From mayankaditya at gmail.com Thu Sep 1 08:42:12 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 1 Sep 2011 12:12:12 +0530 Subject: [Pw_forum] K POINTS Message-ID: Dear All I am doing SCF calculation of ZnSe it has 16 atom and simple cubic structure. I have calculated total energy using Monkhorst pack scheme of k point generation with shift. I got 176 k points while using the kpoint.x utility i found it generates only 120 k points for simple cubic structure. did i make any mistake? or the kpoint.x utility is different from monkhorst method. Thanks -- -- Mayank ?BARC MUMBAI, INDIA From guntram.schmidt at chemie.uni-halle.de Thu Sep 1 12:23:24 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Thu, 01 Sep 2011 12:23:24 +0200 Subject: [Pw_forum] Phonons of molecular crystal In-Reply-To: References: Message-ID: <4E5F5D1C.7060108@chemie.uni-halle.de> Dear All, I want to simulate the infrared spectrum of a molecular crystal. As the phonon calculations usually take weeks to finish, I'd like to ask, wether someone of you has propositions on proper treshold values? I'm using rpb-paw US pseudopotential (revised PBE, as suggested for vdW-potential) and gamma point (also said to be sufficient for molecular crystals). Does the ecutrho of the preceding SCF calculation influence the speed of the phonon calculation? What is a sufficient low value for the tr2_ph to get a reasonable (comparable to experimental values) spectrum? Thanks a lot, Guntram From degironc at sissa.it Thu Sep 1 12:37:48 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 01 Sep 2011 12:37:48 +0200 Subject: [Pw_forum] Phonons of molecular crystal In-Reply-To: <4E5F5D1C.7060108@chemie.uni-halle.de> References: <4E5F5D1C.7060108@chemie.uni-halle.de> Message-ID: <4E5F607C.6080802@sissa.it> Dear Guntram, be careful that vdW-DF functional IS NOT yet implemented in the phonon code Stefano On 09/01/2011 12:23 PM, Guntram Schmidt wrote: > Dear All, > > I want to simulate the infrared spectrum of a molecular crystal. > As the phonon calculations usually take weeks to finish, I'd like to > ask, wether someone of you has propositions on proper treshold values? > > I'm using rpb-paw US pseudopotential (revised PBE, as suggested for > vdW-potential) and gamma point (also said to be sufficient for molecular > crystals). > > Does the ecutrho of the preceding SCF calculation influence the speed of > the phonon calculation? > > What is a sufficient low value for the tr2_ph to get a reasonable > (comparable to experimental values) spectrum? > > > Thanks a lot, > Guntram > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Sep 1 13:26:55 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 1 Sep 2011 13:26:55 +0200 Subject: [Pw_forum] K POINTS In-Reply-To: References: Message-ID: On Sep 1, 2011, at 8:42 , mayank gupta wrote: > I got 176 k points while using the kpoint.x utility i found it > generates > only 120 k points for simple cubic structure. did i make any mistake? kpoint.x yields k-points in the Irreducible Brillouin Zone (IBZ) of the lattice. pw.x yields k-points in the IBZ of the crystal (unless otherwise specified). If the crystal has a lower symmetry than the lattice alone, it may have a larger IBZ and a larger number of inequivalent k-ponts 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 guntram.schmidt at chemie.uni-halle.de Thu Sep 1 13:44:37 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Thu, 01 Sep 2011 13:44:37 +0200 Subject: [Pw_forum] Phonons of molecular crystal In-Reply-To: <4E5F607C.6080802@sissa.it> References: <4E5F5D1C.7060108@chemie.uni-halle.de> <4E5F607C.6080802@sissa.it> Message-ID: <4E5F7025.6070300@chemie.uni-halle.de> Dear Stefano, do you think it is appropiate to use another functional to calculate the phonon spectra of molecular crystals? I just want to have some rough approximation of an IR spectrum and maybe get QHA total energies? Thanks, Guntram Am 01.09.2011 12:37, schrieb Stefano de Gironcoli: > Dear Guntram, > be careful that vdW-DF functional IS NOT yet implemented in the > phonon code > Stefano > > On 09/01/2011 12:23 PM, Guntram Schmidt wrote: >> Dear All, >> >> I want to simulate the infrared spectrum of a molecular crystal. >> As the phonon calculations usually take weeks to finish, I'd like to >> ask, wether someone of you has propositions on proper treshold values? >> >> I'm using rpb-paw US pseudopotential (revised PBE, as suggested for >> vdW-potential) and gamma point (also said to be sufficient for molecular >> crystals). >> >> Does the ecutrho of the preceding SCF calculation influence the speed of >> the phonon calculation? >> >> What is a sufficient low value for the tr2_ph to get a reasonable >> (comparable to experimental values) spectrum? >> >> >> Thanks a lot, >> Guntram >> _______________________________________________ >> 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 From jibanez008 at ikasle.ehu.es Thu Sep 1 18:00:23 2011 From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz) Date: Thu, 1 Sep 2011 18:00:23 +0200 Subject: [Pw_forum] Wannier90, question about units in seedname_hr.dat Message-ID: Dear Wannier90 users, In output file 'seedname_hr.dat' the program W90 stores the Hamiltonian matrix elements in WF basis, in a format that is nicely explained in the W90 Users Guide. However, I could not find the units in which the matrix elements are stored. The dimension, if I am not very wrong, should be Energy (shouldnt?!). I see that most energy-units in W90 are in eV, but I am not sure if this is so in all cases, does anybody know if W90 uses eV energy-units as default? I would really appreciate any kind of help, thanks in advance, -- ?======================================== Julen Iba?ez Azpiroz Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015326 Mail: jibanez008 at ikasle.ehu.es ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110901/ea79088f/attachment.htm From Ari.P.Seitsonen at iki.fi Thu Sep 1 21:27:44 2011 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 1 Sep 2011 21:27:44 +0200 (CEST) Subject: [Pw_forum] Lattice constants with vdW-DF/vdW-DF2 Message-ID: Dear Colleagues, I want to calculate molecules adsorbing on metallic surfaces, and since the adsorption energy of them is know to be small, I would like to apply the vdW-DF/vdW-DF2 for the calculations. When I calculate the lattice constant with those functionals, I seem to get very large lattice constants, 5-10 % larger than the experimental one. An example for bulk, fcc gold is attached. I perform the calculation looping over different values for the lattice constant; the result seems to be independent of the cut-off energies (in this case I have large values for 'ecutwfc'/'ecutrho' because this was the last run for the convergence tests). Thus my question, does any one see something wrong in my input? Since the exchage part of the exchange and correlation is treated with a GGA functional (independently whether I use vdW-DF2 and PW86 or vdW-DF and revPBE) and correlation with LDA, plus an attractive(?) long-range contribution, I would expect lattice constants much closer to the experiments. Greetings from Wroclaw, apsi PS Apologies if the topic of my mail is an FAQ/discussed already! -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- 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 -------------- next part -------------- &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'bulk-Au' pseudo_dir = '/users/aps/usr/espresso/PP_LIBRARY/' outdir = './scratch/' tstress = .true. tprnfor = .true. verbosity = 'high' etot_conv_thr = 1e-6 forc_conv_thr = 1e-5 / &system ibrav = 2 a = 4.60 nat = 1 ntyp = 1 nbnd = 9 occupations = 'smearing' smearing = 'fermi-dirac' degauss = 0.0036749326 ecutwfc = 80 ecutrho = 800 input_dft = 'vdW-DF2' / &electrons conv_thr = 1e-10 mixing_beta = 0.7 / ATOMIC_SPECIES Au 1.00 Au.bp-van_ak.UPF ATOMIC_POSITIONS crystal Au 0 0 0 K_POINTS AUTOMATIC 3*32 0 0 0 From ttduyle at gmail.com Thu Sep 1 21:42:37 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 1 Sep 2011 15:42:37 -0400 Subject: [Pw_forum] Lattice constants with vdW-DF/vdW-DF2 In-Reply-To: References: Message-ID: It is well-known that vdW-DF and vdW-DF2 overestimate lattice parameters of solids See this work: Phys. Rev. B 83, 195131 (2011) -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, Sep 1, 2011 at 3:27 PM, Ari P Seitsonen wrote: > > Dear Colleagues, > > ?I want to calculate molecules adsorbing on metallic surfaces, and since the > adsorption energy of them is know to be small, I would like to apply the > vdW-DF/vdW-DF2 for the calculations. When I calculate the lattice constant > with those functionals, I seem to get very large lattice constants, 5-10 % > larger than the experimental one. An example for bulk, fcc gold is attached. > I perform the calculation looping over different values for the lattice > constant; the result seems to be independent of the cut-off energies (in > this case I have large values for 'ecutwfc'/'ecutrho' because this was the > last run for the convergence tests). > > ?Thus my question, does any one see something wrong in my input? Since the > exchage part of the exchange and correlation is treated with a GGA > functional (independently whether I use vdW-DF2 and PW86 or vdW-DF and > revPBE) and correlation with LDA, plus an attractive(?) long-range > contribution, I would expect lattice constants much closer to the > experiments. > > ? ?Greetings from Wroclaw, > > ? ? ? apsi > > PS Apologies if the topic of my mail is an FAQ/discussed already! > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > ?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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From kucukben at sissa.it Thu Sep 1 21:44:24 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 01 Sep 2011 21:44:24 +0200 Subject: [Pw_forum] Lattice constants with vdW-DF/vdW-DF2 In-Reply-To: References: Message-ID: <20110901214424.it639yoda84ccogg@webmail.sissa.it> ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From kucukben at sissa.it Thu Sep 1 22:33:26 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 01 Sep 2011 22:33:26 +0200 Subject: [Pw_forum] Lattice constants with vdW-DF/vdW-DF2 In-Reply-To: References: <20110901215145.qqb85cdiiokc4cso@webmail.sissa.it> Message-ID: <20110901223326.b42c1l3ogkk0o8oo@webmail.sissa.it> Dear Ari, I see in Modules/funct.f90 that 'VDW-DF2-C09' sets this configuration: SLA+PW+Cooper 09+vdW-DF2 'VDW-DF-C09' instead: SLA+PW+Cooper 09+vdW-DF Cooper 09 (c09x) is the new grad.x i mentioned. While generating the pseudopotentials, as long as you keep grad. exchange as c09x, the grad.correlation should not matter as it is overwritten by the vdWDF/DF2. best, emine Quoting Ari P Seitsonen : > > Dear Emine, > > Thank you very much - I _was_ able to see your emails on the mailing > list. I'll have a look on these alternative exchange functionals - do > you mind telling me what is the syntax for them in the input for Q-E? > And which pseudo potentials (which XC) do you employ with it? > > Thank your again, > > 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 Thu, 1 Sep 2011, Emine Kucukbenli wrote: > >> Hi Ari, >> (I dont see my mail delivered so I am writing again, sorry if >> anyone receives it twice) >> You can try c09x exchange functional which is claimed to solve that issue: >> >> V. R. Cooper, Phys. Rev. B 81, 161104(R) (2010) >> It is recently implemented in QE. >> best, >> emine kucukbenli, phd student, sissa, italy >> >> Quoting Ari P Seitsonen : >> >>> >>> Dear Colleagues, >>> >>> I want to calculate molecules adsorbing on metallic surfaces, and >>> since the adsorption energy of them is know to be small, I would like >>> to apply the vdW-DF/vdW-DF2 for the calculations. When I calculate the >>> lattice constant with those functionals, I seem to get very large >>> lattice constants, 5-10 % larger than the experimental one. An example >>> for bulk, fcc gold is attached. I perform the calculation looping over >>> different values for the lattice constant; the result seems to be >>> independent of the cut-off energies (in this case I have large values >>> for 'ecutwfc'/'ecutrho' because this was the last run for the >>> convergence tests). >>> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From ptao10b at imr.ac.cn Fri Sep 2 02:08:50 2011 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Fri, 2 Sep 2011 08:08:50 +0800 (CST) Subject: [Pw_forum] How to realize the parallel calculation? Message-ID: <9606db.d3b.13227776dba.Coremail.ptao10b@imr.ac.cn> Dear all, The mpi run is used in my calculation, but I hear of that the kpoints cannot be allocated to every cpu unless a parameter is specified in the input file. I don't know it, so my calculation is quite slow. So, dear professors, would you tell me what is the parameter? Thanks a lot! Plato Tao From nkxirainbow at gmail.com Fri Sep 2 05:16:34 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 2 Sep 2011 11:16:34 +0800 Subject: [Pw_forum] How to realize the parallel calculation? In-Reply-To: <9606db.d3b.13227776dba.Coremail.ptao10b@imr.ac.cn> References: <9606db.d3b.13227776dba.Coremail.ptao10b@imr.ac.cn> Message-ID: Dear Tao: On Fri, Sep 2, 2011 at 8:08 AM, ?? wrote: > Dear all, > > The mpi run is used in my calculation, but I hear of that the kpoints > cannot be allocated to every cpu unless a parameter is specified in the > input file. I don't think so. In my experience(a personal computer, not cluster), I just need type "mpirun -np 4 ". "4" is the number of cores. In general, the number of kpoints should be divided by the number of cores. > > So, dear professors, would you tell me what is the parameter? > > Thanks a lot! > > Plato Tao > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110902/ea1508b9/attachment.htm From mohnish.iitk at gmail.com Fri Sep 2 08:15:19 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 2 Sep 2011 11:45:19 +0530 Subject: [Pw_forum] Problem with Bi2Se3 SCF converge In-Reply-To: <000f01cc6786$f1cffc80$d56ff580$@gmail.com> References: <000f01cc6786$f1cffc80$d56ff580$@gmail.com> Message-ID: Try reducing "beta" On Wed, Aug 31, 2011 at 8:07 AM, WF wrote: > Hello everyone,**** > > I am doing calculation of Bi2Se3 with vdW-DF functional, but it > really hard to converge. After several iterations it keeps to prompt things > like:**** > > ** ** > > iteration # 58 ecut= 60.00 Ry beta=0.70**** > > CG style diagonalization**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > **** > > and will not converge in 1000 iteration.**** > > ** ** > > But the calculation of LDA and PBE can converge, however. All > pseudo-potential is generated by ld1.x with same parameters except > functional.**** > > ** ** > > I have tried to change some parameter in SCF but it doesn?t seem > to be helpful. Is there any suggestion for this problem?**** > > ** ** > > Thanks.**** > > ** ** > > F,Wu**** > > ** ** > > -----------------------------------------------------------**** > > F, Wu**** > > College of Chemistry and Molecular Engineering**** > > Peking University**** > > ----------------------------------------------------------**** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110902/6b7cdcf5/attachment.htm From kucukben at sissa.it Fri Sep 2 08:26:22 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Fri, 02 Sep 2011 08:26:22 +0200 Subject: [Pw_forum] How to realize the parallel calculation? In-Reply-To: <9606db.d3b.13227776dba.Coremail.ptao10b@imr.ac.cn> References: <9606db.d3b.13227776dba.Coremail.ptao10b@imr.ac.cn> Message-ID: <20110902082622.b93uqsyqppcow4g8@webmail.sissa.it> Dear Tao, Perhaps you are asking about 'pools' level of parallelization, though it does not have an input parameter attached, there is an option tag: npool. you can read more about it here: http://www.quantum-espresso.org/user_guide/node18.html best, emine kucukbenli, phd student, sissa, italy Quoting ?? : > Dear all, > > The mpi run is used in my calculation, but I hear of that the > kpoints cannot be allocated to every cpu unless a parameter is > specified in the input file. I don't know it, so my calculation is > quite slow. > > So, dear professors, would you tell me what is the parameter? > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From elie.moujaes at hotmail.co.uk Fri Sep 2 15:54:25 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 2 Sep 2011 14:54:25 +0100 Subject: [Pw_forum] total force and number of k-points Message-ID: Dear all, I have a simple question: does the total force acting on a system depend on the number of k-points used? That is in my scf calculation I am using a grid of 4x4x1 for my system whereas the grid must be denser if phonon calculations are taking place I am using 8x8x1. Do I get different total force acting on the system and does it mean I have to relax the crystal twice one for an scf calculation and another for a phonon calculation? Thanks Elie MoujawsUniversity of NottsUniversity ParkNG7 2RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110902/a53b37fd/attachment.htm From giannozz at democritos.it Fri Sep 2 22:55:25 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 2 Sep 2011 22:55:25 +0200 Subject: [Pw_forum] total force and number of k-points In-Reply-To: References: Message-ID: <3D43C19E-A5CF-464A-A893-917CE01246CE@democritos.it> On Sep 2, 2011, at 15:54 , Elie Moujaes wrote: > I have a simple question: does the total force acting > on a system depend on the number of k-points used? not sure what you mean by "total force", but forces on atoms depend upon the number of k-points, for sure > That is in my scf calculation I am using a grid of 4x4x1 > for my system whereas the grid must be denser if phonon > calculations are taking place I am using 8x8x1. Do I get > different total force acting on the system and does it mean > I have to relax the crystal twice one for an scf calculation > and another for a phonon calculation? in principle a system should be relaxed for the same set of parameters (cutoff, k-points) that are used in the subsequent phonon calculation. The difference might be small enough to be negligible, but this is something that should be checked. 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 Fri Sep 2 23:01:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 2 Sep 2011 23:01:45 +0200 Subject: [Pw_forum] Wannier90, question about units in seedname_hr.dat In-Reply-To: References: Message-ID: <2BE8C6EE-6827-47BB-9245-E55B82B2494F@democritos.it> On Sep 1, 2011, at 18:00 , Julen Ibanez Azpiroz wrote: > Dear Wannier90 users, you may have better luck with the Wannier90 mailing list: http://www.democritos.it/mailman/listinfo/wannier 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 windbellklbh at gmail.com Sat Sep 3 03:06:55 2011 From: windbellklbh at gmail.com (WF) Date: Sat, 3 Sep 2011 09:06:55 +0800 Subject: [Pw_forum] Problem with Bi2Se3 SCF converge Message-ID: <000001cc69d5$c7fcb640$57f622c0$@gmail.com> Dear Mohnish: Thanks for our advices. I tried beta = 0.1 and 0.2, and those message is postponed to 100+ iteration, but the convergence still cannot be achieved. On Fri, Sep 2, 2011 at 11:45 AM, mohnish pandey wrote: > Try reducing "beta" >On Wed, Aug 31, 2011 at 8:07 AM, WF wrote: > Hello everyone,**** > > I am doing calculation of Bi2Se3 with vdW-DF functional, but > it really hard to converge. After several iterations it keeps to > prompt things > like:**** > > ** ** > > iteration # 58 ecut= 60.00 Ry beta=0.70**** > > CG style diagonalization**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 1 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > c_bands: 2 eigenvalues not converged**** > > **** > > and will not converge in 1000 iteration.**** > > ** ** > > But the calculation of LDA and PBE can converge, however. All > pseudo-potential is generated by ld1.x with same parameters except > functional.**** > > ** ** > > I have tried to change some parameter in SCF but it doesn?t > seem to be helpful. Is there any suggestion for this problem?**** > > ** ** > > Thanks.**** > > ** ** > > F,Wu**** > > ** ** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > - Regards ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- From elie.moujaes at hotmail.co.uk Sat Sep 3 04:02:04 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sat, 3 Sep 2011 03:02:04 +0100 Subject: [Pw_forum] total force and number of k-points In-Reply-To: <3D43C19E-A5CF-464A-A893-917CE01246CE@democritos.it> References: , <3D43C19E-A5CF-464A-A893-917CE01246CE@democritos.it> Message-ID: Professor Giannozzi, Thanks a lot for your reply. Elie > From: giannozz at democritos.it > Date: Fri, 2 Sep 2011 22:55:25 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] total force and number of k-points > > > On Sep 2, 2011, at 15:54 , Elie Moujaes wrote: > > > I have a simple question: does the total force acting > > on a system depend on the number of k-points used? > > not sure what you mean by "total force", but forces on > atoms depend upon the number of k-points, for sure > > > That is in my scf calculation I am using a grid of 4x4x1 > > for my system whereas the grid must be denser if phonon > > calculations are taking place I am using 8x8x1. Do I get > > different total force acting on the system and does it mean > > I have to relax the crystal twice one for an scf calculation > > and another for a phonon calculation? > > in principle a system should be relaxed for the same set of > parameters (cutoff, k-points) that are used in the subsequent > phonon calculation. The difference might be small enough to > be negligible, but this is something that should be checked. > > 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/20110903/fce43158/attachment.htm From mohnish.iitk at gmail.com Sat Sep 3 06:07:40 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 3 Sep 2011 09:37:40 +0530 Subject: [Pw_forum] Problem with Bi2Se3 SCF converge In-Reply-To: <000001cc69d5$c7fcb640$57f622c0$@gmail.com> References: <000001cc69d5$c7fcb640$57f622c0$@gmail.com> Message-ID: Dear Wu ! Can you please paste your complete input file so that we can take a look and may be able to tell where is the problem. On Sat, Sep 3, 2011 at 6:36 AM, WF wrote: > Dear Mohnish: > Thanks for our advices. I tried beta = 0.1 and 0.2, and those > message is postponed to 100+ iteration, but the convergence still cannot be > achieved. > > > On Fri, Sep 2, 2011 at 11:45 AM, mohnish pandey > wrote: > > Try reducing "beta" > > >On Wed, Aug 31, 2011 at 8:07 AM, WF wrote: > > > Hello everyone,**** > > > > I am doing calculation of Bi2Se3 with vdW-DF functional, but > > it really hard to converge. After several iterations it keeps to > > prompt things > > like:**** > > > > ** ** > > > > iteration # 58 ecut= 60.00 Ry beta=0.70**** > > > > CG style diagonalization**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 1 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > c_bands: 2 eigenvalues not converged**** > > > > **** > > > > and will not converge in 1000 iteration.**** > > > > ** ** > > > > But the calculation of LDA and PBE can converge, however. All > > pseudo-potential is generated by ld1.x with same parameters except > > functional.**** > > > > ** ** > > > > I have tried to change some parameter in SCF but it doesn?t > > seem to be helpful. Is there any suggestion for this problem?**** > > > > ** ** > > > > Thanks.**** > > > > ** ** > > > > F,Wu**** > > > > ** ** > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > - > Regards > > ----------------------------------------------------------- > F, Wu > College of Chemistry and Molecular Engineering > Peking University > ---------------------------------------------------------- > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/6894c488/attachment.htm From jibanez008 at ikasle.ehu.es Sat Sep 3 11:41:47 2011 From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz) Date: Sat, 3 Sep 2011 11:41:47 +0200 Subject: [Pw_forum] Wannier90, question about units in seedname_hr.dat In-Reply-To: <2BE8C6EE-6827-47BB-9245-E55B82B2494F@democritos.it> References: <2BE8C6EE-6827-47BB-9245-E55B82B2494F@democritos.it> Message-ID: Dear Prof. Giannozzi Thank you very much for the answer, I thought QE and W90 shared the mailing list, I will try in W90's, thanks again, -- ?======================================== Julen Iba?ez Azpiroz Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015326 Mail: jibanez008 at ikasle.ehu.es ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/55d6277d/attachment.htm From rajanpandey at gmail.com Sat Sep 3 12:43:05 2011 From: rajanpandey at gmail.com (Rajan Pandey) Date: Sat, 3 Sep 2011 16:13:05 +0530 Subject: [Pw_forum] Method of computing static dielectric constant of materials Message-ID: Dear Quantum Espresso community, I am trying to compute the static dielectric constant of materials using the methodology as implemented in CP code (part of the Quantum Espresso). The method is explained in the example30 of Quantum Espresso distribution. The system discussed is MgO, Ref: P.Umari and A.Pasquarello, Physical Review Letters, 89, p.157602 (2002). The example30 mentioned above has following note: "NOTE: the electronic dipole is defined modulo a factor (2*L=31.824i a.u., during the MD simulation the term "ln det S" changes the Riemann plane, this must be taken into account when addressing the electronic dipole." The above statement is given in the context of a cubic supercell with length L containing 64 atoms of MgO. I am studying a well known system, SiO2 (alpha quartz) for sanity check. I am simulating SiO2 in a 1x1x2 trigonal supercell (18 atoms) as well as in an orthorhombic (in alpha quartz case it will be tetragonal because a = b ) supercell. The ambiguity is that when I use the formula along with the "NOTE" of example30 in Quantum Espresso, mentioned above, I get wrong results for static dielectric constant. However, when I do not use the "NOTE" mentioned above, and by using the formula described in example30, I get the simulated value close to the experimental static dielectric constant of SiO2. This means that the method works for non-cubic unit cells too. I am not able to understand the role of the point mentioned in the NOTE (above) in general, when the formula described in example30 (reiterated below), seems to work. The difference d_Eps between static and high-frequency dielectric constant is given by: d_Eps=4*pi*(D2_el + D2_ion - D1_el - d1_ion)/(0.001 a.u. * Omega) D1(2)_el = electronic contribution of the dipole at the beginning (end) of the relaxation. D1(2)_ion = ionic contribution of the dipole at the beginning (end) of the relaxation. Omega = supercell volume I shall appreciate any comments from community members. Thanks, and regards, Rajan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/eee0c9e2/attachment.htm From rajanpandey at gmail.com Sat Sep 3 12:46:19 2011 From: rajanpandey at gmail.com (Rajan Pandey) Date: Sat, 3 Sep 2011 16:16:19 +0530 Subject: [Pw_forum] Method of computing static dielectric constant of materials In-Reply-To: References: Message-ID: I forgot to add the affiliation in my previous post. Correcting myself, and regret any inconvenience. ---------- Forwarded message ---------- From: Rajan Pandey Date: Sat, Sep 3, 2011 at 4:13 PM Subject: Method of computing static dielectric constant of materials To: PWSCF Forum Dear Quantum Espresso community, I am trying to compute the static dielectric constant of materials using the methodology as implemented in CP code (part of the Quantum Espresso). The method is explained in the example30 of Quantum Espresso distribution. The system discussed is MgO, Ref: P.Umari and A.Pasquarello, Physical Review Letters, 89, p.157602 (2002). The example30 mentioned above has following note: "NOTE: the electronic dipole is defined modulo a factor (2*L=31.824i a.u., during the MD simulation the term "ln det S" changes the Riemann plane, this must be taken into account when addressing the electronic dipole." The above statement is given in the context of a cubic supercell with length L containing 64 atoms of MgO. I am studying a well known system, SiO2 (alpha quartz) for sanity check. I am simulating SiO2 in a 1x1x2 trigonal supercell (18 atoms) as well as in an orthorhombic (in alpha quartz case it will be tetragonal because a = b ) supercell. The ambiguity is that when I use the formula along with the "NOTE" of example30 in Quantum Espresso, mentioned above, I get wrong results for static dielectric constant. However, when I do not use the "NOTE" mentioned above, and by using the formula described in example30, I get the simulated value close to the experimental static dielectric constant of SiO2. This means that the method works for non-cubic unit cells too. I am not able to understand the role of the point mentioned in the NOTE (above) in general, when the formula described in example30 (reiterated below), seems to work. The difference d_Eps between static and high-frequency dielectric constant is given by: d_Eps=4*pi*(D2_el + D2_ion - D1_el - d1_ion)/(0.001 a.u. * Omega) D1(2)_el = electronic contribution of the dipole at the beginning (end) of the relaxation. D1(2)_ion = ionic contribution of the dipole at the beginning (end) of the relaxation. Omega = supercell volume I shall appreciate any comments from community members. Thanks, and regards, Rajan Rajan K. Pandey, Ph.D. Advisory Research Engineer, Semiconductor Research & Development Center India Systems & Technology Engineering Lab IBM India Pvt. Ltd. MD3 1F B354 Manyata Embassy Business Park Nagawara, Outer Ring Road Bangalore - 560045, India Phone: +91-80-28061262 Mobile: +91-9901850981 Email: rajapand at in.ibm.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/dc20ec01/attachment.htm From elie.moujaes at hotmail.co.uk Sat Sep 3 17:23:06 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sat, 3 Sep 2011 16:23:06 +0100 Subject: [Pw_forum] cannot allocate memory error Message-ID: Dear all, I am having a problem when I am running a scf calculation for a 72-atom supercell of Carbon grain boundaries. The calculations start and then after a few minutes stop with the following error: Traceback: not available, compile with -ftrace=frame or -ftrace=fullOperating system error: Cannot allocate memory Memory allocation failed on my desktop at work. I have the espresso-4.2 there. On my laptop at home (where I have downloaded the latest espresso-4.3.2 version). Now I am getting the error : operating system error: cannot allocate memoryout of memory Can anyone tell me what is going on? I am not sure if it is really a memory problem or something else? Thanks Elie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/f915da4d/attachment.htm From ttduyle at gmail.com Sat Sep 3 17:30:00 2011 From: ttduyle at gmail.com (Duy Le) Date: Sat, 3 Sep 2011 11:30:00 -0400 Subject: [Pw_forum] cannot allocate memory error In-Reply-To: References: Message-ID: On Sat, Sep 3, 2011 at 11:23 AM, Elie Moujaes wrote: > Dear all, > I am having a problem when I am running a scf calculation for a 72-atom > supercell of Carbon grain boundaries. The calculations start and then after > a few minutes stop with the following error: > Operating system error: Cannot allocate memory > operating system error: cannot allocate memory > out of memory > Can anyone tell me what is going on? I am not sure if it is really a memory > problem or something else? Yes. It said that. Your system is quite large for running on a personal desktop. Check output to see how much memory you need for this system. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" From elie.moujaes at hotmail.co.uk Sat Sep 3 17:36:31 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sat, 3 Sep 2011 16:36:31 +0100 Subject: [Pw_forum] cannot allocate memory error In-Reply-To: References: , Message-ID: Thanks a lot for the reply ..I was trying to gain some time as I am running other programs on the server at Uni. I guess I will have to do things step by step Thanks again Elie > From: ttduyle at gmail.com > Date: Sat, 3 Sep 2011 11:30:00 -0400 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] cannot allocate memory error > > On Sat, Sep 3, 2011 at 11:23 AM, Elie Moujaes > wrote: > > Dear all, > > I am having a problem when I am running a scf calculation for a 72-atom > > supercell of Carbon grain boundaries. The calculations start and then after > > a few minutes stop with the following error: > > Operating system error: Cannot allocate memory > > operating system error: cannot allocate memory > > out of memory > > Can anyone tell me what is going on? I am not sure if it is really a memory > > problem or something else? > Yes. It said that. Your system is quite large for running on a > personal desktop. Check output to see how much memory you need for > this system. > -------------------------------------------------- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > _______________________________________________ > 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/20110903/f4e56844/attachment-0001.htm From baroni at sissa.it Sat Sep 3 19:17:36 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 3 Sep 2011 19:17:36 +0200 Subject: [Pw_forum] cannot allocate memory error In-Reply-To: References: , Message-ID: <53D61500-AA4B-48E7-B2FC-5C066898D5B5@sissa.it> On Sep 3, 2011, at 5:36 PM, Elie Moujaes wrote: > Thanks a lot for the reply ..I was trying to gain some time as I am running other programs on the server at Uni. I guess I will have to do things step by step that's a very good idea ;-) take care - SB > > Thanks again > > Elie --- 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/20110903/4bb201c8/attachment.htm From guptasanjay.56 at gmail.com Sun Sep 4 11:00:17 2011 From: guptasanjay.56 at gmail.com (Sanjay D. Gupta) Date: Sun, 4 Sep 2011 14:30:17 +0530 Subject: [Pw_forum] Problem while Reading celldm of triclinic structure Message-ID: Dear, Dear QE professionals, I am running a scf calcuation for triclinic strcture but while reading input file it shows "Bad data for namelist object celldm Bad data for namelist object celldm" But program running without any error and giving output without considering the celldm(4) and celldm(5) from the input file. Here with i am pasting the output portion of reading the name list and input file. ************************************************** Part of out put program Program PWSCF v.4.3 starts on 4Sep2011 at 14:17:47 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 Parallel version (MPI), running on 4 processors R & G space division: proc/pool = 4 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... Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used Stick Mesh ---------- nst = 3101, nstw = 449, nsts = 1537 n.st n.stw n.sts n.g n.gw n.gs min 775 112 384 30335 1673 10698 max 776 113 385 30338 1674 10713 3101 449 1537 121343 6695 42829 bravais-lattice index = 14 lattice parameter (a_0) = 8.8896 a.u. unit-cell volume = 897.7308 (a.u.)^3 number of atoms/cell = 6 number of atomic types = 3 number of electrons = 49.00 number of Kohn-Sham states= 30 kinetic-energy cutoff = 50.0000 Ry charge density cutoff = 400.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 local-TF mixing Exchange-correlation = SLA PW PBE PBE (1434) EXX-fraction = 0.00 celldm(1)= 8.889603 celldm(2)= 1.241632 celldm(3)= 1.037384 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.125247 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.155510 1.231855 0.000000 ) a(3) = ( 0.000000 0.000000 1.037384 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 -0.126241 0.000000 ) b(2) = ( 0.000000 0.811784 0.000000 ) b(3) = ( 0.000000 0.000000 0.963964 ) ********************************************************************* here with i am also pasting the input file for further details. &control calculation = 'scf', prefix='CuWO4', restart_mode='from_scratch', outdir='./' pseudo_dir = '/PWSCF/pseudo/', tstress = .true. tprnfor = .true. wf_collect = .true. etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav= 14, celldm(1) = 8.889603025, celldm(2) = 1.241632288, celldm(3) = 1.037383575, celldm(4) = -0.029264993, celldm(5) = -0.043078844, celldm(6) = 0.1252466553, nosym = .true., nat= 6, ntyp= 3, ecutwfc = 50, ecutrho= 400, occupations= 'smearing', smearing= 'm-p', degauss= 0.05, / &electrons mixing_mode = "local-TF", mixing_beta = 0.700000, conv_thr = 1.0d-08, / ATOMIC_SPECIES Cu 63.546 Cu.pbe-n-van_ak.UPF W 183.84 W.pbe-nsp-van.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Cu 0.4953300000E+00 0.6597600000E+00 0.2448100000E+00 W 0.2106000000E-01 0.1734800000E+00 0.2542900000E+00 O 0.2491000000E+00 0.3535000000E+00 0.4245000000E+00 O 0.2145000000E+00 0.8812000000E+00 0.4309000000E+00 O 0.7353000000E+00 0.3803000000E+00 0.9810000000E-01 O 0.7826000000E+00 0.9079000000E+00 0.5330000000E-01 K_POINTS automatic 6 6 6 0 0 0 Please suggest me more. Waiting for positive reply. ~Best Regards ........................................................... Sanjay D. Gupta Research Fellow Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, Mobile-9879666643 email:guptasanjay_56 at yahoo.co.in ........................................................... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/a94d6e2b/attachment.htm From giannozz at democritos.it Sun Sep 4 11:19:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Sep 2011 11:19:24 +0200 Subject: [Pw_forum] Problem while Reading celldm of triclinic structure In-Reply-To: References: Message-ID: <65A2705B-9FDC-47DE-B6D9-E1BC630CA25A@democritos.it> On Sep 4, 2011, at 11:00 , Sanjay D. Gupta wrote: > celldm(4) = ?0.029264993, > celldm(5) = ?0.043078844, the "minus" sign in front of the numbers is not a minus, it is a dash. Compare with the correct character: > celldm(4) = -0.029264993, > celldm(5) = -0.043078844, 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 giuseppe.mattioli at mlib.ism.cnr.it Sun Sep 4 13:37:49 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Sun, 4 Sep 2011 13:37:49 +0200 Subject: [Pw_forum] problems with the new Martins-Troullier O pseudo In-Reply-To: References: Message-ID: <20110904133749.3x4zy8ri84c8www0@webmail.sic.rm.cnr.it> Dear all My 4.3.2 QE version (but I tried also with older ones) crashes when used with the new O.pbe-mt.UPF pseudopotential. No problems with other ones, so the error should depend on the new PP file. The output stops at Program PWSCF v.4.3.2 starts on 4Sep2011 at 13:25:53 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 Parallel version (MPI), running on 4 processors R & G space division: proc/pool = 4 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 stdin rank 0 in job 17 debian_53881 caused collective abort of all ranks exit status of rank 0: killed by signal 9 and my nohup.out file contains ################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_attr (iotk_attr+CHARACTER1_0.f90:207) # CVS Revision: 1.21 ################################################################# application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 What's wrong? Yours Giuseppe Giuseppe Mattioli ISM-CNR Italy From robinshy at gmail.com Sun Sep 4 14:37:09 2011 From: robinshy at gmail.com (Robin H) Date: Sun, 4 Sep 2011 20:37:09 +0800 Subject: [Pw_forum] about PWscf PP generation Message-ID: Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for the first time I met a mistake like this Program LD1 v.4.3.1 starts on 4Sep2011 at 19:53:36 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 Parallel version (MPI), running on 1 processors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from el_config : error # 12 wavefunction 5S found too many times %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 since the input is like this &input title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5D 3 2 1.00 0.00 2.20 2.20 5D 3 2 0.00 0.05 2.20 2.20 6S 1 0 2.00 0.00 2.20 2.20 6S 1 0 0.00 0.05 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.00 Is there anything wrong in my electric configuration of La? as I changed like this : &input title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5S 1 0 2.00 0.00 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.20 5D 3 2 1.00 0.00 2.20 2.20 6S 1 0 1.50 0.00 2.20 2.20 6P 2 1 0.50 0.00 2.20 2.00 the error is still exist like the fomer.what's the error suggest ?I'm wondered that how to write the list of states following the namelist of &inputp.I tried to find some information in the reference of PWscf to make me clear,but this part seemed hard to understand,hope everyone who is sophisticated at PP generation to give me some tips, I'm appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/f9fdfd99/attachment-0001.htm From giannozz at democritos.it Sun Sep 4 15:05:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 4 Sep 2011 15:05:00 +0200 Subject: [Pw_forum] problems with the new Martins-Troullier O pseudo In-Reply-To: <20110904133749.3x4zy8ri84c8www0@webmail.sic.rm.cnr.it> References: <20110904133749.3x4zy8ri84c8www0@webmail.sic.rm.cnr.it> Message-ID: <6D8E5643-1286-4994-A244-9BE4D45C9BF8@democritos.it> On Sep 4, 2011, at 13:37 , giuseppe.mattioli at mlib.ism.cnr.it wrote: > My 4.3.2 QE version (but I tried also with older ones) crashes when > used > with the new O.pbe-mt.UPF pseudopotential. No problems with other ones funny problem: the reason for the crash is a "comment" field pointing to a string longer than 80 characters. I have updated the file on the 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 guptasanjay.56 at gmail.com Sun Sep 4 15:14:28 2011 From: guptasanjay.56 at gmail.com (Sanjay D. Gupta) Date: Sun, 4 Sep 2011 18:44:28 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 51, Issue 7 In-Reply-To: References: Message-ID: ~Best Regards ........................................................... Sanjay D. Gupta Research Fellow Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, Mobile-9879666643 email:guptasanjay_56 at yahoo.co.in ........................................................... On Sun, Sep 4, 2011 at 6:07 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Problem while Reading celldm of triclinic structure > (Sanjay D. Gupta) > 2. Re: Problem while Reading celldm of triclinic structure > (Paolo Giannozzi) > 3. problems with the new Martins-Troullier O pseudo > (giuseppe.mattioli at mlib.ism.cnr.it) > 4. about PWscf PP generation (Robin H) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 4 Sep 2011 14:30:17 +0530 > From: "Sanjay D. Gupta" > Subject: [Pw_forum] Problem while Reading celldm of triclinic > structure > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear, > Dear QE professionals, > I am running a scf calcuation for triclinic strcture but while reading > input file it shows > "Bad data for namelist object celldm > Bad data for namelist object celldm" > > But program running without any error and giving output without considering > the celldm(4) and celldm(5) from the input file. > > Here with i am pasting the output portion of reading the name list and > input file. > > ************************************************** > Part of out put program > > > Program PWSCF v.4.3 starts on 4Sep2011 at 14:17:47 > > 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 > > Parallel version (MPI), running on 4 processors > R & G space division: proc/pool = 4 > > 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... > > Subspace diagonalization in iterative solution of the eigenvalue > problem: > a serial algorithm will be used > > > Stick Mesh > ---------- > nst = 3101, nstw = 449, nsts = 1537 > n.st n.stw n.sts n.g n.gw n.gs > min 775 112 384 30335 1673 10698 > max 776 113 385 30338 1674 10713 > 3101 449 1537 121343 6695 42829 > > > > bravais-lattice index = 14 > lattice parameter (a_0) = 8.8896 a.u. > unit-cell volume = 897.7308 (a.u.)^3 > number of atoms/cell = 6 > number of atomic types = 3 > number of electrons = 49.00 > number of Kohn-Sham states= 30 > kinetic-energy cutoff = 50.0000 Ry > charge density cutoff = 400.0000 Ry > convergence threshold = 1.0E-08 > mixing beta = 0.7000 > number of iterations used = 8 local-TF mixing > Exchange-correlation = SLA PW PBE PBE (1434) > EXX-fraction = 0.00 > > celldm(1)= 8.889603 celldm(2)= 1.241632 celldm(3)= 1.037384 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.125247 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( 0.155510 1.231855 0.000000 ) > a(3) = ( 0.000000 0.000000 1.037384 ) > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( 1.000000 -0.126241 0.000000 ) > b(2) = ( 0.000000 0.811784 0.000000 ) > b(3) = ( 0.000000 0.000000 0.963964 ) > ********************************************************************* > > > here with i am also pasting the input file for further details. > > &control > calculation = 'scf', > prefix='CuWO4', > restart_mode='from_scratch', > outdir='./' > pseudo_dir = '/PWSCF/pseudo/', > tstress = .true. > tprnfor = .true. > wf_collect = .true. > etot_conv_thr = 1.0d-5, > forc_conv_thr = 1.0d-4, > / > &system > ibrav= 14, > celldm(1) = 8.889603025, > celldm(2) = 1.241632288, > celldm(3) = 1.037383575, > celldm(4) = -0.029264993, > celldm(5) = -0.043078844, > celldm(6) = 0.1252466553, > nosym = .true., > nat= 6, > ntyp= 3, > ecutwfc = 50, > ecutrho= 400, > occupations= 'smearing', > smearing= 'm-p', > degauss= 0.05, > / > &electrons > mixing_mode = "local-TF", > mixing_beta = 0.700000, > conv_thr = 1.0d-08, > / > ATOMIC_SPECIES > Cu 63.546 Cu.pbe-n-van_ak.UPF > W 183.84 W.pbe-nsp-van.UPF > O 15.9994 O.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Cu 0.4953300000E+00 0.6597600000E+00 0.2448100000E+00 > W 0.2106000000E-01 0.1734800000E+00 0.2542900000E+00 > O 0.2491000000E+00 0.3535000000E+00 0.4245000000E+00 > O 0.2145000000E+00 0.8812000000E+00 0.4309000000E+00 > O 0.7353000000E+00 0.3803000000E+00 0.9810000000E-01 > O 0.7826000000E+00 0.9079000000E+00 0.5330000000E-01 > K_POINTS automatic > 6 6 6 0 0 0 > > Please suggest me more. > > Waiting for positive reply. > > > > > ~Best Regards > ........................................................... > Sanjay D. Gupta > Research Fellow > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, Mobile-9879666643 > email:guptasanjay_56 at yahoo.co.in > ........................................................... > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110904/a94d6e2b/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Sun, 4 Sep 2011 11:19:24 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Problem while Reading celldm of triclinic > structure > To: PWSCF Forum > Message-ID: <65A2705B-9FDC-47DE-B6D9-E1BC630CA25A at democritos.it> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > On Sep 4, 2011, at 11:00 , Sanjay D. Gupta wrote: > > > celldm(4) = ?0.029264993, > > celldm(5) = ?0.043078844, > > the "minus" sign in front of the numbers is not a minus, > it is a dash. Compare with the correct character: Dear Sir, Thank you very much This was my silly mistake now its working fine. Thanks once again for quick reply. With kind Regards Sanjay D Gupta > > celldm(4) = -0.029264993, > > celldm(5) = -0.043078844, > > 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 > > > > > > > ------------------------------ > > Message: 3 > Date: Sun, 4 Sep 2011 13:37:49 +0200 > From: giuseppe.mattioli at mlib.ism.cnr.it > Subject: [Pw_forum] problems with the new Martins-Troullier O pseudo > To: PWSCF Forum > Message-ID: <20110904133749.3x4zy8ri84c8www0 at webmail.sic.rm.cnr.it> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > > Dear all > > My 4.3.2 QE version (but I tried also with older ones) crashes when > used with the new O.pbe-mt.UPF pseudopotential. No problems with other > ones, so the error should depend on the new PP file. > The output stops at > > Program PWSCF v.4.3.2 starts on 4Sep2011 at 13:25:53 > > 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 > > Parallel version (MPI), running on 4 processors > R & G space division: proc/pool = 4 > > 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 stdin > rank 0 in job 17 debian_53881 caused collective abort of all ranks > exit status of rank 0: killed by signal 9 > > and my nohup.out file contains > > ################################################################## > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_scan_attr (iotk_attr+CHARACTER1_0.f90:207) > # CVS Revision: 1.21 > ################################################################# > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > What's wrong? > > Yours > > Giuseppe > > > Giuseppe Mattioli > ISM-CNR > Italy > > > > > > > ------------------------------ > > Message: 4 > Date: Sun, 4 Sep 2011 20:37:09 +0800 > From: Robin H > Subject: [Pw_forum] about PWscf PP generation > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for > the first time I met a mistake like this > Program LD1 v.4.3.1 starts on 4Sep2011 at 19:53:36 > 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 > Parallel version (MPI), running on 1 processors > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from el_config : error # 12 > wavefunction 5S found too many times > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > since the input is like this > &input > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > nlcc=.true., > tm=.true., > file_pseudopw='La.revPBE.UPF', > / > 5 > 5D 3 2 1.00 0.00 2.20 2.20 > 5D 3 2 0.00 0.05 2.20 2.20 > 6S 1 0 2.00 0.00 2.20 2.20 > 6S 1 0 0.00 0.05 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.00 > Is there anything wrong in my electric configuration of La? > as I changed like this : > &input > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > nlcc=.true., > tm=.true., > file_pseudopw='La.revPBE.UPF', > / > 5 > 5S 1 0 2.00 0.00 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.20 > 5D 3 2 1.00 0.00 2.20 2.20 > 6S 1 0 1.50 0.00 2.20 2.20 > 6P 2 1 0.50 0.00 2.20 2.00 > the error is still exist like the fomer.what's the error suggest ?I'm > wondered that how to write the list of states following the namelist of > &inputp.I tried to find some information in the reference of PWscf to make > me clear,but this part seemed hard to understand,hope everyone who is > sophisticated at PP generation to give me some tips, I'm appreciated. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110904/f9fdfd99/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 51, Issue 7 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/34385c18/attachment-0001.htm From flux_ray12 at 163.com Sun Sep 4 15:55:09 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 4 Sep 2011 21:55:09 +0800 (CST) Subject: [Pw_forum] about PWscf PP generation In-Reply-To: References: Message-ID: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> Of course, since the element Xe already has 5s2 and 5p2~ you can change parameter "config" like: '[Xe] 5d1 6s1.5 6p0.5' -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-04 20:37:09,"Robin H" wrote: Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for the first time I met a mistake like this Program LD1 v.4.3.1 starts on 4Sep2011 at 19:53:36 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); URLhttp://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 Parallel version (MPI), running on 1 processors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from el_config : error # 12 wavefunction 5S found too many times %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 since the input is like this &input title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5D 3 2 1.00 0.00 2.20 2.20 5D 3 2 0.00 0.05 2.20 2.20 6S 1 0 2.00 0.00 2.20 2.20 6S 1 0 0.00 0.05 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.00 Is there anything wrong in my electric configuration of La? as I changed like this : &input title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5S 1 0 2.00 0.00 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.20 5D 3 2 1.00 0.00 2.20 2.20 6S 1 0 1.50 0.00 2.20 2.20 6P 2 1 0.50 0.00 2.20 2.00 the error is still exist like the fomer.what's the error suggest ?I'm wondered that how to write the list of states following the namelist of &inputp.I tried to find some information in the reference of PWscf to make me clear,but this part seemed hard to understand,hope everyone who is sophisticated at PP generation to give me some tips, I'm appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/42f82997/attachment.htm From sternberg at anl.gov Mon Sep 5 05:22:31 2011 From: sternberg at anl.gov (Michael Sternberg) Date: Sun, 4 Sep 2011 22:22:31 -0500 Subject: [Pw_forum] wfc files: heavy I/O, handling for restarts Message-ID: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> Dear fellow users and developers, What's the current wisdom regarding wfc updates hammering a networked file system? Details: I have trouble with what the author of the user guide knowingly calls "excessive I/O", I see users running some 20 .. 40 pw.x processes which concurrently write large wfc files. Those writes choke my Lustre file system. So, count me in as an "angry system manager". I will be throwing more hardware at this problem shortly, but I feel there is room for improvement in other ways. The problem arises because pw.x is being run with the somewhat lazy setting of ESPRESSO_TMPDIR=".", which means all scratch files are being dumped into $PBS_O_WORKDIR, typically somewhere in $HOME or a parallel scratch file system. I wonder to what extent "a modern Parallel File System" as prescribed by the documentation is actually needed, other than the requirement that it provide lots of R/W bandwidth. If one MPI rank writes a file, must this file indeed be seen or even readable by another MPI rank? It appears not - one can run pw.x just fine with $ESPRESSO_TMPDIR pointing to local scratch directories on the nodes. The tricky bits are - stageout, i.e., gathering wfc (and bfgs) files from the nodes upon job termination, regular or otherwise, so as to preserve intermediate results, and - stagein for restarts, i.e., provide to each MPI rank exactly the required .wfc in its local $ESPRESSO_TMPDIR. I did a proof-of-concept using the following code in a PBS/Torque job file: --------------------------------------------------- # $TMPDIR is provided as pointing to a job-specific node-local scratch # directory that is created on all nodes under the same name. export ESPRESSO_TMPDIR=$TMPDIR basename="pwscf" # Scatter wfc restart files awk '{ files_for[$1] = files_for[$1] " '$basename'.wfc" NR } END { for (host in files_for) print host, files_for[host] }' $PBS_NODEFILE \ | while read host files do ssh -n $host "cd $PBS_O_WORKDIR; mv $files $ESPRESSO_TMPDIR/" done # on master host, copy .save directory as well rsync -a $basename.save $ESPRESSO_TMPDIR mpirun -x ESPRESSO_TMPDIR \ -np $(wc -l < $PBS_NODEFILE) \ -machinefile $PBS_NODEFILE \ pw.x -inp input.txt > output.txt # Gather remote files uniq $PBS_NODEFILE \ | while read host do ssh -n $host "rsync -a $TMPDIR/ $PBS_O_WORKDIR/" done --------------------------------------------------- E.g. for a job with nodes=3:ppn=4 the scatter part would distribute the existing files pwscf.wfc{1..12} as follows: ssh -n n340 'cd /home/stern/test/quantum-espresso/restart_test/run8; mv pwscf.wfc5 pwscf.wfc6 pwscf.wfc7 pwscf.wfc8 /tmp/191405.mds01.carboncluster/' ssh -n n342 'cd /home/stern/test/quantum-espresso/restart_test/run8; mv pwscf.wfc9 pwscf.wfc10 pwscf.wfc11 pwscf.wfc12 /tmp/191405.mds01.carboncluster/' ssh -n n339 'cd /home/stern/test/quantum-espresso/restart_test/run8; mv pwscf.wfc1 pwscf.wfc2 pwscf.wfc3 pwscf.wfc4 /tmp/191405.mds01.carboncluster/' rsync -a pwscf.save /tmp/191405.mds01.carboncluster (I chose "mv" rather than "cp" for the proof of concept to be sure there's only one instance per wfc file available.) Now, this is of course cumbersome code to repeat in production job scripts, but the scatter and gather bits could be isolated into utility scripts callable by a single line. Torque provides for Prologue & Epilogue Scripts , but those have rather restrictive runtime environments. Is this something to pursue further? To avoid the stagein file name+number juggling, could the fopen() functions for wfc files (and others) perhaps be wrapped such that if a file is not found in $ESPRESSO_TMPDIR it is read instead from in "." but written to $ESPRESSO_TMPDIR. The stageout is somewhat simpler and in fact not specific to pw.x at all. With best regards, Michael From bamideleibrahim at yahoo.com Mon Sep 5 06:58:18 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Sun, 4 Sep 2011 21:58:18 -0700 (PDT) Subject: [Pw_forum] xspectra calculation error Message-ID: <1315198698.76736.YahooMailNeo@web39408.mail.mud.yahoo.com> Dear all, ?? I am trying to run xspectra calculation on MgSe. Knowing that there is no gipaw pseudopotential for both contributing element on ? the pwscf-pseudo page, i tried to generate one for both Mg and Se. After running scf with this pseudo, i proceed to running the ? xspectra with xspectra.x but to my surprise, it keeps given this error ; ? ?? from allocate_fft : error #???????? 1 ???? the nr"s are too small! Please, can anybody help me out with this? ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/05c3ac7b/attachment.htm From vkarthik at MIT.EDU Mon Sep 5 08:51:22 2011 From: vkarthik at MIT.EDU (vkarthik) Date: Mon, 05 Sep 2011 02:51:22 -0400 Subject: [Pw_forum] Segmentation fault with pp.x Message-ID: <20110905025122.589gwx9kbo00ckok@webmail.mit.edu> Hi, I am using quantum espresso-4.3.2 and running some examples given at the tutorial website on the quantum espresso webpage.http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ PWscf - Simple examples I am trying to run a post process job to determine the charge density. As mentioned in the slides when I run the command prompt> espresso_dir/bin/pp.x < si.pp_rho.in I get en error message Program POST-PROC v.4.3.2 starts on 5Sep2011 at 12:13:38 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 Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input G-vector sticks info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Sum 163 163 61 1459 1459 339 Segmentation fault any help would be appreciated. best, Karthik From crma at sissa.it Mon Sep 5 09:03:43 2011 From: crma at sissa.it (Changru Ma) Date: Mon, 5 Sep 2011 09:03:43 +0200 Subject: [Pw_forum] Segmentation fault with pp.x In-Reply-To: <20110905025122.589gwx9kbo00ckok@webmail.mit.edu> References: <20110905025122.589gwx9kbo00ckok@webmail.mit.edu> Message-ID: Dear Karthik, It's explained in the User Guide. 12.6.0.1 Why is my job crashing with ``segmentation fault''? Possible reasons: too much memory requested; executable or libraries fitted to a different hardware; code bug; compiler bug. The latter are typically not reproducible on different architectures or compilers; code bugs may sometimes be elusive, but typically yield a more reproducible, pattern of problems. Mysterious, unpredictable, erratic errors in parallel execution are almost always coming from bugs in the compiler or/and in the MPI libraries and sometimes even from flaky hardware. Sorry, not our fault. HTH, Changru On 5 Sep, 2011, at 08:51, vkarthik wrote: > Hi, > > I am using quantum espresso-4.3.2 and running some examples given at the > tutorial website on the quantum espresso > webpage.http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ PWscf - Simple > examples > > I am trying to run a post process job to determine the charge density. > As mentioned in the slides when I run the command > prompt> espresso_dir/bin/pp.x < si.pp_rho.in > I get en error message > Program POST-PROC v.4.3.2 starts on 5Sep2011 at 12:13:38 > > 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 > > Info: using nr1, nr2, nr3 values from input > > Info: using nr1s, nr2s, nr3s values from input > > G-vector sticks info > -------------------- > sticks: dense smooth PW G-vecs: dense smooth PW > Sum 163 163 61 1459 1459 339 > > Segmentation fault > > any help would be appreciated. > best, > Karthik > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/9d133c90/attachment-0001.htm From lfhuang at theory.issp.ac.cn Mon Sep 5 09:26:42 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 05 Sep 2011 15:26:42 +0800 Subject: [Pw_forum] =?utf-8?q?Convergence_problem_with_spin-polarized_BLYP?= Message-ID: <20110905072642.22881.qmail@ms.hfcas.ac.cn> Dear QE developers: I am testing generated BLYP US PPs for H and F atoms. Thus, nspin=2 is chosen. The energy convergence is quite good for H if parameterizing carefully, and a satisfactory H_2 dissociation energy of 4.478 eV (the ZPE-corrected binding energy, expt. 4.484 eV) can be obtained. However, when calculating F atom, E_tot always flys away from the value that it ought to be (~-50 Ry). First, I supposed that it might is due to the high localization of wfc and large wfc response, thus I decrease the mixing beta lower and lower, even down to 0.001. However, the convergence problem was not solved. Then, I searched in the PW_FORUM, and I found that the spin-polarized BLYP was not allowed in 2004. So, I want to know does the spin-polarized BLYP still not performance well, although it is allowed now? Best Wishes! Sincerely, L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/ba80ac9a/attachment.htm From matteo.calandra at impmc.jussieu.fr Mon Sep 5 09:43:17 2011 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Mon, 05 Sep 2011 09:43:17 +0200 Subject: [Pw_forum] XSpectra calculation error In-Reply-To: References: Message-ID: <4E647D95.5000309@impmc.jussieu.fr> > > Message: 3 > Date: Sun, 4 Sep 2011 21:58:18 -0700 (PDT) > From: bamidele ibrahim > Subject: [Pw_forum] xspectra calculation error > To: PWSCF Forum > Message-ID: > <1315198698.76736.YahooMailNeo at web39408.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > ?? I am trying to run xspectra calculation on MgSe. Knowing that there is no gipaw pseudopotential for both contributing element on > ? the pwscf-pseudo page, i tried to generate one for both Mg and Se. After running scf with this pseudo, i proceed to running the > ? xspectra with xspectra.x but to my surprise, it keeps given this error ; > > ? ?? from allocate_fft : error #???????? 1 > ???? the nr"s are too small! > Please, can anybody help me out with this? > > ? Dear Adetunji, which version of the code are you using ? Can you first try to run the examples to see that this is not related in some way to your input files or other. Maybe you can send us the input/output files to better understand what are you doing. All the best, M. > Adetunji Bamidele Ibrahim > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/05c3ac7b/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Mon, 05 Sep 2011 02:51:22 -0400 > From: vkarthik > Subject: [Pw_forum] Segmentation fault with pp.x > To: pw_forum at pwscf.org > Message-ID:<20110905025122.589gwx9kbo00ckok at webmail.mit.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I am using quantum espresso-4.3.2 and running some examples given at the > tutorial website on the quantum espresso > webpage.http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ PWscf - Simple > examples > > I am trying to run a post process job to determine the charge density. > As mentioned in the slides when I run the command > prompt> espresso_dir/bin/pp.x< si.pp_rho.in > I get en error message > Program POST-PROC v.4.3.2 starts on 5Sep2011 at 12:13:38 > > 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 > > Info: using nr1, nr2, nr3 values from input > > Info: using nr1s, nr2s, nr3s values from input > > G-vector sticks info > -------------------- > sticks: dense smooth PW G-vecs: dense smooth PW > Sum 163 163 61 1459 1459 339 > > Segmentation fault > > any help would be appreciated. > best, > Karthik > > > > ------------------------------ > > Message: 5 > Date: Mon, 5 Sep 2011 09:03:43 +0200 > From: Changru Ma > Subject: Re: [Pw_forum] Segmentation fault with pp.x > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Karthik, > > It's explained in the User Guide. > > 12.6.0.1 Why is my job crashing with ``segmentation fault''? > > Possible reasons: too much memory requested; executable or libraries fitted to a different hardware; code bug; compiler bug. The latter are typically not reproducible on different architectures or compilers; code bugs may sometimes be elusive, but typically yield a more reproducible, pattern of problems. > > Mysterious, unpredictable, erratic errors in parallel execution are almost always coming from bugs in the compiler or/and in the MPI libraries and sometimes even from flaky hardware. Sorry, not our fault. > > HTH, > Changru > > On 5 Sep, 2011, at 08:51, vkarthik wrote: > >> Hi, >> >> I am using quantum espresso-4.3.2 and running some examples given at the >> tutorial website on the quantum espresso >> webpage.http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ PWscf - Simple >> examples >> >> I am trying to run a post process job to determine the charge density. >> As mentioned in the slides when I run the command >> prompt> espresso_dir/bin/pp.x< si.pp_rho.in >> I get en error message >> Program POST-PROC v.4.3.2 starts on 5Sep2011 at 12:13:38 >> >> 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 >> >> Info: using nr1, nr2, nr3 values from input >> >> Info: using nr1s, nr2s, nr3s values from input >> >> G-vector sticks info >> -------------------- >> sticks: dense smooth PW G-vecs: dense smooth PW >> Sum 163 163 61 1459 1459 339 >> >> Segmentation fault >> >> any help would be appreciated. >> best, >> Karthik >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA& Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/9d133c90/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 51, Issue 9 > *************************************** -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From parthasarathi13 at gmail.com Mon Sep 5 11:34:09 2011 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Mon, 5 Sep 2011 15:04:09 +0530 Subject: [Pw_forum] Quarry about special k-point Message-ID: Dear QE users, I am interested in plotting phonon dispersion curve of a crystal having space group Cmcm (63) [orthorhombic base centred structure with b>c>a]. For that I took some of the special k-points from the website : http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list (for b>a). I want to see phonon branches from 'Gamma' to 'Y' through point 'C' (special k-points as mentioned in that site). 'C' point is given as u-1/2,u+1/2,0 ex. My question is how to write this special k-point path in matdyn.in file. Thanks in advance P. S. Ghosh BARC,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/29ed1d1e/attachment.htm From colonel.sreekar at gmail.com Mon Sep 5 15:55:02 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 5 Sep 2011 19:25:02 +0530 Subject: [Pw_forum] xspectra calculation error Message-ID: > > > Dear all, Respected Mr. Ibrahim, > > ?? I am trying to run xspectra calculation on MgSe. Knowing that there is > no gipaw pseudopotential for both contributing element on > ? the pwscf-pseudo page, i tried to generate one for both Mg and Se. After > running scf with this pseudo, i proceed to running the > ? xspectra with xspectra.x but to my surprise, it keeps given this error ; > > ? ?? from allocate_fft : error #???????? 1 > ???? the nr"s are too small! > Please, can anybody help me out with this? > > A helpful tool(weapon :D) for tracking down errors is to use (learnt from Prof. Gianozzi's replies on the forum) $ grep -e '' */*.f90 In this case,, $ grep -e 'are too small' */*.f90 Results gives the relevant code file where it occurs. $PW/allocate_fft.f90: CALL errore ('allocate_fft', 'the nr"s are too small!', 1) $PW/allocate_fft.f90: CALL errore ('allocate_fft', 'the nrs"s are too small!', 1) A look at the file PW/allocate_fft.f90 suggests that --------------------------------- IF (nrxx.lt.ngm) THEN WRITE( stdout, '(/,4x," nr1=",i4," nr2= ", i4, " nr3=",i4, & &" nrxx = ",i8," ngm=",i8)') nr1, nr2, nr3, nrxx, ngm CALL errore ('allocate_fft', 'the nr"s are too small!', 1) --------------------------------- Here nrxx = nr1*nr2*nr3 (Modules/griddim.f90), the minimal 3D real-space FFT grid required to fit the G-vector sphere with G^2 <= gcut ngm = local number of G vectors (Modules/recvec.f90). I have not generated PPs, but I can only infer that your FFT grid density is not sufficient enough to accommodate the G-vectors. Sincerely, -- Sreekar Guddeti Undergraduate (5th year) Engineering Physics IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/01befa26/attachment.htm From giannozz at democritos.it Mon Sep 5 19:08:54 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 5 Sep 2011 19:08:54 +0200 Subject: [Pw_forum] wfc files: heavy I/O, handling for restarts In-Reply-To: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> References: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> Message-ID: On Sep 5, 2011, at 5:22 , Michael Sternberg wrote: > If one MPI rank writes a file, must this file indeed be seen or even > readable by another MPI rank? no, as long as there is no need to restart from previous interrupted runs or to read wavefunction files for post-processing. The amount of I/O is determined by options "wf_collect" and "disk_io". The latter is also influenced by the number of k-points per process. Note however that this holds only for pw.x; for other executables (e.g. the phonon code) there are no such tricks. In all cases, it should be possible to use local scratch directories with no problem, collect files afterwards, if so desired. In principle, it shouldn't even be needed to collect all files so that they are visibile to all processors, but then you have to convince mpi to send the same process to the same processor as in the previous run! It will however be impossible to restart with a different number (or geometry) of processors. 