From giannozz at democritos.it Sun Feb 1 17:15:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 1 Feb 2009 17:15:14 +0100 Subject: [Pw_forum] PP by atomic.x In-Reply-To: References: Message-ID: On Jan 31, 2009, at 6:45 , Karoly Nemeth wrote: > I am trying to reproduce Ru.pbe-n-van.UPF from the PP library of > PWSCF, > by atomic.x. that PP was generated using the original Vanderbilt code, not by the "atomic" code (whose executable is called "ld1.x", for no better reason than the original code from which it descend used to be called "ld1" once upon a time). The latter uses a different logic to generate US PP. You may find some inspiration in the following sample file for Ru: atomic_doc/pseudo_library/PBE/SRRu.pbe-rrkjus.in Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Sun Feb 1 21:00:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 1 Feb 2009 21:00:12 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <1E4FEB77-157B-4F80-B195-22E8429CCE74@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128230841.x0rzedjqgo4gowo0@mail.democritos.it> <6ac064b60901281420t2b32c8e1mc48c99698d0034bf@mail.gmail.com> <6ac064b60901281607w5f17f081jc82ec82da415f475@mail.gmail.com> <1E4FEB77-157B-4F80-B195-22E8429CCE74@u.northwestern.edu> Message-ID: <433175A8-5B80-4C2E-87F9-1B4E6AD5EB98@democritos.it> On Jan 29, 2009, at 17:21 , David Farrell wrote: > I had been looking through the 'understanding parallelism' section > of the user > manual, and was a bit confused about what is meant by some of the > parameters you can find something else (hopefully better, but not more detailed) in this paper written for the proceedings of an Italian conference on high- performance computing: http://www.fisica.uniud.it/~giannozz/Papers/rimini08.pdf > (not sure which direction though... this part doesn't seem to be > mentioned) 3rd crystal axis (typically z) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From mambom1902 at yahoo.com Mon Feb 2 03:53:48 2009 From: mambom1902 at yahoo.com (loc duong ding) Date: Sun, 1 Feb 2009 18:53:48 -0800 (PST) Subject: [Pw_forum] Error with Xcryden for view input and output of pwscf file Message-ID: <596113.96623.qm@web38803.mail.mud.yahoo.com> Dear all user, I have a problem when using Xcrysden to view input and output file?of pwscf. The error i got was: wrong # args: should be "pwInputPreset file" wrong # args: should be "pwInputPreset file" ??? while executing "pwInputPreset /cygdrive/g/Research/MODELLING/output_model2" ??? ("eval" body line 1) ??? invoked from within "eval $preset $file" ??? (procedure "openExtStruct" line 106) ??? invoked from within "openExtStruct 3 crystal external {sh /home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh} pwi2xsf.xsf_out {PWSCF Input File} ANGS -preset pwInpu..." ??? (menu invoke) ? I did not see this error before. I great appreciate all your instructions. ----------------------------------------------- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com From mpayami at aeoi.org.ir Mon Feb 2 03:07:12 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Mon, 02 Feb 2009 05:37:12 +0330 Subject: [Pw_forum] any published work on Na and Cs Message-ID: Dear ESPRESSOers, We have done some slab calculations based on Stabilized Jellium Model for simple metals of Al, Na, and Cs, and would like to compare our results with those of first-principles. For Al, the results of Ho-Bohnen, Da Silva, and Sferco et al are available in the literature. However, have not find any references on Na and Cs. Has anybody done or aware of those works? Best Regards, Mahmoud Payami Physics Group Atomic Energy Organization of Iran mpayami at aeoi.org.ir From dmitry at korotin.name Mon Feb 2 09:23:43 2009 From: dmitry at korotin.name (Dmitry Korotin) Date: Mon, 2 Feb 2009 09:23:43 +0100 Subject: [Pw_forum] Popularity of Quantum-Espresso Message-ID: <166cd7c60902020023v6d34649aq58c5f7f632663108@mail.gmail.com> Dear QE users and developers, does anyone estimate popularity and wide-spreading of QE code? For example how many papers with QE calculations results were published last year? I am interested in any indexes. -- Best regards, Dmitry Korotin Ph. D. Student, Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From baroni at sissa.it Mon Feb 2 09:43:34 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 2 Feb 2009 09:43:34 +0100 Subject: [Pw_forum] Popularity of Quantum-Espresso In-Reply-To: <166cd7c60902020023v6d34649aq58c5f7f632663108@mail.gmail.com> References: <166cd7c60902020023v6d34649aq58c5f7f632663108@mail.gmail.com> Message-ID: On Feb 2, 2009, at 9:23 AM, Dmitry Korotin wrote: > Dear QE users and developers, > does anyone estimate popularity and wide-spreading of QE code? For > example how many papers with QE calculations results were published > last year? I am interested in any indexes. 227, according to scopus. this figure is likely to be undersetimated because, much to my regret, there is no officially agreed citation policy for quantum espresso. I wish an easy-to-cite QE reference paper will appear somewhen in 2009 thanks for caring Stefan > > > -- > > Best regards, > Dmitry Korotin > > Ph. D. Student, > Institute of Metal Physics > S. Kovalevskaya, 18 > 620041 Ekaterinburg GSP-170 > Russia > _______________________________________________ > 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://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090202/ccbcd973/attachment.htm From sclauzer at sissa.it Mon Feb 2 10:58:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 02 Feb 2009 10:58:39 +0100 Subject: [Pw_forum] something about Pt.pw91-n-van.UPF In-Reply-To: <412f6c680901300814u719ea01nc8dc3b52a11d7684@mail.gmail.com> References: <412f6c680901300814u719ea01nc8dc3b52a11d7684@mail.gmail.com> Message-ID: <4986C3CF.7040908@sissa.it> Dear Vega, as pointed out by Prof. Eyvaz, your system is to be considered "metallic", in the sense that Pt is an open shell atom and there is a set of nearly degenerate levels (nearly because the crystall symmetry breaks the spherical symmerty of the atom) which is not full. The changes in charge density during self-consistency move these levels up and down a bit every cycle, so that their occupancy also changes and therefore the charge density changes somehow "discontinuously" from step to step, preventing the calculation from reaching self-consistency. In order to get a better estimate of the isolated atom energy, I suggest to do a spin polarized calculation (i.e. nspin=2) either using a very small smearing (and check converge with respect to degauss), or fixing occupations (specify occupations='from_input' in the electrons namelist and add the input card OCCUPATIONS after the namelists). You can also fix the total magnetization (=2.0) or, equivalently, the spin multiplicity (=3)instead of occupations. Other suggestions: vega lew wrote: > &CONTROL > , > nstep = 1000 you don't need to specify this in scf calculations. If you want to increase the maximum number of iterations in the scf cycle the corresponding key is electron_maxstep in electrons. > , > nosym = .ture. .TRUE. Regards, GS > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From m.abbasnejad at gmail.com Mon Feb 2 11:59:14 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 2 Feb 2009 14:29:14 +0330 Subject: [Pw_forum] converting pseudopotential In-Reply-To: References: <7699a1950901280433j760f2c2am426645099b021e17@mail.gmail.com> Message-ID: <7699a1950902020259r1049182ftff0bd9562b7cd389@mail.gmail.com> Dear all, Although I attempted so much to compile and run casino2upf.x, I couldn't find it. Would you please help me? Thanks in advance. Yours, Mohaddeseh On Wed, Jan 28, 2009 at 4:24 PM, Lorenzo Paulatto wrote: > On Wed, 28 Jan 2009 13:33:06 +0100, mohaddeseh abbasnejad < > m.abbasnejad at gmail.com> wrote: > > I have found that there is a utility in PWscf > > [...] > > But I couldn't find it. > > Well, have you found it or not? ;-) > In either case it is in upftools/; just eneter the directory and type "make > all". > > > Would you please tell me how I can use it? > > One you have compiled it you can run it from upftools/ like ./casino2upf.x > it'll ask you to provide the name of casino file (for input) and of the UPF > file (for output). > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, End of North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090202/e271135d/attachment.htm From davidfarrell2008 at u.northwestern.edu Mon Feb 2 14:40:51 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Mon, 2 Feb 2009 07:40:51 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <433175A8-5B80-4C2E-87F9-1B4E6AD5EB98@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128230841.x0rzedjqgo4gowo0@mail.democritos.it> <6ac064b60901281420t2b32c8e1mc48c99698d0034bf@mail.gmail.com> <6ac064b60901281607w5f17f081jc82ec82da415f475@mail.gmail.com> <1E4FEB77-157B-4F80-B195-22E8429CCE74@u.northwestern.edu> <433175A8-5B80-4C2E-87F9-1B4E6AD5EB98@democritos.it> Message-ID: <4B51152D-E05C-4968-B9C2-DAA1DE3A9E5D@u.northwestern.edu> I had found that paper and it helped explain a few things, though it didn't help answer my question about the output. Dave On Feb 1, 2009, at 2:00 PM, Paolo Giannozzi wrote: > > On Jan 29, 2009, at 17:21 , David Farrell wrote: > >> I had been looking through the 'understanding parallelism' section >> of the user >> manual, and was a bit confused about what is meant by some of the >> parameters > > you can find something else (hopefully better, but not more detailed) > in this paper > written for the proceedings of an Italian conference on high- > performance computing: > http://www.fisica.uniud.it/~giannozz/Papers/rimini08.pdf > >> (not sure which direction though... this part doesn't seem to be >> mentioned) > > 3rd crystal axis (typically z) > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090202/cfc86a8e/attachment-0001.htm From giannozz at democritos.it Mon Feb 2 15:09:09 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 02 Feb 2009 15:09:09 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <1E4FEB77-157B-4F80-B195-22E8429CCE74@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128230841.x0rzedjqgo4gowo0@mail.democritos.it> <6ac064b60901281420t2b32c8e1mc48c99698d0034bf@mail.gmail.com> <6ac064b60901281607w5f17f081jc82ec82da415f475@mail.gmail.com> <1E4FEB77-157B-4F80-B195-22E8429CCE74@u.northwestern.edu> Message-ID: <4986FE85.2030605@democritos.it> David Farrell wrote: > In my test of 1 pool of 1024 procs with 32 taskgroups, the output looked > like this: > Proc/ planes cols G planes cols G columns G > Pool (dense grid) (smooth grid) (wavefct grid) > 1 15 162 50122 15 162 50122 42 6294 > 2 0 162 50122 0 162 50122 42 6294 > 3 0 162 50122 0 162 50122 42 6294 > 4 0 162 50122 0 162 50122 42 6294 > 5 0 162 50122 0 162 50122 42 6294 > ... > 32 0 164 50136 0 164 50136 42 6290 > 33 15 164 50136 15 164 50136 42 6290 > 34 0 164 50136 0 164 50136 42 6290 > > Which seems to indicate that there are processors that aren't getting > any planes and that the FFT grid is *not* being reproduced within each > taskgroup. or that the output does not reflect what is going pon. This seems to me much more likely, since the goal of the task group stuff is to be able to use a number of processors larger than the number of planes along direction 3, without having processors idling during the FFT Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From tone.kokalj at ijs.si Mon Feb 2 16:08:09 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 02 Feb 2009 16:08:09 +0100 Subject: [Pw_forum] Error with Xcryden for view input and output of pwscf file In-Reply-To: <596113.96623.qm@web38803.mail.mud.yahoo.com> References: <596113.96623.qm@web38803.mail.mud.yahoo.com> Message-ID: <1233587289.2459.10.camel@walk.ijs.si> On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote: > Dear all user, > > I have a problem when using Xcrysden to view input and output file of pwscf. The error i got was: > > wrong # args: should be "pwInputPreset file" You will need to provide more info! How did you load the file (i.e. sequence of steps), what is the actual file (mail it as attachement)? Only then there is a change to help. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From eyvaz_isaev at yahoo.com Mon Feb 2 17:09:16 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 2 Feb 2009 08:09:16 -0800 (PST) Subject: [Pw_forum] something about Pt.pw91-n-van.UPF In-Reply-To: <4986C3CF.7040908@sissa.it> Message-ID: <414839.85741.qm@web65705.mail.ac4.yahoo.com> Dear Gabriele, --- On Mon, 2/2/09, Gabriele Sclauzero wrote: > as pointed out by Prof. Eyvaz, I think there is no need to be so official, just name should be OK. Of course, the signature file is attached every time in order to fulfil the Netiquette. Thanks for your comments, I never did "atomic" calculations and will try to keep in mind the comments. Bests, Eyvaz. > your system is to be considered "metallic", in the sense that Pt is an > open shell atom and there is a set of nearly degenerate levels (nearly > because the crystall symmetry breaks the spherical symmerty > of the atom) which is not full. The changes in charge density during > self-consistency move these levels up and down a bit every cycle, so > that their occupancy also changes and therefore the charge density > changes somehow "discontinuously" from step to step, preventing the > calculation from reaching self-consistency. > > In order to get a better estimate of the isolated atom energy, I suggest >to do a spin polarized calculation (i.e. nspin=2) either using a very > small smearing (and check converge with respect to degauss), or fixing >occupations (specify occupations='from_input' in the electrons namelist >and add the input card OCCUPATIONS after the namelists). You can also >fix the total magnetization (=2.0) or, equivalently, the spin > multiplicity (=3)instead of occupations. > Other suggestions: > > vega lew wrote: > > &CONTROL > > > , > > nstep = 1000 > > you don't need to specify this in scf calculations. If > you want to increase the maximum > number of iterations in the scf cycle the corresponding key > is electron_maxstep in electrons. > > > , > > nosym = .ture. > .TRUE. > > Regards, > > GS > > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical > Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, > Jiangsu, China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > > Office: Room A705, Technical Innovation Building, > Xinmofan Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From marzari at MIT.EDU Mon Feb 2 17:20:52 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 02 Feb 2009 11:20:52 -0500 Subject: [Pw_forum] something about Pt.pw91-n-van.UPF In-Reply-To: <4986C3CF.7040908@sissa.it> References: <412f6c680901300814u719ea01nc8dc3b52a11d7684@mail.gmail.com> <4986C3CF.7040908@sissa.it> Message-ID: <49871D64.3040801@mit.edu> Gabriele Sclauzero wrote: > In order to get a better estimate of the isolated atom energy, I suggest to do a spin > polarized calculation (i.e. nspin=2) either using a very small smearing (and check > converge with respect to degauss), or fixing occupations (specify occupations='from_input' > in the electrons namelist and add the input card OCCUPATIONS after the namelists). > You can also fix the total magnetization (=2.0) or, equivalently, the spin multiplicity > (=3)instead of occupations. A note of caution - if the atom ends up with fractional occupations on equivalent p or d levels, the code will print out in the total energy of the system also the entropic contribution (i.e. it will write E-TS), where S is not zero. (That's why I actually like to call the energy written by PWSCF total free energy, rather than total energy). Looking at the total free energy is the right thing to do in a metal, but not in an atom. Of course, even if S is large (because occupations are not 0 or 1), in the limit of T going to zero -TS goes to zero, but it would be more appropriate to actually look at E (taking the total (free) energy that PWSCF writes, i.e. E-TS, and subtracting to that -TS, that the code also writes, in order to get E). Checking that as a function of smearing [(E-TS)-(-TS)] is constant (this is the difference between the two quantities written by PWSCF in output), while the total (free) energy E-TS is linear, would be a good consistency check. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From amigliore at cmm.upenn.edu Mon Feb 2 18:03:57 2009 From: amigliore at cmm.upenn.edu (Agostino Migliore) Date: Mon, 2 Feb 2009 12:03:57 -0500 (EST) Subject: [Pw_forum] something about Pt.pw91-n-van.UPF Message-ID: <1403.130.91.67.162.1233594237.squirrel@cmm.upenn.edu> Hello Until the smearing is not fully negligible (so that you still have appreciable fractional occupations) also E=F-(-TS)=(E-TS)-(-TS) (that is the difference between the two quantities directly provided by the code) will be a function of the spreading paramater. On the other hand, if you get the energy with a small enough smearing, a good estimate for the energy without smearing is given by the equation [F(T)+E(T)]/2=E(0)+O(T^n), with n>2, which you can find in O. Grotheer and M. Fa?hnle, PRB (1998), 58, 13459. Best, Agostino Migliore CMM, Chemistry Department, UPenn Philadelphia, PA From marzari at MIT.EDU Mon Feb 2 18:36:14 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 02 Feb 2009 12:36:14 -0500 Subject: [Pw_forum] something about Pt.pw91-n-van.UPF In-Reply-To: <1403.130.91.67.162.1233594237.squirrel@cmm.upenn.edu> References: <1403.130.91.67.162.1233594237.squirrel@cmm.upenn.edu> Message-ID: <49872F0E.4060907@mit.edu> Dear Agostino, a couple of points - we are dealing with an atom, and for smearings small enough that occupations do not change as a function of temperature - fractional occupations that are there just because of degeneracies. This is a bit different from the ideal case of the free-electron metal - so for an atom as a function of temperature the total energy E and the entropy S do not change (provided the temperature is smaller than the distance to the next set of empty orbitals), E-TS changes only because of T changing, and S is not zero just because of degeneracy. So my previous post re the atom energies should still hold. Regarding the issue of taking (E+F)/2 (a good idea for a metal, not an atom), that was first introduced by Mike Gillan in 1989 (there is a JPcondmatt from then, I believe, and a later one in 1991 with Alessandro de Vita). That suggestion works only for the energy, but not for antyhing else (forces, stresses, etc...). The Methfessel-Paxton or Marzari-Vanderbilt smearings achieve the same goal of taking (E+F)/2 , but do that variationally (i.e. consistently for forces, stresses, etc...). A long discussion is in chap 4 of http://quasiamore.mit.edu/phd/ . nicola Agostino Migliore wrote: > Hello > > Until the smearing is not fully negligible (so that you still have > appreciable fractional occupations) also E=F-(-TS)=(E-TS)-(-TS) (that is > the difference between the two quantities directly provided by the code) > will be a function of the spreading paramater. On the other hand, if you > get the energy with a small enough smearing, a good estimate for the > energy without smearing is given by the equation > > [F(T)+E(T)]/2=E(0)+O(T^n), with n>2, > > which you can find in > O. Grotheer and M. Fa?hnle, PRB (1998), 58, 13459. > > Best, > Agostino Migliore > CMM, Chemistry Department, UPenn > Philadelphia, PA > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From amigliore at cmm.upenn.edu Mon Feb 2 19:22:37 2009 From: amigliore at cmm.upenn.edu (Agostino Migliore) Date: Mon, 2 Feb 2009 13:22:37 -0500 (EST) Subject: [Pw_forum] something about Pt.pw91-n-van.UPF Message-ID: <2308.130.91.67.162.1233598957.squirrel@cmm.upenn.edu> Hello prof! Quoting Nicola Marzari : > > > Dear Agostino, > > > a couple of points - we are dealing with an atom, and for > smearings small enough that occupations do not change as > a function of temperature - fractional occupations that are > there just because of degeneracies. This is a bit different > from the ideal case of the free-electron metal - so for an atom > as a function of temperature the total energy E and the entropy > S do not change (provided the temperature is smaller than the > distance to the next set of empty orbitals), E-TS changes > only because of T changing, and S is not zero just because > of degeneracy. So my previous post re the atom energies should > still hold. > > Regarding the issue of taking (E+F)/2 (a good idea for > a metal, not an atom), that was first introduced by Mike > Gillan in 1989 (there is a JPcondmatt from then, I believe, > and a later one in 1991 with Alessandro de Vita). That suggestion > works only for the energy, but not for antyhing else (forces, stresses, > etc...). The Methfessel-Paxton or Marzari-Vanderbilt smearings > achieve the same goal of taking (E+F)/2 , but do that variationally > (i.e. consistently for forces, stresses, etc...). A long discussion > is in chap 4 of http://quasiamore.mit.edu/phd/ . > > nicola Thanks for your remarks, which are interesting and allow me to specify something about what I said before. Indeed, in the paper I cited before, the limit for n in the relation [F(T)+E(T)]/2=E(0)+O(T^n), with n>2, (there demonstrated under rather general assumptions) has been pushed up to n=4 (i.e., n even and n>2, so n=4), while it was thought to be n=3 before (e.g., both in M. J. Gillan, J. Phys.: Condens. Matter 1, 689 (1989) and F. Wagner, Th. Laloyaux, and M. Scheffler, Phys. Rev. B 57, 2102 (1998)). So I cited it as the last useful example. And clearly it works only for energy. I agree with you that in the specific case where some levels are degenerate, in a range of smearing values where the occupations don't change, the only change in the free energy associated to fractional occupations is a linear one, depending on T through -TS. In fact, it is a particular case where dS/dT=0 (for a suitable range of T) and dE/dT = T(dS dT)=0 too. Obviously, things can change even with a small fractional occupation of the higher lying levels or some departure from degeneracy of the involved multiplet. So, I spoke in general, having in mind that even in an atomic system you often have a multiplet and there is no exact degeneracy. This was not in contrast with the specific case you were referring to. Best, Agostino Migliore CMM, Chemistry Department, UPenn Philadelphia, PA From davidfarrell2008 at u.northwestern.edu Mon Feb 2 19:30:10 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Mon, 2 Feb 2009 12:30:10 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <20090128231527.uq7wa69a04okwssc@mail.democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> Message-ID: I tried reducing nbnd, diago_david_ndim, mixing_ndim, and still no good. Memory issue seems to remain. In my system I have set nosym = .true. - so I would think the below wouldn't be the problem... or is this flag for a different symmetry operation? Dave On Jan 28, 2009, at 4:15 PM, giannozz at democritos.it wrote: > Quoting Axel Kohlmeyer : > >> however the other use in psymrho.f90/psymrho_mag.f90 is consistent >> with the problem happening at the rho-mixing stage. > > the way parallel symmetrization is implemented now guarantees that a > large system with symmmetry (a strange object, though) will go out > of memory. A workaround should be simple, though > > Paolo > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090202/d3cde6a5/attachment-0001.htm From nemeth at anl.gov Mon Feb 2 21:30:54 2009 From: nemeth at anl.gov (Karoly Nemeth) Date: Mon, 2 Feb 2009 14:30:54 -0600 (CST) Subject: [Pw_forum] PP by atomic.x In-Reply-To: References: Message-ID: Thank you very much Paolo for calling my attention to these example files. The fact that in atomic_doc/pseudo-gen there were example files stopped me from looking also elsewhere for example files. Thanks a lot again: Karoly >> I am trying to reproduce Ru.pbe-n-van.UPF from the PP library of >> PWSCF, >> by atomic.x. > > that PP was generated using the original Vanderbilt code, not by the > "atomic" code (whose executable is called "ld1.x", for no better reason > than the original code from which it descend used to be called "ld1" > once upon a time). The latter uses a different logic to generate US PP. > You may find some inspiration in the following sample file for Ru: > atomic_doc/pseudo_library/PBE/SRRu.pbe-rrkjus.in > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy From yukihiro_okuno at fujifilm.co.jp Tue Feb 3 04:09:37 2009 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Tue, 3 Feb 2009 12:09:37 +0900 Subject: [Pw_forum] On the argument charge for l or d orbital of pseudo potential Message-ID: Dear PWSCF users and developer. I have primitive question of the pseudo charge density. I'm now tring to construct the atomic pseudo charge density of each orbit, calculated the pseudo charge like n(r) = |psi(r)|^2 + \sum_{i,j}Q_{i,j}(r). where psi is pseudo wave function defined in UPF file. And I found the strange results which come from the argument charge Q_{i,j}, in the p (l=1) or d(l=1) pseudo wave function case. There are charge density peak around r=0 ( peak at r=0 ) from the argument charge Q_{i,j}. I think p wave and d wave wave function must have node at r = 0, but the charge density from Q has peak around r = 0. We can see this fact from the values of UPF file simply. For example Zn.pz-van_ak.UPF file it was downloaded from PWSCF site, The d wave pseudo wave function psi has angular momentum l = 2 and the arguement wave function Q_{ij} only comes frol l(i)=l(j)=2 cases ( beta's angular momentum l = 2) case and, the relevant Q's index values in UPF file with l(i)=l(j)=2 are i, j = 5, or 6 . And at the radical point near the origin r(2) = 1.4123607*10^{-6} ( very near the r(1)=0 ), and the relevant values Q_{i,j} are in UPF file r^2Q_{5,5}(r) = 2.983286310*10^{-10} , r^{2}Q_{6,6}=3.54725669 * 10^{-10} r^2Q_{6,5} = -3.2531434588 * 10^{-10}. (The Q function in UPF file is difened as r^{2}Q{r}, multipled by r^{2} , I had cheked this definition in the PWSCF source code and former mail posting http://www.democritos.it/pipermail/pw_forum/2008-November/010758.html http://www.democritos.it/pipermail/pw_forum/2009-January/011188.html ) And we can see, for example, The argument charge density Q_arg around r(2), are Q_{arg} = r^{2{Q_{5,5}/(4.0*pi*r^{2}) = 11.9..... and Q_{5,6}, and Q_{6,6} are same order, and these values are not cancelled by the factors, . Same problem occurs in O.pz-rrkjus.UPF file with pseudo wave function with l=1, I had cheked many times also checked in the Vanderbilt's pseudo potential generation program. Why the argument charge has its value around r (peak at the r = 0) in the case of l=1, or l=2 case? Sincerely. Yukihiro Okuno. From powergreen at gmail.com Tue Feb 3 06:27:46 2009 From: powergreen at gmail.com (Green Power) Date: Tue, 3 Feb 2009 00:27:46 -0500 Subject: [Pw_forum] "Found additional translation" Message-ID: Dear PWscf user, In my outfile, there appear several lines like "Found additional translation: 0.0000 0.5000 -0.5000". Does it mean a supercell in my input? But I directly use the fractional coordinates of cif file from CSD. My system is orthorhombic S8 (Fddd), and atomic postions in the input is as follows. Could you give my any suggestions? Thanks. Tian ATOMIC_POSITIONS {crystal} S 0.8558 0.9527 -0.0485 S 0.7073 0.9798 0.0041 S 0.7842 1.0302 0.0762 S 0.786 0.9077 0.1295 S 0.8942 0.7973 -0.0485 S 0.964 0.8423 0.1295 S 1.0427 0.7702 0.0041 S 0.9658 0.7198 0.0762 S 0.8558 0.4527 0.4515 S 0.7073 0.4798 0.5041 S 0.7842 0.5302 0.5762 S 0.786 0.4077 0.6295 S 0.8942 0.2973 0.4515 S 0.964 0.3423 0.6295 S 1.0427 0.2702 0.5041 S 0.9658 0.2198 0.5762 S 0.3558 0.9527 0.4515 S 0.2073 0.9798 0.5041 S 0.2842 1.0302 0.5762 S 0.286 0.9077 0.6295 S 0.3942 0.7973 0.4515 S 0.464 0.8423 0.6295 S 0.5427 0.7702 0.5041 S 0.4658 0.7198 0.5762 S 0.3558 0.4527 -0.0485 S 0.2073 0.4798 0.0041 S 0.2842 0.5302 0.0762 S 0.286 0.4077 0.1295 S 0.3942 0.2973 -0.0485 S 0.464 0.3423 0.1295 S 0.5427 0.2702 0.0041 S 0.4658 0.2198 0.0762 S 0.1442 0.2027 0.2015 S 0.2927 0.2298 0.2541 S 0.2158 0.2802 0.3262 S 0.214 0.1577 0.3795 S 0.1058 0.0473 0.2015 S 0.036 0.0923 0.3795 S -0.0427 0.0202 0.2541 S 0.0342 -0.0302 0.3262 S 0.1442 0.7027 0.7015 S 0.2927 0.7298 0.7541 S 0.2158 0.7802 0.8262 S 0.214 0.6577 0.8795 S 0.1058 0.5473 0.7015 S 0.036 0.5923 0.8795 S -0.0427 0.5202 0.7541 S 0.0342 0.4698 0.8262 S 0.6442 0.2027 0.7015 S 0.7927 0.2298 0.7541 S 0.7158 0.2802 0.8262 S 0.714 0.1577 0.8795 S 0.6058 0.0473 0.7015 S 0.536 0.0923 0.8795 S 0.4573 0.0202 0.7541 S 0.5342 -0.0302 0.8262 S 0.6442 0.7027 0.2015 S 0.7927 0.7298 0.2541 S 0.7158 0.7802 0.3262 S 0.714 0.6577 0.3795 S 0.6058 0.5473 0.2015 S 0.536 0.5923 0.3795 S 0.4573 0.5202 0.2541 S 0.5342 0.4698 0.3262 S 0.1442 0.0473 1.0485 S 0.2927 0.0202 0.9959 S 0.2158 -0.0302 0.9238 S 0.214 0.0923 0.8705 S 0.1058 0.2027 1.0485 S 0.036 0.1577 0.8705 S -0.0427 0.2298 0.9959 S 0.0342 0.2802 0.9238 S 0.1442 0.5473 0.5485 S 0.2927 0.5202 0.4959 S 0.2158 0.4698 0.4238 S 0.214 0.5923 0.3705 S 0.1058 0.7027 0.5485 S 0.036 0.6577 0.3705 S -0.0427 0.7298 0.4959 S 0.0342 0.7802 0.4238 S 0.6442 0.0473 0.5485 S 0.7927 0.0202 0.4959 S 0.7158 -0.0302 0.4238 S 0.714 0.0923 0.3705 S 0.6058 0.2027 0.5485 S 0.536 0.1577 0.3705 S 0.4573 0.2298 0.4959 S 0.5342 0.2802 0.4238 S 0.6442 0.5473 1.0485 S 0.7927 0.5202 0.9959 S 0.7158 0.4698 0.9238 S 0.714 0.5923 0.8705 S 0.6058 0.7027 1.0485 S 0.536 0.6577 0.8705 S 0.4573 0.7298 0.9959 S 0.5342 0.7802 0.9238 S 0.8558 0.7973 0.7985 S 0.7073 0.7702 0.7459 S 0.7842 0.7198 0.6738 S 0.786 0.8423 0.6205 S 0.8942 0.9527 0.7985 S 0.964 0.9077 0.6205 S 1.0427 0.9798 0.7459 S 0.9658 1.0302 0.6738 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090203/6431cc78/attachment.htm From sclauzer at sissa.it Tue Feb 3 09:34:23 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 03 Feb 2009 09:34:23 +0100 Subject: [Pw_forum] "Found additional translation" In-Reply-To: References: Message-ID: <4988018F.4060400@sissa.it> Green Power wrote: > Dear PWscf user, > In my outfile, there appear several lines like "Found additional > translation: 0.0000 0.5000 -0.5000". Does it mean a supercell in > my input? It should mean exactly that in my knowledge. > But I directly use the fractional coordinates of cif file from > CSD. I don't know if this format can be feed directly to pw input. > My system is orthorhombic S8 (Fddd), and atomic postions in the > input is as follows. Could you give my any suggestions? Thanks. Try to give a look to your system with Xcrysden. You can feed it directly with the pw input like this xcrysden --pwi yourinputfile Please provide affiliation for the next posts, since this is the netiquette of this Forum. Thaks Bests, GS > Tian > > ATOMIC_POSITIONS {crystal} > S 0.8558 0.9527 -0.0485 > S 0.7073 0.9798 0.0041 > S 0.7842 1.0302 0.0762 > S 0.786 0.9077 0.1295 > S 0.8942 0.7973 -0.0485 > S 0.964 0.8423 0.1295 > S 1.0427 0.7702 0.0041 > S 0.9658 0.7198 0.0762 > S 0.8558 0.4527 0.4515 > S 0.7073 0.4798 0.5041 > S 0.7842 0.5302 0.5762 > S 0.786 0.4077 0.6295 > S 0.8942 0.2973 0.4515 > S 0.964 0.3423 0.6295 > S 1.0427 0.2702 0.5041 > S 0.9658 0.2198 0.5762 > S 0.3558 0.9527 0.4515 > S 0.2073 0.9798 0.5041 > S 0.2842 1.0302 0.5762 > S 0.286 0.9077 0.6295 > S 0.3942 0.7973 0.4515 > S 0.464 0.8423 0.6295 > S 0.5427 0.7702 0.5041 > S 0.4658 0.7198 0.5762 > S 0.3558 0.4527 -0.0485 > S 0.2073 0.4798 0.0041 > S 0.2842 0.5302 0.0762 > S 0.286 0.4077 0.1295 > S 0.3942 0.2973 -0.0485 > S 0.464 0.3423 0.1295 > S 0.5427 0.2702 0.0041 > S 0.4658 0.2198 0.0762 > S 0.1442 0.2027 0.2015 > S 0.2927 0.2298 0.2541 > S 0.2158 0.2802 0.3262 > S 0.214 0.1577 0.3795 > S 0.1058 0.0473 0.2015 > S 0.036 0.0923 0.3795 > S -0.0427 0.0202 0.2541 > S 0.0342 -0.0302 0.3262 > S 0.1442 0.7027 0.7015 > S 0.2927 0.7298 0.7541 > S 0.2158 0.7802 0.8262 > S 0.214 0.6577 0.8795 > S 0.1058 0.5473 0.7015 > S 0.036 0.5923 0.8795 > S -0.0427 0.5202 0.7541 > S 0.0342 0.4698 0.8262 > S 0.6442 0.2027 0.7015 > S 0.7927 0.2298 0.7541 > S 0.7158 0.2802 0.8262 > S 0.714 0.1577 0.8795 > S 0.6058 0.0473 0.7015 > S 0.536 0.0923 0.8795 > S 0.4573 0.0202 0.7541 > S 0.5342 -0.0302 0.8262 > S 0.6442 0.7027 0.2015 > S 0.7927 0.7298 0.2541 > S 0.7158 0.7802 0.3262 > S 0.714 0.6577 0.3795 > S 0.6058 0.5473 0.2015 > S 0.536 0.5923 0.3795 > S 0.4573 0.5202 0.2541 > S 0.5342 0.4698 0.3262 > S 0.1442 0.0473 1.0485 > S 0.2927 0.0202 0.9959 > S 0.2158 -0.0302 0.9238 > S 0.214 0.0923 0.8705 > S 0.1058 0.2027 1.0485 > S 0.036 0.1577 0.8705 > S -0.0427 0.2298 0.9959 > S 0.0342 0.2802 0.9238 > S 0.1442 0.5473 0.5485 > S 0.2927 0.5202 0.4959 > S 0.2158 0.4698 0.4238 > S 0.214 0.5923 0.3705 > S 0.1058 0.7027 0.5485 > S 0.036 0.6577 0.3705 > S -0.0427 0.7298 0.4959 > S 0.0342 0.7802 0.4238 > S 0.6442 0.0473 0.5485 > S 0.7927 0.0202 0.4959 > S 0.7158 -0.0302 0.4238 > S 0.714 0.0923 0.3705 > S 0.6058 0.2027 0.5485 > S 0.536 0.1577 0.3705 > S 0.4573 0.2298 0.4959 > S 0.5342 0.2802 0.4238 > S 0.6442 0.5473 1.0485 > S 0.7927 0.5202 0.9959 > S 0.7158 0.4698 0.9238 > S 0.714 0.5923 0.8705 > S 0.6058 0.7027 1.0485 > S 0.536 0.6577 0.8705 > S 0.4573 0.7298 0.9959 > S 0.5342 0.7802 0.9238 > S 0.8558 0.7973 0.7985 > S 0.7073 0.7702 0.7459 > S 0.7842 0.7198 0.6738 > S 0.786 0.8423 0.6205 > S 0.8942 0.9527 0.7985 > S 0.964 0.9077 0.6205 > S 1.0427 0.9798 0.7459 > S 0.9658 1.0302 0.6738 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Feb 3 09:51:48 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 03 Feb 2009 09:51:48 +0100 Subject: [Pw_forum] On the argument charge for l or d orbital of pseudo potential In-Reply-To: References: Message-ID: <498805A4.1050000@sissa.it> yukihiro_okuno at fujifilm.co.jp wrote: > There are charge density peak around r=0 ( peak at r=0 ) from the > argument charge Q_{i,j}. I think it's name is _augmentation_ charge, since you augment (add to) the charge a contribution missing in the pseudo wfcs. > I think p wave and d wave wave function must have node at > > r = 0, but the charge density from Q has peak around r = 0. > > We can see this fact from the values of UPF file simply. > > For example Zn.pz-van_ak.UPF file it was downloaded from PWSCF site, By inspecting that file I noticed: 8 nqf. If not zero, Qij's inside rinner are computed using qfcoef's 1 8.00000000000E-01 2 8.00000000000E-01 3 8.00000000000E-01 4 8.00000000000E-01 5 8.00000000000E-01 So that maybe you have to apply an interpolation formula to get the correct Qij inside rinner (which should be 0.8). Have you taken into account this? If not maybe you should re-read a reply to your post > http://www.democritos.it/pipermail/pw_forum/2009-January/011188.html Bests, GS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From yukihiro_okuno at fujifilm.co.jp Tue Feb 3 11:19:31 2009 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Tue, 3 Feb 2009 19:19:31 +0900 Subject: [Pw_forum] On the argument charge for l or d orbital of pseudo potential Message-ID: Dear PWSCF Users and Dr. Gabriele. Thank you for your reply. >By inspecting that file I noticed: > > 8 nqf. If not zero, Qij's inside rinner are computed using qfcoef's > > 1 8.00000000000E-01 > 2 8.00000000000E-01 > 3 8.00000000000E-01 > 4 8.00000000000E-01 > 5 8.00000000000E-01 > >So that maybe you have to apply an interpolation formula to get the correct Qij inside >rinner (which should be 0.8). Have you taken into account this? If not maybe you should >re-read a reply to your post Of course we tried the interpolation formula and the result was same. Basically, the Qfun(r) is correct also in the region (r < rinner ) as already written in your suggested post. Please see the post. > http://www.democritos.it/pipermail/pw_forum/2009-January/011188.html and furthermore, it can also be seen from the UPF file Zn.pz-van_ak.UPF section with Qij with i=5, j=5 case (which is the case l(i)=2, l(j)=2 ), or i=6, j=6 case (also l(i)=2, l(j)=2 case), the coefficient of Q^{L=0}_{ij}(r) has non zero coefficient C_{0} = 1.495560*10^{2} (for i=5, j=5) with Q^{L=0}_{ij}(r) = r^{L}*(C_{0} + C_{1}*r^{2} + ..... ) , which has weight around r=0 when L=0. L=0 is possible when the angular momentum of beta_{i} and beta_{j} is same, (Q_{ij}) . I think the origin of weight around r=0 of augumentation charge comes from the L=0 component of Q function, and why C_{0} coefficient is not zero for Q_{ij} with l(i)=l(j)=2 case (Zn case) ? Sincerely. Yukihiro Okuno. Yukihiro Okuno. From mpayami at aeoi.org.ir Wed Feb 4 02:06:07 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 3 Feb 2009 17:06:07 -0800 Subject: [Pw_forum] any published work on Na and Cs References: Message-ID: Was my question highly trivial/non-trivial for the community? M.P. ----- Original Message ----- From: "Mahmoud Payami Shabestari" To: Sent: Sunday, February 01, 2009 6:07 PM Subject: [Pw_forum] any published work on Na and Cs > > Dear ESPRESSOers, > We have done some slab calculations based on Stabilized Jellium Model > for simple metals of Al, Na, and Cs, and would like to compare our > results with those of first-principles. For Al, the results of > Ho-Bohnen, Da Silva, and Sferco et al are available in the literature. > However, have not find any references on Na and > Cs. Has anybody done or aware of those works? > > Best Regards, > Mahmoud Payami > > Physics Group > Atomic Energy Organization of Iran > mpayami at aeoi.org.ir > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From baroni at sissa.it Tue Feb 3 15:53:36 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 3 Feb 2009 15:53:36 +0100 Subject: [Pw_forum] 4th "Time-Dependent Density-Functional Theory: Prospects andApplications" Message-ID: Upon request, I am gladly forwarding this advertisement that I just received from A. Rubio --- 4th "Time-Dependent Density-Functional Theory: Prospects and Applications" January 2-15th 2010 Benasque Center for Physics, Spain Organizers: *) E. K. U. Gross *) Miguel A. L. 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This means that scientists new to the field face difficulties in grasping its many aspects that could be alleviated if they could attend a school on time-dependent density functional theory (TDDFT) or Many-Body Techniques (MBT). The school is followed by an international workshop, where the new developments of TDDFT and Many-Body Techniques for the calculation of excitations are discussed. Students attending the school are encouraged to attend the workshop, so they can get in contact with state of the art research in the field. The purpose of the workshop is to bring together leading experts in all these fields with different backgrounds, like density functional, many-body, nuclear physics, quantum chemists, and biophysicists. This allows the exchange of ideas between the different fields and the creation of links between the traditionally separated communities. Tentative program for the school: -------------------------------- The school will be attended by a maximum of around 50 students, and will last 9 days, with theoretical sessions (mostly) in the mornings and practical (tutorial) sessions in the afternoons. The theoretical sessions will consist of four 45m lectures (including discussions) per day. The practical sessions will last for 3 hours per day and a computer will be allocated for every two students. This will allow the students to have some time every day for studying and talking to the teachers. The program of the school starts with basic TDDFT, then continues with more complex theoretical and numerical aspects of TDDFT, and ends with an outline of some of its many applications. Basic knowledge on ground state DFT calculations is required. Also during the school we will address other approaches to describe excited state properties based on either many- body perturbation theory or quantum-chemistry schemes. The preliminary program can be downloaded from http://www.tddft.org/TDDFT2010/2010tddft.htm Tentative list of teachers: --- For the theoretical classes K. Capelle (Sao Carlos, Brazil) - Current DFT and C. Ullrich (U Missouri, USA) Franz Himpsel (USA) - Overview of spectroscopies A. Castro (FU Berlin, Germany) - Propagation schemes Optimal control theory R.W. Godby (York, UK) - Many-Body - GW E.K.U Gross (FU Berlin, Germany) - TDDFT M. Head-Gordon (UC Berkeley, USA) - TDDFT as a tool in chemistry M. Lein (MPI Heidelberg, Germany) - Models for time-dependent phenomena X. Lopez (San Sebastian, Spain) - TDDFT as a tool in biophysics N. Maitra (New York, USA) - Advanced TDDFT I. Tokatly (San Sebastian, Spain) or L. Reining (Paris, France) - Many-Body - BSE R. van Leeuwen (Groningen, The Netherlands) - TDDFT versus Many-Body Stefano Ossicini (Modena, Italy) - Fraud in Science --- For the practical sessions Xavier Andrade (San Sebastian, Spain) Silvana Botti (Paris, France) Alberto Castro (Berlin, Germany) Pablo Garcia (Madrid, Spain) Andrea Marini (Rome, Italy) Conor Hogan (Rome, Italy) Daniele Varsano (Modena, Italy) Yann Pouillon (San Sebastian, Spain) Micael Oliveira (Coimbra, Portugal) During the school we will incentive a close and informal contact between the students and the teachers. Furthermore, the students will be stimulated to talk about their current research activities and future interests. We feel that this is an important point, since young scientists should be involved in the building up of a strong community. The preliminary program of the workshop is: ------------------------------------------- The 4 day workshop will start January 10, 2010 in the afternoon and will end January 15 in the morning. It will include both invited talks on key aspects of TDDFT (45m each), contributed talks (30m) and a poster session. The tentative list of invited speakers is: ** Foundations of TDDFT, new developments and challenges W. Kohn (Santa Barbara, USA) N. Maitra (City University of New York, USA) A. Goerling (Munich, Germany) S. Kuemmel (MPI-Dresden, Germany) K. Burke (Irvine, USA) J. Dobson (Brisbane, Australia) ** Experimental challenges A. Zewail (Pasadena, USA) F. Krauz (Munich, Germany) P.B. Corkum (Ottawa, Canada) G. Gerber (Wuerzburg, Germany) or L. Woeste (Berlin, Germany) ** TD-DMFT, optimal control theory and strong laser fields O. Gritsenko (Amsterdam, The Netherlands) S. Kummel (Dresden, Germany) M. Lein (Kassel, Germany) T. Seidemann (Chicago, USA) ** Excited state dynamics and chemical reactivity O. Sugino (Tokyo, Japan) K. Reuter (Berlin, Germany) J. Hutter (Zurich, Switzerland) Y. Miyamoto (NEC, Japan) F. Martin (Madrid, Spain) ** Molecular Transport T.N. Todorov (Belfast, UK) R. van Leeuwen (Jyvaskyla, Finland) R. Car (Princeton, New Jersey, USA) M. di Ventra (Virginia, USA) R. Baer (Jerusalem, Israel) R. Godby (York, UK) ** Applications: nanotubes, quantum dots, nanostructures, solids and surfaces S.G. Louie (Berkeley, USA) R. Nieminen (Helsinki, Finland) C. Ambrosch-Draxl (Graz, Austria) M. Scheffler (Berlin, Germany) G. Kresse (Wien, Austria) S. Baroni (Trieste, Italy) ** Biological applications E.J. Baerends (Amsterdam, The Netherlands) I. Tavernelli (ETH Zuerich, Switzerland) M. Sprik (Cambridge, UK) F. Furche (Irvine, USA) Klaus Schulten (Illinois, USA) Some of the lecturers at the school will also contribute to the workshop. There will be two contributed talks from the winners of the 2nd Pedro Pascual Prize for the best posters presented at the school. Format of the workshop: ----------------------- We plan an informal workshop with sufficient time for discussions. The informal character of the talks will be encouraged and presentations which are partly tutorial, given the mixed character of the audience, are most welcome. The time for each talk will be divided into 75% for the presentation plus 25% discussion. Speakers will be encouraged to divide their available time into two separate parts if their topic falls under more than one heading. Applications/Support: -------------------- All persons who wish to participate should fill out the application form at http://sophia.ecm.ub.es/2009tddft/ In the comments section, please indicate if you wish to participate in the Summer Summer School or in the Workshop (or in both). School only: As we have a very limited number of places for the school, students will be selected from among an open pool of applicants who have demonstrated a strong interest in computational sciences, applied to chemistry, physics, materials science and biology. Therefore, in order that we can make a reasonable selection, we ask that *all* candidates include in the comments section the following information: *) Date of birth, gender *) Motivation/Why they want to come (just a couple of lines is enough) *) What is their current and previous positions (if PhD or Post- doc state your supervisor). We will *not* accept applications that do not include this information. Furthermore, we will give priority to students willing to participate in both the Summer School and the Workshop. We also have a certain number of grants available that cover traveling and part of the stay in Benasque. If you want to apply for a grant, please indicate explicitly that you wish to be supported in the comments section, and explain why (just a couple of lines is enough). For participants coming from the USA, please check the following address for support: http://www.mcc.uiuc.edu/travel/ ------------------------ P.S: Our apologies if you have received multiple copies of this announcement. _______________________________________________ Octopus-users mailing list Octopus-users at tddft.org http://www.tddft.org/mailman/listinfo/octopus-users From m.abbasnejad at gmail.com Tue Feb 3 20:19:35 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Tue, 3 Feb 2009 22:49:35 +0330 Subject: [Pw_forum] pseudopotential Message-ID: <7699a1950902031119j244d2609p108534123ff6a7a0@mail.gmail.com> Dear all, I am using latest version of PWscf (4.1CVS release). I want to use casino2upf.x utility but I can't find its self explanatory. Would you please help me? Thanks in advance. Regards, Mohaddeseh -- -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran,End of North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090203/85daf53c/attachment.htm From quevedin at gmail.com Tue Feb 3 22:22:05 2009 From: quevedin at gmail.com (Lucas Fernández Seivane) Date: Tue, 3 Feb 2009 21:22:05 +0000 Subject: Únete a Bebo Message-ID: <20090203215228.A8AB6112DA8@democritos.sissa.it> ????nete a Bebo! Cr??eme, ??te encantar??! Descubre por qu??... http://www.bebo.com/in/8585957041a21801311b135 ...................................................................... Este correo electr??nico te ha sido enviado a petici??n de Lucas Fern??ndez Seivane . No has sido agregado a ninguna lista de distribuci??n. Si no deseas recibir invitaciones de NING??N miembro de Bebo, haz clic aqu?? - http://www.bebo.com/unsub/8585957041a21801311 Bebo, Inc., 795 Folsom St, 6th Floor, San Francisco, CA 94107, USA. From quevedin at gmail.com Wed Feb 4 00:30:15 2009 From: quevedin at gmail.com (Lucas Fernandez Seivane) Date: Wed, 4 Feb 2009 00:30:15 +0100 Subject: [Pw_forum] Apologies Message-ID: <2ebe300a0902031530p3431e9acufec7c1cdb3a72183@mail.gmail.com> Hi to all in the list(s) Due to an error, a message from my account was sent to all my contacts regarding an invitation to join a social network called bebo. Please ignore it and apologies for the inconvenience, and keep the good work Lucas From m.abbasnejad at gmail.com Wed Feb 4 08:29:39 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Tue, 3 Feb 2009 23:29:39 -0800 Subject: [Pw_forum] how to convert pseudopotential Message-ID: <7699a1950902032329w78240d59gdb8ba6a13f5dc360@mail.gmail.com> Dear all, Could you please tell me which command I should use in order to convert a pp.data file written in the format of CASINO into a UPF file readable by PWscf? I attempted so much but I couldn't. It wants the number of wavefunction *files* that are using and I don't know what I should do exactly. Thanks in advance. Best Regards, Mohaddeseh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090203/35fd5b51/attachment.htm From giannozz at democritos.it Wed Feb 4 09:42:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 04 Feb 2009 09:42:08 +0100 Subject: [Pw_forum] any published work on Na and Cs In-Reply-To: References: Message-ID: <498954E0.6030301@democritos.it> Mahmoud Payami wrote: > Was my question highly trivial/non-trivial for the community? or maybe nobody knows about Cs and Na surfaces. I don't. