From elie.moujaes at hotmail.co.uk Sun Sep 2 06:09:50 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sun, 2 Sep 2012 05:09:50 +0100 Subject: [Pw_forum] strange results for phonon frequencies. Message-ID: Dear all, Sorry to ask so many questions about computing phonon frequencies but recently i have got some strange results for one of the systems I am working on. My work involves computing phonon frequencies for a 42 carbon at the Gamma point so in total 126 irreducible representations. in a previous calculations, my input was: SCF FILE / &system ibrav= 0, celldm(1) =1.88972599, nat=42, ntyp= 1, ecutwfc =32, ecutrho=128, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.7D0, diago_david_ndim=2, ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ... PH FILE: Phonon calculation for GB60 at gamma point &inputph tr2_ph=1.0d-15, prefix='GrBo42ph', fildvscf='GB60dvscf', elph=.true.,..... The results obtained were: omega( 1) = -4.450324 [THz] = -148.446823 [cm-1] omega( 2) = -3.144068 [THz] = -104.874835 [cm-1] omega( 3) = 2.963314 [THz] = 98.845504 [cm-1] omega( 4) = 3.454797 [THz] = 115.239637 [cm-1] omega( 5) = 3.908880 [THz] = 130.386191 [cm-1]... omega(**) = 47.380063 [THz] = 1580.428796 [cm-1] omega(**) = 47.573318 [THz] = 1586.875087 [cm-1] omega(**) = 47.821300 [THz] = 1595.146853 [cm-1] omega(**) = 48.119632 [THz] = 1605.098137 [cm-1] Where the 2 negative frequencies,as professor Gionazzi repeated several times, could be due to the violation of the ASR rule. For my own piece of mind I repeated the calculation with a better accuracy where ecutrho=256 (8 times ecutwfc which should be the case if an ultrasoft potential is used)and tr2_ph =10^(-17) although mixing_beta was set equal to 0.3 this time. I expected better results but what I got was the following: omega( 1 - 1) = -77614121.2 [cm-1] --> A' I+R omega( 2 - 2) = -13157144.1 [cm-1] --> A' I+R omega( 3 - 3) = -5577066.3 [cm-1] --> A' I+R omega( 4 - 4) = -4332492.8 [cm-1] --> A' I+R omega( 5 - 5) = -4094962.7 [cm-1] --> A' I+R omega( 6 - 6) = -3368158.6 [cm-1] --> A' I+R omega( 7 - 7) = -2781643.0 [cm-1] --> A' I+R omega( 8 - 8) = -2403295.2 [cm-1] --> A' I+R omega( 9 - 9) = -1777809.3 [cm-1] --> A' I+R omega( 10 - 10) = 82.5 [cm-1] --> A'' I+R omega( 11 - 11) = 85.8 [cm-1] --> A'' I+R... omega(120 -120) = 2301243.8 [cm-1] --> A' I+R omega(121 -121) = 2494732.0 [cm-1] --> A' I+R omega(122 -122) = 2788571.0 [cm-1] --> A' I+R omega(123 -123) = 3135326.3 [cm-1] --> A' I+R omega(124 -124) = 3630869.3 [cm-1] --> A' I+R omega(125 -125) = 8808450.4 [cm-1] --> A' I+R What is the reason for those LARGE negative values at the beginning and the LARGE ones at the end? Is it because mixing_beta was changed? Thanks for the help Elie KoukaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120902/ea1e7fd9/attachment.htm From akohlmey at gmail.com Sun Sep 2 08:53:09 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sun, 2 Sep 2012 08:53:09 +0200 Subject: [Pw_forum] strange results for phonon frequencies. In-Reply-To: References: Message-ID: On Sun, Sep 2, 2012 at 6:09 AM, Elie M wrote: > Dear all, > > Sorry to ask so many questions about computing phonon frequencies but > recently i have got some strange results for one of the systems I am working > on. My work involves computing phonon frequencies for a 42 carbon at the > Gamma point so in total 126 irreducible representations. [...] > What is the reason for those LARGE negative values at the beginning and the > LARGE ones at the end? Is it because mixing_beta was changed? no. think about it for a bit and what mixing does. why should mixing_beta change the result? it only should only affect how fast you converge and whether you converge at all. you would get those "strange large" frequencies, when your system is not in the minimum, which is to be expected, if you didn't reoptimize the geometry with the larger density cutoff (which is still on the low side, btw). the procedure is usually the following: 1) you have to choose your cutoffs, so you have well converged forces and derivatives of them 2) you need a well optimized geometry with those settings (you may have to break symmetry by slightly randomizing positions occasionally) 3) you compute phonons. you cannot do 1) after 3) and without 2). cheers, axel. > > > Thanks for the help > > > Elie Koukaes > > University of Nottingham > > NG7 2RD > > UK > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From bfazi90 at gmail.com Sun Sep 2 20:27:26 2012 From: bfazi90 at gmail.com (bf azi) Date: Sun, 2 Sep 2012 22:57:26 +0430 Subject: [Pw_forum] london Message-ID: Hi Dear all What is difference between "London" and "van der Waals interactions"? Bani Adam Faculty of Science Egypt From Ari.P.Seitsonen at iki.fi Sun Sep 2 20:36:18 2012 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Sun, 2 Sep 2012 20:36:18 +0200 (CEST) Subject: [Pw_forum] london In-Reply-To: References: Message-ID: Dear Bani Adam, http://en.wikipedia.org/wiki/Van_der_Waals_force The "dispersion" / "London dispersion" is one of the components in the van der Waals force/interaction. The dispersion is what is usually most difficult to describe with the (semi-)local exchange-correlation functionals, but in the literature there is often confusion about the correct notation. Also the induction/Debye force is not fully described, if I understand correctly. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Sun, 2 Sep 2012, bf azi wrote: > Hi Dear all > > What is difference between "London" and "van der Waals interactions"? > > > Bani Adam > Faculty of Science > Egypt > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Sun Sep 2 21:18:10 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 2 Sep 2012 21:18:10 +0200 Subject: [Pw_forum] strange results for phonon frequencies. In-Reply-To: References: Message-ID: On Sep 2, 2012, at 6:09 , Elie M wrote: > What is the reason for those LARGE negative values at the beginning > and the LARGE ones at the end? > it is impossible to answer without the data and without trying to reproduce them. Not that it irs possible even with the data: reproducing a large phonon calculation requires effort and computer time. It looks like the wrong file were read from the phonon code, though. Try to make two phonon calculations with the same cutoffs, pseudopotentials, everything, for a simpler system (e.g. diamond). P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From florenceliu86 at gmail.com Mon Sep 3 04:16:45 2012 From: florenceliu86 at gmail.com (florence liu) Date: Mon, 3 Sep 2012 10:16:45 +0800 Subject: [Pw_forum] PAW for vdw-DF2 Message-ID: Dear all, I remenber that, it has been mentioned recently, that ld1.x is not able to generate PAW/PP's for vdw-DFs. I am trying to perform a calculation with vdw-DF2 which is made up as NOX-PW-RW86-VDW2. I thought that it might be reasonable to use a PAW which is generated for a functional based on RW86, is that right? I would try the setting dft='NOX-PW-PW96-(anything else?)'. Does anybody can tell whether is settings is reasonable? best wishes florence liu TU Munich -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/ad043a34/attachment.htm From sxr109320 at utdallas.edu Mon Sep 3 06:23:56 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Sun, 2 Sep 2012 23:23:56 -0500 (CDT) Subject: [Pw_forum] EXX_examples Message-ID: <753600100.735133.1346646236871.JavaMail.root@zem1.utdallas.edu> Dear Developers , Quick Question; Is the EXX routine working in version 5.0.1 ? I am trying to run EXX_examples , and it gives me error in finding HSE and PBE0 for molecules? x_gamma_extrapolation is this working for versions 5.0.1 or 4.3.2 ?? Thanks for your help -- Best Regards, Saeedeh Ravandi From lmartinsamos at gmail.com Mon Sep 3 09:48:39 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 3 Sep 2012 09:48:39 +0200 Subject: [Pw_forum] EXX_examples In-Reply-To: <753600100.735133.1346646236871.JavaMail.root@zem1.utdallas.edu> References: <753600100.735133.1346646236871.JavaMail.root@zem1.utdallas.edu> Message-ID: What is exactly the error? because it is implemented (gamma_extrapolation is also working) and I just run the bulk silicon example and everything seems ok! running PBE0 calculation for Si with nq=1,2,4 running the scf calculation for Si with nq = 1 ... done ! total energy = -15.90468197 Ry running the scf calculation for Si with nq = 2 ... done ! total energy = -15.84995846 Ry running the scf calculation for Si with nq = 4 ... best regards Layla 2012/9/3 Saeedeh S Ravandi > Dear Developers , > > > Quick Question; Is the EXX routine working in version 5.0.1 ? > I am trying to run EXX_examples , and it gives me error in finding HSE and > PBE0 for molecules? > x_gamma_extrapolation is this working for versions 5.0.1 or 4.3.2 ?? > > Thanks for your help > -- > Best Regards, > Saeedeh Ravandi > _______________________________________________ > 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/20120903/e108eef0/attachment.htm From lmartinsamos at gmail.com Mon Sep 3 11:16:16 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 3 Sep 2012 11:16:16 +0200 Subject: [Pw_forum] phd felloships announcement Message-ID: Dear all, the ?Slovene Human Resources Development and Scholarship Fund? has open a call for applications for the award of scholarship for postgraduate study in natural science, technology or medicine at educational institutions in the Republic of Slovenia for individual level of education, more precisely for: - Master studies (second level), - Doctoral studies. of nationals of Western Balkans (Republic of Albania, Bosnia and Herzegovina, Republic of Montenegro, Republic of Kosovo, Republic of Macedonia and Republic of Serbia.). The call is open for the year 2012. Deadline for application 21.09.2012. http://www.sklad-kadri.si/si/razpisi-in-objave/naslovnica/razpis/n/stipendije-za-podiplomski-studij-drzavljanov-zahodnega-balkana-v-sloveniji-v-letu-2012-138-jr/ As you know, at University of Nova Gorica, we can offer very interesting opportunities for PhD thesis, in particular in the field of material and surface science (theory and/or experimental). As docent of UNG, we kindly ask you to diffuse this announcement to the interested candidates that can contact us in case they are interested to enroll at our University and they intend to apply for the above mentioned fellowship. Best regards, Layla and Sandra PS contact information lmartinsamos at gmail.com (for theoretical modeling) and sandra.gardonio at ung.si -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/ef763871/attachment.htm From giannozz at democritos.it Mon Sep 3 13:42:33 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 03 Sep 2012 13:42:33 +0200 Subject: [Pw_forum] PAW for vdw-DF2 In-Reply-To: References: Message-ID: <1346672553.12375.7.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-03 at 10:16 +0800, florence liu wrote: > I thought that it might be reasonable to use a PAW which is generated > for a functional based on RW86, is that right? I would try the setting > dft='NOX-PW-PW96-(anything else?)' note that the definition of the vdW-DF2 functional will change in the next release: SLA-PW-RW86, i.e. th eSlater term is no longer contained into the rPW86 functional (the latter contains only the gradient corrections) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From sxr109320 at utdallas.edu Mon Sep 3 14:12:27 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Mon, 3 Sep 2012 07:12:27 -0500 (CDT) Subject: [Pw_forum] EXX_examples , Molecules and InAs Message-ID: <126885844.736104.1346674347107.JavaMail.root@zem1.utdallas.edu> Dear Layala , Thanks for running EXX , my question wasnt about si , I was wondering if the molecules in your examples are working or not ? Do you have any idea, why , I am keep getting this error (as my input file , I am following the example) : This is the error" from read-namelists : error # 88 reading namelists control MY INPUT FILE : & control calculation='scf' restart_mode= 'from_scratch' prefix= ' InAs' pseudo_dir= '$PSEUDO_DIR/' outdir= '$TMP_DIR/' / &system ibrav =2, celldm(1) =11.389792, nat=2, ntyp=2 , nbnd=16, input_dft='hse', nqx1=1nq, nqx2=1nq, nqx3=1nq, ecutwft=18.0, x_gamma_extrapolation = ".TRUE." / &electrons mixing_beta = 0.7D0 / ATOMIC_SPECIES In 114.818 In.pz-bhs.UPF As 74.92160 As.pz-bhs.UPF ATOMIC_POSITIONS In 0.00 0.00 0.00 As 0.25 0.25 0.25 K_POINTS automatic 3 3 3 0 0 0 Best Regards, Saeedeh Ravandi From akohlmey at gmail.com Mon Sep 3 14:16:47 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 3 Sep 2012 14:16:47 +0200 Subject: [Pw_forum] EXX_examples , Molecules and InAs In-Reply-To: <126885844.736104.1346674347107.JavaMail.root@zem1.utdallas.edu> References: <126885844.736104.1346674347107.JavaMail.root@zem1.utdallas.edu> Message-ID: On Mon, Sep 3, 2012 at 2:12 PM, Saeedeh S Ravandi wrote: > Dear Layala , > > Thanks for running EXX , my question wasnt about si , I was wondering if the molecules in your examples are working or not ? > > Do you have any idea, why , I am keep getting this error (as my input file , I am following the example) : This is the error" > > from read-namelists : error # 88 > reading namelists control that error message has nothing to do with EXX, but is a fundamental input syntax error. axel. > > > > MY INPUT FILE : > > & control > > calculation='scf' > restart_mode= 'from_scratch' > prefix= ' InAs' > pseudo_dir= '$PSEUDO_DIR/' > outdir= '$TMP_DIR/' > / > &system > ibrav =2, celldm(1) =11.389792, nat=2, ntyp=2 , nbnd=16, input_dft='hse', nqx1=1nq, nqx2=1nq, nqx3=1nq, ecutwft=18.0, x_gamma_extrapolation = ".TRUE." > / > &electrons > mixing_beta = 0.7D0 > / > ATOMIC_SPECIES > In 114.818 In.pz-bhs.UPF > As 74.92160 As.pz-bhs.UPF > ATOMIC_POSITIONS > In 0.00 0.00 0.00 > As 0.25 0.25 0.25 > K_POINTS automatic > 3 3 3 0 0 0 > > > > > > > > Best Regards, > Saeedeh Ravandi > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From lmartinsamos at gmail.com Mon Sep 3 14:17:07 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 3 Sep 2012 14:17:07 +0200 Subject: [Pw_forum] EXX_examples , Molecules and InAs In-Reply-To: <126885844.736104.1346674347107.JavaMail.root@zem1.utdallas.edu> References: <126885844.736104.1346674347107.JavaMail.root@zem1.utdallas.edu> Message-ID: Dear Saeedeh, your input has two problems: 1) & control -->> write it without space &control 2) nqx1 = 1nq , nqx2=1nq ...-->> nqx1=1 cheers Layla 2012/9/3 Saeedeh S Ravandi > Dear Layala , > > Thanks for running EXX , my question wasnt about si , I was wondering if > the molecules in your examples are working or not ? > > Do you have any idea, why , I am keep getting this error (as my input file > , I am following the example) : This is the error" > > from read-namelists : error # 88 > reading namelists control > > > > > MY INPUT FILE : > > & control > > calculation='scf' > restart_mode= 'from_scratch' > prefix= ' InAs' > pseudo_dir= '$PSEUDO_DIR/' > outdir= '$TMP_DIR/' > / > &system > ibrav =2, celldm(1) =11.389792, nat=2, ntyp=2 , nbnd=16, > input_dft='hse', nqx1=1nq, nqx2=1nq, nqx3=1nq, ecutwft=18.0, > x_gamma_extrapolation = ".TRUE." > / > &electrons > mixing_beta = 0.7D0 > / > ATOMIC_SPECIES > In 114.818 In.pz-bhs.UPF > As 74.92160 As.pz-bhs.UPF > ATOMIC_POSITIONS > In 0.00 0.00 0.00 > As 0.25 0.25 0.25 > K_POINTS automatic > 3 3 3 0 0 0 > > > > > > > > Best Regards, > Saeedeh Ravandi > _______________________________________________ > 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/20120903/30b6486c/attachment.htm From romeda_8 at yahoo.com Mon Sep 3 14:30:57 2012 From: romeda_8 at yahoo.com (Romeda Azeen) Date: Mon, 3 Sep 2012 05:30:57 -0700 (PDT) Subject: [Pw_forum] Pseudopotential for Hafnium (Hf) Message-ID: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> Dear PW Forum, I have a question about of pseudopotential of Hafnium Metal. I want to do some computation on HfV2 under USPP (Vanderbilt's scheme), but I can't find any available USPP of Hafnium. What should I do,will you give me some hints/assistant? Thanks in advance. -- Romeda Azeen Bhavnagar University Bhavnagar 364002 Gujarat, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/de42204d/attachment.htm From romeda_8 at yahoo.com Mon Sep 3 14:32:25 2012 From: romeda_8 at yahoo.com (Romeda Azeen) Date: Mon, 3 Sep 2012 05:32:25 -0700 (PDT) Subject: [Pw_forum] Pseudopotential for Hafnium (Hf) Message-ID: <1346675545.55625.YahooMailNeo@web120406.mail.ne1.yahoo.com> Dear PW Forum, I have a question about of pseudopotential of Hafnium Metal. I want to do some computation on HfV2 under USPP (Vanderbilt's scheme), but I can't find any available USPP of Hafnium. What should I do,will you give me some hints/assistant? Thanks in advance. -- Romeda Azeen Bhavnagar University Bhavnagar 364002 Gujarat, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/5044a32c/attachment.htm From akohlmey at gmail.com Mon Sep 3 14:40:38 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 3 Sep 2012 14:40:38 +0200 Subject: [Pw_forum] Pseudopotential for Hafnium (Hf) In-Reply-To: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> References: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> Message-ID: On Mon, Sep 3, 2012 at 2:30 PM, Romeda Azeen wrote: > Dear PW Forum, > I have a question about of pseudopotential of Hafnium Metal. > I want to do some computation on HfV2 under USPP (Vanderbilt's scheme), but > I can't find any available USPP of Hafnium. > What should I do,will you give me some hints/assistant? if you can't find the pseudopotential, you have to either make it yourself or find a way to convince somebody to do it for you. since generation of pseudopotentials can be tedious and is generally a rather thankless profession, you may need some very good arguments for the latter. cheers, axel. > Thanks in advance. > > -- > Romeda Azeen > Bhavnagar University Bhavnagar 364002 Gujarat, India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From sporevoyager at gmail.com Mon Sep 3 14:53:40 2012 From: sporevoyager at gmail.com (shangy) Date: Mon, 3 Sep 2012 20:53:40 +0800 Subject: [Pw_forum] looking for Er pseudopotential Message-ID: Hi, all I am looking for Er (Erbium) pseudopotential that can run well with QE. The Er pseudopotential is not available in QE pseudopotential table. Though I obtained UPF files of Er by converting the Er pseudopotentials for abinit and Qbox codes, I noted the scf-run does not converge at all with these UPF files. It is highly appreciated that if someone can send the Er pseudopotential to me. Best regards Shangyi Institute of Metal Research, CAS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/398a6c20/attachment-0001.htm From sxr109320 at utdallas.edu Mon Sep 3 15:25:02 2012 From: sxr109320 at utdallas.edu (Saeedeh S Ravandi) Date: Mon, 3 Sep 2012 08:25:02 -0500 (CDT) Subject: [Pw_forum] EXX_examples , Molecules and InAs Message-ID: <1565173025.736216.1346678702290.JavaMail.root@zem1.utdallas.edu> Dear Layla , Unfortunetly , I still get a same error... Poooof sorry for bothering you :/ -- Best Regards, Saeedeh Ravandi From lmartinsamos at gmail.com Mon Sep 3 15:27:03 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 3 Sep 2012 15:27:03 +0200 Subject: [Pw_forum] EXX_examples , Molecules and InAs In-Reply-To: <1565173025.736216.1346678702290.JavaMail.root@zem1.utdallas.edu> References: <1565173025.736216.1346678702290.JavaMail.root@zem1.utdallas.edu> Message-ID: As axel told you also it is a problem with the input! send your current input file. cheers Layla 2012/9/3 Saeedeh S Ravandi > Dear Layla , > > > Unfortunetly , I still get a same error... Poooof > > > sorry for bothering you :/ > > > > -- > Best Regards, > Saeedeh Ravandi > _______________________________________________ > 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/20120903/21263452/attachment.htm From Zbigniew.Lodziana at ifj.edu.pl Mon Sep 3 16:26:16 2012 From: Zbigniew.Lodziana at ifj.edu.pl (Zbigniew Lodziana) Date: Mon, 3 Sep 2012 16:26:16 +0200 Subject: [Pw_forum] GIPAW problems Message-ID: <20120903142113.M49782@ifj.edu.pl> Dear Forum Users & Developers, I am new in QE Forum - welcome to All & congratulations for excellent information exchange here and software. Being new in GIPAW calculations I might have missed the answer browsing the Forum but did not found solution yet. The problem is that I am somehow puzzled by GIPAW calculations: - Using QE 5.0 I did compile it with Intel Fortran, MKL, openmp (more details below). No tuning, no tricks etc. just followed installation guide (./configure & make all). - While pw.x performs nicely, gipaw.x gives results that are difficult for interpretation, and I cannot really locate where the problem is. - Both pw.x and gipaw.x pass self-test; examples were no problem too. However, trying to calculate NMR spectra for slightly complex system calculations with GIPAW give results that seems to be machine dependent to the large extend. Input files and part of output are at the end; shortly "Total NMR chemical shifts in ppm:" is either 16.58 or 134.05 for the same system/element (inputs are simply copied) when calculated on two similar machines. Both computers are Intel based, compiler and libraries differ however: a) intel 11.1 (ifort); mkl 10.3 b) intel 11.1 (ifort); mkl 10.2.5.035 Playing with pseudopotentials, k-points make things even worse.., denser fft grid, density cutoff does not seems to improve results either). I use several other numerical codes on both machines - never had similar problems. I would highly appreciate any suggestions/help toward resolving this problem. best regards & thank you in advance, Zibi Zbigniew Lodziana Polish Academy of Sciences, ul.. Radzikowskiego 152, PL-31-342 Krakow ==================================================================== More detailed output & input. ------------------- Machine (a) Program GIPAW v.5.0 starts on 29Aug2012 ... Parallel version (MPI), running on 36 processors K-points division: npool = 6 R & G space division: proc/pool = 6 ... Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 985 985 263 35145 35145 4831 Max 986 986 264 35146 35146 4833 Sum 5913 5913 1581 210873 210873 28991 ... Total NMR chemical shifts in ppm: --------------------------------------- (adopting the Simpson convention for anisotropy and asymmetry)----------- Atom 1 Ca pos: ( 0.000000 6.787326 7.322301) Total sigma: 1417.43 ... Atom 3 B pos: ( 2.443074 2.731768 3.272940) Total sigma: 134.05 ... Atom 11 O pos: ( 4.532848 1.133423 1.942424) Total sigma: 102.07 ... ================= pw.x Program PWSCF v.5.0 starts on 29Aug2012 the Fermi energy is 10.5803 ev ! total energy = -642.94342958 Ry Harris-Foulkes estimate = -642.94342958 Ry estimated scf accuracy < 2.6E-11 Ry ======================== ========================================================== machine (b) Program GIPAW v.5.0 starts on 30Aug2012 Parallel version (MPI), running on 36 processors K-points division: npool = 6 R & G space division: proc/pool = 6 ... Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 985 985 263 35145 35145 4831 Max 986 986 264 35146 35146 4833 Sum 5913 5913 1581 210873 210873 28991 ... Total NMR chemical shifts in ppm: --------------------------------------- (adopting the Simpson convention for anisotropy and asymmetry)----------- Atom 1 Ca pos: ( 0.000000 6.787326 7.322301) Total sigma: 1001.13 ... Atom 3 B pos: ( 2.443074 2.731768 3.272940) Total sigma: 16.58 ... Atom 11 O pos: ( 4.532848 1.133423 1.942424) Total sigma: 68.51 pw.x Program PWSCF v.5.0 starts on 30Aug2012 the Fermi energy is 10.5803 ev ! total energy = -642.94342958 Ry Harris-Foulkes estimate = -642.94342958 Ry estimated scf accuracy < 2.6E-11 Ry ============================================================= INPUTS: pw.x &control calculation = 'scf' prefix = 'CaB4O7' restart_mode = 'from_scratch' tstress = .true. tprnfor = .true. pseudo_dir = './pseudo/' outdir = './tmp/' / &system ibrav = 0 celldm(1) = 1.0 nat = 24 ntyp = 3 ecutwfc = 110 occupations = 'smearing' smearing = 'mp' degauss = 0.005 / &electrons diagonalization = 'david' diago_thr_init = 1e-4 mixing_mode = 'plain' mixing_beta = 0.1 conv_thr = 1e-10 / ATOMIC_SPECIES Ca 40.078 Ca.pbe-tm-new-dc.UPF B 10.811 B.pbe-tm-new-gipaw-dc.UPF O 15.999 O.pbe-tm-new-gipaw-dc.UPF CELL_PARAMETERS (alat= 1.00000000) 20.248307850 0.000000000 0.000000000 0.000000000 8.343848898 0.000000000 0.000000000 0.000000000 8.006202063 ATOMIC_POSITIONS (crystal) Ca 0.000000000 0.813452700 0.914578653 Ca 0.500000000 0.186731631 0.414667081 B 0.120655733 0.327399041 0.408800535 B 0.379358780 0.672598815 0.908813803 B 0.620641220 0.672598815 0.908813803 B 0.879344267 0.327399041 0.408800535 B 0.250722266 0.822127339 0.383740663 B 0.249297780 0.177848977 0.883744720 B 0.750702220 0.177848977 0.883744720 B 0.749277734 0.822127339 0.383740663 O 0.223863043 0.135839302 0.242614879 O 0.276145474 0.864113231 0.742641343 O 0.723854526 0.864113231 0.742641343 O 0.776136957 0.135839302 0.242614879 O 0.138503036 0.647114168 0.331799880 O 0.361509595 0.352879214 0.831821610 O 0.638490405 0.352879214 0.831821610 O 0.861496964 0.647114168 0.331799880 O 0.133904753 0.274432983 0.747354309 O 0.366136763 0.725573696 0.247375604 O 0.633863237 0.725573696 0.247375604 O 0.866095247 0.274432983 0.747354309 O 0.000000000 0.220447425 0.298885908 O 0.500000000 0.779514715 0.798853668 K_POINTS automatic 2 6 6 1 1 1 ======================================= gipaw.x &inputgipaw job = 'nmr' prefix = 'CaB4O7' tmp_dir = './tmp/' isolve = 0 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .true. / From nicola.marzari at epfl.ch Mon Sep 3 16:31:41 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Mon, 03 Sep 2012 16:31:41 +0200 Subject: [Pw_forum] Pseudopotential for Hafnium (Hf) In-Reply-To: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> References: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> Message-ID: <5044BF4D.5060104@epfl.ch> Dear Romeda, and everyone else, you should try out the ps_library from QE forge. Download it, and ready carefully the AAREADME. Thank Andrea Dal Corso in the process. Report on this list any result that looks odd. We compiled all the pseudos, and they can be found here: http://theossrv1.epfl.ch/index.php?n=Main.Links Look for USPPs using e.g. pbe, i.e. pbe.tgz . Read carefully the readme file mentioned above regarding the different directories pseudopotentials, pseudopotentials_tot, and pseudopotentials_alt. nicola On 03/09/2012 14:30, Romeda Azeen wrote: > Dear PW Forum, > I have a question about of pseudopotential of Hafnium Metal. > I want to do some computation on HfV2 under USPP (Vanderbilt's scheme), > but I can't find any available USPP of Hafnium. > What should I do,will you give me some hints/assistant? > Thanks in advance. > > -- > Romeda Azeen > Bhavnagar University Bhavnagar 364002 Gujarat, India. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From tube77 at gmail.com Mon Sep 3 20:17:25 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Mon, 03 Sep 2012 13:17:25 -0500 Subject: [Pw_forum] Possible bug(?) in q2r.x when using FFT routine in ESSL In-Reply-To: Message-ID: Thank you very much. The temporary workaround that I used is that re-compile the entire source code with FFTW3 instead of ESSL. Then I linked the 'q2r.x' only to the FFTW3 executable and the rest of the executables are remained with ESSL. So the problem is fixed. For some reason, there is memory allocation problem with FFTW3 on AIX so that the 'pw.x' crashes immediately when it calls the FFTW3 routines.. I tried many degrees of freedom when I compiled the FFTW3 (different optimization levels, 32 or 64 bit and etc. ) and modified my user limit. But none of them worked.. But interestingly, the FFTW3 does not complained when it's called from 'q2r.x' .. Anyway, I agree that the best way to fix the problem is to modify the 'cfft3d' routine so that one can call 1d, 2d or 3d ESSL FFT routines depending on the dimensionality of FFT grids.. Thank you. On 9/1/12 2:37 AM, "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. Possible bug(?) in q2r.x when using FFT routine in ESSL > (Jiseok Kim) > 2. Re: Possible bug(?) in q2r.x when using FFT routine in ESSL > (Paolo Giannozzi) > 3. Re: Join to group , confirmation # (Yue-Wen Fang) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 31 Aug 2012 03:19:59 -0500 >From: Jiseok Kim >Subject: [Pw_forum] Possible bug(?) in q2r.x when using FFT routine in > ESSL >To: >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Dear, QE users > >I have been struggling for a while to find out what's going on with q2r.x >The problem was that I could not get rid of the error messages below when >doing q2r.x. > >------------------------------------------------- >DCFT3 : 2538-2030 >The transform length (ARG NO. 9) is not an allowed value. The next higher >allowed value is (2). >------------------------------------------------- > >I've compiled QE-v5.0.1. on AIX6.1(parallel machine) with 'mpxlf' with >ESSL >routines. >So the 'q2r.x' calls 'cfft3d' and then the 'cfft3d' calls 'dcft3' in ESSL >when performing FFT. > >The problem is this. >The 'dcft3' in ESSL only accepts certain values of transforming length as >shown in, > >------------------------------------------------- >http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2F >co >m.ibm.cluster.essl.v5r1.essl100.doc%2Fam501_hscft3.htm >------------------------------------------------- > >so the FFT dimensions (nx, ny, nz), which is read from outputs by ph.x, >should be the values in the table. >Otherwise, the 'dcft3' crashes. > >The FFT dimensions (nx, ny, nz) in q2r.x are equivalent to the (nq1, nq2, >nq3) in ph.x so that the Monkhorst-pack grid for ph.x should be limited by >the values in the table when using the ESSL. > >For example, the Monkhorst-pack grid (16x16x1) for q-points in the case of >two-dimensional supercell, such as graphene, cannot be accepted by the >'dcft3' so we have to avoid using the nq3=1. >(For some reason, the 'dcft3' does not allow odd number of FFT >dimensions..) > >So here is a question. >I wonder if I can use the different Monkhorst-pack grid for pw.x and ph.x >when calculating a phonon dispersion. >For example, can I use the (16x16x1) k-points for pw.x and (16x16x2) >q-points for ph.x. in the case of graphene or some two dimensional >supercell >? >I guess it should not be matter but I just want to be sure .. > >Thank you. > >Sincerely, > >JISEOK KIM, Ph.D. >Postdoctoral Research Associate >Department of Materials Science and Engineering >University of Texas at Dallas >800 W. Campbell Rd. RL10 >Richardson, TX 75080 >(413)386-6285 > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://www.democritos.it/pipermail/pw_forum/attachments/20120831/9bf23f85/ >attachment.html > >------------------------------ > >Message: 2 >Date: Fri, 31 Aug 2012 10:55:54 +0200 >From: Paolo Giannozzi >Subject: Re: [Pw_forum] Possible bug(?) in q2r.x when using FFT > routine in ESSL >To: PWSCF Forum >Message-ID: <1346403354.6068.21.camel at fe12lx.fisica.uniud.it> >Content-Type: text/plain > >The simplest workaround is to move the *.dyn* files to another >machine, compute there the force constants in reciprocal space. >The ultimate solution is to go into Modules/fft_scalar.f90, >edit routine cfft3d in such a way that it can cope with >a dimension of length 1. You need to modify line 1238: > IF( isign /= 0 ) CALL dcft3( f(1), ldx,ldx*ldy, f(1), ldx,ldx*ldy, & > nx,ny,nz, idir, tscale, work(1), lwork) >and call dcft2 instead. You will also need to add initialization of >dft2 in line 1159, definition of needed arrays somewhere around >line 1094. > >Of course you can use any grid of phonon wave-vectors, but it >is a waste of time. > >P. > >On Fri, 2012-08-31 at 03:19 -0500, Jiseok Kim wrote: >> Dear, QE users >> >> >> I have been struggling for a while to find out what's going on with >> q2r.x >> The problem was that I could not get rid of the error messages below >> when doing q2r.x. >> >> >> ------------------------------------------------- >> DCFT3 : 2538-2030 >> The transform length (ARG NO. 9) is not an allowed value. The next >> higher >> allowed value is (2). >> ------------------------------------------------- >> >> >> I've compiled QE-v5.0.1. on AIX6.1(parallel machine) with 'mpxlf' with >> ESSL routines. >> So the 'q2r.x' calls 'cfft3d' and then the 'cfft3d' calls 'dcft3' in >> ESSL when performing FFT. >> >> >> The problem is this. >> The 'dcft3' in ESSL only accepts certain values of transforming length >> as shown in, >> >> >> ------------------------------------------------- >> >>http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2 >>Fcom.ibm.cluster.essl.v5r1.essl100.doc%2Fam501_hscft3.htm >> ------------------------------------------------- >> >> >> so the FFT dimensions (nx, ny, nz), which is read from outputs by >> ph.x, should be the values in the table. >> Otherwise, the 'dcft3' crashes. >> >> >> The FFT dimensions (nx, ny, nz) in q2r.x are equivalent to the (nq1, >> nq2, nq3) in ph.x so that the Monkhorst-pack grid for ph.x should be >> limited by the values in the table when using the ESSL. >> >> >> For example, the Monkhorst-pack grid (16x16x1) for q-points in the >> case of two-dimensional supercell, such as graphene, cannot be >> accepted by the 'dcft3' so we have to avoid using the nq3=1. >> (For some reason, the 'dcft3' does not allow odd number of FFT >> dimensions..) >> >> >> So here is a question. >> I wonder if I can use the different Monkhorst-pack grid for pw.x and >> ph.x when calculating a phonon dispersion. >> For example, can I use the (16x16x1) k-points for pw.x and (16x16x2) >> q-points for ph.x. in the case of graphene or some two dimensional >> supercell ? >> I guess it should not be matter but I just want to be sure .. >> >> >> Thank you. >> >> >> Sincerely, >> >> >> JISEOK KIM, Ph.D. >> Postdoctoral Research Associate >> Department of Materials Science and Engineering >> University of Texas at Dallas >> 800 W. Campbell Rd. RL10 >> Richardson, TX 75080 >> (413)386-6285 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > >------------------------------ > >Message: 3 >Date: Fri, 31 Aug 2012 20:03:34 +0800 >From: Yue-Wen Fang >Subject: Re: [Pw_forum] Join to group , confirmation # >To: PWSCF Forum >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Hello, you have succeeded in subscribing this mail list and you can post >your problems by sending emails to pw_forum at pwscf.org > >Best Regards >Yuewen >East China Normal Univ > >2012/8/29 Saeedeh S Ravandi > >> Hi , >> >> -- >> Best Regards, >> Saeedeh Ravandi >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > >-- >---- >Yue-Wen Fang >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://www.democritos.it/pipermail/pw_forum/attachments/20120831/b3ac7846/ >attachment-0001.htm > >------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > >End of Pw_forum Digest, Vol 63, Issue 1 >*************************************** From romeda_8 at yahoo.com Mon Sep 3 21:26:09 2012 From: romeda_8 at yahoo.com (Romeda Azeen) Date: Mon, 3 Sep 2012 12:26:09 -0700 (PDT) Subject: [Pw_forum] Pseudopotential for Hafnium (Hf) In-Reply-To: <5044BF4D.5060104@epfl.ch> References: <1346675457.25612.YahooMailNeo@web120402.mail.ne1.yahoo.com> <5044BF4D.5060104@epfl.ch> Message-ID: <1346700369.14418.YahooMailNeo@web120406.mail.ne1.yahoo.com> Dear Nicola and also Andrea Dal Corso Thanks, your assistant was very helpful and offered very good advice. Best Regards, Romeda ________________________________ From: Nicola Marzari To: Romeda Azeen ; PWSCF Forum Sent: Monday, September 3, 2012 7:01 PM Subject: Re: [Pw_forum] Pseudopotential for Hafnium (Hf) Dear Romeda, and everyone else, you should try out the ps_library from QE forge. Download it, and ready carefully the AAREADME. Thank Andrea Dal Corso in the process. Report on this list any result that looks odd. We compiled all the pseudos, and they can be found here: http://theossrv1.epfl.ch/index.php?n=Main.Links Look for USPPs using e.g. pbe, i.e. pbe.tgz . Read carefully the readme file mentioned above regarding the different directories pseudopotentials, pseudopotentials_tot, and pseudopotentials_alt. ??? ??? ??? nicola On 03/09/2012 14:30, Romeda Azeen wrote: > Dear PW Forum, > I have a question about of pseudopotential of Hafnium Metal. > I want to do some computation on HfV2 under USPP (Vanderbilt's scheme), > but I can't find any available USPP of Hafnium. > What should I do,will you give me some hints/assistant? > Thanks in advance. > > -- > Romeda Azeen > Bhavnagar University Bhavnagar 364002 Gujarat, India. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/aa523e15/attachment-0001.htm From elie.moujaes at hotmail.co.uk Mon Sep 3 22:21:22 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 3 Sep 2012 21:21:22 +0100 Subject: [Pw_forum] strange results for phonon frequencies. In-Reply-To: References: , Message-ID: > the phonon code, though. Try to make two phonon calculations > with the same cutoffs, pseudopotentials, everything, for a simpler > system (e.g. diamond). will do that. Thank you. Will also check the relaxed system as was also pointed out earlier by prof. Axel. Elie > From: giannozz at democritos.it > Date: Sun, 2 Sep 2012 21:18:10 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] strange results for phonon frequencies. > > On Sep 2, 2012, at 6:09 , Elie M wrote: > > What is the reason for those LARGE negative values at the beginning > > and the LARGE ones at the end? > > > it is impossible to answer without the data and without trying to > reproduce them. Not that it irs possible even with the data: > reproducing a large phonon calculation requires effort and > computer time. It looks like the wrong file were read from > the phonon code, though. Try to make two phonon calculations > with the same cutoffs, pseudopotentials, everything, for a simpler > system (e.g. diamond). > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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/20120903/f9696651/attachment.htm From elie.moujaes at hotmail.co.uk Mon Sep 3 22:46:22 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 3 Sep 2012 21:46:22 +0100 Subject: [Pw_forum] error: wrong order of k-points Message-ID: Dear all, I want to evaluate the electron phonon coefficient at the K point which in my system in terms of 2Pi/a is -0.3363921 0.5833565 0.000000 as read from the scf output. I ran the phonon calculation with a point with negligible difference namely -0.336392 0.5833570 0.000000 and then I decided to stop the calculation and put the exact coordinates of the point above but the code always stops with the error: > > >> from phq_init : error # 1 > >> wrong order of k pointsstopping....Although I have deleted the original .dyn file, I still have the impression that the code still remembers the first put q point. My question is why would it do that although I am changing all the names including fildvscf and is it ok to still run the calculation with the very slightly different initial point or the code will complain after calculating the frequencies and won't evaluate the electron phonon coefficient? Thankss Elie MoukaesUniversity of NottinghamNG7, 2RDUK PH INPUT &inputph tr2_ph=1.0d-19,prefix='GraK',fildvscf='GraphKdvscf',recover=.true.,trans=.true.,elph=.true.,amass(1)=12.0107,amass(2)=1.00794,outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/Graphyne/GraphyneK/BOO',fildyn='GraphK.dyn' /-0.3363921 0.5833565 0.000000 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120903/8d45f0c5/attachment.htm From yuewen.fang at gmail.com Tue Sep 4 12:04:25 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 4 Sep 2012 18:04:25 +0800 Subject: [Pw_forum] How to plot bands perfectly with plotband.x? Message-ID: Dear all, I plotted a bands diagram with plotband.x, but there is some chaos in the diagram (namely the output file *bands.ps*). The diagram was put in the this website: http://www.douban.com/group/topic/32502443/ I also tried to save the bands.xmgr as bands.dat and load it to *origin 8.0 and Xmgrace*, but all failed. The problem still emerged. How to fix this program and curb the problem? Best Regards! -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120904/0478c1f8/attachment.htm From dalcorso at sissa.it Tue Sep 4 13:59:13 2012 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 04 Sep 2012 13:59:13 +0200 Subject: [Pw_forum] How to plot bands perfectly with plotband.x? In-Reply-To: References: Message-ID: <1346759953.28671.15.camel@ulisse.cm.sissa.it> You can try the flag lsym=.true. as input of bands.x and plot all the files that are produced by plotband.x. HTH, Andrea On Tue, 2012-09-04 at 18:04 +0800, Yue-Wen Fang wrote: > Dear all, > > > I plotted a bands diagram with plotband.x, but there is some chaos in > the diagram (namely the output file bands.ps). The diagram was put in > the this website: http://www.douban.com/group/topic/32502443/ > I also tried to save the bands.xmgr as bands.dat and load it to > origin 8.0 and Xmgrace, but all failed. The problem still emerged. > How to fix this program and curb the problem? > > > Best Regards! > > > -- > ---- > Yue-Wen Fang > > > > > > _______________________________________________ > 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 Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From yuewen.fang at gmail.com Tue Sep 4 14:12:27 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 4 Sep 2012 20:12:27 +0800 Subject: [Pw_forum] How to plot bands perfectly with plotband.x? In-Reply-To: <1346759953.28671.15.camel@ulisse.cm.sissa.it> References: <1346759953.28671.15.camel@ulisse.cm.sissa.it> Message-ID: I have use this way you said before, but just got two files name * bands-down-lsym.dat.rap* and *bands-down-lsym.dat*. What's more this flag lsym=.true. costs much more time in computing obviously with 4 processors. PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 2800 fyw 16 0 77416 33m 3332 R 89.9 0.2 5:53.96 bands.x 2834 fyw 16 0 76864 33m 3092 R 89.6 0.2 5:46.15 bands.x 2863 fyw 16 0 76344 33m 3092 R 89.6 0.2 5:48.02 bands.x 2805 fyw 16 0 76992 33m 3092 R 86.9 0.2 5:34.04 bands.x 2012/9/4 Andrea Dal Corso > You can try the flag lsym=.true. as input of bands.x and plot all the > files that are produced by plotband.x. > > HTH, > > Andrea > > On Tue, 2012-09-04 at 18:04 +0800, Yue-Wen Fang wrote: > > Dear all, > > > > > > I plotted a bands diagram with plotband.x, but there is some chaos in > > the diagram (namely the output file bands.ps). The diagram was put in > > the this website: http://www.douban.com/group/topic/32502443/ > > I also tried to save the bands.xmgr as bands.dat and load it to > > origin 8.0 and Xmgrace, but all failed. The problem still emerged. > > How to fix this program and curb the problem? > > > > > > Best Regards! > > > > > > -- > > ---- > > Yue-Wen Fang > > > > > > > > > > > > _______________________________________________ > > 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 Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120904/ae05f0e0/attachment.htm From dalcorso at sissa.it Tue Sep 4 14:18:23 2012 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 04 Sep 2012 14:18:23 +0200 Subject: [Pw_forum] How to plot bands perfectly with plotband.x? In-Reply-To: References: <1346759953.28671.15.camel@ulisse.cm.sissa.it> Message-ID: <1346761103.28671.23.camel@ulisse.cm.sissa.it> Now use plotband.x on bands-down-lsym.dat. Plotband.x reads also the .rap file and produces several files that you can plot with a graphical program. Andrea On Tue, 2012-09-04 at 20:12 +0800, Yue-Wen Fang wrote: > I have use this way you said before, but just got two files > name bands-down-lsym.dat.rap and bands-down-lsym.dat. > What's more this flag lsym=.true. costs much more time in computing > obviously with 4 processors. > > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > > 2800 fyw 16 0 77416 33m 3332 R 89.9 0.2 5:53.96 bands.x > > 2834 fyw 16 0 76864 33m 3092 R 89.6 0.2 5:46.15 bands.x > > 2863 fyw 16 0 76344 33m 3092 R 89.6 0.2 5:48.02 bands.x > > 2805 fyw 16 0 76992 33m 3092 R 86.9 0.2 5:34.04 bands.x > > 2012/9/4 Andrea Dal Corso > You can try the flag lsym=.true. as input of bands.x and plot > all the > files that are produced by plotband.x. > > HTH, > > Andrea > > On Tue, 2012-09-04 at 18:04 +0800, Yue-Wen Fang wrote: > > Dear all, > > > > > > I plotted a bands diagram with plotband.x, but there is some > chaos in > > the diagram (namely the output file bands.ps). The diagram > was put in > > the this website: > http://www.douban.com/group/topic/32502443/ > > I also tried to save the bands.xmgr as bands.dat and load it > to > > origin 8.0 and Xmgrace, but all failed. The problem still > emerged. > > How to fix this program and curb the problem? > > > > > > Best Regards! > > > > > > -- > > ---- > > Yue-Wen Fang > > > > > > > > > > > > > _______________________________________________ > > 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 Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ---- > Yue-Wen Fang > > > > > > > _______________________________________________ > 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 Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From yuewen.fang at gmail.com Tue Sep 4 14:40:26 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 4 Sep 2012 20:40:26 +0800 Subject: [Pw_forum] How to plot bands perfectly with plotband.x? In-Reply-To: <1346761103.28671.23.camel@ulisse.cm.sissa.it> References: <1346759953.28671.15.camel@ulisse.cm.sissa.it> <1346761103.28671.23.camel@ulisse.cm.sissa.it> Message-ID: Dear Andrea, Thank you very much! Owning to your help, I have got a perfect bands diagram without abnormal lines. Your instruction plays a significant role in curbing this problem. Many thanks! Yuewen Fang 2012/9/4 Andrea Dal Corso > Now use plotband.x on bands-down-lsym.dat. Plotband.x reads also > the .rap file and produces several files that you can plot with > a graphical program. > > Andrea > > > On Tue, 2012-09-04 at 20:12 +0800, Yue-Wen Fang wrote: > > I have use this way you said before, but just got two files > > name bands-down-lsym.dat.rap and bands-down-lsym.dat. > > What's more this flag lsym=.true. costs much more time in computing > > obviously with 4 processors. > > > > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > > > > 2800 fyw 16 0 77416 33m 3332 R 89.9 0.2 5:53.96 bands.x > > > > 2834 fyw 16 0 76864 33m 3092 R 89.6 0.2 5:46.15 bands.x > > > > 2863 fyw 16 0 76344 33m 3092 R 89.6 0.2 5:48.02 bands.x > > > > 2805 fyw 16 0 76992 33m 3092 R 86.9 0.2 5:34.04 bands.x > > > > 2012/9/4 Andrea Dal Corso > > You can try the flag lsym=.true. as input of bands.x and plot > > all the > > files that are produced by plotband.x. > > > > HTH, > > > > Andrea > > > > On Tue, 2012-09-04 at 18:04 +0800, Yue-Wen Fang wrote: > > > Dear all, > > > > > > > > > I plotted a bands diagram with plotband.x, but there is some > > chaos in > > > the diagram (namely the output file bands.ps). The diagram > > was put in > > > the this website: > > http://www.douban.com/group/topic/32502443/ > > > I also tried to save the bands.xmgr as bands.dat and load it > > to > > > origin 8.0 and Xmgrace, but all failed. The problem still > > emerged. > > > How to fix this program and curb the problem? > > > > > > > > > Best Regards! > > > > > > > > > -- > > > ---- > > > Yue-Wen Fang > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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 Bonomea 265 Fax. 0039-040-3787249 > > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > ---- > > Yue-Wen Fang > > > > > > > > > > > > > > _______________________________________________ > > 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 Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120904/e124d6c5/attachment-0001.htm From onaiwu.kingsley.nosa at gmail.com Tue Sep 4 21:08:43 2012 From: onaiwu.kingsley.nosa at gmail.com (Onaiwu Kingsley Nosa) Date: Tue, 4 Sep 2012 20:08:43 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 63, Issue 7 In-Reply-To: References: Message-ID: Dear all, Kindly help me with a sample input file to lambda.x. Thanks, Kingsley Onaiwu From tube77 at gmail.com Wed Sep 5 01:04:39 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Tue, 04 Sep 2012 18:04:39 -0500 Subject: [Pw_forum] vc-relax : total force does not converge Message-ID: Dear QE users, I'm having a difficulty on a geometry optimization using 'vc-relax'. I searched forum threads and followed various suggestions but the 'Total force' still does not converge.. (but the pressures seems to be converged) The job steps I've taken as follows, 1. optimized k-point and ecutwfc. 2. optimized lattice parameter using Murnaghan fitting. 3. 'relax' the geometry using the lattice constant obtained from step2, ---------------------------------------------- &control calculation = 'relax', restart_mode = 'from_scratch', prefix = '$NAME', pseudo_dir = '$PSEUDO_DIR/', outdir = '$OUT_DIR/', wf_collect = .TRUE. tstress = .TRUE. tprnfor = .TRUE. etot_conv_thr = 1.d-7 forc_conv_thr = 1.d-6 nstep = 1000 / &system ibrav = 0, celldm(1) = 10.3345 nat = 18, ntyp = 2, ecutwfc = 80.0, / &electrons diagonalization = 'cg', mixing_mode = 'plain', mixing_beta = 0.7, conv_thr = 1.0d-10, / &ions ion_dynamics = 'bfgs' bfgs_ndim = 3 / ATOMIC_SPECIES Si 28.086 Si.pbe-rrkj.UPF H 1.0079 H.pbe-vbc.UPF CELL_PARAMETERS 4.89897948556636 0.00000000000000 0.00000000000000 0.00000000000000 5.19615242270663 0.00000000000000 0.00000000000000 0.00000000000000 0.70710678118655 ATOMIC_POSITIONS angstrom Si 6.65158939652772 10.19066526389879 0.00000000000000 Si 7.76018762928234 9.40676793590657 1.92014846431207 Si 9.97738409479158 10.19066526389879 1.92014846431207 Si 11.08598232754620 9.40676793590657 0.00000000000000 Si 13.30317879305544 10.19066526389879 0.00000000000000 Si 14.41177702581006 9.40676793590657 1.92014846431207 Si 16.62897349131930 10.19066526389879 1.92014846431207 Si 17.73757172407392 9.40676793590657 0.00000000000000 H 6.65158939652772 11.67767298594874 0.00000000000000 H 7.76018762928234 7.91976021385662 1.92014846431207 H 9.97738409479158 11.67767298594874 1.92014846431207 H 11.08598232754620 7.91976021385662 0.00000000000000 H 13.30317879305544 11.67767298594874 0.00000000000000 H 14.41177702581006 7.91976021385662 1.92014846431207 H 16.62897349131930 11.67767298594874 1.92014846431207 H 17.73757172407392 7.91976021385662 0.00000000000000 H 5.24962507127668 9.69499602321547 0.00000000000000 H 19.13953604932496 9.90243717658989 0.00000000000000 K_POINTS automatic 1 1 16 0 0 0 ---------------------------------------------- 4. check if 'Total force' is converged -> OK. 5. Take the final atomic coordinates from step4. 6. Run 'vc-relax' as, ---------------------------------------------- &control calculation = 'vc-relax', restart_mode = 'from_scratch', prefix = '$NAME', pseudo_dir = '$PSEUDO_DIR/', outdir = '$OUT_DIR/', wf_collect = .TRUE. tstress = .TRUE. tprnfor = .TRUE. etot_conv_thr = 1.d-6 forc_conv_thr = 1.d-6 nstep = 10000 / &system ibrav = 0, celldm(1) = 10.3345 nat = 18, ntyp = 2, ecutwfc = 80.0, ecfixed = 70.0, qcutz = 150.0, q2sigma = 4.0, / &electrons diagonalization = 'cg', mixing_mode = 'plain', mixing_beta = 0.7, conv_thr = 1.0d-10, / &ions ion_dynamics = 'bfgs' bfgs_ndim = 3 / &cell cell_dynamics = 'bfgs' press_conv_thr = 0.1d0 press = 0.d0 cell_factor = 2.d0 / ATOMIC_SPECIES Si 28.086 Si.pbe-rrkj.UPF H 1.0079 H.pbe-vbc.UPF CELL_PARAMETERS 4.89897948556636 0.00000000000000 0.00000000000000 0.00000000000000 5.19615242270663 0.00000000000000 0.00000000000000 0.00000000000000 0.70710678118655 ATOMIC_POSITIONS angstrom Si 6.595371055 10.174313717 -0.005918138 Si 7.697686348 9.425353751 1.927575025 Si 9.940638827 10.152944754 1.927571298 Si 11.073523827 9.431959516 -0.005942277 Si 13.315586210 10.165270258 -0.005944217 Si 14.448496999 9.444343582 1.927568680 Si 16.691414457 10.172072841 1.927571881 Si 17.793848036 9.423269303 -0.005921592 H 6.597479872 11.672720999 -0.006012302 H 7.704912055 7.923796337 1.927472273 H 9.942740551 11.655007902 1.927566837 H 11.078852672 7.930134628 -0.005961188 H 13.310208995 11.667097994 -0.005963695 H 14.446478909 7.942288221 1.927563469 H 16.684085788 11.673634035 1.927468080 H 17.791980426 7.924865718 -0.006016781 H 5.166205416 9.718188689 -0.005743345 H 19.222939638 9.879636554 -0.005746296 K_POINTS automatic 1 1 16 0 0 0 ---------------------------------------------- Then the output 'Total force' seems to oscillates and does not converge as shown below, ---------------------------------------------------------------------------- ------------- Total force = 0.000723 Total SCF correction = 0.000009 Total force = 0.000288 Total SCF correction = 0.000010 Total force = 0.000172 Total SCF correction = 0.000001 Total force = 0.000227 Total SCF correction = 0.000005 Total force = 0.000323 Total SCF correction = 0.000005 Total force = 0.000327 Total SCF correction = 0.000004 Total force = 0.000393 Total SCF correction = 0.000004 Total force = 0.000682 Total SCF correction = 0.000004 Total force = 0.000811 Total SCF correction = 0.000006 Total force = 0.000803 Total SCF correction = 0.000007 Total force = 0.000427 Total SCF correction = 0.000001 Total force = 0.000392 Total SCF correction = 0.000002 Total force = 0.000380 Total SCF correction = 0.000001 Total force = 0.000233 Total SCF correction = 0.000001 Total force = 0.000164 Total SCF correction = 0.000001 Total force = 0.000227 Total SCF correction = 0.000001 Total force = 0.000246 Total SCF correction = 0.000000 Total force = 0.000299 Total SCF correction = 0.000001 Total force = 0.000320 Total SCF correction = 0.000001 Total force = 0.000230 Total SCF correction = 0.000001 Total force = 0.000129 Total SCF correction = 0.000001 Total force = 0.000147 Total SCF correction = 0.000000 Total force = 0.000131 Total SCF correction = 0.000001 Total force = 0.000104 Total SCF correction = 0.000000 Total force = 0.000116 Total SCF correction = 0.000001 Total force = 0.000146 Total SCF correction = 0.000000 Total force = 0.000180 Total SCF correction = 0.000001 Total force = 0.000195 Total SCF correction = 0.000000 Total force = 0.000193 Total SCF correction = 0.000001 Total force = 0.000194 Total SCF correction = 0.000001 Total force = 0.000208 Total SCF correction = 0.000000 Total force = 0.000271 Total SCF correction = 0.000001 Total force = 0.000336 Total SCF correction = 0.000000 Total force = 0.000350 Total SCF correction = 0.000001 Total force = 0.000355 Total SCF correction = 0.000001 Total force = 0.000356 Total SCF correction = 0.000001 Total force = 0.000351 Total SCF correction = 0.000000 Total force = 0.000364 Total SCF correction = 0.000000 Total force = 0.000437 Total SCF correction = 0.000000 Total force = 0.000509 Total SCF correction = 0.000000 Total force = 0.000542 Total SCF correction = 0.000002 Total force = 0.000520 Total SCF correction = 0.000001 ---------------------------------------------------------------------------- ------------- I also previously tried without ecfixed, qcutz, q2sigma options but the force did not converge as well. Any suggestions would be greatly appreciated. Thank you. Sincerely, JISEOK KIM, Ph.D. Postdoctoral Research Associate Department of Materials Science and Engineering University of Texas at Dallas 800 W. Campbell Rd. RL10 Richardson, TX 75080 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120904/a0016c76/attachment-0001.htm From rameshchitumalla at gmail.com Wed Sep 5 05:32:11 2012 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Wed, 5 Sep 2012 09:02:11 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 63, Issue 8 In-Reply-To: References: Message-ID: Dear JISEOK KIM, Did you check/visualize your geometry ? The Box is too small and it is far from the Si-H system. > I'm having a difficulty on a geometry optimization using 'vc-relax'. > I searched forum threads and followed various suggestions but the 'Total > force' still does not converge.. > (but the pressures seems to be converged) > > The job steps I've taken as follows, > > 1. optimized k-point and ecutwfc. > 2. optimized lattice parameter using Murnaghan fitting. > 3. 'relax' the geometry using the lattice constant obtained from step2, > > ---------------------------------------------- > &control > calculation = 'relax', > restart_mode = 'from_scratch', > prefix = '$NAME', > pseudo_dir = '$PSEUDO_DIR/', > outdir = '$OUT_DIR/', > wf_collect = .TRUE. > tstress = .TRUE. > tprnfor = .TRUE. > etot_conv_thr = 1.d-7 > forc_conv_thr = 1.d-6 > nstep = 1000 > / > &system > ibrav = 0, > celldm(1) = 10.3345 > nat = 18, > ntyp = 2, > ecutwfc = 80.0, > / > &electrons > diagonalization = 'cg', > mixing_mode = 'plain', > mixing_beta = 0.7, > conv_thr = 1.0d-10, > / > &ions > ion_dynamics = 'bfgs' > bfgs_ndim = 3 > / > ATOMIC_SPECIES > Si 28.086 Si.pbe-rrkj.UPF > H 1.0079 H.pbe-vbc.UPF > CELL_PARAMETERS > .......... > .......... > K_POINTS automatic > 1 1 16 0 0 0 > ---------------------------------------------- > > > 4. check if 'Total force' is converged -> OK. > 5. Take the final atomic coordinates from step4. > 6. Run 'vc-relax' as, > > ---------------------------------------------- > &control > calculation = 'vc-relax', > restart_mode = 'from_scratch', > prefix = '$NAME', > pseudo_dir = '$PSEUDO_DIR/', > outdir = '$OUT_DIR/', > wf_collect = .TRUE. > tstress = .TRUE. > tprnfor = .TRUE. > etot_conv_thr = 1.d-6 > forc_conv_thr = 1.d-6 > nstep = 10000 > / > &system > ibrav = 0, > celldm(1) = 10.3345 > nat = 18, > ntyp = 2, > ecutwfc = 80.0, > ecfixed = 70.0, > qcutz = 150.0, > q2sigma = 4.0, > / > &electrons > diagonalization = 'cg', > mixing_mode = 'plain', > mixing_beta = 0.7, > conv_thr = 1.0d-10, > / > &ions > ion_dynamics = 'bfgs' > bfgs_ndim = 3 > / > &cell > cell_dynamics = 'bfgs' > press_conv_thr = 0.1d0 > press = 0.d0 > cell_factor = 2.d0 > / > ATOMIC_SPECIES > Si 28.086 Si.pbe-rrkj.UPF > H 1.0079 H.pbe-vbc.UPF > --------- > ---------- > K_POINTS automatic > 1 1 16 0 0 0 > ---------------------------------------------- > > > -- *With Best Regards: * *CH. Ramesh Kumar Senior Research Fellow, Computational Chemistry Lab, Indian Institute of Chemical Technology(IICT),* *Tarnaka, ** Hyderabad. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120905/302456f4/attachment.htm From tube77 at gmail.com Wed Sep 5 10:22:48 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Wed, 05 Sep 2012 03:22:48 -0500 Subject: [Pw_forum] vc-relax : total force does not converge In-Reply-To: Message-ID: Dear, Dr. Kumar Yes. I checked the geometry before and after the 'relax' which looks ok ... The atomic distance between neighboring atoms about 12A along x-direction and about 24A along y-direction.. The vacuum region along x-direction might not be large enough but I believe it wouldn't be a problem having considered that the 10~15A of vacuum region usually is accepted. (Please correct me if I'm wrong.) Could I ask what you mean by 'it is far from the Si-H system' ? Thank you very much. Best regards, Jiseok Kim On 9/5/12 2:51 AM, "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: Pw_forum Digest, Vol 63, Issue 8 (Ramesh Kumar) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 5 Sep 2012 09:02:11 +0530 >From: Ramesh Kumar >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 63, Issue 8 >To: pw_forum at pwscf.org >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Dear JISEOK KIM, > >Did you check/visualize your geometry ? > >The Box is too small and it is far from the Si-H system. > > > > >> I'm having a difficulty on a geometry optimization using 'vc-relax'. >> I searched forum threads and followed various suggestions but the 'Total >> force' still does not converge.. >> (but the pressures seems to be converged) >> >> The job steps I've taken as follows, >> >> 1. optimized k-point and ecutwfc. >> 2. optimized lattice parameter using Murnaghan fitting. >> 3. 'relax' the geometry using the lattice constant obtained from step2, >> >> ---------------------------------------------- >> &control >> calculation = 'relax', >> restart_mode = 'from_scratch', >> prefix = '$NAME', >> pseudo_dir = '$PSEUDO_DIR/', >> outdir = '$OUT_DIR/', >> wf_collect = .TRUE. >> tstress = .TRUE. >> tprnfor = .TRUE. >> etot_conv_thr = 1.d-7 >> forc_conv_thr = 1.d-6 >> nstep = 1000 >> / >> &system >> ibrav = 0, >> celldm(1) = 10.3345 >> nat = 18, >> ntyp = 2, >> ecutwfc = 80.0, >> / >> &electrons >> diagonalization = 'cg', >> mixing_mode = 'plain', >> mixing_beta = 0.7, >> conv_thr = 1.0d-10, >> / >> &ions >> ion_dynamics = 'bfgs' >> bfgs_ndim = 3 >> / >> ATOMIC_SPECIES >> Si 28.086 Si.pbe-rrkj.UPF >> H 1.0079 H.pbe-vbc.UPF >> CELL_PARAMETERS >> .......... >> > .......... > >> K_POINTS automatic >> 1 1 16 0 0 0 >> ---------------------------------------------- >> >> >> 4. check if 'Total force' is converged -> OK. >> 5. Take the final atomic coordinates from step4. >> 6. Run 'vc-relax' as, >> >> ---------------------------------------------- >> &control >> calculation = 'vc-relax', >> restart_mode = 'from_scratch', >> prefix = '$NAME', >> pseudo_dir = '$PSEUDO_DIR/', >> outdir = '$OUT_DIR/', >> wf_collect = .TRUE. >> tstress = .TRUE. >> tprnfor = .TRUE. >> etot_conv_thr = 1.d-6 >> forc_conv_thr = 1.d-6 >> nstep = 10000 >> / >> &system >> ibrav = 0, >> celldm(1) = 10.3345 >> nat = 18, >> ntyp = 2, >> ecutwfc = 80.0, >> ecfixed = 70.0, >> qcutz = 150.0, >> q2sigma = 4.0, >> / >> &electrons >> diagonalization = 'cg', >> mixing_mode = 'plain', >> mixing_beta = 0.7, >> conv_thr = 1.0d-10, >> / >> &ions >> ion_dynamics = 'bfgs' >> bfgs_ndim = 3 >> / >> &cell >> cell_dynamics = 'bfgs' >> press_conv_thr = 0.1d0 >> press = 0.d0 >> cell_factor = 2.d0 >> / >> ATOMIC_SPECIES >> Si 28.086 Si.pbe-rrkj.UPF >> H 1.0079 H.pbe-vbc.UPF >> --------- >> > ---------- > >> K_POINTS automatic >> 1 1 16 0 0 0 >> ---------------------------------------------- >> >> >> >-- >*With Best Regards: > >* >*CH. Ramesh Kumar >Senior Research Fellow, >Computational Chemistry Lab, >Indian Institute of Chemical Technology(IICT),* >*Tarnaka, ** >Hyderabad. >* >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://www.democritos.it/pipermail/pw_forum/attachments/20120905/302456f4/ >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 63, Issue 9 >*************************************** From lorenzo.paulatto at impmc.upmc.fr Wed Sep 5 12:06:18 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 5 Sep 2012 12:06:18 +0200 Subject: [Pw_forum] vc-relax : total force does not converge In-Reply-To: References: Message-ID: On 5 September 2012 10:22, Jiseok Kim wrote: > Yes. I checked the geometry before and after the 'relax' which looks ok ... > The atomic distance between neighboring atoms about 12A along x-direction > and about 24A along y-direction.. > The vacuum region along x-direction might not be large enough but I > believe it wouldn't be a problem having considered that the 10~15A of > vacuum region usually is accepted. (Please correct me if I'm wrong.) > I think your forc_conv_thr is just too low, if you want to reach that ridiculous precision you need to reduce the conv_thr and/or increase upscale. I have a couple more observations: 1. why are you using "cg" diagonalization? If the electronic calculation does not converge with the default algorithm, there is probably a problem in your input; changing algorithm will just mask it. 2. why are you mixing ultrasoft (Si) and norm-conserving (H) pseudopotentials? It is not forbidden, but you get the worst of both methods: high wfc cutoff (NC) and high charge density cutoff (US). 