1929911.1254181146242.JavaMail.root@mail1.postech.ac.kr> Message-ID: <4AC20207.6020208@mit.edu> Young Cheol Choi wrote: > Thank you Mr. Ceresoli for your fast reply. > I'm so sorry for not being able to calculate the NMR shift for metallic > system using PWSCF. > > But, I found your paper (Int. J. Quant. Chem. 2009, 109, 3336.), > where you calculated the NMR shift for the metallic system like graphene > or graphite, > and you didn't include the Knight shift. > > 1) so, I thought that it is possible to calculate the NMR shift for > metallic systems using PWSCF, > though it is not considering the Knight shift. Am I right? > (cf. in the case of the Castep code where the same theory (GIPAW) is > implemented, > I could not perform such calculations for the system with fractional > occupation number > ,that is to say, metallic systems.) > > 2) If I'm right, is it meaningful to calculate the NMR shift for > metallic system without the Knight shift? > I'm asking this question cause, as far as I know, the Knight shift > is much larger than chemical shift. Dear Choi, the Int. J. Quant. Chem. paper refers to the so-called "converse" method (JCP 131, 101101). This is not yet available in the CVS version and it's in the list of the 1000+1 things I'm plannig to do. Anyway, we haven't implemented yet the Knight shift, but it should be straightforward. As you mention, in some systems the Knight shift is much larger than the NMR shift, and it doesn't make sense to compute only the latter. However, according to literature, for undoped graphite or graphene, the Kinght shift is small. > 3) lastly, Is it possible to calculate the NMR shift for the > paramagnetic system using PWSCF? > (maybe, spin-polarized calculations for the NMR shift.) The GIPAW code (which does linear response), should work also for spin polarized systems (magnetic insulators). I've never tried though... > Sorry for too many questions. > And thank you very much, Mr. Ceresoli. > > Best regards, > Choi. You are very welcome! Best, Davide From ceresoli at MIT.EDU Tue Sep 29 15:09:46 2009 From: ceresoli at MIT.EDU (Davide Ceresoli) Date: Tue, 29 Sep 2009 09:09:46 -0400 Subject: [Pw_forum] Hyperfine interaction in Li-Mn compounds? In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D256012E52AE@postar.ki.si> References: <001901ca4044$efca0b30$cf5e2190$@ac.kr> <8C0B47760A05FB4AB504C9BCAD32D256012E52AE@postar.ki.si> Message-ID: <4AC2071A.9030103@mit.edu> Gregor Mali wrote: > Dear PWscf/GIPAW users. > > I am studying lithium-manganese oxides and lithium-manganese silicates. > Isotropic shifts of 6Li MAS NMR signals in these compounds are > predominantly determined by the contact hyperfine interaction (Fermi > shifts), i.e. by the interaction between 6Li nuclei and unpaired > electronic spins. > > Is it possible to calculate these hyperfine shifts or the magnitude of > hyperfine interaction by the PWsfc/GIPAW module using job = 'hyperfine'. > I also wonder if the corresponding GIPAW input file requires any > additional input parameters. The option 'hyperfine' is, namely, not > documented in the INPUT_GIPAW.html file. > Dear Gregor, the extra information to enter are the nuclear g-factors for the isotopes. Here is an example for MnO (55Mn and 18O). &inputgipaw job = 'hyperfine' prefix = 'mno' tmp_dir = './scratch/' spline_ps = .true. hfi_output_unit = 'MHz' hfi_nuclear_g_factor(1) = 1.387487 ! 55Mn hfi_nuclear_g_factor(2) = -0.757520 ! 18O / I've got the numbers from webelements.com, under "NMR properties". There, the gyromangnetic ratio \gamma is listed in 10^7 rad T^{-1} s^{-1}. To obtain the g-factor, multiply \hbar and divide by the nuclear magneton (\mu_N): E.g. using the command 'units': You have: 6.6452546e7 hbar / nuclearmagneton T s You want: Definition: 1.3874872 If the nuclear spin is N/2, N>1, you need to divide the output quantities by N. For Li, you should get good results for the Fermi contact, because the unpaired electron are in the 2s orbital. But if the magnetization comes form p and d orbitals, I've found that the core electrons (those not included in the pseudopotential!) polarize opposite to the valence, giving rise to large cancellations in the Fermi contact. I've