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 ying.sun at gradmail.ims.uconn.edu Mon Sep 5 19:42:47 2011 From: ying.sun at gradmail.ims.uconn.edu (Ying Sun) Date: Mon, 05 Sep 2011 13:42:47 -0400 Subject: [Pw_forum] To Dr. Michele Lazzeri about write electron-phonon coupling matrix Message-ID: <20110905174256.020762D16F@mta2.uits.uconn.edu> Dear Dr. Michele Lazzeri, I want to calculate electron phonon coupling for semiconductors, e.g. Si. I try to modify the code to write out the electron phonon matrix. I searched the forum, you said you wrote a patch to write out the matrix element. You know I am a new user, not familiar with FORTRAN, it will be very helpful that you still have the patch,and could help me. Thank you so much for your help~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/6bc4603a/attachment.htm From sks.jnc at gmail.com Mon Sep 5 21:05:02 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Mon, 5 Sep 2011 21:05:02 +0200 Subject: [Pw_forum] wfc files: heavy I/O, handling for restarts In-Reply-To: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> References: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> Message-ID: >>>>>>>> # Scatter wfc restart files awk '{ files_for[$1] = files_for[$1] " '$basename'.wfc" NR } END { for (host in files_for) print host, files_for[host] }' $PBS_NODEFILE \ | while read host files do ssh -n $host "cd $PBS_O_WORKDIR; mv $files $ESPRESSO_TMPDIR/" done # on master host, copy .save directory as well rsync -a $basename.save $ESPRESSO_TMPDIR mpirun -x ESPRESSO_TMPDIR \ -np $(wc -l < $PBS_NODEFILE) \ -machinefile $PBS_NODEFILE \ pw.x -inp input.txt > output.txt # Gather remote files uniq $PBS_NODEFILE \ | while read host do ssh -n $host "rsync -a $TMPDIR/ $PBS_O_WORKDIR/" done ------------------------------ E.g. for a job with nodes=3:ppn=4 the scatter part would distribute the existing files pwscf.wfc{1..12} as follows: <<<<<< Yes, this looks indeed cumbersome. It becomes more painful when one can not know a priori in which nodes his/her job will go, particularly when it is totally decided by the automatic queue decider, depending on the free nodes available. In such a situation, one's restarted job may go to a totally new set of nodes, and phonon calculation can not get necessary files to restart. Then restarting phonon calculation becomes more difficult. It seems, there is a more serious trouble in the recent version of QE. In the version before QE4.2, the QE codes used to replicate the same necessary files to the distributed local disks of all the nodes. In this case, at least phonon calculation can run smoothly instead of crashing. But in the recent version, phonon calculations just stop by complaining that the distributed .wfc files in one node are not visible by another node. If a quick remedy of this problem is not easy, then at least, for the time being, it is better to keep the earlier option of replicating the same .wfc files in all the nodes still working in the version 4.3.1. Other better option can be to implement the "WF_COLLECT" trick, also in phonon code, as it is already there for PW.x. Thanks and regards, Saha SK R&D Assistant JNCASR Bangalore 560064 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/ea2b77e7/attachment-0001.htm From nafiserb at gmail.com Tue Sep 6 07:59:29 2011 From: nafiserb at gmail.com (Nafise Rezaei) Date: Tue, 6 Sep 2011 10:29:29 +0430 Subject: [Pw_forum] heat capacity Message-ID: Dear Prof. Eyvaz Isaev, I want to calculate heat capacity for the Rhombohedral lattice (ibrav= 5). When I try to use QHA package, I have encountered with this message "Trigonal R: not implemented yet". I have seen similar question in mailing list and your reply. But yet I don't know what should be done? Thanks in advance, Nafise --- Nafise Rezaei Dept of Physics, Isfahan University of Technology Isfahan, Iran -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/52b9181f/attachment.htm From giannozz at democritos.it Tue Sep 6 13:06:35 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Sep 2011 13:06:35 +0200 Subject: [Pw_forum] wfc files: heavy I/O, handling for restarts In-Reply-To: References: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> Message-ID: On Sep 5, 2011, at 21:05 , S. K. S. wrote: > In the version before QE4.2, the QE codes used to replicate > the same necessary files to the distributed local disks of all > the nodes. which QE code and which files are you referring to? 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 sks.jnc at gmail.com Tue Sep 6 16:22:22 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Tue, 6 Sep 2011 16:22:22 +0200 Subject: [Pw_forum] wfc files: heavy I/O, handling for restarts In-Reply-To: References: <6061B965-BAA6-40B3-B221-E83B0C5A285D@anl.gov> Message-ID: Dear Prof. Paolo, Thanks a lot for your reply. > which QE code and which files are you referring to? < That is phonon code (ph.x) and the files I mentioned before are given below in detail. With the earlier versions up to 4.1.3, phonon code runs fine and I got following files (bold and underlined items are folders) in the tmp directory of a local disk. The nodes which are used by the codes are node186, 036, 139. node186:/tmpscratch/sksct8/tmp$ ls > *pbmno.save* _phpbmno.com1 _phpbmno.dwf2 _phpbmno.igk3 > _phpbmno.prd3 > pbmno.wfc1 _phpbmno.com2 _phpbmno.dwf3 _phpbmno.mixd1 > _phpbmno.recover > pbmno.wfc2 _phpbmno.com3 _phpbmno.ebar1 _phpbmno.mixd2 > _phpbmno.recover2 > pbmno.wfc3 _phpbmno.dvkb31 _phpbmno.ebar2 _phpbmno.mixd3 > _phpbmno.recover3 > _phpbmno.bar1 _phpbmno.dvkb32 _phpbmno.ebar3 *_phpbmno.phsave** * * > _phpbmno.save* > _phpbmno.bar2 _phpbmno.dvkb33 _phpbmno.igk _phpbmno.prd1 > _phpbmno.bar3 _phpbmno.dwf1 _phpbmno.igk2 _phpbmno.prd2 > node036:/tmpscratch/sksct8/tmp$ ls pbmno.wfc4 _phpbmno.dwf4 _phpbmno.mixd4 _phpbmno.recover4 pbmno.wfc5 _phpbmno.dwf5 _phpbmno.mixd5 _phpbmno.recover5 _phpbmno.bar4 _phpbmno.igk4 _phpbmno.prd4 _phpbmno.wfc4 _phpbmno.bar5 _phpbmno.igk5 _phpbmno.prd5 _phpbmno.wfc5 node139:/tmpscratch/sksct8/tmp$ ls pbmno.wfc6 _phpbmno.bar8 _phpbmno.igk7 _phpbmno.recover6 _phpbmno.wfc8 pbmno.wfc7 _phpbmno.dwf6 _phpbmno.igk8 _phpbmno.recover7 pbmno.wfc8 _phpbmno.dwf7 _phpbmno.prd6 _phpbmno.recover8 _phpbmno.bar6 _phpbmno.dwf8 _phpbmno.prd7 _phpbmno.wfc6 _phpbmno.bar7 _phpbmno.igk6 _phpbmno.prd8 _phpbmno.wfc7 However, with the new version 4.3.1, for the exactly same input files and job scripts I only get these files and nothing else : node045:/tmpscratch/sksct84/tmp$ ls *pbmno.save* pbmno.wfc1 *_ph0* node111:/tmpscratch/sksct84/tmp$ ls pbmno.wfc2 pbmno.wfc3 node092:/tmpscratch/sksct84/tmp$ ls pbmno.wfc4 pbmno.wfc5 node080:/tmpscratch/sksct84/tmp$ ls pbmno.wfc6 pbmno.wfc7 node072:/tmpscratch/sksct84/tmp$ ls pbmno.wfc8 Note that, the used nodes in this time are node045, node111, node092, node080, node072. So it is clear from the above example that somehow in the new version 4.3.1, _phpbmno.save and _phpbmno.phsave goes inside the directory "_ph0" ; And the same phonon calculation, which was running fine with the earlier version, now stops like this way (a bit abruptly and rudely, with out much informations or error messages) : Electric field: Dielectric constant Born effective charges in two ways Atomic displacements: There are 5 irreducible representations Representation 1 3 modes -T_1u G_15 G_4- To be done Representation 2 3 modes -T_1u G_15 G_4- To be done Representation 3 3 modes -T_1u G_15 G_4- To be done Representation 4 3 modes -T_1u G_15 G_4- To be done Representation 5 3 modes -T_2u G_25 G_5- To be done simply with this error : -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 2 with PID 8791 on node node111.cvos.cluster exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [node045:11580] 6 more processes have sent help message help-mpi-api.txt / mpi-abort [node045:11580] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Hope this email explains much better. Thanks and Regards, Saha SK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/78efc62c/attachment.htm From aguiardlm at iq.ufrj.br Tue Sep 6 18:56:43 2011 From: aguiardlm at iq.ufrj.br (Daniel Lima) Date: Tue, 6 Sep 2011 13:56:43 -0300 (BRT) Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <71003022.46734.1315328064932.JavaMail.root@mail.iq.ufrj.br> Message-ID: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> Hi, My name is Daniel Aguiar, and I'm a beginner in Theoretical Calculations. I'm having some troubles with the gipaw.x calculations . The pw.x was sucessed (JOB DONE!!). But in gipaw.x the following mensage appear: At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Fortran runtime error: File '' does not exist I verified in paw_gipaw.f90 and the line is: OPEN ( 14, FILE = filerec_sp ) What's wrong? My nmr input is following below: &inputgipaw job = 'nmr' prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' isolve = 0 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .false. / Thanks in advance and sorry for bad english -- Daniel Lima Marques de Aguiar Universidade Federal do Rio de Janeiro / Centro de Tecnologia Instituto de Qu?mica Programa de P?s Gradua??o em Qu?mica Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/cf36e007/attachment.htm From giannozz at democritos.it Tue Sep 6 19:11:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 6 Sep 2011 19:11:11 +0200 Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> Message-ID: <4A282624-93E6-410C-B182-05AD7DEAB6BA@democritos.it> On Sep 6, 2011, at 18:56 , Daniel Lima wrote: > Thanks in advance and sorry for bad english bad english is not a problem: it is the norm here. The problem is that you haven't specified which version of the code you are talking about. Gipaw, in particular, has undergone serious changes in the last versions 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 kucukben at sissa.it Tue Sep 6 19:11:41 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Tue, 06 Sep 2011 19:11:41 +0200 Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> Message-ID: <20110906191141.y5fu2yfw8wogg8ck@webmail.sissa.it> Hi Daniel, are you sure you are using pseudopotentials that hold gipaw information? if so, send me the pseudo i'll check what is wrong. thanks emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From eugeniofs at iq.ufrj.br Tue Sep 6 19:19:01 2011 From: eugeniofs at iq.ufrj.br (Eugenio Furtado) Date: Tue, 6 Sep 2011 14:19:01 -0300 (BRT) Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <20110906191141.y5fu2yfw8wogg8ck@webmail.sissa.it> Message-ID: <1148323644.46861.1315329541199.JavaMail.root@mail.iq.ufrj.br> you sure you doing the right thing? Did you choose the correct pseudop? your compilation ran perfectly? The system were correctly relaxed? Can you send the pseudos and the input for checks? Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 ----- Mensagem original ----- De: "Emine Kucukbenli" Para: "pw forum" Enviadas: Ter?a-feira, 6 de Setembro de 2011 14:11:41 Assunto: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Hi Daniel, are you sure you are using pseudopotentials that hold gipaw information? if so, send me the pseudo i'll check what is wrong. thanks emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110906/76c1483a/attachment.htm From xijunw at gmail.com Wed Sep 7 01:35:06 2011 From: xijunw at gmail.com (Xijun Wang) Date: Tue, 6 Sep 2011 19:35:06 -0400 Subject: [Pw_forum] ATOMIC_POSITIONS after 'final coordinates' Message-ID: Hi, dear espressors, I'm new to espresso (switching from CPMD) and I have a simple question regarding to the output file of a relax calculation. There is an extra "ATOMIC_POSITIONS" section after the "final coordinates". It is neither the final coordinates, nor the starting coordinates, nor cystal coordinates. What's that? See below the output file. I'd appreciate it if someone can tell me where to find the explanation to the output file in the manual. I have searched the maillist and manual online but find no answer. Xijun Wang -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 *** output file of the relaxation calculation *** ------------------------------------------------------------------------- ... ? ? ?Damped Dynamics: convergence achieved in ?11 steps ? ? ?End of damped dynamics calculation ? ? ?Final energy = ? -3499.4924725209 Ry Begin final coordinates ? ? ?new unit-cell volume = ? 5281.07728 a.u.^3 ( ? 782.57490 Ang^3 ) CELL_PARAMETERS (alat= 19.96079920) ? ?1.000000000 ? 0.000000000 ? 0.000000000 ? ?0.000000000 ? 0.591661302 ? 0.000000000 ? -0.254163181 ? 0.000000000 ? 1.122317102 ATOMIC_POSITIONS (angstrom) Zr ? ? ?-0.000121009 ? 0.000000000 ? 0.000048982 Zr ? ? ? 0.050917464 ? 0.000000000 ? 6.659231281 ... End final coordinates ? ? ?Entering Dynamics: ? ?iteration = ? ?11 ? ? ? = ? 0.78384260 ATOMIC_POSITIONS (angstrom) Zr ? ? ? 0.000033474 ? 0.000000000 ? 0.000130486 Zr ? ? ? 0.050452867 ? 0.000000000 ? 6.659368418 ... Writing output data file rx.damp.save ... From renpj at dicp.ac.cn Wed Sep 7 02:58:15 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Wed, 7 Sep 2011 08:58:15 +0800 Subject: [Pw_forum] How to speed up gipaw? In-Reply-To: References: Message-ID: <20110907085815.6e81dcf0@ren-desktop> Dear all, I'm using gipaw to calculate NMR of a system contain more than 100 atoms, but the first k point haven't been done after more than 40 hours. It's so slow for me. Here is my input: &inputgipaw job = 'nmr' prefix = 'pw' tmp_dir = './tmp/' isolve = 0 conv_threshold=1e-10 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .true. nmr_macroscopic_shape = 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.6667 / Can anyone figure me out how to improve this? PS. My computer is 8 core cpu, and gipaw and QE is compiled with intel mkl lib. Thanks very much! Pengju Ren Dalian Institute of Chemical Physics, Chinese Academy of Science From robinshy at gmail.com Wed Sep 7 04:45:32 2011 From: robinshy at gmail.com (Robin H) Date: Wed, 7 Sep 2011 10:45:32 +0800 Subject: [Pw_forum] about PWscf PP generation In-Reply-To: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> References: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> Message-ID: thank you for your tips,I'm so careless to make such a stupid mistake.After trying for many times I 'm encountered the only problem is how to choose a perfect rc.When I set rc=1.9,in the pseudo_run there is a warning like this: WARNING! Expected number of nodes: 1= 3- 1- 1, number of nodes found: 0. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) Zero norm: self consistency problem; state: 5 (l= 1, j=0.0) and the generated PP is not very well: n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 5S 1( 2.00) -2.85985 -3.28355 0.42370 2 1 5P 1( 6.00) -1.64629 -1.99138 0.34509 2 0 6S 1( 2.00) -0.26736 -0.30023 0.03286 3 2 5D 1( 1.00) -0.22479 -0.44003 0.21524 3 1 6P 1( 0.00) -0.09835 -0.09835 0.00000 this is my input file : &input title='La' zed=57. rel=1, config='[Xe] 6s2.00 5d1.00 6p0.00', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5D 3 2 1.00 0.00 2.00 2.20 5D 3 2 0.00 0.50 2.00 2.20 5S 1 0 2.00 0.00 2.00 2.20 5S 1 0 0.00 0.50 2.00 2.20 5P 2 1 6.00 0.00 1.90 1.90 &test configts(1)='5s2 5p6 6s2 5d1 6p0', I 'm not good at PP generation.And maybe I choose an unproper rc,so I can't get a good result for calculation.You're so kind and so experienced in solving this kind of problem,hope for your advice. ? 2011?9?4? ??9:55?GAO Zhe ??? > Of course, since the element Xe already has 5s2 and 5p2~ you can change > parameter "config" like: '[Xe] 5d1 6s1.5 6p0.5' > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-09-04 20:37:09,"Robin H" wrote: > > Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for > the first time I met a mistake like this > Program LD1 v.4.3.1 starts on 4Sep2011 at 19:53:36 > 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 > Parallel version (MPI), running on 1 processors > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from el_config : error # 12 > wavefunction 5S found too many times > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > since the input is like this > &input > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > nlcc=.true., > tm=.true., > file_pseudopw='La.revPBE.UPF', > / > 5 > 5D 3 2 1.00 0.00 2.20 2.20 > 5D 3 2 0.00 0.05 2.20 2.20 > 6S 1 0 2.00 0.00 2.20 2.20 > 6S 1 0 0.00 0.05 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.00 > Is there anything wrong in my electric configuration of La? > as I changed like this : > &input > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > nlcc=.true., > tm=.true., > file_pseudopw='La.revPBE.UPF', > / > 5 > 5S 1 0 2.00 0.00 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.20 > 5D 3 2 1.00 0.00 2.20 2.20 > 6S 1 0 1.50 0.00 2.20 2.20 > 6P 2 1 0.50 0.00 2.20 2.00 > the error is still exist like the fomer.what's the error suggest ?I'm > wondered that how to write the list of states following the namelist of > &inputp.I tried to find some information in the reference of PWscf to make > me clear,but this part seemed hard to understand,hope everyone who is > sophisticated at PP generation to give me some tips, I'm appreciated. > > > > > _______________________________________________ > 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/20110907/5b5ec167/attachment.htm From giannozz at democritos.it Wed Sep 7 10:54:06 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 10:54:06 +0200 Subject: [Pw_forum] ATOMIC_POSITIONS after 'final coordinates' In-Reply-To: References: Message-ID: <5508B106-C8A2-42A3-B8AA-0B87C18704C0@democritos.it> On Sep 7, 2011, at 1:35 , Xijun Wang wrote: > There is an extra "ATOMIC_POSITIONS" section after the "final > coordinates". It is neither the final coordinates why are you saying this? 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 Wed Sep 7 10:56:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 10:56:33 +0200 Subject: [Pw_forum] about PWscf PP generation In-Reply-To: References: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> Message-ID: <1D263F60-1CC1-4D12-9AF0-F0868F8B5D88@democritos.it> On Sep 7, 2011, at 4:45 , Robin H wrote: > I 'm not good at PP generation nobody is. Did you read atomic_doc/pseudo-gen.tex? it is incomplete but better than nothing 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 davide.ceresoli at materials.ox.ac.uk Wed Sep 7 11:47:09 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Wed, 07 Sep 2011 10:47:09 +0100 Subject: [Pw_forum] How to speed up gipaw? In-Reply-To: <20110907085815.6e81dcf0@ren-desktop> References: <20110907085815.6e81dcf0@ren-desktop> Message-ID: <4E673D9D.2020801@materials.ox.ac.uk> Dear Pengju, on possibility is to use pools, in order to distribute k-points on more CPUs. I always set iverbosity=1 to see some output as the calculation is running (I suffer of empty-output-phobia). To get an idea of the computational cost: I have calculated a complicated silicate mineral with 88 atoms in the unit cell. 4 special k-points. The calculation took 1 day on 16 CPUs. Davide On 01/-10/-28163 08:59 PM, Ren PJ wrote: > Dear all, > I'm using gipaw to calculate NMR of a system contain more than 100 > atoms, but the first k point haven't been done after more than 40 > hours. It's so slow for me. > Here is my input: > &inputgipaw > job =nmr' > prefix =pw' > tmp_dir =./tmp/' > isolve = > conv_threshold -10 > iverbosity = > q_gipaw = .01 > spline_ps =true. > use_nmr_macroscopic_shape =true. > nmr_macroscopic_shape =.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.6667 > / > Can anyone figure me out how to improve this? > PS. My computer is 8 core cpu, and gipaw and QE is compiled with intel > mkl lib. > Thanks very much! > > Pengju Ren > > Dalian Institute of Chemical Physics, > Chinese Academy of Science > From davide.ceresoli at materials.ox.ac.uk Wed Sep 7 11:39:58 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Wed, 07 Sep 2011 10:39:58 +0100 Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> Message-ID: <4E673BEE.3010008@materials.ox.ac.uk> Dear Daniel, this is a fallback situation. When GIPAW pseudopotentials are not available, the code will try to read the 'Paratec reconstruction file'. We did this in the beginning in order to debug the code and make sure we obtained the same results of Paratec. This feature will be removed soon and a clearer error message will be printed. Cheers, Davide On 01/-10/-28163 08:59 PM, Daniel Lima wrote: > Hi, > My name is Daniel Aguiar, and I'm a beginner in Theoretical Calculations. > I'm having some troubles with the gipaw.x calculations. > The pw.x was sucessed (JOB DONE!!). > But in gipaw.x the following mensage appear: > > At line 174 of file paw_gipaw.f90 (unit = 14, file = '') > Fortran runtime error: File '' does not exist > > > I verified in paw_gipaw.f90 and the line is: > > OPEN ( 14, FILE = filerec_sp ) > > What's wrong? > > My nmr input is following below: > > &inputgipaw > job = 'nmr' > prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' > tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' > isolve = 0 > iverbosity = 1 > q_gipaw = 0.01 > spline_ps = .true. > use_nmr_macroscopic_shape = .false. > / From gregor.mali at ki.si Wed Sep 7 12:49:38 2011 From: gregor.mali at ki.si (Gregor Mali) Date: Wed, 7 Sep 2011 12:49:38 +0200 Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <4E673BEE.3010008@materials.ox.ac.uk> References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> <4E673BEE.3010008@materials.ox.ac.uk> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D2560304337B@postar.ki.si> Dear Davide, does the code still require that pseudopotentials for all the species contain the GIPAW reconstruction part. Is it (or will it be) possible that one uses 'non-gipaw' pseudopotentials for the atomic species if one is not interested in NMR shifts or EPR parameters of these species (or if one does not have a proper gipaw pseudopotential for that atomic species)? Best regards. Gregor Gregor Mali Kemijski institut/National Institute of Chemistry Hajdrihova 19 SI-1001 Ljubljana tel. +386 1 47 60 412 fax +386 1 47 60 300 > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Davide Ceresoli > Sent: 7. september 2011 11:40 > To: PWSCF Forum > Subject: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 > (unit = 14, file = '') > > Dear Daniel, > this is a fallback situation. When GIPAW > pseudopotentials are not available, the code will try to read > the 'Paratec reconstruction file'. We did this in the > beginning in order to debug the code and make sure we > obtained the same results of Paratec. This feature will be > removed soon and a clearer error message will be printed. > > Cheers, > Davide > > > On 01/-10/-28163 08:59 PM, Daniel Lima wrote: > > Hi, > > My name is Daniel Aguiar, and I'm a beginner in Theoretical > Calculations. > > I'm having some troubles with the gipaw.x calculations. > > The pw.x was sucessed (JOB DONE!!). > > But in gipaw.x the following mensage appear: > > > > At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Fortran > > runtime error: File '' does not exist > > > > > > I verified in paw_gipaw.f90 and the line is: > > > > OPEN ( 14, FILE = filerec_sp ) > > > > What's wrong? > > > > My nmr input is following below: > > > > &inputgipaw > > job = 'nmr' > > prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' > > tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' > > isolve = 0 > > iverbosity = 1 > > q_gipaw = 0.01 > > spline_ps = .true. > > use_nmr_macroscopic_shape = .false. > > / > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mulwawinfred at gmail.com Wed Sep 7 13:57:14 2011 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Wed, 7 Sep 2011 14:57:14 +0300 Subject: [Pw_forum] (no subject) Message-ID: Dear all, I have tried doing a vc-relax on the attached TiO*2 *rutile supercell, but the calculations stop after a few seconds without giving any error. What might be the problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/7239ed27/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: TiOsc.scf.in1 Type: application/octet-stream Size: 3618 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110907/7239ed27/attachment.obj From kucukben at sissa.it Wed Sep 7 14:09:00 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 07 Sep 2011 14:09:00 +0200 Subject: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '') In-Reply-To: <8C0B47760A05FB4AB504C9BCAD32D2560304337B@postar.ki.si> References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br> <4E673BEE.3010008@materials.ox.ac.uk> <8C0B47760A05FB4AB504C9BCAD32D2560304337B@postar.ki.si> Message-ID: <20110907140900.enq05sxdhsss080g@webmail.sissa.it> Dear Gregor, gipaw is based on paw, as long as it stays so it will always require paw description of the atom.. if you are using a traditional norm conserving or ultrasoft pseudopotential that means you need this description to be calculated and written, which will make it a 'gipaw pseudopotential' If you are using a paw pseudopotential however, everything is already calculated. unfortunately it has not been the default to write down this necessary information. in the future i would like to make it default, such that every paw pseudopotential file already is gipaw-suitable. it is just that there are some details to work out,like,you may want the pw.x to use a different set of projectors (possibly cheaper ones) than gipaw.x part..so we should keep this freedom etc. about not having the paw set for the atoms you are not interested in..what would you propose? the induced magnetic field at a point depends on the induced current in all space..do you suggest a space cut off? or calculating the current response of these atoms we are not interested in without paw constructions? instead there is the 'converse approach' you may want to look at, that sounds more efficient if you are interested in nmr parameters of one atom in huge molecule, for example.. we can hear more from Davide about it. emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From mulwawinfred at yahoo.com Wed Sep 7 14:22:30 2011 From: mulwawinfred at yahoo.com (Winfred Mulwa) Date: Wed, 7 Sep 2011 05:22:30 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Dear all ?????? I have tried doing a vc-relax on the attached TiO2 rutile supercell, the calculations stop after a few minutes without giving any error. What might be the problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/63d5859b/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: TiOsc.scf.in1 Type: application/octet-stream Size: 3619 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110907/63d5859b/attachment-0001.obj From giuseppe.mattioli at mlib.ism.cnr.it Wed Sep 7 14:29:49 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 7 Sep 2011 14:29:49 +0200 Subject: [Pw_forum] [SUSPECTED SPAM-Ironport] (no subject) In-Reply-To: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Message-ID: <201109071429.50039.giuseppe.mattioli@mlib.ism.cnr.it> Dear Winfred I suspect that nobody will help you if you do not: a) choose a meaningful subject for your post (e.g., tio2 supercell unexpected pw.x crash) b) sign your post (with your scientific affiliation) c) provide more details (e.g., QE version, pw.x output, ...) Yours Giuseppe On Wednesday 07 September 2011 14:22:30 Winfred Mulwa wrote: > Dear all > > ?????? I have tried doing a vc-relax on the attached TiO2 rutile supercell, > the calculations stop after a few minutes without giving any error. > > What might be the problem? -- ******************************************************** - 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 crma at sissa.it Wed Sep 7 14:44:05 2011 From: crma at sissa.it (Changru Ma) Date: Wed, 7 Sep 2011 14:44:05 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Message-ID: <6A32BE43-3158-42D2-8614-8EE8CF8AB68F@sissa.it> Dear Winfred, I just have a look at the input you provided. Are you sure this is TiO2 rutile? Please visualize the structure with a software like Xcrysden first. HTH, Changru On 7 Sep, 2011, at 14:22, Winfred Mulwa wrote: > Dear all > > I have tried doing a vc-relax on the attached TiO2 rutile supercell, > the calculations stop after a few minutes without giving any error. > What might be the problem? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/0f1b7804/attachment.htm From giannozz at democritos.it Wed Sep 7 14:47:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 14:47:28 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Message-ID: On Sep 7, 2011, at 14:22 , Winfred Mulwa wrote: > the calculations stop after a few minutes without giving any error. > What might be the problem? http://www.quantum-espresso.org/user_guide/ node52.html#SECTION000121080000000000000 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 flux_ray12 at 163.com Wed Sep 7 15:13:25 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 7 Sep 2011 21:13:25 +0800 (CST) Subject: [Pw_forum] (no subject) In-Reply-To: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Message-ID: According to your input information, nat=48, I think you wanted to make 2x2x2 rutile-TiO2 supercell with a substitutional Nb. However, you setted celldm(1) and ATOMIC_POSITIONS wrong. You may set celldm(1)=1 and keep CELL_PARAMETERS; or keep celldm(1)=8.7 and set CELL_PARAMETERS as 2.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 1.288 For ATOMIC_POSITIONS, you may set it as: ATOMIC_POSITIONS {crystal} O 0.1523998693948630 0.1523998693948630 0.0000000000000000 O 0.3476001306051368 0.3476001306051368 0.0000000000000000 O 0.0976001306051369 0.4023998693948629 0.2500000000000001 O 0.4023998693948629 0.0976001306051369 0.2500000000000001 O 0.6523998693948631 0.1523998693948630 0.0000000000000000 O 0.8476001306051368 0.3476001306051368 0.0000000000000000 O 0.5976001306051370 0.4023998693948629 0.2500000000000001 O 0.9023998693948629 0.0976001306051369 0.2500000000000001 O 0.1523998693948630 0.6523998693948631 0.0000000000000000 O 0.3476001306051368 0.8476001306051368 0.0000000000000000 O 0.0976001306051369 0.9023998693948629 0.2500000000000001 O 0.4023998693948629 0.5976001306051370 0.2500000000000001 O 0.6523998693948631 0.6523998693948631 0.0000000000000000 O 0.8476001306051368 0.8476001306051368 0.0000000000000000 O 0.5976001306051370 0.9023998693948629 0.2500000000000001 O 0.9023998693948629 0.5976001306051370 0.2500000000000001 O 0.1523998693948630 0.1523998693948630 0.5000000000000000 O 0.3476001306051368 0.3476001306051368 0.5000000000000000 O 0.0976001306051369 0.4023998693948629 0.7500000000000001 O 0.4023998693948629 0.0976001306051369 0.7500000000000001 O 0.6523998693948631 0.1523998693948630 0.5000000000000000 O 0.8476001306051368 0.3476001306051368 0.5000000000000000 O 0.5976001306051370 0.4023998693948629 0.7500000000000001 O 0.9023998693948629 0.0976001306051369 0.7500000000000001 O 0.1523998693948630 0.6523998693948631 0.5000000000000000 O 0.3476001306051368 0.8476001306051368 0.5000000000000000 O 0.0976001306051369 0.9023998693948629 0.7500000000000001 O 0.4023998693948629 0.5976001306051370 0.7500000000000001 O 0.6523998693948631 0.6523998693948631 0.5000000000000000 O 0.8476001306051368 0.8476001306051368 0.5000000000000000 O 0.5976001306051370 0.9023998693948629 0.7500000000000001 O 0.9023998693948629 0.5976001306051370 0.7500000000000001 Ti -0.0000000000000000 -0.0000000000000000 0.0000000000000000 Ti 0.2499999999999998 0.2499999999999998 0.2500000000000001 Ti 0.5000000000000000 -0.0000000000000000 0.0000000000000000 Ti 0.7499999999999998 0.2499999999999998 0.2500000000000001 Ti -0.0000000000000000 0.5000000000000000 0.0000000000000000 Ti 0.2499999999999998 0.7499999999999998 0.2500000000000001 Ti 0.5000000000000000 0.5000000000000000 0.0000000000000000 Ti 0.7499999999999998 0.7499999999999998 0.2500000000000001 Ti -0.0000000000000000 -0.0000000000000000 0.5000000000000000 Ti 0.2499999999999998 0.2499999999999998 0.7500000000000001 Ti 0.5000000000000000 -0.0000000000000000 0.5000000000000000 Ti 0.7499999999999998 0.2499999999999998 0.7500000000000001 Ti -0.0000000000000000 0.5000000000000000 0.5000000000000000 Ti 0.2499999999999998 0.7499999999999998 0.7500000000000001 Ti 0.5000000000000000 0.5000000000000000 0.5000000000000000 Ti 0.7499999999999998 0.7499999999999998 0.7500000000000001 -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-07 20:22:30,"Winfred Mulwa" wrote: Dear all I have tried doing a vc-relax on the attached TiO2 rutile supercell, the calculations stop after a few minutes without giving any error. What might be the problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/b844fe2f/attachment.htm From flux_ray12 at 163.com Wed Sep 7 15:16:34 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 7 Sep 2011 21:16:34 +0800 (CST) Subject: [Pw_forum] (no subject) In-Reply-To: References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> Message-ID: <4aacc2a1.e575.132440867bd.Coremail.flux_ray12@163.com> Oh, my mistake, I forgot that bohr is used in QE. So, if you wanna keep CELL_PARAMETERS, you have to set celldm(1) = 1.889725989. Soory~ -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-07 21:13:25,"GAO Zhe" wrote: According to your input information, nat=48, I think you wanted to make 2x2x2 rutile-TiO2 supercell with a substitutional Nb. However, you setted celldm(1) and ATOMIC_POSITIONS wrong. You may set celldm(1)=1 and keep CELL_PARAMETERS; or keep celldm(1)=8.7 and set CELL_PARAMETERS as 2.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 1.288 For ATOMIC_POSITIONS, you may set it as: ATOMIC_POSITIONS {crystal} O 0.1523998693948630 0.1523998693948630 0.0000000000000000 O 0.3476001306051368 0.3476001306051368 0.0000000000000000 O 0.0976001306051369 0.4023998693948629 0.2500000000000001 O 0.4023998693948629 0.0976001306051369 0.2500000000000001 O 0.6523998693948631 0.1523998693948630 0.0000000000000000 O 0.8476001306051368 0.3476001306051368 0.0000000000000000 O 0.5976001306051370 0.4023998693948629 0.2500000000000001 O 0.9023998693948629 0.0976001306051369 0.2500000000000001 O 0.1523998693948630 0.6523998693948631 0.0000000000000000 O 0.3476001306051368 0.8476001306051368 0.0000000000000000 O 0.0976001306051369 0.9023998693948629 0.2500000000000001 O 0.4023998693948629 0.5976001306051370 0.2500000000000001 O 0.6523998693948631 0.6523998693948631 0.0000000000000000 O 0.8476001306051368 0.8476001306051368 0.0000000000000000 O 0.5976001306051370 0.9023998693948629 0.2500000000000001 O 0.9023998693948629 0.5976001306051370 0.2500000000000001 O 0.1523998693948630 0.1523998693948630 0.5000000000000000 O 0.3476001306051368 0.3476001306051368 0.5000000000000000 O 0.0976001306051369 0.4023998693948629 0.7500000000000001 O 0.4023998693948629 0.0976001306051369 0.7500000000000001 O 0.6523998693948631 0.1523998693948630 0.5000000000000000 O 0.8476001306051368 0.3476001306051368 0.5000000000000000 O 0.5976001306051370 0.4023998693948629 0.7500000000000001 O 0.9023998693948629 0.0976001306051369 0.7500000000000001 O 0.1523998693948630 0.6523998693948631 0.5000000000000000 O 0.3476001306051368 0.8476001306051368 0.5000000000000000 O 0.0976001306051369 0.9023998693948629 0.7500000000000001 O 0.4023998693948629 0.5976001306051370 0.7500000000000001 O 0.6523998693948631 0.6523998693948631 0.5000000000000000 O 0.8476001306051368 0.8476001306051368 0.5000000000000000 O 0.5976001306051370 0.9023998693948629 0.7500000000000001 O 0.9023998693948629 0.5976001306051370 0.7500000000000001 Ti -0.0000000000000000 -0.0000000000000000 0.0000000000000000 Ti 0.2499999999999998 0.2499999999999998 0.2500000000000001 Ti 0.5000000000000000 -0.0000000000000000 0.0000000000000000 Ti 0.7499999999999998 0.2499999999999998 0.2500000000000001 Ti -0.0000000000000000 0.5000000000000000 0.0000000000000000 Ti 0.2499999999999998 0.7499999999999998 0.2500000000000001 Ti 0.5000000000000000 0.5000000000000000 0.0000000000000000 Ti 0.7499999999999998 0.7499999999999998 0.2500000000000001 Ti -0.0000000000000000 -0.0000000000000000 0.5000000000000000 Ti 0.2499999999999998 0.2499999999999998 0.7500000000000001 Ti 0.5000000000000000 -0.0000000000000000 0.5000000000000000 Ti 0.7499999999999998 0.2499999999999998 0.7500000000000001 Ti -0.0000000000000000 0.5000000000000000 0.5000000000000000 Ti 0.2499999999999998 0.7499999999999998 0.7500000000000001 Ti 0.5000000000000000 0.5000000000000000 0.5000000000000000 Ti 0.7499999999999998 0.7499999999999998 0.7500000000000001 -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-07 20:22:30,"Winfred Mulwa" wrote: Dear all I have tried doing a vc-relax on the attached TiO2 rutile supercell, the calculations stop after a few minutes without giving any error. What might be the problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/593312ee/attachment-0001.htm From giannozz at democritos.it Wed Sep 7 15:33:31 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 15:33:31 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <4aacc2a1.e575.132440867bd.Coremail.flux_ray12@163.com> References: <1315398150.77703.YahooMailNeo@web113202.mail.gq1.yahoo.com> <4aacc2a1.e575.132440867bd.Coremail.flux_ray12@163.com> Message-ID: <12A5DBBA-7864-45A8-8318-D14768B55161@democritos.it> On Sep 7, 2011, at 15:16 , GAO Zhe wrote: > Oh, my mistake, I forgot that bohr is used in QE. So, if you wanna > keep > CELL_PARAMETERS, you have to set celldm(1) = 1.889725989. while this is possible and legitimate, I do not think it is a wise move to fill "celldm(1)" (or "a") with strange numbers instead of the lattice parameter 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 songsong19840614 at gmail.com Wed Sep 7 15:34:58 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Wed, 7 Sep 2011 21:34:58 +0800 Subject: [Pw_forum] QHA calculated error ! Message-ID: Hi, Recently,I want to calculated the partial_dos of phonon by QHA.Then,I have compiled it and run examples successfully.However,I run the ZnO.fc I calculated is failed. The step is followed: 1.Using ttrinp to generate K point by ...../QHA/bin/tetra.x.../QHA/bin/tetra.x 2.Copy k point into matdy.in and then using .../bin/matdyn.xmatdyn.out to generate 'frequency' 3.Using ../QHA/bin/Partial_phonon_DOS.x < phdos1.in 4.Using ../QHA/bin/phonon_dos.x References: Message-ID: Your file has no directory for output data. On Wed, Sep 7, 2011 at 1:57 PM, Winfred Mulwa wrote: > Dear all, > > I have tried doing a vc-relax on the attached TiO*2 *rutile > supercell, but the calculations stop after a few seconds without > giving any error. What might be the problem? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, The Abdus Salam International Center for Theoretical Physics, Enrico Fermi Building Associate Office 18, Strada Costiera 11, 34014 Trieste, Italy Tel +393382213805, or +39 040 2240 567 pnyawere at gmail.com, pnyawere at ictp.it, God raises the meek from the ground and sits them with Kings. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/50278601/attachment.htm From giannozz at democritos.it Wed Sep 7 16:59:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 16:59:07 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: On Sep 7, 2011, at 16:34 , Phillip Nyawere wrote: > Your file has no directory for output data. not a big problem, though: the code will write to either ESPRESSO_TMPDIR or to the current directory ("./") 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 xijunw at gmail.com Wed Sep 7 17:18:39 2011 From: xijunw at gmail.com (Xijun Wang) Date: Wed, 7 Sep 2011 11:18:39 -0400 Subject: [Pw_forum] ATOMIC_POSITIONS after 'final coordinates' In-Reply-To: <5508B106-C8A2-42A3-B8AA-0B87C18704C0@democritos.it> References: <5508B106-C8A2-42A3-B8AA-0B87C18704C0@democritos.it> Message-ID: On Wed, Sep 7, 2011 at 4:54 AM, Paolo Giannozzi wrote: > > On Sep 7, 2011, at 1:35 , Xijun Wang wrote: > >> There is an extra "ATOMIC_POSITIONS" section after the "final >> coordinates". It is neither the final coordinates > > why are you saying this? P. Because they are different. -XJ > --- > 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 > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From giannozz at democritos.it Wed Sep 7 17:45:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 17:45:26 +0200 Subject: [Pw_forum] ATOMIC_POSITIONS after 'final coordinates' In-Reply-To: References: <5508B106-C8A2-42A3-B8AA-0B87C18704C0@democritos.it> Message-ID: Most likely the damped dynamics algorithm updates the atomic positions one last time before printing them 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 xijunw at gmail.com Wed Sep 7 18:12:03 2011 From: xijunw at gmail.com (Xijun Wang) Date: Wed, 7 Sep 2011 12:12:03 -0400 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: Hi, Winfred, I just tried you input file and I found you have three errors in you input file: (1) You coordinates must not be {crystal}, see manual: crystal : atomic positions are in crystal coordinates, i.e. in relative coordinates of the primitive lattice vectors This means crystal coordinates must be between 0 and 1. (2) Your K_POINTS card should be: K_POINTS {automatic} But you use: K_POINTS (automatic) (3) Please remove the following lines: pot_extrapolation = 'second order' wfc_extrapolation = 'second order' These parameters are for 'damp' algorithm of relaxation. But you are using 'bfgs'. Please refer to the manual/ What's more, there are several extra blank lines somewhere in you input file, I do not know how these will be handled, but remove them if they are not necessary. I suggest, (1) Correct these errors and try it again; (2) If it still crashes, provide the output whatever it come for further discussion; PS: I highly suggest you start from small K_POINTS, 4*4*4 is too large, so you need quite a lot of memories. It may crash if memory could not be allocated to the calculation. What's your hardware configuration (Linux desktop or cluster? How much memory available? ) Xijun On Wed, Sep 7, 2011 at 7:57 AM, Winfred Mulwa wrote: > ? Dear all, > > ??????? I have tried doing a vc-relax on the attached TiO2 rutile supercell, > but the calculations stop after a few seconds without > giving any error.? What might be the problem? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From xijunw at gmail.com Wed Sep 7 18:22:29 2011 From: xijunw at gmail.com (Xijun Wang) Date: Wed, 7 Sep 2011 12:22:29 -0400 Subject: [Pw_forum] ATOMIC_POSITIONS after 'final coordinates' In-Reply-To: References: <5508B106-C8A2-42A3-B8AA-0B87C18704C0@democritos.it> Message-ID: Thanks Paolo. If this is true, then the 'final coordinates' is not actually final. -Xijun On Wed, Sep 7, 2011 at 11:45 AM, Paolo Giannozzi wrote: > Most likely the damped dynamics algorithm updates the > atomic positions one last time before printing them > > 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 > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From trambui at u.boisestate.edu Wed Sep 7 18:45:45 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 7 Sep 2011 10:45:45 -0600 Subject: [Pw_forum] All electron calculation Message-ID: Dear Everyone, * I'm trying to run a quick all electron calculation for Cs. where I have the input file(cs.in) as below: * &input title='Cs', zed=55.0, iswitch=1, dft='PBE', config='[Xe] 6s1 5d0 6p0 ' / *then I run bin/pw.x < cs.in > cs.out. I got an error message saying * "from read_namelists : error # 1 reading namelist control" *what might have been wrong in my code? is pw.x is the right command for all electron calculation? * Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/98986cd8/attachment.htm From gabriele.sclauzero at epfl.ch Wed Sep 7 18:52:27 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 7 Sep 2011 18:52:27 +0200 Subject: [Pw_forum] All electron calculation In-Reply-To: References: Message-ID: <4B5FF5E0-BB4F-4430-AD70-085E870C95FF@epfl.ch> If you want to do all-electron atomic calculations (in spherical symmetry), then you should use ld1.x, not pw.x HTH GS Il giorno 07/set/2011, alle ore 18.45, Tram Bui ha scritto: > Dear Everyone, > I'm trying to run a quick all electron calculation for Cs. where I have the input file(cs.in) as below: > &input > title='Cs', > zed=55.0, > iswitch=1, > dft='PBE', > config='[Xe] 6s1 5d0 6p0 ' > / > then I run bin/pw.x < cs.in > cs.out. I got an error message saying > "from read_namelists : error # 1 > reading namelist control" > what might have been wrong in my code? is pw.x is the right command for all electron calculation? > > > Thank you very much, > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110907/dd14cfe3/attachment-0001.htm From giannozz at democritos.it Wed Sep 7 18:55:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 7 Sep 2011 18:55:26 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: On Sep 7, 2011, at 18:12 , Xijun Wang wrote : > (2) Your K_POINTS card should be: K_POINTS {automatic} > But you use: K_POINTS (automatic) this should not be a problem: the code actually looks for "automatic", not for "(" or "{". Also ignored: blank lines and inappropriate options pot_extrapolation = 'second order', wfc_extrapolation = 'second order' 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 Wed Sep 7 21:25:50 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 20:25:50 +0100 Subject: [Pw_forum] problems with vc-relax Message-ID: Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy = -676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy < 0.17363554 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.000000000 0.000000000 6.503051170 0.000000000 0.000000000 0.000000000 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.000000000 C -10.659793092 -1.160339161 0.000000000 C -12.039843315 -7.112619698 0.000000000 C -12.041158182 -5.732701936 0.000000000 C -10.941089654 -4.881442842 0.000000000...... Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/eec0853b/attachment.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 21:26:33 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 20:26:33 +0100 Subject: [Pw_forum] problems with vc-relax Message-ID: Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy = -676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy < 0.17363554 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.000000000 0.000000000 6.503051170 0.000000000 0.000000000 0.000000000 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.000000000 C -10.659793092 -1.160339161 0.000000000 C -12.039843315 -7.112619698 0.000000000 C -12.041158182 -5.732701936 0.000000000 C -10.941089654 -4.881442842 0.000000000...... Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/df4a8543/attachment-0001.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 21:27:08 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 20:27:08 +0100 Subject: [Pw_forum] problems with vc-relax Message-ID: Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy = -676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy < 0.17363554 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.000000000 0.000000000 6.503051170 0.000000000 0.000000000 0.000000000 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.000000000 C -10.659793092 -1.160339161 0.000000000 C -12.039843315 -7.112619698 0.000000000 C -12.041158182 -5.732701936 0.000000000 C -10.941089654 -4.881442842 0.000000000...... Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/467de01e/attachment.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 21:28:45 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 20:28:45 +0100 Subject: [Pw_forum] problems with vc-relax Message-ID: Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy = -676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy < 0.17363554 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.000000000 0.000000000 6.503051170 0.000000000 0.000000000 0.000000000 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.000000000 C -10.659793092 -1.160339161 0.000000000 C -12.039843315 -7.112619698 0.000000000 C -12.041158182 -5.732701936 0.000000000 C -10.941089654 -4.881442842 0.000000000 ...... Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie Moujaes University of Nott University Park NGT 3RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/17335ac0/attachment-0001.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 21:53:39 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 20:53:39 +0100 Subject: [Pw_forum] problems in vc relax Message-ID: Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy = -676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy < 0.17363554 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: &control prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / &system ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / &electrons conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / &ions ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.000000000 0.000000000 6.503051170 0.000000000 0.000000000 0.000000000 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.000000000 C -10.659793092 -1.160339161 0.000000000 C -12.039843315 -7.112619698 0.000000000 C -12.041158182 -5.732701936 0.000000000 C -10.941089654 -4.881442842 0.000000000 ...... Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie Moujaes University of Nott University Park NGT 3RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/eccff488/attachment-0001.htm From xijunw at gmail.com Wed Sep 7 21:58:37 2011 From: xijunw at gmail.com (Xijun Wang) Date: Wed, 7 Sep 2011 15:58:37 -0400 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: Message-ID: On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > Dear all, > Dear Elie, > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > 4 days of execution and without reaching the desired force threshold. The > following output was obtained : > > Please can anyone advice me on this? Shall I start with the new > configuration and start relaxing again? > I'm also doing some cell relaxation. As I understand, cell optimization is not very easy, and it is common that it does not converge after a very long run. Surely you should restart the calculation to achieve your convergence criteria. You can just change the "restart_mod = 'from_scratch' " to "restart_mode = 'restart' ", and submit the job again to continue from where you stopped. Please be advised that pw.x will read cell parameters / atomic positions, initial density, pseudopotentials from the folder of GBphonon.save, so make sure you copy the folder to computing-nodes. However, I highly suggest you do something to accelerate the convergence. For example, if you do not expect the cell angle to change (i.e. keep angles=90), you may add the following keywords to the &CELL section. cell_dofree = xyz This will greatly reduce the uncertainty of the geometry optimization. and reduce energy/force oscillation. Another great idea is to manually choose x, y and z, then do a relaxation of atomic positions only. and plot the total energy changes with x, y and z. However, be noted that different volume means different numbers of PW basis function, and energy comparison in this way could be a little confusing. Anyway, if volume change is not large, still this would help a lot. Since I'm also a learner, any more comments or correction to my comments are welcome. Thanks Xijun > > Regards > > > > Elie Moujaes > > University of Nott > > University Park > > NGT 3RD > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From xijunw at gmail.com Wed Sep 7 22:20:49 2011 From: xijunw at gmail.com (Xijun Wang) Date: Wed, 7 Sep 2011 16:20:49 -0400 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: Message-ID: Hi, Elie, Please do not repeat sending the same message to the mail list. Also, people will be more happy to help you if you keep your mail neat by removing all the unnecessary blank lines in the input file. Regards, Xijun On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > Dear all, > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > 4 days of execution and without reaching the desired force threshold. The > following output was obtained : > > > > 1st relaxation process: > > > > Total force 0.091 ? Pressure =- 114.1 kbar > > > > 2nd relaxation process: > > > > total force 0.1 ? Pressure = -55 kbar > > > > (new enthalpy < old enthalpy) > > > > 3rd process: > > > > total force = 0.058 ? pressure = -11 kbar > > > > Then in the 4th process, calculations stopped. Here are the last few lines > of the output: > > > > iteration #??2?????ecut=????36.75 Ry?????beta=0.30 > ?????Davidson diagonalization with overlap > ?????c_bands:??5 eigenvalues not converged > ?????c_bands:??1 eigenvalues not converged > ?????c_bands:??3 eigenvalues not converged > ?????c_bands:??1 eigenvalues not converged > ?????c_bands:??4 eigenvalues not converged > ?????c_bands:??4 eigenvalues not converged > ?????c_bands:??4 eigenvalues not converged > ?????c_bands:??4 eigenvalues not converged > ?????c_bands:??5 eigenvalues not converged > ?????c_bands:??5 eigenvalues not converged > ?????c_bands:??2 eigenvalues not converged > ?????c_bands:??2 eigenvalues not converged > ?????ethr =??2.90E-04,??avg # of iterations = 17.6 > > ?????negative rho (up, down):??0.132E-01 0.000E+00 > > ?????total cpu time spent up to now is 382283.13 secs > > ?????total energy??????????????=????-676.77947904 Ry > ?????Harris-Foulkes estimate???=????-676.82846513 Ry > ?????estimated scf accuracy???? > ?????iteration #??3?????ecut=????36.75 Ry?????beta=0.30 > ?????Davidson diagonalization with overlap > ?????c_bands:??1 eigenvalues not converged > ?????c_bands:??1 eigenvalues not converged > ?????c_bands:??2 eigenvalues not converged > ?????c_bands:??3 eigenvalues not converged > > > > The input of the vc-relax is: > > > > &control > > ????prefix='GBphonon', > > ????calculation='vc-relax', > > ????restart_mode='from_scratch', > > ????tstress=.true., > > ????tprnfor=.true, > > ????pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > > ????outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > > > > ?/ > > ?&system > > ????ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, > occupations='smearing', smearing='mp',degauss=0.01 > > / > > ?&electrons > > ????conv_thr=1.D-6, > > ????mixing_beta=0.3D0, > > ????diago_david_ndim=2, > > > > ?/ > > > > &ions > > ?ion_dynamics='bfgs' > > > > / > > $cell > > cell_dynamics='bfgs', > > > > / > > > > CELL_PARAMETERS (alat) > > ??24.064488464???0.000772242???0.000000000 > > ???0.000000000???6.503051170???0.000000000 > > ???0.000000000???0.000000000???8.470514812 > > > > > > ATOMIC_SPECIES > > ?C??12.0107??C.blyp-mt.UPF > > > > ATOMIC_POSITIONS (angstrom) > > C??????-11.330758616??-3.527803203???0.000000000 > > C??????-10.659793092??-1.160339161???0.000000000 > > C??????-12.039843315??-7.112619698???0.000000000 > > C??????-12.041158182??-5.732701936???0.000000000 > > C??????-10.941089654??-4.881442842???0.000000000 > > ...... > > > > Please can anyone advice me on this? Shall I start with the new > configuration and start relaxing again? > > > > Regards > > > > Elie Moujaes > > University of Nott > > University Park > > NGT 3RD > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dept. of Chem and Biochem, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From elie.moujaes at hotmail.co.uk Wed Sep 7 22:39:49 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 21:39:49 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > > cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110907/d18c2aa9/attachment.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 22:43:40 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 21:43:40 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > > cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110907/5d06481e/attachment.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 22:56:39 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 21:56:39 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > > cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110907/5f7d5890/attachment-0001.htm From elie.moujaes at hotmail.co.uk Wed Sep 7 23:15:25 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 22:15:25 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > > cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110907/9b2202ec/attachment.htm From li.chengyang at wmich.edu Wed Sep 7 23:14:53 2011 From: li.chengyang at wmich.edu (Chengyang Li) Date: Wed, 07 Sep 2011 17:14:53 -0400 (EDT) Subject: [Pw_forum] Pseudopotential for Terbium in upf file In-Reply-To: <799764772.213117.1315429715729.JavaMail.root@wmu-mailstore05> Message-ID: <363162858.213291.1315430093930.JavaMail.root@wmu-mailstore05> Dear Users I'm trying to find the pseudopotential for Terbium but it seems like there is no upf file about Terbium. Does any one can share the codes or give me some advice? Thank you. Chengyang Li Department of Physics Western Michigan Univerisity From elie.moujaes at hotmail.co.uk Wed Sep 7 23:22:10 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 7 Sep 2011 22:22:10 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the &CELL section. > > cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110907/38d4a09f/attachment.htm From flux_ray12 at 163.com Thu Sep 8 04:00:04 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 8 Sep 2011 10:00:04 +0800 (CST) Subject: [Pw_forum] Pseudopotential for Terbium in upf file In-Reply-To: <363162858.213291.1315430093930.JavaMail.root@wmu-mailstore05> References: <363162858.213291.1315430093930.JavaMail.root@wmu-mailstore05> Message-ID: <2f96e1ff.11a2d.13246c36a29.Coremail.flux_ray12@163.com> You can try to generate Tb's UPF PP by ld1.x, or transfer from CASTEP's PP file to UPF by usp2upf, which can be downloaded from http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 05:14:53,"Chengyang Li" wrote: >Dear Users > > >I'm trying to find the pseudopotential for Terbium but it seems like there is no upf file about Terbium. Does any one can share the codes or give me some advice? Thank you. > > > > >Chengyang Li > >Department of Physics >Western Michigan Univerisity > >_______________________________________________ >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/20110908/2436fc85/attachment.htm From flux_ray12 at 163.com Thu Sep 8 03:49:31 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 8 Sep 2011 09:49:31 +0800 (CST) Subject: [Pw_forum] All electron calculation In-Reply-To: References: Message-ID: <69befe2d.11631.13246b9c1b0.Coremail.flux_ray12@163.com> QE is pseudo-potential method DFT software instead of all-electron method, unless you make all-electron pseudo-potential by using ld1.x ( I do not guarantee it could be successful ). If you really wanna use all-electron method, you'd better to use the DFT software implemented FLAPW, such like Wien2k. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 00:45:45,"Tram Bui" wrote: Dear Everyone, I'm trying to run a quick all electron calculation for Cs. where I have the input file(cs.in) as below: &input title='Cs', zed=55.0, iswitch=1, dft='PBE', config='[Xe] 6s1 5d0 6p0 ' / then I run bin/pw.x cs.out. I got an error message saying "from read_namelists : error # 1 reading namelist control" what might have been wrong in my code? is pw.x is the right command for all electron calculation? Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/cb0ef0d9/attachment-0001.htm From padmaja_patnaik at yahoo.co.uk Thu Sep 8 07:28:10 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 8 Sep 2011 06:28:10 +0100 (BST) Subject: [Pw_forum] (no subject) Message-ID: <1315459690.99027.YahooMailNeo@web28514.mail.ukl.yahoo.com> Hi All I am doing spin-orbit coupling calculations. To get spin-polarized calculations with spin-orbit coupling mentioned in the input for scf,?? lspinorb=.true., ??? noncolin=.true., ??? starting_magnetization(1)=0.5, ??? starting_magnetization(2)=0.5, After this scf calculations I am doing the nscf calculation and finally the density of states and partial density of states. What I expect is it should give me both up and down spin DOS separately but I didnt get that. usually for calculations without spin-orbit coupling I mention nspin=2 in the input and get spin polarized results with both up and down spin density of states given separately which can be plotted. Please suggest what to do? ?Thanking in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/c638458b/attachment.htm From windbellklbh at gmail.com Thu Sep 8 07:41:38 2011 From: windbellklbh at gmail.com (WF) Date: Thu, 8 Sep 2011 13:41:38 +0800 Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir before calculation? Message-ID: <004a01cc6de9$fcdb9bc0$f692d340$@gmail.com> Hello everyone, Recently I make a small bash script to run a lot of small pw.x calculation one by one. But all of them use same outdir and wfcdir. They are temporary directories and I don't need them ( I only need scf energy, so stdout is enough ). Is it necessary to delete them before starting a new calculation ? Because I have done a lot of calculation, I would like to verify whether this will affect the results to determine whether I should modify the script to restart my calculation again, or just use these result. Best regards, Wu F ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/e9fad8f3/attachment.htm From flux_ray12 at 163.com Thu Sep 8 08:04:48 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 8 Sep 2011 14:04:48 +0800 (CST) Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir before calculation? In-Reply-To: <004a01cc6de9$fcdb9bc0$f692d340$@gmail.com> References: <004a01cc6de9$fcdb9bc0$f692d340$@gmail.com> Message-ID: <1e8bee37.15cc1.13247a3797c.Coremail.flux_ray12@163.com> At least, there are three methods to avoid the effect of last calculation. restart_mode = 'from_scratch' or change prefix or rm -rf $TempDIR/* -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 13:41:38,WF wrote: Hello everyone, Recently I make a small bash script to run a lot of small pw.x calculation one by one. But all of them use same outdir and wfcdir. They are temporary directories and I don?t need them ( I only need scf energy, so stdout is enough ). Is it necessary to delete them before starting a new calculation ? Because I have done a lot of calculation, I would like to verify whether this will affect the results to determine whether I should modify the script to restart my calculation again, or just use these result. Best regards, Wu F ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/22bea0be/attachment.htm From songsong19840614 at gmail.com Thu Sep 8 08:41:11 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Thu, 8 Sep 2011 14:41:11 +0800 Subject: [Pw_forum] Fwd: QHA calculated error ! In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: lucking-pine Date: 2011/9/7 Subject: QHA calculated error ! To: Pw_forum at pwscf.org Hi, Recently,I want to calculated the partial_dos of phonon by QHA.Then,I have compiled it and run examples successfully.However,I run the ZnO.fc I calculated is failed. The step is followed: 1.Using ttrinp to generate K point by ...../QHA/bin/tetra.x.../QHA/bin/tetra.x 2.Copy k point into matdy.in and then using .../bin/matdyn.xmatdyn.out to generate 'frequency' 3.Using ../QHA/bin/Partial_phonon_DOS.x < phdos1.in 4.Using ../QHA/bin/phonon_dos.x References: <2143486237.46751.1315328202966.JavaMail.root@mail.iq.ufrj.br><4E673BEE.3010008@materials.ox.ac.uk><8C0B47760A05FB4AB504C9BCAD32D2560304337B@postar.ki.si> <20110907140900.enq05sxdhsss080g@webmail.sissa.it> Message-ID: <8C0B47760A05FB4AB504C9BCAD32D256030434BE@postar.ki.si> Dear Emine and Davide, Thank you for your informative answers. Gregor > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Emine Kucukbenli > Sent: 7. september 2011 14:09 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 > (unit = 14,file = '') > > Dear Gregor, > gipaw is based on paw, as long as it stays so it will always > require paw description of the atom.. > if you are using a traditional norm conserving or ultrasoft > pseudopotential that means you need this description to be > calculated and written, which will make it a 'gipaw pseudopotential' > If you are using a paw pseudopotential however, everything is > already calculated. unfortunately it has not been the > default to write down this necessary information. in the > future i would like to make it default, such that every paw > pseudopotential file already is gipaw-suitable. > it is just that there are some details to work out,like,you > may want the pw.x to use a different set of projectors > (possibly cheaper ones) than gipaw.x part..so we should keep > this freedom etc. > > about not having the paw set for the atoms you are not > interested in..what would you propose? the induced magnetic > field at a point depends on the induced current in all > space..do you suggest a space cut off? or calculating the > current response of these atoms we are not interested in > without paw constructions? > > instead there is the 'converse approach' you may want to look > at, that sounds more efficient if you are interested in nmr > parameters of one atom in huge molecule, for example.. > we can hear more from Davide about it. > > emine kucukbenli, phd student, sissa, italy > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From windbellklbh at gmail.com Thu Sep 8 09:00:08 2011 From: windbellklbh at gmail.com (WF) Date: Thu, 8 Sep 2011 15:00:08 +0800 Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir Message-ID: <005401cc6df4$f45dfd70$dd19f850$@gmail.com> In my calculation restart_mode="from_scratch" is always used. But I find if a calculation ends with error, it will give different errors depends on the whether the outdir is empty or not. So I wonder whether it affect the calculation results. From giannozz at democritos.it Thu Sep 8 09:00:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 8 Sep 2011 09:00:53 +0200 Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir before calculation? In-Reply-To: <004a01cc6de9$fcdb9bc0$f692d340$@gmail.com> References: <004a01cc6de9$fcdb9bc0$f692d340$@gmail.com> Message-ID: <129E3028-A82E-4C19-8FB1-4640911718A2@democritos.it> On Sep 8, 2011, at 7:41 , WF wrote: > I only need scf energy, so stdout is enough > use option disk_io='none': nothing will be writen to disk 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 gabriele.sclauzero at epfl.ch Thu Sep 8 09:11:33 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 8 Sep 2011 09:11:33 +0200 Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir In-Reply-To: <005401cc6df4$f45dfd70$dd19f850$@gmail.com> References: <005401cc6df4$f45dfd70$dd19f850$@gmail.com> Message-ID: If you do a "nscf" calculation you will need data produced in a previous "scf" run (irrespective of restart_mode), therefore you must specify the correct outdir and prefix. If you specify wrong values, of course that the results will be affected. In some cases the calculation will give an error message. Please sign your posts and provide your affiliation. Thanks. GS Il giorno 08/set/2011, alle ore 09.00, WF ha scritto: > In my calculation restart_mode="from_scratch" is always used. But I find if > a calculation ends with error, it will give different errors depends on the > whether the outdir is empty or not. So I wonder whether it affect the > calculation results. > > _______________________________________________ > 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/20110908/ac777274/attachment.htm From windbellklbh at gmail.com Thu Sep 8 10:02:41 2011 From: windbellklbh at gmail.com (WF) Date: Thu, 8 Sep 2011 16:02:41 +0800 Subject: [Pw_forum] Is it necessary to clear outdir / wfcdir before calculation? Message-ID: <005501cc6dfd$b2f07bc0$18d17340$@gmail.com> Thanks for your advices, I will remove the output if it is not necessary. I am sorry that I don't notice that the title contains a newline mark of which only the first line is copied in my message sent, so it doesn't work properly, i.e. no previous message or affiliation. Best regards, Wu F ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- From mikeat4999 at gmail.com Thu Sep 8 10:02:55 2011 From: mikeat4999 at gmail.com (mike at.) Date: Thu, 8 Sep 2011 11:02:55 +0300 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: On Wed, Sep 7, 2011 at 7:12 PM, Xijun Wang wrote: > > > PS: I highly suggest you start from small K_POINTS, 4*4*4 is too > large, so you need quite a lot of memories. It may crash if memory > could not be allocated to the calculation. What's your hardware > configuration (Linux desktop or cluster? How much memory available? ) > > The work is being done on a pair of sun x2270 calculation nodes, eight physical cores per node with hyperthreading, and 8 GB of memory per node , running CentOS. > Xijun > > > On Wed, Sep 7, 2011 at 7:57 AM, Winfred Mulwa > wrote: > > Dear all, > > > > I have tried doing a vc-relax on the attached TiO2 rutile > supercell, > > but the calculations stop after a few seconds without > > giving any error. What might be the problem? > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- M. O. ATAMBO mikeat4999 at gmail.com student, computational material science group Chepkoilel university college. Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/6690c0da/attachment.htm From janfelix.binder at epfl.ch Thu Sep 8 12:13:26 2011 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Thu, 08 Sep 2011 12:13:26 +0200 Subject: [Pw_forum] All electron calculation In-Reply-To: <69befe2d.11631.13246b9c1b0.Coremail.flux_ray12@163.com> References: <69befe2d.11631.13246b9c1b0.Coremail.flux_ray12@163.com> Message-ID: <4E689546.8040505@epfl.ch> you have to use the ld1.x code. On 09/08/2011 03:49 AM, GAO Zhe wrote: > QE is pseudo-potential method DFT software instead of all-electron > method, unless you make all-electron pseudo-potential by using ld1.x ( > I do not guarantee it could be successful ). > If you really wanna use all-electron method, you'd better to use the > DFT software implemented FLAPW, such like Wien2k. > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-09-08 00:45:45,"Tram Bui" wrote: > > Dear Everyone, > *I'm trying to run a quick all electron calculation for Cs. where > I have the input file(cs.in ) as below: * > &input > title='Cs', > zed=55.0, > iswitch=1, > dft='PBE', > config='[Xe] 6s1 5d0 6p0 ' > / > *then I run bin/pw.x < cs.in > cs.out. I got an > error message saying * > "from read_namelists : error # 1 > reading namelist control" > *what might have been wrong in my code? is pw.x is the right > command for all electron calculation? > > * > Thank you very much, > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > > > _______________________________________________ > 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/20110908/8312b43d/attachment.htm From elie.moujaes at hotmail.co.uk Thu Sep 8 16:26:55 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 8 Sep 2011 15:26:55 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , Message-ID: Hello Xijun, I did not send the e-mail twice intentionally. There was a problem with my e-mail and it kept giving me an error about problems with Windows hotmai hence why it was sent twice without me knowing except now when I opened my e-mail so I apologize for that. Also I wont include blank lines in the input file either. Back to my calculations, I have restarted the calculations, it went fine at first but then I got the error: from scale_h: not enough memory allocated for radial FFT; try restarting with a larger cell_factor. Another simple question: I realized when I restarted everything that the positions of the atoms were the initial ones even before starting the relaxation process where as the k-points used were the NEW ones. Is that normal? or should I have substituted the the C atoms positions by the most recent ones then restart again? Regards Elie > Date: Wed, 7 Sep 2011 16:20:49 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > Hi, Elie, > > Please do not repeat sending the same message to the mail list. Also, > people will be more happy to help you if you keep your mail neat by > removing all the unnecessary blank lines in the input file. > > Regards, > Xijun > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > > Dear all, > > > > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > > > > > 1st relaxation process: > > > > > > > > Total force 0.091 Pressure =- 114.1 kbar > > > > > > > > 2nd relaxation process: > > > > > > > > total force 0.1 Pressure = -55 kbar > > > > > > > > (new enthalpy < old enthalpy) > > > > > > > > 3rd process: > > > > > > > > total force = 0.058 pressure = -11 kbar > > > > > > > > Then in the 4th process, calculations stopped. Here are the last few lines > > of the output: > > > > > > > > iteration # 2 ecut= 36.75 Ry beta=0.30 > > Davidson diagonalization with overlap > > c_bands: 5 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 3 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 4 eigenvalues not converged > > c_bands: 5 eigenvalues not converged > > c_bands: 5 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > ethr = 2.90E-04, avg # of iterations = 17.6 > > > > negative rho (up, down): 0.132E-01 0.000E+00 > > > > total cpu time spent up to now is 382283.13 secs > > > > total energy = -676.77947904 Ry > > Harris-Foulkes estimate = -676.82846513 Ry > > estimated scf accuracy < 0.17363554 Ry > > > > iteration # 3 ecut= 36.75 Ry beta=0.30 > > Davidson diagonalization with overlap > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 3 eigenvalues not converged > > > > > > > > The input of the vc-relax is: > > > > > > > > &control > > > > prefix='GBphonon', > > > > calculation='vc-relax', > > > > restart_mode='from_scratch', > > > > tstress=.true., > > > > tprnfor=.true, > > > > pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > > > > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > > > > > > > > / > > > > &system > > > > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, > > occupations='smearing', smearing='mp',degauss=0.01 > > > > / > > > > &electrons > > > > conv_thr=1.D-6, > > > > mixing_beta=0.3D0, > > > > diago_david_ndim=2, > > > > > > > > / > > > > > > > > &ions > > > > ion_dynamics='bfgs' > > > > > > > > / > > > > $cell > > > > cell_dynamics='bfgs', > > > > > > > > / > > > > > > > > CELL_PARAMETERS (alat) > > > > 24.064488464 0.000772242 0.000000000 > > > > 0.000000000 6.503051170 0.000000000 > > > > 0.000000000 0.000000000 8.470514812 > > > > > > > > > > > > ATOMIC_SPECIES > > > > C 12.0107 C.blyp-mt.UPF > > > > > > > > ATOMIC_POSITIONS (angstrom) > > > > C -11.330758616 -3.527803203 0.000000000 > > > > C -10.659793092 -1.160339161 0.000000000 > > > > C -12.039843315 -7.112619698 0.000000000 > > > > C -12.041158182 -5.732701936 0.000000000 > > > > C -10.941089654 -4.881442842 0.000000000 > > > > ...... > > > > > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Dept. of Chem and Biochem, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110908/48c181bd/attachment-0001.htm From xijunw at gmail.com Thu Sep 8 17:12:24 2011 From: xijunw at gmail.com (Xijun Wang) Date: Thu, 8 Sep 2011 11:12:24 -0400 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: Message-ID: On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes wrote: > Hello Xijun, Hello Elie, > I did not send the e-mail twice intentionally. There was a problem with my > e-mail and it kept giving me an error about problems with Windows hotmai > hence why it was sent twice without me knowing except now when I opened my > e-mail so I apologize for that. Also I wont include blank lines in the input > file either. ?Back to my calculations, I have restarted the calculations, it > went fine at first but then I got the error: > from scale_h: not enough memory allocated for radial FFT; try restarting > with a larger cell_factor. Check the manual for definition of cell_factor. The default value is 1.2, you could try a larger value. What's your new K_POINTS setting? Since you are relax the system, I suggest you start from: K_POINTS {gamma} This will far faster. and need far less memory. > Another simple question: I realized when I restarted everything that the > positions of the atoms were the initial ones even before starting the > relaxation process where as the k-points used were the NEW ones. Is that > normal? or should I have substituted the the C atoms positions by the most > recent ones then restart again? Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode= 'from_scratch' " Regards, - Xijun > Regards > Elie > >> Date: Wed, 7 Sep 2011 16:20:49 -0400 >> From: xijunw at gmail.com >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] problems with vc-relax >> >> Hi, Elie, >> >> Please do not repeat sending the same message to the mail list. Also, >> people will be more happy to help you if you keep your mail neat by >> removing all the unnecessary blank lines in the input file. >> >> Regards, >> Xijun >> >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes >> wrote: >> > Dear all, >> > >> > >> > >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make the >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped >> > after >> > 4 days of execution and without reaching the desired force threshold. >> > The >> > following output was obtained : >> > >> > >> > >> > 1st relaxation process: >> > >> > >> > >> > Total force 0.091 ? Pressure =- 114.1 kbar >> > >> > >> > >> > 2nd relaxation process: >> > >> > >> > >> > total force 0.1 ? Pressure = -55 kbar >> > >> > >> > >> > (new enthalpy < old enthalpy) >> > >> > >> > >> > 3rd process: >> > >> > >> > >> > total force = 0.058 ? pressure = -11 kbar >> > >> > >> > >> > Then in the 4th process, calculations stopped. Here are the last few >> > lines >> > of the output: >> > >> > >> > >> > iteration #??2?????ecut=????36.75 Ry?????beta=0.30 >> > ?????Davidson diagonalization with overlap >> > ?????c_bands:??5 eigenvalues not converged >> > ?????c_bands:??1 eigenvalues not converged >> > ?????c_bands:??3 eigenvalues not converged >> > ?????c_bands:??1 eigenvalues not converged >> > ?????c_bands:??4 eigenvalues not converged >> > ?????c_bands:??4 eigenvalues not converged >> > ?????c_bands:??4 eigenvalues not converged >> > ?????c_bands:??4 eigenvalues not converged >> > ?????c_bands:??5 eigenvalues not converged >> > ?????c_bands:??5 eigenvalues not converged >> > ?????c_bands:??2 eigenvalues not converged >> > ?????c_bands:??2 eigenvalues not converged >> > ?????ethr =??2.90E-04,??avg # of iterations = 17.6 >> > >> > ?????negative rho (up, down):??0.132E-01 0.000E+00 >> > >> > ?????total cpu time spent up to now is 382283.13 secs >> > >> > ?????total energy??????????????=????-676.77947904 Ry >> > ?????Harris-Foulkes estimate???=????-676.82846513 Ry >> > ?????estimated scf accuracy????> > >> > ?????iteration #??3?????ecut=????36.75 Ry?????beta=0.30 >> > ?????Davidson diagonalization with overlap >> > ?????c_bands:??1 eigenvalues not converged >> > ?????c_bands:??1 eigenvalues not converged >> > ?????c_bands:??2 eigenvalues not converged >> > ?????c_bands:??3 eigenvalues not converged >> > >> > >> > >> > The input of the vc-relax is: >> > >> > >> > >> > &control >> > >> > ????prefix='GBphonon', >> > >> > ????calculation='vc-relax', >> > >> > ????restart_mode='from_scratch', >> > >> > ????tstress=.true., >> > >> > ????tprnfor=.true, >> > >> > ????pseudo_dir = >> > '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', >> > >> > ????outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', >> > >> > >> > >> > ?/ >> > >> > ?&system >> > >> > ????ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc >> > =36.749309, >> > occupations='smearing', smearing='mp',degauss=0.01 >> > >> > / >> > >> > ?&electrons >> > >> > ????conv_thr=1.D-6, >> > >> > ????mixing_beta=0.3D0, >> > >> > ????diago_david_ndim=2, >> > >> > >> > >> > ?/ >> > >> > >> > >> > &ions >> > >> > ?ion_dynamics='bfgs' >> > >> > >> > >> > / >> > >> > $cell >> > >> > cell_dynamics='bfgs', >> > >> > >> > >> > / >> > >> > >> > >> > CELL_PARAMETERS (alat) >> > >> > ??24.064488464???0.000772242???0.000000000 >> > >> > ???0.000000000???6.503051170???0.000000000 >> > >> > ???0.000000000???0.000000000???8.470514812 >> > >> > >> > >> > >> > >> > ATOMIC_SPECIES >> > >> > ?C??12.0107??C.blyp-mt.UPF >> > >> > >> > >> > ATOMIC_POSITIONS (angstrom) >> > >> > C??????-11.330758616??-3.527803203???0.000000000 >> > >> > C??????-10.659793092??-1.160339161???0.000000000 >> > >> > C??????-12.039843315??-7.112619698???0.000000000 >> > >> > C??????-12.041158182??-5.732701936???0.000000000 >> > >> > C??????-10.941089654??-4.881442842???0.000000000 >> > >> > ...... >> > >> > >> > >> > Please can anyone advice me on this? Shall I start with the new >> > configuration and start relaxing again? >> > >> > >> > >> > Regards >> > >> > >> > >> > Elie Moujaes >> > >> > University of Nott >> > >> > University Park >> > >> > NGT 3RD >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> >> >> >> -- >> Dept. of Chem and Biochem, Concordia University >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 >> _______________________________________________ >> 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 > > -- Dept. of Chem and Biochem, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From elie.moujaes at hotmail.co.uk Thu Sep 8 17:56:37 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 8 Sep 2011 16:56:37 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: , , , Message-ID: Thanks very much for your suggestions again. I did not know I can use K_POINTS {gamma} (only one point) in the relaxation process as I used K_POINTS {automatic} 7 7 1 in my relaxation process. Regards Elie > Date: Thu, 8 Sep 2011 11:12:24 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes > wrote: > > Hello Xijun, > > Hello Elie, > > > I did not send the e-mail twice intentionally. There was a problem with my > > e-mail and it kept giving me an error about problems with Windows hotmai > > hence why it was sent twice without me knowing except now when I opened my > > e-mail so I apologize for that. Also I wont include blank lines in the input > > file either. Back to my calculations, I have restarted the calculations, it > > went fine at first but then I got the error: > > from scale_h: not enough memory allocated for radial FFT; try restarting > > with a larger cell_factor. > > Check the manual for definition of cell_factor. The default value is > 1.2, you could try a larger value. > > What's your new K_POINTS setting? Since you are relax the system, I > suggest you start from: > > K_POINTS {gamma} > > This will far faster. and need far less memory. > > > Another simple question: I realized when I restarted everything that the > > positions of the atoms were the initial ones even before starting the > > relaxation process where as the k-points used were the NEW ones. Is that > > normal? or should I have substituted the the C atoms positions by the most > > recent ones then restart again? > > Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode= 'from_scratch' " > > Regards, > - Xijun > > > Regards > > Elie > > > >> Date: Wed, 7 Sep 2011 16:20:49 -0400 > >> From: xijunw at gmail.com > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] problems with vc-relax > >> > >> Hi, Elie, > >> > >> Please do not repeat sending the same message to the mail list. Also, > >> people will be more happy to help you if you keep your mail neat by > >> removing all the unnecessary blank lines in the input file. > >> > >> Regards, > >> Xijun > >> > >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > >> wrote: > >> > Dear all, > >> > > >> > > >> > > >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped > >> > after > >> > 4 days of execution and without reaching the desired force threshold. > >> > The > >> > following output was obtained : > >> > > >> > > >> > > >> > 1st relaxation process: > >> > > >> > > >> > > >> > Total force 0.091 Pressure =- 114.1 kbar > >> > > >> > > >> > > >> > 2nd relaxation process: > >> > > >> > > >> > > >> > total force 0.1 Pressure = -55 kbar > >> > > >> > > >> > > >> > (new enthalpy < old enthalpy) > >> > > >> > > >> > > >> > 3rd process: > >> > > >> > > >> > > >> > total force = 0.058 pressure = -11 kbar > >> > > >> > > >> > > >> > Then in the 4th process, calculations stopped. Here are the last few > >> > lines > >> > of the output: > >> > > >> > > >> > > >> > iteration # 2 ecut= 36.75 Ry beta=0.30 > >> > Davidson diagonalization with overlap > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 3 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > ethr = 2.90E-04, avg # of iterations = 17.6 > >> > > >> > negative rho (up, down): 0.132E-01 0.000E+00 > >> > > >> > total cpu time spent up to now is 382283.13 secs > >> > > >> > total energy = -676.77947904 Ry > >> > Harris-Foulkes estimate = -676.82846513 Ry > >> > estimated scf accuracy < 0.17363554 Ry > >> > > >> > iteration # 3 ecut= 36.75 Ry beta=0.30 > >> > Davidson diagonalization with overlap > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > c_bands: 3 eigenvalues not converged > >> > > >> > > >> > > >> > The input of the vc-relax is: > >> > > >> > > >> > > >> > &control > >> > > >> > prefix='GBphonon', > >> > > >> > calculation='vc-relax', > >> > > >> > restart_mode='from_scratch', > >> > > >> > tstress=.true., > >> > > >> > tprnfor=.true, > >> > > >> > pseudo_dir = > >> > '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > >> > > >> > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > >> > > >> > > >> > > >> > / > >> > > >> > &system > >> > > >> > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc > >> > =36.749309, > >> > occupations='smearing', smearing='mp',degauss=0.01 > >> > > >> > / > >> > > >> > &electrons > >> > > >> > conv_thr=1.D-6, > >> > > >> > mixing_beta=0.3D0, > >> > > >> > diago_david_ndim=2, > >> > > >> > > >> > > >> > / > >> > > >> > > >> > > >> > &ions > >> > > >> > ion_dynamics='bfgs' > >> > > >> > > >> > > >> > / > >> > > >> > $cell > >> > > >> > cell_dynamics='bfgs', > >> > > >> > > >> > > >> > / > >> > > >> > > >> > > >> > CELL_PARAMETERS (alat) > >> > > >> > 24.064488464 0.000772242 0.000000000 > >> > > >> > 0.000000000 6.503051170 0.000000000 > >> > > >> > 0.000000000 0.000000000 8.470514812 > >> > > >> > > >> > > >> > > >> > > >> > ATOMIC_SPECIES > >> > > >> > C 12.0107 C.blyp-mt.UPF > >> > > >> > > >> > > >> > ATOMIC_POSITIONS (angstrom) > >> > > >> > C -11.330758616 -3.527803203 0.000000000 > >> > > >> > C -10.659793092 -1.160339161 0.000000000 > >> > > >> > C -12.039843315 -7.112619698 0.000000000 > >> > > >> > C -12.041158182 -5.732701936 0.000000000 > >> > > >> > C -10.941089654 -4.881442842 0.000000000 > >> > > >> > ...... > >> > > >> > > >> > > >> > Please can anyone advice me on this? Shall I start with the new > >> > configuration and start relaxing again? > >> > > >> > > >> > > >> > Regards > >> > > >> > > >> > > >> > Elie Moujaes > >> > > >> > University of Nott > >> > > >> > University Park > >> > > >> > NGT 3RD > >> > > >> > > >> > > >> > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > >> > >> > >> -- > >> Dept. of Chem and Biochem, Concordia University > >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > >> _______________________________________________ > >> 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 > > > > > > > > -- > Dept. of Chem and Biochem, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110908/ba755de6/attachment-0001.htm From li.chengyang at wmich.edu Thu Sep 8 20:50:40 2011 From: li.chengyang at wmich.edu (Chengyang Li) Date: Thu, 08 Sep 2011 14:50:40 -0400 (EDT) Subject: [Pw_forum] Pseudopotential for Terbium in upf file In-Reply-To: <2f96e1ff.11a2d.13246c36a29.Coremail.flux_ray12@163.com> Message-ID: <547350762.238999.1315507840840.JavaMail.root@wmu-mailstore05> I have written an input file and wanted to execute with ld1.x, but I always meet an error ,it said " wavefunction 5S found too many times". &input title='Tb' zed=65. rel=1, config='[Xe] 4f9 5S2.0 5p6.0 6s2.0' iswitch=3, dft='PBE' / &inputp lloc=0, pseudotype=3, file_pseudopw='Tb.pbe-rrkjus.UPF', author='CHENG' / 4 4F 4 3 9.00 0.00 2.40 2.40 1 5S 1 0 2.00 0.00 2.20 2.20 1 5P 2 1 6.00 0.00 2.00 2.00 1 6S 1 0 2.00 0.00 2.20 2.20 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from el_config : error # 13 wavefunction 5S found too many times %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Does anyone know where is my fault? Thank you. Chengyang Li Department of Physics Western Michigan Uniersity ----- Original Message ----- > From: "GAO Zhe" > To: "PWSCF Forum" > Sent: Wednesday, September 7, 2011 9:00:04 PM > Subject: Re: [Pw_forum] Pseudopotential for Terbium in upf file > You can try to generate Tb's UPF PP by ld1.x, or transfer from > CASTEP's PP file to UPF by usp2upf, which can be downloaded from > http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities. > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > At 2011-09-08 05:14:53,"Chengyang Li" wrote: > >Dear Users > > > > > >I'm trying to find the pseudopotential for Terbium but it seems like > >there is no upf file about Terbium. Does any one can share the codes > >or give me some advice? Thank you. > > > > > > > > > >Chengyang Li > > > >Department of Physics > >Western Michigan Univerisity > > > >_______________________________________________ > >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/20110908/7738128b/attachment.htm From kucukben at sissa.it Thu Sep 8 22:06:14 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 08 Sep 2011 22:06:14 +0200 Subject: [Pw_forum] Pseudopotential for Terbium in upf file In-Reply-To: <547350762.238999.1315507840840.JavaMail.root@wmu-mailstore05> References: <547350762.238999.1315507840840.JavaMail.root@wmu-mailstore05> Message-ID: <20110908220614.5iwqub2tc08ww0gs@webmail.sissa.it> Chengyang Li, Xe already has 5s orbital occupied. emine kucukbenli, phd student, sissa , italy Quoting Chengyang Li : > I have written an input file and wanted to execute with ld1.x, but I > always meet an error ,it said " wavefunction 5S found too many > times". &input title='Tb' zed=65. rel=1, config='[Xe] 4f9 5S2.0 > 5p6.0 6s2.0' iswitch=3, dft='PBE' / &inputp lloc=0, pseudotype=3, > file_pseudopw='Tb.pbe-rrkjus.UPF', author='CHENG' / 4 4F 4 3 9.00 > 0.00 2.40 2.40 1 5S 1 0 2.00 0.00 2.20 2.20 1 5P 2 1 6.00 0.00 2.00 > 2.00 1 6S 1 0 2.00 0.00 2.20 2.20 1 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from el_config : error # 13 wavefunction 5S found too many times %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Does anyone know where is my fault? Thank you. Chengyang Li Department of Physics Western Michigan Uniersity ----- Original Message > ----- >> From: "GAO Zhe" >> To: "PWSCF Forum" >> Sent: Wednesday, September 7, 2011 9:00:04 PM >> Subject: Re: [Pw_forum] Pseudopotential for Terbium in upf file >> You can try to generate Tb's UPF PP by ld1.x, or transfer from >> CASTEP's PP file to UPF by usp2upf, which can be downloaded from >> http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities. >> -- >> GAO Zhe >> CMC Lab, MSE, SNU, Seoul, S.Korea >> At 2011-09-08 05:14:53,"Chengyang Li" wrote: >> >Dear Users >> > >> > >> >I'm trying to find the pseudopotential for Terbium but it seems like >> >there is no upf file about Terbium. Does any one can share the codes >> >or give me some advice? Thank you. >> > >> > >> > >> > >> >Chengyang Li >> > >> >Department of Physics >> >Western Michigan Univerisity >> > >> >_______________________________________________ >> >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 > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From windbellklbh at gmail.com Fri Sep 9 01:35:08 2011 From: windbellklbh at gmail.com (WF) Date: Fri, 9 Sep 2011 07:35:08 +0800 Subject: [Pw_forum] problems with vc-relax Message-ID: <006901cc6e7f$f5b58e00$e120aa00$@gmail.com> Is it good enough to relax an arbitrary system with only gamma k-points? I thought it is necessary to do some test with k-points as this effect change from system to system. In my experience, more k-points is necessary for a metal-like system, i.e. graphene. Best regards, Wu, F > Date: Thu, 8 Sep 2011 11:12:24 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes > wrote: > > Hello Xijun, > > Hello Elie, > > > I did not send the e-mail twice intentionally. There was a problem with my > > e-mail and it kept giving me an error about problems with Windows hotmai > > hence why it was sent twice without me knowing except now when I opened my > > e-mail so I apologize for that. Also I wont include blank lines in the input > > file either. Back to my calculations, I have restarted the calculations, it > > went fine at first but then I got the error: > > from scale_h: not enough memory allocated for radial FFT; try restarting > > with a larger cell_factor. > > Check the manual for definition of cell_factor. The default value is > 1.2, you could try a larger value. > > What's your new K_POINTS setting? Since you are relax the system, I > suggest you start from: > > K_POINTS {gamma} > > This will far faster. and need far less memory. > > > Another simple question: I realized when I restarted everything that the > > positions of the atoms were the initial ones even before starting the > > relaxation process where as the k-points used were the NEW ones. Is that > > normal? or should I have substituted the the C atoms positions by the most > > recent ones then restart again? > > Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode= 'from_scratch' " > > Regards, > - Xijun > > > Regards > > Elie > > > >> Date: Wed, 7 Sep 2011 16:20:49 -0400 > >> From: xijunw at gmail.com > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] problems with vc-relax > >> > >> Hi, Elie, > >> > >> Please do not repeat sending the same message to the mail list. Also, > >> people will be more happy to help you if you keep your mail neat by > >> removing all the unnecessary blank lines in the input file. > >> > >> Regards, > >> Xijun > >> > >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > >> wrote: > >> > Dear all, > >> > > >> > > >> > > >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped > >> > after > >> > 4 days of execution and without reaching the desired force threshold. > >> > The > >> > following output was obtained : > >> > > >> > > >> > > >> > 1st relaxation process: > >> > > >> > > >> > > >> > Total force 0.091 Pressure =- 114.1 kbar > >> > > >> > > >> > > >> > 2nd relaxation process: > >> > > >> > > >> > > >> > total force 0.1 Pressure = -55 kbar > >> > > >> > > >> > > >> > (new enthalpy < old enthalpy) > >> > > >> > > >> > > >> > 3rd process: > >> > > >> > > >> > > >> > total force = 0.058 pressure = -11 kbar > >> > > >> > > >> > > >> > Then in the 4th process, calculations stopped. Here are the last few > >> > lines > >> > of the output: > >> > > >> > > >> > > >> > iteration # 2 ecut= 36.75 Ry beta=0.30 > >> > Davidson diagonalization with overlap > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 3 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 4 eigenvalues not converged > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 5 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > ethr = 2.90E-04, avg # of iterations = 17.6 > >> > > >> > negative rho (up, down): 0.132E-01 0.000E+00 > >> > > >> > total cpu time spent up to now is 382283.13 secs > >> > > >> > total energy = -676.77947904 Ry > >> > Harris-Foulkes estimate = -676.82846513 Ry > >> > estimated scf accuracy < 0.17363554 Ry > >> > > >> > iteration # 3 ecut= 36.75 Ry beta=0.30 > >> > Davidson diagonalization with overlap > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 1 eigenvalues not converged > >> > c_bands: 2 eigenvalues not converged > >> > c_bands: 3 eigenvalues not converged > >> > > >> > > >> > > >> > The input of the vc-relax is: > >> > > >> > > >> > > >> > &control > >> > > >> > prefix='GBphonon', > >> > > >> > calculation='vc-relax', > >> > > >> > restart_mode='from_scratch', > >> > > >> > tstress=.true., > >> > > >> > tprnfor=.true, > >> > > >> > pseudo_dir = > >> > '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > >> > > >> > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > >> > > >> > > >> > > >> > / > >> > > >> > &system > >> > > >> > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc > >> > =36.749309, > >> > occupations='smearing', smearing='mp',degauss=0.01 > >> > > >> > / > >> > > >> > &electrons > >> > > >> > conv_thr=1.D-6, > >> > > >> > mixing_beta=0.3D0, > >> > > >> > diago_david_ndim=2, > >> > > >> > > >> > > >> > / > >> > > >> > > >> > > >> > &ions > >> > > >> > ion_dynamics='bfgs' > >> > > >> > > >> > > >> > / > >> > > >> > $cell > >> > > >> > cell_dynamics='bfgs', > >> > > >> > > >> > > >> > / > >> > > >> > > >> > > >> > CELL_PARAMETERS (alat) > >> > > >> > 24.064488464 0.000772242 0.000000000 > >> > > >> > 0.000000000 6.503051170 0.000000000 > >> > > >> > 0.000000000 0.000000000 8.470514812 > >> > > >> > > >> > > >> > > >> > > >> > ATOMIC_SPECIES > >> > > >> > C 12.0107 C.blyp-mt.UPF > >> > > >> > > >> > > >> > ATOMIC_POSITIONS (angstrom) > >> > > >> > C -11.330758616 -3.527803203 0.000000000 > >> > > >> > C -10.659793092 -1.160339161 0.000000000 > >> > > >> > C -12.039843315 -7.112619698 0.000000000 > >> > > >> > C -12.041158182 -5.732701936 0.000000000 > >> > > >> > C -10.941089654 -4.881442842 0.000000000 > >> > > >> > ...... > >> > > >> > > >> > > >> > Please can anyone advice me on this? Shall I start with the new > >> > configuration and start relaxing again? > >> > > >> > > >> > > >> > Regards > >> > > >> > > >> > > >> > Elie Moujaes > >> > > >> > University of Nott > >> > > >> > University Park > >> > > >> > NGT 3RD > >> > > >> > > >> > > >> > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > >> > >> > >> -- > >> Dept. of Chem and Biochem, Concordia University > >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > >> _______________________________________________ > >> 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 > > > > > > > > -- > Dept. of Chem and Biochem, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ----------------------------------------------------------- Wu, F College of Chemistry and Molecular Engineering, Peking University ---------------------------------------------------------- From li.chengyang at wmich.edu Fri Sep 9 05:07:14 2011 From: li.chengyang at wmich.edu (Chengyang Li) Date: Thu, 08 Sep 2011 23:07:14 -0400 (EDT) Subject: [Pw_forum] Pseudopotential for Terbium in upf file In-Reply-To: <20110908220614.5iwqub2tc08ww0gs@webmail.sissa.it> Message-ID: <955543352.248743.1315537634856.JavaMail.root@wmu-mailstore05> Thank you ,I will revise the input file and try it again. Chengyang Li Department of Physics Western Michigan University ----- Original Message ----- > From: "Emine Kucukbenli" > To: "pw forum" > Sent: Thursday, September 8, 2011 3:06:14 PM > Subject: Re: [Pw_forum] Pseudopotential for Terbium in upf file > Chengyang Li, > Xe already has 5s orbital occupied. > emine kucukbenli, phd student, sissa , italy > > > Quoting Chengyang Li : > > > I have written an input file and wanted to execute with ld1.x, but I > > always meet an error ,it said " wavefunction 5S found too many > > times". &input title='Tb' zed=65. rel=1, config='[Xe] 4f9 5S2.0 > > 5p6.0 6s2.0' iswitch=3, dft='PBE' / &inputp lloc=0, pseudotype=3, > > file_pseudopw='Tb.pbe-rrkjus.UPF', author='CHENG' / 4 4F 4 3 9.00 > > 0.00 2.40 2.40 1 5S 1 0 2.00 0.00 2.20 2.20 1 5P 2 1 6.00 0.00 2.00 > > 2.00 1 6S 1 0 2.00 0.00 2.20 2.20 1 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from el_config : error # 13 wavefunction 5S found too many times > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Does anyone know where is my fault? Thank you. Chengyang Li > > Department of Physics Western Michigan Uniersity ----- Original > > Message > > ----- > >> From: "GAO Zhe" > >> To: "PWSCF Forum" > >> Sent: Wednesday, September 7, 2011 9:00:04 PM > >> Subject: Re: [Pw_forum] Pseudopotential for Terbium in upf file > >> You can try to generate Tb's UPF PP by ld1.x, or transfer from > >> CASTEP's PP file to UPF by usp2upf, which can be downloaded from > >> http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities. > >> -- > >> GAO Zhe > >> CMC Lab, MSE, SNU, Seoul, S.Korea > >> At 2011-09-08 05:14:53,"Chengyang Li" > >> wrote: > >> >Dear Users > >> > > >> > > >> >I'm trying to find the pseudopotential for Terbium but it seems > >> >like > >> >there is no upf file about Terbium. Does any one can share the > >> >codes > >> >or give me some advice? Thank you. > >> > > >> > > >> > > >> > > >> >Chengyang Li > >> > > >> >Department of Physics > >> >Western Michigan Univerisity > >> > > >> >_______________________________________________ > >> >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 > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From xijunw at gmail.com Fri Sep 9 05:58:13 2011 From: xijunw at gmail.com (Xijun Wang) Date: Thu, 8 Sep 2011 23:58:13 -0400 Subject: [Pw_forum] problems with vc-relax In-Reply-To: <006901cc6e7f$f5b58e00$e120aa00$@gmail.com> References: <006901cc6e7f$f5b58e00$e120aa00$@gmail.com> Message-ID: Hi, You are right. Tests should be done. I was suggesting "start" from gamma k-points to make a quick relaxation. After this, relaxation with larger k-points could be followed if necessary. Regards, Xijun On Thu, Sep 8, 2011 at 7:35 PM, WF wrote: > Is it good enough to relax an arbitrary system with only gamma k-points? I > thought it is necessary to do some test with k-points as this effect change > from system to system. In my experience, more k-points is necessary for a > metal-like system, i.e. graphene. > > Best regards, > > Wu, F > >> Date: Thu, 8 Sep 2011 11:12:24 -0400 >> From: xijunw at gmail.com >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] problems with vc-relax >> >> On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes >> wrote: >> > Hello Xijun, >> >> Hello Elie, >> >> > I did not send the e-mail twice intentionally. There was a problem with > my >> > e-mail and it kept giving me an error about problems with Windows hotmai >> > hence why it was sent twice without me knowing except now when I opened > my >> > e-mail so I apologize for that. Also I wont include blank lines in the > input >> > file either. ?Back to my calculations, I have restarted the > calculations, it >> > went fine at first but then I got the error: >> > from scale_h: not enough memory allocated for radial FFT; try restarting >> > with a larger cell_factor. >> >> Check the manual for definition of cell_factor. The default value is >> 1.2, you could try a larger value. >> >> What's your new K_POINTS setting? Since you are relax the system, I >> suggest you start from: >> >> ? ? ?K_POINTS {gamma} >> >> This will far faster. and need far less memory. >> >> > Another simple question: I realized when I restarted everything that the >> > positions of the atoms were the initial ones even before starting the >> > relaxation process where as the k-points used were the NEW ones. Is that >> > normal? or should I have substituted the the C atoms positions by the > most >> > recent ones then restart again? >> >> Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode= > 'from_scratch' " >> >> Regards, >> ?- Xijun >> >> > Regards >> > Elie >> > >> >> Date: Wed, 7 Sep 2011 16:20:49 -0400 >> >> From: xijunw at gmail.com >> >> To: pw_forum at pwscf.org >> >> Subject: Re: [Pw_forum] problems with vc-relax >> >> >> >> Hi, Elie, >> >> >> >> Please do not repeat sending the same message to the mail list. Also, >> >> people will be more happy to help you if you keep your mail neat by >> >> removing all the unnecessary blank lines in the input file. >> >> >> >> Regards, >> >> Xijun >> >> >> >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > >> >> wrote: >> >> > Dear all, >> >> > >> >> > >> >> > >> >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make > the >> >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped >> >> > after >> >> > 4 days of execution and without reaching the desired force threshold. >> >> > The >> >> > following output was obtained : >> >> > >> >> > >> >> > >> >> > 1st relaxation process: >> >> > >> >> > >> >> > >> >> > Total force 0.091 ? Pressure =- 114.1 kbar >> >> > >> >> > >> >> > >> >> > 2nd relaxation process: >> >> > >> >> > >> >> > >> >> > total force 0.1 ? Pressure = -55 kbar >> >> > >> >> > >> >> > >> >> > (new enthalpy < old enthalpy) >> >> > >> >> > >> >> > >> >> > 3rd process: >> >> > >> >> > >> >> > >> >> > total force = 0.058 ? pressure = -11 kbar >> >> > >> >> > >> >> > >> >> > Then in the 4th process, calculations stopped. Here are the last few >> >> > lines >> >> > of the output: >> >> > >> >> > >> >> > >> >> > iteration # ?2 ? ? ecut= ? ?36.75 Ry ? ? beta=0.30 >> >> > ? ? ?Davidson diagonalization with overlap >> >> > ? ? ?c_bands: ?5 eigenvalues not converged >> >> > ? ? ?c_bands: ?1 eigenvalues not converged >> >> > ? ? ?c_bands: ?3 eigenvalues not converged >> >> > ? ? ?c_bands: ?1 eigenvalues not converged >> >> > ? ? ?c_bands: ?4 eigenvalues not converged >> >> > ? ? ?c_bands: ?4 eigenvalues not converged >> >> > ? ? ?c_bands: ?4 eigenvalues not converged >> >> > ? ? ?c_bands: ?4 eigenvalues not converged >> >> > ? ? ?c_bands: ?5 eigenvalues not converged >> >> > ? ? ?c_bands: ?5 eigenvalues not converged >> >> > ? ? ?c_bands: ?2 eigenvalues not converged >> >> > ? ? ?c_bands: ?2 eigenvalues not converged >> >> > ? ? ?ethr = ?2.90E-04, ?avg # of iterations = 17.6 >> >> > >> >> > ? ? ?negative rho (up, down): ?0.132E-01 0.000E+00 >> >> > >> >> > ? ? ?total cpu time spent up to now is 382283.13 secs >> >> > >> >> > ? ? ?total energy ? ? ? ? ? ? ?= ? ?-676.77947904 Ry >> >> > ? ? ?Harris-Foulkes estimate ? = ? ?-676.82846513 Ry >> >> > ? ? ?estimated scf accuracy ? ?< ? ? ? 0.17363554 Ry >> >> > >> >> > ? ? ?iteration # ?3 ? ? ecut= ? ?36.75 Ry ? ? beta=0.30 >> >> > ? ? ?Davidson diagonalization with overlap >> >> > ? ? ?c_bands: ?1 eigenvalues not converged >> >> > ? ? ?c_bands: ?1 eigenvalues not converged >> >> > ? ? ?c_bands: ?2 eigenvalues not converged >> >> > ? ? ?c_bands: ?3 eigenvalues not converged >> >> > >> >> > >> >> > >> >> > The input of the vc-relax is: >> >> > >> >> > >> >> > >> >> > &control >> >> > >> >> > ? ? prefix='GBphonon', >> >> > >> >> > ? ? calculation='vc-relax', >> >> > >> >> > ? ? restart_mode='from_scratch', >> >> > >> >> > ? ? tstress=.true., >> >> > >> >> > ? ? tprnfor=.true, >> >> > >> >> > ? ? pseudo_dir = >> >> > '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', >> >> > >> >> > ? ? outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', >> >> > >> >> > >> >> > >> >> > ?/ >> >> > >> >> > ?&system >> >> > >> >> > ? ? ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc >> >> > =36.749309, >> >> > occupations='smearing', smearing='mp',degauss=0.01 >> >> > >> >> > / >> >> > >> >> > ?&electrons >> >> > >> >> > ? ? conv_thr=1.D-6, >> >> > >> >> > ? ? mixing_beta=0.3D0, >> >> > >> >> > ? ? diago_david_ndim=2, >> >> > >> >> > >> >> > >> >> > ?/ >> >> > >> >> > >> >> > >> >> > &ions >> >> > >> >> > ?ion_dynamics='bfgs' >> >> > >> >> > >> >> > >> >> > / >> >> > >> >> > $cell >> >> > >> >> > cell_dynamics='bfgs', >> >> > >> >> > >> >> > >> >> > / >> >> > >> >> > >> >> > >> >> > CELL_PARAMETERS (alat) >> >> > >> >> > ? 24.064488464 ? 0.000772242 ? 0.000000000 >> >> > >> >> > ? ?0.000000000 ? 6.503051170 ? 0.000000000 >> >> > >> >> > ? ?0.000000000 ? 0.000000000 ? 8.470514812 >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > ATOMIC_SPECIES >> >> > >> >> > ?C ?12.0107 ?C.blyp-mt.UPF >> >> > >> >> > >> >> > >> >> > ATOMIC_POSITIONS (angstrom) >> >> > >> >> > C ? ? ?-11.330758616 ?-3.527803203 ? 0.000000000 >> >> > >> >> > C ? ? ?-10.659793092 ?-1.160339161 ? 0.000000000 >> >> > >> >> > C ? ? ?-12.039843315 ?-7.112619698 ? 0.000000000 >> >> > >> >> > C ? ? ?-12.041158182 ?-5.732701936 ? 0.000000000 >> >> > >> >> > C ? ? ?-10.941089654 ?-4.881442842 ? 0.000000000 >> >> > >> >> > ...... >> >> > >> >> > >> >> > >> >> > Please can anyone advice me on this? Shall I start with the new >> >> > configuration and start relaxing again? >> >> > >> >> > >> >> > >> >> > Regards >> >> > >> >> > >> >> > >> >> > Elie Moujaes >> >> > >> >> > University of Nott >> >> > >> >> > University Park >> >> > >> >> > NGT 3RD >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Pw_forum mailing list >> >> > Pw_forum at pwscf.org >> >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> Dept. of Chem and Biochem, Concordia University >> >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) >> >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 >> >> _______________________________________________ >> >> 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 >> > >> > >> >> >> >> -- >> Dept. of Chem and Biochem, Concordia University >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > ----------------------------------------------------------- > Wu, F > College of Chemistry and Molecular Engineering, Peking University > ---------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dept. of Chem and Biochem, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 From songsong19840614 at gmail.com Fri Sep 9 10:47:39 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 9 Sep 2011 16:47:39 +0800 Subject: [Pw_forum] QHA calculated error ! In-Reply-To: References: Message-ID: Both terminal entering step by step and script can not be work when using 'phonon_dos.x > > > ---------- Forwarded message ---------- > From: lucking-pine > Date: 2011/9/7 > Subject: QHA calculated error ! > To: Pw_forum at pwscf.org > > > Hi, > Recently,I want to calculated the partial_dos of phonon by QHA.Then,I > have compiled it and run examples successfully.However,I run the ZnO.fc I > calculated is failed. > The step is followed: > 1.Using ttrinp to generate K point by > ...../QHA/bin/tetra.x.../QHA/bin/tetra.x > 2.Copy k point into matdy.in and then using .../bin/matdyn.xmatdyn.out > to generate 'frequency' > 3.Using ../QHA/bin/Partial_phonon_DOS.x < phdos1.in > 4.Using ../QHA/bin/phonon_dos.x How ever, I get these information instead of runing phonon_dos.x: > natoms== 4 > irec==== 168 > 0.750000000000000 > forrtl: severe (24): end-of-file during read, unit 9, file > /opt/espresso-4.2.1/QHA/Examples/ZnO/phdos.in > Image PC Routine Line Source > > phonon_dos.x 000000000048FCCD Unknown Unknown Unknown > phonon_dos.x 000000000048E7D5 Unknown Unknown Unknown > phonon_dos.x 0000000000440F40 Unknown Unknown Unknown > phonon_dos.x 000000000040778F Unknown Unknown Unknown > phonon_dos.x 0000000000406FC2 Unknown Unknown Unknown > phonon_dos.x 00000000004232EB Unknown Unknown Unknown > phonon_dos.x 00000000004009C1 Unknown Unknown Unknown > phonon_dos.x 00000000004002EC Unknown Unknown Unknown > phonon_dos.x 000000000049B060 Unknown Unknown Unknown > phonon_dos.x 00000000004001B9 Unknown Unknown Unknown > > Norm of the difference between old and new effective charges: > 0.00000000000000000000 > Norm of the difference between old and new force-constants: > 0.00054944988447139730 > Message from routine matdyn: > Z* not found in file ZnO.fc, TO-LO splitting at q=0 will be absent! > A direction for q was not specified:TO-LO splitting will be absent > > > > > > > > > > But I have the phdos.in file.And I try to replace the frequency file using > the file of example of AlAs,the the 'phonon_dos.x ' can be runed. So please > what is wrong in my work. > Thanks. > Best Regards > Pine. > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110909/fcc931d6/attachment.htm From baroni at sissa.it Fri Sep 9 12:02:27 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 9 Sep 2011 12:02:27 +0200 Subject: [Pw_forum] Interatomic force constant In-Reply-To: References: Message-ID: <7178D2C4-99D9-4042-8788-BCA5A7A69008@sissa.it> Dear Mr. Onaiwu, Quantum ESPRESSO can calculate IFCs from first principles, and then it has small utilities for calculating phonon dispersions from the calculated IFCs. Of course, it does not make any sense to sense to "change" the IFCs calculated from first principles, because the ICFs are the *output*, not the input, of the calculations. Once the IFCs are calculated and stored, as said, they can be used to calculated vibrational dispersions. Nothing forbids to change the calculated IFCs for further reuse, provided one knows what one is doing, and why. This being said, it seems to me that the pw forum would be the ideal arena for discussions such as the present one. For that reason, I am forwarding my reply to your enquiry to the forum as well. Best regards, Stefano Baroni On Sep 8, 2011, at 11:33 PM, Onaiwu Kingsley Nosa wrote: > Dear Stefano, > I'm presently doing a phonon calculation of graphene in my Ph.D > research. Please, I'd want to know if there is any way that the > interatomic force constant can be changed in the Quantum espresso > code. I'd be grateful of any assistance in this regard. > Kingsley Onaiwu --- 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/20110909/617f128d/attachment.htm From giannozz at democritos.it Fri Sep 9 12:32:02 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 9 Sep 2011 12:32:02 +0200 Subject: [Pw_forum] QHA calculated error ! In-Reply-To: References: Message-ID: <4BF4959E-F2D5-4FA5-AAF6-6411460C5B24@democritos.it> On Sep 9, 2011, at 10:47 , lucking-pine wrote: > forrtl: severe (24): end-of-file during read, unit 9, file /opt/ > espresso4.2.1/QHA/Examples/ZnO/phdos.in it shouldn't take much to locate an error when it is so clearly described --- 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 songsong19840614 at gmail.com Fri Sep 9 12:42:19 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 9 Sep 2011 18:42:19 +0800 Subject: [Pw_forum] QHA calculated error ! In-Reply-To: <4BF4959E-F2D5-4FA5-AAF6-6411460C5B24@democritos.it> References: <4BF4959E-F2D5-4FA5-AAF6-6411460C5B24@democritos.it> Message-ID: Hi,Paolo I get it. I change the phdos.in 0.75 Zn O to 0.75 Zn Zn O O. But the phdos.in of AlAs of example is Al As, and is not Al Al As As. Why? Could be anyone known? Bests Pine 2011/9/9 Paolo Giannozzi > > On Sep 9, 2011, at 10:47 , lucking-pine wrote: > > > forrtl: severe (24): end-of-file during read, unit 9, file /opt/ > > espresso4.2.1/QHA/Examples/ZnO/phdos.in > > it shouldn't take much to locate an error when it is so clearly > described > --- > 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/20110909/bdbe7e00/attachment.htm From giannozz at democritos.it Fri Sep 9 15:35:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 9 Sep 2011 15:35:07 +0200 Subject: [Pw_forum] QHA calculated error ! In-Reply-To: References: <4BF4959E-F2D5-4FA5-AAF6-6411460C5B24@democritos.it> Message-ID: <2A9E544F-1E28-4032-A7F0-82399D9C0110@democritos.it> On Sep 9, 2011, at 12:42 , lucking-pine wrote: > Zn Zn O O. > But the phdos.in of AlAs of example is > Al As, > and is not > Al Al As As. > Why? wurtzite ZnO? 4 atoms per unit cell. Zincblende AlAs? 2 atoms per unit cell. What does the code expects in 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 songsong19840614 at gmail.com Fri Sep 9 16:04:20 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 9 Sep 2011 22:04:20 +0800 Subject: [Pw_forum] QHA calculated error ! In-Reply-To: <2A9E544F-1E28-4032-A7F0-82399D9C0110@democritos.it> References: <4BF4959E-F2D5-4FA5-AAF6-6411460C5B24@democritos.it> <2A9E544F-1E28-4032-A7F0-82399D9C0110@democritos.it> Message-ID: Hi, Paolo Thanks for your help.I understand now. Bests Pine 2011/9/9 Paolo Giannozzi > > On Sep 9, 2011, at 12:42 , lucking-pine wrote: > > > Zn Zn O O. > > But the phdos.in of AlAs of example is > > Al As, > > and is not > > Al Al As As. > > Why? > > wurtzite ZnO? 4 atoms per unit cell. Zincblende AlAs? > 2 atoms per unit cell. What does the code expects in > 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 > > > > > _______________________________________________ > 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/20110909/e8bf083b/attachment-0001.htm From elie.moujaes at hotmail.co.uk Fri Sep 9 17:00:01 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 9 Sep 2011 16:00:01 +0100 Subject: [Pw_forum] problems with vc-relax In-Reply-To: References: <006901cc6e7f$f5b58e00$e120aa00$@gmail.com>, Message-ID: Thanks all for your suggestions, I did a relaxation of the system with only the gamma point and it was amazingly quick. It was done in 3 hours. The main reason to do the relaxation is because I got negative frequencies while trying to execute ph.x which took a really long time (12 days more or less). The reason for that I guess is the mechanical instability of the system. This is why I want to make sure the system is relaxed before performing ph.x again. I did start again relaxing the system with 4 points now (still going on with oscillations in the total force). My scf file for phonons is with 25 points and the one with scf calculations is with 10 points. Is there a quick way to know if the number of points is sufficient for relation or not or is the only way to take the new coordinates do an scf calculation with say 10 points in my case and check the total force? Regards Elie > Date: Thu, 8 Sep 2011 23:58:13 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > Hi, > > You are right. Tests should be done. I was suggesting "start" from > gamma k-points to make a quick relaxation. After this, relaxation with > larger k-points could be followed if necessary. > > Regards, > Xijun > > On Thu, Sep 8, 2011 at 7:35 PM, WF wrote: > > Is it good enough to relax an arbitrary system with only gamma k-points? I > > thought it is necessary to do some test with k-points as this effect change > > from system to system. In my experience, more k-points is necessary for a > > metal-like system, i.e. graphene. > > > > Best regards, > > > > Wu, F > > > >> Date: Thu, 8 Sep 2011 11:12:24 -0400 > >> From: xijunw at gmail.com > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] problems with vc-relax > >> > >> On Thu, Sep 8, 2011 at 10:26 AM, Elie Moujaes > >> wrote: > >> > Hello Xijun, > >> > >> Hello Elie, > >> > >> > I did not send the e-mail twice intentionally. There was a problem with > > my > >> > e-mail and it kept giving me an error about problems with Windows hotmai > >> > hence why it was sent twice without me knowing except now when I opened > > my > >> > e-mail so I apologize for that. Also I wont include blank lines in the > > input > >> > file either. Back to my calculations, I have restarted the > > calculations, it > >> > went fine at first but then I got the error: > >> > from scale_h: not enough memory allocated for radial FFT; try restarting > >> > with a larger cell_factor. > >> > >> Check the manual for definition of cell_factor. The default value is > >> 1.2, you could try a larger value. > >> > >> What's your new K_POINTS setting? Since you are relax the system, I > >> suggest you start from: > >> > >> K_POINTS {gamma} > >> > >> This will far faster. and need far less memory. > >> > >> > Another simple question: I realized when I restarted everything that the > >> > positions of the atoms were the initial ones even before starting the > >> > relaxation process where as the k-points used were the NEW ones. Is that > >> > normal? or should I have substituted the the C atoms positions by the > > most > >> > recent ones then restart again? > >> > >> Yes, restart again with NEW ATOMIC_POSITIONS and "restart_mode= > > 'from_scratch' " > >> > >> Regards, > >> - Xijun > >> > >> > Regards > >> > Elie > >> > > >> >> Date: Wed, 7 Sep 2011 16:20:49 -0400 > >> >> From: xijunw at gmail.com > >> >> To: pw_forum at pwscf.org > >> >> Subject: Re: [Pw_forum] problems with vc-relax > >> >> > >> >> Hi, Elie, > >> >> > >> >> Please do not repeat sending the same message to the mail list. Also, > >> >> people will be more happy to help you if you keep your mail neat by > >> >> removing all the unnecessary blank lines in the input file. > >> >> > >> >> Regards, > >> >> Xijun > >> >> > >> >> On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > > > >> >> wrote: > >> >> > Dear all, > >> >> > > >> >> > > >> >> > > >> >> > I am relaxing a 60 atom supercell (graphene grain boundary) to make > > the > >> >> > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped > >> >> > after > >> >> > 4 days of execution and without reaching the desired force threshold. > >> >> > The > >> >> > following output was obtained : > >> >> > > >> >> > > >> >> > > >> >> > 1st relaxation process: > >> >> > > >> >> > > >> >> > > >> >> > Total force 0.091 Pressure =- 114.1 kbar > >> >> > > >> >> > > >> >> > > >> >> > 2nd relaxation process: > >> >> > > >> >> > > >> >> > > >> >> > total force 0.1 Pressure = -55 kbar > >> >> > > >> >> > > >> >> > > >> >> > (new enthalpy < old enthalpy) > >> >> > > >> >> > > >> >> > > >> >> > 3rd process: > >> >> > > >> >> > > >> >> > > >> >> > total force = 0.058 pressure = -11 kbar > >> >> > > >> >> > > >> >> > > >> >> > Then in the 4th process, calculations stopped. Here are the last few > >> >> > lines > >> >> > of the output: > >> >> > > >> >> > > >> >> > > >> >> > iteration # 2 ecut= 36.75 Ry beta=0.30 > >> >> > Davidson diagonalization with overlap > >> >> > c_bands: 5 eigenvalues not converged > >> >> > c_bands: 1 eigenvalues not converged > >> >> > c_bands: 3 eigenvalues not converged > >> >> > c_bands: 1 eigenvalues not converged > >> >> > c_bands: 4 eigenvalues not converged > >> >> > c_bands: 4 eigenvalues not converged > >> >> > c_bands: 4 eigenvalues not converged > >> >> > c_bands: 4 eigenvalues not converged > >> >> > c_bands: 5 eigenvalues not converged > >> >> > c_bands: 5 eigenvalues not converged > >> >> > c_bands: 2 eigenvalues not converged > >> >> > c_bands: 2 eigenvalues not converged > >> >> > ethr = 2.90E-04, avg # of iterations = 17.6 > >> >> > > >> >> > negative rho (up, down): 0.132E-01 0.000E+00 > >> >> > > >> >> > total cpu time spent up to now is 382283.13 secs > >> >> > > >> >> > total energy = -676.77947904 Ry > >> >> > Harris-Foulkes estimate = -676.82846513 Ry > >> >> > estimated scf accuracy < 0.17363554 Ry > >> >> > > >> >> > iteration # 3 ecut= 36.75 Ry beta=0.30 > >> >> > Davidson diagonalization with overlap > >> >> > c_bands: 1 eigenvalues not converged > >> >> > c_bands: 1 eigenvalues not converged > >> >> > c_bands: 2 eigenvalues not converged > >> >> > c_bands: 3 eigenvalues not converged > >> >> > > >> >> > > >> >> > > >> >> > The input of the vc-relax is: > >> >> > > >> >> > > >> >> > > >> >> > &control > >> >> > > >> >> > prefix='GBphonon', > >> >> > > >> >> > calculation='vc-relax', > >> >> > > >> >> > restart_mode='from_scratch', > >> >> > > >> >> > tstress=.true., > >> >> > > >> >> > tprnfor=.true, > >> >> > > >> >> > pseudo_dir = > >> >> > '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > >> >> > > >> >> > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > >> >> > > >> >> > > >> >> > > >> >> > / > >> >> > > >> >> > &system > >> >> > > >> >> > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc > >> >> > =36.749309, > >> >> > occupations='smearing', smearing='mp',degauss=0.01 > >> >> > > >> >> > / > >> >> > > >> >> > &electrons > >> >> > > >> >> > conv_thr=1.D-6, > >> >> > > >> >> > mixing_beta=0.3D0, > >> >> > > >> >> > diago_david_ndim=2, > >> >> > > >> >> > > >> >> > > >> >> > / > >> >> > > >> >> > > >> >> > > >> >> > &ions > >> >> > > >> >> > ion_dynamics='bfgs' > >> >> > > >> >> > > >> >> > > >> >> > / > >> >> > > >> >> > $cell > >> >> > > >> >> > cell_dynamics='bfgs', > >> >> > > >> >> > > >> >> > > >> >> > / > >> >> > > >> >> > > >> >> > > >> >> > CELL_PARAMETERS (alat) > >> >> > > >> >> > 24.064488464 0.000772242 0.000000000 > >> >> > > >> >> > 0.000000000 6.503051170 0.000000000 > >> >> > > >> >> > 0.000000000 0.000000000 8.470514812 > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > ATOMIC_SPECIES > >> >> > > >> >> > C 12.0107 C.blyp-mt.UPF > >> >> > > >> >> > > >> >> > > >> >> > ATOMIC_POSITIONS (angstrom) > >> >> > > >> >> > C -11.330758616 -3.527803203 0.000000000 > >> >> > > >> >> > C -10.659793092 -1.160339161 0.000000000 > >> >> > > >> >> > C -12.039843315 -7.112619698 0.000000000 > >> >> > > >> >> > C -12.041158182 -5.732701936 0.000000000 > >> >> > > >> >> > C -10.941089654 -4.881442842 0.000000000 > >> >> > > >> >> > ...... > >> >> > > >> >> > > >> >> > > >> >> > Please can anyone advice me on this? Shall I start with the new > >> >> > configuration and start relaxing again? > >> >> > > >> >> > > >> >> > > >> >> > Regards > >> >> > > >> >> > > >> >> > > >> >> > Elie Moujaes > >> >> > > >> >> > University of Nott > >> >> > > >> >> > University Park > >> >> > > >> >> > NGT 3RD > >> >> > > >> >> > > >> >> > > >> >> > _______________________________________________ > >> >> > Pw_forum mailing list > >> >> > Pw_forum at pwscf.org > >> >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> Dept. of Chem and Biochem, Concordia University > >> >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > >> >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > >> >> _______________________________________________ > >> >> 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 > >> > > >> > > >> > >> > >> > >> -- > >> Dept. of Chem and Biochem, Concordia University > >> 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > >> Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ----------------------------------------------------------- > > Wu, F > > College of Chemistry and Molecular Engineering, Peking University > > ---------------------------------------------------------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dept. of Chem and Biochem, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > _______________________________________________ > 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/20110909/9909bc1e/attachment-0001.htm From parishok at gmail.com Fri Sep 9 17:37:39 2011 From: parishok at gmail.com (pari shok) Date: Fri, 9 Sep 2011 11:37:39 -0400 Subject: [Pw_forum] local density of states on parallel planes Message-ID: Dear All, Hi. I was wondering if QE has a built-in function for calculating local density of states on planes. I need to get the LDOS on different planes parallel to one another. I tried to use ILDOS in post processing. However, I am not sure how possibly I can use the code to get LDOS on different parallel planes. I appreciate your help. P Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110909/f4cc419e/attachment.htm From onaiwu.kingsley.nosa at gmail.com Sat Sep 10 00:57:57 2011 From: onaiwu.kingsley.nosa at gmail.com (Onaiwu Kingsley Nosa) Date: Fri, 9 Sep 2011 23:57:57 +0100 Subject: [Pw_forum] Interatomic force constant In-Reply-To: <7178D2C4-99D9-4042-8788-BCA5A7A69008@sissa.it> References: <7178D2C4-99D9-4042-8788-BCA5A7A69008@sissa.it> Message-ID: Dear Stefano, I thank you for the prompt response to my question. Whenever and wherever I need your assistance again I'll let you know. Best wishes, Kingsley Onaiwu On 9/9/11, Stefano Baroni wrote: > Dear Mr. Onaiwu, > > Quantum ESPRESSO can calculate IFCs from first principles, and then it has > small utilities for calculating phonon dispersions from the calculated IFCs. > Of course, it does not make any sense to sense to "change" the IFCs > calculated from first principles, because the ICFs are the *output*, not the > input, of the calculations. Once the IFCs are calculated and stored, as > said, they can be used to calculated vibrational dispersions. Nothing > forbids to change the calculated IFCs for further reuse, provided one knows > what one is doing, and why. > > This being said, it seems to me that the pw forum would be the ideal arena > for discussions such as the present one. For that reason, I am forwarding my > reply to your enquiry to the forum as well. > > Best regards, > > Stefano Baroni > > On Sep 8, 2011, at 11:33 PM, Onaiwu Kingsley Nosa wrote: > >> Dear Stefano, >> I'm presently doing a phonon calculation of graphene in my Ph.D >> research. Please, I'd want to know if there is any way that the >> interatomic force constant can be changed in the Quantum espresso >> code. I'd be grateful of any assistance in this regard. >> Kingsley Onaiwu > > --- > 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 > > From germaneau at gucas.ac.cn Sat Sep 10 19:03:14 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 10 Sep 2011 13:03:14 -0400 Subject: [Pw_forum] Phonones In-Reply-To: <498390199.17355@test1.gucas.ac.cn> References: <4D6253CF.90409@bham.ac.uk> <454423.44264.qm@web65704.mail.ac4.yahoo.com> <498390199.17355@test1.gucas.ac.cn> Message-ID: <4E6B9852.6080207@gucas.ac.cn> Hey Paul, I got stuck in my phonon calculations .... May I inquire to send me your inputs files. Do you also compute the dispersion curves? Also I wonder whether I have to use a super cell or not. Thank you, ?ric. On 02/22/2011 12:17 PM, Paul Jennings wrote: > Thank you very much, > It now works. > > Cheers, > Paul > > On 21/02/2011 12:37, Eyvaz Isaev wrote: >> Hi, >> >> You could try in two ways: >> >> 1. K_POINTS automatic >> 1 1 1 0 0 0 >> >> This will give you only Gamma point, and G-point tricky will be avoided >> (hopefully). >> >> 2. You can specify in ph.in file >> >> ldisp=.true. >> nq1=2, nq2=2, nq3=2 >> start_q=1 >> last_q=1 >> >> G-point is the first in the q-list generated. >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel& Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Paul Jennings >> To: pw_forum at pwscf.org >> Sent: Mon, February 21, 2011 3:00:15 PM >> Subject: [Pw_forum] Phonones >> >> >> Dear QE users >> >> I try to do a gamma point phonon calculations for say Au6. After doing a SCF >> calculation (at the gamme point) >> and using the input file for ph.x of the form: >> >> Phonons of Au6 at Gamma >> &inputph >> tr2_ph=1.0d-14, >> amass(1)=196.97, >> prefix="Au6_dos", >> outdir="/scratch/heiless", >> fildyn="Au6.dynG", >> / >> 0.0 0.0 0.0 >> >> >> the program comes up with the following error message: >> >> from phq_readin : error # 1 >> cannot start from pw.x data file using Gamma-point tricks >> >> The procedure I used works well for solid Si but unfortunately I don't know what >> the problem for this small >> cluster is. >> >> Any help would be appreciated. >> Many thanks, >> Paul >> >> -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110910/9bf03d37/attachment.htm From germaneau at gucas.ac.cn Sat Sep 10 19:27:00 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 10 Sep 2011 13:27:00 -0400 Subject: [Pw_forum] Phonones In-Reply-To: <515630426.29042@test1.gucas.ac.cn> References: <4D6253CF.90409@bham.ac.uk> <454423.44264.qm@web65704.mail.ac4.yahoo.com> <498390199.17355@test1.gucas.ac.cn> <515630426.29042@test1.gucas.ac.cn> Message-ID: <4E6B9DE4.70204@gucas.ac.cn> Dear all, I apologize for having bothered you, this message was addressed to the forum. ?ric. On 09/10/2011 01:03 PM, Eric Germaneau wrote: > Hey Paul, > > I got stuck in my phonon calculations .... > May I inquire to send me your inputs files. > Do you also compute the dispersion curves? > Also I wonder whether I have to use a super cell or not. > Thank you, > > ?ric. > > On 02/22/2011 12:17 PM, Paul Jennings wrote: >> Thank you very much, >> It now works. >> >> Cheers, >> Paul >> >> On 21/02/2011 12:37, Eyvaz Isaev wrote: >>> Hi, >>> >>> You could try in two ways: >>> >>> 1. K_POINTS automatic >>> 1 1 1 0 0 0 >>> >>> This will give you only Gamma point, and G-point tricky will be avoided >>> (hopefully). >>> >>> 2. You can specify in ph.in file >>> >>> ldisp=.true. >>> nq1=2, nq2=2, nq3=2 >>> start_q=1 >>> last_q=1 >>> >>> G-point is the first in the q-list generated. >>> >>> Bests, >>> Eyvaz. >>> >>> ------------------------------------------------------------------- >>> Prof. Eyvaz Isaev, >>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >>> Sweden >>> >>> Theoretical Physics Department, Moscow State Institute of Steel& Alloys, >>> Russia, >>> >>> isaev at ifm.liu.se,eyvaz_isaev at yahoo.com >>> >>> >>> >>> ----- Original Message ---- >>> From: Paul Jennings >>> To:pw_forum at pwscf.org >>> Sent: Mon, February 21, 2011 3:00:15 PM >>> Subject: [Pw_forum] Phonones >>> >>> >>> Dear QE users >>> >>> I try to do a gamma point phonon calculations for say Au6. After doing a SCF >>> calculation (at the gamme point) >>> and using the input file for ph.x of the form: >>> >>> Phonons of Au6 at Gamma >>> &inputph >>> tr2_ph=1.0d-14, >>> amass(1)=196.97, >>> prefix="Au6_dos", >>> outdir="/scratch/heiless", >>> fildyn="Au6.dynG", >>> / >>> 0.0 0.0 0.0 >>> >>> >>> the program comes up with the following error message: >>> >>> from phq_readin : error # 1 >>> cannot start from pw.x data file using Gamma-point tricks >>> >>> The procedure I used works well for solid Si but unfortunately I don't know what >>> the problem for this small >>> cluster is. >>> >>> Any help would be appreciated. >>> Many thanks, >>> Paul >>> >>> > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110910/28c45230/attachment.htm From elie.moujaes at hotmail.co.uk Sat Sep 10 18:37:12 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sat, 10 Sep 2011 17:37:12 +0100 Subject: [Pw_forum] results of vc-relax Message-ID: Dear all, I have relaxed my 60 Carbon atom system using four k points . everything went ok but i could not understand the final steps of the calculation. I have reached a total force of 0.002024 and a pressure of 0.00 and then teh final positions of the atoms and unit cell were printed. After that a scf calculation started running but with old coordinates where the total force is 0.03 (Of course I will do an scf calculation later with higher points)! I didnt quite understand this final step. i will post the related output for you: convergence has been achieved in 7 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = -0.00023166 -0.00022854 0.00000000 atom 2 type 1 force = -0.00009534 -0.00027625 0.00000000 atom 3 type 1 force = 0.00003632 -0.00007034 0.00000000 atom 4 type 1 force = -0.00007340 -0.00041637 0.00000000 atom 5 type 1 force = 0.00042431 -0.00021307 0.00000000 atom 6 type 1 force = 0.00018754 -0.00011456 0.00000000 atom 7 type 1 force = -0.00013707 -0.00022276 0.00000000 atom 8 type 1 force = -0.00003971 -0.00020683 0.00000000 atom 9 type 1 force = 0.00010279 -0.00012422 0.00000000 atom 10 type 1 force = -0.00039366 -0.00010300 0.00000000 atom 11 type 1 force = 0.00005799 -0.00015878 0.00000000 atom 12 type 1 force = -0.00002702 0.00003237 0.00000000 atom 13 type 1 force = 0.00007204 -0.00008913 0.00000000 atom 14 type 1 force = 0.00017616 0.00003631 0.00000000 atom 15 type 1 force = -0.00014275 0.00000748 0.00000000 atom 16 type 1 force = 0.00007827 -0.00009404 0.00000000 atom 17 type 1 force = -0.00023149 0.00016841 0.00000000 atom 18 type 1 force = -0.00007341 0.00022488 0.00000000 atom 19 type 1 force = -0.00001971 0.00011783 0.00000000 atom 20 type 1 force = -0.00008179 0.00033161 0.00000000 atom 21 type 1 force = -0.00000977 0.00022661 0.00000000 atom 22 type 1 force = 0.00012017 0.00013798 0.00000000 atom 23 type 1 force = 0.00006171 0.00037856 0.00000000 atom 24 type 1 force = 0.00011989 0.00032499 0.00000000 atom 25 type 1 force = -0.00016956 0.00023528 0.00000000 atom 26 type 1 force = -0.00017283 0.00017027 0.00000000 atom 27 type 1 force = 0.00015045 0.00031582 0.00000000 atom 28 type 1 force = -0.00009814 0.00021713 0.00000000 atom 29 type 1 force = 0.00009981 0.00035732 0.00000000 atom 30 type 1 force = 0.00018150 0.00026185 0.00000000 atom 31 type 1 force = -0.00021448 0.00030953 0.00000000 atom 32 type 1 force = -0.00008300 0.00012988 0.00000000 atom 33 type 1 force = 0.00013930 0.00045118 0.00000000 atom 34 type 1 force = -0.00002760 0.00003752 0.00000000 atom 35 type 1 force = -0.00002660 0.00029332 0.00000000 atom 36 type 1 force = 0.00017202 0.00004516 0.00000000 atom 37 type 1 force = -0.00008425 0.00025324 0.00000000 atom 38 type 1 force = 0.00001440 0.00016061 0.00000000 atom 39 type 1 force = -0.00002197 0.00019880 0.00000000 atom 40 type 1 force = 0.00000585 0.00014696 0.00000000 atom 41 type 1 force = 0.00000235 0.00018258 0.00000000 atom 42 type 1 force = -0.00002749 -0.00002578 0.00000000 atom 43 type 1 force = 0.00007404 0.00000508 0.00000000 atom 44 type 1 force = -0.00018007 -0.00012389 0.00000000 atom 45 type 1 force = 0.00005834 0.00007620 0.00000000 atom 46 type 1 force = -0.00012551 0.00000512 0.00000000 atom 47 type 1 force = 0.00017256 -0.00003766 0.00000000 atom 48 type 1 force = -0.00004018 -0.00020654 0.00000000 atom 49 type 1 force = -0.00000882 -0.00014507 0.00000000 atom 50 type 1 force = 0.00005372 -0.00033296 0.00000000 atom 51 type 1 force = 0.00011833 -0.00019327 0.00000000 atom 52 type 1 force = 0.00000983 -0.00023736 0.00000000 atom 53 type 1 force = -0.00006016 -0.00032603 0.00000000 atom 54 type 1 force = 0.00012524 -0.00036276 0.00000000 atom 55 type 1 force = -0.00013815 -0.00016926 0.00000000 atom 56 type 1 force = 0.00008094 -0.00034827 0.00000000 atom 57 type 1 force = -0.00004248 -0.00026122 0.00000000 atom 58 type 1 force = 0.00014510 -0.00027006 0.00000000 atom 59 type 1 force = -0.00010882 -0.00020553 0.00000000 atom 60 type 1 force = 0.00014590 -0.00027631 0.00000000 Total force = 0.002024 Total SCF correction = 0.000078 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 0.00 0.00000014 0.00000012 0.00000000 0.02 0.02 0.00 0.00000012 -0.00000031 0.00000000 0.02 -0.05 0.00 0.00000000 0.00000000 0.00000009 0.00 0.00 0.01 bfgs converged in 15 scf cycles and 14 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) End of BFGS Geometry Optimization Final enthalpy = -676.9794620807 Ry Begin final coordinates new unit-cell volume = 5168.18192 a.u.^3 ( 765.84554 Ang^3 ) CELL_PARAMETERS (alat= 1.88972599) 23.648229443 0.000425529 0.000000000 -0.000095218 6.384489590 0.000000000 0.000000000 0.000000000 5.072434769 ATOMIC_POSITIONS (angstrom) C -11.136635697 -3.462306145 0.000000000 C -10.478248630 -1.147614255 0.000000000 C -11.831433427 -6.994032994 0.000000000 C -11.831426674 -5.638563353 0.000000000 C -10.751387047 -4.799215722 0.000000000 C -10.160334791 -2.499053350 0.000000000 C -8.820668361 -2.960993563 0.000000000 C -8.043295525 -0.710539223 0.000000000 C -9.363023219 -6.653337450 0.000000000 C -9.511314668 -5.268108139 0.000000000 C -8.497854102 -4.325198994 0.000000000 C -7.761245789 -2.065281692 0.000000000 C -6.442142553 -2.516348715 0.000000000 C -5.685573272 -0.238451645 0.000000000 C -6.989896238 -6.169999771 0.000000000 C -7.207798311 -4.786862653 0.000000000 C -6.153437661 -3.877761795 0.000000000 C -5.398176759 -1.599624265 0.000000000 C -4.078396507 -2.050650891 0.000000000 C -3.340982884 0.209300608 0.000000000 C -4.630779203 -5.713828103 0.000000000 C -4.848966184 -4.330636815 0.000000000 C -3.795853019 -3.405318190 0.000000000 C -3.018563685 -1.154861107 0.000000000 C -1.678573660 -1.616001416 0.000000000 C -1.087440337 0.684516495 0.000000000 C -2.327541272 -5.231835461 0.000000000 C -2.475783043 -3.846502013 0.000000000 C -1.360942672 -2.967250287 0.000000000 C -0.702083537 -0.652215387 0.000000000 C 0.687083107 -0.651398642 0.000000000 C 1.072296278 0.685565405 0.000000000 C -0.007674180 -4.859628510 0.000000000 C -0.007610206 -3.504149321 0.000000000 C 1.345555343 -2.966021775 0.000000000 C 1.663374840 -1.614518332 0.000000000 C 3.002953819 -1.152262641 0.000000000 C 3.325731725 0.212052928 0.000000000 C 2.312305445 -5.229824491 0.000000000 C 2.460749293 -3.844602171 0.000000000 C 3.780526654 -3.402480615 0.000000000 C 4.062412584 -2.047656710 0.000000000 C 5.381344182 -1.596005055 0.000000000 C 5.670104386 -0.234973803 0.000000000 C 4.615837048 -5.710336246 0.000000000 C 4.833886474 -4.327275491 0.000000000 C 6.138479775 -3.874324380 0.000000000 C 6.425872787 -2.512933055 0.000000000 C 7.745740874 -2.062243128 0.000000000 C 8.028161853 -0.707596134 0.000000000 C 6.974965715 -6.166773894 0.000000000 C 7.193137352 -4.783632176 0.000000000 C 8.483235865 -4.322476098 0.000000000 C 8.805570186 -2.958360122 0.000000000 C 10.145677264 -2.497405347 0.000000000 C 10.463256819 -1.146031873 0.000000000 C 9.348525512 -6.651067918 0.000000000 C 9.496705023 -5.265832962 0.000000000 C 10.737029931 -4.797874340 0.000000000 C 11.122334580 -3.461139408 0.000000000 End final coordinates A final scf calculation at the relaxed structure. The G-vectors are recalculated. Stick Mesh ---------- nst = 6309, nstw = 1727, nsts = 6309 n.st n.stw n.sts n.g n.gw n.gs min 6309 1727 6309 155597 22181 155597 max 6309 1727 6309 155597 22181 155597 6309 1727 6309 155597 22181 155597 bravais-lattice index = 0 lattice parameter (a_0) = 1.8897 a.u. unit-cell volume = 5168.1819 (a.u.)