3. does it make sense to do vc-relax in a isolated 1D system? Can't the system just rotate if it wants more space? bests regards, and good work -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120905/79086103/attachment.htm From kucukben at sissa.it Wed Sep 5 18:21:34 2012 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 05 Sep 2012 18:21:34 +0200 Subject: [Pw_forum] GIPAW problems In-Reply-To: <20120903142113.M49782@ifj.edu.pl> References: <20120903142113.M49782@ifj.edu.pl> Message-ID: <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> Hi all, Just to update the forum: The problem mentioned in this thread has been solved by the use of occupations='fixed' instead of smearing methods. This might be a good time to remind interested users that the QE-GIPAW implementation is only for insulators for the time being. Although not always, but with some compilers, the unexpected insulator+smearing input configuration could give wrong results as we have seen here. Currently, Davide Ceresoli is updating the code to include metallic systems as well, with this development the mentioned 'bug' would no more appear starting from the next release. Thanks for your feedback! - emine kucukbenli postdoc, epfl, switzerland Quoting Zbigniew Lodziana : > Dear Forum Users & Developers, > > I am new in QE Forum - welcome to All & congratulations for excellent > information exchange here and software. > > Being new in GIPAW calculations I might have missed the answer browsing the > Forum but did not found solution yet. > > The problem is that I am somehow puzzled by GIPAW calculations: > > - Using QE 5.0 I did compile it with Intel Fortran, MKL, openmp (more details > below). No tuning, no tricks etc. just followed installation guide > (./configure & make all). > > - While pw.x performs nicely, gipaw.x gives results that are difficult for > interpretation, and I cannot really locate where the problem is. > > - Both pw.x and gipaw.x pass self-test; examples were no problem too. > > However, trying to calculate NMR spectra for slightly complex system > calculations with GIPAW give results that seems to be machine > dependent to the > large extend. > > Input files and part of output are at the end; shortly "Total NMR chemical > shifts in ppm:" is either 16.58 or 134.05 for the same system/element (inputs > are simply copied) when calculated on two similar machines. > > Both computers are Intel based, compiler and libraries differ however: > a) intel 11.1 (ifort); mkl 10.3 > b) intel 11.1 (ifort); mkl 10.2.5.035 > > Playing with pseudopotentials, k-points make things even worse.., denser fft > grid, density cutoff does not seems to improve results either). I use several > other numerical codes on both machines - never had similar problems. > > I would highly appreciate any suggestions/help toward resolving this problem. > > best regards & thank you in advance, > Zibi > > Zbigniew Lodziana > Polish Academy of Sciences, > ul.. Radzikowskiego 152, > PL-31-342 Krakow > ==================================================================== From suyaqiong1988 at 163.com Thu Sep 6 04:31:31 2012 From: suyaqiong1988 at 163.com (yqsu) Date: Thu, 6 Sep 2012 10:31:31 +0800 Subject: [Pw_forum] clock shew detected Message-ID: <000001cd8bd7$bbf77a40$33e66ec0$@com> Dear sir , When I make the Quantum-Espresso , a problem always appeared about clock skew detected , so I want to know a good way to kill this problem . Thank you for your help . Best wishes ! Su Yaqiong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/6a0fe4af/attachment.htm From prasenjit.jnc at gmail.com Thu Sep 6 05:02:45 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 6 Sep 2012 08:32:45 +0530 Subject: [Pw_forum] GIPAW problems In-Reply-To: <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> Message-ID: In addition to Emine's response I would also like to mention that occupations='fixed' is available only for calculations with a gamma k-point. So for your case you need to use a supercell. Also when you do the gamma-point calculations, set K_POINT{automatic} with 1 1 1 0 0 0 mesh because gipaw does not work with the gamma-point specific subroutines. At least this is the case for version 4.3.2. I do not know whether this has been improved in 5.0 With regards, Prasenjit On 5 September 2012 21:51, Emine Kucukbenli wrote: > Hi all, > Just to update the forum: > The problem mentioned in this thread has been solved by the use of > occupations='fixed' instead of smearing methods. > This might be a good time to remind interested users that the QE-GIPAW > implementation is only for insulators for the time being. Although not > always, but with some compilers, the unexpected insulator+smearing > input configuration could give wrong results as we have seen here. > Currently, Davide Ceresoli is updating the code to include metallic > systems as well, with this development the mentioned 'bug' would no > more appear starting from the next release. > Thanks for your feedback! > - > emine kucukbenli > postdoc, epfl, switzerland > > > Quoting Zbigniew Lodziana : > > > Dear Forum Users & Developers, > > > > I am new in QE Forum - welcome to All & congratulations for excellent > > information exchange here and software. > > > > Being new in GIPAW calculations I might have missed the answer browsing > the > > Forum but did not found solution yet. > > > > The problem is that I am somehow puzzled by GIPAW calculations: > > > > - Using QE 5.0 I did compile it with Intel Fortran, MKL, openmp (more > details > > below). No tuning, no tricks etc. just followed installation guide > > (./configure & make all). > > > > - While pw.x performs nicely, gipaw.x gives results that are difficult > for > > interpretation, and I cannot really locate where the problem is. > > > > - Both pw.x and gipaw.x pass self-test; examples were no problem too. > > > > However, trying to calculate NMR spectra for slightly complex system > > calculations with GIPAW give results that seems to be machine > > dependent to the > > large extend. > > > > Input files and part of output are at the end; shortly "Total NMR > chemical > > shifts in ppm:" is either 16.58 or 134.05 for the same system/element > (inputs > > are simply copied) when calculated on two similar machines. > > > > Both computers are Intel based, compiler and libraries differ however: > > a) intel 11.1 (ifort); mkl 10.3 > > b) intel 11.1 (ifort); mkl 10.2.5.035 > > > > Playing with pseudopotentials, k-points make things even worse.., denser > fft > > grid, density cutoff does not seems to improve results either). I use > several > > other numerical codes on both machines - never had similar problems. > > > > I would highly appreciate any suggestions/help toward resolving this > problem. > > > > best regards & thank you in advance, > > Zibi > > > > Zbigniew Lodziana > > Polish Academy of Sciences, > > ul.. Radzikowskiego 152, > > PL-31-342 Krakow > > ==================================================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/0068671c/attachment-0001.htm From tube77 at gmail.com Thu Sep 6 06:06:23 2012 From: tube77 at gmail.com (Jiseok Kim) Date: Wed, 05 Sep 2012 23:06:23 -0500 Subject: [Pw_forum] vc-relax : total force does not converge (Lorenzo Paulatto) In-Reply-To: Message-ID: Dear, Dr. Lorenzo Paulatto Thank you very much Dr. Paulatto. I'm learning the DFT by myself so there's still lots of things that I have to learn. Regarding the 'forc_conv_thr', I agree with you. Originally I set it to 10^-4 and it converged with both 'relax' and 'vc-relax'. But what happened is that I got negative frequencies (spaghetti-like over the 1D BZ) when I calculate the phonon dispersion. So I decided to go back to the geometry optimization and pushed the 'forc_conv_thr' even lower. I admit that I fail to notice if the 10^6 was too low precision.. 1. why are you using "cg" diagonalization? If the electronic calculation does not converge with the default algorithm, there is probably a problem in your input; changing algorithm will just mask it. => I don't think I have a problem with 'cg' diagonalization.. It converges mostly within 10 iterations.. 2. why are you mixing ultrasoft (Si) and norm-conserving (H) pseudopotentials? It is not forbidden, but you get the worst of both methods: high wfc cutoff (NC) and high charge density cutoff (US). => I'm using 'Si.pbe-rrkj.UPF' and 'H.pbe-vbc.UPF'. As long as I understand, both pseudopotentials are norm-conserving.. Please correct me if I'm wrong. I appreciate your point regarding the mixing that I haven't thought of. 3. does it make sense to do vc-relax in a isolated 1D system? Can't the system just rotate if it wants more space? => I very appreciate that you point this out. I want to learn and hear some advice whether the 'relax' or 'vc-relax' is more appropriate for the isolated system (1D and 2D).. As I've done, the 'relax' does not dramatically modify the geometry. There's only tiny differences in bonding lengths and bonding angles .. As I mentioned, I decided to 'vc-relax' because of the negative frequencies of phonon dispersion.. (I already try to decrease the 'tr2_ph' and 'conv_thr' when doing ph.x) I'm not sure if the negative frequency indicates the 'real' instability or not.. But as far as I understand from literatures this geometry is supposed to be stable.. Also, I'm not sure if the 'vc-relax' can fix the problem.. Thank you very much again. If there is anything that I'm thinking wrong, please correct me. Sincerely, Jiseok Kim > >Message: 2 >Date: Wed, 5 Sep 2012 12:06:18 +0200 >From: Lorenzo Paulatto >Subject: Re: [Pw_forum] vc-relax : total force does not converge >To: PWSCF Forum >Cc: rameshchitumalla at gmail.com, > CAO1fJnvo6EhnZUdMYhURsg2Y9fDQimng16PYiqLUOUCgfCXFFw at mail.gmail.com >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >On 5 September 2012 10:22, Jiseok Kim wrote: > >> Yes. I checked the geometry before and after the 'relax' which looks ok >>... >> The atomic distance between neighboring atoms about 12A along >>x-direction >> and about 24A along y-direction.. >> The vacuum region along x-direction might not be large enough but I >> believe it wouldn't be a problem having considered that the 10~15A of >> vacuum region usually is accepted. (Please correct me if I'm wrong.) >> > >I think your forc_conv_thr is just too low, if you want to reach that >ridiculous precision you need to reduce the conv_thr and/or increase >upscale. I have a couple more observations: > >1. why are you using "cg" diagonalization? If the electronic calculation >does not converge with the default algorithm, there is probably a problem >in your input; changing algorithm will just mask it. >2. why are you mixing ultrasoft (Si) and norm-conserving (H) >pseudopotentials? It is not forbidden, but you get the worst of both >methods: high wfc cutoff (NC) and high charge density cutoff (US). >3. does it make sense to do vc-relax in a isolated 1D system? Can't the >system just rotate if it wants more space? > >bests regards, and good work > >-- >Dr. Lorenzo Paulatto >IdR @ IMPMC -- CNRS & Universit? Paris 6 >phone: +33 (0)1 44275 084 / skype: paulatz >www: http://www-int.impmc.upmc.fr/~paulatto/ >mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://www.democritos.it/pipermail/pw_forum/attachments/20120905/79086103/ >attachment-0001.htm > From elie.moujaes at hotmail.co.uk Thu Sep 6 06:59:58 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 6 Sep 2012 05:59:58 +0100 Subject: [Pw_forum] error when using dynmat.x Message-ID: Dear all, I am trying to get the frequncies of vibrations of a system using the executable dynmat.x but I am getting the error: Image PC Routine Line Source dynmat.x 000000000057FBAD Unknown Unknown Unknowndynmat.x 000000000057E6B5 Unknown Unknown Unknowndynmat.x 000000000052EB90 Unknown Unknown Unknowndynmat.x 00000000004C7A1F Unknown Unknown Unknowndynmat.x 00000000004C7252 Unknown Unknown Unknowndynmat.x 00000000004F9EC1 Unknown Unknown Unknowndynmat.x 0000000000405D53 MAIN__ 115 dynmat.f90dynmat.x 00000000004059DC Unknown Unknown Unknownlibc.so.6 00000036A2E1D974 Unknown Unknown Unknowndynmat.x 00000000004058E9 Unknown Unknown Unknown INPUT: fildyn='Graph.dynG'q(1)=0.0,q(2)=0.0,q(3)=0.0,asr='crystal',filout='Graph.dyn.modes'filxsf='Graph.dyn.axsf' Any help would be appreciated Thanks Elie MoukaesUninversity of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/d4f25117/attachment.htm From akohlmey at gmail.com Thu Sep 6 07:17:42 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 6 Sep 2012 05:17:42 +0000 Subject: [Pw_forum] clock shew detected In-Reply-To: <000001cd8bd7$bbf77a40$33e66ec0$@com> References: <000001cd8bd7$bbf77a40$33e66ec0$@com> Message-ID: <1307112208-1346908665-cardhu_decombobulator_blackberry.rim.net-834622210-@b13.c7.bise7.blackberry> This is an issue of your machine or cluster. It is caused by unsynchronized system clocks between the machine you compile on and its file server. Axel. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: "yqsu" Sender: pw_forum-bounces at pwscf.org Date: Thu, 6 Sep 2012 10:31:31 To: Reply-To: PWSCF Forum Cc: Subject: [Pw_forum] clock shew detected _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From Zbigniew.Lodziana at ifj.edu.pl Thu Sep 6 07:20:55 2012 From: Zbigniew.Lodziana at ifj.edu.pl (Zbigniew Lodziana) Date: Thu, 6 Sep 2012 07:20:55 +0200 Subject: [Pw_forum] GIPAW problems In-Reply-To: References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> Message-ID: <20120906051404.M18256@ifj.edu.pl> Dear Prasenjit & all, ?Thanks for you remark. Actually with kind help of Emine we did run calculations with occupancies "fixed" and with k-points and this seem to work & help. Thus i wonder if gamma point sampling is an additional limitation? If this is so it would result in prohibitive system sizes >1000 atoms.. (for other calculations not mentioned in this thread) I would appreciate clarification of this aspect. best regards, Zibi ---------- Original Message ----------- From: Prasenjit Ghosh To: PWSCF Forum Sent: Thu, 6 Sep 2012 08:32:45 +0530 Subject: Re: [Pw_forum] GIPAW problems > In addition to Emine's response I would also like to mention that occupations='fixed' is available only for calculations with a gamma k-point. So for your case you need to use a supercell. Also when you do the gamma-point calculations, set K_POINT{automatic} with 1 ?1 1 0 0 0 mesh because gipaw does not work with the gamma-point specific subroutines. > At least this is the case for version 4.3.2. I do not know whether this has been improved in 5.0 > > With regards, > > Prasenjit > > On 5 September 2012 21:51, Emine Kucukbenli wrote: > Hi all, > Just to update the forum: > The problem mentioned in this thread has been solved by the use of > occupations='fixed' instead of smearing methods. > This might be a good time to remind interested users that the QE-GIPAW > implementation is only for insulators for the time being. Although not > always, but with some compilers, the unexpected insulator+smearing > input configuration could give wrong results as we have seen here. > Currently, Davide Ceresoli is updating the code to include metallic > systems as well, with this development the mentioned 'bug' would no > more appear starting from the next release. > Thanks for your feedback! > - > emine kucukbenli > postdoc, epfl, switzerland > ------- End of Original Message ------- > > -- > PRASENJIT GHOSH, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/53a804b8/attachment.htm From giannozz at democritos.it Thu Sep 6 08:55:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 Sep 2012 08:55:38 +0200 Subject: [Pw_forum] error when using dynmat.x In-Reply-To: References: Message-ID: <489D3E6F-B354-40F6-AC4E-A4A23943BD8F@democritos.it> On Sep 6, 2012, at 6:59 , Elie M wrote: > Image PC Routine Line > Source > > dynmat.x 000000000057FBAD Unknown Unknown > Unknown > dynmat.x 000000000057E6B5 Unknown Unknown > Unknown > dynmat.x 000000000052EB90 Unknown Unknown > Unknown > dynmat.x 00000000004C7A1F Unknown Unknown > Unknown > dynmat.x 00000000004C7252 Unknown Unknown > Unknown > dynmat.x 00000000004F9EC1 Unknown Unknown > Unknown > dynmat.x 0000000000405D53 MAIN__ 115 > dynmat.f90 > dynmat.x 00000000004059DC Unknown Unknown > Unknown > libc.so.6 00000036A2E1D974 Unknown Unknown > Unknown > dynmat.x 00000000004058E9 Unknown Unknown > Unknown the only piece of information that comes out from your error message is that something happens at line 115 fo dynmat.f90. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lorenzo.paulatto at impmc.upmc.fr Thu Sep 6 08:57:34 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 6 Sep 2012 08:57:34 +0200 Subject: [Pw_forum] error when using dynmat.x In-Reply-To: References: Message-ID: On 6 September 2012 06:59, Elie M wrote: > dynmat.x 0000000000405D53 MAIN__ 115 > dynmat.f90 > > Dear Elie, this looks like a problem reading the input. > fildyn='Graph.dynG' > q(1)=0.0, > q(2)=0.0, > q(3)=0.0, > asr='crystal', > filout='Graph.dyn.modes' > filxsf='Graph.dyn.axsf' > > Did you bracket that input between "&input" and "/"? If you did, there may be strange characters in you input file. Check it with "cat -v input" bests > Any help would be appreciated > > Thanks > > Elie Moukaes > Uninversity of Notts > NG7 2RD > UK > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/2f492918/attachment-0001.htm From giannozz at democritos.it Thu Sep 6 08:58:06 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 Sep 2012 08:58:06 +0200 Subject: [Pw_forum] vc-relax : total force does not converge (Lorenzo Paulatto) In-Reply-To: References: Message-ID: <30F0F278-72F9-49F6-ACB6-FB7123EEC3B1@democritos.it> On Sep 6, 2012, at 6:06 , Jiseok Kim wrote: > => I don't think I have a problem with 'cg' diagonalization. maybe not, but it is usually slower than the default Davidson diagonalization P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wang.riping.81 at gmail.com Thu Sep 6 09:52:14 2012 From: wang.riping.81 at gmail.com (Riping Wang) Date: Thu, 6 Sep 2012 16:52:14 +0900 Subject: [Pw_forum] oscillation of P T in cp Message-ID: Dear developers, when I use vc-cp calculations in quantum espresso 5.0, I have a question: in this code, how much is normal oscillation of pressure and temperature that could be controlled? Thank you very much. WANG Riping 2012.9.6 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), +81-858-43-1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/c26d1152/attachment.htm From wang.riping.81 at gmail.com Thu Sep 6 09:54:24 2012 From: wang.riping.81 at gmail.com (Riping Wang) Date: Thu, 6 Sep 2012 16:54:24 +0900 Subject: [Pw_forum] supercell for cpmd Message-ID: Dear developers, when I use cpmd in quantum espresso, I have a question: In this code , is it better to use supercell for achieving a stable pressure and temperature? Thank you very much. WANG Riping 2012.9.6 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), +81-858-43-1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/2e446c02/attachment.htm From prasenjit.jnc at gmail.com Thu Sep 6 10:51:43 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 6 Sep 2012 14:21:43 +0530 Subject: [Pw_forum] GIPAW problems In-Reply-To: <20120906051404.M18256@ifj.edu.pl> References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> <20120906051404.M18256@ifj.edu.pl> Message-ID: Dear Zibi, I am not sure about that. I checked the documentation of QE 5.0 (INPUT_PW.txt).....it says that now one can perform calculations with occupations='fixed' for more than one k-point, however, you need to set nbnd. I tried to do the calculation with a simple example given below: &control calculation='scf', restart_mode='from_scratch', pseudo_dir='/pghosh/pslibrary.0.2.2/pbe/WORK/test/' outdir='./' ! verbosity='high' / &system ibrav=1, celldm(1)=14.0, nat=1, ntyp=1, nbnd=13, nosym=.true., ecutwfc=27.0, ecutrho=216.0, occupations='from_input', / &electrons mixing_beta=0.25, conv_thr=1.0E-8, / ATOMIC_SPECIES O 15.99994 O.pbe-gipaw_uspp.UPF ATOMIC_POSITIONS O 0.000000000 0.000000000 0.000000000 K_POINTS {automatic} 2 2 2 0 0 0 OCCUPATIONS 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.1073 0.1071 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0614 0.0431 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0614 0.0520 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0719 0.0528 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0616 0.0377 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0608 0.0529 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0678 0.0531 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1250 0.0548 0.0544 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 However, the code is reading only the first 13 values and ignoring the rest of them. I do not know why. Also today while trying to download gipaw, it says they have removed version 5.0 because of a bug with USPP. Any comments on this will be highly appreciated. With regards, Prasenjit On 6 September 2012 10:50, Zbigniew Lodziana wrote: > Dear Prasenjit & all, > > Thanks for you remark. > > Actually with kind help of Emine we did run calculations with occupancies > "fixed" and with k-points and this seem to work & help. Thus i wonder if > gamma point sampling is an additional limitation? > If this is so it would result in prohibitive system sizes >1000 atoms.. > (for other calculations not mentioned in this thread) > > I would appreciate clarification of this aspect. > > best regards, > Zibi > > *---------- Original Message -----------* > From: Prasenjit Ghosh > To: PWSCF Forum > Sent: Thu, 6 Sep 2012 08:32:45 +0530 > Subject: Re: [Pw_forum] GIPAW problems > > > In addition to Emine's response I would also like to mention that > occupations='fixed' is available only for calculations with a gamma > k-point. So for your case you need to use a supercell. Also when you do the > gamma-point calculations, set K_POINT{automatic} with 1 1 1 0 0 0 mesh > because gipaw does not work with the gamma-point specific subroutines. > > At least this is the case for version 4.3.2. I do not know whether this > has been improved in 5.0 > > > > With regards, > > > > Prasenjit > > > > On 5 September 2012 21:51, Emine Kucukbenli wrote: > > > >> Hi all, >> > Just to update the forum: >> > The problem mentioned in this thread has been solved by the use of >> > occupations='fixed' instead of smearing methods. >> > This might be a good time to remind interested users that the QE-GIPAW >> > implementation is only for insulators for the time being. Although not >> > always, but with some compilers, the unexpected insulator+smearing >> > input configuration could give wrong results as we have seen here. >> > Currently, Davide Ceresoli is updating the code to include metallic >> > systems as well, with this development the mentioned 'bug' would no >> > more appear starting from the next release. >> > Thanks for your feedback! >> > - >> > emine kucukbenli >> > postdoc, epfl, switzerland >> > ------- End of Original Message ------- >> > > > > -- > > PRASENJIT GHOSH, > > IISER Pune, > > First floor, Central Tower, Sai Trinity Building > > Garware Circle, Sutarwadi, Pashan > > Pune, Maharashtra 411021, India > > > > Phone: +91 (20) 2590 8203 > > Fax: +91 (20) 2589 9790 > -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/db27f675/attachment.htm From gabriele.sclauzero at epfl.ch Thu Sep 6 11:31:53 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 6 Sep 2012 11:31:53 +0200 Subject: [Pw_forum] GIPAW problems In-Reply-To: References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> <20120906051404.M18256@ifj.edu.pl> Message-ID: Hello, Il giorno 06/set/2012, alle ore 10.51, Prasenjit Ghosh ha scritto: > Dear Zibi, > > I am not sure about that. I checked the documentation of QE 5.0 (INPUT_PW.txt).....it says that now one can perform calculations with occupations='fixed' for more than one k-point, however, you need to set nbnd. Are you speaking about "fixed" occupations, or rather of occupations "from_input"? They are not the same option. In the first case the occupations are chosen by the code, in the second you have to supply them in the input file. Also, in the first case there is no need to specify nbnd, unless you want to change the default (nelec/2 for spin unpolarized calculations). The restriction to the Gamma point does not apply to the first case. From a quick glance to the code, it seems to me that it still applies to the second case, even if not stated (anymore?) in the input description. That's why part of your input is ignored, the code reads just nbnd*nspin values from the OCCUPATIONS card. HTH GS > > I tried to do the calculation with a simple example given below: > > &control > calculation='scf', > restart_mode='from_scratch', > pseudo_dir='/pghosh/pslibrary.0.2.2/pbe/WORK/test/' > outdir='./' > ! verbosity='high' > / > &system > ibrav=1, > celldm(1)=14.0, > nat=1, > ntyp=1, > nbnd=13, > nosym=.true., > ecutwfc=27.0, > ecutrho=216.0, > occupations='from_input', > / > &electrons > mixing_beta=0.25, > conv_thr=1.0E-8, > / > ATOMIC_SPECIES > O 15.99994 O.pbe-gipaw_uspp.UPF > ATOMIC_POSITIONS > O 0.000000000 0.000000000 0.000000000 > K_POINTS {automatic} > 2 2 2 0 0 0 > OCCUPATIONS > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1073 0.1071 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0614 0.0431 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0614 0.0520 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0719 0.0528 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0616 0.0377 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0608 0.0529 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0678 0.0531 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0548 0.0544 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > > However, the code is reading only the first 13 values and ignoring the rest of them. I do not know why. > > Also today while trying to download gipaw, it says they have removed version 5.0 because of a bug with USPP. > > Any comments on this will be highly appreciated. > > With regards, > > Prasenjit ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/e15c0f46/attachment-0001.htm From prasenjit.jnc at gmail.com Thu Sep 6 11:55:49 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 6 Sep 2012 15:25:49 +0530 Subject: [Pw_forum] GIPAW problems In-Reply-To: References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> <20120906051404.M18256@ifj.edu.pl> Message-ID: Dear Gabriele, Thanks for the clarification...... I am sorry for the confusion.....i meant occupations='from_input'. Since it does not say that it works only for one k-point, I thought that the restriction might have been moved. With regards, Prasenjit On 6 September 2012 15:01, Gabriele Sclauzero wrote: > > Hello, > > Il giorno 06/set/2012, alle ore 10.51, Prasenjit Ghosh ha scritto: > > Dear Zibi, > > I am not sure about that. I checked the documentation of QE 5.0 > (INPUT_PW.txt).....it says that now one can perform calculations with > occupations='fixed' for more than one k-point, however, you need to set > nbnd. > > > Are you speaking about "fixed" occupations, or rather of occupations > "from_input"? They are not the same option. > In the first case the occupations are chosen by the code, in the second > you have to supply them in the input file. > Also, in the first case there is no need to specify nbnd, unless you want > to change the default (nelec/2 for spin unpolarized calculations). > The restriction to the Gamma point does not apply to the first case. > From a quick glance to the code, it seems to me that it still applies to > the second case, even if not stated (anymore?) in the input description. > That's why part of your input is ignored, the code reads just nbnd*nspin > values from the OCCUPATIONS card. > > > HTH > > GS > > > > I tried to do the calculation with a simple example given below: > > &control > calculation='scf', > restart_mode='from_scratch', > pseudo_dir='/pghosh/pslibrary.0.2.2/pbe/WORK/test/' > outdir='./' > ! verbosity='high' > / > &system > ibrav=1, > celldm(1)=14.0, > nat=1, > ntyp=1, > nbnd=13, > nosym=.true., > ecutwfc=27.0, > ecutrho=216.0, > occupations='from_input', > / > &electrons > mixing_beta=0.25, > conv_thr=1.0E-8, > / > ATOMIC_SPECIES > O 15.99994 O.pbe-gipaw_uspp.UPF > ATOMIC_POSITIONS > O 0.000000000 0.000000000 0.000000000 > K_POINTS {automatic} > 2 2 2 0 0 0 > OCCUPATIONS > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1250 0.1250 0.1250 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.1073 0.1071 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0614 0.0431 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0614 0.0520 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0719 0.0528 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0616 0.0377 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0608 0.0529 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0678 0.0531 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.1250 0.0548 0.0544 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 > > However, the code is reading only the first 13 values and ignoring the > rest of them. I do not know why. > > Also today while trying to download gipaw, it says they have removed > version 5.0 because of a bug with USPP. > > Any comments on this will be highly appreciated. > > With regards, > > Prasenjit > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/87d189a8/attachment.htm From baroni at sissa.it Thu Sep 6 12:20:26 2012 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 6 Sep 2012 05:20:26 -0500 Subject: [Pw_forum] clock shew detected In-Reply-To: <1307112208-1346908665-cardhu_decombobulator_blackberry.rim.net-834622210-@b13.c7.bise7.blackberry> References: <000001cd8bd7$bbf77a40$33e66ec0$@com> <1307112208-1346908665-cardhu_decombobulator_blackberry.rim.net-834622210-@b13.c7.bise7.blackberry> Message-ID: <160C43D2-46DE-433E-9EFB-2ECD2CF54FF7@sissa.it> To avoid any misunderstandings about Axel's advice, please do not "kill" your system administrator ... SB On Sep 6, 2012, at 12:17 AM, Axel Kohlmeyer wrote: > This is an issue of your machine or cluster. It is caused by unsynchronized system clocks between the machine you compile on and its file server. Axel. > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > > -----Original Message----- > From: "yqsu" > Sender: pw_forum-bounces at pwscf.org > Date: Thu, 6 Sep 2012 10:31:31 > To: > Reply-To: PWSCF Forum > Cc: > Subject: [Pw_forum] clock shew detected > > _______________________________________________ > 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 --- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/d6d261eb/attachment.htm From giannozz at democritos.it Thu Sep 6 13:26:06 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 Sep 2012 13:26:06 +0200 Subject: [Pw_forum] GIPAW problems In-Reply-To: References: <20120903142113.M49782@ifj.edu.pl> <20120905182134.Horde.ueIjOx8V4mxQR3wOabK2u1A@webmail.sissa.it> <20120906051404.M18256@ifj.edu.pl> Message-ID: <010FF308-D4EB-4092-9AD8-4F1A09D0C21A@democritos.it> On Sep 6, 2012, at 11:31 , Gabriele Sclauzero wrote: > Are you speaking about "fixed" occupations, or rather of > occupations "from_input"? [...] > The restriction to the Gamma point does not apply to the first > case. From a quick glance > to the code, it seems to me that it still applies to the second case I vaguely remember removing such restriction some time ago P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Thu Sep 6 16:15:07 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 6 Sep 2012 15:15:07 +0100 Subject: [Pw_forum] error when using dynmat.x In-Reply-To: References: , Message-ID: Thanks very much for your help. Elie Date: Thu, 6 Sep 2012 08:57:34 +0200 From: lorenzo.paulatto at impmc.upmc.fr To: pw_forum at pwscf.org Subject: Re: [Pw_forum] error when using dynmat.x On 6 September 2012 06:59, Elie M wrote: dynmat.x 0000000000405D53 MAIN__ 115 dynmat.f90 Dear Elie,this looks like a problem reading the input. fildyn='Graph.dynG'q(1)=0.0, q(2)=0.0,q(3)=0.0,asr='crystal',filout='Graph.dyn.modes'filxsf='Graph.dyn.axsf' Did you bracket that input between "&input" and "/"?If you did, there may be strange characters in you input file. Check it with "cat -v input" bests Any help would be appreciated Thanks Elie MoukaesUninversity of NottsNG7 2RDUK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6phone: +33 (0)1 44275 084 / skype: paulatzwww: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 _______________________________________________ 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/20120906/dc528879/attachment-0001.htm From rainbee1988 at gmail.com Fri Sep 7 02:28:59 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 6 Sep 2012 20:28:59 -0400 Subject: [Pw_forum] supercell Message-ID: Hi everyone, When we want to use a supercell, how to determine the cell parameters? What kind of reactions are considered between supercells? Thanks, Ruibin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120906/58c78eca/attachment.htm From pandey.bramha at gmail.com Fri Sep 7 08:28:28 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Fri, 7 Sep 2012 11:58:28 +0530 Subject: [Pw_forum] full version of QE-5.0-GPU Message-ID: Dear Sir / Developers, I am the user of quantum espresso since last two years and currently using the 'espresso-4.3.2' version. I want to install new version of quantum espresso-5.0-GPU But not able to download it as a full packages like espresso-4.3.2. Sir i was also tried by command::: svn checkout svn://qeforge.qe-forge.org/svnroot/q-e/branches/espresso-PRACE but getting the error::: svn: Can't connect to host 'qeforge.qe-forge.org': Connection refused ::: Sir plz tell me how can i get the espresso-5.0-GPU in full version? Thanks in advanced for your kind helps. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/bdb5d623/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Fri Sep 7 08:43:56 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 7 Sep 2012 08:43:56 +0200 Subject: [Pw_forum] full version of QE-5.0-GPU In-Reply-To: References: Message-ID: On 7 September 2012 08:28, Bramha Pandey wrote: > svn checkout svn:// > qeforge.qe-forge.org/svnroot/q-e/branches/espresso-PRACE > > but getting the error::: > svn: Can't connect to host 'qeforge.qe-forge.org': Connection refused ::: > > Sir plz tell me how can i get the espresso-5.0-GPU in full version? > > The asn address you are using does not look right to me (the server was changed some time ago) plz check the new SVN access procedure here : < http://qe-forge.org/gf/project/q-e-gpu/scmsvn/?action=AccessInfo> -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/37213035/attachment.htm From pandey.bramha at gmail.com Fri Sep 7 09:03:00 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Fri, 7 Sep 2012 12:33:00 +0530 Subject: [Pw_forum] full version of QE-5.0-GPU In-Reply-To: References: Message-ID: Thank you Lorenzo Paulatto Sir, it is working. On Fri, Sep 7, 2012 at 12:13 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > On 7 September 2012 08:28, Bramha Pandey wrote: > >> svn checkout svn:// >> qeforge.qe-forge.org/svnroot/q-e/branches/espresso-PRACE >> >> but getting the error::: >> svn: Can't connect to host 'qeforge.qe-forge.org': Connection refused ::: >> >> Sir plz tell me how can i get the espresso-5.0-GPU in full version? >> >> > The asn address you are using does not look right to me (the server was > changed some time ago) > plz check the new SVN access procedure here : < > http://qe-forge.org/gf/project/q-e-gpu/scmsvn/?action=AccessInfo> > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/185836b7/attachment.htm From yccheng.nju at gmail.com Fri Sep 7 11:00:32 2012 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 7 Sep 2012 12:00:32 +0300 Subject: [Pw_forum] W full relativistic pseudopotential Message-ID: Dear All, I need W full relativistic pseudopotential to check the spin-orbital effect on band structure. However, I found that there is no such pseudopotential in QE pseudolist and pslibrary0.2.5. Would you please kindly help me to solve this problem? Thank you in advance. Best, -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com From lmartinsamos at gmail.com Fri Sep 7 11:23:18 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 7 Sep 2012 11:23:18 +0200 Subject: [Pw_forum] supercell In-Reply-To: References: Message-ID: DEar Riubin, a supercell is just when you replicate along x,y and z a primitive cell. The cell paramenters are such just (in the orthorombic case): number_of_replicas_along_x * a, number_of_replicas_along_y*b, number_of_replicas_alog_z * c, where a, b, and c are the primitive cell parameters. For better understanding all this you should read an introduction to crystallography and solid state physics. As we are in periodic boundary conditions the supercell is interacting with its images of course as in a primitive cell calculation. define better your question. (after reading a text book of crystallography and of solid state). cheers Layla 2012/9/7 Ruibin Liu > Hi everyone, > > When we want to use a supercell, how to determine the cell parameters? > What kind of reactions are considered between supercells? > > Thanks, > Ruibin > > > > _______________________________________________ > 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/20120907/48e72ff8/attachment.htm From flux_ray12 at 163.com Fri Sep 7 12:44:20 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 7 Sep 2012 18:44:20 +0800 (CST) Subject: [Pw_forum] W full relativistic pseudopotential In-Reply-To: References: Message-ID: <13a10ecb.e75b.139a0549092.Coremail.flux_ray12@163.com> Dear Yingchun: Few days ago, Prof. Marzari provided the compiled "pslib" in this maillist. Any one can download them at: http://theossrv1.epfl.ch/index.php?n=Main.Links For example, in rel-pbe, you can find W.rel-pbe-spn-rrkjus.UPF, the basic information of this file is: author="ADC" date="15Jun2012" comment="" element=" W" pseudo_type="USPP" relativistic="full" is_ultrasoft="T" is_paw="F" is_coulomb="F" has_so="T" has_wfc="F" has_gipaw="F" paw_as_gipaw="F" core_correction="T" functional="PBE" -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-09-07 17:00:32,"???" wrote: >Dear All, >I need W full relativistic pseudopotential to check the spin-orbital >effect on band structure. >However, I found that there is no such pseudopotential in QE >pseudolist and pslibrary0.2.5. >Would you please kindly help me to solve this problem? >Thank you in advance. >Best, >-- >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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/fb0a62db/attachment.htm From yccheng.nju at gmail.com Fri Sep 7 14:13:37 2012 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Fri, 7 Sep 2012 15:13:37 +0300 Subject: [Pw_forum] W full relativistic pseudopotential In-Reply-To: <13a10ecb.e75b.139a0549092.Coremail.flux_ray12@163.com> References: <13a10ecb.e75b.139a0549092.Coremail.flux_ray12@163.com> Message-ID: Dear Zhe, Many thanks. It is very helpful. Best, Yingchun 2012/9/7 GAO Zhe : > Dear Yingchun: > Few days ago, Prof. Marzari provided the compiled "pslib" in this maillist. > Any one can download them at: > http://theossrv1.epfl.ch/index.php?n=Main.Links > For example, in rel-pbe, you can find W.rel-pbe-spn-rrkjus.UPF, the basic > information of this file is: > author="ADC" > date="15Jun2012" > comment="" > element=" W" > pseudo_type="USPP" > relativistic="full" > is_ultrasoft="T" > is_paw="F" > is_coulomb="F" > has_so="T" > has_wfc="F" > has_gipaw="F" > paw_as_gipaw="F" > core_correction="T" > functional="PBE" > > -- > GAO Zhe > CMC Lab, Materials Science & Engineering Department, > Seoul National University, South Korea > > > > At 2012-09-07 17:00:32,"???" wrote: >>Dear All, >>I need W full relativistic pseudopotential to check the spin-orbital >>effect on band structure. >>However, I found that there is no such pseudopotential in QE >>pseudolist and pslibrary0.2.5. >>Would you please kindly help me to solve this problem? >>Thank you in advance. >>Best, >>-- >>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 > > > > > _______________________________________________ > 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 From spiga.filippo at gmail.com Fri Sep 7 15:37:49 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 7 Sep 2012 15:37:49 +0200 Subject: [Pw_forum] full version of QE-5.0-GPU In-Reply-To: References: Message-ID: <249CEBF9-E8DD-4A51-879D-1FBBDC9E75DE@gmail.com> Dear Bramha, I strongly suggest you to use the packages available here: http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseView&release_id=119 In fact, the branch "espresso-PRACE" is going to disappear very soon (it is a matter of days) because a new repository, directly linked as external to the main QE repository, will be active in very short time (it's a matter of days, finally!). If you are looking to the repository access in order to extend the GPU capabilities of the current code feel free to drop me an email and I will be glad to give you an access to the dedicated repository. We are always looking for new collaborators. Best Regards, Filippo On Sep 7, 2012, at 9:03 AM, Bramha Pandey wrote: > Thank you Lorenzo Paulatto Sir, it is working. > > On Fri, Sep 7, 2012 at 12:13 PM, Lorenzo Paulatto wrote: > On 7 September 2012 08:28, Bramha Pandey wrote: > svn checkout svn://qeforge.qe-forge.org/svnroot/q-e/branches/espresso-PRACE > > but getting the error::: > svn: Can't connect to host 'qeforge.qe-forge.org': Connection refused ::: > > Sir plz tell me how can i get the espresso-5.0-GPU in full version? > > > The asn address you are using does not look right to me (the server was changed some time ago) > plz check the new SVN access procedure here : > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/9615aa0f/attachment-0001.htm From pchen at ion.chem.utk.edu Fri Sep 7 19:16:39 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Fri, 7 Sep 2012 13:16:39 -0400 Subject: [Pw_forum] Density of states Message-ID: Dear All, I calculated the total density of states (in the attachment) for both afm and fm states of an insulator. I shifted the curves so that the band gap starts at 0 eV. In the top figure, the Fermi energy obtained from the scf calculation falls between the gap. So if I plot Fermi surface, can I get reliable result? In the bottom figure, I shifted the spin down DOS of fm state so that it can match with the spin down DOS of afm state. I am not sure if that is the right way to show the DOS difference of these two states. Another question is about the accuracy of calculation. In the scf calculation, I made the total energy converged within 0.001 Ry with related to the ecutwfc, degauss, kpoints... Then I did band structure calculation. Can I say the error of calculated band energy is within 0.001 Ry? Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/e568acd6/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: dos.pdf Type: application/pdf Size: 38350 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120907/e568acd6/attachment-0001.pdf From jiachen at princeton.edu Fri Sep 7 19:34:42 2012 From: jiachen at princeton.edu (jia chen) Date: Fri, 7 Sep 2012 13:34:42 -0400 Subject: [Pw_forum] Density of states In-Reply-To: References: Message-ID: Dear Peng, Regarding to your first question, I don't think you can plot Fermi surface for insulators, since there is no states at fermi level. The second one, in my opinion, you probably don't want to shift spin down level along because relative positions of spin up and down is meaningful and Fermi energy is uniquely defined for the whole system. Bests Jia On Fri, Sep 7, 2012 at 1:16 PM, Peng Chen wrote: > Dear All, > > I calculated the total density of states (in the attachment) for both afm > and fm states of an insulator. I shifted the curves so that the band gap > starts at 0 eV. In the top figure, the Fermi energy obtained from the scf > calculation falls between the gap. So if I plot Fermi surface, can I get > reliable result? In the bottom figure, I shifted the spin down DOS of fm > state so that it can match with the spin down DOS of afm state. I am not > sure if that is the right way to show the DOS difference of these two > states. > > Another question is about the accuracy of calculation. In the scf > calculation, I made the total energy converged within 0.001 Ry with related > to the ecutwfc, degauss, kpoints... Then I did band structure calculation. > Can I say the error of calculated band energy is within 0.001 Ry? > > > > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Jia Chen webpage: www.princeton.edu/~jiachen From flux_ray12 at 163.com Fri Sep 7 20:49:35 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 8 Sep 2012 02:49:35 +0800 (CST) Subject: [Pw_forum] Density of states In-Reply-To: References: Message-ID: <4f584527.122a4.139a210d4f0.Coremail.flux_ray12@163.com> Dear Peng: To show the difference between DOSes, the best way is put the Fermi level at same place. Normally, (E-Ef) is preferred by lots of researches as the variable of x-axes. Manually shifting DOS for matching is not a good idea, since HOMO should be the standard and adjusted to the same position (although Fermi level given by PWscf is LUMO for semiconductor or insulator). BTW, in PWscf, nscf calculation also provides Fermi energy, which usually is slightly different with that from scf calculation and displayed by setting verbosity='high' in &control namelist. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-09-08 01:16:39,"Peng Chen" wrote: Dear All, I calculated the total density of states (in the attachment) for both afm and fm states of an insulator. I shifted the curves so that the band gap starts at 0 eV. In the top figure, the Fermi energy obtained from the scf calculation falls between the gap. So if I plot Fermi surface, can I get reliable result? In the bottom figure, I shifted the spin down DOS of fm state so that it can match with the spin down DOS of afm state. I am not sure if that is the right way to show the DOS difference of these two states. Another question is about the accuracy of calculation. In the scf calculation, I made the total energy converged within 0.001 Ry with related to the ecutwfc, degauss, kpoints... Then I did band structure calculation. Can I say the error of calculated band energy is within 0.001 Ry? Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120908/7e79df07/attachment.htm From rainbee1988 at gmail.com Fri Sep 7 20:50:13 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Fri, 7 Sep 2012 14:50:13 -0400 Subject: [Pw_forum] IOTK library Message-ID: I checked that file and found that it's already Q_REAL_SPACE, but I encountered similar problems like ######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 ######################################################################################################################## How to fix it? -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/00638629/attachment.htm From akohlmey at gmail.com Fri Sep 7 20:53:41 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 7 Sep 2012 20:53:41 +0200 Subject: [Pw_forum] IOTK library In-Reply-To: References: Message-ID: On Fri, Sep 7, 2012 at 8:50 PM, Ruibin Liu wrote: > I checked that file and found that it's already Q_REAL_SPACE, but I > encountered similar problems like > ######################################################################################################################## > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20 > ######################################################################################################################## > How to fix it? i think the consensus is that you have to use a better compiler. one that works correctly and is not broken like older versions of gfortran. axel. > > -- > Liu, Ruibin > Department of Chemistry > Duke University > Durham, NC, 27708 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From bfazi90 at gmail.com Fri Sep 7 22:09:58 2012 From: bfazi90 at gmail.com (bf azi) Date: Sat, 8 Sep 2012 00:39:58 +0430 Subject: [Pw_forum] generate pseudopotential Message-ID: Hi Dear all I want to generate PBE Norm-conserving pseudopotential for Boron and Nitrogen. Can any body give me input file? Thanks a lot Bani Adam Faculty of Science Egypt From 200210qb at gmail.com Fri Sep 7 22:45:22 2012 From: 200210qb at gmail.com (Bo Qiu) Date: Fri, 7 Sep 2012 16:45:22 -0400 Subject: [Pw_forum] electron phonon coupling in semiconductors Message-ID: Dear developers and users, I'm new to QE and want to do some electron phonon calculation to reproduce the el-ph scattering rates similar to that reported in this paper: "First-principles calculations of electron mobilities in silicon: Phonon and Coulomb scattering" Restrepo et al, Appl. Phys. Lett. 94, 212103 (2009). This paper used QE package as well. However, when I tried to run a silicon el-ph calculation by modifying the example input files for Al, the program complained "el-ph calculations for metals only". I tried to suppress the error message and ran the code. It output the el-ph coupling constants etc. similar to Al case, however, I've no idea if the results make sense. For semiconductors, the code should have no problem calculating the el-ph matrix elements g and should be able to give band energies and Fermi energy as needed to compute phonon linewidth. So I'm confused why QE cannot do el-ph for semiconductors? Could you please help me understand it a little bit? Thanks! Please excuse me if the answer is obvious. Thanks a lot! Bo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/c66cefd5/attachment.htm From pchen at ion.chem.utk.edu Sat Sep 8 01:36:29 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Fri, 7 Sep 2012 19:36:29 -0400 Subject: [Pw_forum] Density of states In-Reply-To: <4f584527.122a4.139a210d4f0.Coremail.flux_ray12@163.com> References: <4f584527.122a4.139a210d4f0.Coremail.flux_ray12@163.com> Message-ID: Thanks, Jia and Gao. Your suggestions are helpful. On Fri, Sep 7, 2012 at 2:49 PM, GAO Zhe wrote: > Dear Peng: > To show the difference between DOSes, the best way is put the Fermi level > at same place. Normally, (E-Ef) is preferred by lots of researches as the > variable of x-axes. Manually shifting DOS for matching is not a good idea, > since HOMO should be the standard and adjusted to the same position > (although Fermi level given by PWscf is LUMO for semiconductor or > insulator). > BTW, in PWscf, nscf calculation also provides Fermi energy, which usually > is slightly different with that from scf calculation and displayed by > setting verbosity='high' in &control namelist. > > -- > GAO Zhe > CMC Lab, Materials Science & Engineering Department, > Seoul National University, South Korea > > > At 2012-09-08 01:16:39,"Peng Chen" wrote: > > Dear All, > > I calculated the total density of states (in the attachment) for both afm > and fm states of an insulator. I shifted the curves so that the band gap > starts at 0 eV. In the top figure, the Fermi energy obtained from the scf > calculation falls between the gap. So if I plot Fermi surface, can I get > reliable result? In the bottom figure, I shifted the spin down DOS of fm > state so that it can match with the spin down DOS of afm state. I am not > sure if that is the right way to show the DOS difference of these two > states. > > Another question is about the accuracy of calculation. In the scf > calculation, I made the total energy converged within 0.001 Ry with related > to the ecutwfc, degauss, kpoints... Then I did band structure > calculation. Can I say the error of calculated band energy is within 0.001 > Ry? > > > > Best Regards. > Peng > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120907/a35fa46a/attachment-0001.htm From elie.moujaes at hotmail.co.uk Sat Sep 8 07:41:07 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 8 Sep 2012 06:41:07 +0100 Subject: [Pw_forum] comparison of ph.x and dynmat.x results Message-ID: Dear all, I have done phonon calculations at the Gamma point to find the vibrational frequencies of a system I am working on and I got three negative frequencies; the results are: q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -11.303890 [THz] = -377.057178 [cm-1] omega( 2) = -11.228798 [THz] = -374.552397 [cm-1] omega( 3) = -1.493780 [THz] = -49.827127 [cm-1] omega( 4) = 1.499866 [THz] = 50.030148 [cm-1] omega( 5) = 2.192955 [THz] = 73.149113 [cm-1] omega( 6) = 11.690342 [THz] = 389.947822 [cm-1] omega( 7) = 15.929343 [THz] = 531.345701 [cm-1] omega( 8) = 17.762801 [THz] = 592.503255 [cm-1] omega( 9) = 17.814756 [THz] = 594.236307 [cm-1] omega(10) = 22.128875 [THz] = 738.139807 [cm-1] omega(11) = 24.754227 [THz] = 825.712121 [cm-1] omega(12) = 25.174421 [THz] = 839.728307 [cm-1] omega(13) = 25.229402 [THz] = 841.562251 [cm-1] omega(14) = 31.677488 [THz] = 1056.647257 [cm-1] omega(15) = 32.931458 [THz] = 1098.475192 [cm-1] omega(16) = 32.974208 [THz] = 1099.901170 [cm-1] omega(17) = 37.529033 [THz] = 1251.833794 [cm-1] omega(18) = 37.585396 [THz] = 1253.713860 [cm-1] omega(19) = 38.689108 [THz] = 1290.529726 [cm-1] omega(20) = 44.468725 [THz] = 1483.317012 [cm-1] omega(21) = 44.490793 [THz] = 1484.053106 [cm-1] omega(22) = 100.618488 [THz] = 3356.271501 [cm-1] omega(23) = 100.705119 [THz] = 3359.161186 [cm-1] omega(24) = 103.337467 [THz] = 3446.966862 [cm-1] To check whether the first three freqnecies are the accoustic ones and not instabilities i applied dynmat.x with asr='crystal' and got: mode [cm-1] [THz] IR 1 -377.06 -11.3039 0.0000 2 -374.55 -11.2287 0.0000 3 0.00 0.0000 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 0.0000 6 406.11 12.1749 0.0000 7 531.35 15.9293 0.0000 8 592.50 17.7628 0.0000 9 594.24 17.8148 0.0000 10 738.13 22.1286 0.0000 11 828.85 24.8482 0.0000 12 839.68 25.1730 0.0000 13 841.62 25.2311 0.0000 14 1056.65 31.6775 0.0000 15 1099.09 32.9498 0.0000 16 1099.25 32.9547 0.0000 17 1251.32 37.5135 0.0000 18 1253.47 37.5781 0.0000 19 1290.53 38.6891 0.0000 20 1483.05 44.4608 0.0000 21 1485.30 44.5283 0.0000 22 3356.09 100.6131 0.0000 23 3359.58 100.7178 0.0000 24 3446.96 103.3373 0.0000 As it is seen, the freqencies are very close but the thing and the system is stable! Howevere,I could not understand is about the first 5 frequencies: i still got the first two negative but in addition i have 3 more zero frequencies; does it mean we have five accoustic modes due to the symmetry of this particular system? Thanks in advance Elie KoujaesUniversity of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120908/95064031/attachment.htm From degironc at sissa.it Sat Sep 8 09:17:05 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 08 Sep 2012 09:17:05 +0200 Subject: [Pw_forum] comparison of ph.x and dynmat.x results In-Reply-To: References: Message-ID: <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> negative (imaginary) frequencies signal instabilities. acoustic modes (i.e. rigid global translations on the crystal) at gamma should always have zero frequencies but for numerical reasons they can result in small positive or negative values that can be fixed by the acoustic sum rule. in your case the modee at -49, 50 and 73 are the acoustic modes that vanish after ASR inclusion. the modes around -370 are other modes and they are unstable.. move the atoms of your structure along one of this modes and relax it again. this will probably break a symmetry that prevented your system to reach complete relaxation stefano Quoting Elie M : > Dear all, I have done phonon calculations at the Gamma point to find > the vibrational frequencies of a system I am working on and I got > three negative frequencies; the results are: > q = ( 0.000000000 0.000000000 0.000000000 ) > > ************************************************************************** > omega( 1) = -11.303890 [THz] = -377.057178 [cm-1] > omega( 2) = -11.228798 [THz] = -374.552397 [cm-1] omega( > 3) = -1.493780 [THz] = -49.827127 [cm-1] omega( 4) = > 1.499866 [THz] = 50.030148 [cm-1] omega( 5) = > 2.192955 [THz] = 73.149113 [cm-1] omega( 6) = > 11.690342 [THz] = 389.947822 [cm-1] omega( 7) = > 15.929343 [THz] = 531.345701 [cm-1] omega( 8) = > 17.762801 [THz] = 592.503255 [cm-1] omega( 9) = > 17.814756 [THz] = 594.236307 [cm-1] omega(10) = > 22.128875 [THz] = 738.139807 [cm-1] omega(11) = > 24.754227 [THz] = 825.712121 [cm-1] omega(12) = > 25.174421 [THz] = 839.728307 [cm-1] omega(13) = > 25.229402 [THz] = 841.562251 [cm-1] omega(14) = > 31.677488 [THz] = 1056.647257 [cm-1] omega(15) = > 32.931458 [THz] = 1098.475192 [cm-1] omega(16) = > 32.974208 [THz] = 1099.901170 [cm-1] omega(17) = > 37.529033 [THz] = 1251.833794 [cm-1] omega(18) = > 37.585396 [THz] = 1253.713860 [cm-1] omega(19) = > 38.689108 [THz] = 1290.529726 [cm-1] omega(20) = > 44.468725 [THz] = 1483.317012 [cm-1] omega(21) = > 44.490793 [THz] = 1484.053106 [cm-1] omega(22) = > 100.618488 [THz] = 3356.271501 [cm-1] omega(23) = > 100.705119 [THz] = 3359.161186 [cm-1] omega(24) = > 103.337467 [THz] = 3446.966862 [cm-1] > To check whether the first three freqnecies are the accoustic ones > and not instabilities i applied dynmat.x with asr='crystal' and got: > mode [cm-1] [THz] IR 1 -377.06 -11.3039 > 0.0000 2 -374.55 -11.2287 0.0000 3 0.00 0.0000 > 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 > 0.0000 6 406.11 12.1749 0.0000 7 531.35 15.9293 > 0.0000 8 592.50 17.7628 0.0000 9 594.24 > 17.8148 0.0000 10 738.13 22.1286 0.0000 11 828.85 > 24.8482 0.0000 12 839.68 25.1730 0.0000 13 841.62 > 25.2311 0.0000 14 1056.65 31.6775 0.0000 15 > 1099.09 32.9498 0.0000 16 1099.25 32.9547 0.0000 17 > 1251.32 37.5135 0.0000 18 1253.47 37.5781 0.0000 19 > 1290.53 38.6891 0.0000 20 1483.05 44.4608 0.0000 > 21 1485.30 44.5283 0.0000 22 3356.09 100.6131 0.0000 > 23 3359.58 100.7178 0.0000 24 3446.96 103.3373 0.0000 > As it is seen, the freqencies are very close but the thing and the > system is stable! Howevere,I could not understand is about the first > 5 frequencies: i still got the first two negative but in addition i > have 3 more zero frequencies; does it mean we have five accoustic > modes due to the symmetry of this particular system? > > Thanks in advance > Elie KoujaesUniversity of NottsNG7 2RDUK From giannozz at democritos.it Sat Sep 8 09:43:33 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 8 Sep 2012 09:43:33 +0200 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information In-Reply-To: References: Message-ID: On Aug 31, 2012, at 22:55 , Matthew M Montemore wrote: > I just wanted to make the community aware of this issue and help out > anyone having similar problems. your help is very much appreciated. It will be even more appreciated if you provide an example of a pseudopotential that works if you remove the input data section ( ... I guess), doesn't work as is (please also provide you definition of "doesn't work": yields an error while reading the pseudopotential file?). I hadn't checked if the pseudopotentials with the new input information actually work, but I don't see any reason why they shouldn't (and the only one I just tried seems to have no problem) Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lorenzo.paulatto at impmc.upmc.fr Sat Sep 8 11:58:52 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Sat, 8 Sep 2012 11:58:52 +0200 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information In-Reply-To: References: Message-ID: On 8 September 2012 09:43, Paolo Giannozzi wrote: > > > I just wanted to make the community aware of this issue and help out > > anyone having similar problems. > > Some time ago i noticed that if the "author" or "comment" field includes the character "<" that the xml parser cannot read the pseudopotential file. Can you check if your input falls in the same case? bests -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120908/5509af06/attachment.htm From elie.moujaes at hotmail.co.uk Sat Sep 8 15:41:08 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 8 Sep 2012 14:41:08 +0100 Subject: [Pw_forum] comparison of ph.x and dynmat.x results In-Reply-To: <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> References: , <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> Message-ID: Yes, I thought that the non zero negative frequencies that remained still signal instability. Will do what you suggested. Thanks Elie > Date: Sat, 8 Sep 2012 09:17:05 +0200 > From: degironc at sissa.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] comparison of ph.x and dynmat.x results > > negative (imaginary) frequencies signal instabilities. > acoustic modes (i.e. rigid global translations on the crystal) at > gamma should always have zero frequencies but for numerical reasons > they can result in small positive or negative values that can be fixed > by the acoustic sum rule. > > in your case the modee at -49, 50 and 73 are the acoustic modes that > vanish after ASR inclusion. > the modes around -370 are other modes and they are unstable.. > > move the atoms of your structure along one of this modes and relax it again. > this will probably break a symmetry that prevented your system to > reach complete relaxation > > stefano > > > Quoting Elie M : > > > Dear all, I have done phonon calculations at the Gamma point to find > > the vibrational frequencies of a system I am working on and I got > > three negative frequencies; the results are: > > q = ( 0.000000000 0.000000000 0.000000000 ) > > > > ************************************************************************** > > omega( 1) = -11.303890 [THz] = -377.057178 [cm-1] > > omega( 2) = -11.228798 [THz] = -374.552397 [cm-1] omega( > > 3) = -1.493780 [THz] = -49.827127 [cm-1] omega( 4) = > > 1.499866 [THz] = 50.030148 [cm-1] omega( 5) = > > 2.192955 [THz] = 73.149113 [cm-1] omega( 6) = > > 11.690342 [THz] = 389.947822 [cm-1] omega( 7) = > > 15.929343 [THz] = 531.345701 [cm-1] omega( 8) = > > 17.762801 [THz] = 592.503255 [cm-1] omega( 9) = > > 17.814756 [THz] = 594.236307 [cm-1] omega(10) = > > 22.128875 [THz] = 738.139807 [cm-1] omega(11) = > > 24.754227 [THz] = 825.712121 [cm-1] omega(12) = > > 25.174421 [THz] = 839.728307 [cm-1] omega(13) = > > 25.229402 [THz] = 841.562251 [cm-1] omega(14) = > > 31.677488 [THz] = 1056.647257 [cm-1] omega(15) = > > 32.931458 [THz] = 1098.475192 [cm-1] omega(16) = > > 32.974208 [THz] = 1099.901170 [cm-1] omega(17) = > > 37.529033 [THz] = 1251.833794 [cm-1] omega(18) = > > 37.585396 [THz] = 1253.713860 [cm-1] omega(19) = > > 38.689108 [THz] = 1290.529726 [cm-1] omega(20) = > > 44.468725 [THz] = 1483.317012 [cm-1] omega(21) = > > 44.490793 [THz] = 1484.053106 [cm-1] omega(22) = > > 100.618488 [THz] = 3356.271501 [cm-1] omega(23) = > > 100.705119 [THz] = 3359.161186 [cm-1] omega(24) = > > 103.337467 [THz] = 3446.966862 [cm-1] > > To check whether the first three freqnecies are the accoustic ones > > and not instabilities i applied dynmat.x with asr='crystal' and got: > > mode [cm-1] [THz] IR 1 -377.06 -11.3039 > > 0.0000 2 -374.55 -11.2287 0.0000 3 0.00 0.0000 > > 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 > > 0.0000 6 406.11 12.1749 0.0000 7 531.35 15.9293 > > 0.0000 8 592.50 17.7628 0.0000 9 594.24 > > 17.8148 0.0000 10 738.13 22.1286 0.0000 11 828.85 > > 24.8482 0.0000 12 839.68 25.1730 0.0000 13 841.62 > > 25.2311 0.0000 14 1056.65 31.6775 0.0000 15 > > 1099.09 32.9498 0.0000 16 1099.25 32.9547 0.0000 17 > > 1251.32 37.5135 0.0000 18 1253.47 37.5781 0.0000 19 > > 1290.53 38.6891 0.0000 20 1483.05 44.4608 0.0000 > > 21 1485.30 44.5283 0.0000 22 3356.09 100.6131 0.0000 > > 23 3359.58 100.7178 0.0000 24 3446.96 103.3373 0.0000 > > As it is seen, the freqencies are very close but the thing and the > > system is stable! Howevere,I could not understand is about the first > > 5 frequencies: i still got the first two negative but in addition i > > have 3 more zero frequencies; does it mean we have five accoustic > > modes due to the symmetry of this particular system? > > > > Thanks in advance > > Elie KoujaesUniversity of NottsNG7 2RDUK > > > _______________________________________________ > 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/20120908/5bb024a5/attachment.htm From Matthew.Montemore at Colorado.EDU Sat Sep 8 23:03:21 2012 From: Matthew.Montemore at Colorado.EDU (Matthew M Montemore) Date: Sat, 8 Sep 2012 15:03:21 -0600 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information In-Reply-To: References: Message-ID: <6A5A4CC6-FAFD-493F-BE0D-A14050D5202E@colorado.edu> > > your help is very much appreciated. It will be even more appreciated > if you provide an example of a pseudopotential that works if you > remove the input data section ( ... I guess), > doesn't work as is (please also provide you definition of "doesn't work": > yields an error while reading the pseudopotential file?). I hadn't checked > if the pseudopotentials with the new input information actually work, but > I don't see any reason why they shouldn't (and the only one I just tried > seems to have no problem) > > Paolo > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > The top of an offending pseudopotential (C for PW91) is below. I had the same problem with other functionals, too. All the PPs I tried with Lorenzo Paulatto as the author required me to delete to (as you surmised), and those with "ADC" as the author did not have this problem. (I suppose that could be a coincidence; it was just something I noticed.) When I used the C PP without deleting that section, the code would run up through 'Reading input from qe.in' and then quit, but I don't think it gave an error message. I think the only file it generated was the .out file. As you say, it seems odd that this section would cause any problems, but that seems to be the case for me. Hope that helps. Matt Montemore University of Colorado Boulder Generated using "atomic" code by A. Dal Corso v.5.0.1 svn rev. 9381 Author: "Lorenzo Paulatto" /paulatto at sissa.it/ Generation date: 27Aug2012 Pseudopotential type: PAW Element: C Functional: SLA PW GGX GGC Suggested minimum cutoff for wavefunctions: 37. Ry Suggested minimum cutoff for charge density: 147. Ry The Pseudo was generated with a Scalar-Relativistic Calculation L component and cutoff radius for Local Potential: 2 1.1000 Valence configuration: nl pn l occ Rcut Rcut US E pseu 2S 1 0 2.00 1.000 1.300 -1.014050 2P 2 1 2.00 1.000 1.450 -0.392710 Generation configuration: 2S 1 0 2.00 1.000 1.300 -1.014042 2S 1 0 0.00 1.000 1.300 0.050000 2P 2 1 2.00 1.000 1.450 -0.392707 2P 2 1 0.00 1.000 1.450 0.050000 3D 3 2 -2.00 1.100 1.100 0.100000 Pseudization used: troullier-martins &input title='C', zed=6, rel=1, config='[He] 2s2 2p2 3d-2', iswitch=3, dft='PW91' / &inputp lpaw=.true., pseudotype=3, file_pseudopw='C.pw91-n-kjpaw.UPF', author='"Lorenzo Paulatto" ', lloc=2, which_augfun ='BESSEL', rmatch_augfun=1.1, nlcc=.true., new_core_ps=.true., rcore=0.8, tm=.true. / 5 2S 1 0 2.00 0.00 1.00 1.30 0.0 2S 1 0 0.00 0.05 1.00 1.30 0.0 2P 2 1 2.00 0.00 1.00 1.45 0.0 2P 2 1 0.00 0.05 1.00 1.45 0.0 3D 3 2 -2.00 0.10 1.10 1.10 0.0 1.519803275924194E-004 1.538920047781704E-004 1.558277279027637E-004 1.577877994268756E-004 1.597725256156700E-004 1.617822165866515E-004 1.638171863581231E-004 1.658777528982519E-004 From raamesh123 at rediffmail.com Sat Sep 8 20:37:50 2012 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 8 Sep 2012 18:37:50 -0000 Subject: [Pw_forum] =?utf-8?q?Error/Warning_in_Ph=2Ex?