implemented the core relaxation in an experimental version of the code. I haven't put it in the CVS, because it's not perfect, and one should carefully check if the results make sense. If you are interested, send me an e-mail. > Best regards. > > Gregor Mali Best, Davide From javier.fuhr at gmail.com Tue Sep 29 16:10:13 2009 From: javier.fuhr at gmail.com (Javier Fuhr) Date: Tue, 29 Sep 2009 11:10:13 -0300 Subject: [Pw_forum] bug in mm_dispersion.f90 Message-ID: Hi, I think I've found a bug in the calculation of the dispersion energy/force/stress when doing a parallel calculation with more than one pool. In mm_dispersion.f90, the sum between the processes is only done intra_pool but not inter_pool. Here is a diff between the version 4.1 and a possible corrected one (I'm not an expert in the paralelization of QE...): ----------------------------- 261c261 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 362a363 > CALL mp_sum ( energy_london , inter_pool_comm ) 377c378 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 503a505 > CALL mp_sum ( force_london , inter_pool_comm ) 519c521 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, inter_pool_comm 660a663 > CALL mp_sum ( stres_london , inter_pool_comm ) ----------------------------- Regards, Javier -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies - Div. Colisiones At?micas Centro At?mico Bariloche Bariloche - Argentina TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/71fb90ee/attachment.htm From sclauzer at sissa.it Tue Sep 29 16:25:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 29 Sep 2009 16:25:11 +0200 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: References: Message-ID: <4AC218C7.9080805@sissa.it> Dear Javier, Javier Fuhr wrote: > Hi, > I think I've found a bug in the calculation of the dispersion > energy/force/stress when doing a parallel calculation with more than one > pool. In mm_dispersion.f90, the sum between the processes is only done > intra_pool but not inter_pool. I don't know that (pretty new) part of the code, but at a first glance to that subroutine I would say that you must be wrong. The parallelization is done inside each pool over atoms, hence you only need to collect the partial sums over subsets of atoms from the processes in the pool. Using more than one pool will not improve the speedup of that part of the code, but neither change the result of energy_london. If you have (reproducible) evidence that the same calculation performed with more than one pool gives a different result, please provide some simple input file. Thanks, GS > Here is a diff between the version 4.1 and a possible corrected one (I'm > not an expert in the paralelization of QE...): > ----------------------------- > 261c261 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 362a363 > > CALL mp_sum ( energy_london , inter_pool_comm ) > 377c378 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 503a505 > > CALL mp_sum ( force_london , inter_pool_comm ) > 519c521 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 660a663 > > CALL mp_sum ( stres_london , inter_pool_comm ) > ----------------------------- > > Regards, > Javier > > -- > Dr. Javier Daniel Fuhr > Grupo F?sica de Superficies - Div. Colisiones At?micas > Centro At?mico Bariloche > Bariloche - Argentina > TE : ++54 2944 44 5100 Int. 5524 > FAX: ++54 2944 44 5299 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From degironc at sissa.it Tue Sep 29 16:48:03 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 29 Sep 2009 16:48:03 +0200 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: References: Message-ID: <4AC21E23.7030904@sissa.it> Hi , thank you for your contribution. Have you tested the 4.1 version and verified that it has a bug ? I mean, have you done a parallel calculation with and w/o pools and seen that they give different results ? Moreover, have you tested your modified version and seen that it is working correctly ? do you have simple example where this can be seen ? best regards, stefano de Gironcoli - SISSA and DEMOCRITOS Javier Fuhr wrote: > Hi, > I think I've found a bug in the calculation of the dispersion > energy/force/stress when doing a parallel calculation