^3 number of atoms/cell = 60 number of atomic types = 1 number of electrons = 240.00 number of Kohn-Sham states= 144 kinetic-energy cutoff = 36.7493 Ry charge density cutoff = 146.9972 Ry convergence threshold = 1.0E-08 mixing beta = 0.3000 number of iterations used = 8 plain mixing Exchange-correlation = SLA LYP B88 BLYP (1313) EXX-fraction = 0.00 celldm(1)= 1.889726 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) = ( 23.648229 0.000426 0.000000 ) a(2) = ( -0.000095 6.384490 0.000000 ) a(3) = ( 0.000000 0.000000 5.072435 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 0.042286 0.000001 0.000000 ) b(2) = ( -0.000003 0.156630 0.000000 ) b(3) = ( 0.000000 0.000000 0.197144 ) PseudoPot. # 1 for C read from file C.blyp-mt.UPF MD5 check sum: 9707c83c4328ed89710f741247262d6d Pseudo is Norm-conserving, Zval = 4.0 Generated by new atomic code, or converted to UPF format Using radial grid of 279 points, 1 beta functions with: l(1) = 0 atomic species valence mass pseudopotential C 4.00 12.01070 C ( 1.00) 2 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (a_0 units) 1 C tau( 1) = ( -11.1366365 -3.4623064 0.0000000 ) 2 C tau( 2) = ( -10.4782494 -1.1476143 0.0000000 ) 3 C tau( 3) = ( -11.8314343 -6.9940335 0.0000000 ) 4 C tau( 4) = ( -11.8314276 -5.6385638 0.0000000 ) 5 C tau( 5) = ( -10.7513879 -4.7992161 0.0000000 ) 6 C tau( 6) = ( -10.1603356 -2.4990535 0.0000000 ) 7 C tau( 7) = ( -8.8206690 -2.9609938 0.0000000 ) 8 C tau( 8) = ( -8.0432961 -0.7105393 0.0000000 ) 9 C tau( 9) = ( -9.3630239 -6.6533380 0.0000000 ) 10 C tau( 10) = ( -9.5113154 -5.2681085 0.0000000 ) 11 C tau( 11) = ( -8.4978547 -4.3251993 0.0000000 ) 12 C tau( 12) = ( -7.7612464 -2.0652818 0.0000000 ) 13 C tau( 13) = ( -6.4421430 -2.5163489 0.0000000 ) 14 C tau( 14) = ( -5.6855737 -0.2384517 0.0000000 ) 15 C tau( 15) = ( -6.9898968 -6.1700002 0.0000000 ) 16 C tau( 16) = ( -7.2077989 -4.7868630 0.0000000 ) 17 C tau( 17) = ( -6.1534381 -3.8777621 0.0000000 ) 18 C tau( 18) = ( -5.3981772 -1.5996244 0.0000000 ) 19 C tau( 19) = ( -4.0783968 -2.0506510 0.0000000 ) 20 C tau( 20) = ( -3.3409831 0.2093006 0.0000000 ) 21 C tau( 21) = ( -4.6307796 -5.7138285 0.0000000 ) 22 C tau( 22) = ( -4.8489666 -4.3306371 0.0000000 ) 23 C tau( 23) = ( -3.7958533 -3.4053184 0.0000000 ) 24 C tau( 24) = ( -3.0185639 -1.1548612 0.0000000 ) 25 C tau( 25) = ( -1.6785738 -1.6160015 0.0000000 ) 26 C tau( 26) = ( -1.0874404 0.6845165 0.0000000 ) 27 C tau( 27) = ( -2.3275414 -5.2318359 0.0000000 ) 28 C tau( 28) = ( -2.4757832 -3.8465023 0.0000000 ) 29 C tau( 29) = ( -1.3609428 -2.9672505 0.0000000 ) 30 C tau( 30) = ( -0.7020836 -0.6522154 0.0000000 ) 31 C tau( 31) = ( 0.6870832 -0.6513987 0.0000000 ) 32 C tau( 32) = ( 1.0722964 0.6855655 0.0000000 ) 33 C tau( 33) = ( -0.0076742 -4.8596289 0.0000000 ) 34 C tau( 34) = ( -0.0076102 -3.5041496 0.0000000 ) 35 C tau( 35) = ( 1.3455554 -2.9660220 0.0000000 ) 36 C tau( 36) = ( 1.6633750 -1.6145185 0.0000000 ) 37 C tau( 37) = ( 3.0029540 -1.1522627 0.0000000 ) 38 C tau( 38) = ( 3.3257320 0.2120529 0.0000000 ) 39 C tau( 39) = ( 2.3123056 -5.2298249 0.0000000 ) 40 C tau( 40) = ( 2.4607495 -3.8446025 0.0000000 ) 41 C tau( 41) = ( 3.7805269 -3.4024809 0.0000000 ) 42 C tau( 42) = ( 4.0624129 -2.0476569 0.0000000 ) 43 C tau( 43) = ( 5.3813446 -1.5960052 0.0000000 ) 44 C tau( 44) = ( 5.6701048 -0.2349738 0.0000000 ) 45 C tau( 45) = ( 4.6158374 -5.7103367 0.0000000 ) 46 C tau( 46) = ( 4.8338868 -4.3272758 0.0000000 ) 47 C tau( 47) = ( 6.1384802 -3.8743247 0.0000000 ) 48 C tau( 48) = ( 6.4258733 -2.5129332 0.0000000 ) 49 C tau( 49) = ( 7.7457415 -2.0622433 0.0000000 ) 50 C tau( 50) = ( 8.0281625 -0.7075962 0.0000000 ) 51 C tau( 51) = ( 6.9749662 -6.1667744 0.0000000 ) 52 C tau( 52) = ( 7.1931379 -4.7836325 0.0000000 ) 53 C tau( 53) = ( 8.4832365 -4.3224764 0.0000000 ) 54 C tau( 54) = ( 8.8055709 -2.9583603 0.0000000 ) 55 C tau( 55) = ( 10.1456780 -2.4974055 0.0000000 ) 56 C tau( 56) = ( 10.4632576 -1.1460320 0.0000000 ) 57 C tau( 57) = ( 9.3485262 -6.6510684 0.0000000 ) 58 C tau( 58) = ( 9.4967057 -5.2658334 0.0000000 ) 59 C tau( 59) = ( 10.7370307 -4.7978747 0.0000000 ) 60 C tau( 60) = ( 11.1223354 -3.4611397 0.0000000 ) number of k points= 4 Methfessel-Paxton smearing, width (Ry)= 0.0100 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.5000000 k( 2) = ( 0.0000014 -0.0783148 0.0000000), wk = 0.5000000 k( 3) = ( -0.0211432 -0.0000003 0.0000000), wk = 0.5000000 k( 4) = ( -0.0211418 -0.0783151 0.0000000), wk = 0.5000000 G cutoff = 13.2968 ( 155597 G-vectors) FFT grid: (180, 48, 60) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 42.82 Mb ( 19488, 144) NL pseudopotentials 17.84 Mb ( 19488, 60) Each V/rho on FFT grid 7.91 Mb ( 518400) Each G-vector array 1.19 Mb ( 155597) G-vector shells 0.31 Mb ( 40485) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 85.64 Mb ( 19488, 288) Each subspace H/S matrix 1.27 Mb ( 288, 288) Each matrix 0.13 Mb ( 60, 144) Arrays for rho mixing 63.28 Mb ( 518400, 8) Initial potential from superposition of free atoms starting charge 239.99701, renormalised to 240.00000 Starting wfc are 240 atomic wfcs Writing output data file GBphonon.save NEW-OLD atomic charge density approx. for the potential total cpu time spent up to now is 96526.99 secs per-process dynamical memory: 220.9 Mb Self-consistent Calculation iteration # 1 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 3 eigenvalues not converged ethr = 1.00E-06, avg # of iterations = 13.5 total cpu time spent up to now is 97868.40 secs total energy = -675.93103902 Ry Harris-Foulkes estimate = -678.38890554 Ry estimated scf accuracy < 7.56949546 Ry iteration # 2 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 3.15E-03, avg # of iterations = 1.2 total cpu time spent up to now is 98075.26 secs total energy = -674.91899415 Ry Harris-Foulkes estimate = -676.18211072 Ry estimated scf accuracy < 2.47001517 Ry iteration # 3 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.03E-03, avg # of iterations = 2.5 total cpu time spent up to now is 98411.72 secs total energy = -675.26750433 Ry Harris-Foulkes estimate = -675.26356434 Ry estimated scf accuracy < 0.06905617 Ry iteration # 4 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 3 eigenvalues not converged ethr = 2.88E-05, avg # of iterations = 7.0 total cpu time spent up to now is 98801.53 secs total energy = -675.28057655 Ry Harris-Foulkes estimate = -675.27896696 Ry estimated scf accuracy < 0.02728775 Ry iteration # 5 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.14E-05, avg # of iterations = 5.0 total cpu time spent up to now is 99053.52 secs total energy = -675.28396488 Ry Harris-Foulkes estimate = -675.28230406 Ry estimated scf accuracy < 0.01000062 Ry iteration # 6 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 4.17E-06, avg # of iterations = 2.0 total cpu time spent up to now is 99290.41 secs total energy = -675.28425959 Ry Harris-Foulkes estimate = -675.28447913 Ry estimated scf accuracy < 0.00054950 Ry iteration # 7 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 2.29E-07, avg # of iterations = 3.5 total cpu time spent up to now is 99671.95 secs total energy = -675.28435295 Ry Harris-Foulkes estimate = -675.28441044 Ry estimated scf accuracy < 0.00024572 Ry iteration # 8 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.02E-07, avg # of iterations = 2.0 total cpu time spent up to now is 100071.99 secs total energy = -675.28437469 Ry Harris-Foulkes estimate = -675.28439044 Ry estimated scf accuracy < 0.00003998 Ry iteration # 9 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.67E-08, avg # of iterations = 2.0 total cpu time spent up to now is 100822.69 secs total energy = -675.28438219 Ry Harris-Foulkes estimate = -675.28438332 Ry estimated scf accuracy < 0.00000411 Ry iteration # 10 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 1.71E-09, avg # of iterations = 2.5 total cpu time spent up to now is 101307.73 secs total energy = -675.28438274 Ry Harris-Foulkes estimate = -675.28438314 Ry estimated scf accuracy < 0.00000239 Ry iteration # 11 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 9.97E-10, avg # of iterations = 1.0 total cpu time spent up to now is 101597.34 secs total energy = -675.28438313 Ry Harris-Foulkes estimate = -675.28438309 Ry estimated scf accuracy < 0.00000062 Ry iteration # 12 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 2.60E-10, avg # of iterations = 2.0 total cpu time spent up to now is 102202.40 secs total energy = -675.28438326 Ry Harris-Foulkes estimate = -675.28438322 Ry estimated scf accuracy < 0.00000010 Ry iteration # 13 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 4.01E-11, avg # of iterations = 2.5 total cpu time spent up to now is 102672.08 secs total energy = -675.28438329 Ry Harris-Foulkes estimate = -675.28438327 Ry estimated scf accuracy < 0.00000002 Ry iteration # 14 ecut= 36.75 Ry beta=0.30 Davidson diagonalization with overlap ethr = 8.32E-12, avg # of iterations = 2.5 total cpu time spent up to now is 103132.95 secs End of self-consistent calculation k = 0.0000 0.0000 0.0000 ( 19435 PWs) bands (ev): -16.1105 -15.9400 -15.9028 -15.3899 -15.3269 -14.4925 -14.3852 -13.5572 -13.4851 -13.3432 -13.3341 -13.2901 -13.1277 -13.0976 -13.0853 -12.8106 -12.8102 -12.6787 -12.4321 -11.9329 -11.8942 -11.8907 -11.7608 -11.4548 -11.2232 -10.8510 -10.7521 -10.4622 -10.3492 -9.5348 -9.0982 -8.8746 -8.8580 -8.7453 -8.5649 -7.5485 -7.2407 -7.1685 -7.0442 -6.9935 -6.9162 -6.4214 -6.2120 -6.1961 -6.0192 -5.8501 -5.5010 -5.5004 -5.4773 -5.4559 -5.4025 -5.1819 -5.0707 -5.0049 -4.9206 -4.6560 -4.5173 -4.3270 -4.2838 -4.2829 -4.0523 -3.8182 -3.6408 -3.6038 -3.6035 -3.5747 -3.5697 -3.3586 -2.9692 -2.9511 -2.9081 -2.8951 -2.8046 -2.7990 -2.7445 -2.6985 -2.6316 -2.5962 -2.5100 -2.4138 -1.8402 -1.7837 -1.7784 -1.7712 -1.7633 -1.6141 -1.1204 -0.7558 -0.7471 -0.7264 -0.6149 -0.5840 -0.5345 -0.5258 -0.5249 -0.4170 -0.2763 -0.2489 -0.1183 -0.0052 0.0484 0.1827 0.2858 0.3454 0.4650 0.5868 0.7685 0.8965 0.9923 1.0004 1.0122 1.0901 1.1478 1.4496 1.5720 1.8444 1.9995 2.4419 2.9194 3.2187 5.2105 5.6981 5.9428 6.3866 6.4559 6.5191 6.7340 7.5621 7.5888 7.8629 7.8951 7.9492 8.2668 8.8552 9.1482 9.3369 9.4423 9.4499 9.5399 9.5673 9.7398 9.8912 11.1185 11.4378 k = 0.0000-0.0783 0.0000 ( 19466 PWs) bands (ev): -15.6517 -15.5778 -15.2889 -15.2748 -15.2211 -14.9984 -14.8292 -14.7424 -14.6042 -14.3891 -13.9279 -13.8031 -13.6681 -13.4547 -12.6906 -12.4682 -12.4224 -12.1783 -11.1843 -10.9925 -10.7139 -10.6740 -10.6016 -10.4996 -10.3756 -10.2295 -10.2275 -9.8650 -9.7618 -9.7229 -9.3807 -9.3710 -9.0198 -8.9437 -8.8897 -8.7407 -8.5853 -8.4872 -8.4854 -8.4821 -7.5835 -7.4368 -7.2700 -6.9806 -6.4622 -6.3311 -6.2986 -6.0334 -5.8932 -5.8400 -5.6204 -5.4213 -4.5577 -4.4310 -4.4015 -4.2787 -4.2520 -4.0494 -4.0200 -3.6295 -3.1581 -3.0103 -2.9060 -2.8668 -2.8429 -2.8022 -2.7720 -2.6602 -2.6320 -2.6134 -2.5694 -2.3951 -2.3874 -2.3198 -2.3165 -2.2829 -2.2470 -2.1788 -2.0829 -2.0230 -1.9826 -1.8943 -1.8092 -1.7244 -1.4949 -1.4404 -1.4098 -1.2594 -1.2428 -1.1466 -1.1089 -1.1058 -1.0636 -1.0121 -0.9795 -0.9207 -0.7969 -0.6342 -0.5826 -0.3513 -0.3468 -0.1784 -0.1587 0.1848 0.2478 0.3239 0.4499 0.6617 1.5936 1.6266 1.8076 1.9473 2.0437 2.4118 2.5146 2.5829 2.6248 3.1742 3.3944 3.6197 4.5206 4.7813 5.4431 5.7138 5.7201 5.8512 5.9326 6.0091 6.0517 6.5563 7.0985 7.2540 7.2698 7.3037 7.3130 7.5010 7.5144 7.5228 7.6140 8.1340 8.2848 8.3010 8.3625 9.0265 k =-0.0211 0.0000 0.0000 ( 19418 PWs) bands (ev): -16.0636 -16.0629 -15.6863 -15.6859 -14.9420 -14.9419 -13.8776 -13.8773 -13.4356 -13.4353 -13.3799 -13.3791 -13.0700 -13.0696 -12.9863 -12.9861 -12.4901 -12.4896 -12.2914 -12.2909 -12.1316 -12.1313 -11.3417 -11.3413 -11.1378 -11.1375 -10.6432 -10.6428 -9.8781 -9.8779 -9.2881 -9.2878 -8.3816 -8.3812 -8.0080 -8.0078 -7.8002 -7.7999 -6.6544 -6.6543 -6.3665 -6.3660 -6.1572 -6.1570 -6.0457 -6.0454 -5.7802 -5.7797 -5.4793 -5.4791 -5.1959 -5.1955 -5.0290 -5.0285 -4.9769 -4.9761 -4.3365 -4.3361 -4.1123 -4.1119 -3.7602 -3.7596 -3.7026 -3.7022 -3.4997 -3.4992 -3.3770 -3.3762 -3.3000 -3.2998 -3.1069 -3.1064 -2.9930 -2.9923 -2.5581 -2.5579 -2.3929 -2.3927 -2.2436 -2.2435 -2.1318 -2.1316 -1.7511 -1.7509 -1.4096 -1.4091 -1.0808 -1.0806 -0.8139 -0.8138 -0.7049 -0.7047 -0.6446 -0.6441 -0.2563 -0.2561 -0.2273 -0.2272 -0.1267 -0.1264 0.2430 0.2435 0.4640 0.4645 0.6024 0.6029 0.6567 0.6569 0.8070 0.8076 0.9531 0.9533 1.4051 1.4053 1.8162 1.8163 2.1889 2.1893 3.0691 3.0694 5.4446 5.4447 6.0191 6.0193 6.8356 6.8360 6.9488 6.9490 7.3731 7.3733 8.4700 8.4705 8.6117 8.6120 8.8474 8.8477 9.4137 9.4139 9.7701 9.7706 9.8057 9.8059 11.2712 11.2714 k =-0.0211-0.0783 0.0000 ( 19488 PWs) bands (ev): -15.6214 -15.6208 -15.2717 -15.2707 -15.1319 -15.1315 -14.8091 -14.8088 -14.3960 -14.3958 -14.0525 -14.0520 -13.2818 -13.2818 -12.9570 -12.9569 -11.8392 -11.8390 -11.5482 -11.5478 -10.5901 -10.5890 -10.3943 -10.3939 -10.1142 -10.1136 -10.0432 -10.0429 -9.9500 -9.9497 -9.4102 -9.4097 -9.1729 -9.1728 -8.8023 -8.8020 -8.4542 -8.4534 -8.2340 -8.2335 -7.6463 -7.6462 -7.1582 -7.1579 -6.5509 -6.5507 -6.2019 -6.2015 -5.5012 -5.5007 -5.2325 -5.2322 -5.0814 -5.0812 -4.7136 -4.7133 -3.5130 -3.5128 -3.3978 -3.3973 -3.3637 -3.3632 -3.1075 -3.1070 -3.0403 -3.0399 -2.8841 -2.8833 -2.6166 -2.6164 -2.3976 -2.3968 -2.3716 -2.3715 -2.2263 -2.2258 -2.0059 -2.0057 -1.9949 -1.9948 -1.7782 -1.7778 -1.7172 -1.7171 -1.6406 -1.6406 -1.4859 -1.4854 -1.4658 -1.4654 -1.1457 -1.1454 -0.8782 -0.8772 -0.8317 -0.8312 -0.5465 -0.5460 -0.4203 -0.4202 -0.2485 -0.2484 -0.2317 -0.2315 0.0586 0.0591 1.0865 1.0868 1.2592 1.2596 1.8451 1.8461 2.2328 2.2330 2.6411 2.6414 2.9102 2.9105 3.5128 3.5129 4.6129 4.6131 5.5580 5.5585 5.8395 5.8397 6.0228 6.0234 6.2412 6.2414 7.0157 7.0159 7.9685 7.9688 8.8115 8.8117 10.0171 10.0174 10.7767 10.7775 12.0124 12.0128 12.6085 12.6087 the Fermi energy is 3.7061 ev ! total energy = -675.28438329 Ry Harris-Foulkes estimate = -675.28438329 Ry estimated scf accuracy < 2.5E-09 Ry The total energy is the sum of the following terms: one-electron contribution = -836.97825237 Ry hartree contribution = 509.14934796 Ry xc contribution = -210.28068853 Ry ewald contribution = -137.17530398 Ry smearing contrib. (-TS) = 0.00051363 Ry convergence has been achieved in 14 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = -0.00154345 0.00045749 0.00000000 atom 2 type 1 force = -0.00258721 0.00366714 0.00000000 atom 3 type 1 force = 0.00000284 -0.01063271 0.00000000 atom 4 type 1 force = -0.00007521 0.00103385 0.00000000 atom 5 type 1 force = -0.00401147 0.00395919 0.00000000 atom 6 type 1 force = 0.00600015 -0.00102293 0.00000000 atom 7 type 1 force = -0.00317351 -0.00046456 0.00000000 atom 8 type 1 force = 0.00041501 0.00263023 0.00000000 atom 9 type 1 force = -0.00094612 -0.00214746 0.00000000 atom 10 type 1 force = 0.00690756 -0.00274464 0.00000000 atom 11 type 1 force = -0.00085401 0.00134915 0.00000000 atom 12 type 1 force = 0.00147346 -0.00139797 0.00000000 atom 13 type 1 force = -0.00095223 0.00073438 0.00000000 atom 14 type 1 force = 0.00099285 0.00074729 0.00000000 atom 15 type 1 force = -0.00176871 -0.00025741 0.00000000 atom 16 type 1 force = 0.00250360 -0.00122082 0.00000000 atom 17 type 1 force = -0.00101200 -0.00046904 0.00000000 atom 18 type 1 force = 0.00108857 -0.00071837 0.00000000 atom 19 type 1 force = -0.00156277 0.00157943 0.00000000 atom 20 type 1 force = 0.00087677 -0.00114774 0.00000000 atom 21 type 1 force = -0.00255842 0.00137277 0.00000000 atom 22 type 1 force = 0.00174042 0.00039477 0.00000000 atom 23 type 1 force = -0.00039148 -0.00245676 0.00000000 atom 24 type 1 force = 0.00311733 0.00052315 0.00000000 atom 25 type 1 force = -0.00592174 0.00119325 0.00000000 atom 26 type 1 force = 0.00432491 -0.00396108 0.00000000 atom 27 type 1 force = -0.00716398 0.00294264 0.00000000 atom 28 type 1 force = 0.00090590 0.00226821 0.00000000 atom 29 type 1 force = 0.00255827 -0.00359421 0.00000000 atom 30 type 1 force = 0.00147190 -0.00047087 0.00000000 atom 31 type 1 force = -0.00151315 -0.00031945 0.00000000 atom 32 type 1 force = -0.00448141 -0.00407288 0.00000000 atom 33 type 1 force = 0.00005817 -0.00101782 0.00000000 atom 34 type 1 force = 0.00001197 0.01056477 0.00000000 atom 35 type 1 force = -0.00252121 -0.00359095 0.00000000 atom 36 type 1 force = 0.00600131 0.00096190 0.00000000 atom 37 type 1 force = -0.00315214 0.00053108 0.00000000 atom 38 type 1 force = -0.00076425 -0.00139719 0.00000000 atom 39 type 1 force = 0.00717927 0.00286864 0.00000000 atom 40 type 1 force = -0.00093000 0.00221263 0.00000000 atom 41 type 1 force = 0.00040036 -0.00262290 0.00000000 atom 42 type 1 force = 0.00154382 0.00135163 0.00000000 atom 43 type 1 force = -0.00087931 -0.00095723 0.00000000 atom 44 type 1 force = -0.00086909 0.00056525 0.00000000 atom 45 type 1 force = 0.00240722 0.00121490 0.00000000 atom 46 type 1 force = -0.00163452 0.00027701 0.00000000 atom 47 type 1 force = 0.00088315 -0.00069315 0.00000000 atom 48 type 1 force = 0.00107763 0.00078044 0.00000000 atom 49 type 1 force = -0.00158534 -0.00165004 0.00000000 atom 50 type 1 force = -0.00032938 0.00245890 0.00000000 atom 51 type 1 force = 0.00164351 -0.00049716 0.00000000 atom 52 type 1 force = -0.00245292 -0.00133947 0.00000000 atom 53 type 1 force = 0.00079499 0.00116456 0.00000000 atom 54 type 1 force = 0.00314131 -0.00057332 0.00000000 atom 55 type 1 force = -0.00592807 -0.00114677 0.00000000 atom 56 type 1 force = 0.00256109 0.00354809 0.00000000 atom 57 type 1 force = 0.00086023 -0.00234414 0.00000000 atom 58 type 1 force = -0.00710063 -0.00286617 0.00000000 atom 59 type 1 force = 0.00430490 0.00398674 0.00000000 atom 60 type 1 force = 0.00141527 0.00045577 0.00000000 Total force = 0.031711 Total SCF correction = 0.000095 Thank you Elie MoujaesUniversity Of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110910/ffb9d4e5/attachment-0001.htm From kacper.druzbicki at uj.edu.pl Sat Sep 10 18:55:44 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Sat, 10 Sep 2011 18:55:44 +0200 Subject: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. Message-ID: Dear QE users, I started to work with organic molecular crystals, trying to simulate phonon spectra at gamma, using ultrasoft pps. I deal with monoclinic systems, with the point group P21/c. I tested the procedure with Glycine example, and everything works good and I got all the needed results. However, when I turned into bigger system, with the 186 atomic unit cell, I stuck with no progress... Being more strictly, I got the inproper phonon number 3N-7 instead of 3N and nothing more. The program gives: Atomic displacements: There are 551 irreducible representations The output ends with the listing: 'Representation 551 1 modes -B To be done' and the program does not give any more results for the next hours. I wait for the line: 'Alpha used in Ewald sum = ...' but I got nothing more than the previously mentioned line. The program seems to still work or sleep. I was given no error commands. Is there any limitation of ph.x? I have no idea. I use QE ver 4.3. Could anyone check if this error occurs also at one's machine? ---------------------------------------- My pw.x input only for gamma looks like: ---------------------------------------- &CONTROL title = freq , calculation = 'scf' , outdir = '...' , wfcdir = '...' , pseudo_dir = '...' , prefix = 'freq' restart_mode = 'from_scratch' , wf_collect = .true. , disk_io = 'high' , etot_conv_thr = 1.0d-6 , forc_conv_thr = 1.0d-4 , tstress = .true. , tprnfor = .true. , nstep = 1000 , / &SYSTEM ibrav = 0 , celldm(1) = 16.657934589 , nat = 186, ntyp = 4, ecutwfc = 35.0, ecutrho = 420.0, nosym = .false. , occupations = 'fixed' , london = .true. , / &ELECTRONS electron_maxstep = 100 , conv_thr = 1.D-8 , / &IONS ion_dynamics = 'bfgs' , upscale = 100 , / ATOMIC_SPECIES H 1.0080000162 H.pbe-van_bm.UPF C 12.0109996796 C.pbe-van_bm.UPF O 15.9989995956 O.pbe-van_bm.UPF S 32.0600013733 S.pbe-van_bm.UPF ATOMIC_POSITIONS crystal H 0.661768681 0.098938508 0.027981564 H 0.681762733 0.422126036 0.031147779 H 0.710600002 0.241252285 0.075540824 H 0.911720569 0.232557783 0.003204964 H 0.943244272 0.047148948 0.046896512 H 0.972545308 0.440972636 0.088760388 H 0.950707533 0.612471994 0.043453200 H 1.185165475 0.402837986 0.019740732 H 1.203284961 0.228642875 0.064947666 H 1.221684226 0.614171074 0.105831184 H 1.209382169 0.794360264 0.061215766 H 1.453593378 0.605397048 0.041178042 H 1.463518767 0.417260867 0.085244173 H 1.475307338 0.982108249 0.084496779 H 1.714729329 0.769004805 0.064951907 H 1.715288127 0.587554612 0.109713614 H 1.743518237 0.911226534 0.113518402 H 1.509304424 1.247931787 0.231211728 H 1.386058504 1.174258073 0.295461176 H 1.191306726 0.502931257 0.245636813 H 1.316250165 0.575294755 0.182169779 H 0.893771048 1.295612503 0.360400800 H 0.761039631 1.259598293 0.422215413 H 1.008108016 0.590340566 0.452448120 H 1.135128158 0.624540850 0.391020982 H 0.648719144 1.227335666 0.469467460 H 0.763991964 0.536420331 0.563538388 H 0.896497028 0.561587838 0.501851000 H 0.376539444 1.064666579 0.578561984 H 0.545745742 1.212353752 0.599222472 H 0.538123549 0.976303068 0.663073142 H 0.369942960 0.822943867 0.644368047 H 0.229716969 1.218967098 0.639126983 H 0.400019790 1.387811998 0.648770996 H 0.265047891 1.390814172 0.709924789 H 0.433376628 1.216281792 0.718987372 H 0.285565507 0.824365684 0.709221575 H 0.115807400 0.995779167 0.699976088 H 0.152134669 1.184020951 0.769102402 H 0.322228589 1.014627013 0.779622204 H 0.182893915 0.619844993 0.770979600 H 0.015685456 0.776052371 0.753332990 H 0.002737958 0.974709477 0.821894297 H 0.163534225 0.797629807 0.840392847 H 0.023344300 0.408511721 0.821105841 H -0.130002493 0.581670416 0.798432853 H -0.194915353 0.436797122 0.865661373 H -0.176560036 0.759211830 0.867488521 H 1.028352538 0.070629138 0.110395323 H 0.519225839 1.200934848 0.530432834 H -0.661768681 0.598938508 -0.027981564 H -0.681762733 0.922126036 -0.031147779 H -0.710600002 0.741252285 -0.075540824 H -0.911720569 0.732557783 -0.003204964 H -0.943244272 0.547148948 -0.046896512 H -0.972545308 0.940972636 -0.088760388 H -0.950707533 1.112471994 -0.043453200 H -1.185165475 0.902837986 -0.019740732 H -1.203284961 0.728642875 -0.064947666 H -1.221684226 1.114171074 -0.105831184 H -1.209382169 1.294360264 -0.061215766 H -1.453593378 1.105397048 -0.041178042 H -1.463518767 0.917260867 -0.085244173 H -1.475307338 1.482108249 -0.084496779 H -1.714729329 1.269004805 -0.064951907 H -1.715288127 1.087554612 -0.109713614 H -1.743518237 1.411226534 -0.113518402 H -1.509304424 1.747931787 -0.231211728 H -1.386058504 1.674258073 -0.295461176 H -1.191306726 1.002931257 -0.245636813 H -1.316250165 1.075294755 -0.182169779 H -0.893771048 1.795612503 -0.360400800 H -0.761039631 1.759598293 -0.422215413 H -1.008108016 1.090340566 -0.452448120 H -1.135128158 1.124540850 -0.391020982 H -0.648719144 1.727335666 -0.469467460 H -0.763991964 1.036420331 -0.563538388 H -0.896497028 1.061587838 -0.501851000 H -0.376539444 1.564666579 -0.578561984 H -0.545745742 1.712353752 -0.599222472 H -0.538123549 1.476303068 -0.663073142 H -0.369942960 1.322943867 -0.644368047 H -0.229716969 1.718967098 -0.639126983 H -0.400019790 1.887811998 -0.648770996 H -0.265047891 1.890814172 -0.709924789 H -0.433376628 1.716281792 -0.718987372 H -0.285565507 1.324365684 -0.709221575 H -0.115807400 1.495779167 -0.699976088 H -0.152134669 1.684020951 -0.769102402 H -0.322228589 1.514627013 -0.779622204 H -0.182893915 1.119844993 -0.770979600 H -0.015685456 1.276052371 -0.753332990 H -0.002737958 1.474709477 -0.821894297 H -0.163534225 1.297629807 -0.840392847 H -0.023344300 0.908511721 -0.821105841 H 0.130002493 1.081670416 -0.798432853 H 0.194915353 0.936797122 -0.865661373 H 0.176560036 1.259211830 -0.867488521 H -1.028352538 0.570629138 -0.110395323 H -0.519225839 1.700934848 -0.530432834 C 0.728626073 0.247846465 0.042949839 C 0.897257843 0.228567865 0.035882951 C 0.991608644 0.432184810 0.056290207 C 1.162712851 0.408352227 0.052014096 C 1.250254561 0.614003344 0.073945031 C 1.422956546 0.597403014 0.072808333 C 1.510805079 0.797517587 0.096365924 C 1.682218122 0.765376759 0.096401475 C 1.493392597 0.965045277 0.164303769 C 1.419409399 0.917075161 0.202532030 C 1.437605810 1.088108355 0.234344671 C 1.370320486 1.045060059 0.270417400 C 1.285697223 0.831478396 0.274741096 C 1.262762418 0.663341646 0.242720274 C 1.331037594 0.707067434 0.206818178 C 1.100399465 0.998738832 0.333047067 C 1.025413889 0.965865742 0.371204165 C 0.918960523 1.143196747 0.381035001 C 0.843020449 1.119102854 0.416023991 C 0.869604614 0.920841679 0.442786750 C 0.978117537 0.745082717 0.432720528 C 1.053410257 0.766435675 0.397459061 C 0.788234475 0.900829236 0.480009277 C 0.679146019 1.075428018 0.489672275 C 0.602553582 1.060416950 0.524937543 C 0.634725753 0.867223703 0.552057444 C 0.740272222 0.688005555 0.542753758 C 0.815236501 0.705216057 0.507480167 C 0.477997872 1.041743804 0.600201196 C 0.433639298 0.998353147 0.642851284 C 0.341562634 1.214634984 0.656597975 C 0.320799886 1.215139294 0.702050041 C 0.229701620 1.001803114 0.716450120 C 0.210334357 1.008835185 0.762057114 C 0.117374876 0.792492225 0.774781777 C 0.065005624 0.798437840 0.817618721 C -0.040687694 0.584039698 0.823740250 C -0.114120058 0.587470196 0.863754139 C -0.728626073 0.747846465 -0.042949839 C -0.897257843 0.728567865 -0.035882951 C -0.991608644 0.932184810 -0.056290207 C -1.162712851 0.908352227 -0.052014096 C -1.250254561 1.114003344 -0.073945031 C -1.422956546 1.097403014 -0.072808333 C -1.510805079 1.297517587 -0.096365924 C -1.682218122 1.265376759 -0.096401475 C -1.493392597 1.465045277 -0.164303769 C -1.419409399 1.417075161 -0.202532030 C -1.437605810 1.588108355 -0.234344671 C -1.370320486 1.545060059 -0.270417400 C -1.285697223 1.331478396 -0.274741096 C -1.262762418 1.163341646 -0.242720274 C -1.331037594 1.207067434 -0.206818178 C -1.100399465 1.498738832 -0.333047067 C -1.025413889 1.465865742 -0.371204165 C -0.918960523 1.643196747 -0.381035001 C -0.843020449 1.619102854 -0.416023991 C -0.869604614 1.420841679 -0.442786750 C -0.978117537 1.245082717 -0.432720528 C -1.053410257 1.266435675 -0.397459061 C -0.788234475 1.400829236 -0.480009277 C -0.679146019 1.575428018 -0.489672275 C -0.602553582 1.560416950 -0.524937543 C -0.634725753 1.367223703 -0.552057444 C -0.740272222 1.188005555 -0.542753758 C -0.815236501 1.205216057 -0.507480167 C -0.477997872 1.541743804 -0.600201196 C -0.433639298 1.498353147 -0.642851284 C -0.341562634 1.714634984 -0.656597975 C -0.320799886 1.715139294 -0.702050041 C -0.229701620 1.501803114 -0.716450120 C -0.210334357 1.508835185 -0.762057114 C -0.117374876 1.292492225 -0.774781777 C -0.065005624 1.298437840 -0.817618721 C 0.040687694 1.084039698 -0.823740250 C 0.114120058 1.087470196 -0.863754139 O 1.462981550 0.780361038 0.137590003 O 1.568838954 1.147058099 0.158030833 O 1.077559129 1.176306183 0.310832186 O 0.568594584 0.838837730 0.587936942 O -1.462981550 1.280361038 -0.137590003 O -1.568838954 1.647058099 -0.158030833 O -1.077559129 1.676306183 -0.310832186 O -0.568594584 1.338837730 -0.587936942 S 1.221642499 0.747224350 0.321956022 S -1.221642499 1.247224350 -0.321956022 CELL_PARAMETERS {cubic} 0.996736750691604 0.000000000000000 -0.080720825586998 0.000000000000000 0.621667612603949 0.000000000000000 0.000000000000000 0.000000000000000 3.755870678483857 K_POINTS automatic 1 1 1 0 0 0 --------------------------- And here is my ph.x input: --------------------------- nodnoopt &INPUTPH outdir = '...' , prefix = 'freq' , tr2_ph = 1.0d-14, ldisp = .false., nogg = .true., trans = .true., epsil = .true., elph = .false., fpol = .false. , elop = .false., lraman = .false., recover = .false. , amass(1) = 1.0080000162 , amass(2) = 12.0109996796 , amass(3) = 15.9989995956 , amass(4) = 32.0600013733 , iverbosity = 0 , / 0.0 0.0 0.0 Thank you in advance! Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 From giannozz at democritos.it Sat Sep 10 20:26:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 10 Sep 2011 20:26:40 +0200 Subject: [Pw_forum] results of vc-relax In-Reply-To: References: Message-ID: On Sep 10, 2011, at 18:37 , Elie Moujaes wrote: > I didnt quite understand this final step http://www.democritos.it/pipermail/pw_forum/2011-April/020154.html The problem mentioned at the end has been meanwhile solved in v.4.3.2 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 10 20:29:08 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sat, 10 Sep 2011 19:29:08 +0100 Subject: [Pw_forum] results of vc-relax In-Reply-To: References: , Message-ID: Prof. Giannozzi, Thanks for the answer Elie > From: giannozz at democritos.it > Date: Sat, 10 Sep 2011 20:26:40 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] results of vc-relax > > > On Sep 10, 2011, at 18:37 , Elie Moujaes wrote: > > > I didnt quite understand this final step > > http://www.democritos.it/pipermail/pw_forum/2011-April/020154.html > > The problem mentioned at the end has been meanwhile solved > in v.4.3.2 > > 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/20110910/d4a7c719/attachment.htm From onaiwu.kingsley.nosa at gmail.com Sat Sep 10 21:50:09 2011 From: onaiwu.kingsley.nosa at gmail.com (Onaiwu Kingsley Nosa) Date: Sat, 10 Sep 2011 20:50:09 +0100 Subject: [Pw_forum] Installation failure Message-ID: Dear All, I currently use QE version 4.0.5. In an attempt to install version 4.3, 'make' stopped with the error msg: make[1]:** No rule to make target '../PW/libpw.a', needed by 'phcg.x'. Stop. I'll be grateful if any body can assist in resolving this problem. Kingsley Onaiwu From ying.sun at gradmail.ims.uconn.edu Sun Sep 11 02:31:57 2011 From: ying.sun at gradmail.ims.uconn.edu (ying.sun at gradmail.ims.uconn.edu) Date: Sat, 10 Sep 2011 20:31:57 -0400 Subject: [Pw_forum] How to modify code and recompile? Message-ID: I want to modify a file in Quantum ESPRESSO, let it write out a matrix I want. It will be a minor modificataion. When I try to modify code, *.f90, it says read only and will not let me change it. How to recompile it? Looks like in ABINIT , just modify the file and reissue "make "will do. Any suggestions will be appreciated!! Thanks a lot! \ Ying sun Institute of materials science university of connecticut From faccin.giovani at gmail.com Sun Sep 11 03:43:39 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Sat, 10 Sep 2011 21:43:39 -0400 Subject: [Pw_forum] How to modify code and recompile? In-Reply-To: References: Message-ID: Dear Ying, Looks like a permissions issue. Assuming you are in a Linux/Unix environment, and that the QE files are somewhere inside your home folder, try this at the command line, inside the folder where the files are: chmod 666 filename And them try to modify something and save the file. If the file can be read/written, a "ls -la" will give you something like this: gfaccin at jacare ~/lixo/saves $ ls -la -rw-rw-rw- 1 gfaccin gfaccin 14 Sep 10 22:36 filename in which the rw-rw-rw means, respectively, that user, group and everyone are allowed to read and write to that file. You can of course change those permissions in any way you find adequate. Best, Giovani Faccin UFMS - Brazil 2011/9/10 > I want to modify a file in Quantum ESPRESSO, let it write out a > matrix I want. It will be a minor modificataion. > When I try to modify code, *.f90, it says read only and will not > let me change it. How to recompile it? > Looks like in ABINIT , just modify the file and reissue "make > "will do. > Any suggestions will be appreciated!! > Thanks a lot! > \ > Ying sun > Institute of materials science > university of connecticut > > > _______________________________________________ > 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/20110910/cc9aba2a/attachment-0001.htm From robinshy at gmail.com Sun Sep 11 14:25:30 2011 From: robinshy at gmail.com (Robin H) Date: Sun, 11 Sep 2011 20:25:30 +0800 Subject: [Pw_forum] about PWscf PP generation In-Reply-To: <1D263F60-1CC1-4D12-9AF0-F0868F8B5D88@democritos.it> References: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> <1D263F60-1CC1-4D12-9AF0-F0868F8B5D88@democritos.it> Message-ID: I can't find the answer to my question in the manual,so I put my question on the forum.I never wanted to make troubles.I think maybe someone has ever been confused by this kind of problem,and if they have solved it,could please to share the method with me.I 'm so appreciate it.It's much better to discuss than to work alone in the office. 2011/9/7 Paolo Giannozzi > > On Sep 7, 2011, at 4:45 , Robin H wrote: > > > I 'm not good at PP generation > > nobody is. Did you read atomic_doc/pseudo-gen.tex? > it is incomplete but better than nothing > > 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/20110911/d0b01a34/attachment.htm From kucukben at sissa.it Sun Sep 11 14:55:32 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 11 Sep 2011 14:55:32 +0200 Subject: [Pw_forum] about PWscf PP generation In-Reply-To: References: <1683710e.d316.13234b8a686.Coremail.flux_ray12@163.com> <1D263F60-1CC1-4D12-9AF0-F0868F8B5D88@democritos.it> Message-ID: <20110911145532.v493tccisw8ko84w@webmail.sissa.it> Dear Robin, It takes some trial and error to generate a good pseudopotential. the more complex your atom is, harder it may get. So why dont you try starting with something simple? It is really not easy to guess the best rcut values without carefully examining the atom. If I may, i would suggest you to start with something simple, draw the atomic orbitals, study the shape of pseduo orbitals for each cut off you choose and change them systematically. Watch also the logarithmic derivatives for ghosts. if you are generating a paw one, also watch the behavior of partial wave expansion curves. Do this for a simple system, actually, do it for a system that you already know the working set of parameters, like the ones in pslibrary project that you can download from qe-forge..once you find a reasonable range for all the parameters you can start refining them for a better pseudo. And once you have a better idea about how each parameter affects the pseudopotential in the simpler system, i think it gets a tad easier to move on to harder-to-generate pseudopotentials. best, emine kucukbenli, phd student, sissa, italy Quoting Robin H : > I can't find the answer to my question in the manual,so I put my question > on the forum.I never wanted to make troubles.I think maybe someone has ever > been confused by this kind of problem,and if they have solved it,could > please to share the method with me.I 'm so appreciate it.It's much better to > discuss than to work alone in the office. > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From giannozz at democritos.it Sun Sep 11 17:40:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 11 Sep 2011 17:40:46 +0200 Subject: [Pw_forum] Installation failure In-Reply-To: References: Message-ID: On Sep 10, 2011, at 21:50 , Onaiwu Kingsley Nosa wrote: > make[1]:** No rule to make target '../PW/libpw.a', needed by > 'phcg.x'. Stop. you cannot get such a message unless you do something weird 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 11 17:45:37 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 11 Sep 2011 17:45:37 +0200 Subject: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. In-Reply-To: References: Message-ID: <7AE5909B-49EC-4635-A79E-666A39E129D6@democritos.it> On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > However, when I turned into bigger system, with the 186 atomic unit > cell a phonon calculation for such a big cell will take a serious amount of time. You should try to estimate it from smaller calculations. 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 kacper.druzbicki at uj.edu.pl Sun Sep 11 18:00:56 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Sun, 11 Sep 2011 18:00:56 +0200 Subject: [Pw_forum] ODP: Re: Ph.x problem. No results. Wrong irreducible representations number. In-Reply-To: <7AE5909B-49EC-4635-A79E-666A39E129D6@democritos.it> References: <7AE5909B-49EC-4635-A79E-666A39E129D6@democritos.it> Message-ID: Dear Prof. Gianozzi, Thank you for your suggestion. Well, actually I am interested only (or at least) in the IR spectrum. I would like to use USPP so I would like to avoid the gamma trick. I know it's a quite big system, however, I found no problems with the system size when using CASTEP in this purpose. Thus, I thought that QE might also handle it. I have more serious computation resources for QE that for CASTEP. QE solve SCF step for this system in ~20 seconds. I solve the wrong irreducible representations number by turning off the symmetry. However it didn't solve the whole problem. The ph.x still idles. With best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 ----- Wiadomo?? oryginalna ----- Od: Paolo Giannozzi Data: Niedziela, Wrzesie? 11, 2011 5:46 pm Temat: Re: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. Do: PWSCF Forum > On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > > > However, when I turned into bigger system, with the 186 atomic unit > > > cell > > a phonon calculation for such a big cell will take a serious amount > of time. > You should try to estimate it from smaller calculations. > > 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 kacper.druzbicki at uj.edu.pl Sun Sep 11 18:16:39 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Sun, 11 Sep 2011 18:16:39 +0200 Subject: [Pw_forum] Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP Message-ID: Dear QE users, I hope that you wouldn't mind if I ask does anybody know any source of PBE Norm-Conserving PP for Sulfur, Nitrogen and Chlorine? I cannot found them anywhere. I would appreciate if someone could share them with me... With kind regards, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 From giannozz at democritos.it Sun Sep 11 18:45:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 11 Sep 2011 18:45:45 +0200 Subject: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. In-Reply-To: References: Message-ID: On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > london = .true. this is not currently implemented in the phonon code (and could cause the latter to crash / hang) 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 kacper.druzbicki at uj.edu.pl Sun Sep 11 20:10:30 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Sun, 11 Sep 2011 20:10:30 +0200 Subject: [Pw_forum] ODP: Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP In-Reply-To: References: Message-ID: The problem have been solved by Emine Kucukbenli, who linked me to pslibrary project in qe-forge. Just to summarize and educate newbies like me: http://qe-forge.org/projects/pslibrary/ I also got the needed pseudos from the abinit page: http://www.abinit.org/downloads/psp-links/pseudopotentials Thank you very much! Casper Definitely it's a great library. Did not know about it. I found all the data I needed. I looked for NC pseudos due to some ph.x restrictions. Besides, I wanted to get PBE NC, and the sulfur pseudo with D orbitals included. I also found the needed data at abinit webpage, but the one for Sulfur does not include D states, which are IMO important in structural studies of sulfur including organic compounds. I also found BLYP norm conserving pps at QE page. However, I performed some benchmark for the compound I study, within isolated molecule approach. As a result I found that PBE works as good as B3LYP in the prediction of vibrational spectra in this case, and also works well with CASTEP and DMOL3, while BLYP delivered the worst results, along with OLYP and LDA. Thank you! With the best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 ----- Wiadomo?? oryginalna ----- Od: "Kacper Dru?bicki" Data: Niedziela, Wrzesie? 11, 2011 6:16 pm Temat: [Pw_forum] Sulfur, Nitrogen, Chlorine PBE Norm-Conserving PP Do: pw_forum at pwscf.org > Dear QE users, > > I hope that you wouldn't mind if I ask does anybody know any source of > PBE Norm-Conserving PP for Sulfur, Nitrogen and Chlorine? I cannot > found them anywhere. I would appreciate if someone could share them > with me... > > With kind regards, > Casper > > Kacper Dru?bicki, > Faculty of Chemistry, > Department of Chemical Physics, > Jagiellonian University, > Ingardena Street 3, 30-060 Krak?w, Poland > phone: +48 12 6632265 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From kacper.druzbicki at uj.edu.pl Sun Sep 11 22:21:29 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Sun, 11 Sep 2011 22:21:29 +0200 Subject: [Pw_forum] ODP: Re: Ph.x problem. No results. Wrong irreducible representations number. In-Reply-To: References: Message-ID: Thank you, Sir! It's seems that now it's finally running. The program has already turned into Electric Fields Calculation section, and it looks that it's ok now. It progressively iterating. I still wonder why it lost the thread of symmetry, giving the inproper normal modes number. It's monoclinic system (which I notice that QE define in a specific way) and I built the geometry by importing the coordinates and the cell parameters from CASTEP. When opened via Xcrysden or J-Ice, the geometry seems to be allright. All the cell parameters are correct. Loss of normal mode symmetry for such a low symmetric system is not a problem to me. However, It's courious. With kind regards, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 ----- Wiadomo?? oryginalna ----- Od: Paolo Giannozzi Data: Niedziela, Wrzesie? 11, 2011 6:46 pm Temat: Re: [Pw_forum] Ph.x problem. No results. Wrong irreducible representations number. Do: PWSCF Forum > On Sep 10, 2011, at 18:55 , Kacper Dru?bicki wrote: > > > london = .true. > > this is not currently implemented in the phonon code (and could > cause the latter to crash / hang) > > 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 elie.moujaes at hotmail.co.uk Sun Sep 11 23:20:13 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Sun, 11 Sep 2011 22:20:13 +0100 Subject: [Pw_forum] relaxation of the 60 C atom supercell Message-ID: Dear all, I am still "fighting" with the 60 carbon atom system that I am trying to relax. I did a relaxation using 4 k-points and I got the system relaxed then I did an scf calculation with 25 points (for phonon calculations) and the total force is 0.099839. Does this mean that using 4 points is not enough? how many points do I have to consider as 25 points would really take a lot of time? Shall I relax for 10 k-points, the same as I was doing for an scf calculation? Can anyone advise me on that? Thanks again and sorry to disturb you with that many times. I am trying to avoid the negative frequencies that I obtained before totally relaxing the crystal. Elie MUniversity of Nottng7 2rduk -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110911/51adbb5d/attachment-0001.htm From izaakw89 at yahoo.com Mon Sep 12 03:21:37 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Sun, 11 Sep 2011 18:21:37 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <1315790497.76558.YahooMailNeo@web43402.mail.sp1.yahoo.com> Dear all, I am trying to create a model Hamiltonian which is written in the attached file equation.png. I want to know if we can calculate the parameters such as ea?eb?xa? U ?JH ?t in this Hamiltonian using plane wave methods as implemented in QUANTUM ESPRESSO? Thank you for your help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110911/a38b97cf/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: equation..PNG Type: image/png Size: 33432 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110911/a38b97cf/attachment-0001.png From mohnish.iitk at gmail.com Mon Sep 12 05:40:57 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 12 Sep 2011 09:10:57 +0530 Subject: [Pw_forum] relaxation of the 60 C atom supercell In-Reply-To: References: Message-ID: Dear Ellie, For phonon calculation you definitely need to converge forces and energy to much accuracy. First check the convergence for these two for relax calculation then do phonon calculation. On Mon, Sep 12, 2011 at 2:50 AM, Elie Moujaes wrote: > Dear all, > I am still "fighting" with the 60 carbon atom system that I am trying to > relax. I did a relaxation using 4 k-points and I got the system relaxed then > I did an scf calculation with 25 points (for phonon calculations) and the > total force is 0.099839. Does this mean that using 4 points is not enough? > how many points do I have to consider as 25 points would really take a lot > of time? Shall I relax for 10 k-points, the same as I was doing for an scf > calculation? Can anyone advise me on that? > Thanks again and sorry to disturb you with that many times. I am trying to > avoid the negative frequencies that I obtained before totally relaxing the > crystal. > > Elie M > University of Nott > ng7 2rd > uk > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- From padmaja_patnaik at yahoo.co.uk Mon Sep 12 07:06:14 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Mon, 12 Sep 2011 06:06:14 +0100 (BST) Subject: [Pw_forum] Doubt in spin-orbit coupling results Message-ID: <1315803974.96266.YahooMailNeo@web28505.mail.ukl.yahoo.com> Hi All I am doing spin-orbit coupling calculations. To get spin-polarized calculations with spin-orbit coupling I mentioned in the input for scf, ?lspinorb=.true., ?noncolin=.true., ?starting_magnetization(1)=0.5, ?starting_magnetization(2)=0.5, After this scf calculations I am doing the nscf calculation and finally the density of states and partial density of states. What I expect is it should give me both up and down spin DOS separately but I didnt get that. The input,? nspin=2 in the input and get spin polarized results with both up and down spin density of states given separately which can be plotted. Can anybody please suggest what to do? Another doubt is the total magnetic moment is found to be zero (with spin-orbit interaction) which was earlier (without spin-orbit interaction) found to be 2 BohrMagneton./cell. Thanking in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110912/1fcd1d25/attachment.htm From mayankaditya at gmail.com Mon Sep 12 16:17:24 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 12 Sep 2011 19:47:24 +0530 Subject: [Pw_forum] PHONON ON GRID Message-ID: Dear Users I am try to calculate phonon on GRID. I have run example which is given in example directory. But during the execution of run_example it stopped with error message " /run_example: 200: Syntax error: Bad fd number". Mayank ?BARC MUMBAI, INDIA From izaakw89 at yahoo.com Mon Sep 12 20:06:08 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 12 Sep 2011 11:06:08 -0700 (PDT) Subject: [Pw_forum] Parameters for a model Hamiltonian In-Reply-To: <1315790497.76558.YahooMailNeo@web43402.mail.sp1.yahoo.com> References: <1315790497.76558.YahooMailNeo@web43402.mail.sp1.yahoo.com> Message-ID: <1315850768.59133.YahooMailNeo@web43414.mail.sp1.yahoo.com> Dear all, I am trying to create a model Hamiltonian which is written in the attached file equation.png. I want to know if we can calculate the parameters such as ea?eb?xa? U ?JH ?t in this Hamiltonian using plane wave methods as implemented in QUANTUM ESPRESSO? Thank you for your help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110912/ac982457/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: equation..PNG Type: image/png Size: 33432 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110912/ac982457/attachment-0001.png From lorenzo.paulatto at impmc.upmc.fr Mon Sep 12 21:17:13 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 12 Sep 2011 21:17:13 +0200 Subject: [Pw_forum] PHONON ON GRID In-Reply-To: References: Message-ID: In data 12 settembre 2011 alle ore 16:17:24, mayank gupta ha scritto: > I am try to calculate phonon on GRID. I have run example which is > given in example directory. But during the execution of run_example it > stopped with error message " /run_example: 200: Syntax error: Bad fd > number". Dear Mayank, the "phonon on GRID" project from qe-forge is used to run the phonon code on a very specific hardware infrastracture; it is NOT a system to run ph.x for a grid of q points. If what you want to do is actually run ph.x on the GRID hardware, I cannot help you... if on the other hand you have only want to do a phonon dispersion calculation please have at the keywords ldisp and nq1, nq2, nq3 in the phonon documentation. best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From trambui at u.boisestate.edu Mon Sep 12 23:02:31 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 12 Sep 2011 15:02:31 -0600 Subject: [Pw_forum] charge density calculation with plotrho.x Message-ID: Dear Everyone, I've been having the issue of trying to run plotrho.x to convert my data from "2Dplotrho.dat" to "2Dplotrho.ps", and this is what I got on the screen: forrtl: severe (64): input conversion error, unit 5, file stdin Image PC Routine Line Source plotrho.x 00000000004A216D Unknown Unknown Unknown plotrho.x 00000000004A0C75 Unknown Unknown Unknown plotrho.x 00000000004510F9 Unknown Unknown Unknown plotrho.x 0000000000412F3F Unknown Unknown Unknown plotrho.x 0000000000412772 Unknown Unknown Unknown plotrho.x 00000000004346DB Unknown Unknown Unknown plotrho.x 0000000000432268 Unknown Unknown Unknown plotrho.x 0000000000404C78 MAIN__ 114 plotrho.f90 plotrho.x 000000000040343C Unknown Unknown Unknown libc.so.6 00007F789A630586 Unknown Unknown Unknown plotrho.x 0000000000403339 Unknown Unknown Unknown Would you give me information on how to fix this problem? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110912/c9fc675f/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Sep 12 23:41:54 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 12 Sep 2011 23:41:54 +0200 Subject: [Pw_forum] charge density calculation with plotrho.x In-Reply-To: References: Message-ID: In data 12 settembre 2011 alle ore 23:02:31, Tram Bui ha scritto: > forrtl: severe (64): input conversion error, unit 5, file stdin > ... > Would you give me information on how to fix this problem? > Dear Tram, there must be an error somewhere in your input, it is difficult to say what it could be without seeing it. In case recheck best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From helen at fh.huji.ac.il Tue Sep 13 11:11:07 2011 From: helen at fh.huji.ac.il (helen at fh.huji.ac.il) Date: Tue, 13 Sep 2011 12:11:07 +0300 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe Message-ID: <20110913121107.13782ctls7eb263o@webmail.huji.ac.il> Dear QE users, I need a LDA norm-conserving pseudopotential for Fe, and later for transition metals in general. In the quantum-espresso library I found a PBE norm-conserving pseudo-potential : Fe.pbe-sp-mt_gipaw.UPF . Does anyone know where I can obtain a LDA norm-conserving Fe pseudo-potential, in a format which pwscf can use? (I saw there are libraries in a different format in abinit.org) Thank you for your help, Dr. Helen Eisenberg, Post-doc, Fritz-Haber Research Center, Hebrew University, Jerusalem ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From renpj at dicp.ac.cn Tue Sep 13 11:41:16 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Tue, 13 Sep 2011 17:41:16 +0800 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe In-Reply-To: <20110913121107.13782ctls7eb263o@webmail.huji.ac.il> References: <20110913121107.13782ctls7eb263o@webmail.huji.ac.il> Message-ID: <20110913174116.4b2dbe44@ren-desktop> On Tue, 13 Sep 2011 12:11:07 +0300 helen at fh.huji.ac.il wrote: > Dear QE users, > I need a LDA norm-conserving pseudopotential for Fe, and later for > transition metals in general. In the quantum-espresso library I > found a PBE norm-conserving pseudo-potential : > Fe.pbe-sp-mt_gipaw.UPF . Does anyone know where I can obtain a LDA > norm-conserving Fe pseudo-potential, in a format which pwscf can use? > (I saw there are libraries in a different format in abinit.org) > Thank you for your help, > Dr. Helen Eisenberg, > Post-doc, Fritz-Haber Research Center, Hebrew University, Jerusalem > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Dear Helen If you have a abinit format PP, you can convert it to pwscf format by the tools fhi2upf in upftools/ directory. I suggest you read http://www.quantum-espresso.org/pseudo-notes.php for more information. Good luck! Pengju Ren From giuseppe.mattioli at mlib.ism.cnr.it Tue Sep 13 15:23:08 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 13 Sep 2011 15:23:08 +0200 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe In-Reply-To: <20110913121107.13782ctls7eb263o@webmail.huji.ac.il> References: <20110913121107.13782ctls7eb263o@webmail.huji.ac.il> Message-ID: <201109131523.08988.giuseppe.mattioli@mlib.ism.cnr.it> Dear Helen A better solution: learn to generate PPs and everybody will ask you for collaboration...:-) Actually (and more seriously), it should not be difficult to use the generation data contained into the library Fe.pbe-sp-mt_gipaw.UPF file and create a brand new Fe.lda-sp-mt.UPF file with ld1.x (which is the QE executable to generate PPs). You can find a very nice guide to the PP generation in yourQE/atomic_doc/pseudo-gen.pdf HTH Giuseppe On Tuesday 13 September 2011 11:11:07 helen at fh.huji.ac.il wrote: > Dear QE users, > I need a LDA norm-conserving pseudopotential for Fe, and later for > transition metals in general. In the quantum-espresso library I found > a PBE norm-conserving pseudo-potential : Fe.pbe-sp-mt_gipaw.UPF . Does > anyone know where I can obtain a LDA norm-conserving Fe > pseudo-potential, in a format which pwscf can use? (I saw there are > libraries in a different format in abinit.org) > Thank you for your help, > Dr. Helen Eisenberg, > Post-doc, Fritz-Haber Research Center, Hebrew University, Jerusalem > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - 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 mlib.ism.cnr.it Tue Sep 13 16:08:02 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 13 Sep 2011 16:08:02 +0200 Subject: [Pw_forum] hybrid functionals and vc-relax calculations Message-ID: <201109131608.02381.giuseppe.mattioli@mlib.ism.cnr.it> Dear all Are "vc-relax" bfgs calculations implemented when using hybrid functionals? I read Stefano's examples/EXX_example/README file which says "no!" WHAT PROPERTIES CAN I COMPUTE ? Energy and forces (thanks to Hellmann-Feynman theorem forces do not require extra calculations). In principle also stresses but the corresponding formulas have not yet been coded. So structural optimization is OK if the cell shape is kept fixed. So I've performed several "relax" calculations and fitted a multi-parameter (for ZnO wurtzite, that is, a non-cubic cell... boring) E(a,c) equation. Then I've tried a "vc-relax" calculation... And it seems to do something! It has gone quite well for the first three scf steps (negligible pressure after 2 steps), then it has started to dance around fixed values (the BFGS counter stuck at iteration 2) P= 68.29 P= 18.73 P= 0.82 P= 19.84 P= 19.18 P= 18.84 P= 6.06 P= 19.30 P= 19.02 P= 18.80 P= 6.06 P= 19.30 P= 19.02 P= 18.80 P= 6.06 P= 19.30 P= 19.02 P= 18.80 P= 6.06 P= 19.30 P= 19.02 P= 18.80 P= 6.06 P= 19.30 P= 19.02 P= 18.80 P= 6.06 P= 19.30 P= 19.02 P= 18.80 Then I stopped (smoothly) and restarted the calculation, and it is now dancing around different values P= 6.19 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 P= 6.22 P= 20.85 and the BFGS is still stuck number of scf cycles = 46 number of bfgs steps = 2 Maybe the question is intrinsically fool (thou shall not perform unsupported calculations...), but what am I calculating? Yours Giuseppe &control calculation = 'vc-relax' restart_mode='restart', prefix='zno-4at-vcr-hse-k443s-cw80', pseudo_dir = '/home/giuseppe/PP_UPF/', outdir='/data/giuseppe/zno/bulk/hse/run/tmp/', tstress=.true., tprnfor=.true., nstep=50, etot_conv_thr=1.0E-5, forc_conv_thr=1.0D-4, / &system ibrav=4, A=3.2691493, B=3.2691493, C=5.1976911, cosAB=-0.500000, cosBC=0.000000, cosAC=0.000000, nat=4, ntyp=2, ecutwfc=80.0, occupations='smearing', degauss=0.01, nspin=1, input_dft='hse', nqx1 = 4, nqx2 = 4, nqx3 = 3, / &electrons diagonalization='david', mixing_mode='plain' mixing_beta=0.3 conv_thr=1.0d-9 electron_maxstep=200 / &ions ion_dynamics='bfgs' / &cell cell_dynamics='bfgs', press =0.0, / ATOMIC_SPECIES Zn 65.409 Zn.pbe-rrkj.UPF O 15.999 O.pbe-mt.UPF ATOMIC_POSITIONS {crystal} Zn 0.000000 0.000000 0.377000 Zn 0.333333 0.666666 0.877000 O 0.000000 0.000000 0.000000 O 0.333333 0.666666 0.500000 K_POINTS {automatic} 4, 4, 3, 1, 1, 1 -- ******************************************************** - 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 songsong19840614 at gmail.com Tue Sep 13 16:38:43 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Tue, 13 Sep 2011 22:38:43 +0800 Subject: [Pw_forum] SCF errror with the converted pseudopotential Message-ID: Hi, Recently,I want to calculate the Raman property of ZnO.But the pwscf have no nc-pp for Zn.So,I download espudopotentials of 30-Zn.LDA.fhi and 08-O.LDA.fhi from abinit web. And I use fhi2upf.x chang fhi to upf. The step is followed: 1.Zn /whatever/fhi2upf.x 30-Zn.LDA.fhi label1, occupancy > 4s 2 label1, occupancy > 3d 10 label1, occupancy > 3p 6 label1, occupancy > 3s 2 2.O /whatever/fhi2upf.x 08-O.LDA.fhi label1, occupancy > 2p 2 label1, occupancy > 2s 2 label1, occupancy > 1s 2 label1, occupancy > 1s 2 And the I run the SCF,but is error note: 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... file Zn.LDA.fhi.UPF: wavefunction(s) 3d 3s renormalized %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readpp : error # 2 inconsistent DFT read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110913/0ad9bd86/attachment.htm From caperott at ucs.br Tue Sep 13 19:35:52 2011 From: caperott at ucs.br (Claudio Perottoni) Date: Tue, 13 Sep 2011 14:35:52 -0300 Subject: [Pw_forum] phonon dispersion from IFC Message-ID: <4E6F9478.9050204@ucs.br> Hi, I just finished a very lengthy calculation of the phonon dispersion spectrum for a 132-atom structure using DFPT and interatomic force constants. I wonder could the same IFCs be used to calculate the phonon spectrum for the same compound, now optimized at a different pressure, i.e., with different lattice parameters and atomic positions, without the need to perform the full calculation of phonons and dynamical matrices and generate new IFCs all over again ? Thanks for your attention! Regards, Claudio -- ****************************************************************** Dr. Cl?udio A. Perottoni Universidade de Caxias do Sul Centro de Ci?ncias Exatas e Tecnologia Rua Francisco Get?lio Vargas, 1130 95070-560 Caxias do Sul - RS - Brazil Phone: +55 54 3218 2607 http://www.ucs.br/ccet/defq/caperott/ ****************************************************************** From baroni at sissa.it Tue Sep 13 20:16:38 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 13 Sep 2011 20:16:38 +0200 Subject: [Pw_forum] phonon dispersion from IFC In-Reply-To: <4E6F9478.9050204@ucs.br> References: <4E6F9478.9050204@ucs.br> Message-ID: How would the dynamical matrices ever know that the lattice parameter has changed, if you do not recalculate them? Unless you have a model to predict the dependence of the IFCs upon pressure/latt param ... SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 13/set/2011, at 19:35, Claudio Perottoni wrote: > Hi, > > I just finished a very lengthy calculation of the phonon dispersion > spectrum for a 132-atom structure using DFPT and interatomic force > constants. I wonder could the same IFCs be used to calculate the phonon > spectrum for the same compound, now optimized at a different pressure, > i.e., with different lattice parameters and atomic positions, without > the need to perform the full calculation of phonons and dynamical > matrices and generate new IFCs all over again ? > > Thanks for your attention! > > Regards, > > Claudio > > -- > ****************************************************************** > Dr. Cl?udio A. Perottoni > > Universidade de Caxias do Sul > Centro de Ci?ncias Exatas e Tecnologia > Rua Francisco Get?lio Vargas, 1130 > 95070-560 Caxias do Sul - RS - Brazil > Phone: +55 54 3218 2607 > http://www.ucs.br/ccet/defq/caperott/ > ****************************************************************** > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From caperott at ucs.br Tue Sep 13 20:25:19 2011 From: caperott at ucs.br (Claudio Perottoni) Date: Tue, 13 Sep 2011 15:25:19 -0300 Subject: [Pw_forum] phonon dispersion from IFC In-Reply-To: References: <4E6F9478.9050204@ucs.br> Message-ID: <4E6FA00F.2080305@ucs.br> Dear Stefano, Yes, that's right. I just wanted to be sure before start another (lengthy) calculation. Thank you very much! Regards, Claudio On 13-Sep-11 15:16, Stefano Baroni wrote: > How would the dynamical matrices ever know that the lattice parameter has changed, if you do not recalculate them? Unless you have a model to predict the dependence of the IFCs upon pressure/latt param ... SB > > -- > Stefano Baroni, Trieste -- swift message written and sent on the go > > On 13/set/2011, at 19:35, Claudio Perottoni wrote: > >> Hi, >> >> I just finished a very lengthy calculation of the phonon dispersion >> spectrum for a 132-atom structure using DFPT and interatomic force >> constants. I wonder could the same IFCs be used to calculate the phonon >> spectrum for the same compound, now optimized at a different pressure, >> i.e., with different lattice parameters and atomic positions, without >> the need to perform the full calculation of phonons and dynamical >> matrices and generate new IFCs all over again ? >> >> Thanks for your attention! >> >> Regards, >> >> Claudio >> >> -- >> ****************************************************************** >> Dr. Cl?udio A. Perottoni >> >> Universidade de Caxias do Sul >> Centro de Ci?ncias Exatas e Tecnologia >> Rua Francisco Get?lio Vargas, 1130 >> 95070-560 Caxias do Sul - RS - Brazil >> Phone: +55 54 3218 2607 >> http://www.ucs.br/ccet/defq/caperott/ >> ****************************************************************** >> >> _______________________________________________ >> 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. Cl?udio A. Perottoni Universidade de Caxias do Sul Centro de Ci?ncias Exatas e Tecnologia Rua Francisco Get?lio Vargas, 1130 95070-560 Caxias do Sul - RS - Brazil Phone: +55 54 3218 2607 http://www.ucs.br/ccet/defq/caperott/ ****************************************************************** From giannozz at democritos.it Tue Sep 13 21:00:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 13 Sep 2011 21:00:48 +0200 Subject: [Pw_forum] SCF errror with the converted pseudopotential In-Reply-To: References: Message-ID: On Sep 13, 2011, at 16:38 , lucking-pine wrote: > from readpp : error # 2 > inconsistent DFT read http://www.quantum-espresso.org/user_guide/ node52.html#SECTION000121060000000000000 --- 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 Trinh.Vo at jpl.nasa.gov Tue Sep 13 20:46:53 2011 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Tue, 13 Sep 2011 11:46:53 -0700 Subject: [Pw_forum] Cu PP for LDA+U Message-ID: Dear All, I am doing a test calculation for YBa2Cu3O6 compound. I go through all the Pps on PWSCF website. I noticed a comment in a link "details" for the PP "Cu-pbe-d-rrkjus.UPF." a comment, "The original version of this pseudopotential file contained unnormalized atomic orbitals, which could be a source of trouble for LDA+U calculations.On April 26, 2006 an updated version, containing normalized atomic orbitals, was uploaded to the site." Does it mean that any PP that have unnormalized atomic orbitals will give unreliable results in LDA+U calculation. I used the PP "Cu-pbe-n-van_gipaw.UPF" for one test calculation, and I got a message in the output "WARNING: atomic wfc # 6 for atom type 3 has zero norm WARNING: atomic wfc # 6 for atom type 4 has zero norm WARNING: atomic wfc # 6 for atom type 5 has zero norm WARNING: atomic wfc # 2 for atom type 6 has zero norm WARNING: atomic wfc # 4 for atom type 6 has zero norm" I guess the message may be the unnormalized atomic wfc. However, using both Pps above, I still have metallic solution, while it should have been an insulator. I guess the problem is not just unnormalized atomic wfc but other things (e.g occupation matrix,?), and I have to figure it out. Thank you, Trinh Computation Group JPL/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110913/c5560970/attachment.htm From martins at if.uff.br Tue Sep 13 21:28:16 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Tue, 13 Sep 2011 16:28:16 -0300 Subject: [Pw_forum] Convergence problem with Ni/Ni3Al system Message-ID: <20110913162816.16777b0mg64j6tow@webmail.if.uff.br> Dear all, I'm studying the Ni/Ni3Al system. In order to estimate the value of the interface energy, I built several supercells keeping Nx = Ny = 1 (the Ni and Ni3Al lattice parameters are commensurated) and vary the number of unitary cells along the z direction, but constraining the numbers of Ni and Ni3Al cells to be equal. For small systems, nz = 2 and nz = 4, the calculations runned without any problem. However, for nz = 6 and nz = 8 I'm having problems of convergency: the quantum espresso is unable to reach the minimum value of energy. I tried several modifications: i) Increase ecutwfc and the k-point sampling; ii) Increase ecutrho; iii) Modify the ion and cell dynamics options; iv) ... Bellow I send the input file. I appeciate any help to solve this problem. If someone want to write me directly to my personal e-mail, fell free! One last information: I tried too to run only a SCF calculation... and the result not converged. Thanks in advance, Adriano Martins (Universidade Federal Fluminense - Brazil) -------------------- Typical Input File ------------------------------- &control calculation = 'vc-relax', restart_mode='from_scratch' prefix='NiNi3Al' tstress = .true. tprnfor = .true. pseudo_dir = '/home/martins/programas/espresso-4.3.2/pseudo/', outdir='/home/martins/calculos/QE/NiNi3Al/nx1ny1nz6/' / &system ibrav = 0, celldm(1) = 40.35, nat = 24, ntyp = 2, ecutwfc = 40.0, ecutrho = 320, nspin = 2, starting_magnetization(1) = 0.0, starting_magnetization(2) = 0.2, occupations = 'smearing', smearing = 'gaussian', degauss = 0.02, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.70 conv_thr = 1.0d-6 / &ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / CELL_PARAMETERS 0.16667 0.00000 0.00000 0.00000 0.16667 0.00000 0.00000 0.00000 1.00000 ATOMIC_SPECIES Al 26.981 Al.pbe-sp-van.UPF Ni 58.693 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS alat Ni 0.00000 0.00000 0.00000 Ni 0.00000 0.08333 0.08333 Ni 0.08333 0.08333 0.00000 Ni 0.08333 0.00000 0.08333 Ni 0.00000 0.00000 0.16667 Ni 0.00000 0.08333 0.25000 Ni 0.08333 0.08333 0.16667 Ni 0.08333 0.00000 0.25000 Ni 0.00000 0.00000 0.33333 Ni 0.00000 0.08333 0.41667 Ni 0.08333 0.08333 0.33333 Ni 0.08333 0.00000 0.41667 Al 0.00000 0.00000 0.50000 Ni 0.00000 0.08333 0.58333 Ni 0.08333 0.08333 0.50000 Ni 0.08333 0.00000 0.58333 Al 0.00000 0.00000 0.66667 Ni 0.00000 0.08333 0.75000 Ni 0.08333 0.08333 0.66667 Ni 0.08333 0.00000 0.75000 Al 0.00000 0.00000 0.83333 Ni 0.00000 0.08333 0.91667 Ni 0.08333 0.08333 0.83333 Ni 0.08333 0.00000 0.91667 K_POINTS automatic 8 8 2 1 1 1 ---------------------------------------------------------------------- ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From matteo at umn.edu Tue Sep 13 23:41:56 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 13 Sep 2011 16:41:56 -0500 Subject: [Pw_forum] Cu PP for LDA+U In-Reply-To: References: Message-ID: On Tue, Sep 13, 2011 at 1:46 PM, Vo, Trinh (388C) wrote: > Dear All, > > I am doing a test calculation for YBa2Cu3O6 compound. I go through all the > Pps on PWSCF website. I noticed a comment in a link "details" for the PP > "Cu-pbe-d-rrkjus.UPF." a comment, > "The original version of this pseudopotential file contained unnormalized > > atomic orbitals, which could be a source of trouble for LDA+U calculations.On April 26, 2006 an updated version, containing normalized atomic orbitals, > was uploaded to the site." > > Does it mean that any PP that have unnormalized atomic orbitals will give unreliable results in LDA+U calculation. > > Dear Trinh, no. actually the code now normalizes the atomic wfcs whose norm is not one at the beginning of the calculation. So whether atomic wfcs are normalized or not should not matter at all. I don't know much about PAW so I cannot help with the rest. regards, Matteo > I used the PP "Cu-pbe-n-van_gipaw.UPF" for one test calculation, and I got a message in the output > > "WARNING: atomic wfc # 6 for atom type 3 has zero norm > WARNING: atomic wfc # 6 for atom type 4 has zero norm > WARNING: atomic wfc # 6 for atom type 5 has zero norm > WARNING: atomic wfc # 2 for atom type 6 has zero norm > WARNING: atomic wfc # 4 for atom type 6 has zero norm" > > I guess the message may be the unnormalized atomic wfc. > > However, using both Pps above, I still have metallic solution, while it should have been an insulator. I guess the problem is not just unnormalized atomic wfc but other things (e.g occupation matrix,?), and I have to figure it out. > > Thank you, > > Trinh > > Computation Group > > JPL/CalTech > > > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110913/13c58a6d/attachment.htm From Trinh.Vo at jpl.nasa.gov Tue Sep 13 23:49:28 2011 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Tue, 13 Sep 2011 14:49:28 -0700 Subject: [Pw_forum] Cu PP for LDA+U In-Reply-To: Message-ID: Dear Mateo, Thank you very much. Trinh From: Matteo Cococcioni > Reply-To: PWSCF Forum > Date: Tue, 13 Sep 2011 14:41:56 -0700 To: PWSCF Forum > Subject: Re: [Pw_forum] Cu PP for LDA+U On Tue, Sep 13, 2011 at 1:46 PM, Vo, Trinh (388C) > wrote: Dear All, I am doing a test calculation for YBa2Cu3O6 compound. I go through all the Pps on PWSCF website. I noticed a comment in a link "details" for the PP "Cu-pbe-d-rrkjus.UPF." a comment, "The original version of this pseudopotential file contained unnormalized atomic orbitals, which could be a source of trouble for LDA+U calculations.On April 26, 2006 an updated version, containing normalized atomic orbitals, was uploaded to the site." Does it mean that any PP that have unnormalized atomic orbitals will give unreliable results in LDA+U calculation. Dear Trinh, no. actually the code now normalizes the atomic wfcs whose norm is not one at the beginning of the calculation. So whether atomic wfcs are normalized or not should not matter at all. I don't know much about PAW so I cannot help with the rest. regards, Matteo I used the PP "Cu-pbe-n-van_gipaw.UPF" for one test calculation, and I got a message in the output "WARNING: atomic wfc # 6 for atom type 3 has zero norm WARNING: atomic wfc # 6 for atom type 4 has zero norm WARNING: atomic wfc # 6 for atom type 5 has zero norm WARNING: atomic wfc # 2 for atom type 6 has zero norm WARNING: atomic wfc # 4 for atom type 6 has zero norm" I guess the message may be the unnormalized atomic wfc. However, using both Pps above, I still have metallic solution, while it should have been an insulator. I guess the problem is not just unnormalized atomic wfc but other things (e.g occupation matrix,?), and I have to figure it out. Thank you, Trinh Computation Group JPL/CalTech _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110913/f2bb4ed8/attachment.htm From konda.physics at gmail.com Wed Sep 14 11:14:08 2011 From: konda.physics at gmail.com (kondaiah samudrala) Date: Wed, 14 Sep 2011 14:44:08 +0530 Subject: [Pw_forum] regarding structural optimization Message-ID: Dear all, I am doing test calculations for orthorhombic layered compounds having van der waals forces. i calculated the volume by varying c/a, b/a and a with energy and taken the minimum values of c/a, b/a and a. But my volume change is surprisingly 2% with experimental ( even van der waals forces having). I tried with the "vc-relax" for same system i found 12% volume change with experimental.I tried with psedopotentials also and the results are same. I am very thankful any to solve this problem. Thanks in advance S.Appalakondaiah Research Scholar University of hyderabad Hyderabad India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110914/62e67db8/attachment.htm From maalygharib at gmail.com Wed Sep 14 12:48:52 2011 From: maalygharib at gmail.com (maaly) Date: Wed, 14 Sep 2011 13:48:52 +0300 Subject: [Pw_forum] modifying sumpdos.f90 Message-ID: Dear all, I need to modify sumpdos.f90 to sum one of the pdos(up) and pdos(dwn) columns for selected atoms instead of summing ldos(up) and ldos(dwn) and i'm not that familiar with fortran, so it will be very great if any one can tell me how. Best regards, Maaly Ghariballah Graduate student Alneelain university,sudan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110914/2ae13982/attachment.htm From songsong19840614 at gmail.com Wed Sep 14 13:25:54 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Wed, 14 Sep 2011 19:25:54 +0800 Subject: [Pw_forum] SCF errror with the converted pseudopotential In-Reply-To: References: Message-ID: Hi, Paolo Thanks for your advice.But the main problem I want to know is if the way which I converted pseudopotential is right or wrong?And could tell me the reason? The information is very few by only reading atomic_doc/pseudo-gen.pdf. 2011/9/14 Paolo Giannozzi > > On Sep 13, 2011, at 16:38 , lucking-pine wrote: > > > from readpp : error # 2 > > inconsistent DFT read > > > http://www.quantum-espresso.org/user_guide/ > node52.html#SECTION000121060000000000000 > --- > 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/20110914/efcc6a6e/attachment.htm From elbuesta at icqmail.com Wed Sep 14 14:34:29 2011 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Wed, 