= Message-ID: <20120908183750.12451.qmail@f4mail-235-195.rediffmail.com> Dear All During phonon calculation i get a message like this. Tried to find the answer in the pw_forum got something similar but couldnt figure wat it is. Can anyone please help me in this regard Cannot match namelist object name electron_phonon namelist read: missplaced = sign Cannot match namelist object name interpolated',^M with regards ramesh 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/20120908/764a9dac/attachment.htm From pchen at ion.chem.utk.edu Sun Sep 9 04:35:48 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Sat, 8 Sep 2012 22:35:48 -0400 Subject: [Pw_forum] Occupation number Message-ID: Hi All, When I tried to do GGA/GGA+U computation on Ni3V2O8, the occupation number of Ni looks a little weird. In this compound, d orbitals of Ni split into t2g (dxy, dxz,dyz) and eg (dx^2-y^2, dz^2) because of NiO6 octahedral coordination. So the down spin will occupy t2g states. But both GGA and GGA+U results show the occupation of dxz, dyz and dx^2-y^2. I tried to write occupation matrix using starting_ns_eigenvalue so that the occupation can be dxy, dxz and dyz, but the scf calculation can not reach convergence. Any suggestion is appreciated! GGA after the first iteration: eigenvalues: 0.059 0.066 0.075 0.146 0.161 eigenvectors: 0.009 0.001 0.000 0.000 0.990 0.000 0.000 0.997 0.003 0.000 0.076 0.924 0.000 0.000 0.000 0.916 0.075 0.000 0.000 0.009 0.000 0.000 0.003 0.997 0.000 occupations: 0.160 0.001 0.000 -0.010 0.000 0.001 0.075 0.000 0.000 -0.004 0.000 0.000 0.066 -0.002 0.001 -0.010 0.000 -0.002 0.060 0.000 0.000 -0.004 0.001 0.000 0.146 GGA after scf convergence: eigenvalues: 0.336 0.364 0.987 0.988 0.991 eigenvectors: 0.030 0.968 0.002 0.000 0.000 0.001 0.000 0.026 0.822 0.151 0.000 0.000 0.063 0.175 0.761 0.000 0.001 0.909 0.002 0.088 0.968 0.030 0.000 0.001 0.000 occupations: 0.364 -0.003 -0.014 0.022 0.005 -0.003 0.988 -0.001 0.000 -0.024 -0.014 -0.001 0.990 0.001 0.001 0.022 0.000 0.001 0.987 -0.001 0.005 -0.024 0.001 -0.001 0.338 GGA+U after the first iteration: eigenvalues: 0.071 0.079 0.095 0.157 0.172 eigenvectors: 0.008 0.000 0.000 0.000 0.992 0.024 0.363 0.607 0.006 0.000 0.000 0.630 0.369 0.001 0.000 0.967 0.006 0.018 0.000 0.008 0.000 0.000 0.006 0.993 0.000 occupations: 0.171 0.001 0.001 -0.009 0.000 0.001 0.089 -0.008 -0.003 -0.005 0.001 -0.008 0.085 0.001 0.002 -0.009 -0.003 0.001 0.072 0.000 0.000 -0.005 0.002 0.000 0.157 GGA+U after scf convergence: eigenvalues: 0.265 0.306 0.995 0.996 0.996 eigenvectors: 0.010 0.988 0.001 0.000 0.000 0.001 0.000 0.003 0.919 0.077 0.000 0.000 0.098 0.060 0.841 0.000 0.001 0.897 0.020 0.082 0.989 0.010 0.000 0.001 0.000 occupations: 0.307 -0.002 -0.014 0.023 0.004 -0.002 0.995 0.000 0.000 -0.024 -0.014 0.000 0.996 0.001 0.000 0.023 0.000 0.001 0.994 -0.001 0.004 -0.024 0.000 -0.001 0.266 -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120908/9ac62cf4/attachment-0001.htm From degironc at sissa.it Sun Sep 9 13:31:55 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 09 Sep 2012 13:31:55 +0200 Subject: [Pw_forum] Occupation number In-Reply-To: References: Message-ID: <504C7E2B.3080202@sissa.it> are you sure the code is not correct? how are the oxygen octahedra oriented in your case? a rotation of pi/4 around z would do.. stefano On 09/09/2012 04:35 AM, Peng Chen wrote: > Hi All, > > When I tried to do GGA/GGA+U computation on Ni3V2O8, the occupation number > of Ni looks a little weird. In this compound, d orbitals of Ni split into > t2g (dxy, dxz,dyz) and eg (dx^2-y^2, dz^2) because of NiO6 octahedral > coordination. So the down spin will occupy t2g states. But both GGA and > GGA+U results show the occupation of dxz, dyz and dx^2-y^2. I tried to > write occupation matrix using starting_ns_eigenvalue so that the > occupation can be dxy, dxz and dyz, but the scf calculation can not reach > convergence. Any suggestion is appreciated! > > > GGA after the first iteration: > eigenvalues: > 0.059 0.066 0.075 0.146 0.161 > eigenvectors: > 0.009 0.001 0.000 0.000 0.990 > 0.000 0.000 0.997 0.003 0.000 > 0.076 0.924 0.000 0.000 0.000 > 0.916 0.075 0.000 0.000 0.009 > 0.000 0.000 0.003 0.997 0.000 > occupations: > 0.160 0.001 0.000 -0.010 0.000 > 0.001 0.075 0.000 0.000 -0.004 > 0.000 0.000 0.066 -0.002 0.001 > -0.010 0.000 -0.002 0.060 0.000 > 0.000 -0.004 0.001 0.000 0.146 > > GGA after scf convergence: > eigenvalues: > 0.336 0.364 0.987 0.988 0.991 > eigenvectors: > 0.030 0.968 0.002 0.000 0.000 > 0.001 0.000 0.026 0.822 0.151 > 0.000 0.000 0.063 0.175 0.761 > 0.000 0.001 0.909 0.002 0.088 > 0.968 0.030 0.000 0.001 0.000 > occupations: > 0.364 -0.003 -0.014 0.022 0.005 > -0.003 0.988 -0.001 0.000 -0.024 > -0.014 -0.001 0.990 0.001 0.001 > 0.022 0.000 0.001 0.987 -0.001 > 0.005 -0.024 0.001 -0.001 0.338 > > > GGA+U after the first iteration: > eigenvalues: > 0.071 0.079 0.095 0.157 0.172 > eigenvectors: > 0.008 0.000 0.000 0.000 0.992 > 0.024 0.363 0.607 0.006 0.000 > 0.000 0.630 0.369 0.001 0.000 > 0.967 0.006 0.018 0.000 0.008 > 0.000 0.000 0.006 0.993 0.000 > occupations: > 0.171 0.001 0.001 -0.009 0.000 > 0.001 0.089 -0.008 -0.003 -0.005 > 0.001 -0.008 0.085 0.001 0.002 > -0.009 -0.003 0.001 0.072 0.000 > 0.000 -0.005 0.002 0.000 0.157 > > GGA+U after scf convergence: > eigenvalues: > 0.265 0.306 0.995 0.996 0.996 > eigenvectors: > 0.010 0.988 0.001 0.000 0.000 > 0.001 0.000 0.003 0.919 0.077 > 0.000 0.000 0.098 0.060 0.841 > 0.000 0.001 0.897 0.020 0.082 > 0.989 0.010 0.000 0.001 0.000 > occupations: > 0.307 -0.002 -0.014 0.023 0.004 > -0.002 0.995 0.000 0.000 -0.024 > -0.014 0.000 0.996 0.001 0.000 > 0.023 0.000 0.001 0.994 -0.001 > 0.004 -0.024 0.000 -0.001 0.266 > > > > > _______________________________________________ > 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/20120909/66f1589b/attachment.htm From pchen at ion.chem.utk.edu Sun Sep 9 17:35:02 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Sun, 9 Sep 2012 11:35:02 -0400 Subject: [Pw_forum] Occupation number In-Reply-To: <504C7E2B.3080202@sissa.it> References: <504C7E2B.3080202@sissa.it> Message-ID: Thanks Dr. Gironcoli. You are right! In xy plane, the oxygen atoms indeed lie in between xy axes. Best Regards. Peng On Sun, Sep 9, 2012 at 7:31 AM, Stefano de Gironcoli wrote: > are you sure the code is not correct? > how are the oxygen octahedra oriented in your case? > a rotation of pi/4 around z would do.. > stefano > > > On 09/09/2012 04:35 AM, Peng Chen wrote: > > Hi All, > > When I tried to do GGA/GGA+U computation on Ni3V2O8, the occupation number > of Ni looks a little weird. In this compound, d orbitals of Ni split into > t2g (dxy, dxz,dyz) and eg (dx^2-y^2, dz^2) because of NiO6 octahedral > coordination. So the down spin will occupy t2g states. But both GGA and > GGA+U results show the occupation of dxz, dyz and dx^2-y^2. I tried to > write occupation matrix using starting_ns_eigenvalue so that the > occupation can be dxy, dxz and dyz, but the scf calculation can not reach > convergence. Any suggestion is appreciated! > > > GGA after the first iteration: > eigenvalues: > 0.059 0.066 0.075 0.146 0.161 > eigenvectors: > 0.009 0.001 0.000 0.000 0.990 > 0.000 0.000 0.997 0.003 0.000 > 0.076 0.924 0.000 0.000 0.000 > 0.916 0.075 0.000 0.000 0.009 > 0.000 0.000 0.003 0.997 0.000 > occupations: > 0.160 0.001 0.000 -0.010 0.000 > 0.001 0.075 0.000 0.000 -0.004 > 0.000 0.000 0.066 -0.002 0.001 > -0.010 0.000 -0.002 0.060 0.000 > 0.000 -0.004 0.001 0.000 0.146 > > GGA after scf convergence: > eigenvalues: > 0.336 0.364 0.987 0.988 0.991 > eigenvectors: > 0.030 0.968 0.002 0.000 0.000 > 0.001 0.000 0.026 0.822 0.151 > 0.000 0.000 0.063 0.175 0.761 > 0.000 0.001 0.909 0.002 0.088 > 0.968 0.030 0.000 0.001 0.000 > occupations: > 0.364 -0.003 -0.014 0.022 0.005 > -0.003 0.988 -0.001 0.000 -0.024 > -0.014 -0.001 0.990 0.001 0.001 > 0.022 0.000 0.001 0.987 -0.001 > 0.005 -0.024 0.001 -0.001 0.338 > > > GGA+U after the first iteration: > eigenvalues: > 0.071 0.079 0.095 0.157 0.172 > eigenvectors: > 0.008 0.000 0.000 0.000 0.992 > 0.024 0.363 0.607 0.006 0.000 > 0.000 0.630 0.369 0.001 0.000 > 0.967 0.006 0.018 0.000 0.008 > 0.000 0.000 0.006 0.993 0.000 > occupations: > 0.171 0.001 0.001 -0.009 0.000 > 0.001 0.089 -0.008 -0.003 -0.005 > 0.001 -0.008 0.085 0.001 0.002 > -0.009 -0.003 0.001 0.072 0.000 > 0.000 -0.005 0.002 0.000 0.157 > > GGA+U after scf convergence: > eigenvalues: > 0.265 0.306 0.995 0.996 0.996 > eigenvectors: > 0.010 0.988 0.001 0.000 0.000 > 0.001 0.000 0.003 0.919 0.077 > 0.000 0.000 0.098 0.060 0.841 > 0.000 0.001 0.897 0.020 0.082 > 0.989 0.010 0.000 0.001 0.000 > occupations: > 0.307 -0.002 -0.014 0.023 0.004 > -0.002 0.995 0.000 0.000 -0.024 > -0.014 0.000 0.996 0.001 0.000 > 0.023 0.000 0.001 0.994 -0.001 > 0.004 -0.024 0.000 -0.001 0.266 > > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://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/20120909/b039298b/attachment.htm From giannozz at democritos.it Sun Sep 9 18:59:50 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 9 Sep 2012 18:59:50 +0200 Subject: [Pw_forum] Error/Warning in Ph.x In-Reply-To: <20120908183750.12451.qmail@f4mail-235-195.rediffmail.com> References: <20120908183750.12451.qmail@f4mail-235-195.rediffmail.com> Message-ID: <16CD730C-C46F-4877-9D74-C1ED97E132CC@democritos.it> On Sep 8, 2012, at 20:37 , ramesh kumar wrote: > During phonon calculation i get a message like this. > Tried to find the answer in the pw_forum got > something similar but couldnt figure what it is. it is either a mistake or a spurious character in your input P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Sep 9 19:02:20 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 9 Sep 2012 19:02:20 +0200 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information In-Reply-To: <6A5A4CC6-FAFD-493F-BE0D-A14050D5202E@colorado.edu> References: <6A5A4CC6-FAFD-493F-BE0D-A14050D5202E@colorado.edu> Message-ID: <4BB50CD6-31E6-464D-A479-0252E48823C8@democritos.it> On Sep 8, 2012, at 23:03 , Matthew M Montemore wrote: > author='"Lorenzo Paulatto" ', remove "<" and ">" in this line P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From raamesh123 at rediffmail.com Mon Sep 10 13:53:10 2012 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 10 Sep 2012 11:53:10 -0000 Subject: [Pw_forum] =?utf-8?q?Error/Warning_in_Ph=2Ex_=28Paolo_Giannozzi?= =?utf-8?q?=29?= In-Reply-To: Message-ID: <1347263012.S.11409.21756.H.TnB3X2ZvcnVtLXJlcXVlc3RAcHdzY2Yub3JnAFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDYzLCBJc3N1ZSAyMQ__.RU.rfs215, rfs215, 950, 500.f4-235-237.old.1347277990.2923@webmail.rediffmail.com> Dear Prof Paolo Thank you for the answer. Here with i am attaching my input file. Electron-phonon coefficients for pd2ZrGa12.2nm-alpha &inputph tr2_ph=1.0d-10, prefix='pd2ZrGa12.2nm-alpha', fildvscf='Pd2ZrGadv', amass(1)= 91.224 amass(2)= 106.42 amass(3)= 69.723 outdir='/home/ramesh/tmp/', fildyn='Pd2ZrGa.dyn', electron_phonon='interpolated', trans=.true., ldisp=.true. nq1=2, nq2=2, nq3=2 / Apart from the error msg the calculation is running and showing convergence for all the modes. with regards ramesh 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/20120910/50762b6a/attachment.htm From pchen at ion.chem.utk.edu Mon Sep 10 16:35:39 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 10 Sep 2012 10:35:39 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem Message-ID: Dear All, I tried to calculate an insulator Ni3V2O3 using pbe norm conserving pp from pslibrary. But the energy related with ecutwfc is not converged. It reaches minimum at ecutwfc=80 Ry. But when I fix ecutrho=320 Ry and increase ecutwfc, it starts to decrease monotonically. I am not sure if the system reaches the convergence at ecutwfc=80 Ry. (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) ecutrho=4*ecutwfc ecutwfc energy total force 30 -1086.672528 1.335253 40 -1119.972723 0.690327 50 -1129.973333 0.690484 60 -1134.622157 0.640747 70 -1136.892534 0.617201 80 -1137.666471 0.616635 90 -1137.620919 0.610216 100 -1137.238099 0.615361 110 -1136.89911 0.62063 120 -1136.866006 0.622763 Fixing ecutrho=360 Ry 80 -1137.58272 0.62097 84 -1137.73562 0.61824 88 -1137.84215 0.61622 92 -1137.91512 0.61511 96 -1137.96457 0.61475 100 -1137.99772 0.61473 -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120910/0114cd73/attachment.htm From xjamesmao at gmail.com Mon Sep 10 18:17:13 2012 From: xjamesmao at gmail.com (James Mao) Date: Mon, 10 Sep 2012 12:17:13 -0400 Subject: [Pw_forum] question about pp for Raman calculation Message-ID: <000301cd8f6f$bd7d4de0$3877e9a0$@com> Hi dear all, I am new to qe, as well as computations in solid states. I am trying to calculate a Raman spectrum for a crystal, and have a question: for pp used in a photon calculation, does the result still make sense if the different atoms' pp have different source? Namely, different xc func (pz, vwn, ..., but same xc approx such as LDA), or different psp class (mt, hbs, vbc...). The reason for asking this question is that it seems photon code can only calculate Raman for LDA pp, and they cannot be relativistic, ultrasoft or paw. So the choice is really limited. For example, I cannot find an available pp for F atom to perform the calculation, and no suitable pp from same source for C, O, N. I think the correct way probably is to learn how to generate pp by myself, but it might take a while to learn and I would like to set up the calculation first. I have used pz-vbc for C and pz-mt for O, but cannot find any available LDA pp for F which is not ultrasoft and paw. Any help will be greatly appreciated! Best, J. Mao ----------------------------------------------- postdoc, department of chemistry, university of pittsburgh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120910/889594b0/attachment.htm From giannozz at democritos.it Mon Sep 10 18:22:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 18:22:41 +0200 Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <000301cd8f6f$bd7d4de0$3877e9a0$@com> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> Message-ID: <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-10 at 12:17 -0400, James Mao wrote: > cannot find any available LDA pp for F which is not ultrasoft > and paw. there's a reason: norm-conserving F is very hard. Anyway, if you follow the links in the pseudopotential page of the quantum espresso web site, you will find for sure some norm-conserving LDA PP for F. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From akohlmey at gmail.com Mon Sep 10 18:24:53 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 10 Sep 2012 18:24:53 +0200 Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> Message-ID: On Mon, Sep 10, 2012 at 6:22 PM, Paolo Giannozzi wrote: > On Mon, 2012-09-10 at 12:17 -0400, James Mao wrote: > >> cannot find any available LDA pp for F which is not ultrasoft >> and paw. > > there's a reason: norm-conserving F is very hard. Anyway, if you > follow the links in the pseudopotential page of the quantum espresso > web site, you will find for sure some norm-conserving LDA PP for F. ...and you should probably also start looking for a bigger/faster computer, so you can afford the cutoff. ;) axel. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From jen7182 at hotmail.com Mon Sep 10 18:26:55 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Mon, 10 Sep 2012 12:26:55 -0400 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: References: Message-ID: I'm trying to instal on a Cray XE6 and when I use 'make all' I get this error concerning 'global_version.mod'. I've tried to find this on the website/forum etc but I haven't seen it mentioned, could anyone tell me what this mod is and where it's located? test -d bin || mkdir bin cd install ; make -f extlibs_makefile libiotk make[1]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/install' if test ! -d ../S3DE; then \ (gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ if test -e Makefile_iotk; then \ (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ if test -e iotk_config.h; then \ (cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi cd ../S3DE/iotk/src; make lib+util; make[2]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/S3DE/iotk/src' make[2]: Nothing to be done for `lib+util'. make[2]: Leaving directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/S3DE/iotk/src' cd ../bin; ln -fs ../S3DE/iotk/tools/iotk .; \ ln -fs ../S3DE/iotk/src/iotk.x .; \ ln -fs ../S3DE/iotk/src/iotk_print_kinds.x .; \ cd ../; ln -fs S3DE/iotk iotk make[1]: Leaving directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/install' ( cd Modules ; if test "make" = "" ; then make TLDEPS= all ; \ else make TLDEPS= all ; fi ) make[1]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/Modules' ftn -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA -I../include -I../iotk/src -I. -c environment.f90 environment.f90:18.56: USE global_version, ONLY: version_number, svn_revision 1 Fatal Error: Can't open module file 'global_version.mod' for reading at (1): No such file or directory Thank you, J. Wohlwend Universal Technology Corp. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120910/929160b4/attachment.htm From bamideleibrahim at yahoo.com Mon Sep 10 18:40:16 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Mon, 10 Sep 2012 09:40:16 -0700 (PDT) Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <000301cd8f6f$bd7d4de0$3877e9a0$@com> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> Message-ID: <1347295216.73642.YahooMailNeo@web39405.mail.mud.yahoo.com> Dear James, You can check the pslibrary pp here .'http://qe-forge.org/gf/project/pslibrary/frs/' ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: James Mao To: Pw_forum at pwscf.org Sent: Monday, September 10, 2012 5:17 PM Subject: [Pw_forum] question about pp for Raman calculation Hi dear all, ? I am new to qe, as well as computations in solid states. I am trying to calculate a Raman spectrum for a crystal, and have a question: for pp used in a photon calculation, does the result still make sense if the different atoms' pp have different source? Namely, different xc func (pz, vwn, ..., but same xc approx such as LDA), or different psp class (mt, hbs, vbc...). ? The reason for asking this question is that it seems photon code can only calculate Raman for LDA pp, and they cannot be relativistic, ultrasoft or paw. So the choice is really limited. For example, I cannot find an available pp for F atom to perform the calculation, and no suitable pp from same source for C, O, N. I think the correct way probably is to learn how to generate pp by myself, but it might take a while to learn and I would like to set up the calculation first. I have used pz-vbc for C and pz-mt for O, but cannot find any available LDA pp for F which is not ultrasoft and paw. ? Any help will be greatly appreciated! ? Best, J. Mao ----------------------------------------------- postdoc, department of chemistry, university of pittsburgh _______________________________________________ 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/20120910/09ae46f4/attachment-0001.htm From giannozz at democritos.it Mon Sep 10 18:46:07 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 18:46:07 +0200 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: References: Message-ID: <1347295567.17175.61.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-10 at 12:26 -0400, Jennifer Wohlwend wrote: > I get this error concerning 'global_version.mod' go into Modules/, type "make version.f90". It should produce a file version.f90 from version.f90.in (see Makefile and ../install/update_version if you want to understand what is going on). If it doesn't, please report any error message. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From jen7182 at hotmail.com Mon Sep 10 18:57:07 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Mon, 10 Sep 2012 12:57:07 -0400 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: <1347295567.17175.61.camel@fe12lx.fisica.uniud.it> References: , , <1347295567.17175.61.camel@fe12lx.fisica.uniud.it> Message-ID: It says: make: `version.f90' is up to date. after, I tried make all again and received the same message When I looked at version.f90, it was empty J. Wohlwend Universal Technology Corp. > From: giannozz at democritos.it > To: pw_forum at pwscf.org > Date: Mon, 10 Sep 2012 18:46:07 +0200 > Subject: Re: [Pw_forum] make error (module global_version.mod) > > On Mon, 2012-09-10 at 12:26 -0400, Jennifer Wohlwend wrote: > > > I get this error concerning 'global_version.mod' > > > go into Modules/, type "make version.f90". It should produce > a file version.f90 from version.f90.in (see Makefile and > ../install/update_version if you want to understand what is > going on). If it doesn't, please report any error message. > > P. > -- > Paolo Giannozzi, IOM-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/20120910/7589d97a/attachment.htm From giannozz at democritos.it Mon Sep 10 19:18:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 19:18:58 +0200 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: References: , , <1347295567.17175.61.camel@fe12lx.fisica.uniud.it> Message-ID: <6DA522D8-5F89-4EDD-AD16-0745F5D58567@democritos.it> On Sep 10, 2012, at 18:57 , Jennifer Wohlwend wrote: > When I looked at version.f90, it was empty remove version.f90, retry. If it is still empty: edit ../install/update_version, removing redirections to /dev/null (things like this: "2> /dev/null > /dev/null"). Set the script to verbose (not sure whether #!/bin/sh -x will do the job). Run again ../install/update_version, report what happens, what is in file version.f90.tmp if any If no quick solution is found, just copy version.f90.in to version.f90 P. > > J. Wohlwend > Universal Technology Corp. > > > From: giannozz at democritos.it > > To: pw_forum at pwscf.org > > Date: Mon, 10 Sep 2012 18:46:07 +0200 > > Subject: Re: [Pw_forum] make error (module global_version.mod) > > > > On Mon, 2012-09-10 at 12:26 -0400, Jennifer Wohlwend wrote: > > > > > I get this error concerning 'global_version.mod' > > > > > > go into Modules/, type "make version.f90". It should produce > > a file version.f90 from version.f90.in (see Makefile and > > ../install/update_version if you want to understand what is > > going on). If it doesn't, please report any error message. > > > > P. > > -- > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > > _______________________________________________ > > 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 --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Mon Sep 10 20:48:23 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 10 Sep 2012 19:48:23 +0100 Subject: [Pw_forum] comparison of ph.x and dynmat.x results In-Reply-To: <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> References: , <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> Message-ID: Professor de Gironcoli, First of all. thanks for your suggestion. Concerning moving the atoms along the modes, how can this be done? How do we know their directions? Vizualizing them in XCrysDen, for example, would not help I guess because they will be set to zero Thanks in advance. Elie > Date: Sat, 8 Sep 2012 09:17:05 +0200 > From: degironc at sissa.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] comparison of ph.x and dynmat.x results > > negative (imaginary) frequencies signal instabilities. > acoustic modes (i.e. rigid global translations on the crystal) at > gamma should always have zero frequencies but for numerical reasons > they can result in small positive or negative values that can be fixed > by the acoustic sum rule. > > in your case the modee at -49, 50 and 73 are the acoustic modes that > vanish after ASR inclusion. > the modes around -370 are other modes and they are unstable.. > > move the atoms of your structure along one of this modes and relax it again. > this will probably break a symmetry that prevented your system to > reach complete relaxation > > stefano > > > Quoting Elie M : > > > Dear all, I have done phonon calculations at the Gamma point to find > > the vibrational frequencies of a system I am working on and I got > > three negative frequencies; the results are: > > q = ( 0.000000000 0.000000000 0.000000000 ) > > > > ************************************************************************** > > omega( 1) = -11.303890 [THz] = -377.057178 [cm-1] > > omega( 2) = -11.228798 [THz] = -374.552397 [cm-1] omega( > > 3) = -1.493780 [THz] = -49.827127 [cm-1] omega( 4) = > > 1.499866 [THz] = 50.030148 [cm-1] omega( 5) = > > 2.192955 [THz] = 73.149113 [cm-1] omega( 6) = > > 11.690342 [THz] = 389.947822 [cm-1] omega( 7) = > > 15.929343 [THz] = 531.345701 [cm-1] omega( 8) = > > 17.762801 [THz] = 592.503255 [cm-1] omega( 9) = > > 17.814756 [THz] = 594.236307 [cm-1] omega(10) = > > 22.128875 [THz] = 738.139807 [cm-1] omega(11) = > > 24.754227 [THz] = 825.712121 [cm-1] omega(12) = > > 25.174421 [THz] = 839.728307 [cm-1] omega(13) = > > 25.229402 [THz] = 841.562251 [cm-1] omega(14) = > > 31.677488 [THz] = 1056.647257 [cm-1] omega(15) = > > 32.931458 [THz] = 1098.475192 [cm-1] omega(16) = > > 32.974208 [THz] = 1099.901170 [cm-1] omega(17) = > > 37.529033 [THz] = 1251.833794 [cm-1] omega(18) = > > 37.585396 [THz] = 1253.713860 [cm-1] omega(19) = > > 38.689108 [THz] = 1290.529726 [cm-1] omega(20) = > > 44.468725 [THz] = 1483.317012 [cm-1] omega(21) = > > 44.490793 [THz] = 1484.053106 [cm-1] omega(22) = > > 100.618488 [THz] = 3356.271501 [cm-1] omega(23) = > > 100.705119 [THz] = 3359.161186 [cm-1] omega(24) = > > 103.337467 [THz] = 3446.966862 [cm-1] > > To check whether the first three freqnecies are the accoustic ones > > and not instabilities i applied dynmat.x with asr='crystal' and got: > > mode [cm-1] [THz] IR 1 -377.06 -11.3039 > > 0.0000 2 -374.55 -11.2287 0.0000 3 0.00 0.0000 > > 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 > > 0.0000 6 406.11 12.1749 0.0000 7 531.35 15.9293 > > 0.0000 8 592.50 17.7628 0.0000 9 594.24 > > 17.8148 0.0000 10 738.13 22.1286 0.0000 11 828.85 > > 24.8482 0.0000 12 839.68 25.1730 0.0000 13 841.62 > > 25.2311 0.0000 14 1056.65 31.6775 0.0000 15 > > 1099.09 32.9498 0.0000 16 1099.25 32.9547 0.0000 17 > > 1251.32 37.5135 0.0000 18 1253.47 37.5781 0.0000 19 > > 1290.53 38.6891 0.0000 20 1483.05 44.4608 0.0000 > > 21 1485.30 44.5283 0.0000 22 3356.09 100.6131 0.0000 > > 23 3359.58 100.7178 0.0000 24 3446.96 103.3373 0.0000 > > As it is seen, the freqencies are very close but the thing and the > > system is stable! Howevere,I could not understand is about the first > > 5 frequencies: i still got the first two negative but in addition i > > have 3 more zero frequencies; does it mean we have five accoustic > > modes due to the symmetry of this particular system? > > > > Thanks in advance > > Elie KoujaesUniversity of NottsNG7 2RDUK > > > _______________________________________________ > 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/20120910/b1b1d691/attachment.htm From xjamesmao at gmail.com Mon Sep 10 20:49:21 2012 From: xjamesmao at gmail.com (James Mao) Date: Mon, 10 Sep 2012 14:49:21 -0400 Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> Message-ID: <000001cd8f85$00570e20$01052a60$@com> Dr. Giannozzi, I checked the pslibrary and NNIN vault links. All LDA PP there for F are paw or ultrasoft. It seems there are more LDA PP in abinit website. But they are in different format. Maybe I should try my luck to convert them to PP format in QE. Best, J. Mao ---- Department of Chemistry, University of Pittsburgh -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Monday, September 10, 2012 12:23 PM To: PWSCF Forum Subject: Re: [Pw_forum] question about pp for Raman calculation On Mon, 2012-09-10 at 12:17 -0400, James Mao wrote: > cannot find any available LDA pp for F which is not ultrasoft and paw. there's a reason: norm-conserving F is very hard. Anyway, if you follow the links in the pseudopotential page of the quantum espresso web site, you will find for sure some norm-conserving LDA PP for F. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From xjamesmao at gmail.com Mon Sep 10 20:49:21 2012 From: xjamesmao at gmail.com (James Mao) Date: Mon, 10 Sep 2012 14:49:21 -0400 Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <1347295216.73642.YahooMailNeo@web39405.mail.mud.yahoo.com> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347295216.73642.YahooMailNeo@web39405.mail.mud.yahoo.com> Message-ID: <000701cd8f85$0269c180$073d4480$@com> Hi Adetunji, I did checked the PSLibrary 2.0.5 pp. But all LDA pp there are either us (ultrasoft) or paw, which are not supported by photon Raman code. Best, J. Mao ------------------------- Department of chemistry, University of pittsburgh From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of bamidele ibrahim Sent: Monday, September 10, 2012 12:40 PM To: PWSCF Forum Subject: Re: [Pw_forum] question about pp for Raman calculation Dear James, You can check the pslibrary pp here .'http://qe-forge.org/gf/project/pslibrary/frs/' ---------------------------------------------------------------------------- ----------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. ---------------------------------------------------------------------------- ----------------------- _____ From: James Mao To: Pw_forum at pwscf.org Sent: Monday, September 10, 2012 5:17 PM Subject: [Pw_forum] question about pp for Raman calculation Hi dear all, I am new to qe, as well as computations in solid states. I am trying to calculate a Raman spectrum for a crystal, and have a question: for pp used in a photon calculation, does the result still make sense if the different atoms' pp have different source? Namely, different xc func (pz, vwn, ..., but same xc approx such as LDA), or different psp class (mt, hbs, vbc...). The reason for asking this question is that it seems photon code can only calculate Raman for LDA pp, and they cannot be relativistic, ultrasoft or paw. So the choice is really limited. For example, I cannot find an available pp for F atom to perform the calculation, and no suitable pp from same source for C, O, N. I think the correct way probably is to learn how to generate pp by myself, but it might take a while to learn and I would like to set up the calculation first. I have used pz-vbc for C and pz-mt for O, but cannot find any available LDA pp for F which is not ultrasoft and paw. Any help will be greatly appreciated! Best, J. Mao ----------------------------------------------- postdoc, department of chemistry, university of pittsburgh _______________________________________________ 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/20120910/cf7362e1/attachment-0001.htm From giannozz at democritos.it Mon Sep 10 20:52:55 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 20:52:55 +0200 Subject: [Pw_forum] question about pp for Raman calculation In-Reply-To: <000001cd8f85$00570e20$01052a60$@com> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> <000001cd8f85$00570e20$01052a60$@com> Message-ID: <1A6307F6-783E-44A8-8095-C8D04916F1DD@democritos.it> On Sep 10, 2012, at 20:49 , James Mao wrote: > It seems there are more LDA PP in abinit website. But they are > in different format. Maybe I should try my luck to convert them > to PP format in QE. there is a converter from FHI format P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Matthew.Montemore at Colorado.EDU Mon Sep 10 21:11:09 2012 From: Matthew.Montemore at Colorado.EDU (Matthew M Montemore) Date: Mon, 10 Sep 2012 13:11:09 -0600 Subject: [Pw_forum] Problem with Pseudopotentials and Input Information In-Reply-To: References: Message-ID: > > > On Sep 8, 2012, at 23:03 , Matthew M Montemore wrote: > >> author='"Lorenzo Paulatto" ', > > remove "<" and ">" in this line > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > Yep, that fixed it. Thanks for your help, and to the others who came up with the same solution. Matt Montemore University of Colorado Boulder From vinayhegde at jncasr.ac.in Mon Sep 10 21:13:49 2012 From: vinayhegde at jncasr.ac.in (Vinay Hegde) Date: Tue, 11 Sep 2012 00:43:49 +0530 Subject: [Pw_forum] comparison of ph.x and dynmat.x results In-Reply-To: References: <20120908091705.Horde.zhtAWx8V4mxQSvDxjXeWR4A@webmail.sissa.it> Message-ID: Dear Elie, > > First of all. thanks for your suggestion. Concerning moving the atoms along > the modes, how can this be done? How do we know their directions? > Use the eigenvectors (of the dynamical matrix) corresponding to the unstable eigenvalues to move the atoms of your structure. Relax your structure after that. Hope this helps, Vinay -- Vinay Ishwar Hegde Graduate Student Theoretical Sciences Unit (TSU) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur, Bangalore 560 064 Email: vinayhegde at jncasr.ac.in Phone: +91-96639-92336 From giannozz at democritos.it Mon Sep 10 21:45:40 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 21:45:40 +0200 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: On Sep 10, 2012, at 16:35 , Peng Chen wrote: > I tried to calculate an insulator Ni3V2O3 using pbe norm conserving > pp from pslibrary. But the energy related with ecutwfc is not > converged. It reaches minimum at ecutwfc=80 Ry. But when I fix > ecutrho=320 Ry and increase ecutwfc, it starts to decrease > monotonically. I am not sure if the system reaches the convergence > at ecutwfc=80 Ry. > (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) if it is an insulator, why are you using smearing? Apart from this: with norm-conserving PP, ecutwfc is the only parameter defining the basis set. You should not set ecutrho. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jen7182 at hotmail.com Mon Sep 10 21:57:17 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Mon, 10 Sep 2012 15:57:17 -0400 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: <6DA522D8-5F89-4EDD-AD16-0745F5D58567@democritos.it> References: , , , , <1347295567.17175.61.camel@fe12lx.fisica.uniud.it>, , <6DA522D8-5F89-4EDD-AD16-0745F5D58567@democritos.it> Message-ID: Thank you so much for your suggestion, removing the /dev/null statements produced another error so I copied version.f90.in to version.f90 and it was successful. Thank you again! J. Wohlwend > From: giannozz at democritos.it > Date: Mon, 10 Sep 2012 19:18:58 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] make error (module global_version.mod) > > > On Sep 10, 2012, at 18:57 , Jennifer Wohlwend wrote: > > > When I looked at version.f90, it was empty > > remove version.f90, retry. If it is still empty: > edit ../install/update_version, removing > redirections to /dev/null (things like this: > "2> /dev/null > /dev/null"). > Set the script to verbose (not sure whether > #!/bin/sh -x will do the job). Run again > ../install/update_version, report what > happens, what is in file version.f90.tmp if any > > If no quick solution is found, just copy version.f90.in > to version.f90 > > P. > > > > J. Wohlwend > > Universal Technology Corp. > > > > > From: giannozz at democritos.it > > > To: pw_forum at pwscf.org > > > Date: Mon, 10 Sep 2012 18:46:07 +0200 > > > Subject: Re: [Pw_forum] make error (module global_version.mod) > > > > > > On Mon, 2012-09-10 at 12:26 -0400, Jennifer Wohlwend wrote: > > > > > > > I get this error concerning 'global_version.mod' > > > > > > > > > go into Modules/, type "make version.f90". It should produce > > > a file version.f90 from version.f90.in (see Makefile and > > > ../install/update_version if you want to understand what is > > > going on). If it doesn't, please report any error message. > > > > > > P. > > > -- > > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > > > > > _______________________________________________ > > > 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 > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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/20120910/5eeb6b09/attachment.htm From giannozz at democritos.it Mon Sep 10 22:03:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 22:03:41 +0200 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: References: , , , , <1347295567.17175.61.camel@fe12lx.fisica.uniud.it>, , <6DA522D8-5F89-4EDD-AD16-0745F5D58567@democritos.it> Message-ID: <55621D1C-F3A1-4582-897D-AC886F6A6515@democritos.it> On Sep 10, 2012, at 21:57 , Jennifer Wohlwend wrote: > Thank you so much for your suggestion, removing the /dev/null > statements produced another error WHICH ERROR ?!? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Sep 10 22:07:14 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Sep 2012 22:07:14 +0200 Subject: [Pw_forum] electron phonon coupling in semiconductors In-Reply-To: References: Message-ID: <2A1F20B3-C5EA-4CB9-8E94-46283073FDFA@democritos.it> On Sep 7, 2012, at 22:45 , Bo Qiu wrote: > why QE cannot do el-ph for semiconductors? because - as explained too many times - QE calculates the "electron-phonon coupling coefficient \lambda", something that exists only in metals. Electon-phonon matrix elements are also calculated, but if you want to do something else than calculating \lambda with them, you have to modify the code P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pchen at ion.chem.utk.edu Mon Sep 10 23:02:09 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 10 Sep 2012 17:02:09 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: Dear Dr. Giannozzi, Thanks for your reply. I use smearing for computing the band structure in afm and fm states. It looks there is still a lot to learn. If I use occupation=fixed to calculate afm/fm states, shall I just set tot_magnetization=0 or 1? If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So the results are the same as the following, and the energy doesn't decrease monotonically. I tried to decrease degauss to 0.005 Ry, I got the similar results. What I can do to make the energy converge? ecutrho=4*ecutwfc ecutwfc energy total force 30 -1086.672528 1.335253 40 -1119.972723 0.690327 50 -1129.973333 0.690484 60 -1134.622157 0.640747 70 -1136.892534 0.617201 *80 -1137.666471 0.616635* 90 -1137.620919 0.610216 100 -1137.238099 0.615361 110 -1136.89911 0.62063 120 -1136.866006 0.622763 On Mon, Sep 10, 2012 at 3:45 PM, Paolo Giannozzi wrote: > > On Sep 10, 2012, at 16:35 , Peng Chen wrote: > > > I tried to calculate an insulator Ni3V2O3 using pbe norm conserving > > pp from pslibrary. But the energy related with ecutwfc is not > > converged. It reaches minimum at ecutwfc=80 Ry. But when I fix > > ecutrho=320 Ry and increase ecutwfc, it starts to decrease > > monotonically. I am not sure if the system reaches the convergence > > at ecutwfc=80 Ry. > > (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) > > if it is an insulator, why are you using smearing? Apart from this: > with norm-conserving PP, ecutwfc is the only parameter defining > the basis set. You should not set ecutrho. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120910/e93125e1/attachment-0001.htm From jiachenchem at gmail.com Mon Sep 10 23:17:34 2012 From: jiachenchem at gmail.com (Jia Chen) Date: Mon, 10 Sep 2012 17:17:34 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: Dear Peng, For AFM case, you can set tot_magentization = 0, for FM case, you need to know tot_magnetization from experiments or previous calculations. Or you can use the int(absolute magnetization) from you AFM calculations. Trying to converge total energy with respect to wave function cutoff is usually not a good idea. If you just want to choose a good cutoff energy for calculations, first thing you can do is to look into those pseudopotentials you are using. If you can find recommended cutoffs, you probably can just use the highest cutoffs in your system. Bests Jia On Mon, Sep 10, 2012 at 5:02 PM, Peng Chen wrote: > Dear Dr. Giannozzi, > > Thanks for your reply. I use smearing for computing the band structure in > afm and fm states. It looks there is still a lot to learn. If I use > occupation=fixed to calculate afm/fm states, shall I just set > tot_magnetization=0 or 1? > > If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So the > results are the same as the following, and the energy doesn't decrease > monotonically. I tried to decrease degauss to 0.005 Ry, I got the similar > results. What I can do to make the energy converge? > > ecutrho=4*ecutwfc > ecutwfc energy total force > 30 -1086.672528 1.335253 > 40 -1119.972723 0.690327 > 50 -1129.973333 0.690484 > 60 -1134.622157 0.640747 > 70 -1136.892534 0.617201 > 80 -1137.666471 0.616635 > 90 -1137.620919 0.610216 > 100 -1137.238099 0.615361 > 110 -1136.89911 0.62063 > 120 -1136.866006 0.622763 > > On Mon, Sep 10, 2012 at 3:45 PM, Paolo Giannozzi > wrote: >> >> >> On Sep 10, 2012, at 16:35 , Peng Chen wrote: >> >> > I tried to calculate an insulator Ni3V2O3 using pbe norm conserving >> > pp from pslibrary. But the energy related with ecutwfc is not >> > converged. It reaches minimum at ecutwfc=80 Ry. But when I fix >> > ecutrho=320 Ry and increase ecutwfc, it starts to decrease >> > monotonically. I am not sure if the system reaches the convergence >> > at ecutwfc=80 Ry. >> > (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) >> >> if it is an insulator, why are you using smearing? Apart from this: >> with norm-conserving PP, ecutwfc is the only parameter defining >> the basis set. You should not set ecutrho. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. 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 > > > > > -- > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Jia Chen webpage: www.princeton.edu/~jiachen From pchen at ion.chem.utk.edu Tue Sep 11 03:48:10 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 10 Sep 2012 21:48:10 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: Dear Jia, I checked those pp and there are not recommended cutoffs. When I use occupation=fixed, the results are similar as those from occupation=smearing (reach minimum at 80 Ry) . And the scf doesn't converge when ecutwfc=60 Ry. Ecutwfc energy total force 50 -1129.7209 0.7937 60 no convergence 70 -1136.6081 0.7066 80 -1137.3776 0.7059 90 -1137.3342 0.6997 100 -1136.9523 0.7056 On Mon, Sep 10, 2012 at 5:17 PM, Jia Chen wrote: > Dear Peng, > > For AFM case, you can set tot_magentization = 0, for FM case, you need > to know tot_magnetization from experiments or previous calculations. > Or you can use the int(absolute magnetization) from you AFM > calculations. > > Trying to converge total energy with respect to wave function cutoff > is usually not a good idea. If you just want to choose a good cutoff > energy for calculations, first thing you can do is to look into those > pseudopotentials you are using. If you can find recommended cutoffs, > you probably can just use the highest cutoffs in your system. > > Bests > Jia > > On Mon, Sep 10, 2012 at 5:02 PM, Peng Chen wrote: > > Dear Dr. Giannozzi, > > > > Thanks for your reply. I use smearing for computing the band structure in > > afm and fm states. It looks there is still a lot to learn. If I use > > occupation=fixed to calculate afm/fm states, shall I just set > > tot_magnetization=0 or 1? > > > > If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So > the > > results are the same as the following, and the energy doesn't decrease > > monotonically. I tried to decrease degauss to 0.005 Ry, I got the similar > > results. What I can do to make the energy converge? > > > > ecutrho=4*ecutwfc > > ecutwfc energy total force > > 30 -1086.672528 1.335253 > > 40 -1119.972723 0.690327 > > 50 -1129.973333 0.690484 > > 60 -1134.622157 0.640747 > > 70 -1136.892534 0.617201 > > 80 -1137.666471 0.616635 > > 90 -1137.620919 0.610216 > > 100 -1137.238099 0.615361 > > 110 -1136.89911 0.62063 > > 120 -1136.866006 0.622763 > > > > On Mon, Sep 10, 2012 at 3:45 PM, Paolo Giannozzi > > > wrote: > >> > >> > >> On Sep 10, 2012, at 16:35 , Peng Chen wrote: > >> > >> > I tried to calculate an insulator Ni3V2O3 using pbe norm conserving > >> > pp from pslibrary. But the energy related with ecutwfc is not > >> > converged. It reaches minimum at ecutwfc=80 Ry. But when I fix > >> > ecutrho=320 Ry and increase ecutwfc, it starts to decrease > >> > monotonically. I am not sure if the system reaches the convergence > >> > at ecutwfc=80 Ry. > >> > (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) > >> > >> if it is an insulator, why are you using smearing? Apart from this: > >> with norm-conserving PP, ecutwfc is the only parameter defining > >> the basis set. You should not set ecutrho. > >> > >> P. > >> --- > >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > >> Univ. 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 > > > > > > > > > > -- > > Best Regards. > > Peng > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Jia Chen > webpage: www.princeton.edu/~jiachen > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120910/a00e8a29/attachment.htm From jiachenchem at gmail.com Tue Sep 11 05:10:24 2012 From: jiachenchem at gmail.com (Jia Chen) Date: Mon, 10 Sep 2012 23:10:24 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: O norm-conserving usually need 70Ry, since you have d electrons in your system, they may require higher cutoff. Some people calculate lattice constants to justify their choice of cutoff, but It finally depends on what do you study. Not much more I can say about it... On Mon, Sep 10, 2012 at 9:48 PM, Peng Chen wrote: > Dear Jia, > > I checked those pp and there are not recommended cutoffs. When I use > occupation=fixed, the results are similar as those from occupation=smearing > (reach minimum at 80 Ry) . And the scf doesn't converge when ecutwfc=60 Ry. > > Ecutwfc energy total force > 50 -1129.7209 0.7937 > 60 no convergence > 70 -1136.6081 0.7066 > 80 -1137.3776 0.7059 > 90 -1137.3342 0.6997 > 100 -1136.9523 0.7056 > > On Mon, Sep 10, 2012 at 5:17 PM, Jia Chen wrote: >> >> Dear Peng, >> >> For AFM case, you can set tot_magentization = 0, for FM case, you need >> to know tot_magnetization from experiments or previous calculations. >> Or you can use the int(absolute magnetization) from you AFM >> calculations. >> >> Trying to converge total energy with respect to wave function cutoff >> is usually not a good idea. If you just want to choose a good cutoff >> energy for calculations, first thing you can do is to look into those >> pseudopotentials you are using. If you can find recommended cutoffs, >> you probably can just use the highest cutoffs in your system. >> >> Bests >> Jia >> >> On Mon, Sep 10, 2012 at 5:02 PM, Peng Chen wrote: >> > Dear Dr. Giannozzi, >> > >> > Thanks for your reply. I use smearing for computing the band structure >> > in >> > afm and fm states. It looks there is still a lot to learn. If I use >> > occupation=fixed to calculate afm/fm states, shall I just set >> > tot_magnetization=0 or 1? >> > >> > If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So >> > the >> > results are the same as the following, and the energy doesn't decrease >> > monotonically. I tried to decrease degauss to 0.005 Ry, I got the >> > similar >> > results. What I can do to make the energy converge? >> > >> > ecutrho=4*ecutwfc >> > ecutwfc energy total force >> > 30 -1086.672528 1.335253 >> > 40 -1119.972723 0.690327 >> > 50 -1129.973333 0.690484 >> > 60 -1134.622157 0.640747 >> > 70 -1136.892534 0.617201 >> > 80 -1137.666471 0.616635 >> > 90 -1137.620919 0.610216 >> > 100 -1137.238099 0.615361 >> > 110 -1136.89911 0.62063 >> > 120 -1136.866006 0.622763 >> > >> > On Mon, Sep 10, 2012 at 3:45 PM, Paolo Giannozzi >> > >> > wrote: >> >> >> >> >> >> On Sep 10, 2012, at 16:35 , Peng Chen wrote: >> >> >> >> > I tried to calculate an insulator Ni3V2O3 using pbe norm conserving >> >> > pp from pslibrary. But the energy related with ecutwfc is not >> >> > converged. It reaches minimum at ecutwfc=80 Ry. But when I fix >> >> > ecutrho=320 Ry and increase ecutwfc, it starts to decrease >> >> > monotonically. I am not sure if the system reaches the convergence >> >> > at ecutwfc=80 Ry. >> >> > (smearing=mv, Degauss=0.01 Ry and kpoints = 4 4 3) >> >> >> >> if it is an insulator, why are you using smearing? Apart from this: >> >> with norm-conserving PP, ecutwfc is the only parameter defining >> >> the basis set. You should not set ecutrho. >> >> >> >> P. >> >> --- >> >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> >> Univ. 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 >> > >> > >> > >> > >> > -- >> > Best Regards. >> > Peng >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Jia Chen >> webpage: www.princeton.edu/~jiachen >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Jia Chen webpage: www.princeton.edu/~jiachen From 200210qb at gmail.com Tue Sep 11 06:11:39 2012 From: 200210qb at gmail.com (Bo Qiu) Date: Tue, 11 Sep 2012 00:11:39 -0400 Subject: [Pw_forum] electron phonon coupling in semiconductors In-Reply-To: <2A1F20B3-C5EA-4CB9-8E94-46283073FDFA@democritos.it> References: <2A1F20B3-C5EA-4CB9-8E94-46283073FDFA@democritos.it> Message-ID: Dear Paolo, Thanks a lot for the explanations! So can I say if I just need Electon-phonon matrix elements (I'll modify code from there to compute other quantities like electron linewidth), there should be no fundamental difficulty for QE to compute them correctly for semiconductors? Thanks a lot again! Bo On Mon, Sep 10, 2012 at 4:07 PM, Paolo Giannozzi wrote: > > On Sep 7, 2012, at 22:45 , Bo Qiu wrote: > > > why QE cannot do el-ph for semiconductors? > > because - as explained too many times - QE calculates the > "electron-phonon coupling coefficient \lambda", something > that exists only in metals. Electon-phonon matrix elements > are also calculated, but if you want to do something else > than calculating \lambda with them, you have to modify the > code > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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/20120911/92477ae3/attachment.htm From giannozz at democritos.it Tue Sep 11 09:16:07 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Sep 2012 09:16:07 +0200 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: References: Message-ID: <1347347767.26330.8.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-10 at 17:02 -0400, Peng Chen wrote: > If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So > the results are the same as the following, and the energy doesn't > decrease monotonically. it has to. The only reason for which the energy might not decrease monotonically is the presence of the nonlinear core correction in pseudpotentials. If you increase even more the cutoff, sooner or later it has to converge. Note that Ni is a very hard element. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From tsakhrawi at yahoo.com Tue Sep 11 10:06:42 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Tue, 11 Sep 2012 09:06:42 +0100 (BST) Subject: [Pw_forum] error 1 Message-ID: <1347350802.77920.YahooMailNeo@web133005.mail.ir2.yahoo.com> Dr. Gianozzi i am new in pwscf calculations: wen calculating lattice the code stops!!!!! ???? Program PWSCF v.4.2??????? starts on 10Sep2012 at 14:52:45 ???? This program is part of the open-source Quantum ESPRESSO suite ???? for quantum simulation of materials; please acknowledge ???????? "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); ????????? URL http://www.quantum-espresso.org", ???? in publications or presentations arising from this work. More details at ???? http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO ???? 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 ???? Waiting for input... ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from? iosys? : error #???????? 1 ????? invalid lattice parameters ( celldm or a ) ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120911/af4f85b2/attachment.htm From amirhosseinba67 at gmail.com Tue Sep 11 11:50:16 2012 From: amirhosseinba67 at gmail.com (Amir hosseini) Date: Tue, 11 Sep 2012 14:20:16 +0430 Subject: [Pw_forum] GPU Message-ID: Dear all I was run a same example on Quantum espresso 5.0 with and without GPU compalibity but my result very amazing. Without GPU, time spending 806s but with GPU, time spending 1600s!!!! From akohlmey at gmail.com Tue Sep 11 11:52:40 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 11 Sep 2012 11:52:40 +0200 Subject: [Pw_forum] GPU In-Reply-To: References: Message-ID: On Tue, Sep 11, 2012 at 11:50 AM, Amir hosseini wrote: > Dear all > > I was run a same example on Quantum espresso 5.0 with and without GPU > compalibity but my result very amazing. not necessarily. > Without GPU, time spending 806s but with GPU, time spending 1600s!!!! benchmarks are completely useless without context: what kind of a GPU do you have and what kind of machine (processor, bus) are you running on? are you running in parallel or serial? axel. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From spiga.filippo at gmail.com Tue Sep 11 13:31:43 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 11 Sep 2012 13:31:43 +0200 Subject: [Pw_forum] GPU In-Reply-To: References: Message-ID: <2CE2178B-44F0-4668-B0C7-BA4568E52B59@gmail.com> Dear Amir, I am afraid most of the examples provided with the suite are excellent examples to understand how to create an input files and deal with multiple parameters of PWscf. But those examples are not suitable for a performance-oriented benchmarking activity. If you want to assess the performance of your CPU+GPU workstation (or cluster) you might need to try some input cases a bit more computational intensive. GPU support has been introduced to tackle heavy computational calculations, by taking advantage by the acceleration provided by the graphic cards. If the test takes one minutes or less using only the GPU, there is no point to look for any additional acceleration with a GPU. I suggest AUSURF112, you can find it here: http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse&frs_package_id=36 ( or the archive "pwscf-small-benchmark.tar.gz") I'll take as personal stuff to provide a small set of new benchmarks (with reference outputs) only for the GPU package. Please, subscribe the mailing-list dedicated to the GPU version of the code here http://qe-forge.org/mailman/listinfo/q-e-gpgpu I will be glad to help you go through any issue you might encounter. Regards, Filippo On Sep 11, 2012, at 11:50 AM, Amir hosseini wrote: > Dear all > > I was run a same example on Quantum espresso 5.0 with and without GPU > compalibity but my result very amazing. > Without GPU, time spending 806s but with GPU, time spending 1600s!!!! -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120911/87a20467/attachment.htm From jen7182 at hotmail.com Tue Sep 11 15:12:46 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Tue, 11 Sep 2012 09:12:46 -0400 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: <55621D1C-F3A1-4582-897D-AC886F6A6515@democritos.it> References: , , , , , , <1347295567.17175.61.camel@fe12lx.fisica.uniud.it>, , , , <6DA522D8-5F89-4EDD-AD16-0745F5D58567@democritos.it>, , <55621D1C-F3A1-4582-897D-AC886F6A6515@democritos.it> Message-ID: + '[' 0 = 0 ']' ++ svnversion -n + svn_rev='Unversioned directory' + test -f version.f90 + mv version.f90.tmp version.f90 mv: cannot stat `version.f90.tmp': No such file or directory > From: giannozz at democritos.it > Date: Mon, 10 Sep 2012 22:03:41 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] make error (module global_version.mod) > > > On Sep 10, 2012, at 21:57 , Jennifer Wohlwend wrote: > > > Thank you so much for your suggestion, removing the /dev/null > > statements produced another error > > WHICH ERROR ?!? > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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/20120911/35fe8f81/attachment.htm From thomas.gruber at physik.tu-freiberg.de Tue Sep 11 15:22:16 2012 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Tue, 11 Sep 2012 15:22:16 +0200 Subject: [Pw_forum] wrong total_weight error with matdyn Message-ID: <504F3B08.8050603@physik.tu-freiberg.de> Dear all, I have done a phonon calculation for a huge system and got finally the dynamical matrix. &inputph tr2_ph=1.0d-13, prefix='Li12Si7.0.0.1', recover=.true. ldisp=.true., nq1=1,nq2=1,nq3=1, amass(1)=28.086, amass(2)=6.914, outdir='./' fildyn='Li12Si7.0.0.1.full.dyn', / To exploit the acoustic sum rule I run q2r.x &input fildyn='Li12Si7.0.0.1.full.dyn', zasr='crystal', flfrc='q2r.fc' / and finally matdyn.x &input asr='crystal', amass(1)=28.086, amass(2)=6.914, flfrc='q2r.fc', flfrq='matdyn.freq.phdos' nk1=1,nk2=1,nk3=1 / But I get the error message with matdyn.x: Norm of the difference between old and new force-constants: 7.87014401166549149025 0.833333333333333 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from frc_blk : error # 1 wrong total_weight %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I looked in the PW_forum and found two threads, but they had no solutions: http://www.democritos.it/pipermail/pw_forum/2008-November/010604.html http://www.democritos.it/pipermail/pw_forum/2011-March/019851.html My system is orthorhombic and the beginning of my *.dyn file is: 2 152 0 1.8897261 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 cubic 8.342943957 0.000000000 0.000000000 0.000000000 19.224088437 0.000000000 0.000000000 0.000000000 14.029483693 1 'Si ' 25598.8229845270 2 'Li ' 6301.72549010253 and the only strange thing I found is that it is identified as cubic. Another orthorhombic system from me (which worked) is identified as hexagonal. But when I change cubic to hexagonal in q2r.fc, then matdyn.x encounter the same problem. Can someone give me a hint how to calculate my phonon frequencies with acoustic sum rule? Best Regards. -- Thomas Gruber Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392006 Email: thomas.gruber at physik.tu-freiberg.de From giannozz at democritos.it Tue Sep 11 15:46:48 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Sep 2012 15:46:48 +0200 Subject: [Pw_forum] wrong total_weight error with matdyn In-Reply-To: <504F3B08.8050603@physik.tu-freiberg.de> References: <504F3B08.8050603@physik.tu-freiberg.de> Message-ID: <1347371208.29270.4.camel@fe12lx.fisica.uniud.it> On Tue, 2012-09-11 at 15:22 +0200, Thomas Gruber wrote: > I looked in the PW_forum and found two threads, but they had no solutions: > http://www.democritos.it/pipermail/pw_forum/2008-November/010604.html > http://www.democritos.it/pipermail/pw_forum/2011-March/019851.html but there is a hint: "try to increase the VERY VERY SAFE RANGE to 3 times nr1,nr2,nr3" (search for it in file matdyn.f90) > and the only strange thing I found is that it is identified as cubic. this just means that the symmetry group is a subgroup of a cubic group and not of an hexagonal group. This has been removed in recent versions, by the way P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Sep 11 17:20:25 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Sep 2012 17:20:25 +0200 Subject: [Pw_forum] wrong total_weight error with matdyn In-Reply-To: <504F3B08.8050603@physik.tu-freiberg.de> References: <504F3B08.8050603@physik.tu-freiberg.de> Message-ID: <1347376825.29588.11.camel@fe12lx.fisica.uniud.it> On Tue, 2012-09-11 at 15:22 +0200, Thomas Gruber wrote: > Can someone give me a hint how to calculate my phonon > frequencies with acoustic sum rule? just heard a suggestion: since you have just one phonon wave-vector, you can use dynmat.x instead of q2r.x+matdyn.x P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From Zbigniew.Lodziana at ifj.edu.pl Tue Sep 11 18:00:34 2012 From: Zbigniew.Lodziana at ifj.edu.pl (Zbigniew Lodziana) Date: Tue, 11 Sep 2012 18:00:34 +0200 Subject: [Pw_forum] quadrupole monents & GIPAW & a problem Message-ID: <20120911155139.M83411@ifj.edu.pl> Dear users & developers, While calculating quadrupole moments with GIPAW I have experienced a strange output that confuses me and it is difficult for interpretation, at least to me. Performing calculations for LiBO2 (with occupancies = fixed!) efg calculations provide for Boron: (a) Cq= 0.0208 MHz eta= 0.00000 (b) Cq= 2.0747 MHz eta= 0.00000 (c) Cq= 0.0228 MHz eta= 0.00000 Where (a) is with TM potential [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-new-gipaw-dc.UPF?attredirects=0]; (b) also TM [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-gipaw.UPF?attredirects=0]; (c) with ultrasoft. Experimental value is Cq=2.56, eta=0.6; theoretical report Cq=2.552, eta=0.54 Test calculations with other more accurate potentials unfortunately do not solve problem. And the problem is that the worst description of the valence states provides (at least numerically) best Cq; besides it is difficult to understand how small changes in the valence state might result in so large ? two orders of magnitude ? changes in the core region. For other systems changes are even 3 orders. Structural parameters are reasonable. For oxygen I did not found such a large variations, for Al Cq is reasonable. Does anyone experienced similar problems or has any hint where the problem could origin form? Thank you in advance, Best regards, Zibi Pw.x ? 5.0 Gipaw.x 5.0 (version 4.3a gives similar results) ----------------------------------- Pw.x &control calculation = 'scf' prefix = 'LiBO2' restart_mode = 'from_scratch' pseudo_dir = './pseudo/' outdir = './tmp/' verbosity = 'high' wf_collect=.true. / &system ibrav = 0 celldm(1) = 1.0 nat = 16 ntyp = 3 ecutwfc = 110 ecutrho = 1000 spline_ps = .true. occupations = 'fixed' / &electrons diagonalization = 'david' diago_thr_init = 1e-4 mixing_mode = 'plain' mixing_beta = 0.1 conv_thr = 1e-10 / ATOMIC_SPECIES Li 6.941 Li.pbe-tm-gipaw-dc.UPF B 10.811 B.pbe-tm-gipaw.UPF O 15.999 O.pbe-tm-new-gipaw-dc.UPF CELL_PARAMETERS (alat= 1.00000000) 8.020588949 0.000000000 0.000000000 0.000000000 8.020588949 0.000000000 0.000000000 0.000000000 12.497695405 ATOMIC_POSITIONS (crystal) Li 0.000000000 0.000000000 0.500000000 Li 0.500000000 0.000000000 0.249999998 Li 0.500000000 0.500000000 0.000000000 Li 0.000000000 0.500000000 0.750000002 B 0.000000000 0.000000000 0.000000000 B 0.500000000 0.000000000 0.750000000 B 0.500000000 0.500000000 0.500000000 B 0.000000000 0.500000000 0.250000000 O 0.154649384 0.249987860 0.125014658 O 0.845350616 0.750012140 0.125014658 O 0.249987860 0.845350616 0.874985342 O 0.750012140 0.154649384 0.874985342 O 0.345350616 0.250012141 0.625014658 O 0.654649384 0.749987859 0.625014658 O 0.749987859 0.345350616 0.374985342 O 0.250012141 0.654649384 0.374985342 K_POINTS automatic 4 4 4 1 1 1 ------------------------------------------ Gipaw.x &inputgipaw job = 'efg' prefix = 'LiBO2' tmp_dir = './tmp/' iverbosity = 11 spline_ps = .true. Q_efg(1) = 4.06 ! 7Li Q_efg(2) = 4.06 ! 11B Q_efg(3) = 2.55 ! 17O ! q_gipaw = 0.01 / Q_efg for Li might not be perfect but shall not matter. From spiga.filippo at gmail.com Tue Sep 11 20:41:06 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 11 Sep 2012 20:41:06 +0200 Subject: [Pw_forum] make error (module global_version.mod) In-Reply-To: References: Message-ID: <8D285BA3-6C6A-4898-8D1B-EB4762F37C5E@gmail.com> Dear Jennifer, all CRAY XE6 machines have PGI compiler. I do suggest to use that compiler instead of the GNU GFORTRAN. On a CRAY machine I just did these steps to compile and run: [log into the system] $ module swap PrgEnv-cray PrgEnv-pgi $ svn checkout svn+ssh://spigafi at qeforge.qe-forge.org/svnroot/q-e/trunk/espresso $ cd espresso $ ./configure --enable-openmp --enable-parallel --with-scalapack $ vim make.sys added manually "-D__IOTK_WORKAROUND1" at the end of "DFLAGS" line $ make all And I do not have any problem at all. All the executable are under "bin/" $ ls bin average.x cp.x ev.x iotk.x neb.x plotproj.x pw2gw.x q2qstar.x wannier_plot.x band_plot.x d3.x fqha.x kpoints.x path_interpolation.x plotrho.x pw2wannier90.x q2r.x wfdd.x bands_FS.x dist.x generate_vdW_kernel_table.x kvecs_FS.x phcg.x pmw.x pwcond.x sumpdos.x bands.x dos.x initial_state.x lambda.x ph.x pp.x pw_export.x turbo_lanczos.x bgw2pw.x dynmat.x iotk ld1.x plan_avg.x projwfc.x pwi2xsf.x turbo_spectrum.x cppp.x epsilon.x iotk_print_kinds.x matdyn.x plotband.x pw2bgw.x pw.x wannier_ham.x Now, despite what people can imagine, every CRAY machine deployed can have different environment. For example on the machine I usually use for tests since it is a developer machine (half XE6, half XE6) I do have to unload some modules to make QE running properly. On another CRAY, in a HPC centre here in Switzerland, there is also Intel compiler as option and the system is slightly different compared to the other. So my recipe should work, 99% of the cases. I strongly suggest you to use PGI, also for a performance point of view. If you only have the GNU compiler (weird situation, CRAY usually sells the full package) I should give a more detailed look to your issue. I can also help to figure out your environment but I need the output of the command "module list" just after you logged in into the system. I can see that you work for a private company, if you feel more comfortable to share specific details of your system in private is perfectly understandable. Happy computing. Best Regards, Filippo On Sep 10, 2012, at 6:26 PM, Jennifer Wohlwend wrote: > I'm trying to instal on a Cray XE6 and when I use 'make all' I get this error concerning 'global_version.mod'. I've tried to find this on the website/forum etc but I haven't seen it mentioned, could anyone tell me what this mod is and where it's located? > > test -d bin || mkdir bin > cd install ; make -f extlibs_makefile libiotk > make[1]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/install' > if test ! -d ../S3DE; then \ > (gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ > if test -e Makefile_iotk; then \ > (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ > if test -e iotk_config.h; then \ > (cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi > cd ../S3DE/iotk/src; make lib+util; > make[2]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/S3DE/iotk/src' > make[2]: Nothing to be done for `lib+util'. > make[2]: Leaving directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/S3DE/iotk/src' > cd ../bin; ln -fs ../S3DE/iotk/tools/iotk .; \ > ln -fs ../S3DE/iotk/src/iotk.x .; \ > ln -fs ../S3DE/iotk/src/iotk_print_kinds.x .; \ > cd ../; ln -fs S3DE/iotk iotk > make[1]: Leaving directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/install' > ( cd Modules ; if test "make" = "" ; then make TLDEPS= all ; \ > else make TLDEPS= all ; fi ) > make[1]: Entering directory `/lustre/workspace/rick_dir/QE_dir/QE5.0/espresso-5.0.1/Modules' > ftn -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA -I../include -I../iotk/src -I. -c environment.f90 > environment.f90:18.56: > USE global_version, ONLY: version_number, svn_revision > 1 > Fatal Error: Can't open module file 'global_version.mod' for reading at (1): No such file or directory > > Thank you, > J. Wohlwend > Universal Technology Corp. -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120911/fe3496c2/attachment.htm From pchen at ion.chem.utk.edu Tue Sep 11 23:06:28 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Tue, 11 Sep 2012 17:06:28 -0400 Subject: [Pw_forum] pbe with norm conserving pp convergence problem In-Reply-To: <1347347767.26330.8.camel@fe12lx.fisica.uniud.it> References: <1347347767.26330.8.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Dr. Giannozzi, It looks like the energy doesn't converge up to 200 Ry as shown in the attached figure. On Tue, Sep 11, 2012 at 3:16 AM, Paolo Giannozzi wrote: > On Mon, 2012-09-10 at 17:02 -0400, Peng Chen wrote: > > > If I didn't set ecutrho, the default value of ecutrho is 4*ecutwfc. So > > the results are the same as the following, and the energy doesn't > > decrease monotonically. > > it has to. The only reason for which the energy might not decrease > monotonically is the presence of the nonlinear core correction in > pseudpotentials. If you increase even more the cutoff, sooner or later > it has to converge. Note that Ni is a very hard element. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120911/8a6bbbaa/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Graph29.pdf Type: application/pdf Size: 8624 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120911/8a6bbbaa/attachment-0001.pdf From davide.ceresoli at istm.cnr.it Wed Sep 12 10:32:11 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Wed, 12 Sep 2012 10:32:11 +0200 Subject: [Pw_forum] quadrupole monents & GIPAW & a problem In-Reply-To: <20120911155139.M83411@ifj.edu.pl> References: <20120911155139.M83411@ifj.edu.pl> Message-ID: <5050488B.7080000@istm.cnr.it> Dear Zibi, could you check with me whether your crystal is the gamma phase? experiments report Cq=0.042 MHz and eta=0.0 (Vorotilova, Dmitrieva and Samoson, 1987). B is an nearly cubic environment and the tetragonal symmetry should yield an axial tensor, hence vanishing eta. Anyway, I recognize that B.pbe-tm-gipaw.UPF has some problems. It did work for NMR of small molecules, but I never tested it in solid state systems, I'm sorry. The last thing to check, is the tensor convention. I think I'm using the Haeberlen convention, which is the same used by the Simpson code (http://anorganik.uni-tuebingen.de/klaus/nmr/index.php?p=conventions/csa/csa). HTH. Best, Davide On 09/11/2012 06:00 PM, Zbigniew Lodziana wrote: > Dear users & developers, > > While calculating quadrupole moments with GIPAW I have experienced a strange > output that confuses me and it is difficult for interpretation, at least to me. > > Performing calculations for LiBO2 (with occupancies = fixed!) efg calculations > provide for Boron: > (a) Cq= 0.0208 MHz eta= 0.00000 > (b) Cq= 2.0747 MHz eta= 0.00000 > (c) Cq= 0.0228 MHz eta= 0.00000 > > Where > (a) is with TM potential > [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-new-gipaw-dc.UPF?attredirects=0]; > > (b) also TM > [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-gipaw.UPF?attredirects=0]; > > (c) with ultrasoft. > > Experimental value is Cq=2.56, eta=0.6; theoretical report Cq=2.552, eta=0.54 > > Test calculations with other more accurate potentials unfortunately do not > solve problem. > > And the problem is that the worst description of the valence states provides > (at least numerically) best Cq; besides it is difficult to understand how > small changes in the valence state might result in so large ? two orders of > magnitude ? changes in the core region. For other systems changes are even 3 > orders. > > Structural parameters are reasonable. > > For oxygen I did not found such a large variations, for Al Cq is reasonable. > > Does anyone experienced similar problems or has any hint where the problem > could origin form? > > Thank you in advance, > Best regards, > > Zibi > > > Pw.x ? 