with more than > one pool. In mm_dispersion.f90, the sum between the processes is only > done intra_pool but not inter_pool. > Here is a diff between the version 4.1 and a possible corrected one > (I'm not an expert in the paralelization of QE...): > ----------------------------- > 261c261 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 362a363 > > CALL mp_sum ( energy_london , inter_pool_comm ) > 377c378 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 503a505 > > CALL mp_sum ( force_london , inter_pool_comm ) > 519c521 > < USE mp_global, ONLY : mpime , nproc , intra_pool_comm > --- > > USE mp_global, ONLY : mpime , nproc , intra_pool_comm, > inter_pool_comm > 660a663 > > CALL mp_sum ( stres_london , inter_pool_comm ) > ----------------------------- > > Regards, > Javier > > -- > Dr. Javier Daniel Fuhr > Grupo F?sica de Superficies - Div. Colisiones At?micas > Centro At?mico Bariloche > Bariloche - Argentina > TE : ++54 2944 44 5100 Int. 5524 > FAX: ++54 2944 44 5299 > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From javier.fuhr at gmail.com Tue Sep 29 17:12:10 2009 From: javier.fuhr at gmail.com (Javier Fuhr) Date: Tue, 29 Sep 2009 12:12:10 -0300 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: <4AC218C7.9080805@sissa.it> References: <4AC218C7.9080805@sissa.it> Message-ID: Dear Gabriele and Stefano, Thanks for your answers, On Tue, Sep 29, 2009 at 11:25 AM, Gabriele Sclauzero wrote: > Dear Javier, > > I don't know that (pretty new) part of the code, but at a first glance to > that > subroutine I would say that you must be wrong. > The parallelization is done inside each pool over atoms, hence you only > need to collect > the partial sums over subsets of atoms from the processes in the pool. > Using more than one pool will not improve the speedup of that part of the > code, but > neither change the result of energy_london. > > The parallelization is done to all processes (nproc), and if I understand correctly the sum should be performed over all processes. Looking better at the different parallelizations, I think the correct way is to replace, in mm_dispersion.f90, intra_pool_comm by world_comm, i.e., the diff between original and modified file is: ----------------------------- 261c261 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , world_comm 362c362 < 999 CALL mp_sum ( energy_london , intra_pool_comm ) --- > 999 CALL mp_sum ( energy_london , world_comm ) 377c377 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , world_comm 503c503 < 999 CALL mp_sum ( force_london , intra_pool_comm ) --- > 999 CALL mp_sum ( force_london , world_comm ) 519c519 < USE mp_global, ONLY : mpime , nproc , intra_pool_comm --- > USE mp_global, ONLY : mpime , nproc , world_comm 660c660 < 999 CALL mp_sum ( stres_london , intra_pool_comm ) --- > 999 CALL mp_sum ( stres_london , world_comm ) ----------------------------- > If you have (reproducible) evidence that the same calculation performed > with more than one > pool gives a different result, please provide some simple input file. > > Thanks, > > GS > > I attach an input file which the original version of the subroutine gives me Dispersion Correction = -0.05035543 Ry for "-npool 1", and Dispersion Correction = -0.02587314 Ry for "-npool 2". With the modified version of mm_dispersion.f90, I get the same value for 1 o 2 pools. -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies Divisi?n Colisiones At?micas Centro At?mico Bariloche TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/add9d603/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: gaas.scf.in Type: application/octet-stream Size: 493 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090929/add9d603/attachment-0001.obj From ps at ned.sims.nrc.ca Tue Sep 29 17:23:05 2009 From: ps at ned.sims.nrc.ca (Serguei Patchkovskii) Date: Tue, 29 Sep 2009 11:23:05 -0400 (EDT) Subject: [Pw_forum] About NMR calculations for metallic system. In-Reply-To: <4AC20207.6020208@mit.edu> References: <1929911.1254181146242.JavaMail.root@mail1.postech.ac.kr> <4AC20207.6020208@mit.edu> Message-ID: On Tue, 29 Sep 2009, Davide Ceresoli wrote: > > 3) lastly, Is it possible to calculate the NMR shift for the > > paramagnetic