14 Sep 2011 08:34:29 -0400 (EDT) Subject: [Pw_forum] Convergence problem with Ni/Ni3Al system In-Reply-To: <20110913162816.16777b0mg64j6tow@webmail.if.uff.br> References: <20110913162816.16777b0mg64j6tow@webmail.if.uff.br> Message-ID: <8CE40F1C7C4AA9F-5B8-3C6F0@webmail-m053.sysops.aol.com> Dear Adriano Martins, if the SCF calculation is not converging, than you should reduce the mixing_beta parameter. I never performed calculations on your specific system, but for the Ni-X surfaces that I've studied I had to use a mixing_beta should equal to 0.05-0.4 in order to reach convergence. I hope it helps, Fabio Negreiros Ribeiro IPCF - CNR Pisa, Italy -----Original Message----- From: martins To: pw_forum Sent: Tue, Sep 13, 2011 9:28 pm Subject: [Pw_forum] Convergence problem with Ni/Ni3Al system Dear all, I'm studying the Ni/Ni3Al system. In order to estimate the value of the interface energy, I built several supercells keeping Nx = Ny = 1 (the Ni and Ni3Al lattice parameters are commensurated) and vary the number of unitary cells along the z direction, but constraining the numbers of Ni and Ni3Al cells to be equal. For small systems, nz = 2 and nz = 4, the calculations runned without any problem. However, for nz = 6 and nz = 8 I'm having problems of convergency: the quantum espresso is unable to reach the minimum value of energy. I tried several modifications: i) Increase ecutwfc and the k-point sampling; ii) Increase ecutrho; iii) Modify the ion and cell dynamics options; iv) ... Bellow I send the input file. I appeciate any help to solve this problem. If someone want to write me directly to my personal e-mail, fell free! One last information: I tried too to run only a SCF calculation... and the result not converged. Thanks in advance, Adriano Martins (Universidade Federal Fluminense - Brazil) -------------------- Typical Input File ------------------------------- &control calculation = 'vc-relax', restart_mode='from_scratch' prefix='NiNi3Al' tstress = .true. tprnfor = .true. pseudo_dir = '/home/martins/programas/espresso-4.3.2/pseudo/', outdir='/home/martins/calculos/QE/NiNi3Al/nx1ny1nz6/' / &system ibrav = 0, celldm(1) = 40.35, nat = 24, ntyp = 2, ecutwfc = 40.0, ecutrho = 320, nspin = 2, starting_magnetization(1) = 0.0, starting_magnetization(2) = 0.2, occupations = 'smearing', smearing = 'gaussian', degauss = 0.02, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.70 conv_thr = 1.0d-6 / &ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / CELL_PARAMETERS 0.16667 0.00000 0.00000 0.00000 0.16667 0.00000 0.00000 0.00000 1.00000 ATOMIC_SPECIES Al 26.981 Al.pbe-sp-van.UPF Ni 58.693 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS alat Ni 0.00000 0.00000 0.00000 Ni 0.00000 0.08333 0.08333 Ni 0.08333 0.08333 0.00000 Ni 0.08333 0.00000 0.08333 Ni 0.00000 0.00000 0.16667 Ni 0.00000 0.08333 0.25000 Ni 0.08333 0.08333 0.16667 Ni 0.08333 0.00000 0.25000 Ni 0.00000 0.00000 0.33333 Ni 0.00000 0.08333 0.41667 Ni 0.08333 0.08333 0.33333 Ni 0.08333 0.00000 0.41667 Al 0.00000 0.00000 0.50000 Ni 0.00000 0.08333 0.58333 Ni 0.08333 0.08333 0.50000 Ni 0.08333 0.00000 0.58333 Al 0.00000 0.00000 0.66667 Ni 0.00000 0.08333 0.75000 Ni 0.08333 0.08333 0.66667 Ni 0.08333 0.00000 0.75000 Al 0.00000 0.00000 0.83333 Ni 0.00000 0.08333 0.91667 Ni 0.08333 0.08333 0.83333 Ni 0.08333 0.00000 0.91667 K_POINTS automatic 8 8 2 1 1 1 ---------------------------------------------------------------------- ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110914/9edb0f40/attachment.htm From ttduyle at gmail.com Wed Sep 14 16:40:49 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 14 Sep 2011 10:40:49 -0400 Subject: [Pw_forum] modifying sumpdos.f90 In-Reply-To: References: Message-ID: On Wed, Sep 14, 2011 at 6:48 AM, maaly wrote: > Dear all, > I?need to modify sumpdos.f90 to sum??one of the pdos(up) and pdos(dwn) > columns for selected atoms instead of summing ldos(up) and ldos(dwn) > and i'm not that familiar with fortran, Fortran is not the only option. And you don't have to modify sumpdos.f90 and you should not mess it up if you are not familiar with Fortran >so it will be very?great if any one > can tell me how. You can use any plotting softwares to do the job. Even Microsoft Excel can help you :) -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" > > > > > > Best regards, > > Maaly Ghariballah > Graduate student > Alneelain university,sudan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From baroni at sissa.it Wed Sep 14 16:48:01 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 14 Sep 2011 15:48:01 +0100 Subject: [Pw_forum] modifying sumpdos.f90 In-Reply-To: References: Message-ID: <3AB6189C-EBDE-4CE9-9C7D-39FB1FD2F59F@sissa.it> still, learning some fortran would not be such a bad idea, for people doing our job ... SB On Sep 14, 2011, at 3:40 PM, Duy Le wrote: > On Wed, Sep 14, 2011 at 6:48 AM, maaly wrote: >> Dear all, >> I need to modify sumpdos.f90 to sum one of the pdos(up) and pdos(dwn) >> columns for selected atoms instead of summing ldos(up) and ldos(dwn) >> and i'm not that familiar with fortran, > > Fortran is not the only option. And you don't have to modify > sumpdos.f90 and you should not mess it up if you are not familiar with > Fortran >> so it will be very great if any one >> can tell me how. > You can use any plotting softwares to do the job. Even Microsoft Excel > can help you :) > > -------------------------------------------------- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > >> >> >> >> >> >> Best regards, >> >> Maaly Ghariballah >> Graduate student >> Alneelain university,sudan >> _______________________________________________ >> 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/20110914/a618de84/attachment-0001.htm From giacsport at libero.it Wed Sep 14 17:04:37 2011 From: giacsport at libero.it (giacsport at libero.it) Date: Wed, 14 Sep 2011 17:04:37 +0200 (CEST) Subject: [Pw_forum] A psudopotential for Manganese (LDA NC) Message-ID: <2389636.7101611316012677523.JavaMail.root@wmail39> Dear All, I am looking for a tested pseudopotential for Manganese, LDA and Norm Conserving. Both 7e- and 13e- in the valence would be ok. I took a look on the database and I noticed that for Mn there is only USPP and GGA. I also read in the forum the suggestion in case to use a high cutoff for such pseudo (pssibly 130 Ry) Has anyone something to share with me? Excuse me for asking, but I am not very good in generating pseudopotential by myself. Thanks in advance. My very best, Giacomo Giacomo Giorgi, Department of Chemical Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan From renpj at dicp.ac.cn Wed Sep 14 17:17:00 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Wed, 14 Sep 2011 23:17:00 +0800 Subject: [Pw_forum] A psudopotential for Manganese (LDA NC) In-Reply-To: <2389636.7101611316012677523.JavaMail.root@wmail39> References: <2389636.7101611316012677523.JavaMail.root@wmail39> Message-ID: <20110914231700.586f32ad@ren-desktop> On Wed, 14 Sep 2011 17:04:37 +0200 (CEST) "giacsport at libero.it" wrote: > Dear All, > I am looking for a tested pseudopotential for > Manganese, LDA and Norm Conserving. Both 7e- and 13e- in the valence > would be ok. I took a look on the database and I noticed that for Mn > there is only USPP and GGA. I also read in the forum the suggestion > in case to use a high cutoff for such pseudo (pssibly 130 Ry) > > Has anyone something to share with me? Excuse me for asking, but I am > not very good in generating pseudopotential by myself. > > > Thanks in advance. > > My very best, > Giacomo > > > > > > Giacomo Giorgi, > Department of Chemical Engineering, > The University of Tokyo, > Hongo, Bunkyo-ku, Tokyo, > Japan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum You can find PP of Mn in this website, http://charter.cnf.cornell.edu/ , you need to convert the PP to the format of pwscf by using the tools in upftools/ directory. As I know, NCPP need a higher cutoff than USPP. Pengju From windbellklbh at gmail.com Thu Sep 15 04:31:37 2011 From: windbellklbh at gmail.com (WF) Date: Thu, 15 Sep 2011 10:31:37 +0800 Subject: [Pw_forum] Error: fft order too large Message-ID: <000001cc734f$9a6ae890$cf40b9b0$@gmail.com> Hello everyone, I am calculating a surface slab model of MoS2. My parameter works well with 5~11 layers. But with 13 layers ( 39 atoms total ), it gives %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% from good_fft_order : error # 2241 fft order too large %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Decreasing Ecutwfc/Ecutrho can eliminate these problem. But these Ecutwfc/Ecutrho is determined by convergence test of bulk lattice parameter test, so I would like to find a way to solve this problem without decreasing Ecutwfc/Ecutrho. Is there any suggestion ? My input file is like this: ( all 5~11layers input files are just same except atoms related part ) ====================================== &control calculation = 'relax' restart_mode = 'from_scratch' tstress = .true. tprnfor = .true. outdir = './out' wfcdir = './wfc' prefix = 'MoS2' / &system ntyp = 2 nat = 39 ibrav = 4 celldm(1) = 6.108157 celldm(3) = 40.745230 ecutwfc = 100.0 ecutrho = 800.0 london = .false. / &electrons diagonalization = 'cg' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.00d-08 / &ions ion_dynamics = 'bfgs' ion_positions = 'default' / ATOMIC_SPECIES S 32.070000 S.vdwDF-tmus-tmc.UPF Mo 95.940000 Mo.vdwDF-rrkjus-tmc.UPF (Atomic position is negelected for it is too long) K_POINTS automatic 8 8 1 1 1 1 ===================================== Best Regards, F, Wu ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110915/862b0759/attachment.htm From giannozz at democritos.it Thu Sep 15 08:16:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 15 Sep 2011 08:16:15 +0200 Subject: [Pw_forum] Error: fft order too large In-Reply-To: <000001cc734f$9a6ae890$cf40b9b0$@gmail.com> References: <000001cc734f$9a6ae890$cf40b9b0$@gmail.com> Message-ID: On Sep 15, 2011, at 4:31 , WF wrote: > from good_fft_order : error # 2241 fft order too > large > > Is there any suggestion ? > look into the code. You will find that there is a maximum fft dimension (nfftx, currently set to 2048). There is nothing special about this number: it is just a check. If you really need a FFT dimension larger than 2048, just increase nfftx and recompile 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 fratesi at mater.unimib.it Fri Sep 16 08:56:11 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 16 Sep 2011 08:56:11 +0200 (CEST) Subject: [Pw_forum] modifying sumpdos.f90 In-Reply-To: References: Message-ID: Dear Maaly, as a first and simple modification, you could change what is read from the file. The key line is the READ statement below, which puts the contents of column1 into egrid, of column2 into pdos(up) and column3 into pdos(dw) (if nspin==2) (from file sumpdos.f90). DO ie = 1, ngrid READ(10, *, IOSTAT=ios ) egrid(ie), pdos(ie, 1:nspin, ifile) IF (ios/=0) & CALL errore("sumpdos", "reading first line in "//trim(file(ifile)), ie ) ENDDO Learning Fortran would be of help by sure. Still, you might find more convenient to use some scripting to perform some simple yet very specific operations as the one you mention here. As an example, let me write below a bash script I recently used to sum the p_z-PDOS. ========================= #!/bin/bash n=0 prefix=YOUR_PREFIX # loop over files to be summed for file in $prefix.pdos_atm*\(p\) ; do n=$((n+1)) echo "including file: " $file # get pz PDOS from file $file (spin-unpolarized: get 3rd column) awk '(NR>1) {print $3}' $file > pz_$n done # get energies (1st column) awk '(NR>1) {print $1}' *.pdos_tot > en # paste PDOS energies, sum, write results paste en pz_* | awk '{tot=0; for (i=2;i<=NF;i++) {tot=tot+$i}; print $1, tot}' > $prefix.pdos_pz # delete temporary files rm pz_* en ========================= On Wed, 14 Sep 2011, maaly wrote: > Dear all, > > > I need to modify sumpdos.f90 to sum one of the pdos(up) and pdos(dwn) > columns for selected atoms instead of summing ldos(up) and ldos(dwn) > and i'm not that familiar with fortran, so it will be very great if any one > can tell me how. > > > > > > Best regards, > > Maaly Ghariballah > Graduate student > Alneelain university,sudan > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy Phone: +39 02 6448 5183 email: fratesi at mater.unimib.it From flux_ray12 at 163.com Fri Sep 16 17:39:46 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 16 Sep 2011 23:39:46 +0800 (CST) Subject: [Pw_forum] regarding structural optimization In-Reply-To: References: Message-ID: <872839b.1e316.13272e4c123.Coremail.flux_ray12@163.com> Because of your question without any details, I can only answer it generally. For getting convergency lattice parameter by energy-volume method, you can read the paper,Acta Materialia 54 (2006) 1641-1657, in which the author discussed that issue by Wien2k code. Or, if you want to use "vc-relax", you'd better decrease the convergence threshold to very small number with convergence cutoff energy, k-mesh and so on. One more to be noted is that the minimum energy configuration corresponds to zero force, but minimum enthalpy corresponds to zero force and stress. In "vc-relax" case, we try to find zero both for force and stress instead of only for total energy. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-14 17:14:08,"kondaiah samudrala" wrote: Dear all, I am doing test calculations for orthorhombic layered compounds having van der waals forces. i calculated the volume by varying c/a, b/a and a with energy and taken the minimum values of c/a, b/a and a. But my volume change is surprisingly 2% with experimental ( even van der waals forces having). I tried with the "vc-relax" for same system i found 12% volume change with experimental.I tried with psedopotentials also and the results are same. I am very thankful any to solve this problem. Thanks in advance S.Appalakondaiah Research Scholar University of hyderabad Hyderabad India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110916/3bc17b0d/attachment.htm From flux_ray12 at 163.com Fri Sep 16 17:44:42 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 16 Sep 2011 23:44:42 +0800 (CST) Subject: [Pw_forum] SCF errror with the converted pseudopotential In-Reply-To: References: Message-ID: <77da908f.1e35f.13272e9433c.Coremail.flux_ray12@163.com> Therefore, you have to use the examples at atomic_doc/***_library, too. The problem of fhi-ncpp converting, may be solved only by Abinit or FHI98 developers, because of the lack of basic information in pp files. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-14 19:25:54,lucking-pine wrote: Hi, Paolo Thanks for your advice.But the main problem I want to know is if the way which I converted pseudopotential is right or wrong?And could tell me the reason? The information is very few by only reading atomic_doc/pseudo-gen.pdf. 2011/9/14 Paolo Giannozzi On Sep 13, 2011, at 16:38 , lucking-pine wrote: > from readpp : error # 2 > inconsistent DFT read http://www.quantum-espresso.org/user_guide/ node52.html#SECTION000121060000000000000 --- 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/20110916/295624e3/attachment.htm From raamesh123 at rediffmail.com Sat Sep 17 13:57:19 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 17 Sep 2011 11:57:19 -0000 Subject: [Pw_forum] =?utf-8?q?from_check=5Fatoms_=3A_error_=23?= Message-ID: <20110917115719.22641.qmail@f6mail-145-79.rediffmail.com> Dear All I am trying to make a tetragonal supercell with 32 atoms but got this error from check_atoms : error # 1 atoms # 1 and # 2 overlap! I tried searching forum got the answer like because of the equivalent atom positions it shows the error. So i tried to use p1 space group (triclinic cell) but i am unable to get rid of the error. Anyboday faced this problem earlier please help me in this regard... Thankyou 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/20110917/7c0bc34c/attachment.htm From mahdi_fn109 at yahoo.com Sat Sep 17 14:20:03 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Sat, 17 Sep 2011 05:20:03 -0700 (PDT) Subject: [Pw_forum] problem in plot bandstructure Message-ID: <1316262003.27580.YahooMailNeo@web43144.mail.sp1.yahoo.com> Dear all, i am trying to plot bandstructure, but i have a problem that marked red in picture attached. what should i do? ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110917/cc58338c/attachment.htm From flux_ray12 at 163.com Sat Sep 17 15:37:28 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 17 Sep 2011 21:37:28 +0800 (CST) Subject: [Pw_forum] from check_atoms : error # In-Reply-To: <20110917115719.22641.qmail@f6mail-145-79.rediffmail.com> References: <20110917115719.22641.qmail@f6mail-145-79.rediffmail.com> Message-ID: <7295bb6e.6859.132779b2392.Coremail.flux_ray12@163.com> Definitely, this error means that No.1 and No.2 atoms were at same or very close position. You'd better check your ATOMIC_POSITIONS instead of changing ibrav. Without your "input" file, I cannot tell any thing detailed. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-17 19:57:19,"ramesh kumar" wrote: Dear All I am trying to make a tetragonal supercell with 32 atoms but got this error from check_atoms : error # 1 atoms # 1 and # 2 overlap! I tried searching forum got the answer like because of the equivalent atom positions it shows the error. So i tried to use p1 space group (triclinic cell) but i am unable to get rid of the error. Anyboday faced this problem earlier please help me in this regard... Thankyou With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 Treat yourself at a restaurant, spa, resort and much more withRediff Deal ho jaye! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110917/76715521/attachment.htm From mohnish.iitk at gmail.com Sat Sep 17 18:34:23 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 17 Sep 2011 22:04:23 +0530 Subject: [Pw_forum] from check_atoms : error # In-Reply-To: <20110917115719.22641.qmail@f6mail-145-79.rediffmail.com> References: <20110917115719.22641.qmail@f6mail-145-79.rediffmail.com> Message-ID: Dear Ramesh! Visualize the structure with Xcrysden. You may be figure out the problem by yourself. On Sat, Sep 17, 2011 at 5:27 PM, ramesh kumar wrote: > Dear All > > I am trying to make a tetragonal supercell with 32 atoms but got this error > > > from check_atoms : error # 1 > atoms # 1 and # 2 overlap! > > I tried searching forum got the answer like because of the equivalent atom > positions it shows the > error. So i tried to use p1 space group (triclinic cell) but i am unable to > get rid of the error. > Anyboday faced this problem earlier please help me in this regard... > > Thankyou > > With regards > > K. Ramesh Kumar > Research Scholar > Department of Physics > IIT-Madras > Chennai-600 036 > > > Treat yourself at a restaurant, spa, resort and much more with *Rediff > Deal ho jaye! > * > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110917/dd93d07e/attachment.htm From maalygharib at gmail.com Sat Sep 17 21:53:53 2011 From: maalygharib at gmail.com (maaly) Date: Sat, 17 Sep 2011 22:53:53 +0300 Subject: [Pw_forum] Pw_forum Digest, Vol 51, Issue 43 In-Reply-To: References: Message-ID: Dear Guido, These are very useful two pieces of information for me. and since i have the luxury of two options now, i guess i will save modifying the sumpdos for some other time. I tried the bash scripting because it's safer, I modified it a lil bit to sum over all columns, and yes ! it worked. you really helped ... thank you! On Fri, Sep 16, 2011 at 10:32 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > Today's Topics: > > 1. Re: modifying sumpdos.f90 (Guido Fratesi) > > > ---------- Forwarded message ---------- > From: Guido Fratesi > To: PWSCF Forum > Date: Fri, 16 Sep 2011 08:56:11 +0200 (CEST) > Subject: Re: [Pw_forum] modifying sumpdos.f90 > Dear Maaly, > > as a first and simple modification, you could change what is read from the > file. The key line is the READ statement below, which puts the contents of > column1 into egrid, of column2 into pdos(up) and column3 into pdos(dw) (if > nspin==2) (from file sumpdos.f90). > > DO ie = 1, ngrid > READ(10, *, IOSTAT=ios ) egrid(ie), pdos(ie, 1:nspin, ifile) > IF (ios/=0) & > CALL errore("sumpdos", "reading first line in > "//trim(file(ifile)), ie ) > ENDDO > > > Learning Fortran would be of help by sure. Still, you might find more > convenient to use some scripting to perform some simple yet very specific > operations as the one you mention here. As an example, let me write below a > bash script I recently used to sum the p_z-PDOS. > > ========================= > > #!/bin/bash > > n=0 > prefix=YOUR_PREFIX > > # loop over files to be summed > for file in $prefix.pdos_atm*\(p\) ; do > n=$((n+1)) > echo "including file: " $file > > # get pz PDOS from file $file (spin-unpolarized: get 3rd column) > awk '(NR>1) {print $3}' $file > pz_$n > > done > > # get energies (1st column) > awk '(NR>1) {print $1}' *.pdos_tot > en > > # paste PDOS energies, sum, write results > paste en pz_* | awk '{tot=0; for (i=2;i<=NF;i++) {tot=tot+$i}; print $1, > tot}' > $prefix.pdos_pz > > # delete temporary files > rm pz_* en > > ========================= > > > On Wed, 14 Sep 2011, maaly wrote: > > Dear all, >> >> >> I need to modify sumpdos.f90 to sum one of the pdos(up) and pdos(dwn) >> columns for selected atoms instead of summing ldos(up) and ldos(dwn) >> and i'm not that familiar with fortran, so it will be very great if any >> one >> can tell me how. >> >> >> >> >> >> Best regards, >> >> Maaly Ghariballah >> Graduate student >> Alneelain university,sudan >> >> > -- > Guido Fratesi > > Dipartimento di Scienza dei Materiali > Universita` degli Studi di Milano-Bicocca > via Cozzi 53, 20125 Milano, Italy > > Phone: +39 02 6448 5183 > email: fratesi at mater.unimib.it > > > _______________________________________________ > 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/20110917/4ea43c89/attachment.htm From konda.physics at gmail.com Sun Sep 18 09:47:00 2011 From: konda.physics at gmail.com (kondaiah samudrala) Date: Sun, 18 Sep 2011 13:17:00 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 51, Issue 44 In-Reply-To: References: Message-ID: Dear Sir, Thank you for your reply. I am sorry for not sending complete details. Here i am running Black phosphorous, which is layered compound and reported that havng huge van der waals forces. Genarally systems having van der waals forces shows volume change( either 10-12% underestimate in LDA or 5-6% overestimate in GGA) with experimental volume in DFT calculations. In my case,CASTEP and VASP i got similar variation in volume. But in PwSCF, i got 2% volume change with experimental volume. Here i used 50Ry cutoff and 10X10X10 K-mesh is used for my calculations. For energy minimum i used upto 10e-8 .Where as in "vc-relax" calculations i got 10% volume change with experimental volume. please give your suggestions for my problem. If it is need i will send my b/a, c/a and a calculation input and output files to your mail. with regards S.Appalakondaiah Research scholar University of Hyderabad Hyderabad -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110918/f0641585/attachment.htm From konda.physics at gmail.com Wed Sep 14 11:34:19 2011 From: konda.physics at gmail.com (konda) Date: Wed, 14 Sep 2011 15:04:19 +0530 Subject: [Pw_forum] regarding structural optimization Message-ID: <1315992859.2949.1.camel@konda> Dear all I am doing test calculations for orthorhombic layered compounds having van der waals forces. i calculated the volume by varying c/a, b/a and a with energy and taken the minimum values of c/a, b/a and a. But my volume change is surprisingly 2% with experimental ( even van der waals forces having). I tried with the "vc-relax" for same system i found 12% volume change with experimental.I tried with psedopotentials also and the results are same. I am very thankful any to solve this problem. Thanks in advance S.Appalakondaiah Research Scholar University of hyderabad Hyderabad India From konda.physics at gmail.com Sun Sep 18 16:57:27 2011 From: konda.physics at gmail.com (konda) Date: Sun, 18 Sep 2011 20:27:27 +0530 Subject: [Pw_forum] Regarding Structral optimization Message-ID: <1316357847.6139.2.camel@konda> Dear Sir, Thank you for your reply. I am sorry for not sending complete details. Here i am running Black phosphorous, which is layered compound crystallizes in orthorhombic structure and reported that having huge van der waals forces. Generally systems having van der waals forces shows volume change( either 10-12% underestimate in LDA or 5-6% overestimate in GGA) with experimental volume in DFT calculations. In my case,CASTEP and VASP i got similar variation in volume. But in PwSCF, i got 2% volume change with experimental volume. Here i used 50Ry cutoff and 10X10X10 K-mesh is used for my calculations. For energy minimum i used up to 10e-8 . Where as in "vc-relax" calculations i got 10% volume change with experimental volume. please give your suggestions for my problem. If it is need i will send my b/a, c/a and a calculation input and output files to your mail. with regards S.Appalakondaiah Research scholar University of Hyderabad Hyderabad From bdslipun at gmail.com Sun Sep 18 17:09:27 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 18 Sep 2011 20:39:27 +0530 Subject: [Pw_forum] elastic constants Message-ID: can any one suggest me how to find the elastic constants in CsCl phase because i know by distortion stress strain relation i can find the elastic constants in B 1 phase (nacl) by orthorombhic and tetragonal distortion what is the difference between two phase determining the elastic constants b d sahoo(reserch scholar) barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110918/7dcb7e49/attachment.htm From flux_ray12 at 163.com Sun Sep 18 19:01:34 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 19 Sep 2011 01:01:34 +0800 (CST) Subject: [Pw_forum] elastic constants In-Reply-To: References: Message-ID: <11dd95c.4.1327d7c5d87.Coremail.flux_ray12@163.com> In my opinion, the methods, to find elastic constants for both of CsCl-structure and NaCl-structure, should be same principlely, because of the cubic lattice. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-18 23:09:27,"bhabya sahoo" wrote: can any one suggest me how to find the elastic constants in CsCl phase because i know by distortion stress strain relation i can find the elastic constants in B 1 phase (nacl) by orthorombhic and tetragonal distortion what is the difference between two phase determining the elastic constants b d sahoo(reserch scholar) barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110919/d178f073/attachment.htm From raamesh123 at rediffmail.com Sun Sep 18 19:12:48 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 18 Sep 2011 17:12:48 -0000 Subject: [Pw_forum] =?utf-8?q?from_check=5Fatoms_=3A_error_=23_=3A_Problem?= =?utf-8?q?_solved?= Message-ID: <20110918171248.2936.qmail@f6mail-145-189.rediffmail.com> Dear All Thankyou very much for all the replies. the problem about overlap of atoms is solved. That was a input file mistake instead of crystal i used alat. And instead of elongate c axis i wrongly made a axis to elongate thankyou for all the suggestions. 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/20110918/5b68228f/attachment.htm From bdslipun at gmail.com Sun Sep 18 19:44:55 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 18 Sep 2011 23:14:55 +0530 Subject: [Pw_forum] elastic constants Message-ID: i calculated c44 be 47 for equilibrium volume for B1 phase for some ScC how can i calculate for B2 phase? if same for a single volume c44 may be same? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110918/5d6df58e/attachment.htm From swapnil.chandratre at gmail.com Mon Sep 19 02:39:19 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 18 Sep 2011 19:39:19 -0500 Subject: [Pw_forum] warning: symmetry operation # x not allowed Message-ID: Hi, I am trying to perform scf on porous graphene nanoribbon, i receive the following warning, I read some posts related to the same, and also the user manual, The user manual said, its not actually an error, does it mean, I can perform the simulation with the warning existing and use for my purpose or do I have to resolve it to make the results meaningful. I read playing around with ecutrho may help. I am trying that as well. I am attaching my input file as well. Can anyone help ? *warning:* symmetry operation # 2 not allowed. fractional translation: 0.0000000 -0.0374763 0.0000000 in crystal coordinates warning: symmetry operation # 4 not allowed. fractional translation: 0.0000000 -0.0374763 -0.0000031 in crystal coordinates warning: symmetry operation # 5 not allowed. fractional translation: 0.0000000 -0.0374763 -0.0000031 in crystal coordinates warning: symmetry operation # 7 not allowed. fractional translation: 0.0000000 -0.0374763 0.0000000 in crystal coordinates INPUT FILE &control calculation = 'scf' restart_mode = 'from_scratch' pseudo_dir = '/home/s/schandratre/Espresso/pseudo' outdir = '/home/s/schandratre/Espresso/circular' / &system ibrav = 0 celldm(1) = 1.8897261 nat=78 ntyp=2 ecutwfc=25.0 ecutrho =300.0 , / &electrons conv_thr = 1.0d-6, mixing_beta=0.05, / ATOMIC_SPECIES C 12.0000 C.pz-vbc.UPF H 1.00000 H.pz-vbc.UPF ATOMIC_POSITIONS {angstrom} C 5.000000e+00 7.045491e+00 2.841720e+00 C 5.000000e+00 8.275992e+00 3.552150e+00 C 5.000000e+00 7.045491e+00 1.420860e+00 C 5.000000e+00 9.506493e+00 2.841720e+00 C 5.000000e+00 1.073699e+01 3.552150e+00 C 5.000000e+00 8.275992e+00 7.104300e-01 C 5.000000e+00 9.506493e+00 1.420860e+00 C 5.000000e+00 1.196749e+01 2.841720e+00 C 5.000000e+00 1.319800e+01 3.552150e+00 C 5.000000e+00 1.073699e+01 7.104300e-01 C 5.000000e+00 1.196749e+01 1.420860e+00 C 5.000000e+00 1.442850e+01 2.841720e+00 C 5.000000e+00 1.565900e+01 3.552150e+00 C 5.000000e+00 1.319800e+01 7.104300e-01 C 5.000000e+00 1.442850e+01 1.420860e+00 C 5.000000e+00 1.688950e+01 2.841720e+00 C 5.000000e+00 1.812000e+01 3.552150e+00 C 5.000000e+00 1.565900e+01 7.104300e-01 C 5.000000e+00 1.688950e+01 1.420860e+00 C 5.000000e+00 1.935050e+01 2.841720e+00 C 5.000000e+00 1.812000e+01 7.104300e-01 C 5.000000e+00 1.935050e+01 1.420860e+00 H 5.000000e+00 6.091997e+00 3.392220e+00 H 5.000000e+00 6.091997e+00 8.703600e-01 C 5.000000e+00 7.045491e+00 7.104300e+00 C 5.000000e+00 8.275992e+00 7.814730e+00 C 5.000000e+00 7.045491e+00 5.683440e+00 C 5.000000e+00 9.506493e+00 7.104300e+00 C 5.000000e+00 1.073699e+01 7.814730e+00 C 5.000000e+00 8.275992e+00 4.973010e+00 C 5.000000e+00 9.506493e+00 5.683440e+00 C 5.000000e+00 1.073699e+01 4.973010e+00 C 5.000000e+00 1.565900e+01 7.814730e+00 C 5.000000e+00 1.688950e+01 7.104300e+00 C 5.000000e+00 1.812000e+01 7.814730e+00 C 5.000000e+00 1.565900e+01 4.973010e+00 C 5.000000e+00 1.688950e+01 5.683440e+00 C 5.000000e+00 1.935050e+01 7.104300e+00 C 5.000000e+00 1.812000e+01 4.973010e+00 C 5.000000e+00 1.935050e+01 5.683440e+00 H 5.000000e+00 6.091997e+00 7.654800e+00 H 5.000000e+00 6.091997e+00 5.132940e+00 C 5.000000e+00 7.045491e+00 1.136688e+01 C 5.000000e+00 8.275992e+00 1.207731e+01 C 5.000000e+00 7.045491e+00 9.946020e+00 C 5.000000e+00 9.506493e+00 1.136688e+01 C 5.000000e+00 1.073699e+01 1.207731e+01 C 5.000000e+00 8.275992e+00 9.235590e+00 C 5.000000e+00 9.506493e+00 9.946020e+00 C 5.000000e+00 1.196749e+01 1.136688e+01 C 5.000000e+00 1.319800e+01 1.207731e+01 C 5.000000e+00 1.073699e+01 9.235590e+00 C 5.000000e+00 1.196749e+01 9.946020e+00 C 5.000000e+00 1.442850e+01 1.136688e+01 C 5.000000e+00 1.565900e+01 1.207731e+01 C 5.000000e+00 1.319800e+01 9.235590e+00 C 5.000000e+00 1.442850e+01 9.946020e+00 C 5.000000e+00 1.688950e+01 1.136688e+01 C 5.000000e+00 1.812000e+01 1.207731e+01 C 5.000000e+00 1.565900e+01 9.235590e+00 C 5.000000e+00 1.688950e+01 9.946020e+00 C 5.000000e+00 1.935050e+01 1.136688e+01 C 5.000000e+00 1.812000e+01 9.235590e+00 C 5.000000e+00 1.935050e+01 9.946020e+00 H 5.000000e+00 6.091997e+00 1.191738e+01 H 5.000000e+00 6.091997e+00 9.395520e+00 H 5.000000e+00 1.319800e+01 4.653150e+00 H 5.000000e+00 2.030399e+01 3.392220e+00 H 5.000000e+00 2.030399e+01 8.703600e-01 H 5.000000e+00 1.169049e+01 7.264230e+00 H 5.000000e+00 1.169049e+01 5.523510e+00 H 5.000000e+00 1.470550e+01 7.264230e+00 H 5.000000e+00 1.470550e+01 5.523510e+00 H 5.000000e+00 2.030399e+01 7.654800e+00 H 5.000000e+00 2.030399e+01 5.132940e+00 H 5.000000e+00 1.319800e+01 8.134590e+00 H 5.000000e+00 2.030399e+01 1.191738e+01 H 5.000000e+00 2.030399e+01 9.395520e+00 CELL_PARAMETERS 10.000000 0.000000 0.0000000 0.0000000 25.44250 0.0000000 0.0000000 0.000000 12.787700 K_POINTS {automatic} 1 1 23 0 0 0 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110918/abd5c3af/attachment-0001.htm From degironc at sissa.it Mon Sep 19 09:13:48 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 19 Sep 2011 09:13:48 +0200 Subject: [Pw_forum] warning: symmetry operation # x not allowed In-Reply-To: References: Message-ID: <4E76EBAC.50809@sissa.it> It's a warning. It says, as explained several times in this forum, that the code cannot accept, for technical reasons associated to fft grid dimensions and fractional translations being incommensurate, a symmetry operation that would be otherwise acceptable. The number of k-points is increased accordingly so that the calculation is still correct, only takes more time. Hope this helps, stefano On 09/19/2011 02:39 AM, swapnil chandratre wrote: > Hi, > > I am trying to perform scf on porous graphene nanoribbon, i receive the > following warning, I read some posts related to the same, and also the user > manual, The user manual said, its not actually an error, does it mean, I can > perform the simulation with the warning existing and use for my purpose or > do I have to resolve it to make the results meaningful. I read playing > around with ecutrho may help. I am trying that as well. I am attaching my > input file as well. Can anyone help ? > > *warning:* symmetry operation # 2 not allowed. fractional translation: > 0.0000000 -0.0374763 0.0000000 in crystal coordinates > warning: symmetry operation # 4 not allowed. fractional translation: > 0.0000000 -0.0374763 -0.0000031 in crystal coordinates > warning: symmetry operation # 5 not allowed. fractional translation: > 0.0000000 -0.0374763 -0.0000031 in crystal coordinates > warning: symmetry operation # 7 not allowed. fractional translation: > 0.0000000 -0.0374763 0.0000000 in crystal coordinates > > INPUT FILE > &control > calculation = 'scf' > restart_mode = 'from_scratch' > pseudo_dir = '/home/s/schandratre/Espresso/pseudo' > outdir = '/home/s/schandratre/Espresso/circular' > > / > &system > > ibrav = 0 > > celldm(1) = 1.8897261 > nat=78 > ntyp=2 > ecutwfc=25.0 > ecutrho =300.0 > , > / > &electrons > conv_thr = 1.0d-6, > mixing_beta=0.05, > / > > ATOMIC_SPECIES > C 12.0000 C.pz-vbc.UPF > H 1.00000 H.pz-vbc.UPF > > ATOMIC_POSITIONS {angstrom} > C 5.000000e+00 7.045491e+00 2.841720e+00 > C 5.000000e+00 8.275992e+00 3.552150e+00 > C 5.000000e+00 7.045491e+00 1.420860e+00 > C 5.000000e+00 9.506493e+00 2.841720e+00 > C 5.000000e+00 1.073699e+01 3.552150e+00 > C 5.000000e+00 8.275992e+00 7.104300e-01 > C 5.000000e+00 9.506493e+00 1.420860e+00 > C 5.000000e+00 1.196749e+01 2.841720e+00 > C 5.000000e+00 1.319800e+01 3.552150e+00 > C 5.000000e+00 1.073699e+01 7.104300e-01 > C 5.000000e+00 1.196749e+01 1.420860e+00 > C 5.000000e+00 1.442850e+01 2.841720e+00 > C 5.000000e+00 1.565900e+01 3.552150e+00 > C 5.000000e+00 1.319800e+01 7.104300e-01 > C 5.000000e+00 1.442850e+01 1.420860e+00 > C 5.000000e+00 1.688950e+01 2.841720e+00 > C 5.000000e+00 1.812000e+01 3.552150e+00 > C 5.000000e+00 1.565900e+01 7.104300e-01 > C 5.000000e+00 1.688950e+01 1.420860e+00 > C 5.000000e+00 1.935050e+01 2.841720e+00 > C 5.000000e+00 1.812000e+01 7.104300e-01 > C 5.000000e+00 1.935050e+01 1.420860e+00 > H 5.000000e+00 6.091997e+00 3.392220e+00 > H 5.000000e+00 6.091997e+00 8.703600e-01 > C 5.000000e+00 7.045491e+00 7.104300e+00 > C 5.000000e+00 8.275992e+00 7.814730e+00 > C 5.000000e+00 7.045491e+00 5.683440e+00 > C 5.000000e+00 9.506493e+00 7.104300e+00 > C 5.000000e+00 1.073699e+01 7.814730e+00 > C 5.000000e+00 8.275992e+00 4.973010e+00 > C 5.000000e+00 9.506493e+00 5.683440e+00 > C 5.000000e+00 1.073699e+01 4.973010e+00 > C 5.000000e+00 1.565900e+01 7.814730e+00 > C 5.000000e+00 1.688950e+01 7.104300e+00 > C 5.000000e+00 1.812000e+01 7.814730e+00 > C 5.000000e+00 1.565900e+01 4.973010e+00 > C 5.000000e+00 1.688950e+01 5.683440e+00 > C 5.000000e+00 1.935050e+01 7.104300e+00 > C 5.000000e+00 1.812000e+01 4.973010e+00 > C 5.000000e+00 1.935050e+01 5.683440e+00 > H 5.000000e+00 6.091997e+00 7.654800e+00 > H 5.000000e+00 6.091997e+00 5.132940e+00 > C 5.000000e+00 7.045491e+00 1.136688e+01 > C 5.000000e+00 8.275992e+00 1.207731e+01 > C 5.000000e+00 7.045491e+00 9.946020e+00 > C 5.000000e+00 9.506493e+00 1.136688e+01 > C 5.000000e+00 1.073699e+01 1.207731e+01 > C 5.000000e+00 8.275992e+00 9.235590e+00 > C 5.000000e+00 9.506493e+00 9.946020e+00 > C 5.000000e+00 1.196749e+01 1.136688e+01 > C 5.000000e+00 1.319800e+01 1.207731e+01 > C 5.000000e+00 1.073699e+01 9.235590e+00 > C 5.000000e+00 1.196749e+01 9.946020e+00 > C 5.000000e+00 1.442850e+01 1.136688e+01 > C 5.000000e+00 1.565900e+01 1.207731e+01 > C 5.000000e+00 1.319800e+01 9.235590e+00 > C 5.000000e+00 1.442850e+01 9.946020e+00 > C 5.000000e+00 1.688950e+01 1.136688e+01 > C 5.000000e+00 1.812000e+01 1.207731e+01 > C 5.000000e+00 1.565900e+01 9.235590e+00 > C 5.000000e+00 1.688950e+01 9.946020e+00 > C 5.000000e+00 1.935050e+01 1.136688e+01 > C 5.000000e+00 1.812000e+01 9.235590e+00 > C 5.000000e+00 1.935050e+01 9.946020e+00 > H 5.000000e+00 6.091997e+00 1.191738e+01 > H 5.000000e+00 6.091997e+00 9.395520e+00 > H 5.000000e+00 1.319800e+01 4.653150e+00 > H 5.000000e+00 2.030399e+01 3.392220e+00 > H 5.000000e+00 2.030399e+01 8.703600e-01 > H 5.000000e+00 1.169049e+01 7.264230e+00 > H 5.000000e+00 1.169049e+01 5.523510e+00 > H 5.000000e+00 1.470550e+01 7.264230e+00 > H 5.000000e+00 1.470550e+01 5.523510e+00 > H 5.000000e+00 2.030399e+01 7.654800e+00 > H 5.000000e+00 2.030399e+01 5.132940e+00 > H 5.000000e+00 1.319800e+01 8.134590e+00 > H 5.000000e+00 2.030399e+01 1.191738e+01 > H 5.000000e+00 2.030399e+01 9.395520e+00 > > CELL_PARAMETERS > 10.000000 0.000000 0.0000000 > 0.0000000 25.44250 0.0000000 > 0.0000000 0.000000 12.787700 > > K_POINTS {automatic} > 1 1 23 0 0 0 > > > > _______________________________________________ > 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/20110919/dc01bc56/attachment.htm From songsong19840614 at gmail.com Mon Sep 19 16:32:33 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Mon, 19 Sep 2011 22:32:33 +0800 Subject: [Pw_forum] about raman? Message-ID: Hi, Recently,I calculate raman using the pseudopotential converted from abinit.com.The phonon which I tested is similiar with using US-PP. and the phonon frequency of ZnO at gamma point(cm-1): 98.2,260.5,389.8,407.3,438.7,555.6 The Raman Intensity is follow: # mode [cm-1] [THz] IR Raman depol 1 0.00 0.0000 0.0000 948.1738 0.0915 2 0.00 0.0000 0.0000 458.1870 0.7494 3 0.00 0.0000 0.0000 458.7942 0.7467 4 103.07 3.0901 0.0000 48273.1493 0.7500 5 103.07 3.0901 0.0000 48273.1493 0.7500 6 245.38 7.3564 0.0000 0.0000 0.7422 7 398.89 11.9584 27.8734 65515.9354 0.2194 8 407.61 12.2199 91.7357 318320.9101 0.7500 9 407.61 12.2199 91.7357 318320.9101 0.7500 10 456.47 13.6846 0.0000 581667.8712 0.7500 11 456.47 13.6846 0.0000 581667.8712 0.7500 12 591.18 17.7231 0.0000 0.0000 0.7444 the max value is 581667,I don't know if it is right. My input is: 1.pw.x &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/lucking-pine/ZnO/915-IR' , pseudo_dir = '/home/lucking-pine/pseudopotential' , prefix = 'ZnO' , etot_conv_thr = 1.0D-6 , forc_conv_thr = 1.0D-5 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, celldm(1) = 6.026, celldm(3) = 1.613, nat = 4, ntyp = 2, ecutwfc = 47 , ecutrho = 380 , / &ELECTRONS conv_thr = 1.0d-12 , mixing_mode = 'plain' , mixing_beta = 0.6 , diagonalization = 'david' , / ATOMIC_SPECIES Zn 65.40900 30-Zn.LDA.fhi.UPF O 15.99940 08-O.LDA.fhi.UPF ATOMIC_POSITIONS crystal Zn 0.333333333 0.666666667 0.000000000 0 0 0 Zn 0.666666667 0.333333333 0.500000000 0 0 0 O 0.333333333 0.666666667 0.379000000 0 0 0 O 0.666666667 0.333333333 0.879000000 0 0 0 K_POINTS automatic 4 4 4 0 0 0 2.ph.x phonons of ZnO &INPUTPH outdir = '/home/lucking-pine/ZnO/915-IR' , prefix = 'ZnO' , fildyn = 'ZnO_IR.dyn' , fildrho = 'ZnO_IR.drho' , ldisp = .false., trans = .true., epsil = .true., elph = .false., fpol = .false. , elop = .true., lraman = .true., recover = .false. , amass(1) = 65.4090, amass(2) = 15.9994, tr2_ph = 1.0d-12 , / 0 0 0 3.dynamat.x &input fildyn='ZnO_IR.dyn', asr='crystal', filout='ZnO_raman.out' filmol='ZnO_raman.mold' filxsf='ZnO_raman.axsf' / Best Regards Yun Song,Kang Physics Department of Inner Mongolia University P.R.China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110919/0c1c5a87/attachment.htm From faccin.giovani at gmail.com Tue Sep 20 02:50:03 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Mon, 19 Sep 2011 20:50:03 -0400 Subject: [Pw_forum] 64 bit GPU-enabled QE Message-ID: Dear QE users, The GPU-enabled version of QE, listed here, appears to have been released only for the i386 architecture. This fails to compile on x86_64 OS, with errors like this: */usr/local/cuda_4.0.17/include/cublas.h(608): error #140: too many arguments in function call cublasStatus_t error = cublasSrotmg_v2(handle, sd1, sd2, sx1, sy1, sparam); ^ compilation aborted for cuda_env.c (code 4)* My question: is there a 64 bit compatible version of the espresso-GPU code available for testing? Thanks! Giovani M. Faccin UFMS - Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110919/95a3a778/attachment-0001.htm From germaneau at gucas.ac.cn Tue Sep 20 16:03:46 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Tue, 20 Sep 2011 10:03:46 -0400 Subject: [Pw_forum] 64 bit GPU-enabled QE In-Reply-To: <516478561.01614@test1.gucas.ac.cn> References: <516478561.01614@test1.gucas.ac.cn> Message-ID: <4E789D42.3010402@gucas.ac.cn> Dear Giovani, Please post your question the the mailing dedicated to QE on GPU. This is not the right place. Thank you, ?ric. PS : by the way, QE on GPU this working on x86_64 architecture. On 09/19/2011 08:50 PM, Giovani Faccin wrote: > Dear QE users, > > The GPU-enabled version of QE, listed here > , appears to have been released > only for the i386 architecture. This fails to compile on x86_64 OS, > with errors like this: > > //usr/local/cuda_4.0.17/include/cublas.h(608): error #140: too many > arguments in function call > cublasStatus_t error = cublasSrotmg_v2(handle, sd1, sd2, sx1, > sy1, sparam); > ^ > > compilation aborted for cuda_env.c (code 4)/ > > My question: is there a 64 bit compatible version of the espresso-GPU > code available for testing? > > Thanks! > > Giovani M. Faccin > UFMS - Brazil > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/f49c794f/attachment.htm From renpj at dicp.ac.cn Tue Sep 20 04:50:55 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Tue, 20 Sep 2011 10:50:55 +0800 Subject: [Pw_forum] pw.x error running on cluster Message-ID: <20110920105055.5cdd2caa@ren-desktop> Dear all when I running pw.x on cluster there is a error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... from electrons : error # 1 charge is wrong: smearing is needed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% but no error appeared when running on PC. NO ERROR occur during compiling on cluster but warning: : warning #5117: Bad # preprocessor line. Here is my input file: &control calculation = 'scf' restart_mode = 'from_scratch' prefix = 'benzene' tstress = .false. tprnfor = .true. pseudo_dir = './pseudo/' outdir = './tmp/' / &system ibrav = 8 celldm(1) = 24.4265999286 celldm(2) = 0.948940120687 celldm(3) = 0.618907628037 nat = 12 ntyp = 2 ecutwfc = 35 ecutrho = 350 spline_ps = .true. / &electrons diagonalization = 'david' conv_thr = 1e-8 / ATOMIC_SPECIES C 12.000 C.pbe-rrkjus-gipaw-dc.UPF H 2.000 H.pbe-rrkjus-gipaw-dc.UPF K_POINTS automatic 1 1 1 0 0 0 ATOMIC_POSITIONS angstrom C 0.000000 1.391862 0.000000 C 1.205388 0.695931 0.000000 C 1.205388 -0.695931 0.000000 C 0.000000 -1.391862 0.000000 C -1.205388 -0.695931 0.000000 C -1.205388 0.695931 0.000000 H 0.000000 2.475623 0.000000 H 2.143952 1.237811 0.000000 H 2.143952 -1.237811 0.000000 H 0.000000 -2.475623 0.000000 H -2.143952 -1.237811 0.000000 H -2.143952 1.237811 0.000000 Thank you. ================================================ ??? Pengju Ren renpj at dicp.ac.cn State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 zhongshan Road, Dalian, 116023, P.R. China From bamideleibrahim at yahoo.com Tue Sep 20 09:41:54 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Tue, 20 Sep 2011 00:41:54 -0700 (PDT) Subject: [Pw_forum] Doping semiconductor Message-ID: <1316504514.43044.YahooMailNeo@web39412.mail.mud.yahoo.com> Dear all, ??? I am interested in doping some semiconductor with some metals. But, i don't understand how to prepared the input file. I have run series of scf,nscf and? even plotted the band structure, dos and ?charge density of most of the semiconductor am interested in. But now, i want to investigate the effect of doing on the semiconductor of interest. I will be delighted if anybody with an idea on how to do this can share his or her experience on this with me. Thanks ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/7acb0ded/attachment.htm From rameshchitumalla at gmail.com Tue Sep 20 11:01:28 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Tue, 20 Sep 2011 14:31:28 +0530 Subject: [Pw_forum] pw.x error running on cluster Message-ID: Dear Pengju Ren, It seems there is no problem with your input file as I successfully completed the task with your input file with in couple of minutes with 20 processors. Just I added wfcdir = "/tmp", and changed the pseudo potentials as H 1.000 H.pw91-van_ak.UPF C 12.000 C.pw91-van_ak.UPF Of-course these changes may not be the correct reason for your error. And one more thing THE MASS OF 'H' ATOM IS *1, which also not a matter in scf/nscf calculations.* * * *Hope this helps you.* > Message: 2 > Date: Tue, 20 Sep 2011 10:50:55 +0800 > From: Ren PJ > Subject: [Pw_forum] pw.x error running on cluster > To: PWSCF Forum > Message-ID: <20110920105055.5cdd2caa at ren-desktop> > Content-Type: text/plain; charset=UTF-8 > > > Dear all > > when I running pw.x on cluster there is a error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > from electrons : error # 1 > charge is wrong: smearing is needed > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > but no error appeared when running on PC. NO ERROR occur during > compiling on cluster but warning: > : warning #5117: Bad # preprocessor line. > > Here is my input file: > &control > calculation = 'scf' > restart_mode = 'from_scratch' > prefix = 'benzene' > tstress = .false. > tprnfor = .true. > pseudo_dir = './pseudo/' > outdir = './tmp/' > / > &system > ibrav = 8 > celldm(1) = 24.4265999286 > celldm(2) = 0.948940120687 > celldm(3) = 0.618907628037 > nat = 12 > ntyp = 2 > ecutwfc = 35 > ecutrho = 350 > spline_ps = .true. > / > &electrons > diagonalization = 'david' > conv_thr = 1e-8 > / > > ATOMIC_SPECIES > C 12.000 C.pbe-rrkjus-gipaw-dc.UPF > H 2.000 H.pbe-rrkjus-gipaw-dc.UPF > > K_POINTS automatic > 1 1 1 0 0 0 > > ATOMIC_POSITIONS angstrom > C 0.000000 1.391862 0.000000 > C 1.205388 0.695931 0.000000 > C 1.205388 -0.695931 0.000000 > C 0.000000 -1.391862 0.000000 > C -1.205388 -0.695931 0.000000 > C -1.205388 0.695931 0.000000 > H 0.000000 2.475623 0.000000 > H 2.143952 1.237811 0.000000 > H 2.143952 -1.237811 0.000000 > H 0.000000 -2.475623 0.000000 > H -2.143952 -1.237811 0.000000 > H -2.143952 1.237811 0.000000 > > Thank you. > > ================================================ > ??? > Pengju Ren > renpj at dicp.ac.cn > State Key Laboratory of Catalysis, > Dalian Institute of Chemical Physics, > Chinese Academy of Sciences > 457 zhongshan Road, Dalian, 116023, P.R. China > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 51, Issue 49 > **************************************** > -- *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/20110920/b4974de7/attachment.htm From eariel99 at gmail.com Tue Sep 20 11:55:35 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 20 Sep 2011 11:55:35 +0200 Subject: [Pw_forum] about raman? Message-ID: Neither do I know if the values are correct, it depends on the units, and very details. You should search for experimental values of Raman cross sections in ZnO and compare with yur numbers. However, it is crucial to know what is printed at the output. Regarding the units, in dynmat.f90 I can read ! Raman cross sections are in units of bohr^4/(Ry mass unit) write (6,'(5x,"Raman cross sections are in A^4/amu units")'). I guess A means Angstrom, but I am not sure that the comment and the write statement are consisten. Also, I think that cross section should have units of area. In any case, it is quite common to report Raman cross sections in "arbitrary units" due to experimental difficulties to precisely determine them. please, see PRB 54, 7830 (1996) and take a look at dynmat.f90 to see exactly what is printed on the column Raman. It corresponds to a particular configuration of incoming and outgoing polarisations and scattering direction. Pay attentio to this part of dynmat.f90 alpha = (raman(1,1,nu) + raman(2,2,nu) + raman(3,3,nu))/3.d0 beta2 = ( (raman(1,1,nu) - raman(2,2,nu))**2 + & (raman(1,1,nu) - raman(3,3,nu))**2 + & (raman(2,2,nu) - raman(3,3,nu))**2 + 6.d0 * & (raman(1,2,nu)**2 + raman(1,3,nu)**2 + raman(2,3,nu)**2) )/2.d0 write (6,'(i5,f10.2,2f10.4,f15.4,f10.4)') & nu, freq, freq*cm1thz, infrared(nu), & (45.d0*alpha**2 + 7.0d0*beta2)*r1fac, & 3.d0*beta2/(45.d0*alpha**2 + 4.0d0*beta2) (45.d0*alpha**2 + 7.0d0*beta2)*r1fac is what is written on column "Raman" Good luck -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 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). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/eb4a9a0c/attachment.htm From gabriele.sclauzero at epfl.ch Tue Sep 20 12:03:40 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 20 Sep 2011 12:03:40 +0200 Subject: [Pw_forum] local density of states on parallel planes In-Reply-To: References: Message-ID: <25D90436-C6D6-4094-B2BA-16FFF9CEE73F@epfl.ch> Hello P Shok, I think you can extract the LDOS (calculated at the Fermi energy), or the ILDOS, using pp.x and then use the code average.x to make the planar averages. The ILDOS is integrated in energy (not space), therefore is still a function of the position in the unit cell, as the LDOS calculated at some specific energy. Please provide your affiliation next time. HTH GS Il giorno 09/set/2011, alle ore 17.37, pari shok ha scritto: > Dear All, > Hi. > I was wondering if QE has a built-in function for calculating local density of states on planes. I need to get the LDOS on different planes parallel to one another. > I tried to use ILDOS in post processing. However, I am not sure how possibly I can use the code to get LDOS on different parallel planes. > I appreciate your help. > P Shok > _______________________________________________ > 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/20110920/27873b0b/attachment-0001.htm From damien.connetable at ensiacet.fr Tue Sep 20 12:13:15 2011 From: damien.connetable at ensiacet.fr (damien) Date: Tue, 20 Sep 2011 12:13:15 +0200 Subject: [Pw_forum] Ge pseudopotential Message-ID: <4E78673B.4070704@ensiacet.fr> Dear all, First at all, I would to thanks PWSCF developpers for their indirect help in my research. I looking for a Ge pseudpotential. In the data base, we can find different pseudo for Ge, but none has been generated with the pw91 or pbe functionals. Is there someone who has generated Ge pseudopotential with such type of functional. sincerely D. Conn?table CIRIMAT Toulouse, France -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/d64dccb7/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: damien_connetable.vcf Type: text/x-vcard Size: 411 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110920/d64dccb7/attachment.vcf From gabriele.sclauzero at epfl.ch Tue Sep 20 12:28:58 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 20 Sep 2011 12:28:58 +0200 Subject: [Pw_forum] Doubt in spin-orbit coupling results In-Reply-To: <1315803974.96266.YahooMailNeo@web28505.mail.ukl.yahoo.com> References: <1315803974.96266.YahooMailNeo@web28505.mail.ukl.yahoo.com> Message-ID: Dear Padmaja Patnaik, in order to include spin-orbit interaction in the KS equations (lspinorb=.true.) one needs to use a formalism for noncollinear magnetization (noncolin=.true.). This means that there is no preferential axis for the magnetization, which is a vector field, (m_x(r),m_y(r),m_z(r)) in this case. Therefore, in general one cannot define "spin up" and "spin down" (unless the ground state of the system is collinear, e.g. m_x=m_y=0 for each r). That's why the code does not give two distinct components of the DOS in the noncollinear formalism. What you should do depends on what you are looking for... first I would suggest that you try to understand the difference between the collinear and noncollinear formalisms, in order to be able to interpret the results. About the total magnetic moment, I can't say anything because you didn't say a word about your system. GS Il giorno 12/set/2011, alle ore 07.06, Padmaja Patnaik ha scritto: > Hi All > > I am doing spin-orbit coupling calculations. To get spin-polarized calculations with spin-orbit coupling I mentioned in the input for scf, > lspinorb=.true., > noncolin=.true., > starting_magnetization(1)=0.5, > starting_magnetization(2)=0.5, > After this scf calculations I am doing the nscf calculation and finally the density of states and partial density of states. What I expect is it should give me both up and down spin DOS separately but I didnt get that. The input, nspin=2 in the input and get spin polarized results with both up and down spin density of states given separately which can be plotted. Can anybody please suggest what to do? Another doubt is the total magnetic moment is found to be zero (with spin-orbit interaction) which was earlier (without spin-orbit interaction) found to be 2 BohrMagneton./cell. > > Thanking in advance, > regards > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? 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/20110920/ac78e621/attachment.htm From arvifis at gmail.com Tue Sep 20 12:37:53 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Tue, 20 Sep 2011 07:37:53 -0300 Subject: [Pw_forum] Doping semiconductor In-Reply-To: <1316504514.43044.YahooMailNeo@web39412.mail.mud.yahoo.com> References: <1316504514.43044.YahooMailNeo@web39412.mail.mud.yahoo.com> Message-ID: Dear Adetunji, if you want to dope some semiconductor, probably you need build a supercell of your compound and change an atom of the semiconductor by another one (* Substitutional* doping) or put an atom (dope atom) among the semiconductor atoms (interstitial doping). Best. PhD stdn. Arles V. Gil Rebaza IFLP - Argentina 2011/9/20 bamidele ibrahim > Dear all, > I am interested in doping some semiconductor with some metals. But, i > don't understand how > to prepared the input file. I have run series of scf,nscf and even plotted > the band structure, dos and > charge density of most of the semiconductor am interested in. But now, i > want to investigate the effect > of doing on the semiconductor of interest. I will be delighted if anybody > with an idea on how to do this can > share his or her experience on this with me. > Thanks > > Adetunji Bamidele Ibrahim > Department of physics,University of Agriculture, > Abeokuta, Ogun State,Nigeria. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/36ec8532/attachment.htm From giannozz at democritos.it Tue Sep 20 12:47:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Sep 2011 12:47:39 +0200 Subject: [Pw_forum] Ge pseudopotential In-Reply-To: <4E78673B.4070704@ensiacet.fr> References: <4E78673B.4070704@ensiacet.fr> Message-ID: On Sep 20, 2011, at 12:13 , damien wrote: > Is there someone who has generated Ge pseudopotential with such > type of functional. if you cannot find it in the links reported here: http://www.quantum-espresso.org/pseudo-notes.php likely it doesn't exist 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 Tue Sep 20 12:56:04 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Sep 2011 12:56:04 +0200 Subject: [Pw_forum] about raman? In-Reply-To: References: Message-ID: On Sep 20, 2011, at 11:55 , Eduardo Ariel Menendez Proupin wrote: > Regarding the units, in dynmat.f90 I can read > ! Raman cross sections are in units of bohr^4/(Ry mass unit) > write (6,'(5x,"Raman cross sections are in A^4/amu units")'). > I guess A means Angstrom exactly > but I am not sure that the comment and the write statement are > consistent I hope they are, since some time ago I spent a non-negligible amount of time figuring out the correct units so that absolute Raman cross sections could be calculated. I don't remember much about it, but the attached document should contain the results of my elucubrations P. -------------- next part -------------- A non-text attachment was scrubbed... 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I looked in the forum but I did not find an answer. Thanks in advance! Very best, Giacomo ------------------------ Giacomo GIORGI Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan E-mail: giacomo at tcl.t.u-tokyo.ac.jp From giannozz at democritos.it Tue Sep 20 14:59:16 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Sep 2011 14:59:16 +0200 Subject: [Pw_forum] hgh to UPF In-Reply-To: <29558046.8939811316521368950.JavaMail.defaultUser@defaultHost> References: <29558046.8939811316521368950.JavaMail.defaultUser@defaultHost> Message-ID: <3C58655E-CEAB-4409-9F61-98CAA8BBB81B@democritos.it> On Sep 20, 2011, at 14:22 , giacsport at libero.it wrote: > Is there a .hgh to .UPF pseudo converter? the answer to all questions like "is there a converter from format X to .UPF" is invariably "if it is not mentioned, there isn't any, and you are welcome to contribute one" (something that nobody ever does). However ... Recently the cpmd2upf converter has been extended to HGH pseudopotentials. The conversion works by projecting onto a radial logarithmic grid, so it may introduce minor numerical differences wrt CPMD results. From the first tests, differences seem to be sufficiently small and should not affect the physics (or the chemistry). The new converter is available in the SVN version of QE: see http://qe-forge.org/scm/?group_id=10 After conversion, it is convenient to generate the atomic (pseudo-)orbitals using code ld1.x. Attached is an example of ld1.x input for Zr: it reads the converted file Zr-q12.UPF, and (among other things) produces an output UPF file Zr.wfc.UPF, containing (pseudo-)orbitals and (pseudo-)charge density. You can directly use the latter file, but I prefer to replace the and fields in the converted file with those of the output UPF file. You will need to edit the "number_of_wfc" field as well. Please carefully check if everything is working properly! P. -------------- next part -------------- A non-text attachment was scrubbed... Name: zr.in Type: application/octet-stream Size: 220 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110920/06321aae/attachment.obj -------------- next part -------------- --- 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 renpj at dicp.ac.cn Tue Sep 20 15:38:26 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Tue, 20 Sep 2011 21:38:26 +0800 Subject: [Pw_forum] pw.x error running on cluster In-Reply-To: References: Message-ID: <20110920213826.4eb5caff@ren-desktop> Thanks for your answer. I think maybe it is the problem of parallel environment or using a old version intel compiler (11.0). I have contact to administrator for this problem. ================================================ ??? Pengju Ren renpj at dicp.ac.cn State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 zhongshan Road, Dalian, 116023, P.R. China On Tue, 20 Sep 2011 14:31:28 +0530 Ramesh Kumar wrote: > Dear Pengju Ren, > > It seems there is no problem with your input file as I successfully > completed the task with your input file with in couple of minutes > with 20 processors. > > Just I added wfcdir = "/tmp", and changed the pseudo > potentials as > > H 1.000 H.pw91-van_ak.UPF > C 12.000 C.pw91-van_ak.UPF > > Of-course these changes may not be the correct reason for your error. > > And one more thing THE MASS OF 'H' ATOM IS *1, which also not a > matter in scf/nscf calculations.* > * > * > *Hope this helps you.* > > > From payam.norouzzadeh at gmail.com Tue Sep 20 17:59:01 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Tue, 20 Sep 2011 10:59:01 -0500 Subject: [Pw_forum] BltzTrap interface Message-ID: Dear Espresso Users Does anyone how to use QE with bltztrap code to calculate transport coefficients? Is there any interface? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/3dc1ea02/attachment.htm From giannozz at democritos.it Tue Sep 20 18:10:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 20 Sep 2011 18:10:21 +0200 Subject: [Pw_forum] BltzTrap interface In-Reply-To: References: Message-ID: <59640F62-A4EA-4FA2-9F84-0545D9389649@democritos.it> On Sep 20, 2011, at 17:59 , Payam Norouzzadeh wrote: > Does anyone how to use QE with bltztrap code to calculate transport > coefficients? Is there any interface? bltztrap? you mean the "BoltzTraP" code, http://www.icams.de/content/ departments/ams/madsen/boltztrap.html ? 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 jlgr at super.unam.mx Tue Sep 20 18:19:50 2011 From: jlgr at super.unam.mx (Jose Luis Gordillo Ruiz) Date: Tue, 20 Sep 2011 11:19:50 -0500 (CDT) Subject: [Pw_forum] problems with examples Message-ID: Hi, I'm compiling QE 4.3.2 with Intel 12.0.2.137 Build 20110112 in a Intel(R) Xeon(R) CPU X5670 Compilation worked fine, but when running the examples, some of them didn't finish. For instance, example34 ends the "running the dynamic polarizability calculation" step with this message: iter # 80 charge diff. 1.99621241 thresh_veff 0.00960000 **********unstability happens********** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 6 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... while example35 ends "running pw.x at Gamma for O2 with noncolin=.true." step with iteration # 8 ecut= 45.00 Ry beta=0.50 Davidson diagonalization with overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from c_bands : error # 1 too many bands are not converged %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I've got similar results both for using MKL or internal BLAS. anny suggestions? thank you in advance Jose Luis Gordillo Supercomputo - UNAM From ZChen at cau.edu Tue Sep 20 20:55:28 2011 From: ZChen at cau.edu (Chen, Zhifan) Date: Tue, 20 Sep 2011 14:55:28 -0400 Subject: [Pw_forum] Xe pseudopotentials Message-ID: Hi all, I am looking for Xe ultrasoft pseudopotential with 4d,5s,5p as valence electrons. I can Use ABINIT fhi pseudopotential and make conversion from fhi format to USP. However, Xe NC pseudopotential has only 5s, 5p as valence electron. I am new to the generate pseudopotential . Any information is welcome. Thanks Zhifan Chen Clark Atlanta University USA From parishok at gmail.com Tue Sep 20 22:01:58 2011 From: parishok at gmail.com (pari shok) Date: Tue, 20 Sep 2011 16:01:58 -0400 Subject: [Pw_forum] .SAVE files Message-ID: Dear All, Hi. I have a very silly question (I am sorry), but I need a wise answer! I lost the ".SAVE" files of the structures I made; however, I have the ".pw/wfc" files. I was wondering if there is a way to do the pp.x, and band structure simulation without ".SAVE" files. If positive, how? Thanks a lot. Yours P. Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110920/bf845a89/attachment.htm From giannozz at democritos.it Wed Sep 21 09:24:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Sep 2011 09:24:48 +0200 Subject: [Pw_forum] .SAVE files In-Reply-To: References: Message-ID: <1316589888.24621.0.camel@fe12lx.fisica.uniud.it> On Tue, 2011-09-20 at 16:01 -0400, pari shok wrote: > I lost the ".SAVE" files of the structures I made; however, I have the > ".pw/wfc" files. I was wondering if there is a way to do the pp.x no, there isn't any P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Sep 21 10:11:35 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Sep 2011 10:11:35 +0200 Subject: [Pw_forum] problems with examples In-Reply-To: References: Message-ID: <1316592695.27156.7.camel@fe12lx.fisica.uniud.it> On Tue, 2011-09-20 at 11:19 -0500, Jose Luis Gordillo Ruiz wrote: > For instance, example34 ends the "running the dynamic polarizability calculation" > step with this message [...] example34 tests a rather exotic and basically unmaintained calculation. Unless somebody needs that particular feature, just ignore it > while example35 ends "running pw.x at Gamma for O2 with noncolin=.true." it works for me. Have you tried to run it in serial or in parallel? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From mahdi_fn109 at yahoo.com Wed Sep 21 10:14:44 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Wed, 21 Sep 2011 01:14:44 -0700 (PDT) Subject: [Pw_forum] problem in plot bandstructure Message-ID: <1316592884.24136.YahooMailNeo@web43136.mail.sp1.yahoo.com> Dear all, i am trying to plot bandstructure, but i have a problem. as you see in picture attached, conduction band that follow red line, cross with valence band (green line) and in continuance it form valence band and valence band form conduction band that it's not possible in real bandstructure, what is wrong? what should i do? ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/4269ca47/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: BStr2.jpg Type: image/jpeg Size: 116955 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110921/4269ca47/attachment-0001.jpg From konda.physics at gmail.com Wed Sep 21 10:48:05 2011 From: konda.physics at gmail.com (kondaiah samudrala) Date: Wed, 21 Sep 2011 14:18:05 +0530 Subject: [Pw_forum] Regarding structural optimization Message-ID: Dear Sir, (1) Here i am running Black phosphorous, which is layered compound crystallizes in orthorhombic structure and reported that having huge van der waals forces. Generally systems having van der waals forces shows huge volume change( either 10-12% underestimate in LDA or 5-6% overestimate in GGA) with experimental volume in DFT calculations. In my case, CASTEP and VASP i got similar variation in volume. But in PwSCF, i got 2% volume change with experimental volume. Here i used 50Ry cutoff and 10X10X10 K-mesh is used for my calculations. For energy minimum i used up to 10e-8 . Where as in "vc-relax" calculations i got 10% volume change with experimental volume. please give your suggestions for my problem. If it is need i will send my b/a, c/a and a calculation input and output files to your mail. (2) What is the difference in structural optimization between normal process( optimizain c/a, b/a and a with energy) and "vc-relax"? Thanks in advance. with regards S.Appalakondaiah Research scholar University of Hyderabad Hyderabad -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/1166c7a0/attachment.htm From padmaja_patnaik at yahoo.co.uk Wed Sep 21 12:10:05 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 21 Sep 2011 11:10:05 +0100 (BST) Subject: [Pw_forum] Doubt in spin-orbit coupling results In-Reply-To: References: Message-ID: <1316599805.78995.YahooMailNeo@web28505.mail.ukl.yahoo.com> Thanks a lot GS. I was waiting for some suggestions. As u have advised I need to study more about collinear and non-collinear formalism. About the system I am working on --? SiC doped with Cr. I am taking various supercells and Cr as a dilute impurity, doing relaxed and unrelaxed calcualtions for magnetic properties. Hope this is enough and would expect some suggestions for the magnetic moment problem. Thanks and regards, Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India ________________________________ Message: 2 Date: Tue, 20 Sep 2011 12:28:58 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] Doubt in spin-orbit coupling results To: Padmaja Patnaik ,??? PWSCF Forum ??? Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear? Padmaja Patnaik, ? ? in order to include spin-orbit interaction in the KS equations (lspinorb=.true.) one needs to use a formalism for noncollinear magnetization (noncolin=.true.). This means that there is no preferential axis for the magnetization, which is a vector field, (m_x(r),m_y(r),m_z(r)) in this case. Therefore, in general one cannot define "spin up" and "spin down" (unless the ground state of the system is collinear, e.g. m_x=m_y=0 for each r). That's why the code does not give two distinct components of the DOS in the noncollinear formalism. What you should do depends on what you are looking for... first I would suggest that you try to understand the difference between the collinear and noncollinear formalisms, in order to be able to interpret the results. About the total magnetic moment, I can't say anything because you didn't say a word about your system. GS Il giorno 12/set/2011, alle ore 07.06, Padmaja Patnaik ha scritto: > Hi All > > I am doing spin-orbit coupling calculations. To get spin-polarized calculations with spin-orbit coupling I mentioned in the input for scf, >? lspinorb=.true., >? noncolin=.true., >? starting_magnetization(1)=0.5, >? starting_magnetization(2)=0.5, > After this scf calculations I am doing the nscf calculation and finally the density of states and partial density of states. What I expect is it should give me both up and down spin DOS separately but I didnt get that. The input,? nspin=2 in the input and get spin polarized results with both up and down spin density of states given separately which can be plotted. Can anybody please suggest what to do? Another doubt is the total magnetic moment is found to be zero (with spin-orbit interaction) which was earlier (without spin-orbit interaction) found to be 2 BohrMagneton./cell. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/a1f32d71/attachment.htm From gabriele.sclauzero at epfl.ch Wed Sep 21 12:34:48 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 21 Sep 2011 12:34:48 +0200 Subject: [Pw_forum] Doubt in spin-orbit coupling results In-Reply-To: <1316599805.78995.YahooMailNeo@web28505.mail.ukl.yahoo.com> References: <1316599805.78995.YahooMailNeo@web28505.mail.ukl.yahoo.com> Message-ID: <98BD7A90-D4A8-4255-B952-6AB676EA601A@epfl.ch> Il giorno 21/set/2011, alle ore 12.10, Padmaja Patnaik ha scritto: > Thanks a lot GS. > I was waiting for some suggestions. As u have advised I need to study more about collinear and non-collinear formalism. About the system I am working on -- SiC doped with Cr. I am taking various supercells and Cr as a dilute impurity, doing relaxed and unrelaxed calcualtions for magnetic properties. Hope this is enough and would expect some suggestions for the magnetic moment problem. > Mmh, not easy to say... if there is a magnetic anisotropy, then you need to choose also the correct orientation of the magnetization (see angle1 and angle2) vector on the impurity in order to be sure that the calculation converges to the ground state. On which atoms do you put the starting magnetization? (what are species 1 and 2?) Are you using smearing? It would be easier if you post (or send privately) your input file and the relvant part of the output. GS > > Thanks and regards, > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > Message: 2 > Date: Tue, 20 Sep 2011 12:28:58 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Doubt in spin-orbit coupling results > To: Padmaja Patnaik , PWSCF Forum > > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Padmaja Patnaik, > > in order to include spin-orbit interaction in the KS equations (lspinorb=.true.) one needs to use a formalism for noncollinear magnetization (noncolin=.true.). This means that there is no preferential axis for the magnetization, which is a vector field, (m_x(r),m_y(r),m_z(r)) in this case. > Therefore, in general one cannot define "spin up" and "spin down" (unless the ground state of the system is collinear, e.g. m_x=m_y=0 for each r). That's why the code does not give two distinct components of the DOS in the noncollinear formalism. > > What you should do depends on what you are looking for... first I would suggest that you try to understand the difference between the collinear and noncollinear formalisms, in order to be able to interpret the results. > > About the total magnetic moment, I can't say anything because you didn't say a word about your system. > > > GS > > Il giorno 12/set/2011, alle ore 07.06, Padmaja Patnaik ha scritto: > > > Hi All > > > > I am doing spin-orbit coupling calculations. To get spin-polarized calculations with spin-orbit coupling I mentioned in the input for scf, > > lspinorb=.true., > > noncolin=.true., > > starting_magnetization(1)=0.5, > > starting_magnetization(2)=0.5, > > After this scf calculations I am doing the nscf calculation and finally the density of states and partial density of states. What I expect is it should give me both up and down spin DOS separately but I didnt get that. The input, nspin=2 in the input and get spin polarized results with both up and down spin density of states given separately which can be plotted. Can anybody please suggest what to do? Another doubt is the total magnetic moment is found to be zero (with spin-orbit interaction) which was earlier (without spin-orbit interaction) found to be 2 BohrMagneton./cell. > > > > > _______________________________________________ > 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/20110921/4e45ccb2/attachment.htm From payam.norouzzadeh at gmail.com Wed Sep 21 17:21:54 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Wed, 21 Sep 2011 10:21:54 -0500 Subject: [Pw_forum] BoltzTrap interface Message-ID: Prof.Giannozzi You are right. I am looking for an interface for BoltzTrap code. http://www.icams.de/content/departments/ams/madsen/boltztrap.html Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/37e5fe92/attachment-0001.htm From mona at suin.edu.sd Wed Sep 21 17:19:59 2011 From: mona at suin.edu.sd (Mona M.O. Elfadil) Date: Wed, 21 Sep 2011 18:19:59 +0300 Subject: [Pw_forum] cluster timing & delay -v.lousy way- Message-ID: Dear all, We had run an example -Q.E.3.0.1- from your package few days ago on a linux cluster- CentOS 5-, and it worked although we had no BLAS, LAPACK nor an FFTW packages previously installed - not surprising,since you have said so in your user guide-. Then we had tried an experimental data. It took a single CPU 10 min to get the results. While, unfortunately, it took a 16 CPUs more than 40 min to process the same data. We had tried the following: - Referring to your user guide: It needs a detailed physics background which is unavailable at the moment. - Downloading these mathematical packages: FFTW 3.1.2-3 & FFTW 2.1.5-2 LAPACK 3_0-2 BLAS 3_0-2 (RPM versions) In the configuration phase of Q.E. it said that both LAPACK and FFTW are not found although BLASS was successfully configured. We could not find FFTWND in our internet search(As a packet). But in your archive you have said it is not an error. Assuming that all other factors are well, what could be the cause?? (P.S.: we are the system administrators) -- Your sincerely, Mona Elfadil SudREN - Network Engineer www.suin.edu.sd +249911319113 From jlgr at super.unam.mx Wed Sep 21 17:29:40 2011 From: jlgr at super.unam.mx (Jose Luis Gordillo Ruiz) Date: Wed, 21 Sep 2011 10:29:40 -0500 (CDT) Subject: [Pw_forum] problems with examples In-Reply-To: <1316592695.27156.7.camel@fe12lx.fisica.uniud.it> References: <1316592695.27156.7.camel@fe12lx.fisica.uniud.it> Message-ID: > On Tue, 2011-09-20 at 11:19 -0500, Jose Luis Gordillo Ruiz wrote: > > > > For instance, example34 ends the "running the dynamic polarizability calculation" > > step with this message [...] > > example34 tests a rather exotic and basically unmaintained calculation. > Unless somebody needs that particular feature, just ignore it > ok. > > while example35 ends "running pw.x at Gamma for O2 with noncolin=.true." > > it works for me. Have you tried to run it in serial or in parallel? > serial in both cases (internal and MKL). > 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 crma at sissa.it Wed Sep 21 17:38:10 2011 From: crma at sissa.it (Changru Ma) Date: Wed, 21 Sep 2011 17:38:10 +0200 Subject: [Pw_forum] cluster timing & delay -v.lousy way- In-Reply-To: References: Message-ID: <9501C7A2-BE94-45B3-8CCC-50CC782E1EA9@sissa.it> Dear Mona Elfadil, Q.E.3.0 was released on 2005. I would suggest you to try the newest version 4.3.2 first. You can find it here: http://www.quantum-espresso.org/download.php HTH, Changru On 21 Sep, 2011, at 17:19, Mona M.O. Elfadil wrote: > Dear all, > We had run an example -Q.E.3.0.1- from your package few days ago > on a linux cluster- CentOS 5-, and it worked although we had no > BLAS, LAPACK nor an FFTW packages previously installed - not > surprising,since you have said so in your user guide-. > Then we had tried an experimental data. It took a single CPU 10 min to get > the results. While, unfortunately, it took a 16 CPUs more than 40 min to > process the same data. > We had tried the following: > - Referring to your user guide: It needs a detailed physics background > which is unavailable at the moment. > - Downloading these mathematical packages: > FFTW 3.1.2-3 & FFTW 2.1.5-2 > LAPACK 3_0-2 > BLAS 3_0-2 > (RPM versions) > In the configuration phase of Q.E. it said that both LAPACK and FFTW are > not found although BLASS was successfully configured. > > We could not find FFTWND in our internet search(As a packet). But in your > archive you have said it is not an error. > > Assuming that all other factors are well, what could be the cause?? > > (P.S.: we are the system administrators) > > -- > Your sincerely, > Mona Elfadil > SudREN - Network Engineer > www.suin.edu.sd > +249911319113 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- From giannozz at democritos.it Wed Sep 21 18:13:47 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 21 Sep 2011 18:13:47 +0200 Subject: [Pw_forum] problems with examples In-Reply-To: References: <1316592695.27156.7.camel@fe12lx.fisica.uniud.it> Message-ID: <1316621628.5410.15.camel@fe12lx.fisica.uniud.it> On Wed, 2011-09-21 at 10:29 -0500, Jose Luis Gordillo Ruiz wrote: > serial in both cases (internal and MKL) I see; I had the version with EXX compiled. It is an unfortunate case in which at the very end a too small convergence threshold is set, resulting in non-convergence. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From trambui at u.boisestate.edu Wed Sep 21 23:37:45 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 21 Sep 2011 15:37:45 -0600 Subject: [Pw_forum] charge density plot in xcrysden Message-ID: Dear Everyone, I have an output file of the SiC bulk charge density (bulk.xsf). I open it using xcrysden and do data grid to get the display of color-plane and isoline, etc. I'd also like to make the isoline with different color other than just the gray scale, how can I do so in xcrysden? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/ca94dc20/attachment.htm From aguiardlm at iq.ufrj.br Thu Sep 22 00:23:16 2011 From: aguiardlm at iq.ufrj.br (Daniel Lima) Date: Wed, 21 Sep 2011 19:23:16 -0300 (BRT) Subject: [Pw_forum] Questions about pseudopotential generation. In-Reply-To: <1569721047.84865.1316643685777.JavaMail.root@mail.iq.ufrj.br> Message-ID: <412439261.84871.1316643796133.JavaMail.root@mail.iq.ufrj.br> Dear All, My name is Daniel Aguiar and I?m a begginer in? "pseudopotential generation art". My PhD thesis is about o rganic molecules solid state NMR GIPAW calculations? and in QE website?gipaw pseudopotentials are limited. So, I?m trying build my own pseudopotentials. I?m following the classical Silicon example ( ? http://www.fisica.uniud.it/~giannozz/Corsi/MetNum/LectureNotes/metnum-ex2.pdf ?and http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf ) and some aspects of the tutorials / exercises are not clear for me. 1) A typical value to logarithmic derivative ? is the midpoint of a typical bonding, or the ionic /covalent radii. The?chemical bonding is?variable to organic molecules, so?my choice is the ionic radius of Silicon. ?However the example value to rlderiv is 2.1, but the silicon is 1.11 ?. How it works ? 2) How can I get a razoable value to logarithimic derivative energy parameters ( eminld, emaxld and deld) ? . In? example the value s are eminld=-11.0, emaxld=2.0 and deld=0.01d0, but I think that for other atoms these values can change for a good pseudopotential generation. 3)?In ?last lines, there?is a list of informations ?about the pseudization. In this input section, I can?t understand the third column significance . What this numbers means ? 2) How can I get a razoable value to logarithimic derivative energy parameters ( eminld, emaxld and deld) ? . In? example the value s are eminld=-11.0, emaxld=2.0 and deld=0.01d0, but I think that for other atoms these values can change for a good pseudopotential generation. 3)?In ?last lines, there?is a list of informations ?about the pseudization. In this input section, I can?t understand the third column significance . What this numbers means ? 4) The matching radii? for s, p and d silicon orbitals is 2.4. How can I calculate the matching radii for other atoms ? Anyone have some reference to do this ? Sorry if my question sounds stupid, Thanks in advance, -- Daniel Lima Marques de Aguiar Universidade Federal do Rio de Janeiro / Centro de Tecnologia Instituto de Qu?mica Programa de P?s Gradua??o em Qu?mica Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 -- Daniel Lima Marques de Aguiar Universidade Federal do Rio de Janeiro / Centro de Tecnologia Instituto de Qu?mica Programa de P?s Gradua??o em Qu?mica Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/a439859c/attachment.htm From aryjunior at gmail.com Thu Sep 22 00:52:36 2011 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 21 Sep 2011 19:52:36 -0300 Subject: [Pw_forum] Questions about pseudopotential generation. In-Reply-To: <412439261.84871.1316643796133.JavaMail.root@mail.iq.ufrj.br> References: <1569721047.84865.1316643685777.JavaMail.root@mail.iq.ufrj.br> <412439261.84871.1316643796133.JavaMail.root@mail.iq.ufrj.br> Message-ID: Hi Daniel, Take a look at http://www.quantum-espresso.org/input-syntax/INPUT_LD1.htmland also check a very recent post ([Pw_forum] about PWscf PP generation) answered by Emine Kucukbenli in this forum. Best, -- Ary Rodrigues Ferreira Junior Universidade Federal de Juiz de Fora Departamento de Qu?mica On Wed, Sep 21, 2011 at 7:23 PM, Daniel Lima wrote: > Dear All, > > > > My name is Daniel Aguiar and I?m a begginer in "pseudopotential generation > art". > > My PhD thesis is about organic molecules solid state NMR GIPAW > calculations and in QE website gipaw pseudopotentials are limited. So, I?m > trying build my own pseudopotentials. > > I?m following the classical Silicon example ( > http://www.fisica.uniud.it/~giannozz/Corsi/MetNum/LectureNotes/metnum-ex2.pdf and > http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf) and some aspects of the > tutorials/exercises are not clear for me. > > > > 1) A typical value to logarithmic derivative is the midpoint of a typical > bonding, or the ionic/covalent radii. The chemical bonding is variable to > organic molecules, so my choice is the ionic radius of Silicon. However the > example value to rlderiv is 2.1, but the silicon is 1.11 ?. How it works? > > > > 2) How can I get a razoable value to logarithimic derivative energy > parameters ( eminld, emaxld and deld)?. In example the values are > eminld=-11.0, emaxld=2.0 and deld=0.01d0, but I think that for other atoms > these values can change for a good pseudopotential generation. > > > > 3) In last lines, there is a list of informations about the pseudization. > In this input section, I can?t understand the third column significance. > What this numbers means? > > > > 4) The matching radii for s, p and d silicon orbitals is 2.4. How can I > calculate the matching radii for other atoms? Anyone have some reference > to do this? > > > > Sorry if my question sounds stupid, > > > > Thanks in advance, > > > > -- > Daniel Lima Marques de Aguiar > Universidade Federal do Rio de Janeiro / Centro de Tecnologia > Instituto de Qu?mica > Programa de P?s Gradua??o em Qu?mica > Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 > > _______________________________________________ > 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/20110921/ecd5a4d6/attachment-0001.htm From kucukben at sissa.it Thu Sep 22 01:09:39 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 22 Sep 2011 01:09:39 +0200 Subject: [Pw_forum] Questions about pseudopotential generation. In-Reply-To: <412439261.84871.1316643796133.JavaMail.root@mail.iq.ufrj.br> References: <412439261.84871.1316643796133.JavaMail.root@mail.iq.ufrj.br> Message-ID: <20110922010939.yntpplt2ucs0gcw0@webmail.sissa.it> Dear Daniel, I think you can find the answers to your questions in the guide inside the QE distribution (new address in svn version is atomic/Doc) plus these: http://people.sissa.it/~dalcorso/lectures/lecture_pseudo_sb_2009.pdf http://www.impmc.upmc.fr/~paulatto/shanghai.pdf I am linking the PAW one (the second) in case you want to do GIPAW calculations. It is important to understand the PAW formalism before doing so. cheers, emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From roccad at gmail.com Thu Sep 22 02:13:50 2011 From: roccad at gmail.com (dario rocca) Date: Wed, 21 Sep 2011 17:13:50 -0700 Subject: [Pw_forum] FFT on a small mesh Message-ID: Dear Developers I would be interested in calculating the FFT with a small reciprocal space cutoff. Namely beyond the FFT for wavefunctions and density I would like to use an additional FFT on an "object" that requires a cutoff smaller than the wavefunctions (but of course the real space mesh would still be the same). All the standard FFT machinery seems very specialized to the wavefunction/density case, and I was wondering if there is an easy option or if someone has developed more general subroutines and is willing to share them. Thanks for your help Dario Rocca, UCDavis -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/85ec9c27/attachment.htm From giannozz at democritos.it Thu Sep 22 08:30:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Sep 2011 08:30:05 +0200 Subject: [Pw_forum] FFT on a small mesh In-Reply-To: References: Message-ID: <835C1FDE-082C-426A-A975-DC69EE4D7ECE@democritos.it> On Sep 22, 2011, at 2:13 , dario rocca wrote: > Dear Developers (reminder: the proper place where to contact developers is the q-e- developers mailing list on qe-forge.org) > I would be interested in calculating the FFT with a small > reciprocal space cutoff. > Namely beyond the FFT for wavefunctions and density I would like to > use an > additional FFT on an "object" that requires a cutoff smaller than > the wavefunctions > (but of course the real space mesh would still be the same). All > the standard > FFT machinery seems very specialized to the wavefunction/density case it is, by construction. In the most recent versions, however, the FFT stuff is encapsulated into a few "descriptors" that are initialized in a few specific routines. Note that the CP code has a third grid, the "small box" grid, a subset of the dense grid in real space.This is used to deal with augmentation charges in the USPP framework. You may want to have a look at it. I have heard of work done to speed up exact exchange and GW calculations, consisting in performing the needed FFT with a lower cutoff. Nothing has yet percolated to the current development version, though. 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 mona at suin.edu.sd Thu Sep 22 08:39:42 2011 From: mona at suin.edu.sd (Mona M.O. Elfadil) Date: Thu, 22 Sep 2011 09:39:42 +0300 Subject: [Pw_forum] cluster timing & delay -v.lousy way- In-Reply-To: <9501C7A2-BE94-45B3-8CCC-50CC782E1EA9@sissa.it> References: <9501C7A2-BE94-45B3-8CCC-50CC782E1EA9@sissa.it> Message-ID: Dear Changru, Since there are other programs included such as Yambo which are not compatible with the recent version of Q.E. , this version is used -- Your sincerely, Mona Elfadil SudREN - Network Engineer www.suin.edu.sd +249911319113 > Dear Mona Elfadil, > > Q.E.3.0 was released on 2005. I would suggest you to try the newest > version 4.3.2 first. You can find it here: > > http://www.quantum-espresso.org/download.php > > HTH, > Changru > > On 21 Sep, 2011, at 17:19, Mona M.O. Elfadil wrote: > >> Dear all, >> We had run an example -Q.E.3.0.1- from your package few days ago >> on a linux cluster- CentOS 5-, and it worked although we had no >> BLAS, LAPACK nor an FFTW packages previously installed - not >> surprising,since you have said so in your user guide-. >> Then we had tried an experimental data. It took a single CPU 10 min to >> get >> the results. While, unfortunately, it took a 16 CPUs more than 40 min to >> process the same data. >> We had tried the following: >> - Referring to your user guide: It needs a detailed physics background >> which is unavailable at the moment. >> - Downloading these mathematical packages: >> FFTW 3.1.2-3 & FFTW 2.1.5-2 >> LAPACK 3_0-2 >> BLAS 3_0-2 >> (RPM versions) >> In the configuration phase of Q.E. it said that both LAPACK and FFTW are >> not found although BLASS was successfully configured. >> >> We could not find FFTWND in our internet search(As a packet). But in >> your >> archive you have said it is not an error. >> >> Assuming that all other factors are well, what could be the cause?? >> >> (P.S.: we are the system administrators) >> >> -- >> Your sincerely, >> Mona Elfadil >> SudREN - Network Engineer >> www.suin.edu.sd >> +249911319113 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > _______________________________________________ > 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/20110922/3a38642e/attachment.htm From baroni at sissa.it Thu Sep 22 08:54:49 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 22 Sep 2011 08:54:49 +0200 Subject: [Pw_forum] charge density plot in xcrysden In-Reply-To: References: Message-ID: <2796E1D4-010A-4755-AC79-A40B375E0892@sissa.it> Hi! I do not know how to help you. If you do not assistance on this mailing list, you may want to try with a specific mailing list for xcrysden users, which, I am sure, must exist. Good luck - SB On Sep 21, 2011, at 11:37 PM, Tram Bui wrote: > Dear Everyone, > I have an output file of the SiC bulk charge density (bulk.xsf). I open it using xcrysden and do data grid to get the display of color-plane and isoline, etc. I'd also like to make the isoline with different color other than just the gray scale, how can I do so in xcrysden? > > Regards, > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110922/6aecad08/attachment.htm From baroni at sissa.it Thu Sep 22 08:57:02 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 22 Sep 2011 08:57:02 +0200 Subject: [Pw_forum] FFT on a small mesh In-Reply-To: References: Message-ID: <14D6FF6A-7503-4E8C-AA53-95F5609056E8@sissa.it> I know that Paolo Umari has already implemented this feature in "his" GW codes, and possibly in pw.x as well. Don't know, though, if in his private version or in the svn one. PAOLO: any hints? Stefano B On Sep 22, 2011, at 2:13 AM, dario rocca wrote: > Dear Developers > I would be interested in calculating the FFT with a small reciprocal > space cutoff. Namely beyond the FFT for wavefunctions > and density I would like to use an additional FFT on an "object" that requires a cutoff smaller than the > wavefunctions (but of course the real space mesh would still be the same). All the standard > FFT machinery seems very specialized to the > wavefunction/density case, and I was wondering if there is an easy option or if someone > has developed more general subroutines and is willing to share them. > Thanks for your help > Dario Rocca, UCDavis > _______________________________________________ > 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/20110922/3cae09dc/attachment-0001.htm From flux_ray12 at 163.com Thu Sep 22 10:20:11 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 22 Sep 2011 16:20:11 +0800 (CST) Subject: [Pw_forum] cluster timing & delay -v.lousy way- In-Reply-To: References: <9501C7A2-BE94-45B3-8CCC-50CC782E1EA9@sissa.it> Message-ID: <6c763a0c.febb.13290387422.Coremail.flux_ray12@163.com> Yambo can be easily compiled with QE-4.x in Debian-based system, but with a makefile problem in RedHat-based system (lack of seperator '\'). However, you can compile it seperately, i.e., download Yambo-code fromhttp://www.yambo-code.org/ and compile. Actually, I reported this problem in Yambo's forum half year before~ http://www.yambo-code.org/forum/viewtopic.php?f=1&t=300 -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-22 14:39:42,"Mona M.O. Elfadil" wrote: Dear Changru, Since there are other programs included such as Yambo which are not compatible with the recent version of Q.E. , this version is used -- Your sincerely, Mona Elfadil SudREN - Network Engineer www.suin.edu.sd +249911319113 > Dear Mona Elfadil, > > Q.E.3.0 was released on 2005. I would suggest you to try the newest > version 4.3.2 first. You can find it here: > > http://www.quantum-espresso.org/download.php > > HTH, > Changru > > On 21 Sep, 2011, at 17:19, Mona M.O. Elfadil wrote: > >> Dear all, >> We had run an example -Q.E.3.0.1- from your package few days ago >> on a linux cluster- CentOS 5-, and it worked although we had no >> BLAS, LAPACK nor an FFTW packages previously installed - not >> surprising,since you have said so in your user guide-. >> Then we had tried an experimental data. It took a single CPU 10 min to >> get >> the results. While, unfortunately, it took a 16 CPUs more than 40 min to >> process the same data. >> We had tried the following: >> - Referring to your user guide: It needs a detailed physics background >> which is unavailable at the moment. >> - Downloading these mathematical packages: >> FFTW 3.1.2-3 & FFTW 2.1.5-2 >> LAPACK 3_0-2 >> BLAS 3_0-2 >> (RPM versions) >> In the configuration phase of Q.E. it said that both LAPACK and FFTW are >> not found although BLASS was successfully configured. >> >> We could not find FFTWND in our internet search(As a packet). But in >> your >> archive you have said it is not an error. >> >> Assuming that all other factors are well, what could be the cause?? >> >> (P.S.: we are the system administrators) >> >> -- >> Your sincerely, >> Mona Elfadil >> SudREN - Network Engineer >> www.suin.edu.sd >> +249911319113 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >>Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email:crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > _______________________________________________ > 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/20110922/4604d3c6/attachment.htm From helen at fh.huji.ac.il Thu Sep 22 10:29:49 2011 From: helen at fh.huji.ac.il (helen at fh.huji.ac.il) Date: Thu, 22 Sep 2011 11:29:49 +0300 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe: to Pengju Ren Message-ID: <20110922112949.93621vlzbbw65ick@webmail.huji.ac.il> Dear Pengju Ren, Thank you very much for your reply. I've tried using fhi2upf.f90 in the upftools directory to covert the .fhi file I downloaded from the abinit site. My problem is that it asks me for the label and occupancy of the wavefunctions, and I don't know what was used to generate the fhi file on the abinit site. There appear to be 4 wavefunctions in this file so I tried guessing that they were 3s,3p,3d and 4s, as these are the obvious choices. However the generated UPF file then lists: Generated using Fritz-Haber code Author: unknown Generation date: as well iron, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder Perdew/Wang (1992), l 1 The Pseudo was generated with a Scalar-Relativistic Calculation nl pn l occ Rcut Rcut US E pseu 3s 0 0 2.00 0.00000000000 0.00000000000 0.00000000000 3p 0 1 6.00 0.00000000000 0.00000000000 0.00000000000 3d 0 2 6.00 0.00000000000 0.00000000000 0.00000000000 4s 0 3 2.00 0.00000000000 0.00000000000 0.00000000000 and the angular momentum values do not make sense This is the info given in the fhi file: iron, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder Perdew/Wang (1992), l= 1 local 26.000 8.000 011001 zatom,zion,pspdat 6 7 3 1 521 0 pspcod,pspxc,lmax,lloc,mmax,r2well 0.000 0.000 0.000 rchrg, fchrg, qchrg 5--- These two lines are available for giving more information, later 6 7-Here follows the cpi file from the fhi98pp code- 8.00000E+00 4 I would be very grateful for any help with this, Dr.Helen Eisenberg, Post-doc, Fritz-Haber Research Center, Hebrew University, Jerusalem Dear Helen If you have a abinit format PP, you can convert it to pwscf format by the tools fhi2upf in upftools/ directory. I suggest you read http://www.quantum-espresso.org/pseudo-notes.php for more information. Good luck! Pengju Ren ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From giannozz at democritos.it Thu Sep 22 14:06:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Sep 2011 14:06:03 +0200 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe: to Pengju Ren In-Reply-To: <20110922112949.93621vlzbbw65ick@webmail.huji.ac.il> References: <20110922112949.93621vlzbbw65ick@webmail.huji.ac.il> Message-ID: <1316693163.12553.14.camel@fe12lx.fisica.uniud.it> On Thu, 2011-09-22 at 11:29 +0300, helen at fh.huji.ac.il wrote: > My problem is that it asks me for the label and occupancy of the > wavefunctions, and I don't know what was used to generate the > fhi file on the abinit site. guess something sensible, then verify if it works. The wavefunction label is used only for the printout of projected dos. The l value is used, but I think that the code always assume s-p-d-f ordering. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From eariel99 at gmail.com Thu Sep 22 14:38:15 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 22 Sep 2011 14:38:15 +0200 Subject: [Pw_forum] epsilon.x and scissor shift renormalization of momentum operator Message-ID: Hi all, Recently a reviewer has warned me about a problem of the dielectric function calculation that I performed using the epsilon code, where I applied the scissor shift (option shift in the input) to correct the infamous gap problem. Following the referee's criticism I got to an article by Rodolfo del Sole and Rafaello Girlanda, PRB 48, 11780 (1993), when a scissor shift is applied to correct the LDA underestimation of the transition energies, the momentum matrix elements must be multiplied by (Ec-Ev)/(Ec0-Ev0), (see unnumbered equation after Eq. (15) in the cited paper) , where Ec0-Ev0 is the LDA transition energy and Ec-Ev=Ec0-Ev0 +\Delta ( \Delta is the scissor shift). Equivalently, one can replace the \omega^2 in the denominator by (\omega-\Delta/\hbar)^2 (Eq. 17 and 19 of the above article) . As shown by del Sole and Girlanda (and repeated many times in the literature) this is a simple approximation for the fact that "exact" transition energies Ec-Ev arise from non-local self-energy (e.g. from GW) and for non-local one electron hamiltonians the interaction with an electromagnetivc wabe is not longer A.p. It is very easy to set this correction in the code epsilon.x, for example , in subroutine eps_calc one can change etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift ....... epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2) * intersmear * w* & RYTOEV**3 * (focc(iband1,ik))/ & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2) * RYTOEV**3 * & (focc(iband1,ik)) * & (etrans**2 - w**2 ) / & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) by the following etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift shift_renorm = ( etrans/(etrans-shift) )**2 epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2) *shift_renorm* intersmear * w* & RYTOEV**3 * (focc(iband1,ik))/ & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2) *shift_renorm* RYTOEV**3 * & (focc(iband1,ik)) * & (etrans**2 - w**2 ) / & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) and similarly in a few other parts of the code. This is equivalent to replace epsilon_2(omega) by epsilon2(omega- shift/hbar) , at least for small broadening parameter so that the "delta function" is sharp , and it corrects automatically the real part of the dielectric function. This is valid for LDA, and in principle not valid for GGA, although I suspect that in practice gives the same results. In fact I would appreciate a feedback to this comment. Best regards -- 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). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/1201fad8/attachment.htm From neto.baldini at gmail.com Thu Sep 22 14:40:01 2011 From: neto.baldini at gmail.com (Ettore Baldini-Neto) Date: Thu, 22 Sep 2011 09:40:01 -0300 Subject: [Pw_forum] NEB procedure Message-ID: Dear users, I have some questions regarding a NEB calculation. As input to a neb file I should use, at least, the initial and final positions (both well previously relaxed). What I want is to calculated the energy barrier for the transition of a metal from one stable position (let's say a hollow position on a C ring) to another one (also stable but with slightly higher total energy than first, let's say the Top position). When I use just the initial and final positions and perform the calculations, asking the code to automatically divide the grid, I get an ascendent curve form the first to the last as expected. But at a position just before the Top position I also expect the energy barrier to be a little higher than the energy at this final site (Top) because the metal is at a unstable position. So here are is my question, a very basic one since I have no previous experience with this kind of calculation. I can put more intermediate images, automatically or by hand, in order to better mapping the region around this position (Top). In the second case, should these intermediate images be previously optimized or the neb does it for me?? Thanks in advance, *************************************************************************************** Ettore Baldini-Neto Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil *************************************************************************************** From lmartinsamos at gmail.com Thu Sep 22 14:46:55 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Thu, 22 Sep 2011 14:46:55 +0200 Subject: [Pw_forum] NEB procedure In-Reply-To: References: Message-ID: Dear Ettore, you can put more intermediate images by hand and the NEB algorythm will "relax" then for you. I put relax within "" because neb relaxes along the perpendicular directions of the chain. best regards Layla 2011/9/22 Ettore Baldini-Neto > Dear users, > > I have some questions regarding a NEB calculation. > > As input to a neb file I should use, at least, the initial and final > positions (both well previously relaxed). > What I want is to calculated the energy barrier for the transition of a > metal from one stable position (let's say a hollow position on a C ring) to > another one (also stable but with slightly higher total energy than first, > let's say the Top position). > > When I use just the initial and final positions and perform the > calculations, asking the code to automatically divide the grid, I get an > ascendent curve form the first to the last as expected. > But at a position just before the Top position I also expect the energy > barrier to be a little higher than the energy at this final site (Top) > because the metal is at a unstable position. > > So here are is my question, a very basic one since I have no previous > experience with this kind of calculation. > > I can put more intermediate images, automatically or by hand, in order to > better mapping the region around this position (Top). > In the second case, should these intermediate images be previously > optimized or the neb does it for me?? > > Thanks in advance, > > > > *************************************************************************************** > Ettore Baldini-Neto > Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil > > *************************************************************************************** > _______________________________________________ > 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/20110922/e7bf1c0d/attachment.htm From neto.baldini at gmail.com Thu Sep 22 14:49:07 2011 From: neto.baldini at gmail.com (Ettore Baldini-Neto) Date: Thu, 22 Sep 2011 09:49:07 -0300 Subject: [Pw_forum] NEB procedure In-Reply-To: References: Message-ID: <1FF59654-F1B3-4807-9B73-B9D3450B088D@gmail.com> Thanks Layla, Bests Ettore On Sep 22, 2011, at 9:46 AM, Layla Martin-Samos wrote: > Dear Ettore, you can put more intermediate images by hand and the NEB algorythm will "relax" then for you. I put relax within "" because neb relaxes along the perpendicular directions of the chain. > > best regards > > Layla > > 2011/9/22 Ettore Baldini-Neto > Dear users, > > I have some questions regarding a NEB calculation. > > As input to a neb file I should use, at least, the initial and final positions (both well previously relaxed). > What I want is to calculated the energy barrier for the transition of a metal from one stable position (let's say a hollow position on a C ring) to another one (also stable but with slightly higher total energy than first, let's say the Top position). > > When I use just the initial and final positions and perform the calculations, asking the code to automatically divide the grid, I get an ascendent curve form the first to the last as expected. > But at a position just before the Top position I also expect the energy barrier to be a little higher than the energy at this final site (Top) because the metal is at a unstable position. > > So here are is my question, a very basic one since I have no previous experience with this kind of calculation. > > I can put more intermediate images, automatically or by hand, in order to better mapping the region around this position (Top). > In the second case, should these intermediate images be previously optimized or the neb does it for me?? > > Thanks in advance, > > > *************************************************************************************** > Ettore Baldini-Neto > Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil > *************************************************************************************** > _______________________________________________ > 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/20110922/672c2137/attachment.htm From helen at fh.huji.ac.il Thu Sep 22 16:53:09 2011 From: helen at fh.huji.ac.il (helen at fh.huji.ac.il) Date: Thu, 22 Sep 2011 17:53:09 +0300 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe Message-ID: <20110922175309.14974atuytx1mv40@webmail.huji.ac.il> Thank you for your help. My problem is the fhi2upf code doesn't include values for principle number and assumes a s-p-d-f ordering, which doesn't make sense for Fe which doesn't have any occupied f orbitals. DO i=1, nwfs PRINT '("Wavefunction # ",i1,": label, occupancy > ",$)', i READ (5,*) els(i), oc(i) nns (i) = 0 lchi(i) = i-1 rcut(i) = 0.0d0 rcutus(i)= 0.0d0 epseu(i) = 0.0d0 ENDDO Could they have used 3s3p3d3f and ignored 4s completely in the fhi file? Is this the way the fhi2upf code is written because that is how fhi files are organized (only s-p-d-f ordering)? Or should I manually change the UPF file afterwards to have a more likely 3s3p3d4s ordering? Thank you again, Helen Dr. Helen Eisenberg Fritz-Haber, Hebrew University, Israel On Thu, 2011-09-22 at 11:29 +0300, helen at fh.huji.ac.il wrote: My problem is that it asks me for the label and occupancy of the wavefunctions, and I don't know what was used to generate the fhi file on the abinit site. guess something sensible, then verify if it works. The wavefunction label is used only for the printout of projected dos. The l value is used, but I think that the code always assume s-p-d-f ordering. P. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From luleon13 at gmail.com Thu Sep 22 19:13:19 2011 From: luleon13 at gmail.com (Luis Antonio Leon Martinez) Date: Thu, 22 Sep 2011 12:13:19 -0500 Subject: [Pw_forum] from cp_read_cell : error # 2 Message-ID: Dear users. I have problems when I try to run cp calculations on Quantum Espresso 4.3. Below show the input and output files: Input # Ions + Cell + Electronic dynamics &CONTROL title = ' Silicon ', calculation = 'vc-cp', restart_mode = 'restart', ndr = 52, ndw = 52, nstep = 500, iprint = 10, isave = 100, tstress = .TRUE., tprnfor = .TRUE., dt = 8.0d0, etot_conv_thr = 1.d-9, ekin_conv_thr = 1.d-4, prefix = 'si' pseudo_dir = './' outdir = './' / &SYSTEM ibrav = 14, celldm(1) = 10.2, celldm(2) = 1.0, celldm(3) = 1.0, celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0, nat = 8, ntyp = 1, ecutwfc = 16.0, ecfixed = 14.0, qcutz = 14.0, q2sigma = 2.0 / &ELECTRONS emass = 400.d0, emass_cutoff = 1.0d0, orthogonalization = 'ortho', electron_dynamics = 'verlet', electron_damping = 0.1, ! electron_velocities = 'zero', electron_temperature = 'not_controlled', / &IONS ion_dynamics = 'verlet', ! ion_velocities = 'zero', ion_temperature = 'not_controlled', / &CELL cell_dynamics = 'pr', ! cell_velocities = 'zero', press = 0.0d0, wmass = 70000.0 / ATOMIC_SPECIES Si 28.0d0 Si.pz-vbc.UPF ATOMIC_POSITIONS (crystal) Si 0.0000 0.0000 0.0000 1 1 1 Si 0.5000 0.5000 0.0000 1 1 1 Si 0.0000 0.5000 0.5000 1 1 1 Si 0.5000 0.0000 0.5000 1 1 1 Si 0.2500 0.2500 0.2500 1 1 1 Si 0.7500 0.7500 0.2500 1 1 1 Si 0.2500 0.7500 0.7500 1 1 1 Si 0.7500 0.2500 0.7500 1 1 1 Output Program CP v.4.3 starts on 22Sep2011 at 12: 4:24 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 Waiting for input... Job Title: Silicon Atomic Pseudopotentials Parameters ---------------------------------- Reading pseudopotential for specie # 1 from file : ./Si.pz-vbc.UPF file type is 20: UPF Main Simulation Parameters (from input) --------------------------------------- Restart Mode = 1 restart Number of MD Steps = 500 Print out every 10 MD Steps Reads from unit = 52 Writes to unit = 52 MD Simulation time step = 8.00 Electronic fictitious mass (emass) = 400.00 emass cut-off = 1.00 Simulation Cell Parameters (from input) external pressure = 0.00 [KBar] wmass (read from input) = 70000.00 [AU] ibrav = 14 alat = 10.20000000 a1 = 10.20000000 0.00000000 0.00000000 a2 = 0.00000000 10.20000000 0.00000000 a3 = 0.00000000 0.00000000 10.20000000 b1 = 0.09803922 0.00000000 0.00000000 b2 = 0.00000000 0.09803922 0.00000000 b3 = 0.00000000 0.00000000 0.09803922 omega = 1061.20800000 Energy Cut-offs --------------- Ecutwfc = 16.0 Ry, Ecutrho = 64.0 Ry, Ecuts = 64.0 Ry Gcutwfc = 6.5 , Gcutrho = 13.0 Gcuts = 13.0 modified kinetic energy functional, with parameters: ecutz = 14.0000 ecsig = 2.0000 ecfix = 14.00 NOTA BENE: refg, mmx = 0.050000 2560 Eigenvalues calculated without the kinetic term contribution Orthog. with lagrange multipliers : eps = 0.10E-07, max = 20 Electron dynamics with newton equations Electron dynamics : the temperature is not controlled Electronic states ----------------- Number of Electron = 32, of States = 16 Occupation numbers : 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 Exchange and correlations functionals ------------------------------------- Using Local Density Approximation with Exchange functional: SLATER Correlation functional: PERDEW AND ZUNGER Exchange-correlation = SLA PZ NOGX NOGC (1100) EXX-fraction = 0.00 Ions Simulation Parameters -------------------------- Ions are allowed to move Ions dynamics with newton equations the temperature is computed for 24 degrees of freedom ion dynamics with fricp = 0.0000 and greasp = 1.0000 Ionic position (from input) sorted by specie, and converted to real a.u. coordinates Species 1 atoms = 8 mass = 51040.88 (a.u.), 28.00 (amu) rcmax = 0.50 (a.u.) 0.000000 0.000000 0.000000 5.100000 5.100000 0.000000 0.000000 5.100000 5.100000 5.100000 0.000000 5.100000 2.550000 2.550000 2.550000 7.650000 7.650000 2.550000 2.550000 7.650000 7.650000 7.650000 2.550000 7.650000 Ionic position will be re-read from restart file All atoms are allowed to move Ionic temperature is not controlled Cell Dynamics Parameters (from STDIN) ------------------------------------- internal stress tensor calculated Starting cell generated from CELLDM Cell parameters will be re-read from restart file Volume dynamics with newton equations Volume dynamics: the temperature is not controlled Constant PRESSURE Molecular dynamics: External pressure (GPa) = 0.00 Volume mass = 70000.00 Verbosity: iprsta = 1 Simulation dimensions initialization ------------------------------------ unit vectors of full simulation cell in real space: in reciprocal space (units 2pi/alat): 1 10.2000 0.0000 0.0000 1.0000 0.0000 0.0000 2 0.0000 10.2000 0.0000 0.0000 1.0000 0.0000 3 0.0000 0.0000 10.2000 0.0000 0.0000 1.0000 Stick Mesh ---------- nst = 259, nstw = 69, nsts = 259 n.st n.stw n.sts n.g n.gw n.gs min 517 137 517 9093 1189 9093 max 517 137 517 9093 1189 9093 517 137 517 9093 1189 9093 Real Mesh --------- Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 25 25 25 25 25 25 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 25 25 25 Local number of cell to store the grid ( nrxx ) = 15625 Number of x-y planes for each processors: nr3l = 25 Smooth Real Mesh ---------------- Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 25 25 25 25 25 25 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 25 25 25 Local number of cell to store the grid ( nrxx ) = 15625 Number of x-y planes for each processors: nr3sl = 25 Reciprocal Space Mesh --------------------- Large Mesh Global(ngm_g) MinLocal MaxLocal Average 4547 4547 4547 4547.00 Smooth Mesh Global(ngms_g) MinLocal MaxLocal Average 4547 4547 4547 4547.00 Wave function Mesh Global(ngw_g) MinLocal MaxLocal Average 595 595 595 595.00 System geometry initialization ------------------------------ Scaled positions from standard input Si 0.000000E+00 0.000000E+00 0.000000E+00 Si 0.500000E+00 0.500000E+00 0.000000E+00 Si 0.000000E+00 0.500000E+00 0.500000E+00 Si 0.500000E+00 0.000000E+00 0.500000E+00 Si 0.250000E+00 0.250000E+00 0.250000E+00 Si 0.750000E+00 0.750000E+00 0.250000E+00 Si 0.250000E+00 0.750000E+00 0.750000E+00 Si 0.750000E+00 0.250000E+00 0.750000E+00 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cp_read_cell : error # 2 cannot open restart file for reading: .//si_52.save/data-file.xml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... STOP 2 Now, I want to know if you you have a list of errors showed in this program, for instance, error # 1, error # 2, and so on. This is an example proposed in a tutorial. What can I do? Thanks for your colaboration. Luis A. Leon. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/b40d02cf/attachment-0001.htm From tone.kokalj at ijs.si Thu Sep 22 19:16:11 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 22 Sep 2011 19:16:11 +0200 Subject: [Pw_forum] NEB procedure In-Reply-To: References: Message-ID: <1316711771.3150.23.camel@catalyst.ijs.si> Dear Ettore, putting intermediate images will not help to locate the presumable maximum in your case. (increasing the num_of_images may help though, but even that can be insufficient if transition state is very close to final state) Intermediate images are used to do a better initial guess of the reaction path. Intermediate images are not really used, but all the input images (initial+intermediates+final) are connected so as to produce a piecewise-linear path and then the EQUIDISTANT linear interpolation is performed on this piecewise-linear path. In your case you should set the CI_scheme = 'manual' and specify as the climbing image the last image before the final image in the CLIMBING_IMAGES card, i.e.: &PATH num_of_images = N CI_scheme = 'manual' ... / CLIMBING_IMAGES N-1 By doing that the N-1'th image will climb up to the transition state (TS) by the CI-NEB scheme, provided the TS is indeed there before the top site. Best regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From neto.baldini at gmail.com Thu Sep 22 19:25:55 2011 From: neto.baldini at gmail.com (Ettore Baldini-Neto) Date: Thu, 22 Sep 2011 14:25:55 -0300 Subject: [Pw_forum] NEB procedure In-Reply-To: <1316711771.3150.23.camel@catalyst.ijs.si> References: <1316711771.3150.23.camel@catalyst.ijs.si> Message-ID: <46CC6237-8D82-459A-B886-543EF8431F69@gmail.com> Thanks a lot Anton, Best regards, Ettore On Sep 22, 2011, at 2:16 PM, Tone Kokalj wrote: > Dear Ettore, > > putting intermediate images will not help to locate the presumable > maximum in your case. > > (increasing the num_of_images may help though, but even that can be > insufficient if transition state is very close to final state) > > > Intermediate images are used to do a better initial guess of the > reaction path. Intermediate images are not really used, but all the > input images (initial+intermediates+final) are connected so as to > produce a piecewise-linear path and then the EQUIDISTANT linear > interpolation is performed on this piecewise-linear path. > > In your case you should set the CI_scheme = 'manual' > and specify as the climbing image the last image before the final image > in the CLIMBING_IMAGES card, i.e.: > > &PATH > num_of_images = N > CI_scheme = 'manual' > ... > / > > CLIMBING_IMAGES > N-1 > > By doing that the N-1'th image will climb up to the transition state > (TS) by the CI-NEB scheme, provided the TS is indeed there before the > top site. > > Best regards, > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Sep 22 19:25:43 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Sep 2011 19:25:43 +0200 Subject: [Pw_forum] from cp_read_cell : error # 2 In-Reply-To: References: Message-ID: <12843FC3-0BA6-47CD-B9EF-BA4CC4B8A90F@democritos.it> On Sep 22, 2011, at 19:13 , Luis Antonio Leon Martinez wrote: > cannot open restart file for reading: .//si_52.save/data-file.xml did you run with "restart_mode='from_scratch" first? 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 tone.kokalj at ijs.si Thu Sep 22 19:27:20 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 22 Sep 2011 19:27:20 +0200 Subject: [Pw_forum] charge density plot in xcrysden In-Reply-To: References: Message-ID: <1316712441.3150.31.camel@catalyst.ijs.si> On Wed, 2011-09-21 at 15:37 -0600, Tram Bui wrote: > Dear Everyone, > I have an output file of the SiC bulk charge density (bulk.xsf). I > open it using xcrysden and do data grid to get the display of > color-plane and isoline, etc. I'd also like to make the isoline with > different color other than just the gray scale, how can I do so in > xcrysden? Dear Tram, Here you will find the information you need: http://www.xcrysden.org/doc/plane1control.html Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bdslipun at gmail.com Thu Sep 22 19:30:43 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 22 Sep 2011 23:00:43 +0530 Subject: [Pw_forum] stable phase Message-ID: i am calulated b1 to b2 transition of some metal carbide i found b1 to b2 transition at 140 gpa from phonon dispersion i found dyanamical unstabilty at 140 gpa b1 phase but i am also found b2 is dyanamical unstable(in X and M) directions so i thought there must be other phase which may be stable at 140 gpa for this calculated L10 phase which will less enthalpy than b2 at 140 gpa but also this shows imaginary frequency in X direction so what is the stable phase? b d sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/f727dc07/attachment.htm From giannozz at democritos.it Thu Sep 22 19:32:08 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Sep 2011 19:32:08 +0200 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe In-Reply-To: <20110922175309.14974atuytx1mv40@webmail.huji.ac.il> References: <20110922175309.14974atuytx1mv40@webmail.huji.ac.il> Message-ID: <43BFBDAF-A05D-43D1-BE0A-59660215E521@democritos.it> On Sep 22, 2011, at 16:53 , helen at fh.huji.ac.il wrote: > My problem is the fhi2upf code doesn't include values for principle > number and assumes a s-p-d-f ordering, which doesn't make sense > for Fe which doesn't have any occupied f orbitals. I wouldn't be so sure that it doesn't make sense. A PP for Fe could have been generated using 4s2 4p0 3d6 4f0 states. > Could they have used 3s3p3d3f and ignored 4s completely in the fhi > file? 3f, unlikely, but another possibility is 3s2 3p6 3d6 4f0, with no 4s and 4p states > Is this the way the fhi2upf code is written because that is how > fhi files are organized (only s-p-d-f ordering)? he who originally wrote the fhi2upf converter (not myself) had to dig into the format of the fhi file and to make some educated guess. I have no evidence until now that those guesses were not good. > Fritz-Haber so YOU are from FHI, you should know what is inside those files... 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 luleon13 at gmail.com Thu Sep 22 19:32:35 2011 From: luleon13 at gmail.com (Luis Antonio Leon Martinez) Date: Thu, 22 Sep 2011 12:32:35 -0500 Subject: [Pw_forum] from cp_read_cell : error # 2 In-Reply-To: <12843FC3-0BA6-47CD-B9EF-BA4CC4B8A90F@democritos.it> References: <12843FC3-0BA6-47CD-B9EF-BA4CC4B8A90F@democritos.it> Message-ID: Hi, no. I have tried the examples that comes with the program, and I get the same error. I have changed this order, and I get the same error. I do not know. Thanks for your collaboration. On Thu, Sep 22, 2011 at 12:25 PM, Paolo Giannozzi wrote: > > On Sep 22, 2011, at 19:13 , Luis Antonio Leon Martinez wrote: > > > cannot open restart file for reading: .//si_52.save/data-file.xml > > did you run with "restart_mode='from_scratch" first? > > 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/20110922/a9eebc18/attachment.htm From Michael.Mehl at nrl.navy.mil Thu Sep 22 19:43:28 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Thu, 22 Sep 2011 13:43:28 -0400 Subject: [Pw_forum] stable phase In-Reply-To: References: Message-ID: <4E7B73C0.2030109@nrl.navy.mil> If you found a phonon with an imaginary frequency, then you can find a supercell of the L10 structure, displace the atoms in it according to the symmetry of the phonon, and relax the structure to obtain another structure with lower energy (enthalpy if you are working at fixed pressure). Here's how I did it: Michael J. Mehl, Gus L. W. Hart and Stefano Curtarolo Density functional study of the L10??IrV transition in IrV and RhV Journal of Alloys and Compounds Volume 509, Issue 3, 21 January 2011, Pages 560-567 http://dx.doi.org/10.1016/j.jallcom.2010.08.102 Note that the instabilities we found in the IrV L10 structure will not necessarily be the same as you find in L10 M-C. On 09/22/2011 01:30 PM, bhabya sahoo wrote: > i am calulated b1 to b2 transition of some metal carbide > i found b1 to b2 transition at 140 gpa > from phonon dispersion i found dyanamical unstabilty at 140 gpa b1 phase > but i am also > found b2 is dyanamical unstable(in X and M) directions so i thought > there must be other phase which may be stable at 140 gpa > for this calculated L10 phase which will less enthalpy than b2 at 140 > gpa but also this shows imaginary frequency in X direction > so what is the stable phase? > > b d sahoo barc > mumbai > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From luleon13 at gmail.com Thu Sep 22 19:52:51 2011 From: luleon13 at gmail.com (Luis Antonio Leon Martinez) Date: Thu, 22 Sep 2011 12:52:51 -0500 Subject: [Pw_forum] Other example with cpx problem on qe-43 Message-ID: Dear users. Here I describe other example with error when I use cp.x command. Input # Electronic + Ionic Dynamic + NOSE thermostat on ions &CONTROL title = ' Water Molecule ', calculation = 'cp', ndr = 52, ndw = 52, nstep = 400, iprint = 10, isave = 100, tstress = .TRUE., tprnfor = .TRUE., dt = 4.0d0, etot_conv_thr = 1.d-9, ekin_conv_thr = 1.d-4, prefix = 'h2o_mol' pseudo_dir = './' outdir = './' / &SYSTEM ibrav = 14, celldm(1) = 10.0, celldm(2) = 1.0, celldm(3) = 1.0, celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0, nat = 3, ntyp = 2, ecutwfc = 70.0, / &ELECTRONS emass = 300.d0, emass_cutoff = 2.5d0, orthogonalization = 'ortho', electron_dynamics = 'verlet', electron_velocities = 'zero', / &IONS ion_dynamics = 'verlet', ion_temperature = 'nose', ion_velocities='zero' tempw = 43.0, fnosep = 70 / ATOMIC_SPECIES O 16.0d0 O.BLYP.UPF H 1.00d0 H.fpmd.UPF ATOMIC_POSITIONS (bohr) O 5.0099 5.0099 5.0000 0 0 0 H 6.8325 4.7757 4.9999 1 1 1 H 4.7757 6.8325 4.9998 1 1 1 Output Program CP v.4.3 starts on 22Sep2011 at 12:47: 6 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 Waiting for input... Job Title: Water Molecule Atomic Pseudopotentials Parameters ---------------------------------- Reading pseudopotential for specie # 1 from file : ./O.BLYP.UPF file type is 20: UPF Reading pseudopotential for specie # 2 from file : ./H.fpmd.UPF file type is 20: UPF Main Simulation Parameters (from input) --------------------------------------- Restart Mode = 1 restart Number of MD Steps = 400 Print out every 10 MD Steps Reads from unit = 52 Writes to unit = 52 MD Simulation time step = 4.00 Electronic fictitious mass (emass) = 300.00 emass cut-off = 2.50 Simulation Cell Parameters (from input) external pressure = 0.00 [KBar] wmass (calculated) = 2493.41 [AU] ibrav = 14 alat = 10.00000000 a1 = 10.00000000 0.00000000 0.00000000 a2 = 0.00000000 10.00000000 0.00000000 a3 = 0.00000000 0.00000000 10.00000000 b1 = 0.10000000 0.00000000 0.00000000 b2 = 0.00000000 0.10000000 0.00000000 b3 = 0.00000000 0.00000000 0.10000000 omega = 1000.00000000 Energy Cut-offs --------------- Ecutwfc = 70.0 Ry, Ecutrho = 280.0 Ry, Ecuts = 280.0 Ry Gcutwfc = 13.3 , Gcutrho = 26.6 Gcuts = 26.6 NOTA BENE: refg, mmx = 0.050000 11200 Eigenvalues calculated without the kinetic term contribution Orthog. with lagrange multipliers : eps = 0.10E-07, max = 20 Electron dynamics with newton equations Electron dynamics : the temperature is not controlled Electronic states ----------------- Number of Electron = 8, of States = 4 Occupation numbers : 2.00 2.00 2.00 2.00 Exchange and correlations functionals ------------------------------------- Using Local Density Approximation with Exchange functional: SLATER Correlation functional: LEE, YANG, AND PARR Using Generalized Gradient Corrections with Exchange functional: BECKE Correlation functional: PERDEW AND WANG Exchange-correlation = BLYP (1313) EXX-fraction = 0.00 Ions Simulation Parameters -------------------------- Ions are allowed to move Ions dynamics with newton equations the temperature is computed for 6 degrees of freedom ion dynamics with fricp = 0.0000 and greasp = 1.0000 Zero initial momentum for ions Ionic position (from input) sorted by specie, and converted to real a.u. coordinates Species 1 atoms = 1 mass = 29166.22 (a.u.), 16.00 (amu) rcmax = 0.50 (a.u.) 5.009900 5.009900 5.000000 Species 2 atoms = 2 mass = 1822.89 (a.u.), 1.00 (amu) rcmax = 0.50 (a.u.) 6.832500 4.775700 4.999900 4.775700 6.832500 4.999800 Ionic position will be re-read from restart file NOT all atoms are allowed to move indx ..x.. ..y.. ..z.. 1 F F F Ionic temperature control via nose thermostat ion dynamics with nose` temperature control: temperature required = 43.00000 (kelvin) NH chain length = 1 active degrees of freedom = 6 time steps per nose osc. = 147 nose` frequency(es) = 70.000 the requested type of NH chains is 0 total number of thermostats used 1 0 0 ionic degrees of freedom for each chain 9 nose` mass(es) for chain 1 = 14.437 atom i (in sorted order) is assigned to this thermostat : 1 1 1 Cell Dynamics Parameters (from STDIN) ------------------------------------- internal stress tensor calculated Starting cell generated from CELLDM Cell parameters will be re-read from restart file Constant VOLUME Molecular dynamics cell parameters are not allowed to move Verbosity: iprsta = 1 Simulation dimensions initialization ------------------------------------ unit vectors of full simulation cell in real space: in reciprocal space (units 2pi/alat): 1 10.0000 0.0000 0.0000 1.0000 0.0000 0.0000 2 0.0000 10.0000 0.0000 0.0000 1.0000 0.0000 3 0.0000 0.0000 10.0000 0.0000 0.0000 1.0000 Stick Mesh ---------- nst = 1117, nstw = 277, nsts = 1117 n.st n.stw n.sts n.g n.gw n.gs min 2233 553 2233 79117 9843 79117 max 2233 553 2233 79117 9843 79117 2233 553 2233 79117 9843 79117 Real Mesh --------- Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 54 54 54 54 54 54 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 54 54 54 Local number of cell to store the grid ( nrxx ) = 157464 Number of x-y planes for each processors: nr3l = 54 Smooth Real Mesh ---------------- Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 54 54 54 54 54 54 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 54 54 54 Local number of cell to store the grid ( nrxx ) = 157464 Number of x-y planes for each processors: nr3sl = 54 Reciprocal Space Mesh --------------------- Large Mesh Global(ngm_g) MinLocal MaxLocal Average 39559 39559 39559 39559.00 Smooth Mesh Global(ngms_g) MinLocal MaxLocal Average 39559 39559 39559 39559.00 Wave function Mesh Global(ngw_g) MinLocal MaxLocal Average 4922 4922 4922 4922.00 System geometry initialization ------------------------------ Scaled positions from standard input O 0.500990E+00 0.500990E+00 0.500000E+00 H 0.683250E+00 0.477570E+00 0.499990E+00 H 0.477570E+00 0.683250E+00 0.499980E+00 Position components with 0 are kept fixed ia x y z 1 0 0 0 2 1 1 1 3 1 1 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cp_read_cell : error # 1 cannot open restart file for reading: .//h2o_mol_52.save/data-file.xml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... STOP 2 Thanks for your attention. Luis A. Leon. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/24a86cfb/attachment-0001.htm From mayankaditya at gmail.com Thu Sep 22 20:03:54 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 22 Sep 2011 23:33:54 +0530 Subject: [Pw_forum] Symmetry problem in phonon Message-ID: Dear All I have done phonon calculation of a BCT system. I have chosen 2x2x2 q mesh for phonon calculation. While in real space force constant calculation (q2r.x) I am getting the waring and it says " fft-check warning: sum of imaginary terms =10-6". i ignored it and calculate the phonon frequencies. From symmetry at zone boundary along 001 all the phonon frequencies are doubly degenerate which is experimentally observed but i didn't get the degeneracy. the frequencies at 001 are differ by about 1-5 meV. kindly advice. Thanks Mayank Research student BARC mumbai From giannozz at democritos.it Thu Sep 22 20:15:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 22 Sep 2011 20:15:41 +0200 Subject: [Pw_forum] from cp_read_cell : error # 2 In-Reply-To: References: <12843FC3-0BA6-47CD-B9EF-BA4CC4B8A90F@democritos.it> Message-ID: On Sep 22, 2011, at 19:32 , Luis Antonio Leon Martinez wrote: > Hi, no then you are trying to restart from a nonexistent restart file. You need to understand how a Car-Parrinello simulation works before starting to run anything. 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 trambui at u.boisestate.edu Thu Sep 22 22:54:32 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 22 Sep 2011 14:54:32 -0600 Subject: [Pw_forum] charge density map Message-ID: Dear Everyone, I have done my charge density calculation and the contour maps for my bulk SiC. I also see the scale based on the thermometer around each atom (Si, C). But my questions is what should I focus on in order to help me understand the charge density map ? what information can I get out of the charge density contour maps? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/81987074/attachment.htm From swapnil.chandratre at gmail.com Fri Sep 23 00:31:50 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 22 Sep 2011 17:31:50 -0500 Subject: [Pw_forum] semi conducting / metallic Message-ID: Dear users, The question I have is not very technical. I just wanted put a doubt ahead. I submitted a metallic structure ( what I analyzed using bandstructures from other software) into espresso. and I did not define smearing and degauss, but I did not receive and warning or error of system is metallic. definer smearing etc. Does this mean I have analyzed the bandstructure in a wrong way when I visualized it , or it happens. Can anyone comment -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/41cd590f/attachment.htm From trambui at u.boisestate.edu Fri Sep 23 01:09:54 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 22 Sep 2011 17:09:54 -0600 Subject: [Pw_forum] band structure calculation Message-ID: Dear Everyone, I have run DOS calculation on my bulk SiC and I also wonder how to do the band structure and plot the band structure. Would you give me some information or some examples regarding generating the band structure? Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/f9ff7ce8/attachment.htm From mikeat4999 at gmail.com Fri Sep 23 07:39:24 2011 From: mikeat4999 at gmail.com (mike at.) Date: Fri, 23 Sep 2011 08:39:24 +0300 Subject: [Pw_forum] band structure calculation In-Reply-To: References: Message-ID: Bui, Have you taken a look at at example01, example13 and example22 in your espresso$VER/examples directory? also, Look at Thursday, 22 July in this page: http://users.aims.ac.za/~sandro/ On Fri, Sep 23, 2011 at 2:09 AM, Tram Bui wrote: > Dear Everyone, > I have run DOS calculation on my bulk SiC and I also wonder how to do > the band structure and plot the band structure. Would you give me some > information or some examples regarding generating the band structure? > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- M. O. ATAMBO mikeat4999 at gmail.com M Phil. student, computational material science group Chepkoilel university college, Department of Physics, Eldoret, Kenya, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110923/3d776daf/attachment.htm From flux_ray12 at 163.com Fri Sep 23 08:44:45 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 23 Sep 2011 14:44:45 +0800 (CST) Subject: [Pw_forum] Does VCA method give positive formation energy? Message-ID: <371e8666.a1f9.13295077220.Coremail.flux_ray12@163.com> Dear QE developers and users: Hi. I am using Quantum-ESPRESSO v4.2.1 to deal with DFPT and QHA. Because of the computational limitation of my PC, I chose VCA method to compare the phonon dispersion and thermo-properties change as a function of compositions. The system I calculated was ZrC-ZrN. Since based on our experiments, we have known that the Zr(CN) solid-solution is possible to produce. PW91 xc-functional has been selected at 13x13x13 k-points mesh with ecutwfc=40Ry and ecutrho=400Ry. The q-mesh was 4x4x4. Structure of ZrC, ZrN and Zr(CN) is Fm-3m (NaCl Structure). The Vanderbilt ultrasoft pseudo-potential of C and N were combined by virtual.x in certain ratio. However, I found the formation energy: Ff[T, Zr(CNx)] = F[T, Zr(CNx)] - (1-x) * F[T, ZrC] - x * F[T, ZrN] was always positive number. Then, I checked ZrC, ZrN and Zr(CN0.5) carefully by both of 'vc-relax' and E-V curve for total energy calculation. Finally, I found thatE[Zr(CN0.5)] - 0.5 * E[ZrC] - 0.5 * E[ZrN] was about +0.4Ry/cell, that means+525.088kJ/mol. According to thermodynamics principle, Zr(CN0.5) cannot be prepared. However, when I tried supercell-doping method, the formation energy was negative ( about-10kJ/mol ). Therefore, I want to know why VCA method gives positive formation energy. Is it reasonable? If it should be like this, then can we believe the phonon result from VCA as reliable one? Any suggestion will be welcomed. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110923/b7d640da/attachment.htm From helen at fh.huji.ac.il Fri Sep 23 09:15:55 2011 From: helen at fh.huji.ac.il (helen at fh.huji.ac.il) Date: Fri, 23 Sep 2011 10:15:55 +0300 Subject: [Pw_forum] LDA norm-conserving pseudopotential for Fe Message-ID: <20110923101555.54152hhgfv332neo@webmail.huji.ac.il> Thanks so much for your help. I'll try some of these possibilities. > so YOU are from FHI, you should know what is inside those files... I'm from the Fritz-Haber Center for Molecular Research at the Hebrew University....not the same Fritz Haber Institute :) Helen ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From songsong19840614 at gmail.com Fri Sep 23 13:48:47 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 23 Sep 2011 19:48:47 +0800 Subject: [Pw_forum] Xe pseudopotentials In-Reply-To: References: Message-ID: I just converted the pseudopotential of fhi of Zn and O.For O atom,I try this way: 2s 2 2p 4 3s 0 3p 0 For Xe atom, I think you can try 5s 2 5p 6 5d 0 5f 0 Best Regards Yun Song,Kang Physics Department of Inner Mongolia University P.R.China 2011/9/21 Chen, Zhifan > Hi all, > I am looking for Xe ultrasoft pseudopotential with 4d,5s,5p as > valence electrons. I can > Use ABINIT fhi pseudopotential and make conversion from fhi format to > USP. However, Xe NC pseudopotential has only 5s, 5p as valence electron. > I am new to the generate pseudopotential > . Any information is welcome. > > Thanks > > Zhifan Chen > Clark Atlanta University > USA > _______________________________________________ > 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/20110923/edd4556a/attachment.htm From parishok at gmail.com Fri Sep 23 19:51:59 2011 From: parishok at gmail.com (pari shok) Date: Fri, 23 Sep 2011 13:51:59 -0400 Subject: [Pw_forum] LDOS on parallel planes Message-ID: Dear All, It is embarrassing for me to say that although I've read almost all emails in QE Archive on finding the local density of states on parallel planes of structures, I couldn't find a way to calculate them from your kind guidance. As far as I found, QE calculates the integrated local density of states in different energies (with post processing code). In ILDOS input file, it is possible to define different planes by ei(i), i=1,2,3. I was wondering whether by changing x0(i), i=1,2,3 (origin of the those planes defined by ei(i)), it would be possible to get the LODS on parallel planes. If positive, how can I possibly change x0(i) to get LDOS on parallel planes. Otherwise, if there is a way to find LDOS on parallel planes. I deeply appreciate your help. Yours P Shokri graduate student UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110923/6021a179/attachment.htm From mehrnooshhazrati at gmail.com Fri Sep 23 21:39:41 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Fri, 23 Sep 2011 23:09:41 +0330 Subject: [Pw_forum] a request Message-ID: Hi dear users, I need a paper but i don't have access to that. I'll be thankful, if some one sent it to me ! *Acta Cryst.* (1952). *5*, 356-361 LINK : [ doi:10.1107/S0365110X52001064 ] An X-ray study of boron nitrideR. S. Pease Thank you :) -- *""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""* **** Mehrnoosh Kh. Hazrati **** **** Master Student of Computational Physical Chemistry,KNTU,Tehran **** *** Phone : +989123436300 *** *** Mail : mehrnooshhazrati at gmail.com *** *"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110923/7c8de68c/attachment.htm From windbellklbh at gmail.com Sat Sep 24 11:45:49 2011 From: windbellklbh at gmail.com (WF) Date: Sat, 24 Sep 2011 17:45:49 +0800 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with PDOS Message-ID: <003d01cc7a9e$c050bd40$40f237c0$@gmail.com> Hello everyone, I recently do a vc-relax calculation of Ru metal of PBE norm-conserving PP. The PP input is like this, which is slightly modified from that in atomic_doc: -------------------------------------------------------------- &input title='Ru', zed=44.0, rel=1, config='[Kr] 4d6.0 5s2.0 5p0', iswitch=3, dft='pbe' / &inputp pseudotype=2, file_pseudopw='Ru.pbe-rrkjnc.UPF', author='TM', lloc=0, nlcc=.true., rcore = 0.9, / 3 5P 2 1 0.00 -0.099963 2.40 2.40 0.0 4D 3 2 6.00 0.00 1.90 2.40 0.0 5S 1 0 2.00 0.00 2.30 2.40 0.0 -------------------------------------------------------------------------- If the 5P energy is set to 0.00 ( which means energy of all-electron calculation ), the a axis of result is identical to that when the energy is set to -0.09963 ( the all electron result copied from ld1.x output ). However, in .UPF file, 2 wavefunctions and 3 projectors are generated if the energy is 0.00, all of 4D, 5S and 5P will appear in PDOS ( by projwfc.x ), but only 2 projectors are obtained otherwise and 5P will not appear in further PDOS calculation. I don't know how to make PDOS of all of 4D, 5S and 5P if the energy is not 0.00. Can anyone give some advices ? Thanks. Best regards, Wu F ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- From flux_ray12 at 163.com Sat Sep 24 13:56:20 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 24 Sep 2011 19:56:20 +0800 (CST) Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with PDOS In-Reply-To: <003d01cc7a9e$c050bd40$40f237c0$@gmail.com> References: <003d01cc7a9e$c050bd40$40f237c0$@gmail.com> Message-ID: <29026e9f.15611.1329b4b1211.Coremail.flux_ray12@163.com> Even though I cannot give you any suggestion to generate a better NCPP for Ru, you can try to convert a fhi NCPP to UPF by upftools/fhi2upf.x. Here: http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html#Ru3, you can find both of the fhi file and parameters. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-24 17:45:49,WF wrote: >Hello everyone, > I recently do a vc-relax calculation of Ru metal of PBE >norm-conserving PP. > >The PP input is like this, which is slightly modified from that in >atomic_doc: >-------------------------------------------------------------- >&input > title='Ru', > zed=44.0, > rel=1, > config='[Kr] 4d6.0 5s2.0 5p0', > iswitch=3, > dft='pbe' > / > &inputp > pseudotype=2, > file_pseudopw='Ru.pbe-rrkjnc.UPF', > author='TM', > lloc=0, > nlcc=.true., > rcore = 0.9, > / >3 >5P 2 1 0.00 -0.099963 2.40 2.40 0.0 >4D 3 2 6.00 0.00 1.90 2.40 0.0 >5S 1 0 2.00 0.00 2.30 2.40 0.0 >-------------------------------------------------------------------------- > >If the 5P energy is set to 0.00 ( which means energy of all-electron >calculation ), the a axis of result is identical to that when the energy is >set to -0.09963 ( the all electron result copied from ld1.x output ). >However, in .UPF file, 2 wavefunctions and 3 projectors are generated if the >energy is 0.00, all of 4D, 5S and 5P will appear in PDOS ( by projwfc.x ), >but only 2 projectors are obtained otherwise and 5P will not appear in >further PDOS calculation. I don't know how to make PDOS of all of 4D, 5S and >5P if the energy is not 0.00. Can anyone give some advices ? Thanks. > >Best regards, > >Wu F > >----------------------------------------------------------- >F, Wu >College of Chemistry and Molecular Engineering >Peking University >---------------------------------------------------------- > >_______________________________________________ >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/20110924/75069ebf/attachment.htm From baroni at sissa.it Sat Sep 24 14:56:15 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 24 Sep 2011 14:56:15 +0200 Subject: [Pw_forum] charge density map In-Reply-To: References: Message-ID: <50B121B7-CC76-4A34-8819-FFBE2686C964@sissa.it> I think that this kind of questions should be better addressed to (and answered by) a local supervisor ... SB On Sep 22, 2011, at 10:54 PM, Tram Bui wrote: > Dear Everyone, > I have done my charge density calculation and the contour maps for my bulk SiC. I also see the scale based on the thermometer around each atom (Si, C). But my questions is what should I focus on in order to help me understand the charge density map ? what information can I get out of the charge density contour maps? > > Regards, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110924/fd15eb71/attachment.htm From baroni at sissa.it Sat Sep 24 15:00:43 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 24 Sep 2011 15:00:43 +0200 Subject: [Pw_forum] a request In-Reply-To: References: Message-ID: I am pretty sure that posting the paper you request in this mailing list would result in a violation of some copyright law. If anybody ever wants to reply to this post, please do it in private. Thanks - SB On Sep 23, 2011, at 9:39 PM, Mehrnoosh Hazrati wrote: > Hi dear users, > > I need a paper but i don't have access to that. I'll be thankful, if some one sent it to me ! > > Acta Cryst. (1952). 5, 356-361 LINK : [ doi:10.1107/S0365110X52001064 ] > > An X-ray study of boron nitride > > R. S. Pease > > > Thank you :) > > -- > """""""""""""""""""""""""""""""""""""""""""""""""""""""""""" > *** Mehrnoosh Kh. Hazrati *** > *** Master Student of Computational Physical Chemistry,KNTU,Tehran *** > *** Phone : +989123436300 *** > *** Mail : mehrnooshhazrati at gmail.com *** > """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110924/1c04523a/attachment-0001.htm From trambui at u.boisestate.edu Sat Sep 24 21:59:52 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Sat, 24 Sep 2011 12:59:52 -0700 Subject: [Pw_forum] band structure calculation In-Reply-To: References: Message-ID: Dear Mike Thank you very much for all the information. Tram On Thu, Sep 22, 2011 at 10:39 PM, mike at. wrote: > Bui, > Have you taken a look at at example01, example13 and example22 in your > espresso$VER/examples directory? also, > Look at Thursday, 22 July in this page: > http://users.aims.ac.za/~sandro/ > > > On Fri, Sep 23, 2011 at 2:09 AM, Tram Bui wrote: > >> Dear Everyone, >> I have run DOS calculation on my bulk SiC and I also wonder how to do >> the band structure and plot the band structure. Would you give me some >> information or some examples regarding generating the band structure? >> >> Thank you very much, >> >> Tram Bui >> >> M.S. Materials Science & Engineering >> trambui at u.boisestate.edu >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > M. O. ATAMBO > mikeat4999 at gmail.com > M Phil. student, computational material science group > Chepkoilel university college, Department of Physics, > Eldoret, Kenya, > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110924/9138dad3/attachment.htm From windbellklbh at gmail.com Sun Sep 25 04:58:28 2011 From: windbellklbh at gmail.com (WF) Date: Sun, 25 Sep 2011 10:58:28 +0800 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with PDOS Message-ID: <004601cc7b2f$037a5550$0a6efff0$@gmail.com> The FHI file seems doesn't contain all information necessary and hard to convert. However, my problem here is not about the quality of the PP, but how to show 5P in later PDOS calculation. Currently PDOS of Ru metal with PP that energy of 5P is not 0.00 will give result that the PDOS of 5P does not exists. On 24 Sep, 2011 ,at 19:56:20, GAO Zhe wrote: >Even though I cannot give you any suggestion to generate a better NCPP for Ru, you can try to convert a fhi NCPP to UPF by upftools/fhi2upf.x. Here: http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html#Ru3, you can find both of the fhi file and parameters. > > >-- >GAO Zhe >CMC Lab, MSE, SNU, Seoul, S.Korea > > > > >At 2011-09-24 17:45:49,WF wrote: >>Hello everyone, >> I recently do a vc-relax calculation of Ru metal of PBE >>norm-conserving PP. >> >>The PP input is like this, which is slightly modified from that in >>atomic_doc: >>-------------------------------------------------------------- >>&input >> title='Ru', >> zed=44.0, >> rel=1, >> config='[Kr] 4d6.0 5s2.0 5p0', >> iswitch=3, >> dft='pbe' >> / >> &inputp >> pseudotype=2, >> file_pseudopw='Ru.pbe-rrkjnc.UPF', >> author='TM', >> lloc=0, >> nlcc=.true., >> rcore = 0.9, >> / >>3 >>5P 2 1 0.00 -0.099963 2.40 2.40 0.0 4D 3 2 6.00 0.00 1.90 >>2.40 0.0 5S 1 0 2.00 0.00 2.30 2.40 0.0 >>----------------------------------------------------------------------- >>--- >> >>If the 5P energy is set to 0.00 ( which means energy of all-electron >>calculation ), the a axis of result is identical to that when the >>energy is set to -0.09963 ( the all electron result copied from ld1.x output ). >>However, in .UPF file, 2 wavefunctions and 3 projectors are generated >>if the energy is 0.00, all of 4D, 5S and 5P will appear in PDOS ( by >>projwfc.x ), but only 2 projectors are obtained otherwise and 5P will >>not appear in further PDOS calculation. I don't know how to make PDOS >>of all of 4D, 5S and 5P if the energy is not 0.00. Can anyone give some advices ? Thanks. >> >>Best regards, >> >>Wu F >> >>----------------------------------------------------------- >>F, Wu >>College of Chemistry and Molecular Engineering Peking University >>---------------------------------------------------------- >> > ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110925/647781e1/attachment.htm From mahdi_fn109 at yahoo.com Sun Sep 25 17:31:57 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Sun, 25 Sep 2011 08:31:57 -0700 (PDT) Subject: [Pw_forum] error in example01 Message-ID: <1316964717.7209.YahooMailNeo@web43134.mail.sp1.yahoo.com> Dear all, i am trying to run example01, si bandstructure, but i have an error, ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ???? task #???????? 0 ???? from iosys : error #???????? 1 ???? diagonalization $diago not implemented ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% i changed diagonalization, but i reached segmentation fault, what is that? how can i solve it? ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110925/5de09d4b/attachment.htm From zhiting at MIT.EDU Sun Sep 25 18:22:44 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Sun, 25 Sep 2011 12:22:44 -0400 Subject: [Pw_forum] Too many bands are not converged from nscf calculation In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997A65@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A65@EXPO20.exchange.mit.edu> Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A73@EXPO20.exchange.mit.edu> Dear all, I first did scf calculation and it finished. Then I run nscf, but always got error message: "Too many bands are not converged" and then it stopped. I had read a few posts before and tried to reduce mixing-beta from 0.7 to 0.4 and even to 0.05, but same error. Also, I have tried to change the diagolization='david' to 'cg', same error. My input files are following: scf_in: &control calculation = 'scf' restart_mode='from_scratch' prefix='PbSeAl' tstress = .true. tprnfor = .true. pseudo_dir = "..." outdir = "..." / &system ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3 , ecutwfc = 60, noncolin = .TRUE. lspinorb = .TRUE. occupations = 'smearing' smearing = 'mv' degauss = 0.01 / &electrons mixing_beta = 0.7D0 conv_thr = 1.0d-10 / ATOMIC_SPECIES Al 26.98 Al.rel-pz-nc.UPF Pb 207.21 Pb.rel-pz-nc.UPF Se 78.96 Se.rel-pz-nc.UPF ATOMIC_POSITIONS Al 0.000000 0.000000 0.000000 Pb 0.500000 0.000000 0.000000 Pb 0.250000 0.250000 0.000000 Pb 0.750000 0.250000 0.000000 Pb 0.000000 0.500000 0.000000 Pb 0.500000 0.500000 0.000000 Pb 0.250000 0.750000 0.000000 Pb 0.750000 0.750000 0.000000 Pb 0.250000 0.000000 0.250000 Pb 0.750000 0.000000 0.250000 Pb 0.000000 0.250000 0.250000 Pb 0.500000 0.250000 0.250000 Pb 0.250000 0.500000 0.250000 Pb 0.750000 0.500000 0.250000 Pb 0.000000 0.750000 0.250000 Pb 0.500000 0.750000 0.250000 Pb 0.000000 0.000000 0.500000 Pb 0.500000 0.000000 0.500000 Pb 0.250000 0.250000 0.500000 Pb 0.750000 0.250000 0.500000 Pb 0.000000 0.500000 0.500000 Pb 0.500000 0.500000 0.500000 Pb 0.250000 0.750000 0.500000 Pb 0.750000 0.750000 0.500000 Pb 0.250000 0.000000 0.750000 Pb 0.750000 0.000000 0.750000 Pb 0.000000 0.250000 0.750000 Pb 0.500000 0.250000 0.750000 Pb 0.250000 0.500000 0.750000 Pb 0.750000 0.500000 0.750000 Pb 0.000000 0.750000 0.750000 Pb 0.500000 0.750000 0.750000 Se 0.250000 0.000000 0.000000 Se 0.750000 0.000000 0.000000 Se 0.000000 0.250000 0.000000 Se 0.500000 0.250000 0.000000 Se 0.250000 0.500000 0.000000 Se 0.750000 0.500000 0.000000 Se 0.000000 0.750000 0.000000 Se 0.500000 0.750000 0.000000 Se 0.000000 0.000000 0.250000 Se 0.500000 0.000000 0.250000 Se 0.250000 0.250000 0.250000 Se 0.750000 0.250000 0.250000 Se 0.000000 0.500000 0.250000 Se 0.500000 0.500000 0.250000 Se 0.250000 0.750000 0.250000 Se 0.750000 0.750000 0.250000 Se 0.250000 0.000000 0.500000 Se 0.750000 0.000000 0.500000 Se 0.000000 0.250000 0.500000 Se 0.500000 0.250000 0.500000 Se 0.250000 0.500000 0.500000 Se 0.750000 0.500000 0.500000 Se 0.000000 0.750000 0.500000 Se 0.500000 0.750000 0.500000 Se 0.000000 0.000000 0.750000 Se 0.500000 0.000000 0.750000 Se 0.250000 0.250000 0.750000 Se 0.750000 0.250000 0.750000 Se 0.000000 0.500000 0.750000 Se 0.500000 0.500000 0.750000 Se 0.250000 0.750000 0.750000 Se 0.750000 0.750000 0.750000 K_POINTS (automatic) 4 4 4 0 0 0 nscf_in: &control calculation = 'nscf' prefix='PbSeAl' tstress = .true. tprnfor = .true. pseudo_dir = "..." outdir = "..." / &system ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 ecutwfc = 60, noncolin = .TRUE. lspinorb = .TRUE. occupations = 'tetrahedra' / &electrons mixing_beta = 0.05D0 conv_thr = 1.0d-10 diagonalization = 'david' / ATOMIC_SPECIES Al 26.98 Al.rel-pz-nc.UPF Pb 207.21 Pb.rel-pz-nc.UPF Se 78.96 Se.rel-pz-nc.UPF ATOMIC_POSITIONS Al 0.000000 0.000000 0.000000 Pb 0.500000 0.000000 0.000000 Pb 0.250000 0.250000 0.000000 Pb 0.750000 0.250000 0.000000 Pb 0.000000 0.500000 0.000000 Pb 0.500000 0.500000 0.000000 Pb 0.250000 0.750000 0.000000 Pb 0.750000 0.750000 0.000000 Pb 0.250000 0.000000 0.250000 Pb 0.750000 0.000000 0.250000 Pb 0.000000 0.250000 0.250000 Pb 0.500000 0.250000 0.250000 Pb 0.250000 0.500000 0.250000 Pb 0.750000 0.500000 0.250000 Pb 0.000000 0.750000 0.250000 Pb 0.500000 0.750000 0.250000 Pb 0.000000 0.000000 0.500000 Pb 0.500000 0.000000 0.500000 Pb 0.250000 0.250000 0.500000 Pb 0.750000 0.250000 0.500000 Pb 0.000000 0.500000 0.500000 Pb 0.500000 0.500000 0.500000 Pb 0.250000 0.750000 0.500000 Pb 0.750000 0.750000 0.500000 Pb 0.250000 0.000000 0.750000 Pb 0.750000 0.000000 0.750000 Pb 0.000000 0.250000 0.750000 Pb 0.500000 0.250000 0.750000 Pb 0.250000 0.500000 0.750000 Pb 0.750000 0.500000 0.750000 Pb 0.000000 0.750000 0.750000 Pb 0.500000 0.750000 0.750000 Se 0.250000 0.000000 0.000000 Se 0.750000 0.000000 0.000000 Se 0.000000 0.250000 0.000000 Se 0.500000 0.250000 0.000000 Se 0.250000 0.500000 0.000000 Se 0.750000 0.500000 0.000000 Se 0.000000 0.750000 0.000000 Se 0.500000 0.750000 0.000000 Se 0.000000 0.000000 0.250000 Se 0.500000 0.000000 0.250000 Se 0.250000 0.250000 0.250000 Se 0.750000 0.250000 0.250000 Se 0.000000 0.500000 0.250000 Se 0.500000 0.500000 0.250000 Se 0.250000 0.750000 0.250000 Se 0.750000 0.750000 0.250000 Se 0.250000 0.000000 0.500000 Se 0.750000 0.000000 0.500000 Se 0.000000 0.250000 0.500000 Se 0.500000 0.250000 0.500000 Se 0.250000 0.500000 0.500000 Se 0.750000 0.500000 0.500000 Se 0.000000 0.750000 0.500000 Se 0.500000 0.750000 0.500000 Se 0.000000 0.000000 0.750000 Se 0.500000 0.000000 0.750000 Se 0.250000 0.250000 0.750000 Se 0.750000 0.250000 0.750000 Se 0.000000 0.500000 0.750000 Se 0.500000 0.500000 0.750000 Se 0.250000 0.750000 0.750000 Se 0.750000 0.750000 0.750000 K_POINTS (automatic) 8 8 8 0 0 0 Can anyone help me with this? Thanks a lot, Zhiting Tian PhD student Mechanical Engineering Department Massachusetts Institute of Technology Email: zhiting at mit.edu From giannozz at democritos.it Sun Sep 25 18:28:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Sep 2011 18:28:53 +0200 Subject: [Pw_forum] error in example01 In-Reply-To: <1316964717.7209.YahooMailNeo@web43134.mail.sp1.yahoo.com> References: <1316964717.7209.YahooMailNeo@web43134.mail.sp1.yahoo.com> Message-ID: <0F1E0807-99BD-4202-B33C-4B45203AD620@democritos.it> On Sep 25, 2011, at 17:31 , Mahdi Faqieh nasiri wrote: > i am trying to run example01, si bandstructure, but i have an error > from iosys : error # 1 > diagonalization $diago not implemented you cannot get this error unless - the exampes/example01/run_example script is corrupted or was modified, or - your unix shell does not work as expected 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 25 18:31:16 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Sep 2011 18:31:16 +0200 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with PDOS In-Reply-To: <004601cc7b2f$037a5550$0a6efff0$@gmail.com> References: <004601cc7b2f$037a5550$0a6efff0$@gmail.com> Message-ID: <5D52CEDF-A225-407D-9E03-EF27DFE40EE6@democritos.it> On Sep 25, 2011, at 4:58 , WF wrote: > my problem here is [...] how to show 5P in later PDOS calculation > you need atomic wavefunctions for a bound 5P state in the pseudopotential file 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 henod2001 at yahoo.com Sun Sep 25 20:07:47 2011 From: henod2001 at yahoo.com (henry odhiambo) Date: Sun, 25 Sep 2011 11:07:47 -0700 (PDT) Subject: [Pw_forum] DOS calculation for hexagonal Ge2Sb2Te5 (GST) Message-ID: <1316974067.66662.YahooMailClassic@web121013.mail.ne1.yahoo.com> Dear all, I am trying to calculate the DOS for hexagonal Ge2Sb2Te5 (GST). When I do a nscf calculation, it crashes and I get the following error message: ? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 1 from read_rho_xml : error # 1 dimensions do not match %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ? The input file (script) is attached. Where could the problem be? Please help. ? Yours, Henry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110925/e5eeb9e3/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: gst.nscf.in Type: application/octet-stream Size: 756 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110925/e5eeb9e3/attachment.obj From giannozz at democritos.it Sun Sep 25 20:24:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 25 Sep 2011 20:24:40 +0200 Subject: [Pw_forum] DOS calculation for hexagonal Ge2Sb2Te5 (GST) In-Reply-To: <1316974067.66662.YahooMailClassic@web121013.mail.ne1.yahoo.com> References: <1316974067.66662.YahooMailClassic@web121013.mail.ne1.yahoo.com> Message-ID: On Sep 25, 2011, at 20:07 , henry odhiambo wrote: > from read_rho_xml : error # 1 > dimensions do not match the FFT dimensions in scf and non-scf calculations must be the same. This implies that you should use the same cutoff(s) with the same cell. Note that different FFT libraries have different restrictions on allowed FFT dimensions. If you want to perform the non-scf calculation from scf data produced by a different machine, you may need to explicitly set the FFT dimensions in 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 giuseppe.mattioli at mlib.ism.cnr.it Sun Sep 25 21:12:38 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Sun, 25 Sep 2011 21:12:38 +0200 Subject: [Pw_forum] Too many bands are not converged from nscf calculation In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997A73@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A65@EXPO20.exchange.mit.edu> <1675BB3F3586E9459BBC8B9812C3532020C7997A73@EXPO20.exchange.mit.edu> Message-ID: <20110925211238.wmbxiyst6oogowsc@webmail.sic.rm.cnr.it> Dear Zhiting > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 your 64-atom alloy supercell should contain much more than 18 occupied bands. If you want to calculate 18 unoccupied bands you should set the nband parameter to "number_of_occupied_levels+18". HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Citando Zhiting Tian : > Dear all, > > I first did scf calculation and it finished. Then I run nscf, but > always got error message: "Too many bands are not converged" and > then it stopped. > I had read a few posts before and tried to reduce mixing-beta from > 0.7 to 0.4 and even to 0.05, but same error. Also, I have tried to > change the diagolization='david' to 'cg', same error. > > My input files are following: > scf_in: > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='PbSeAl' > tstress = .true. > tprnfor = .true. > pseudo_dir = "..." > outdir = "..." > / > &system > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3 , > ecutwfc = 60, > noncolin = .TRUE. > lspinorb = .TRUE. > occupations = 'smearing' > smearing = 'mv' > degauss = 0.01 > / > &electrons > mixing_beta = 0.7D0 > conv_thr = 1.0d-10 > / > ATOMIC_SPECIES > Al 26.98 Al.rel-pz-nc.UPF > Pb 207.21 Pb.rel-pz-nc.UPF > Se 78.96 Se.rel-pz-nc.UPF > > ATOMIC_POSITIONS > Al 0.000000 0.000000 0.000000 > Pb 0.500000 0.000000 0.000000 > Pb 0.250000 0.250000 0.000000 > Pb 0.750000 0.250000 0.000000 > Pb 0.000000 0.500000 0.000000 > Pb 0.500000 0.500000 0.000000 > Pb 0.250000 0.750000 0.000000 > Pb 0.750000 0.750000 0.000000 > Pb 0.250000 0.000000 0.250000 > Pb 0.750000 0.000000 0.250000 > Pb 0.000000 0.250000 0.250000 > Pb 0.500000 0.250000 0.250000 > Pb 0.250000 0.500000 0.250000 > Pb 0.750000 0.500000 0.250000 > Pb 0.000000 0.750000 0.250000 > Pb 0.500000 0.750000 0.250000 > Pb 0.000000 0.000000 0.500000 > Pb 0.500000 0.000000 0.500000 > Pb 0.250000 0.250000 0.500000 > Pb 0.750000 0.250000 0.500000 > Pb 0.000000 0.500000 0.500000 > Pb 0.500000 0.500000 0.500000 > Pb 0.250000 0.750000 0.500000 > Pb 0.750000 0.750000 0.500000 > Pb 0.250000 0.000000 0.750000 > Pb 0.750000 0.000000 0.750000 > Pb 0.000000 0.250000 0.750000 > Pb 0.500000 0.250000 0.750000 > Pb 0.250000 0.500000 0.750000 > Pb 0.750000 0.500000 0.750000 > Pb 0.000000 0.750000 0.750000 > Pb 0.500000 0.750000 0.750000 > Se 0.250000 0.000000 0.000000 > Se 0.750000 0.000000 0.000000 > Se 0.000000 0.250000 0.000000 > Se 0.500000 0.250000 0.000000 > Se 0.250000 0.500000 0.000000 > Se 0.750000 0.500000 0.000000 > Se 0.000000 0.750000 0.000000 > Se 0.500000 0.750000 0.000000 > Se 0.000000 0.000000 0.250000 > Se 0.500000 0.000000 0.250000 > Se 0.250000 0.250000 0.250000 > Se 0.750000 0.250000 0.250000 > Se 0.000000 0.500000 0.250000 > Se 0.500000 0.500000 0.250000 > Se 0.250000 0.750000 0.250000 > Se 0.750000 0.750000 0.250000 > Se 0.250000 0.000000 0.500000 > Se 0.750000 0.000000 0.500000 > Se 0.000000 0.250000 0.500000 > Se 0.500000 0.250000 0.500000 > Se 0.250000 0.500000 0.500000 > Se 0.750000 0.500000 0.500000 > Se 0.000000 0.750000 0.500000 > Se 0.500000 0.750000 0.500000 > Se 0.000000 0.000000 0.750000 > Se 0.500000 0.000000 0.750000 > Se 0.250000 0.250000 0.750000 > Se 0.750000 0.250000 0.750000 > Se 0.000000 0.500000 0.750000 > Se 0.500000 0.500000 0.750000 > Se 0.250000 0.750000 0.750000 > Se 0.750000 0.750000 0.750000 > > K_POINTS (automatic) > 4 4 4 0 0 0 > > nscf_in: > > &control > calculation = 'nscf' > prefix='PbSeAl' > tstress = .true. > tprnfor = .true. > pseudo_dir = "..." > outdir = "..." > / > &system > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > ecutwfc = 60, > noncolin = .TRUE. > lspinorb = .TRUE. > occupations = 'tetrahedra' > / > &electrons > mixing_beta = 0.05D0 > conv_thr = 1.0d-10 > diagonalization = 'david' > / > ATOMIC_SPECIES > Al 26.98 Al.rel-pz-nc.UPF > Pb 207.21 Pb.rel-pz-nc.UPF > Se 78.96 Se.rel-pz-nc.UPF > > ATOMIC_POSITIONS > Al 0.000000 0.000000 0.000000 > Pb 0.500000 0.000000 0.000000 > Pb 0.250000 0.250000 0.000000 > Pb 0.750000 0.250000 0.000000 > Pb 0.000000 0.500000 0.000000 > Pb 0.500000 0.500000 0.000000 > Pb 0.250000 0.750000 0.000000 > Pb 0.750000 0.750000 0.000000 > Pb 0.250000 0.000000 0.250000 > Pb 0.750000 0.000000 0.250000 > Pb 0.000000 0.250000 0.250000 > Pb 0.500000 0.250000 0.250000 > Pb 0.250000 0.500000 0.250000 > Pb 0.750000 0.500000 0.250000 > Pb 0.000000 0.750000 0.250000 > Pb 0.500000 0.750000 0.250000 > Pb 0.000000 0.000000 0.500000 > Pb 0.500000 0.000000 0.500000 > Pb 0.250000 0.250000 0.500000 > Pb 0.750000 0.250000 0.500000 > Pb 0.000000 0.500000 0.500000 > Pb 0.500000 0.500000 0.500000 > Pb 0.250000 0.750000 0.500000 > Pb 0.750000 0.750000 0.500000 > Pb 0.250000 0.000000 0.750000 > Pb 0.750000 0.000000 0.750000 > Pb 0.000000 0.250000 0.750000 > Pb 0.500000 0.250000 0.750000 > Pb 0.250000 0.500000 0.750000 > Pb 0.750000 0.500000 0.750000 > Pb 0.000000 0.750000 0.750000 > Pb 0.500000 0.750000 0.750000 > Se 0.250000 0.000000 0.000000 > Se 0.750000 0.000000 0.000000 > Se 0.000000 0.250000 0.000000 > Se 0.500000 0.250000 0.000000 > Se 0.250000 0.500000 0.000000 > Se 0.750000 0.500000 0.000000 > Se 0.000000 0.750000 0.000000 > Se 0.500000 0.750000 0.000000 > Se 0.000000 0.000000 0.250000 > Se 0.500000 0.000000 0.250000 > Se 0.250000 0.250000 0.250000 > Se 0.750000 0.250000 0.250000 > Se 0.000000 0.500000 0.250000 > Se 0.500000 0.500000 0.250000 > Se 0.250000 0.750000 0.250000 > Se 0.750000 0.750000 0.250000 > Se 0.250000 0.000000 0.500000 > Se 0.750000 0.000000 0.500000 > Se 0.000000 0.250000 0.500000 > Se 0.500000 0.250000 0.500000 > Se 0.250000 0.500000 0.500000 > Se 0.750000 0.500000 0.500000 > Se 0.000000 0.750000 0.500000 > Se 0.500000 0.750000 0.500000 > Se 0.000000 0.000000 0.750000 > Se 0.500000 0.000000 0.750000 > Se 0.250000 0.250000 0.750000 > Se 0.750000 0.250000 0.750000 > Se 0.000000 0.500000 0.750000 > Se 0.500000 0.500000 0.750000 > Se 0.250000 0.750000 0.750000 > Se 0.750000 0.750000 0.750000 > > K_POINTS (automatic) > 8 8 8 0 0 0 > > > Can anyone help me with this? > > Thanks a lot, > Zhiting Tian > PhD student > Mechanical Engineering Department > Massachusetts Institute of Technology > Email: zhiting at mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zhiting at MIT.EDU Sun Sep 25 22:59:48 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Sun, 25 Sep 2011 16:59:48 -0400 Subject: [Pw_forum] Too many bands are not converged from nscf calculation Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A76@EXPO20.exchange.mit.edu> I see. That's silly mistake. Since I set nbnd=18 for 2 atoms testing case and forgot to change it. Now I have removed nbnd, but got the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 1273 problems computing cholesky stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Does it mean that I need to change the diagonalization? Thanks, Zhiting ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of giuseppe.mattioli at mlib.ism.cnr.it [giuseppe.mattioli at mlib.ism.cnr.it] Sent: Sunday, September 25, 2011 3:12 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Too many bands are not converged from nscf calculation Dear Zhiting > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 your 64-atom alloy supercell should contain much more than 18 occupied bands. If you want to calculate 18 unoccupied bands you should set the nband parameter to "number_of_occupied_levels+18". HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Citando Zhiting Tian : > Dear all, > > I first did scf calculation and it finished. Then I run nscf, but > always got error message: "Too many bands are not converged" and > then it stopped. > I had read a few posts before and tried to reduce mixing-beta from > 0.7 to 0.4 and even to 0.05, but same error. Also, I have tried to > change the diagolization='david' to 'cg', same error. > > My input files are following: > scf_in: > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='PbSeAl' > tstress = .true. > tprnfor = .true. > pseudo_dir = "..." > outdir = "..." > / > &system > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3 , > ecutwfc = 60, > noncolin = .TRUE. > lspinorb = .TRUE. > occupations = 'smearing' > smearing = 'mv' > degauss = 0.01 > / > &electrons > mixing_beta = 0.7D0 > conv_thr = 1.0d-10 > / > ATOMIC_SPECIES > Al 26.98 Al.rel-pz-nc.UPF > Pb 207.21 Pb.rel-pz-nc.UPF > Se 78.96 Se.rel-pz-nc.UPF > > ATOMIC_POSITIONS > Al 0.000000 0.000000 0.000000 > Pb 0.500000 0.000000 0.000000 > Pb 0.250000 0.250000 0.000000 > Pb 0.750000 0.250000 0.000000 > Pb 0.000000 0.500000 0.000000 > Pb 0.500000 0.500000 0.000000 > Pb 0.250000 0.750000 0.000000 > Pb 0.750000 0.750000 0.000000 > Pb 0.250000 0.000000 0.250000 > Pb 0.750000 0.000000 0.250000 > Pb 0.000000 0.250000 0.250000 > Pb 0.500000 0.250000 0.250000 > Pb 0.250000 0.500000 0.250000 > Pb 0.750000 0.500000 0.250000 > Pb 0.000000 0.750000 0.250000 > Pb 0.500000 0.750000 0.250000 > Pb 0.000000 0.000000 0.500000 > Pb 0.500000 0.000000 0.500000 > Pb 0.250000 0.250000 0.500000 > Pb 0.750000 0.250000 0.500000 > Pb 0.000000 0.500000 0.500000 > Pb 0.500000 0.500000 0.500000 > Pb 0.250000 0.750000 0.500000 > Pb 0.750000 0.750000 0.500000 > Pb 0.250000 0.000000 0.750000 > Pb 0.750000 0.000000 0.750000 > Pb 0.000000 0.250000 0.750000 > Pb 0.500000 0.250000 0.750000 > Pb 0.250000 0.500000 0.750000 > Pb 0.750000 0.500000 0.750000 > Pb 0.000000 0.750000 0.750000 > Pb 0.500000 0.750000 0.750000 > Se 0.250000 0.000000 0.000000 > Se 0.750000 0.000000 0.000000 > Se 0.000000 0.250000 0.000000 > Se 0.500000 0.250000 0.000000 > Se 0.250000 0.500000 0.000000 > Se 0.750000 0.500000 0.000000 > Se 0.000000 0.750000 0.000000 > Se 0.500000 0.750000 0.000000 > Se 0.000000 0.000000 0.250000 > Se 0.500000 0.000000 0.250000 > Se 0.250000 0.250000 0.250000 > Se 0.750000 0.250000 0.250000 > Se 0.000000 0.500000 0.250000 > Se 0.500000 0.500000 0.250000 > Se 0.250000 0.750000 0.250000 > Se 0.750000 0.750000 0.250000 > Se 0.250000 0.000000 0.500000 > Se 0.750000 0.000000 0.500000 > Se 0.000000 0.250000 0.500000 > Se 0.500000 0.250000 0.500000 > Se 0.250000 0.500000 0.500000 > Se 0.750000 0.500000 0.500000 > Se 0.000000 0.750000 0.500000 > Se 0.500000 0.750000 0.500000 > Se 0.000000 0.000000 0.750000 > Se 0.500000 0.000000 0.750000 > Se 0.250000 0.250000 0.750000 > Se 0.750000 0.250000 0.750000 > Se 0.000000 0.500000 0.750000 > Se 0.500000 0.500000 0.750000 > Se 0.250000 0.750000 0.750000 > Se 0.750000 0.750000 0.750000 > > K_POINTS (automatic) > 4 4 4 0 0 0 > > nscf_in: > > &control > calculation = 'nscf' > prefix='PbSeAl' > tstress = .true. > tprnfor = .true. > pseudo_dir = "..." > outdir = "..." > / > &system > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > ecutwfc = 60, > noncolin = .TRUE. > lspinorb = .TRUE. > occupations = 'tetrahedra' > / > &electrons > mixing_beta = 0.05D0 > conv_thr = 1.0d-10 > diagonalization = 'david' > / > ATOMIC_SPECIES > Al 26.98 Al.rel-pz-nc.UPF > Pb 207.21 Pb.rel-pz-nc.UPF > Se 78.96 Se.rel-pz-nc.UPF > > ATOMIC_POSITIONS > Al 0.000000 0.000000 0.000000 > Pb 0.500000 0.000000 0.000000 > Pb 0.250000 0.250000 0.000000 > Pb 0.750000 0.250000 0.000000 > Pb 0.000000 0.500000 0.000000 > Pb 0.500000 0.500000 0.000000 > Pb 0.250000 0.750000 0.000000 > Pb 0.750000 0.750000 0.000000 > Pb 0.250000 0.000000 0.250000 > Pb 0.750000 0.000000 0.250000 > Pb 0.000000 0.250000 0.250000 > Pb 0.500000 0.250000 0.250000 > Pb 0.250000 0.500000 0.250000 > Pb 0.750000 0.500000 0.250000 > Pb 0.000000 0.750000 0.250000 > Pb 0.500000 0.750000 0.250000 > Pb 0.000000 0.000000 0.500000 > Pb 0.500000 0.000000 0.500000 > Pb 0.250000 0.250000 0.500000 > Pb 0.750000 0.250000 0.500000 > Pb 0.000000 0.500000 0.500000 > Pb 0.500000 0.500000 0.500000 > Pb 0.250000 0.750000 0.500000 > Pb 0.750000 0.750000 0.500000 > Pb 0.250000 0.000000 0.750000 > Pb 0.750000 0.000000 0.750000 > Pb 0.000000 0.250000 0.750000 > Pb 0.500000 0.250000 0.750000 > Pb 0.250000 0.500000 0.750000 > Pb 0.750000 0.500000 0.750000 > Pb 0.000000 0.750000 0.750000 > Pb 0.500000 0.750000 0.750000 > Se 0.250000 0.000000 0.000000 > Se 0.750000 0.000000 0.000000 > Se 0.000000 0.250000 0.000000 > Se 0.500000 0.250000 0.000000 > Se 0.250000 0.500000 0.000000 > Se 0.750000 0.500000 0.000000 > Se 0.000000 0.750000 0.000000 > Se 0.500000 0.750000 0.000000 > Se 0.000000 0.000000 0.250000 > Se 0.500000 0.000000 0.250000 > Se 0.250000 0.250000 0.250000 > Se 0.750000 0.250000 0.250000 > Se 0.000000 0.500000 0.250000 > Se 0.500000 0.500000 0.250000 > Se 0.250000 0.750000 0.250000 > Se 0.750000 0.750000 0.250000 > Se 0.250000 0.000000 0.500000 > Se 0.750000 0.000000 0.500000 > Se 0.000000 0.250000 0.500000 > Se 0.500000 0.250000 0.500000 > Se 0.250000 0.500000 0.500000 > Se 0.750000 0.500000 0.500000 > Se 0.000000 0.750000 0.500000 > Se 0.500000 0.750000 0.500000 > Se 0.000000 0.000000 0.750000 > Se 0.500000 0.000000 0.750000 > Se 0.250000 0.250000 0.750000 > Se 0.750000 0.250000 0.750000 > Se 0.000000 0.500000 0.750000 > Se 0.500000 0.500000 0.750000 > Se 0.250000 0.750000 0.750000 > Se 0.750000 0.750000 0.750000 > > K_POINTS (automatic) > 8 8 8 0 0 0 > > > Can anyone help me with this? > > Thanks a lot, > Zhiting Tian > PhD student > Mechanical Engineering Department > Massachusetts Institute of Technology > Email: zhiting at mit.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 From windbellklbh at gmail.com Mon Sep 26 01:23:51 2011 From: windbellklbh at gmail.com (WF) Date: Mon, 26 Sep 2011 07:23:51 +0800 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with Message-ID: <004f01cc7bda$317f1200$947d3600$@gmail.com> Thanks for your advices. How can I get bound 5P states ? In my opinion a state has energy lower than 0 is bound, but regardless what the 5P energy in ld1.x input file is ( I test the range from -0.1 to 1.50 ), no 5P orbital is found in PDOS calculation, which only appear when 5P energy is set to 0.00 . On Sep 25, 2011, at 18:31:16, Paolo Giannozzi wrote: >> my problem here is [...] how to show 5P in later PDOS calculation >> >you need atomic wavefunctions for a bound 5P state in the pseudopotential file > >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 ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- From mikeat4999 at gmail.com Mon Sep 26 07:20:26 2011 From: mikeat4999 at gmail.com (mike at.) Date: Mon, 26 Sep 2011 08:20:26 +0300 Subject: [Pw_forum] band structure calculation In-Reply-To: References: Message-ID: On Sat, Sep 24, 2011 at 10:59 PM, Tram Bui wrote: > Dear Mike > Thank you very much for all the information. > glad i could help. > Tram > > > On Thu, Sep 22, 2011 at 10:39 PM, mike at. wrote: > >> Bui, >> Have you taken a look at at example01, example13 and example22 in your >> espresso$VER/examples directory? also, >> Look at Thursday, 22 July in this page: >> http://users.aims.ac.za/~sandro/ >> >> >> On Fri, Sep 23, 2011 at 2:09 AM, Tram Bui wrote: >> >>> Dear Everyone, >>> I have run DOS calculation on my bulk SiC and I also wonder how to do >>> the band structure and plot the band structure. Would you give me some >>> information or some examples regarding generating the band structure? >>> >>> Thank you very much, >>> >>> Tram Bui >>> >>> M.S. Materials Science & Engineering >>> trambui at u.boisestate.edu >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> M. O. ATAMBO >> mikeat4999 at gmail.com >> M Phil. student, computational material science group >> Chepkoilel university college, Department of Physics, >> Eldoret, Kenya, >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- M. O. ATAMBO mikeat4999 at gmail.com M Phil. student, computational material science group Chepkoilel university college, Department of Physics, Eldoret, Kenya, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110926/1e126a6d/attachment.htm From giannozz at democritos.it Mon Sep 26 08:30:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 26 Sep 2011 08:30:12 +0200 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with In-Reply-To: <004f01cc7bda$317f1200$947d3600$@gmail.com> References: <004f01cc7bda$317f1200$947d3600$@gmail.com> Message-ID: <48568824-7C56-49A5-8934-DEBD6E04BB6E@democritos.it> On Sep 26, 2011, at 1:23 , WF wrote: > regardless what the 5P energy in ld1.x input file is (...), no 5P > orbital is > found in PDOS calculation, which only appear when 5P energy is set > to 0.00 . energy = 0.00 => "use energy of the bound state" energy /=0.00 => "use specified energy for pseudization" It is clumsy and unclear but it was done that way and now it cannot be changed without breaking existing data. Anyway, it is documented. In the latter case, the pseudo-wavefunction is not used for projection: it is not guaranteed to be a bund state 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 giuseppe.mattioli at mlib.ism.cnr.it Mon Sep 26 10:08:14 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 26 Sep 2011 10:08:14 +0200 Subject: [Pw_forum] Too many bands are not converged from nscf calculation In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997A76@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A76@EXPO20.exchange.mit.edu> Message-ID: <201109261008.14535.giuseppe.mattioli@mlib.ism.cnr.it> Dear Zhiting This erratic behaviour may occur quite often, and it is sometimes difficult to track down. I can only suggest to increase the ecutwfc value: 60 Ry could be not enough for your norm conserving pseudopotentials. HTH Giuseppe P.S. > conv_thr = 1.0d-10 too tight for an scf calculation. 1.0d-8 should be enough. On Sunday 25 September 2011 22:59:48 Zhiting Tian wrote: > I see. That's silly mistake. Since I set nbnd=18 for 2 atoms testing case > and forgot to change it. Now I have removed nbnd, but got the following > error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 1273 > > problems computing cholesky > stopping ... > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Does it mean that I need to change the diagonalization? > Thanks, > Zhiting > > ________________________________________ > From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of > giuseppe.mattioli at mlib.ism.cnr.it [giuseppe.mattioli at mlib.ism.cnr.it] Sent: > Sunday, September 25, 2011 3:12 PM > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Too many bands are not converged from nscf > calculation > > Dear Zhiting > > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > > your 64-atom alloy supercell should contain much more than 18 occupied > bands. If you want to calculate 18 unoccupied bands you should set the > nband parameter to "number_of_occupied_levels+18". > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Citando Zhiting Tian : > > Dear all, > > > > I first did scf calculation and it finished. Then I run nscf, but > > always got error message: "Too many bands are not converged" and > > then it stopped. > > I had read a few posts before and tried to reduce mixing-beta from > > 0.7 to 0.4 and even to 0.05, but same error. Also, I have tried to > > change the diagolization='david' to 'cg', same error. > > > > My input files are following: > > scf_in: > > > > &control > > calculation = 'scf' > > restart_mode='from_scratch' > > prefix='PbSeAl' > > tstress = .true. > > tprnfor = .true. > > pseudo_dir = "..." > > outdir = "..." > > / > > &system > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3 , > > ecutwfc = 60, > > noncolin = .TRUE. > > lspinorb = .TRUE. > > occupations = 'smearing' > > smearing = 'mv' > > degauss = 0.01 > > / > > &electrons > > mixing_beta = 0.7D0 > > conv_thr = 1.0d-10 > > / > > ATOMIC_SPECIES > > Al 26.98 Al.rel-pz-nc.UPF > > Pb 207.21 Pb.rel-pz-nc.UPF > > Se 78.96 Se.rel-pz-nc.UPF > > > > ATOMIC_POSITIONS > > Al 0.000000 0.000000 0.000000 > > Pb 0.500000 0.000000 0.000000 > > Pb 0.250000 0.250000 0.000000 > > Pb 0.750000 0.250000 0.000000 > > Pb 0.000000 0.500000 0.000000 > > Pb 0.500000 0.500000 0.000000 > > Pb 0.250000 0.750000 0.000000 > > Pb 0.750000 0.750000 0.000000 > > Pb 0.250000 0.000000 0.250000 > > Pb 0.750000 0.000000 0.250000 > > Pb 0.000000 0.250000 0.250000 > > Pb 0.500000 0.250000 0.250000 > > Pb 0.250000 0.500000 0.250000 > > Pb 0.750000 0.500000 0.250000 > > Pb 0.000000 0.750000 0.250000 > > Pb 0.500000 0.750000 0.250000 > > Pb 0.000000 0.000000 0.500000 > > Pb 0.500000 0.000000 0.500000 > > Pb 0.250000 0.250000 0.500000 > > Pb 0.750000 0.250000 0.500000 > > Pb 0.000000 0.500000 0.500000 > > Pb 0.500000 0.500000 0.500000 > > Pb 0.250000 0.750000 0.500000 > > Pb 0.750000 0.750000 0.500000 > > Pb 0.250000 0.000000 0.750000 > > Pb 0.750000 0.000000 0.750000 > > Pb 0.000000 0.250000 0.750000 > > Pb 0.500000 0.250000 0.750000 > > Pb 0.250000 0.500000 0.750000 > > Pb 0.750000 0.500000 0.750000 > > Pb 0.000000 0.750000 0.750000 > > Pb 0.500000 0.750000 0.750000 > > Se 0.250000 0.000000 0.000000 > > Se 0.750000 0.000000 0.000000 > > Se 0.000000 0.250000 0.000000 > > Se 0.500000 0.250000 0.000000 > > Se 0.250000 0.500000 0.000000 > > Se 0.750000 0.500000 0.000000 > > Se 0.000000 0.750000 0.000000 > > Se 0.500000 0.750000 0.000000 > > Se 0.000000 0.000000 0.250000 > > Se 0.500000 0.000000 0.250000 > > Se 0.250000 0.250000 0.250000 > > Se 0.750000 0.250000 0.250000 > > Se 0.000000 0.500000 0.250000 > > Se 0.500000 0.500000 0.250000 > > Se 0.250000 0.750000 0.250000 > > Se 0.750000 0.750000 0.250000 > > Se 0.250000 0.000000 0.500000 > > Se 0.750000 0.000000 0.500000 > > Se 0.000000 0.250000 0.500000 > > Se 0.500000 0.250000 0.500000 > > Se 0.250000 0.500000 0.500000 > > Se 0.750000 0.500000 0.500000 > > Se 0.000000 0.750000 0.500000 > > Se 0.500000 0.750000 0.500000 > > Se 0.000000 0.000000 0.750000 > > Se 0.500000 0.000000 0.750000 > > Se 0.250000 0.250000 0.750000 > > Se 0.750000 0.250000 0.750000 > > Se 0.000000 0.500000 0.750000 > > Se 0.500000 0.500000 0.750000 > > Se 0.250000 0.750000 0.750000 > > Se 0.750000 0.750000 0.750000 > > > > K_POINTS (automatic) > > 4 4 4 0 0 0 > > > > nscf_in: > > > > &control > > calculation = 'nscf' > > prefix='PbSeAl' > > tstress = .true. > > tprnfor = .true. > > pseudo_dir = "..." > > outdir = "..." > > / > > &system > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > > ecutwfc = 60, > > noncolin = .TRUE. > > lspinorb = .TRUE. > > occupations = 'tetrahedra' > > / > > &electrons > > mixing_beta = 0.05D0 > > conv_thr = 1.0d-10 > > diagonalization = 'david' > > / > > ATOMIC_SPECIES > > Al 26.98 Al.rel-pz-nc.UPF > > Pb 207.21 Pb.rel-pz-nc.UPF > > Se 78.96 Se.rel-pz-nc.UPF > > > > ATOMIC_POSITIONS > > Al 0.000000 0.000000 0.000000 > > Pb 0.500000 0.000000 0.000000 > > Pb 0.250000 0.250000 0.000000 > > Pb 0.750000 0.250000 0.000000 > > Pb 0.000000 0.500000 0.000000 > > Pb 0.500000 0.500000 0.000000 > > Pb 0.250000 0.750000 0.000000 > > Pb 0.750000 0.750000 0.000000 > > Pb 0.250000 0.000000 0.250000 > > Pb 0.750000 0.000000 0.250000 > > Pb 0.000000 0.250000 0.250000 > > Pb 0.500000 0.250000 0.250000 > > Pb 0.250000 0.500000 0.250000 > > Pb 0.750000 0.500000 0.250000 > > Pb 0.000000 0.750000 0.250000 > > Pb 0.500000 0.750000 0.250000 > > Pb 0.000000 0.000000 0.500000 > > Pb 0.500000 0.000000 0.500000 > > Pb 0.250000 0.250000 0.500000 > > Pb 0.750000 0.250000 0.500000 > > Pb 0.000000 0.500000 0.500000 > > Pb 0.500000 0.500000 0.500000 > > Pb 0.250000 0.750000 0.500000 > > Pb 0.750000 0.750000 0.500000 > > Pb 0.250000 0.000000 0.750000 > > Pb 0.750000 0.000000 0.750000 > > Pb 0.000000 0.250000 0.750000 > > Pb 0.500000 0.250000 0.750000 > > Pb 0.250000 0.500000 0.750000 > > Pb 0.750000 0.500000 0.750000 > > Pb 0.000000 0.750000 0.750000 > > Pb 0.500000 0.750000 0.750000 > > Se 0.250000 0.000000 0.000000 > > Se 0.750000 0.000000 0.000000 > > Se 0.000000 0.250000 0.000000 > > Se 0.500000 0.250000 0.000000 > > Se 0.250000 0.500000 0.000000 > > Se 0.750000 0.500000 0.000000 > > Se 0.000000 0.750000 0.000000 > > Se 0.500000 0.750000 0.000000 > > Se 0.000000 0.000000 0.250000 > > Se 0.500000 0.000000 0.250000 > > Se 0.250000 0.250000 0.250000 > > Se 0.750000 0.250000 0.250000 > > Se 0.000000 0.500000 0.250000 > > Se 0.500000 0.500000 0.250000 > > Se 0.250000 0.750000 0.250000 > > Se 0.750000 0.750000 0.250000 > > Se 0.250000 0.000000 0.500000 > > Se 0.750000 0.000000 0.500000 > > Se 0.000000 0.250000 0.500000 > > Se 0.500000 0.250000 0.500000 > > Se 0.250000 0.500000 0.500000 > > Se 0.750000 0.500000 0.500000 > > Se 0.000000 0.750000 0.500000 > > Se 0.500000 0.750000 0.500000 > > Se 0.000000 0.000000 0.750000 > > Se 0.500000 0.000000 0.750000 > > Se 0.250000 0.250000 0.750000 > > Se 0.750000 0.250000 0.750000 > > Se 0.000000 0.500000 0.750000 > > Se 0.500000 0.500000 0.750000 > > Se 0.250000 0.750000 0.750000 > > Se 0.750000 0.750000 0.750000 > > > > K_POINTS (automatic) > > 8 8 8 0 0 0 > > > > > > Can anyone help me with this? > > > > Thanks a lot, > > Zhiting Tian > > PhD student > > Mechanical Engineering Department > > Massachusetts Institute of Technology > > Email: zhiting at mit.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 > _______________________________________________ > 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 songsong19840614 at gmail.com Mon Sep 26 15:14:54 2011 From: songsong19840614 at gmail.com (Yun song,Kang) Date: Mon, 26 Sep 2011 21:14:54 +0800 Subject: [Pw_forum] Too many bands are not converged from nscf calculation In-Reply-To: <201109261008.14535.giuseppe.mattioli@mlib.ism.cnr.it> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A76@EXPO20.exchange.mit.edu> <201109261008.14535.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Hi,Zhiting Tian "Too many bands are not converged" can be solved for two way: 1.increase ecutwfc 2.decrease conv_thr or both do them. Best Regards -- Yun Song,Kang Physical Science and Technology of Inner Mongolia University. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110926/8f5f3309/attachment.htm From amyassin29 at gmail.com Mon Sep 26 18:30:06 2011 From: amyassin29 at gmail.com (Ahmad Yassin) Date: Mon, 26 Sep 2011 19:30:06 +0300 Subject: [Pw_forum] mpif90 compiler that uses ifort Message-ID: Hello all; I had a problem in installing QE 4.0.3 using Intel Compiler... the ./configure step runs smooth if using gcc and gfortran, but when using icc and ifort it gives me the following warnings: configure: WARNING: serial/parallel compiler mismatch detected configure: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler is ifort looking it up, I found a previous email in the mailing list ( http://www.democritos.it/pipermail/pw_forum/2009-June/013265.html) stating that you have a mismatch between parallel (mpif90) and serial (gfortran) compiler. This is something "configure" warns you about. Use "./configure F90=gfortran", or, better, install a mpif90 compiler that uses ifort I tried to reinstall OpenMPI, using icc and ifort to compile its source, but the conflict is still there... Is there anyway to make mpif90 use ifort ? or is there any other parallel compiler using ifort? Ahmad Yassin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110926/d3f16bf1/attachment.htm From windbellklbh at gmail.com Mon Sep 26 18:32:43 2011 From: windbellklbh at gmail.com (WF) Date: Tue, 27 Sep 2011 00:32:43 +0800 Subject: [Pw_forum] Problem of the energy of orbital in ld1.x with Message-ID: <005c01cc7c69$ed696760$c83c3620$@gmail.com> On Sep 26, 2011, at 8:30, Paolo Giannozzi wrote: > energy = 0.00 => "use energy of the bound state" > energy /=0.00 => "use specified energy for pseudization" > It is clumsy and unclear but it was done that way and now it cannot > be changed > without breaking existing data. Anyway, it is documented. > In the latter case, the pseudo-wavefunction is not used for projection: > it is not guaranteed to be a bund state Yes it is documented in atomic package related guide, but I have not understand it clearly until you explain this. Thanks very much for your patience guidance. Best regards, Wu ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- From jtmullen at ncsu.edu Mon Sep 26 19:10:44 2011 From: jtmullen at ncsu.edu (Jeff Mullen) Date: Mon, 26 Sep 2011 13:10:44 -0400 Subject: [Pw_forum] mpif90 compiler that uses ifort In-Reply-To: References: Message-ID: Hello Ahmad I recently compiled QE with ifort and had the same issue. I resolved by first setting the OMPI_MPF90 environment variable to be ifort. For example, in the bash shell export OMPI_MPIF90=ifort then compiling, I explicitly set all the F##=ifort and MPIF90=mpif90 ./configure MPIF90=mpif90 F90=ifort F77=ifort This eliminated the constant references to gfortran. You can find more about OPENMPI settings for compiling applications at http://www.open-mpi.org/faq/?category=mpi-apps Good Luck Jeff Mullen Physics North Carolina State University On Mon, Sep 26, 2011 at 12:30 PM, Ahmad Yassin wrote: > Hello all; > I had a problem in installing QE 4.0.3 using Intel Compiler... the > ./configure step runs smooth if using gcc and gfortran, but when using icc > and ifort it gives me the following warnings: > > configure: WARNING: serial/parallel compiler mismatch detected > configure: WARNING: parallel compiler mpif90 uses gfortran, but serial > compiler is ifort > > looking it up, I found a previous email in the mailing list ( > http://www.democritos.it/pipermail/pw_forum/2009-June/013265.html) stating > that > > you have a mismatch between parallel (mpif90) and > serial (gfortran) compiler. This is something > "configure" warns you about. Use > "./configure F90=gfortran", or, better, install > a mpif90 compiler that uses ifort > > I tried to reinstall OpenMPI, using icc and ifort to compile its source, > but the conflict is still there... Is there anyway to make mpif90 use ifort > ? or is there any other parallel compiler using ifort? > > Ahmad Yassin > > > > > _______________________________________________ > 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/20110926/23848923/attachment.htm From flux_ray12 at 163.com Tue Sep 27 03:46:42 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 27 Sep 2011 09:46:42 +0800 (CST) Subject: [Pw_forum] mpif90 compiler that uses ifort In-Reply-To: References: Message-ID: <2b32df6a.2a72.132a890005f.Coremail.flux_ray12@163.com> In my case, I installed ifort 2011 at first, and then compiled OpenMPI by ifort with command: ./configure --prefix=/**** FC=ifort After "make install" OpenMPI, the $MPIBIN=/**/OpenMPI/bin and $MPILIB=/***/OpenMPI/Lib have been added into .bashrc file through the method: $PATH=$MPIBIN:$PATH and $LD_LIBRARY_PATH=$MPILIB:$LD_LIBRARY_PATH. When compiling QE v4.3.2, only ./configure was needed, then ifort and mpif90 would be chosen automaticly (if compiled before, "make clean" first) Hope this method can work in your case. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-27 00:30:06,"Ahmad Yassin" wrote: Hello all; I had a problem in installing QE 4.0.3 using Intel Compiler... the ./configure step runs smooth if using gcc and gfortran, but when using icc and ifort it gives me the following warnings: configure: WARNING: serial/parallel compiler mismatch detected configure: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler is ifort looking it up, I found a previous email in the mailing list (http://www.democritos.it/pipermail/pw_forum/2009-June/013265.html) stating that you have a mismatch between parallel (mpif90) and serial (gfortran) compiler. This is something "configure" warns you about. Use "./configure F90=gfortran", or, better, install a mpif90 compiler that uses ifort I tried to reinstall OpenMPI, using icc and ifort to compile its source, but the conflict is still there... Is there anyway to make mpif90 use ifort ? or is there any other parallel compiler using ifort? Ahmad Yassin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/caefa21c/attachment-0001.htm From padmaja_patnaik at yahoo.co.uk Tue Sep 27 08:24:52 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 27 Sep 2011 07:24:52 +0100 (BST) Subject: [Pw_forum] Finding effective mass Message-ID: <1317104692.84608.YahooMailNeo@web28514.mail.ukl.yahoo.com> Dear All Is it possible to calculate effective mass using k.p method in quantum espresso? Regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/fbd5d5d7/attachment.htm From giannozz at democritos.it Tue Sep 27 10:34:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 27 Sep 2011 10:34:33 +0200 Subject: [Pw_forum] Finding effective mass In-Reply-To: <1317104692.84608.YahooMailNeo@web28514.mail.ukl.yahoo.com> References: <1317104692.84608.YahooMailNeo@web28514.mail.ukl.yahoo.com> Message-ID: <1317112473.13690.6.camel@fe12lx.fisica.uniud.it> On Tue, 2011-09-27 at 07:24 +0100, Padmaja Patnaik wrote: > Is it possible to calculate effective mass using k.p method in quantum espresso? no, it is not implemented. Anyway, as far as I remember, the k.p method works for local (pseudo)potentials only P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From eariel99 at gmail.com Tue Sep 27 15:40:48 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 27 Sep 2011 15:40:48 +0200 Subject: [Pw_forum] Finding effective mass Message-ID: Dear Padmaja, Quantum ESPRESSO calculates the band energies by a method different from k.p. If you want to calculate an effective mass you can use QE to calculate the band energies in the neighborhood of the desired k-point and then obtain the effective mass doing numerical derivation. If you want to get inside he code, you can extract the matrix elements of the momentum operator and program the calculation of the effective mass. Due to the non-locality of the pseudopotentials, as well as of the GGA functionals, I am not sure if the expressions found in the 50's classic papers (e.g. Kohn&Luttinger) can be applied. In presence of non local hamiltonian it is not true that p/m=[H,r]/ihbar I know that for optical properties, the momentum operator in the A.p interaction hamiltonian has to be replaced by a generalized operator. See, e.g., PRB48, 11789 (1993) and PRB 73, 045112 (2006). Hence, I suspect you would have to repeat the derivation made in the classic papers, or find where it is done (and let me know your findings). Best regards Eduardo ---------- Mensaje reenviado ---------- From: Padmaja Patnaik To: "pw_forum at pwscf.org" Date: Tue, 27 Sep 2011 07:24:52 +0100 (BST) Subject: [Pw_forum] Finding effective mass Dear All Is it possible to calculate effective mass using k.p method in quantum espresso? -- 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). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/1b9b54fc/attachment.htm From vkarthik at MIT.EDU Tue Sep 27 16:29:45 2011 From: vkarthik at MIT.EDU (vkarthik) Date: Tue, 27 Sep 2011 10:29:45 -0400 Subject: [Pw_forum] PostProcessing the .save file on another machine Message-ID: <20110927102945.9fg00wls044ocscg@webmail.mit.edu> Hi, I had a technical question on performing post process functions like bands.x. I use a supercomputer to run my scf calculations. Once done, I am interested in transferring the prefix.save file into my QE on my laptop (same QE version as the one installed in the mainframe of the supercomputer). Whenever I try to process any job on my laptop, it fails to run and gives an error saying cannot open the charge-density.dat file from the outdir. Are the contents of the .save file very specific to the computer architecture used for running the QE code ? Is there anyway, I can process the data from my personal computer ? Best, Karthik From izaakw89 at yahoo.com Tue Sep 27 23:10:09 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Tue, 27 Sep 2011 14:10:09 -0700 (PDT) Subject: [Pw_forum] Magnetic Anisotropy using PAW In-Reply-To: References: Message-ID: <1317157809.77783.YahooMailNeo@web43406.mail.sp1.yahoo.com> Dear all, I would like to calculate the magnetic anisotropy of some materials using PAW potentials instead of US pseudopotentials. Is the calculation of magnetic anisotropy using PAW already implemented in QE? Any references on this subject would be of great help. Thank you. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/cb34162a/attachment.htm From amar.shugani at gmail.com Wed Sep 28 08:27:48 2011 From: amar.shugani at gmail.com (amar shugani) Date: Tue, 27 Sep 2011 23:27:48 -0700 Subject: [Pw_forum] problem about ibrav no. Message-ID: Respected sir, my compound is molybdenum disilicide .when i am putting ibrav no. 7 correct structure is not forming when i am giving 6 structure is same as given on crystal structure site but MoSi2 is bct for which ibrav no. is 7 sir,guide me about this and tell me whether my input file and structure is correct or not -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/6aad4a42/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mosi2new Type: application/octet-stream Size: 844 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110927/6aad4a42/attachment.obj From flux_ray12 at 163.com Wed Sep 28 08:58:51 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 28 Sep 2011 14:58:51 +0800 (CST) Subject: [Pw_forum] problem about ibrav no. In-Reply-To: References: Message-ID: <1d28c1dc.f5a8.132aed42618.Coremail.flux_ray12@163.com> I do not know whether your structure was right or not unless you provide the data base of MoSi. However, you can determine the strcutre by CELL_PARAMETER and ATOMIC_POSITIONS, which can be obtained by the utility, spacegroup, in ELK/Exciting code according ICSD. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-28 14:27:48,"amar shugani" wrote: Respected sir, my compound is molybdenum disilicide .when i am putting ibrav no. 7 correct structure is not forming when i am giving 6 structure is same as given on crystal structure site but MoSi2 is bct for which ibrav no. is 7 sir,guide me about this and tell me whether my input file and structure is correct or not -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110928/c5f19f84/attachment.htm From giannozz at democritos.it Wed Sep 28 09:48:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 28 Sep 2011 09:48:59 +0200 Subject: [Pw_forum] PostProcessing the .save file on another machine In-Reply-To: <20110927102945.9fg00wls044ocscg@webmail.mit.edu> References: <20110927102945.9fg00wls044ocscg@webmail.mit.edu> Message-ID: <1317196139.16750.19.camel@fe12lx.fisica.uniud.it> On Tue, 2011-09-27 at 10:29 -0400, vkarthik wrote: > Are the contents of the .save file very specific to the computer architecture > used for running the QE code ? they aren't "very" specific, but they specific enough to make reading a file produced on a different machine a nontrivial task. In principle, machines with the same binary representation of numbers should be able to exchange files, but then there is the big-endian vs little-endian stuff etc. Also note that the following may apply to your case: http://www.democritos.it/pipermail/pw_forum/2011-September/022043.html > Is there anyway, I can process the data from my personal computer ? try the iotk_copy utility: it converts from binary to text and back. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From joshiniharika20 at yahoo.in Wed Sep 28 14:59:02 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Wed, 28 Sep 2011 18:29:02 +0530 (IST) Subject: [Pw_forum] problem in xspectra calculations Message-ID: <1317214742.49087.YahooMailClassic@web95706.mail.in.yahoo.com> Hello, I am trying the test xspectra calculation for diamond. The scf and fermi energy calculations run fine, but the xanes calculation remains incomplete. In its output file, at the end it says 'Could not find the element? C in the table of K edge energies!' I'm using quantum espresso v4.3.2 Can anyone suggest what possibly is wrong? Below are the inputs for scf, fermi energy and xanes calculations. &control ??? calculation='scf', pseudo_dir = './Matteo/Gipaw_Pseudo_Generation/C_Hole', ??? outdir='./tmp/', ??? prefix='diamondh', ??? verbosity='high' ?/ ?&system ??? ibrav = 1, ??? celldm(1) = 6.740256, ??? nat=8, ??? ntyp=2, ??? nbnd=17, ??? ecutwfc=40.0, ??? tot_charge=+1.0, ?/ ?&electrons ??? mixing_beta = 0.3, ?/ ATOMIC_SPECIES Ch 12.0 C.star1s-pbe-mt_gipaw.UPF C 12.0 C.pbe-mt_gipaw.UPF ATOMIC_POSITIONS crystal Ch 0.0 0.0 0.0 C 0.0 0.5 0.5 C 0.5 0.0 0.5 C 0.5 0.5 0.0 C 0.75 0.75 0.25 C 0.75 0.25 0.75 C 0.25 0.75 0.75 C 0.25 0.25 0.25 K_POINTS automatic 4 4 4 0 0 0 ?input for calculating? fermi energy... &input_xspectra ??? calculation='fermi_level', ??? prefix='diamondh', ??? outdir='./tmp/', ??? xread_wf=.true., ?/ ?&plot ?/ ?&pseudos ??? filecore='Ch1.wfc', ?/ ?&cut_occ ?/ 4 4 4 0 0 0 input for xanes.... ?&input_xspectra ??? calculation='xanes_dipole', ??? prefix='diamondh', ??? outdir='./tmp/', ??? xniter=1000, ??? xcheck_conv=50, ??? xepsilon(1)=1.0, ??? xepsilon(2)=0.0, ??? xepsilon(3)=0.0, ??? xiabs=1, ??? x_save_file='diamondh.xspectra.sav', ??? ef_r=0.94036945, ??? xerror=0.001, ?/ ?&plot ??? xnepoint=1000, ??? xgamma=0.8, ??? xemin=-10.0, ??? xemax=30.0, ??? terminator=.true., ??? cut_occ_states=.false., ?/ ?&pseudos ??? filecore='Ch1.wfc', ??? r_paw(1)=3.2, ?/ ?&cut_occ ?/ 4 4 4 1 1 1 Thanking in advance. -Niharika Joshi (project student, IISER Pune) ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110928/6d334959/attachment.htm From trambui at u.boisestate.edu Wed Sep 28 19:17:17 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 28 Sep 2011 11:17:17 -0600 Subject: [Pw_forum] Charge density: what min and max values represent? Message-ID: Dear Everyone, I have got the data below from my output of 2D charge density calculation. I ran my work for two different defects type in bulk SiC (2x2x2 super cell): - One defect with Cs sits at C site (1/4 1/4 1/4 position), I got this information below Min, Max, imaginary charge: 0.000143 0.391420 0.000000 - One defect with Cs sits at Si site (1/2 1/2 0 position) and I got the information below Min, Max, imaginary charge: -0.000006 0.393416 0.000000 *My question are what does it mean when the min charge density is negative? and what difference does it make between the negative min charge density and positive min charge dendity. * Also, when I do the density of state calculation for the cells above (SiC with Cs at substitutional site of C and Si), I found an extra peak in the band gap and : for Cs at C site in SiC, the extra peak is close to the conduction band minimum for Cs at Si site in SiC, the extra peak is closed to the valence band maxnimum *So does it have something to do with the charge density, I found to be starting with negative and postitive above?I mean is there a correlation here or they are totally from different thing? * I'm sorry if my questions are confusing or do not make any sense, and I really appreciate any input you have for me. Best Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110928/18158c81/attachment.htm From zhiting at MIT.EDU Wed Sep 28 22:01:43 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Wed, 28 Sep 2011 16:01:43 -0400 Subject: [Pw_forum] Error running dos.x Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A82@EXPO20.exchange.mit.edu> Dear all, I am running dos.x. I have succeeded in running it couple of times. But for most of the time, I get the error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from pp_check_file : error # 2 file /home/.../PbSedos.save not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% But I have checked and the folder PbSedos.save is definitely there. I am using the same version of espresso and I don't think version should be a problem. Sometimes, I get the error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from dos : error # 1 pools not implemented, or incorrect file read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Or %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Anyone could give me some hints? Thanks, Zhiting Tian Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge, MA 02139 From zhiting at MIT.EDU Wed Sep 28 22:04:21 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Wed, 28 Sep 2011 16:04:21 -0400 Subject: [Pw_forum] Too many bands are not converged from nscf calculation In-Reply-To: <201109261008.14535.giuseppe.mattioli@mlib.ism.cnr.it> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A76@EXPO20.exchange.mit.edu>, <201109261008.14535.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A83@EXPO20.exchange.mit.edu> I have increased my conv_thr to 1.0d-8 and I am using nbnd=500, occupation='tetrahedra' for nscf. But I got the error message and the program stopped. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from tweights : error # 1 bad Fermi energy %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Any suggestions? Thanks, Zhiting ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Giuseppe Mattioli [giuseppe.mattioli at mlib.ism.cnr.it] Sent: Monday, September 26, 2011 4:08 AM To: PWSCF Forum Subject: Re: [Pw_forum] Too many bands are not converged from nscf calculation Dear Zhiting This erratic behaviour may occur quite often, and it is sometimes difficult to track down. I can only suggest to increase the ecutwfc value: 60 Ry could be not enough for your norm conserving pseudopotentials. HTH Giuseppe P.S. > conv_thr = 1.0d-10 too tight for an scf calculation. 1.0d-8 should be enough. On Sunday 25 September 2011 22:59:48 Zhiting Tian wrote: > I see. That's silly mistake. Since I set nbnd=18 for 2 atoms testing case > and forgot to change it. Now I have removed nbnd, but got the following > error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from cdiaghg : error # 1273 > > problems computing cholesky > stopping ... > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Does it mean that I need to change the diagonalization? > Thanks, > Zhiting > > ________________________________________ > From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of > giuseppe.mattioli at mlib.ism.cnr.it [giuseppe.mattioli at mlib.ism.cnr.it] Sent: > Sunday, September 25, 2011 3:12 PM > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Too many bands are not converged from nscf > calculation > > Dear Zhiting > > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > > your 64-atom alloy supercell should contain much more than 18 occupied > bands. If you want to calculate 18 unoccupied bands you should set the > nband parameter to "number_of_occupied_levels+18". > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Citando Zhiting Tian : > > Dear all, > > > > I first did scf calculation and it finished. Then I run nscf, but > > always got error message: "Too many bands are not converged" and > > then it stopped. > > I had read a few posts before and tried to reduce mixing-beta from > > 0.7 to 0.4 and even to 0.05, but same error. Also, I have tried to > > change the diagolization='david' to 'cg', same error. > > > > My input files are following: > > scf_in: > > > > &control > > calculation = 'scf' > > restart_mode='from_scratch' > > prefix='PbSeAl' > > tstress = .true. > > tprnfor = .true. > > pseudo_dir = "..." > > outdir = "..." > > / > > &system > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3 , > > ecutwfc = 60, > > noncolin = .TRUE. > > lspinorb = .TRUE. > > occupations = 'smearing' > > smearing = 'mv' > > degauss = 0.01 > > / > > &electrons > > mixing_beta = 0.7D0 > > conv_thr = 1.0d-10 > > / > > ATOMIC_SPECIES > > Al 26.98 Al.rel-pz-nc.UPF > > Pb 207.21 Pb.rel-pz-nc.UPF > > Se 78.96 Se.rel-pz-nc.UPF > > > > ATOMIC_POSITIONS > > Al 0.000000 0.000000 0.000000 > > Pb 0.500000 0.000000 0.000000 > > Pb 0.250000 0.250000 0.000000 > > Pb 0.750000 0.250000 0.000000 > > Pb 0.000000 0.500000 0.000000 > > Pb 0.500000 0.500000 0.000000 > > Pb 0.250000 0.750000 0.000000 > > Pb 0.750000 0.750000 0.000000 > > Pb 0.250000 0.000000 0.250000 > > Pb 0.750000 0.000000 0.250000 > > Pb 0.000000 0.250000 0.250000 > > Pb 0.500000 0.250000 0.250000 > > Pb 0.250000 0.500000 0.250000 > > Pb 0.750000 0.500000 0.250000 > > Pb 0.000000 0.750000 0.250000 > > Pb 0.500000 0.750000 0.250000 > > Pb 0.000000 0.000000 0.500000 > > Pb 0.500000 0.000000 0.500000 > > Pb 0.250000 0.250000 0.500000 > > Pb 0.750000 0.250000 0.500000 > > Pb 0.000000 0.500000 0.500000 > > Pb 0.500000 0.500000 0.500000 > > Pb 0.250000 0.750000 0.500000 > > Pb 0.750000 0.750000 0.500000 > > Pb 0.250000 0.000000 0.750000 > > Pb 0.750000 0.000000 0.750000 > > Pb 0.000000 0.250000 0.750000 > > Pb 0.500000 0.250000 0.750000 > > Pb 0.250000 0.500000 0.750000 > > Pb 0.750000 0.500000 0.750000 > > Pb 0.000000 0.750000 0.750000 > > Pb 0.500000 0.750000 0.750000 > > Se 0.250000 0.000000 0.000000 > > Se 0.750000 0.000000 0.000000 > > Se 0.000000 0.250000 0.000000 > > Se 0.500000 0.250000 0.000000 > > Se 0.250000 0.500000 0.000000 > > Se 0.750000 0.500000 0.000000 > > Se 0.000000 0.750000 0.000000 > > Se 0.500000 0.750000 0.000000 > > Se 0.000000 0.000000 0.250000 > > Se 0.500000 0.000000 0.250000 > > Se 0.250000 0.250000 0.250000 > > Se 0.750000 0.250000 0.250000 > > Se 0.000000 0.500000 0.250000 > > Se 0.500000 0.500000 0.250000 > > Se 0.250000 0.750000 0.250000 > > Se 0.750000 0.750000 0.250000 > > Se 0.250000 0.000000 0.500000 > > Se 0.750000 0.000000 0.500000 > > Se 0.000000 0.250000 0.500000 > > Se 0.500000 0.250000 0.500000 > > Se 0.250000 0.500000 0.500000 > > Se 0.750000 0.500000 0.500000 > > Se 0.000000 0.750000 0.500000 > > Se 0.500000 0.750000 0.500000 > > Se 0.000000 0.000000 0.750000 > > Se 0.500000 0.000000 0.750000 > > Se 0.250000 0.250000 0.750000 > > Se 0.750000 0.250000 0.750000 > > Se 0.000000 0.500000 0.750000 > > Se 0.500000 0.500000 0.750000 > > Se 0.250000 0.750000 0.750000 > > Se 0.750000 0.750000 0.750000 > > > > K_POINTS (automatic) > > 4 4 4 0 0 0 > > > > nscf_in: > > > > &control > > calculation = 'nscf' > > prefix='PbSeAl' > > tstress = .true. > > tprnfor = .true. > > pseudo_dir = "..." > > outdir = "..." > > / > > &system > > ibrav= 1, celldm(1)= 22.52, nat= 64, ntyp= 3, nbnd=18 > > ecutwfc = 60, > > noncolin = .TRUE. > > lspinorb = .TRUE. > > occupations = 'tetrahedra' > > / > > &electrons > > mixing_beta = 0.05D0 > > conv_thr = 1.0d-10 > > diagonalization = 'david' > > / > > ATOMIC_SPECIES > > Al 26.98 Al.rel-pz-nc.UPF > > Pb 207.21 Pb.rel-pz-nc.UPF > > Se 78.96 Se.rel-pz-nc.UPF > > > > ATOMIC_POSITIONS > > Al 0.000000 0.000000 0.000000 > > Pb 0.500000 0.000000 0.000000 > > Pb 0.250000 0.250000 0.000000 > > Pb 0.750000 0.250000 0.000000 > > Pb 0.000000 0.500000 0.000000 > > Pb 0.500000 0.500000 0.000000 > > Pb 0.250000 0.750000 0.000000 > > Pb 0.750000 0.750000 0.000000 > > Pb 0.250000 0.000000 0.250000 > > Pb 0.750000 0.000000 0.250000 > > Pb 0.000000 0.250000 0.250000 > > Pb 0.500000 0.250000 0.250000 > > Pb 0.250000 0.500000 0.250000 > > Pb 0.750000 0.500000 0.250000 > > Pb 0.000000 0.750000 0.250000 > > Pb 0.500000 0.750000 0.250000 > > Pb 0.000000 0.000000 0.500000 > > Pb 0.500000 0.000000 0.500000 > > Pb 0.250000 0.250000 0.500000 > > Pb 0.750000 0.250000 0.500000 > > Pb 0.000000 0.500000 0.500000 > > Pb 0.500000 0.500000 0.500000 > > Pb 0.250000 0.750000 0.500000 > > Pb 0.750000 0.750000 0.500000 > > Pb 0.250000 0.000000 0.750000 > > Pb 0.750000 0.000000 0.750000 > > Pb 0.000000 0.250000 0.750000 > > Pb 0.500000 0.250000 0.750000 > > Pb 0.250000 0.500000 0.750000 > > Pb 0.750000 0.500000 0.750000 > > Pb 0.000000 0.750000 0.750000 > > Pb 0.500000 0.750000 0.750000 > > Se 0.250000 0.000000 0.000000 > > Se 0.750000 0.000000 0.000000 > > Se 0.000000 0.250000 0.000000 > > Se 0.500000 0.250000 0.000000 > > Se 0.250000 0.500000 0.000000 > > Se 0.750000 0.500000 0.000000 > > Se 0.000000 0.750000 0.000000 > > Se 0.500000 0.750000 0.000000 > > Se 0.000000 0.000000 0.250000 > > Se 0.500000 0.000000 0.250000 > > Se 0.250000 0.250000 0.250000 > > Se 0.750000 0.250000 0.250000 > > Se 0.000000 0.500000 0.250000 > > Se 0.500000 0.500000 0.250000 > > Se 0.250000 0.750000 0.250000 > > Se 0.750000 0.750000 0.250000 > > Se 0.250000 0.000000 0.500000 > > Se 0.750000 0.000000 0.500000 > > Se 0.000000 0.250000 0.500000 > > Se 0.500000 0.250000 0.500000 > > Se 0.250000 0.500000 0.500000 > > Se 0.750000 0.500000 0.500000 > > Se 0.000000 0.750000 0.500000 > > Se 0.500000 0.750000 0.500000 > > Se 0.000000 0.000000 0.750000 > > Se 0.500000 0.000000 0.750000 > > Se 0.250000 0.250000 0.750000 > > Se 0.750000 0.250000 0.750000 > > Se 0.000000 0.500000 0.750000 > > Se 0.500000 0.500000 0.750000 > > Se 0.250000 0.750000 0.750000 > > Se 0.750000 0.750000 0.750000 > > > > K_POINTS (automatic) > > 8 8 8 0 0 0 > > > > > > Can anyone help me with this? > > > > Thanks a lot, > > Zhiting Tian > > PhD student > > Mechanical Engineering Department > > Massachusetts Institute of Technology > > Email: zhiting at mit.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 > _______________________________________________ > 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 From flux_ray12 at 163.com Thu Sep 29 02:17:40 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 29 Sep 2011 08:17:40 +0800 (CST) Subject: [Pw_forum] Error running dos.x In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997A82@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A82@EXPO20.exchange.mit.edu> Message-ID: <7afd36a0.641.132b28b353d.Coremail.flux_ray12@163.com> Why not trywf_collect = .true. anddisk_io = 'default' in pw.x ? At least, when I calculatednscf afterscf, it does not work if disk_io = 'low'. The similar thing may occur indos.x case. Good luck. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-29 04:01:43,"Zhiting Tian" wrote: >Dear all, > >I am running dos.x. I have succeeded in running it couple of times. But for most of the time, I get the error message: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from pp_check_file : error # 2 > file /home/.../PbSedos.save not found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >But I have checked and the folder PbSedos.save is definitely there. I am using the same version of espresso and I don't think version should be a problem. > >Sometimes, I get the error message: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from dos : error # 1 > pools not implemented, or incorrect file read > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >Or >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > reading inputpp namelist > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > >Anyone could give me some hints? > >Thanks, >Zhiting Tian >Department of Mechanical Engineering >Massachusetts Institute of Technology >Cambridge, MA 02139 >_______________________________________________ >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/20110929/13b66832/attachment.htm From zhiting at MIT.EDU Thu Sep 29 05:04:55 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Wed, 28 Sep 2011 23:04:55 -0400 Subject: [Pw_forum] projwfc.x error Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A85@EXPO20.exchange.mit.edu> Dear all, I searched on forum but didn't see this error. I got the error message as following: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from d_matrix_so : error # 19 D_S (j=1/2) for this symmetry operation is not unitary %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My in_pdos is: &inputpp prefix='PbSedos', outdir='/home/.../tmp' Emin=-10,Emax=15,DeltaE=0.1 / Does anyone know how to solve it? Thanks a lot. Zhiting Tian Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge, MA 02139 From zhiting at MIT.EDU Thu Sep 29 05:05:34 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Wed, 28 Sep 2011 23:05:34 -0400 Subject: [Pw_forum] Error running dos.x In-Reply-To: <7afd36a0.641.132b28b353d.Coremail.flux_ray12@163.com> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A82@EXPO20.exchange.mit.edu>, <7afd36a0.641.132b28b353d.Coremail.flux_ray12@163.com> Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997A86@EXPO20.exchange.mit.edu> Thanks. I have fixed the problem. I set npool to be 4 at the beginning, but I guess that for dos.x, I should not have npool > 1. wf_collect is a good point since I have never paid attention to this keyword. In this case, since dos.x doesn't read wave function, it is OK. But I will keep it in mind for the cases where wave functions are read. Zhiting ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of GAO Zhe [flux_ray12 at 163.com] Sent: Wednesday, September 28, 2011 8:17 PM To: PWSCF Forum Subject: Re: [Pw_forum] Error running dos.x Why not try wf_collect = .true. and disk_io = 'default' in pw.x ? At least, when I calculated nscf after scf, it does not work if disk_io = 'low'. The similar thing may occur in dos.x case. Good luck. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-29 04:01:43,"Zhiting Tian" wrote: >Dear all, > >I am running dos.x. I have succeeded in running it couple of times. But for most of the time, I get the error message: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from pp_check_file : error # 2 > file /home/.../PbSedos.save not found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >But I have checked and the folder PbSedos.save is definitely there. I am using the same version of espresso and I don't think version should be a problem. > >Sometimes, I get the error message: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from dos : error # 1 > pools not implemented, or incorrect file read > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >Or >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > reading inputpp namelist > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > >Anyone could give me some hints? > >Thanks, >Zhiting Tian >Department of Mechanical Engineering >Massachusetts Institute of Technology >Cambridge, MA 02139 >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum From amyassin29 at gmail.com Thu Sep 29 14:48:25 2011 From: amyassin29 at gmail.com (Ahmad Yassin) Date: Thu, 29 Sep 2011 15:48:25 +0300 Subject: [Pw_forum] mpif90 compiler that uses ifort In-Reply-To: <2b32df6a.2a72.132a890005f.Coremail.flux_ray12@163.com> References: <2b32df6a.2a72.132a890005f.Coremail.flux_ray12@163.com> Message-ID: I found that I can use OpenMPI with Intel compilers without recompiling it... just by setting the environmental variables OMPI_CC=icc, OMPI_CXX=icpc, OMPI_F77=ifort, and OMPI_FC=ifort . I'd be sure when doing the ./configure to set CC=icc, CXX=icpc, FC & F77 = ifort... Thank you all a lot... Ahmad Yassin 2011/9/27 GAO Zhe > In my case, I installed ifort 2011 at first, and then compiled OpenMPI by > ifort with command: > ./configure --prefix=/**** FC=ifort > After "make install" OpenMPI, the $MPIBIN=/**/OpenMPI/bin and > $MPILIB=/***/OpenMPI/Lib have been added into .bashrc file through the > method: $PATH=$MPIBIN:$PATH and $LD_LIBRARY_PATH=$MPILIB:$LD_LIBRARY_PATH. > When compiling QE v4.3.2, only ./configure was needed, then ifort and > mpif90 would be chosen automaticly (if compiled before, "make clean" first) > Hope this method can work in your case. > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-09-27 00:30:06,"Ahmad Yassin" wrote: > > Hello all; > I had a problem in installing QE 4.0.3 using Intel Compiler... the > ./configure step runs smooth if using gcc and gfortran, but when using icc > and ifort it gives me the following warnings: > > configure: WARNING: serial/parallel compiler mismatch detected > configure: WARNING: parallel compiler mpif90 uses gfortran, but serial > compiler is ifort > > looking it up, I found a previous email in the mailing list ( > http://www.democritos.it/pipermail/pw_forum/2009-June/013265.html) stating > that > > you have a mismatch between parallel (mpif90) and > serial (gfortran) compiler. This is something > "configure" warns you about. Use > "./configure F90=gfortran", or, better, install > a mpif90 compiler that uses ifort > > I tried to reinstall OpenMPI, using icc and ifort to compile its source, > but the conflict is still there... Is there anyway to make mpif90 use ifort > ? or is there any other parallel compiler using ifort? > > Ahmad Yassin > > > > > > > _______________________________________________ > 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/20110929/dcc81cfd/attachment.htm From swapnil.chandratre at gmail.com Fri Sep 30 00:41:04 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 29 Sep 2011 17:41:04 -0500 Subject: [Pw_forum] Graphene Sheet with Antidots Message-ID: Hi, I am sending the input file I am using for a graphene sheet with H passivated antidots, the script is taking very long time to converge. The simulations converge in 20 steps but it is taking terribly long. Can anyone comment on what changes can help bringing the time consumed down? &control calculation = 'scf' restart_mode = 'from_scratch' pseudo_dir = '/work/s/sharma/schandratre/pseudo' outdir = '/work/s/sharma/schandratre/triangular02strain' / &system ibrav = 0 celldm(1) = 1.8897261 nat=222 ntyp=2 ecutwfc=30.0 ecutrho = 300.0 , / &electrons conv_thr = 1.0d-6, mixing_beta=0.05, / ATOMIC_SPECIES C 12.0000 C.pz-vbc.UPF H 1.00000 H.pz-vbc.UPF ATOMIC_POSITIONS {angstrom} C 5.000000e+00 2.841730e+00 2.447465e+01 C 5.000000e+00 3.552160e+00 2.321954e+01 C 5.000000e+00 1.420870e+00 2.447465e+01 C 5.000000e+00 2.841730e+00 2.196443e+01 C 5.000000e+00 3.552160e+00 2.070932e+01 C 5.000000e+00 7.104400e-01 2.321954e+01 C 5.000000e+00 1.420870e+00 2.196443e+01 C 5.000000e+00 2.841730e+00 1.945421e+01 C 5.000000e+00 3.552160e+00 1.819910e+01 C 5.000000e+00 7.104400e-01 2.070932e+01 C 5.000000e+00 1.420870e+00 1.945421e+01 C 5.000000e+00 2.841730e+00 1.694399e+01 C 5.000000e+00 3.552160e+00 1.568888e+01 C 5.000000e+00 7.104400e-01 1.819910e+01 C 5.000000e+00 1.420870e+00 1.694399e+01 C 5.000000e+00 2.841730e+00 1.443377e+01 C 5.000000e+00 3.552160e+00 1.317866e+01 C 5.000000e+00 7.104400e-01 1.568888e+01 C 5.000000e+00 1.420870e+00 1.443377e+01 C 5.000000e+00 2.841730e+00 1.192354e+01 C 5.000000e+00 3.552160e+00 1.066843e+01 C 5.000000e+00 7.104400e-01 1.317866e+01 C 5.000000e+00 1.420870e+00 1.192354e+01 C 5.000000e+00 2.841730e+00 9.413323e+00 C 5.000000e+00 3.552160e+00 8.158212e+00 C 5.000000e+00 7.104400e-01 1.066843e+01 C 5.000000e+00 1.420870e+00 9.413323e+00 C 5.000000e+00 2.841730e+00 6.903101e+00 C 5.000000e+00 3.552160e+00 5.647990e+00 C 5.000000e+00 7.104400e-01 8.158212e+00 C 5.000000e+00 1.420870e+00 6.903101e+00 C 5.000000e+00 2.841730e+00 4.392879e+00 C 5.000000e+00 3.552160e+00 3.137768e+00 C 5.000000e+00 7.104400e-01 5.647990e+00 C 5.000000e+00 1.420870e+00 4.392879e+00 C 5.000000e+00 2.841730e+00 1.882658e+00 C 5.000000e+00 3.552160e+00 6.275467e-01 C 5.000000e+00 7.104400e-01 3.137768e+00 C 5.000000e+00 1.420870e+00 1.882658e+00 C 5.000000e+00 7.104400e-01 6.275467e-01 C 5.000000e+00 7.104310e+00 2.447465e+01 C 5.000000e+00 7.814740e+00 2.321954e+01 C 5.000000e+00 5.683450e+00 2.447465e+01 C 5.000000e+00 7.104310e+00 2.196443e+01 C 5.000000e+00 7.814740e+00 2.070932e+01 C 5.000000e+00 4.973020e+00 2.321954e+01 C 5.000000e+00 5.683450e+00 2.196443e+01 C 5.000000e+00 7.104310e+00 1.945421e+01 C 5.000000e+00 7.814740e+00 1.819910e+01 C 5.000000e+00 4.973020e+00 2.070932e+01 C 5.000000e+00 5.683450e+00 1.945421e+01 C 5.000000e+00 7.104310e+00 1.694399e+01 C 5.000000e+00 4.973020e+00 1.819910e+01 C 5.000000e+00 5.683450e+00 1.694399e+01 C 5.000000e+00 4.973020e+00 1.568888e+01 C 5.000000e+00 5.683450e+00 1.443377e+01 C 5.000000e+00 7.104310e+00 1.192354e+01 C 5.000000e+00 7.814740e+00 1.066843e+01 C 5.000000e+00 4.973020e+00 1.317866e+01 C 5.000000e+00 5.683450e+00 1.192354e+01 C 5.000000e+00 7.104310e+00 9.413323e+00 C 5.000000e+00 7.814740e+00 8.158212e+00 C 5.000000e+00 4.973020e+00 1.066843e+01 C 5.000000e+00 5.683450e+00 9.413323e+00 C 5.000000e+00 7.104310e+00 6.903101e+00 C 5.000000e+00 7.814740e+00 5.647990e+00 C 5.000000e+00 4.973020e+00 8.158212e+00 C 5.000000e+00 5.683450e+00 6.903101e+00 C 5.000000e+00 7.104310e+00 4.392879e+00 C 5.000000e+00 7.814740e+00 3.137768e+00 C 5.000000e+00 4.973020e+00 5.647990e+00 C 5.000000e+00 5.683450e+00 4.392879e+00 C 5.000000e+00 7.104310e+00 1.882658e+00 C 5.000000e+00 7.814740e+00 6.275467e-01 C 5.000000e+00 4.973020e+00 3.137768e+00 C 5.000000e+00 5.683450e+00 1.882658e+00 C 5.000000e+00 4.973020e+00 6.275467e-01 C 5.000000e+00 1.136689e+01 2.447465e+01 C 5.000000e+00 1.207732e+01 2.321954e+01 C 5.000000e+00 9.946030e+00 2.447465e+01 C 5.000000e+00 1.136689e+01 2.196443e+01 C 5.000000e+00 1.207732e+01 2.070932e+01 C 5.000000e+00 9.235600e+00 2.321954e+01 C 5.000000e+00 9.946030e+00 2.196443e+01 C 5.000000e+00 1.136689e+01 1.945421e+01 C 5.000000e+00 1.207732e+01 1.819910e+01 C 5.000000e+00 9.235600e+00 2.070932e+01 C 5.000000e+00 9.946030e+00 1.945421e+01 C 5.000000e+00 1.136689e+01 1.694399e+01 C 5.000000e+00 9.235600e+00 1.819910e+01 C 5.000000e+00 9.946030e+00 1.694399e+01 C 5.000000e+00 9.235600e+00 8.158212e+00 C 5.000000e+00 9.946030e+00 6.903101e+00 C 5.000000e+00 1.136689e+01 4.392879e+00 C 5.000000e+00 1.207732e+01 3.137768e+00 C 5.000000e+00 9.235600e+00 5.647990e+00 C 5.000000e+00 9.946030e+00 4.392879e+00 C 5.000000e+00 1.136689e+01 1.882658e+00 C 5.000000e+00 1.207732e+01 6.275467e-01 C 5.000000e+00 9.235600e+00 3.137768e+00 C 5.000000e+00 9.946030e+00 1.882658e+00 C 5.000000e+00 9.235600e+00 6.275467e-01 C 5.000000e+00 1.562947e+01 2.447465e+01 C 5.000000e+00 1.633990e+01 2.321954e+01 C 5.000000e+00 1.420861e+01 2.447465e+01 C 5.000000e+00 1.562947e+01 2.196443e+01 C 5.000000e+00 1.633990e+01 2.070932e+01 C 5.000000e+00 1.349818e+01 2.321954e+01 C 5.000000e+00 1.420861e+01 2.196443e+01 C 5.000000e+00 1.562947e+01 1.945421e+01 C 5.000000e+00 1.633990e+01 1.819910e+01 C 5.000000e+00 1.349818e+01 2.070932e+01 C 5.000000e+00 1.420861e+01 1.945421e+01 C 5.000000e+00 1.562947e+01 1.694399e+01 C 5.000000e+00 1.349818e+01 1.819910e+01 C 5.000000e+00 1.420861e+01 1.694399e+01 C 5.000000e+00 1.633990e+01 8.158212e+00 C 5.000000e+00 1.562947e+01 6.903101e+00 C 5.000000e+00 1.633990e+01 5.647990e+00 C 5.000000e+00 1.562947e+01 4.392879e+00 C 5.000000e+00 1.633990e+01 3.137768e+00 C 5.000000e+00 1.420861e+01 4.392879e+00 C 5.000000e+00 1.562947e+01 1.882658e+00 C 5.000000e+00 1.633990e+01 6.275467e-01 C 5.000000e+00 1.349818e+01 3.137768e+00 C 5.000000e+00 1.420861e+01 1.882658e+00 C 5.000000e+00 1.349818e+01 6.275467e-01 C 5.000000e+00 1.989205e+01 2.447465e+01 C 5.000000e+00 2.060248e+01 2.321954e+01 C 5.000000e+00 1.847119e+01 2.447465e+01 C 5.000000e+00 1.989205e+01 2.196443e+01 C 5.000000e+00 2.060248e+01 2.070932e+01 C 5.000000e+00 1.776076e+01 2.321954e+01 C 5.000000e+00 1.847119e+01 2.196443e+01 C 5.000000e+00 1.989205e+01 1.945421e+01 C 5.000000e+00 2.060248e+01 1.819910e+01 C 5.000000e+00 1.776076e+01 2.070932e+01 C 5.000000e+00 1.847119e+01 1.945421e+01 C 5.000000e+00 1.989205e+01 1.694399e+01 C 5.000000e+00 2.060248e+01 1.568888e+01 C 5.000000e+00 1.776076e+01 1.819910e+01 C 5.000000e+00 1.847119e+01 1.694399e+01 C 5.000000e+00 1.989205e+01 1.443377e+01 C 5.000000e+00 2.060248e+01 1.317866e+01 C 5.000000e+00 1.989205e+01 1.192354e+01 C 5.000000e+00 2.060248e+01 1.066843e+01 C 5.000000e+00 1.847119e+01 1.192354e+01 C 5.000000e+00 1.989205e+01 9.413323e+00 C 5.000000e+00 2.060248e+01 8.158212e+00 C 5.000000e+00 1.776076e+01 1.066843e+01 C 5.000000e+00 1.847119e+01 9.413323e+00 C 5.000000e+00 1.989205e+01 6.903101e+00 C 5.000000e+00 2.060248e+01 5.647990e+00 C 5.000000e+00 1.776076e+01 8.158212e+00 C 5.000000e+00 1.847119e+01 6.903101e+00 C 5.000000e+00 1.989205e+01 4.392879e+00 C 5.000000e+00 2.060248e+01 3.137768e+00 C 5.000000e+00 1.776076e+01 5.647990e+00 C 5.000000e+00 1.847119e+01 4.392879e+00 C 5.000000e+00 1.989205e+01 1.882658e+00 C 5.000000e+00 2.060248e+01 6.275467e-01 C 5.000000e+00 1.776076e+01 3.137768e+00 C 5.000000e+00 1.847119e+01 1.882658e+00 C 5.000000e+00 1.776076e+01 6.275467e-01 C 5.000000e+00 2.415463e+01 2.447465e+01 C 5.000000e+00 2.486506e+01 2.321954e+01 C 5.000000e+00 2.273377e+01 2.447465e+01 C 5.000000e+00 2.415463e+01 2.196443e+01 C 5.000000e+00 2.486506e+01 2.070932e+01 C 5.000000e+00 2.202334e+01 2.321954e+01 C 5.000000e+00 2.273377e+01 2.196443e+01 C 5.000000e+00 2.415463e+01 1.945421e+01 C 5.000000e+00 2.486506e+01 1.819910e+01 C 5.000000e+00 2.202334e+01 2.070932e+01 C 5.000000e+00 2.273377e+01 1.945421e+01 C 5.000000e+00 2.415463e+01 1.694399e+01 C 5.000000e+00 2.486506e+01 1.568888e+01 C 5.000000e+00 2.202334e+01 1.819910e+01 C 5.000000e+00 2.273377e+01 1.694399e+01 C 5.000000e+00 2.415463e+01 1.443377e+01 C 5.000000e+00 2.486506e+01 1.317866e+01 C 5.000000e+00 2.202334e+01 1.568888e+01 C 5.000000e+00 2.273377e+01 1.443377e+01 C 5.000000e+00 2.415463e+01 1.192354e+01 C 5.000000e+00 2.486506e+01 1.066843e+01 C 5.000000e+00 2.202334e+01 1.317866e+01 C 5.000000e+00 2.273377e+01 1.192354e+01 C 5.000000e+00 2.415463e+01 9.413323e+00 C 5.000000e+00 2.486506e+01 8.158212e+00 C 5.000000e+00 2.202334e+01 1.066843e+01 C 5.000000e+00 2.273377e+01 9.413323e+00 C 5.000000e+00 2.415463e+01 6.903101e+00 C 5.000000e+00 2.486506e+01 5.647990e+00 C 5.000000e+00 2.202334e+01 8.158212e+00 C 5.000000e+00 2.273377e+01 6.903101e+00 C 5.000000e+00 2.415463e+01 4.392879e+00 C 5.000000e+00 2.486506e+01 3.137768e+00 C 5.000000e+00 2.202334e+01 5.647990e+00 C 5.000000e+00 2.273377e+01 4.392879e+00 C 5.000000e+00 2.415463e+01 1.882658e+00 C 5.000000e+00 2.486506e+01 6.275467e-01 C 5.000000e+00 2.202334e+01 3.137768e+00 C 5.000000e+00 2.273377e+01 1.882658e+00 C 5.000000e+00 2.202334e+01 6.275467e-01 H 5.000000e+00 7.654810e+00 1.597142e+01 H 5.000000e+00 6.784450e+00 1.443377e+01 H 5.000000e+00 7.654810e+00 1.289611e+01 H 5.000000e+00 8.915740e+00 1.066843e+01 H 5.000000e+00 1.191739e+01 1.597142e+01 H 5.000000e+00 9.395530e+00 1.597142e+01 H 5.000000e+00 9.786100e+00 9.130776e+00 H 5.000000e+00 1.104703e+01 6.903101e+00 H 5.000000e+00 1.191739e+01 5.365443e+00 H 5.000000e+00 1.617997e+01 1.597142e+01 H 5.000000e+00 1.365811e+01 1.597142e+01 H 5.000000e+00 1.578940e+01 9.130776e+00 H 5.000000e+00 1.452847e+01 6.903101e+00 H 5.000000e+00 1.365811e+01 5.365443e+00 H 5.000000e+00 1.792069e+01 1.597142e+01 H 5.000000e+00 1.879105e+01 1.443377e+01 H 5.000000e+00 1.792069e+01 1.289611e+01 H 5.000000e+00 1.665976e+01 1.066843e+01 CELL_PARAMETERS 10.000000 0.000000 0.0000000 0.0000000 25.57550 0.0000000 0.0000000 0.000000 25.102200 K_POINTS {automatic} 1 6 6 0 0 0 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110929/5d22d9e3/attachment-0001.htm From masoudnahali at gmail.com Fri Sep 30 01:20:29 2011 From: masoudnahali at gmail.com (Masoud) Date: Fri, 30 Sep 2011 01:20:29 +0200 Subject: [Pw_forum] Graphene Sheet with Antidots Message-ID: Dear Swapnil The charge density cutoff of C and H Norm-Conserving pseudo-potentials should be set to a lower value say 4 times greater than plane-wave cutoff. Then you can increase it to examine the convergence issue. I hope it helps. Best Wishes Masoud ---------------------------------------- Masoud Nahali, Ph. D Student International School for Advanced Studies (SISSA) Sharif University of Technology P Save a Tree . . . Please don't print this e-mail unless you really need to. Swapnil wrote : > > Hi, > > I am sending the input file I am using for a graphene sheet with H > passivated antidots, the script is taking very long time to converge. The > simulations converge in 20 steps but it is taking terribly long. Can anyone > comment on what changes can help bringing the time consumed down? > > &control > calculation = 'scf' > restart_mode = 'from_scratch' > pseudo_dir = '/work/s/sharma/schandratre/pseudo' > outdir = '/work/s/sharma/schandratre/triangular02strain' > > / > &system > > ibrav = 0 > > celldm(1) = 1.8897261 > nat=222 > ntyp=2 > ecutwfc=30.0 > ecutrho = 300.0 > , > / > &electrons > conv_thr = 1.0d-6, > mixing_beta=0.05, > / > > ATOMIC_SPECIES > C 12.0000 C.pz-vbc.UPF > H 1.00000 H.pz-vbc.UPF > > ATOMIC_POSITIONS {angstrom} > C 5.000000e+00 2.841730e+00 2.447465e+01 > C 5.000000e+00 3.552160e+00 2.321954e+01 > C 5.000000e+00 1.420870e+00 2.447465e+01 > C 5.000000e+00 2.841730e+00 2.196443e+01 > C 5.000000e+00 3.552160e+00 2.070932e+01 > C 5.000000e+00 7.104400e-01 2.321954e+01 > C 5.000000e+00 1.420870e+00 2.196443e+01 > C 5.000000e+00 2.841730e+00 1.945421e+01 > C 5.000000e+00 3.552160e+00 1.819910e+01 > C 5.000000e+00 7.104400e-01 2.070932e+01 > C 5.000000e+00 1.420870e+00 1.945421e+01 > C 5.000000e+00 2.841730e+00 1.694399e+01 > C 5.000000e+00 3.552160e+00 1.568888e+01 > C 5.000000e+00 7.104400e-01 1.819910e+01 > C 5.000000e+00 1.420870e+00 1.694399e+01 > C 5.000000e+00 2.841730e+00 1.443377e+01 > C 5.000000e+00 3.552160e+00 1.317866e+01 > C 5.000000e+00 7.104400e-01 1.568888e+01 > C 5.000000e+00 1.420870e+00 1.443377e+01 > C 5.000000e+00 2.841730e+00 1.192354e+01 > C 5.000000e+00 3.552160e+00 1.066843e+01 > C 5.000000e+00 7.104400e-01 1.317866e+01 > C 5.000000e+00 1.420870e+00 1.192354e+01 > C 5.000000e+00 2.841730e+00 9.413323e+00 > C 5.000000e+00 3.552160e+00 8.158212e+00 > C 5.000000e+00 7.104400e-01 1.066843e+01 > C 5.000000e+00 1.420870e+00 9.413323e+00 > C 5.000000e+00 2.841730e+00 6.903101e+00 > C 5.000000e+00 3.552160e+00 5.647990e+00 > C 5.000000e+00 7.104400e-01 8.158212e+00 > C 5.000000e+00 1.420870e+00 6.903101e+00 > C 5.000000e+00 2.841730e+00 4.392879e+00 > C 5.000000e+00 3.552160e+00 3.137768e+00 > C 5.000000e+00 7.104400e-01 5.647990e+00 > C 5.000000e+00 1.420870e+00 4.392879e+00 > C 5.000000e+00 2.841730e+00 1.882658e+00 > C 5.000000e+00 3.552160e+00 6.275467e-01 > C 5.000000e+00 7.104400e-01 3.137768e+00 > C 5.000000e+00 1.420870e+00 1.882658e+00 > C 5.000000e+00 7.104400e-01 6.275467e-01 > C 5.000000e+00 7.104310e+00 2.447465e+01 > C 5.000000e+00 7.814740e+00 2.321954e+01 > C 5.000000e+00 5.683450e+00 2.447465e+01 > C 5.000000e+00 7.104310e+00 2.196443e+01 > C 5.000000e+00 7.814740e+00 2.070932e+01 > C 5.000000e+00 4.973020e+00 2.321954e+01 > C 5.000000e+00 5.683450e+00 2.196443e+01 > C 5.000000e+00 7.104310e+00 1.945421e+01 > C 5.000000e+00 7.814740e+00 1.819910e+01 > C 5.000000e+00 4.973020e+00 2.070932e+01 > C 5.000000e+00 5.683450e+00 1.945421e+01 > C 5.000000e+00 7.104310e+00 1.694399e+01 > C 5.000000e+00 4.973020e+00 1.819910e+01 > C 5.000000e+00 5.683450e+00 1.694399e+01 > C 5.000000e+00 4.973020e+00 1.568888e+01 > C 5.000000e+00 5.683450e+00 1.443377e+01 > C 5.000000e+00 7.104310e+00 1.192354e+01 > C 5.000000e+00 7.814740e+00 1.066843e+01 > C 5.000000e+00 4.973020e+00 1.317866e+01 > C 5.000000e+00 5.683450e+00 1.192354e+01 > C 5.000000e+00 7.104310e+00 9.413323e+00 > C 5.000000e+00 7.814740e+00 8.158212e+00 > C 5.000000e+00 4.973020e+00 1.066843e+01 > C 5.000000e+00 5.683450e+00 9.413323e+00 > C 5.000000e+00 7.104310e+00 6.903101e+00 > C 5.000000e+00 7.814740e+00 5.647990e+00 > C 5.000000e+00 4.973020e+00 8.158212e+00 > C 5.000000e+00 5.683450e+00 6.903101e+00 > C 5.000000e+00 7.104310e+00 4.392879e+00 > C 5.000000e+00 7.814740e+00 3.137768e+00 > C 5.000000e+00 4.973020e+00 5.647990e+00 > C 5.000000e+00 5.683450e+00 4.392879e+00 > C 5.000000e+00 7.104310e+00 1.882658e+00 > C 5.000000e+00 7.814740e+00 6.275467e-01 > C 5.000000e+00 4.973020e+00 3.137768e+00 > C 5.000000e+00 5.683450e+00 1.882658e+00 > C 5.000000e+00 4.973020e+00 6.275467e-01 > C 5.000000e+00 1.136689e+01 2.447465e+01 > C 5.000000e+00 1.207732e+01 2.321954e+01 > C 5.000000e+00 9.946030e+00 2.447465e+01 > C 5.000000e+00 1.136689e+01 2.196443e+01 > C 5.000000e+00 1.207732e+01 2.070932e+01 > C 5.000000e+00 9.235600e+00 2.321954e+01 > C 5.000000e+00 9.946030e+00 2.196443e+01 > C 5.000000e+00 1.136689e+01 1.945421e+01 > C 5.000000e+00 1.207732e+01 1.819910e+01 > C 5.000000e+00 9.235600e+00 2.070932e+01 > C 5.000000e+00 9.946030e+00 1.945421e+01 > C 5.000000e+00 1.136689e+01 1.694399e+01 > C 5.000000e+00 9.235600e+00 1.819910e+01 > C 5.000000e+00 9.946030e+00 1.694399e+01 > C 5.000000e+00 9.235600e+00 8.158212e+00 > C 5.000000e+00 9.946030e+00 6.903101e+00 > C 5.000000e+00 1.136689e+01 4.392879e+00 > C 5.000000e+00 1.207732e+01 3.137768e+00 > C 5.000000e+00 9.235600e+00 5.647990e+00 > C 5.000000e+00 9.946030e+00 4.392879e+00 > C 5.000000e+00 1.136689e+01 1.882658e+00 > C 5.000000e+00 1.207732e+01 6.275467e-01 > C 5.000000e+00 9.235600e+00 3.137768e+00 > C 5.000000e+00 9.946030e+00 1.882658e+00 > C 5.000000e+00 9.235600e+00 6.275467e-01 > C 5.000000e+00 1.562947e+01 2.447465e+01 > C 5.000000e+00 1.633990e+01 2.321954e+01 > C 5.000000e+00 1.420861e+01 2.447465e+01 > C 5.000000e+00 1.562947e+01 2.196443e+01 > C 5.000000e+00 1.633990e+01 2.070932e+01 > C 5.000000e+00 1.349818e+01 2.321954e+01 > C 5.000000e+00 1.420861e+01 2.196443e+01 > C 5.000000e+00 1.562947e+01 1.945421e+01 > C 5.000000e+00 1.633990e+01 1.819910e+01 > C 5.000000e+00 1.349818e+01 2.070932e+01 > C 5.000000e+00 1.420861e+01 1.945421e+01 > C 5.000000e+00 1.562947e+01 1.694399e+01 > C 5.000000e+00 1.349818e+01 1.819910e+01 > C 5.000000e+00 1.420861e+01 1.694399e+01 > C 5.000000e+00 1.633990e+01 8.158212e+00 > C 5.000000e+00 1.562947e+01 6.903101e+00 > C 5.000000e+00 1.633990e+01 5.647990e+00 > C 5.000000e+00 1.562947e+01 4.392879e+00 > C 5.000000e+00 1.633990e+01 3.137768e+00 > C 5.000000e+00 1.420861e+01 4.392879e+00 > C 5.000000e+00 1.562947e+01 1.882658e+00 > C 5.000000e+00 1.633990e+01 6.275467e-01 > C 5.000000e+00 1.349818e+01 3.137768e+00 > C 5.000000e+00 1.420861e+01 1.882658e+00 > C 5.000000e+00 1.349818e+01 6.275467e-01 > C 5.000000e+00 1.989205e+01 2.447465e+01 > C 5.000000e+00 2.060248e+01 2.321954e+01 > C 5.000000e+00 1.847119e+01 2.447465e+01 > C 5.000000e+00 1.989205e+01 2.196443e+01 > C 5.000000e+00 2.060248e+01 2.070932e+01 > C 5.000000e+00 1.776076e+01 2.321954e+01 > C 5.000000e+00 1.847119e+01 2.196443e+01 > C 5.000000e+00 1.989205e+01 1.945421e+01 > C 5.000000e+00 2.060248e+01 1.819910e+01 > C 5.000000e+00 1.776076e+01 2.070932e+01 > C 5.000000e+00 1.847119e+01 1.945421e+01 > C 5.000000e+00 1.989205e+01 1.694399e+01 > C 5.000000e+00 2.060248e+01 1.568888e+01 > C 5.000000e+00 1.776076e+01 1.819910e+01 > C 5.000000e+00 1.847119e+01 1.694399e+01 > C 5.000000e+00 1.989205e+01 1.443377e+01 > C 5.000000e+00 2.060248e+01 1.317866e+01 > C 5.000000e+00 1.989205e+01 1.192354e+01 > C 5.000000e+00 2.060248e+01 1.066843e+01 > C 5.000000e+00 1.847119e+01 1.192354e+01 > C 5.000000e+00 1.989205e+01 9.413323e+00 > C 5.000000e+00 2.060248e+01 8.158212e+00 > C 5.000000e+00 1.776076e+01 1.066843e+01 > C 5.000000e+00 1.847119e+01 9.413323e+00 > C 5.000000e+00 1.989205e+01 6.903101e+00 > C 5.000000e+00 2.060248e+01 5.647990e+00 > C 5.000000e+00 1.776076e+01 8.158212e+00 > C 5.000000e+00 1.847119e+01 6.903101e+00 > C 5.000000e+00 1.989205e+01 4.392879e+00 > C 5.000000e+00 2.060248e+01 3.137768e+00 > C 5.000000e+00 1.776076e+01 5.647990e+00 > C 5.000000e+00 1.847119e+01 4.392879e+00 > C 5.000000e+00 1.989205e+01 1.882658e+00 > C 5.000000e+00 2.060248e+01 6.275467e-01 > C 5.000000e+00 1.776076e+01 3.137768e+00 > C 5.000000e+00 1.847119e+01 1.882658e+00 > C 5.000000e+00 1.776076e+01 6.275467e-01 > C 5.000000e+00 2.415463e+01 2.447465e+01 > C 5.000000e+00 2.486506e+01 2.321954e+01 > C 5.000000e+00 2.273377e+01 2.447465e+01 > C 5.000000e+00 2.415463e+01 2.196443e+01 > C 5.000000e+00 2.486506e+01 2.070932e+01 > C 5.000000e+00 2.202334e+01 2.321954e+01 > C 5.000000e+00 2.273377e+01 2.196443e+01 > C 5.000000e+00 2.415463e+01 1.945421e+01 > C 5.000000e+00 2.486506e+01 1.819910e+01 > C 5.000000e+00 2.202334e+01 2.070932e+01 > C 5.000000e+00 2.273377e+01 1.945421e+01 > C 5.000000e+00 2.415463e+01 1.694399e+01 > C 5.000000e+00 2.486506e+01 1.568888e+01 > C 5.000000e+00 2.202334e+01 1.819910e+01 > C 5.000000e+00 2.273377e+01 1.694399e+01 > C 5.000000e+00 2.415463e+01 1.443377e+01 > C 5.000000e+00 2.486506e+01 1.317866e+01 > C 5.000000e+00 2.202334e+01 1.568888e+01 > C 5.000000e+00 2.273377e+01 1.443377e+01 > C 5.000000e+00 2.415463e+01 1.192354e+01 > C 5.000000e+00 2.486506e+01 1.066843e+01 > C 5.000000e+00 2.202334e+01 1.317866e+01 > C 5.000000e+00 2.273377e+01 1.192354e+01 > C 5.000000e+00 2.415463e+01 9.413323e+00 > C 5.000000e+00 2.486506e+01 8.158212e+00 > C 5.000000e+00 2.202334e+01 1.066843e+01 > C 5.000000e+00 2.273377e+01 9.413323e+00 > C 5.000000e+00 2.415463e+01 6.903101e+00 > C 5.000000e+00 2.486506e+01 5.647990e+00 > C 5.000000e+00 2.202334e+01 8.158212e+00 > C 5.000000e+00 2.273377e+01 6.903101e+00 > C 5.000000e+00 2.415463e+01 4.392879e+00 > C 5.000000e+00 2.486506e+01 3.137768e+00 > C 5.000000e+00 2.202334e+01 5.647990e+00 > C 5.000000e+00 2.273377e+01 4.392879e+00 > C 5.000000e+00 2.415463e+01 1.882658e+00 > C 5.000000e+00 2.486506e+01 6.275467e-01 > C 5.000000e+00 2.202334e+01 3.137768e+00 > C 5.000000e+00 2.273377e+01 1.882658e+00 > C 5.000000e+00 2.202334e+01 6.275467e-01 > H 5.000000e+00 7.654810e+00 1.597142e+01 > H 5.000000e+00 6.784450e+00 1.443377e+01 > H 5.000000e+00 7.654810e+00 1.289611e+01 > H 5.000000e+00 8.915740e+00 1.066843e+01 > H 5.000000e+00 1.191739e+01 1.597142e+01 > H 5.000000e+00 9.395530e+00 1.597142e+01 > H 5.000000e+00 9.786100e+00 9.130776e+00 > H 5.000000e+00 1.104703e+01 6.903101e+00 > H 5.000000e+00 1.191739e+01 5.365443e+00 > H 5.000000e+00 1.617997e+01 1.597142e+01 > H 5.000000e+00 1.365811e+01 1.597142e+01 > H 5.000000e+00 1.578940e+01 9.130776e+00 > H 5.000000e+00 1.452847e+01 6.903101e+00 > H 5.000000e+00 1.365811e+01 5.365443e+00 > H 5.000000e+00 1.792069e+01 1.597142e+01 > H 5.000000e+00 1.879105e+01 1.443377e+01 > H 5.000000e+00 1.792069e+01 1.289611e+01 > H 5.000000e+00 1.665976e+01 1.066843e+01 > > CELL_PARAMETERS > 10.000000 0.000000 0.0000000 > 0.0000000 25.57550 0.0000000 > 0.0000000 0.000000 25.102200 > > K_POINTS {automatic} > 1 6 6 0 0 0 > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/9a5e0eb5/attachment-0001.htm From g0800703 at nus.edu.sg Fri Sep 30 04:30:44 2011 From: g0800703 at nus.edu.sg (He Jinghui) Date: Fri, 30 Sep 2011 10:30:44 +0800 Subject: [Pw_forum] installing input file builder: gdis-0.99 Message-ID: <4E8529D4.8060208@nus.edu.sg> Dear All: I was wondering who has successively installed the latest version of gdis: 0.99. Now the official release version is 0.90-3, but it doesn't support the pwscf input/output file format. I tried to use cvs to download the 0.99 version and to install it. The installation went well without any error, but after installation, the software cannot start a GUI, exit without any error message. Any idea? Thank you in advance! OS: linux mint 10 -64 bit gnome no library files missing reported regards He Jinghui Department of Chemistry national university of Singapore From germaneau at gucas.ac.cn Fri Sep 30 16:52:06 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 30 Sep 2011 10:52:06 -0400 Subject: [Pw_forum] installing input file builder: gdis-0.99 In-Reply-To: <517349080.05423@test1.gucas.ac.cn> References: <517349080.05423@test1.gucas.ac.cn> Message-ID: <4E85D796.8020101@gucas.ac.cn> Hey Jinghui, Are you sure the last version is 0.99? From the website it's 0.90 and actually GDIS does not support QE files. I run it without any issue on 32 and 64 bit machines. You may have to go to Xcrysgen or J-ICE for using QE files (still limited unfortunately). Best, ?ric. On 09/29/2011 10:30 PM, He Jinghui wrote: > Dear All: > > I was wondering who has successively installed the latest version of > gdis: 0.99. Now the official release version is 0.90-3, but it doesn't > support the pwscf input/output file format. I tried to use cvs to > download the 0.99 version and to install it. The installation went well > without any error, but after installation, the software cannot start a > GUI, exit without any error message. Any idea? > Thank you in advance! > > OS: linux mint 10 -64 bit gnome > no library files missing reported > > regards > He Jinghui > Department of Chemistry > national university of Singapore > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/4f0c1f35/attachment.htm From flux_ray12 at 163.com Fri Sep 30 05:13:51 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 30 Sep 2011 11:13:51 +0800 (CST) Subject: [Pw_forum] installing input file builder: gdis-0.99 In-Reply-To: <4E8529D4.8060208@nus.edu.sg> References: <4E8529D4.8060208@nus.edu.sg> Message-ID: <259dd673.c6f3.132b852dd98.Coremail.flux_ray12@163.com> To Jinghui: I haven't tried GDIS. But, I still think you can start the software through terminate, then some error may display if it doesn't work. To Eric: Now, the lastest version is 0.99, you can download from: https://df.arcs.org.au/ARCS/worldview/GDIS/ -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-30 10:30:44,"He Jinghui" wrote: >Dear All: > >I was wondering who has successively installed the latest version of >gdis: 0.99. Now the official release version is 0.90-3, but it doesn't >support the pwscf input/output file format. I tried to use cvs to >download the 0.99 version and to install it. The installation went well >without any error, but after installation, the software cannot start a >GUI, exit without any error message. Any idea? >Thank you in advance! > >OS: linux mint 10 -64 bit gnome >no library files missing reported > >regards >He Jinghui >Department of Chemistry >national university of Singapore > > > >_______________________________________________ >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/20110930/08dd1f73/attachment.htm From germaneau at gucas.ac.cn Fri Sep 30 17:22:26 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 30 Sep 2011 11:22:26 -0400 Subject: [Pw_forum] installing input file builder: gdis-0.99 In-Reply-To: <517351075.06456@test1.gucas.ac.cn> References: <4E8529D4.8060208@nus.edu.sg> <517351075.06456@test1.gucas.ac.cn> Message-ID: <4E85DEB2.9020708@gucas.ac.cn> Very good! I did nor know that! So, I try and let you know guys. On 09/29/2011 11:13 PM, GAO Zhe wrote: > To Jinghui: > I haven't tried GDIS. But, I still think you can start the software > through terminate, then some error may display if it doesn't work. > To Eric: > Now, the lastest version is 0.99, you can download from: > https://df.arcs.org.au/ARCS/worldview/GDIS/ > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-09-30 10:30:44,"He Jinghui" wrote: > >Dear All: > > > >I was wondering who has successively installed the latest version of > >gdis: 0.99. Now the official release version is 0.90-3, but it doesn't > >support the pwscf input/output file format. I tried to use cvs to > >download the 0.99 version and to install it. The installation went well > >without any error, but after installation, the software cannot start a > >GUI, exit without any error message. Any idea? > >Thank you in advance! > > > >OS: linux mint 10 -64 bit gnome > >no library files missing reported > > > >regards > >He Jinghui > >Department of Chemistry > >national university of Singapore > > > > > > > >_______________________________________________ > >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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/16df3d73/attachment.htm From germaneau at gucas.ac.cn Fri Sep 30 17:25:03 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 30 Sep 2011 11:25:03 -0400 Subject: [Pw_forum] Spin polarization Message-ID: <4E85DF4F.8090109@gucas.ac.cn> Dear all, I work on Boron Nitride structures and got confused about the use spin polarization in that case. Well, some people say that one have to but I have papers which described DFT calculations on BN without it. So, I'm wondering how much spin polarization influence the cell relaxation and scf calculations, and whether it has some influence on phonon for instance. Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/39934d79/attachment.htm From germaneau at gucas.ac.cn Fri Sep 30 17:54:31 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 30 Sep 2011 11:54:31 -0400 Subject: [Pw_forum] installing input file builder: gdis-0.99 In-Reply-To: <517349080.05423@test1.gucas.ac.cn> References: <517349080.05423@test1.gucas.ac.cn> Message-ID: <4E85E637.2070705@gucas.ac.cn> Hey Jinghui, I'm sorry I did not know about this version. So, I quickly tried and on my i686 machine. I can compile and run it without crashing but I can no longer export figure, even using povray. I tried to open QE input and output files (good it may handle it) but can not see *.in out *.out files. On my x86_64 I can not even compile. By the way, it does not seem to me to be the right place for talking about gdis, I mean that may bother most of QE users. So, why not continue this conversation privately? (I'm not aware of any gdis mailing list) Best, ?ric. On 09/29/2011 10:30 PM, He Jinghui wrote: > Dear All: > > I was wondering who has successively installed the latest version of > gdis: 0.99. Now the official release version is 0.90-3, but it doesn't > support the pwscf input/output file format. I tried to use cvs to > download the 0.99 version and to install it. The installation went well > without any error, but after installation, the software cannot start a > GUI, exit without any error message. Any idea? > Thank you in advance! > > OS: linux mint 10 -64 bit gnome > no library files missing reported > > regards > He Jinghui > Department of Chemistry > national university of Singapore > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/c508b50d/attachment-0001.htm From g0800703 at nus.edu.sg Fri Sep 30 06:12:46 2011 From: g0800703 at nus.edu.sg (He Jinghui) Date: Fri, 30 Sep 2011 12:12:46 +0800 Subject: [Pw_forum] installing input file builder: gdis-0.99 Message-ID: <4E8541BE.505@nus.edu.sg> Dear Gao Zhe: Yes, I run it from a terminal by typing : "./gdis", But nothing happened. BTW: How do you prepare the input file? PWgui + xcrysden? is there any builder can modify atom positions and save in pwscf input file? This is what i am looking for. Would you mind sharing your experience with me? This is my first day dealing with QE :). Thank you very much! Jinghui From swapnil.chandratre at gmail.com Fri Sep 30 06:38:41 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 29 Sep 2011 23:38:41 -0500 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: Hi, This is the output i get, the file is not updated. I see the wavefunctions file being updated but there is no update on the output while. Any suggestions? Program PWSCF v.4.3 starts on 29Sep2011 at 20: 2:15 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 Parallel version (MPI), running on 24 processors R & G space division: proc/pool = 24 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... file H.pz-vbc.UPF: wavefunction(s) 1S renormalized Subspace diagonalization in iterative solution of the eigenvalue problem: parallel, distributed-memory algorithm (size of sub-group: 3* 3 procs) Stick Mesh ---------- nst = 8705, nstw = 2253, nsts = 8705 n.st n.stw n.sts n.g n.gw n.gs min 362 93 362 39280 5165 39280 max 363 94 363 39289 5170 39289 8705 2253 8705 942815 124019 942815 bravais-lattice index = 0 lattice parameter (a_0) = 1.8897 a.u. unit-cell volume = 42474.8966 (a.u.)^3 number of atoms/cell = 222 number of atomic types = 2 number of electrons = 834.00 number of Kohn-Sham states= 417 kinetic-energy cutoff = 30.0000 Ry charge density cutoff = 120.0000 Ry convergence threshold = 1.0E-06 mixing beta = 0.0500 number of iterations used = 8 plain mixing Exchange-correlation = SLA PZ NOGX NOGC (1100) EXX-fraction = 0.00 celldm(1)= 1.889726 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) = ( 10.000000 0.000000 0.000000 ) a(2) = ( 0.000000 25.575500 0.000000 ) a(3) = ( 0.000000 0.000000 24.610000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 0.100000 0.000000 0.000000 ) b(2) = ( 0.000000 0.039100 0.000000 ) b(3) = ( 0.000000 0.000000 0.040634 ) PseudoPot. # 1 for C read from file C.pz-vbc.UPF MD5 check sum: 8129035fc53e2fa5aad48791fe6e510b Pseudo is Norm-conserving, Zval = 4.0 Generated by new atomic code, or converted to UPF format Using radial grid of 269 points, 1 beta functions with: l(1) = 0 PseudoPot. # 2 for H read from file H.pz-vbc.UPF MD5 check sum: aa329623744ed3b79b6c0d10dade6a79 Pseudo is Norm-conserving, Zval = 1.0 Generated by new atomic code, or converted to UPF format Using radial grid of 131 points, 0 beta functions with: atomic species valence mass pseudopotential C 4.00 12.00000 C ( 1.00) H 1.00 1.00000 H ( 1.00) 4 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (a_0 units) 1 C tau( 1) = ( 5.0000001 2.8417300 23.9947604 ) 2 C tau( 2) = ( 5.0000001 3.5521601 22.7642604 ) 3 C tau( 3) = ( 5.0000001 1.4208700 23.9947604 ) 4 C tau( 4) = ( 5.0000001 2.8417300 21.5337604 ) 5 C tau( 5) = ( 5.0000001 3.5521601 20.3032604 ) 6 C tau( 6) = ( 5.0000001 0.7104400 22.7642604 ) 7 C tau( 7) = ( 5.0000001 1.4208700 21.5337604 ) 8 C tau( 8) = ( 5.0000001 2.8417300 19.0727503 ) 9 C tau( 9) = ( 5.0000001 3.5521601 17.8422503 ) 10 C tau( 10) = ( 5.0000001 0.7104400 20.3032604 ) 11 C tau( 11) = ( 5.0000001 1.4208700 19.0727503 ) 12 C tau( 12) = ( 5.0000001 2.8417300 16.6117503 ) 13 C tau( 13) = ( 5.0000001 3.5521601 15.3812503 ) 14 C tau( 14) = ( 5.0000001 0.7104400 17.8422503 ) 15 C tau( 15) = ( 5.0000001 1.4208700 16.6117503 ) 16 C tau( 16) = ( 5.0000001 2.8417300 14.1507502 ) 17 C tau( 17) = ( 5.0000001 3.5521601 12.9202502 ) 18 C tau( 18) = ( 5.0000001 0.7104400 15.3812503 ) 19 C tau( 19) = ( 5.0000001 1.4208700 14.1507502 ) 20 C tau( 20) = ( 5.0000001 2.8417300 11.6897502 ) 21 C tau( 21) = ( 5.0000001 3.5521601 10.4592502 ) 22 C tau( 22) = ( 5.0000001 0.7104400 12.9202502 ) 23 C tau( 23) = ( 5.0000001 1.4208700 11.6897502 ) 24 C tau( 24) = ( 5.0000001 2.8417300 9.2287482 ) 25 C tau( 25) = ( 5.0000001 3.5521601 7.9982471 ) 26 C tau( 26) = ( 5.0000001 0.7104400 10.4592502 ) 27 C tau( 27) = ( 5.0000001 1.4208700 9.2287482 ) 28 C tau( 28) = ( 5.0000001 2.8417300 6.7677461 ) 29 C tau( 29) = ( 5.0000001 3.5521601 5.5372451 ) 30 C tau( 30) = ( 5.0000001 0.7104400 7.9982471 ) 31 C tau( 31) = ( 5.0000001 1.4208700 6.7677461 ) 32 C tau( 32) = ( 5.0000001 2.8417300 4.3067441 ) 33 C tau( 33) = ( 5.0000001 3.5521601 3.0762441 ) 34 C tau( 34) = ( 5.0000001 0.7104400 5.5372451 ) 35 C tau( 35) = ( 5.0000001 1.4208700 4.3067441 ) 36 C tau( 36) = ( 5.0000001 2.8417300 1.8457430 ) 37 C tau( 37) = ( 5.0000001 3.5521601 0.6152419 ) 38 C tau( 38) = ( 5.0000001 0.7104400 3.0762441 ) 39 C tau( 39) = ( 5.0000001 1.4208700 1.8457430 ) 40 C tau( 40) = ( 5.0000001 0.7104400 0.6152419 ) 41 C tau( 41) = ( 5.0000001 7.1043101 23.9947604 ) 42 C tau( 42) = ( 5.0000001 7.8147401 22.7642604 ) 43 C tau( 43) = ( 5.0000001 5.6834501 23.9947604 ) 44 C tau( 44) = ( 5.0000001 7.1043101 21.5337604 ) 45 C tau( 45) = ( 5.0000001 7.8147401 20.3032604 ) 46 C tau( 46) = ( 5.0000001 4.9730201 22.7642604 ) 47 C tau( 47) = ( 5.0000001 5.6834501 21.5337604 ) 48 C tau( 48) = ( 5.0000001 7.1043101 19.0727503 ) 49 C tau( 49) = ( 5.0000001 7.8147401 17.8422503 ) 50 C tau( 50) = ( 5.0000001 4.9730201 20.3032604 ) 51 C tau( 51) = ( 5.0000001 5.6834501 19.0727503 ) 52 C tau( 52) = ( 5.0000001 7.1043101 16.6117503 ) 53 C tau( 53) = ( 5.0000001 4.9730201 17.8422503 ) 54 C tau( 54) = ( 5.0000001 5.6834501 16.6117503 ) 55 C tau( 55) = ( 5.0000001 4.9730201 15.3812503 ) 56 C tau( 56) = ( 5.0000001 5.6834501 14.1507502 ) 57 C tau( 57) = ( 5.0000001 7.1043101 11.6897502 ) 58 C tau( 58) = ( 5.0000001 7.8147401 10.4592502 ) 59 C tau( 59) = ( 5.0000001 4.9730201 12.9202502 ) 60 C tau( 60) = ( 5.0000001 5.6834501 11.6897502 ) 61 C tau( 61) = ( 5.0000001 7.1043101 9.2287482 ) 62 C tau( 62) = ( 5.0000001 7.8147401 7.9982471 ) 63 C tau( 63) = ( 5.0000001 4.9730201 10.4592502 ) 64 C tau( 64) = ( 5.0000001 5.6834501 9.2287482 ) 65 C tau( 65) = ( 5.0000001 7.1043101 6.7677461 ) 66 C tau( 66) = ( 5.0000001 7.8147401 5.5372451 ) 67 C tau( 67) = ( 5.0000001 4.9730201 7.9982471 ) 68 C tau( 68) = ( 5.0000001 5.6834501 6.7677461 ) 69 C tau( 69) = ( 5.0000001 7.1043101 4.3067441 ) 70 C tau( 70) = ( 5.0000001 7.8147401 3.0762441 ) 71 C tau( 71) = ( 5.0000001 4.9730201 5.5372451 ) 72 C tau( 72) = ( 5.0000001 5.6834501 4.3067441 ) 73 C tau( 73) = ( 5.0000001 7.1043101 1.8457430 ) 74 C tau( 74) = ( 5.0000001 7.8147401 0.6152419 ) 75 C tau( 75) = ( 5.0000001 4.9730201 3.0762441 ) 76 C tau( 76) = ( 5.0000001 5.6834501 1.8457430 ) 77 C tau( 77) = ( 5.0000001 4.9730201 0.6152419 ) 78 C tau( 78) = ( 5.0000001 11.3668902 23.9947604 ) 79 C tau( 79) = ( 5.0000001 12.0773202 22.7642604 ) 80 C tau( 80) = ( 5.0000001 9.9460302 23.9947604 ) 81 C tau( 81) = ( 5.0000001 11.3668902 21.5337604 ) 82 C tau( 82) = ( 5.0000001 12.0773202 20.3032604 ) 83 C tau( 83) = ( 5.0000001 9.2356002 22.7642604 ) 84 C tau( 84) = ( 5.0000001 9.9460302 21.5337604 ) 85 C tau( 85) = ( 5.0000001 11.3668902 19.0727503 ) 86 C tau( 86) = ( 5.0000001 12.0773202 17.8422503 ) 87 C tau( 87) = ( 5.0000001 9.2356002 20.3032604 ) 88 C tau( 88) = ( 5.0000001 9.9460302 19.0727503 ) 89 C tau( 89) = ( 5.0000001 11.3668902 16.6117503 ) 90 C tau( 90) = ( 5.0000001 9.2356002 17.8422503 ) 91 C tau( 91) = ( 5.0000001 9.9460302 16.6117503 ) 92 C tau( 92) = ( 5.0000001 9.2356002 7.9982471 ) 93 C tau( 93) = ( 5.0000001 9.9460302 6.7677461 ) 94 C tau( 94) = ( 5.0000001 11.3668902 4.3067441 ) 95 C tau( 95) = ( 5.0000001 12.0773202 3.0762441 ) 96 C tau( 96) = ( 5.0000001 9.2356002 5.5372451 ) 97 C tau( 97) = ( 5.0000001 9.9460302 4.3067441 ) 98 C tau( 98) = ( 5.0000001 11.3668902 1.8457430 ) 99 C tau( 99) = ( 5.0000001 12.0773202 0.6152419 ) 100 C tau(100) = ( 5.0000001 9.2356002 3.0762441 ) 101 C tau(101) = ( 5.0000001 9.9460302 1.8457430 ) 102 C tau(102) = ( 5.0000001 9.2356002 0.6152419 ) 103 C tau(103) = ( 5.0000001 15.6294703 23.9947604 ) 104 C tau(104) = ( 5.0000001 16.3399003 22.7642604 ) 105 C tau(105) = ( 5.0000001 14.2086102 23.9947604 ) 106 C tau(106) = ( 5.0000001 15.6294703 21.5337604 ) 107 C tau(107) = ( 5.0000001 16.3399003 20.3032604 ) 108 C tau(108) = ( 5.0000001 13.4981802 22.7642604 ) 109 C tau(109) = ( 5.0000001 14.2086102 21.5337604 ) 110 C tau(110) = ( 5.0000001 15.6294703 19.0727503 ) 111 C tau(111) = ( 5.0000001 16.3399003 17.8422503 ) 112 C tau(112) = ( 5.0000001 13.4981802 20.3032604 ) 113 C tau(113) = ( 5.0000001 14.2086102 19.0727503 ) 114 C tau(114) = ( 5.0000001 15.6294703 16.6117503 ) 115 C tau(115) = ( 5.0000001 13.4981802 17.8422503 ) 116 C tau(116) = ( 5.0000001 14.2086102 16.6117503 ) 117 C tau(117) = ( 5.0000001 16.3399003 7.9982471 ) 118 C tau(118) = ( 5.0000001 15.6294703 6.7677461 ) 119 C tau(119) = ( 5.0000001 16.3399003 5.5372451 ) 120 C tau(120) = ( 5.0000001 15.6294703 4.3067441 ) 121 C tau(121) = ( 5.0000001 16.3399003 3.0762441 ) 122 C tau(122) = ( 5.0000001 14.2086102 4.3067441 ) 123 C tau(123) = ( 5.0000001 15.6294703 1.8457430 ) 124 C tau(124) = ( 5.0000001 16.3399003 0.6152419 ) 125 C tau(125) = ( 5.0000001 13.4981802 3.0762441 ) 126 C tau(126) = ( 5.0000001 14.2086102 1.8457430 ) 127 C tau(127) = ( 5.0000001 13.4981802 0.6152419 ) 128 C tau(128) = ( 5.0000001 19.8920503 23.9947604 ) 129 C tau(129) = ( 5.0000001 20.6024804 22.7642604 ) 130 C tau(130) = ( 5.0000001 18.4711903 23.9947604 ) 131 C tau(131) = ( 5.0000001 19.8920503 21.5337604 ) 132 C tau(132) = ( 5.0000001 20.6024804 20.3032604 ) 133 C tau(133) = ( 5.0000001 17.7607603 22.7642604 ) 134 C tau(134) = ( 5.0000001 18.4711903 21.5337604 ) 135 C tau(135) = ( 5.0000001 19.8920503 19.0727503 ) 136 C tau(136) = ( 5.0000001 20.6024804 17.8422503 ) 137 C tau(137) = ( 5.0000001 17.7607603 20.3032604 ) 138 C tau(138) = ( 5.0000001 18.4711903 19.0727503 ) 139 C tau(139) = ( 5.0000001 19.8920503 16.6117503 ) 140 C tau(140) = ( 5.0000001 20.6024804 15.3812503 ) 141 C tau(141) = ( 5.0000001 17.7607603 17.8422503 ) 142 C tau(142) = ( 5.0000001 18.4711903 16.6117503 ) 143 C tau(143) = ( 5.0000001 19.8920503 14.1507502 ) 144 C tau(144) = ( 5.0000001 20.6024804 12.9202502 ) 145 C tau(145) = ( 5.0000001 19.8920503 11.6897502 ) 146 C tau(146) = ( 5.0000001 20.6024804 10.4592502 ) 147 C tau(147) = ( 5.0000001 18.4711903 11.6897502 ) 148 C tau(148) = ( 5.0000001 19.8920503 9.2287482 ) 149 C tau(149) = ( 5.0000001 20.6024804 7.9982471 ) 150 C tau(150) = ( 5.0000001 17.7607603 10.4592502 ) 151 C tau(151) = ( 5.0000001 18.4711903 9.2287482 ) 152 C tau(152) = ( 5.0000001 19.8920503 6.7677461 ) 153 C tau(153) = ( 5.0000001 20.6024804 5.5372451 ) 154 C tau(154) = ( 5.0000001 17.7607603 7.9982471 ) 155 C tau(155) = ( 5.0000001 18.4711903 6.7677461 ) 156 C tau(156) = ( 5.0000001 19.8920503 4.3067441 ) 157 C tau(157) = ( 5.0000001 20.6024804 3.0762441 ) 158 C tau(158) = ( 5.0000001 17.7607603 5.5372451 ) 159 C tau(159) = ( 5.0000001 18.4711903 4.3067441 ) 160 C tau(160) = ( 5.0000001 19.8920503 1.8457430 ) 161 C tau(161) = ( 5.0000001 20.6024804 0.6152419 ) 162 C tau(162) = ( 5.0000001 17.7607603 3.0762441 ) 163 C tau(163) = ( 5.0000001 18.4711903 1.8457430 ) 164 C tau(164) = ( 5.0000001 17.7607603 0.6152419 ) 165 C tau(165) = ( 5.0000001 24.1546304 23.9947604 ) 166 C tau(166) = ( 5.0000001 24.8650604 22.7642604 ) 167 C tau(167) = ( 5.0000001 22.7337704 23.9947604 ) 168 C tau(168) = ( 5.0000001 24.1546304 21.5337604 ) 169 C tau(169) = ( 5.0000001 24.8650604 20.3032604 ) 170 C tau(170) = ( 5.0000001 22.0233404 22.7642604 ) 171 C tau(171) = ( 5.0000001 22.7337704 21.5337604 ) 172 C tau(172) = ( 5.0000001 24.1546304 19.0727503 ) 173 C tau(173) = ( 5.0000001 24.8650604 17.8422503 ) 174 C tau(174) = ( 5.0000001 22.0233404 20.3032604 ) 175 C tau(175) = ( 5.0000001 22.7337704 19.0727503 ) 176 C tau(176) = ( 5.0000001 24.1546304 16.6117503 ) 177 C tau(177) = ( 5.0000001 24.8650604 15.3812503 ) 178 C tau(178) = ( 5.0000001 22.0233404 17.8422503 ) 179 C tau(179) = ( 5.0000001 22.7337704 16.6117503 ) 180 C tau(180) = ( 5.0000001 24.1546304 14.1507502 ) 181 C tau(181) = ( 5.0000001 24.8650604 12.9202502 ) 182 C tau(182) = ( 5.0000001 22.0233404 15.3812503 ) 183 C tau(183) = ( 5.0000001 22.7337704 14.1507502 ) 184 C tau(184) = ( 5.0000001 24.1546304 11.6897502 ) 185 C tau(185) = ( 5.0000001 24.8650604 10.4592502 ) 186 C tau(186) = ( 5.0000001 22.0233404 12.9202502 ) 187 C tau(187) = ( 5.0000001 22.7337704 11.6897502 ) 188 C tau(188) = ( 5.0000001 24.1546304 9.2287482 ) 189 C tau(189) = ( 5.0000001 24.8650604 7.9982471 ) 190 C tau(190) = ( 5.0000001 22.0233404 10.4592502 ) 191 C tau(191) = ( 5.0000001 22.7337704 9.2287482 ) 192 C tau(192) = ( 5.0000001 24.1546304 6.7677461 ) 193 C tau(193) = ( 5.0000001 24.8650604 5.5372451 ) 194 C tau(194) = ( 5.0000001 22.0233404 7.9982471 ) 195 C tau(195) = ( 5.0000001 22.7337704 6.7677461 ) 196 C tau(196) = ( 5.0000001 24.1546304 4.3067441 ) 197 C tau(197) = ( 5.0000001 24.8650604 3.0762441 ) 198 C tau(198) = ( 5.0000001 22.0233404 5.5372451 ) 199 C tau(199) = ( 5.0000001 22.7337704 4.3067441 ) 200 C tau(200) = ( 5.0000001 24.1546304 1.8457430 ) 201 C tau(201) = ( 5.0000001 24.8650604 0.6152419 ) 202 C tau(202) = ( 5.0000001 22.0233404 3.0762441 ) 203 C tau(203) = ( 5.0000001 22.7337704 1.8457430 ) 204 C tau(204) = ( 5.0000001 22.0233404 0.6152419 ) 205 H tau(205) = ( 5.0000001 7.6548101 15.6582603 ) 206 H tau(206) = ( 5.0000001 6.7844501 14.1507502 ) 207 H tau(207) = ( 5.0000001 7.6548101 12.6432402 ) 208 H tau(208) = ( 5.0000001 8.9157402 10.4592502 ) 209 H tau(209) = ( 5.0000001 11.9173902 15.6582603 ) 210 H tau(210) = ( 5.0000001 9.3955302 15.6582603 ) 211 H tau(211) = ( 5.0000001 9.7861002 8.9517412 ) 212 H tau(212) = ( 5.0000001 11.0470302 6.7677461 ) 213 H tau(213) = ( 5.0000001 11.9173902 5.2602381 ) 214 H tau(214) = ( 5.0000001 16.1799703 15.6582603 ) 215 H tau(215) = ( 5.0000001 13.6581102 15.6582603 ) 216 H tau(216) = ( 5.0000001 15.7894003 8.9517412 ) 217 H tau(217) = ( 5.0000001 14.5284703 6.7677461 ) 218 H tau(218) = ( 5.0000001 13.6581102 5.2602381 ) 219 H tau(219) = ( 5.0000001 17.9206903 15.6582603 ) 220 H tau(220) = ( 5.0000001 18.7910503 14.1507502 ) 221 H tau(221) = ( 5.0000001 17.9206903 12.6432402 ) 222 H tau(222) = ( 5.0000001 16.6597603 10.4592502 ) number of k points= 16 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0555556 k( 2) = ( 0.0000000 0.0000000 0.0067723), wk = 0.1111111 k( 3) = ( 0.0000000 0.0000000 0.0135446), wk = 0.1111111 k( 4) = ( 0.0000000 0.0000000 -0.0203169), wk = 0.0555556 k( 5) = ( 0.0000000 0.0065167 0.0000000), wk = 0.1111111 k( 6) = ( 0.0000000 0.0065167 0.0067723), wk = 0.2222222 k( 7) = ( 0.0000000 0.0065167 0.0135446), wk = 0.2222222 k( 8) = ( 0.0000000 0.0065167 -0.0203169), wk = 0.1111111 k( 9) = ( 0.0000000 0.0130333 0.0000000), wk = 0.1111111 k( 10) = ( 0.0000000 0.0130333 0.0067723), wk = 0.2222222 k( 11) = ( 0.0000000 0.0130333 0.0135446), wk = 0.2222222 k( 12) = ( 0.0000000 0.0130333 -0.0203169), wk = 0.1111111 k( 13) = ( 0.0000000 -0.0195500 0.0000000), wk = 0.0555556 k( 14) = ( 0.0000000 -0.0195500 0.0067723), wk = 0.1111111 k( 15) = ( 0.0000000 -0.0195500 0.0135446), wk = 0.1111111 k( 16) = ( 0.0000000 -0.0195500 -0.0203169), wk = 0.0555556 G cutoff = 10.8547 ( 942815 G-vectors) FFT grid: ( 72,180,180) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 31.31 Mb ( 4920, 417) NL pseudopotentials 15.31 Mb ( 4920, 204) Each V/rho on FFT grid 1.58 Mb ( 103680) Each G-vector array 0.30 Mb ( 39289) G-vector shells 0.14 Mb ( 18612) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 125.22 Mb ( 4920,1668) Each subspace H/S matrix 42.45 Mb ( 1668,1668) Each matrix 1.30 Mb ( 204, 417) Arrays for rho mixing 12.66 Mb ( 103680, 8) Initial potential from superposition of free atoms Check: negative starting charge= -0.108545 starting charge 833.99370, renormalised to 834.00000 negative rho (up, down): 0.109E+00 0.000E+00 Starting wfc are 834 atomic wfcs On Thu, Sep 29, 2011 at 6:20 PM, Masoud wrote: > Dear Swapnil > > The charge density cutoff of C and H Norm-Conserving pseudo-potentials > should be set to a lower value say 4 times greater than plane-wave cutoff. > Then you can increase it to examine the convergence issue. I hope it helps. > > > > > Best Wishes > > Masoud > > > > ---------------------------------------- > Masoud Nahali, Ph. D Student > International School for Advanced Studies (SISSA) > Sharif University of Technology > P Save a Tree . . . Please don't print this e-mail unless you really need > to. > > > > Swapnil wrote : >> > > >> Hi, >> >> I am sending the input file I am using for a graphene sheet with H >> passivated antidots, the script is taking very long time to converge. The >> simulations converge in 20 steps but it is taking terribly long. Can >> anyone >> comment on what changes can help bringing the time consumed down? >> >> &control >> calculation = 'scf' >> restart_mode = 'from_scratch' >> pseudo_dir = '/work/s/sharma/schandratre/pseudo' >> outdir = '/work/s/sharma/schandratre/triangular02strain' >> >> / >> &system >> >> ibrav = 0 >> >> celldm(1) = 1.8897261 >> nat=222 >> ntyp=2 >> ecutwfc=30.0 >> ecutrho = 300.0 >> , >> / >> &electrons >> conv_thr = 1.0d-6, >> mixing_beta=0.05, >> / >> >> ATOMIC_SPECIES >> C 12.0000 C.pz-vbc.UPF >> H 1.00000 H.pz-vbc.UPF >> >> ATOMIC_POSITIONS {angstrom} >> C 5.000000e+00 2.841730e+00 2.447465e+01 >> C 5.000000e+00 3.552160e+00 2.321954e+01 >> C 5.000000e+00 1.420870e+00 2.447465e+01 >> C 5.000000e+00 2.841730e+00 2.196443e+01 >> C 5.000000e+00 3.552160e+00 2.070932e+01 >> C 5.000000e+00 7.104400e-01 2.321954e+01 >> C 5.000000e+00 1.420870e+00 2.196443e+01 >> C 5.000000e+00 2.841730e+00 1.945421e+01 >> C 5.000000e+00 3.552160e+00 1.819910e+01 >> C 5.000000e+00 7.104400e-01 2.070932e+01 >> C 5.000000e+00 1.420870e+00 1.945421e+01 >> C 5.000000e+00 2.841730e+00 1.694399e+01 >> C 5.000000e+00 3.552160e+00 1.568888e+01 >> C 5.000000e+00 7.104400e-01 1.819910e+01 >> C 5.000000e+00 1.420870e+00 1.694399e+01 >> C 5.000000e+00 2.841730e+00 1.443377e+01 >> C 5.000000e+00 3.552160e+00 1.317866e+01 >> C 5.000000e+00 7.104400e-01 1.568888e+01 >> C 5.000000e+00 1.420870e+00 1.443377e+01 >> C 5.000000e+00 2.841730e+00 1.192354e+01 >> C 5.000000e+00 3.552160e+00 1.066843e+01 >> C 5.000000e+00 7.104400e-01 1.317866e+01 >> C 5.000000e+00 1.420870e+00 1.192354e+01 >> C 5.000000e+00 2.841730e+00 9.413323e+00 >> C 5.000000e+00 3.552160e+00 8.158212e+00 >> C 5.000000e+00 7.104400e-01 1.066843e+01 >> C 5.000000e+00 1.420870e+00 9.413323e+00 >> C 5.000000e+00 2.841730e+00 6.903101e+00 >> C 5.000000e+00 3.552160e+00 5.647990e+00 >> C 5.000000e+00 7.104400e-01 8.158212e+00 >> C 5.000000e+00 1.420870e+00 6.903101e+00 >> C 5.000000e+00 2.841730e+00 4.392879e+00 >> C 5.000000e+00 3.552160e+00 3.137768e+00 >> C 5.000000e+00 7.104400e-01 5.647990e+00 >> C 5.000000e+00 1.420870e+00 4.392879e+00 >> C 5.000000e+00 2.841730e+00 1.882658e+00 >> C 5.000000e+00 3.552160e+00 6.275467e-01 >> C 5.000000e+00 7.104400e-01 3.137768e+00 >> C 5.000000e+00 1.420870e+00 1.882658e+00 >> C 5.000000e+00 7.104400e-01 6.275467e-01 >> C 5.000000e+00 7.104310e+00 2.447465e+01 >> C 5.000000e+00 7.814740e+00 2.321954e+01 >> C 5.000000e+00 5.683450e+00 2.447465e+01 >> C 5.000000e+00 7.104310e+00 2.196443e+01 >> C 5.000000e+00 7.814740e+00 2.070932e+01 >> C 5.000000e+00 4.973020e+00 2.321954e+01 >> C 5.000000e+00 5.683450e+00 2.196443e+01 >> C 5.000000e+00 7.104310e+00 1.945421e+01 >> C 5.000000e+00 7.814740e+00 1.819910e+01 >> C 5.000000e+00 4.973020e+00 2.070932e+01 >> C 5.000000e+00 5.683450e+00 1.945421e+01 >> C 5.000000e+00 7.104310e+00 1.694399e+01 >> C 5.000000e+00 4.973020e+00 1.819910e+01 >> C 5.000000e+00 5.683450e+00 1.694399e+01 >> C 5.000000e+00 4.973020e+00 1.568888e+01 >> C 5.000000e+00 5.683450e+00 1.443377e+01 >> C 5.000000e+00 7.104310e+00 1.192354e+01 >> C 5.000000e+00 7.814740e+00 1.066843e+01 >> C 5.000000e+00 4.973020e+00 1.317866e+01 >> C 5.000000e+00 5.683450e+00 1.192354e+01 >> C 5.000000e+00 7.104310e+00 9.413323e+00 >> C 5.000000e+00 7.814740e+00 8.158212e+00 >> C 5.000000e+00 4.973020e+00 1.066843e+01 >> C 5.000000e+00 5.683450e+00 9.413323e+00 >> C 5.000000e+00 7.104310e+00 6.903101e+00 >> C 5.000000e+00 7.814740e+00 5.647990e+00 >> C 5.000000e+00 4.973020e+00 8.158212e+00 >> C 5.000000e+00 5.683450e+00 6.903101e+00 >> C 5.000000e+00 7.104310e+00 4.392879e+00 >> C 5.000000e+00 7.814740e+00 3.137768e+00 >> C 5.000000e+00 4.973020e+00 5.647990e+00 >> C 5.000000e+00 5.683450e+00 4.392879e+00 >> C 5.000000e+00 7.104310e+00 1.882658e+00 >> C 5.000000e+00 7.814740e+00 6.275467e-01 >> C 5.000000e+00 4.973020e+00 3.137768e+00 >> C 5.000000e+00 5.683450e+00 1.882658e+00 >> C 5.000000e+00 4.973020e+00 6.275467e-01 >> C 5.000000e+00 1.136689e+01 2.447465e+01 >> C 5.000000e+00 1.207732e+01 2.321954e+01 >> C 5.000000e+00 9.946030e+00 2.447465e+01 >> C 5.000000e+00 1.136689e+01 2.196443e+01 >> C 5.000000e+00 1.207732e+01 2.070932e+01 >> C 5.000000e+00 9.235600e+00 2.321954e+01 >> C 5.000000e+00 9.946030e+00 2.196443e+01 >> C 5.000000e+00 1.136689e+01 1.945421e+01 >> C 5.000000e+00 1.207732e+01 1.819910e+01 >> C 5.000000e+00 9.235600e+00 2.070932e+01 >> C 5.000000e+00 9.946030e+00 1.945421e+01 >> C 5.000000e+00 1.136689e+01 1.694399e+01 >> C 5.000000e+00 9.235600e+00 1.819910e+01 >> C 5.000000e+00 9.946030e+00 1.694399e+01 >> C 5.000000e+00 9.235600e+00 8.158212e+00 >> C 5.000000e+00 9.946030e+00 6.903101e+00 >> C 5.000000e+00 1.136689e+01 4.392879e+00 >> C 5.000000e+00 1.207732e+01 3.137768e+00 >> C 5.000000e+00 9.235600e+00 5.647990e+00 >> C 5.000000e+00 9.946030e+00 4.392879e+00 >> C 5.000000e+00 1.136689e+01 1.882658e+00 >> C 5.000000e+00 1.207732e+01 6.275467e-01 >> C 5.000000e+00 9.235600e+00 3.137768e+00 >> C 5.000000e+00 9.946030e+00 1.882658e+00 >> C 5.000000e+00 9.235600e+00 6.275467e-01 >> C 5.000000e+00 1.562947e+01 2.447465e+01 >> C 5.000000e+00 1.633990e+01 2.321954e+01 >> C 5.000000e+00 1.420861e+01 2.447465e+01 >> C 5.000000e+00 1.562947e+01 2.196443e+01 >> C 5.000000e+00 1.633990e+01 2.070932e+01 >> C 5.000000e+00 1.349818e+01 2.321954e+01 >> C 5.000000e+00 1.420861e+01 2.196443e+01 >> C 5.000000e+00 1.562947e+01 1.945421e+01 >> C 5.000000e+00 1.633990e+01 1.819910e+01 >> C 5.000000e+00 1.349818e+01 2.070932e+01 >> C 5.000000e+00 1.420861e+01 1.945421e+01 >> C 5.000000e+00 1.562947e+01 1.694399e+01 >> C 5.000000e+00 1.349818e+01 1.819910e+01 >> C 5.000000e+00 1.420861e+01 1.694399e+01 >> C 5.000000e+00 1.633990e+01 8.158212e+00 >> C 5.000000e+00 1.562947e+01 6.903101e+00 >> C 5.000000e+00 1.633990e+01 5.647990e+00 >> C 5.000000e+00 1.562947e+01 4.392879e+00 >> C 5.000000e+00 1.633990e+01 3.137768e+00 >> C 5.000000e+00 1.420861e+01 4.392879e+00 >> C 5.000000e+00 1.562947e+01 1.882658e+00 >> C 5.000000e+00 1.633990e+01 6.275467e-01 >> C 5.000000e+00 1.349818e+01 3.137768e+00 >> C 5.000000e+00 1.420861e+01 1.882658e+00 >> C 5.000000e+00 1.349818e+01 6.275467e-01 >> C 5.000000e+00 1.989205e+01 2.447465e+01 >> C 5.000000e+00 2.060248e+01 2.321954e+01 >> C 5.000000e+00 1.847119e+01 2.447465e+01 >> C 5.000000e+00 1.989205e+01 2.196443e+01 >> C 5.000000e+00 2.060248e+01 2.070932e+01 >> C 5.000000e+00 1.776076e+01 2.321954e+01 >> C 5.000000e+00 1.847119e+01 2.196443e+01 >> C 5.000000e+00 1.989205e+01 1.945421e+01 >> C 5.000000e+00 2.060248e+01 1.819910e+01 >> C 5.000000e+00 1.776076e+01 2.070932e+01 >> C 5.000000e+00 1.847119e+01 1.945421e+01 >> C 5.000000e+00 1.989205e+01 1.694399e+01 >> C 5.000000e+00 2.060248e+01 1.568888e+01 >> C 5.000000e+00 1.776076e+01 1.819910e+01 >> C 5.000000e+00 1.847119e+01 1.694399e+01 >> C 5.000000e+00 1.989205e+01 1.443377e+01 >> C 5.000000e+00 2.060248e+01 1.317866e+01 >> C 5.000000e+00 1.989205e+01 1.192354e+01 >> C 5.000000e+00 2.060248e+01 1.066843e+01 >> C 5.000000e+00 1.847119e+01 1.192354e+01 >> C 5.000000e+00 1.989205e+01 9.413323e+00 >> C 5.000000e+00 2.060248e+01 8.158212e+00 >> C 5.000000e+00 1.776076e+01 1.066843e+01 >> C 5.000000e+00 1.847119e+01 9.413323e+00 >> C 5.000000e+00 1.989205e+01 6.903101e+00 >> C 5.000000e+00 2.060248e+01 5.647990e+00 >> C 5.000000e+00 1.776076e+01 8.158212e+00 >> C 5.000000e+00 1.847119e+01 6.903101e+00 >> C 5.000000e+00 1.989205e+01 4.392879e+00 >> C 5.000000e+00 2.060248e+01 3.137768e+00 >> C 5.000000e+00 1.776076e+01 5.647990e+00 >> C 5.000000e+00 1.847119e+01 4.392879e+00 >> C 5.000000e+00 1.989205e+01 1.882658e+00 >> C 5.000000e+00 2.060248e+01 6.275467e-01 >> C 5.000000e+00 1.776076e+01 3.137768e+00 >> C 5.000000e+00 1.847119e+01 1.882658e+00 >> C 5.000000e+00 1.776076e+01 6.275467e-01 >> C 5.000000e+00 2.415463e+01 2.447465e+01 >> C 5.000000e+00 2.486506e+01 2.321954e+01 >> C 5.000000e+00 2.273377e+01 2.447465e+01 >> C 5.000000e+00 2.415463e+01 2.196443e+01 >> C 5.000000e+00 2.486506e+01 2.070932e+01 >> C 5.000000e+00 2.202334e+01 2.321954e+01 >> C 5.000000e+00 2.273377e+01 2.196443e+01 >> C 5.000000e+00 2.415463e+01 1.945421e+01 >> C 5.000000e+00 2.486506e+01 1.819910e+01 >> C 5.000000e+00 2.202334e+01 2.070932e+01 >> C 5.000000e+00 2.273377e+01 1.945421e+01 >> C 5.000000e+00 2.415463e+01 1.694399e+01 >> C 5.000000e+00 2.486506e+01 1.568888e+01 >> C 5.000000e+00 2.202334e+01 1.819910e+01 >> C 5.000000e+00 2.273377e+01 1.694399e+01 >> C 5.000000e+00 2.415463e+01 1.443377e+01 >> C 5.000000e+00 2.486506e+01 1.317866e+01 >> C 5.000000e+00 2.202334e+01 1.568888e+01 >> C 5.000000e+00 2.273377e+01 1.443377e+01 >> C 5.000000e+00 2.415463e+01 1.192354e+01 >> C 5.000000e+00 2.486506e+01 1.066843e+01 >> C 5.000000e+00 2.202334e+01 1.317866e+01 >> C 5.000000e+00 2.273377e+01 1.192354e+01 >> C 5.000000e+00 2.415463e+01 9.413323e+00 >> C 5.000000e+00 2.486506e+01 8.158212e+00 >> C 5.000000e+00 2.202334e+01 1.066843e+01 >> C 5.000000e+00 2.273377e+01 9.413323e+00 >> C 5.000000e+00 2.415463e+01 6.903101e+00 >> C 5.000000e+00 2.486506e+01 5.647990e+00 >> C 5.000000e+00 2.202334e+01 8.158212e+00 >> C 5.000000e+00 2.273377e+01 6.903101e+00 >> C 5.000000e+00 2.415463e+01 4.392879e+00 >> C 5.000000e+00 2.486506e+01 3.137768e+00 >> C 5.000000e+00 2.202334e+01 5.647990e+00 >> C 5.000000e+00 2.273377e+01 4.392879e+00 >> C 5.000000e+00 2.415463e+01 1.882658e+00 >> C 5.000000e+00 2.486506e+01 6.275467e-01 >> C 5.000000e+00 2.202334e+01 3.137768e+00 >> C 5.000000e+00 2.273377e+01 1.882658e+00 >> C 5.000000e+00 2.202334e+01 6.275467e-01 >> H 5.000000e+00 7.654810e+00 1.597142e+01 >> H 5.000000e+00 6.784450e+00 1.443377e+01 >> H 5.000000e+00 7.654810e+00 1.289611e+01 >> H 5.000000e+00 8.915740e+00 1.066843e+01 >> H 5.000000e+00 1.191739e+01 1.597142e+01 >> H 5.000000e+00 9.395530e+00 1.597142e+01 >> H 5.000000e+00 9.786100e+00 9.130776e+00 >> H 5.000000e+00 1.104703e+01 6.903101e+00 >> H 5.000000e+00 1.191739e+01 5.365443e+00 >> H 5.000000e+00 1.617997e+01 1.597142e+01 >> H 5.000000e+00 1.365811e+01 1.597142e+01 >> H 5.000000e+00 1.578940e+01 9.130776e+00 >> H 5.000000e+00 1.452847e+01 6.903101e+00 >> H 5.000000e+00 1.365811e+01 5.365443e+00 >> H 5.000000e+00 1.792069e+01 1.597142e+01 >> H 5.000000e+00 1.879105e+01 1.443377e+01 >> H 5.000000e+00 1.792069e+01 1.289611e+01 >> H 5.000000e+00 1.665976e+01 1.066843e+01 >> >> CELL_PARAMETERS >> 10.000000 0.000000 0.0000000 >> 0.0000000 25.57550 0.0000000 >> 0.0000000 0.000000 25.102200 >> >> K_POINTS {automatic} >> 1 6 6 0 0 0 >> >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next 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URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110929/2538be54/attachment-0001.htm From giannozz at democritos.it Fri Sep 30 07:23:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Sep 2011 07:23:46 +0200 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: On Sep 30, 2011, at 6:38 , swapnil chandratre wrote: > This is the output i get, the file is not updated. I see the > wavefunctions file being updated but there is no update > on the output while. remember that in many operating systems, the output is buffered. Nothing is written until the buffer is full. 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 swapnil.chandratre at gmail.com Fri Sep 30 07:27:27 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Fri, 30 Sep 2011 00:27:27 -0500 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: Thanks Paolo, I did many simulations and encountered this for the first time. I think what happens here is, because it doesnt update the output regularly, it ultimately utilizes all the available disk space and then I get an message saying error writing to file. On Fri, Sep 30, 2011 at 12:23 AM, Paolo Giannozzi wrote: > > On Sep 30, 2011, at 6:38 , swapnil chandratre wrote: > > > This is the output i get, the file is not updated. I see the > > wavefunctions file being updated but there is no update > > on the output while. > > remember that in many operating systems, the output is > buffered. Nothing is written until the buffer is full. > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/ca03dfe2/attachment.htm From giannozz at democritos.it Fri Sep 30 07:49:43 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Sep 2011 07:49:43 +0200 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: On Sep 30, 2011, at 7:27 , swapnil chandratre wrote: > it ultimately utilizes all the available disk space and > then I get an message saying error writing to file. so the problem is clear: you either need to increase thedisk space, or to reduce the size of the calculation. 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 swapnil.chandratre at gmail.com Fri Sep 30 07:54:09 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Fri, 30 Sep 2011 00:54:09 -0500 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: Thanks Paolo, I will try to increase my available disk space. Thanks. On Fri, Sep 30, 2011 at 12:49 AM, Paolo Giannozzi wrote: > > On Sep 30, 2011, at 7:27 , swapnil chandratre wrote: > > > it ultimately utilizes all the available disk space and > > then I get an message saying error writing to file. > > so the problem is clear: you either need to increase > thedisk space, or to reduce the size of the calculation. > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/b4c7860b/attachment.htm From swapnil.chandratre at gmail.com Fri Sep 30 07:55:02 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Fri, 30 Sep 2011 00:55:02 -0500 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: Can you suggest some way to reduce the size of calculation, I dont have the liberty to make the system smaller. On Fri, Sep 30, 2011 at 12:54 AM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Thanks Paolo, > > I will try to increase my available disk space. Thanks. > > > On Fri, Sep 30, 2011 at 12:49 AM, Paolo Giannozzi wrote: > >> >> On Sep 30, 2011, at 7:27 , swapnil chandratre wrote: >> >> > it ultimately utilizes all the available disk space and >> > then I get an message saying error writing to file. >> >> so the problem is clear: you either need to increase >> thedisk space, or to reduce the size of the calculation. >> >> 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 >> > > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/1731eeca/attachment.htm From germaneau at gucas.ac.cn Fri Sep 30 20:03:45 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 30 Sep 2011 14:03:45 -0400 Subject: [Pw_forum] installing input file builder: gdis-0.99 In-Reply-To: <517354572.27599@gscas.net.cn> References: <517354572.27599@gscas.net.cn> Message-ID: <4E860481.3000406@gucas.ac.cn> Dear Jinghui, As I've already mention, have a look to J-ICE , it does handle qe input and output files ... ?ric. On 09/30/2011 12:12 AM, He Jinghui wrote: > Dear Gao Zhe: > > Yes, I run it from a terminal by typing : "./gdis", But nothing happened. > BTW: How do you prepare the input file? PWgui + xcrysden? is there any > builder can modify atom positions and save in pwscf input file? This is > what i am looking for. Would you mind sharing your experience with me? > This is my first day dealing with QE :). > > Thank you very much! > > Jinghui > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/f201b857/attachment.htm From giannozz at democritos.it Fri Sep 30 08:37:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 30 Sep 2011 08:37:05 +0200 Subject: [Pw_forum] Graphene Sheet with Antidots In-Reply-To: References: Message-ID: <57251512-E614-493B-8B4D-401C4780CBE6@democritos.it> On Sep 30, 2011, at 7:55 , swapnil chandratre wrote: > Can you suggest some way to reduce the size of calculation the usual ones: reduce size of the cell, number of bands, number of k-points, number of plane waves (i.e. cutoff) 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 ams751 at psu.edu Fri Sep 30 20:42:38 2011 From: ams751 at psu.edu (Alejandro Suarez) Date: Fri, 30 Sep 2011 14:42:38 -0400 Subject: [Pw_forum] ESM and spin polarized ionic relaxations Message-ID: Hello, I have recently tried running an ionic relaxation with a cell using the effective screening medium (ESM) method, but have run into a hanging issue. Whenever I try running the relaxation, the program hangs after the first scf minimization converges and before the forces on the atoms are calculated. The output stops immediately after the ESM charge and potential are printed. What's interesting is this error also happens when I set the esm boundary conditions to "pbc" which should remove any implementation of ESM should it not? The relaxation runs without problems when all esm related variables are removed. This issue is reproducible on 4.3.1 and 4.3.2. Is ESM just not yet able to do 'relax' runs? Thank you for any help you may provide. My input file is attached below: -------------------------------------------- &control calculation='relax', restart_mode='from_scratch', prefix='qe-test', pseudo_dir='/usr/global/qe/4.3.2/pseudo', outdir='/gpfs/home/ams751/scratch/test', tprnfor = .TRUE. / &system ibrav = 0, celldm(1) = 1.889725989, tot_charge=0, nat= 2, ntyp= 2, ecutwfc = 22.05, starting_magnetization(2) = 1.0 nspin = 2, nosym=.TRUE. occupations='smearing', smearing='gauss', degauss=0.004 assume_isolated='esm', esm_bc='pbc' / &electrons mixing_beta = 0.7 / &ions / ATOMIC_SPECIES C 12.000000 C.pbe-rrkjus.UPF H 1.000000 H.pbe-rrkjus.UPF CELL_PARAMETERS 12.3000000000000000 0.0000000000000000 0.0000000000000000 -6.1500000000000000 10.6521120000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 20.0000000000000000 ATOMIC_POSITIONS (crystal) C 0.46667 0.53333 0.00000 H 0.46667 0.53333 0.05000 K_POINTS automatic 1 1 1 0 0 0 Alejandro Suarez Graduate Student Department of Physics Penn State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/ecd25a70/attachment.htm From alex124678 at nc.rr.com Fri Sep 30 23:25:38 2011 From: alex124678 at nc.rr.com (Alex Shearer) Date: Fri, 30 Sep 2011 14:25:38 -0700 Subject: [Pw_forum] GADGET and PWSCF Message-ID: <4E8633D2.7070608@nc.rr.com> Esteemed Colleagues, I am interested in using PWSCF to calculate the properties of molecules self assembled onto crystal faces. These calculations are often done in VASP, but I would prefer to use PWSCF because I find it easier to work with and can run test jobs on a local machine rather than our cluster. The geometries of adsorption are often non-trivial; in papers dealing with similar systems, a tool known as GADGET is often used for geometry optimizations (see reference below). It seems that this tool, written in python, is designed to work in conjunction with VASP itself. A. Track; F. Rissner; G. Heimel, L. Romaner; D. Kafer; A. Bashir; G. M. Rangger; O. T. Hofmann; T. Bucko; G Witte; E. Zojer.J Phys. Chem C 2010, 114, 2677-2684. So, my two questions are: 1. Is there a similar geometry optimization package that is appropriate for use with PWSCF? 2. If there is no such package, does anyone have experience using GADGET in conjunction with PWSCF? Many thanks, Alex Shearer Graduate student; University of California, Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/696c4817/attachment.htm