5.0 > Gipaw.x 5.0 > (version 4.3a gives similar results) > ----------------------------------- > Pw.x > > &control > calculation = 'scf' > prefix = 'LiBO2' > restart_mode = 'from_scratch' > pseudo_dir = './pseudo/' > outdir = './tmp/' > verbosity = 'high' > wf_collect=.true. > / > &system > ibrav = 0 > celldm(1) = 1.0 > nat = 16 > ntyp = 3 > ecutwfc = 110 > ecutrho = 1000 > spline_ps = .true. > occupations = 'fixed' > / > &electrons > diagonalization = 'david' > diago_thr_init = 1e-4 > mixing_mode = 'plain' > mixing_beta = 0.1 > conv_thr = 1e-10 > / > > ATOMIC_SPECIES > Li 6.941 Li.pbe-tm-gipaw-dc.UPF > B 10.811 B.pbe-tm-gipaw.UPF > O 15.999 O.pbe-tm-new-gipaw-dc.UPF > > CELL_PARAMETERS (alat= 1.00000000) > 8.020588949 0.000000000 0.000000000 > 0.000000000 8.020588949 0.000000000 > 0.000000000 0.000000000 12.497695405 > > ATOMIC_POSITIONS (crystal) > Li 0.000000000 0.000000000 0.500000000 > Li 0.500000000 0.000000000 0.249999998 > Li 0.500000000 0.500000000 0.000000000 > Li 0.000000000 0.500000000 0.750000002 > B 0.000000000 0.000000000 0.000000000 > B 0.500000000 0.000000000 0.750000000 > B 0.500000000 0.500000000 0.500000000 > B 0.000000000 0.500000000 0.250000000 > O 0.154649384 0.249987860 0.125014658 > O 0.845350616 0.750012140 0.125014658 > O 0.249987860 0.845350616 0.874985342 > O 0.750012140 0.154649384 0.874985342 > O 0.345350616 0.250012141 0.625014658 > O 0.654649384 0.749987859 0.625014658 > O 0.749987859 0.345350616 0.374985342 > O 0.250012141 0.654649384 0.374985342 > > K_POINTS automatic > 4 4 4 1 1 1 > ------------------------------------------ > Gipaw.x > > &inputgipaw > job = 'efg' > prefix = 'LiBO2' > tmp_dir = './tmp/' > iverbosity = 11 > spline_ps = .true. > Q_efg(1) = 4.06 ! 7Li > Q_efg(2) = 4.06 ! 11B > Q_efg(3) = 2.55 ! 17O > ! q_gipaw = 0.01 > / > Q_efg for Li might not be perfect but shall not matter. > > -- +--------------------------------------------------------------+ Davide Ceresoli CNR Institute of Molecular Science and Technology (CNR-ISTM) c/o University of Milan, via Golgi 19, 20133 Milan, Italy Email: davide.ceresoli at istm.cnr.it Phone: +39-02-50314276, +39-347-1001570 (mobile) Skype: dceresoli +--------------------------------------------------------------+ From Max.Lawson at unige.ch Wed Sep 12 13:29:54 2012 From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=) Date: Wed, 12 Sep 2012 13:29:54 +0200 Subject: [Pw_forum] upf_v1_format option no more available in 5.0.1 ' Message-ID: <50507232.3090000@unige.ch> Dear QE users and developpers, It seems that the upf_v1_format switch is no more available for ld1/5.0.1 though it is still for ld1/5.0. Is this correct ? Or should I use an other option ? Thanks in advance for your answer. Best, Max -- Latevi Max LAWSON DAKU Universite de Geneve - Sciences II Quai Ernest-Ansermet 30 Tel: (41) 22/379 6548 CH-1211 Geneve 4 Fax: (41) 22/379 6103 From giannozz at democritos.it Wed Sep 12 14:12:10 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Sep 2012 14:12:10 +0200 Subject: [Pw_forum] upf_v1_format option no more available in 5.0.1 ' In-Reply-To: <50507232.3090000@unige.ch> References: <50507232.3090000@unige.ch> Message-ID: <9B5B7B0D-49D4-4301-8605-145CC6A5AE54@democritos.it> On Sep 12, 2012, at 13:29 , Lat?vi Max LAWSON DAKU wrote: > It seems that the upf_v1_format switch is no more available > for ld1/5.0.1 though it is still for ld1/5.0. Is this correct ? it is. The pseudopotential file will be generated into v.2 UPF format. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From thomas.gruber at physik.tu-freiberg.de Wed Sep 12 15:33:24 2012 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Wed, 12 Sep 2012 15:33:24 +0200 Subject: [Pw_forum] wrong total_weight error with matdyn In-Reply-To: References: Message-ID: <50508F24.2000205@physik.tu-freiberg.de> >> I looked in the PW_forum and found two threads, but they had no solutions: >> http://www.democritos.it/pipermail/pw_forum/2008-November/010604.html >> http://www.democritos.it/pipermail/pw_forum/2011-March/019851.html > but there is a hint: > "try to increase the VERY VERY SAFE RANGE to 3 times nr1,nr2,nr3" > (search for it in file matdyn.f90) I already found this line before, but I found it somehow strange to "exclude" the weight test. I thought the weight should be correct, when calculating the frequencies. >> Can someone give me a hint how to calculate my phonon >> frequencies with acoustic sum rule? > just heard a suggestion: since you have just one phonon > wave-vector, you can use dynmat.x instead of q2r.x+matdyn.x > I tried dynmat.x and it worked, thank you very much. Best regards, Thomas -- Thomas Gruber Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392006 Email: thomas.gruber at physik.tu-freiberg.de From Max.Lawson at unige.ch Wed Sep 12 15:46:26 2012 From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=) Date: Wed, 12 Sep 2012 15:46:26 +0200 Subject: [Pw_forum] upf_v1_format option no more available in 5.0.1 ' In-Reply-To: <9B5B7B0D-49D4-4301-8605-145CC6A5AE54@democritos.it> References: <50507232.3090000@unige.ch> <9B5B7B0D-49D4-4301-8605-145CC6A5AE54@democritos.it> Message-ID: <50509232.80605@unige.ch> Dear Paolo, Thanks for your answer. I will go with ld1/5.0 to also generate the PSPs in the v.1 UPF format; the virtual.x program being able to only deal with v.1 UPF. All the best, Max On 12. 09. 12 14:12, Paolo Giannozzi wrote: > On Sep 12, 2012, at 13:29 , Lat?vi Max LAWSON DAKU wrote: > >> It seems that the upf_v1_format switch is no more available >> for ld1/5.0.1 though it is still for ld1/5.0. Is this correct ? > it is. The pseudopotential file will be generated into v.2 UPF format. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Latevi Max LAWSON DAKU Universite de Geneve - Sciences II Quai Ernest-Ansermet 30 Tel: (41) 22/379 6548 CH-1211 Geneve 4 Fax: (41) 22/379 6103 From Zbigniew.Lodziana at ifj.edu.pl Wed Sep 12 16:34:02 2012 From: Zbigniew.Lodziana at ifj.edu.pl (Zbigniew Lodziana) Date: Wed, 12 Sep 2012 16:34:02 +0200 Subject: [Pw_forum] quadrupole monents & GIPAW & a problem In-Reply-To: <5050488B.7080000@istm.cnr.it> References: <20120911155139.M83411@ifj.edu.pl> <5050488B.7080000@istm.cnr.it> Message-ID: <20120912142737.M29176@ifj.edu.pl> Dear Davide, The structure is gamma (tetragonal symmetry) according to J. Chem. Phys. 44, 3348 (1966), all borons are tetrahedrally coordinated to oxygen. Convention is ok. i think. There might be some confusion in the literature indeed. I will re-check for other system ans report asap. Thanks for help, best regards, Zibi ---------- Original Message ----------- From: Davide Ceresoli To: PWSCF Forum Sent: Wed, 12 Sep 2012 10:32:11 +0200 Subject: Re: [Pw_forum] quadrupole monents & GIPAW & a problem > Dear Zibi, > could you check with me whether your crystal is the gamma > phase? experiments report Cq=0.042 MHz and eta=0.0 (Vorotilova, > Dmitrieva and Samoson, 1987). B is an nearly cubic environment > and the tetragonal symmetry should yield an axial tensor, hence > vanishing eta. > > Anyway, I recognize that B.pbe-tm-gipaw.UPF has some problems. > It did work for NMR of small molecules, but I never tested it > in solid state systems, I'm sorry. > > The last thing to check, is the tensor convention. I think I'm > using the Haeberlen convention, which is the same used by the > Simpson code > > (http://anorganik.uni- > tuebingen.de/klaus/nmr/index.php?p=conventions/csa/csa). > > HTH. > > Best, > Davide > > On 09/11/2012 06:00 PM, Zbigniew Lodziana wrote: > > Dear users & developers, > > > > While calculating quadrupole moments with GIPAW I have experienced a strange > > output that confuses me and it is difficult for interpretation, at least to me. > > > > Performing calculations for LiBO2 (with occupancies = fixed!) efg calculations > > provide for Boron: > > (a) Cq= 0.0208 MHz eta= 0.00000 > > (b) Cq= 2.0747 MHz eta= 0.00000 > > (c) Cq= 0.0228 MHz eta= 0.00000 > > > > Where > > (a) is with TM potential > > [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-new-gipaw-dc.UPF?attredirects=0]; > > > > (b) also TM > > [https://sites.google.com/site/dceresoli/pseudopotentials/B.pbe-tm-gipaw.UPF?attredirects=0]; > > > > (c) with ultrasoft. > > > > Experimental value is Cq=2.56, eta=0.6; theoretical report Cq=2.552, eta=0.54 > > > > Test calculations with other more accurate potentials unfortunately do not > > solve problem. > > > > And the problem is that the worst description of the valence states provides > > (at least numerically) best Cq; besides it is difficult to understand how > > small changes in the valence state might result in so large ? two orders of > > magnitude ? changes in the core region. For other systems changes are even 3 > > orders. > > > > Structural parameters are reasonable. > > > > For oxygen I did not found such a large variations, for Al Cq is reasonable. > > > > Does anyone experienced similar problems or has any hint where the problem > > could origin form? > > > > Thank you in advance, > > Best regards, > > > > Zibi > > > > > > Pw.x ? 5.0 > > Gipaw.x 5.0 > > (version 4.3a gives similar results) > > ----------------------------------- > > Pw.x > > > > &control > > calculation = 'scf' > > prefix = 'LiBO2' > > restart_mode = 'from_scratch' > > pseudo_dir = './pseudo/' > > outdir = './tmp/' > > verbosity = 'high' > > wf_collect=.true. > > / > > &system > > ibrav = 0 > > celldm(1) = 1.0 > > nat = 16 > > ntyp = 3 > > ecutwfc = 110 > > ecutrho = 1000 > > spline_ps = .true. > > occupations = 'fixed' > > / > > &electrons > > diagonalization = 'david' > > diago_thr_init = 1e-4 > > mixing_mode = 'plain' > > mixing_beta = 0.1 > > conv_thr = 1e-10 > > / > > > > ATOMIC_SPECIES > > Li 6.941 Li.pbe-tm-gipaw-dc.UPF > > B 10.811 B.pbe-tm-gipaw.UPF > > O 15.999 O.pbe-tm-new-gipaw-dc.UPF > > > > CELL_PARAMETERS (alat= 1.00000000) > > 8.020588949 0.000000000 0.000000000 > > 0.000000000 8.020588949 0.000000000 > > 0.000000000 0.000000000 12.497695405 > > > > ATOMIC_POSITIONS (crystal) > > Li 0.000000000 0.000000000 0.500000000 > > Li 0.500000000 0.000000000 0.249999998 > > Li 0.500000000 0.500000000 0.000000000 > > Li 0.000000000 0.500000000 0.750000002 > > B 0.000000000 0.000000000 0.000000000 > > B 0.500000000 0.000000000 0.750000000 > > B 0.500000000 0.500000000 0.500000000 > > B 0.000000000 0.500000000 0.250000000 > > O 0.154649384 0.249987860 0.125014658 > > O 0.845350616 0.750012140 0.125014658 > > O 0.249987860 0.845350616 0.874985342 > > O 0.750012140 0.154649384 0.874985342 > > O 0.345350616 0.250012141 0.625014658 > > O 0.654649384 0.749987859 0.625014658 > > O 0.749987859 0.345350616 0.374985342 > > O 0.250012141 0.654649384 0.374985342 > > > > K_POINTS automatic > > 4 4 4 1 1 1 > > ------------------------------------------ > > Gipaw.x > > > > &inputgipaw > > job = 'efg' > > prefix = 'LiBO2' > > tmp_dir = './tmp/' > > iverbosity = 11 > > spline_ps = .true. > > Q_efg(1) = 4.06 ! 7Li > > Q_efg(2) = 4.06 ! 11B > > Q_efg(3) = 2.55 ! 17O > > ! q_gipaw = 0.01 > > / > > Q_efg for Li might not be perfect but shall not matter. > > > > > > -- > +--------------------------------------------------------------+ > Davide Ceresoli > CNR Institute of Molecular Science and Technology (CNR-ISTM) > c/o University of Milan, via Golgi 19, 20133 Milan, Italy > Email: davide.ceresoli at istm.cnr.it > Phone: +39-02-50314276, +39-347-1001570 (mobile) > Skype: dceresoli > +--------------------------------------------------------------+ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ------- End of Original Message ------- From tianlan at caltech.edu Thu Sep 13 00:33:19 2012 From: tianlan at caltech.edu (Tian Lan) Date: Wed, 12 Sep 2012 15:33:19 -0700 Subject: [Pw_forum] The cell blowing up in MD simulation Message-ID: Hi all, I am trying to run the MD simulation on Ag2O of cuprite structure, with a 2 by 2 by 2 supercell. I find it cannot converge. I just started to do MD on QE, so I cannot figure out what is going on. Your help is appreciated very much. The scf calculation gives a good convergence, including the phonon frequencies calculated by PH., I also run the vc-relax, it converged too and gives an optimized lattice parameter very close to experimental data. Then I used those parameters running MD, cp.x, however, even in the first relaxation step with the constant volume, it is hard to converge. And only if ortho_max is set to 1000, the orthonormalization cannot be fulfilled. After the job is done, I find the final total stress exceeds 200 GPa. Then I restart, with a random atom displacement, it does not help. I then run the vc-cp, the cell keeps going larger, like blowing up. The temperature cannot converge as well, and far from the target. I think it is not surprising, since the initial stress in NVE is so high. I also changed the cell back to the primitive one. It performs in the same way, so I think the supercell is not the problem. I am very confused about what is happening. It appears to be a contradiction, I expected a good structure from scf calculation should more or less agree with the MD run. The basic setup is like this: I used ultrasoft potential Ag.pbe-d-rrkjus.UPF and O.pbe-rrkjus.UPF. I followed most of default settings, except, emass=700, and the emass_cutoff=3, nr1b=10, ecutwfc=30 (tried 20 to 70). The # of valence electrons are, 11 for Ag and 6 for O. If you have experience about it, please give me a hint. I can provide more information if needed. Best, Tian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120912/e0bf000f/attachment-0001.htm From amei2 at illinois.edu Thu Sep 13 04:29:39 2012 From: amei2 at illinois.edu (amei2 at illinois.edu) Date: Wed, 12 Sep 2012 21:29:39 -0500 Subject: [Pw_forum] pb_small error Message-ID: Kind Developers, I compiled EPW without problems, however when I try the pb_small example, I get the following error when running epw.x before the "Imposing acoustic sum rule on the dynamical matrix" routine: forrtl: severe (36): attempt to access non-existent record, unit 24, file /Users/amei2/Applications/espresso/EPW236old/examples/pb_small/epw/tmp/./pb.igk Image PC Routine Line Source epw.x 00000001005D26FD Unknown Unknown Unknown epw.x 00000001005D10C4 Unknown Unknown Unknown epw.x 000000010059B82E Unknown Unknown Unknown epw.x 000000010052E8B4 Unknown Unknown Unknown epw.x 000000010052DFBC Unknown Unknown Unknown epw.x 0000000100552116 Unknown Unknown Unknown epw.x 00000001005505A2 Unknown Unknown Unknown epw.x 000000010030DDC8 Unknown Unknown Unknown epw.x 00000001002A4862 Unknown Unknown Unknown epw.x 00000001002A9EB9 Unknown Unknown Unknown epw.x 00000001002AD8A6 Unknown Unknown Unknown epw.x 00000001002D6B63 Unknown Unknown Unknown epw.x 0000000100000CBC Unknown Unknown Unknown epw.x 0000000100000C74 Unknown Unknown Unknown I suspect it is connected with the way readigk.f90 is reading the file. I am using ifort version 12 and have tried using -convert big_endian and -assume byterecl to no avail. Any help is appreciated, Thanks, Antonio -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120912/509fa48a/attachment.htm From jarkko.vahakangas at oulu.fi Thu Sep 13 07:14:18 2012 From: jarkko.vahakangas at oulu.fi (=?iso-8859-1?Q?Jarkko_V=E4h=E4kangas?=) Date: Thu, 13 Sep 2012 08:14:18 +0300 Subject: [Pw_forum] No compatible Gipaw and Quantum Espresso available Message-ID: Hi all, I am intend to start NMR properties with Gipaw package. Currently the only qe-gipaw version which one can download from qe-forge is 4.3.1 and I have not succeed in compiling it with Quantum Epresso version 4.3.2 (which is the oldest QE in qe-forge). So, could you help me to get started with NMR calculations? BR, Jarkko From giannozz at democritos.it Thu Sep 13 08:11:36 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 08:11:36 +0200 Subject: [Pw_forum] No compatible Gipaw and Quantum Espresso available In-Reply-To: References: Message-ID: <96BA9A96-853B-43BD-BC7B-E5B758BA4ECD@democritos.it> On Sep 13, 2012, at 7:14 , Jarkko V?h?kangas wrote: > Currently the only qe-gipaw version which one can download > from qe-forge is 4.3.1 and I have not succeed in compiling it > with Quantum Epresso version 4.3.2 (which is the oldest QE > in qe-forge). it isn't P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jarkko.vahakangas at oulu.fi Thu Sep 13 08:36:48 2012 From: jarkko.vahakangas at oulu.fi (=?iso-8859-1?Q?Jarkko_V=E4h=E4kangas?=) Date: Thu, 13 Sep 2012 09:36:48 +0300 Subject: [Pw_forum] No compatible Gipaw and Quantum Espresso available In-Reply-To: <96BA9A96-853B-43BD-BC7B-E5B758BA4ECD@democritos.it> References: <96BA9A96-853B-43BD-BC7B-E5B758BA4ECD@democritos.it> Message-ID: <04810506-026C-46F4-8284-57039FBD109F@oulu.fi> Hi again, so, I must make myself more clear: I do not have QE version which is supported with qe-gipaw 4.3.1. How can I get that kind of? Is it possible to put it to qe-forge? thanks, Jarkko > >> Currently the only qe-gipaw version which one can download >> from qe-forge is 4.3.1 and I have not succeed in compiling it >> with Quantum Epresso version 4.3.2 (which is the oldest QE >> in qe-forge). > > it isn't > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > From giannozz at democritos.it Thu Sep 13 09:47:50 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 09:47:50 +0200 Subject: [Pw_forum] No compatible Gipaw and Quantum Espresso available In-Reply-To: <04810506-026C-46F4-8284-57039FBD109F@oulu.fi> References: <96BA9A96-853B-43BD-BC7B-E5B758BA4ECD@democritos.it> <04810506-026C-46F4-8284-57039FBD109F@oulu.fi> Message-ID: <1347522470.32734.1.camel@fe12lx.fisica.uniud.it> On Thu, 2012-09-13 at 09:36 +0300, Jarkko V?h?kangas wrote: > I do not have QE version which is supported with qe-gipaw 4.3.1. I don't know which one, but it should be QE 4.3.1 > How can I get that kind of? > Is it possible to put it to qe-forge? it is already there: http://qe-forge.org/gf/download/frsrelease/76/159/espresso-4.3.1.tar.gz P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu Sep 13 09:48:42 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 09:48:42 +0200 Subject: [Pw_forum] pb_small error In-Reply-To: References: Message-ID: <1347522522.32734.3.camel@fe12lx.fisica.uniud.it> Note that EPW works only in conjunction with an old QE version P. On Wed, 2012-09-12 at 21:29 -0500, amei2 at illinois.edu wrote: > Kind Developers, > > > I compiled EPW without problems, however when I try the pb_small > example, I get the following error when running epw.x before the > "Imposing acoustic sum rule on the dynamical matrix" routine: > > > forrtl: severe (36): attempt to access non-existent record, unit 24, > file /Users/amei2/Applications/espresso/EPW236old/examples/pb_small/epw/tmp/./pb.igk > Image PC Routine Line > Source > epw.x 00000001005D26FD Unknown Unknown > Unknown > epw.x 00000001005D10C4 Unknown Unknown > Unknown > epw.x 000000010059B82E Unknown Unknown > Unknown > epw.x 000000010052E8B4 Unknown Unknown > Unknown > epw.x 000000010052DFBC Unknown Unknown > Unknown > epw.x 0000000100552116 Unknown Unknown > Unknown > epw.x 00000001005505A2 Unknown Unknown > Unknown > epw.x 000000010030DDC8 Unknown Unknown > Unknown > epw.x 00000001002A4862 Unknown Unknown > Unknown > epw.x 00000001002A9EB9 Unknown Unknown > Unknown > epw.x 00000001002AD8A6 Unknown Unknown > Unknown > epw.x 00000001002D6B63 Unknown Unknown > Unknown > epw.x 0000000100000CBC Unknown Unknown > Unknown > epw.x 0000000100000C74 Unknown Unknown > Unknown > > > I suspect it is connected with the way readigk.f90 is reading the > file. I am using ifort version 12 and have tried using -convert > big_endian and -assume byterecl to no avail. > > > Any help is appreciated, > > > Thanks, > > > Antonio > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu Sep 13 10:19:17 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 10:19:17 +0200 Subject: [Pw_forum] upf_v1_format option no more available in 5.0.1 ' In-Reply-To: <50509232.80605@unige.ch> References: <50507232.3090000@unige.ch> <9B5B7B0D-49D4-4301-8605-145CC6A5AE54@democritos.it> <50509232.80605@unige.ch> Message-ID: <1347524357.32734.6.camel@fe12lx.fisica.uniud.it> On Wed, 2012-09-12 at 15:46 +0200, Lat?vi Max LAWSON DAKU wrote: > the virtual.x program being able to only deal with v.1 UPF. anybody volunteering to extend upftools/virtual.f90 to UPF v.2? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu Sep 13 10:22:56 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 10:22:56 +0200 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: References: Message-ID: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> On Wed, 2012-09-12 at 15:33 -0700, Tian Lan wrote: > I expected a good structure from scf calculation should more or less > agree with the MD run. it does. First of all, you should verify that you can get the same energy (within numerical noise, and not forgetting the Ha to Ry conversion) with pw.x and cp.x (beware the different defaults for atomic positions in input). In the latter case, just perform an electronic minimization at fixed atoms. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu Sep 13 10:29:59 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 10:29:59 +0200 Subject: [Pw_forum] wrong total_weight error with matdyn In-Reply-To: <50508F24.2000205@physik.tu-freiberg.de> References: <50508F24.2000205@physik.tu-freiberg.de> Message-ID: <1347524999.32734.18.camel@fe12lx.fisica.uniud.it> On Wed, 2012-09-12 at 15:33 +0200, Thomas Gruber wrote: > I found it somehow strange to "exclude" the weight test you shouldn't exclude the test: if the weight is not correct, the results will also be not correct. Apparently the algorithm doesn't work well when you have force constants only in the unit cell (your case, since you have just one phonon wave vector). Not sure why P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From pandey.bramha at gmail.com Thu Sep 13 16:54:18 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Thu, 13 Sep 2012 20:24:18 +0530 Subject: [Pw_forum] gamma phonon calculation error using phcg.x Message-ID: Dear Users and Developers I was tried to calculate the phonon at gamma by phcg.x program. But it was giving the error:::: %%%%%%%%%%%%%%%%%%%%%% from cg_readin : error # 1 double grid not implemented %%%%%%%%%%%%%%%%%%%%%%%% stopping ... when i was running with ph.x same error was occurred. I am using espresso-4.3.2 version and the scf.in and Ph.in file are given bellow : lit.scf.in &control calculation = 'scf' restart_mode='from_scratch', pseudo_dir = '/', outdir='' prefix = 'litG' , tprnfor = .true. , tstress = .true., / &SYSTEM ibrav = 7, celldm(1) = 12.03, celldm(3) = 1.95, nat = 8, ntyp = 3, ecutwfc =95, ecutrho = 550 , / &ELECTRONS conv_thr = 1.0d-9 , mixing_beta = 0.7 , / &IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES Li 6.94100 Li.pz-n-vbc.UPF In 114.82000 In.pz-bhs.UPF Te 127.60000 Te.pz-bhs.UPF ATOMIC_POSITIONS alat Li 0.000000000 0.000000000 0.000000000 0 0 0 Li 0.500000000 0.000000000 0.500000000 0 0 0 In -0.000000000 0.500000000 0.500000000 0 0 0 In 0.500000000 0.500000000 0.000000000 0 0 0 Te 0.249557073 0.250000000 0.250000000 1 0 0 Te 0.247556589 0.750000000 0.750000000 1 0 0 Te 0.750000000 0.254391217 0.750000000 0 1 0 Te 0.750000000 0.743348455 0.250000000 0 1 0 K_POINTS gamma Phcg.in &INPUTPH outdir = '/home/bramha/tmp/' , prefix = 'litG' , fildyn = '/home/bramha/lit/dyn' , recover = .true., trans = .true., epsil = .true., amass(1) = 6.94100, amass(2) = 114.82000, amass(3) = 127.60000, asr=.true., raman = .true., deltatau = 0.01, nderiv = 2, tr2_ph = 1.0d-14 , / 0 0 0 Any suggestions are appreciated regarding this error. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120913/d7486e4c/attachment.htm From giannozz at democritos.it Thu Sep 13 17:00:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 13 Sep 2012 17:00:21 +0200 Subject: [Pw_forum] gamma phonon calculation error using phcg.x In-Reply-To: References: Message-ID: <1347548421.6870.1.camel@fe12lx.fisica.uniud.it> On Thu, 2012-09-13 at 20:24 +0530, Bramha Pandey wrote: > from cg_readin : error # 1 > double grid not implemented > ecutwfc =95, > ecutrho = 550 4*95 = 380 < 550. You are uyusing a grid for charge density that is different from the one for Kohn-Sham orbitals P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From pandey.bramha at gmail.com Thu Sep 13 19:28:06 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Thu, 13 Sep 2012 22:58:06 +0530 Subject: [Pw_forum] gamma phonon calculation error using phcg.x In-Reply-To: <1347548421.6870.1.camel@fe12lx.fisica.uniud.it> References: <1347548421.6870.1.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo Sir, Thank you very much. that problem was solved. On Thu, Sep 13, 2012 at 8:30 PM, Paolo Giannozzi wrote: > On Thu, 2012-09-13 at 20:24 +0530, Bramha Pandey wrote: > > > from cg_readin : error # 1 > > double grid not implemented > > > ecutwfc =95, > > ecutrho = 550 > > 4*95 = 380 < 550. You are uyusing a grid for charge density > that is different from the one for Kohn-Sham orbitals > > P. > > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120913/a51d67fd/attachment.htm From lmartinsamos at gmail.com Fri Sep 14 00:34:27 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 14 Sep 2012 00:34:27 +0200 Subject: [Pw_forum] No compatible Gipaw and Quantum Espresso available In-Reply-To: <1347522470.32734.1.camel@fe12lx.fisica.uniud.it> References: <96BA9A96-853B-43BD-BC7B-E5B758BA4ECD@democritos.it> <04810506-026C-46F4-8284-57039FBD109F@oulu.fi> <1347522470.32734.1.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Jarkko, you can also try with the developement version. just follow the instructions at http://www.qe-forge.org/gf/project/q-e/scmsvn/?action=AccessInfo best regards Layla 2012/9/13 Paolo Giannozzi > On Thu, 2012-09-13 at 09:36 +0300, Jarkko V?h?kangas wrote: > > > I do not have QE version which is supported with qe-gipaw 4.3.1. > > I don't know which one, but it should be QE 4.3.1 > > > How can I get that kind of? > > Is it possible to put it to qe-forge? > > it is already there: > http://qe-forge.org/gf/download/frsrelease/76/159/espresso-4.3.1.tar.gz > > P. > -- > Paolo Giannozzi, IOM-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/20120914/b0a96e43/attachment-0001.htm From tianlan at caltech.edu Fri Sep 14 00:36:51 2012 From: tianlan at caltech.edu (Tian Lan) Date: Thu, 13 Sep 2012 15:36:51 -0700 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> Message-ID: Thank you. I did not notice the unit difference in pw.x and cp.x. But it seems that the energies that both codes obtained agree well. I pasted the results in the following. The first one is the result from vc-relax operated on one unit cell, the total energy is -358.1 Ry, this is very close to my original setup with scf calculation. The second one is from cp.x operated on 2 by 2 by 2 supercell, with fixed atom positions(ion and cell_dynamics are set to 'none'), the energy is -1410 au==-2820 Ry. I don't know whether this is a big difference, but I cannot find an obvious error, but the pressure is quite high, like100GPa, and it is sensitive to the setup especially $electron part. I don't quite get your point about the default positions of atoms in pw and cp. In both codes, I used 'crystal', and in the supercell, all the ratios are in reference to this cubic supercell. I don't think the atom positions have much problem from the result. Thank you! Tian --------------------------------------------------------------------------------------------- pw.x ------------------------------------------------------------------------------------------ total energy = -358.09688074 Ry Harris-Foulkes estimate = -358.09688074 Ry estimated scf accuracy < 9.1E-14 Ry The total energy is the sum of the following terms: one-electron contribution = -98.88874403 Ry hartree contribution = 94.24811082 Ry xc contribution = -60.23256770 Ry ewald contribution = -293.22367983 Ry convergence has been achieved in 27 iterations Forces acting on atoms (Ry/au): atom 1 type 2 force = 0.00000000 0.00000000 0.00000000 atom 2 type 2 force = 0.00000000 0.00000000 -0.00000000 atom 3 type 2 force = 0.00000000 -0.00000000 -0.00000000 atom 4 type 2 force = -0.00000000 0.00000000 -0.00000000 atom 5 type 1 force = 0.00000000 0.00000000 0.00000000 atom 6 type 1 force = 0.00000000 0.00000000 0.00000000 Total force = 0.000000 Total SCF correction = 0.000000 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -0.08 -0.00000054 0.00000000 0.00000000 -0.08 0.00 0.00 0.00000000 -0.00000054 0.00000000 0.00 -0.08 0.00 0.00000000 0.00000000 -0.00000054 0.00 0.00 -0.08 bfgs converged in 5 scf cycles and 2 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) End of BFGS Geometry Optimization Final enthalpy = -358.0968807430 Ry Begin final coordinates new unit-cell volume = 774.49676 a.u.^3 ( 114.76858 Ang^3 ) CELL_PARAMETERS (alat= 9.15690000) 1.002900997 0.000000000 0.000000000 0.000000000 1.002900997 0.000000000 0.000000000 0.000000000 1.002900997 ATOMIC_POSITIONS (crystal) Ag 0.250000000 0.250000000 0.250000000 Ag 0.750000000 0.750000000 0.250000000 Ag 0.250000000 0.750000000 0.750000000 Ag 0.750000000 0.250000000 0.750000000 O 0.000000000 0.000000000 0.000000000 O 0.500000000 0.500000000 0.500000000 End final coordinates ------------------------------------------------------------------------------------ cp.x ------------------------------------------------------------------------------------ Partial temperatures (for each ionic specie) Species Temp (K) Mean Square Displacement (a.u.) 1 0.00 0.0000 2 0.00 0.0000 nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0 100 0.00092 0.0 0.0 -1431.80272 -1431.80272 -1431.80272 -1431.80180 0.0000 0.0000 0.0000 0.0000 writing restart file: ./Ag2O_51.save restart file written in 39.227 sec. Averaged Physical Quantities accomulated this run ekinc : 7.61699 7.61699 (AU) ekin : 374.63650 374.63650 (AU) epot : -1373.54937 -1373.54937 (AU) total energy : -1410.67335 -1410.67335 (AU) temperature : 0.00000 0.00000 (K ) enthalpy : -1410.67335 -1410.67335 (AU) econs : -1410.67335 -1410.67335 (AU) pressure : 93.03124 93.03124 (Gpa) volume : 6148.60237 6148.60237 (AU) On Thu, Sep 13, 2012 at 1:22 AM, Paolo Giannozzi wrote: > On Wed, 2012-09-12 at 15:33 -0700, Tian Lan wrote: > > > I expected a good structure from scf calculation should more or less > > agree with the MD run. > > it does. First of all, you should verify that you can get the same > energy (within numerical noise, and not forgetting the Ha to Ry > conversion) with pw.x and cp.x (beware the different defaults > for atomic positions in input). In the latter case, just perform > an electronic minimization at fixed atoms. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 138-78, Pasadena, CA, 91125 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120913/6189f3fe/attachment.htm From giannozz at democritos.it Fri Sep 14 16:30:01 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Sep 2012 16:30:01 +0200 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> Message-ID: <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> On Thu, 2012-09-13 at 15:36 -0700, Tian Lan wrote: > But it seems that the energies that both codes obtained agree well. I > pasted the results in the following. The first one is the result from > vc-relax operated on one unit cell, the total energy is -358.1 Ry, > this is very close to my original setup with scf calculation. The > second one is from cp.x operated on 2 by 2 by 2 supercell, with fixed > atom positions(ion and cell_dynamics are set to 'none'), the energy is > -1410 au==-2820 Ry. I don't know whether this is a big difference the energy is -1431.80272 Ha or so, i.e. -1431.80272/8 Ha per cell, i.e. 357.95Ry. Close (358.097) but not very close. Note however that you need to compare equivalent results, i.e. same cell, same k-points, or a cell and a supercell but with equivalent k-points. Also note that the treatment of the augmentation charge via the "small boxes" requires some testing in order to find a suitable value for input variables nr1b, nr2b, nr3b. The resulting pressure may also change quite a bit. > I don't quite get your point about the default positions of atoms in > pw and cp. In both codes, I used 'crystal' perfect: it is of no concern for you. If you do not specify anything, cp will assume borh radii and pw lattice parameters, or something like this, as explained in the documentation P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From yuewen.fang at gmail.com Sat Sep 15 14:58:48 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Sat, 15 Sep 2012 20:58:48 +0800 Subject: [Pw_forum] How to make use of PSlibrary? Message-ID: Dear all? I heard that we can *download* pseudopotential and* share* my pseudopotential with others in *PSlibrary*, but I cannot find the steps to do this work at PSlibrary website: http://qe-forge.org/projects/*pslibrary* Does someone know? Best Regards! -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120915/0131d113/attachment.htm From bamideleibrahim at yahoo.com Sat Sep 15 15:23:56 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Sat, 15 Sep 2012 06:23:56 -0700 (PDT) Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: References: Message-ID: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> Dear Yue, What exactly do you want to do? Do you want to download pslibrary pseudopotentiasl? if yes, then follow this link ''http://qe-forge.org/gf/project/pslibrary/frs/''. Hope this help. ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: Yue-Wen Fang To: PWSCF Forum Sent: Saturday, September 15, 2012 1:58 PM Subject: [Pw_forum] How to make use of PSlibrary? Dear all? I heard that we can download pseudopotential andshare my pseudopotential with others in PSlibrary, but I cannot find the steps to do this work at PSlibrary website:? http://qe-forge.org/projects/pslibrary? Does someone know? Best Regards! -- ---- Yue-Wen Fang _______________________________________________ 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/20120915/0a33f495/attachment.htm From sohailphysics at yahoo.co.in Sun Sep 16 17:15:39 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Sun, 16 Sep 2012 23:15:39 +0800 (SGT) Subject: [Pw_forum] Density of states Message-ID: <1347808539.29675.YahooMailClassic@web190906.mail.sg3.yahoo.com> Dear QE Users I am trying to find DOS for MoS? using version 5.0.1 I have already done this using version 4.2.1 around one month back The only difference i noticed that i have to use &dos instead of &inputpp and rest others i believe it should be same Can anyone help me in this regard ?? Input file is attached &dos ??? outdir = './OUT' ??? prefix? = 'MoS' ??? Emin = -7.00, Emax = 13.00 ??? DeltaE = 0.001, ??? fildos = 'MoS.dos.dat' --------------------------------------------------------------------- Sohail AhmadAssistant ProfessorDepartment of PhysicsKing Khalid UniversityAbha, Saudi Arabia?Contact:???+966 (0) 556776986 (M) -------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120916/0196524b/attachment.htm From physics.skgupta at gmail.com Sun Sep 16 17:17:24 2012 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Sun, 16 Sep 2012 08:17:24 -0700 Subject: [Pw_forum] Density of states In-Reply-To: <1347808539.29675.YahooMailClassic@web190906.mail.sg3.yahoo.com> References: <1347808539.29675.YahooMailClassic@web190906.mail.sg3.yahoo.com> Message-ID: Yes, no further change is required. best skg On Sun, Sep 16, 2012 at 8:15 AM, Sohail Ahmad wrote: > > Dear QE Users > > I am trying to find DOS for MoS using version 5.0.1 > > I have already done this using version 4.2.1 around one month back > > The only difference i noticed that i have to use &dos instead of &inputpp > and rest others i believe it should be same > > Can anyone help me in this regard ?? > > Input file is attached > > &dos > outdir = './OUT' > prefix = 'MoS' > Emin = -7.00, Emax = 13.00 > DeltaE = 0.001, > fildos = 'MoS.dos.dat' > > --------------------------------------------------------------------- > > *Sohail Ahmad* > > Assistant Professor > > Department of Physics > > King Khalid University > > Abha, Saudi Arabia > > > > Contact: +966 (0) 556776986 (M) > -------------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120916/e341208e/attachment.htm From florenceliu86 at gmail.com Mon Sep 17 08:17:49 2012 From: florenceliu86 at gmail.com (florence liu) Date: Mon, 17 Sep 2012 14:17:49 +0800 Subject: [Pw_forum] hse06 vs pbe0 Message-ID: Dear all, i am trying various hydride functionals for my calculations, and i have noticed that the time required for the same system calculated with PBE0 and with HSE06 are comparable. this seems kind of strange to me as the original publicaltion of HSE06 (Hyde et al. J Chem Phys, 2003, 118, 8207) claims that, it should be less computationally demanding. Has any body compared the computation time required for these two functionals in QE? my input for both the PBE0 and HSE06 calculations are like &control (...) / &system ibrav= 0, nat= 32, ntyp= 1, ecutwfc = 58.79798, occupations='smearing', smearing='gaussian', degauss= 0.00367487 / &electrons / &ions / &cell / The functional are specified via the pseudopotential. The output shows "Exchange-correlation = PBE0 ( 6 4 8 4 0)" and "Exchange-correlation = HSE ( 1 412 4 0)", so QE should have taken the right functionals. An other, rather technical question, is it possible that the current geometry in a optimization using hybrid functional is not printed in the output, when using "standard" settings? If so, what do i have to change in order to get the current geometry? best wishes, florence TU Munich -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/0825fcb1/attachment.htm From giannozz at democritos.it Mon Sep 17 09:15:34 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Sep 2012 09:15:34 +0200 Subject: [Pw_forum] hse06 vs pbe0 In-Reply-To: References: Message-ID: <1347866134.16725.7.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-17 at 14:17 +0800, florence liu wrote: > I have noticed that the time required for the same system calculated > with PBE0 and with HSE06 are comparable. this seems kind of strange to > me as the original publicaltion of HSE06 (Hyde et al. J Chem Phys, > 2003, 118, 8207) claims that, it should be less computationally > demanding. with the current implementation and with plane waves, there is no advantage in using HSE wrt any other hybrid functional > An other, rather technical question, is it possible that the current > geometry in a optimization using hybrid functional is not printed in > the output, when using "standard" settings? I don't see why it shouldn't. The optimization algorithm does not depend upon the specific functional used. All it needs are forces and energies P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From pourazar2012 at gmail.com Mon Sep 17 09:28:29 2012 From: pourazar2012 at gmail.com (yavar pour azar) Date: Mon, 17 Sep 2012 11:58:29 +0430 Subject: [Pw_forum] How to calculate the adsorption energy of ion (charged particle) on the surface of semiconductor? Message-ID: Dear QE users I want to calculate adsorption energy and structural parameters for the adsorption of some ions on the surface of semiconductor, is this similar to calculation of neutral particle or other procedure is required? I would be appreciate if anyone refer me to detailed reference to do this. Thanks in advance ----------------------------------------- Yavar Taghipour Azar Physics Group, AEOI Tehran, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/5a24dc88/attachment.htm From yuewen.fang at gmail.com Mon Sep 17 10:09:33 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:09:33 +0800 Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> References: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> Message-ID: Dear Adetunji, I opened your website link, but I just saw a file named pslibrary.0.2.5.tar.gz (19.55 Kb),does i t contain the pseudopotentials? Regards! 2012/9/15 bamidele ibrahim > Dear Yue, > What exactly do you want to do? Do you want to download pslibrary > pseudopotentiasl? if yes, then follow this link '' > http://qe-forge.org/gf/project/pslibrary/frs/''. > Hope this help. > > > --------------------------------------------------------------------------------------------------- > Adetunji Bamidele Ibrahim(PhD Student) > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > > --------------------------------------------------------------------------------------------------- > > ------------------------------ > *From:* Yue-Wen Fang > *To:* PWSCF Forum > *Sent:* Saturday, September 15, 2012 1:58 PM > *Subject:* [Pw_forum] How to make use of PSlibrary? > > Dear all? > > I heard that we can *download* pseudopotential and* share* my > pseudopotential with others in *PSlibrary*, but I cannot find the steps > to do this work at PSlibrary website: http://qe-forge.org/projects/* > pslibrary* > Does someone know? > > Best Regards! > > -- > ---- > Yue-Wen Fang > > > > > _______________________________________________ > 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 > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/8083a387/attachment.htm From giannozz at democritos.it Mon Sep 17 10:14:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Sep 2012 10:14:39 +0200 Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: References: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> Message-ID: <1347869679.17120.5.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-17 at 16:09 +0800, Yue-Wen Fang wrote: > I opened your website link, but I just saw a file named > pslibrary.0.2.5.tar.gz (19.55 Kb),does i t contain the > pseudopotentials? >From the pseudopotential page of the qe web site: If you do not find here the pseudopotentials you need, please have a look at the PSlibrary project on QE-forge: it contains input data for generating many more pseudopotentials (generated files can be found here). "You can observe a lot by watching" (Yogi Berra) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From yuewen.fang at gmail.com Mon Sep 17 10:18:08 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:18:08 +0800 Subject: [Pw_forum] Density of states In-Reply-To: <1347808539.29675.YahooMailClassic@web190906.mail.sg3.yahoo.com> References: <1347808539.29675.YahooMailClassic@web190906.mail.sg3.yahoo.com> Message-ID: just use* dos* instead of inputpp similarly, if you intend to calculate LDOS and PDOS, just instead of inputpp by using* projwfc* * * *Best Regards!* *Yuewen Fang* *Shanghai, China * 2012/9/16 Sohail Ahmad > > Dear QE Users > > I am trying to find DOS for MoS using version 5.0.1 > > I have already done this using version 4.2.1 around one month back > > The only difference i noticed that i have to use &dos instead of &inputpp > and rest others i believe it should be same > > Can anyone help me in this regard ?? > > Input file is attached > > &dos > outdir = './OUT' > prefix = 'MoS' > Emin = -7.00, Emax = 13.00 > DeltaE = 0.001, > fildos = 'MoS.dos.dat' > > --------------------------------------------------------------------- > > *Sohail Ahmad* > > Assistant Professor > > Department of Physics > > King Khalid University > > Abha, Saudi Arabia > > > > Contact: +966 (0) 556776986 (M) > -------------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/18d9074c/attachment.htm From garcia.risueno at gmail.com Mon Sep 17 10:20:16 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 10:20:16 +0200 Subject: [Pw_forum] pw.x does not work Message-ID: Dear Espresso experts I am making my first steps in Espresso. Unfortunately, I am still unable to make it run. After doing $ configure and $ make pw (Espresso 4), everything is all right. Howver, if I do $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > si.scf.out No error message appears, but the scf calculation is not performed. The out file ends with: Initial potential from superposition of free atoms starting charge 9.99966, renormalised to 10.00000 T F Could anybody help me? Thank you very much -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/a5fd6014/attachment.htm From yuewen.fang at gmail.com Mon Sep 17 10:20:47 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:20:47 +0800 Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: <1347869679.17120.5.camel@fe12lx.fisica.uniud.it> References: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> <1347869679.17120.5.camel@fe12lx.fisica.uniud.it> Message-ID: Dear* *Paolo, In fact, I want to find the input data of generating PP, but I haven't found them in the website. Can you give me the link? Best Regards! 2012/9/17 Paolo Giannozzi > On Mon, 2012-09-17 at 16:09 +0800, Yue-Wen Fang wrote: > > > I opened your website link, but I just saw a file named > > pslibrary.0.2.5.tar.gz (19.55 Kb),does i t contain the > > pseudopotentials? > > >From the pseudopotential page of the qe web site: > If you do not find here the pseudopotentials you need, please have a > look at the PSlibrary project on QE-forge: it contains input data > for generating many more pseudopotentials (generated files can be > found here). > > "You can observe a lot by watching" (Yogi Berra) > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/5d0a155c/attachment.htm From yuewen.fang at gmail.com Mon Sep 17 10:27:22 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:27:22 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Dear Pablo, I think you'd better show your input file if possible because the given information is too limited. Best Regards! Yuewen Fang 2012/9/17 Pablo Garc?a Risue?o > Dear Espresso experts > > I am making my first steps in Espresso. Unfortunately, I am still unable > to make it run. After doing $ configure and $ make pw (Espresso 4), > everything is all right. Howver, if I do > > $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > > si.scf.out > > No error message appears, but the scf calculation is not performed. The > out file ends with: > > Initial potential from superposition of free atoms > > starting charge 9.99966, renormalised to 10.00000 > T F > > Could anybody help me? Thank you very much > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/13cc11c4/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Sep 17 10:32:50 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 17 Sep 2012 10:32:50 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: On 17 September 2012 10:20, Pablo Garc?a Risue?o wrote: > Dear Espresso experts > > I am making my first steps in Espresso. Unfortunately, I am still unable > to make it run. After doing $ configure and $ make pw (Espresso 4), > everything is all right. Howver, if I do > > $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > > si.scf.out > Dear Pablo, I would bet there is some problem with the GPU environment; there is a specific mailing list for this version of QE: . The GPU developers read this mailing list regularly, but you may have a faster and more pertinent response by writing directly there. bests -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/d17ff2a0/attachment-0001.htm From garcia.risueno at gmail.com Mon Sep 17 10:34:00 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 10:34:00 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Dear Fang Thank you very much. The input is a very standard one: &control prefix='silicon', pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' outdir = '.', / &system ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, ecutwfc = 12.0, / &electrons / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 2 0.25 0.25 0.75 3.0 0.25 0.25 0.25 1.0 It corresponds to a tutorial example. If I use the input below, the result is the same &control prefix='nickel' outdir='.' pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', / &system ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, ecutwfc = 24.0, ecutrho = 288.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 nspin = 2, starting_magnetization(1)=0.7, / &electrons / ATOMIC_SPECIES Ni 58.69 NiUS.RRKJ3.UPF ATOMIC_POSITIONS Ni 0.0 0.0 0.0 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 &control prefix='nickel' outdir='.' pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', / &system ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, ecutwfc = 24.0, ecutrho = 288.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 nspin = 2, starting_magnetization(1)=0.7, / / &electrons / ATOMIC_SPECIES Ni 58.69 NiUS.RRKJ3.UPF ATOMIC_POSITIONS Ni 0.0 0.0 0.0 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 I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > si.scf.out Thank you very much, and best regards 2012/9/17 Yue-Wen Fang > Dear Pablo, > > I think you'd better show your input file if possible because the given > information is too limited. > > Best Regards! > Yuewen Fang > > 2012/9/17 Pablo Garc?a Risue?o > >> Dear Espresso experts >> >> I am making my first steps in Espresso. Unfortunately, I am still unable >> to make it run. After doing $ configure and $ make pw (Espresso 4), >> everything is all right. Howver, if I do >> >> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > >> si.scf.out >> >> No error message appears, but the scf calculation is not performed. The >> out file ends with: >> >> Initial potential from superposition of free atoms >> >> starting charge 9.99966, renormalised to 10.00000 >> T F >> >> Could anybody help me? Thank you very much >> >> -- >> -- >> >> Dr. Pablo Garc?a Risue?o >> >> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >> (Claudia-Draxl Group), 12489 Berlin, Germany >> >> Tel. +49 030 20937904 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ---- > Yue-Wen Fang > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/9d7b58ea/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Sep 17 10:34:43 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 17 Sep 2012 10:34:43 +0200 Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: References: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> Message-ID: On 17 September 2012 10:09, Yue-Wen Fang wrote: > Dear Adetunji, > > I opened your website link, but I just saw a file named > pslibrary.0.2.5.tar.gz (19.55 > Kb),does i t contain the pseudopotentials? > > I can assure you that it does not contain anything illegal or dangerous. You can safely try to download it. bests -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/588169a3/attachment.htm From garcia.risueno at gmail.com Mon Sep 17 10:35:49 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 10:35:49 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Dear Lorenzo I think I did not express properly in my first email. Actually the problem is given by the Espresso 4 version, not by the 5.0.1-GPU one... Thank you very much, and best regards 2012/9/17 Lorenzo Paulatto > On 17 September 2012 10:20, Pablo Garc?a Risue?o > wrote: > >> Dear Espresso experts >> >> I am making my first steps in Espresso. Unfortunately, I am still unable >> to make it run. After doing $ configure and $ make pw (Espresso 4), >> everything is all right. Howver, if I do >> >> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > >> si.scf.out >> > > Dear Pablo, > > I would bet there is some problem with the GPU environment; there is a > specific mailing list for this version of QE: . > The GPU developers read this mailing list regularly, but you may have a > faster and more pertinent response by writing directly there. > > bests > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/731c86af/attachment-0001.htm From yuewen.fang at gmail.com Mon Sep 17 10:44:08 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:44:08 +0800 Subject: [Pw_forum] How to make use of PSlibrary? In-Reply-To: References: <1347715436.81491.YahooMailNeo@web39401.mail.mud.yahoo.com> Message-ID: Dear Lorenzo, Paolo and Adetunji, I have downloaded it and got many pp generation codes. Thank you for your help. It will help me generate more pp. Thank you! Best Regards! Yuewen Fang 2012/9/17 Lorenzo Paulatto > On 17 September 2012 10:09, Yue-Wen Fang wrote: > >> Dear Adetunji, >> >> I opened your website link, but I just saw a file named >> pslibrary.0.2.5.tar.gz (19.55 >> Kb),does i t contain the pseudopotentials? >> >> > I can assure you that it does not contain anything illegal or dangerous. > You can safely try to download it. > > bests > > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/091377b4/attachment.htm From yuewen.fang at gmail.com Mon Sep 17 10:48:58 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:48:58 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: It seems that you lost the tag "*calculation*", check it! 2012/9/17 Pablo Garc?a Risue?o > Dear Fang > > Thank you very much. The input is a very standard one: > > &control > prefix='silicon', > pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' > outdir = '.', > / > &system > ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, > ecutwfc = 12.0, > / > &electrons > / > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS > 2 > 0.25 0.25 0.75 3.0 > 0.25 0.25 0.25 1.0 > > It corresponds to a tutorial example. If I use the input below, the result > is the same > > &control > prefix='nickel' > outdir='.' > pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 > nspin = 2, starting_magnetization(1)=0.7, > / > &electrons > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > 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 > > &control > prefix='nickel' > outdir='.' > pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 > nspin = 2, starting_magnetization(1)=0.7, > / > / > &electrons > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > 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 > > I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > si.scf.out > > Thank you very much, and best regards > > > > 2012/9/17 Yue-Wen Fang > >> Dear Pablo, >> >> I think you'd better show your input file if possible because the given >> information is too limited. >> >> Best Regards! >> Yuewen Fang >> >> 2012/9/17 Pablo Garc?a Risue?o >> >>> Dear Espresso experts >>> >>> I am making my first steps in Espresso. Unfortunately, I am still unable >>> to make it run. After doing $ configure and $ make pw (Espresso 4), >>> everything is all right. Howver, if I do >>> >>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > >>> si.scf.out >>> >>> No error message appears, but the scf calculation is not performed. The >>> out file ends with: >>> >>> Initial potential from superposition of free atoms >>> >>> starting charge 9.99966, renormalised to 10.00000 >>> T F >>> >>> Could anybody help me? Thank you very much >>> >>> -- >>> -- >>> >>> Dr. Pablo Garc?a Risue?o >>> >>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>> (Claudia-Draxl Group), 12489 Berlin, Germany >>> >>> Tel. +49 030 20937904 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/bce58a48/attachment.htm From yuewen.fang at gmail.com Mon Sep 17 10:50:46 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 16:50:46 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: calculationCHARACTER*Default:*'scf' a string describing the task to be performed: 'scf', 'nscf', 'bands', 'relax', 'md', 'vc-relax', 'vc-md' (vc = variable-cell). 2012/9/17 Pablo Garc?a Risue?o > Dear Fang > > Thank you very much. The input is a very standard one: > > &control > prefix='silicon', > pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' > outdir = '.', > / > &system > ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, > ecutwfc = 12.0, > / > &electrons > / > ATOMIC_SPECIES > Si 28.086 Si.vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS > 2 > 0.25 0.25 0.75 3.0 > 0.25 0.25 0.25 1.0 > > It corresponds to a tutorial example. If I use the input below, the result > is the same > > &control > prefix='nickel' > outdir='.' > pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 > nspin = 2, starting_magnetization(1)=0.7, > / > &electrons > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > 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 > > &control > prefix='nickel' > outdir='.' > pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', > / > &system > ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 > nspin = 2, starting_magnetization(1)=0.7, > / > / > &electrons > / > ATOMIC_SPECIES > Ni 58.69 NiUS.RRKJ3.UPF > ATOMIC_POSITIONS > Ni 0.0 0.0 0.0 > 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 > > I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > si.scf.out > > Thank you very much, and best regards > > > > 2012/9/17 Yue-Wen Fang > >> Dear Pablo, >> >> I think you'd better show your input file if possible because the given >> information is too limited. >> >> Best Regards! >> Yuewen Fang >> >> 2012/9/17 Pablo Garc?a Risue?o >> >>> Dear Espresso experts >>> >>> I am making my first steps in Espresso. Unfortunately, I am still unable >>> to make it run. After doing $ configure and $ make pw (Espresso 4), >>> everything is all right. Howver, if I do >>> >>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > >>> si.scf.out >>> >>> No error message appears, but the scf calculation is not performed. The >>> out file ends with: >>> >>> Initial potential from superposition of free atoms >>> >>> starting charge 9.99966, renormalised to 10.00000 >>> T F >>> >>> Could anybody help me? Thank you very much >>> >>> -- >>> -- >>> >>> Dr. Pablo Garc?a Risue?o >>> >>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>> (Claudia-Draxl Group), 12489 Berlin, Germany >>> >>> Tel. +49 030 20937904 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/3ae1c138/attachment-0001.htm From garcia.risueno at gmail.com Mon Sep 17 10:56:17 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 10:56:17 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Dear Fang. I also tried with calculation='scf' in the control block (I think it is actually default), but the result is the same (actually I think I am running the version 2.1.4). The complete output is Program PWSCF v.2.1.4 starts ... Today is 17Sep2012 at 10:54: 6 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx =10 npk =40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 ASIER: minus_q: T bravais-lattice index = 2 lattice parameter (a_0) = 10.2000 a.u. unit-cell volume = 265.3020 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 1 kinetic-energy cutoff = 12.0000 Ry charge density cutoff = 48.0000 Ry convergence threshold = 1.0E-06 beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PZ NOGX NOGC (1100) iswitch = 0 celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( -0.500000 0.000000 0.500000 ) a(2) = ( 0.000000 0.500000 0.500000 ) a(3) = ( -0.500000 0.500000 0.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( -1.000000 -1.000000 1.000000 ) b(2) = ( 1.000000 1.000000 1.000000 ) b(3) = ( -1.000000 1.000000 -1.000000 ) PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0 (in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000) atomic species valence mass pseudopotential Si 4.00 28.08600 Si( 1.00) 48 Sym.Ops. (with inversion) Cartesian axes site n. atom positions (a_0 units) 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 ) number of k points= 2 cart. coord. in units 2pi/a_0 k( 1) = ( 0.2500000 0.2500000 0.7500000 ), wk = 1.5000000 k( 2) = ( 0.2500000 0.2500000 0.2500000 ), wk = 0.5000000 G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, 16) nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 186 nelec = 8.00 nkb = 8 ngl = 43 Initial potential from superposition of free atoms starting charge 7.99901, renormalised to 8.00000 T F Best regards 2012/9/17 Yue-Wen Fang > calculation CHARACTER*Default:* 'scf' > > a string describing the task to be performed: > 'scf', > 'nscf', > 'bands', > 'relax', > 'md', > 'vc-relax', > 'vc-md' > > (vc = variable-cell). > > > 2012/9/17 Pablo Garc?a Risue?o > >> Dear Fang >> >> Thank you very much. The input is a very standard one: >> >> &control >> prefix='silicon', >> pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' >> outdir = '.', >> / >> &system >> ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, >> ecutwfc = 12.0, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Si 28.086 Si.vbc.UPF >> ATOMIC_POSITIONS >> Si 0.00 0.00 0.00 >> Si 0.25 0.25 0.25 >> K_POINTS >> 2 >> 0.25 0.25 0.75 3.0 >> 0.25 0.25 0.25 1.0 >> >> It corresponds to a tutorial example. If I use the input below, the >> result is the same >> >> &control >> prefix='nickel' >> outdir='.' >> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >> / >> &system >> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >> ecutwfc = 24.0, ecutrho = 288.0, >> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >> nspin = 2, starting_magnetization(1)=0.7, >> / >> &electrons >> / >> ATOMIC_SPECIES >> Ni 58.69 NiUS.RRKJ3.UPF >> ATOMIC_POSITIONS >> Ni 0.0 0.0 0.0 >> 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 >> >> &control >> prefix='nickel' >> outdir='.' >> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >> / >> &system >> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >> ecutwfc = 24.0, ecutrho = 288.0, >> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >> nspin = 2, starting_magnetization(1)=0.7, >> / >> / >> &electrons >> / >> ATOMIC_SPECIES >> Ni 58.69 NiUS.RRKJ3.UPF >> ATOMIC_POSITIONS >> Ni 0.0 0.0 0.0 >> 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 >> >> I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > >> si.scf.out >> >> Thank you very much, and best regards >> >> >> >> 2012/9/17 Yue-Wen Fang >> >>> Dear Pablo, >>> >>> I think you'd better show your input file if possible because the given >>> information is too limited. >>> >>> Best Regards! >>> Yuewen Fang >>> >>> 2012/9/17 Pablo Garc?a Risue?o >>> >>>> Dear Espresso experts >>>> >>>> I am making my first steps in Espresso. Unfortunately, I am still >>>> unable to make it run. After doing $ configure and $ make pw (Espresso 4), >>>> everything is all right. Howver, if I do >>>> >>>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in > >>>> si.scf.out >>>> >>>> No error message appears, but the scf calculation is not performed. The >>>> out file ends with: >>>> >>>> Initial potential from superposition of free atoms >>>> >>>> starting charge 9.99966, renormalised to 10.00000 >>>> T F >>>> >>>> Could anybody help me? Thank you very much >>>> >>>> -- >>>> -- >>>> >>>> Dr. Pablo Garc?a Risue?o >>>> >>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>> >>>> Tel. +49 030 20937904 >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> ---- >>> Yue-Wen Fang >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> -- >> >> Dr. Pablo Garc?a Risue?o >> >> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >> (Claudia-Draxl Group), 12489 Berlin, Germany >> >> Tel. +49 030 20937904 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ---- > Yue-Wen Fang > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/e71ef185/attachment-0001.htm From yuewen.fang at gmail.com Mon Sep 17 11:00:05 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 17:00:05 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Dear Pablo, I think you'e better use the latest version. 2012/9/17 Pablo Garc?a Risue?o > Dear Fang. I also tried with calculation='scf' in the control block (I > think it is actually default), but the result is the same (actually I think > I am running the version 2.1.4). The complete output is > > Program PWSCF v.2.1.4 starts ... > Today is 17Sep2012 at 10:54: 6 > > Ultrasoft (Vanderbilt) Pseudopotentials > > Current dimensions of program pwscf are: > ntypx =10 npk =40000 lmax = 3 > nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 > ASIER: minus_q: T > > > bravais-lattice index = 2 > lattice parameter (a_0) = 10.2000 a.u. > unit-cell volume = 265.3020 (a.u.)^3 > number of atoms/cell = 2 > number of atomic types = 1 > kinetic-energy cutoff = 12.0000 Ry > charge density cutoff = 48.0000 Ry > convergence threshold = 1.0E-06 > beta = 0.7000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PZ NOGX NOGC (1100) > iswitch = 0 > > celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( -0.500000 0.000000 0.500000 ) > a(2) = ( 0.000000 0.500000 0.500000 ) > a(3) = ( -0.500000 0.500000 0.000000 ) > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( -1.000000 -1.000000 1.000000 ) > b(2) = ( 1.000000 1.000000 1.000000 ) > b(3) = ( -1.000000 1.000000 -1.000000 ) > > > PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0 > (in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000) > > atomic species valence mass pseudopotential > Si 4.00 28.08600 Si( 1.00) > > 48 Sym.Ops. (with inversion) > > > Cartesian axes > > site n. atom positions (a_0 units) > 1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 > ) > 2 Si tau( 2) = ( 0.2500000 0.2500000 0.2500000 > ) > > number of k points= 2 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.2500000 0.2500000 0.7500000 ), wk = 1.5000000 > k( 2) = ( 0.2500000 0.2500000 0.2500000 ), wk = 0.5000000 > > G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, 16) > nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 186 > nelec = 8.00 nkb = 8 ngl = 43 > > > Initial potential from superposition of free atoms > > starting charge 7.99901, renormalised to 8.00000 > T F > > > Best regards > > 2012/9/17 Yue-Wen Fang > >> calculation CHARACTER*Default:* 'scf' >> >> a string describing the task to be performed: >> 'scf', >> 'nscf', >> 'bands', >> 'relax', >> 'md', >> 'vc-relax', >> 'vc-md' >> >> (vc = variable-cell). >> >> >> 2012/9/17 Pablo Garc?a Risue?o >> >>> Dear Fang >>> >>> Thank you very much. The input is a very standard one: >>> >>> &control >>> prefix='silicon', >>> pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' >>> outdir = '.', >>> / >>> &system >>> ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, >>> ecutwfc = 12.0, >>> / >>> &electrons >>> / >>> ATOMIC_SPECIES >>> Si 28.086 Si.vbc.UPF >>> ATOMIC_POSITIONS >>> Si 0.00 0.00 0.00 >>> Si 0.25 0.25 0.25 >>> K_POINTS >>> 2 >>> 0.25 0.25 0.75 3.0 >>> 0.25 0.25 0.25 1.0 >>> >>> It corresponds to a tutorial example. If I use the input below, the >>> result is the same >>> >>> &control >>> prefix='nickel' >>> outdir='.' >>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>> / >>> &system >>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>> ecutwfc = 24.0, ecutrho = 288.0, >>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>> nspin = 2, starting_magnetization(1)=0.7, >>> / >>> &electrons >>> / >>> ATOMIC_SPECIES >>> Ni 58.69 NiUS.RRKJ3.UPF >>> ATOMIC_POSITIONS >>> Ni 0.0 0.0 0.0 >>> 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 >>> >>> &control >>> prefix='nickel' >>> outdir='.' >>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>> / >>> &system >>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>> ecutwfc = 24.0, ecutrho = 288.0, >>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>> nspin = 2, starting_magnetization(1)=0.7, >>> / >>> / >>> &electrons >>> / >>> ATOMIC_SPECIES >>> Ni 58.69 NiUS.RRKJ3.UPF >>> ATOMIC_POSITIONS >>> Ni 0.0 0.0 0.0 >>> 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 >>> >>> I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > >>> si.scf.out >>> >>> Thank you very much, and best regards >>> >>> >>> >>> 2012/9/17 Yue-Wen Fang >>> >>>> Dear Pablo, >>>> >>>> I think you'd better show your input file if possible because the given >>>> information is too limited. >>>> >>>> Best Regards! >>>> Yuewen Fang >>>> >>>> 2012/9/17 Pablo Garc?a Risue?o >>>> >>>>> Dear Espresso experts >>>>> >>>>> I am making my first steps in Espresso. Unfortunately, I am still >>>>> unable to make it run. After doing $ configure and $ make pw (Espresso 4), >>>>> everything is all right. Howver, if I do >>>>> >>>>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in> si.scf.out >>>>> >>>>> No error message appears, but the scf calculation is not performed. >>>>> The out file ends with: >>>>> >>>>> Initial potential from superposition of free atoms >>>>> >>>>> starting charge 9.99966, renormalised to 10.00000 >>>>> T F >>>>> >>>>> Could anybody help me? Thank you very much >>>>> >>>>> -- >>>>> -- >>>>> >>>>> Dr. Pablo Garc?a Risue?o >>>>> >>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>> >>>>> Tel. +49 030 20937904 >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>>> >>>> >>>> >>>> -- >>>> ---- >>>> Yue-Wen Fang >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> -- >>> >>> Dr. Pablo Garc?a Risue?o >>> >>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>> (Claudia-Draxl Group), 12489 Berlin, Germany >>> >>> Tel. +49 030 20937904 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/f69abd51/attachment-0001.htm From garcia.risueno at gmail.com Mon Sep 17 11:03:58 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 11:03:58 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Hi! The problem is that this concrete version is expected to be well suited to some additional code that other scientist wrote some years ago, so we agreed I would use this version to avoid further problems... 