system using PWSCF? > > (maybe, spin-polarized calculations for the NMR shift.) > The GIPAW code (which does linear response), should work > also for spin polarized systems (magnetic insulators). > I've never tried though... Unlike NMR chemical shifts of closed-shell systems, chemical shift in paramagnetic species is a statistical (rather than a response) property. Generally speaking, you need to know all spin-Hamiltonian parameters to calculate it - the shielding tensor, the hyperfine tensor, the g-tensor, and (if you radical sites are of a spin higher than 1/2) the zero-field splitting parameters. You may also need to know the spin-spin and spin-lattice relaxation times, or at least have an idea as to their magnitude relative to the NMR time scale. You'll get a better idea of what's involved in such calculation from our (by now slightly dated, but still basically OK) review: S. Moon and S. Patchkovskii, "First-Principles Calculations of Paramagnetic NMR Shifts", pp. 325-338, in M. Kaupp, M. Buehl, and V.G. Malkin (eds), "Calculation of NMR and EPR Parameters", Wiley-VCH, 2004. For the simplest possible case (isolates spin-1/2 paramagnetic centres, relaxing rapidly on the NMR time scale) you may be able to get everything you need from GIPAW - but a fair bit of a bit of coaxing and head-scratching is likely to be involved ... Have fun, Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 Skype: Serguei.Patchkovskii E-mail: Serguei.Patchkovskii at nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From giannozz at democritos.it Tue Sep 29 19:14:36 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Sep 2009 19:14:36 +0200 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: References: <4AC218C7.9080805@sissa.it> Message-ID: <9A4683A5-EEAB-4680-BE1B-D1443C8195C9@democritos.it> On Sep 29, 2009, at 17:12 , Javier Fuhr wrote: > The parallelization is done to all processes (nproc), and > if I understand correctly the sum should be performed > over all processes. Looking better at the different > parallelizations, I think the correct way is to replace, > in mm_dispersion.f90, intra_pool_comm by world_comm I think you are (almost) right. "image" parallelization, useful for NEB calculations, implies different atomic positions on different groups of processors. So the correct communicator is "intra_image_comm", containing nproc_image processors. Attached the (hopefully) correct Modules/mm_dispersion.f90. Thank you for reporting this bug and its (quasi-)fix Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: mm_dispersion.f90 Type: application/octet-stream Size: 20001 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090929/50246bf3/attachment.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From javier.fuhr at gmail.com Tue Sep 29 20:49:11 2009 From: javier.fuhr at gmail.com (Javier Fuhr) Date: Tue, 29 Sep 2009 15:49:11 -0300 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: <9A4683A5-EEAB-4680-BE1B-D1443C8195C9@democritos.it> References: <4AC218C7.9080805@sissa.it> <9A4683A5-EEAB-4680-BE1B-D1443C8195C9@democritos.it> Message-ID: On Tue, Sep 29, 2009 at 2:14 PM, Paolo Giannozzi wrote: > > > I think you are (almost) right. "image" parallelization, useful > for NEB calculations, implies different atomic positions on > different groups of processors. So the correct communicator > is "intra_image_comm", containing nproc_image processors. > Attached the (hopefully) correct Modules/mm_dispersion.f90. > Thank you for reporting this bug and its (quasi-)fix > > Paolo > > Thank you Paolo for the correct fix. An additional doubt: although I am not using the value given by "Harris-Foulkes estimate", when converged, shouldn't it be the same than "total energy"? Looking at PW/electrons.f90, it seems to me that lines 473-475 (at least line 475 for the dispersion energy) should have the equivalent for hwf_energy. Regards, Javier -- Dr. Javier Daniel Fuhr Grupo F?sica de Superficies Divisi?n Colisiones At?micas Centro At?mico Bariloche TE : ++54 2944 44 5100 Int. 5524 FAX: ++54 2944 44 5299 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090929/03572284/attachment-0001.htm From giannozz at democritos.it Tue Sep 29 