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 4 09:46:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 04 Feb 2009 09:46:12 +0100 Subject: [Pw_forum] how to convert pseudopotential In-Reply-To: <7699a1950902032329w78240d59gdb8ba6a13f5dc360@mail.gmail.com> References: <7699a1950902032329w78240d59gdb8ba6a13f5dc360@mail.gmail.com> Message-ID: <498955D4.2030607@democritos.it> mohaddeseh abbasnejad wrote: > Could you please tell me which command I should use in order to convert > a pp.data file written in the format of CASINO into a UPF file casino2upf.x > I attempted so much but I couldn't. > It wants the number of wavefunction *files* that are using and I don't > know what I should do exactly. if you want to convert A into B, you need A. Apparently in this case A includes wavefunction files. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From mpayami at aeoi.org.ir Wed Feb 4 11:29:47 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Wed, 04 Feb 2009 13:59:47 +0330 Subject: [Pw_forum] any published work on Na and Cs In-Reply-To: <498954E0.6030301@democritos.it> References: <498954E0.6030301@democritos.it> Message-ID: > Mahmoud Payami wrote: > > > Was my question highly trivial/non-trivial for the community? > > or maybe nobody knows about Cs and Na surfaces. I don't. > > Paolo Ciao Paolo, Thank you so much. Best regards, Mahmoud > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From djaithania at hotmail.com Wed Feb 4 11:42:31 2009 From: djaithania at hotmail.com (hania djani-ait aissa) Date: Wed, 4 Feb 2009 10:42:31 +0000 Subject: [Pw_forum] problem with ibrav=13 again Message-ID: Dear all, i am doing calculation on C2/m monoclinic base centered structure. Infortunately, things don't work;no symmetry in the output and weird structure viewed bu Xcrysden.I checked the coordinates with an other code (Wien2k) where everything seemed to go well, giving the exact number of symmetry operations and the expected structure in Xcrysden. by the way, i am working on Pwscf version 3.2, where the bug ibrav=13 is fixed for good!!! please help me to figure out the problem, here is my input file: &control calculation = 'scf' restart_mode = 'from_scratch' pseudo_dir = '/home/hania//pseudo/ outdir = '/home/hania//tmp/' / &system ibrav=13 celldm(1)=31.067, celldm(2)=0.234, celldm(3)=0.5, celldm(4)=-0.213, nat=18 ntyp=3 ecutwfc=35.0 ecutrho=200.0, occupations = 'fixed' / &electrons conv_thr = 1e-6, mixing_beta=0.7, /ATOMIC_SPECIES W 183.84 W.pz-bhs.UPF Bi 208.98 083-Bi-ca-d-vgrp_ji.uspp.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS alat W 0.4981 0.117 0.15035 W 0.5019 0.117 0.34965 Bi 0.3341 0.000 0.46565 Bi 0.6659 0.000 0.03435 Bi 0.3213 0.000 0.1975 ???????????????????.. ????????????????????. ????????????????????. O 0.5054 0.000 0.34435 O 0.5753 0.117 0.25435 O 0.4247 0.117 0.24565 O 0.5696 0.117 0.0867 O 0.4304 0.117 0.4133 O 0.3972 0.117 0.08225 O 0.6028 0.117 0.41775 K_POINTS {automatic} 3 6 6 1 1 1 thanks in advance, Hania Djani-Ait Aissa ph.d. student Centre de D?veloppement des Technologies Avanc?es (CDTA)Baba Hassen Alger, Alg?rieDivision Milieux Ionis?es & Lasers Phone: (+213)21351044; Fax:(+213)21351039http://www.cdta.dz _________________________________________________________________ D?couvrez Windows Live Spaces et cr?ez votre site Web perso en quelques clics ! http://spaces.live.com/signup.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090204/2c94e67e/attachment.htm From sclauzer at sissa.it Wed Feb 4 11:56:00 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 04 Feb 2009 11:56:00 +0100 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: References: Message-ID: <49897440.90305@sissa.it> hania djani-ait aissa wrote: > Dear all, > i am doing calculation on C2/m monoclinic base centered structure. > Infortunately, things don't work;no symmetry in the output and weird > structure viewed bu Xcrysden.I checked the coordinates with an other > code (Wien2k) where everything seemed to go well, giving the exact > number of symmetry operations and the expected structure in Xcrysden. by > the way, i am working on Pwscf version 3.2, where the bug ibrav=13 is > fixed for good!!! > please help me to figure out the problem, If you want to be helped you should send the full input file (I don't understand why you omit some of the atomic positions, which could be relevant to solve your problem). Your (partial) structure does not look so wierd to me when inspecting it with xcrysden (but I don't know this system, so maybe I'm wrong). Maybe you did not find the symmetry you expected because you specified the atomic postion with too low accuracy, so try to specify them with more significant digits (at least 6 or more) and try running pw.x again. GS > here is my input file: > > &control > calculation = 'scf' > restart_mode = 'from_scratch' > pseudo_dir = '/home/hania//pseudo/ > outdir = '/home/hania//tmp/' > / > &system > ibrav=13 > celldm(1)=31.067, > celldm(2)=0.234, > celldm(3)=0.5, > celldm(4)=-0.213, > nat=18 > ntyp=3 > ecutwfc=35.0 > ecutrho=200.0, > occupations = 'fixed' > > / > &electrons > conv_thr = 1e-6, > mixing_beta=0.7, > / > ATOMIC_SPECIES > > W 183.84 W.pz-bhs.UPF > Bi 208.98 083-Bi-ca-d-vgrp_ji.uspp.UPF > O 15.9994 O.pz-van_ak.UPF > > ATOMIC_POSITIONS alat > W 0.4981 0.117 0.15035 > W 0.5019 0.117 0.34965 > Bi 0.3341 0.000 0.46565 > Bi 0.6659 0.000 0.03435 > Bi 0.3213 0.000 0.1975 > ???????????????????.. > ????????????????????. > > ????????????????????. > > O 0.5054 0.000 0.34435 > O 0.5753 0.117 0.25435 > O 0.4247 0.117 0.24565 > O 0.5696 0.117 0.0867 > O 0.4304 0.117 0.4133 > O 0.3972 0.117 0.08225 > O 0.6028 0.117 0.41775 > > K_POINTS {automatic} > 3 6 6 1 1 1 > > > thanks in advance, > > Hania Djani-Ait Aissa > ph.d. student > > Centre de D?veloppement des Technologies Avanc?es (CDTA) > Baba Hassen Alger, Alg?rie > Division Milieux Ionis?es & Lasers > Phone: (+213)21351044; Fax:(+213)21351039 > http://www.cdta.dz > > > ------------------------------------------------------------------------ > Tous vos amis discutent sur Messenger, et vous ? T?l?chargez Messenger, > c'est gratuit ! > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Wed Feb 4 11:55:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 04 Feb 2009 11:55:55 +0100 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: References: Message-ID: <4989743B.2040205@democritos.it> hania djani-ait aissa wrote: > I checked the coordinates with an other code (Wien2k) > where everything seemed, to go well, giving the exact > number of symmetry operations and the expected structure which demonstrates nothing, since it is not obvious that Wien2k and Q-E use the same convention to describe the case ibrav=13. What Q-E uses is described IN DETAIL in the documentation. If you have evidence that what the documentation says is not what the code does, please provide evidence Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From tone.kokalj at ijs.si Wed Feb 4 12:00:45 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 04 Feb 2009 12:00:45 +0100 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: References: Message-ID: <1233745245.4412.18.camel@walk.ijs.si> On Wed, 2009-02-04 at 10:42 +0000, hania djani-ait aissa wrote: > Dear all, > i am doing calculation on C2/m monoclinic base centered structure. > Infortunately, things don't work;no symmetry in the output and weird > structure viewed bu Xcrysden. As for the xcrysden, it is important to use 1.5.* version of the code, where the "ibrav" lattices have been (hopefully) syncronised with the current definitions in pwscf. The version 1.4.1 will do it wrong. If you still experience weird structure diplsay by xcrysden-1.5.* for ibrav=13 let me know. Please post the whole input file. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From djaithania at hotmail.com Wed Feb 4 12:23:55 2009 From: djaithania at hotmail.com (hania djani-ait aissa) Date: Wed, 4 Feb 2009 11:23:55 +0000 Subject: [Pw_forum] problem with ibrav=13 again Message-ID: Dear all, thank you for your quick reply, the structure should look as stacked multilayers of Bi2O2 slabs and perovskites ones along a-axis. i will use the latest version of Xcrysden and check if the problem still persist. here my total input file: &control calculation = 'scf' restart_mode = 'from_scratch' pseudo_dir = '/home/hania/pseudo/' outdir = '/home/hania/tmp/' / &system ibrav=0 celldm(1)=31.067, celldm(2)=0.234, celldm(3)=0.5, celldm(4)=-0.213, nat=18 ntyp=3 ecutwfc=35.0 ecutrho=200.0, occupations = 'fixed' / &electrons conv_thr = 1e-6, mixing_beta=0.7, /ATOMIC_SPECIES W 183.84 W.pz-bhs.UPF Bi 208.98 083-Bi-ca-d-vgrp_ji.uspp.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS alat W 0.4981 0.117 0.15035 W 0.5019 0.117 0.34965 Bi 0.3341 0.000 0.46565 Bi 0.6659 0.000 0.03435 Bi 0.3213 0.000 0.1975 Bi 0.6787 0.000 0.3025 O 0.2469 0.000 0.0585 O 0.7531 0.000 0.4415 O 0.2313 0.117 0.1819 O 0.7686 0.117 0.3181 O 0.4946 0.000 0.15565 O 0.5054 0.000 0.34435 O 0.5753 0.117 0.25435 O 0.4247 0.117 0.24565 O 0.5696 0.117 0.0867 O 0.4304 0.117 0.4133 O 0.3972 0.117 0.08225 O 0.6028 0.117 0.41775 K_POINTS {automatic} 3 6 6 1 1 1 thanks again Hania djani-Ait Aissa _________________________________________________________________ D?couvrez toutes les possibilit?s de communication avec vos proches http://www.microsoft.com/windows/windowslive/default.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090204/c627e9cb/attachment.htm From tone.kokalj at ijs.si Wed Feb 4 13:26:02 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 04 Feb 2009 13:26:02 +0100 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: References: Message-ID: <1233750362.4412.28.camel@walk.ijs.si> On Wed, 2009-02-04 at 11:23 +0000, hania djani-ait aissa wrote: > Dear all, > thank you for your quick reply, the structure should look as stacked > multilayers of Bi2O2 slabs and perovskites ones along a-axis. i will > use the latest version of Xcrysden and check if the problem still > persist. here my total input file: Based on your input, I just checked that the new xcrysden version uses the lattice for ibrav=13 as specified in the pwscf documentation for ibrav13, i.e.: celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a, celldm(4)=cos(ab) v1 = ( a/2, 0, -c/2), v2 = (b*cos(gamma), b*sin(gamma), 0), v3 = ( a/2, 0, c/2), where gamma is the angle between axis a and b There is indeed some problem in your structure: some Bi and O atoms are too close (only 1.1 Angs). Please check the coordinates of atoms 5, 6, 7 and 8 (in particular the two oxygens). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From djaithania at hotmail.com Wed Feb 4 15:11:56 2009 From: djaithania at hotmail.com (hania djani-ait aissa) Date: Wed, 4 Feb 2009 14:11:56 +0000 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: <1233750362.4412.28.camel@walk.ijs.si> References: <1233750362.4412.28.camel@walk.ijs.si> Message-ID: thanks for reply, actually, the problem is that the data collected by neutron diffraction gives a non-standard A2/m structure with a=8.37Angstrom, b=3.85A. c=16.44 and Beta >90?=102.334?. for pwscf recognize my structure i had to transforme A2/m to C2/m by swapping a and c axis and swapping x and z coordinates. however pwscf gives for ibrav=13 celldm(4)=cos(gamma) and my angle is Beta between ac. hania> From: tone.kokalj at ijs.si> To: pw_forum at pwscf.org> Date: Wed, 4 Feb 2009 13:26:02 +0100> Subject: Re: [Pw_forum] problem with ibrav=13 again> > On Wed, 2009-02-04 at 11:23 +0000, hania djani-ait aissa wrote:> > Dear all,> > thank you for your quick reply, the structure should look as stacked> > multilayers of Bi2O2 slabs and perovskites ones along a-axis. i will> > use the latest version of Xcrysden and check if the problem still> > persist. here my total input file:> > Based on your input, I just checked that the new xcrysden version uses> the lattice for ibrav=13 as specified in the pwscf documentation for> ibrav13, i.e.:> > celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a, celldm(4)=cos(ab)> > v1 = ( a/2, 0, -c/2),> v2 = (b*cos(gamma), b*sin(gamma), 0),> v3 = ( a/2, 0, c/2),> > where gamma is the angle between axis a and b> > There is indeed some problem in your structure: some Bi and O atoms are> too close (only 1.1 Angs). Please check the coordinates of atoms 5, 6, 7> and 8 (in particular the two oxygens).> > Regards, Tone> -- > Anton Kokalj> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822)> > Please, if possible, avoid sending me Word or PowerPoint attachments.> See: http://www.gnu.org/philosophy/no-word-attachments.html> > _______________________________________________> Pw_forum mailing list> Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ Vous voulez savoir ce que vous pouvez faire avec le nouveau Windows Live?? Lancez-vous ! http://www.microsoft.com/windows/windowslive/default.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090204/bc5631a7/attachment.htm From djaithania at hotmail.com Wed Feb 4 15:14:07 2009 From: djaithania at hotmail.com (hania djani-ait aissa) Date: Wed, 4 Feb 2009 14:14:07 +0000 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: <1233750362.4412.28.camel@walk.ijs.si> References: <1233750362.4412.28.camel@walk.ijs.si> Message-ID: thanks for reply, actually, the problem is that the data collected by neutron diffraction gives a non-standard A2/m structure with a=8.37Angstrom, b=3.85A. c=16.44 and Beta >90?=102.334?. for pwscf recognize my structure i had to transforme A2/m to C2/m by swapping a and c axis and swapping x and z coordinates. however pwscf gives for ibrav=13 celldm(4)=cos(gamma) and my angle is Beta between ac. hania> From: tone.kokalj at ijs.si> To: pw_forum at pwscf.org> Date: Wed, 4 Feb 2009 13:26:02 +0100> Subject: Re: [Pw_forum] problem with ibrav=13 again> > On Wed, 2009-02-04 at 11:23 +0000, hania djani-ait aissa wrote:> > Dear all,> > thank you for your quick reply, the structure should look as stacked> > multilayers of Bi2O2 slabs and perovskites ones along a-axis. i will> > use the latest version of Xcrysden and check if the problem still> > persist. here my total input file:> > Based on your input, I just checked that the new xcrysden version uses> the lattice for ibrav=13 as specified in the pwscf documentation for> ibrav13, i.e.:> > celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a, celldm(4)=cos(ab)> > v1 = ( a/2, 0, -c/2),> v2 = (b*cos(gamma), b*sin(gamma), 0),> v3 = ( a/2, 0, c/2),> > where gamma is the angle between axis a and b> > There is indeed some problem in your structure: some Bi and O atoms are> too close (only 1.1 Angs). Please check the coordinates of atoms 5, 6, 7> and 8 (in particular the two oxygens).> > Regards, Tone> -- > Anton Kokalj> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822)> > Please, if possible, avoid sending me Word or PowerPoint attachments.> See: http://www.gnu.org/philosophy/no-word-attachments.html> > _______________________________________________> Pw_forum mailing list> Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ Sur Windows Live Ideas, d?couvrez en exclusivit? de nouveaux services en ligne... si nouveaux qu'ils ne sont pas encore sortis officiellement sur le march? ! http://ideas.live.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090204/4181afad/attachment.htm From degironc at sissa.it Wed Feb 4 15:15:54 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 04 Feb 2009 15:15:54 +0100 Subject: [Pw_forum] problem with ibrav=13 again In-Reply-To: References: <1233750362.4412.28.camel@walk.ijs.si> Message-ID: <4989A31A.5010507@sissa.it> one possibility cound be to use ibrav=0 and then provide the bravais lattice vector as required by your cell via the CELL_PARAMETERS card... Hope this helps stefano hania djani-ait aissa wrote: > thanks for reply, > actually, the problem is that the data collected by neutron > diffraction gives a non-standard A2/m structure with a=8.37Angstrom, > b=3.85A. c=16.44 and Beta >90?=102.334?. for pwscf recognize my > structure i had to transforme A2/m to C2/m by swapping a and c axis > and swapping x and z coordinates. however pwscf gives for ibrav=13 > celldm(4)=cos(gamma) and my angle is Beta between ac. > > hania > > From: tone.kokalj at ijs.si > > To: pw_forum at pwscf.org > > Date: Wed, 4 Feb 2009 13:26:02 +0100 > > Subject: Re: [Pw_forum] problem with ibrav=13 again > > > > On Wed, 2009-02-04 at 11:23 +0000, hania djani-ait aissa wrote: > > > Dear all, > > > thank you for your quick reply, the structure should look as stacked > > > multilayers of Bi2O2 slabs and perovskites ones along a-axis. i will > > > use the latest version of Xcrysden and check if the problem still > > > persist. here my total input file: > > > > Based on your input, I just checked that the new xcrysden version uses > > the lattice for ibrav=13 as specified in the pwscf documentation for > > ibrav13, i.e.: > > > > celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a, celldm(4)=cos(ab) > > > > v1 = ( a/2, 0, -c/2), > > v2 = (b*cos(gamma), b*sin(gamma), 0), > > v3 = ( a/2, 0, c/2), > > > > where gamma is the angle between axis a and b > > > > There is indeed some problem in your structure: some Bi and O atoms are > > too close (only 1.1 Angs). Please check the coordinates of atoms 5, 6, 7 > > and 8 (in particular the two oxygens). > > > > Regards, Tone > > -- > > Anton Kokalj > > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > > > Please, if possible, avoid sending me Word or PowerPoint attachments. > > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------------------------------------------------ > Vous voulez savoir ce que vous pouvez faire avec le nouveau Windows > Live ? Lancez-vous ! > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ierrea001 at ikasle.ehu.es Thu Feb 5 11:58:41 2009 From: ierrea001 at ikasle.ehu.es (Ion Errea Lope) Date: Thu, 05 Feb 2009 11:58:41 +0100 Subject: [Pw_forum] Norm-conserving Na pseudopotential Message-ID: <1233831521.7217.29.camel@lcpybm> Dear users and developers, Lately I am calculating the phonons of Na at high pressure (65-105 GPa). At these pressures core overlap is significant and 2s and 2p states should be treated as valence electrons. However, phonons calculated with the ultra-soft pseudopotentials available at http://www.quantum-espresso.org/pseudo.php are really difficult to converge at q points close to gamma. This is not so if the norm-conserving Na.pz-n-vbc.UPF pseudo, with just 3s states in the valence, is used. Nevertheless, cores overlap and I do not trust my phonon calculation at all. Considering these aspects, I wonder if someone has ever generated a norm-conserving pseudopotential of Na including 2s and 2p states in the valence. I could try to generate one myself (actually I made some attempts), but considering my null experience generating pseudopotentials, this may not be a good idea. I would be very grateful if someone that has generated such a pseudo could send it to me, or at least give me some hints towards its generation with ld1.x code. Thanks in advance and kind regards, Ion -- ?======================================== Ion Errea Lope *Donostia International Physics Center (DIPC) *Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015322 Mail: ierrea001 at ikasle.ehu.es ======================================== From alexandra.carvalho at epfl.ch Thu Feb 5 15:49:26 2009 From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch) Date: Thu, 05 Feb 2009 15:49:26 +0100 Subject: [Pw_forum] specify occupation with k-points Message-ID: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> Dear Pwscf users, I have a shallow acceptor defect with an unpaired electron (in a semiconductor) that so far I have treated using smearing. However, to test the influence of the filling, I would like to set the occupation of the Kohn-Sham levels in the following manners: 1 - specify that band number # is filled/empty in all the k-points; and 2 - specify that band number # is empty at gamma, but filled at all the other k-points I would be very greatful if someone could suggest me a way of specifying this, since I could not find a suitable option in the manual. Thank you for your attention. Alexandra Carvalho EPFL Lausanne, Switzerland From sclauzer at sissa.it Thu Feb 5 16:07:01 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Feb 2009 16:07:01 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> Message-ID: <498B0095.8020103@sissa.it> Dear Alexandra, alexandra.carvalho at epfl.ch wrote: > Dear Pwscf users, > > I have a shallow acceptor defect with an unpaired electron (in a > semiconductor) > that so far I have treated using smearing. > However, to test the influence of the filling, I > would like to set the occupation of the Kohn-Sham levels > in the following manners: > > 1 - specify that band number # is filled/empty in all the k-points; > and > 2 - specify that band number # is empty at gamma, but filled at all > the other k-points I think that you can do this only for single-k point calculations, by specifying occupations='from_input' in the electrons namelist and adding an input card called OCCUPATIONS at the end of your input file (please check Doc/INPUT_PW.txt for more info). If you want to do it for a calculation with more than one k-poit I think you must do some haking within the code. My suggestion is to search for the keyword tfixed_occ inside the PW source files to start with. Good work, GS > > I would be very greatful if someone could suggest me a way of specifying this, > since I could not find a suitable option in the manual. > > Thank you for your attention. > > Alexandra Carvalho > EPFL Lausanne, Switzerland > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From powergreen at gmail.com Thu Feb 5 17:13:58 2009 From: powergreen at gmail.com (Green Power) Date: Thu, 5 Feb 2009 11:13:58 -0500 Subject: [Pw_forum] Imposed symmetry Message-ID: Dear PWscf users, I wonder if PWscf can deal with imposed symmetry for structural relaxation calculations. If so, dose the imposed symmetry speed up the calculations? Thanks in advance. Tian Georgetown University Washington DC 20057 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090205/383feee6/attachment.htm From sclauzer at sissa.it Thu Feb 5 17:38:07 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Feb 2009 17:38:07 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: References: Message-ID: <498B15EF.6040207@sissa.it> Green Power wrote: > Dear PWscf users, > I wonder if PWscf can deal with imposed symmetry for structural > relaxation calculations. If so, dose the imposed symmetry speed up the > calculations? Thanks in advance. The symmetry is determined at the beginning of the run and depends on the bravais lattice, atomic positions and maybe other stuff (like starting magnetization for noncolinear calculations with SO). Everything is symmetrizing with this initial symmetry which holds during all the relaxation. You may want to break symmetry, rather than imposing it, when doing structural relaxations in order not to be confined in a subspace of configurations. If you want to impose constraints, well, that's another story... GS > > Tian > Georgetown University > Washington DC 20057 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From baroni at sissa.it Thu Feb 5 21:26:37 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 5 Feb 2009 21:26:37 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <498B0095.8020103@sissa.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> Message-ID: <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> Dear Alexandra & Gabriele, I know little of the details of Gabriele's answer, which I am sure is totally right. On top of that, I would say that there would be little point to use k-point sampling to describe a defect, which would require a supercell in any case. Stefano On Feb 5, 2009, at 4:07 PM, Gabriele Sclauzero wrote: > Dear Alexandra, > > alexandra.carvalho at epfl.ch wrote: >> Dear Pwscf users, >> >> I have a shallow acceptor defect with an unpaired electron (in a >> semiconductor) >> that so far I have treated using smearing. >> However, to test the influence of the filling, I >> would like to set the occupation of the Kohn-Sham levels >> in the following manners: >> >> 1 - specify that band number # is filled/empty in all the k-points; >> and >> 2 - specify that band number # is empty at gamma, but filled at all >> the other k-points > > I think that you can do this only for single-k point calculations, > by specifying > > occupations='from_input' > > in the electrons namelist and adding an input card called > OCCUPATIONS at the end of your > input file (please check Doc/INPUT_PW.txt for more info). > If you want to do it for a calculation with more than one k-poit I > think you must do some > haking within the code. > My suggestion is to search for the keyword tfixed_occ inside the PW > source files to start > with. > > Good work, > > GS > > >> >> I would be very greatful if someone could suggest me a way of >> specifying this, >> since I could not find a suitable option in the manual. >> >> Thank you for your attention. >> >> Alexandra Carvalho >> EPFL Lausanne, Switzerland >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090205/ffdfdf8d/attachment-0001.htm From marzari at MIT.EDU Thu Feb 5 21:30:33 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 05 Feb 2009 15:30:33 -0500 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> Message-ID: <498B4C69.8030104@mit.edu> Stefano Baroni wrote: > Dear Alexandra & Gabriele, > > I know little of the details of Gabriele's answer, which I am sure is > totally right. On top of that, I would say that there would be little > point to use k-point sampling to describe a defect, which would require > a supercell in any case. > > Stefano > Ciao Stefano, in realta', se ricordo bene, la gente pensava che la vacancy formation energy del silicio richeidesse celle enormi (samplate a gamma), ma in realta' bastavano celle piccole, samplate meglio. Cioe' e' un problema elettronico vs/ elastico - puo' essere che l'interezione elastica diventi neglibile per sistemi in cui il silicio bulk richiede ancora sampling decenti. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From baroni at sissa.it Thu Feb 5 21:35:55 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 5 Feb 2009 21:35:55 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <498B15EF.6040207@sissa.it> References: <498B15EF.6040207@sissa.it> Message-ID: <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> Gabriele is totally right. Let me elaborate a little bit on his arguments, though. Geometry optimization is based on energy minimization, which procedes by varying the structural parameters (nuclear coordinates, unit-cell shape/size) using various algorithms, all of which vary the struc parameters along energy derivatives (forces and stress). When the ground state is nondegenerate, energy derivatives have the same symmetry as the the geometry of the system. Energy minimization, therefore, cannot break any symmetry unless: i) random displacements are introduced on purpose (as suggested by Gabriele, and as sometimes done); ii) some noise comes in unporposedly, because of numerical accuracy (this is often coped is, again as suggested by Gabriele, by explicitly simmetrizing the resulting forces), or iii) if the ground state is degenerate, giving rise to Jahn-Teller distortions. I do not expect to have been very pedagogic, but hope nevertheless to have offered some food for thoughts. Stefano On Feb 5, 2009, at 5:38 PM, Gabriele Sclauzero wrote: > > Green Power wrote: >> Dear PWscf users, >> I wonder if PWscf can deal with imposed symmetry for structural >> relaxation calculations. If so, dose the imposed symmetry speed up >> the >> calculations? Thanks in advance. > > The symmetry is determined at the beginning of the run and depends > on the bravais lattice, > atomic positions and maybe other stuff (like starting magnetization > for noncolinear > calculations with SO). > Everything is symmetrizing with this initial symmetry which holds > during all the relaxation. > You may want to break symmetry, rather than imposing it, when doing > structural relaxations > in order not to be confined in a subspace of configurations. > > If you want to impose constraints, well, that's another story... > > GS > > >> >> Tian >> Georgetown University >> Washington DC 20057 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090205/d2e7e396/attachment.htm From afloris at physik.fu-berlin.de Thu Feb 5 22:15:00 2009 From: afloris at physik.fu-berlin.de (Andrea Floris) Date: Thu, 5 Feb 2009 22:15:00 +0100 (CET) Subject: [Pw_forum] spin in solve_e Message-ID: Dear users, I would like to have a confirmation: has LSDA (nspin=2) been implemented in PH/solve_e.f90 (Electric Fields Calculation) in the last version of the code? In version 3.2 an error occurred, in 4.0.2 the line has been commented out. Was this comment written just to make the code not stopping? thanks, Andrea --------------- Dr. Andrea Floris Institut f"ur Theoretische Physik Freie Universit"at Berlin Arnimallee 14 D-14195 Berlin Germany Tel +49-30-838-53029 Fax +49-30-838-55258 e-mail: andrea.floris at fu-berlin.de From egk at gatech.edu Thu Feb 5 23:06:40 2009 From: egk at gatech.edu (Kim, Eung-Gun) Date: Thu, 5 Feb 2009 17:06:40 -0500 (EST) Subject: [Pw_forum] BLYP Vanderbilt pseudos for F and Cl In-Reply-To: <642151515.2527791233871548024.JavaMail.root@mail4.gatech.edu> Message-ID: <823208399.2527981233871600507.JavaMail.root@mail4.gatech.edu> Dear PWscf Community, May I kindly ask anyone to share BLYP Vanderbilt pseudos for F and Cl? Thank you very much. Best, EG -- + - | E.-G. Kim, Ph.D. | School of Chemistry and Biochemistry | 901 Atlantic Drive NW | Georgia Institute of Technology | Atlanta, GA 30332 | U.S.A. + - | +1.215.327.7315 | egk at gatech.edu + - From thmason24 at yahoo.com Fri Feb 6 01:14:39 2009 From: thmason24 at yahoo.com (Timothy Mason) Date: Thu, 5 Feb 2009 16:14:39 -0800 (PST) Subject: [Pw_forum] Imposed symmetry Message-ID: <321924.62954.qm@web81806.mail.mud.yahoo.com> Dear Stefano, >> ii) some noise comes >in unporposedly, because of numerical accuracy >>(this is often coped is, >again as suggested by Gabriele, by explicitly >>>simmetrizing the resulting >forces), does this imply that a good fix to the checkallsym error in vc-relax is to increase ecut to avoid numerical errors that would break the symmetry during vc-relax? Tim Mason University of Missouri St. Louis From marzari at MIT.EDU Fri Feb 6 01:40:46 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 05 Feb 2009 19:40:46 -0500 Subject: [Pw_forum] lack of ECC on Intel core i7 Message-ID: <498B870E.9000303@mit.edu> Dear All, a question not directly q-e related, but probably relevant to the community. Does anyone have any sense about the importance of error corrections for dynamical memory ? The new intel core i7 do not support ECC, but are much faster than then older processors. Having a calculation done quickly and incorrectly is preferable to having one done slowly and carefully (it's the 21st century, after all), but I was wondering if anyone had some opinion or expertise. We bought a core i7 for testing, but chose the extreme edition, and it broke after a few hours... We do have an older cluster (2006) of core 2 duos, without ECC, and the calculations are ok (the cluster is not very reliable, though - not sure if it's related). nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From lex at phys.ufl.edu Fri Feb 6 05:31:14 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Thu, 05 Feb 2009 23:31:14 -0500 Subject: [Pw_forum] Vc-relax Message-ID: <498BBD12.4010603@phys.ufl.edu> Hello everyone, I have a question (or two, rather) regarding the vc-relax methods in PWSCF. First, is there a need for a high energy cutoff, or high number of kpoints? Second, having tried using it previously, I've found that the lattice constants are updated by very very small increments. What sets the scale on the size changes? Thanks, A.F. Kemper Department of Physics and QTP University of Florda From baroni at sissa.it Fri Feb 6 08:13:30 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 6 Feb 2009 08:13:30 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <321924.62954.qm@web81806.mail.mud.yahoo.com> References: <321924.62954.qm@web81806.mail.mud.yahoo.com> Message-ID: <30673674-A3F6-470E-987E-CFBDC7A663FB@sissa.it> On Feb 6, 2009, at 1:14 AM, Timothy Mason wrote: > > Dear Stefano, > >>> ii) some noise comes >in unporposedly, because of numerical >>> accuracy >>(this is often coped is, >again as suggested by >>> Gabriele, by explicitly >>>simmetrizing the resulting >forces), > > does this imply that a good fix to the checkallsym error in vc-relax > is to increase ecut to avoid numerical errors that would break the > symmetry during vc-relax? I do not think so. I confess not to know what the "checkallsym error" is, but any errors done by reducing the basis set cannot break any symmetry. I was rather referring to small roundoff errors that may accumulate during the computation. Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090206/98053318/attachment.htm From giannozz at democritos.it Fri Feb 6 09:06:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 Feb 2009 09:06:10 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> Message-ID: <498BEF72.9020401@democritos.it> Stefano Baroni wrote: > On top of that, I would say that there would be little point to use > k-point sampling to describe a defect, which would require a supercell > in any case. yes and no. There are cases in which relatively small supercells describe well the defect (i.e. the interaction of the defect with its periodic replica is small) but do not describe well the underlying crystal structure if one uses the Gama point only. In those cases, using k-points makes sense. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Feb 6 09:14:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 Feb 2009 09:14:23 +0100 Subject: [Pw_forum] spin in solve_e In-Reply-To: References: Message-ID: <498BF15F.5080202@democritos.it> Andrea Floris wrote: > I would like to have a confirmation: has LSDA (nspin=2) > been implemented in PH/solve_e.f90 (Electric Fields Calculation) > in the last version of the code? In version 3.2 an error occurred, > in 4.0.2 the line has been commented out. Was this comment written > just to make the code not stopping? I don't know exactly what the status of LSDA+Electric field is. I think it is implemented and working, but if you perform a LSDA calculation in the usual way, i.e. using smearing as in metals, the code will complain that you are trying to perform a calculation for electric fields in a metal Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Fri Feb 6 09:32:36 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 6 Feb 2009 09:32:36 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <498BEF72.9020401@democritos.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> <498BEF72.9020401@democritos.it> Message-ID: you got a point, Paolo, I think - thanks Stefano On Feb 6, 2009, at 9:06 AM, Paolo Giannozzi wrote: > Stefano Baroni wrote: > >> On top of that, I would say that there would be little point to use >> k-point sampling to describe a defect, which would require a >> supercell >> in any case. > > yes and no. There are cases in which relatively small supercells > describe well the defect (i.e. the interaction of the defect with its > periodic replica is small) but do not describe well the underlying > crystal structure if one uses the Gama point only. In those cases, > using k-points makes sense. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090206/142285ca/attachment.htm From paulatto at sissa.it Fri Feb 6 09:38:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 06 Feb 2009 09:38:15 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <321924.62954.qm@web81806.mail.mud.yahoo.com> References: <321924.62954.qm@web81806.mail.mud.yahoo.com> Message-ID: On Fri, 06 Feb 2009 01:14:39 +0100, Timothy Mason wrote: > does this imply that a good fix to the checkallsym error in vc-relax is > to increase ecut to avoid numerical errors that would break the symmetry > during vc-relax? It can help, but a better solution would be to upgrade quantum espresso to more recent version, where that problem has been fixed (adding an additional active enforcement of the symmetry). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Fri Feb 6 09:42:21 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 06 Feb 2009 09:42:21 +0100 Subject: [Pw_forum] Vc-relax In-Reply-To: <498BBD12.4010603@phys.ufl.edu> References: <498BBD12.4010603@phys.ufl.edu> Message-ID: On Fri, 06 Feb 2009 05:31:14 +0100, Lex Kemper wrote: > First, is there a need for a high energy cutoff, or high number of > kpoints? Dear Lex, your calculation must be well converger wrt kpoints and cutoff; if it is a small system, it is often better to increase cutoff an kpoints a bit more than the bare minimum and don't worry about it anymore. > Second, having tried using it previously, I've found that the lattice > constants are updated by very very small increments. What sets the scale > on the size changes? It depends on the algorithm you are using. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From dalcorso at sissa.it Fri Feb 6 09:52:41 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Fri, 06 Feb 2009 09:52:41 +0100 Subject: [Pw_forum] spin in solve_e In-Reply-To: References: Message-ID: <1233910361.3313.7.camel@dhpc-5-20.sissa.it> On Thu, 2009-02-05 at 22:15 +0100, Andrea Floris wrote: > Dear users, > I would like to have a confirmation: has LSDA (nspin=2) been implemented > in PH/solve_e.f90 (Electric Fields Calculation) in the last version of the > code? In version 3.2 an error occurred, in 4.0.2 the line has been > commented out. Was this comment written just to make the code not > stopping? > I think nspin=2 is dealt with correctly in solve_e, but to simulate a magnetic insulator with LDSA you need to constrain the magnetization and DFPT with constraints is not implemented yet. Using noncolin=.true. without constraints, instead should work in the CVS version (this is now in a test phase so please report any bug you can find). Andrea > thanks, > Andrea > > --------------- > Dr. Andrea Floris > Institut f"ur Theoretische Physik > Freie Universit"at Berlin > Arnimallee 14 > D-14195 Berlin > Germany > Tel +49-30-838-53029 > Fax +49-30-838-55258 > e-mail: andrea.floris at fu-berlin.de > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From sclauzer at sissa.it Fri Feb 6 10:12:40 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 06 Feb 2009 10:12:40 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> Message-ID: <498BFF08.6040907@sissa.it> Stefano Baroni wrote: > parameters along energy derivatives (forces and stress). When the ground > state is nondegenerate, energy derivatives have the same symmetry as the > the geometry of the system. Please Stefano help me to understand this point, which is not clear to me. If the ground state is degenerate (you meant degenerate at a fixed external potential, i.e. fixed atomic geometry, am I right?) you could reach a lower energy by lowering the symmetry: do you think this is possible in practical calculations. I thought that you could only end up in a configuration with higher symmetry than the starting one, not lower. From the theoretical point of view, is it correct to apply the standard formulation of HK theorem to a system with degenerate GS (is the HK mapping still valid?). Gabriele > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From alexandra.carvalho at epfl.ch Fri Feb 6 10:28:54 2009 From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch) Date: Fri, 06 Feb 2009 10:28:54 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <498BEF72.9020401@democritos.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> <498BEF72.9020401@democritos.it> Message-ID: <20090206102854.zu2r0j7jusgwwk4w@webmail.epfl.ch> Dear Gabriele, Nicola, Stefano and Paolo, Thank you very much for your helpful replies and comments. In fact, I sould lile to confirm that the electrical level of this defect calculated at gamma converges faster with the system size than that calculated with multiple k-points. However, it seems that the type of filling that I use will affect the convergence. Alexandra Carvalho Quoting Paolo Giannozzi : > Stefano Baroni wrote: > >> On top of that, I would say that there would be little point to use >> k-point sampling to describe a defect, which would require a supercell >> in any case. > > yes and no. There are cases in which relatively small supercells > describe well the defect (i.e. the interaction of the defect with its > periodic replica is small) but do not describe well the underlying > crystal structure if one uses the Gama point only. In those cases, > using k-points makes sense. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From guido.roma at cea.fr Fri Feb 6 09:51:04 2009 From: guido.roma at cea.fr (Guido Roma) Date: Fri, 06 Feb 2009 09:51:04 +0100 Subject: [Pw_forum] specify occupation with k-points In-Reply-To: <498BEF72.9020401@democritos.it> References: <20090205154926.vs5kq8sgyoggoccw@webmail.epfl.ch> <498B0095.8020103@sissa.it> <3C09BDA5-F18C-484C-88C8-93BFDB3358D4@sissa.it> <498BEF72.9020401@democritos.it> Message-ID: <498BF9F8.8070108@cea.fr> Paolo Giannozzi wrote: > Stefano Baroni wrote: > > >> On top of that, I would say that there would be little point to use >> k-point sampling to describe a defect, which would require a supercell >> in any case. >> > > yes and no. There are cases in which relatively small supercells > describe well the defect (i.e. the interaction of the defect with its > periodic replica is small) but do not describe well the underlying > crystal structure if one uses the Gama point only. In those cases, > using k-points makes sense. > > Paolo > There are also cases (for example Si interstitials in SiC) in which a defect level in the gap is still dispersed with relatively large supercells but using K-points allows to have relatively well converged total (i.e. formation energy). It has been proposed (Bernardini et al. Eur. Phys. J. B, v38, p437 (2004)) to impose the same occupation occuring at Gamma to the other k-points (where spurious breaking of degeneracies could appear). My impression is that this cumbersome procedure can be dangerous as, I believe, it does not give the DFT ground state (which, as badly converged as it can be with the supercell size, is what we are looking for). I would be happy to have the feeling of others in the list on this point. Guido -------------- next part -------------- A non-text attachment was scrubbed... Name: guido_roma.vcf Type: text/x-vcard Size: 260 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090206/f9466b5e/attachment.vcf From thmason24 at yahoo.com Fri Feb 6 15:42:17 2009 From: thmason24 at yahoo.com (Timothy Mason) Date: Fri, 6 Feb 2009 06:42:17 -0800 (PST) Subject: [Pw_forum] Imposed symmetry Message-ID: <373319.92301.qm@web81807.mail.mud.yahoo.com> Hi Lorenzo, in what version was this fixed introduced please? thanks, Tim Mason University of Missouri St. Louis >> does this imply that a good fix to the checkallsym error in vc-relax is to >> increase ecut to avoid numerical errors that would break the symmetry during >> vc-relax? > > It can help, but a better solution would be to upgrade quantum espresso to > more recent version, where that problem has been fixed (adding an additional > active enforcement of the symmetry). > > cheers > From paulatto at sissa.it Fri Feb 6 15:54:57 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 06 Feb 2009 15:54:57 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <373319.92301.qm@web81807.mail.mud.yahoo.com> References: <373319.92301.qm@web81807.mail.mud.yahoo.com> Message-ID: On Fri, 06 Feb 2009 15:42:17 +0100, Timothy Mason wrote: > Hi Lorenzo, > > in what version was this fixed introduced please? > 4.0.1, if I remember correctly -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From erjunkan at mail.ustc.edu.cn Fri Feb 6 17:14:14 2009 From: erjunkan at mail.ustc.edu.cn (ErJun Kan) Date: Sat, 07 Feb 2009 00:14:14 +0800 Subject: [Pw_forum] error in pwcond.x calculations Message-ID: <433936854.28232@ustc.edu.cn> Dear all, I want to calculate transport of one magnetic systems with QE 4.04 version. But pwcond.x always gives error messages in the calculations, and and I can't recognize any mistakes in my input. The input items are: !For calculations of tranport &inputcond outdir='./', prefixl='al', prefixs = 'gan' tran_file='trans.gan1', ikind=1, iofspin = 2 energy0=2.95d0, denergy=-0.1d0, ewind=3.d0, epsproj=1.d-6, nz1 =5 / 1 0.0 0.0 1.0 40 !SCF calculations: # self-consistent calculation for gan &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', outdir='./' prefix='gan' / &system ibrav = 0, nat= 96, ntyp= 3, ecutwfc = 20.0, nspin = 2 starting_magnetization(1)=0.7 occupations='smearing', smearing='gaussian', degauss=0.01 / &electrons diagonalization='$diago' mixing_mode = 'plain' electron_maxstep = 200 conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Mn 54.938 Mn.pbe-sp-van.UPF Ga 69.72 Ga.pbe-nsp-van.UPF N 14.00 N.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} Ga -0.0001657758759119 0.4818194083996286 0.0182938409064565 Ga 0.1667274772312116 0.0195694130995621 0.9990694956596797 Ga 0.5000164056660824 0.0275423908315948 0.9983838280839206 Ga 0.8332760609810573 0.0195102813279311 0.9990674813820080 Ga 0.3343449833004964 0.4871849918764722 0.0164388913198390 Ga 0.6658508541371895 0.4872145844903105 0.0164924601108568 Ga -0.0002943530538455 0.9969585128911231 0.0739962112659120 Ga 0.3333532449819225 0.0007723748545170 0.0729112240197635 Ga 0.6669243039679955 0.0006897210790763 0.0729287345988502 Ga 0.1684085461182105 0.4951198331347210 0.0992729841981305 Ga 0.5000669979934426 0.4977723574841029 0.0992272818270406 Ga 0.8318449912608433 0.4936237423118682 0.1004135848917636 Ga 0.1672070782004766 0.9927820601371106 0.1538426320734469 Ga 0.4995602878201254 0.9979632509617761 0.1528810399759821 Ga 0.8332084532887823 0.9972896887596313 0.1539174144427966 Ga 0.6651617852986196 0.4993749825682515 0.1813823613900334 Ga 0.0000000000000000 0.0000000000000000 0.2347412425949784 Ga 0.3333333333333357 0.0000000000000000 0.2347412425949784 Ga 0.6666666666666643 0.0000000000000000 0.2347412425949784 Ga 0.1666666666666643 0.5000000000000000 0.2608236028833062 Ga 0.5000000000000000 0.5000000000000000 0.2608236028833062 Ga 0.8333333333333357 0.5000000000000000 0.2608236028833062 Ga 0.1666666666666643 0.0000000000000000 0.3129883234599689 Ga 0.5000000000000000 0.0000000000000000 0.3129883234599689 Ga 0.8333333333333357 0.0000000000000000 0.3129883234599689 Ga 0.0000000000000000 0.5000000000000000 0.3390706837482966 Ga 0.3333333333333357 0.5000000000000000 0.3390706837482966 ............ K_POINTS (automatic) 4 7 1 0 0 0 CELL_PARAMETERS { cubic} 18.034 0.0000 0.0000 0.0000 9.7980 0.0000 0.0000 0.0000 66.535 &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', outdir='./', prefix='al' tprnfor = .true. tstress = .true. / &system ibrav = 6, celldm(1) =20.0, celldm(3) =0.225, nat= 1, ntyp= 1, nspin = 1, ecutwfc = 25.0, ecutrho = 150.0 occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons diagonalization='$diago' mixing_mode = 'plain' electron_maxstep = 200 conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.98 Al.pbe-rrkj.UPF ATOMIC_POSITIONS Al 0.00 0.00 0.00 K_POINTS (automatic) 1 1 24 1 1 1 And the end of output of pwcond.x calculations: k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 ngper, shell number = 355 100 ngper, n2d = 355 355 Application 1942431 exit codes: 139 Application 1942431 exit signals: Killed Application 1942431 resources: utime 0, stime 0 From giannozz at democritos.it Fri Feb 6 17:23:18 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 Feb 2009 17:23:18 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <433936854.28232@ustc.edu.cn> References: <433936854.28232@ustc.edu.cn> Message-ID: <498C63F6.8020605@democritos.it> ErJun Kan wrote: > Application 1942431 exit codes: 139 > Application 1942431 exit signals: Killed out of memory? -- Paolo Giannozzi, Democritos and University of Udine, Italy From erjunkan at mail.ustc.edu.cn Fri Feb 6 17:35:36 2009 From: erjunkan at mail.ustc.edu.cn (ErJun Kan) Date: Sat, 07 Feb 2009 00:35:36 +0800 Subject: [Pw_forum] error in pwcond.x calculations Message-ID: <433938136.12707@ustc.edu.cn> Hi, Palo, Thank you! I will try the cases with reduced atoms and cell. In your mail: >From: Paolo Giannozzi >Reply-To: PWSCF Forum >To: ErJun Kan , PWSCF Forum >Subject: Re: [Pw_forum] error in pwcond.x calculations >Date:Fri, 06 Feb 2009 17:23:18 +0100 > >ErJun Kan wrote: > > > Application 1942431 exit codes: 139 > > Application 1942431 exit signals: Killed > > out of memory? > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Fri Feb 6 21:43:34 2009 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 6 Feb 2009 21:43:34 +0100 Subject: [Pw_forum] Imposed symmetry In-Reply-To: <498BFF08.6040907@sissa.it> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> Message-ID: On Feb 6, 2009, at 10:12 AM, Gabriele Sclauzero wrote: Gabriele: > Stefano Baroni wrote: >> parameters along energy derivatives (forces and stress). When the >> ground >> state is nondegenerate, energy derivatives have the same symmetry >> as the >> the geometry of the system. > > Please Stefano help me to understand this point, which is not clear > to me. If the ground > state is degenerate (you meant degenerate at a fixed external > potential, i.e. fixed atomic > geometry, am I right?) YES > you could reach a lower energy by lowering the symmetry: do you > think this is possible in practical calculations. This is possible in reality (in fact, the Jahn-Teller effect is exactly this). Whether or not this is possible "in practice" depends on how faithfully "practice" mimics "reality" (out of the metaphor: on how calculations are done). > I thought that you could only end up in > a configuration with higher symmetry than the starting one, not lower. it depends ... when the nuclear geometry is such that the ground state is degenerate, it may happen that two or more Born-Oppenheimer surfaces (each one corresponding to a different degenerate state) intersect at that geometry in such a way that the gradients along each one of the surfaces does not vanish. In the nondegenerate case, symmetry trivially imposes that forces along symmetry-breaking directions vanish. In the degenerate case, the situation is more tricky: symmetry imposes that the SUM of the forces corresponding to different degenerate states vanish. Which implies that you can lower the energy by breaking the symmetry along one of the intersecting BO energy surfaces > From the theoretical point of view, is it correct to apply the > standard formulation of > HK theorem to a system with degenerate GS (is the HK mapping still > valid?) this problem used to be a very popular and controversial one, some time ago. I do not know the "politically correct" answer. Let me give you mine. 1) strictly, the usual derivation of DFT does not hold for degenerate states 2) That derivation can be easily extended to a (arbitrarily small) finite temperature (Mermin's DFT does that) 3) at finite temperature, degeneracy does not matter. DFT holds, the Hellmann-Feynman theorem applies. only one BO surface exists, no symmetry breaking distortions would occur 4) at zero temperature complications arise and the BO surface would develop a cusp, corresponding to different forces along different directions. common sense is restored "in practice" by considering infinitesimal distortions of the high-simmetry geometry. the limit of the forces as the distortion goes to zero would depend on dierction, which is exactly a amnifestation of the Jahn-Teller effect (or at least, so it seems to me) Ciao Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090206/a499a8ad/attachment-0001.htm From nazari at iasbs.ac.ir Sat Feb 7 16:37:18 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Sat, 7 Feb 2009 15:37:18 -0000 (UTC) Subject: [Pw_forum] nspin=2/Band structure In-Reply-To: References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> Message-ID: <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> Dear All, If a spin polarize calculation with fixed occupation is run how the band structure for majority and minority spin can be ploted? In the output data there exist k points and related energies for spin up and spin down. Do the band structure can be ploted from these data? From m.abbasnejad at gmail.com Sat Feb 7 15:13:17 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Sat, 7 Feb 2009 17:43:17 +0330 Subject: [Pw_forum] scf calculation Message-ID: <7699a1950902070613m52ea5705i80d67322d8846512@mail.gmail.com> Dear all, I want to do scf calculation for Ni. I used tabulated pseudopotential from CASINO and converted it to one appropriate for PWscf.. As I run it, it gives me such an error: Program PWSCF v.4.1CVS starts ... Today is 7Feb2009 at 17:37:51 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_pseudo_nl : error # 1 Reading pseudo file (BETA) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Would you please help me? Thanks in advance. Mohaddeseh -- -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, End of North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090207/9bb8c481/attachment.htm From erjunkan at mail.ustc.edu.cn Sat Feb 7 20:45:42 2009 From: erjunkan at mail.ustc.edu.cn (ErJun Kan) Date: Sun, 08 Feb 2009 03:45:42 +0800 Subject: [Pw_forum] error in pwcond.x calculations Message-ID: <434035942.21533@ustc.edu.cn> Dear all, I have reduced the size of cell, it still does not work. what is the problem? thank you. +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++ ! SCF calculation part: # self-consistent calculation &control calculation='scf' restart_mode='from_scratch', pseudo_dir = './', outdir='./' prefix='gan' / &system ibrav = 0, nat = 36 ntyp= 3, ecutwfc = 15.0, nspin = 2 starting_magnetization(1)=0.7 occupations='smearing', smearing='gaussian', degauss=0.01 / &electrons diagonalization='$diago' mixing_mode = 'plain' electron_maxstep = 200 conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Mn 54.938 Mn.pbe-sp-van.UPF Ga 69.72 Ga.pbe-nsp-van.UPF N 14.00 N.pbe-van_ak.UPF ATOMIC_POSITIONS {angstrom} Mn 1.590000000 0.000000000 -6.425908496 Ga 4.770000000 0.000000000 -6.425908496 Ga 7.950000000 0.000000000 -6.425908496 Ga -0.000000000 0.000000000 -3.671947712 Ga 3.180000000 0.000000000 -3.671947712 Ga 6.360000000 0.000000000 -3.671947712 Ga 1.590000000 0.000000000 -0.917986928 Ga 4.770000000 0.000000000 -0.917986928 Ga 7.950000000 0.000000000 -0.917986928 Ga -0.000000000 2.591500000 -5.507921568 Ga 3.180000000 2.591500000 -5.507921568 Ga 6.360000000 2.591500000 -5.507921568 Ga 1.590000000 2.591500000 -2.753960784 Ga 4.770000000 2.591500000 -2.753960784 Ga 7.950000000 2.591500000 -2.753960784 Ga -0.000000000 2.591500000 0.000000000 Ga 3.180000000 2.591500000 0.000000000 Ga 6.360000000 2.591500000 0.000000000 N -0.000000000 4.542899554 -5.507921568 N 3.180000000 4.542899554 -5.507921568 N 6.360000000 4.542899554 -5.507921568 N 1.590000000 4.542899554 -2.753960784 N 4.770000000 4.542899554 -2.753960784 N 7.950000000 4.542899554 -2.753960784 N -0.000000000 4.542899554 0.000000000 N 3.180000000 4.542899554 0.000000000 N 6.360000000 4.542899554 0.000000000 N 1.590000000 1.951399554 -6.425908496 N 4.770000000 1.951399554 -6.425908496 N 7.950000000 1.951399554 -6.425908496 N -0.000000000 1.951399554 -3.671947712 N 3.180000000 1.951399554 -3.671947712 N 6.360000000 1.951399554 -3.671947712 N 1.590000000 1.951399554 -0.917986928 N 4.770000000 1.951399554 -0.917986928 N 7.950000000 1.951399554 -0.917986928 K_POINTS (automatic) 3 7 3 0 0 0 CELL_PARAMETERS { cubic} 18.034 0.0000 0.0000 0.0000 9.7980 0.0000 0.0000 0.0000 15.6181 +++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++ SCF calculatons show no any problems, and the total energy is well converged. $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ !and the pwcond.x calculation part: &inputcond outdir='./', prefixl='gan', prefixs = 'gan' tran_file='trans.gan1', ikind=1, iofspin = 2 energy0=2.95d0, denergy=-0.1d0, ewind=3.d0, epsproj=1.d-6, nz1 =6 / 1 0.0 0.0 1.0 20 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ For electric conductivity calculations, the error signals: k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 ngper, shell number = 211 62 ngper, n2d = 211 211 Application 2036109 exit signals: Killed Application 2036109 resources: utime 0, stime 0 Becasue the number of atoms is small now, I do not think the problem is caused by out of memory. In your mail: >From: Paolo Giannozzi >Reply-To: PWSCF Forum >To: ErJun Kan , PWSCF Forum >Subject: Re: [Pw_forum] error in pwcond.x calculations >Date:Fri, 06 Feb 2009 17:23:18 +0100 > >ErJun Kan wrote: > > > Application 1942431 exit codes: 139 > > Application 1942431 exit signals: Killed > > out of memory? > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From meghdad_saeedian at yahoo.com Sun Feb 8 15:46:06 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Sun, 8 Feb 2009 06:46:06 -0800 (PST) Subject: [Pw_forum] relaxation Message-ID: <249641.14083.qm@web31404.mail.mud.yahoo.com> Dear all, I am trying to relax Ni atom by using the converted pseudopotential of CASINO format (http://www.tcm.phy.cam.ac.uk/~mdt26/casino2_pseudopotentials.html). But the pressure obtained from it is too far of the desired value. That's according to it: ??????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=******** ? -0.59082488?? 0.00000000?? 0.00000000???? -86913.33????? 0.00????? 0.00 ?? 0.00000000? -0.59082488?? 0.00000000????????? 0.00 -86913.33????? 0.00 ?? 0.00000000?? 0.00000000? -0.59082488 ? ? ? ?? 0.00????? 0.00 -86913.33 Would you please help me and tell me where the problem is? I have also attached the converted pseudopotential file as well as? the input and output files. Thanks in advance. Yours, Saeedian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090208/25147d27/attachment.htm From eyvaz_isaev at yahoo.com Sun Feb 8 16:20:40 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 8 Feb 2009 07:20:40 -0800 (PST) Subject: [Pw_forum] relaxation In-Reply-To: <249641.14083.qm@web31404.mail.mud.yahoo.com> Message-ID: <111265.34239.qm@web65705.mail.ac4.yahoo.com> Dear Meghdad, I have a very simple question: are you sure these pseudopotentials taken from CASINO library are suitable for QE? Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sun, 2/8/09, meghdad saeedian wrote: > From: meghdad saeedian > Subject: [Pw_forum] relaxation > To: "PWscf" > Date: Sunday, February 8, 2009, 5:46 PM > Dear all, > > I am trying to relax Ni atom by using the converted > pseudopotential of CASINO format > (http://www.tcm.phy.cam.ac.uk/~mdt26/casino2_pseudopotentials.html). > > But the pressure obtained from it is > too far of the desired value. That's according to it: > > ??????? total?? stress? > (Ry/bohr**3)?????????????????? > (kbar)???? P=******** > ? -0.59082488?? 0.00000000?? 0.00000000???? > -86913.33????? 0.00????? 0.00 > ?? 0.00000000? -0.59082488?? > 0.00000000????????? 0.00 -86913.33????? 0.00 > ?? 0.00000000?? > 0.00000000? -0.59082488 ? ? ? ?? 0.00????? 0.00 > -86913.33 > > Would you please help me and tell me where the problem is? > I have also attached the converted pseudopotential file as > well as? the input and output files. > Thanks in advance. > > Yours, > Saeedian > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Sun Feb 8 16:26:32 2009 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 8 Feb 2009 16:26:32 +0100 Subject: [Pw_forum] relaxation In-Reply-To: <111265.34239.qm@web65705.mail.ac4.yahoo.com> References: <111265.34239.qm@web65705.mail.ac4.yahoo.com> Message-ID: I have an even simpler question: what do you mean by "relaxing an atom" Stefano oh, yes: please let us know your current affiliation ... On Feb 8, 2009, at 4:20 PM, Eyvaz Isaev wrote: > Dear Meghdad, > > I have a very simple question: are you sure these pseudopotentials > taken from CASINO library are suitable for QE? > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & > Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping > University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Sun, 2/8/09, meghdad saeedian > wrote: > >> From: meghdad saeedian >> Subject: [Pw_forum] relaxation >> To: "PWscf" >> Date: Sunday, February 8, 2009, 5:46 PM >> Dear all, >> >> I am trying to relax Ni atom by using the converted >> pseudopotential of CASINO format >> (http://www.tcm.phy.cam.ac.uk/~mdt26/casino2_pseudopotentials.html). >> >> But the pressure obtained from it is >> too far of the desired value. That's according to it: >> >> total stress >> (Ry/bohr**3) >> (kbar) P=******** >> -0.59082488 0.00000000 0.00000000 >> -86913.33 0.00 0.00 >> 0.00000000 -0.59082488 >> 0.00000000 0.00 -86913.33 0.00 >> 0.00000000 >> 0.00000000 -0.59082488 0.00 0.00 >> -86913.33 >> >> Would you please help me and tell me where the problem is? >> I have also attached the converted pseudopotential file as >> well as the input and output files. >> Thanks in advance. >> >> Yours, >> Saeedian >> >> >> >> >> >> _______________________________________________ >> 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://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090208/c9100a02/attachment.htm From m.abbasnejad at gmail.com Sun Feb 8 16:27:51 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Sun, 8 Feb 2009 07:27:51 -0800 Subject: [Pw_forum] relaxation In-Reply-To: <111265.34239.qm@web65705.mail.ac4.yahoo.com> References: <249641.14083.qm@web31404.mail.mud.yahoo.com> <111265.34239.qm@web65705.mail.ac4.yahoo.com> Message-ID: <7699a1950902080727o7f2af798wd14ce68b6d6634db@mail.gmail.com> Dear Professor Eyvaz, Thanks for your comment. To be honest, no. But I decide to run this calculation in order to prepare a suitable input file for CASINO program. Unfortunately this program can't read pseudopotentials of PWscf form. I was wondering if you could help me? Best wishes, Mohaddeseh -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090208/6098bf64/attachment.htm From eyvaz_isaev at yahoo.com Sun Feb 8 17:17:28 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 8 Feb 2009 08:17:28 -0800 (PST) Subject: [Pw_forum] relaxation In-Reply-To: <7699a1950902080727o7f2af798wd14ce68b6d6634db@mail.gmail.com> Message-ID: <764952.71261.qm@web65713.mail.ac4.yahoo.com> Dear Mohaddeseh, It looks like a mystery (and non-ethique) to receive an mail of you, though my question was addressed to meghdad saeedian. Anyway, I am not familiar with CASINO (casino, too), and it is another story (it is a horse of another color). As far as I am not aware of your particular problem, most likely, not. If you can explain what do you want to study, then you have more chance. Bests, Eyvaz. --- On Sun, 2/8/09, mohaddeseh abbasnejad wrote: > From: mohaddeseh abbasnejad > Subject: Re: [Pw_forum] relaxation > To: eyvaz_isaev at yahoo.com, "PWSCF Forum" > Date: Sunday, February 8, 2009, 6:27 PM > Dear Professor Eyvaz, > > Thanks for your comment. > To be honest, no. But I decide to run this calculation in > order to prepare a > suitable input file for CASINO program. Unfortunately this > program can't > read pseudopotentials of PWscf form. > I was wondering if you could help me? > > Best wishes, > Mohaddeseh > > -------------------------------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > -------------------------------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From naylin.nll at gmail.com Mon Feb 9 04:06:08 2009 From: naylin.nll at gmail.com (Nay Lin) Date: Mon, 9 Feb 2009 11:06:08 +0800 Subject: [Pw_forum] PWscf on YCGwin Message-ID: <619d39dc0902081906g7c5d7eb8l59a7eb470df5ef61@mail.gmail.com> Dear all, I am new to Pwscf. I managed to compile the latest package of pwscf with GFORTRAN on Cygwin. although i compiled it, Does anyone have problem running on the Cygwin system? regards Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090209/a68c4980/attachment.htm From lzh-ming at 163.com Mon Feb 9 04:59:50 2009 From: lzh-ming at 163.com (lzh-ming) Date: Mon, 9 Feb 2009 11:59:50 +0800 (CST) Subject: [Pw_forum] PWscf on YCGwin In-Reply-To: <619d39dc0902081906g7c5d7eb8l59a7eb470df5ef61@mail.gmail.com> References: <619d39dc0902081906g7c5d7eb8l59a7eb470df5ef61@mail.gmail.com> Message-ID: <23200832.153881234151990579.JavaMail.coremail@bj163app120.163.com> No problem. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090209/03d1d6d0/attachment.htm From meghdad_saeedian at yahoo.com Mon Feb 9 08:45:08 2009 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Sun, 8 Feb 2009 23:45:08 -0800 (PST) Subject: [Pw_forum] Phonon DOS Message-ID: <24356.29744.qm@web31407.mail.mud.yahoo.com> Dear all How can i separate PDOS (phonon DOS) to acoustical phonon dos and optical phonon dos? Thanks in advance Sincerely yours saeedian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090208/e0aa975b/attachment.htm From lex at phys.ufl.edu Mon Feb 9 08:54:54 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Mon, 09 Feb 2009 02:54:54 -0500 Subject: [Pw_forum] ph.x error message Message-ID: <498FE14E.5010203@phys.ufl.edu> Hello everyone, I'm attempting to calculate the phonon DOS and a^2F(w) for a metallic system. I've run an scf calculation, and was going through the steps (as in example 7). Here is the elph.in file: eph coupling for SNP &INPUTPH outdir = './tmp' prefix = 'SNP' tr2_ph = 1.0d-10 fildyn = 'SNP.dyn' fildvscf = 'SNP.dv' trans = .true. elph = .true. ldisp = .true. nq1 = 9 nq2 = 9 nq3 = 5 / The error I get is, after the SCF steps: ************************************************************************** electron-phonon interaction ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from lint : error # 1 cannot locate k point xk %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Could someone help me fix this problem? Thanks, Lex Kemper Department of Physics University of Florida From sclauzer at sissa.it Mon Feb 9 08:59:40 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 08:59:40 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <434035942.21533@ustc.edu.cn> References: <434035942.21533@ustc.edu.cn> Message-ID: <498FE26C.3050302@sissa.it> ErJun Kan wrote: > Dear all, > > I have reduced the size of cell, it still does not work. > what is the problem? thank you. I think that pwcond was not programmed in order to work with ibrav=0. Why don't you use an orthorhombic cell type? You should be able to specify atomic positions of your system also with that ibrav. > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > !and the pwcond.x calculation part: > &inputcond > outdir='./', > prefixl='gan', > prefixs = 'gan' Another problem could be here: why do you specify the same prefix for both left lead and scattering region? Are you sure you understood the meaning of those prefixes? If not, please try to read some documentation and if it's still not clear you can ask to this forum. > tran_file='trans.gan1', > ikind=1, > iofspin = 2 > energy0=2.95d0, > denergy=-0.1d0, > ewind=3.d0, > epsproj=1.d-6, > nz1 =6 > / > 1 > 0.0 0.0 1.0 > 20 > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > For electric conductivity calculations, the error signals: > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > ngper, shell number = 211 62 > ngper, n2d = 211 211 > Application 2036109 exit signals: Killed > Application 2036109 resources: utime 0, stime 0 > > Becasue the number of atoms is small now, I do not think the problem is caused > by out of memory. Sorry, but wouldn't it be nice if you sign your posts and provide affiliation? (since this is the netiquette of this forum). Thanks! BTW, the name of Paolo is Paolo, not Palo... Gabriele -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Feb 9 09:12:41 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 09:12:41 +0100 Subject: [Pw_forum] scf calculation -> Problems with pseudopotential converted from CASINO In-Reply-To: <7699a1950902070613m52ea5705i80d67322d8846512@mail.gmail.com> References: <7699a1950902070613m52ea5705i80d67322d8846512@mail.gmail.com> Message-ID: <498FE579.5040307@sissa.it> Dear Mohaddeseh, I think you should specify a more appropriate topic for your problem, so that you'll have more probability that someone which can solve the real issue will notice your mail. Said that, all I can tell you while you wait for a more precise reply is that there was a problem while reading your pseudopotential (which is also what the error message tells you...). This means that the PP file you got from conversion has not been digested by pw.x. This may be due to many factors: the conversion failed, the file is corrupted... You have to specify more details on your pseudo-conversion in order to be helped. GS mohaddeseh abbasnejad wrote: > Dear all, > > I want to do scf calculation for Ni. I used tabulated pseudopotential > from CASINO > and converted it to one appropriate for PWscf.. > As I run it, it gives me such an error: > > Program PWSCF v.4.1CVS starts ... > Today is 7Feb2009 at 17:37:51 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_pseudo_nl : error # 1 > Reading pseudo file (BETA) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > Would you please help me? > > Thanks in advance. > > Mohaddeseh > > > -- > -------------------------------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, End of North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > -------------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Feb 9 09:29:35 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 09:29:35 +0100 Subject: [Pw_forum] nspin=2/Band structure In-Reply-To: <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> Message-ID: <498FE96F.8060904@sissa.it> Dear (?) we would like to know your name and affiliation, if possible. nazari at iasbs.ac.ir wrote: > > Dear All, > > > If a spin polarize calculation with fixed occupation is run how the band > > structure for majority and minority spin can be ploted? Yes of course it can. You can do a nscf run after the scf calculations has converged (if you want to plot bands on a set of k-points different from that use for the self-consistency) and then use the post-processing tools bands.x and plotband.x. You can find many tutorials on that, goggling something like 'pwscf plot bands', or simply have a look to some examples in the example/ directory. It shouldn't be difficult to port that examples to your specific system. > > In the output data there exist k points and related energies for spin up > > and spin down. Do the band structure can be ploted from these data? You can even do this way, if you know a little bit of scripting with bash, awk or sed, but it would not be convenient in my opinion, since you already have the tools do do that in the QE distribution... Bests, GS > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From smogunov at sissa.it Mon Feb 9 09:21:30 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Mon, 9 Feb 2009 09:21:30 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <434035942.21533@ustc.edu.cn> References: <434035942.21533@ustc.edu.cn> Message-ID: <200902090921.31005.smogunov@sissa.it> Dear ErJun Kan What kind of system do you study? For conductance calculation you should have two semi-infinite left and right metallic leads connected by some scattering region which should match PERFECTLY to the leads. What are the leads and the scattering region in your case? Regards, Alexander On Saturday 07 February 2009 20:45, ErJun Kan wrote: > Dear all, > > I have reduced the size of cell, it still does not work. > what is the problem? thank you. > +++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++++++++++++++++++++++++++++++++++++++++++++++ > ! SCF calculation part: > # self-consistent calculation > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = './', > outdir='./' > prefix='gan' > / > &system > ibrav = 0, > nat = 36 > ntyp= 3, > ecutwfc = 15.0, > nspin = 2 > starting_magnetization(1)=0.7 > occupations='smearing', > smearing='gaussian', > degauss=0.01 > / > &electrons > diagonalization='$diago' > mixing_mode = 'plain' > electron_maxstep = 200 > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Mn 54.938 Mn.pbe-sp-van.UPF > Ga 69.72 Ga.pbe-nsp-van.UPF > N 14.00 N.pbe-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > Mn 1.590000000 0.000000000 -6.425908496 > Ga 4.770000000 0.000000000 -6.425908496 > Ga 7.950000000 0.000000000 -6.425908496 > Ga -0.000000000 0.000000000 -3.671947712 > Ga 3.180000000 0.000000000 -3.671947712 > Ga 6.360000000 0.000000000 -3.671947712 > Ga 1.590000000 0.000000000 -0.917986928 > Ga 4.770000000 0.000000000 -0.917986928 > Ga 7.950000000 0.000000000 -0.917986928 > Ga -0.000000000 2.591500000 -5.507921568 > Ga 3.180000000 2.591500000 -5.507921568 > Ga 6.360000000 2.591500000 -5.507921568 > Ga 1.590000000 2.591500000 -2.753960784 > Ga 4.770000000 2.591500000 -2.753960784 > Ga 7.950000000 2.591500000 -2.753960784 > Ga -0.000000000 2.591500000 0.000000000 > Ga 3.180000000 2.591500000 0.000000000 > Ga 6.360000000 2.591500000 0.000000000 > N -0.000000000 4.542899554 -5.507921568 > N 3.180000000 4.542899554 -5.507921568 > N 6.360000000 4.542899554 -5.507921568 > N 1.590000000 4.542899554 -2.753960784 > N 4.770000000 4.542899554 -2.753960784 > N 7.950000000 4.542899554 -2.753960784 > N -0.000000000 4.542899554 0.000000000 > N 3.180000000 4.542899554 0.000000000 > N 6.360000000 4.542899554 0.000000000 > N 1.590000000 1.951399554 -6.425908496 > N 4.770000000 1.951399554 -6.425908496 > N 7.950000000 1.951399554 -6.425908496 > N -0.000000000 1.951399554 -3.671947712 > N 3.180000000 1.951399554 -3.671947712 > N 6.360000000 1.951399554 -3.671947712 > N 1.590000000 1.951399554 -0.917986928 > N 4.770000000 1.951399554 -0.917986928 > N 7.950000000 1.951399554 -0.917986928 > K_POINTS (automatic) > 3 7 3 0 0 0 > CELL_PARAMETERS { cubic} > 18.034 0.0000 0.0000 > 0.0000 9.7980 0.0000 > 0.0000 0.0000 15.6181 > +++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++++++++++++++++++++++++++++++++++++++++++++++++ > SCF calculatons show no any problems, and the total energy > is well converged. > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > !and the pwcond.x calculation part: > &inputcond > outdir='./', > prefixl='gan', > prefixs = 'gan' > tran_file='trans.gan1', > ikind=1, > iofspin = 2 > energy0=2.95d0, > denergy=-0.1d0, > ewind=3.d0, > epsproj=1.d-6, > nz1 =6 > / > 1 > 0.0 0.0 1.0 > 20 > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > For electric conductivity calculations, the error signals: > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > ngper, shell number = 211 62 > ngper, n2d = 211 211 > Application 2036109 exit signals: Killed > Application 2036109 resources: utime 0, stime 0 > > Becasue the number of atoms is small now, I do not think the problem is > caused by out of memory. > > In your mail: > >From: Paolo Giannozzi > >Reply-To: PWSCF Forum > >To: ErJun Kan , > > PWSCF Forum > > >Subject: Re: [Pw_forum] error in pwcond.x calculations > >Date:Fri, 06 Feb 2009 17:23:18 +0100 > > > >ErJun Kan wrote: > > > Application 1942431 exit codes: 139 > > > Application 1942431 exit signals: Killed > > > > out of memory? > > > > -- > > Paolo Giannozzi, Democritos and University of Udine, Italy > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From smogunov at sissa.it Mon Feb 9 09:40:33 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Mon, 9 Feb 2009 09:40:33 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <498FE26C.3050302@sissa.it> References: <434035942.21533@ustc.edu.cn> <498FE26C.3050302@sissa.it> Message-ID: <200902090940.34033.smogunov@sissa.it> On Monday 09 February 2009 08:59, Gabriele Sclauzero wrote: > ErJun Kan wrote: > > Dear all, > > > > I have reduced the size of cell, it still does not work. > > what is the problem? thank you. > > I think that pwcond was not programmed in order to work with ibrav=0. Why > don't you use an orthorhombic cell type? You should be able to specify > atomic positions of your system also with that ibrav. PWCOND should also work for ibrav=0 if the cell is MONOCLINIC... once again. Regards, A. > > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > !and the pwcond.x calculation part: > > &inputcond > > outdir='./', > > prefixl='gan', > > prefixs = 'gan' > > Another problem could be here: why do you specify the same prefix for both > left lead and scattering region? Are you sure you understood the meaning of > those prefixes? If not, please try to read some documentation and if it's > still not clear you can ask to this forum. > > > tran_file='trans.gan1', > > ikind=1, > > iofspin = 2 > > energy0=2.95d0, > > denergy=-0.1d0, > > ewind=3.d0, > > epsproj=1.d-6, > > nz1 =6 > > / > > 1 > > 0.0 0.0 1.0 > > 20 > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > For electric conductivity calculations, the error signals: > > > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > > > ngper, shell number = 211 62 > > ngper, n2d = 211 211 > > Application 2036109 exit signals: Killed > > Application 2036109 resources: utime 0, stime 0 > > > > Becasue the number of atoms is small now, I do not think the problem is > > caused by out of memory. > > Sorry, but wouldn't it be nice if you sign your posts and provide > affiliation? (since this is the netiquette of this forum). Thanks! > > BTW, the name of Paolo is Paolo, not Palo... > > Gabriele From giannozz at democritos.it Mon Feb 9 10:20:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 09 Feb 2009 10:20:17 +0100 Subject: [Pw_forum] ph.x error message In-Reply-To: <498FE14E.5010203@phys.ufl.edu> References: <498FE14E.5010203@phys.ufl.edu> Message-ID: <498FF551.5030403@democritos.it> Lex Kemper wrote: > from lint : error # 1 > cannot locate k point xk there are constraints on k-point grids that you can use. See the README of example 7. Also note that allowed grids must not break the symmetry of the material under examination Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From baris.malcioglu at gmail.com Mon Feb 9 10:55:18 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Mon, 9 Feb 2009 10:55:18 +0100 Subject: [Pw_forum] scf calculation In-Reply-To: <7699a1950902070613m52ea5705i80d67322d8846512@mail.gmail.com> References: <7699a1950902070613m52ea5705i80d67322d8846512@mail.gmail.com> Message-ID: Dear Mohaddeseh, Although I can not help you with the exact reason why you are getting this error, on a technical point of view, the error message means that the beta functions (used in calculating the norm) can not be read from the file you have created. My first guess would be that your assumption of "and converted it to one appropriate for PWscf" might be wrong. If you have prepared i.e. an USPP, a first starting point might be to check in the PP file that the number of projectors and sections are consistent, meshes are consistent, etc. Best, O. Baris Malcioglu SISSA CM sector. On Sat, Feb 7, 2009 at 3:13 PM, mohaddeseh abbasnejad wrote: > Dear all, > > I want to do scf calculation for Ni. I used tabulated pseudopotential from > CASINO > and converted it to one appropriate for PWscf.. > As I run it, it gives me such an error: > > Program PWSCF v.4.1CVS starts ... > Today is 7Feb2009 at 17:37:51 > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > Current dimensions of program pwscf are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_pseudo_nl : error # 1 > Reading pseudo file (BETA) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > Would you please help me? > > Thanks in advance. > > Mohaddeseh > > > -- > -------------------------------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, End of North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > -------------------------------------------------------------------------------- > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From eyvaz_isaev at yahoo.com Mon Feb 9 11:26:38 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 9 Feb 2009 02:26:38 -0800 (PST) Subject: [Pw_forum] Phonon DOS In-Reply-To: <24356.29744.qm@web31407.mail.mud.yahoo.com> Message-ID: <564321.65522.qm@web65703.mail.ac4.yahoo.com> Dear Meghdad, I will send you the code which does much more than you expected. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 2/9/09, meghdad saeedian wrote: > From: meghdad saeedian > Subject: [Pw_forum] Phonon DOS > To: "PWscf" > Date: Monday, February 9, 2009, 10:45 AM > Dear all > > How can i separate PDOS (phonon DOS) to acoustical phonon > dos and optical phonon dos? > > Thanks in advance > > Sincerely yours > saeedian > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From jdai3 at mail.ustc.edu.cn Mon Feb 9 12:27:53 2009 From: jdai3 at mail.ustc.edu.cn (Dai) Date: Mon, 9 Feb 2009 19:27:53 +0800 Subject: [Pw_forum] Phonon DOS References: <434175280.10327@ustc.edu.cn> Message-ID: <434178871.28918@ustc.edu.cn> Dear Prof. Isaev, Would you please send me a copy of the code you mentioned, thanks. 2009-02-09 Best regards, Jun Dai ============================================================= Jun Dai Ph.D. Candidate, Hefei National Laboratory For Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China Tel.: 86-551-3606428 Fax.: 86-551-3602969 E-mail: jdai3 at mail.ustc.edu.cn ============================================================= ???? Eyvaz Isaev ????? 2009-02-09 18:28:00 ???? PWSCF Forum ??? ??? Re: [Pw_forum] Phonon DOS Dear Meghdad, I will send you the code which does much more than you expected. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 2/9/09, meghdad saeedian wrote: > From: meghdad saeedian > Subject: [Pw_forum] Phonon DOS > To: "PWscf" > Date: Monday, February 9, 2009, 10:45 AM > Dear all > > How can i separate PDOS (phonon DOS) to acoustical phonon > dos and optical phonon dos? > > Thanks in advance > > Sincerely yours > saeedian > > > > > _______________________________________________ > 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/20090209/e792bcfd/attachment.htm From nazari at iasbs.ac.ir Mon Feb 9 16:25:57 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 9 Feb 2009 15:25:57 -0000 (UTC) Subject: [Pw_forum] nspin=2/Band structure In-Reply-To: <498FE96F.8060904@sissa.it> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> <498FE96F.8060904@sissa.it> Message-ID: <6861.213.176.122.17.1234193157.squirrel@mail.iasbs.ac.ir> Dear Gabriele Sclauzero, Sorry for forgetting my name. You are wright but when I run spin polarized calculation along with occupation=fixed or tetrahedra for calculating bands.x after nscf calculation the program stops with this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bands : error # 1 The bands code with constrained magnetization has not been tested %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Would you please let me know what is the problem? Regards Fariba Nazari IASBS From sclauzer at sissa.it Mon Feb 9 13:35:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 13:35:46 +0100 Subject: [Pw_forum] nspin=2/Band structure In-Reply-To: <6861.213.176.122.17.1234193157.squirrel@mail.iasbs.ac.ir> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> <498FE96F.8060904@sissa.it> <6861.213.176.122.17.1234193157.squirrel@mail.iasbs.ac.ir> Message-ID: <49902322.7020800@sissa.it> nazari at iasbs.ac.ir wrote: > > > > Dear Gabriele Sclauzero, > > Sorry for forgetting my name. > > You are wright but when I run spin polarized calculation along with > > occupation=fixed or tetrahedra for calculating bands.x after nscf > > calculation the program stops with this error: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from bands : error # 1 > The bands code with constrained magnetization has not been tested > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From this output it seems like you're constraining magnetization, through the keyword constrained_magnetization As the error message says, the bands program has not been tested in this case, but you may want to try it anyway (at your risk: simply remove the corresponding call to errore subroutine in the PP/bands.f90 source file and recompile) and eventually report/fix bugs, if any. If you're NOT using constrained_magnetization, then it should work smoothly, if it is not the case please send input and output files. If using tethraedra, you should be careful, maybe some parts of the postprocessing codes do not support this option (though I'm not sure). Regards GS > > Would you please let me know what is the problem? > > Regards > Fariba Nazari > IASBS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Feb 9 14:02:07 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 14:02:07 +0100 Subject: [Pw_forum] nspin=2/Band structure In-Reply-To: <6861.213.176.122.17.1234193157.squirrel@mail.iasbs.ac.ir> References: <498B15EF.6040207@sissa.it> <81436D25-106F-444E-A485-BBB75A2516FA@sissa.it> <498BFF08.6040907@sissa.it> <21402.213.176.122.17.1234021038.squirrel@mail.iasbs.ac.ir> <498FE96F.8060904@sissa.it> <6861.213.176.122.17.1234193157.squirrel@mail.iasbs.ac.ir> Message-ID: <4990294F.6050306@sissa.it> nazari at iasbs.ac.ir wrote: > > > > Dear Gabriele Sclauzero, > > Sorry for forgetting my name. > > You are wright but when I run spin polarized calculation along with > > occupation=fixed or tetrahedra for calculating bands.x after nscf > > calculation the program stops with this error: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from bands : error # 1 > The bands code with constrained magnetization has not been tested > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Looking into the code, I realized that this happens in spin-polarized calculations also if your treating your system as an insulator (which is dealt fixing the number of up and down electrons, thus the total magnetization). Actually I don't know if the bands program can be applied safely, but in alternative you can always use occupations='smearing' and specify a very small degauss (and also remember to turn on magnetization using starting_magnetization keyword, if your system is actually magnetic). GS > > Would you please let me know what is the problem? > > Regards > Fariba Nazari > IASBS > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From erjunkan at mail.ustc.edu.cn Mon Feb 9 17:21:48 2009 From: erjunkan at mail.ustc.edu.cn (ErJun Kan) Date: Tue, 10 Feb 2009 00:21:48 +0800 Subject: [Pw_forum] error in pwcond.x calculations Message-ID: <434196508.19237@ustc.edu.cn> Hi, Alexander, Thank you! I want to calculate the conductivity of GaN:Mn film. In my case, I has used the leads same as the scattering region. Unfortunately, it does not work. Bests, Erjun Kan ============================================================= Erjun Kan Department of Chemistry, North Carolina State University Raleigh, North Carolina, USA E-mail: erjunkan at mail.ustc.edu.cn or ekan at ncsu.edu ============================================================= In your mail: >From: Alexander Smogunov >Reply-To: PWSCF Forum >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] error in pwcond.x calculations >Date:Mon, 9 Feb 2009 09:21:30 +0100 > >Dear ErJun Kan > What kind of system do you study? > For conductance calculation you should have two semi-infinite > left and right metallic leads connected by some scattering region > which should match PERFECTLY to the leads. What are the leads and the > scattering region in your case? > Regards, > Alexander > > > On Saturday 07 February 2009 20:45, ErJun Kan wrote: > > Dear all, > > > > I have reduced the size of cell, it still does not work. > > what is the problem? thank you. > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > ! SCF calculation part: > > # self-consistent calculation > > &control > > calculation='scf' > > restart_mode='from_scratch', > > pseudo_dir = './', > > outdir='./' > > prefix='gan' > > / > > &system > > ibrav = 0, > > nat = 36 > > ntyp= 3, > > ecutwfc = 15.0, > > nspin = 2 > > starting_magnetization(1)=0.7 > > occupations='smearing', > > smearing='gaussian', > > degauss=0.01 > > / > > &electrons > > diagonalization='$diago' > > mixing_mode = 'plain' > > electron_maxstep = 200 > > conv_thr = 1.0e-8 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Mn 54.938 Mn.pbe-sp-van.UPF > > Ga 69.72 Ga.pbe-nsp-van.UPF > > N 14.00 N.pbe-van_ak.UPF > > ATOMIC_POSITIONS {angstrom} > > Mn 1.590000000 0.000000000 -6.425908496 > > Ga 4.770000000 0.000000000 -6.425908496 > > Ga 7.950000000 0.000000000 -6.425908496 > > Ga -0.000000000 0.000000000 -3.671947712 > > Ga 3.180000000 0.000000000 -3.671947712 > > Ga 6.360000000 0.000000000 -3.671947712 > > Ga 1.590000000 0.000000000 -0.917986928 > > Ga 4.770000000 0.000000000 -0.917986928 > > Ga 7.950000000 0.000000000 -0.917986928 > > Ga -0.000000000 2.591500000 -5.507921568 > > Ga 3.180000000 2.591500000 -5.507921568 > > Ga 6.360000000 2.591500000 -5.507921568 > > Ga 1.590000000 2.591500000 -2.753960784 > > Ga 4.770000000 2.591500000 -2.753960784 > > Ga 7.950000000 2.591500000 -2.753960784 > > Ga -0.000000000 2.591500000 0.000000000 > > Ga 3.180000000 2.591500000 0.000000000 > > Ga 6.360000000 2.591500000 0.000000000 > > N -0.000000000 4.542899554 -5.507921568 > > N 3.180000000 4.542899554 -5.507921568 > > N 6.360000000 4.542899554 -5.507921568 > > N 1.590000000 4.542899554 -2.753960784 > > N 4.770000000 4.542899554 -2.753960784 > > N 7.950000000 4.542899554 -2.753960784 > > N -0.000000000 4.542899554 0.000000000 > > N 3.180000000 4.542899554 0.000000000 > > N 6.360000000 4.542899554 0.000000000 > > N 1.590000000 1.951399554 -6.425908496 > > N 4.770000000 1.951399554 -6.425908496 > > N 7.950000000 1.951399554 -6.425908496 > > N -0.000000000 1.951399554 -3.671947712 > > N 3.180000000 1.951399554 -3.671947712 > > N 6.360000000 1.951399554 -3.671947712 > > N 1.590000000 1.951399554 -0.917986928 > > N 4.770000000 1.951399554 -0.917986928 > > N 7.950000000 1.951399554 -0.917986928 > > K_POINTS (automatic) > > 3 7 3 0 0 0 > > CELL_PARAMETERS { cubic} > > 18.034 0.0000 0.0000 > > 0.0000 9.7980 0.0000 > > 0.0000 0.0000 15.6181 > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > SCF calculatons show no any problems, and the total energy > > is well converged. > > > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > !and the pwcond.x calculation part: > > &inputcond > > outdir='./', > > prefixl='gan', > > prefixs = 'gan' > > tran_file='trans.gan1', > > ikind=1, > > iofspin = 2 > > energy0=2.95d0, > > denergy=-0.1d0, > > ewind=3.d0, > > epsproj=1.d-6, > > nz1 =6 > > / > > 1 > > 0.0 0.0 1.0 > > 20 > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > For electric conductivity calculations, the error signals: > > > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > > > ngper, shell number = 211 62 > > ngper, n2d = 211 211 > > Application 2036109 exit signals: Killed > > Application 2036109 resources: utime 0, stime 0 > > > > Becasue the number of atoms is small now, I do not think the problem is > > caused by out of memory. > > > > In your mail: > > >From: Paolo Giannozzi > > >Reply-To: PWSCF Forum > > >To: ErJun Kan , > > > > PWSCF Forum > > > > >Subject: Re: [Pw_forum] error in pwcond.x calculations > > >Date:Fri, 06 Feb 2009 17:23:18 +0100 > > > > > >ErJun Kan wrote: > > > > Application 1942431 exit codes: 139 > > > > Application 1942431 exit signals: Killed > > > > > > out of memory? > > > > > > -- > > > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > > 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 m.abbasnejad at gmail.com Mon Feb 9 17:23:26 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 9 Feb 2009 19:53:26 +0330 Subject: [Pw_forum] pw2casino.x Message-ID: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> Dear all, I used the post-proceeding program pw2casino.x to deal with the input file as follows, but get the error result : &inputpp prefix = 'silicon', outdir = '/home/mohaddeseh/tmp/' filplot = 'density' plot_num = 3 / Program POST-PROC v.4.1CVS starts ... Today is 9Feb2009 at 19:47:28 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from pw2casino : error # 19 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Would you please help me? Thanks in advance. Yours, Mohaddeseh -- -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090209/e6cf5de5/attachment.htm From erjunkan at mail.ustc.edu.cn Mon Feb 9 17:26:39 2009 From: erjunkan at mail.ustc.edu.cn (ErJun Kan) Date: Tue, 10 Feb 2009 00:26:39 +0800 Subject: [Pw_forum] error in pwcond.x calculations Message-ID: <434196799.23017@ustc.edu.cn> Hi, Gabriele, Thank you for your reply. In your mail: >From: Gabriele Sclauzero >Reply-To: PWSCF Forum >To: ErJun Kan , PWSCF Forum >Subject: Re: [Pw_forum] error in pwcond.x calculations >Date:Mon, 09 Feb 2009 08:59:40 +0100 > > > ErJun Kan wrote: > > Dear all, > > > > I have reduced the size of cell, it still does not work. > > what is the problem? thank you. > > I think that pwcond was not programmed in order to work with ibrav=0. Why don't you use an > orthorhombic cell type? You should be able to specify atomic positions of your system also > with that ibrav. I will try different ibrav to see the difference. > > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > !and the pwcond.x calculation part: > > &inputcond > > outdir='./', > > prefixl='gan', > > prefixs = 'gan' > > Another problem could be here: why do you specify the same prefix for both left lead and > scattering region? Are you sure you understood the meaning of those prefixes? If not, > please try to read some documentation and if it's still not clear you can ask to this forum. In my case, I will use the same leads, but with different scattering region. The only ambiguous point is whether the leads can be a semiconductor or insulator? > > > > tran_file='trans.gan1', > > ikind=1, > > iofspin = 2 > > energy0=2.95d0, > > denergy=-0.1d0, > > ewind=3.d0, > > epsproj=1.d-6, > > nz1 =6 > > / > > 1 > > 0.0 0.0 1.0 > > 20 > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > For electric conductivity calculations, the error signals: > > > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > > > ngper, shell number = 211 62 > > ngper, n2d = 211 211 > > Application 2036109 exit signals: Killed > > Application 2036109 resources: utime 0, stime 0 > > > > Becasue the number of atoms is small now, I do not think the problem is caused > > by out of memory. > > Sorry, but wouldn't it be nice if you sign your posts and provide affiliation? (since this > is the netiquette of this forum). Thanks! Sorry, I have supplied the informations. Thank you. > > BTW, the name of Paolo is Paolo, not Palo... > > Gabriele > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ============================================================= Erjun Kan Department of Chemistry, North Carolina State University Raleigh, North Carolina, USA E-mail: erjunkan at mail.ustc.edu.cn or ekan at ncsu.edu ============================================================= From sclauzer at sissa.it Mon Feb 9 17:29:53 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 17:29:53 +0100 Subject: [Pw_forum] pw2casino.x In-Reply-To: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> References: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> Message-ID: <49905A01.1030101@sissa.it> Very easy to understand, if you have a little knowledge of Fortran90: there was an error in reading the inputpp namelist! It seems that this namelist includes only prefix and outdir keywords, as you can check at the beginning of the source file PP/pw2casino.f90. IMPLICIT NONE INTEGER :: ios NAMELIST / inputpp / prefix, outdir CALL start_postproc(nd_nmbr) Regards GS mohaddeseh abbasnejad wrote: > Dear all, > > I used the post-proceeding program pw2casino.x to deal with the input > file as follows, > but get the error result : > > &inputpp > prefix = 'silicon', > outdir = '/home/mohaddeseh/tmp/' > filplot = 'density' > plot_num = 3 > / > > > > Program POST-PROC v.4.1CVS starts ... > Today is 9Feb2009 at 19:47:28 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from pw2casino : error # 19 > reading inputpp namelist > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > Would you please help me? > Thanks in advance. > > Yours, > Mohaddeseh > -- > -------------------------------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > -------------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From manoj at phys.ufl.edu Mon Feb 9 17:32:50 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 9 Feb 2009 11:32:50 -0500 (EST) Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <434196508.19237@ustc.edu.cn> Message-ID: Hey Erjun, Alexander, I have noticed one thing that is odd. For ewind =3, or any value of it less than 100, the code does basis reduction, which is not happening in this case. have a look at this- ngper, shell number = 211 62 ngper, n2d = 211 211 So, i think something is wrong with ewind. I would suggest trying some other values of ewind and see what happenes. Regards, Manoj Srivastava Department of Physics University of Florida On Tue, 10 Feb 2009, ErJun Kan wrote: > Hi, Alexander, > > Thank you! > > I want to calculate the conductivity of GaN:Mn film. > In my case, I has used the leads same as the scattering region. > Unfortunately, it does not work. > > Bests, > Erjun Kan > > ============================================================= > Erjun Kan > Department of Chemistry, North Carolina State University > Raleigh, North Carolina, USA > E-mail: erjunkan at mail.ustc.edu.cn or > ekan at ncsu.edu > ============================================================= > > > > In your mail: > >From: Alexander Smogunov > >Reply-To: PWSCF Forum > >To: pw_forum at pwscf.org > >Subject: Re: [Pw_forum] error in pwcond.x calculations > >Date:Mon, 9 Feb 2009 09:21:30 +0100 > > > >Dear ErJun Kan > > What kind of system do you study? > > For conductance calculation you should have two semi-infinite > > left and right metallic leads connected by some scattering region > > which should match PERFECTLY to the leads. What are the leads and the > > scattering region in your case? > > Regards, > > Alexander > > > > > > > > > > On Saturday 07 February 2009 20:45, ErJun Kan wrote: > > > Dear all, > > > > > > I have reduced the size of cell, it still does not work. > > > what is the problem? thank you. > > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > > ! SCF calculation part: > > > # self-consistent calculation > > > &control > > > calculation='scf' > > > restart_mode='from_scratch', > > > pseudo_dir = './', > > > outdir='./' > > > prefix='gan' > > > / > > > &system > > > ibrav = 0, > > > nat = 36 > > > ntyp= 3, > > > ecutwfc = 15.0, > > > nspin = 2 > > > starting_magnetization(1)=0.7 > > > occupations='smearing', > > > smearing='gaussian', > > > degauss=0.01 > > > / > > > &electrons > > > diagonalization='$diago' > > > mixing_mode = 'plain' > > > electron_maxstep = 200 > > > conv_thr = 1.0e-8 > > > mixing_beta = 0.7 > > > / > > > ATOMIC_SPECIES > > > Mn 54.938 Mn.pbe-sp-van.UPF > > > Ga 69.72 Ga.pbe-nsp-van.UPF > > > N 14.00 N.pbe-van_ak.UPF > > > ATOMIC_POSITIONS {angstrom} > > > Mn 1.590000000 0.000000000 -6.425908496 > > > Ga 4.770000000 0.000000000 -6.425908496 > > > Ga 7.950000000 0.000000000 -6.425908496 > > > Ga -0.000000000 0.000000000 -3.671947712 > > > Ga 3.180000000 0.000000000 -3.671947712 > > > Ga 6.360000000 0.000000000 -3.671947712 > > > Ga 1.590000000 0.000000000 -0.917986928 > > > Ga 4.770000000 0.000000000 -0.917986928 > > > Ga 7.950000000 0.000000000 -0.917986928 > > > Ga -0.000000000 2.591500000 -5.507921568 > > > Ga 3.180000000 2.591500000 -5.507921568 > > > Ga 6.360000000 2.591500000 -5.507921568 > > > Ga 1.590000000 2.591500000 -2.753960784 > > > Ga 4.770000000 2.591500000 -2.753960784 > > > Ga 7.950000000 2.591500000 -2.753960784 > > > Ga -0.000000000 2.591500000 0.000000000 > > > Ga 3.180000000 2.591500000 0.000000000 > > > Ga 6.360000000 2.591500000 0.000000000 > > > N -0.000000000 4.542899554 -5.507921568 > > > N 3.180000000 4.542899554 -5.507921568 > > > N 6.360000000 4.542899554 -5.507921568 > > > N 1.590000000 4.542899554 -2.753960784 > > > N 4.770000000 4.542899554 -2.753960784 > > > N 7.950000000 4.542899554 -2.753960784 > > > N -0.000000000 4.542899554 0.000000000 > > > N 3.180000000 4.542899554 0.000000000 > > > N 6.360000000 4.542899554 0.000000000 > > > N 1.590000000 1.951399554 -6.425908496 > > > N 4.770000000 1.951399554 -6.425908496 > > > N 7.950000000 1.951399554 -6.425908496 > > > N -0.000000000 1.951399554 -3.671947712 > > > N 3.180000000 1.951399554 -3.671947712 > > > N 6.360000000 1.951399554 -3.671947712 > > > N 1.590000000 1.951399554 -0.917986928 > > > N 4.770000000 1.951399554 -0.917986928 > > > N 7.950000000 1.951399554 -0.917986928 > > > K_POINTS (automatic) > > > 3 7 3 0 0 0 > > > CELL_PARAMETERS { cubic} > > > 18.034 0.0000 0.0000 > > > 0.0000 9.7980 0.0000 > > > 0.0000 0.0000 15.6181 > > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > > SCF calculatons show no any problems, and the total energy > > > is well converged. > > > > > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > > !and the pwcond.x calculation part: > > > &inputcond > > > outdir='./', > > > prefixl='gan', > > > prefixs = 'gan' > > > tran_file='trans.gan1', > > > ikind=1, > > > iofspin = 2 > > > energy0=2.95d0, > > > denergy=-0.1d0, > > > ewind=3.d0, > > > epsproj=1.d-6, > > > nz1 =6 > > > / > > > 1 > > > 0.0 0.0 1.0 > > > 20 > > > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ > > > For electric conductivity calculations, the error signals: > > > > > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > > > > > ngper, shell number = 211 62 > > > ngper, n2d = 211 211 > > > Application 2036109 exit signals: Killed > > > Application 2036109 resources: utime 0, stime 0 > > > > > > Becasue the number of atoms is small now, I do not think the problem is > > > caused by out of memory. > > > > > > In your mail: > > > >From: Paolo Giannozzi > > > >Reply-To: PWSCF Forum > > > >To: ErJun Kan , > > > > > > PWSCF Forum > > > > > > >Subject: Re: [Pw_forum] error in pwcond.x calculations > > > >Date:Fri, 06 Feb 2009 17:23:18 +0100 > > > > > > > >ErJun Kan wrote: > > > > > Application 1942431 exit codes: 139 > > > > > Application 1942431 exit signals: Killed > > > > > > > > out of memory? > > > > > > > > -- > > > > Paolo Giannozzi, Democritos and University of Udine, Italy > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > _______________________________________________ > > > 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 > From sclauzer at sissa.it Mon Feb 9 17:45:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 17:45:45 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: <434196799.23017@ustc.edu.cn> References: <434196799.23017@ustc.edu.cn> Message-ID: <49905DB9.6090806@sissa.it> ErJun Kan wrote: > I will try different ibrav to see the difference. As Alexander pointed you can even use monoclinic cells, of which the orthorombic cells should be a subset (with cos(ab)=0), if I'm not mistaken. > >>> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ >>> !and the pwcond.x calculation part: >>> &inputcond >>> outdir='./', >>> prefixl='gan', >>> prefixs = 'gan' >> Another problem could be here: why do you specify the same prefix for both left > lead and >> scattering region? Are you sure you understood the meaning of those prefixes? If > not, >> please try to read some documentation and if it's still not clear you can ask to > this forum. > In my case, I will use the same leads, but with different scattering region. And so why do you specify the same prefix for both the left lead and the scatetring region??? (the right lead is assumed to be identical to the left one, in your input) Please first have a look at the examples in the examples/ directory and try to practice with them (and understand the meaning of parameters and input keywords). > The > only ambiguous point is whether the leads can be a semiconductor or insulator? In principle the leads should be metallic, I don't know if this formulation of ballistic transport makes sense with semiconductors or insulators. In practice the transmission calculations should be feasible, but it makes no sense to use the same cell as both the lead AND the scattering region (which have conceptually different meanings!). You should make clear to yourself what you want to calculate, first of all. GS > >> > > ============================================================= > Erjun Kan > Department of Chemistry, North Carolina State University > Raleigh, North Carolina, USA > E-mail: erjunkan at mail.ustc.edu.cn or > ekan at ncsu.edu > ============================================================= > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Feb 9 17:52:33 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 17:52:33 +0100 Subject: [Pw_forum] error in pwcond.x calculations In-Reply-To: References: Message-ID: <49905F51.5000906@sissa.it> You're totally right, the basis set reduction does not actually reduce the basis in this particular case and with these values of ewind and epsproj (but basis reduction is not much effective in this kind of systems). I think it's not safe to reduce ewind below 3.0, since it could lead to wrong complex band dispersions. I would suggest to try and encreasing eps_proj up to 1.d-5, which could help in reducing the basis set (however convergency with respect to these two parameters should be always checked, if not using the full basis). GS Manoj Srivastava wrote: > Hey Erjun, Alexander, > I have noticed one thing that is odd. For ewind =3, or any value of it > less than 100, the code does basis reduction, which is not happening in > this case. have a look at this- > ngper, shell number = 211 62 > ngper, n2d = 211 211 > > So, i think something is wrong with ewind. I would suggest trying some > other values of ewind and see what happenes. > > Regards, > Manoj Srivastava > Department of Physics > University of Florida > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From m.abbasnejad at gmail.com Mon Feb 9 17:54:05 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 9 Feb 2009 20:24:05 +0330 Subject: [Pw_forum] pw2casino.x In-Reply-To: <49905A01.1030101@sissa.it> References: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> <49905A01.1030101@sissa.it> Message-ID: <7699a1950902090854m1ed00454p5ca7be46578640ac@mail.gmail.com> Dear Gabriele, Thank you so much. I have another question too. If I use the simplest input file as follows, &inputpp prefix = 'silicon', outdir = '/home/mohaddeseh/tmp/' / the output is as follows and doesn't contain any information about Geometry, G vectors and so on. Program POST-PROC v.4.1CVS starts ... Today is 9Feb2009 at 20:11:23 Writing file pwfn.data for program CASINO Kinetic energy 3.01269703220284 Local energy -2.26291401756337 Non-Local energy 1.61122312220330 Ewald energy -8.34402473115134 xc contribution -2.37920332238950 hartree energy 0.525427024055568 Total energy -7.83679489264251 Would you please make a comment? Best wishes, Mohaddeseh -- -------------------------------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir -------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090209/23e54138/attachment-0001.htm From giannozz at democritos.it Mon Feb 9 17:59:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 09 Feb 2009 17:59:47 +0100 Subject: [Pw_forum] pw2casino.x In-Reply-To: <7699a1950902090854m1ed00454p5ca7be46578640ac@mail.gmail.com> References: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> <49905A01.1030101@sissa.it> <7699a1950902090854m1ed00454p5ca7be46578640ac@mail.gmail.com> Message-ID: <49906103.7050601@democritos.it> mohaddeseh abbasnejad wrote: > the output is as follows and doesn't contain any information > about Geometry, G vectors and so on. > > Program POST-PROC v.4.1CVS starts ... > Today is 9Feb2009 at 20:11:23 > > Writing file pwfn.data for program CASINO this is where the output is written: file pwfn.data -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Mon Feb 9 18:01:08 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Feb 2009 18:01:08 +0100 Subject: [Pw_forum] pw2casino.x In-Reply-To: <7699a1950902090854m1ed00454p5ca7be46578640ac@mail.gmail.com> References: <7699a1950902090823i86746cdn8dbd462e9b008b40@mail.gmail.com> <49905A01.1030101@sissa.it> <7699a1950902090854m1ed00454p5ca7be46578640ac@mail.gmail.com> Message-ID: <49906154.50204@sissa.it> mohaddeseh abbasnejad wrote: > Dear Gabriele, > > Thank you so much. > I have another question too. > If I use the simplest input file as follows, > > &inputpp > prefix = 'silicon', > outdir = '/home/mohaddeseh/tmp/' > / > > the output is as follows and doesn't contain any information > about Geometry, G vectors and so on. Why should it? Maybe it was not programmed in order to do that... I guess that since pw2casino.x should read the restart files produced by pw.x (i.e. those in /home/mohaddeseh/tmp/silicon.save), you can get information about the geometry from the output of pw.x run which produced those restart files (or from the restart files themselves, which are not all human readable anyway). GS > > Program POST-PROC v.4.1CVS starts ... > Today is 9Feb2009 at 20:11:23 > > Writing file pwfn.data for program CASINO > Kinetic energy 3.01269703220284 > Local energy -2.26291401756337 > Non-Local energy 1.61122312220330 > Ewald energy -8.34402473115134 > xc contribution -2.37920332238950 > hartree energy 0.525427024055568 > Total energy -7.83679489264251 > > Would you please make a comment? > > Best wishes, > Mohaddeseh > > -- > -------------------------------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > -------------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From manoj at phys.ufl.edu Mon Feb 9 23:03:16 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Mon, 9 Feb 2009 17:03:16 -0500 (EST) Subject: [Pw_forum] symmetry operations in PW Message-ID: Dear PWSCF users and developers, I was looking into the code where it calculates symmerty operations for the group. Now the symmetry operations are defined as ' 90 deg rotation - cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] I did not understand the point of defining rotation about z and -z axis. Is this because of some numerical constraint? Also, there are elements with 'theta' and '-theta' rotation in the same group. I was just wondering the reason behind this. Any help will be appreciated. Regards, Manoj Srivastava Department of Physics University of Florida Gainesville, FL, USA. From quantumdft at gmail.com Tue Feb 10 06:35:52 2009 From: quantumdft at gmail.com (vega lew) Date: Tue, 10 Feb 2009 13:35:52 +0800 Subject: [Pw_forum] something about Pt.pw91-n-van.UPF In-Reply-To: <412f6c680902092123y4862cc7id0d017000da4bcd5@mail.gmail.com> References: <2308.130.91.67.162.1233598957.squirrel@cmm.upenn.edu> <412f6c680902092123y4862cc7id0d017000da4bcd5@mail.gmail.com> Message-ID: <412f6c680902092135g54dfa66cs9bb822b0d24c6380@mail.gmail.com> Dear all, thank you very much for all the comments and hints to my question. I just return from winter vacation. sorry for such a late responding to this mail. actually, my real question is not just limited to total (free) energy of Pt. This is a part of study for Pt atoms on titania surface, for example, anatase (101), as reported in J. Phys. Chem. B 2006, 110, 7463. I think the system is not metallic, but semiconductive system When I want to calculated the binding energy between the surface and the Pt atom, I need to have three total (free) energies, E(Pt), E(surf.), E(relaxed)(Pt @ surf.). Mr. Paolo Giannozzi (Democritos and University of Udine, Italy) used to tell me that 'all energies should be calculated with the same cell, cutoff, k-points, at the equilibrium geometry of the respective system...'. So the E(Pt), E(surf.), E(relaxed)(Pt @ surf.) should use the same parameters during the calculation. But there is some trouble for me to calculate the E(Pt) using the same parameters as E(surf.), E(relaxed)(Pt @ surf.). Do you think I should adjust the paremeter for E(surf.), E(relaxed)(Pt @ surf.), which should be better for E(Pt) calculation? in order to make better understanding of my question, i'll show my input file for E(Pt @ surf.). and the E(surf.) is calculated by just removing the Pt atoms from the input file as well as related parameters, such as nat, ntyp etc. &CONTROL title = 'anatase 101 Pt1_3' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , prefix = 'anatase 101 Pt1_3' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 8, celldm(1) =19.6144, celldm(2) = 1.0955, celldm(3) = 1.7218, nat = 73, ntyp = 3, nosym = .true. , ecutwfc = 30, ecutrho = 300, / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF Pt 195.09000 Pt.pw91-n-van.UPF ATOMIC_POSITIONS crystal Ti 0.45574 0.08471 0.04088 0 0 0 Ti 0.58876 0.08481 0.24889 1 1 1 Ti 0.95575 0.25138 0.04088 0 0 0 Ti 0.08876 0.25148 0.24889 1 1 1 Ti 0.23909 0.25138 0.09024 0 0 0 Ti 0.36002 0.25140 0.28435 1 1 1 Ti 0.73908 0.08471 0.09024 0 0 0 Ti 0.86002 0.08473 0.28435 1 1 1 O 0.63518 0.08471 0.00000 0 0 0 O 0.77165 0.08470 0.19890 1 1 1 O 0.13518 0.25138 0.00000 0 0 0 O 0.27165 0.25137 0.19890 1 1 1 O 0.41852 0.25138 0.04936 0 0 0 O 0.55009 0.25139 0.24981 1 1 1 O 0.91852 0.08471 0.04936 0 0 0 O 0.05009 0.08472 0.24980 1 1 1 O 0.55965 0.08471 0.13112 0 0 0 O 0.70209 0.08473 0.32993 1 1 1 O 0.05965 0.25138 0.13112 0 0 0 O 0.20208 0.25139 0.32993 1 1 1 O 0.77631 0.25138 0.08176 0 0 0 O 0.91188 0.25139 0.29614 1 1 1 O 0.27631 0.08471 0.08176 0 0 0 O 0.41187 0.08472 0.29614 1 1 1 Ti 0.45574 0.41804 0.04088 0 0 0 Ti 0.58876 0.41814 0.24889 1 1 1 Ti 0.95575 0.58471 0.04088 0 0 0 Ti 0.08876 0.58481 0.24889 1 1 1 Ti 0.23909 0.58471 0.09024 0 0 0 Ti 0.36002 0.58473 0.28435 1 1 1 Ti 0.73908 0.41804 0.09024 0 0 0 Ti 0.86002 0.41806 0.28435 1 1 1 O 0.63518 0.41804 0.00000 0 0 0 O 0.77165 0.41804 0.19890 1 1 1 O 0.13518 0.58471 0.00000 0 0 0 O 0.27165 0.58470 0.19890 1 1 1 O 0.41852 0.58471 0.04936 0 0 0 O 0.55009 0.58472 0.24981 1 1 1 O 0.91852 0.41804 0.04936 0 0 0 O 0.05009 0.41805 0.24981 1 1 1 O 0.55965 0.41804 0.13112 0 0 0 O 0.70208 0.41806 0.32993 1 1 1 O 0.05965 0.58471 0.13112 0 0 0 O 0.20208 0.58473 0.32993 1 1 1 O 0.77631 0.58471 0.08176 0 0 0 O 0.91188 0.58472 0.29614 1 1 1 O 0.27631 0.41804 0.08176 0 0 0 O 0.41187 0.41806 0.29614 1 1 1 Ti 0.45574 0.75138 0.04088 0 0 0 Ti 0.58876 0.75148 0.24889 1 1 1 Ti 0.95575 0.91804 0.04088 0 0 0 Ti 0.08876 0.91814 0.24889 1 1 1 Ti 0.23909 0.91804 0.09024 0 0 0 Ti 0.36002 0.91806 0.28435 1 1 1 Ti 0.73908 0.75138 0.09024 0 0 0 Ti 0.86002 0.75140 0.28435 1 1 1 O 0.63518 0.75138 0.00000 0 0 0 O 0.77165 0.75137 0.19890 1 1 1 O 0.13518 0.91804 0.00000 0 0 0 O 0.27165 0.91804 0.19890 1 1 1 O 0.41852 0.91804 0.04936 0 0 0 O 0.55009 0.91805 0.24981 1 1 1 O 0.91852 0.75138 0.04936 0 0 0 O 0.05009 0.75138 0.24981 1 1 1 O 0.55965 0.75138 0.13112 0 0 0 O 0.70208 0.75139 0.32993 1 1 1 O 0.05965 0.91804 0.13112 0 0 0 O 0.20208 0.91806 0.32993 1 1 1 O 0.77631 0.91804 0.08176 0 0 0 O 0.91188 0.91806 0.29614 1 1 1 O 0.27631 0.75138 0.08176 0 0 0 O 0.41187 0.75139 0.29614 1 1 1 Pt 0.58876 0.41814 0.41980 1 1 1 K_POINTS gamma thanks for reading vega -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090210/cdf81aad/attachment-0001.htm From lfhuang at theory.issp.ac.cn Tue Feb 10 06:43:51 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 10 Feb 2009 13:43:51 +0800 Subject: [Pw_forum] =?utf-8?q?coordination_system_for_polarizations_in_mat?= =?utf-8?q?dyn=2Emodes?= Message-ID: <20090210054351.27213.qmail@ms.hfcas.ac.cn> Hello everyone: Could anyone tell me what the coordination system for the polarizations (epsilon) of vibrating atoms is in the output file matdyn.modes of matdyn.x? Is it Cartesian coordination(I guess so)? or lattice coordination? I'd like to appreciate any help! Best Wishes! Yours Sincerely L.F.Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090210/115c4569/attachment.htm From alexandra.carvalho at epfl.ch Tue Feb 10 08:01:22 2009 From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch) Date: Tue, 10 Feb 2009 08:01:22 +0100 Subject: [Pw_forum] symmetry operations in PW In-Reply-To: References: Message-ID: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> Dear Manoj, I do not know about the definitions intrinsic to pwscf, but in group theory directed opperations are not allways equivalent. In this case, the rotations about -z and z will be inequivalent if there is no opperation of the group which reverses the sense of the z axis. For example, in the T group there are 8 C3 opperations although there are only four cube diagonals- see Tinkham "Group Theory and Quantum mechanics" 2003 pp 58. Alexandra Carvalho EPFL Lausanne Quoting Manoj Srivastava : > Dear PWSCF users and developers, > I was looking into the code where it calculates symmerty operations for > the group. Now the symmetry operations are defined as ' 90 deg rotation - > cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] > I did not understand the point of defining rotation about z and -z > axis. Is this because of some numerical constraint? Also, there are > elements with 'theta' and '-theta' rotation in the same group. I was just > wondering the reason behind this. Any help will be appreciated. > > Regards, > Manoj Srivastava > Department of Physics > University of Florida > Gainesville, FL, USA. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Feb 10 09:24:12 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Feb 2009 09:24:12 +0100 Subject: [Pw_forum] symmetry operations in PW In-Reply-To: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> References: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> Message-ID: <499139AC.1020808@sissa.it> Dear Manoj and Alexandra, in my limited and maybe naive knowledge of group theory I think that alexandra.carvalho at epfl.ch wrote: > Dear Manoj, > > I do not know about the definitions intrinsic to pwscf, > but in group theory directed opperations are not allways equivalent. Rotation of 90 deg about z and about -z are _different_ operations (in every group to which they belong...). Maybe pwscf uses a naive way to call symmetry operations, but you may call rotation of 90 deg about -z as "rotation of -90 deg about z" so maybe it's more clear (do you know the right hand rule?). If the rotation of 90 deg about z is present, also the rotation of -90 deg about z must be present (from the definition of group), as well as the rotation of 180 deg about z (which you can obtain by applying the rotation of 90 twice). This gives you a C_4 symmetry about the z axis (then if you will add more symmetry operations you will have higher symmetry). > In this case, the rotations about -z and z will be inequivalent > if there is no opperation of the group which reverses the sense of the z axis. I don't understand what do you mean by "equivalent/inequivalent" in this case... Hope it helps, GS > > For example, in the T group there are 8 C3 opperations although there > are only four cube diagonals- see Tinkham "Group Theory and Quantum > mechanics" 2003 pp 58. > > Alexandra Carvalho > EPFL Lausanne > > Quoting Manoj Srivastava : > >> Dear PWSCF users and developers, >> I was looking into the code where it calculates symmerty operations for >> the group. Now the symmetry operations are defined as ' 90 deg rotation - >> cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] >> I did not understand the point of defining rotation about z and -z >> axis. Is this because of some numerical constraint? Also, there are >> elements with 'theta' and '-theta' rotation in the same group. I was just >> wondering the reason behind this. Any help will be appreciated. >> >> Regards, >> Manoj Srivastava >> Department of Physics >> University of Florida >> Gainesville, FL, USA. >> >> _______________________________________________ >> 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 > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From alexandra.carvalho at epfl.ch Tue Feb 10 10:19:33 2009 From: alexandra.carvalho at epfl.ch (alexandra.carvalho at epfl.ch) Date: Tue, 10 Feb 2009 10:19:33 +0100 Subject: [Pw_forum] symmetry operations in PW In-Reply-To: <499139AC.1020808@sissa.it> References: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> <499139AC.1020808@sissa.it> Message-ID: <1234257573.499146a58bb2a@webmail.epfl.ch> Dear Gabriele and Manoj, In fact I should clarify that I meant that rotations about directed axes belong to different classes if the axes are not inverted by symmetry. (The word 'equivalent' was a poor choice...) Alexandra Quoting Gabriele Sclauzero : > Dear Manoj and Alexandra, > > in my limited and maybe naive knowledge of group theory I think that > > alexandra.carvalho at epfl.ch wrote: > > Dear Manoj, > > > > I do not know about the definitions intrinsic to pwscf, > > but in group theory directed opperations are not allways equivalent. > > > Rotation of 90 deg about z and about -z are _different_ operations (in every > group to > which they belong...). Maybe pwscf uses a naive way to call symmetry > operations, but you > may call rotation of 90 deg about -z as "rotation of -90 deg about z" so > maybe it's more > clear (do you know the right hand rule?). > If the rotation of 90 deg about z is present, also the rotation of -90 deg > about z must be > present (from the definition of group), as well as the rotation of 180 deg > about z (which > you can obtain by applying the rotation of 90 twice). This gives you a C_4 > symmetry about > the z axis (then if you will add more symmetry operations you will have > higher symmetry). > > > In this case, the rotations about -z and z will be inequivalent > > if there is no opperation of the group which reverses the sense of the z > axis. > > I don't understand what do you mean by "equivalent/inequivalent" in this > case... > > Hope it helps, > > GS > > > > > For example, in the T group there are 8 C3 opperations although there > > are only four cube diagonals- see Tinkham "Group Theory and Quantum > > mechanics" 2003 pp 58. > > > > Alexandra Carvalho > > EPFL Lausanne > > > > Quoting Manoj Srivastava : > > > >> Dear PWSCF users and developers, > >> I was looking into the code where it calculates symmerty operations for > >> the group. Now the symmetry operations are defined as ' 90 deg rotation - > >> cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] > >> I did not understand the point of defining rotation about z and -z > >> axis. Is this because of some numerical constraint? Also, there are > >> elements with 'theta' and '-theta' rotation in the same group. I was just > >> wondering the reason behind this. Any help will be appreciated. > >> > >> Regards, > >> Manoj Srivastava > >> Department of Physics > >> University of Florida > >> Gainesville, FL, USA. > >> > >> _______________________________________________ > >> 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 > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Feb 10 11:24:28 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Feb 2009 11:24:28 +0100 Subject: [Pw_forum] symmetry operations in PW In-Reply-To: <1234257573.499146a58bb2a@webmail.epfl.ch> References: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> <499139AC.1020808@sissa.it> <1234257573.499146a58bb2a@webmail.epfl.ch> Message-ID: <499155DC.8080701@sissa.it> Dear Alexandra, alexandra.carvalho at epfl.ch wrote: > Dear Gabriele and Manoj, > > In fact I should clarify that I meant that rotations about directed axes belong > to different classes if the axes are not inverted by symmetry. OK, I agree. Anyway when pwscf lists symmetry operations includes all elements of the symmetry group (which may or may not belong to the same class, this is irrelevant at this stage). The important point here is that those two rotations must always appear together, otherwise you will not obtain a group. GS > (The word 'equivalent' was a poor choice...) > > Alexandra > > Quoting Gabriele Sclauzero : > >> Dear Manoj and Alexandra, >> >> in my limited and maybe naive knowledge of group theory I think that >> >> alexandra.carvalho at epfl.ch wrote: >>> Dear Manoj, >>> >>> I do not know about the definitions intrinsic to pwscf, >>> but in group theory directed opperations are not allways equivalent. >> >> Rotation of 90 deg about z and about -z are _different_ operations (in every >> group to >> which they belong...). Maybe pwscf uses a naive way to call symmetry >> operations, but you >> may call rotation of 90 deg about -z as "rotation of -90 deg about z" so >> maybe it's more >> clear (do you know the right hand rule?). >> If the rotation of 90 deg about z is present, also the rotation of -90 deg >> about z must be >> present (from the definition of group), as well as the rotation of 180 deg >> about z (which >> you can obtain by applying the rotation of 90 twice). This gives you a C_4 >> symmetry about >> the z axis (then if you will add more symmetry operations you will have >> higher symmetry). >> >> > In this case, the rotations about -z and z will be inequivalent >>> if there is no opperation of the group which reverses the sense of the z >> axis. >> >> I don't understand what do you mean by "equivalent/inequivalent" in this >> case... >> >> Hope it helps, >> >> GS >> >>> For example, in the T group there are 8 C3 opperations although there >>> are only four cube diagonals- see Tinkham "Group Theory and Quantum >>> mechanics" 2003 pp 58. >>> >>> Alexandra Carvalho >>> EPFL Lausanne >>> >>> Quoting Manoj Srivastava : >>> >>>> Dear PWSCF users and developers, >>>> I was looking into the code where it calculates symmerty operations for >>>> the group. Now the symmetry operations are defined as ' 90 deg rotation - >>>> cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] >>>> I did not understand the point of defining rotation about z and -z >>>> axis. Is this because of some numerical constraint? Also, there are >>>> elements with 'theta' and '-theta' rotation in the same group. I was just >>>> wondering the reason behind this. Any help will be appreciated. >>>> >>>> Regards, >>>> Manoj Srivastava >>>> Department of Physics >>>> University of Florida >>>> Gainesville, FL, USA. >>>> >>>> _______________________________________________ >>>> 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 >>> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From eyvaz_isaev at yahoo.com Tue Feb 10 13:13:44 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 10 Feb 2009 04:13:44 -0800 (PST) Subject: [Pw_forum] coordination system for polarizations in matdyn.modes In-Reply-To: <20090210054351.27213.qmail@ms.hfcas.ac.cn> Message-ID: <734464.38315.qm@web65710.mail.ac4.yahoo.com> Dear Huang, > the polarizations (epsilon) of vibrating atoms is in the output file This looks somewhat strange. I mean mixed "polarization and epsilon". > Is it Cartesian coordination(I guess so)? If you mean displacements in matdyn.modes, it is, you are right. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 2/10/09, lfhuang wrote: > From: lfhuang > Subject: [Pw_forum] coordination system for polarizations in matdyn.modes > To: "pw_forum" > Date: Tuesday, February 10, 2009, 8:43 AM > Hello everyone: > Could anyone tell me what the coordination system for > the polarizations (epsilon) of vibrating atoms is in the > output > file matdyn.modes of matdyn.x? Is it Cartesian > coordination(I guess so)? or lattice coordination? > > I'd like to appreciate any help! > > Best Wishes! > > Yours Sincerely > L.F.Huang > ------ > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials > Sciences, > Instutue of Solid State Physics,the Chinese Academy of > Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn (website of our theory > group) > http://www.issp.ac.cn (website of our institute) > ====================================================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From manoj at phys.ufl.edu Tue Feb 10 16:00:07 2009 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Tue, 10 Feb 2009 10:00:07 -0500 (EST) Subject: [Pw_forum] symmetry operations in PW In-Reply-To: <499155DC.8080701@sissa.it> Message-ID: Dear Alexandra and Gabriele, Thank you for the help. -manoj On Tue, 10 Feb 2009, Gabriele Sclauzero wrote: > Dear Alexandra, > > alexandra.carvalho at epfl.ch wrote: > > Dear Gabriele and Manoj, > > > > In fact I should clarify that I meant that rotations about directed axes belong > > to different classes if the axes are not inverted by symmetry. > > OK, I agree. Anyway when pwscf lists symmetry operations includes all elements of the > symmetry group (which may or may not belong to the same class, this is irrelevant at this > stage). The important point here is that those two rotations must always appear together, > otherwise you will not obtain a group. > > GS > > > > (The word 'equivalent' was a poor choice...) > > > > Alexandra > > > > Quoting Gabriele Sclauzero : > > > >> Dear Manoj and Alexandra, > >> > >> in my limited and maybe naive knowledge of group theory I think that > >> > >> alexandra.carvalho at epfl.ch wrote: > >>> Dear Manoj, > >>> > >>> I do not know about the definitions intrinsic to pwscf, > >>> but in group theory directed opperations are not allways equivalent. > >> > >> Rotation of 90 deg about z and about -z are _different_ operations (in every > >> group to > >> which they belong...). Maybe pwscf uses a naive way to call symmetry > >> operations, but you > >> may call rotation of 90 deg about -z as "rotation of -90 deg about z" so > >> maybe it's more > >> clear (do you know the right hand rule?). > >> If the rotation of 90 deg about z is present, also the rotation of -90 deg > >> about z must be > >> present (from the definition of group), as well as the rotation of 180 deg > >> about z (which > >> you can obtain by applying the rotation of 90 twice). This gives you a C_4 > >> symmetry about > >> the z axis (then if you will add more symmetry operations you will have > >> higher symmetry). > >> > >> > In this case, the rotations about -z and z will be inequivalent > >>> if there is no opperation of the group which reverses the sense of the z > >> axis. > >> > >> I don't understand what do you mean by "equivalent/inequivalent" in this > >> case... > >> > >> Hope it helps, > >> > >> GS > >> > >>> For example, in the T group there are 8 C3 opperations although there > >>> are only four cube diagonals- see Tinkham "Group Theory and Quantum > >>> mechanics" 2003 pp 58. > >>> > >>> Alexandra Carvalho > >>> EPFL Lausanne > >>> > >>> Quoting Manoj Srivastava : > >>> > >>>> Dear PWSCF users and developers, > >>>> I was looking into the code where it calculates symmerty operations for > >>>> the group. Now the symmetry operations are defined as ' 90 deg rotation - > >>>> cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] > >>>> I did not understand the point of defining rotation about z and -z > >>>> axis. Is this because of some numerical constraint? Also, there are > >>>> elements with 'theta' and '-theta' rotation in the same group. I was just > >>>> wondering the reason behind this. Any help will be appreciated. > >>>> > >>>> Regards, > >>>> Manoj Srivastava > >>>> Department of Physics > >>>> University of Florida > >>>> Gainesville, FL, USA. > >>>> > >>>> _______________________________________________ > >>>> 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 > >>> > >> -- > >> > >> > >> o ------------------------------------------------ o > >> | Gabriele Sclauzero, PhD Student | > >> | c/o: SISSA & CNR-INFM Democritos, | > >> | via Beirut 2-4, 34014 Trieste (Italy) | > >> | email: sclauzer at sissa.it | > >> | phone: +39 040 3787 511 | > >> | skype: gurlonotturno | > >> o ------------------------------------------------ o > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From aryjunior at gmail.com Tue Feb 10 18:07:16 2009 From: aryjunior at gmail.com (Ary Junior) Date: Tue, 10 Feb 2009 15:07:16 -0200 Subject: [Pw_forum] Problems with phonon calculation Message-ID: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> Hello, I have a very large system and I must do a phonon calculation. This calculation takes months, so I want to do with only few atoms. But the variable nat_todo seems to not work. When I enable the variable for a little system, it only makes the calculation ph.x to the atoms that I ask, but with my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it continues making 3*n representations. Thanks very much! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090210/3071b678/attachment.htm From baroni at sissa.it Tue Feb 10 19:46:00 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 10 Feb 2009 19:46:00 +0100 Subject: [Pw_forum] symmetry operations in PW In-Reply-To: <1234257573.499146a58bb2a@webmail.epfl.ch> References: <20090210080122.5cad5i4lu88kgk8o@webmail.epfl.ch> <499139AC.1020808@sissa.it> <1234257573.499146a58bb2a@webmail.epfl.ch> Message-ID: <0119B836-D88B-4500-BBDE-74C2F42149E5@sissa.it> Alexandra: are you by any chance a student/collaborator of Alfonso's? One of the few persons that I know, still able to teach group theory, and the one who taught me long ago, when group theory was not yet considered archeo-physics in our community. Cheers - Stefano On Feb 10, 2009, at 10:19 AM, alexandra.carvalho at epfl.ch wrote: > Dear Gabriele and Manoj, > > In fact I should clarify that I meant that rotations about directed > axes belong > to different classes if the axes are not inverted by symmetry. > (The word 'equivalent' was a poor choice...) > > Alexandra > > Quoting Gabriele Sclauzero : > >> Dear Manoj and Alexandra, >> >> in my limited and maybe naive knowledge of group theory I think >> that >> >> alexandra.carvalho at epfl.ch wrote: >>> Dear Manoj, >>> >>> I do not know about the definitions intrinsic to pwscf, >>> but in group theory directed opperations are not allways equivalent. >> >> >> Rotation of 90 deg about z and about -z are _different_ operations >> (in every >> group to >> which they belong...). Maybe pwscf uses a naive way to call symmetry >> operations, but you >> may call rotation of 90 deg about -z as "rotation of -90 deg about >> z" so >> maybe it's more >> clear (do you know the right hand rule?). >> If the rotation of 90 deg about z is present, also the rotation of >> -90 deg >> about z must be >> present (from the definition of group), as well as the rotation of >> 180 deg >> about z (which >> you can obtain by applying the rotation of 90 twice). This gives >> you a C_4 >> symmetry about >> the z axis (then if you will add more symmetry operations you will >> have >> higher symmetry). >> >>> In this case, the rotations about -z and z will be inequivalent >>> if there is no opperation of the group which reverses the sense of >>> the z >> axis. >> >> I don't understand what do you mean by "equivalent/inequivalent" in >> this >> case... >> >> Hope it helps, >> >> GS >> >>> >>> For example, in the T group there are 8 C3 opperations although >>> there >>> are only four cube diagonals- see Tinkham "Group Theory and Quantum >>> mechanics" 2003 pp 58. >>> >>> Alexandra Carvalho >>> EPFL Lausanne >>> >>> Quoting Manoj Srivastava : >>> >>>> Dear PWSCF users and developers, >>>> I was looking into the code where it calculates symmerty >>>> operations for >>>> the group. Now the symmetry operations are defined as ' 90 deg >>>> rotation - >>>> cart. axis [0,0,-1]', & ' 90 deg rotation - cart. axis [0,0,1] >>>> I did not understand the point of defining rotation about z and -z >>>> axis. Is this because of some numerical constraint? Also, there are >>>> elements with 'theta' and '-theta' rotation in the same group. I >>>> was just >>>> wondering the reason behind this. Any help will be appreciated. >>>> >>>> Regards, >>>> Manoj Srivastava >>>> Department of Physics >>>> University of Florida >>>> Gainesville, FL, USA. >>>> >>>> _______________________________________________ >>>> 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 >>> >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090210/dfbb3b08/attachment-0001.htm From andrewlee.cp at gmail.com Wed Feb 11 02:51:12 2009 From: andrewlee.cp at gmail.com (Andrew Lee) Date: Wed, 11 Feb 2009 09:51:12 +0800 Subject: [Pw_forum] Problems with phonon calculation In-Reply-To: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> References: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> Message-ID: I have a related question. With the current version of PWSCF, is it possible only to do the electric field perturbation? If possible, how to setup the input parameters? Thanks Best, Zhenyu University of Science and Technology of China Hefei, Anhui 230026, China On Wed, Feb 11, 2009 at 1:07 AM, Ary Junior wrote: > Hello, > > I have a very large system and I must do a phonon calculation. This > calculation takes months, so I want to do with only few atoms. But the > variable nat_todo seems to not work. When I enable the variable for a little > system, it only makes the calculation ph.x to the atoms that I ask, but with > my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it > continues making 3*n representations. > > Thanks very much! > > _______________________________________________ > 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/20090211/c68e1774/attachment.htm From lfhuang at theory.issp.ac.cn Wed Feb 11 07:28:41 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 11 Feb 2009 14:28:41 +0800 Subject: [Pw_forum] =?utf-8?q?coordination_system_for_polarizations_in_mat?= =?utf-8?q?dyn=2Emodes?= Message-ID: <20090211062841.14569.qmail@ms.hfcas.ac.cn> Dear prof. Isaev: Thank you for your help and correction! Yes I had mixed "polarization" and "epsilon" due to not taking the designation "polarization" seriously before. Thank you very much! Best Wishes! Yours Sincerely L.F.Huang > Date: Tue, 10 Feb 2009 04:13:44 -0800 (PST) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] coordination system for polarizations in > matdyn.modes > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=utf-8 > > Dear Huang, > > > the polarizations (epsilon) of vibrating atoms is in the output file > > This looks somewhat strange. I mean mixed "polarization and epsilon". > > > Is it Cartesian coordination(I guess so)? > > If you mean displacements in matdyn.modes, it is, you are right. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Tue, 2/10/09, lfhuang wrote: > > > From: lfhuang > > Subject: [Pw_forum] coordination system for polarizations in matdyn.modes > > To: "pw_forum" > > Date: Tuesday, February 10, 2009, 8:43 AM > > Hello everyone: > > Could anyone tell me what the coordination system for > > the polarizations (epsilon) of vibrating atoms is in the > > output > > file matdyn.modes of matdyn.x? Is it Cartesian > > coordination(I guess so)? or lattice coordination? > > > > I'd like to appreciate any help! > > > > Best Wishes! > > > > Yours Sincerely > > L.F.Huang > > ------ > > ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/e590bcb0/attachment.htm From lanhaiping at gmail.com Wed Feb 11 12:49:40 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 11 Feb 2009 19:49:40 +0800 Subject: [Pw_forum] Problems with phonon calculation In-Reply-To: References: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> Message-ID: Hi, Zhenyu, I think you may try to run the $espresso/example/example30, and take a look at README. Regards, Hai-Ping On Wed, Feb 11, 2009 at 9:51 AM, Andrew Lee wrote: > I have a related question. With the current version of PWSCF, is it > possible only to do the electric field perturbation? If possible, how to > setup the input parameters? Thanks > Best, > Zhenyu > > University of Science and Technology of China > Hefei, Anhui 230026, China > > On Wed, Feb 11, 2009 at 1:07 AM, Ary Junior wrote: > >> Hello, >> >> I have a very large system and I must do a phonon calculation. This >> calculation takes months, so I want to do with only few atoms. But the >> variable nat_todo seems to not work. When I enable the variable for a little >> system, it only makes the calculation ph.x to the atoms that I ask, but with >> my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it >> continues making 3*n representations. >> >> Thanks very much! >> >> _______________________________________________ >> 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 > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/886892b2/attachment.htm From lanhaiping at gmail.com Wed Feb 11 12:51:49 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 11 Feb 2009 19:51:49 +0800 Subject: [Pw_forum] Problems with phonon calculation In-Reply-To: References: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> Message-ID: Sorry, I just mis-typed. example31 should be the script for finite-electric field scheme implemented in PWSCF. regards, On Wed, Feb 11, 2009 at 7:49 PM, lan haiping wrote: > Hi, Zhenyu, > I think you may try to run the $espresso/example/example30, and take a look > at README. > > Regards, > Hai-Ping > > > On Wed, Feb 11, 2009 at 9:51 AM, Andrew Lee wrote: > >> I have a related question. With the current version of PWSCF, is it >> possible only to do the electric field perturbation? If possible, how to >> setup the input parameters? Thanks >> Best, >> Zhenyu >> >> University of Science and Technology of China >> Hefei, Anhui 230026, China >> >> On Wed, Feb 11, 2009 at 1:07 AM, Ary Junior wrote: >> >>> Hello, >>> >>> I have a very large system and I must do a phonon calculation. This >>> calculation takes months, so I want to do with only few atoms. But the >>> variable nat_todo seems to not work. When I enable the variable for a little >>> system, it only makes the calculation ph.x to the atoms that I ask, but with >>> my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it >>> continues making 3*n representations. >>> >>> Thanks very much! >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/73d31ac2/attachment.htm From davidfarrell2008 at u.northwestern.edu Wed Feb 11 15:11:43 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Wed, 11 Feb 2009 08:11:43 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <4992D013.9030905@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> Message-ID: <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> Yes, but only just in the last few days. I also CC'd this to the PWSCF list. I travelled out to a meeting at Argonne's LCF (where the BG is hosted), and was able to begin to work more closely with Nichols Romero on the issue. I was able to try the following systems (a pw BOMD run on Li4BN3H10 crystal with an initial temperature and periodic boundaries, no vacuum in the supercell) all run in vn mode. 432 atoms (960 electrons) on 1024, 4096, 8192 procs 576 atoms (1280 electrons) on 1024, 2048, 4096 procs 864 atoms (1920 electrons) on 1024, 2048, 4096 procs What I found is (with with -ntg 8 and -ndiag 1): - In all cases, the 1024 proc case was able to get into at the electronic loop and complete at least one SCF step (before the runtime got too long and it was killed) - In all cases, the runs on greater than 1024 procs died before outputing SCF step data. The complaint found in the stderr files was the 'from n_plane_waves : error # 1' and 'no PWs!' error. In the 8192 proc case (ntg 64 ndiag 1), the error was 'wrong ngm' - but I think that is actually the same error (data spread too thin) - just manifest in a different way. - All of the systems on all processors had the following complaints in the beginning of stdout: Iterative solution of the eigenvalue problem Too few electrons for parallel algorithm we need at least as many bands as SQRT(nproc) a serial algorithm will be used Message from routine data_structure: some processors have no planes Message from routine data_structure: some processors have no smooth planes .... Regardless of if they were able to successfully enter the SCF steps or not. The error about the number of bands I think may be erroneous - but would have to dig through the code a bit more to be sure. - ndiag > 1 doesn't work in any case is pointing toward the idea that the parallel orthogonalization isn't working. The error spat out are like this (from the 432 atom case on 1024 procs with -ntg 8 -ndiag 128: from pdpotf : error # 1 problems computing cholesky decomposition I can try a 1008 atom case (2240 electrons) and the above system as a 1152 atom case (2560 electrons) - I have a feeling that may break down because of memory issues even at 1024 procs, but I have a feeling getting to the bottom of why the above cases fail so spectacularly will be required if I want to get to a larger system on more procs. I also haven't touched the taskgroup thing to see what, if any, trouble that is causing. I also tried the above with the CVS version with SCALAPACK and seemed to get the same behavior. If I am able to get to run say ~2500-3000 electrons on 4192 cores, I will consider that a win. But right now, it seems that 1024 is about as high as I can go. Dave On Feb 11, 2009, at 7:18 AM, Paolo Giannozzi wrote: > Hi, any news on your BG problem? Paolo > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/284be401/attachment.htm From mjfmartins at ice.ufjf.br Wed Feb 11 17:10:57 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Wed, 11 Feb 2009 14:10:57 -0200 Subject: [Pw_forum] Problems with phonon calculation In-Reply-To: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> References: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> Message-ID: <85d7d5fd0902110810k629dda5bj747036d7c2bf51e5@mail.gmail.com> Ary, Your scf calculation is configured with the variable "nosym = . false ". Change, set true. Mateus. 2009/2/10 Ary Junior > Hello, > > I have a very large system and I must do a phonon calculation. This > calculation takes months, so I want to do with only few atoms. But the > variable nat_todo seems to not work. When I enable the variable for a little > system, it only makes the calculation ph.x to the atoms that I ask, but with > my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it > continues making 3*n representations. > > Thanks very much! > > _______________________________________________ > 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/20090211/1ee69585/attachment.htm From giannozz at democritos.it Wed Feb 11 19:00:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 11 Feb 2009 19:00:05 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> Message-ID: <49931225.3010904@democritos.it> David Farrell wrote: > 432 atoms (960 electrons) on 1024, 4096, 8192 procs > 576 atoms (1280 electrons) on 1024, 2048, 4096 procs > 864 atoms (1920 electrons) on 1024, 2048, 4096 procs I recently run a test (with CP) of 838 atoms and 2311 electrons on as little as 64 processors (and I think it would also fit into 32 processors). 8192 processors for 432 atoms is way off mark, unless you can use other parallelization levels. > - ndiag > 1 doesn't work in any case is pointing toward the idea that > the parallel orthogonalization isn't working. last time I tried on a BG, it was working (after I fixed a problem, which was on the BG side, not on Q-E side). Please provide a test job (the smaller you have, of course) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Wed Feb 11 20:16:30 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Wed, 11 Feb 2009 13:16:30 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <4992D013.9030905@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> Message-ID: <9F1AF4DF-3376-4771-A664-FB0404E14040@u.northwestern.edu> I was able to make a bit more progress - at least in the direction of seeing what is breaking as I get to larger numbers of electrons. It seems to be mainly due to a number of large allocates which all of the processes carry out. I don't yet know enough about the code to know, but I suspect these aren't all necessary. I have found 2 that have caused problems in different runs. The first was the problem that Axel pointed out earlier in this thread, the next is this one: In my periodic bulk case (1156 atoms, 2560 electrons), running on 1024 procs in vn mode (256 nodes, 512 MB RAM/process): "add_vuspsi.f90", line 78: 1525-108 Error encountered while attempting to allocate a data object. The program will stop. - at this line, there is an allocate that is the size of: (number of projectors for the atom types) x (number of states).... (so something like 4736 * 1536 ... ~55 MB) which seems to be kicking it over the limit. This prevented the system from getting to where it would ouput info about the SCF steps. My memory report output for this run looks like: Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 3.35 Mb ( 143,1536) NL pseudopotentials 10.33 Mb ( 143,4736) Each V/rho on FFT grid 0.78 Mb ( 51200) Each G-vector array 0.01 Mb ( 1006) G-vector shells 0.00 Mb ( 488) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 6.70 Mb ( 143,6144) Each subspace H/S matrix 288.00 Mb ( 6144,6144) Each matrix 55.50 Mb ( 4736,1536) Arrays for rho mixing 6.25 Mb ( 51200, 8) So I am guessing that something just isn't getting split up right or at least not very efficiently - probably the Hamiltonian and Overlap matrices as a start. The above case in dual mode (512 nodes, 1 GB RAM/process) was able to get into the SCF stages, and do some output: Self-consistent Calculation iteration # 1 ecut= 38.22 Ry beta=0.70 Davidson diagonalization with overlap but then died with the following memory-related error: "regterg.f90", line 108: 1525-108 Error encountered while attempting to allocate a data object. The program will stop. Which appears to be caused by an allocation that looks like the # planewaves * # states (or some subset of them). I guess this isn't really a surprise to you guys, and I am not really sure what to do about it, but at least I am now getting some idea of what is causing the breakdown. Dave On Feb 11, 2009, at 7:18 AM, Paolo Giannozzi wrote: > Hi, any news on your BG problem? Paolo > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/cabaa17c/attachment.htm From lshulenburger at ciw.edu Wed Feb 11 20:23:51 2009 From: lshulenburger at ciw.edu (Luke Shulenburger) Date: Wed, 11 Feb 2009 14:23:51 -0500 (EST) Subject: [Pw_forum] i/o question Message-ID: <54343.10.1.20.105.1234380231.squirrel@mail.ciw.edu> Hello, I'm using pwscf to generate wavefunctions for quantum Monte Carlo calculations and have run into an I/O oddity I wanted to solicit advice about. My calculations proceed as follows: scf calculation -> nscf calculation with specific k-points -> pw2casino for output. Thinking that the nscf calculation would need significantly fewer resources than the scf, I used 64 processors for the scf, 16 for the nscf and than 1 for pw2casino (I need everything written to a single file at the end). In order for this to work, I specified wf_collect=.true. in both the scf and nscf input files. Both of those tasks completed without incident but pw2casino died with an I/O error (unable to read file). However, I rerun everything using the same number of processors for scf and nscf, and only having wf_collect=.true. in the second step, everything runs perfectly. Looking into the output directory I notice two things. When I have wf_collect in both files, I still end up with 64 .wfc* files in the directory as well as having directories for all of the k-points from the scf calculation in the outdir/prefix.save/ directory. Is it possible this is confusing pw2casino? Is there some way this problem could be remedied or am I making some logical mistake with the way I'm attempting to use the code? Thanks, Luke Shulenburger Geophysical Laboratory Carnegie Institution of Washington (lshulenburger at ciw.edu) From davidfarrell2008 at u.northwestern.edu Wed Feb 11 20:57:36 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Wed, 11 Feb 2009 13:57:36 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <49931225.3010904@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> Message-ID: <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> >> - ndiag > 1 doesn't work in any case is pointing toward the idea >> that the parallel orthogonalization isn't working. > > last time I tried on a BG, it was working (after I fixed a problem, > which was on the BG side, not on Q-E side). Please provide a test > job (the smaller you have, of course) I was just looking through the code and the errors I got, and noticed in ptoolkit.f90 several places where there appears a variable INFO and info - in the 'problems with cholesky' errors, the loops that execute them seem to have these mixed to my eyes. For example: IF( ( myrow == ( jb - 1 ) ) .AND. ( mycol == ( jb - 1 ) ) ) THEN CALL DPOTRF( 'L', jnr, sll, ldx, INFO ) IF( info /= 0 ) & CALL errore( " pdpotf ", " problems computing cholesky decomposition ", ABS( info ) ) END IF Now, I am not too familiar with fortran - but I would suspect this could cause some issues with this depending on compiler options. Also, there is a declaration for both INFO and info in the file. I am trying to change these to be consistent, to see if it makes a difference. Dave David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/78149ae3/attachment.htm From giannozz at democritos.it Wed Feb 11 21:03:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 11 Feb 2009 21:03:42 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> Message-ID: <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> On Feb 11, 2009, at 20:57 , David Farrell wrote: > I was just looking through the code and the errors I got, and > noticed in > ptoolkit.f90 several places where there appears a variable INFO and > info BG is a stupid machine, but not THAT stupid. Fortran is case- independent. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Wed Feb 11 21:08:14 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Wed, 11 Feb 2009 14:08:14 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> Message-ID: <256C6697-0817-4345-8282-D058F9F74100@u.northwestern.edu> Indeed it isn't - so that was a dead end. Guess I'll have to look into why the call to the lapack lib is failing. On Feb 11, 2009, at 2:03 PM, Paolo Giannozzi wrote: > > On Feb 11, 2009, at 20:57 , David Farrell wrote: > >> I was just looking through the code and the errors I got, and >> noticed in >> ptoolkit.f90 several places where there appears a variable INFO and >> info > > BG is a stupid machine, but not THAT stupid. Fortran is case- > independent. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/789170ef/attachment-0001.htm From w2agz at pacbell.net Thu Feb 12 04:58:44 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 11 Feb 2009 19:58:44 -0800 Subject: [Pw_forum] Format of charge-density.dat Message-ID: <00b801c98cc6$348a9380$9d9fba80$@net> I realize charge-density.dat is stored in iotk binary format and the reasons why. But is there any documentation illuminating the layout of the file or how to access the data stored therein? I've poked around in the source code of chden and electrons but it's not terribly obvious how they load the data, which I assume is a necessary task somewhere in these two routines.at least not in four or five minutes of manual scanning. All I really want to do is write a (hopefully small) Fortran routine to load data from charge-density.dat into a four (x, y, z, rho) by number-of-points array. Maybe there's even an iotk subroutine someone has laying around to do just that. BTW, I assume the units are electrons/cubic-au as a function of x, y, z? Best to all, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090211/0b91777f/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Feb 12 05:27:54 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 11 Feb 2009 23:27:54 -0500 (EST) Subject: [Pw_forum] Format of charge-density.dat In-Reply-To: <00b801c98cc6$348a9380$9d9fba80$@net> References: <00b801c98cc6$348a9380$9d9fba80$@net> Message-ID: On Wed, 11 Feb 2009, Paul M. Grant wrote: PG> I realize charge-density.dat is stored in iotk binary format and the reasons PG> why. But is there any documentation illuminating the layout of the file or PG> how to access the data stored therein? I've poked around in the source code PG> of chden and electrons but it's not terribly obvious how they load the data, PG> which I assume is a necessary task somewhere in these two routines.at least PG> not in four or five minutes of manual scanning. All I really want to do is PG> write a (hopefully small) Fortran routine to load data from PG> charge-density.dat into a four (x, y, z, rho) by number-of-points array. PG> Maybe there's even an iotk subroutine someone has laying around to do just PG> that. paul, there is an example code, qexml.f90 (check out qexml_write/read_rho()) that should demonstrate how to read iotk files. not sure whether it still works, though. it has not been touched in a while. if you are more concerned about a fast result rather than performance, why don't you use pp.x to convert it into (gaussian) .cube format, which is plain text and easier to read into fortran. the way it is usually read is that you just have one 3-dim array, with the grid vector index positions as the indices. if you give me a hint about what exactly you're after, perhaps i can give you a more specific suggestion. PG> BTW, I assume the units are electrons/cubic-au as a function of x, y, z? right, at least that is what i remember, summing over the indivdual rho entries and multiplying with the volume of a single voxel should yield the total number of electrons. cheers, axel. PG> PG> Best to all, -Paul PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford (2005-2008) PG> EPRI Science Fellow (Retired) PG> IBM Research Staff Member Emeritus PG> w2agz at pacbell.net PG> http://www.w2agz.com PG> PG> PG> PG> PG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From w2agz at pacbell.net Thu Feb 12 06:04:08 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 11 Feb 2009 21:04:08 -0800 Subject: [Pw_forum] Format of charge-density.dat In-Reply-To: References: <00b801c98cc6$348a9380$9d9fba80$@net> Message-ID: <012d01c98ccf$5632d2a0$029877e0$@net> Hey Axel, thanks. My agenda is really to get rho(r) into an ascii file of size 4xn that I can load it as an array into APL2 to play around with...I thought the Fortran description would be more familiar to the PWscf community. I'm playing around with coding some PP apps in APL2. I'll look into pp.x as you suggest as a way to get such a file. It's 9 PM out here in California, which means midnight on your part of the globe...do you ever sleep? Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Wednesday, February 11, 2009 8:28 PM To: Paul M. Grant Cc: 'PWSCF Forum' Subject: Re: [Pw_forum] Format of charge-density.dat On Wed, 11 Feb 2009, Paul M. Grant wrote: PG> I realize charge-density.dat is stored in iotk binary format and the reasons PG> why. But is there any documentation illuminating the layout of the file or PG> how to access the data stored therein? I've poked around in the source code PG> of chden and electrons but it's not terribly obvious how they load the data, PG> which I assume is a necessary task somewhere in these two routines.at least PG> not in four or five minutes of manual scanning. All I really want to do is PG> write a (hopefully small) Fortran routine to load data from PG> charge-density.dat into a four (x, y, z, rho) by number-of-points array. PG> Maybe there's even an iotk subroutine someone has laying around to do just PG> that. paul, there is an example code, qexml.f90 (check out qexml_write/read_rho()) that should demonstrate how to read iotk files. not sure whether it still works, though. it has not been touched in a while. if you are more concerned about a fast result rather than performance, why don't you use pp.x to convert it into (gaussian) .cube format, which is plain text and easier to read into fortran. the way it is usually read is that you just have one 3-dim array, with the grid vector index positions as the indices. if you give me a hint about what exactly you're after, perhaps i can give you a more specific suggestion. PG> BTW, I assume the units are electrons/cubic-au as a function of x, y, z? right, at least that is what i remember, summing over the indivdual rho entries and multiplying with the volume of a single voxel should yield the total number of electrons. cheers, axel. PG> PG> Best to all, -Paul PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford (2005-2008) PG> EPRI Science Fellow (Retired) PG> IBM Research Staff Member Emeritus PG> w2agz at pacbell.net PG> http://www.w2agz.com PG> PG> PG> PG> PG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From paulatto at sissa.it Thu Feb 12 09:20:12 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 12 Feb 2009 09:20:12 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <256C6697-0817-4345-8282-D058F9F74100@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> <256C6697-0817-4345-8282-D058F9F74100@u.northwestern.edu> Message-ID: On Wed, 11 Feb 2009 21:08:14 +0100, David Farrell wrote: > Indeed it isn't - so that was a dead end. Guess I'll have to look into > why the call to the lapack lib is failing. That subroutine is usually where error originated in the most remotes parts of the code finally emerge. There are dozens of possible errors that will not cause any apparent problem for a while, until the errors accumulate enough to break positive definiteness of the matrix. Some possible reasons (in not very strict order of plausibility): 1. especially with USPP, atoms too close together will break several approximations, this may happen after a few ionic optimization iterations 2. bad pseudopotential, with a ghost state at high energy 3. smearing is too low, especially with mexfeld-paxton or marzari-vanderbilt smearings 4. cutoff is too low 5. bad interpolation of wavefunctions over ionic dynamic steps 6. some error in the algorithm cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sclauzer at sissa.it Thu Feb 12 09:44:02 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 Feb 2009 09:44:02 +0100 Subject: [Pw_forum] i/o question In-Reply-To: <54343.10.1.20.105.1234380231.squirrel@mail.ciw.edu> References: <54343.10.1.20.105.1234380231.squirrel@mail.ciw.edu> Message-ID: <4993E152.2070401@sissa.it> Hi Luke, Luke Shulenburger wrote: > Hello, > > I'm using pwscf to generate wavefunctions for quantum Monte Carlo > calculations and have run into an I/O oddity I wanted to solicit advice > about. My calculations proceed as follows: scf calculation -> nscf > calculation with specific k-points -> pw2casino for output. Thinking that > the nscf calculation would need significantly fewer resources than the > scf, I used 64 processors for the scf, 16 for the nscf and than 1 for > pw2casino (I need everything written to a single file at the end). In > order for this to work, I specified wf_collect=.true. in both the scf and > nscf input files. Both of those tasks completed without incident but > pw2casino died with an I/O error (unable to read file). Which file? Can you try to identify the missing file? And which version of QE are you using? > However, I rerun > everything using the same number of processors for scf and nscf, and only > having wf_collect=.true. in the second step, everything runs perfectly. > > Looking into the output directory I notice two things. When I have > wf_collect in both files, I still end up with 64 .wfc* files in the > directory as well as having directories for all of the k-points from the > scf calculation in the outdir/prefix.save/ directory. I don't know if all the *.wfc?? files will be deleted when you specify wf_collect=.TRUE. (I guess so, after having a look to PW/stop_run.f90), but you should have the eigenvectors (i.e. the wavefunction coefficients) for each k-point stored in the corresponding directory as a evc.dat file. Those should be enough to restart/postproc the run (if it ended smoothly), since pw2casino (as postproc) uses pw subroutines to read the restart files and fill the variables. GS > Is it possible this > is confusing pw2casino? Is there some way this problem could be remedied > or am I making some logical mistake with the way I'm attempting to use the > code? > > Thanks, > > Luke Shulenburger > Geophysical Laboratory > Carnegie Institution of Washington > (lshulenburger at ciw.edu) > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Thu Feb 12 09:52:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 09:52:49 +0100 Subject: [Pw_forum] i/o question In-Reply-To: <54343.10.1.20.105.1234380231.squirrel@mail.ciw.edu> References: <54343.10.1.20.105.1234380231.squirrel@mail.ciw.edu> Message-ID: On Feb 11, 2009, at 20:23 , Luke Shulenburger wrote: > Is there some way this problem could be remedied before trying to remedy a problem, one has to be sure that the problem exists and is reproducible. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Feb 12 09:54:15 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 09:54:15 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> <256C6697-0817-4345-8282-D058F9F74100@u.northwestern.edu> Message-ID: <33E6C922-9583-488C-8F1E-3C3B35BB0016@democritos.it> On Feb 12, 2009, at 9:20 , Lorenzo Paulatto wrote: > That subroutine is usually where error originated in the most > remotes parts of the code finally emerge. There are dozens of > possible errors that will not cause any apparent problem for a > while, until the errors accumulate enough to break positive > definiteness of the matrix. this is a different case: if the subspace diagonalization it works on one processor, it has to work on more that one processor as well Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From zhukov at ihim.uran.ru Thu Feb 12 09:59:33 2009 From: zhukov at ihim.uran.ru (Vladlen Zhukov Windows) Date: Thu, 12 Feb 2009 13:59:33 +0500 Subject: [Pw_forum] Non-standard band populations in semiconductors Message-ID: <001601c98cf0$38f1cc20$2b88a8c0@ZHUKOV> Dear all, It happens sometimes to have a non-standard population of bands calculated with Espresso. E.g., in the Journ. Phys. Cond. Matter, 19 (2007) 425218 the conductivity band of semiconducting LiH was populated with a small number of doping electrons, VCA approximation. My case is that I need, within non-scf scheme, a hole in the valence band of a semiconductor and electron in the conductivity band. I wonder if there is a simple tool in Espresso to perform such trick? Vladlen P. Zhukov, Prof. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/437db3db/attachment.htm From aryjunior at gmail.com Thu Feb 12 12:46:48 2009 From: aryjunior at gmail.com (Ary Junior) Date: Thu, 12 Feb 2009 09:46:48 -0200 Subject: [Pw_forum] Problems with phonon calculation In-Reply-To: <85d7d5fd0902110810k629dda5bj747036d7c2bf51e5@mail.gmail.com> References: <4c9c61c20902100907y53fbc7fekc958395dc5b42673@mail.gmail.com> <85d7d5fd0902110810k629dda5bj747036d7c2bf51e5@mail.gmail.com> Message-ID: <4c9c61c20902120346r4a3c914bm3b0fd0e6abaafe84@mail.gmail.com> Hi Mateus, it works!!! Thank you very much!!! Ary Junior On Wed, Feb 11, 2009 at 2:10 PM, MATEUS JOS? FERNANDES MARTINS < mjfmartins at ice.ufjf.br> wrote: > Ary, > > Your scf calculation is configured with the variable "nosym = . false ". > Change, set true. > > Mateus. > > 2009/2/10 Ary Junior > >> Hello, >> >> I have a very large system and I must do a phonon calculation. This >> calculation takes months, so I want to do with only few atoms. But the >> variable nat_todo seems to not work. When I enable the variable for a little >> system, it only makes the calculation ph.x to the atoms that I ask, but with >> my system of interest, no matter if I insert nat_todo, nrapp or maxirr, it >> continues making 3*n representations. >> >> Thanks very much! >> >> _______________________________________________ >> 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/20090212/542b21d2/attachment.htm From davidfarrell2008 at u.northwestern.edu Thu Feb 12 13:44:54 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 06:44:54 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <33E6C922-9583-488C-8F1E-3C3B35BB0016@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <639DAFE1-CA3F-4ECE-89E1-589D81CDE012@u.northwestern.edu> <8B8F9AD6-D228-416A-86C7-6D8B238F67C9@democritos.it> <256C6697-0817-4345-8282-D058F9F74100@u.northwestern.edu> <33E6C922-9583-488C-8F1E-3C3B35BB0016@democritos.it> Message-ID: <8139909F-2400-4E18-AD25-DA7B24D8B949@u.northwestern.edu> Indeed - the serial diagonalization cases seem to be fine. Paolo, did you get the files I sent over yesterday? I think the list may have bounced them - but I had CC'd you on it. Dave On Feb 12, 2009, at 2:54 AM, Paolo Giannozzi wrote: > > On Feb 12, 2009, at 9:20 , Lorenzo Paulatto wrote: > >> That subroutine is usually where error originated in the most >> remotes parts of the code finally emerge. There are dozens of >> possible errors that will not cause any apparent problem for a >> while, until the errors accumulate enough to break positive >> definiteness of the matrix. > > this is a different case: if the subspace diagonalization it works on > one processor, > it has to work on more that one processor as well > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/5870eb29/attachment.htm From giannozz at democritos.it Thu Feb 12 13:53:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 13:53:23 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> Message-ID: <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> On Feb 11, 2009, at 19:41 , David Farrell wrote: > Let me know if the attachment doesn't make it through it didn't to the mailing list (max attachment size 40kB), but I received it. Attached is what I got (for a scf calculation) on a cray xt5. Apart from the bogus values of planes printed in the output, everything else seems ok, including parallel subspace diagonalization (scalapack) on 121 processors. Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: test432.out.gz Type: application/x-gzip Size: 10672 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090212/8f96970e/attachment-0001.bin -------------- next part -------------- --- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Thu Feb 12 14:01:54 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 07:01:54 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> Message-ID: <2A1F9F3D-9522-461F-8FFF-C048F9295DE6@u.northwestern.edu> OK - I have been working with version 4.0.4 of pw that has been compiled with only the internal espresso libraries (just to check that it isn't an IBM library thing). The errors still appear. I am trying my 'simple' periodic 1152 atom cell (a larger version of the one I sent you) on as few processors as I can, to see if that helps anything. The behavior at 128 and 512 was the same as 1024, dying in the cholesky decomposition routine. Dave On Feb 12, 2009, at 6:53 AM, Paolo Giannozzi wrote: > On Feb 11, 2009, at 19:41 , David Farrell wrote: > >> Let me know if the attachment doesn't make it through > > it didn't to the mailing list (max attachment size 40kB), but > I received it. Attached is what I got (for a scf calculation) on > a cray xt5. Apart from the bogus values of planes printed in > the output, everything else seems ok, including parallel > subspace diagonalization (scalapack) on 121 processors. > > Paolo > > > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/cf1677a1/attachment.htm From giannozz at democritos.it Thu Feb 12 14:33:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 14:33:42 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <2A1F9F3D-9522-461F-8FFF-C048F9295DE6@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> <2A1F9F3D-9522-461F-8FFF-C048F9295DE6@u.northwestern.edu> Message-ID: <25DD2350-31A0-4E75-882D-A00575D066E3@democritos.it> On Feb 12, 2009, at 14:01 , David Farrell wrote: > OK - I have been working with version 4.0.4 of pw that has > been compiled with only the internal espresso libraries (just > to check that it isn't an IBM library thing). The errors still appear. the same example works on the cray with internal libraries as well. > I am trying my 'simple' periodic 1152 atom cell try first to reproduce the example I sent. There is no way you can run large jobs without distributing the subspace matrices. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Thu Feb 12 15:06:35 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 08:06:35 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> Message-ID: Just to add to my last email, I tried to reproduce your results (and it looks like you emailed the list back before I had a chance to finish this) I found when I took the 432 atom system I sent you, and ran it on 128 cores in smp mode (1 MPI process/node - 2 GB per process) it did work (-ntg 32 -ndiag 121 as well as -ntg 4 -ndiag 121) - the system didn't fit into memory in vn mode (4 mpi processes/node - 512 MB per process). the error in the vn mode case was: '"fft_parallel.f90", line 104: 1525-108 Error encountered while attempting to allocate a data object. The program will stop.' I then tried the system in dual mode (2 mpi processes/node - 1 GB per process) using -ntg 4 and -ndiag 121. In this case, the cholesky error came up: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% task # 12 from pdpotf : error # 1 problems computing cholesky decomposition %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% I then tried the dual mode case with -ntg 4 and -ndiag 100 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% task # 11 from pdpotf : error # 1 problems computing cholesky decomposition %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% So now I am left wondering if I am not trying to spread the work out too much (sounds like this was the case) and that is what is leading to these cholesky errors. But the dual mode error seems to point to something else going on. Dave On Feb 12, 2009, at 6:53 AM, Paolo Giannozzi wrote: > On Feb 11, 2009, at 19:41 , David Farrell wrote: > >> Let me know if the attachment doesn't make it through > > it didn't to the mailing list (max attachment size 40kB), but > I received it. Attached is what I got (for a scf calculation) on > a cray xt5. Apart from the bogus values of planes printed in > the output, everything else seems ok, including parallel > subspace diagonalization (scalapack) on 121 processors. > > Paolo > > > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/f70be33a/attachment.htm From giannozz at democritos.it Thu Feb 12 15:54:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 15:54:35 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> Message-ID: <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> On Feb 12, 2009, at 15:06 , David Farrell wrote: > I found when I took the 432 atom system I sent you, and ran it on > 128 cores in smp mode > (1 MPI process/node - 2 GB per process) it did work (-ntg 32 -ndiag > 121 32 task groups? that's a lot > as well as -ntg 4 -ndiag 121) 4 looks more reasonable in my opinion > - the system didn't fit into memory in vn mode (4 mpi processes/ > node - > 512 MB per process) that job requires approx. 