2012/9/17 Yue-Wen Fang > Dear Pablo, > > I think you'e better use the latest version. > > > 2012/9/17 Pablo Garc?a Risue?o > >> Dear Fang. I also tried with calculation='scf' in the control block (I >> think it is actually default), but the result is the same (actually I think >> I am running the version 2.1.4). The complete output is >> >> Program PWSCF v.2.1.4 starts ... >> Today is 17Sep2012 at 10:54: 6 >> >> Ultrasoft (Vanderbilt) Pseudopotentials >> >> Current dimensions of program pwscf are: >> ntypx =10 npk =40000 lmax = 3 >> nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 >> ASIER: minus_q: T >> >> >> bravais-lattice index = 2 >> lattice parameter (a_0) = 10.2000 a.u. >> unit-cell volume = 265.3020 (a.u.)^3 >> number of atoms/cell = 2 >> number of atomic types = 1 >> kinetic-energy cutoff = 12.0000 Ry >> charge density cutoff = 48.0000 Ry >> convergence threshold = 1.0E-06 >> beta = 0.7000 >> number of iterations used = 8 plain mixing >> Exchange-correlation = SLA PZ NOGX NOGC (1100) >> iswitch = 0 >> >> celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000 >> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 >> >> crystal axes: (cart. coord. in units of a_0) >> a(1) = ( -0.500000 0.000000 0.500000 ) >> a(2) = ( 0.000000 0.500000 0.500000 ) >> a(3) = ( -0.500000 0.500000 0.000000 ) >> >> reciprocal axes: (cart. coord. in units 2 pi/a_0) >> b(1) = ( -1.000000 -1.000000 1.000000 ) >> b(2) = ( 1.000000 1.000000 1.000000 ) >> b(3) = ( -1.000000 1.000000 -1.000000 ) >> >> >> PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0 >> (in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000) >> >> atomic species valence mass pseudopotential >> Si 4.00 28.08600 Si( 1.00) >> >> 48 Sym.Ops. (with inversion) >> >> >> Cartesian axes >> >> site n. atom positions (a_0 units) >> 1 Si tau( 1) = ( 0.0000000 0.0000000 >> 0.0000000 ) >> 2 Si tau( 2) = ( 0.2500000 0.2500000 >> 0.2500000 ) >> >> number of k points= 2 >> cart. coord. in units 2pi/a_0 >> k( 1) = ( 0.2500000 0.2500000 0.7500000 ), wk = >> 1.5000000 >> k( 2) = ( 0.2500000 0.2500000 0.2500000 ), wk = >> 0.5000000 >> >> G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, 16) >> nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 186 >> nelec = 8.00 nkb = 8 ngl = 43 >> >> >> Initial potential from superposition of free atoms >> >> starting charge 7.99901, renormalised to 8.00000 >> T F >> >> >> Best regards >> >> 2012/9/17 Yue-Wen Fang >> >>> calculation CHARACTER*Default:* 'scf' >>> >>> a string describing the task to be performed: >>> 'scf', >>> 'nscf', >>> 'bands', >>> 'relax', >>> 'md', >>> 'vc-relax', >>> 'vc-md' >>> >>> (vc = variable-cell). >>> >>> >>> 2012/9/17 Pablo Garc?a Risue?o >>> >>>> Dear Fang >>>> >>>> Thank you very much. The input is a very standard one: >>>> >>>> &control >>>> prefix='silicon', >>>> pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' >>>> outdir = '.', >>>> / >>>> &system >>>> ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, >>>> ecutwfc = 12.0, >>>> / >>>> &electrons >>>> / >>>> ATOMIC_SPECIES >>>> Si 28.086 Si.vbc.UPF >>>> ATOMIC_POSITIONS >>>> Si 0.00 0.00 0.00 >>>> Si 0.25 0.25 0.25 >>>> K_POINTS >>>> 2 >>>> 0.25 0.25 0.75 3.0 >>>> 0.25 0.25 0.25 1.0 >>>> >>>> It corresponds to a tutorial example. If I use the input below, the >>>> result is the same >>>> >>>> &control >>>> prefix='nickel' >>>> outdir='.' >>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>> / >>>> &system >>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>> ecutwfc = 24.0, ecutrho = 288.0, >>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>> nspin = 2, starting_magnetization(1)=0.7, >>>> / >>>> &electrons >>>> / >>>> ATOMIC_SPECIES >>>> Ni 58.69 NiUS.RRKJ3.UPF >>>> ATOMIC_POSITIONS >>>> Ni 0.0 0.0 0.0 >>>> 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 >>>> >>>> &control >>>> prefix='nickel' >>>> outdir='.' >>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>> / >>>> &system >>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>> ecutwfc = 24.0, ecutrho = 288.0, >>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>> nspin = 2, starting_magnetization(1)=0.7, >>>> / >>>> / >>>> &electrons >>>> / >>>> ATOMIC_SPECIES >>>> Ni 58.69 NiUS.RRKJ3.UPF >>>> ATOMIC_POSITIONS >>>> Ni 0.0 0.0 0.0 >>>> 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 >>>> >>>> I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > >>>> si.scf.out >>>> >>>> Thank you very much, and best regards >>>> >>>> >>>> >>>> 2012/9/17 Yue-Wen Fang >>>> >>>>> Dear Pablo, >>>>> >>>>> I think you'd better show your input file if possible because the >>>>> given information is too limited. >>>>> >>>>> Best Regards! >>>>> Yuewen Fang >>>>> >>>>> 2012/9/17 Pablo Garc?a Risue?o >>>>> >>>>>> Dear Espresso experts >>>>>> >>>>>> I am making my first steps in Espresso. Unfortunately, I am still >>>>>> unable to make it run. After doing $ configure and $ make pw (Espresso 4), >>>>>> everything is all right. Howver, if I do >>>>>> >>>>>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in> si.scf.out >>>>>> >>>>>> No error message appears, but the scf calculation is not performed. >>>>>> The out file ends with: >>>>>> >>>>>> Initial potential from superposition of free atoms >>>>>> >>>>>> starting charge 9.99966, renormalised to 10.00000 >>>>>> T F >>>>>> >>>>>> Could anybody help me? Thank you very much >>>>>> >>>>>> -- >>>>>> -- >>>>>> >>>>>> Dr. Pablo Garc?a Risue?o >>>>>> >>>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>>> >>>>>> Tel. +49 030 20937904 >>>>>> >>>>>> _______________________________________________ >>>>>> Pw_forum mailing list >>>>>> Pw_forum at pwscf.org >>>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> ---- >>>>> Yue-Wen Fang >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>>> >>>> >>>> >>>> -- >>>> -- >>>> >>>> Dr. Pablo Garc?a Risue?o >>>> >>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>> >>>> Tel. +49 030 20937904 >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> ---- >>> Yue-Wen Fang >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> -- >> >> Dr. Pablo Garc?a Risue?o >> >> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >> (Claudia-Draxl Group), 12489 Berlin, Germany >> >> Tel. +49 030 20937904 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ---- > Yue-Wen Fang > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/54e3965c/attachment-0001.htm From yuewen.fang at gmail.com Mon Sep 17 11:08:15 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 17:08:15 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: Em... Then I advise you to check the Doc directory(~/espresso**/Doc), you may get some instructions from the PW.html. Have a try. 2012/9/17 Pablo Garc?a Risue?o > Hi! The problem is that this concrete version is expected to be well > suited to some additional code that other scientist wrote some years ago, > so we agreed I would use this version to avoid further problems... > > > > > 2012/9/17 Yue-Wen Fang > >> Dear Pablo, >> >> I think you'e better use the latest version. >> >> >> 2012/9/17 Pablo Garc?a Risue?o >> >>> Dear Fang. I also tried with calculation='scf' in the control block (I >>> think it is actually default), but the result is the same (actually I think >>> I am running the version 2.1.4). The complete output is >>> >>> Program PWSCF v.2.1.4 starts ... >>> Today is 17Sep2012 at 10:54: 6 >>> >>> Ultrasoft (Vanderbilt) Pseudopotentials >>> >>> Current dimensions of program pwscf are: >>> ntypx =10 npk =40000 lmax = 3 >>> nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 >>> ASIER: minus_q: T >>> >>> >>> bravais-lattice index = 2 >>> lattice parameter (a_0) = 10.2000 a.u. >>> unit-cell volume = 265.3020 (a.u.)^3 >>> number of atoms/cell = 2 >>> number of atomic types = 1 >>> kinetic-energy cutoff = 12.0000 Ry >>> charge density cutoff = 48.0000 Ry >>> convergence threshold = 1.0E-06 >>> beta = 0.7000 >>> number of iterations used = 8 plain mixing >>> Exchange-correlation = SLA PZ NOGX NOGC (1100) >>> iswitch = 0 >>> >>> celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000 >>> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 >>> >>> crystal axes: (cart. coord. in units of a_0) >>> a(1) = ( -0.500000 0.000000 0.500000 ) >>> a(2) = ( 0.000000 0.500000 0.500000 ) >>> a(3) = ( -0.500000 0.500000 0.000000 ) >>> >>> reciprocal axes: (cart. coord. in units 2 pi/a_0) >>> b(1) = ( -1.000000 -1.000000 1.000000 ) >>> b(2) = ( 1.000000 1.000000 1.000000 ) >>> b(3) = ( -1.000000 1.000000 -1.000000 ) >>> >>> >>> PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0 >>> (in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000) >>> >>> atomic species valence mass pseudopotential >>> Si 4.00 28.08600 Si( 1.00) >>> >>> 48 Sym.Ops. (with inversion) >>> >>> >>> Cartesian axes >>> >>> site n. atom positions (a_0 units) >>> 1 Si tau( 1) = ( 0.0000000 0.0000000 >>> 0.0000000 ) >>> 2 Si tau( 2) = ( 0.2500000 0.2500000 >>> 0.2500000 ) >>> >>> number of k points= 2 >>> cart. coord. in units 2pi/a_0 >>> k( 1) = ( 0.2500000 0.2500000 0.7500000 ), wk = >>> 1.5000000 >>> k( 2) = ( 0.2500000 0.2500000 0.2500000 ), wk = >>> 0.5000000 >>> >>> G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, >>> 16) >>> nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 186 >>> nelec = 8.00 nkb = 8 ngl = 43 >>> >>> >>> Initial potential from superposition of free atoms >>> >>> starting charge 7.99901, renormalised to 8.00000 >>> T F >>> >>> >>> Best regards >>> >>> 2012/9/17 Yue-Wen Fang >>> >>>> calculation CHARACTER*Default:* 'scf' >>>> >>>> a string describing the task to be performed: >>>> 'scf', >>>> 'nscf', >>>> 'bands', >>>> 'relax', >>>> 'md', >>>> 'vc-relax', >>>> 'vc-md' >>>> >>>> (vc = variable-cell). >>>> >>>> >>>> 2012/9/17 Pablo Garc?a Risue?o >>>> >>>>> Dear Fang >>>>> >>>>> Thank you very much. The input is a very standard one: >>>>> >>>>> &control >>>>> prefix='silicon', >>>>> pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' >>>>> outdir = '.', >>>>> / >>>>> &system >>>>> ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, >>>>> ecutwfc = 12.0, >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Si 28.086 Si.vbc.UPF >>>>> ATOMIC_POSITIONS >>>>> Si 0.00 0.00 0.00 >>>>> Si 0.25 0.25 0.25 >>>>> K_POINTS >>>>> 2 >>>>> 0.25 0.25 0.75 3.0 >>>>> 0.25 0.25 0.25 1.0 >>>>> >>>>> It corresponds to a tutorial example. If I use the input below, the >>>>> result is the same >>>>> >>>>> &control >>>>> prefix='nickel' >>>>> outdir='.' >>>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>>> / >>>>> &system >>>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>>> ecutwfc = 24.0, ecutrho = 288.0, >>>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>>> nspin = 2, starting_magnetization(1)=0.7, >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Ni 58.69 NiUS.RRKJ3.UPF >>>>> ATOMIC_POSITIONS >>>>> Ni 0.0 0.0 0.0 >>>>> 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 >>>>> >>>>> &control >>>>> prefix='nickel' >>>>> outdir='.' >>>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>>> / >>>>> &system >>>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>>> ecutwfc = 24.0, ecutrho = 288.0, >>>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>>> nspin = 2, starting_magnetization(1)=0.7, >>>>> / >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Ni 58.69 NiUS.RRKJ3.UPF >>>>> ATOMIC_POSITIONS >>>>> Ni 0.0 0.0 0.0 >>>>> 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 >>>>> >>>>> I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > >>>>> si.scf.out >>>>> >>>>> Thank you very much, and best regards >>>>> >>>>> >>>>> >>>>> 2012/9/17 Yue-Wen Fang >>>>> >>>>>> Dear Pablo, >>>>>> >>>>>> I think you'd better show your input file if possible because the >>>>>> given information is too limited. >>>>>> >>>>>> Best Regards! >>>>>> Yuewen Fang >>>>>> >>>>>> 2012/9/17 Pablo Garc?a Risue?o >>>>>> >>>>>>> Dear Espresso experts >>>>>>> >>>>>>> I am making my first steps in Espresso. Unfortunately, I am still >>>>>>> unable to make it run. After doing $ configure and $ make pw (Espresso 4), >>>>>>> everything is all right. Howver, if I do >>>>>>> >>>>>>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in> si.scf.out >>>>>>> >>>>>>> No error message appears, but the scf calculation is not performed. >>>>>>> The out file ends with: >>>>>>> >>>>>>> Initial potential from superposition of free atoms >>>>>>> >>>>>>> starting charge 9.99966, renormalised to 10.00000 >>>>>>> T F >>>>>>> >>>>>>> Could anybody help me? Thank you very much >>>>>>> >>>>>>> -- >>>>>>> -- >>>>>>> >>>>>>> Dr. Pablo Garc?a Risue?o >>>>>>> >>>>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>>>> >>>>>>> Tel. +49 030 20937904 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Pw_forum mailing list >>>>>>> Pw_forum at pwscf.org >>>>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ---- >>>>>> Yue-Wen Fang >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Pw_forum mailing list >>>>>> Pw_forum at pwscf.org >>>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> -- >>>>> >>>>> Dr. Pablo Garc?a Risue?o >>>>> >>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>> >>>>> Tel. +49 030 20937904 >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>>> >>>> >>>> >>>> -- >>>> ---- >>>> Yue-Wen Fang >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> -- >>> >>> Dr. Pablo Garc?a Risue?o >>> >>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>> (Claudia-Draxl Group), 12489 Berlin, Germany >>> >>> Tel. +49 030 20937904 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/699b3831/attachment-0001.htm From yuewen.fang at gmail.com Mon Sep 17 11:09:36 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Mon, 17 Sep 2012 17:09:36 +0800 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: If the problems still remains, jsut send emails to my personal emailbox. Best Regards! 2012/9/17 Pablo Garc?a Risue?o > Hi! The problem is that this concrete version is expected to be well > suited to some additional code that other scientist wrote some years ago, > so we agreed I would use this version to avoid further problems... > > > > > 2012/9/17 Yue-Wen Fang > >> Dear Pablo, >> >> I think you'e better use the latest version. >> >> >> 2012/9/17 Pablo Garc?a Risue?o >> >>> Dear Fang. I also tried with calculation='scf' in the control block (I >>> think it is actually default), but the result is the same (actually I think >>> I am running the version 2.1.4). The complete output is >>> >>> Program PWSCF v.2.1.4 starts ... >>> Today is 17Sep2012 at 10:54: 6 >>> >>> Ultrasoft (Vanderbilt) Pseudopotentials >>> >>> Current dimensions of program pwscf are: >>> ntypx =10 npk =40000 lmax = 3 >>> nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8 >>> ASIER: minus_q: T >>> >>> >>> bravais-lattice index = 2 >>> lattice parameter (a_0) = 10.2000 a.u. >>> unit-cell volume = 265.3020 (a.u.)^3 >>> number of atoms/cell = 2 >>> number of atomic types = 1 >>> kinetic-energy cutoff = 12.0000 Ry >>> charge density cutoff = 48.0000 Ry >>> convergence threshold = 1.0E-06 >>> beta = 0.7000 >>> number of iterations used = 8 plain mixing >>> Exchange-correlation = SLA PZ NOGX NOGC (1100) >>> iswitch = 0 >>> >>> celldm(1)= 10.200000 celldm(2)= 0.000000 celldm(3)= 0.000000 >>> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 >>> >>> crystal axes: (cart. coord. in units of a_0) >>> a(1) = ( -0.500000 0.000000 0.500000 ) >>> a(2) = ( 0.000000 0.500000 0.500000 ) >>> a(3) = ( -0.500000 0.500000 0.000000 ) >>> >>> reciprocal axes: (cart. coord. in units 2 pi/a_0) >>> b(1) = ( -1.000000 -1.000000 1.000000 ) >>> b(2) = ( 1.000000 1.000000 1.000000 ) >>> b(3) = ( -1.000000 1.000000 -1.000000 ) >>> >>> >>> PSEUDO 1 is Si zval = 4.0 lmax= 1 lloc= 0 >>> (in numerical form: 431 grid points, xmin = 0.00, dx = 0.0000) >>> >>> atomic species valence mass pseudopotential >>> Si 4.00 28.08600 Si( 1.00) >>> >>> 48 Sym.Ops. (with inversion) >>> >>> >>> Cartesian axes >>> >>> site n. atom positions (a_0 units) >>> 1 Si tau( 1) = ( 0.0000000 0.0000000 >>> 0.0000000 ) >>> 2 Si tau( 2) = ( 0.2500000 0.2500000 >>> 0.2500000 ) >>> >>> number of k points= 2 >>> cart. coord. in units 2pi/a_0 >>> k( 1) = ( 0.2500000 0.2500000 0.7500000 ), wk = >>> 1.5000000 >>> k( 2) = ( 0.2500000 0.2500000 0.2500000 ), wk = >>> 0.5000000 >>> >>> G cutoff = 126.4975 ( 1459 G-vectors) FFT grid: ( 16, 16, >>> 16) >>> nbndx = 16 nbnd = 4 natomwfc = 8 npwx = 186 >>> nelec = 8.00 nkb = 8 ngl = 43 >>> >>> >>> Initial potential from superposition of free atoms >>> >>> starting charge 7.99901, renormalised to 8.00000 >>> T F >>> >>> >>> Best regards >>> >>> 2012/9/17 Yue-Wen Fang >>> >>>> calculation CHARACTER*Default:* 'scf' >>>> >>>> a string describing the task to be performed: >>>> 'scf', >>>> 'nscf', >>>> 'bands', >>>> 'relax', >>>> 'md', >>>> 'vc-relax', >>>> 'vc-md' >>>> >>>> (vc = variable-cell). >>>> >>>> >>>> 2012/9/17 Pablo Garc?a Risue?o >>>> >>>>> Dear Fang >>>>> >>>>> Thank you very much. The input is a very standard one: >>>>> >>>>> &control >>>>> prefix='silicon', >>>>> pseudo_dir='/users/sol/risueno/Asier/esp4/pseudo' >>>>> outdir = '.', >>>>> / >>>>> &system >>>>> ibrav= 2, celldm(1) =10.2, nat= 2, ntyp= 1, >>>>> ecutwfc = 12.0, >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Si 28.086 Si.vbc.UPF >>>>> ATOMIC_POSITIONS >>>>> Si 0.00 0.00 0.00 >>>>> Si 0.25 0.25 0.25 >>>>> K_POINTS >>>>> 2 >>>>> 0.25 0.25 0.75 3.0 >>>>> 0.25 0.25 0.25 1.0 >>>>> >>>>> It corresponds to a tutorial example. If I use the input below, the >>>>> result is the same >>>>> >>>>> &control >>>>> prefix='nickel' >>>>> outdir='.' >>>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>>> / >>>>> &system >>>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>>> ecutwfc = 24.0, ecutrho = 288.0, >>>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>>> nspin = 2, starting_magnetization(1)=0.7, >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Ni 58.69 NiUS.RRKJ3.UPF >>>>> ATOMIC_POSITIONS >>>>> Ni 0.0 0.0 0.0 >>>>> 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 >>>>> >>>>> &control >>>>> prefix='nickel' >>>>> outdir='.' >>>>> pseudo_dir = '/users/sol/risueno/Asier/esp4/pseudo', >>>>> / >>>>> &system >>>>> ibrav=2, celldm(1) =6.48, nat=1, ntyp=1, >>>>> ecutwfc = 24.0, ecutrho = 288.0, >>>>> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02 >>>>> nspin = 2, starting_magnetization(1)=0.7, >>>>> / >>>>> / >>>>> &electrons >>>>> / >>>>> ATOMIC_SPECIES >>>>> Ni 58.69 NiUS.RRKJ3.UPF >>>>> ATOMIC_POSITIONS >>>>> Ni 0.0 0.0 0.0 >>>>> 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 >>>>> >>>>> I am executing pw.x with $ $espresso_dir/bin/pw.x < si.scf.in > >>>>> si.scf.out >>>>> >>>>> Thank you very much, and best regards >>>>> >>>>> >>>>> >>>>> 2012/9/17 Yue-Wen Fang >>>>> >>>>>> Dear Pablo, >>>>>> >>>>>> I think you'd better show your input file if possible because the >>>>>> given information is too limited. >>>>>> >>>>>> Best Regards! >>>>>> Yuewen Fang >>>>>> >>>>>> 2012/9/17 Pablo Garc?a Risue?o >>>>>> >>>>>>> Dear Espresso experts >>>>>>> >>>>>>> I am making my first steps in Espresso. Unfortunately, I am still >>>>>>> unable to make it run. After doing $ configure and $ make pw (Espresso 4), >>>>>>> everything is all right. Howver, if I do >>>>>>> >>>>>>> $ /users/sol/risueno/Desktop/espresso-5.0.1-GPU/bin/pw.x < si.scf.in> si.scf.out >>>>>>> >>>>>>> No error message appears, but the scf calculation is not performed. >>>>>>> The out file ends with: >>>>>>> >>>>>>> Initial potential from superposition of free atoms >>>>>>> >>>>>>> starting charge 9.99966, renormalised to 10.00000 >>>>>>> T F >>>>>>> >>>>>>> Could anybody help me? Thank you very much >>>>>>> >>>>>>> -- >>>>>>> -- >>>>>>> >>>>>>> Dr. Pablo Garc?a Risue?o >>>>>>> >>>>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>>>> >>>>>>> Tel. +49 030 20937904 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Pw_forum mailing list >>>>>>> Pw_forum at pwscf.org >>>>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ---- >>>>>> Yue-Wen Fang >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Pw_forum mailing list >>>>>> Pw_forum at pwscf.org >>>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> -- >>>>> >>>>> Dr. Pablo Garc?a Risue?o >>>>> >>>>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>>>> (Claudia-Draxl Group), 12489 Berlin, Germany >>>>> >>>>> Tel. +49 030 20937904 >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>>> >>>> >>>> >>>> -- >>>> ---- >>>> Yue-Wen Fang >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> -- >>> >>> Dr. Pablo Garc?a Risue?o >>> >>> Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 >>> (Claudia-Draxl Group), 12489 Berlin, Germany >>> >>> Tel. +49 030 20937904 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl > Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/36d27e77/attachment-0001.htm From giannozz at democritos.it Mon Sep 17 11:17:26 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Sep 2012 11:17:26 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: <1347873446.18108.6.camel@fe12lx.fisica.uniud.it> On Mon, 2012-09-17 at 10:56 +0200, Pablo Garc?a Risue?o wrote: > I also tried with calculation='scf' in the control block (I think > it is actually default) it is > but the result is the same (actually I think I am running the version 2.1.4) released 2005-06-17 ... anyway: it compiles and work, at least for the first case you sent (simple Si). Unless, of course, it is a locally modified version, as some additional lines in the output seem to indicate, P. --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From garcia.risueno at gmail.com Mon Sep 17 11:24:57 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Mon, 17 Sep 2012 11:24:57 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: <1347873446.18108.6.camel@fe12lx.fisica.uniud.it> References: <1347873446.18108.6.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo Did you download this version with svn? Could you explain me how you did it? Best 2012/9/17 Paolo Giannozzi > On Mon, 2012-09-17 at 10:56 +0200, Pablo Garc?a Risue?o wrote: > > > I also tried with calculation='scf' in the control block (I think > > it is actually default) > > it is > > > but the result is the same (actually I think I am running the version > 2.1.4) > > released 2005-06-17 ... anyway: it compiles and work, at least for the > first case you sent (simple Si). Unless, of course, it is a locally > modified version, as some additional lines in the output seem to > indicate, > > P. > --- > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/aa4304a8/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Sep 17 11:28:49 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 17 Sep 2012 11:28:49 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: <1347873446.18108.6.camel@fe12lx.fisica.uniud.it> Message-ID: On 17 September 2012 11:24, Pablo Garc?a Risue?o wrote: > Dear Paolo > > Did you download this version with svn? Could you explain me how you did > it? > > Best > Go to the QE download page: http://www.quantum-espresso.org/?page_id=16 and follow the "Previous versions up to and including v.4.1.2 can be found here." link at the end. bests -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/3506601f/attachment.htm From wangfenggong at gmail.com Mon Sep 17 22:13:52 2012 From: wangfenggong at gmail.com (Fenggong Wang) Date: Mon, 17 Sep 2012 16:13:52 -0400 Subject: [Pw_forum] Wired and large (4Ry) total energy difference on different machines Message-ID: Dear everyone: Recently we got quite different total energy using exactly the same input files for pwscf cacluation when running on different machines. On one machine, the total energy of the first ionic step is: ! total energy = -3188.41593157 Ry Harris-Foulkes estimate = -3188.41560923 Ry estimated scf accuracy < 0.00005695 Ry The total energy is the sum of the following terms: one-electron contribution = -55000.39131345 Ry hartree contribution = 27705.53744978 Ry xc contribution = -530.25923399 Ry ewald contribution = 24636.69787808 Ry electric field correction = 0.00107603 Ry smearing contrib. (-TS) = -0.00178802 Ry while on the other one, it is: ! total energy = -3184.04215443 Ry Harris-Foulkes estimate = -3184.04248811 Ry estimated scf accuracy < 0.00007177 Ry The total energy is the sum of the following terms: one-electron contribution = -55000.21479459 Ry hartree contribution = 27705.35347136 Ry xc contribution = -525.87732678 Ry ewald contribution = 24636.69787808 Ry electric field correction = 0.00042900 Ry smearing contrib. (-TS) = -0.00181150 Ry As we can see, the energy difference is mainly from the xc part. During the ionic relaxation, the large energy difference maintains. This is wired and we have no idea of what the problem is. Since the partial core correction is used for the Al pseudopotential, does the large difference have something related to the Al psps? Could any one have any idea or hint about this? Thank you. Our input files are enclosed as follows for your reference: &control calculation = 'relax' prefix='lao_sto_1+10ucs_surf', nstep=200, pseudo_dir ='./' outdir='./' verbosity = 'high' nstep = 200 dipfield = .true. tefield = .true. restart_mode = 'from_scratch' / &system ibrav= 6, celldm(1)=7.279889198, celldm(2)=1, celldm(3)=15.5 nat=60, ntyp= 5, ecutwfc = 50, occupations='smearing', degauss = 0.01 nspin = 1 edir = 3, eopreg=0.03, emaxpos=0.860 / &electrons mixing_mode = 'plain' mixing_beta = 0.10 conv_thr = 1.0e-4 startingwfc='random' startingpot='atomic' / &ions ion_dynamics = 'bfgs', pot_extrapolation = 'atomic', upscale = 100, trust_radius_ini = 0.5, / ATOMIC_SPECIES La 138.9055 La_LDA.upf Al 26.9815 Al_LDA.upf Sr 87.6200 Sr_LDA.upf Ti 47.8670 Ti_LDA.upf O 15.9994 O_LDA.upf K_POINTS {automatic} 6 6 1 0 0 0ATOMIC_POSITIONS (angstrom) O 1.926180751 0.000000000 1.932851169 O 1.926180751 0.000000000 5.806416120 O 1.926180751 0.000000000 9.690288605 O 1.926180751 0.000000000 13.570435914 O 1.926180751 0.000000000 17.444898624 O 1.926180751 0.000000000 21.316455327 O 1.926180751 0.000000000 25.188371707 O 1.926180751 0.000000000 29.064620363 O 1.926180751 0.000000000 32.947258569 O 1.926180751 0.000000000 36.826561486 O 1.926180751 0.000000000 40.718241080 O 1.926180751 0.000000000 44.413343364 O 1.926180751 1.926180751 -0.022898252 O 1.926180751 1.926180751 3.855269167 O 1.926180751 1.926180751 7.733476374 O 1.926180751 1.926180751 11.614174551 O 1.926180751 1.926180751 15.491455293 O 1.926180751 1.926180751 19.364662145 O 1.926180751 1.926180751 23.236913267 O 1.926180751 1.926180751 27.111740990 O 1.926180751 1.926180751 30.990883340 O 1.926180751 1.926180751 34.870585517 O 1.926180751 1.926180751 38.750367991 O 1.926180751 1.926180751 42.575880071 O 0.000000000 1.926180751 1.932851169 O 0.000000000 1.926180751 5.806416120 O 0.000000000 1.926180751 9.690288605 O 0.000000000 1.926180751 13.570435914 O 0.000000000 1.926180751 17.444898624 O 0.000000000 1.926180751 21.316455327 O 0.000000000 1.926180751 25.188371707 O 0.000000000 1.926180751 29.064620363 O 0.000000000 1.926180751 32.947258569 O 0.000000000 1.926180751 36.826561486 O 0.000000000 1.926180751 40.718241080 O 0.000000000 1.926180751 44.413343364 Ti 1.926180751 1.926180751 1.835084398 Ti 1.926180751 1.926180751 5.714812422 Ti 1.926180751 1.926180751 9.595819437 Ti 1.926180751 1.926180751 13.476028107 Ti 1.926180751 1.926180751 17.351541485 Ti 1.926180751 1.926180751 21.223872514 Ti 1.926180751 1.926180751 25.096507617 Ti 1.926180751 1.926180751 28.972779773 Ti 1.926180751 1.926180751 32.853697401 Ti 1.926180751 1.926180751 36.735490165 Ti 1.926180751 1.926180751 40.630380050 Al 1.926180751 1.926180751 44.503275725 Sr 0.000000000 0.000000000 -0.079993855 Sr 0.000000000 0.000000000 3.786562857 Sr 0.000000000 0.000000000 7.660339507 Sr 0.000000000 0.000000000 11.541763403 Sr 0.000000000 0.000000000 15.419292965 Sr 0.000000000 0.000000000 19.292333803 Sr 0.000000000 0.000000000 23.163762621 Sr 0.000000000 0.000000000 27.037320220 Sr 0.000000000 0.000000000 30.916125648 Sr 0.000000000 0.000000000 34.794891468 Sr 0.000000000 0.000000000 38.659475210 La 0.000000000 0.000000000 42.684568538 -- Dr. Fenggong Wang Postdoctoral Researcher Department of Chemistry University of Pennsylvania 231 South 34th Street, BOX 314 Philadelphia, PA 19104-6323 e-mail: wangfenggong at gmail.com; fenggong at sas.upenn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/573edb66/attachment.htm From giannozz at democritos.it Mon Sep 17 22:27:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Sep 2012 22:27:35 +0200 Subject: [Pw_forum] Wired and large (4Ry) total energy difference on different machines In-Reply-To: References: Message-ID: <79022521-6C41-4D22-9F10-FD3161318938@democritos.it> On Sep 17, 2012, at 22:13 , Fenggong Wang wrote: > Recently we got quite different total energy using exactly > the same input files for pwscf calcuation when running > on different machines. make a diff of the outputs, just to be sure that everything else is the same. Small differences between different machines/number of processors/compilers/libraries/phases of the moon are unavoidable. 4Ry is definitely too much. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wangfenggong at gmail.com Mon Sep 17 23:18:22 2012 From: wangfenggong at gmail.com (Fenggong Wang) Date: Mon, 17 Sep 2012 17:18:22 -0400 Subject: [Pw_forum] Wired and large (4Ry) total energy difference on different machines In-Reply-To: <79022521-6C41-4D22-9F10-FD3161318938@democritos.it> References: <79022521-6C41-4D22-9F10-FD3161318938@democritos.it> Message-ID: Dear Prof. Giannozzi: Thank you very much. I checked the diff of the outputs. The first part (before calculating) of the output is essentially the same except some trivial information. The main difference starts from the first iteration. In output1, it is: Computed dipole along edir(3) : Elec. dipole -0.7303 Ry au, -1.8561 Debye Ion. dipole -0.6420 Ry au, -1.6317 Debye Dipole 42.0156 Ry au, 106.7936 Debye Dipole field 0.0883 Ry au Potential amp. -19.3274 Ry Total length 109.4531 bohr Starting wfc are random total cpu time spent up to now is 9.8 secs per-process dynamical memory: 163.1 Mb Self-consistent Calculation iteration # 1 ecut= 50.00 Ry beta=0.10 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 17.1 negative rho (up, down): 0.195E-03 0.000E+00 Adding external electric field Computed dipole along edir(3) : Elec. dipole 3.4941 Ry au, 8.8811 Debye Ion. dipole -0.6420 Ry au, -1.6317 Debye Dipole -1968.2460 Ry au, -5002.8089 Debye Dipole field -4.1360 Ry au Potential amp. 905.4020 Ry Total length 109.4531 bohr total cpu time spent up to now is 178.7 secs while in output2 it is: Computed dipole along edir(3) : Elec. dipole -0.7303 Ry au, -1.8561 Debye Ion. dipole -0.6420 Ry au, -1.6317 Debye Dipole 42.0156 Ry au, 106.7936 Debye Dipole field 0.0883 Ry au Potential amp. -19.3274 Ry Total length 109.4531 bohr Starting wfc are random total cpu time spent up to now is 4.5 secs per-process dynamical memory: 24.2 Mb Self-consistent Calculation iteration # 1 ecut= 50.00 Ry beta=0.10 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 18.5 negative rho (up, down): 0.196E-03 0.000E+00 Adding external electric field Computed dipole along edir(3) : Elec. dipole 3.4862 Ry au, 8.8612 Debye Ion. dipole -0.6420 Ry au, -1.6317 Debye Dipole -1964.5250 Ry au, -4993.3512 Debye Dipole field -4.1282 Ry au Potential amp. 903.6903 Ry Total length 109.4531 bohr total cpu time spent up to now is 58.6 secs Thank you. Fenggong On Mon, Sep 17, 2012 at 4:27 PM, Paolo Giannozzi wrote: > > On Sep 17, 2012, at 22:13 , Fenggong Wang wrote: > > > Recently we got quite different total energy using exactly > > the same input files for pwscf calcuation when running > > on different machines. > > make a diff of the outputs, just to be sure that everything > else is the same. > > Small differences between different machines/number of > processors/compilers/libraries/phases of the moon are > unavoidable. 4Ry is definitely too much. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Dr. Fenggong Wang Postdoctoral Researcher Department of Chemistry University of Pennsylvania 231 South 34th Street, BOX 314 Philadelphia, PA 19104-6323 e-mail: wangfenggong at gmail.com; fenggong at sas.upenn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/edd43b3a/attachment.htm From iyad.ne at gmail.com Tue Sep 18 04:52:48 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Mon, 17 Sep 2012 22:52:48 -0400 Subject: [Pw_forum] el-ph in Nb Message-ID: Dear PWSCF users, I am interested in el-ph calculations in Nb. I am studying the effect of k-mesh size, smearing width, and smearing type on the el-ph constant and phonon linewidths. I am comparing Gaussian (gauss) and Fermi-Dirac (fd) using smearing width 0.022Ry =0.30 eV. I am also using 64 64 64 k-mesh for el-ph and 16 16 16 k-mesh for the scf calculations. The calculations are performed with QE-5.0. However, in case of Fermi-Dirac smearing the phonon calculations (ph.x) proceed smoothly, whereas in case of Gaussian smearing the the phonon calculations stops from the beginning with an error message : too many kpoints ==> Why it works in case of (fd) and not in case of (gauss) smearing??????? below is my input file for the el-ph calculations: &control calculation='scf', restart_mode='from_scratch', title='Nb', outdir='./', prefix='Nb', pseudo_dir='./', wf_collect=.true., / &system ibrav=3, celldm(1)=6.1389, nat=1, ntyp=1, ecutwfc=60.0, ecutrho=480.0, occupations='smearing', degauss=0.022, smearing='gauss', la2F= .true., / &electrons conv_thr=1.0d-8, mixing_mode='plain', mixing_beta=0.7, diagonalization='cg', / ATOMIC_SPECIES Nb 92.906 Nb.pz-sp-van.UPF ATOMIC_POSITIONS {alat} Nb 0.00 0.00 0.00 K_POINTS {automatic} 64 64 64 0 0 0 Kindest Regards, ___________________________ IYAD I. AL-QASIR, PhD Postdoc Research Associate X-Ray and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division Oak Ridge National Lab Oak Ridge, TN -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120917/c5d05d70/attachment.htm From spiga.filippo at gmail.com Tue Sep 18 09:44:46 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 18 Sep 2012 09:44:46 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: Message-ID: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> Dear Pablo, thanks to express interest in the GPU accelerated version of PWscf! I grab your input file and I am going to do some tests this morning. Please confirm that is "espresso-4.3.2-GPU.tar.gz" the package that generates the crash. If you tried with the code in the espresso-PRACE branch please do your test again. that code is old and not properly aligned (and we are going to delete that branch very very soon!). I am not excluding some dirt deep bugs espresso-4.3.2-GPU, we moved forward with the implementation and now the 5.0 is the reference build. I will keep you posted privately after I performed some tests. The ML for GPU issue is http://qe-forge.org/mailman/listinfo/q-e-gpgpu Regards, Filippo On Sep 17, 2012, at 10:35 AM, Pablo Garc?a Risue?o wrote: > I think I did not express properly in my first email. Actually the problem is given by the Espresso 4 version, not by the 5.0.1-GPU one... -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/749b6c8a/attachment.htm From garcia.risueno at gmail.com Tue Sep 18 09:49:20 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Tue, 18 Sep 2012 09:49:20 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> References: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> Message-ID: Dear Filippo Thank you very much for your help. Unfortunately, the version that is crashing is actually v.2.1.4 (I have to use it because it is well suited to some functions that were written some years ago...). When I run pw.x with the attached input, I obtain the attached output, where the scf is not actually run, but no error message is given. Have you ever found something like this? Best regards 2012/9/18 Filippo Spiga > Dear Pablo, > > thanks to express interest in the GPU accelerated version of PWscf! > > I grab your input file and I am going to do some tests this morning. > Please confirm that is "espresso-4.3.2-GPU.tar.gz" the package that > generates the crash. If you tried with the code in the espresso-PRACE > branch please do your test again. that code is old and not properly aligned > (and we are going to delete that branch very very soon!). > > I am not excluding some dirt deep bugs espresso-4.3.2-GPU, we moved > forward with the implementation and now the 5.0 is the reference build. I > will keep you posted privately after I performed some tests. > > The ML for GPU issue is http://qe-forge.org/mailman/listinfo/q-e-gpgpu > > Regards, > Filippo > > On Sep 17, 2012, at 10:35 AM, Pablo Garc?a Risue?o < > garcia.risueno at gmail.com> wrote: > > I think I did not express properly in my first email. Actually the problem > is given by the Espresso 4 version, not by the 5.0.1-GPU one... > > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/cbe5be4a/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: si.scf.in Type: application/octet-stream Size: 462 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120918/cbe5be4a/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: si.scf.out Type: application/octet-stream Size: 2540 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120918/cbe5be4a/attachment-0003.obj From giannozz at democritos.it Tue Sep 18 09:53:40 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 18 Sep 2012 09:53:40 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> Message-ID: <1347954820.30299.11.camel@fe12lx.fisica.uniud.it> You should first of all try the provided examples. If they don't work, there is something wrong either in your compiler/libraries/machine/whatever, or in your changes P. On Tue, 2012-09-18 at 09:49 +0200, Pablo Garc?a Risue?o wrote: > Dear Filippo > > Thank you very much for your help. Unfortunately, the version that is > crashing is actually v.2.1.4 (I have to use it because it is well > suited to some functions that were written some years ago...). When I > run pw.x with the attached input, I obtain the attached output, where > the scf is not actually run, but no error message is given. Have you > ever found something like this? > > Best regards > > > > 2012/9/18 Filippo Spiga > Dear Pablo, > > > thanks to express interest in the GPU accelerated version of > PWscf! > > > I grab your input file and I am going to do some tests this > morning. Please confirm that is "espresso-4.3.2-GPU.tar.gz" > the package that generates the crash. If you tried with the > code in the espresso-PRACE branch please do your test again. > that code is old and not properly aligned (and we are going to > delete that branch very very soon!). > > > I am not excluding some dirt deep bugs espresso-4.3.2-GPU, we > moved forward with the implementation and now the 5.0 is the > reference build. I will keep you posted privately after I > performed some tests. > > > The ML for GPU issue > is http://qe-forge.org/mailman/listinfo/q-e-gpgpu > > > Regards, > Filippo > > > On Sep 17, 2012, at 10:35 AM, Pablo Garc?a Risue?o > wrote: > > I think I did not express properly in my first email. > > Actually the problem is given by the Espresso 4 version, not > > by the 5.0.1-GPU one... > > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: > filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David > Hilbert > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > -- > > Dr. Pablo Garc?a Risue?o > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 > (Claudia-Draxl Group), 12489 Berlin, Germany > > Tel. +49 030 20937904 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From spiga.filippo at gmail.com Tue Sep 18 10:14:30 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Tue, 18 Sep 2012 10:14:30 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: References: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> Message-ID: <9B9C696F-457A-40EC-9526-BB148648EFCD@gmail.com> On Sep 18, 2012, at 9:49 AM, Pablo Garc?a Risue?o wrote: > v.2.1.4 Such an old version? Sure? Have you tried to merge your changes to the current release? It is a effort that it might be worth for future investigations? F. -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/775c58b3/attachment.htm From garcia.risueno at gmail.com Tue Sep 18 11:04:35 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Tue, 18 Sep 2012 11:04:35 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: <1347954820.30299.11.camel@fe12lx.fisica.uniud.it> References: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> <1347954820.30299.11.camel@fe12lx.fisica.uniud.it> Message-ID: Actually they does not work. How could I find what is wrong in my compiler/libraries/machine/whatever? The 2.1.4 version that my colleague sent me compiles (after commenting the line with mpif90 in the configure), but the examples crash. The 2.1.4 version downloaded from the website gives error when doing make pw (messages attached), how may I avoid them? (which file should I modify) Thank you very much 2012/9/18 Paolo Giannozzi > You should first of all try the provided examples. If > they don't work, there is something wrong either in > your compiler/libraries/machine/whatever, or in your > changes > > P. > > On Tue, 2012-09-18 at 09:49 +0200, Pablo Garc?a Risue?o wrote: > > Dear Filippo > > > > Thank you very much for your help. Unfortunately, the version that is > > crashing is actually v.2.1.4 (I have to use it because it is well > > suited to some functions that were written some years ago...). When I > > run pw.x with the attached input, I obtain the attached output, where > > the scf is not actually run, but no error message is given. Have you > > ever found something like this? > > > > Best regards > > > > > > > > 2012/9/18 Filippo Spiga > > Dear Pablo, > > > > > > thanks to express interest in the GPU accelerated version of > > PWscf! > > > > > > I grab your input file and I am going to do some tests this > > morning. Please confirm that is "espresso-4.3.2-GPU.tar.gz" > > the package that generates the crash. If you tried with the > > code in the espresso-PRACE branch please do your test again. > > that code is old and not properly aligned (and we are going to > > delete that branch very very soon!). > > > > > > I am not excluding some dirt deep bugs espresso-4.3.2-GPU, we > > moved forward with the implementation and now the 5.0 is the > > reference build. I will keep you posted privately after I > > performed some tests. > > > > > > The ML for GPU issue > > is http://qe-forge.org/mailman/listinfo/q-e-gpgpu > > > > > > Regards, > > Filippo > > > > > > On Sep 17, 2012, at 10:35 AM, Pablo Garc?a Risue?o > > wrote: > > > I think I did not express properly in my first email. > > > Actually the problem is given by the Espresso 4 version, not > > > by the 5.0.1-GPU one... > > > > > > -- > > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: > > filippo.spiga > > > > ?Nobody will drive us out of Cantor's paradise.? ~ David > > Hilbert > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > -- > > > > Dr. Pablo Garc?a Risue?o > > > > Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 > > (Claudia-Draxl Group), 12489 Berlin, Germany > > > > Tel. +49 030 20937904 > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/94f6bf31/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: error_pw_disable-parallel.log Type: application/octet-stream Size: 23390 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120918/94f6bf31/attachment-0001.obj From garcia.risueno at gmail.com Tue Sep 18 11:05:13 2012 From: garcia.risueno at gmail.com (=?ISO-8859-1?Q?Pablo_Garc=EDa_Risue=F1o?=) Date: Tue, 18 Sep 2012 11:05:13 +0200 Subject: [Pw_forum] pw.x does not work In-Reply-To: <9B9C696F-457A-40EC-9526-BB148648EFCD@gmail.com> References: <42F4A4CB-8599-491E-B026-1EFEC4D92717@gmail.com> <9B9C696F-457A-40EC-9526-BB148648EFCD@gmail.com> Message-ID: Hi! I thought it would be wiser to try to make work the simplest version first... 2012/9/18 Filippo Spiga > On Sep 18, 2012, at 9:49 AM, Pablo Garc?a Risue?o < > garcia.risueno at gmail.com> wrote: > > v.2.1.4 > > > Such an old version? Sure? > > Have you tried to merge your changes to the current release? It is a > effort that it might be worth for future investigations? > > F. > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -- Dr. Pablo Garc?a Risue?o Institut f?r Physik, Humboldt Universit?t, Newtonstrasse 15 (Claudia-Draxl Group), 12489 Berlin, Germany Tel. +49 030 20937904 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/b64ed467/attachment.htm From yuewen.fang at gmail.com Tue Sep 18 14:55:11 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 18 Sep 2012 20:55:11 +0800 Subject: [Pw_forum] charge density difference calculation error! Message-ID: Dear all, It happened a problem to me when calculating the charge density difference. *My input*: &inputpp / &plot nfile = 2 filepp(1) = 'SRO-up.rho' *(SRO-up.rho is a file which records the charge density data of this system, it was given at last step)* filepp(2) = 'SROup-doping.rho' weight(1) = 1.0 weight(2) = -1.0 iflag = 2 output_format = 3 fileout = 'test_diff.xsf' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, nx=56, ny=40 / *The output*: R & G space division: proc/pool = 4 Reading header from file SRO-up.rho Reading data from file SRO-up.rho %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from chdens : error # 1 *incompatible nr1x or nr2x (I haven't found what nr1x means)* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from chdens : error # 1 incompatible nr1x or nr2x %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from chdens : error # 1 incompatible nr1x or nr2x %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from chdens : error # 1 incompatible nr1x or nr2x %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... p0_22690: p4_error: : 0 rm_l_1_22720: (0.140625) net_send: could not write to fd=5, errno = 32 rm_l_3_22778: (0.058594) net_send: could not write to fd=5, errno = 32 p0_22690: (4.222656) net_send: could not write to fd=4, errno = 32 p1_22695: (4.144531) net_send: could not write to fd=5, errno = 32 p3_22753: (4.062500) net_send: could not write to fd=5, errno = 32 -- ---- Yue-Wen Fang Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/77e73f80/attachment.htm From gabriele.sclauzero at epfl.ch Tue Sep 18 15:07:23 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 18 Sep 2012 15:07:23 +0200 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: Il giorno 18/set/2012, alle ore 14.55, Yue-Wen Fang ha scritto: > Dear all, > It happened a problem to me when calculating the charge density difference. > My input: > &inputpp > / > &plot > nfile = 2 > filepp(1) = 'SRO-up.rho' (SRO-up.rho is a file which records the charge density data of this system, it was given at last step) > filepp(2) = 'SROup-doping.rho' > weight(1) = 1.0 > weight(2) = -1.0 > iflag = 2 > output_format = 3 > fileout = 'test_diff.xsf' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > The output: > R & G space division: proc/pool = 4 > Reading header from file SRO-up.rho > Reading data from file SRO-up.rho > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from chdens : error # 1 > incompatible nr1x or nr2x (I haven't found what nr1x means) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... Most probably there is a size mismatch between the two cells, or you used a different cutoff for the two calculations. Please check. GS ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/2d769162/attachment.htm From yuewen.fang at gmail.com Tue Sep 18 15:32:08 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 18 Sep 2012 21:32:08 +0800 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: The cells are same size and the cutoff is also same. The difference is that in the second cell I used a pseudopotential generated by virtual.x (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal approximation method to simulate the SRO system doped by nitrogen. Best wishes! 2012/9/18 Gabriele Sclauzero > > Il giorno 18/set/2012, alle ore 14.55, Yue-Wen Fang ha scritto: > > Dear all, > It happened a problem to me when calculating the charge density > difference. > *My input*: > &inputpp > / > &plot > nfile = 2 > filepp(1) = 'SRO-up.rho' *(SRO-up.rho is a file which records the > charge density data of this system, it was given at last step)* > filepp(2) = 'SROup-doping.rho' > weight(1) = 1.0 > weight(2) = -1.0 > iflag = 2 > output_format = 3 > fileout = 'test_diff.xsf' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > *The output*: > R & G space division: proc/pool = 4 > Reading header from file SRO-up.rho > Reading data from file SRO-up.rho > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from chdens : error # 1 > *incompatible nr1x or nr2x (I haven't found what nr1x means)* > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > Most probably there is a size mismatch between the two cells, or you used > a different cutoff for the two calculations. Please check. > > > GS > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/c274b97c/attachment-0001.htm From gabriele.sclauzero at epfl.ch Tue Sep 18 16:42:09 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 18 Sep 2012 16:42:09 +0200 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: Could you please provide the header of the two density files? Thanks, GS Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto: > The cells are same size and the cutoff is also same. The difference is that in the second cell I used a pseudopotential generated by virtual.x (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal approximation method to simulate the SRO system doped by nitrogen. > > Best wishes! ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/bb012d7b/attachment.htm From yuewen.fang at gmail.com Tue Sep 18 17:09:25 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Tue, 18 Sep 2012 23:09:25 +0800 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: Do you mean the output file? the header of output file in xsf* with Nitrogen doping*: CRYSTAL PRIMVEC 3.905001297 0.000000000 0.000000000 0.000000000 3.905001297 0.000000000 0.000000000 0.000000000 3.905001297 PRIMCOORD 5 1 Sr 0.000000000 0.000000000 0.000000000 Ru 1.952500649 1.952500649 1.952500649 O 1.952500649 0.000000000 1.952500649 O 0.000000000 1.952500649 1.952500649 O 1.952500649 1.952500649 0.000000000 ???????? ???????? the header of output file in xsf* without Nitrogen doping*: CRYSTAL PRIMVEC 3.905001297 0.000000000 0.000000000 0.000000000 3.905001297 0.000000000 0.000000000 0.000000000 3.905001297 PRIMCOORD 5 1 Sr 0.000000000 0.000000000 0.000000000 Ru 1.952500649 1.952500649 1.952500649 O 1.952500649 0.000000000 1.952500649 O 0.000000000 1.952500649 1.952500649 O 1.952500649 1.952500649 0.000000000 The two headers are same. Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory building and go to sleep. Thank you for your help. Best wishes! Yuewen Fang 2012/9/18 Gabriele Sclauzero > Could you please provide the header of the two density files? > > Thanks, > > GS > > > Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto: > > The cells are same size and the cutoff is also same. The difference is > that in the second cell I used a pseudopotential generated by virtual.x > (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual > crystal approximation method to simulate the SRO system doped by nitrogen. > > Best wishes! > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/59503712/attachment.htm From iyad.ne at gmail.com Tue Sep 18 23:17:04 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Tue, 18 Sep 2012 17:17:04 -0400 Subject: [Pw_forum] el-ph in Nb In-Reply-To: References: Message-ID: Dear PWSCF users, I am interested in el-ph calculations in Nb. I am studying the effect of k-mesh size, smearing width, and smearing type on the el-ph constant and phonon linewidths. I am comparing Gaussian (gauss) and Fermi-Dirac (fd) using smearing width 0.022Ry =0.30 eV. I am also using 64 64 64 k-mesh for el-ph and 16 16 16 k-mesh for the scf calculations. The calculations are performed with QE-5.0. However, in case of Fermi-Dirac smearing the phonon calculations (ph.x) proceed smoothly, whereas in case of Gaussian smearing the the phonon calculations stops from the beginning with an error message : too many kpoints ==> Why it works in case of (fd) and not in case of (gauss) smearing??????? below is my input file for the el-ph calculations: &control calculation='scf', restart_mode='from_scratch', title='Nb', outdir='./', prefix='Nb', pseudo_dir='./', wf_collect=.true., / &system ibrav=3, celldm(1)=6.1389, nat=1, ntyp=1, ecutwfc=60.0, ecutrho=480.0, occupations='smearing', degauss=0.022, smearing='gauss', la2F= .true., / &electrons conv_thr=1.0d-8, mixing_mode='plain', mixing_beta=0.7, diagonalization='cg', / ATOMIC_SPECIES Nb 92.906 Nb.pz-sp-van.UPF ATOMIC_POSITIONS {alat} Nb 0.00 0.00 0.00 K_POINTS {automatic} 64 64 64 0 0 0 Kindest Regards, ___________________________ IYAD I. AL-QASIR, PhD Postdoc Research Associate X-Ray and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division Oak Ridge National Lab Oak Ridge, TN -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120918/d6403a5d/attachment.htm From subhra at iitg.ernet.in Wed Sep 19 08:14:19 2012 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Wed, 19 Sep 2012 11:44:19 +0530 Subject: [Pw_forum] Queries regarding fixed-spin moment phonon calculations and DFPT+U Message-ID: <832a83bbddf2714c11d4d42d4525beed.squirrel@webmail.iitg.ernet.in> To The Developers of QE, I am curious to know whether the following would be possible by QE-5.0.1? 1) Fixed-spin moment phonon calculation for a metallic system. 2) Is DFPT+U (PRB 84, 161102(R)) implemented in QE-5.0.1? I would really appreciate a response. Subhradip ************************************************************************ Dr. Subhradip Ghosh Associate Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From gabriele.sclauzero at epfl.ch Wed Sep 19 09:38:32 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 19 Sep 2012 09:38:32 +0200 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: I mean the header (the first 4 lines at least) of the density files that you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the xsf files. Those lines contain information about the fft grid and are read by pp.x to check consistency between the grids in the two files. GS Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto: > Do you mean the output file? > the header of output file in xsf with Nitrogen doping: > CRYSTAL > PRIMVEC > 3.905001297 0.000000000 0.000000000 > 0.000000000 3.905001297 0.000000000 > 0.000000000 0.000000000 3.905001297 > PRIMCOORD > 5 1 > Sr 0.000000000 0.000000000 0.000000000 > Ru 1.952500649 1.952500649 1.952500649 > O 1.952500649 0.000000000 1.952500649 > O 0.000000000 1.952500649 1.952500649 > O 1.952500649 1.952500649 0.000000000 > ???????? > ???????? > > the header of output file in xsf without Nitrogen doping: > CRYSTAL > PRIMVEC > 3.905001297 0.000000000 0.000000000 > 0.000000000 3.905001297 0.000000000 > 0.000000000 0.000000000 3.905001297 > PRIMCOORD > 5 1 > Sr 0.000000000 0.000000000 0.000000000 > Ru 1.952500649 1.952500649 1.952500649 > O 1.952500649 0.000000000 1.952500649 > O 0.000000000 1.952500649 1.952500649 > O 1.952500649 1.952500649 0.000000000 > > The two headers are same. > Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory building and go to sleep. > Thank you for your help. > > Best wishes! > Yuewen Fang > > 2012/9/18 Gabriele Sclauzero > Could you please provide the header of the two density files? > > Thanks, > > GS > > > Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto: > >> The cells are same size and the cutoff is also same. The difference is that in the second cell I used a pseudopotential generated by virtual.x (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual crystal approximation method to simulate the SRO system doped by nitrogen. >> >> Best wishes! > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ---- > Yue-Wen Fang > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/85298e7d/attachment-0001.htm From yuewen.fang at gmail.com Wed Sep 19 10:05:25 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Wed, 19 Sep 2012 16:05:25 +0800 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: &inputpp prefix = 'SRO' outdir = './' filplot = 'SROcharge' plot_num= 0 spin_component=1 / &plot nfile = 1 filepp(1) = 'SROcharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'SRO-up.rho' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, nx=56, ny=40 / &inputpp prefix = 'SRO' outdir = './' filplot = 'SROcharge' plot_num= 0 spin_component=1 / &plot nfile = 1 filepp(1) = 'SROcharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'SROup-doping.rho' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, nx=56, ny=40 / 2012/9/19 Gabriele Sclauzero > > I mean the header (the first 4 lines at least) of the density files that > you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not > the xsf files. > Those lines contain information about the fft grid and are read by pp.x to > check consistency between the grids in the two files. > > GS > > Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto: > > Do you mean the output file? > the header of output file in xsf* with Nitrogen doping*: > CRYSTAL > PRIMVEC > 3.905001297 0.000000000 0.000000000 > 0.000000000 3.905001297 0.000000000 > 0.000000000 0.000000000 3.905001297 > PRIMCOORD > 5 1 > Sr 0.000000000 0.000000000 0.000000000 > Ru 1.952500649 1.952500649 1.952500649 > O 1.952500649 0.000000000 1.952500649 > O 0.000000000 1.952500649 1.952500649 > O 1.952500649 1.952500649 0.000000000 > ???????? > ???????? > > the header of output file in xsf* without Nitrogen doping*: > CRYSTAL > PRIMVEC > 3.905001297 0.000000000 0.000000000 > 0.000000000 3.905001297 0.000000000 > 0.000000000 0.000000000 3.905001297 > PRIMCOORD > 5 1 > Sr 0.000000000 0.000000000 0.000000000 > Ru 1.952500649 1.952500649 1.952500649 > O 1.952500649 0.000000000 1.952500649 > O 0.000000000 1.952500649 1.952500649 > O 1.952500649 1.952500649 0.000000000 > > The two headers are same. > Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory > building and go to sleep. > Thank you for your help. > > Best wishes! > Yuewen Fang > > 2012/9/18 Gabriele Sclauzero > >> Could you please provide the header of the two density files? >> >> Thanks, >> >> GS >> >> >> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto: >> >> The cells are same size and the cutoff is also same. The difference is >> that in the second cell I used a pseudopotential generated by virtual.x >> (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual >> crystal approximation method to simulate the SRO system doped by nitrogen. >> >> Best wishes! >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> * PH H2 462, Station 3, CH-1015 Lausanne* >> >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ---- > Yue-Wen Fang > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/71295339/attachment.htm From yuewen.fang at gmail.com Wed Sep 19 10:15:34 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Wed, 19 Sep 2012 16:15:34 +0800 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: The input files are listed here. In fact, there is no difference. 2012/9/19 Yue-Wen Fang > > &inputpp > prefix = 'SRO' > outdir = './' > filplot = 'SROcharge' > plot_num= 0 > spin_component=1 > / > &plot > nfile = 1 > filepp(1) = 'SROcharge' > weight(1) = 1.0 > iflag = 2 > output_format = 2 > fileout = 'SRO-up.rho' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > > &inputpp > prefix = 'SRO' > outdir = './' > filplot = 'SROcharge' > plot_num= 0 > spin_component=1 > / > &plot > nfile = 1 > filepp(1) = 'SROcharge' > weight(1) = 1.0 > iflag = 2 > output_format = 2 > fileout = 'SROup-doping.rho' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > > > 2012/9/19 Gabriele Sclauzero > >> >> I mean the header (the first 4 lines at least) of the density files that >> you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not >> the xsf files. >> Those lines contain information about the fft grid and are read by pp.x >> to check consistency between the grids in the two files. >> >> GS >> >> Il giorno 18/set/2012, alle ore 17.09, Yue-Wen Fang ha scritto: >> >> Do you mean the output file? >> the header of output file in xsf* with Nitrogen doping*: >> CRYSTAL >> PRIMVEC >> 3.905001297 0.000000000 0.000000000 >> 0.000000000 3.905001297 0.000000000 >> 0.000000000 0.000000000 3.905001297 >> PRIMCOORD >> 5 1 >> Sr 0.000000000 0.000000000 0.000000000 >> Ru 1.952500649 1.952500649 1.952500649 >> O 1.952500649 0.000000000 1.952500649 >> O 0.000000000 1.952500649 1.952500649 >> O 1.952500649 1.952500649 0.000000000 >> ???????? >> ???????? >> >> the header of output file in xsf* without Nitrogen doping*: >> CRYSTAL >> PRIMVEC >> 3.905001297 0.000000000 0.000000000 >> 0.000000000 3.905001297 0.000000000 >> 0.000000000 0.000000000 3.905001297 >> PRIMCOORD >> 5 1 >> Sr 0.000000000 0.000000000 0.000000000 >> Ru 1.952500649 1.952500649 1.952500649 >> O 1.952500649 0.000000000 1.952500649 >> O 0.000000000 1.952500649 1.952500649 >> O 1.952500649 1.952500649 0.000000000 >> >> The two headers are same. >> Wow, it is 23 o'clock here (Shanghai, China), I have to leave laboratory >> building and go to sleep. >> Thank you for your help. >> >> Best wishes! >> Yuewen Fang >> >> 2012/9/18 Gabriele Sclauzero >> >>> Could you please provide the header of the two density files? >>> >>> Thanks, >>> >>> GS >>> >>> >>> Il giorno 18/set/2012, alle ore 15.32, Yue-Wen Fang ha scritto: >>> >>> The cells are same size and the cutoff is also same. The difference is >>> that in the second cell I used a pseudopotential generated by virtual.x >>> (the pp mix N.*.UPF and O.