21:21:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Sep 2009 21:21:49 +0200 Subject: [Pw_forum] bug in mm_dispersion.f90 In-Reply-To: References: <4AC218C7.9080805@sissa.it> <9A4683A5-EEAB-4680-BE1B-D1443C8195C9@democritos.it> Message-ID: <9F035D79-9BBF-4B27-AAED-4A263C6FE829@democritos.it> On Sep 29, 2009, at 20:49 , Javier Fuhr wrote: > An additional doubt: although I am not using the value given by > "Harris-Foulkes estimate", when converged, shouldn't it be the > same than "total energy"? it should, if all terms are there! apparently in some cases there are missing terms in the Harris-Foulkes energy. Thank you for noticing this as well P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yuminqian at gmail.com Wed Sep 30 03:22:13 2009 From: yuminqian at gmail.com (yumin qian) Date: Wed, 30 Sep 2009 09:22:13 +0800 Subject: [Pw_forum] spin orbital structure in crystal In-Reply-To: <4AC06375.4090307@sissa.it> References: <4AC06375.4090307@sissa.it> Message-ID: Thanks for your reply ,I will try it . 2009/9/28 Gabriele Sclauzero > > yumin qian wrote: > > Is there anyone konw how to draw a picture of spin or d orbit > > orientation on a crystal lattice . > > The spin orientation can be plotted via pp.x using plot_num=6 for collinear > LSDA, or > plot_num=13 for noncollinear calculations. > > For orbital ordering you can devise something to visualize in a way that > you like the > information given by projwfc.x, which projects KS eigenstates onto atomic > wave-functions > (including the 5 d orbitals on the atoms which have those orbitals in > valence). > > HTH > > GS > > > > Is there any tool that can be used. > > Many thanks . > > > > -- > > Sincerely Y. M. Qian > > Lab.of Condensed Matter Theory and Materials Computation > > Institute of Physics > > Chinese Academy of Sciences > > Tel: + 8610 8264 9147 > > E-Mail:yuminqian at gmail.com E-Mail%3Ayuminqian at gmail.com > > > P.O.Box 603 Beijing 100190 > > China > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/ba121585/attachment.htm From decboy9 at gmail.com Wed Sep 30 08:02:27 2009 From: decboy9 at gmail.com (dev sharma) Date: Wed, 30 Sep 2009 11:32:27 +0530 Subject: [Pw_forum] Re : electro-optic properties In-Reply-To: References: Message-ID: Hi 2 All, i have sent this mail some days ago but i didnt get any reply from the forum . Please have a look on my question and advice. Thanks in advance, Take care, Dev sharma, University of Delhi, I want to know that can we calculate the dielectric constant , electro-optic coefficient as a function of external electric field. Like if i want to increase electric field in Z direction gradually , what is change in dielectric constant , electro optic properties and non linear optical properties???? which parameters to apply ?? which inputs to be added ??? Sir what i think, i have to do the following things 1) Scf with these extra parameters tefield=.true., edir = 3 (Z dierection) emaxpos= 0.5D0,(it means that electric field is maximum at c/2 where c is the lattice constant along z axis) eopreg=0.1D0 (I dident get the Zone meaning) eamp= 1.9 *(10 raise to power -15) V/m,( only this electric field i have to vary and calculate optical properties at diffrent values) 2) pw.x with calculation =phonon with above same parameters 3) Ph.x (phonon at gamma) Please advice, Thanks, Take care Dev Sharma, Univeristy of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/53116b0f/attachment.htm From kazempoor2000 at yahoo.com Wed Sep 30 12:23:20 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 30 Sep 2009 03:23:20 -0700 (PDT) Subject: [Pw_forum] symmetry of defect state Message-ID: <290030.71709.qm@web112507.mail.gq1.yahoo.com> Hi Does anyone knows how to determine the symmetry of the defect state introduced in gap or how to join the the relaxation of atoms around the defect by the changing point group? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/0725c58b/attachment.htm From kazempoor2000 at yahoo.com Wed Sep 30 12:57:40 2009 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Wed, 30 Sep 2009 03:57:40 -0700 (PDT) Subject: [Pw_forum] defect symmetry Message-ID: <460994.96430.qm@web112503.mail.gq1.yahoo.com> Hi Does anyone knows how to determine the symmetry of the defect state introduced in gap or how to join the the relaxation of atoms around the defect by the changing point group? thanks a lot Ali Kazempour Physics department, Isfahan University of Technology 84156 Isfahan, Iran. Tel-1: +98 311 391 3733 Fax: +98 311 391 2376 Tel-2: +98 311 391 2375 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/f76f567f/attachment.htm From udayagiri3 at gmail.com Wed Sep 30 17:48:41 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 30 Sep 2009 21:18:41 +0530 Subject: [Pw_forum] convergence test for chromium Message-ID: Dear all I did convergence tests for chromium. The ecut value i obtained for energy converged to 1mRyd is 60Ryd! which i believe is very high for an Ultra Soft PP can somebody tell me if i am doing something wrong. Given below are my sample input file and ecut vs total energy. &control calculation = 'scf', restart_mode='from_scratch', outdir='/home/sai/softwares/espresso-4.0.1/workspace/temp', prefix='chromium' pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/', / &system ibrav=3 celldm(1)=5.450000, nat=1, ntyp=1 ecutwfc=15, ecutrho=150, occupations='smearing', smearing='mp', degauss=0.005000 / &electrons conv_thr=1.D-8, diagonalization='david', mixing_mode='plain', mixing_beta= 0.3 electron_maxstep=1000 / ATOMIC_SPECIES Cr 51.9961 Cr.pbe-sp-van.UPF ATOMIC_POSITIONS (crystal) Cr 0.00000000 0.00000000 0.00000000 K_POINTS {automatic} 12 12 12 0 0 0 ecut energy 15 -171.52805273 20 -173.85044031 25 -174.14015464 30 -174.15592557 35 -174.16252481 40 -174.17616814 45 -174.18792735 50 -174.19506225 55 -174.19773267 60 -174.19824847 -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/a1963d66/attachment.htm From paulatto at sissa.it Wed Sep 30 18:00:53 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 30 Sep 2009 18:00:53 +0200 Subject: [Pw_forum] convergence test for chromium In-Reply-To: References: Message-ID: In data 30 settembre 2009 alle ore 17:48:41, udayagiri sai babu ha scritto: > Dear all > I did convergence tests for chromium. The ecut value i obtained for > energy converged to 1mRyd is 60Ryd! which i believe is very high for an > Ultra Soft PP can somebody tell me if i am doing something wrong. Given > below are my > sample input file and ecut vs total energy. Dear Udayagiri, what about the cutoff for charge density? One good procedure to find a nicely converged cutoff is to increase ecutwfc until it converges than set ecutrho to 4*ecutwfc and reduce ecutwfc keeping ecutrho fixed. Maybe you can fix ecutrho to 240 and see how low you can go with ecutwfc best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From udayagiri3 at gmail.com Wed Sep 30 19:04:39 2009 From: udayagiri3 at gmail.com (udayagiri sai babu) Date: Wed, 30 Sep 2009 22:34:39 +0530 Subject: [Pw_forum] convergence test for chromium In-Reply-To: References: Message-ID: Dear Lorenzo paulatto I did not understand what you said but i am using ecutrho=10*ecutwfc. On Wed, Sep 30, 2009 at 9:30 PM, Lorenzo Paulatto wrote: > In data 30 settembre 2009 alle ore 17:48:41, udayagiri sai babu > ha scritto: > > > Dear all > > I did convergence tests for chromium. The ecut value i obtained for > > energy converged to 1mRyd is 60Ryd! which i believe is very high for an > > Ultra Soft PP can somebody tell me if i am doing something wrong. Given > > below are my > > sample input file and ecut vs total energy. > > Dear Udayagiri, > what about the cutoff for charge density? > One good procedure to find a nicely converged cutoff is to increase > ecutwfc until it converges than set ecutrho to 4*ecutwfc and reduce > ecutwfc keeping ecutrho fixed. > > Maybe you can fix ecutrho to 240 and see how low you can go with ecutwfc > > best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- U.Saibabu PhD student, Deformation mechanisms modeling group, Materials engineering department, IISc Bangalore, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/6f5b1b29/attachment.htm From aryjunior at gmail.com Wed Sep 30 20:15:33 2009 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 30 Sep 2009 15:15:33 -0300 Subject: [Pw_forum] convergence test for chromium In-Reply-To: References: Message-ID: <4c9c61c20909301115r7fe80662q7fb3ae8171fc8ee1@mail.gmail.com> Hi Lorenzo, I did exactly what you said and I got the same convergence chart on both tests... I'm working with g-alumina and ultrasoft pp... My first convergence test suggested an ecutwfc value between 50Ry-70Ry... Then I used ecutrho = 280Ry for the second test... It means that I can use ecutrho = 4*ecutwfc, right? []s Ary Junior On Wed, Sep 30, 2009 at 1:00 PM, Lorenzo Paulatto wrote: > In data 30 settembre 2009 alle ore 17:48:41, udayagiri sai babu > ha scritto: > > > Dear all > > I did convergence tests for chromium. The ecut value i obtained for > > energy converged to 1mRyd is 60Ryd! which i believe is very high for an > > Ultra Soft PP can somebody tell me if i am doing something wrong. Given > > below are my > > sample input file and ecut vs total energy. > > Dear Udayagiri, > what about the cutoff for charge density? > One good procedure to find a nicely converged cutoff is to increase > ecutwfc until it converges than set ecutrho to 4*ecutwfc and reduce > ecutwfc keeping ecutrho fixed. > > Maybe you can fix ecutrho to 240 and see how low you can go with ecutwfc > > best regards > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- http://lattes.cnpq.br/8221674673413336 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/8fc5ccc7/attachment.htm From ttduyle at gmail.com Wed Sep 30 20:55:53 2009 From: ttduyle at gmail.com (Duy Le) Date: Wed, 30 Sep 2009 14:55:53 -0400 Subject: [Pw_forum] convergence test for chromium In-Reply-To: <4c9c61c20909301115r7fe80662q7fb3ae8171fc8ee1@mail.gmail.com> References: <4c9c61c20909301115r7fe80662q7fb3ae8171fc8ee1@mail.gmail.com> Message-ID: <8974d3b20909301155s45287ae8m8e4f3fb7335a7bb9@mail.gmail.com> Hi, The USPP which includes sp semicore could lead you to that such ecut if it is not a very good PP. Ecutrho should be about 10-14*ecut and you should also make sure that the k-point sampling is good enough. Good luck. On Wed, Sep 30, 2009 at 2:15 PM, Ary Junior wrote: > Hi Lorenzo, I did exactly what you said and I got the same convergence > chart on both tests... I'm working with g-alumina and ultrasoft pp... My > first convergence test suggested an ecutwfc value between 50Ry-70Ry... Then > I used ecutrho = 280Ry for the second test... It means that I can use > ecutrho = 4*ecutwfc, right? > > []s > > Ary Junior > > > On Wed, Sep 30, 2009 at 1:00 PM, Lorenzo Paulatto wrote: > >> In data 30 settembre 2009 alle ore 17:48:41, udayagiri sai babu >> ha scritto: >> >> > Dear all >> > I did convergence tests for chromium. The ecut value i obtained for >> > energy converged to 1mRyd is 60Ryd! which i believe is very high for an >> > Ultra Soft PP can somebody tell me if i am doing something wrong. Given >> > below are my >> > sample input file and ecut vs total energy. >> >> Dear Udayagiri, >> what about the cutoff for charge density? >> One good procedure to find a nicely converged cutoff is to increase >> ecutwfc until it converges than set ecutrho to 4*ecutwfc and reduce >> ecutwfc keeping ecutrho fixed. >> >> Maybe you can fix ecutrho to 240 and see how low you can go with ecutwfc >> >> best regards >> >> >> -- >> Lorenzo Paulatto >> SISSA & DEMOCRITOS (Trieste) >> phone: +39 040 3787 511 >> skype: paulatz >> www: http://people.sissa.it/~paulatto/ >> >> *** save italian brains *** >> http://saveitalianbrains.wordpress.com/ >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > http://lattes.cnpq.br/8221674673413336 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090930/ccf4fc30/attachment-0001.htm From liuyongduo at hotmail.com Wed Sep 30 22:43:39 2009 From: liuyongduo at hotmail.com (=?gb2312?B?wfXTwO7s?=) Date: Thu, 1 Oct 2009 04:43:39 +0800 Subject: [Pw_forum] Projected DOS Message-ID: Dear all Does any body know what is the setting of Wigner Seitz radii in the DOS projection? What is the default value and how to reset it? Thanks very much! Yongduo Liu Materials Science & Engineering University of California, Los Angeles _________________________________________________________________ ?????????????????msn????? http://ditu.live.com/?form=TL&swm=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20091001/94301650/attachment.htm