100Mb of dynamically allocated RAM per process, plus a few tens of Mb of work space. Why it does not fit into 512Mb is a mystery, unless each process comes with a copy of all libraries. If this is the case, the maximum you can fit into 512Mb is a code printing "Hello world" in parallel. By the way: the default number of bands in metallic calculations can be trimmed by a significant amount (e.g. 500 instead of 576) > I then tried the system in dual mode (2 mpi processes/node - 1 GB > per process) > using -ntg 4 and -ndiag 121. In this case, the cholesky error came up: the code performs exactly the same operations, independently on how the MPI processes are distributed. It looks like yet another BlueGene weirdness, like this: http://www.democritos.it:8888/O-sesame/chngview?cn=5777 http://www.democritos.it:8888/O-sesame/chngview?cn=5932 that however affected only the internal parallel diagonalization, not the new scalapack algorithm. I do not see any evidence that there is anything wrong with the code itself. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Thu Feb 12 16:18:14 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 09:18:14 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> Message-ID: <688BD310-CFE2-4828-B655-54A6B9330C33@u.northwestern.edu> >> I found when I took the 432 atom system I sent you, and ran it on >> 128 cores in smp mode >> (1 MPI process/node - 2 GB per process) it did work (-ntg 32 -ndiag >> 121 > > 32 task groups? that's a lot Yeah - I ran that by mistake. But I figured I'd mention it anyway > > >> as well as -ntg 4 -ndiag 121) > > 4 looks more reasonable in my opinion > Right. >> - the system didn't fit into memory in vn mode (4 mpi processes/ >> node - >> 512 MB per process) > > that job requires approx. 100Mb of dynamically allocated RAM per > process, plus > a few tens of Mb of work space. Why it does not fit into 512Mb is a > mystery, > unless each process comes with a copy of all libraries. If this is > the case, the > maximum you can fit into 512Mb is a code printing "Hello world" in > parallel. > Yeah - I am very curious about this. I was actually *very* surprised when this happened. > By the way: the default number of bands in metallic calculations can > be trimmed > by a significant amount (e.g. 500 instead of 576) > >> I then tried the system in dual mode (2 mpi processes/node - 1 GB >> per process) >> using -ntg 4 and -ndiag 121. In this case, the cholesky error came >> up: > > > the code performs exactly the same operations, independently on how > the MPI > processes are distributed. It looks like yet another BlueGene > weirdness, like this: > http://www.democritos.it:8888/O-sesame/chngview?cn=5777 > http://www.democritos.it:8888/O-sesame/chngview?cn=5932 > that however affected only the internal parallel diagonalization, > not the new > scalapack algorithm. I do not see any evidence that there is > anything wrong > with the code itself. > OK - so perhaps I should try this same run with scalapack enabled instead just to be sure of what happens and that I haven't miscompiled anything. That is only available in the latest CVS versions right? Dave David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/10e2af13/attachment-0001.htm From giannozz at democritos.it Thu Feb 12 17:51:11 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Feb 2009 17:51:11 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <688BD310-CFE2-4828-B655-54A6B9330C33@u.northwestern.edu> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> <688BD310-CFE2-4828-B655-54A6B9330C33@u.northwestern.edu> Message-ID: <7C35357E-AD7F-46FD-A9F5-D9B62E319807@democritos.it> On Feb 12, 2009, at 16:18 , David Farrell wrote: > OK - so perhaps I should try this same run with scalapack enabled > instead > just to be sure of what happens and that I haven't miscompiled > anything. > That is only available in the latest CVS versions right? right. You need option "-D__SCALAPACK" and to link to blacs and scalapack Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Thu Feb 12 18:23:04 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 11:23:04 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <7C35357E-AD7F-46FD-A9F5-D9B62E319807@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> <688BD310-CFE2-4828-B655-54A6B9330C33@u.northwestern.edu> <7C35357E-AD7F-46FD-A9F5-D9B62E319807@democritos.it> Message-ID: <8A8315DF-983F-4D5B-A2D5-1F8BB7C34421@u.northwestern.edu> OK, I tried the Jan 12 2009 snapshot from the website with the BG/P scalapack, blacs, goto and lapack. Things compiled fine. When I ran on 128 cores in vn mode with -ntg 4 -ndiag 121, I got a cholesky error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% task # 103 from rdiaghg : error # 102 problems computing cholesky %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% When I ran on 128 cores in dual mode with -ntg 4 -ndiag 121, I got the cholesky error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%% task # 118 from rdiaghg : error # 102 problems computing cholesky %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% When I ran on 128 cores in smp mode with -ntg 4 -ndiag 121, it ran fine. I am going to pull down the latest CVS version and see if that changes anything. It sounds like this shouldn't be a memory issue (and I don't get any memory errors in stderr), but I may have to see if I can reproduce this on a very small scale to see if it is something else. Something that according to the memory output should only use a couple hundred MB at most shouldn't require more than 1 GB to run. Dave On Feb 12, 2009, at 10:51 AM, Paolo Giannozzi wrote: > On Feb 12, 2009, at 16:18 , David Farrell wrote: > >> OK - so perhaps I should try this same run with scalapack enabled >> instead >> just to be sure of what happens and that I haven't miscompiled >> anything. >> That is only available in the latest CVS versions right? > > right. You need option "-D__SCALAPACK" and to link to blacs and > scalapack > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/fcf8391e/attachment.htm From davidfarrell2008 at u.northwestern.edu Thu Feb 12 19:24:38 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 12:24:38 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <7C35357E-AD7F-46FD-A9F5-D9B62E319807@democritos.it> References: <2507FF00-6FE9-481B-A3FD-81C4E26131C8@u.northwestern.edu> <20090128231527.uq7wa69a04okwssc@mail.democritos.it> <4992D013.9030905@democritos.it> <3B537690-395A-4CD3-A1F1-D2440AACF123@u.northwestern.edu> <49931225.3010904@democritos.it> <4B634F3D-55CF-4A9A-850D-C7A36630B3EA@u.northwestern.edu> <7C5E23B7-5F17-461C-90DC-8B68FA4A5EF5@democritos.it> <37525474-24BB-4CA5-A1BE-A3ED05F046FB@democritos.it> <688BD310-CFE2-4828-B655-54A6B9330C33@u.northwestern.edu> <7C35357E-AD7F-46FD-A9F5-D9B62E319807@democritos.it> Message-ID: <619DFC2E-E71E-414F-A449-02A872579B25@u.northwestern.edu> I pulled down the current CVS version, compiled as I did with the previous snapshot and got the same behavior: When I ran on 128 cores in vn mode with -ntg 4 -ndiag 121, I got a cholesky error: When I ran on 128 cores in dual mode with -ntg 4 -ndiag 121, I got the cholesky error: When I ran on 128 cores in smp mode with -ntg 4 -ndiag 121, it ran fine. I guess I have 2 options: 1) try larger systems in SMP mode with the CVS version, see how big I can get before things blow up. I'll just have to deal with the extra cost of the idle CPUs. 2) climb into the code with a debugger to see if I can see anything going on (things I am interested in now are how much memory is actually available to the code, how much it is using, if there is something funny going on in the different modes). I'll probably have to construct a smaller system that does the same thing first. I don't want to abandon PW/CP just yet because this code has demonstrated decent physics, and other codes would require me to do develop PPs that give me results I can be confident in or way too much work to get them scalable. Unfortunately - I also need to get it running on the BG/P as I have a big allocation on that machine that is otherwise wasted. Dave David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/457df989/attachment.htm From Max.Lawson at unige.ch Thu Feb 12 18:32:10 2009 From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=) Date: Thu, 12 Feb 2009 18:32:10 +0100 Subject: [Pw_forum] ld1 & search of ghost states Message-ID: <49945D1A.2070203@unige.ch> Dear Q.-E. users, I have a question about the use of the ld1 code and the identification of ghost states. I am trying to generate a norm-conserving TM PP for iron (xc=blyp), with the 3s and 3p semicores states treated as valence states. The reference configuration used is: '[Ne] 3s2 3p6 3d6 4s0 4p0'. I generated one with the fhi98pp package, but I would like to also do it with the LD1 code, using the blyp and also other more recent functionals. According to my understanding of the LD1 manual (INPUT_LD1.html), testing the generated PP with a basis set of Bessel functions allow the identification of ghost states. In order to see how this shows up, I used too large cutoff radii ('rcut') for generating the PP (pseudotype=1). This one was stored in a UPF file. *) I used lloc=0 and, during the test, the following warning was issued >>> Computing logarithmic derivative in 2.19388 WARNING! Expected number of nodes: 0= 2- 1- 1, number of nodes found: 1. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) Computing logarithmic derivative in 2.19388 Computing the partial wave expansion no projector for channel: 0 <<< I therefore guessed that a ghost state at least appears in the L=1 channel (according to my understanding of "ascheqps.f90"). *) The calculation of the logarithm was followed by a test of the PP: >>> Fe scalar relativistic calculation atomic number is 26.00 valence charge is 16.00 dft =BLYP lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 mesh =1191 r(mesh) = 101.18024 xmin = -7.00 dx = 0.01250 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 3S 1( 2.00) -8.25458 -8.25457 0.00000 2 1 3P 1( 6.00) -5.76444 -5.76444 0.00000 3 2 3D 1( 6.00) -1.89183 -1.89183 0.00000 2 0 4S 1( 0.00) -1.50529 -1.74603 0.24073 3 1 4P 1( 0.00) -1.07194 -1.13184 0.05990 eps = 7.2E-15 iter = 23 Etot = -2543.705260 Ry, -1271.852630 Ha, -34608.870131 eV Etotps = -237.821799 Ry, -118.910899 Ha, -3235.730128 eV ... <<< *) Then, there is the test with the basis set of Bessel functions. But no warning or error message was printed during this test: >>> Box size (a.u.) : 30.0 Cutoff (Ry) : 50.0 N = 1 N = 2 N = 3 E(L=0) = -8.2690 Ry -1.7535 Ry -0.6442 Ry E(L=1) = -5.8198 Ry -1.1415 Ry -0.4622 Ry E(L=2) = -1.9392 Ry -0.5486 Ry -0.2724 Ry Cutoff (Ry) : 55.0 N = 1 N = 2 N = 3 E(L=0) = -8.2692 Ry -1.7535 Ry -0.6442 Ry E(L=1) = -5.8266 Ry -1.1429 Ry -0.4626 Ry E(L=2) = -1.9629 Ry -0.5508 Ry -0.2732 Ry ..etc... <<< By looking at the source (test_bessel.f90), I understood that no such a warning or error message is to be printed. The reading of the above eigenvalues does not help me tell whether there is a ghost state or not: I'm clearly missing something !! Probably something very obvious *) My guess is that I actually should use the semilocal form of the PP to compute the eigenvalue spectrum and compare this spectrum with the above one. Is this correct ? If so, how should I proceed ? I thanks you in advance for your advice and/or help. Best regards, Max -- *********************************************** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *********************************************** From davidfarrell2008 at u.northwestern.edu Thu Feb 12 22:59:21 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Thu, 12 Feb 2009 15:59:21 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <31583015.2201101234466186195.JavaMail.root@zimbra> References: <31583015.2201101234466186195.JavaMail.root@zimbra> Message-ID: <079A7FF0-BC13-4E15-A55E-A5C444535B17@u.northwestern.edu> I set up an 864 atom run (so this has 1920 electrons, 960 states), and varied the number of nodes (the nodes were operating in smp mode so 1 node == 1 core) I ran the following cases successfully (with the current CVS version of pw, scalapack enabled): 512 cores, -ntg 8 -ndiag 256 256 cores, -ntg 8 -ndiag 256 128 cores, -ntg 4 -ndiag 121 64 cores, -ntg 4 -ndiag 64 32 cores, -ntg 4 -ndiag 25 it seemed to crash at 16 cores, -ntg 4 -ndiag 16 - the error was: 'pw.x: /bglhome/bgbuild/V1R2M0_200_2008-080513P/ppc/bgp/comm/sys/build- dcmf/include/devices/dma/DMAMulticast.h:568: static int DCMF ::DMA ::DMAMulticast::Registration::McastLongPacketHandler(void*, DCMF::DMA::DMAMulticast::PacketHeader*, void*, char*, int) [with TDesc = DMA_MemoryFifoDescriptor]: Assertion `recv != __null' failed.' Comparing this to the 432 atom run at 128 cores, I am not convinced that the issue between different modes is due to not enough memory per core. This system is twice as large, so shouldn't have worked on 32 cores if we assume linear scaling in memory usage. To put it another way: if we assume that the 432 atom case required more than 1 GB RAM/core to run at 128 cores (despite the output saying otherwise), then 864 would require more than 2 GB RAM/core at 128 cores. If we assume that memory consumption scales linearly, then at 64 cores, I should have seen a problem (since it would presumably need something more than 2 GB/core). Certainly by 32 cores (where it would need 4 GB/core). But I don't. On the up side, this likely means that I *can* run a big system (I'll have to play around to find out how big - especially when I get into adding a vacuum region). The down side is that I have to do it in smp mode and have 3 idle cores/node. Dave On Feb 12, 2009, at 1:16 PM, Nichols A. Romero wrote: > David, > > Just to clarify you mean. > > 128 nodes in vn mode = 512 cores > 128 nodes in dual mode = 256 cores > 128 nodes in smp mode = 128 cores > > Nichols A. Romero, Ph.D. > Argonne Leadership Computing Facility > Argonne National Laboratory > Building 360 Room L-146 > 9700 South Cass Avenue > Argonne, IL 60490 > (630) 252-3441 > > > ----- Original Message ----- > From: "David Farrell" > To: "PWSCF Forum" > Cc: "Nichols A. Romero" > Sent: Thursday, February 12, 2009 12:24:38 PM GMT -06:00 US/Canada > Central > Subject: Re: [Pw_forum] PW taskgroups and a large run on a BG/P > > > I pulled down the current CVS version, compiled as I did with the > previous snapshot and got the same behavior: > > > When I ran on 128 cores in vn mode with -ntg 4 -ndiag 121, I got a > cholesky error: > > > When I ran on 128 cores in dual mode with -ntg 4 -ndiag 121, I got > the cholesky error: > > > > When I ran on 128 cores in smp mode with -ntg 4 -ndiag 121, it ran > fine. > > > I guess I have 2 options: > > > 1) try larger systems in SMP mode with the CVS version, see how big > I can get before things blow up. I'll just have to deal with the > extra cost of the idle CPUs. > > > 2) climb into the code with a debugger to see if I can see anything > going on (things I am interested in now are how much memory is > actually available to the code, how much it is using, if there is > something funny going on in the different modes). I'll probably have > to construct a smaller system that does the same thing first. > > > I don't want to abandon PW/CP just yet because this code has > demonstrated decent physics, and other codes would require me to do > develop PPs that give me results I can be confident in or way too > much work to get them scalable. Unfortunately - I also need to get > it running on the BG/P as I have a big allocation on that machine > that is otherwise wasted. > > > Dave > > > > > > > > David E. Farrell > Post-Doctoral Fellow > Department of Materials Science and Engineering > Northwestern University > email: d-farrell2 at northwestern.edu David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090212/47527f9a/attachment-0001.htm From w2agz at pacbell.net Fri Feb 13 02:40:41 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Thu, 12 Feb 2009 17:40:41 -0800 Subject: [Pw_forum] Format of charge-density.dat In-Reply-To: References: <00b801c98cc6$348a9380$9d9fba80$@net> Message-ID: <003001c98d7c$14bcd2f0$3e3678d0$@net> OK, now I got it! Thanks, Axel (and Lex Kemper who e-mailed me off-forum). I actually use pp.x a lot, with plot_num=0 (or 6) and output_format=5 (xcrysden), and before posting this matter to the forum I poked around a lot in the postproc.f90 and chdens.f90 code and their output looking for what I wanted. I never knew what output_format=6 was for...I thought it might be for "Gaussian" one of PWscf's "alternatives." I'll test it out...I assume the "cube" indices are mapable onto the unit cell parameters and units (au?) in some fashion? BTW, I never could figure out or get answered what plot_num=3 was doing in a plot preparation utility, so I've modified the Fortran code for epsilon.x and dos.x to explicitly calculate the DOS at Ef. If anyone wants the code, e-mail me. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Wednesday, February 11, 2009 8:28 PM To: Paul M. Grant Cc: 'PWSCF Forum' Subject: Re: [Pw_forum] Format of charge-density.dat On Wed, 11 Feb 2009, Paul M. Grant wrote: PG> I realize charge-density.dat is stored in iotk binary format and the reasons PG> why. But is there any documentation illuminating the layout of the file or PG> how to access the data stored therein? I've poked around in the source code PG> of chden and electrons but it's not terribly obvious how they load the data, PG> which I assume is a necessary task somewhere in these two routines.at least PG> not in four or five minutes of manual scanning. All I really want to do is PG> write a (hopefully small) Fortran routine to load data from PG> charge-density.dat into a four (x, y, z, rho) by number-of-points array. PG> Maybe there's even an iotk subroutine someone has laying around to do just PG> that. paul, there is an example code, qexml.f90 (check out qexml_write/read_rho()) that should demonstrate how to read iotk files. not sure whether it still works, though. it has not been touched in a while. if you are more concerned about a fast result rather than performance, why don't you use pp.x to convert it into (gaussian) .cube format, which is plain text and easier to read into fortran. the way it is usually read is that you just have one 3-dim array, with the grid vector index positions as the indices. if you give me a hint about what exactly you're after, perhaps i can give you a more specific suggestion. PG> BTW, I assume the units are electrons/cubic-au as a function of x, y, z? right, at least that is what i remember, summing over the indivdual rho entries and multiplying with the volume of a single voxel should yield the total number of electrons. cheers, axel. PG> PG> Best to all, -Paul PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford (2005-2008) PG> EPRI Science Fellow (Retired) PG> IBM Research Staff Member Emeritus PG> w2agz at pacbell.net PG> http://www.w2agz.com PG> PG> PG> PG> PG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From sanjeev0302 at rediffmail.com Fri Feb 13 05:41:53 2009 From: sanjeev0302 at rediffmail.com (Sanjeev K. Gupta) Date: 13 Feb 2009 04:41:53 -0000 Subject: [Pw_forum] STEP-4 [Phonon] Message-ID: <20090213044153.26458.qmail@f4mail-235-243.rediffmail.com> Dear PWSCF user, We get all phonons postive in step 4, but in step 5 some are negative.Does one really need to go for the step 5 for phonon dispersion curves. If yes then suggest the modification for step 5. Sanjeev Gupta S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/8f946ee9/attachment.htm From zhukov at ihim.uran.ru Fri Feb 13 06:59:34 2009 From: zhukov at ihim.uran.ru (Vladlen Zhukov Windows) Date: Fri, 13 Feb 2009 10:59:34 +0500 Subject: [Pw_forum] nelec problem Message-ID: <000d01c98da0$40b5cd70$2b88a8c0@ZHUKOV> Dear all, This message is an addition to my previous one. I try to make calculations for semiconductor with one electron in the conductivity band. I supposed that is was possible by setting NELEC in SYSTEM equal to the number of electrons in neutral cell plus one. The extra charge, as it follows from the manual, has to be compensated by positive backgrounds. But it does not work! The answer of the code is 'charge is wrong'. Why? Is it still not implemented? Vladlen P. Zhukov, chief research associate, Institute of Solid State Chemistry, Russian Academy of Sciences, Ekaterinburg, Russia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/25aad409/attachment.htm From giannozz at democritos.it Fri Feb 13 09:00:58 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Feb 2009 09:00:58 +0100 Subject: [Pw_forum] nelec problem In-Reply-To: <000d01c98da0$40b5cd70$2b88a8c0@ZHUKOV> References: <000d01c98da0$40b5cd70$2b88a8c0@ZHUKOV> Message-ID: <499528BA.9050408@democritos.it> Vladlen Zhukov Windows wrote > I supposed that is was possible by setting NELEC in SYSTEM > equal to the number of electrons in neutral cell plus one. it is possible (it is NOT possible, however, to add an electron into the conduction band and a hole in the valence band) > The extra charge, as it follows from the manual, has to be > compensated by positive backgrounds. But it does not work! it does, if you do things properly > The answer of the code is 'charge is wrong'. you should treat the system as a metal Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Fri Feb 13 09:33:28 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Feb 2009 09:33:28 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: <49945D1A.2070203@unige.ch> References: <49945D1A.2070203@unige.ch> Message-ID: On Thu, 12 Feb 2009 18:32:10 +0100, Lat??vi Max LAWSON DAKU wrote: > WARNING! Expected number of nodes: 0= 2- 1- 1, number of > nodes found: 1. The specific Warning means that the first iteration of the self-consistency process found the wrong number of nodes (e.g. not the one you asked for), but the fact that convergence actually succeeded means that it could later recover and produce something. It doesn't necessarily means that there is a ghost state. If you are putting semicore states in valence, you will have two states (let's call them inner and outer) with the same angular momentum. When you are generating the PP you can either ask for the external state to have 0 nodes (e.g. setting L=S+1) or one node (L=S+2. Both choices are ok, which one is better depends on the details. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Fri Feb 13 10:09:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Feb 2009 10:09:14 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: References: <49945D1A.2070203@unige.ch> Message-ID: <499538BA.6090904@democritos.it> Lorenzo Paulatto wrote: > If you are putting semicore states in valence, you will have two states (let's call > them inner and outer) with the same angular momentum. When you are generating the PP > you can either ask for the external state to have 0 nodes (e.g. setting L=S+1) > or one node (L=S+2. Both choices are ok, which one is better depends on the details. for norm-conserving PP I don't think you can: the inner one must have 0 nodes, the outer one 1 Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From zhukov at ihim.uran.ru Fri Feb 13 10:19:27 2009 From: zhukov at ihim.uran.ru (Vladlen Zhukov Windows) Date: Fri, 13 Feb 2009 14:19:27 +0500 Subject: [Pw_forum] (no subject) Message-ID: <000e01c98dbc$2b9171d0$2b88a8c0@ZHUKOV> Many thanks to Paolo Giannozzi for the prompt answer! Everything is all right now, and I have no problems more! ---------------------------------------------------------------------- Vladlen P. Zhukov, chief research associate, Institute of Solid State Chemistry, Russian Academy of Sciences, Ekaterinburg, Russia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/95bbccc5/attachment.htm From giannozz at democritos.it Fri Feb 13 10:33:46 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Feb 2009 10:33:46 +0100 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <079A7FF0-BC13-4E15-A55E-A5C444535B17@u.northwestern.edu> References: <31583015.2201101234466186195.JavaMail.root@zimbra> <079A7FF0-BC13-4E15-A55E-A5C444535B17@u.northwestern.edu> Message-ID: <49953E7A.3070300@democritos.it> In conclusion, and if I understand correctly: PWscf runs only with 1 MPI process per core, but it runs 800+ atoms in as little as 32 processes or in as much as 512, as I was expecting. This confirms my opinion that the problem is on the BG side and not on the PWscf side, since there is NOTHING in the fortran code that depends upon where the MPI processes are running. Of course one can never rule out the possibility that some obscure bug is triggered only in that special cases, but it seems to me highly unlikely. Implementation of mixed MPI-openMPI parallelization is under development, but it wil take some time. In the meantime, if you can link openMPI-aware mathematical libraries, you might get some speedup. If you do not need k-points, and if you know how to deal with metallic systems, you might try CP instead of PWscf - it is better tested for large systems - but I don't expect a different behavior, since the routines performing parallel subspace diagonalization are the same that perform iterative orthonormalization, so the trouble is likely to move from "cholesky" to "ortho". You might try to find out what is wrong, since you have two cases that should yield exactly the same results but don't. It may take a lot of time and lead to no result, though. You may also try to raise this issue with the technical staff of the computing center. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From davidfarrell2008 at u.northwestern.edu Fri Feb 13 13:25:26 2009 From: davidfarrell2008 at u.northwestern.edu (David Farrell) Date: Fri, 13 Feb 2009 06:25:26 -0600 Subject: [Pw_forum] PW taskgroups and a large run on a BG/P In-Reply-To: <49953E7A.3070300@democritos.it> References: <31583015.2201101234466186195.JavaMail.root@zimbra> <079A7FF0-BC13-4E15-A55E-A5C444535B17@u.northwestern.edu> <49953E7A.3070300@democritos.it> Message-ID: I think this summary is about right. At least I can run something now and have an idea of what it is. I will probably also be transitioning to cp for my runs. I have been working with the folks at the supercomputing center, and will continue in hopes of finding out what is causing the trouble. Thanks, Dave On Feb 13, 2009, at 3:33 AM, Paolo Giannozzi wrote: > In conclusion, and if I understand correctly: > > PWscf runs only with 1 MPI process per core, but > it runs 800+ atoms in as little as 32 processes > or in as much as 512, as I was expecting. > > This confirms my opinion that the problem is on the > BG side and not on the PWscf side, since there is > NOTHING in the fortran code that depends upon where > the MPI processes are running. Of course one can > never rule out the possibility that some obscure > bug is triggered only in that special cases, but > it seems to me highly unlikely. > > Implementation of mixed MPI-openMPI parallelization > is under development, but it wil take some time. In > the meantime, if you can link openMPI-aware > mathematical libraries, you might get some speedup. > > If you do not need k-points, and if you know how to > deal with metallic systems, you might try CP instead > of PWscf - it is better tested for large systems - but > I don't expect a different behavior, since the routines > performing parallel subspace diagonalization are the > same that perform iterative orthonormalization, so the > trouble is likely to move from "cholesky" to "ortho". > > You might try to find out what is wrong, since you have > two cases that should yield exactly the same results > but don't. It may take a lot of time and lead to no > result, though. You may also try to raise this issue > with the technical staff of the computing center. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy David E. Farrell Post-Doctoral Fellow Department of Materials Science and Engineering Northwestern University email: d-farrell2 at northwestern.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/97886a3d/attachment.htm From giannozz at democritos.it Fri Feb 13 14:55:06 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Feb 2009 14:55:06 +0100 Subject: [Pw_forum] Format of charge-density.dat In-Reply-To: <003001c98d7c$14bcd2f0$3e3678d0$@net> References: <00b801c98cc6$348a9380$9d9fba80$@net> <003001c98d7c$14bcd2f0$3e3678d0$@net> Message-ID: <49957BBA.2030404@democritos.it> Paul M. Grant wrote: > BTW, I never could figure out or get answered what plot_num=3 was doing it calculates f(r) = \sum_i |\psi_i(r)|^2 \delta(\epsilon_i-E_F) I think. No idea who is using it for what purpose, though. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From Max.Lawson at unige.ch Fri Feb 13 14:58:35 2009 From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=) Date: Fri, 13 Feb 2009 14:58:35 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: <499538BA.6090904@democritos.it> References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> Message-ID: <49957C8B.1080204@unige.ch> Dear Paolo, Dear Lorenzo, I thank you a lot for your answers: I do understand that I should not worry about these warnings. I played a little bit further with the code. I generated a PP using a meaningless input and, as expected :-) , the "Bessel" test gave me a weird eigenvalue spectrum, and the ghost states could also be nicely seen in the logarithmic derivatives. Lorenzo: I unfortunately am a bit confused by your statement about the fact that the construction of the outer state can be made such that this one has zero or one node. Shouldn't the two pseudo-states be orthogonal ? At this point, Paolo: the distinction you make between NC and NC pseudopotentials add a bit more to my confusion. Could you please elaborate more on these subtleties or point me to a paper dealing with them ? All the best, Max Paolo Giannozzi wrote: > Lorenzo Paulatto wrote: > > >> If you are putting semicore states in valence, you will have two states (let's call >> > > them inner and outer) with the same angular momentum. When you are > generating the PP > > you can either ask for the external state to have 0 nodes (e.g. > setting L=S+1) > >> or one node (L=S+2. Both choices are ok, which one is better depends on the >> > details. > > for norm-conserving PP I don't think you can: the inner one must have > 0 nodes, the outer one 1 > > Paolo > -- *********************************************** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/2a8f94b2/attachment-0001.htm From giannozz at democritos.it Fri Feb 13 15:14:32 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Feb 2009 15:14:32 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: <49957C8B.1080204@unige.ch> References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> <49957C8B.1080204@unige.ch> Message-ID: <49958048.9010702@democritos.it> Lat?vi Max LAWSON DAKU wrote: > At this point, Paolo: the distinction you make between > NC and NC pseudopotentials did I? > add a bit more to my confusion. In norm-conserving PPs, the inner pseudo-state is nodeless, so the outer pseudo-state must have one node in order to be orthogonal to the previous. With ultrasoft PP a generalized orthogonality constraint - with an overlap matrix - is enforced. In principle, this does not require that the soft parts of the pseudo-states have a different number of nodes. This is why I pointed out that my statement was valid only for norm-conserving PPs Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From Max.Lawson at unige.ch Fri Feb 13 15:24:59 2009 From: Max.Lawson at unige.ch (=?ISO-8859-1?Q?Lat=E9vi_Max_LAWSON_DAKU?=) Date: Fri, 13 Feb 2009 15:24:59 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: <49958048.9010702@democritos.it> References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> <49957C8B.1080204@unige.ch> <49958048.9010702@democritos.it> Message-ID: <499582BB.3090402@unige.ch> Many thanks, Paolo, for your explanations. And, I'm sorry for the typo (NC vs non-NC :-) ) Regards, Max Paolo Giannozzi wrote: > Lat?vi Max LAWSON DAKU wrote: > > >> At this point, Paolo: the distinction you make between >> NC and NC pseudopotentials >> > > did I? > > >> add a bit more to my confusion. >> > > In norm-conserving PPs, the inner pseudo-state is nodeless, > so the outer pseudo-state must have one node in order to be > orthogonal to the previous. With ultrasoft PP a generalized > orthogonality constraint - with an overlap matrix - is enforced. > In principle, this does not require that the soft parts of > the pseudo-states have a different number of nodes. This is > why I pointed out that my statement was valid only for > norm-conserving PPs > > Paolo > -- *********************************************** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/e2f0a5bc/attachment.htm From paulatto at sissa.it Fri Feb 13 15:33:52 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Feb 2009 15:33:52 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: <49957C8B.1080204@unige.ch> References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> <49957C8B.1080204@unige.ch> Message-ID: On Fri, 13 Feb 2009 14:58:35 +0100, Lat??vi Max LAWSON DAKU wrote: > > I thank you a lot for your answers: I do understand that > I should not worry about these warnings. Sometimes, when you are trying to generate a PP you get problems with self-consistency; it may be difficult to understand which is the "bad" state giving problem (assumed there there is only one, and your configuration is not totally wrong), that's why I've added that message. Keeping in mind your concerns, I may try to reword it in a less scary way. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From Max.Lawson at unige.ch Fri Feb 13 16:59:28 2009 From: Max.Lawson at unige.ch (=?UTF-8?B?TGF0w6l2aSBNYXggTEFXU09OIERBS1U=?=) Date: Fri, 13 Feb 2009 16:59:28 +0100 Subject: [Pw_forum] ld1 & search of ghost states In-Reply-To: References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> <49957C8B.1080204@unige.ch> Message-ID: <499598E0.8090505@unige.ch> Dear Lorenzo, Many thanks for your additional explanations. I also did appreciate a lot your previous explanations. It's simply that I don't generate PP routinely, yet :-) and that I probably tend to be too(?) peaky about the (gory) details; especially before burning thousands cpu-hours. All the best, Max Lorenzo Paulatto wrote: > On Fri, 13 Feb 2009 14:58:35 +0100, Lat??vi Max LAWSON DAKU wrote: > >> I thank you a lot for your answers: I do understand that >> I should not worry about these warnings. >> > > Sometimes, when you are trying to generate a PP you get problems with self-consistency; it may be difficult to understand which is the "bad" state giving problem (assumed there there is only one, and your configuration is not totally wrong), that's why I've added that message. Keeping in mind your concerns, I may try to reword it in a less scary way. > > regards > > > > -- *********************************************** Latevi Max LAWSON DAKU Departement de chimie physique Universite de Geneve - Sciences II 30, quai Ernest-Ansermet CH-1211 Geneve 4 Switzerland Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103 *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090213/339e97c7/attachment.htm From eyvaz_isaev at yahoo.com Fri Feb 13 19:21:25 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 13 Feb 2009 10:21:25 -0800 (PST) Subject: [Pw_forum] STEP-4 [Phonon] In-Reply-To: <20090213044153.26458.qmail@f4mail-235-243.rediffmail.com> Message-ID: <725083.59511.qm@web65708.mail.ac4.yahoo.com> Dear Sanjeev, Until you describe your problem more exactly, no one can help you. I think nobody (except you) can understand what they are these mystery 4 steps. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 2/13/09, Sanjeev K. Gupta wrote: From: Sanjeev K. Gupta Subject: [Pw_forum] STEP-4 [Phonon] To: pw_forum at pwscf.org Date: Friday, February 13, 2009, 7:41 AM Dear PWSCF user, We get all phonons postive in step 4, but in step 5 some are negative.Does one really need to go for the step 5 for phonon dispersion curves. If yes then suggest the modification for step 5. Sanjeev Gupta S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From marc at fq.edu.uy Fri Feb 13 19:47:27 2009 From: marc at fq.edu.uy (marc at fq.edu.uy) Date: Fri, 13 Feb 2009 16:47:27 -0200 (UYST) Subject: [Pw_forum] H pseudopotential In-Reply-To: <499598E0.8090505@unige.ch> References: <49945D1A.2070203@unige.ch> <499538BA.6090904@democritos.it> <49957C8B.1080204@unige.ch> <499598E0.8090505@unige.ch> Message-ID: <49564.200.40.206.198.1234550847.squirrel@webmail.fq.edu.uy> Hi I looking for a H pseudopotential H.blyp-mt.UPF, isn't in Q/E homepage, any suggestion ? Many thanks. Marc Marc Segovia Facultad de Quimica Universidad de la Republica Uruguay From eyvaz_isaev at yahoo.com Fri Feb 13 21:40:13 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 13 Feb 2009 12:40:13 -0800 (PST) Subject: [Pw_forum] H pseudopotential In-Reply-To: <49564.200.40.206.198.1234550847.squirrel@webmail.fq.edu.uy> Message-ID: <237288.79923.qm@web65716.mail.ac4.yahoo.com> Hi Marc, I will send you personally H_MT_BLYP.psp taken from CPMD/pseudo_ext_lib in order to keep the forum clean. But you have to convert it to UPF using cpmd2upf.x from /upftools. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 2/13/09, marc at fq.edu.uy wrote: > From: marc at fq.edu.uy > Subject: [Pw_forum] H pseudopotential > To: "PWSCF Forum" > Date: Friday, February 13, 2009, 9:47 PM > Hi > > I looking for a H pseudopotential H.blyp-mt.UPF, isn't > in Q/E homepage, > any suggestion ? > Many thanks. > Marc > > > Marc Segovia > Facultad de Quimica > Universidad de la Republica > Uruguay > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From marc at fq.edu.uy Fri Feb 13 22:08:52 2009 From: marc at fq.edu.uy (Marc Segovia) Date: Fri, 13 Feb 2009 19:08:52 -0200 Subject: [Pw_forum] H pseudopotential In-Reply-To: <237288.79923.qm@web65716.mail.ac4.yahoo.com> References: <237288.79923.qm@web65716.mail.ac4.yahoo.com> Message-ID: <4995E164.3040307@fq.edu.uy> Dear Eyvaz Many thanks for the file and explanation how to convert. Nice weekend Marc Eyvaz Isaev escribi?: > Hi Marc, > > I will send you personally H_MT_BLYP.psp taken from CPMD/pseudo_ext_lib in order to keep the forum clean. But you have to convert it to UPF using cpmd2upf.x from /upftools. > > Bests, > Eyvaz. > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Fri, 2/13/09, marc at fq.edu.uy wrote: > > >> From: marc at fq.edu.uy >> Subject: [Pw_forum] H pseudopotential >> To: "PWSCF Forum" >> Date: Friday, February 13, 2009, 9:47 PM >> Hi >> >> I looking for a H pseudopotential H.blyp-mt.UPF, isn't >> in Q/E homepage, >> any suggestion ? >> Many thanks. >> Marc >> >> >> Marc Segovia >> Facultad de Quimica >> Universidad de la Republica >> Uruguay >> >> _______________________________________________ >> 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 > ------------------------------------------------------------------------ > > > No virus found in this incoming message. > Checked by AVG - www.avg.com > Version: 8.0.233 / Virus Database: 270.10.23/1951 - Release Date: 02/10/09 17:44:00 > > From adrian.voslab at googlemail.com Fri Feb 13 23:19:55 2009 From: adrian.voslab at googlemail.com (Adrian) Date: Fri, 13 Feb 2009 22:19:55 +0000 Subject: [Pw_forum] ibrav=13 Message-ID: <4995F20B.30002@gmail.com> Dear All, I would greatly appreciate some help with using ibrav=13. Does it require the coordinates in the conventional unit cell or those corresponding to the primitive? No matter what I've tried it just doesn't seem to be right. Many thanks, Adrian Newcastle University Chem Eng. & Advanced Materials UK From degironc at sissa.it Sat Feb 14 00:29:36 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 14 Feb 2009 00:29:36 +0100 Subject: [Pw_forum] ibrav=13 In-Reply-To: <4995F20B.30002@gmail.com> References: <4995F20B.30002@gmail.com> Message-ID: <49960260.6010401@sissa.it> In pwscf you need to specify the position of all the atoms in the primitive unit cell of your Bravais lattice as it is defined by three Bravais lattice vectors (printed at the beginning of the output of any run). Coordinates are given using the ATOMIC_POSITIONS card... Pay attention that if you are using the default format (alat), positions are given in cartesian coordinates in unit of alat(=celldm(1)). If you want to use crystal coordinates (that is fractions of the BL vectors) you should use the following syntax ATOMIC_POSITION crystal hope this helps, stefano Adrian wrote: > Dear All, > > I would greatly appreciate some help with using ibrav=13. Does it > require the coordinates in the conventional unit cell or those > corresponding to the primitive? No matter what I've tried it just > doesn't seem to be right. > Many thanks, > Adrian > Newcastle University > Chem Eng. & Advanced Materials > UK > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From lex at phys.ufl.edu Sat Feb 14 00:45:04 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Fri, 13 Feb 2009 18:45:04 -0500 Subject: [Pw_forum] ibrav=13 In-Reply-To: <49960260.6010401@sissa.it> References: <4995F20B.30002@gmail.com> <49960260.6010401@sissa.it> Message-ID: <49960600.5080501@phys.ufl.edu> Two things that might help as well: (1) The lattice vectors are also printed in the INPUT_PW files (2) XCrySDen does a decent job of interpreting input files/coordinates (although I've had a bit of trouble with bct lattices, so be careful) so you can check your inputfile. Lex Kemper Stefano de Gironcoli wrote: > In pwscf you need to specify the position of all the atoms in the > primitive unit cell of your Bravais lattice as it is defined by three > Bravais lattice vectors (printed at the beginning of the output of any > run). > Coordinates are given using the ATOMIC_POSITIONS card... > Pay attention that if you are using the default format (alat), positions > are given in cartesian coordinates in unit of alat(=celldm(1)). > If you want to use crystal coordinates (that is fractions of the BL > vectors) you should use the following syntax > ATOMIC_POSITION crystal > > hope this helps, > stefano > > Adrian wrote: >> Dear All, >> >> I would greatly appreciate some help with using ibrav=13. Does it >> require the coordinates in the conventional unit cell or those >> corresponding to the primitive? No matter what I've tried it just >> doesn't seem to be right. >> Many thanks, >> Adrian >> Newcastle University >> Chem Eng. & Advanced Materials >> UK >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From adrian.voslab at googlemail.com Sat Feb 14 14:21:50 2009 From: adrian.voslab at googlemail.com (Adrian) Date: Sat, 14 Feb 2009 13:21:50 +0000 Subject: [Pw_forum] ibrav=13 thanks In-Reply-To: References: Message-ID: <4996C56E.8020200@gmail.com> Thank you all for your swift reply. I decided to go with ibrav=0 after a literature search, there is a debate whether Fe5C2 is monoclinic or triclinic. Adrian Newcastle University, UK > ------------------------------------------------------------------------ > > Today's Topics: > > 1. Re: ibrav=13 (Lex Kemper) > > > ------------------------------------------------------------------------ > > Subject: > Re: [Pw_forum] ibrav=13 > From: > Lex Kemper > Date: > Fri, 13 Feb 2009 18:45:04 -0500 > To: > PWSCF Forum > > To: > PWSCF Forum > > > Two things that might help as well: > > (1) The lattice vectors are also printed in the INPUT_PW files > (2) XCrySDen does a decent job of interpreting input files/coordinates > (although I've had a bit of trouble with bct lattices, so be careful) so > you can check your inputfile. > > Lex Kemper > > Stefano de Gironcoli wrote: > >> In pwscf you need to specify the position of all the atoms in the >> primitive unit cell of your Bravais lattice as it is defined by three >> Bravais lattice vectors (printed at the beginning of the output of any >> run). >> Coordinates are given using the ATOMIC_POSITIONS card... >> Pay attention that if you are using the default format (alat), positions >> are given in cartesian coordinates in unit of alat(=celldm(1)). >> If you want to use crystal coordinates (that is fractions of the BL >> vectors) you should use the following syntax >> ATOMIC_POSITION crystal >> >> hope this helps, >> stefano >> >> Adrian wrote: >> >>> Dear All, >>> >>> I would greatly appreciate some help with using ibrav=13. Does it >>> require the coordinates in the conventional unit cell or those >>> corresponding to the primitive? No matter what I've tried it just >>> doesn't seem to be right. >>> Many thanks, >>> Adrian >>> Newcastle University >>> Chem Eng. & Advanced Materials >>> UK >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mpayami at aeoi.org.ir Sat Feb 14 18:01:34 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sat, 14 Feb 2009 09:01:34 -0800 Subject: [Pw_forum] openmpi-1.3 References: <4996C56E.8020200@gmail.com> Message-ID: Hi ALL, Has anybody succeeded running QE using openmpi-1.3? I get the following error message: %%%%%%%%%%%%%% from read_namelists: error #1 reading namelist control %%%%%%%%%%%%%%%%% %%%%%%%%%%%%%% from read_namelists: error #1 reading namelist control %%%%%%%%%%%%%%%%% stopping.... stopping.... On the other hand it is ok with openmpi-1.2.8. Any comments highly appreciated. Mahmoud Payami From eyvaz_isaev at yahoo.com Sat Feb 14 19:39:24 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 14 Feb 2009 10:39:24 -0800 (PST) Subject: [Pw_forum] openmpi-1.3 In-Reply-To: Message-ID: <821225.5649.qm@web65704.mail.ac4.yahoo.com> Dear Mahmoud, Are you absolutely sure that both files you used are the same? Did you try re-run after you got this message? Several times I had such kind message, but just restarting the message disappeared. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 2/14/09, Mahmoud Payami wrote: > From: Mahmoud Payami > Subject: [Pw_forum] openmpi-1.3 > To: "PWSCF Forum" > Date: Saturday, February 14, 2009, 8:01 PM > Hi ALL, > > Has anybody succeeded running QE using openmpi-1.3? > > I get the following error message: > > > %%%%%%%%%%%%%% > from read_namelists: error #1 > reading namelist control > %%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%% > from read_namelists: error #1 > reading namelist control > %%%%%%%%%%%%%%%%% > stopping.... > stopping.... > > On the other hand it is ok with openmpi-1.2.8. > Any comments highly appreciated. > > Mahmoud Payami > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From powergreen at gmail.com Sat Feb 14 20:05:14 2009 From: powergreen at gmail.com (Green Power) Date: Sat, 14 Feb 2009 14:05:14 -0500 Subject: [Pw_forum] Molecular radicals Message-ID: Hi, Can anyone give me an example for molecular radical calculations, for example,the triplet oxygen molecule? Should I set the multiplicity, magnetization, band occupation or anything else? I did search the archive, but I get even more puzzled by the explanations. Probably, an example would help me understand the problem. Thanks. Qian Clemson University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090214/6903f11e/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Feb 14 20:33:47 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 14 Feb 2009 14:33:47 -0500 (EST) Subject: [Pw_forum] openmpi-1.3 In-Reply-To: References: <4996C56E.8020200@gmail.com> Message-ID: On Sat, 14 Feb 2009, Mahmoud Payami wrote: MP> Hi ALL, MP> MP> Has anybody succeeded running QE using openmpi-1.3? MP> MP> I get the following error message: this error message comes from the fortran compiler runtime, not from MPI, and usually indicates a not 100% conformant input file or a typo. could it be that your two openmpi compilations use a different compiler (or compiler version) and that one of the compilers is more picky about correct namelist syntax than the other? cheers, axel. MP> MP> MP> %%%%%%%%%%%%%% MP> from read_namelists: error #1 MP> reading namelist control MP> %%%%%%%%%%%%%%%%% MP> %%%%%%%%%%%%%% MP> from read_namelists: error #1 MP> reading namelist control MP> %%%%%%%%%%%%%%%%% MP> stopping.... MP> stopping.... MP> MP> On the other hand it is ok with openmpi-1.2.8. MP> Any comments highly appreciated. MP> MP> Mahmoud Payami MP> MP> MP> MP> _______________________________________________ MP> Pw_forum mailing list MP> Pw_forum at pwscf.org MP> http://www.democritos.it/mailman/listinfo/pw_forum MP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Sat Feb 14 20:40:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 14 Feb 2009 20:40:23 +0100 Subject: [Pw_forum] openmpi-1.3 In-Reply-To: References: <4996C56E.8020200@gmail.com> Message-ID: <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> On Feb 14, 2009, at 18:01 , Mahmoud Payami wrote: > Has anybody succeeded running QE using openmpi-1.3? > I get the following error message: [...] > from read_namelists: error #1 > reading namelist control [...] > On the other hand it is ok with openmpi-1.2.8. try pw.x/cp.x -inp "input file name" . It happens more often than not that MPI installations are confused by input redirection (pw.x/cp.x < "input file name"). Maybe your newer version is not installed in exactly the same way as your previous one Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Sat Feb 14 20:46:06 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 14 Feb 2009 14:46:06 -0500 (EST) Subject: [Pw_forum] Molecular radicals In-Reply-To: References: Message-ID: On Sat, 14 Feb 2009, Green Power wrote: GP> Hi, Can anyone give me an example for molecular radical calculations, for GP> example,the triplet oxygen molecule? Should I set the multiplicity, qian, as always, it would help if you explained a little more about your background and what exactly you are trying to achieve and last but not least, which code you are using. Q-E has two codes, pw.x and cp.x, that can compute single point energys and MD of molecules. in pw.x, and i guess that is the result of your confusion, there are several redundant ways of defining a triplet state. i'd recommend you use multiplicity=3 and occupations='fixed'. apart from the fact, that triplet oxygen is a pathological case, all you need is to do is to set a sufficiently large cell and use gamma point only. that'll get you to where a (more adequate) regular quantum chemistry code would get. GP> magnetization, band occupation or anything else? I did search the archive, GP> but I get even more puzzled by the explanations. Probably, an example would GP> help me understand the problem. my guess is that you are mostly confused by the different nomenclatures and requirements that affect people calculating bulk magnetic materials. cheers, axel. GP> Thanks. GP> GP> Qian GP> Clemson University GP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From nguyenhalvt at yahoo.com Sun Feb 15 03:54:58 2009 From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha) Date: Sat, 14 Feb 2009 18:54:58 -0800 (PST) Subject: [Pw_forum] Pseudopotential for Mg-PBE in upf file Message-ID: <531402.95201.qm@web31003.mail.mud.yahoo.com> Dear PWscf Users, I can not find where to get Mg-PBE upf potential, Does anyone share this PP or give me some advice? Thank you so much for your help. Nguyen, Ngoc Ha Hanoi National University of Education Faculty of Chemistry Department of Physical Chemistry Tel: Office: 04/8330842 Home: 04/7891674 Mobile: 0989133436 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090214/04dea914/attachment.htm From mpayami at aeoi.org.ir Sun Feb 15 04:34:56 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sun, 15 Feb 2009 07:04:56 +0330 Subject: [Pw_forum] openmpi-1.3 In-Reply-To: <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> References: <4996C56E.8020200@gmail.com> <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> Message-ID: Dear Axel, Eyvaz, and Paolo, Thank you so much for your comments. Paolo's suggestion resolved my problem. In fact, I created two versions "openmpi_1.2.8" and "openmpi_1.3", and correspondingly two versions "QE-1.2.8" and "QE-1.3". In all preparations, I used the same intel compiler 11 (lc_prof_11), and in each case I modified ".bashtc" for "LD_LIBRARY_PATH" and "openmpi/bin". using two pools, each with two cores, I got the message: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< [mahmoud at node0]$ mpirun --hostfile myhost -np 4 /opt/espresso404_32/bin/pw.x < Au2.in Program PWSCF v.4.0.4 starts ... Today is 15Feb2009 at 3:56:30 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------------------- 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 19267 on node condmat2 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [node0:24707] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node0:24707] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Best regards, Mahmoud > On Feb 14, 2009, at 18:01 , Mahmoud Payami wrote: > > > Has anybody succeeded running QE using openmpi-1.3? > > I get the following error message: [...] > > from read_namelists: error #1 > > reading namelist control [...] > > On the other hand it is ok with openmpi-1.2.8. > > try pw.x/cp.x -inp "input file name" . It happens more often than > not that MPI installations are confused by input redirection > (pw.x/cp.x < "input file name"). Maybe your newer version is > not installed in exactly the same way as your previous one > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sanjeev0302 at rediffmail.com Sun Feb 15 06:15:57 2009 From: sanjeev0302 at rediffmail.com (Sanjeev K. Gupta) Date: 15 Feb 2009 05:15:57 -0000 Subject: [Pw_forum] STEP-4 [Phonon] Message-ID: <1234549285.S.3878.47224.f4mail-235-209.rediffmail.com.old.replied.1234674957.43863@webmail.rediffmail.com> Respected sir, I am working on some noble nitride system. I want to calculate phonon dispersion curve. For that I have calculate phonon frequency at [0 0 0], [-0.25 0.25 -0.25], [0.5 -0.5 0.5], [0.0 0.5 0.0], [0.75 -0.25 0.75], [0.5 0.0 0.5], [0.0 -1.0 0.0], [-0.5 -1.0 0.0], which is coming positive. (all this calculation, i have done using espresso code and phonon frequency obtained by using STEP_4 under FONONI folder). Now i want to plot the phonon dispersion?, Sir, Plz. suggest me how i do that and these q-point are sufficient to plot PDC? Kind Regards Sanjeev On Fri, 13 Feb 2009 23:51:25 +0530 wrote >Dear Sanjeev, > >Until you describe your problem more exactly, no one can help you. > >I think nobody (except you) can understand what they are these mystery 4 steps. > >Bests, >Eyvaz. > >------------------------------------------------------------------- > >Prof. Eyvaz Isaev, > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden >Condensed Matter Theory Group, Uppsala University, Sweden >Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > >--- On Fri, 2/13/09, Sanjeev K. Gupta wrote: >From: Sanjeev K. Gupta >Subject: [Pw_forum] STEP-4 [Phonon] >To: pw_forum at pwscf.org >Date: Friday, February 13, 2009, 7:41 AM > >Dear PWSCF user, > > >We get all phonons postive in step 4, but in step 5 some are negative.Does one really need to go for the step 5 for phonon dispersion curves. If yes then suggest the modification for step 5. > > >Sanjeev Gupta > >S. K. Gupta > >PhD Candidate, > >Dept. of Physics, > >Bhavnagar University. > >Bhavnagar, 364 002., Gujarat. > > > >_______________________________________________ >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 > S. K. Gupta PhD Candidate, Dept. of Physics, Bhavnagar University. Bhavnagar, 364 002., Gujarat. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090215/60caad45/attachment.htm From w2agz at pacbell.net Sun Feb 15 06:49:17 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sat, 14 Feb 2009 21:49:17 -0800 Subject: [Pw_forum] Atom 01 not found Message-ID: <010d01c98f31$246925d0$6d3b7170$@net> On running pp.x with the namelist below trying to get a "cube gauss file" I get the error listed below. No problem with other "output_format"s like 3 and/or 5. *********************************************************** Program POST-PROC v.4.0 starts ... Today is 14Feb2009 at 21:27:11 Calling punch_plot, plot_num = 0 Writing data to file af-CuO.rho_cube_2.rho Reading data from file af-CuO.rho_cube_2.rho Writing data to be plotted to file af-CuO.rho_cube_2.dat Atom O1 not found ************************************************************* &inputpp prefix = 'af-CuO', outdir = '/home/pmpgrant/Research_Projects/DFT_Calculations/af_RS_CuO/CuO', filplot = 'af-CuO.rho_cube_2.rho', plot_num = 0, spin_component = 2, / &plot nfile = 1, filepp(1) = 'af-CuO.rho_cube_2.rho', weight(1) = 1.0, iflag = 3, output_format = 6, fileout = 'af-CuO.rho_cube_2.dat', / Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090214/c21d35ce/attachment.htm From mpayami at aeoi.org.ir Sun Feb 15 14:06:47 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 15 Feb 2009 05:06:47 -0800 Subject: [Pw_forum] Benchmarking: openmpi-1.3 vs openmpi-1.2.8 Message-ID: Dear ALL, I performed a benchmarking test using openmpi-1.2.8 and openmpi-1.3 for a 2-atom Au cluster. The out files show that in all parts "1.3" takes shorter time than "1.2.8". However, the wall time in "1.3" is slightly increased. I do not know how to resolve it. Is the bottleneck the connection cables? Bests, Mahmoud Payami ---------------------------------------- #out_1.2.8 PWSCF : 2m 5.29s CPU time, 4m43.10s wall time init_run : 9.50s CPU electrons : 108.91s CPU forces : 5.90s CPU Called by init_run: wfcinit : 1.58s CPU potinit : 3.84s CPU Called by electrons: c_bands : 32.38s CPU ( 10 calls, 3.238 s avg) sum_band : 29.74s CPU ( 10 calls, 2.974 s avg) v_of_rho : 25.64s CPU ( 10 calls, 2.564 s avg) newd : 12.15s CPU ( 10 calls, 1.215 s avg) mix_rho : 5.26s CPU ( 10 calls, 0.526 s avg) Called by c_bands: init_us_2 : 0.12s CPU ( 21 calls, 0.006 s avg) regterg : 32.10s CPU ( 10 calls, 3.210 s avg) Called by *egterg: h_psi : 31.51s CPU ( 43 calls, 0.733 s avg) s_psi : 0.20s CPU ( 43 calls, 0.005 s avg) g_psi : 0.06s CPU ( 32 calls, 0.002 s avg) rdiaghg : 1.19s CPU ( 41 calls, 0.029 s avg) Called by h_psi: add_vuspsi : 0.17s CPU ( 43 calls, 0.004 s avg) General routines calbec : 2.26s CPU ( 57 calls, 0.040 s avg) cft3s : 82.62s CPU ( 595 calls, 0.139 s avg) interpolate : 9.35s CPU ( 20 calls, 0.467 s avg) davcio : 0.00s CPU ( 9 calls, 0.000 s avg) Parallel routines fft_scatter : 64.88s CPU ( 595 calls, 0.109 s avg) ---------------------------------------------------------------------------------------- #out-1.3 PWSCF : 1m55.59s CPU time, 4m44.04s wall time init_run : 8.69s CPU electrons : 100.47s CPU forces : 5.55s CPU Called by init_run: wfcinit : 1.46s CPU potinit : 3.41s CPU Called by electrons: c_bands : 30.14s CPU ( 10 calls, 3.014 s avg) sum_band : 27.11s CPU ( 10 calls, 2.711 s avg) v_of_rho : 23.62s CPU ( 10 calls, 2.362 s avg) newd : 11.95s CPU ( 10 calls, 1.195 s avg) mix_rho : 4.47s CPU ( 10 calls, 0.447 s avg) Called by c_bands: init_us_2 : 0.10s CPU ( 21 calls, 0.005 s avg) regterg : 29.87s CPU ( 10 calls, 2.987 s avg) Called by *egterg: h_psi : 29.42s CPU ( 43 calls, 0.684 s avg) s_psi : 0.18s CPU ( 43 calls, 0.004 s avg) g_psi : 0.06s CPU ( 32 calls, 0.002 s avg) rdiaghg : 1.05s CPU ( 41 calls, 0.026 s avg) Called by h_psi: add_vuspsi : 0.16s CPU ( 43 calls, 0.004 s avg) General routines calbec : 1.63s CPU ( 57 calls, 0.029 s avg) cft3s : 75.61s CPU ( 595 calls, 0.127 s avg) interpolate : 8.18s CPU ( 20 calls, 0.409 s avg) davcio : 0.00s CPU ( 9 calls, 0.000 s avg) Parallel routines fft_scatter : 57.22s CPU ( 595 calls, 0.096 s avg)>>>> Has anybody succeeded running QE using openmpi-1.3?>>> I get the following error message: [...]>>> from read_namelists: error #1>>> reading namelist control [...]>>> On the other hand it is ok with openmpi-1.2.8.>>>> try pw.x/cp.x -inp "input file name" . It happens more often than>> not that MPI installations are confused by input redirection>> (pw.x/cp.x < "input file name"). Maybe your newer version is>> not installed in exactly the same way as your previous one>>>> Paolo>> --->> Paolo Giannozzi, Democritos and University of Udine, Italy>>>>>> _______________________________________________>> Pw_forum mailing list>> Pw_forum at pwscf.org>> http://www.democritos.it/mailman/listinfo/pw_forum>>>>> From mpayami at aeoi.org.ir Sun Feb 15 11:54:45 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Sun, 15 Feb 2009 02:54:45 -0800 Subject: [Pw_forum] Benchmarking: openmpi-1.3 vs openmpi-1.2.8 References: <4996C56E.8020200@gmail.com> <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> Message-ID: <7920EE04A94045AB9C75E5C665DBDB8F@ctpm> Dear ALL, I performed a benchmarking test using openmpi-1.2.8 and openmpi-1.3 for a 2-atom Au cluster. The out files show that in all parts "1.3" takes shorter time than "1.2.8". However, the wall time in "1.3" is slightly increased. I do not know how to resolve it. Is the bottleneck the connection cables? Bests, Mahmoud Payami ---------------------------------------- #out_1.2.8 PWSCF : 2m 5.29s CPU time, 4m43.10s wall time init_run : 9.50s CPU electrons : 108.91s CPU forces : 5.90s CPU Called by init_run: wfcinit : 1.58s CPU potinit : 3.84s CPU Called by electrons: c_bands : 32.38s CPU ( 10 calls, 3.238 s avg) sum_band : 29.74s CPU ( 10 calls, 2.974 s avg) v_of_rho : 25.64s CPU ( 10 calls, 2.564 s avg) newd : 12.15s CPU ( 10 calls, 1.215 s avg) mix_rho : 5.26s CPU ( 10 calls, 0.526 s avg) Called by c_bands: init_us_2 : 0.12s CPU ( 21 calls, 0.006 s avg) regterg : 32.10s CPU ( 10 calls, 3.210 s avg) Called by *egterg: h_psi : 31.51s CPU ( 43 calls, 0.733 s avg) s_psi : 0.20s CPU ( 43 calls, 0.005 s avg) g_psi : 0.06s CPU ( 32 calls, 0.002 s avg) rdiaghg : 1.19s CPU ( 41 calls, 0.029 s avg) Called by h_psi: add_vuspsi : 0.17s CPU ( 43 calls, 0.004 s avg) General routines calbec : 2.26s CPU ( 57 calls, 0.040 s avg) cft3s : 82.62s CPU ( 595 calls, 0.139 s avg) interpolate : 9.35s CPU ( 20 calls, 0.467 s avg) davcio : 0.00s CPU ( 9 calls, 0.000 s avg) Parallel routines fft_scatter : 64.88s CPU ( 595 calls, 0.109 s avg) ---------------------------------------------------------------------------------------- #out-1.3 PWSCF : 1m55.59s CPU time, 4m44.04s wall time init_run : 8.69s CPU electrons : 100.47s CPU forces : 5.55s CPU Called by init_run: wfcinit : 1.46s CPU potinit : 3.41s CPU Called by electrons: c_bands : 30.14s CPU ( 10 calls, 3.014 s avg) sum_band : 27.11s CPU ( 10 calls, 2.711 s avg) v_of_rho : 23.62s CPU ( 10 calls, 2.362 s avg) newd : 11.95s CPU ( 10 calls, 1.195 s avg) mix_rho : 4.47s CPU ( 10 calls, 0.447 s avg) Called by c_bands: init_us_2 : 0.10s CPU ( 21 calls, 0.005 s avg) regterg : 29.87s CPU ( 10 calls, 2.987 s avg) Called by *egterg: h_psi : 29.42s CPU ( 43 calls, 0.684 s avg) s_psi : 0.18s CPU ( 43 calls, 0.004 s avg) g_psi : 0.06s CPU ( 32 calls, 0.002 s avg) rdiaghg : 1.05s CPU ( 41 calls, 0.026 s avg) Called by h_psi: add_vuspsi : 0.16s CPU ( 43 calls, 0.004 s avg) General routines calbec : 1.63s CPU ( 57 calls, 0.029 s avg) cft3s : 75.61s CPU ( 595 calls, 0.127 s avg) interpolate : 8.18s CPU ( 20 calls, 0.409 s avg) davcio : 0.00s CPU ( 9 calls, 0.000 s avg) Parallel routines fft_scatter : 57.22s CPU ( 595 calls, 0.096 s avg) > >> Has anybody succeeded running QE using openmpi-1.3? >> I get the following error message: [...] >> from read_namelists: error #1 >> reading namelist control [...] >> On the other hand it is ok with openmpi-1.2.8. > > try pw.x/cp.x -inp "input file name" . It happens more often than > not that MPI installations are confused by input redirection > (pw.x/cp.x < "input file name"). Maybe your newer version is > not installed in exactly the same way as your previous one > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Sun Feb 15 18:44:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 15 Feb 2009 18:44:47 +0100 Subject: [Pw_forum] Atom 01 not found In-Reply-To: <010d01c98f31$246925d0$6d3b7170$@net> References: <010d01c98f31$246925d0$6d3b7170$@net> Message-ID: On Feb 15, 2009, at 6:49 , Paul M. Grant wrote > Atom O1 not found > should have been fixed here: http://www.democritos.it:8888/O-sesame/chngview?cn=6108 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Sun Feb 15 18:45:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 15 Feb 2009 18:45:55 +0100 Subject: [Pw_forum] Benchmarking: openmpi-1.3 vs openmpi-1.2.8 In-Reply-To: <7920EE04A94045AB9C75E5C665DBDB8F@ctpm> References: <4996C56E.8020200@gmail.com> <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> <7920EE04A94045AB9C75E5C665DBDB8F@ctpm> Message-ID: <6247DCE3-F2A1-42AB-B424-BE6CC9B1A959@democritos.it> On Feb 15, 2009, at 11:54 , Mahmoud Payami wrote: > The out files show that in all parts "1.3" takes shorter time than > "1.2.8". > However, the wall time in "1.3" is slightly increased. I do not > know how to > resolve it. don't trust too much small differences in short runs Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Sun Feb 15 19:44:17 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 15 Feb 2009 13:44:17 -0500 (EST) Subject: [Pw_forum] Benchmarking: openmpi-1.3 vs openmpi-1.2.8 In-Reply-To: <7920EE04A94045AB9C75E5C665DBDB8F@ctpm> References: <4996C56E.8020200@gmail.com> <5EAFA262-4E62-40C1-844B-1F4C330699A6@democritos.it> <7920EE04A94045AB9C75E5C665DBDB8F@ctpm> Message-ID: On Sun, 15 Feb 2009, Mahmoud Payami wrote: MP> Dear ALL, MP> MP> I performed a benchmarking test using openmpi-1.2.8 and openmpi-1.3 for a MP> 2-atom Au cluster. MP> The out files show that in all parts "1.3" takes shorter time than "1.2.8". MP> However, the wall time in "1.3" is slightly increased. I do not know how to MP> resolve it. Is the bottleneck the connection cables? MP> Bests, MP> Mahmoud Payami MP> MP> ---------------------------------------- MP> #out_1.2.8 MP> PWSCF : 2m 5.29s CPU time, 4m43.10s wall time wow. your wall time is over double the CPU time. this is _bad_. over half of your cpu power is wasted. what kind of setup are you running? what interconnect? what types of machines? without context there is little to learn from this. [...] MP> #out-1.3 MP> PWSCF : 1m55.59s CPU time, 4m44.04s wall time same here. in practice on the wall time matters, so there is no significant difference. but it also is highly likely, that you are not running in an efficient way. this is not really useful in telling you anything about the two mpi versions. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From w2agz at pacbell.net Sun Feb 15 20:57:21 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 15 Feb 2009 11:57:21 -0800 Subject: [Pw_forum] Atom 01 not found In-Reply-To: References: <010d01c98f31$246925d0$6d3b7170$@net> Message-ID: <013601c98fa7$9d760e40$d8622ac0$@net> Thanks, Paolo. I'll insert these patches later today. Two quick questions: 1) Is there a utility you use to automate the insertion of patches, and 2) Will there be a new release of QE coming soon? Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Sunday, February 15, 2009 9:45 AM To: PWSCF Forum Subject: Re: [Pw_forum] Atom 01 not found On Feb 15, 2009, at 6:49 , Paul M. Grant wrote > Atom O1 not found > should have been fixed here: http://www.democritos.it:8888/O-sesame/chngview?cn=6108 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Sun Feb 15 21:15:31 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 15 Feb 2009 15:15:31 -0500 (EST) Subject: [Pw_forum] Atom 01 not found In-Reply-To: <013601c98fa7$9d760e40$d8622ac0$@net> References: <010d01c98f31$246925d0$6d3b7170$@net> <013601c98fa7$9d760e40$d8622ac0$@net> Message-ID: On Sun, 15 Feb 2009, Paul M. Grant wrote: PG> Thanks, Paolo. PG> PG> I'll insert these patches later today. PG> PG> Two quick questions: 1) Is there a utility you use to automate the insertion yes. it is called "patch" (see 'man patch'). ;) if you download a patch from the cvs via the web interface, you should click on the "patchset" link and save the resulting file as text and then use: patch -b -p# < patchfile in the directory of the files to be patched, where # is the number of forward slashes to be removed from the pathnames in the patch file. cheers, axel. PG> of patches, and 2) Will there be a new release of QE coming soon? PG> PG> Paul M. Grant, PhD PG> Principal, W2AGZ Technologies PG> Visiting Scholar, Applied Physics, Stanford (2005-2008) PG> EPRI Science Fellow (Retired) PG> IBM Research Staff Member Emeritus PG> w2agz at pacbell.net PG> http://www.w2agz.com PG> ? PG> ? PG> PG> PG> -----Original Message----- PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On PG> Behalf Of Paolo Giannozzi PG> Sent: Sunday, February 15, 2009 9:45 AM PG> To: PWSCF Forum PG> Subject: Re: [Pw_forum] Atom 01 not found PG> PG> PG> On Feb 15, 2009, at 6:49 , Paul M. Grant wrote PG> > Atom O1 not found PG> > PG> should have been fixed here: PG> http://www.democritos.it:8888/O-sesame/chngview?cn=6108 PG> PG> Paolo PG> --- PG> Paolo Giannozzi, Democritos and University of Udine, Italy PG> PG> PG> _______________________________________________ PG> Pw_forum mailing list PG> Pw_forum at pwscf.org PG> http://www.democritos.it/mailman/listinfo/pw_forum PG> PG> PG> _______________________________________________ PG> Pw_forum mailing list PG> Pw_forum at pwscf.org PG> http://www.democritos.it/mailman/listinfo/pw_forum PG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From w2agz at pacbell.net Sun Feb 15 22:52:15 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 15 Feb 2009 13:52:15 -0800 Subject: [Pw_forum] Atom 01 not found In-Reply-To: References: <010d01c98f31$246925d0$6d3b7170$@net> Message-ID: <014601c98fb7$aae4d380$00ae7a80$@net> Sorry, Paolo, the fix didn't work...the code still seems to not recognize O(oxygen)1. I checked the changed atomic_number.f90 and capital.f90 codes twice against the patch, and my changes compiled and "made" successfully. Incidentally, take a look at the following lines from the patch: atom(2:2)=capital(atm(1:1)) else if (atm(1:1) == ' ') then +! +! Case : atm=' X*' +! atom(2:2)=capital(atm(2:2)) + atom(2:2)=capital(atm(1:1)) else Isn't the line + atom(2:2)=capital(atm(1:1)) somewhat redundant? Should it be "atom(1:1)=..."? Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Sunday, February 15, 2009 9:45 AM To: PWSCF Forum Subject: Re: [Pw_forum] Atom 01 not found On Feb 15, 2009, at 6:49 , Paul M. Grant wrote > Atom O1 not found > should have been fixed here: http://www.democritos.it:8888/O-sesame/chngview?cn=6108 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From w2agz at pacbell.net Sun Feb 15 23:18:03 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 15 Feb 2009 14:18:03 -0800 Subject: [Pw_forum] Atom 01 not found In-Reply-To: <014601c98fb7$aae4d380$00ae7a80$@net> References: <010d01c98f31$246925d0$6d3b7170$@net> <014601c98fb7$aae4d380$00ae7a80$@net> Message-ID: <014701c98fbb$4541db50$cfc591f0$@net> NEVER MIND! I forgot to re-make the PP directory. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paul M. Grant Sent: Sunday, February 15, 2009 1:52 PM To: 'PWSCF Forum' Subject: Re: [Pw_forum] Atom 01 not found Sorry, Paolo, the fix didn't work...the code still seems to not recognize O(oxygen)1. I checked the changed atomic_number.f90 and capital.f90 codes twice against the patch, and my changes compiled and "made" successfully. Incidentally, take a look at the following lines from the patch: atom(2:2)=capital(atm(1:1)) else if (atm(1:1) == ' ') then +! +! Case : atm=' X*' +! atom(2:2)=capital(atm(2:2)) + atom(2:2)=capital(atm(1:1)) else Isn't the line + atom(2:2)=capital(atm(1:1)) somewhat redundant? Should it be "atom(1:1)=..."? Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Sunday, February 15, 2009 9:45 AM To: PWSCF Forum Subject: Re: [Pw_forum] Atom 01 not found On Feb 15, 2009, at 6:49 , Paul M. Grant wrote > Atom O1 not found > should have been fixed here: http://www.democritos.it:8888/O-sesame/chngview?cn=6108 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Sun Feb 15 23:23:51 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 15 Feb 2009 17:23:51 -0500 (EST) Subject: [Pw_forum] Atom 01 not found In-Reply-To: <014601c98fb7$aae4d380$00ae7a80$@net> References: <010d01c98f31$246925d0$6d3b7170$@net> <014601c98fb7$aae4d380$00ae7a80$@net> Message-ID: On Sun, 15 Feb 2009, Paul M. Grant wrote: PMG> Sorry, Paolo, the fix didn't work...the code still seems to not recognize PMG> O(oxygen)1. I checked the changed atomic_number.f90 and capital.f90 codes PMG> twice against the patch, and my changes compiled and "made" successfully. PMG> Incidentally, take a look at the following lines from the patch: PMG> PMG> atom(2:2)=capital(atm(1:1)) PMG> else if (atm(1:1) == ' ') then PMG> +! PMG> +! Case : atm=' X*' PMG> +! PMG> atom(2:2)=capital(atm(2:2)) PMG> + atom(2:2)=capital(atm(1:1)) PMG> else PMG> PMG> Isn't the line PMG> + atom(2:2)=capital(atm(1:1)) PMG> somewhat redundant? Should it be "atom(1:1)=..."? nope. it has to be deleted. have a look at the list of elements above in the code. they have a leading blank. however, your case of "O1" should be handled in the if brach above. so this bug should not affect you. cheers, axel. PMG> PMG> Paul M. Grant, PhD PMG> Principal, W2AGZ Technologies PMG> Visiting Scholar, Applied Physics, Stanford (2005-2008) PMG> EPRI Science Fellow (Retired) PMG> IBM Research Staff Member Emeritus PMG> w2agz at pacbell.net PMG> http://www.w2agz.com PMG> ? PMG> ? PMG> PMG> PMG> -----Original Message----- PMG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On PMG> Behalf Of Paolo Giannozzi PMG> Sent: Sunday, February 15, 2009 9:45 AM PMG> To: PWSCF Forum PMG> Subject: Re: [Pw_forum] Atom 01 not found PMG> PMG> PMG> On Feb 15, 2009, at 6:49 , Paul M. Grant wrote PMG> > Atom O1 not found PMG> > PMG> should have been fixed here: PMG> http://www.democritos.it:8888/O-sesame/chngview?cn=6108 PMG> PMG> Paolo PMG> --- PMG> Paolo Giannozzi, Democritos and University of Udine, Italy PMG> PMG> PMG> _______________________________________________ PMG> Pw_forum mailing list PMG> Pw_forum at pwscf.org PMG> http://www.democritos.it/mailman/listinfo/pw_forum PMG> PMG> _______________________________________________ PMG> Pw_forum mailing list PMG> Pw_forum at pwscf.org PMG> http://www.democritos.it/mailman/listinfo/pw_forum PMG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Mon Feb 16 09:01:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Feb 2009 09:01:48 +0100 Subject: [Pw_forum] Atom 01 not found In-Reply-To: References: <010d01c98f31$246925d0$6d3b7170$@net> <014601c98fb7$aae4d380$00ae7a80$@net> Message-ID: <49991D6C.9040509@democritos.it> Axel Kohlmeyer wrote: > PMG> Isn't the line > PMG> + atom(2:2)=capital(atm(1:1)) > PMG> somewhat redundant? Should it be "atom(1:1)=..."? > > nope. it has to be deleted. fixed, thanks. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Feb 16 09:18:29 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Feb 2009 09:18:29 +0100 Subject: [Pw_forum] Atom 01 not found In-Reply-To: <013601c98fa7$9d760e40$d8622ac0$@net> References: <010d01c98f31$246925d0$6d3b7170$@net> <013601c98fa7$9d760e40$d8622ac0$@net> Message-ID: <49992155.7050704@democritos.it> Paul M. Grant wrote: > Will there be a new release of QE coming soon? I think there have been enough changes since the latest release to justify a new one soon. The exact definition "soon" is however not yet clear...Anyway: from time to time, CVS snapshots are made available on the download page. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From mahmoud.payami at gmail.com Mon Feb 16 14:18:30 2009 From: mahmoud.payami at gmail.com (Mahmoud Payami) Date: Mon, 16 Feb 2009 16:48:30 +0330 Subject: [Pw_forum] Benchmarking: openmpi-1.3 vs openmpi-1.2.8 Message-ID: <118b978f0902160518j1ee65843x12e130f3e71938fd@mail.gmail.com> Dear Axel and Paolo, Thank you for the comments. For Paolo's advice, I repeated the same job more than 5 times, the results differed within some percent of second, so I can trust at least on "PWSCF : 1m58.00s CPU time, 4m44.00s wall time". On the other hand, for Axel's advice, I eliminated the interconnection factor just by running on a single box with 2 cores (P4 3.2G), and obtained the acceptable result: "PWSCF : 1m58.54s CPU time, 2m10.72s wall time". :-) The wall time is decreased to less than half of the run on 4 cores in 2 boxes, and now "wall time" and "cpu time" are more or less the same. Thank you again! cheers, mahmoud -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090216/a08bba85/attachment.htm From powergreen at gmail.com Mon Feb 16 21:57:44 2009 From: powergreen at gmail.com (Green Power) Date: Mon, 16 Feb 2009 15:57:44 -0500 Subject: [Pw_forum] Hydrogen dissociation test Message-ID: Hi, All, I wonder how to do broken symmetry calculations for a hydrogen molecule with a separation larger than 3.0 a.u. using pw.x code. As I understand, the in the region larger then 3.0 a.u. separation, the restricted wavefountion method, for instance the RHF, would fail, and UHF method or correlation method is needed. I don't know how to break the symmetry of alpha spin and beta spin using pw.x code. I tried to do that by spin-polarized calculations using the following input. The energy is 0.05 a.u.lower than the sipn-unpolarized method at he hydrogen separation of 2.4333672 angstom. But at the sepration of 2.0100254, the spin-polarized method gave much energy then sipn-unpolarized. Could you please check my input file? Mabye I have smething wrong. Another question is about the binding energy of hydrgen molecule. I calculated the total engergy of H2 at 0.74 angstrom bond distanced and the energy H atom, and comapred the energy difference, I got a binding energy much higher than the experimental value of 436 kj/mol. I guess I did not calculate the energy of Hydrogen atom properly. Could you give me any suggestion how to do that? Thank you. Qian *INPUT: Spin-polarized calculation* &control / &system ibrav = 1 celldm(1) = 30.0 nat = 2 ntyp = 1 nosym=.true., starting_magnetization(1)=1.0 nspin =2 ecutwfc = 60.0 occupations = 'smearing' degauss = 0.01 smearing = 'gaussian' / &electrons conv_thr = 1.0d-8 / ATOMIC_SPECIES H 1.00 H.vbc.UPF ATOMIC_POSITIONS {angstrom} H 0.0 0.0 0.0 H 2.4333672 0.0 0.0 K_POINTS AUTOMATIC 1 1 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090216/aa410663/attachment.htm From akohlmey at cmm.chem.upenn.edu Mon Feb 16 22:11:25 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 16 Feb 2009 16:11:25 -0500 (EST) Subject: [Pw_forum] Hydrogen dissociation test In-Reply-To: References: Message-ID: On Mon, 16 Feb 2009, Green Power wrote: GP> Hi, All, GP> I wonder how to do broken symmetry calculations for a hydrogen molecule with GP> a separation larger than 3.0 a.u. using pw.x code. As I understand, the i GP> the region larger then 3.0 a.u. separation, the restricted wavefountion GP> method, for instance the RHF, would fail, and UHF method or correlation please do not confuse pw.x with a "normal" quantum chemistry program (like gamess, gaussian etc.). if you want to scan the breaking of an H-H bond, you have to use a multi-determinant method. pw.x (and cp.x) use(s) DFT exclusively. GP> method is needed. I don't know how to break the symmetry of alpha spin and GP> beta spin using pw.x code. I tried to do that by spin-polarized calculations you have to assign two hydrogen atom types. H1, H2 and then initialize their magnetization in opposing directions. GP> using the following input. The energy is 0.05 a.u.lower than the GP> sipn-unpolarized method at he hydrogen separation of 2.4333672 angstom. But GP> at the sepration of 2.0100254, the spin-polarized method gave much energy GP> then sipn-unpolarized. Could you please check my input file? Mabye I have GP> smething wrong. GP> GP> Another question is about the binding energy of hydrgen molecule. I GP> calculated the total engergy of H2 at 0.74 angstrom bond distanced and the GP> energy H atom, and comapred the energy difference, I got a binding energy GP> much higher than the experimental value of 436 kj/mol. I guess I did not what experiment? have you computed the minimum H-H distance first? GP> calculate the energy of Hydrogen atom properly. Could you give me any GP> suggestion how to do that? doing this kind of calculation is not as simple as with a code using an atom centered basis set. you are always computing a supercell (and its vacuum) and you have to make sure that this cell is large enough, so that periodic interactions don't matter, as well as you have to make sure that atoms stay at their relative positions, since with plane waves and a small(ish) cutoff, the total energy depends to some degree on the position of an atom in space (so-called ripples). finally, you should factor in that you are using an LDA pseudopotential, and LDA has a tendency to overbind. not sure whether that explains your observations, since you don't say how much your result deviates. in general, i suggest you have an extensive look at the mailing list archives which contain many answers and explanations to your kind of beginner questions. cheers, axel. GP> Thank you. GP> GP> Qian GP> GP> GP> *INPUT: Spin-polarized calculation* GP> &control GP> / GP> &system GP> ibrav = 1 GP> celldm(1) = 30.0 GP> nat = 2 GP> ntyp = 1 GP> nosym=.true., GP> starting_magnetization(1)=1.0 GP> nspin =2 GP> ecutwfc = 60.0 GP> occupations = 'smearing' GP> degauss = 0.01 GP> smearing = 'gaussian' GP> / GP> &electrons GP> conv_thr = 1.0d-8 GP> / GP> ATOMIC_SPECIES GP> H 1.00 H.vbc.UPF GP> ATOMIC_POSITIONS {angstrom} GP> H 0.0 0.0 0.0 GP> H 2.4333672 0.0 0.0 GP> K_POINTS AUTOMATIC GP> 1 1 1 0 0 0 GP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From somesh.kb at gmail.com Mon Feb 16 23:08:40 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Mon, 16 Feb 2009 23:08:40 +0100 Subject: [Pw_forum] Relaxation of AlN surface Message-ID: Dear All, I am a new to PWSCF. I am trying to relax a surface slab of AlN which has 32 atoms. However, the system is not achieving convergence. The input file is : &control calculation = 'relax' restart_mode='from_scratch', prefix='AlN', nstep = 100, tprnfor = .true., etot_conv_thr = 1.d-8, pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', outdir='.' / &system ibrav= 4, celldm(1) = 11.71623992919922, celldm(3) = 4.513,nat=32, ntyp= 2, ecutwfc =30.0, ecutrho = 400, nspin =1, / &electrons electron_maxstep=150, conv_thr = 1.D-6, mixing_mode = 'local-TF', mixing_beta = 0.2, / &ions ion_dynamics='bfgs', phase_space = 'full' / ATOMIC_SPECIES Al 26.98154 Al.pw91-n-van.UPF N 14.00674 N.pw91-van_ak.UPF ATOMIC_POSITIONS {angstrom} Al 1.549999937 4.474454315 14.919999921 1 1 1 Al 1.549999937 4.474454315 9.919999843 0 0 0 Al -0.000000015 7.159132936 14.919999921 1 1 1 Al -0.000000015 7.159132936 9.919999843 0 0 0 Al 4.649999842 4.474454315 14.919999921 1 1 1 Al 4.649999842 4.474454315 9.919999843 0 0 0 Al 3.099999890 7.159132936 14.919999921 1 1 1 Al 3.099999890 7.159132936 9.919999843 0 0 0 N 1.549999937 4.474454315 6.818997379 0 0 0 N 1.549999937 4.474454315 11.778997301 0 0 0 N -0.000000015 7.159132936 6.818997379 0 0 0 N -0.000000015 7.159132936 11.778997301 0 0 0 N 4.649999842 4.474454315 6.818997379 0 0 0 N 4.649999842 4.474454315 11.778997301 0 0 0 N 3.099999890 7.159132936 6.818997379 0 0 0 N 3.099999890 7.159132936 11.778997301 0 0 0 Al 3.099991178 3.579566454 7.439985857 0 0 0 Al 3.099991178 3.579566454 12.399985779 0 0 0 Al 1.549991226 6.264245075 7.439985857 0 0 0 Al 1.549991226 6.264245075 12.399985779 0 0 0 Al 6.199991083 3.579566454 7.439985857 0 0 0 Al 6.199991083 3.579566454 12.399985779 0 0 0 Al 4.649991131 6.264245075 7.439985857 0 0 0 Al 4.649991131 6.264245075 12.399985779 0 0 0 N 3.099991178 3.579566454 9.298983315 0 0 0 N 3.099991178 3.579566454 14.258983237 1 1 1 N 1.549991226 6.264245075 9.298983315 0 0 0 N 1.549991226 6.264245075 14.258983237 1 1 1 N 6.199991083 3.579566454 9.298983315 0 0 0 N 6.199991083 3.579566454 14.258983237 1 1 1 N 4.649991131 6.264245075 9.298983315 0 0 0 N 4.649991131 6.264245075 14.258983237 1 1 1 K_POINTS {GAMMA} I am allowing only the top two layers to relax. Using --- grep scf < *.out ...... the output is the following : estimated scf accuracy < 21.54311123 Ry estimated scf accuracy < 16.91216138 Ry estimated scf accuracy < 6.80358058 Ry estimated scf accuracy < 10.02440462 Ry estimated scf accuracy < 5.42211905 Ry estimated scf accuracy < 3.98570225 Ry estimated scf accuracy < 3.63368556 Ry estimated scf accuracy < 2.80935163 Ry estimated scf accuracy < 2.18832175 Ry estimated scf accuracy < 1.88438498 Ry estimated scf accuracy < 1.34984265 Ry estimated scf accuracy < 1.15892961 Ry estimated scf accuracy < 1.08983405 Ry estimated scf accuracy < 11.86322500 Ry estimated scf accuracy < 9.08655092 Ry estimated scf accuracy < 10.92075279 Ry estimated scf accuracy < 11.43007849 Ry ................. The system never attain convergence. Can anyone kindly suggest the possible source of error on my part. Regards, Somesh ............................... Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 From eyvaz_isaev at yahoo.com Tue Feb 17 00:03:14 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 16 Feb 2009 15:03:14 -0800 (PST) Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: Message-ID: <415464.16574.qm@web65710.mail.ac4.yahoo.com> Dear Somesh, Looking at your structure by means of XCrysDen have shown you have a slab with vacuum on both sides. Most likely, your system is metallized due to surface states and you should consider it as metallic turning on "occupations" and related keywords. Please have a look at /DOC/INPUT_PW. Hope this helps. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 2/17/09, Somesh Kumar Bhattacharya wrote: > From: Somesh Kumar Bhattacharya > Subject: [Pw_forum] Relaxation of AlN surface > To: pw_forum at pwscf.org > Date: Tuesday, February 17, 2009, 1:08 AM > Dear All, > > I am a new to PWSCF. > > I am trying to relax a surface slab of AlN which has 32 > atoms. > However, the system is not achieving convergence. > > The input file is : > > &control > calculation = 'relax' > restart_mode='from_scratch', > prefix='AlN', > nstep = 100, > tprnfor = .true., > etot_conv_thr = 1.d-8, > pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', > outdir='.' > / > &system > ibrav= 4, celldm(1) = 11.71623992919922, > celldm(3) = 4.513,nat=32, ntyp= 2, > ecutwfc =30.0, ecutrho = 400, nspin =1, > / > &electrons > electron_maxstep=150, > conv_thr = 1.D-6, > mixing_mode = 'local-TF', > mixing_beta = 0.2, > / > &ions > ion_dynamics='bfgs', > phase_space = 'full' > / > ATOMIC_SPECIES > Al 26.98154 Al.pw91-n-van.UPF > N 14.00674 N.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > Al 1.549999937 4.474454315 14.919999921 1 1 1 > Al 1.549999937 4.474454315 9.919999843 0 0 0 > Al -0.000000015 7.159132936 14.919999921 1 1 1 > Al -0.000000015 7.159132936 9.919999843 0 0 0 > Al 4.649999842 4.474454315 14.919999921 1 1 1 > Al 4.649999842 4.474454315 9.919999843 0 0 0 > Al 3.099999890 7.159132936 14.919999921 1 1 1 > Al 3.099999890 7.159132936 9.919999843 0 0 0 > N 1.549999937 4.474454315 6.818997379 0 0 0 > N 1.549999937 4.474454315 11.778997301 0 0 0 > N -0.000000015 7.159132936 6.818997379 0 0 0 > N -0.000000015 7.159132936 11.778997301 0 0 0 > N 4.649999842 4.474454315 6.818997379 0 0 0 > N 4.649999842 4.474454315 11.778997301 0 0 0 > N 3.099999890 7.159132936 6.818997379 0 0 0 > N 3.099999890 7.159132936 11.778997301 0 0 0 > Al 3.099991178 3.579566454 7.439985857 0 0 0 > Al 3.099991178 3.579566454 12.399985779 0 0 0 > Al 1.549991226 6.264245075 7.439985857 0 0 0 > Al 1.549991226 6.264245075 12.399985779 0 0 0 > Al 6.199991083 3.579566454 7.439985857 0 0 0 > Al 6.199991083 3.579566454 12.399985779 0 0 0 > Al 4.649991131 6.264245075 7.439985857 0 0 0 > Al 4.649991131 6.264245075 12.399985779 0 0 0 > N 3.099991178 3.579566454 9.298983315 0 0 0 > N 3.099991178 3.579566454 14.258983237 1 1 1 > N 1.549991226 6.264245075 9.298983315 0 0 0 > N 1.549991226 6.264245075 14.258983237 1 1 1 > N 6.199991083 3.579566454 9.298983315 0 0 0 > N 6.199991083 3.579566454 14.258983237 1 1 1 > N 4.649991131 6.264245075 9.298983315 0 0 0 > N 4.649991131 6.264245075 14.258983237 1 1 1 > K_POINTS {GAMMA} > > > I am allowing only the top two layers to relax. > > Using --- grep scf < *.out ...... the output is the > following : > > estimated scf accuracy < 21.54311123 Ry > estimated scf accuracy < 16.91216138 Ry > estimated scf accuracy < 6.80358058 Ry > estimated scf accuracy < 10.02440462 Ry > estimated scf accuracy < 5.42211905 Ry > estimated scf accuracy < 3.98570225 Ry > estimated scf accuracy < 3.63368556 Ry > estimated scf accuracy < 2.80935163 Ry > estimated scf accuracy < 2.18832175 Ry > estimated scf accuracy < 1.88438498 Ry > estimated scf accuracy < 1.34984265 Ry > estimated scf accuracy < 1.15892961 Ry > estimated scf accuracy < 1.08983405 Ry > estimated scf accuracy < 11.86322500 Ry > estimated scf accuracy < 9.08655092 Ry > estimated scf accuracy < 10.92075279 Ry > estimated scf accuracy < 11.43007849 Ry > ................. > > The system never attain convergence. > > Can anyone kindly suggest the possible source of error on > my part. > > Regards, > Somesh > ............................... > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical > Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From zhukov at ihim.uran.ru Tue Feb 17 05:00:48 2009 From: zhukov at ihim.uran.ru (Vladlen Zhukov Windows) Date: Tue, 17 Feb 2009 09:00:48 +0500 Subject: [Pw_forum] Relaxation of AlN surface References: Message-ID: <003701c990b4$514be090$2b88a8c0@ZHUKOV> Hi! Are you shure that the atomic coordinates are correct? In fact, estimated scf accuracy is too big from the very beginning. Although I am also novice in PW-calculations, I relaxed recently anatase very successfully, so my impression is that PW is beautifull is this respect. ---------------------------------------------------------------------- Vladlen P. Zhukov, chief research associate, Institute of Solid State Chemistry, Russian Academy of Sciences, Ekaterinburg, Russia ----- Original Message ----- From: "Somesh Kumar Bhattacharya" To: Sent: Tuesday, February 17, 2009 3:08 AM Subject: [Pw_forum] Relaxation of AlN surface > Dear All, > > I am a new to PWSCF. > > I am trying to relax a surface slab of AlN which has 32 atoms. > However, the system is not achieving convergence. > > The input file is : > > &control > calculation = 'relax' > restart_mode='from_scratch', > prefix='AlN', > nstep = 100, > tprnfor = .true., > etot_conv_thr = 1.d-8, > pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', > outdir='.' > / > &system > ibrav= 4, celldm(1) = 11.71623992919922, > celldm(3) = 4.513,nat=32, ntyp= 2, > ecutwfc =30.0, ecutrho = 400, nspin =1, > / > &electrons > electron_maxstep=150, > conv_thr = 1.D-6, > mixing_mode = 'local-TF', > mixing_beta = 0.2, > / > &ions > ion_dynamics='bfgs', > phase_space = 'full' > / > ATOMIC_SPECIES > Al 26.98154 Al.pw91-n-van.UPF > N 14.00674 N.