*.UPF), in the other words, i used the virtual >>> crystal approximation method to simulate the SRO system doped by nitrogen. >>> >>> Best wishes! >>> >>> >>> >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA >>> * PH H2 462, Station 3, CH-1015 Lausanne* >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ---- >> Yue-Wen Fang >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> * PH H2 462, Station 3, CH-1015 Lausanne* >> >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ---- > Yue-Wen Fang > > > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/f4493ddd/attachment-0001.htm From gabriele.sclauzero at epfl.ch Wed Sep 19 10:37:44 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 19 Sep 2012 10:37:44 +0200 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: It seems to me that you have not completely understood how to use pp.x. If you take the difference between SRO-up.rho and SROup-doping.rho obtained with the inputs here below you will get zero, because they will contain the same charge density. You see why? GS Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto: > The input files are listed here. In fact, there is no difference. > > 2012/9/19 Yue-Wen Fang > > &inputpp > prefix = 'SRO' > outdir = './' > filplot = 'SROcharge' > plot_num= 0 > spin_component=1 > / > &plot > nfile = 1 > filepp(1) = 'SROcharge' > weight(1) = 1.0 > iflag = 2 > output_format = 2 > fileout = 'SRO-up.rho' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > > &inputpp > prefix = 'SRO' > outdir = './' > filplot = 'SROcharge' > plot_num= 0 > spin_component=1 > / > &plot > nfile = 1 > filepp(1) = 'SROcharge' > weight(1) = 1.0 > iflag = 2 > output_format = 2 > fileout = 'SROup-doping.rho' > e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, > nx=56, ny=40 > / > > > 2012/9/19 Gabriele Sclauzero > > I mean the header (the first 4 lines at least) of the density files that you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the xsf files. > Those lines contain information about the fft grid and are read by pp.x to check consistency between the grids in the two files. > > GS ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/eaf223c4/attachment.htm From gabriele.sclauzero at epfl.ch Wed Sep 19 10:45:27 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 19 Sep 2012 10:45:27 +0200 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: Moreover, this is not the way to proceed. The files read in chdens.f90 (filepp(*) in the &plot section) are those listed in the &inputpp section (filplot). They can be produced in the same run of pp.x or in a previous run(s). If you need charge differences you need to run twice pp.x specifying only the &inputpp section, and then once more using only the &plot section. HTH GS Il giorno 19/set/2012, alle ore 10.37, Gabriele Sclauzero ha scritto: > > It seems to me that you have not completely understood how to use pp.x. > If you take the difference between SRO-up.rho and SROup-doping.rho obtained with the inputs here below you will get zero, because they will contain the same charge density. You see why? > > GS > > > Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto: > >> The input files are listed here. In fact, there is no difference. >> >> 2012/9/19 Yue-Wen Fang >> >> &inputpp >> prefix = 'SRO' >> outdir = './' >> filplot = 'SROcharge' >> plot_num= 0 >> spin_component=1 >> / >> &plot >> nfile = 1 >> filepp(1) = 'SROcharge' >> weight(1) = 1.0 >> iflag = 2 >> output_format = 2 >> fileout = 'SRO-up.rho' >> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, >> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, >> nx=56, ny=40 >> / >> >> &inputpp >> prefix = 'SRO' >> outdir = './' >> filplot = 'SROcharge' >> plot_num= 0 >> spin_component=1 >> / >> &plot >> nfile = 1 >> filepp(1) = 'SROcharge' >> weight(1) = 1.0 >> iflag = 2 >> output_format = 2 >> fileout = 'SROup-doping.rho' >> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, >> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, >> nx=56, ny=40 >> / >> >> >> 2012/9/19 Gabriele Sclauzero >> >> I mean the header (the first 4 lines at least) of the density files that you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not the xsf files. >> Those lines contain information about the fft grid and are read by pp.x to check consistency between the grids in the two files. >> >> GS > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/3b588bb5/attachment-0001.htm From yuewen.fang at gmail.com Wed Sep 19 11:02:39 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Wed, 19 Sep 2012 17:02:39 +0800 Subject: [Pw_forum] charge density difference calculation error! In-Reply-To: References: Message-ID: Dear Gabriele, The attachment is the charge density given by pp.x. Left pic is no doping and the right pic is N doped. These pictures present differently, so I think the charge density shouldn't be zero. 2012/9/19 Gabriele Sclauzero > > It seems to me that you have not completely understood how to use pp.x. > If you take the difference between SRO-up.rho and SROup-doping.rho > obtained with the inputs here below you will get zero, because they will > contain the same charge density. You see why? > > GS > > > Il giorno 19/set/2012, alle ore 10.15, Yue-Wen Fang ha scritto: > > The input files are listed here. In fact, there is no difference. > > 2012/9/19 Yue-Wen Fang > >> >> &inputpp >> prefix = 'SRO' >> outdir = './' >> filplot = 'SROcharge' >> plot_num= 0 >> spin_component=1 >> / >> &plot >> nfile = 1 >> filepp(1) = 'SROcharge' >> weight(1) = 1.0 >> iflag = 2 >> output_format = 2 >> fileout = 'SRO-up.rho' >> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, >> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, >> nx=56, ny=40 >> / >> >> &inputpp >> prefix = 'SRO' >> outdir = './' >> filplot = 'SROcharge' >> plot_num= 0 >> spin_component=1 >> / >> &plot >> nfile = 1 >> filepp(1) = 'SROcharge' >> weight(1) = 1.0 >> iflag = 2 >> output_format = 2 >> fileout = 'SROup-doping.rho' >> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, >> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, >> x0(1) =0.0, x0(2)=0.50, x0(3) = 0.0, >> nx=56, ny=40 >> / >> >> >> 2012/9/19 Gabriele Sclauzero >> >>> >>> I mean the header (the first 4 lines at least) of the density files that >>> you are supplying to pp.x to make the plot ( filepp(1) and filepp(2) ), not >>> the xsf files. >>> Those lines contain information about the fft grid and are read by pp.x >>> to check consistency between the grids in the two files. >>> >>> GS >>> >> > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/c7771737/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: no doping and doping charge density.jpg Type: image/jpeg Size: 25387 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120919/c7771737/attachment-0001.jpg From d.tiana at bath.ac.uk Wed Sep 19 14:29:00 2012 From: d.tiana at bath.ac.uk (Davide Tiana) Date: Wed, 19 Sep 2012 13:29:00 +0100 Subject: [Pw_forum] doubts (problems?) in DOS calculation Message-ID: <20120919132900.Horde.NGl0D81vlIJQWbqMSq4167A@webmail.bath.ac.uk> Dear all, I am trying to calculate DOS and projected DOS for a semiconducting 1D hybrid (i.e. metal-organic) polymer. The band gap I found is about 0.4. However when I try to calculate DOS I don't find 0 contribution at the Fermi level nor a band gap around it. I am in doubt and I think something wrong happened (namely I made some errors). How can I check that everything is fine and-or explain this behaviour? By the way here what I've done: pw optimisation pw band calculation pw nscf calculation dos dos calculation (at first instance I did't make but finding something "weird" in the total projwfc I run it to check) projwfc projected dos calc thanks a lot From yuewen.fang at gmail.com Wed Sep 19 14:57:55 2012 From: yuewen.fang at gmail.com (Yue-Wen Fang) Date: Wed, 19 Sep 2012 20:57:55 +0800 Subject: [Pw_forum] doubts (problems?) in DOS calculation In-Reply-To: <20120919132900.Horde.NGl0D81vlIJQWbqMSq4167A@webmail.bath.ac.uk> References: <20120919132900.Horde.NGl0D81vlIJQWbqMSq4167A@webmail.bath.ac.uk> Message-ID: When calculate DOS, you should make a scf calculation first, then nscf, last is bands and dos. 2012/9/19 Davide Tiana > Dear all, > I am trying to calculate DOS and projected DOS for a semiconducting 1D > hybrid (i.e. metal-organic) polymer. The band gap I found is about > 0.4. However when I try to calculate DOS I don't find 0 contribution > at the Fermi level nor a band gap around it. I am in doubt and I think > something wrong happened (namely I made some errors). How can I check > that everything is fine and-or explain this behaviour? > > By the way here what I've done: > > pw optimisation > pw band calculation > pw nscf calculation > dos dos calculation (at first instance I did't make but finding > something "weird" in the total projwfc I run it to check) > projwfc projected dos calc > > thanks a lot > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---- Yue-Wen Fang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/b65a1488/attachment.htm From bamideleibrahim at yahoo.com Wed Sep 19 14:58:30 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Wed, 19 Sep 2012 05:58:30 -0700 (PDT) Subject: [Pw_forum] doubts (problems?) in DOS calculation In-Reply-To: <20120919132900.Horde.NGl0D81vlIJQWbqMSq4167A@webmail.bath.ac.uk> References: <20120919132900.Horde.NGl0D81vlIJQWbqMSq4167A@webmail.bath.ac.uk> Message-ID: <1348059510.33238.YahooMailNeo@web39405.mail.mud.yahoo.com> Dear Tiana, Nobody can figure out your problem if you did not provide your input file. For meaning assistance in this forum, always provide your input file. ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: Davide Tiana To: pw-mailing_list Sent: Wednesday, September 19, 2012 1:29 PM Subject: [Pw_forum] doubts (problems?) in DOS calculation Dear all, I am trying to calculate DOS and projected DOS for a semiconducting 1D? hybrid (i.e. metal-organic) polymer. The band gap I found is about? 0.4. However when I try to calculate DOS I don't find 0 contribution? at the Fermi level nor a band gap around it. I am in doubt and I think? something wrong happened (namely I made some errors). How can I check? that everything is fine and-or explain this behaviour? By the way here what I've done: pw optimisation pw band calculation pw nscf calculation dos dos calculation (at first instance I did't make but finding? something "weird" in the total projwfc I run it to check) projwfc projected dos calc thanks a lot _______________________________________________ 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/20120919/31f77560/attachment.htm From saurabhbajaj2 at gmail.com Thu Sep 20 01:04:36 2012 From: saurabhbajaj2 at gmail.com (Saurabh Bajaj) Date: Wed, 19 Sep 2012 19:04:36 -0400 Subject: [Pw_forum] QHA code questions In-Reply-To: References: Message-ID: Dear PW forum, I was using the QHA code within QE-5.0.1 to calculate thermodynamic properties of Si , that is included in the Examples/ folder. From the output file Si.QHA.out, the entropy is 4.687*k_B at T=300 K (RT), which leads to a free energy of vibration of about ?T*S = -0.1211 eV/atom. Isn?t this entropy too high? Even for AlAs in the Examples/ folder, this value is ?T*S = -0.1756 eV/atom, which is higher than the maximum configurational entropy of an ideal solution = -0.0179 eV/atom. Thank you Saurabh Bajaj California Institute of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/154e41c2/attachment.htm From hrachk at gmail.com Thu Sep 20 04:00:47 2012 From: hrachk at gmail.com (Hrachya Kyureghian) Date: Wed, 19 Sep 2012 21:00:47 -0500 Subject: [Pw_forum] Delta-sol method Message-ID: Dear all, I am interested in semiconductors, and so, in band gaps. It seems that pw calculations give large errors for band gaps. Recently I came across this paper: Chan and Ceder, Phys. Rev. Lett., 105, 196403 (2010), in which the authors say their method, Delta-sol, which is a generalization of Delta-scf, gives much more accurate results for band gaps. Does anyone happen to know if this method is implemented in QE; or, as someone told me, it is even not a mater of coding in QE but just a matter of playing with input parameters; or perhaps you know if it has been implemented with some other software? Thanks. Hrach University of Nebraska-Lincoln -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120919/2b56186f/attachment.htm From tsakhrawi at yahoo.com Thu Sep 20 11:45:43 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Thu, 20 Sep 2012 10:45:43 +0100 (BST) Subject: [Pw_forum] pw.x Message-ID: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> I made ??a pw.xcalculation for the compound FeRh to estimate the value of a, the problem is thatI always find a value that doubles the expected value Do you have any idea what to do thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/7c4b6916/attachment.htm From pandey.bramha at gmail.com Thu Sep 20 11:58:10 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Thu, 20 Sep 2012 15:28:10 +0530 Subject: [Pw_forum] pw.x In-Reply-To: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> References: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> Message-ID: Could you please give your affiliation before posting in this forum.??? Without your input file no one can exactly estimate what is going wrong in your system. On Thu, Sep 20, 2012 at 3:15 PM, Sakhrawi Taoufek wrote: > I made ??a pw.x calculation for the compound FeRh to estimate the value > of a, the problem is that I always find a value that doubles the expected > value > Do you have any idea what to do > thank you > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/10f63e11/attachment.htm From bamideleibrahim at yahoo.com Thu Sep 20 11:59:55 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Thu, 20 Sep 2012 02:59:55 -0700 (PDT) Subject: [Pw_forum] pw.x In-Reply-To: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> References: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> Message-ID: <1348135195.7609.YahooMailNeo@web39404.mail.mud.yahoo.com> Dear Taoufek, What type of exchange correlation are you using? ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: Sakhrawi Taoufek To: "Pw_forum at pwscf.org" Sent: Thursday, September 20, 2012 10:45 AM Subject: [Pw_forum] pw.x I made ??a pw.xcalculation for the compound FeRh to estimate the value of a, the problem is thatI always find a value that doubles the expected value Do you have any idea what to do thank you _______________________________________________ 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/20120920/84e92db5/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu Sep 20 12:02:14 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 20 Sep 2012 12:02:14 +0200 Subject: [Pw_forum] pw.x In-Reply-To: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> References: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> Message-ID: <201209201202.14441.giuseppe.mattioli@ism.cnr.it> Dear Sakhrawi Taoufek Please always sign your posts to this forum with your name and scientific affiliation. Please provide a meaningful subject. pw.x is one of the QE executables, and has little to do with your FeRh problem Please provide your input file, and explain your problem in a better way. Nobody can help you on this forum otherwise. Yours Giuseppe On Thursday 20 September 2012 11:45:43 Sakhrawi Taoufek wrote: > I made ??a pw.xcalculation for the compound FeRh to estimate the value of > a, the problem is thatI always find a value that doubles the expected > value Do you have any idea what to do > thank you -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From vioiancu at gmail.com Thu Sep 20 15:39:22 2012 From: vioiancu at gmail.com (Violeta Iancu) Date: Thu, 20 Sep 2012 15:39:22 +0200 Subject: [Pw_forum] revPBE pseudo potentials Message-ID: Dear All, We are trying to calculate a weakly adsorbed molecule on a metallic substrate using a vdW-DF functional. Does anyone know where to find the revPBE pseudo potentials? Thank you very much, Violeta Violeta Iancu Laboratory of Solid-State Physics and Magnetism Katholieke Universiteit Leuven Celestijnenlaan 200 D, B-3001 Leuven, Belgium -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/73065a51/attachment.htm From aryjunior at gmail.com Thu Sep 20 15:53:05 2012 From: aryjunior at gmail.com (Ary Junior) Date: Thu, 20 Sep 2012 10:53:05 -0300 Subject: [Pw_forum] revPBE pseudo potentials In-Reply-To: References: Message-ID: Hi, You can start from the pslibrary project ( http://qe-forge.org/gf/project/pslibrary/ )... Ary Junior Universidade Federal de Juiz de Fora - Brazil On Thu, Sep 20, 2012 at 10:39 AM, Violeta Iancu wrote: > > Dear All, > > We are trying to calculate a weakly adsorbed molecule on a metallic > substrate using a vdW-DF functional. Does anyone know where to find the > revPBE pseudo potentials? > > Thank you very much, > > Violeta > > > Violeta Iancu > Laboratory of Solid-State Physics and Magnetism > Katholieke Universiteit Leuven > Celestijnenlaan 200 D, B-3001 Leuven, Belgium > > > > _______________________________________________ > 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/20120920/a90e0c7e/attachment.htm From xinli at lbl.gov Thu Sep 20 16:22:48 2012 From: xinli at lbl.gov (Xin Li) Date: Thu, 20 Sep 2012 07:22:48 -0700 Subject: [Pw_forum] Can't get converged results when using ESM method In-Reply-To: References: Message-ID: Dear all, I meet a big problem when doing ESM calculations that all the calculations couldn't get converged. The input is posted below and the efforts I made are, 1, using different degauss 2, using different ecutwfc 3, using different esm_bc 4, using different number of cores 5, using different tot_charge 6, searching on the pw_forum It can be converged when tot_charge=0. But otherwise, it can't and just run out of all the steps. The strange thing is the total energies in each step vary quite differently. For example, at step #47, the total energy is -7776.16619281 Ry, at step #52, the total energy is -5612.51355642 Ry, but step #53, the total energy is -8825.13517388 Ry. just doesn't have trend to converge. For esm_bc, pbc and bc1 were tested, but none of them worked. Hope you can help me out of this issue. Thanks a lot. Best, Xin LBNL, CA ##############INPUT, pw.in################### &control calculation='scf' prefix='HOPG' pseudo_dir='/' outdir='./' wf_collect=.TRUE. disk_io='low' restart_mode='from_scratch' / &system ibrav=8 , a=4.2384 , b=2.447 , c=32.0875 nat=16, ntyp=1, tot_charge=-2 nbnd=96, occupations='smearing', degauss=0.0019 ecutwfc=35, ecutrho=300 assume_isolated = 'esm', esm_bc='bc1' / &electrons electron_maxstep=300 conv_thr=1.0d-7 mixing_mode='local-TF' mixing_beta=0.1 / ATOMIC_SPECIES C 12.00 C.pbe-van_bm.UPF ATOMIC_POSITIONS angstrom C 0.000000000 1.223500013 11.521874905 C 1.412785889 1.223500013 11.521874905 C 2.119199991 0.000000000 11.521874905 C 3.531985754 0.000000000 11.521874905 C 0.000000000 1.223500013 14.834999979 C 0.706414102 0.000000000 14.834999979 C 2.119199991 0.000000000 14.834999979 C 2.825614220 1.223500013 14.834999979 C 0.000000000 1.223500013 18.148125053 C 1.412785889 1.223500013 18.148125053 C 2.119199991 0.000000000 18.148125053 C 3.531985754 0.000000000 18.148125053 C 0.000000000 1.223500013 21.461249470 C 0.706414102 0.000000000 21.461249470 C 2.119199991 0.000000000 21.461249470 C 2.825614220 1.223500013 21.461249470 K_POINTS automatic 17 31 1 0 0 0 ############################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/12b7b8fa/attachment-0001.htm From ma at nano.ku.dk Thu Sep 20 15:55:18 2012 From: ma at nano.ku.dk (Martin Andersson) Date: Thu, 20 Sep 2012 15:55:18 +0200 Subject: [Pw_forum] revPBE pseudo potentials In-Reply-To: References: Message-ID: <505B2046.2010808@nano.ku.dk> You can download pseudos from THEOS as wel: http://theossrv1.epfl.ch/index.php?n=Main.Links Cheers, Martin Andersson University of Copenhagen Den 2012-09-20 3:39 PM, Violeta Iancu skrev: > > Dear All, > > We are trying to calculate a weakly adsorbed molecule on a metallic > substrate using a vdW-DF functional. Does anyone know where to find > the revPBE pseudo potentials? > > Thank you very much, > > Violeta > > > Violeta Iancu > Laboratory of Solid-State Physics and Magnetism > Katholieke Universiteit Leuven > Celestijnenlaan 200 D, B-3001 Leuven, Belgium > > > > > _______________________________________________ > 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/20120920/744004d4/attachment.htm From stewart at cnf.cornell.edu Thu Sep 20 16:15:36 2012 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Thu, 20 Sep 2012 10:15:36 -0400 Subject: [Pw_forum] PW91 bug in QE 4.3.2 Message-ID: <505B2508.1060406@cnf.cornell.edu> Hi everyone, I was reading through the items fixed in the new version of Quantum Espresso (5.0.x) and I came across the following line for the PW91 bug. * VERY NASTY bug: exchange-correlation keyword 'PW91' was incorrectly interpreted (PZ LDA instead of PW) in all 4.3.x versions I assume this hasn't been corrected in the 4.3.x versions that are available on the web. Also, is there anything in the output file that gives us a clue that this error occurs (other than doing a direct comparison with version 5). It looks like the output file just prints the pseudopotential details read in from the pseudopotential file. Thanks, Derek -- ################################ Derek Stewart, Ph. D. Senior Research Associate http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From tsakhrawi at yahoo.com Thu Sep 20 16:33:53 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Thu, 20 Sep 2012 15:33:53 +0100 (BST) Subject: [Pw_forum] revPBE pseudo potentials In-Reply-To: References: Message-ID: <1348151633.94798.YahooMailNeo@web133001.mail.ir2.yahoo.com> in this cite you choose your element and you see all pseudopotentials http://www.quantum-espresso.org/?page_id=190 Sakhraoui Taoufik d?partement de physique, facult? des sciences de monastir Monastir, Tunisia ________________________________ De?: Ary Junior ??: PWSCF Forum Envoy? le : Jeudi 20 septembre 2012 15h53 Objet?: Re: [Pw_forum] revPBE pseudo potentials Hi, You can start from the pslibrary project ( http://qe-forge.org/gf/project/pslibrary/ )... Ary Junior Universidade Federal de Juiz de Fora - Brazil On Thu, Sep 20, 2012 at 10:39 AM, Violeta Iancu wrote: >Dear All, > > >We are trying to calculate a weakly adsorbed molecule on a metallic substrate using a vdW-DF functional. ?Does anyone know where to find the revPBE pseudo potentials?? > > >Thank you very much, > > >Violeta > > > >Violeta Iancu >Laboratory of Solid-State Physics and Magnetism >Katholieke Universiteit Leuven >Celestijnenlaan 200 D, B-3001 Leuven, Belgium > > >_______________________________________________ >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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/46c7c102/attachment.htm From tsakhrawi at yahoo.com Thu Sep 20 17:49:02 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Thu, 20 Sep 2012 16:49:02 +0100 (BST) Subject: [Pw_forum] (no subject) Message-ID: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> i'am trying to estimate celldm(1) for the compound FeRh, the problem is thatI always find a value that doubles the expected value ------------------------------------------------------------------------ # self-consistent calculation cat > ferh_fm.scf.in << EOF ?&control ??? prefix='FeRh_fm', ??? pseudo_dir = '$pseudo_dir/', ??? outdir='$outdir/' ?/ ?&system ??? ibrav= 3, ??? celldm(1) =$alat, ??? nat=? 2, ??? ntyp= 2, ??? ecutwfc = 30, ??? nbnd = 16, ??? occupations='smearing', ??? smearing='mv', ??? degauss=0.022, ? / ? &electrons mixing_mode = 'plain' , mixing_beta = 0.4, diagonalization = 'david' , conv_thr = 1.0e-7, electron_maxstep=1000, ?/ ATOMIC_SPECIES ?Fe 55.85??? Fe.pz-nd-rrkjus.UPF ?Rh 102.91?? Rh.pz-rrkjus.UPF ATOMIC_POSITIONS {crystal} ?? Fe????? 0.00000000? 0.00000000? 0.00000000 ?? Rh????? 0.50000000? 0.50000000? 0.50000000 K_POINTS {automatic} ?? 12 12 12 1 1 1 EOF $espresso_dir/bin/pw.x < ferh_fm.scf.in > ferh_fm.scf.out grep -e 'lattice parameter' -e ! ferh_fm.scf.out | \ ????? awk '/lattice/{alat=$(NF-1)}/!/{print alat, $(NF-1)}' >> ferh_fm.etot_vs_alat ------------------------------------------------ Sakhraoui TaoufikUnit? de Recherche Physique des Solides D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/1a7fa595/attachment.htm From bamideleibrahim at yahoo.com Thu Sep 20 18:22:05 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Thu, 20 Sep 2012 09:22:05 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> References: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> Message-ID: <1348158125.80673.YahooMailNeo@web39403.mail.mud.yahoo.com> Dear Taoufek, Try and view your structure with xcrysden with this input file. you will notice that the structure is not perfect enough. Thereafter, set your ibrav=1 and view again. With this, you will noticed that the actual structure you are expected to used is what you will see. Hope this help. ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: Sakhrawi Taoufek To: "Pw_forum at pwscf.org" Sent: Thursday, September 20, 2012 4:49 PM Subject: [Pw_forum] (no subject) i'am trying to estimate celldm(1) for the compound FeRh, the problem is thatI always find a value that doubles the expected value ------------------------------------------------------------------------ # self-consistent calculation cat > ferh_fm.scf.in << EOF ?&control ??? prefix='FeRh_fm', ??? pseudo_dir = '$pseudo_dir/', ??? outdir='$outdir/' ?/ ?&system ??? ibrav= 3, ??? celldm(1) =$alat, ??? nat=? 2, ??? ntyp= 2, ??? ecutwfc = 30, ??? nbnd = 16, ??? occupations='smearing', ??? smearing='mv', ??? degauss=0.022, ? / ? &electrons mixing_mode = 'plain' , mixing_beta = 0.4, diagonalization = 'david' , conv_thr = 1.0e-7, electron_maxstep=1000, ?/ ATOMIC_SPECIES ?Fe 55.85??? Fe.pz-nd-rrkjus.UPF ?Rh 102.91?? Rh.pz-rrkjus.UPF ATOMIC_POSITIONS {crystal} ?? Fe????? 0.00000000? 0.00000000? 0.00000000 ?? Rh????? 0.50000000? 0.50000000? 0.50000000 K_POINTS {automatic} ?? 12 12 12 1 1 1 EOF $espresso_dir/bin/pw.x < ferh_fm.scf.in > ferh_fm.scf.out grep -e 'lattice parameter' -e ! ferh_fm.scf.out | \ ????? awk '/lattice/{alat=$(NF-1)}/!/{print alat, $(NF-1)}' >> ferh_fm.etot_vs_alat ------------------------------------------------ Sakhraoui TaoufikUnit? de Recherche Physique des Solides D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. _______________________________________________ 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/20120920/b9657573/attachment-0001.htm From yzunt at yahoo.com Thu Sep 20 18:39:34 2012 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Thu, 20 Sep 2012 09:39:34 -0700 (PDT) Subject: [Pw_forum] bands.data Message-ID: <1348159174.21438.YahooMailNeo@web111207.mail.gq1.yahoo.com> Hi, In trying to get bands data to be used in plotting band for simple graphene unit cell, the out put files for bands.in shows the erro details given below. ?Program POST-PROC v.4.1.2? starts ... ???? Today is 21Sep2012 at? 0:17:35 ???? file C.pz-rrkjus.UPF: wavefunction(s)? 2S renormalized ???? negative rho (up, down):? 0.396E-04 0.000E+00 ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from davcio : error #??????? 10 ???? error while reading from file ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... Please I need the possible solution. Thank you Yusuf. Postgraduate Student -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/157ad44f/attachment.htm From lmartinsamos at gmail.com Thu Sep 20 18:41:25 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Thu, 20 Sep 2012 18:41:25 +0200 Subject: [Pw_forum] bands.data In-Reply-To: <1348159174.21438.YahooMailNeo@web111207.mail.gq1.yahoo.com> References: <1348159174.21438.YahooMailNeo@web111207.mail.gq1.yahoo.com> Message-ID: Dear Yusuf, this error means that the program is not finding something he needs! take a look at the paths and the files produced by the precedent pw.x calculation and control that evrything is in the right place. best regards Layla 2012/9/20 Yusuf Zuntu > Hi, > In trying to get bands data to be used in plotting band for simple > graphene unit cell, the out put files for bands.in shows the erro details > given below. > > Program POST-PROC v.4.1.2 starts ... > Today is 21Sep2012 at 0:17:35 > file C.pz-rrkjus.UPF: wavefunction(s) 2S renormalized > > negative rho (up, down): 0.396E-04 0.000E+00 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > Please I need the possible solution. > Thank you > Yusuf. > Postgraduate Student > > > > > _______________________________________________ > 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/20120920/611d72c1/attachment.htm From azadi at uni-mainz.de Thu Sep 20 18:35:03 2012 From: azadi at uni-mainz.de (Sam Azadi) Date: Thu, 20 Sep 2012 17:35:03 +0100 Subject: [Pw_forum] CrayXE6 Message-ID: <505B45B7.3080708@uni-mainz.de> Dear PWSCF developers, Stuck in compiling on CrayXE6 machines, using "ftn" wrapper, GNU compiler suits "PrgEnv-gnu", and "acml" libraries. Really appreciate any comment/example/experience ... Yours Sam -- *************************************************** Sam Azadi Institute of Physical Chemistry and Center for Computational Sciences Johannes Gutenberg University Mainz Staudinger Weg 9, D-55128 Mainz,Germany Tel: +49 6131 3926844 *************************************************** From giovanni.pizzi at epfl.ch Thu Sep 20 19:24:07 2012 From: giovanni.pizzi at epfl.ch (Giovanni Pizzi) Date: Thu, 20 Sep 2012 17:24:07 +0000 Subject: [Pw_forum] CrayXE6 In-Reply-To: <505B45B7.3080708@uni-mainz.de> References: <505B45B7.3080708@uni-mainz.de> Message-ID: Dear Sam, You may want to take a look to the instructions to compile on the rosa machine at CSCS, Switzerland, which is a CrayXE6 (with the PGI compiler, though) provided by Filippo Spiga and that you can find here: http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2Ftrunk%2Fespresso%2Finstall%2FREADME.CSCS_rosa&view=markup Best, -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 319 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31159 On 20 Sep 2012, at 6:35 PM, Sam Azadi wrote: > Dear PWSCF developers, > > Stuck in compiling on CrayXE6 machines, > using "ftn" wrapper, GNU compiler suits "PrgEnv-gnu", and "acml" libraries. > Really appreciate any comment/example/experience ... > > Yours > Sam > > -- > *************************************************** > Sam Azadi > Institute of Physical Chemistry and > Center for Computational Sciences > Johannes Gutenberg University Mainz > Staudinger Weg 9, D-55128 Mainz,Germany > Tel: +49 6131 3926844 > *************************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From spiga.filippo at gmail.com Thu Sep 20 19:51:26 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Thu, 20 Sep 2012 19:51:26 +0200 Subject: [Pw_forum] CrayXE6 In-Reply-To: <505B45B7.3080708@uni-mainz.de> References: <505B45B7.3080708@uni-mainz.de> Message-ID: Dear Sam, please send me the config.log so I can take a look (even if I knew it is not working). As Giovanni mention, try PrgEnv-pgi plus the standard CRAY libsci (the default for almost 99% of CRAY systems). If for some reason PGI is not available or you need GNU we can work on the configure in order to make it able to produce a correct make.sys Regards, Filippo On Sep 20, 2012, at 6:35 PM, Sam Azadi wrote: > Dear PWSCF developers, > > Stuck in compiling on CrayXE6 machines, > using "ftn" wrapper, GNU compiler suits "PrgEnv-gnu", and "acml" libraries. > Really appreciate any comment/example/experience ... > > Yours > Sam -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/28da7e2c/attachment.htm From giannozz at democritos.it Thu Sep 20 21:11:42 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 Sep 2012 21:11:42 +0200 Subject: [Pw_forum] PW91 bug in QE 4.3.2 In-Reply-To: <505B2508.1060406@cnf.cornell.edu> References: <505B2508.1060406@cnf.cornell.edu> Message-ID: <2CA04FD4-77C9-46E3-8754-81EB17402A7F@democritos.it> On Sep 20, 2012, at 16:15 , Derek Stewart wrote: > I assume this hasn't been corrected in the 4.3.x versions that are > available on the web. it hasn't (and will never be) > Also, is there anything in the output file that gives us a clue that > this error occurs look at the line "Exchange-correlation": it should look like Exchange-correlation = SLA PW GGX GGC ( 1 4 2 2 0) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From pchen at ion.chem.utk.edu Thu Sep 20 21:15:06 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Thu, 20 Sep 2012 15:15:06 -0400 Subject: [Pw_forum] spin direction Message-ID: Dear All, In the Quantum Espresso, can I specify spin direction? E.g, in the unit cell, spins of M1 and M2 are along c direction (spin of M1 is opposite to that of M2), whereas spins of M3 and M4 are in b direction. Can I simulate this magnetic structure in QE? Thank you in advance for any help you can provide. -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/8ce3168f/attachment.htm From vioiancu at gmail.com Thu Sep 20 21:21:22 2012 From: vioiancu at gmail.com (Violeta Iancu) Date: Thu, 20 Sep 2012 21:21:22 +0200 Subject: [Pw_forum] revPBE pseudo potentials In-Reply-To: <505B2046.2010808@nano.ku.dk> References: <505B2046.2010808@nano.ku.dk> Message-ID: Thank you very much for the answers! Any idea if there are any pseudos available for vdw-df-c09 functional? Thank you, Violeta Iancu KU Leuven On Thu, Sep 20, 2012 at 3:55 PM, Martin Andersson wrote: > You can download pseudos from THEOS as wel: > > http://theossrv1.epfl.ch/index.php?n=Main.Links > > Cheers, > Martin Andersson > University of Copenhagen > > > Den 2012-09-20 3:39 PM, Violeta Iancu skrev: > > > Dear All, > > We are trying to calculate a weakly adsorbed molecule on a metallic > substrate using a vdW-DF functional. Does anyone know where to find the > revPBE pseudo potentials? > > Thank you very much, > > Violeta > > > Violeta Iancu > Laboratory of Solid-State Physics and Magnetism > Katholieke Universiteit Leuven > Celestijnenlaan 200 D, B-3001 Leuven, Belgium > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Violeta -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/b689052e/attachment-0001.htm From giannozz at democritos.it Thu Sep 20 21:35:10 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 Sep 2012 21:35:10 +0200 Subject: [Pw_forum] spin direction In-Reply-To: References: Message-ID: On Sep 20, 2012, at 21:15 , Peng Chen wrote: > In the Quantum Espresso, can I specify spin direction? E.g, in the > unit cell, spins of M1 and M2 are along c direction (spin of M1 is > opposite to that of M2), whereas spins of M3 and M4 are in b > direction. Can I simulate this magnetic structure in QE? yes, it is called "noncolinear magnetization" P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Sep 20 21:36:14 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 Sep 2012 21:36:14 +0200 Subject: [Pw_forum] revPBE pseudo potentials In-Reply-To: References: <505B2046.2010808@nano.ku.dk> Message-ID: <44818206-EFF6-4700-BBDF-E892ABCFEA71@democritos.it> On Sep 20, 2012, at 21:21 , Violeta Iancu wrote: > Any idea if there are any pseudos available for vdw-df-c09 functional? currently there are no pseudos for nonlocal functionals P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From xjamesmao at gmail.com Thu Sep 20 23:12:48 2012 From: xjamesmao at gmail.com (James Mao) Date: Thu, 20 Sep 2012 17:12:48 -0400 Subject: [Pw_forum] wrong result from converted abinit LDA FHI PP In-Reply-To: <1A6307F6-783E-44A8-8095-C8D04916F1DD@democritos.it> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> <000001cd8f85$00570e20$01052a60$@com> <1A6307F6-783E-44A8-8095-C8D04916F1DD@democritos.it> Message-ID: <003c01cd9774$b0a9a200$11fce600$@com> Dear all, I learned how to generate and test PPs in the past several days, and generated NC-LDA PPs for oxygen and carbon using PSLibrary code for practice. They were tested using ld1.x first, then a CO2 vibrational run to compare with results from known pbe-rrkjus PPs, as well as all electrons results. Everything looks fine. I also converted fhi PP from Abinit and tested them. The results of ld1 test looks fine: e(eigen) of AE-PS and \delta E are small, wfc and logarithmic derivative match AE results. However, the results of CO2 vibrational calculations using these converted PPs are completely wrong. My question is: what could cause a completely wrong result of photon calculation for PPs which look fine in ld1 code test? I don't think I messed up the converting. But if anyone would like to help, just let me know and I will send you the converted PPs for your testing. Another thing is that although pbe-rrkjus PPs produced best results, they also produced negative frequencies, is it normal? In all cases I ran a "relax" calculation first to make sure the geometry was optimized. I am learning everything in solid states calculations, so any comments are welcome and will be greatly appreciated! James Mao ------------ Postdoc, Department of Chemistry University of Pittsburgh ------------ Here is the all electron results: [cm-1] 641 1373 2438 results from pbe-rrkjus PPs: # mode [cm-1] [THz] IR 1 -188.02 -5.6368 0.0000 2 -188.02 -5.6368 0.0000 3 0.00 0.0000 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 0.0000 6 658.64 19.7456 0.4938 7 658.64 19.7456 0.4938 8 1304.71 39.1142 0.0000 9 2340.86 70.1772 12.1795 results from NC LDA PPs I generated using PSLibrary code: # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 218.30 6.5444 0.0000 5 218.30 6.5444 0.0000 6 577.10 17.3010 0.0521 7 577.10 17.3010 0.0521 8 1303.15 39.0676 0.0000 9 2386.77 71.5536 11.0101 results (WRONG!) from LDA PPs converted from Abinit fhi files: # mode [cm-1] [THz] IR 1 -219.57 -6.5825 0.0000 2 -219.57 -6.5825 0.0000 3 0.00 0.0000 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 0.0000 6 246.28 7.3833 0.1700 7 246.28 7.3833 0.1700 8 499.18 14.9652 0.0000 9 675.29 20.2448 9.8485 rlx input: &control calculation='relax', restart_mode='from_scratch', prefix='co2' pseudo_dir='./pseudos' outdir='./' tprnfor = .true. / &system ibrav = 1, celldm(1) =20.0, nat= 3, ntyp= 2, ecutwfc = 30.0, ecutrho = 300.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions ion_dynamics="bfgs", / ATOMIC_SPECIES C 12.01 06-C.LDA.fhi.UPF O 16.01 08-O.LDA.fhi.UPF ATOMIC_POSITIONS (angstrom) C 0.000000 0.000000 0.000000 O 0.000000 0.000000 1.220000 O 0.000000 0.000000 -1.220000 K_POINTS (automatic) 1 1 1 0 0 0 From rainbee1988 at gmail.com Thu Sep 20 23:57:36 2012 From: rainbee1988 at gmail.com (Ruibin Liu) Date: Thu, 20 Sep 2012 17:57:36 -0400 Subject: [Pw_forum] IOTK library In-Reply-To: References: Message-ID: It seems not easy to fix in that way. I am following the examples here http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_pwscf_ex.pdf and I get in trouble in the second step of nscf calculation. Here is the detailed error information: # WARNING: there are pending errors # PENDING ERROR (ierr=1) # ERROR IN: iotk_tag_parse (iotk_misc.f90:999) # CVS Revision: 1.39 # Wrong syntax in tag tag=1984) Info: automatically converted from PWSCF format F The Pseudo was generated with a Non-Relativistic # ERROR IN: iotk_scan (iotk_scan.f90:829) # CVS Revision: 1.23 # direction control=2 # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=2) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 What happened? Thanks, Ruibin On Fri, Sep 7, 2012 at 2:53 PM, Axel Kohlmeyer wrote: > On Fri, Sep 7, 2012 at 8:50 PM, Ruibin Liu wrote: > > I checked that file and found that it's already Q_REAL_SPACE, but I > > encountered similar problems like > > > ######################################################################################################################## > > # FROM IOTK LIBRARY, VERSION 1.2.0 > > # UNRECOVERABLE ERROR (ierr=1) > > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > > # CVS Revision: 1.23 > > # foundl > > # ERROR IN: iotk_close_read (iotk_files.f90:746) > > # CVS Revision: 1.20 > > > ######################################################################################################################## > > How to fix it? > > i think the consensus is that you have to use > a better compiler. one that works correctly and > is not broken like older versions of gfortran. > > axel. > > > > > > -- > > Liu, Ruibin > > Department of Chemistry > > Duke University > > Durham, NC, 27708 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- *Liu, Ruibin* Department of Chemistry Duke University Durham, NC, 27708 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120920/2e1c205f/attachment.htm From spiga.filippo at gmail.com Fri Sep 21 00:41:13 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 21 Sep 2012 00:41:13 +0200 Subject: [Pw_forum] IOTK library In-Reply-To: References: Message-ID: <53F784B9-B31B-459B-A95E-DA4A26CA516B@gmail.com> It might be worth to try to compile with some special flags for IOTK. I am not expert of that library at all but, for example on CRAY machines, it does not work if you do not manually add the macro "-D__IOTK_WORKAROUND1" to DFLAGS in the make.sys Now, fortunately (or not, it depends how you look at the situation), there are 9 different "workaround", so -D__IOTK_WORKAROUND{1?9}. A lot of combinations? Looking at the code and looking at the IOTK configure, the first 6 macros are "documented" but there is not clear explanation (not clear for me) about the other 3. Try come combinations? you might be lucky. Regards, Filippo On Sep 20, 2012, at 11:57 PM, Ruibin Liu wrote: > It seems not easy to fix in that way. > I am following the examples here http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_pwscf_ex.pdf > and I get in trouble in the second step of nscf calculation. Here is the detailed error information: > # WARNING: there are pending errors > # PENDING ERROR (ierr=1) > # ERROR IN: iotk_tag_parse (iotk_misc.f90:999) > # CVS Revision: 1.39 > # Wrong syntax in tag > tag=1984) Info: automatically converted from PWSCF format F The Pseudo was generated with a Non-Relativistic > # ERROR IN: iotk_scan (iotk_scan.f90:829) > # CVS Revision: 1.23 > # direction > control=2 > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20 > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=2) > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20 > > What happened? > > Thanks, > Ruibin > > On Fri, Sep 7, 2012 at 2:53 PM, Axel Kohlmeyer wrote: > On Fri, Sep 7, 2012 at 8:50 PM, Ruibin Liu wrote: > > I checked that file and found that it's already Q_REAL_SPACE, but I > > encountered similar problems like > > ######################################################################################################################## > > # FROM IOTK LIBRARY, VERSION 1.2.0 > > # UNRECOVERABLE ERROR (ierr=1) > > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > > # CVS Revision: 1.23 > > # foundl > > # ERROR IN: iotk_close_read (iotk_files.f90:746) > > # CVS Revision: 1.20 > > ######################################################################################################################## > > How to fix it? > > i think the consensus is that you have to use > a better compiler. one that works correctly and > is not broken like older versions of gfortran. > > axel. > > > > > > -- > > Liu, Ruibin > > Department of Chemistry > > Duke University > > Durham, NC, 27708 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Liu, Ruibin > Department of Chemistry > Duke University > Durham, NC, 27708 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/ca85f15c/attachment-0001.htm From akohlmey at gmail.com Fri Sep 21 00:47:10 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 21 Sep 2012 00:47:10 +0200 Subject: [Pw_forum] IOTK library In-Reply-To: References: Message-ID: On Thu, Sep 20, 2012 at 11:57 PM, Ruibin Liu wrote: > It seems not easy to fix in that way. how so? which compiler and which version of it *are* you using? testing yet another input doesn't prove anything. axel. > I am following the examples here > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_pwscf_ex.pdf > and I get in trouble in the second step of nscf calculation. Here is the > detailed error information: > # WARNING: there are pending errors > # PENDING ERROR (ierr=1) > # ERROR IN: iotk_tag_parse (iotk_misc.f90:999) > # CVS Revision: 1.39 > # Wrong syntax in tag > tag=1984) Info: automatically converted from PWSCF format F The > Pseudo was generated with a Non-Relativistic > # ERROR IN: iotk_scan (iotk_scan.f90:829) > # CVS Revision: 1.23 > # direction > control=2 > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20 > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=2) > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20 > > What happened? > > Thanks, > Ruibin > > On Fri, Sep 7, 2012 at 2:53 PM, Axel Kohlmeyer wrote: >> >> On Fri, Sep 7, 2012 at 8:50 PM, Ruibin Liu wrote: >> > I checked that file and found that it's already Q_REAL_SPACE, but I >> > encountered similar problems like >> > >> > ######################################################################################################################## >> > # FROM IOTK LIBRARY, VERSION 1.2.0 >> > # UNRECOVERABLE ERROR (ierr=1) >> > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) >> > # CVS Revision: 1.23 >> > # foundl >> > # ERROR IN: iotk_close_read (iotk_files.f90:746) >> > # CVS Revision: 1.20 >> > >> > ######################################################################################################################## >> > How to fix it? >> >> i think the consensus is that you have to use >> a better compiler. one that works correctly and >> is not broken like older versions of gfortran. >> >> axel. >> >> >> > >> > -- >> > Liu, Ruibin >> > Department of Chemistry >> > Duke University >> > Durham, NC, 27708 >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >> International Centre for Theoretical Physics, Trieste. Italy. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Liu, Ruibin > Department of Chemistry > Duke University > Durham, NC, 27708 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From akohlmey at gmail.com Fri Sep 21 00:51:09 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 21 Sep 2012 00:51:09 +0200 Subject: [Pw_forum] wrong result from converted abinit LDA FHI PP In-Reply-To: <003c01cd9774$b0a9a200$11fce600$@com> References: <000301cd8f6f$bd7d4de0$3877e9a0$@com> <1347294161.17175.47.camel@fe12lx.fisica.uniud.it> <000001cd8f85$00570e20$01052a60$@com> <1A6307F6-783E-44A8-8095-C8D04916F1DD@democritos.it> <003c01cd9774$b0a9a200$11fce600$@com> Message-ID: On Thu, Sep 20, 2012 at 11:12 PM, James Mao wrote: > Dear all, > > I learned how to generate and test PPs in the past several days, and > generated NC-LDA PPs for oxygen and carbon using PSLibrary code for > practice. They were tested using ld1.x first, then a CO2 vibrational > run to compare with results from known pbe-rrkjus PPs, as well as all > electrons results. Everything looks fine. > I also converted fhi PP from Abinit and tested them. The results of > ld1 test looks fine: e(eigen) of AE-PS and \delta E are small, wfc > and logarithmic derivative match AE results. However, the results of > CO2 vibrational calculations using these converted PPs are completely > wrong. My question is: what could cause a completely wrong result of > photon calculation for PPs which look fine in ld1 code test? the problem is your complete neglect of the differences between ultra-soft and norm-conserving pseudopotentials in your input. your input is for ultra-softs, for NC you need a higher wavefunction cutoff. and usually the "hardest" potential, in your case oxygen determines the cutoff needed. try using 70 ry and then crank it up in steps to, say, 120ry or even 150ry. also you should not set the density cutoff, as it should be 4x the wfc cutoff (which is the default). you should observe some convergence to consistent values this way, and i would bet they are not as wrong as your current one. cheers, axel. > > I don't think I messed up the converting. But if anyone would like to > help, just let me know and I will send you the converted PPs for your > testing. > > Another thing is that although pbe-rrkjus PPs produced best results, > they also produced negative frequencies, is it normal? In all cases I > ran a "relax" calculation first to make sure the geometry was optimized. > > I am learning everything in solid states calculations, so any comments > are welcome and will be greatly appreciated! > > James Mao > ------------ > Postdoc, Department of Chemistry > University of Pittsburgh > ------------ > > Here is the all electron results: > [cm-1] > 641 > 1373 > 2438 > > results from pbe-rrkjus PPs: > > # mode [cm-1] [THz] IR > 1 -188.02 -5.6368 0.0000 > 2 -188.02 -5.6368 0.0000 > 3 0.00 0.0000 0.0000 > 4 0.00 0.0000 0.0000 > 5 0.00 0.0000 0.0000 > 6 658.64 19.7456 0.4938 > 7 658.64 19.7456 0.4938 > 8 1304.71 39.1142 0.0000 > 9 2340.86 70.1772 12.1795 > > results from NC LDA PPs I generated using PSLibrary code: > > # mode [cm-1] [THz] IR > 1 0.00 0.0000 0.0000 > 2 0.00 0.0000 0.0000 > 3 0.00 0.0000 0.0000 > 4 218.30 6.5444 0.0000 > 5 218.30 6.5444 0.0000 > 6 577.10 17.3010 0.0521 > 7 577.10 17.3010 0.0521 > 8 1303.15 39.0676 0.0000 > 9 2386.77 71.5536 11.0101 > > results (WRONG!) from LDA PPs converted from Abinit fhi files: > > # mode [cm-1] [THz] IR > 1 -219.57 -6.5825 0.0000 > 2 -219.57 -6.5825 0.0000 > 3 0.00 0.0000 0.0000 > 4 0.00 0.0000 0.0000 > 5 0.00 0.0000 0.0000 > 6 246.28 7.3833 0.1700 > 7 246.28 7.3833 0.1700 > 8 499.18 14.9652 0.0000 > 9 675.29 20.2448 9.8485 > > rlx input: > > &control > calculation='relax', > restart_mode='from_scratch', > prefix='co2' > pseudo_dir='./pseudos' > outdir='./' > tprnfor = .true. > / > &system > ibrav = 1, celldm(1) =20.0, nat= 3, ntyp= 2, > ecutwfc = 30.0, ecutrho = 300.0 > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > &ions > ion_dynamics="bfgs", > / > ATOMIC_SPECIES > C 12.01 06-C.LDA.fhi.UPF > O 16.01 08-O.LDA.fhi.UPF > ATOMIC_POSITIONS (angstrom) > C 0.000000 0.000000 0.000000 > O 0.000000 0.000000 1.220000 > O 0.000000 0.000000 -1.220000 > K_POINTS (automatic) > 1 1 1 0 0 0 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. From ferretti at mit.edu Fri Sep 21 00:53:30 2012 From: ferretti at mit.edu (ferretti at mit.edu) Date: Fri, 21 Sep 2012 00:53:30 +0200 (CEST) Subject: [Pw_forum] IOTK library Message-ID: Hi everyone, if I rememebr correctly, the workarounds of iotk can be switched on all together by using -D__IOTK_SAFEST regarding the problem you are describing, you may also want to check if special/protected xml charatcer are used in the description strings of your pseudo file... this used to be one reason for iotk failing similarly to what you have found... take care Andrea > It might be worth to try to compile with some special flags for IOTK. I am > not expert of that library at all but, for > example on CRAY machines, it does not work if you do not manually add the > macro "-D__IOTK_WORKAROUND1" to DFLAGS in the > make.sys > Now, fortunately (or not, it depends how you look at the situation), there > are 9 different "workaround", > so?-D__IOTK_WORKAROUND{1?9}. A lot of combinations??Looking at the code and > looking at the IOTK configure, the first 6 > macros are "documented" but there is not clear explanation (not clear for me) > about the other 3. > > Try come combinations??you might be lucky. > > Regards, > Filippo > > > > On Sep 20, 2012, at 11:57 PM, Ruibin Liu wrote: > > It seems not easy to fix in that way.?I am following the examples > here?http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_pwscf_ex.pdf > and I get in trouble in the second step of nscf?calculation. Here is the > detailed error information: > # WARNING: there are pending errors > # PENDING ERROR (ierr=1) > # ERROR IN: iotk_tag_parse (iotk_misc.f90:999) > # CVS Revision: 1.39? > # Wrong syntax in tag > tag=1984) Info: automatically converted from PWSCF format ? ? F ? ? ? ?The > Pseudo was generated with a > Non-Relativistic? > # ERROR IN: iotk_scan (iotk_scan.f90:829) > # CVS Revision: 1.23? > # direction > control=2 > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23? > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20? > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=2) > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23? > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20? > > What happened? > > Thanks, > Ruibin > > On Fri, Sep 7, 2012 at 2:53 PM, Axel Kohlmeyer wrote: > On Fri, Sep 7, 2012 at 8:50 PM, Ruibin Liu > wrote: > > I checked that file and found that it's already Q_REAL_SPACE, but I > > encountered similar problems like > > > ######################################################################################################################## > > # FROM IOTK LIBRARY, VERSION 1.2.0 > > # UNRECOVERABLE ERROR (ierr=1) > > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > > # CVS Revision: 1.23 > > # foundl > > # ERROR IN: iotk_close_read (iotk_files.f90:746) > > # CVS Revision: 1.20 > > > ######################################################################################################################## > > How to fix it? > > i think the consensus is that you have to use > a better compiler. one that works correctly and > is not broken like older versions of gfortran. > > axel. > > > > > > -- > > Liu, Ruibin > > Department of Chemistry > > Duke University > > Durham, NC, 27708 > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer ?akohlmey at gmail.com ?http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Liu, Ruibin Department of Chemistry > Duke University > Durham, NC, 27708 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate? > CADMOS - Chair of Numerical Algorithms?and HPC (ANCHP) > ?cole Polytechnique F?d?rale de?Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me?~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's?paradise.? ~ David Hilbert > > > -- Andrea Ferretti S3 Center, Istituto Nanoscienze, CNR via Campi 213/A, 41125, Modena, Italy Tel: +39 059 2055322; Skype: andrea_ferretti URL: http://www.nano.cnr.it From pchen at ion.chem.utk.edu Fri Sep 21 06:16:12 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Fri, 21 Sep 2012 00:16:12 -0400 Subject: [Pw_forum] spin direction In-Reply-To: References: Message-ID: Dear Dr. Giannozzi, Thanks for your note! In some afm structures, there is "spin canting" due to the Dzyaloshinskii-Moriya interaction. Does noncolinear magnetization calculation in QE involve spin canting effect? I also tried to use LDA+U with noncolinear magnetization calculation, but it only works for lda_plus_u_kind=1. In that case, I don't know what is the value of Hubbard_J . Whereas, when lda_plus_u_kind=0, the U can be computed by linear-response method of Cococcioni et al.. So can I consider lda_plus_u_kind=0 is the same condition as: lda_plus_u_kind=1 and Hubbard_J = 0? On Thu, Sep 20, 2012 at 3:35 PM, Paolo Giannozzi wrote: > > On Sep 20, 2012, at 21:15 , Peng Chen wrote: > > > In the Quantum Espresso, can I specify spin direction? E.g, in the > > unit cell, spins of M1 and M2 are along c direction (spin of M1 is > > opposite to that of M2), whereas spins of M3 and M4 are in b > > direction. Can I simulate this magnetic structure in QE? > > yes, it is called "noncolinear magnetization" > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/040383ff/attachment.htm From giuseppe.mattioli at ism.cnr.it Fri Sep 21 10:25:39 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 21 Sep 2012 10:25:39 +0200 Subject: [Pw_forum] spin direction In-Reply-To: References: Message-ID: <201209211025.39969.giuseppe.mattioli@ism.cnr.it> Dear Peng Look at the PW_INPUT documentation ("noncolin" variable and related quantities) and at example06 in the PW dir. HTH Giuseppe On Thursday 20 September 2012 21:15:06 Peng Chen wrote: > Dear All, > > In the Quantum Espresso, can I specify spin direction? E.g, in the unit > cell, spins of M1 and M2 are along c direction (spin of M1 is opposite to > that of M2), whereas spins of M3 and M4 are in b direction. Can I simulate > this magnetic structure in QE? Thank you in advance for any help you can > provide. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giuseppe.mattioli at ism.cnr.it Fri Sep 21 10:26:59 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 21 Sep 2012 10:26:59 +0200 Subject: [Pw_forum] spin direction Message-ID: <201209211026.59842.giuseppe.mattioli@ism.cnr.it> It seems you've already done it... Sorry! On Thursday 20 September 2012 21:15:06 Peng Chen wrote: > Dear All, > > In the Quantum Espresso, can I specify spin direction? E.g, in the unit > cell, spins of M1 and M2 are along c direction (spin of M1 is opposite to > that of M2), whereas spins of M3 and M4 are in b direction. Can I simulate > this magnetic structure in QE? Thank you in advance for any help you can > provide. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From thomas.gruber at physik.tu-freiberg.de Fri Sep 21 11:01:51 2012 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Fri, 21 Sep 2012 11:01:51 +0200 Subject: [Pw_forum] specific q-point with phonon splitting Message-ID: <505C2CFF.30903@physik.tu-freiberg.de> Dear all, I am doing phonon calculations with splitting in q-points and irreducible representations. Do to negative frequencies at the last q-point I do some convergence test only with the last q-point. It is possible to calculate the whole q-point at once without calculating the other and get the frequencies with "start_q" and "last_q". But I have to split into representations because the system is too big. When I run final calculation with "recover=.true." then the calculation finds all *.xml files but it stop the the error code: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from openfilq : error # 1 file LiSi.k8.q4.tr2-14.0.4.4.wfc not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I found out that when I run a final calculation with several q-points and "start_q=1" it works to every q-point, but if start_q is not equal to 1 then I get the above error message. Why is it possible to calculate a q-point at once but not with splitting? Best regards, Thomas Gruber -- Thomas Gruber Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392006 Email: thomas.gruber at physik.tu-freiberg.de From tsakhrawi at yahoo.com Fri Sep 21 11:10:08 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Fri, 21 Sep 2012 10:10:08 +0100 (BST) Subject: [Pw_forum] celldm Message-ID: <1348218608.40576.YahooMailNeo@web133005.mail.ir2.yahoo.com> Dear pwsf users, I made ??a pw.xcalculation for the compound FeRh to estimate the value of celldm(1), the problem is thatI always find a value that doubles the expected value Do you have any idea what to do thank you My input : ----------------------------------------------------------------------------------- for alat in 8.0 8.2 8.4 8.6 8.8 9.0 9.2 9.4 9.6 ;do # self-consistent calculation cat > ferh_nm.scf.in << EOF ?&control ??? prefix='FeRh_nm', ??? pseudo_dir = '$pseudo_dir/', ??? outdir='$outdir/' ??? !verbosity = 'high', ?/ ?&system??? ??? ibrav= 3, ??? celldm(1) =$alat, ??? nat=? 2, ??? ntyp= 2, ??? ecutwfc =30, ??? nbnd = 16, ??? occupations='smearing', ??? smearing='gaussian', ??? degauss=0.02, ? / ? &electrons mixing_mode = 'plain' , mixing_beta = 0.4, diagonalization = 'david' , conv_thr = 1.0d-7, electron_maxstep=1000, ?/ ATOMIC_SPECIES ?Fe 55.85??? Fe.pz-nd-rrkjus.UPF ?Rh 102.91?? Rh.pz-rrkjus.UPF ATOMIC_POSITIONS {Crystal} ?? Fe????? 0.00000000? 0.00000000? 0.00000000 ?? Rh????? 0.50000000? 0.50000000? 0.50000000 K_POINTS {automatic} ?? 3 3 3 1 1 1 EOF $espresso_dir/bin/pw.x < ferh_nm.scf.in > ferh_nm.scf.out ----------------------------------------------------------------------------------------- Sakhraoui Taoufik depatement de physique, facult? des sciences de Monastir Monastir, Tunisie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/ab014446/attachment.htm From giannozz at democritos.it Fri Sep 21 11:24:16 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Sep 2012 11:24:16 +0200 Subject: [Pw_forum] celldm In-Reply-To: <1348218608.40576.YahooMailNeo@web133005.mail.ir2.yahoo.com> References: <1348218608.40576.YahooMailNeo@web133005.mail.ir2.yahoo.com> Message-ID: <1348219456.13559.31.camel@fe12lx.fisica.uniud.it> On Fri, 2012-09-21 at 10:10 +0100, Sakhrawi Taoufek wrote: > I made ??a pw.x calculation for the compound FeRh to estimate the value of celldm(1), > the problem is that I always find a value that doubles the expected value you know that celldm(1) is in Bohr radii and not in Angsttrom, don't you? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Sep 21 11:25:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Sep 2012 11:25:39 +0200 Subject: [Pw_forum] specific q-point with phonon splitting In-Reply-To: <505C2CFF.30903@physik.tu-freiberg.de> References: <505C2CFF.30903@physik.tu-freiberg.de> Message-ID: <1348219539.13559.33.camel@fe12lx.fisica.uniud.it> Please specify which version of the code you are using P. On Fri, 2012-09-21 at 11:01 +0200, Thomas Gruber wrote: > Dear all, > > I am doing phonon calculations with splitting in q-points and > irreducible representations. Do to negative frequencies at the last > q-point I do some convergence test only with the last q-point. It is > possible to calculate the whole q-point at once without calculating the > other and get the frequencies with "start_q" and "last_q". But I have to > split into representations because the system is too big. When I run > final calculation with "recover=.true." then the calculation finds all > *.xml files but it stop the the error code: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from openfilq : error # 1 > file LiSi.k8.q4.tr2-14.0.4.4.wfc not found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > I found out that when I run a final calculation with several q-points > and "start_q=1" it works to every q-point, but if start_q is not equal > to 1 then I get the above error message. Why is it possible to calculate > a q-point at once but not with splitting? > > Best regards, > > Thomas Gruber > -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Sep 21 11:29:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Sep 2012 11:29:58 +0200 Subject: [Pw_forum] Queries regarding fixed-spin moment phonon calculations and DFPT+U In-Reply-To: <832a83bbddf2714c11d4d42d4525beed.squirrel@webmail.iitg.ernet.in> References: <832a83bbddf2714c11d4d42d4525beed.squirrel@webmail.iitg.ernet.in> Message-ID: <1348219798.13559.35.camel@fe12lx.fisica.uniud.it> On Wed, 2012-09-19 at 11:44 +0530, Subhradip Ghosh wrote: > I am curious to know whether the following would be possible by QE-5.0.1? > > 1) Fixed-spin moment phonon calculation for a metallic system. > 2) Is DFPT+U (PRB 84, 161102(R)) implemented in QE-5.0.1? 1) Not sure, I don't think so 2) no P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From baroni at sissa.it Fri Sep 21 11:56:12 2012 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 21 Sep 2012 11:56:12 +0200 Subject: [Pw_forum] pw.x In-Reply-To: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> References: <1348134343.4729.YahooMailNeo@web133002.mail.ir2.yahoo.com> Message-ID: <5B67CCDE-3515-47D9-8ADE-5370BB901647@sissa.it> convert from Bohr radii to Angstroms? (just guessing ...) - SB On Sep 20, 2012, at 11:45 AM, Sakhrawi Taoufek wrote: > I made ??a pw.x calculation for the compound FeRh to estimate the value of a, the problem is that I always find a value that doubles the expected value > Do you have any idea what to do > thank you > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/26222972/attachment-0001.htm From thomas.gruber at physik.tu-freiberg.de Fri Sep 21 12:32:21 2012 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Fri, 21 Sep 2012 12:32:21 +0200 Subject: [Pw_forum] specific q-point with phonon splitting In-Reply-To: References: Message-ID: <505C4235.4090409@physik.tu-freiberg.de> I am using Version 4.3.2 Thomas Gruber Please specify which version of the code you are using P. On Fri, 2012-09-21 at 11:01 +0200, Thomas Gruber wrote: > Dear all, > > I am doing phonon calculations with splitting in q-points and > irreducible representations. Do to negative frequencies at the last > q-point I do some convergence test only with the last q-point. It is > possible to calculate the whole q-point at once without calculating the > other and get the frequencies with "start_q" and "last_q". But I have to > split into representations because the system is too big. When I run > final calculation with "recover=.true." then the calculation finds all > *.xml files but it stop the the error code: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from openfilq : error # 1 > file LiSi.k8.q4.tr2-14.0.4.4.wfc not found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > I found out that when I run a final calculation with several q-points > and "start_q=1" it works to every q-point, but if start_q is not equal > to 1 then I get the above error message. Why is it possible to calculate > a q-point at once but not with splitting? > > Best regards, > > Thomas Gruber -- Thomas Gruber Institut f?r Theoretische Physik TU Bergakademie Freiberg Leipziger Str. 23, 09599 Freiberg, Germany Tel: +49 (0)3731 392006 Email: thomas.gruber at physik.tu-freiberg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/409bd998/attachment.htm From prasenjit.jnc at gmail.com Fri Sep 21 14:44:53 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 21 Sep 2012 18:14:53 +0530 Subject: [Pw_forum] NMR calculation of CDCl3 Message-ID: Dear all, I want to calculate the 13C NMR spectra of CDCl3, where D is the deuterium......How do I incorporate the fact that D has one extra neutron in it? Or since we are interested in the C NMR spectra, it will not effect the calculation? With regards, Prasenjit -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/5d6eab4d/attachment.htm From mustardt at onid.orst.edu Fri Sep 21 15:02:29 2012 From: mustardt at onid.orst.edu (TJ Mustard) Date: Fri, 21 Sep 2012 06:02:29 -0700 Subject: [Pw_forum] Fwd: Error when compiling GPU version of QE In-Reply-To: References: Message-ID: Hi all, I have gotten the MPI CPU and serial GPU versions to install nicely, but I am having some problems with the MPI GPU version. I configured with this: > > ./configure --enable-cuda --enable-parallel --with-internal-blas --with-internal-lapack --with-gpu-arch=20 --with-cuda-dir=/usr/local/cuda --enable-phigemm And make: > > make pw -j 6 Slightly off topic but if I --enable-magma I lose my FFT libraries...What?! I have compiled the CPU version with Intel MKL libraries and have no real reason for using the internal libraries. It does not matter which library sources I use I will always get this cuda_env_para.o error. (Sometimes in conjuction with a cuda memory error as well.) My error occurs like this... > > ... > mpif90 -O3 -g -fopenmp -x f95-cpp-input -fopenmp -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA -D__CUDA -D__GPU_NVIDIA_20 -D__PHIGEMM -D__CUDA_QE_TIMING -D__OPENMP -I../include -I/root/espresso-5.0.1-GPU/phiGEMM/include -I/usr/local/cuda/include -I../iotk/src -I. -c cuda_env_para.f90 > In file cuda_env_para.f90:40 > world > 1 > Error: Syntax error in argument list at (1) > make[1]: *** [cuda_env_para.o] Error 1 > make[1]: *** Waiting for unfinished jobs.... > make[1]: Leaving directory `/root/espresso-5.0.1-GPU/Modules' > make: *** [mods] Error 2 Anything would be grateful. Thank you, Thomas J. L. Mustard Graduate Student Department of Chemistry Oregon State University P.S. I have intel 11.1 C/CPP/ifort installed as well as the mkl. Also fftw3 in double precision and CUDA 4.0. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/3663f3ee/attachment.htm From spiga.filippo at gmail.com Fri Sep 21 15:29:28 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 21 Sep 2012 15:29:28 +0200 Subject: [Pw_forum] Error when compiling GPU version of QE In-Reply-To: References: Message-ID: <44EAF8F0-9DD0-4F57-9BAA-521CE8897C5A@gmail.com> Hi Thomas, please subscribe and use the q-e-gpgpu at qe-forge.org ML (link: http://qe-forge.org/mailman/listinfo/q-e-gpgpu). Then try with INTEL and MKL f you have the Intel suite. GNU GCC/GFORTRAN should be ALWAYS the last thing to try. > Slightly off topic but if I --enable-magma I lose my FFT libraries...What?! > Can you send me the config.log? > I have compiled the CPU version with Intel MKL libraries and have no real reason for using the internal libraries. It does not matter which library sources I use I will always get this cuda_env_para.o error. (Sometimes in conjuction with a cuda memory error as well.) > > My error occurs like this... > > > > ... > > mpif90 -O3 -g -fopenmp -x f95-cpp-input -fopenmp -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA -D__CUDA -D__GPU_NVIDIA_20 -D__PHIGEMM -D__CUDA_QE_TIMING -D__OPENMP -I../include -I/root/espresso-5.0.1-GPU/phiGEMM/include -I/usr/local/cuda/include -I../iotk/src -I. -c cuda_env_para.f90 > > In file cuda_env_para.f90:40 > > world > > 1 > > Error: Syntax error in argument list at (1) > > make[1]: *** [cuda_env_para.o] Error 1 > > make[1]: *** Waiting for unfinished jobs.... > > make[1]: Leaving directory `/root/espresso-5.0.1-GPU/Modules' > > make: *** [mods] Error 2 > Can you tell me the version of your GFORTRAN compiler? Did you try to compile the parallel version with INTEL? Regards, Filippo -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/32fb8811/attachment.htm From spiga.filippo at gmail.com Fri Sep 21 15:32:39 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 21 Sep 2012 15:32:39 +0200 Subject: [Pw_forum] Error when compiling GPU version of QE In-Reply-To: <44EAF8F0-9DD0-4F57-9BAA-521CE8897C5A@gmail.com> References: <44EAF8F0-9DD0-4F57-9BAA-521CE8897C5A@gmail.com> Message-ID: I forgot to mention: try also without using the "-j" option in the make. F. On Sep 21, 2012, at 3:29 PM, Filippo Spiga wrote: > Can you tell me the version of your GFORTRAN compiler? Did you try to compile the parallel version with INTEL? -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/e538e488/attachment-0001.htm From igirotto at ictp.it Fri Sep 21 15:41:14 2012 From: igirotto at ictp.it (Ivan Girotto) Date: Fri, 21 Sep 2012 15:41:14 +0200 Subject: [Pw_forum] Fwd: Error when compiling GPU version of QE In-Reply-To: References: Message-ID: <505C6E7A.6010807@ictp.it> Hi Thomas, adding the option -ffree-line-length-190 within your make.sys file should do it. F90FLAGS = $(FFLAGS) -x f95-cpp-input -fopenmp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) -ffree-line-length-190 However, all Filippo said about the Intel compiler still remains. Use it, whether it is possible. Ivan On 21/09/2012 15:02, TJ Mustard wrote: > Anything would be grateful. From pandey.bramha at gmail.com Fri Sep 21 15:42:03 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Fri, 21 Sep 2012 19:12:03 +0530 Subject: [Pw_forum] 'hse' in pw run can not converges Message-ID: Dear Developers and Users, I was calculating the band structure of ZB-InN using 'hse' hybrid functional. It gives the reasonable band gap opening but the run was goes on and can't stop. Here i am giving some sort of it's output. Firstly sorry for giving long output data...but have no choice... Please give me a ray of hope to converges of hse calculation in pw.x. input.... &control calculation = 'scf' restart_mode='restart', pseudo_dir = '/pseudo/' , outdir='/tmp/' , prefix = 'innexx' , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 9.90, nat = 2, ntyp = 2, nbnd = 8, ecutwfc = 130, input_dft = 'hse', nqx1 = 1, nqx2 = 1, nqx3 = 1, x_gamma_extrapolation = .TRUE., / &ELECTRONS conv_thr = 1.0d-11 , mixing_beta = 0.7 , / ATOMIC_SPECIES In 114.81400 In.pz-bhs.UPF N 14.01000 N.pz-vbc.UPF ATOMIC_POSITIONS alat In 0.000000000 0.000000000 0.000000000 N 0.250000000 0.250000000 0.250000000 K_POINTS 36 0.5 0.5 0.5 1 .. .. ... Output, At k= 0 0 0 points only.. k = 0.0000 0.0000 0.0000 ( 5985 PWs) bands (ev): -10.0435 2.6536 2.8935 2.8935 2.8935 11.6834 11.6834 11.6834 highest occupied, lowest unoccupied level (ev): 2.8935 2.8935 EXX: now go back to refine exchange calculation -2.4962685539301832 highest occupied, lowest unoccupied level (ev): 1.4312 4.4034 -2.4962685539301832 -2.4966288035394730 -2.4978367300949738 est. exchange err (dexx) = 0.00042384 Ry ! total energy = -24.15032730 Ry highest occupied, lowest unoccupied level (ev): 1.4134 4.4023 -2.4978367300949738 -2.4980591338705209 -2.4984413942151975 est. exchange err (dexx) = 0.00007993 Ry ! total energy = -24.15054868 Ry highest occupied, lowest unoccupied level (ev): 1.4066 4.4806 -2.4995084229633417 -2.4995690173056424 -2.4997151620876128 est. exchange err (dexx) = 0.00004278 Ry ! total energy = -24.15103886 Ry .... ... .... .... est. exchange err (dexx) = 0.00000009 Ry ! total energy = -24.15145297 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006821135594719 -2.5006822803381836 -2.5006825016241492 est. exchange err (dexx) = 0.00000003 Ry ! total energy = -24.15145336 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006830182691306 -2.5006823182635491 -2.5006816409825148 est. exchange err (dexx) = 0.00000001 Ry ! total energy = -24.15145346 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006827878685880 -2.5006825627249212 -2.5006823476519933 est. exchange err (dexx) = 0.00000001 Ry ! total energy = -24.15145351 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006823476519933 -2.5006827558468370 -2.5006831719007772 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145351 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006831719007772 -2.5006824586209802 -2.5006817515742186 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145352 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006817515742186 -2.5006821655655500 -2.5006825845917415 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145353 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006827994750860 -2.5006825695782151 -2.5006823413433099 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145367 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006823413433099 -2.5006827420502393 -2.5006831444189488 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145368 Ry highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 -2.5006831444189488 -2.5006824325837682 -2.5006817224109170 est. exchange err (dexx) = 0.00000000 Ry ! total energy = -24.15145368 Ry .... ..... ..... goes on for atleast total time will take approximate 14 hrs but not stop the run. Please any type of comment is appreciable. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/284018bf/attachment.htm From j.moeller1 at physics.ox.ac.uk Fri Sep 21 15:25:37 2012 From: j.moeller1 at physics.ox.ac.uk (Johannes Moeller) Date: Fri, 21 Sep 2012 13:25:37 +0000 Subject: [Pw_forum] Phonon omega or nu? Factors of 2pi Message-ID: <4B0CE3CF73346E42B35D348620A82F5D20DA653E@EXCHNG14.physics.ox.ac.uk> Hello all, A quick question about the definition of the phonon frequency omega. Is the omega output by Espresso an angular or a linear frequency (omega/2pi)? I.e. is this converted into an energy by multiplying by hbar or h? Comparing simple vibrational modes of molecules (eg. of CO2) in cm^-1 to experimental values gives good agreement with experimental data, which are usually referred to as a liner frequency nu or 1/lambda rather than an angular frequency omega. This suggests that the value that Espresso outputs is nu and not omega(2pi*nu) as the name implies? The values output by Espresso in THz and cm^-1 seem to be related simply by a factor of c (no factors of 2pi). I'm using QE 5.01 but I don't think this is version specific. Many thanks, Johannes ------------------------------- Johannes Moeller Department of Physics University of Oxford Parks Road Oxford OX1 3PU, UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/a765c8d7/attachment.htm From sbajaj at caltech.edu Fri Sep 21 16:02:25 2012 From: sbajaj at caltech.edu (Saurabh Bajaj) Date: Fri, 21 Sep 2012 10:02:25 -0400 Subject: [Pw_forum] Phonon omega or nu? Factors of 2pi In-Reply-To: <4B0CE3CF73346E42B35D348620A82F5D20DA653E@EXCHNG14.physics.ox.ac.uk> References: <4B0CE3CF73346E42B35D348620A82F5D20DA653E@EXCHNG14.physics.ox.ac.uk> Message-ID: Yes, you are right. The numbers with units /cm are wavenumbers (nu-bar). Frequency, nu (/s) = c (cm/s) * nu-bar (/cm) Lamda (cm) = 1/nu-bar (/cm) Energy = hbar (energy-s) * nu (/s) Saurabh Bajaj California Institute of Technology On Fri, Sep 21, 2012 at 9:25 AM, Johannes Moeller < j.moeller1 at physics.ox.ac.uk> wrote: > Hello all, > > A quick question about the definition of the phonon frequency omega. Is > the omega output by Espresso an angular or a linear frequency (omega/2pi)? > I.e. is this converted into an energy by multiplying by hbar or h? > > Comparing simple vibrational modes of molecules (eg. of CO2) in cm^-1 to > experimental values gives good agreement with experimental data, which are > usually referred to as a liner frequency nu or 1/lambda rather than an > angular frequency omega. This suggests that the value that Espresso outputs > is nu and not omega(2pi*nu) as the name implies? > > The values output by Espresso in THz and cm^-1 seem to be related simply > by a factor of c (no factors of 2pi). I'm using QE 5.01 but I don't think > this is version specific. > > Many thanks, > Johannes > > ------------------------------- > Johannes Moeller > Department of Physics > University of Oxford > Parks Road > Oxford OX1 3PU, UK > > > _______________________________________________ > 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/20120921/5b7155d3/attachment-0001.htm From mustardt at onid.orst.edu Fri Sep 21 16:03:08 2012 From: mustardt at onid.orst.edu (TJ Mustard) Date: Fri, 21 Sep 2012 07:03:08 -0700 Subject: [Pw_forum] Error when compiling GPU version of QE In-Reply-To: References: <44EAF8F0-9DD0-4F57-9BAA-521CE8897C5A@gmail.com> Message-ID: Thanks will do. On Fri, Sep 21, 2012 at 6:32 AM, Filippo Spiga wrote: > I forgot to mention: try also without using the "-j" option in the make. > > F. > > On Sep 21, 2012, at 3:29 PM, Filippo Spiga > wrote: > > Can you tell me the version of your GFORTRAN compiler? Did you try to > compile the parallel version with INTEL? > > > -- > Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate > CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) > ?cole Polytechnique F?d?rale de Lausanne (EPFL) > http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thomas J. L. Mustard Graduate Student Department of Chemistry Oregon State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/30646df7/attachment.htm From giuseppe.mattioli at ism.cnr.it Fri Sep 21 16:15:18 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 21 Sep 2012 16:15:18 +0200 Subject: [Pw_forum] 'hse' in pw run can not converges In-Reply-To: References: Message-ID: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> Dear Brahma > &ELECTRONS > conv_thr = 1.0d-11 , > / You require a very strict convergence threshold on wfcs... 1.0d-7 may be sufficient for scf calculations. > nqx1 = 1, nqx2 = 1, nqx3 = 1, You should check the convergence of such mesh. The above 1 1 1 could be quite poor. HTH Giuseppe On Friday 21 September 2012 15:42:03 Bramha Pandey wrote: > Dear Developers and Users, > I was calculating the band structure of ZB-InN using 'hse' hybrid > functional. It gives the reasonable band gap opening but the run was goes > on and can't stop. Here i am giving some sort of it's output. > Firstly sorry for giving long output data...but have no choice... > Please give me a ray of hope to converges of hse calculation in pw.x. > input.... > > &control > calculation = 'scf' > restart_mode='restart', > pseudo_dir = '/pseudo/' , > outdir='/tmp/' , > prefix = 'innexx' , > tprnfor = .true. , > > / > &SYSTEM > ibrav = 2, > celldm(1) = 9.90, > nat = 2, > ntyp = 2, > nbnd = 8, > ecutwfc = 130, > input_dft = 'hse', > nqx1 = 1, nqx2 = 1, nqx3 = 1, > x_gamma_extrapolation = .TRUE., > > / > &ELECTRONS > conv_thr = 1.0d-11 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > In 114.81400 In.pz-bhs.UPF > N 14.01000 N.pz-vbc.UPF > ATOMIC_POSITIONS alat > In 0.000000000 0.000000000 0.000000000 > N 0.250000000 0.250000000 0.250000000 > K_POINTS > 36 > 0.5 0.5 0.5 1 > .. > .. > ... > Output, At k= 0 0 0 points only.. > k = 0.0000 0.0000 0.0000 ( 5985 PWs) bands (ev): > > -10.0435 2.6536 2.8935 2.8935 2.8935 11.6834 11.6834 11.6834 > > highest occupied, lowest unoccupied level (ev): 2.8935 2.8935 > EXX: now go back to refine exchange calculation > -2.4962685539301832 > > > highest occupied, lowest unoccupied level (ev): 1.4312 4.4034 > -2.4962685539301832 -2.4966288035394730 > -2.4978367300949738 > est. exchange err (dexx) = 0.00042384 Ry > ! total energy = -24.15032730 Ry > > highest occupied, lowest unoccupied level (ev): 1.4134 4.4023 > -2.4978367300949738 -2.4980591338705209 > -2.4984413942151975 > est. exchange err (dexx) = 0.00007993 Ry > ! total energy = -24.15054868 Ry > > highest occupied, lowest unoccupied level (ev): 1.4066 4.4806 > -2.4995084229633417 -2.4995690173056424 > -2.4997151620876128 > est. exchange err (dexx) = 0.00004278 Ry > > ! total energy = -24.15103886 Ry > > .... > ... > .... > .... > > est. exchange err (dexx) = 0.00000009 Ry > > ! total energy = -24.15145297 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006821135594719 -2.5006822803381836 > -2.5006825016241492 > est. exchange err (dexx) = 0.00000003 Ry > > ! total energy = -24.15145336 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006830182691306 -2.5006823182635491 > -2.5006816409825148 > est. exchange err (dexx) = 0.00000001 Ry > > ! total energy = -24.15145346 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006827878685880 -2.5006825627249212 > -2.5006823476519933 > est. exchange err (dexx) = 0.00000001 Ry > > ! total energy = -24.15145351 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006823476519933 -2.5006827558468370 > -2.5006831719007772 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145351 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006831719007772 -2.5006824586209802 > -2.5006817515742186 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145352 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006817515742186 -2.5006821655655500 > -2.5006825845917415 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145353 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006827994750860 -2.5006825695782151 > -2.5006823413433099 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145367 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006823413433099 -2.5006827420502393 > -2.5006831444189488 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145368 Ry > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > -2.5006831444189488 -2.5006824325837682 > -2.5006817224109170 > est. exchange err (dexx) = 0.00000000 Ry > > ! total energy = -24.15145368 Ry > .... > ..... > ..... > goes on for atleast total time will take approximate 14 hrs but not stop > the run. > > Please any type of comment is appreciable. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From j.moeller1 at physics.ox.ac.uk Fri Sep 21 16:21:06 2012 From: j.moeller1 at physics.ox.ac.uk (Johannes Moeller) Date: Fri, 21 Sep 2012 14:21:06 +0000 Subject: [Pw_forum] Phonon omega or nu? Factors of 2pi In-Reply-To: References: Message-ID: <4B0CE3CF73346E42B35D348620A82F5D20DA6B01@EXCHNG14.physics.ox.ac.uk> Thanks very much for your reply Saurabh, That's what I thought as well, though if the "omega" output by Espresso is a linear frequency it should be Energy = h (energy-s) * nu (/s) rather than hbar. This is not what I would naturally do if I was a given a number "omega". So if this indeed is correct, I think the naming of the phonon output frequency should be revised. Best wishes, Johannes From: Saurabh Bajaj > Date: 21 September 2012 15:02:25 GMT+01:00 To: PWSCF Forum > Subject: Re: [Pw_forum] Phonon omega or nu? Factors of 2pi Reply-To: PWSCF Forum > Yes, you are right. The numbers with units /cm are wavenumbers (nu-bar). Frequency, nu (/s) = c (cm/s) * nu-bar (/cm) Lamda (cm) = 1/nu-bar (/cm) Energy = hbar (energy-s) * nu (/s) Saurabh Bajaj California Institute of Technology On Fri, Sep 21, 2012 at 9:25 AM, Johannes Moeller > wrote: Hello all, A quick question about the definition of the phonon frequency omega. Is the omega output by Espresso an angular or a linear frequency (omega/2pi)? I.e. is this converted into an energy by multiplying by hbar or h? Comparing simple vibrational modes of molecules (eg. of CO2) in cm^-1 to experimental values gives good agreement with experimental data, which are usually referred to as a liner frequency nu or 1/lambda rather than an angular frequency omega. This suggests that the value that Espresso outputs is nu and not omega(2pi*nu) as the name implies? The values output by Espresso in THz and cm^-1 seem to be related simply by a factor of c (no factors of 2pi). I'm using QE 5.01 but I don't think this is version specific. Many thanks, Johannes ------------------------------- Johannes Moeller Department of Physics University of Oxford Parks Road Oxford OX1 3PU, UK _______________________________________________ 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 ------------------------------- Johannes Moeller Department of Physics University of Oxford Parks Road Oxford OX1 3PU, UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/f782139f/attachment-0001.htm From tsakhrawi at yahoo.com Fri Sep 21 16:22:38 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Fri, 21 Sep 2012 15:22:38 +0100 (BST) Subject: [Pw_forum] Tr : (no subject) In-Reply-To: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> References: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> Message-ID: <1348237358.37180.YahooMailNeo@web133004.mail.ir2.yahoo.com> i'am trying to estimate celldm(1) for the compound FeRh, the problem is thatI always find a value that doubles the expected value ------------------------------------------------------------------------ # self-consistent calculation cat > ferh_fm.scf.in << EOF ?&control ??? prefix='FeRh_fm', ??? pseudo_dir = '$pseudo_dir/', ??? outdir='$outdir/' ?/ ?&system ??? ibrav= 3, ??? celldm(1) =$alat, ??? nat=? 2, ??? ntyp= 2, ??? ecutwfc = 30, ??? nbnd = 16, ??? occupations='smearing', ??? smearing='mv', ??? degauss=0.022, ? / ? &electrons mixing_mode = 'plain' , mixing_beta = 0.4, diagonalization = 'david' , conv_thr = 1.0e-7, electron_maxstep=1000, ?/ ATOMIC_SPECIES ?Fe 55.85??? Fe.pz-nd-rrkjus.UPF ?Rh 102.91?? Rh.pz-rrkjus.UPF ATOMIC_POSITIONS {crystal} ?? Fe????? 0.00000000? 0.00000000? 0.00000000 ?? Rh????? 0.50000000? 0.50000000? 0.50000000 K_POINTS {automatic} ?? 8 8 8 1 1 1 EOF $espresso_dir/bin/pw.x < ferh_fm.scf.in > ferh_fm.scf.out grep -e 'lattice parameter' -e ! ferh_fm.scf.out | \ ????? awk '/lattice/{alat=$(NF-1)}/!/{print alat, $(NF-1)}' >> ferh_fm.etot_vs_alat ------------------------------------------------ Sakhraoui TaoufikUnit? de Recherche Physique des Solides D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/11a7406d/attachment.htm From giannozz at democritos.it Fri Sep 21 16:30:51 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Sep 2012 16:30:51 +0200 Subject: [Pw_forum] Tr : (no subject) In-Reply-To: <1348237358.37180.YahooMailNeo@web133004.mail.ir2.yahoo.com> References: <1348156142.53707.YahooMailNeo@web133004.mail.ir2.yahoo.com> <1348237358.37180.YahooMailNeo@web133004.mail.ir2.yahoo.com> Message-ID: <1348237851.17452.1.camel@fe12lx.fisica.uniud.it> On Fri, 2012-09-21 at 15:22 +0100, Sakhrawi Taoufek wrote: > i'am trying to estimate celldm(1) for the compound FeRh, the problem > is that I always find a value that doubles the expected value dobling the number of your messages will not cut your result into half. Looking more carefully at your data might, though. Have you looked at your data using xcrysden? no? please do and verify if the structure you have is what you want -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From silas.silva at ufabc.edu.br Fri Sep 21 19:10:48 2012 From: silas.silva at ufabc.edu.br (Silas Silva) Date: Fri, 21 Sep 2012 14:10:48 -0300 Subject: [Pw_forum] Question of a system administrator about pw.x usage Message-ID: <20120921171047.GK1967@auron.ufabc.int.br> Hello all, I'm a system administrator of the High Performance Computing Center at Universidade Federal do ABC - Brazil (http://hpc.ufabc.edu.br/). I'm not used about the internals of scientific research and the tools you are used, but we have ran into problems regarding pw.x usage of one of the users we support. She has a simple job submission file that run pw.x, with an input and an output file. After hours of execution, the system load increases absurdly. We can see it is I/O stuff, but we could not discover why it happens later in the execution of the program nor how to fix it. In this cluster, we use NFS for both "distributed scratch" and home folders (we know we should use a modern parallel file system, but it is not possible for the moment), but each node has a big local scratch partition. Some questions: 1. Why I/O happens later in the execution of pw.x? 2. Documentation (here: http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/node18.html#SECTION00043100000000000000) is not clear about the "distributed" or "collected" work. Although it has some tips, I still wonder about suggesting to our user about the best configuration. What can be "parallelized"? What may remain in one place? 3. Is there any flag or configuration we can pass to pw.x to see what it is doing? Any debug flag? 4. Variables you place in input file are documented anywhere? Thank you very much. -- Silas Silva From pandey.bramha at gmail.com Fri Sep 21 19:43:28 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Fri, 21 Sep 2012 23:13:28 +0530 Subject: [Pw_forum] 'hse' in pw run can not converges In-Reply-To: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> References: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> Message-ID: Thank you very much Dear Mattioli Sir , it works. Can please give a clue to obtained the Al.pz-bhs.UPF (Al LDA with bhs funtionals essentially NormConversing) pseudopotential as i am very poor to generate it myself and not obtained it in pslibrary. it's a very bad habit i know but i have no option except taking help at this stage for my research. thanks in advanced for your kind help. On Fri, Sep 21, 2012 at 7:45 PM, Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it> wrote: > > Dear Brahma > > > &ELECTRONS > > conv_thr = 1.0d-11 , > > / > > You require a very strict convergence threshold on wfcs... > 1.0d-7 may be sufficient for scf calculations. > > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > You should check the convergence of such mesh. The above 1 1 1 could be > quite poor. > > HTH > > Giuseppe > > > On Friday 21 September 2012 15:42:03 Bramha Pandey wrote: > > Dear Developers and Users, > > I was calculating the band structure of ZB-InN using 'hse' hybrid > > functional. It gives the reasonable band gap opening but the run was goes > > on and can't stop. Here i am giving some sort of it's output. > > Firstly sorry for giving long output data...but have no choice... > > Please give me a ray of hope to converges of hse calculation in pw.x. > > input.... > > > > &control > > calculation = 'scf' > > restart_mode='restart', > > pseudo_dir = '/pseudo/' , > > outdir='/tmp/' , > > prefix = 'innexx' , > > tprnfor = .true. , > > > > / > > &SYSTEM > > ibrav = 2, > > celldm(1) = 9.90, > > nat = 2, > > ntyp = 2, > > nbnd = 8, > > ecutwfc = 130, > > input_dft = 'hse', > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > x_gamma_extrapolation = .TRUE., > > > > / > > &ELECTRONS > > conv_thr = 1.0d-11 , > > mixing_beta = 0.7 , > > / > > ATOMIC_SPECIES > > In 114.81400 In.pz-bhs.UPF > > N 14.01000 N.pz-vbc.UPF > > ATOMIC_POSITIONS alat > > In 0.000000000 0.000000000 0.000000000 > > N 0.250000000 0.250000000 0.250000000 > > K_POINTS > > 36 > > 0.5 0.5 0.5 1 > > .. > > .. > > ... > > Output, At k= 0 0 0 points only.. > > k = 0.0000 0.0000 0.0000 ( 5985 PWs) bands (ev): > > > > -10.0435 2.6536 2.8935 2.8935 2.8935 11.6834 11.6834 > 11.6834 > > > > highest occupied, lowest unoccupied level (ev): 2.8935 2.8935 > > EXX: now go back to refine exchange calculation > > -2.4962685539301832 > > > > > > highest occupied, lowest unoccupied level (ev): 1.4312 4.4034 > > -2.4962685539301832 -2.4966288035394730 > > -2.4978367300949738 > > est. exchange err (dexx) = 0.00042384 Ry > > ! total energy = -24.15032730 Ry > > > > highest occupied, lowest unoccupied level (ev): 1.4134 4.4023 > > -2.4978367300949738 -2.4980591338705209 > > -2.4984413942151975 > > est. exchange err (dexx) = 0.00007993 Ry > > ! total energy = -24.15054868 Ry > > > > highest occupied, lowest unoccupied level (ev): 1.4066 4.4806 > > -2.4995084229633417 -2.4995690173056424 > > -2.4997151620876128 > > est. exchange err (dexx) = 0.00004278 Ry > > > > ! total energy = -24.15103886 Ry > > > > .... > > ... > > .... > > .... > > > > est. exchange err (dexx) = 0.00000009 Ry > > > > ! total energy = -24.15145297 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006821135594719 -2.5006822803381836 > > -2.5006825016241492 > > est. exchange err (dexx) = 0.00000003 Ry > > > > ! total energy = -24.15145336 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006830182691306 -2.5006823182635491 > > -2.5006816409825148 > > est. exchange err (dexx) = 0.00000001 Ry > > > > ! total energy = -24.15145346 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006827878685880 -2.5006825627249212 > > -2.5006823476519933 > > est. exchange err (dexx) = 0.00000001 Ry > > > > ! total energy = -24.15145351 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006823476519933 -2.5006827558468370 > > -2.5006831719007772 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145351 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006831719007772 -2.5006824586209802 > > -2.5006817515742186 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145352 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006817515742186 -2.5006821655655500 > > -2.5006825845917415 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145353 Ry > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006827994750860 -2.5006825695782151 > > -2.5006823413433099 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145367 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006823413433099 -2.5006827420502393 > > -2.5006831444189488 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145368 Ry > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > -2.5006831444189488 -2.5006824325837682 > > -2.5006817224109170 > > est. exchange err (dexx) = 0.00000000 Ry > > > > ! total energy = -24.15145368 Ry > > .... > > ..... > > ..... > > goes on for atleast total time will take approximate 14 hrs but not stop > > the run. > > > > Please any type of comment is appreciable. > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/577d6e87/attachment-0001.htm From spiga.filippo at gmail.com Fri Sep 21 22:38:04 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 21 Sep 2012 22:38:04 +0200 Subject: [Pw_forum] Question of a system administrator about pw.x usage In-Reply-To: <20120921171047.GK1967@auron.ufabc.int.br> References: <20120921171047.GK1967@auron.ufabc.int.br> Message-ID: Dear Silas, Unfortunately there are few things you can do to improve the performance of a NFS-based distributed file system. Try to keep as less I/O as possible (flag disk_io = 'none' in the input) I remember you can tell to PW to write each wfc.XX files in the local scratch (am I wrong? something changed?) by simply point the output directory to the local scratch (but it might be necessary to specify something else?). Then at the end by using a epilogue script (this is for PBS/TORQUE, other resource managers have the same capability but the file might have a different name) you can collect in a central point all the files for post-processing. You do not reduce the amount of data that you move but by using rcp or other tricks you can definitely reduce the overall loss in performance due to the data movement on the network. The other fact is ? you have to write the epilogue script by yourself. It can be bash or csh or even python. A scripting exercise :-) Let's wait for other suggestion of true experts? HTH F. On Sep 21, 2012, at 7:10 PM, Silas Silva wrote: > Hello all, > > I'm a system administrator of the High Performance Computing Center at > Universidade Federal do ABC - Brazil (http://hpc.ufabc.edu.br/). I'm > not used about the internals of scientific research and the tools you > are used, but we have ran into problems regarding pw.x usage of one of > the users we support. > > She has a simple job submission file that run pw.x, with an input and an > output file. After hours of execution, the system load increases > absurdly. We can see it is I/O stuff, but we could not discover why it > happens later in the execution of the program nor how to fix it. > > In this cluster, we use NFS for both "distributed scratch" and home > folders (we know we should use a modern parallel file system, but it is > not possible for the moment), but each node has a big local scratch > partition. > > Some questions: > > 1. Why I/O happens later in the execution of pw.x? > > 2. Documentation (here: http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/node18.html#SECTION00043100000000000000) > is not clear about the "distributed" or "collected" work. Although > it has some tips, I still wonder about suggesting to our user about > the best configuration. What can be "parallelized"? What may remain > in one place? > > 3. Is there any flag or configuration we can pass to pw.x to see what it > is doing? Any debug flag? > > 4. Variables you place in input file are documented anywhere? > > Thank you very much. > > -- > Silas Silva > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Mr. Filippo SPIGA, M.Sc., Ph.D. Candidate CADMOS - Chair of Numerical Algorithms and HPC (ANCHP) ?cole Polytechnique F?d?rale de Lausanne (EPFL) http://anchp.epfl.ch ~ http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/78fd5cae/attachment.htm From spmmal at gmail.com Fri Sep 21 22:41:14 2012 From: spmmal at gmail.com (Caloma Trumica) Date: Fri, 21 Sep 2012 16:41:14 -0400 Subject: [Pw_forum] SYMMETRY REFERENCE Message-ID: Dear All, I found it is difficult to understand some routine like "set_irr", which shows how to obtain the irreducible representations involved in phonon calculations. Could you please recommend some textbook or references related with the crystal symmetry. Thank you very much! Caloma -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120921/ef3960bd/attachment.htm From 1009ukumar at gmail.com Sat Sep 22 03:12:16 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Sat, 22 Sep 2012 06:42:16 +0530 Subject: [Pw_forum] SYMMETRY REFERENCE In-Reply-To: References: Message-ID: Hi Caloma, A good for group theory is : Space groups for solid state scientists, by Gerald Burns, Anthony Michael Glazer. good luck regards, sonu ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== On Sat, Sep 22, 2012 at 2:11 AM, Caloma Trumica wrote: > Dear All, > > I found it is difficult to understand some routine like "set_irr", which > shows how to obtain the irreducible representations involved in phonon > calculations. > > Could you please recommend some textbook or references related with the > crystal symmetry. > > Thank you very much! > > Caloma > > _______________________________________________ > 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/20120922/ef2d5717/attachment.htm From himanshu at iopb.res.in Sat Sep 22 05:46:30 2012 From: himanshu at iopb.res.in (himanshu at iopb.res.in) Date: Sat, 22 Sep 2012 09:16:30 +0530 Subject: [Pw_forum] Regarding davcio error Message-ID: Dear QE users, when i run my scf calculation ,i encounter following error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... i am really very thankful if any of you have solution to get rid off this error. himanshu From pandey.bramha at gmail.com Sat Sep 22 06:23:56 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sat, 22 Sep 2012 09:53:56 +0530 Subject: [Pw_forum] Regarding davcio error In-Reply-To: References: Message-ID: Dear Himanshu, can you please give firstly your affiliation with posting your problem in this forum. Regarding this error, you can try with cleaning your 'tmp' directory and then start again. On Sat, Sep 22, 2012 at 9:16 AM, wrote: > Dear QE users, > when i run my scf calculation ,i encounter following error > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > i am really very thankful if any of you have solution to > get rid off this error. > > himanshu > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120922/36867d01/attachment.htm From davide.ceresoli at istm.cnr.it Sat Sep 22 10:32:52 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Sat, 22 Sep 2012 10:32:52 +0200 Subject: [Pw_forum] NMR calculation of CDCl3 In-Reply-To: References: Message-ID: <505D77B4.3000306@istm.cnr.it> Dear Prasenjit, as far you are considering a frozen geometry, there is no difference between H and D. Only zero point motion will be affected. Deuterium NMR is exactly the same as H NMR, except that experimentally the D signal is weak, noisy and broad. In practice, D substitution is used to suppress selected H resonances. Best wishes, Davide On 09/21/2012 02:44 PM, Prasenjit Ghosh wrote: > Dear all, > > I want to calculate the 13C NMR spectra of CDCl3, where D is the > deuterium......How do I incorporate the fact that D has one extra neutron in it? > Or since we are interested in the C NMR spectra, it will not effect the calculation? > > With regards, > > Prasenjit > > -- > PRASENJIT GHOSH, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 From prasenjit.jnc at gmail.com Sat Sep 22 12:02:18 2012 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Sat, 22 Sep 2012 15:32:18 +0530 Subject: [Pw_forum] NMR calculation of CDCl3 In-Reply-To: <505D77B4.3000306@istm.cnr.it> References: <505D77B4.3000306@istm.cnr.it> Message-ID: Dear Davide, Thanks a lot for the explanation. With regards, Prasenjit On 22 September 2012 14:02, Davide Ceresoli wrote: > Dear Prasenjit, > as far you are considering a frozen geometry, there is no > difference between H and D. Only zero point motion will be > affected. Deuterium NMR is exactly the same as H NMR, except > that experimentally the D signal is weak, noisy and broad. In > practice, D substitution is used to suppress selected H resonances. > > Best wishes, > Davide > > > > On 09/21/2012 02:44 PM, Prasenjit Ghosh wrote: > > Dear all, > > > > I want to calculate the 13C NMR spectra of CDCl3, where D is the > > deuterium......How do I incorporate the fact that D has one extra > neutron in it? > > Or since we are interested in the C NMR spectra, it will not effect the > calculation? > > > > With regards, > > > > Prasenjit > > > > -- > > PRASENJIT GHOSH, > > IISER Pune, > > First floor, Central Tower, Sai Trinity Building > > Garware Circle, Sutarwadi, Pashan > > Pune, Maharashtra 411021, India > > > > Phone: +91 (20) 2590 8203 > > Fax: +91 (20) 2589 9790 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120922/2b4864b2/attachment.htm From giannozz at democritos.it Sat Sep 22 14:00:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Sep 2012 14:00:28 +0200 Subject: [Pw_forum] SYMMETRY REFERENCE In-Reply-To: References: Message-ID: On Sep 21, 2012, at 22:41 , Caloma Trumica wrote: > I found it is difficult to understand some routine like "set_irr" you are not the only one: the implementation of symmetries in the phonon code is rather complex. You do not need to understand everything, though, unless you want to modify the code. Why are you interested in that part of the code? > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Sep 22 14:10:34 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Sep 2012 14:10:34 +0200 Subject: [Pw_forum] Question of a system administrator about pw.x usage In-Reply-To: <20120921171047.GK1967@auron.ufabc.int.br> References: <20120921171047.GK1967@auron.ufabc.int.br> Message-ID: On Sep 21, 2012, at 19:10 , Silas Silva wrote: > After hours of execution, the system load increases absurdly. > We can see it is I/O stuff, but we could not discover why it > happens later in the execution of the program nor how to fix it. because at the end of the execution the code, if so instructed (input variable "wf_collect"), collects big arrays that are distributed across all processors to a single processor, that in turn writes them to disk. This is needed only if you want to use those data for further processing. > 3. Is there any flag or configuration we can pass to pw.x to see > what it > is doing? Any debug flag? no. There is nothing to debug anyway: it is well known that one should not read or even worse write big files via NFS > 4. Variables you place in input file are documented anywhere? of course they are: in PW/Doc/INPUT_PW.* and in the www.quantum-espresso.org web site P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From spmmal at gmail.com Sat Sep 22 19:39:04 2012 From: spmmal at gmail.com (Caloma Trumica) Date: Sat, 22 Sep 2012 13:39:04 -0400 Subject: [Pw_forum] SYMMETRY REFERENCE In-Reply-To: References: Message-ID: Hi Sonu, Thank you so much! On Fri, Sep 21, 2012 at 9:12 PM, Sonu Kumar <1009ukumar at gmail.com> wrote: > Hi Caloma, > > A good for group theory is : > > Space groups for solid state scientists, > by Gerald Burns, Anthony Michael Glazer. > > good luck > > regards, > sonu > > ========================================== > Sonu Kumar > Phd Student,Physics Department > Indian Institute of Technology ,Delhi-110016, India > web:-http://www.iitd.ac.in/ > ========================================== > > > > On Sat, Sep 22, 2012 at 2:11 AM, Caloma Trumica wrote: > >> Dear All, >> >> I found it is difficult to understand some routine like "set_irr", which >> shows how to obtain the irreducible representations involved in phonon >> calculations. >> >> Could you please recommend some textbook or references related with the >> crystal symmetry. >> >> Thank you very much! >> >> Caloma >> >> _______________________________________________ >> 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/20120922/85f8bc5b/attachment.htm From pandey.bramha at gmail.com Sun Sep 23 07:13:59 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sun, 23 Sep 2012 10:43:59 +0530 Subject: [Pw_forum] info regarding r.x code Message-ID: Dear Users and Developers, How can i get the r.x code for the calculation of U parameter in quantum espresso-5.0.1. Any kind of help is heartily appreciable. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120923/1daf03f9/attachment.htm From mpayami at aeoi.org.ir Sun Sep 23 09:52:10 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sun, 23 Sep 2012 11:22:10 +0330 Subject: [Pw_forum] How to calculate the adsorption energy of ion (charged particle) on the surface of semiconductor? In-Reply-To: References: Message-ID: Dear Yavar, take a look at the following link of a post from Paolo: http://www.democritos.it/pipermail/pw_forum/2007-January/005694.html mahmoud -----Original Message----- From: yavar pour azar To: PWSCF Forum Date: Mon, 17 Sep 2012 11:58:29 +0430 Subject: [Pw_forum] How to calculate the adsorption energy of ion (charged particle) on the surface of semiconductor? Dear QE users I want to calculate adsorption energy and structural parameters for the adsorption of some ions on the surface of semiconductor, is this similar to calculation of neutral particle or other procedure is required? I would be appreciate if anyone refer me to detailed reference to do this. Thanks in advance ----------------------------------------- Yavar Taghipour Azar Physics Group, AEOI Tehran, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120923/3b11f099/attachment.htm From pchen at ion.chem.utk.edu Sun Sep 23 17:08:12 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Sun, 23 Sep 2012 11:08:12 -0400 Subject: [Pw_forum] info regarding r.x code In-Reply-To: References: Message-ID: Dear Pandey, You can find r.x in the exercises of "Matteo Cococcioni,Examples of spin-polarized and DFT+U calculations" in the link: http://media.quantum-espresso.org/santa_barbara_2009_07/index.php. And you can follow the "instructions of LDA+U" to calculate U. On Sun, Sep 23, 2012 at 1:13 AM, Bramha Pandey wrote: > Dear Users and Developers, > How can i get the r.x code for the calculation of U parameter in quantum > espresso-5.0.1. > Any kind of help is heartily appreciable. > > -- > Thanks and Regards > Bramha Prasad Pandey > Ph.D Student Indian School of Mines(ISM) > Dhanbad, INDIA. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120923/b9505960/attachment.htm From aakimov at z.rochester.edu Sun Sep 23 16:43:34 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sun, 23 Sep 2012 10:43:34 -0400 (EDT) Subject: [Pw_forum] Error in routine scale_h (1) Message-ID: <604767151.39747.1348411414087.JavaMail.root@z.rochester.edu> Dear all, I'm trying to optimize a relatively large system such as 2 C60 / unit cell. So i start with relatively large cell dimensions. I'm doing vc-relax calculations with either 'damp'&'damp-pr' or 'bfgs'&'bfgs' for ionic and cell dynamics options. However, after some number (~50-70) of successful (ionic/cell) steps the calculations crash with the error: Error in routine scale_h (1): Not enough space allocated for radial FFT: try restarting with a larger cell_factor. It seems like this happens when the size of the simulation cell changes by some notable amount with respect to the starting one. Perhaps, the program automatically changes the plane wave basis set (increases). If i restart the calculations with the latest (most optimal) configuration of the system and the same amount of memory allocated, the further optimization can proceed some more time (also ~50 - 70 steps) before next crash. So in principle it is still possible to achieve the convergence with this sequence of operations, but it is quite inconvenient to reset the calculations every 50-70 steps. So my question: is there any way to avoid this and get optimized results without intermediate crashes (apart from increasing the amount of memory reserved in the beginning)? Thank you, Alexey -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From pandey.bramha at gmail.com Sun Sep 23 18:24:48 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sun, 23 Sep 2012 21:54:48 +0530 Subject: [Pw_forum] info regarding r.x code In-Reply-To: References: Message-ID: Thank you very much Dear Chen Sir for your kind help. On Sun, Sep 23, 2012 at 8:38 PM, Peng Chen wrote: > Dear Pandey, > > You can find r.x in the exercises of "Matteo Cococcioni,Examples of > spin-polarized and DFT+U calculations" in the link: > http://media.quantum-espresso.org/santa_barbara_2009_07/index.php. And > you can follow the "instructions of LDA+U" to calculate U. > > > > On Sun, Sep 23, 2012 at 1:13 AM, Bramha Pandey wrote: > >> Dear Users and Developers, >> How can i get the r.x code for the calculation of U parameter in quantum >> espresso-5.0.1. >> Any kind of help is heartily appreciable. >> >> -- >> Thanks and Regards >> Bramha Prasad Pandey >> Ph.D Student Indian School of Mines(ISM) >> Dhanbad, INDIA. >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Best Regards. > Peng > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120923/72111707/attachment.htm From ma at nano.ku.dk Sun Sep 23 21:33:15 2012 From: ma at nano.ku.dk (Martin Andersson) Date: Sun, 23 Sep 2012 21:33:15 +0200 Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <604767151.39747.1348411414087.JavaMail.root@z.rochester.edu> References: <604767151.39747.1348411414087.JavaMail.root@z.rochester.edu> Message-ID: <505F63FB.1020408@nano.ku.dk> Set cell_factor (in &cell) to a number higher than the default like suggested... That should work. Cheers, Martin Andersson University of Copenhagen Den 2012-09-23 4:43 PM, Alexey Akimov skrev: > Dear all, > > I'm trying to optimize a relatively large system such as 2 C60 / unit cell. So i start with relatively large cell dimensions. I'm doing vc-relax calculations with either 'damp'&'damp-pr' or 'bfgs'&'bfgs' for ionic and cell dynamics options. However, after some number (~50-70) of successful (ionic/cell) steps the calculations crash with the error: > > Error in routine scale_h (1): > Not enough space allocated for radial FFT: try restarting with a larger cell_factor. > > It seems like this happens when the size of the simulation cell changes by some notable amount with respect to the starting one. Perhaps, the program automatically changes the plane wave basis set (increases). If i restart the calculations with the latest (most optimal) configuration of the system and the same amount of memory allocated, the further optimization can proceed some more time (also ~50 - 70 steps) before next crash. So in principle it is still possible to achieve the convergence with this sequence of operations, but it is quite inconvenient to reset the calculations every 50-70 steps. > > So my question: is there any way to avoid this and get optimized results without intermediate crashes (apart from increasing the amount of memory reserved in the beginning)? > > Thank you, > Alexey > > From giannozz at democritos.it Sun Sep 23 22:19:05 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 23 Sep 2012 22:19:05 +0200 Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <604767151.39747.1348411414087.JavaMail.root@z.rochester.edu> References: <604767151.39747.1348411414087.JavaMail.root@z.rochester.edu> Message-ID: <19050A59-AE2E-461B-B6B7-3FFD5EC988EC@democritos.it> On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > If i restart the calculations with the latest (most optimal) > configuration of the system and the same amount of memory > allocated, the further optimization can proceed some more time > (also ~50 - 70 steps) before next crash. this should not happen, unless your optimization procedure keeps oscillating between large and small volumes. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sun Sep 23 22:27:23 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 23 Sep 2012 22:27:23 +0200 Subject: [Pw_forum] 'hse' in pw run can not converges In-Reply-To: References: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> Message-ID: <0E2879E3-A574-4B34-AD08-4A4253C99410@democritos.it> On Sep 21, 2012, at 19:43 , Bramha Pandey wrote: > Can please give a clue to obtained the Al.pz-bhs.UPF (Al LDA with > bhs funtionals essentially NormConversing) pseudopotential as i am > very poor to generate it myself and not obtained it in pslibrary. can you please write understandable sentences? Al.pz-bhs.UPF = Aluminium, Perdew-Zunger functional (LDA), Bachelet-Hamann-Schlueter: Phys.Rev. B 26, 4199 (1982) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From aakimov at z.rochester.edu Sun Sep 23 23:42:16 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sun, 23 Sep 2012 17:42:16 -0400 (EDT) Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <19050A59-AE2E-461B-B6B7-3FFD5EC988EC@democritos.it> Message-ID: <1451914513.41198.1348436536144.JavaMail.root@z.rochester.edu> my unit cell is not oscillating, but rather shrinking. shouldn't the basis size (number of plane waves) be bigger for larger cell, so the bigger cell would determine the maximal amount of memory for simulation even if the cell contracts? ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Sunday, September 23, 2012 1:19:05 PM Subject: Re: [Pw_forum] Error in routine scale_h (1) On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > If i restart the calculations with the latest (most optimal) > configuration of the system and the same amount of memory > allocated, the further optimization can proceed some more time > (also ~50 - 70 steps) before next crash. this should not happen, unless your optimization procedure keeps oscillating between large and small volumes. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. 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 -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From aakimov at z.rochester.edu Sun Sep 23 23:44:49 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sun, 23 Sep 2012 17:44:49 -0400 (EDT) Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <505F63FB.1020408@nano.ku.dk> Message-ID: <1398477988.41205.1348436689684.JavaMail.root@z.rochester.edu> Ok. I'll try this option, thank you for suggestion. In conjunction to this feature, will the memory required for calculation increase with increased cell_factor? how fast? ----- Original Message ----- From: "Martin Andersson" To: "PWSCF Forum" Sent: Sunday, September 23, 2012 12:33:15 PM Subject: Re: [Pw_forum] Error in routine scale_h (1) Set cell_factor (in &cell) to a number higher than the default like suggested... That should work. Cheers, Martin Andersson University of Copenhagen Den 2012-09-23 4:43 PM, Alexey Akimov skrev: > Dear all, > > I'm trying to optimize a relatively large system such as 2 C60 / unit cell. So i start with relatively large cell dimensions. I'm doing vc-relax calculations with either 'damp'&'damp-pr' or 'bfgs'&'bfgs' for ionic and cell dynamics options. However, after some number (~50-70) of successful (ionic/cell) steps the calculations crash with the error: > > Error in routine scale_h (1): > Not enough space allocated for radial FFT: try restarting with a larger cell_factor. > > It seems like this happens when the size of the simulation cell changes by some notable amount with respect to the starting one. Perhaps, the program automatically changes the plane wave basis set (increases). If i restart the calculations with the latest (most optimal) configuration of the system and the same amount of memory allocated, the further optimization can proceed some more time (also ~50 - 70 steps) before next crash. So in principle it is still possible to achieve the convergence with this sequence of operations, but it is quite inconvenient to reset the calculations every 50-70 steps. > > So my question: is there any way to avoid this and get optimized results without intermediate crashes (apart from increasing the amount of memory reserved in the beginning)? > > Thank you, > Alexey > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From degironc at sissa.it Sun Sep 23 23:58:47 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 23 Sep 2012 23:58:47 +0200 Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <1451914513.41198.1348436536144.JavaMail.root@z.rochester.edu> References: <1451914513.41198.1348436536144.JavaMail.root@z.rochester.edu> Message-ID: <505F8617.70206@sissa.it> as your cell shrinks the energy cutoff corresponding to your set of plane wave increases and it this exceeds a the maximum values in the precalculated psedopotential table (some 20% higher than the specified ecut by default if i remember correctly) the code stops. You can increase this limit with the cell_factor variable. However if this keeps happening it means that your cell was way too large ! stefano On 09/23/2012 11:42 PM, Alexey Akimov wrote: > my unit cell is not oscillating, but rather shrinking. shouldn't the basis size (number of plane waves) be bigger for larger cell, so the bigger cell would determine the maximal amount of memory for simulation even if the cell contracts? > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Sunday, September 23, 2012 1:19:05 PM > Subject: Re: [Pw_forum] Error in routine scale_h (1) > > > On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > >> If i restart the calculations with the latest (most optimal) >> configuration of the system and the same amount of memory >> allocated, the further optimization can proceed some more time >> (also ~50 - 70 steps) before next crash. > this should not happen, unless your optimization procedure keeps > oscillating between large and > small volumes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > From aakimov at z.rochester.edu Mon Sep 24 04:14:14 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Sun, 23 Sep 2012 22:14:14 -0400 (EDT) Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <505F8617.70206@sissa.it> Message-ID: <272832362.42101.1348452854675.JavaMail.root@z.rochester.edu> I see. Thank you for the explanation! Alexey ----- Original Message ----- From: "Stefano de Gironcoli" To: "pw forum" Sent: Sunday, September 23, 2012 2:58:47 PM Subject: Re: [Pw_forum] Error in routine scale_h (1) as your cell shrinks the energy cutoff corresponding to your set of plane wave increases and it this exceeds a the maximum values in the precalculated psedopotential table (some 20% higher than the specified ecut by default if i remember correctly) the code stops. You can increase this limit with the cell_factor variable. However if this keeps happening it means that your cell was way too large ! stefano On 09/23/2012 11:42 PM, Alexey Akimov wrote: > my unit cell is not oscillating, but rather shrinking. shouldn't the basis size (number of plane waves) be bigger for larger cell, so the bigger cell would determine the maximal amount of memory for simulation even if the cell contracts? > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Sunday, September 23, 2012 1:19:05 PM > Subject: Re: [Pw_forum] Error in routine scale_h (1) > > > On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > >> If i restart the calculations with the latest (most optimal) >> configuration of the system and the same amount of memory >> allocated, the further optimization can proceed some more time >> (also ~50 - 70 steps) before next crash. > this should not happen, unless your optimization procedure keeps > oscillating between large and > small volumes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From giuseppe.mattioli at ism.cnr.it Mon Sep 24 10:27:01 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Mon, 24 Sep 2012 10:27:01 +0200 Subject: [Pw_forum] 'hse' in pw run can not converges In-Reply-To: References: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> Message-ID: <201209241027.01507.giuseppe.mattioli@ism.cnr.it> Dear Brahma I'm afraid I'm not. I've never employed Bachelet-Hamann-Schluter pseudopotentials in my calculations and I do not know if there are still codes that generate them. Why do not you try with Martins- Troullier pseudopotentials? There is plenty of them in the ps library, and you can build your own pseudopotential with ld1.x Yours Giuseppe On Friday 21 September 2012 19:43:28 Bramha Pandey wrote: > Thank you very much Dear Mattioli Sir , it works. > > Can please give a clue to obtained the Al.pz-bhs.UPF (Al LDA with bhs > funtionals essentially NormConversing) pseudopotential as i am very poor to > generate it myself and not obtained it in pslibrary. > it's a very bad habit i know but i have no option except taking help at > this stage for my research. > > thanks in advanced for your kind help. > > On Fri, Sep 21, 2012 at 7:45 PM, Giuseppe Mattioli < > > giuseppe.mattioli at ism.cnr.it> wrote: > > Dear Brahma > > > > > &ELECTRONS > > > > > > conv_thr = 1.0d-11 , > > > > > > / > > > > You require a very strict convergence threshold on wfcs... > > 1.0d-7 may be sufficient for scf calculations. > > > > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > > > You should check the convergence of such mesh. The above 1 1 1 could be > > quite poor. > > > > HTH > > > > Giuseppe > > > > On Friday 21 September 2012 15:42:03 Bramha Pandey wrote: > > > Dear Developers and Users, > > > I was calculating the band structure of ZB-InN using 'hse' hybrid > > > functional. It gives the reasonable band gap opening but the run was > > > goes on and can't stop. Here i am giving some sort of it's output. > > > Firstly sorry for giving long output data...but have no choice... > > > Please give me a ray of hope to converges of hse calculation in pw.x. > > > input.... > > > > > > &control > > > > > > calculation = 'scf' > > > restart_mode='restart', > > > pseudo_dir = '/pseudo/' , > > > outdir='/tmp/' , > > > prefix = 'innexx' , > > > tprnfor = .true. , > > > > > > / > > > > > > &SYSTEM > > > > > > ibrav = 2, > > > > > > celldm(1) = 9.90, > > > > > > nat = 2, > > > > > > ntyp = 2, > > > > > > nbnd = 8, > > > > > > ecutwfc = 130, > > > > > > input_dft = 'hse', > > > > > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > > x_gamma_extrapolation = .TRUE., > > > > > > / > > > &ELECTRONS > > > > > > conv_thr = 1.0d-11 , > > > > > > mixing_beta = 0.7 , > > > > > > / > > > > > > ATOMIC_SPECIES > > > > > > In 114.81400 In.pz-bhs.UPF > > > > > > N 14.01000 N.pz-vbc.UPF > > > > > > ATOMIC_POSITIONS alat > > > > > > In 0.000000000 0.000000000 0.000000000 > > > > > > N 0.250000000 0.250000000 0.250000000 > > > > > > K_POINTS > > > 36 > > > > > > 0.5 0.5 0.5 1 > > > > > > .. > > > .. > > > ... > > > Output, At k= 0 0 0 points only.. > > > > > > k = 0.0000 0.0000 0.0000 ( 5985 PWs) bands (ev): > > > -10.0435 2.6536 2.8935 2.8935 2.8935 11.6834 11.6834 > > > > 11.6834 > > > > > highest occupied, lowest unoccupied level (ev): 2.8935 > > > 2.8935 EXX: now go back to refine exchange calculation > > > > > > -2.4962685539301832 > > > > > > highest occupied, lowest unoccupied level (ev): 1.4312 4.4034 > > > > > > -2.4962685539301832 -2.4966288035394730 > > > > > > -2.4978367300949738 > > > > > > est. exchange err (dexx) = 0.00042384 Ry > > > > > > ! total energy = -24.15032730 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4134 4.4023 > > > > > > -2.4978367300949738 -2.4980591338705209 > > > > > > -2.4984413942151975 > > > > > > est. exchange err (dexx) = 0.00007993 Ry > > > > > > ! total energy = -24.15054868 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4066 4.4806 > > > > > > -2.4995084229633417 -2.4995690173056424 > > > > > > -2.4997151620876128 > > > > > > est. exchange err (dexx) = 0.00004278 Ry > > > > > > ! total energy = -24.15103886 Ry > > > > > > .... > > > ... > > > .... > > > .... > > > > > > est. exchange err (dexx) = 0.00000009 Ry > > > > > > ! total energy = -24.15145297 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > > > > -2.5006821135594719 -2.5006822803381836 > > > > > > -2.5006825016241492 > > > > > > est. exchange err (dexx) = 0.00000003 Ry > > > > > > ! total energy = -24.15145336 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > > > > -2.5006830182691306 -2.5006823182635491 > > > > > > -2.5006816409825148 > > > > > > est. exchange err (dexx) = 0.00000001 Ry > > > > > > ! total energy = -24.15145346 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > > > > -2.5006827878685880 -2.5006825627249212 > > > > > > -2.5006823476519933 > > > > > > est. exchange err (dexx) = 0.00000001 Ry > > > > > > ! total energy = -24.15145351 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006823476519933 -2.5006827558468370 > > > > > > -2.5006831719007772 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145351 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006831719007772 -2.5006824586209802 > > > > > > -2.5006817515742186 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145352 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006817515742186 -2.5006821655655500 > > > > > > -2.5006825845917415 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145353 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006827994750860 -2.5006825695782151 > > > > > > -2.5006823413433099 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145367 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006823413433099 -2.5006827420502393 > > > > > > -2.5006831444189488 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145368 Ry > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > -2.5006831444189488 -2.5006824325837682 > > > > > > -2.5006817224109170 > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > ! total energy = -24.15145368 Ry > > > .... > > > ..... > > > ..... > > > goes on for atleast total time will take approximate 14 hrs but not > > > stop the run. > > > > > > Please any type of comment is appreciable. > > > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00015 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From d.tiana at bath.ac.uk Mon Sep 24 10:35:45 2012 From: d.tiana at bath.ac.uk (Davide Tiana) Date: Mon, 24 Sep 2012 09:35:45 +0100 Subject: [Pw_forum] doubts (problems?) in DOS calculation In-Reply-To: References: Message-ID: <20120924093545.Horde.mONackKGDPZQYBthJffQxCA@webmail.bath.ac.uk> does scf is not included in optimisation? > > ------------------------------ > > Message: 2 > Date: Wed, 19 Sep 2012 20:57:55 +0800 > From: Yue-Wen Fang > Subject: Re: [Pw_forum] doubts (problems?) in DOS calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > When calculate DOS, you should make a scf calculation first, then nscf, > last is bands and dos. > > 2012/9/19 Davide Tiana > >> Dear all, >> I am trying to calculate DOS and projected DOS for a semiconducting 1D >> hybrid (i.e. metal-organic) polymer. The band gap I found is about >> 0.4. However when I try to calculate DOS I don't find 0 contribution >> at the Fermi level nor a band gap around it. I am in doubt and I think >> something wrong happened (namely I made some errors). How can I check >> that everything is fine and-or explain this behaviour? >> >> By the way here what I've done: >> >> pw optimisation >> pw band calculation >> pw nscf calculation >> dos dos calculation (at first instance I did't make but finding >> something "weird" in the total projwfc I run it to check) >> projwfc projected dos calc >> >> thanks a lot >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > ---- > Yue-Wen Fang > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: From akohlmey at gmail.com Mon Sep 24 11:32:28 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 24 Sep 2012 09:32:28 +0000 Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <272832362.42101.1348452854675.JavaMail.root@z.rochester.edu> References: <505F8617.70206@sissa.it> <272832362.42101.1348452854675.JavaMail.root@z.rochester.edu> Message-ID: <2111222266-1348479151-cardhu_decombobulator_blackberry.rim.net-331047699-@b16.c7.bise7.blackberry> And I venture an educated guess here, but looks toMe that you could save yourself a lot of time and effort with a small number of well picked single point calculations and thus obtained a much better initialnguess. For your system it should be easy enough to pick a cell that is a bit too large and a bit too small and a few in between. Variable cell calculation far from equilibrium always converge very slow. Axel -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: Alexey Akimov Sender: pw_forum-bounces at pwscf.org Date: Sun, 23 Sep 2012 22:14:14 To: PWSCF Forum Reply-To: PWSCF Forum Subject: Re: [Pw_forum] Error in routine scale_h (1) I see. Thank you for the explanation! Alexey ----- Original Message ----- From: "Stefano de Gironcoli" To: "pw forum" Sent: Sunday, September 23, 2012 2:58:47 PM Subject: Re: [Pw_forum] Error in routine scale_h (1) as your cell shrinks the energy cutoff corresponding to your set of plane wave increases and it this exceeds a the maximum values in the precalculated psedopotential table (some 20% higher than the specified ecut by default if i remember correctly) the code stops. You can increase this limit with the cell_factor variable. However if this keeps happening it means that your cell was way too large ! stefano On 09/23/2012 11:42 PM, Alexey Akimov wrote: > my unit cell is not oscillating, but rather shrinking. shouldn't the basis size (number of plane waves) be bigger for larger cell, so the bigger cell would determine the maximal amount of memory for simulation even if the cell contracts? > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Sunday, September 23, 2012 1:19:05 PM > Subject: Re: [Pw_forum] Error in routine scale_h (1) > > > On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > >> If i restart the calculations with the latest (most optimal) >> configuration of the system and the same amount of memory >> allocated, the further optimization can proceed some more time >> (also ~50 - 70 steps) before next crash. > this should not happen, unless your optimization procedure keeps > oscillating between large and > small volumes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From aakimov at z.rochester.edu Mon Sep 24 17:50:10 2012 From: aakimov at z.rochester.edu (Alexey Akimov) Date: Mon, 24 Sep 2012 11:50:10 -0400 (EDT) Subject: [Pw_forum] Error in routine scale_h (1) In-Reply-To: <2111222266-1348479151-cardhu_decombobulator_blackberry.rim.net-331047699-@b16.c7.bise7.blackberry> Message-ID: <1651979242.50469.1348501810788.JavaMail.root@z.rochester.edu> Good point, thank you! Alexey ----- Original Message ----- From: "Axel Kohlmeyer" To: "PWSCF Forum" Sent: Monday, September 24, 2012 2:32:28 AM Subject: Re: [Pw_forum] Error in routine scale_h (1) And I venture an educated guess here, but looks toMe that you could save yourself a lot of time and effort with a small number of well picked single point calculations and thus obtained a much better initialnguess. For your system it should be easy enough to pick a cell that is a bit too large and a bit too small and a few in between. Variable cell calculation far from equilibrium always converge very slow. Axel -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: Alexey Akimov Sender: pw_forum-bounces at pwscf.org Date: Sun, 23 Sep 2012 22:14:14 To: PWSCF Forum Reply-To: PWSCF Forum Subject: Re: [Pw_forum] Error in routine scale_h (1) I see. Thank you for the explanation! Alexey ----- Original Message ----- From: "Stefano de Gironcoli" To: "pw forum" Sent: Sunday, September 23, 2012 2:58:47 PM Subject: Re: [Pw_forum] Error in routine scale_h (1) as your cell shrinks the energy cutoff corresponding to your set of plane wave increases and it this exceeds a the maximum values in the precalculated psedopotential table (some 20% higher than the specified ecut by default if i remember correctly) the code stops. You can increase this limit with the cell_factor variable. However if this keeps happening it means that your cell was way too large ! stefano On 09/23/2012 11:42 PM, Alexey Akimov wrote: > my unit cell is not oscillating, but rather shrinking. shouldn't the basis size (number of plane waves) be bigger for larger cell, so the bigger cell would determine the maximal amount of memory for simulation even if the cell contracts? > > ----- Original Message ----- > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Sunday, September 23, 2012 1:19:05 PM > Subject: Re: [Pw_forum] Error in routine scale_h (1) > > > On Sep 23, 2012, at 16:43 , Alexey Akimov wrote: > >> If i restart the calculations with the latest (most optimal) >> configuration of the system and the same amount of memory >> allocated, the further optimization can proceed some more time >> (also ~50 - 70 steps) before next crash. > this should not happen, unless your optimization procedure keeps > oscillating between large and > small volumes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu _______________________________________________ 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 -- Dr. Alexey V. Akimov Postdoctoral Research Associate Department of Chemistry University of Rochester aakimov at z.rochester.edu From elie.moujaes at hotmail.co.uk Mon Sep 24 19:14:15 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 24 Sep 2012 18:14:15 +0100 Subject: [Pw_forum] QE-5.0.1 Message-ID: Dear All, Can anyone give me the link to where I can download the Quantum-espresso-5.0.01 version? I could not find it on the quantum espresso website -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120924/8c270715/attachment-0001.htm From bamideleibrahim at yahoo.com Mon Sep 24 19:57:17 2012 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Mon, 24 Sep 2012 10:57:17 -0700 (PDT) Subject: [Pw_forum] QE-5.0.1 In-Reply-To: References: Message-ID: <1348509437.26238.YahooMailNeo@web39406.mail.mud.yahoo.com> Here it is http://qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse&frs_package_id=18 but next time unvail your identity in this community. ? --------------------------------------------------------------------------------------------------- Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. --------------------------------------------------------------------------------------------------- ________________________________ From: Elie M To: "pw_forum at pwscf.org" Sent: Monday, September 24, 2012 6:14 PM Subject: [Pw_forum] QE-5.0.1 Dear All, Can anyone give me the link to where I can download the Quantum-espresso-5.0.01 version? I could not find it on the quantum espresso website _______________________________________________ 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/20120924/0489df73/attachment.htm From pchen at ion.chem.utk.edu Mon Sep 24 21:38:43 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 24 Sep 2012 15:38:43 -0400 Subject: [Pw_forum] U of vanadium Message-ID: Dear All, I did LDA+U calculation on Ni3V2O8, and got the U of V (vanadium) -1.7 eV. I am not sure if it is reasonable. I checked the occupation number of vanadium. All d orbitals are filled almost evenly. Whereas, I expected to see only 3 occupied orbitals. I tried to set inital occupation number by starting_ns_eigenvalue. But the results are the same after iterations. Dr. Kulik mentioned that "if 3d and 4s are comparably filled and their energies are close, then 3d and 4s shells should be included directly in the U calculation". So I am wondering if this is the case for vanadium and can QE calculate U with both 3d and 4s shells? Thank you in advance for any help you can provide! spin 1 eigenvalues: 0.441 0.448 0.480 0.505 0.513 eigenvectors: 0.813 0.183 0.000 0.004 0.000 0.012 0.018 0.028 0.211 0.731 0.001 0.001 0.576 0.248 0.174 0.001 0.001 0.394 0.533 0.071 0.174 0.797 0.001 0.004 0.024 occupations: 0.442 0.003 0.002 -0.003 -0.002 0.003 0.509 -0.006 -0.001 0.011 0.002 -0.006 0.492 -0.013 -0.002 -0.003 -0.001 -0.013 0.496 0.001 -0.002 0.011 -0.002 0.001 0.448 -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120924/02a7df81/attachment.htm From jen7182 at hotmail.com Mon Sep 24 22:28:32 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Mon, 24 Sep 2012 16:28:32 -0400 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: References: Message-ID: I have recently installed 5.0.1 and have tried to run a ph.x test-case of the Al system in example 03 (in the PHonon examples) but I'm running into an error in the scf phase of the example. I've run a simple Si scf input which ran without incident so I'm not sure where this is coming from. Input: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './' , wfcdir = './' , pseudo_dir = '/app2/espresso/pseudo/' , prefix = 'al' , / &SYSTEM ibrav = 2, celldm(1) = 7.5, nat = 1, ntyp = 1, ecutwfc = 15.0 , occupations = 'smearing' , degauss = 0.05 , smearing = 'methfessel-paxton' , la2F = .true., / &ELECTRONS conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.98 Al.vbc.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 K_POINTS {automatic} 16 16 16 0 0 0 OUTPUT: Program PWSCF v.5.0.1 starts on 24Sep2012 at 15:48:43 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote.php Parallel version (MPI), running on 32 processors R & G space division: proc/pool = 32 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 Waiting for input... Reading input from standard input Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 3 3 1 25 25 6 Max 4 4 2 29 29 8 Sum 121 121 55 869 869 229 Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found Message from routine sym_rho_init: likely internal error: no G-vectors found bravais-lattice index = 2 lattice parameter (alat) = 7.5000 a.u. unit-cell volume = 105.4688 (a.u.)^3 number of atoms/cell = 1 number of atomic types = 1 number of electrons = 3.00 number of Kohn-Sham states= 6 kinetic-energy cutoff = 15.0000 Ry charge density cutoff = 60.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0) EXX-fraction = 0.00 celldm(1)= 7.500000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of alat) a(1) = ( -0.500000 0.000000 0.500000 ) a(2) = ( 0.000000 0.500000 0.500000 ) a(3) = ( -0.500000 0.500000 0.000000 ) reciprocal axes: (cart. coord. in units 2 pi/alat) b(1) = ( -1.000000 -1.000000 1.000000 ) b(2) = ( 1.000000 1.000000 1.000000 ) b(3) = ( -1.000000 1.000000 -1.000000 ) PseudoPot. # 1 for Al read from file: /app2/espresso/pseudo/Al.vbc.UPF MD5 check sum: c34c8b369e81ee50c191f4345b5f621b Pseudo is Norm-conserving, Zval = 3.0 Generated by new atomic code, or converted to UPF format Using radial grid of 171 points, 2 beta functions with: l(1) = 0 l(2) = 1 atomic species valence mass pseudopotential Al 3.00 26.98000 Al( 1.00) 48 Sym. Ops., with inversion, found Cartesian axes site n. atom positions (alat units) 1 Al tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) number of k points= 145 Methfessel-Paxton smearing, width (Ry)= 0.0500 Number of k-points >= 100: set verbosity='high' to print them. Dense grid: 869 G-vectors FFT dimensions: ( 15, 15, 15) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.00 Mb ( 6, 6) NL pseudopotentials 0.00 Mb ( 6, 4) Each V/rho on FFT grid 0.00 Mb ( 225) Each G-vector array 0.00 Mb ( 26) G-vector shells 0.00 Mb ( 18) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 0.00 Mb ( 6, 24) Each subspace H/S matrix 0.01 Mb ( 24, 24) Each matrix 0.00 Mb ( 4, 6) Arrays for rho mixing 0.03 Mb ( 225, 8) writing wfc files to a dedicated directory Initial potential from superposition of free atoms starting charge 2.99794, renormalised to 3.00000 Starting wfc are 9 randomized atomic wfcs total cpu time spent up to now is 0.3 secs per-process dynamical memory: 0.8 Mb Self-consistent Calculation iteration # 1 ecut= 15.00 Ry beta=0.70 Davidson diagonalization with overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Error in routine cdiaghg (31): S matrix not positive definite %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Application 1984917 exit codes: 134 Application 1984917 resources: utime ~1s, stime ~1s Thank you for your time, J. Wohlwend Universal Technology Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120924/bd4e52e5/attachment-0001.htm From pchen at ion.chem.utk.edu Tue Sep 25 03:53:28 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 24 Sep 2012 21:53:28 -0400 Subject: [Pw_forum] U calculation with noncollinear spins Message-ID: Dear All, It looks like the noncollinear calculation only supports lda_plus_u_kind=1 currently, and it can not be used with Hubbard_alpha to calculate U. So is there a way to calculate U for lda_plus_u_kind=1 or will noncollinear calculation support lda_plus_u_kind=0 in the near future? -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120924/b4794acc/attachment.htm From matteo at umn.edu Tue Sep 25 05:08:54 2012 From: matteo at umn.edu (Matteo Cococcioni) Date: Mon, 24 Sep 2012 22:08:54 -0500 Subject: [Pw_forum] U calculation with noncollinear spins In-Reply-To: References: Message-ID: Dear Peng, I'm not expert of the non collinear implementation but I would expect the U to not depend strongly on the orientation of localized magnetic moments. So, at first approximation, you could use the one you compute the usual way, from collinear magnetism. HTH, Matteo On Mon, Sep 24, 2012 at 8:53 PM, Peng Chen wrote: > Dear All, > > It looks like the noncollinear calculation only supports lda_plus_u_kind=1 > currently, and it can not be used with Hubbard_alpha to calculate U. So is > there a way to calculate U for lda_plus_u_kind=1 or will noncollinear > calculation support lda_plus_u_kind=0 in the near future? > > -- > Best Regards. > Peng > > _______________________________________________ > 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 pchen at ion.chem.utk.edu Tue Sep 25 05:37:47 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Mon, 24 Sep 2012 23:37:47 -0400 Subject: [Pw_forum] U calculation with noncollinear spins In-Reply-To: References: Message-ID: Dear Dr. Matteo, Thanks for your reply! That is very useful. I will try and see what is the result. On Mon, Sep 24, 2012 at 11:08 PM, Matteo Cococcioni wrote: > Dear Peng, > > I'm not expert of the non collinear implementation but I would expect > the U to not depend strongly on the orientation of localized magnetic > moments. So, at first approximation, you could use the one you compute > the usual way, from collinear magnetism. > > HTH, > > Matteo > > > > On Mon, Sep 24, 2012 at 8:53 PM, Peng Chen wrote: > > Dear All, > > > > It looks like the noncollinear calculation only supports > lda_plus_u_kind=1 > > currently, and it can not be used with Hubbard_alpha to calculate U. So > is > > there a way to calculate U for lda_plus_u_kind=1 or will noncollinear > > calculation support lda_plus_u_kind=0 in the near future? > > > > -- > > Best Regards. > > Peng > > > > _______________________________________________ > > 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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120924/b8f116fc/attachment.htm From giannozz at democritos.it Tue Sep 25 08:18:00 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 Sep 2012 08:18:00 +0200 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: References: Message-ID: <13FC6B14-1DE4-49B2-89FF-BE1BCCFB97C5@democritos.it> On Sep 24, 2012, at 22:28 , Jennifer Wohlwend wrote: > Parallel version (MPI), running on 32 processors > R & G space division: proc/pool = 32 32 processors for crystal Al? wow! As a rule, parallellism should work even for too many processors, but if you push the code into extreme regions, it may still fail. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From 1009ukumar at gmail.com Tue Sep 25 10:00:26 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Tue, 25 Sep 2012 13:30:26 +0530 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: References: Message-ID: Hi, In your output, i noticed Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0) > i think it should be (1100) not (11000)? regards, sk ========================================== S. Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120925/509d99ff/attachment.htm From degironc at sissa.it Tue Sep 25 10:10:18 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 25 Sep 2012 10:10:18 +0200 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: References: Message-ID: <506166EA.2040308@sissa.it> (1 1 0 0 0) is fine, or at least consistent with SLA PZ recently a new level of XC complexity has been added with the van der Waals explicitely non local functionals... if this term is absent the fifth digit is 0 stefano On 09/25/2012 10:00 AM, Sonu Kumar wrote: > Hi, > > In your output, i noticed > > Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0) > i think it should be (1100) not (11000)? > > > regards, > sk > ========================================== > S. Kumar > Phd Student,Physics Department > Indian Institute of Technology ,Delhi-110016, India > web:-http://www.iitd.ac.in/ > ========================================== > > > > _______________________________________________ > 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/20120925/aab92b8c/attachment.htm From kajalmh18 at gmail.com Tue Sep 25 12:37:03 2012 From: kajalmh18 at gmail.com (Kajal Jindal) Date: Tue, 25 Sep 2012 16:07:03 +0530 Subject: [Pw_forum] Error while parsing atomic positions Message-ID: Hi, I am trying to do the scf calculation on unit cell GaAs. But i am continously observing an error "Error while parsing atomic positions" while running it. I have checked the program several times but still not able to troubleshoot. I am attaching my input and output file result along. *input file* &control calculation='scf' restart_mode='from_scratch' prefix='GaAs' wf_collect=.true., pseudo_dir = '/root/pseudo', outdir='/root/poonamGaAs/temp', / &system ibrav=2, nat=10, ntyp= 2,celldm(1) = 10.20, ecutwfc = 25.0,ecutrho=300, occupations ='fixed', / &electrons mixing_beta = 0.1 mixing_mode = 'plain' conv_thr = 1.0e-5 diagonalization = 'david' / ATOMIC_SPECIES Ga 69.72 Ga.pbe-n-van.UPF As 74.92 As.pbe-n-van.UPF ATOMIC_POSITIONS {crystal} Ga 0.O 0.0 1.0 Ga 1.0 0.0 0.0 Ga 0.5 0.0 0.5 As 0.75 0.25 0.75 As 0.25 0.25 0.25 Ga 0.5 0.5 1.0 Ga 1.0 0.5 0.5 As 0.25 0.75 0.75 As 0.75 0.75 0.25 Ga 0.0 1.0 0.0 K_POINTS {automatic} 4 4 2 0 0 0 *Output file is *[eval_infix.c] A parsing error occurred helper string: 0.O error code: Error: invalid token: O Program PWSCF v.4.3.1 starts on 25Sep2012 at 15:39:46 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO 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 Waiting for input... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from card_atomic_positions : error # 1 Error while parsing atomic position card. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I have tried running this file with all the versions of quantum espresso but error is same.. I will be highly thankful if somebody can give some suggestion. Thanks and Regards, Kajal Jindal University of Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120925/dc5d721b/attachment.htm From baroni at sissa.it Tue Sep 25 12:47:38 2012 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 25 Sep 2012 12:47:38 +0200 Subject: [Pw_forum] Error while parsing atomic positions In-Reply-To: References: Message-ID: <2238AD15-AB9B-45B0-9B08-283AD16F20DD@sissa.it> On Sep 25, 2012, at 12:37 PM, Kajal Jindal wrote: > Hi, > > I am trying to do the scf calculation on unit cell GaAs. But i am continously observing an error "Error while parsing atomic positions" while running it. I have checked the program several times but still not able to troubleshoot. I am attaching my input and output file result along. > > input file > > &control > calculation='scf' > restart_mode='from_scratch' > prefix='GaAs' > wf_collect=.true., > pseudo_dir = '/root/pseudo', > outdir='/root/poonamGaAs/temp', > > / > &system > ibrav=2, nat=10, ntyp= 2,celldm(1) = 10.20, > ecutwfc = 25.0,ecutrho=300, occupations ='fixed', > > / > &electrons > mixing_beta = 0.1 > mixing_mode = 'plain' > conv_thr = 1.0e-5 > diagonalization = 'david' > / > > ATOMIC_SPECIES > Ga 69.72 Ga.pbe-n-van.UPF > As 74.92 As.pbe-n-van.UPF > ATOMIC_POSITIONS {crystal} > Ga 0.O 0.0 1.0 this is an "O" (like Omar), not a "0" (zero) 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120925/004fca9b/attachment.htm From 1009ukumar at gmail.com Tue Sep 25 13:16:26 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Tue, 25 Sep 2012 16:46:26 +0530 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: <506166EA.2040308@sissa.it> References: <506166EA.2040308@sissa.it> Message-ID: Thank you Prof. Stefano de Gironcoli for this information. But, the confusion arose because there was not "character" keyword corresponding to vander Waals functional, like we have SLA, PZ, NOGX, NOGC for exchange, correlation terms ....etc. with regards, SK ========================================== S. Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== On Tue, Sep 25, 2012 at 1:40 PM, Stefano de Gironcoli wrote: > (1 1 0 0 0) is fine, or at least consistent with SLA PZ > recently a new level of XC complexity has been added with the van der > Waals explicitely non local functionals... if this term is absent the fifth > digit is 0 > > stefano > > On 09/25/2012 10:00 AM, Sonu Kumar wrote: > > Hi, > > In your output, i noticed > > Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0) > > i think it should be (1100) not (11000)? > > > regards, > sk > ========================================== > S. Kumar > Phd Student,Physics Department > Indian Institute of Technology ,Delhi-110016, India > web:-http://www.iitd.ac.in/ > ========================================== > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://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/20120925/22d9eedc/attachment-0001.htm From eariel99 at gmail.com Tue Sep 25 13:44:43 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 25 Sep 2012 13:44:43 +0200 Subject: [Pw_forum] Error while parsing atomic positions Message-ID: As S. Baroni noticed with better aye than me, "O" is different from "0", but also you have set too many atoms positions are equivalent due to translational symmetry. Positions (0,0,0), (1,0,0), (0,1,0), etc are the same. Also, with ibrav=2, you need to set only the positions of ONE Ga and ONE As in the primitive unit cell, and also nat=2. ATOMIC_POSITIONS {crystal} Ga 0.O 0.0 1.0 Ga 1.0 0.0 0.0 Ga 0.5 0.0 0.5 As 0.75 0.25 0.75 As 0.25 0.25 0.25 Ga 0.5 0.5 1.0 Ga 1.0 0.5 0.5 As 0.25 0.75 0.75 As 0.75 0.75 0.25 Ga 0.0 1.0 0.0 ---------- Mensaje reenviado ---------- From: Kajal Jindal To: PWSCF Forum Cc: Date: Tue, 25 Sep 2012 16:07:03 +0530 Subject: [Pw_forum] Error while parsing atomic positions Hi, I am trying to do the scf calculation on unit cell GaAs. But i am continously observing an error "Error while parsing atomic positions" while running it. I have checked the program several times but still not able to troubleshoot. I am attaching my input and output file result along. *input file* &control calculation='scf' restart_mode='from_scratch' prefix='GaAs' wf_collect=.true., pseudo_dir = '/root/pseudo', outdir='/root/poonamGaAs/temp', / &system ibrav=2, nat=10, ntyp= 2,celldm(1) = 10.20, ecutwfc = 25.0,ecutrho=300, occupations ='fixed', / &electrons mixing_beta = 0.1 mixing_mode = 'plain' conv_thr = 1.0e-5 diagonalization = 'david' / ATOMIC_SPECIES Ga 69.72 Ga.pbe-n-van.UPF As 74.92 As.pbe-n-van.UPF ATOMIC_POSITIONS {crystal} Ga 0.O 0.0 1.0 Ga 1.0 0.0 0.0 Ga 0.5 0.0 0.5 As 0.75 0.25 0.75 As 0.25 0.25 0.25 Ga 0.5 0.5 1.0 Ga 1.0 0.5 0.5 As 0.25 0.75 0.75 As 0.75 0.75 0.25 Ga 0.0 1.0 0.0 K_POINTS {automatic} 4 4 2 0 0 0 -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120925/79fa37e4/attachment.htm From akohlmey at gmail.com Tue Sep 25 13:52:50 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 25 Sep 2012 11:52:50 +0000 Subject: [Pw_forum] Error while parsing atomic positions In-Reply-To: References: Message-ID: <853442096-1348574017-cardhu_decombobulator_blackberry.rim.net-865875493-@b16.c7.bise7.blackberry> O vs 0 is the reason why smart people use a font where the zero has a slash added. No eagle eye needed. Same goes for other similar looking characters. Axel. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: Eduardo Ariel Menendez Proupin Sender: pw_forum-bounces at pwscf.org Date: Tue, 25 Sep 2012 13:44:43 To: Reply-To: PWSCF Forum Subject: Re: [Pw_forum] Error while parsing atomic positions _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From jen7182 at hotmail.com Tue Sep 25 15:07:19 2012 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Tue, 25 Sep 2012 09:07:19 -0400 Subject: [Pw_forum] Error in routine cdiaghg S matrix not positive definite In-Reply-To: <13FC6B14-1DE4-49B2-89FF-BE1BCCFB97C5@democritos.it> References: , , <13FC6B14-1DE4-49B2-89FF-BE1BCCFB97C5@democritos.it> Message-ID: Thank you! That was the problem, I reduced the number of processors and everything finished. ~J Wohlwend UTC > From: giannozz at democritos.it > Date: Tue, 25 Sep 2012 08:18:00 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Error in routine cdiaghg S matrix not positive definite > > > On Sep 24, 2012, at 22:28 , Jennifer Wohlwend wrote: > > > Parallel version (MPI), running on 32 processors > > R & G space division: proc/pool = 32 > > 32 processors for crystal Al? wow! > > As a rule, parallellism should work even for too many processors, > but if you push the code into extreme regions, it may still fail. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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/20120925/8ec77e2a/attachment.htm From yzunt at yahoo.com Wed Sep 26 11:32:42 2012 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Wed, 26 Sep 2012 02:32:42 -0700 (PDT) Subject: [Pw_forum] relax issue In-Reply-To: References: Message-ID: <1348651962.7286.YahooMailNeo@web111209.mail.gq1.yahoo.com> Hi, Can some one help explain the meaning of the erro stated below: ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? from calbec : error #???????? 1 ???? size mismatch ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? stopping ... Am trying to relax Fe-structure comprising 32 C and dimers. Thank you Yusuf ________________________________ From: Paolo Giannozzi To: PWSCF Forum Sent: Saturday, September 22, 2012 8:00 PM Subject: Re: [Pw_forum] SYMMETRY REFERENCE On Sep 21, 2012, at 22:41 , Caloma Trumica wrote: > I found it is difficult to understand some routine like "set_irr" you are not the only one: the implementation of symmetries in the phonon code is rather complex. You do not need to understand everything, though, unless you want to modify the code. Why are you interested in that part of the code? > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. 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/20120926/eeda082c/attachment.htm From giannozz at democritos.it Wed Sep 26 11:45:23 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 Sep 2012 11:45:23 +0200 Subject: [Pw_forum] relax issue In-Reply-To: <1348651962.7286.YahooMailNeo@web111209.mail.gq1.yahoo.com> References: <1348651962.7286.YahooMailNeo@web111209.mail.gq1.yahoo.com> Message-ID: On Sep 26, 2012, at 11:32 , Yusuf Zuntu wrote: > from calbec : error # 1 > size mismatch this is an internal check that should never give an error. If the error is reproducible on a different machine, please provide the details of what you did: which code and which version, input data, serial or parallel and how parallel, etc. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yzunt at yahoo.com Wed Sep 26 12:15:32 2012 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT) Subject: [Pw_forum] ecutwfc convergence In-Reply-To: <2238AD15-AB9B-45B0-9B08-283AD16F20DD@sissa.it> References: <2238AD15-AB9B-45B0-9B08-283AD16F20DD@sissa.it> Message-ID: <1348654532.82296.YahooMailNeo@web111211.mail.gq1.yahoo.com> Hi, I need clarification on kinetic energy cutoff. I have a system comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in? convergence w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the unit cell. Thank you for anticipated reply. Yusuf ________________________________ From: Stefano Baroni To: PWSCF Forum Sent: Tuesday, September 25, 2012 6:47 PM Subject: Re: [Pw_forum] Error while parsing atomic positions On Sep 25, 2012, at 12:37 PM, Kajal Jindal wrote: Hi, > >I am trying to do the scf calculation on unit cell GaAs. But i am continously observing an error "Error while parsing atomic positions" while running it. I have checked the program several times but still not able to troubleshoot. I am attaching my input and output file result along. > >input file > >&control >??? calculation='scf' >??? restart_mode='from_scratch' >??? prefix='GaAs' >??? wf_collect=.true., >??? pseudo_dir = '/root/pseudo', >??? outdir='/root/poonamGaAs/temp', >??? >?/ >?&system >??? ibrav=2, nat=10, ntyp= 2,celldm(1) = 10.20, >??? ecutwfc = 25.0,ecutrho=300, occupations ='fixed',? >? >?/ >?&electrons >??? mixing_beta = 0.1 >??? mixing_mode = 'plain'? >??? conv_thr =? 1.0e-5 >??? diagonalization = 'david'?? >?/ >? >ATOMIC_SPECIES >Ga? 69.72? Ga.pbe-n-van.UPF? >As? 74.92? As.pbe-n-van.UPF >ATOMIC_POSITIONS {crystal} >Ga 0.O? 0.0? 1.0 > this is an "O" (like Omar), not a "0" (zero) 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 _______________________________________________ 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/20120926/7f9a02fe/attachment.htm From eariel99 at gmail.com Wed Sep 26 13:09:19 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 26 Sep 2012 13:09:19 +0200 Subject: [Pw_forum] functionals and pseudopotentials for bandgap. Message-ID: Dear fellows, I am swimming (but not diving yet) in the sea of hybrid functionals. I need to estimate bandgap corrections of a crystal made of benzene-like molecules. After some googling, I am almost at the same place, but looking to the HSE functional, and I tested the HSE and the TPSS with the example of silicon. I request a few advise, these are my dubts 1) Does the metaGGA functional TPSS improves the bandgap ? 2) What pseudopotential (i.e. what functional) can be used for a calculation with HSE? 3) What kind of pseudoptential are the CPBE*nlcc.RRKJ3 in EXX_example 4) I would appreciate a recommendation of a published benchmark on the performance of different functionals for the gap. Thanks -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/a8985300/attachment-0001.htm From eariel99 at gmail.com Wed Sep 26 13:18:25 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 26 Sep 2012 13:18:25 +0200 Subject: [Pw_forum] ecutwfc convergence Message-ID: Dear Yusufm ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used for the atoms in the molecule or the crystal. If your molecule is C32 and have no other elements, you can make tests with a C2 (which does not exists, I guess), and the cutoffs for C32. Anyway, if your are going to calculate something that it is not the total energy or the DOS, let's say, the phonons, or the Raman spectrum, it is reasonable that you test the effect of the cutoff first on C2 and then on C32. ---------- Mensaje reenviado ---------- From: Yusuf Zuntu To: PWSCF Forum Cc: Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT) Subject: [Pw_forum] ecutwfc convergence Hi, I need clarification on kinetic energy cutoff. I have a system comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in convergence w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the unit cell. Thank you for anticipated reply. Yusuf -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/ebeb7ceb/attachment.htm From yzunt at yahoo.com Wed Sep 26 13:51:08 2012 From: yzunt at yahoo.com (Yusuf Zuntu) Date: Wed, 26 Sep 2012 04:51:08 -0700 (PDT) Subject: [Pw_forum] ecutwfc convergence In-Reply-To: References: Message-ID: <1348660268.822.YahooMailNeo@web111214.mail.gq1.yahoo.com> Dear Manasaje The system is graphene with 32 carbon atoms. The cutoff is not specified in the pseudo and I need it before proceeding to other SCF and nscf calculations and believe, cutoff is a property of an atom in question. So can I still go ahead with the atoms in the unit cell. Thank you for your quick response Yusuf ________________________________ From: Eduardo Ariel Menendez Proupin To: pw_forum at pwscf.org Sent: Wednesday, September 26, 2012 7:18 PM Subject: Re: [Pw_forum] ecutwfc convergence Dear Yusufm? ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used for the atoms in the molecule or the crystal. If your molecule is C32 and have no other elements, you can make tests with a C2 (which does not exists, I guess), and the cutoffs for C32.? Anyway, if your are going to calculate something that it is not the total energy or the DOS, let's say, the phonons, or the Raman spectrum, it is reasonable that you test the effect of the cutoff first on C2 and then on C32.? ---------- Mensaje reenviado ---------- From:?Yusuf Zuntu To:?PWSCF Forum Cc:? Date:?Wed, 26 Sep 2012 03:15:32 -0700 (PDT) Subject:?[Pw_forum] ecutwfc convergence Hi, I need clarification on kinetic energy cutoff. I have a system comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in? convergence w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the unit cell. Thank you for anticipated reply. Yusuf _______________________________________________ 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/20120926/9ffec4c4/attachment.htm From eariel99 at gmail.com Wed Sep 26 14:44:30 2012 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 26 Sep 2012 14:44:30 +0200 Subject: [Pw_forum] ecutwfc convergence Message-ID: Dear Yusuf The cutoff depends on the pseudopotential that you use, not just on the atom. Different pseudopotentials for the same atoms have different cutoff. Also, some properties requiere higher cutoffs than others. For example, forces and relative energies need lower cutoff than total energy and stress. Using higher values does not harm, just take longer time and more computer resources. Some programs include recommended cutoffs in the pseudopotential, but the user is still responsible of testing it. If you want a starting parameter for graphene, use C.pz-vbc.UPF with ecutwfc = 60.0 , or C.pbe-rrkjus.UPF with ecutwfc = 30.0 and ecutrho = 180.0 the above work reasonably well to relax the structures with fixed cell, and to get the bands and DOS. I fou want to calculate elastic properties or LDA+U or PBE+U, or calculate conductance, etc, etc, these cutoffs may be too low. Yo need to do tests increasing the values until you see no change in the property that you want to calculate. If you plan to adsorb other atoms (e.g. oxygen) on the graphene, then determine cutoffs that are valid for the full system and do all the calculations with the same parameters. Dear Manasaje The system is graphene with 32 carbon atoms. The cutoff is not specified in the pseudo and I need it before proceeding to other SCF and nscf calculations and believe, cutoff is a property of an atom in question. So can I still go ahead with the atoms in the unit cell. Thank you for your quick response Yusuf ________________________________ From: Eduardo Ariel Menendez Proupin > To: pw_forum at pwscf.org Sent: Wednesday, September 26, 2012 7:18 PM Subject: Re: [Pw_forum] ecutwfc convergence Dear Yusufm ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used for the atoms in the molecule or the crystal. If your molecule is C32 and have no other elements, you can make tests with a C2 (which does not exists, I guess), and the cutoffs for C32. Anyway, if your are going to calculate something that it is not the total energy or the DOS, let's say, the phonons, or the Raman spectrum, it is reasonable that you test the effect of the cutoff first on C2 and then on C32. ---------- Mensaje reenviado ---------- From: Yusuf Zuntu > To: PWSCF Forum > Cc: Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT) Subject: [Pw_forum] ecutwfc convergence Hi, I need clarification on kinetic energy cutoff. I have a system comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in convergence w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the unit cell. Thank you for anticipated reply. Yusuf -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/ebaa437a/attachment.htm From annetindele at yahoo.fr Wed Sep 26 14:45:57 2012 From: annetindele at yahoo.fr (anne etindele) Date: Wed, 26 Sep 2012 13:45:57 +0100 (BST) Subject: [Pw_forum] polarizability of metals using ph.x Message-ID: <1348663557.44488.YahooMailNeo@web133003.mail.ir2.yahoo.com> Dear all I am trying to determine the frequency dependent polarisability of metals like Pt and Al using ph.x code. Here is the input I made for the case of Pt: phonons of pt at Gamma ?&inputph ? tr2_ph=1.0d-15, ? trans=.false., ? fpol=.true., ? amass(1)=195.078, ? prefix='Pt', ? outdir='$TMP_DIR' ? fildyn='pt.dynG', ?/ 0.0 0.0 0.0 FREQUENCIES ?4 ?0.5d0 ?1.0d0 ?1.5d0 ?5.0d0 In the output file I don't have any value of polarizability. Do I need to modify or to add another parameter? ? Anne Justine ETINDELE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/365044dc/attachment-0001.htm From flima at if.usp.br Wed Sep 26 17:23:22 2012 From: flima at if.usp.br (Filipe Camargo Dalmatti Alves Lima) Date: Wed, 26 Sep 2012 12:23:22 -0300 Subject: [Pw_forum] ecutwfc convergence In-Reply-To: References: Message-ID: Dear Yusuf, I agree with everyone has said to you, but I just want to comment: "When the cutoff is enough?" I think this is your question, right? The best way to learn it is by testing your system with different parameters. For example: if you think that you need the best total energy description you should create a series of test varying the cutoff and testing the Total Energy. So, For a system you will run X simulations using different cutoffs 20 ry (200 ry), 25 ry (250 ry), 30 (300), 40 (400), 60 (600), ... (Remember charge density description (ecutrho) should change as you increase the kinect energy cutoff) For instance, lets pretend you obtained the following total energies: using 20 Ry = -20 eV using 25 Ry = -22 eV using 30 Ry = -22.501 eV using 40 Ry = -22.623 eV using 60 Ry = -22.625 eV In a perfect world as much ecutwfc is higher better would be your result. (if it does not happening, probably you are doing something wrong, like a poor k point description, etc) But do you need the best possible? In my example, there is a 2 eV difference by between 20 Ry and 25 Ry, so, it might not be a good idea use 20 Ry. However, comparing 30 and 40 ry, you have ~0.1 eV difference. Is this enough for the property that you are looking for? In some cases it could be enough, in others it won't. If you are looking at conformational changes that are around 0.5 eV probably you will need to increase your ecutwfc. You can use this procedure in all properties that you are interested in. In DOS case, you might compare if the DOS are changing as the cutoff increases. In summary: - The parameters that you choose are not changing the physics of your results. - They have a good relationship between correctness/computational time. - They are reasonable when you compare your work with the literature. - Your tests should be (relatively) fast since you don't want waste your machine time. That's it, I hope it will help you. Also, I hope I didn't make any mistake in my comment! :) Best regards, -- _________________________________________ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones: (11) 3091-6881 (USP) (11) 8249-4628 (TIM) On Wed, Sep 26, 2012 at 9:44 AM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Dear Yusuf > The cutoff depends on the pseudopotential that you use, not just on the > atom. Different pseudopotentials for the same atoms have different cutoff. > Also, some properties requiere higher cutoffs than others. For example, > forces and relative energies need lower cutoff than total energy and > stress. Using higher values does not harm, just take longer time and more > computer resources. Some programs include recommended cutoffs in the > pseudopotential, but the user is still responsible of testing it. > > If you want a starting parameter for graphene, use > C.pz-vbc.UPF with ecutwfc = 60.0 , > or > C.pbe-rrkjus.UPF with ecutwfc = 30.0 and ecutrho = 180.0 > > > the above work reasonably well to relax the structures with fixed cell, and to get the bands and DOS. I fou want to calculate elastic properties or LDA+U or PBE+U, or calculate conductance, etc, etc, these cutoffs may be too low. Yo need to do tests increasing the values until you see no change in the property that you want to calculate. > > If you plan to adsorb other atoms (e.g. oxygen) on the graphene, then determine cutoffs that are valid for the full system and do all the calculations with the same parameters. > > > > Dear Manasaje > > The system is graphene with 32 carbon atoms. The cutoff is not specified in the pseudo and I need it before proceeding to other SCF and nscf calculations and believe, cutoff is a property of an atom in question. So can I still go ahead with the atoms in the unit cell. Thank you for your quick response > Yusuf > > > ______________________________ > __ > From: Eduardo Ariel Menendez Proupin > > To: pw_forum at pwscf.org > Sent: Wednesday, September 26, 2012 7:18 PM > Subject: Re: [Pw_forum] ecutwfc convergence > > > Dear Yusufm > > ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used for the atoms in the molecule or the crystal. If your molecule is C32 and have no other elements, you can make tests with a C2 (which does not exists, I guess), and the cutoffs for C32. > > Anyway, if your are going to calculate something that it is not the total energy or the DOS, let's say, the phonons, or the Raman spectrum, it is reasonable that you test the effect of the cutoff first on C2 and then on C32. > ---------- Mensaje reenviado ---------- > From: Yusuf Zuntu > > To: PWSCF Forum > > Cc: > Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT) > Subject: [Pw_forum] ecutwfc convergence > > Hi, > I need clarification on kinetic energy cutoff. I have a system comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in convergence w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the unit cell. > Thank you for anticipated reply. > Yusuf > > -- > > > Eduardo Menendez Proupin > Departamento de Qu?mica Fisica Aplicada > Facultad de Ciencias > Universidad Aut?noma de Madrid > 28049 Madrid, Spain > Phone: +34 91 497 6706 > > On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad > de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez > > "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez > padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, > pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n > que le es otorgada. Pero la grandeza del hombre est? precisamente en querer > mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay > grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, > inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, > reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro > de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar > su grandeza, su m?xima medida en el Reino de este Mundo*". > Alejo Carpentier, El reino de este mundo, (1949). > > "...man never knows for who he suffers and waits. He suffers and waits and > works for peoples he will never meet, and who at the same time will suffer > and wait and work for others who will also not be happy, as man always > desires a happiness that is beyond the lot that he is given. But the > greatness of man is precisely in wanting to improve what he is. In > assigning himself Tasks. In the Kingdom of Heaven there is no greatness to > conquer, for everything there is an established hierarchy, the unknown is > unobscured, existence is without end, sacrifice, rest, and delight are > impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful > within his misery, capable of loving in the middle of calamity, man can > only find his greatness, his full self-realization, in the Kingdom of this > World." - Alejo Carpentier > > > _______________________________________________ > 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/20120926/880a0790/attachment.htm From tianlan at caltech.edu Wed Sep 26 19:19:14 2012 From: tianlan at caltech.edu (Tian Lan) Date: Wed, 26 Sep 2012 10:19:14 -0700 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> Message-ID: Hi sir, Thank you. I am trying to keep every setup the same in CP.x and Pw.x as you suggested. You mentioned that the k-points should be the same. But I cannot find the input card like &K_Points in cp.x, how could I control the k sampling? I only find the charge meshing commands like nr1...in &System. So I guess cp.x used some default setup or some different algorithm in MD calculation? Best, Tian On Fri, Sep 14, 2012 at 7:30 AM, Paolo Giannozzi wrote: > On Thu, 2012-09-13 at 15:36 -0700, Tian Lan wrote: > > > But it seems that the energies that both codes obtained agree well. I > > pasted the results in the following. The first one is the result from > > vc-relax operated on one unit cell, the total energy is -358.1 Ry, > > this is very close to my original setup with scf calculation. The > > second one is from cp.x operated on 2 by 2 by 2 supercell, with fixed > > atom positions(ion and cell_dynamics are set to 'none'), the energy is > > -1410 au==-2820 Ry. I don't know whether this is a big difference > > the energy is -1431.80272 Ha or so, i.e. -1431.80272/8 Ha per cell, > i.e. 357.95Ry. Close (358.097) but not very close. Note however that > you need to compare equivalent results, i.e. same cell, same k-points, > or a cell and a supercell but with equivalent k-points. Also note > that the treatment of the augmentation charge via the "small boxes" > requires some testing in order to find a suitable value for input > variables nr1b, nr2b, nr3b. The resulting pressure may also change > quite a bit. > > > I don't quite get your point about the default positions of atoms in > > pw and cp. In both codes, I used 'crystal' > > perfect: it is of no concern for you. If you do not specify anything, > cp will assume borh radii and pw lattice parameters, or something > like this, as explained in the documentation > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 138-78, Pasadena, CA, 91125 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/4272621e/attachment.htm From pandey.bramha at gmail.com Wed Sep 26 19:29:44 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Wed, 26 Sep 2012 22:59:44 +0530 Subject: [Pw_forum] 'hse' in pw run can not converges In-Reply-To: <201209241027.01507.giuseppe.mattioli@ism.cnr.it> References: <201209211615.18741.giuseppe.mattioli@ism.cnr.it> <201209241027.01507.giuseppe.mattioli@ism.cnr.it> Message-ID: Thank you Prof. Giuseppe, and Prof. Paolo, i will try from MT pseudopotential and try to built it myself. On Mon, Sep 24, 2012 at 1:57 PM, Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it> wrote: > > Dear Brahma > I'm afraid I'm not. I've never employed Bachelet-Hamann-Schluter > pseudopotentials in my calculations > and I do not know if there are still codes that generate them. Why do not > you try with Martins- > Troullier pseudopotentials? There is plenty of them in the ps library, and > you can build your own > pseudopotential with ld1.x > Yours > Giuseppe > > On Friday 21 September 2012 19:43:28 Bramha Pandey wrote: > > Thank you very much Dear Mattioli Sir , it works. > > > > Can please give a clue to obtained the Al.pz-bhs.UPF (Al LDA with bhs > > funtionals essentially NormConversing) pseudopotential as i am very poor > to > > generate it myself and not obtained it in pslibrary. > > it's a very bad habit i know but i have no option except taking help at > > this stage for my research. > > > > thanks in advanced for your kind help. > > > > On Fri, Sep 21, 2012 at 7:45 PM, Giuseppe Mattioli < > > > > giuseppe.mattioli at ism.cnr.it> wrote: > > > Dear Brahma > > > > > > > &ELECTRONS > > > > > > > > conv_thr = 1.0d-11 , > > > > > > > > / > > > > > > You require a very strict convergence threshold on wfcs... > > > 1.0d-7 may be sufficient for scf calculations. > > > > > > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > > > > > You should check the convergence of such mesh. The above 1 1 1 could be > > > quite poor. > > > > > > HTH > > > > > > Giuseppe > > > > > > On Friday 21 September 2012 15:42:03 Bramha Pandey wrote: > > > > Dear Developers and Users, > > > > I was calculating the band structure of ZB-InN using 'hse' hybrid > > > > functional. It gives the reasonable band gap opening but the run was > > > > goes on and can't stop. Here i am giving some sort of it's output. > > > > Firstly sorry for giving long output data...but have no choice... > > > > Please give me a ray of hope to converges of hse calculation in pw.x. > > > > input.... > > > > > > > > &control > > > > > > > > calculation = 'scf' > > > > restart_mode='restart', > > > > pseudo_dir = '/pseudo/' , > > > > outdir='/tmp/' , > > > > prefix = 'innexx' , > > > > tprnfor = .true. , > > > > > > > > / > > > > > > > > &SYSTEM > > > > > > > > ibrav = 2, > > > > > > > > celldm(1) = 9.90, > > > > > > > > nat = 2, > > > > > > > > ntyp = 2, > > > > > > > > nbnd = 8, > > > > > > > > ecutwfc = 130, > > > > > > > > input_dft = 'hse', > > > > > > > > nqx1 = 1, nqx2 = 1, nqx3 = 1, > > > > x_gamma_extrapolation = .TRUE., > > > > > > > > / > > > > &ELECTRONS > > > > > > > > conv_thr = 1.0d-11 , > > > > > > > > mixing_beta = 0.7 , > > > > > > > > / > > > > > > > > ATOMIC_SPECIES > > > > > > > > In 114.81400 In.pz-bhs.UPF > > > > > > > > N 14.01000 N.pz-vbc.UPF > > > > > > > > ATOMIC_POSITIONS alat > > > > > > > > In 0.000000000 0.000000000 0.000000000 > > > > > > > > N 0.250000000 0.250000000 0.250000000 > > > > > > > > K_POINTS > > > > 36 > > > > > > > > 0.5 0.5 0.5 1 > > > > > > > > .. > > > > .. > > > > ... > > > > Output, At k= 0 0 0 points only.. > > > > > > > > k = 0.0000 0.0000 0.0000 ( 5985 PWs) bands (ev): > > > > -10.0435 2.6536 2.8935 2.8935 2.8935 11.6834 11.6834 > > > > > > 11.6834 > > > > > > > highest occupied, lowest unoccupied level (ev): 2.8935 > > > > 2.8935 EXX: now go back to refine exchange calculation > > > > > > > > -2.4962685539301832 > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4312 4.4034 > > > > > > > > -2.4962685539301832 -2.4966288035394730 > > > > > > > > -2.4978367300949738 > > > > > > > > est. exchange err (dexx) = 0.00042384 Ry > > > > > > > > ! total energy = -24.15032730 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4134 4.4023 > > > > > > > > -2.4978367300949738 -2.4980591338705209 > > > > > > > > -2.4984413942151975 > > > > > > > > est. exchange err (dexx) = 0.00007993 Ry > > > > > > > > ! total energy = -24.15054868 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4066 4.4806 > > > > > > > > -2.4995084229633417 -2.4995690173056424 > > > > > > > > -2.4997151620876128 > > > > > > > > est. exchange err (dexx) = 0.00004278 Ry > > > > > > > > ! total energy = -24.15103886 Ry > > > > > > > > .... > > > > ... > > > > .... > > > > .... > > > > > > > > est. exchange err (dexx) = 0.00000009 Ry > > > > > > > > ! total energy = -24.15145297 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > > > > > -2.5006821135594719 -2.5006822803381836 > > > > > > > > -2.5006825016241492 > > > > > > > > est. exchange err (dexx) = 0.00000003 Ry > > > > > > > > ! total energy = -24.15145336 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > > > > > -2.5006830182691306 -2.5006823182635491 > > > > > > > > -2.5006816409825148 > > > > > > > > est. exchange err (dexx) = 0.00000001 Ry > > > > > > > > ! total energy = -24.15145346 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 4.5809 > > > > > > > > -2.5006827878685880 -2.5006825627249212 > > > > > > > > -2.5006823476519933 > > > > > > > > est. exchange err (dexx) = 0.00000001 Ry > > > > > > > > ! total energy = -24.15145351 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006823476519933 -2.5006827558468370 > > > > > > > > -2.5006831719007772 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145351 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006831719007772 -2.5006824586209802 > > > > > > > > -2.5006817515742186 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145352 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006817515742186 -2.5006821655655500 > > > > > > > > -2.5006825845917415 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145353 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006827994750860 -2.5006825695782151 > > > > > > > > -2.5006823413433099 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145367 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006823413433099 -2.5006827420502393 > > > > > > > > -2.5006831444189488 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145368 Ry > > > > > > > > highest occupied, lowest unoccupied level (ev): 1.4052 > 4.5809 > > > > -2.5006831444189488 -2.5006824325837682 > > > > > > > > -2.5006817224109170 > > > > > > > > est. exchange err (dexx) = 0.00000000 Ry > > > > > > > > ! total energy = -24.15145368 Ry > > > > .... > > > > ..... > > > > ..... > > > > goes on for atleast total time will take approximate 14 hrs but not > > > > stop the run. > > > > > > > > Please any type of comment is appreciable. > > > > > > -- > > > ******************************************************** > > > - Article premier - Les hommes naissent et demeurent > > > libres et ?gaux en droits. Les distinctions sociales > > > ne peuvent ?tre fond?es que sur l'utilit? commune > > > - Article 2 - Le but de toute association politique > > > est la conservation des droits naturels et > > > imprescriptibles de l'homme. Ces droits sont la libert?, > > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > > ******************************************************** > > > > > > Giuseppe Mattioli > > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > > v. Salaria Km 29,300 - C.P. 10 > > > I 00015 - Monterotondo Stazione (RM) > > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > > E-mail: > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/454f9ecb/attachment-0001.htm From giannozz at democritos.it Wed Sep 26 19:31:14 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 Sep 2012 19:31:14 +0200 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> Message-ID: <176BAED4-B5D1-46ED-9872-CF860E90B419@democritos.it> On Sep 26, 2012, at 19:19 , Tian Lan wrote: > I cannot find the input card like &K_Points in cp.x, how could I > control the k sampling? you cannot: CP uses Gamma-point (k=0) sampling only P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From tianlan at caltech.edu Wed Sep 26 19:55:31 2012 From: tianlan at caltech.edu (Tian Lan) Date: Wed, 26 Sep 2012 10:55:31 -0700 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: <176BAED4-B5D1-46ED-9872-CF860E90B419@democritos.it> References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> <176BAED4-B5D1-46ED-9872-CF860E90B419@democritos.it> Message-ID: Hi, Thank you. So It means that I cannot exactly copy the setup of scf calculation to the cp calculation because in scf I used a much denser k-mesh but cp calculation only uses the Gamma point. Then how could I do the best to eliminate this difference in the MD calculation? I just find a blowing supercell in MD that otherwise in equilibrium in scf. You said last time that my two calculations, though energies are similar in both calculation but not that close, so ask me to use the exactly the same setup in MD as that in scf. And maybe nr1b sets are also senstive parameters. According to your experience, what should I modify then? Best, Tian On Wed, Sep 26, 2012 at 10:31 AM, Paolo Giannozzi wrote: > > On Sep 26, 2012, at 19:19 , Tian Lan wrote: > > > I cannot find the input card like &K_Points in cp.x, how could I > > control the k sampling? > > you cannot: CP uses Gamma-point (k=0) sampling only > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. 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 > -- Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 138-78, Pasadena, CA, 91125 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120926/b0079e14/attachment.htm From wparker at anl.gov Wed Sep 26 19:47:16 2012 From: wparker at anl.gov (William Parker) Date: Wed, 26 Sep 2012 12:47:16 -0500 Subject: [Pw_forum] functionals and pseudopotentials for bandgap. In-Reply-To: References: Message-ID: <2C5D7C1B-617A-45E6-951B-1FF1803D44F1@anl.gov> Hi Eduardo, TPSS does not significantly change the DFT band gap with respect to PBE. See these papers: http://dx.doi.org/10.1063/1.3698285 http://dx.doi.org/10.1063/1.3076922 http://dx.doi.org/10.1063/1.1760074 PBE pseudopotentials have usually been used with HSE since HSE's correlation is the same as PBE. See, for example: http://dx.doi.org/10.1063/1.4722993 The pseudopotentials in PW/examples/EXX_example/pseudos are all RRKJ-type PBE pseudopotentials. The first paper I mentioned tested a large number of functionals on a fairly large number of systems. If you don't like Gaussian basis sets, there is also this paper (no meta-GGAs, though): http://dx.doi.org/10.1063/1.3524336 Enjoy your exploration of the wide world of density functionals! --William ********************************************************* William D. Parker phone: +1 (630) 252-3388 Argonne Scholar Argonne Leadership Computing Facility Building 240, Office 1-D.26 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 U.S.A. ********************************************************* On Sep 26, 2012, at 6:09 AM, Eduardo Ariel Menendez Proupin wrote: > Dear fellows, > > I am swimming (but not diving yet) in the sea of hybrid functionals. I need to estimate bandgap corrections of a crystal made of benzene-like molecules. After some googling, I am almost at the same place, but looking to the HSE functional, and I tested the HSE and the TPSS with the example of silicon. I request a few advise, these are my dubts > > 1) Does the metaGGA functional TPSS improves the bandgap ? > > 2) What pseudopotential (i.e. what functional) can be used for a calculation with HSE? > > 3) What kind of pseudoptential are the CPBE*nlcc.RRKJ3 in EXX_example > > 4) I would appreciate a recommendation of a published benchmark on the performance of different functionals for the gap. > > Thanks > > -- > > > Eduardo Menendez Proupin > Departamento de Qu?mica Fisica Aplicada > Facultad de Ciencias > Universidad Aut?noma de Madrid > 28049 Madrid, Spain > Phone: +34 91 497 6706 > > On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez > > "Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo". > Alejo Carpentier, El reino de este mundo, (1949). > > "...man never knows for who he suffers and waits. He suffers and waits and works for peoples he will never meet, and who at the same time will suffer and wait and work for others who will also not be happy, as man always desires a happiness that is beyond the lot that he is given. But the greatness of man is precisely in wanting to improve what he is. In assigning himself Tasks. In the Kingdom of Heaven there is no greatness to conquer, for everything there is an established hierarchy, the unknown is unobscured, existence is without end, sacrifice, rest, and delight are impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful within his misery, capable of loving in the middle of calamity, man can only find his greatness, his full self-realization, in the Kingdom of this World." - Alejo Carpentier > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Wed Sep 26 22:03:44 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 26 Sep 2012 22:03:44 +0200 Subject: [Pw_forum] The cell blowing up in MD simulation In-Reply-To: References: <1347524576.32734.11.camel@fe12lx.fisica.uniud.it> <1347633001.11464.49.camel@fe12lx.fisica.uniud.it> <176BAED4-B5D1-46ED-9872-CF860E90B419@democritos.it> Message-ID: <26C27CAC-7D61-4D17-BB12-82AFBBB725FA@democritos.it> On Sep 26, 2012, at 19:55 , Tian Lan wrote: > So It means that I cannot exactly copy the setup of scf calculation > to the cp calculation > because in scf I used a much denser k-mesh but cp calculation only > uses the Gamma > point. Then how could I do the best to eliminate this difference in > the MD calculation? > I just find a blowing supercell in MD that otherwise in equilibrium > in scf. the simplest and fastest test is to compare the results of self- consistent calculations for cp.x (no dynamics, just electronic minimization) and for pw.x for the same data (use card K_POINTS gamma). Compare the energies and the stresses. The choice of nr1b, nr2b, nr3b (if needed) is not completely obvious: you have to find a compromise between speed (incrases for decreasing values), and accuracy, taking into account that accuracy doesn't actually improve if you increase those values beyond some limits (useless long-range oscillations of the augmentation charges is all you see) Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lmartinsamos at gmail.com Thu Sep 27 11:10:16 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Thu, 27 Sep 2012 11:10:16 +0200 Subject: [Pw_forum] 1th october: mailing lists maintenance Message-ID: Dear all, on monday the 1th october since 12 am to 3 pm (Central Europe Time) the mailing lists pw_forum and pw_users will be provisory unavailable due to maintenance activities. Depending on your location, you may experience connection problems even after 3 pm. The normal activity will be fully recovered once the DNS have been propagated everywhere. sorry for the inconvenience this may cause and thank you for your understanding Layla -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120927/513c4d4c/attachment.htm From pandey.bramha at gmail.com Fri Sep 28 16:03:06 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Fri, 28 Sep 2012 19:33:06 +0530 Subject: [Pw_forum] info regarding r.x code In-Reply-To: References: Message-ID: Dear Users and developers... i am facing to compile the r.x code in my system. i have ifort and gfortron compile in ubuntu 12.04 in single system. As i issued the ./comp_resp_mat.j >>>>> ifort -o r.x resp_mat.f90 -L/opt/intel/mkl/lib/ia32 -lmkl_lapack \ -lmkl_ia32 -lguide -lpthread <<<<<< i got the following error. ld: cannot find -lmkl_lapack ld: cannot find -lmkl_ia32 ld: cannot find -lguide your cooperation is appreciated in any form. On Sun, Sep 23, 2012 at 9:54 PM, Bramha Pandey wrote: > Thank you very much Dear Chen Sir for your kind help. > > > On Sun, Sep 23, 2012 at 8:38 PM, Peng Chen wrote: > >> Dear Pandey, >> >> You can find r.x in the exercises of "Matteo Cococcioni,Examples of >> spin-polarized and DFT+U calculations" in the link: >> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php. And >> you can follow the "instructions of LDA+U" to calculate U. >> >> >> >> On Sun, Sep 23, 2012 at 1:13 AM, Bramha Pandey wrote: >> >>> Dear Users and Developers, >>> How can i get the r.x code for the calculation of U parameter in quantum >>> espresso-5.0.1. >>> Any kind of help is heartily appreciable. >>> >>> -- >>> Thanks and Regards >>> Bramha Prasad Pandey >>> Ph.D Student Indian School of Mines(ISM) >>> Dhanbad, INDIA. >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> Best Regards. >> Peng >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Thanks and Regards > Bramha Prasad Pandey > Ph.D Student Indian School of Mines(ISM) > Dhanbad, INDIA. > > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120928/dc092cbf/attachment.htm From ananyamondol3 at gmail.com Fri Sep 28 18:03:27 2012 From: ananyamondol3 at gmail.com (Ananya Mondal) Date: Fri, 28 Sep 2012 12:03:27 -0400 Subject: [Pw_forum] how to print trajectory and velocity pw.x Message-ID: Hi, I am a new user of quantum espresso. I have downloaded one MD input file from http://www.vlab.msi.umn.edu/events/download/ and able to run the molecular dynamics on the ground-state BO surface using the pw.x (quantum espresso 5.0.1). The out files are like md.out, pwscf.md, pwscf.mix1, pwscf.msd.dat, pwscf.rdf.dat, pwscf.wfc1, From tsakhrawi at yahoo.com Fri Sep 28 18:06:44 2012 From: tsakhrawi at yahoo.com (Sakhrawi Taoufek) Date: Fri, 28 Sep 2012 17:06:44 +0100 (BST) Subject: [Pw_forum] starting_magnetization Message-ID: <1348848404.37644.YahooMailNeo@web133006.mail.ir2.yahoo.com> Dear all, i want to calculate the ferromagnetique structure for Fe compound, in the litterature i find that the magnetic moment is 2.84. in the pwscf_input : -1< starting_magnetization<1 i can't understand the relation between starting_magnetization and the magnetic moment???? there is any adea?? thinks in advance --------------------------------------------------------------------- Sakhraoui Taoufik PhD student Research Unit of Solid State Physics F.S.Monastir, Tunisia --------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120928/a16e1d08/attachment.htm From giannozz at democritos.it Fri Sep 28 18:23:23 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 28 Sep 2012 18:23:23 +0200 Subject: [Pw_forum] starting_magnetization In-Reply-To: <1348848404.37644.YahooMailNeo@web133006.mail.ir2.yahoo.com> References: <1348848404.37644.YahooMailNeo@web133006.mail.ir2.yahoo.com> Message-ID: <1348849403.27328.0.camel@fe12lx.fisica.uniud.it> On Fri, 2012-09-28 at 17:06 +0100, Sakhrawi Taoufek wrote: > i can't understand the relation between starting_magnetization and the > magnetic moment???? starting_magnetization is used only to break the symmetry and has no relation with the final magnetization P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From cyrille.barreteau at cea.fr Fri Sep 28 18:44:59 2012 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Fri, 28 Sep 2012 16:44:59 +0000 Subject: [Pw_forum] RE : starting_magnetization In-Reply-To: <1348849403.27328.0.camel@fe12lx.fisica.uniud.it> References: <1348848404.37644.YahooMailNeo@web133006.mail.ir2.yahoo.com>, <1348849403.27328.0.camel@fe12lx.fisica.uniud.it> Message-ID: <6E80B49CBC3D9F4694B510228B88EE3C20A7D7@E-EXDAGE-A1.extra.cea.fr> Let me add that it can have an influence on the final magnetization in cases where several metastable magnetic solution coexist. Whenever you observe such dependence on the starting magnetization it is safe to do some kind of fixed spin moment calculation. Cyrille ============================================================ Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay cellphone: +33 (0)6 47 53 66 52 IRAMIS, SPCSI, Bat. 462 fax : +33 (0)1 69 08 84 46 91191 Gif sur Yvette Cedex email: cyrille.barreteau at cea.fr FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ============================================================== ________________________________________ De : pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] de la part de Paolo Giannozzi [giannozz at democritos.it] Date d'envoi : vendredi 28 septembre 2012 18:23 ? : Sakhrawi Taoufek; PWSCF Forum Objet : Re: [Pw_forum] starting_magnetization On Fri, 2012-09-28 at 17:06 +0100, Sakhrawi Taoufek wrote: > i can't understand the relation between starting_magnetization and the > magnetic moment???? starting_magnetization is used only to break the symmetry and has no relation with the final magnetization P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From alramtor at gmail.com Sat Sep 29 01:13:18 2012 From: alramtor at gmail.com (Alfredo Ramirez) Date: Fri, 28 Sep 2012 19:13:18 -0400 Subject: [Pw_forum] Density electronic Message-ID: Hi everybody, Who knows where I can find the explicit value of ground density electronic of one system, when I finish a run on pwscf code. Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120928/5dbd1680/attachment.htm From giannozz at democritos.it Sat Sep 29 10:17:42 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 29 Sep 2012 10:17:42 +0200 Subject: [Pw_forum] Density electronic In-Reply-To: References: Message-ID: <98B1C76F-FD9D-4E09-A27F-2B137702165F@democritos.it> On Sep 29, 2012, at 1:13 , Alfredo Ramirez wrote: > Who knows where I can find the explicit value of > ground density electronic of one system, in file charge-density.dat . Note however that this is in binary format. If you need to access the charge density, you may want to take inspiration from the various postprocessing codes in PP/src P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Sat Sep 29 18:31:29 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 29 Sep 2012 17:31:29 +0100 Subject: [Pw_forum] electron phonon calculation at the Gamma point Message-ID: Dear all, I am trying to do el-ph calculations only at the Gamma point for graphene (as I want to compare it to another system where the calculations are only feasible at the Gamma point). However the values I am getting for lambda for graphene AT THE GAMMA POINT are really high: degauss lambda 0.005 13.442600 0.015 2.303600 0.020 1.756000 0.025 1.436000 0.030 1.228800 0.035 1.085800 0.040 0.983000 0.045 0.906400 0.050 0.847800I am using a 90 x90 x1 grid (in scf) for graphene. It is already known that lambda for graphene is ~0.02. (1) Do the above results mean that one cannot calculate el-ph coefficients unless on a grid of phonons and then are the calculations -at the Gamma point ONLY- useless and unexact? (2) or does this mean that the results did not converge due to a small k-mesh in the scf calculations (90x90x1) and I need to increase it to say 400x400x1? Any suggestions of any kind would also be ahighly appreciated. Thanks for your help Elie MUniversity of NottsNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120929/29525685/attachment.htm From pandey.bramha at gmail.com Sun Sep 30 07:22:07 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sun, 30 Sep 2012 10:52:07 +0530 Subject: [Pw_forum] Segmentation fault (core dumped) to run a script Message-ID: Dear Developers and users, When i am trying to run one simple script, i get the Segmentation fault (core dumped) for the two value (9.8 and 9.9) of alat. The following script which i am using #!/bin/sh #################################################################### # # define the following variables according to your needs # #espresso_dir=/home/bramha/espresso-5.0.1 #outdir1=/home/bramha/tmp #pseudo_dir=/home/bramha/espresso-5.0.1/pseudo #################################################################### for alat in 9.8 9.9 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 ; do # self-consistent calculation cat > si.scf.in << EOF &control restart_mode='from_scratch', prefix='silicon', pseudo_dir = '/home/bramha/espresso-5.0.1/pseudo', outdir='/home/bramha/tmp' / &system ibrav= 2, celldm(1) =$alat, nat= 2, ntyp= 1, ecutwfc = 20.0, / &electrons / ATOMIC_SPECIES Si 28.086 Si.pz-vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS automatic 4 4 4 1 1 1 EOF /home/bramha/espresso-5.0.1/bin/pw.x < si.scf.in > si.scf.out grep -e 'lattice parameter' -e ! si.scf.out | \ awk '/lattice/{alat=$(NF-1)}/!/{print alat, $(NF-1)}' >> si.etot_vs_alat done Please any type of comments are appreciated. -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120930/bd5b8165/attachment.htm From pandey.bramha at gmail.com Sun Sep 30 09:34:12 2012 From: pandey.bramha at gmail.com (Bramha Pandey) Date: Sun, 30 Sep 2012 13:04:12 +0530 Subject: [Pw_forum] Segmentation fault (core dumped) to run a script In-Reply-To: References: Message-ID: Please Ignore this mail, i was making a mistake it was working now perfectly. Error was coming to take very less value of ecut(20Ry) for normconversing pseudopotential. As i have increased it to 35-40 Ry, it has run perfectly without showing any error. On Sun, Sep 30, 2012 at 10:52 AM, Bramha Pandey wrote: > Dear Developers and users, > When i am trying to run one simple script, i get the Segmentation fault > (core dumped) for the two value (9.8 and 9.9) of alat. > The following script which i am using > #!/bin/sh > #################################################################### > # > # define the following variables according to your needs > # > #espresso_dir=/home/bramha/espresso-5.0.1 > #outdir1=/home/bramha/tmp > #pseudo_dir=/home/bramha/espresso-5.0.1/pseudo > #################################################################### > > for alat in 9.8 9.9 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 ; do > > # self-consistent calculation > cat > si.scf.in << EOF > &control > restart_mode='from_scratch', > prefix='silicon', > pseudo_dir = '/home/bramha/espresso-5.0.1/pseudo', > outdir='/home/bramha/tmp' > / > &system > ibrav= 2, celldm(1) =$alat, nat= 2, ntyp= 1, > ecutwfc = 20.0, > / > &electrons > / > ATOMIC_SPECIES > Si 28.086 Si.pz-vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS automatic > 4 4 4 1 1 1 > EOF > > /home/bramha/espresso-5.0.1/bin/pw.x < si.scf.in > si.scf.out > > grep -e 'lattice parameter' -e ! si.scf.out | \ > awk '/lattice/{alat=$(NF-1)}/!/{print alat, $(NF-1)}' >> > si.etot_vs_alat > > done > > Please any type of comments are appreciated. > > -- > Thanks and Regards > Bramha Prasad Pandey > Ph.D Student Indian School of Mines(ISM) > Dhanbad, INDIA. > > -- Thanks and Regards Bramha Prasad Pandey Ph.D Student Indian School of Mines(ISM) Dhanbad, INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120930/3725448e/attachment.htm From baroni at sissa.it Sun Sep 30 21:24:35 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 30 Sep 2012 21:24:35 +0200 Subject: [Pw_forum] polarizability of metals using ph.x In-Reply-To: <1348663557.44488.YahooMailNeo@web133003.mail.ir2.yahoo.com> References: <1348663557.44488.YahooMailNeo@web133003.mail.ir2.yahoo.com> Message-ID: <3CEF66C3-35DD-4B95-AEB8-4604EC274F99@sissa.it> Dear Anne, I am not sure I understand what you actually expect. The electronic polarizability? (i.e. the dielecric constant such as probed by eels?) For that you would need a tddft calculation, which is not implemented in ph.x ... SB On Sep 26, 2012, at 2:45 PM, anne etindele wrote: > Dear all > > I am trying to determine the frequency dependent polarisability of metals like > Pt and Al using ph.x code. Here is the input I made for the case of Pt: > > phonons of pt at Gamma > &inputph > tr2_ph=1.0d-15, > trans=.false., > fpol=.true., > amass(1)=195.078, > prefix='Pt', > outdir='$TMP_DIR' > fildyn='pt.dynG', > / > 0.0 0.0 0.0 > > FREQUENCIES > 4 > 0.5d0 > 1.0d0 > 1.5d0 > 5.0d0 > > In the output file I don't have any value of polarizability. Do I need > to modify or to add another parameter? > > Anne Justine ETINDELE > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120930/4b2fff1f/attachment.htm