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > Al 1.549999937 4.474454315 14.919999921 1 1 1 > Al 1.549999937 4.474454315 9.919999843 0 0 0 > Al -0.000000015 7.159132936 14.919999921 1 1 1 > Al -0.000000015 7.159132936 9.919999843 0 0 0 > Al 4.649999842 4.474454315 14.919999921 1 1 1 > Al 4.649999842 4.474454315 9.919999843 0 0 0 > Al 3.099999890 7.159132936 14.919999921 1 1 1 > Al 3.099999890 7.159132936 9.919999843 0 0 0 > N 1.549999937 4.474454315 6.818997379 0 0 0 > N 1.549999937 4.474454315 11.778997301 0 0 0 > N -0.000000015 7.159132936 6.818997379 0 0 0 > N -0.000000015 7.159132936 11.778997301 0 0 0 > N 4.649999842 4.474454315 6.818997379 0 0 0 > N 4.649999842 4.474454315 11.778997301 0 0 0 > N 3.099999890 7.159132936 6.818997379 0 0 0 > N 3.099999890 7.159132936 11.778997301 0 0 0 > Al 3.099991178 3.579566454 7.439985857 0 0 0 > Al 3.099991178 3.579566454 12.399985779 0 0 0 > Al 1.549991226 6.264245075 7.439985857 0 0 0 > Al 1.549991226 6.264245075 12.399985779 0 0 0 > Al 6.199991083 3.579566454 7.439985857 0 0 0 > Al 6.199991083 3.579566454 12.399985779 0 0 0 > Al 4.649991131 6.264245075 7.439985857 0 0 0 > Al 4.649991131 6.264245075 12.399985779 0 0 0 > N 3.099991178 3.579566454 9.298983315 0 0 0 > N 3.099991178 3.579566454 14.258983237 1 1 1 > N 1.549991226 6.264245075 9.298983315 0 0 0 > N 1.549991226 6.264245075 14.258983237 1 1 1 > N 6.199991083 3.579566454 9.298983315 0 0 0 > N 6.199991083 3.579566454 14.258983237 1 1 1 > N 4.649991131 6.264245075 9.298983315 0 0 0 > N 4.649991131 6.264245075 14.258983237 1 1 1 > K_POINTS {GAMMA} > > > I am allowing only the top two layers to relax. > > Using --- grep scf < *.out ...... the output is the following : > > estimated scf accuracy < 21.54311123 Ry > estimated scf accuracy < 16.91216138 Ry > estimated scf accuracy < 6.80358058 Ry > estimated scf accuracy < 10.02440462 Ry > estimated scf accuracy < 5.42211905 Ry > estimated scf accuracy < 3.98570225 Ry > estimated scf accuracy < 3.63368556 Ry > estimated scf accuracy < 2.80935163 Ry > estimated scf accuracy < 2.18832175 Ry > estimated scf accuracy < 1.88438498 Ry > estimated scf accuracy < 1.34984265 Ry > estimated scf accuracy < 1.15892961 Ry > estimated scf accuracy < 1.08983405 Ry > estimated scf accuracy < 11.86322500 Ry > estimated scf accuracy < 9.08655092 Ry > estimated scf accuracy < 10.92075279 Ry > estimated scf accuracy < 11.43007849 Ry > ................. > > The system never attain convergence. > > Can anyone kindly suggest the possible source of error on my part. > > Regards, > Somesh > ............................... > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From lanhaiping at gmail.com Tue Feb 17 05:46:02 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 17 Feb 2009 12:46:02 +0800 Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: References: Message-ID: Hi, Somesh , How do you think about the thread for electron scf : conv_thr = 1.D-6 ? And only gamma k-point sampling for your cell seems not enough . regards, On Tue, Feb 17, 2009 at 6:08 AM, Somesh Kumar Bhattacharya < somesh.kb at gmail.com> wrote: > Dear All, > > I am a new to PWSCF. > > I am trying to relax a surface slab of AlN which has 32 atoms. > However, the system is not achieving convergence. > > The input file is : > > &control > calculation = 'relax' > restart_mode='from_scratch', > prefix='AlN', > nstep = 100, > tprnfor = .true., > etot_conv_thr = 1.d-8, > pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', > outdir='.' > / > &system > ibrav= 4, celldm(1) = 11.71623992919922, > celldm(3) = 4.513,nat=32, ntyp= 2, > ecutwfc =30.0, ecutrho = 400, nspin =1, > / > &electrons > electron_maxstep=150, > conv_thr = 1.D-6, > mixing_mode = 'local-TF', > mixing_beta = 0.2, > / > &ions > ion_dynamics='bfgs', > phase_space = 'full' > / > ATOMIC_SPECIES > Al 26.98154 Al.pw91-n-van.UPF > N 14.00674 N.pw91-van_ak.UPF > ATOMIC_POSITIONS {angstrom} > Al 1.549999937 4.474454315 14.919999921 1 1 1 > Al 1.549999937 4.474454315 9.919999843 0 0 0 > Al -0.000000015 7.159132936 14.919999921 1 1 1 > Al -0.000000015 7.159132936 9.919999843 0 0 0 > Al 4.649999842 4.474454315 14.919999921 1 1 1 > Al 4.649999842 4.474454315 9.919999843 0 0 0 > Al 3.099999890 7.159132936 14.919999921 1 1 1 > Al 3.099999890 7.159132936 9.919999843 0 0 0 > N 1.549999937 4.474454315 6.818997379 0 0 0 > N 1.549999937 4.474454315 11.778997301 0 0 0 > N -0.000000015 7.159132936 6.818997379 0 0 0 > N -0.000000015 7.159132936 11.778997301 0 0 0 > N 4.649999842 4.474454315 6.818997379 0 0 0 > N 4.649999842 4.474454315 11.778997301 0 0 0 > N 3.099999890 7.159132936 6.818997379 0 0 0 > N 3.099999890 7.159132936 11.778997301 0 0 0 > Al 3.099991178 3.579566454 7.439985857 0 0 0 > Al 3.099991178 3.579566454 12.399985779 0 0 0 > Al 1.549991226 6.264245075 7.439985857 0 0 0 > Al 1.549991226 6.264245075 12.399985779 0 0 0 > Al 6.199991083 3.579566454 7.439985857 0 0 0 > Al 6.199991083 3.579566454 12.399985779 0 0 0 > Al 4.649991131 6.264245075 7.439985857 0 0 0 > Al 4.649991131 6.264245075 12.399985779 0 0 0 > N 3.099991178 3.579566454 9.298983315 0 0 0 > N 3.099991178 3.579566454 14.258983237 1 1 1 > N 1.549991226 6.264245075 9.298983315 0 0 0 > N 1.549991226 6.264245075 14.258983237 1 1 1 > N 6.199991083 3.579566454 9.298983315 0 0 0 > N 6.199991083 3.579566454 14.258983237 1 1 1 > N 4.649991131 6.264245075 9.298983315 0 0 0 > N 4.649991131 6.264245075 14.258983237 1 1 1 > K_POINTS {GAMMA} > > > I am allowing only the top two layers to relax. > > Using --- grep scf < *.out ...... the output is the following : > > estimated scf accuracy < 21.54311123 Ry > estimated scf accuracy < 16.91216138 Ry > estimated scf accuracy < 6.80358058 Ry > estimated scf accuracy < 10.02440462 Ry > estimated scf accuracy < 5.42211905 Ry > estimated scf accuracy < 3.98570225 Ry > estimated scf accuracy < 3.63368556 Ry > estimated scf accuracy < 2.80935163 Ry > estimated scf accuracy < 2.18832175 Ry > estimated scf accuracy < 1.88438498 Ry > estimated scf accuracy < 1.34984265 Ry > estimated scf accuracy < 1.15892961 Ry > estimated scf accuracy < 1.08983405 Ry > estimated scf accuracy < 11.86322500 Ry > estimated scf accuracy < 9.08655092 Ry > estimated scf accuracy < 10.92075279 Ry > estimated scf accuracy < 11.43007849 Ry > ................. > > The system never attain convergence. > > Can anyone kindly suggest the possible source of error on my part. > > Regards, > Somesh > ............................... > Somesh Kr. Bhattacharya > Post Doctoral Fellow > Room No. 263, > Leonardo Building, > The Abdus Salam International Centre for Theoretical Physics > Strada Costiera, 11 > I-34014 Trieste > Italy > Phone: +39-040-2240399 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090217/22bdfca7/attachment.htm From rajanpnano at gmail.com Tue Feb 17 08:11:31 2009 From: rajanpnano at gmail.com (Raj Pandey) Date: Tue, 17 Feb 2009 12:41:31 +0530 Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) Message-ID: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Dear PWSCF developers and users, I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg or gif movie from "file.axsf" (about 152 coordinate steps), I get the following error at 70th step: ERROR: while executing exec /usr/bin/convert /home/rajan/xcrys_tmp/xc_13003/tmp.ppm /home/rajan/xcrys_tmp/xc_13003/anime69.jpg I will greatly appreciate your help/suggestion. Thanks, From giannozz at democritos.it Tue Feb 17 10:00:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 10:00:30 +0100 Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: References: Message-ID: <499A7CAE.8050109@democritos.it> lan haiping wrote: > How do you think about the thread for electron scf : conv_thr = 1.D-6 ? I think it is quite good. Consider that it will be reduced during structural optimization. What is meaningless (way too small) is the following: etot_conv_thr = 1.d-8 This is however irrelevant for scf convergence. > And only gamma k-point sampling for your cell only gamma may be sufficient or not, one has to verify. I would try a denser grid in the xy direction. The main problem in this case is however that the system is treated as an insulator. It should be sufficient to add a few more bands and a broadening, as explained by Eyvaz Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Feb 17 10:18:42 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 10:18:42 +0100 Subject: [Pw_forum] STEP-4 [Phonon] In-Reply-To: <1234549285.S.3878.47224.f4mail-235-209.rediffmail.com.old.replied.1234674957.43863@webmail.rediffmail.com> References: <1234549285.S.3878.47224.f4mail-235-209.rediffmail.com.old.replied.1234674957.43863@webmail.rediffmail.com> Message-ID: <499A80F2.3030108@democritos.it> Sanjeev K. Gupta wrote: > Now i want to plot the phonon dispersion?, Sir, Plz. suggest me > how i do that and these q-point are sufficient to plot PDC? please have a look at example 06 Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Tue Feb 17 10:24:12 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 17 Feb 2009 10:24:12 +0100 Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: References: Message-ID: <499A823C.2010907@sissa.it> On top of all other suggestions, I just want to add that it is not sage to ask for an energy convergence threshold (for relaxation) as strict as etot_conv_thr = 1.d-8, while you use only conv_thr = 1.D-6 for the self consistency threshold. My suggestion is to choose conv_thr = 1.D-8 and leave etot_conv_thr to the default (unless you have some specific needing). Also consider increasing upscale from its default value. GS lan haiping wrote: > Hi, Somesh , > How do you think about the thread for electron scf : conv_thr = 1.D-6 ? > And only gamma k-point sampling for your cell > seems not enough . > > regards, > > On Tue, Feb 17, 2009 at 6:08 AM, Somesh Kumar Bhattacharya > > wrote: > > Dear All, > > I am a new to PWSCF. > > I am trying to relax a surface slab of AlN which has 32 atoms. > However, the system is not achieving convergence. > > The input file is : > > &control > calculation = 'relax' > restart_mode='from_scratch', > prefix='AlN', > nstep = 100, > tprnfor = .true., > etot_conv_thr = 1.d-8, > pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', > outdir='.' > / > &system > ibrav= 4, celldm(1) = 11.71623992919922, > celldm(3) = 4.513,nat=32, ntyp= 2, > ecutwfc =30.0, ecutrho = 400, nspin =1, > / > &electrons > electron_maxstep=150, > conv_thr = 1.D-6, > mixing_mode = 'local-TF', > mixing_beta = 0.2, > / > &ions > ion_dynamics='bfgs', > phase_space = 'full' > / -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Tue Feb 17 10:27:22 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 10:27:22 +0100 Subject: [Pw_forum] Pseudopotential for Mg-PBE in upf file In-Reply-To: <531402.95201.qm@web31003.mail.mud.yahoo.com> References: <531402.95201.qm@web31003.mail.mud.yahoo.com> Message-ID: <499A82FA.8080609@democritos.it> Nguyen Ngoc Ha wrote: > I can not find where to get Mg-PBE upf potential, > Does anyone share this PP or give me some advice? please generate one with this input file (it is in the CVS version of the pseudppotential library) and report if it works well Paolo &input atom='Mg', rel=1, config='[Ne] 3s2 3p0 3d-1' iswitch=3, dft='PBE', / &inputp lloc=2, pseudotype=2, nlcc=.true., file_pseudopw='Mg.pbe-n-rrkj.UPF', author='PG' / 3 3S 1 0 2.00 0.00 2.50 2.50 3P 2 1 0.00 0.00 2.70 2.70 3D 3 2 -2.00 0.25 2.30 2.30 -- Paolo Giannozzi, Democritos and University of Udine, Italy From baris.malcioglu at gmail.com Tue Feb 17 10:40:07 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Tue, 17 Feb 2009 10:40:07 +0100 Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) In-Reply-To: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> References: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Message-ID: Dear Raj, If you are absolutely sure Imagemagick is working correctly in your system, try exporting the 70th frame to a pixmap file yourself. You may get a more descriptive error. Maybe you should try xcrysden mailing list at (http://www.democritos.it/mailman/listinfo/xcrysden) for more definitive answers. Best, O. Baris Malcioglu SISSA CM sector. On Tue, Feb 17, 2009 at 8:11 AM, Raj Pandey wrote: > Dear PWSCF developers and users, > > I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed > whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg > or gif movie from "file.axsf" (about 152 coordinate steps), I get the > following error at 70th step: > > ERROR: while executing > exec /usr/bin/convert > /home/rajan/xcrys_tmp/xc_13003/tmp.ppm > /home/rajan/xcrys_tmp/xc_13003/anime69.jpg > > I will greatly appreciate your help/suggestion. > > Thanks, > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From m.abbasnejad at gmail.com Tue Feb 17 10:53:54 2009 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Tue, 17 Feb 2009 13:23:54 +0330 Subject: [Pw_forum] vc-relax Message-ID: <7699a1950902170153hefda508j565ade6c95f19615@mail.gmail.com> Dear all, I was trying to do "vc-relax" for an orthorhombic unit cell consisting of 24 ions. I also put "nosym=.true.". At the end, I received this error: " End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping " Would you please help me? Yours, Mohaddeseh -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090217/459aa053/attachment.html From lanhaiping at gmail.com Tue Feb 17 11:12:31 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 17 Feb 2009 18:12:31 +0800 Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) In-Reply-To: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> References: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Message-ID: Hi, You should install gimp , a GNU image processor ! And please supply your affiliation . regards On Tue, Feb 17, 2009 at 3:11 PM, Raj Pandey wrote: > Dear PWSCF developers and users, > > I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed > whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg > or gif movie from "file.axsf" (about 152 coordinate steps), I get the > following error at 70th step: > > ERROR: while executing > exec /usr/bin/convert > /home/rajan/xcrys_tmp/xc_13003/tmp.ppm > /home/rajan/xcrys_tmp/xc_13003/anime69.jpg > > I will greatly appreciate your help/suggestion. > > Thanks, > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090217/5ba183d7/attachment.htm From giannozz at democritos.it Tue Feb 17 11:17:59 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 11:17:59 +0100 Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: References: Message-ID: <499A8ED7.9000408@democritos.it> lan haiping wrote: > How do you think about the thread for electron scf : conv_thr = 1.D-6 ? I think it is quite good. Consider that it will be reduced during structural optimization. What is meaningless (way too small) is the following: etot_conv_thr = 1.d-8 This is however irrelevant for scf convergence. > And only gamma k-point sampling for your cell seems not enough . gamma may or may not be sufficient; I would try a denser grid in the xy direction. The main problem in this case is however that the system is treated as an insulator. It is sufficient to add a few more bands and a broadening, as explained by Eyvaz Paolo (apologies if this message arrives twice: there was some problem on the mailing list this morning) -- Paolo Giannozzi, Democritos and University of Udine, Italy From tone.kokalj at ijs.si Tue Feb 17 11:42:18 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 17 Feb 2009 11:42:18 +0100 Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) In-Reply-To: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> References: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Message-ID: <1234867338.23760.7.camel@walk.ijs.si> On Tue, 2009-02-17 at 12:41 +0530, Raj Pandey wrote: > Dear PWSCF developers and users, > > I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed > whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg > or gif movie from "file.axsf" (about 152 coordinate steps), I get the > following error at 70th step: > > ERROR: while executing > exec /usr/bin/convert > /home/rajan/xcrys_tmp/xc_13003/tmp.ppm > /home/rajan/xcrys_tmp/xc_13003/anime69.jpg > > I will greatly appreciate your help/suggestion. I strongly suggest you install one of the 1.6 release canditate versions (i.e. 1.5.*, goto: http://www.xcrysden.org/Download.html#__toc__1 ). There the movie-making has been 1000% improved. I strongly believe the problem will disappear in new version? Moreover mpeg_encode is obsolete, it has been replaced by ppmtompeg, although for movie-making in the new version I recommend mencoder (i.e. mplayer's encoder). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From cyrille.barreteau at cea.fr Tue Feb 17 12:04:14 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Tue, 17 Feb 2009 12:04:14 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: <7699a1950902170153hefda508j565ade6c95f19615@mail.gmail.com> References: <7699a1950902170153hefda508j565ade6c95f19615@mail.gmail.com> Message-ID: <499A99AE.4010205@cea.fr> Dear Mohaddeseh Well, just read the message: It just means that the convergence criterion has not been reached after 100 steps... You can increase the number of step (nstep) or be less stringent on the convergence. How small are your forces and stress? cyrille mohaddeseh abbasnejad wrote: > Dear all, > > I was trying to do "vc-relax" for an orthorhombic unit cell consisting > of 24 ions. > I also put "nosym=.true.". > At the end, I received this error: > > " End of self-consistent calculation > convergence NOT achieved after 100 iterations: stopping " > > Would you please help me? > > Yours, > Mohaddeseh > > > -- > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/IRAMIS/SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html ================================================================== From paulatto at sissa.it Tue Feb 17 13:22:25 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 17 Feb 2009 13:22:25 +0100 Subject: [Pw_forum] vc-relax In-Reply-To: <499A99AE.4010205@cea.fr> References: <7699a1950902170153hefda508j565ade6c95f19615@mail.gmail.com> <499A99AE.4010205@cea.fr> Message-ID: On Tue, 17 Feb 2009 12:04:14 +0100, Cyrille Barreteau wrote: >> " End of self-consistent calculation >> convergence NOT achieved after 100 iterations: stopping " I think this is the electronic convergence, not the ionic... anyway with so few details I can't really give meaningful advice. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From abejeme at yahoo.com Tue Feb 17 13:24:11 2009 From: abejeme at yahoo.com (abeje menkir) Date: Tue, 17 Feb 2009 04:24:11 -0800 (PST) Subject: [Pw_forum] to change my e mail address ! Message-ID: <798449.12018.qm@web111503.mail.gq1.yahoo.com> dear sir , i changed my e-mail address from abejeme at yahoo.com to abejemenkir at yahoo.com .would you subscribe me with a new address abejemenkir at yahoo.com instead of old one.and i prefer any kinds of information by the new one not by the old one. thank you !! From somesh.kb at gmail.com Tue Feb 17 13:44:20 2009 From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya) Date: Tue, 17 Feb 2009 13:44:20 +0100 Subject: [Pw_forum] Relaxation of AlN surface In-Reply-To: <415464.16574.qm@web65710.mail.ac4.yahoo.com> References: <415464.16574.qm@web65710.mail.ac4.yahoo.com> Message-ID: Dear Prof. Eyvaz, Thanks a lot for your suggestion. I have introduced the key words occupations etc. and the system is achieving convergence. To comment on some suggestions on a denser grid, the system is attaining convergence for GAMMA point only. Though I would like to test the k-point sampling. Moreover, Giuseppe Mattioli's suggestion seems more plausible to me as it is known that the intragap states arising from the dangling bonds will affect the energy gap. However, for III-V and II-VI semiconductors the passivation by ordinary hydrogen is not enough as explained by Chelikowsky et. al. I have worked earlier on CdTe and othe II-VI semiconductor clusters and have found the same. In accordance with the paper and from my past experience, the best result is obtained by the use of fictitious hydrogen atom (H*) where Z for H* is different than 1. A usual choice is H* (Z=1.5) for cation and H*(Z=0.5) for anion in case of II-VI materials and H* (Z=1.25) and H* (Z=0.75) for cations and anions respectively for III-V materials. Regards, Somesh On Tue, Feb 17, 2009 at 12:03 AM, Eyvaz Isaev wrote: > Dear Somesh, > > Looking at your structure by means of XCrysDen have shown you have a slab with vacuum on both sides. Most likely, your system is metallized due to surface states and you should consider it as metallic turning on "occupations" and related keywords. Please have a look at /DOC/INPUT_PW. > > Hope this helps. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Tue, 2/17/09, Somesh Kumar Bhattacharya wrote: > >> From: Somesh Kumar Bhattacharya >> Subject: [Pw_forum] Relaxation of AlN surface >> To: pw_forum at pwscf.org >> Date: Tuesday, February 17, 2009, 1:08 AM >> Dear All, >> >> I am a new to PWSCF. >> >> I am trying to relax a surface slab of AlN which has 32 >> atoms. >> However, the system is not achieving convergence. >> >> The input file is : >> >> &control >> calculation = 'relax' >> restart_mode='from_scratch', >> prefix='AlN', >> nstep = 100, >> tprnfor = .true., >> etot_conv_thr = 1.d-8, >> pseudo_dir = '~/QE/espresso-4.0.3/pseudo/', >> outdir='.' >> / >> &system >> ibrav= 4, celldm(1) = 11.71623992919922, >> celldm(3) = 4.513,nat=32, ntyp= 2, >> ecutwfc =30.0, ecutrho = 400, nspin =1, >> / >> &electrons >> electron_maxstep=150, >> conv_thr = 1.D-6, >> mixing_mode = 'local-TF', >> mixing_beta = 0.2, >> / >> &ions >> ion_dynamics='bfgs', >> phase_space = 'full' >> / >> ATOMIC_SPECIES >> Al 26.98154 Al.pw91-n-van.UPF >> N 14.00674 N.pw91-van_ak.UPF >> ATOMIC_POSITIONS {angstrom} >> Al 1.549999937 4.474454315 14.919999921 1 1 1 >> Al 1.549999937 4.474454315 9.919999843 0 0 0 >> Al -0.000000015 7.159132936 14.919999921 1 1 1 >> Al -0.000000015 7.159132936 9.919999843 0 0 0 >> Al 4.649999842 4.474454315 14.919999921 1 1 1 >> Al 4.649999842 4.474454315 9.919999843 0 0 0 >> Al 3.099999890 7.159132936 14.919999921 1 1 1 >> Al 3.099999890 7.159132936 9.919999843 0 0 0 >> N 1.549999937 4.474454315 6.818997379 0 0 0 >> N 1.549999937 4.474454315 11.778997301 0 0 0 >> N -0.000000015 7.159132936 6.818997379 0 0 0 >> N -0.000000015 7.159132936 11.778997301 0 0 0 >> N 4.649999842 4.474454315 6.818997379 0 0 0 >> N 4.649999842 4.474454315 11.778997301 0 0 0 >> N 3.099999890 7.159132936 6.818997379 0 0 0 >> N 3.099999890 7.159132936 11.778997301 0 0 0 >> Al 3.099991178 3.579566454 7.439985857 0 0 0 >> Al 3.099991178 3.579566454 12.399985779 0 0 0 >> Al 1.549991226 6.264245075 7.439985857 0 0 0 >> Al 1.549991226 6.264245075 12.399985779 0 0 0 >> Al 6.199991083 3.579566454 7.439985857 0 0 0 >> Al 6.199991083 3.579566454 12.399985779 0 0 0 >> Al 4.649991131 6.264245075 7.439985857 0 0 0 >> Al 4.649991131 6.264245075 12.399985779 0 0 0 >> N 3.099991178 3.579566454 9.298983315 0 0 0 >> N 3.099991178 3.579566454 14.258983237 1 1 1 >> N 1.549991226 6.264245075 9.298983315 0 0 0 >> N 1.549991226 6.264245075 14.258983237 1 1 1 >> N 6.199991083 3.579566454 9.298983315 0 0 0 >> N 6.199991083 3.579566454 14.258983237 1 1 1 >> N 4.649991131 6.264245075 9.298983315 0 0 0 >> N 4.649991131 6.264245075 14.258983237 1 1 1 >> K_POINTS {GAMMA} >> >> >> I am allowing only the top two layers to relax. >> >> Using --- grep scf < *.out ...... the output is the >> following : >> >> estimated scf accuracy < 21.54311123 Ry >> estimated scf accuracy < 16.91216138 Ry >> estimated scf accuracy < 6.80358058 Ry >> estimated scf accuracy < 10.02440462 Ry >> estimated scf accuracy < 5.42211905 Ry >> estimated scf accuracy < 3.98570225 Ry >> estimated scf accuracy < 3.63368556 Ry >> estimated scf accuracy < 2.80935163 Ry >> estimated scf accuracy < 2.18832175 Ry >> estimated scf accuracy < 1.88438498 Ry >> estimated scf accuracy < 1.34984265 Ry >> estimated scf accuracy < 1.15892961 Ry >> estimated scf accuracy < 1.08983405 Ry >> estimated scf accuracy < 11.86322500 Ry >> estimated scf accuracy < 9.08655092 Ry >> estimated scf accuracy < 10.92075279 Ry >> estimated scf accuracy < 11.43007849 Ry >> ................. >> >> The system never attain convergence. >> >> Can anyone kindly suggest the possible source of error on >> my part. >> >> Regards, >> Somesh >> ............................... >> Somesh Kr. Bhattacharya >> Post Doctoral Fellow >> Room No. 263, >> Leonardo Building, >> The Abdus Salam International Centre for Theoretical >> Physics >> Strada Costiera, 11 >> I-34014 Trieste >> Italy >> Phone: +39-040-2240399 >> _______________________________________________ >> 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 > -- Somesh Kr. Bhattacharya Post Doctoral Fellow Room No. 263, Leonardo Building, The Abdus Salam International Centre for Theoretical Physics Strada Costiera, 11 I-34014 Trieste Italy Phone: +39-040-2240399 From j.antonio.montoya at gmail.com Tue Feb 17 14:05:13 2009 From: j.antonio.montoya at gmail.com (j.antonio.montoya at gmail.com) Date: Tue, 17 Feb 2009 13:05:13 +0000 Subject: [Pw_forum] vc-relax Message-ID: <673094003-1234875944-cardhu_decombobulator_blackberry.rim.net-1854269717-@bxe241.bisx.prod.on.blackberry> Dear Cyrille, From my experience (not for the particular case that you ask) I got this problem whenever the starting point was sort of unphysical (very short bond lengths and stuff like that) and/or the mixing_beta parameter in &electrons was set too high (the default value is high for many cases). Please check your structure with XcrysDen and if everything is fine just put a lower mixing (0.48 works for me) and/or try also using a different starting point for you wave functions. J Montoya. ------Original Message------ From: Lorenzo Paulatto Sender: pw_forum-bounces at pwscf.org To: PWSCF Forum ReplyTo: PWSCF Forum Sent: Feb 17, 2009 7:22 AM Subject: Re: [Pw_forum] vc-relax On Tue, 17 Feb 2009 12:04:14 +0100, Cyrille Barreteau wrote: >> " End of self-consistent calculation >> convergence NOT achieved after 100 iterations: stopping " I think this is the electronic convergence, not the ionic... anyway with so few details I can't really give meaningful advice. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum Sent via BlackBerry by AT&T From giannozz at democritos.it Tue Feb 17 14:33:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 14:33:27 +0100 Subject: [Pw_forum] to change my e mail address ! In-Reply-To: <798449.12018.qm@web111503.mail.gq1.yahoo.com> References: <798449.12018.qm@web111503.mail.gq1.yahoo.com> Message-ID: <499ABCA7.3060203@democritos.it> abeje menkir wrote: > i changed my e-mail address from abejeme at yahoo.com to abejemenkir at yahoo.com > would you subscribe me with a new address abejemenkir at yahoo.com instead of old one the only way to do this is to unsubscribe the previous address and subscribe with the new one. You (and nobody else) can do this: http://www.democritos.it/mailman/listinfo/pw_forum Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From elandry at andrew.cmu.edu Tue Feb 17 15:22:49 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Tue, 17 Feb 2009 09:22:49 -0500 Subject: [Pw_forum] Example 06 - problem with phonon calculation Message-ID: <001301c9910b$3677abd0$44390280@eLandry> Hi, I'm trying to run example 6, but I'm running into some problems. The scf calculation appears to work but I get an error message when running the phonon calculation (below). I've also included the full output from the alas.ph.out file. Thanks in advance. Eric Landry Mechanical Engineering Ph.D. Candidate, Carnegie Mellon University SCREEN OUTPUT: "/home/eric/espresso-4.0.4/examples/example06 : starting This example shows how to calculate interatomic force constants in real space for AlAs in zincblende structure. executables directory: /home/eric/espresso-4.0.4/bin pseudo directory: /home/eric/espresso-4.0.4/pseudo temporary directory: /home/eric/tmp checking that needed directories and files exist... done running pw.x as: /home/eric/espresso-4.0.4/bin/pw.x running ph.x as: /home/eric/espresso-4.0.4/bin/ph.x running q2r.x as: /home/eric/espresso-4.0.4/bin/q2r.x running matdyn.x as: /home/eric/espresso-4.0.4/bin/matdyn.x cleaning /home/eric/tmp... done running the scf calculation... done running the phonon calculation ..../run_example: line 136: 28035 Aborted $PH_COMMAND < alas.ph.in > alas.ph.out Error condition encountered during test: exit status = 134 Aborting" alas.ph.out FILE: " Program PHONON v.4.0.4 starts ... Today is 12Feb2009 at 11:53:48 Parallel version (MPI) Number of processors in use: 1 Ultrasoft (Vanderbilt) Pseudopotentials Planes per process (thick) : nr3 = 20 npp = 20 ncplane = 400 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 20 241 2445 20 241 2445 85 459 Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points ( 8q-points): N xq(1) xq(2) xq(3) 1 0.00000 0.00000 0.00000 2 -0.25000 0.25000 -0.25000 3 0.50000 -0.50000 0.50000 4 0.00000 0.50000 0.00000 5 0.75000 -0.25000 0.75000 6 0.50000 0.00000 0.50000 7 0.00000 -1.00000 0.00000 8 -0.50000 -1.00000 0.00000 bravais-lattice index = 2 lattice parameter (a_0) = 10.5000 a.u. unit-cell volume = 289.4063 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 2 kinetic-energy cut-off = 16.0000 Ry charge density cut-off = 64.0000 Ry convergence threshold = 1.0E-12 beta = 0.7000 number of iterations used = 4 Exchange-correlation = SLA PZ NOGX NOGC (1100) celldm(1)= 10.50000 celldm(2)= 0.00000 celldm(3)= 0.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of a_0) a(1) = ( -0.5000 0.0000 0.5000 ) a(2) = ( 0.0000 0.5000 0.5000 ) a(3) = ( -0.5000 0.5000 0.0000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( -1.0000 -1.0000 1.0000 ) b(2) = ( 1.0000 1.0000 1.0000 ) b(3) = ( -1.0000 1.0000 -1.0000 ) Atoms inside the unit cell: Cartesian axes site n. atom mass positions (a_0 units) 1 Al 26.9800 tau( 1) = ( 0.00000 0.00000 0.00000 ) 2 As 74.9200 tau( 2) = ( 0.25000 0.25000 0.25000 ) Computing dynamical matrix for q = ( 0.00000 0.00000 0.00000 ) 25 Sym.Ops. (with q -> -q+G ) G cutoff = 178.7306 ( 2445 G-vectors) FFT grid: ( 20, 20, 20) number of k points= 2 cart. coord. in units 2pi/a_0 k( 1) = ( 0.2500000 0.2500000 0.2500000), wk = 0.5000000 k( 2) = ( 0.2500000 0.2500000 0.7500000), wk = 1.5000000 PseudoPot. # 1 for Al read from file Al.vbc.UPF Pseudo is Norm-conserving, Zval = 3.0 Generated by new atomic code, or converted to UPF format Using radial grid of 171 points, 2 beta functions with: l(1) = 0 l(2) = 1 PseudoPot. # 2 for As read from file As.gon.UPF Pseudo is Norm-conserving, Zval = 5.0 Generated by new atomic code, or converted to UPF format Using radial grid of 525 points, 2 beta functions with: l(1) = 0 l(2) = 1 Atomic displacements: There are 2 irreducible representations Representation 1 3 modes - To be done Representation 2 3 modes - To be done PHONON : 0.52s CPU time, 0.48s wall time Alpha used in Ewald sum = 0.7000 Electric Fields Calculation" From nguyenhalvt at yahoo.com Tue Feb 17 15:32:48 2009 From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha) Date: Tue, 17 Feb 2009 06:32:48 -0800 (PST) Subject: [Pw_forum] Pseudopotential for Mg-PBE in upf file In-Reply-To: Message-ID: <610599.59614.qm@web31008.mail.mud.yahoo.com> Dear Paolo, Thanks for your kindness. I'v just created a new PBE-PP from your input then tested to calculate lattice parameters of MgO (cubic), k-points = 6x6x6, Ecut = 25 ryd; here are results: ? Using PBE-PP:??????????????????????????????????????? a = 4.144 angstroms Using PBE-PP (modiffied from PW91-PP): a = 4.180 angstroms Experimental data:?????????????????????????????????? a = 4.211 angstroms ? Best Regards, Nguyen, Ngoc Ha Hanoi National University of Education Faculty of Chemistry Department of Physical Chemistry Tel: Office: 04/8330842 Home: 04/7891674 Mobile: 0989133436 ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090217/bb7114b2/attachment-0001.htm From akohlmey at cmm.chem.upenn.edu Tue Feb 17 15:36:40 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 17 Feb 2009 09:36:40 -0500 (EST) Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) In-Reply-To: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> References: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Message-ID: On Tue, 17 Feb 2009, Raj Pandey wrote: RP> Dear PWSCF developers and users, RP> RP> I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed RP> whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg RP> or gif movie from "file.axsf" (about 152 coordinate steps), I get the RP> following error at 70th step: RP> RP> ERROR: while executing RP> exec /usr/bin/convert RP> /home/rajan/xcrys_tmp/xc_13003/tmp.ppm RP> /home/rajan/xcrys_tmp/xc_13003/anime69.jpg RP> RP> I will greatly appreciate your help/suggestion. have you checked whether you have enough diskspace? making movies is quite demanding wrt storage. cheers, axel. RP> RP> Thanks, RP> _______________________________________________ RP> Pw_forum mailing list RP> Pw_forum at pwscf.org RP> http://www.democritos.it/mailman/listinfo/pw_forum RP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Tue Feb 17 15:48:36 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Feb 2009 15:48:36 +0100 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <001301c9910b$3677abd0$44390280@eLandry> References: <001301c9910b$3677abd0$44390280@eLandry> Message-ID: <499ACE44.3080706@democritos.it> Eric Landry wrote: > I get an error message when running the phonon calculation (below) which compiler? the phonon code is miscompiled quite often Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From rajanpnano at gmail.com Tue Feb 17 17:07:07 2009 From: rajanpnano at gmail.com (Raj Pandey) Date: Tue, 17 Feb 2009 21:37:07 +0530 Subject: [Pw_forum] Error: while making mpeg/gif movie using xcrysden-bin-static (version 1.4.1) In-Reply-To: References: <48b8698d0902162311t25e59459had2e7e0965b81431@mail.gmail.com> Message-ID: <48b8698d0902170807k272f2f81n3a2b1aae6e5d89db@mail.gmail.com> Dear Axel, Thanks for your input. Of course I have plenty of disk space (200 GB empty) and memory (8 GB). I believe the problem was something else with the version 1.4.1, because I tried making movie with the same version on three different systems and got the same problem. The problem has been rectified when I installed the latest snapshot of xcrysden (version 1.5.17). Thanks to Anton. I could make the movie out of the same .axsf file with new version, without any issue. Thanks and regards, Rajan IBM I On Tue, Feb 17, 2009 at 8:06 PM, Axel Kohlmeyer wrote: > On Tue, 17 Feb 2009, Raj Pandey wrote: > > RP> Dear PWSCF developers and users, > RP> > RP> I am using xcrysden (XCrySDen-1.4.1bin-static). I have also installed > RP> whirlgif, and mpeg_encode (/usr/bin). When I am trying to make a mpeg > RP> or gif movie from "file.axsf" (about 152 coordinate steps), I get the > RP> following error at 70th step: > RP> > RP> ERROR: while executing > RP> exec /usr/bin/convert > RP> /home/rajan/xcrys_tmp/xc_13003/tmp.ppm > RP> /home/rajan/xcrys_tmp/xc_13003/anime69.jpg > RP> > RP> I will greatly appreciate your help/suggestion. > > have you checked whether you have enough diskspace? > > making movies is quite demanding wrt storage. > > cheers, > axel. > > RP> > RP> Thanks, > RP> _______________________________________________ > RP> Pw_forum mailing list > RP> Pw_forum at pwscf.org > RP> http://www.democritos.it/mailman/listinfo/pw_forum > RP> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090217/f668b096/attachment.htm From meheut at impmc.jussieu.fr Wed Feb 18 01:04:54 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Wed, 18 Feb 2009 01:04:54 +0100 Subject: [Pw_forum] phonon calculation crashes In-Reply-To: <68B0D4C9-AB3E-48F1-8585-D22C354B2CAD@sissa.it> References: <740492.33195.qm@web65702.mail.ac4.yahoo.com> <68B0D4C9-AB3E-48F1-8585-D22C354B2CAD@sissa.it> Message-ID: <20090218010454.40593zs5758vh4me@www-ext.impmc.jussieu.fr> Dear all, thank you very much for your help. The calculation, which took one week, went finally fine. The maximum dimension of irreducible representations in the case of this system is 3 at gamma but 6 for the 0 0 -1 q-point, in case you would like to know. Thanks again, Merlin ESS department at UCLA Quoting Stefano Baroni : > I am a bit confused. I thought that the maximum dimension of any > irrep of any point group compatible with lattice translations was > 3. The number 4 may arise form complications with non-symmorphic > groups (such as at the X point of the diamond structure), which I > used to me kind of familiar with, but that I do not remember any > longer. I am surprised that the need of any irrep larger that 4 may > ever arise, but this surprise may well be due to the rustiness of > my knowledge in group theory - Cheers - Stefano B > > On Jan 30, 2009, at 10:45 AM, Eyvaz Isaev wrote: > >> Dear Merlin, >> >> This one is also a famous message, though I did heard about it >> since long time. >> >> Well, this means you have more dimension for irreducible >> reperesentations that allowed by default, max_irr_dim=4. See >> phcom.f90 for sure. >> >> So, you can just increase this parameter (up to a reasonable value >> 6, 8, ... ) in phcom.f90 and recompile ph.x. >> Then it should work. >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Theoretical Physics Department, Moscow State Institute of Steel & >> Alloys, Russia, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping >> University, Sweden >> Condensed Matter Theory Group, Uppsala University, Sweden >> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> --- On Fri, 1/30/09, merlin meheut wrote: >> >>> From: merlin meheut >>> Subject: [Pw_forum] phonon calculation crashes >>> To: "PWSCF Forum" >>> Date: Friday, January 30, 2009, 6:19 AM >>> Dear all, >>> >>> I have had a strange crash on a phonon calculation, with >>> version >>> 3.2.3: I have calculated the dynamical matrix of the >>> structure at >>> gamma, at q-point (0;0.5;-0.5), both without problems, but >>> I cannot >>> calculate the (0;0;-1) q-point without having this error: >>> >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> %%%%%%%%%% >>> from set_irr : error # 2 >>> npert > max_irr_dim >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> %%%%%%%%%% >>> >>> I don't know what this means. The structure I am >>> calculating is very >>> big (80 atoms), so maybe it is related, I don't know. >>> >>> Follows the input files: >>> >>> --------------------------- scf input file: >>> pyrope Pavese 1995 (30K) cubique centre >>> &control >>> calculation = 'scf', >>> restart_mode = 'from_scratch' , >>> prefix = 'PYROPE', >>> disk_io = 'default' , >>> pseudo_dir = './', >>> outdir = '/tmp/', >>> tprnfor = .true., >>> tstress = .true., >>> /&end >>> &system >>> ibrav =3, celldm(1)=21.9096, >>> nat =80, ntyp = 4, ecutwfc = 80.0 >>> /&end >>> &electrons >>> electron_maxstep = 60, >>> conv_thr = 1.d-7 , >>> mixing_mode = 'plain', >>> startingwfc = 'atomic', >>> mixing_beta = 0.4, >>> diagonalization = 'david_overlap', >>> /&end >>> ATOMIC_SPECIES >>> Al 26.9815 Al.pbe2 >>> Mg 23.9850 Mgpbe1_mt.ncpp >>> Si 27.9769 Si.pbe2 >>> O 15.9949 O.pbe >>> ATOMIC_POSITIONS crystal >>> Si 0.62500000 0.62500000 0.25000000 >>> (...) >>> >>> K_POINTS {crystal} >>> 1 >>> 0.25 0.25 0.25 1 >>> ------------------------------------------------------------------- >>> >>> ------------------------------------------nscf input file: >>> >>> pyrope Pavese 1995 (30K) cubique centre >>> &control >>> calculation = 'phonon', >>> restart_mode = 'from_scratch' , >>> prefix = 'PYROPE', >>> disk_io = 'default' , >>> pseudo_dir = './', >>> outdir = '/tmp/', >>> tprnfor = .true., >>> tstress = .true., >>> /&end >>> &system >>> ibrav =3, celldm(1)=21.9096, >>> nat =80, ntyp = 4, ecutwfc = 80.0 >>> /&end >>> &electrons >>> electron_maxstep = 60, >>> conv_thr = 1.d-7 , >>> mixing_mode = 'plain', >>> startingwfc = 'atomic', >>> mixing_beta = 0.4, >>> diagonalization = 'david_overlap', >>> /&end >>> &phonon >>> xqq(1)= 0.0000000, xqq(2)= 0.0000000, xqq(3)= -1.0000000 >>> /&end >>> ATOMIC_SPECIES >>> Al 26.9815 Al.pbe2 >>> Mg 23.9850 Mgpbe1_mt.ncpp >>> Si 27.9769 Si.pbe2 >>> O 15.9949 O.pbe >>> ATOMIC_POSITIONS crystal >>> Si 0.62500000 0.62500000 0.25000000 >>> Si 0.87500000 0.87500000 0.75000000 >>> (....) >>> >>> K_POINTS {crystal} >>> 1 >>> 0.25 0.25 0.25 1 >>> ------------------------------------------------------------------- >>> >>> -----------------------ph input file: >>> >>> Pyrope m2 >>> &inputph >>> amass(1)=26.9815, >>> amass(2)=23.9850, >>> amass(3)=27.9769, >>> amass(4)=15.9949, >>> alpha_mix(1) = 0.7, >>> tr2_ph = 1.0D-16, >>> prefix='PYROPE', >>> fildyn='mat.strelD.bald.m3', >>> epsil =.false., >>> trans =.true., >>> zue = .false., >>> outdir='/tmp/' >>> /&end >>> 0.0 0.0 -1.0000000 >>> ----------------------------------------------------- >>> >>> >>> Has anyone an idea on the importance or the origin of this >>> error? >>> >>> Thanks for any hints, >>> >>> Best regards, >>> >>> Merlin Meheut >>> >>> ESS department at UCLA >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> Merlin M?heut >>> professional adress: >>> 595 Charles Young Drive East >>> 3806 Geology Building >>> Los Angeles, California 90095-1597 >>> United States of America >>> tel: 310 825 7934 >>> cell phone: 310 893 4253 >>> >>> ---------------------------------------------------------------- >>> 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 >> >> >> >> _______________________________________________ >> 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://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une > morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From lanhaiping at gmail.com Wed Feb 18 08:33:43 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 18 Feb 2009 15:33:43 +0800 Subject: [Pw_forum] DCC correction to electrostatic potential Message-ID: Dear All, I did test calculations on DCC correction implemented in CVS version. I came to problems when i examine the results of electrostatic potential. Would you please give me some hints ? My test calculation is a CNT (10,10) system, and the setting for DCC correction is which_compensation ='dcc', ecutcoarse = 100.0, n_charge_compensation= 5, nlev = 4, whichbc(1)= 0, whichbc(2)=0, whichbc(3)=1, But the final fermi energy i obtained is -3.99 eV, which is not consistent with previous report on workfunction of CNTs(about 4.6 eV ). Best, Hai-Ping -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090218/c1a8ab13/attachment.htm From panda.deng.pan at gmail.com Wed Feb 18 12:02:25 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Wed, 18 Feb 2009 19:02:25 +0800 Subject: [Pw_forum] problem with the inputs of the 'bands.x' Message-ID: Dear All, It has the error massage while running the bands.x for plotting a band structure.Please someone tell me where I was wrong. The error message are from bands : error # 4 pools not implemented and I used this file to prosess the bands.x: PARA_PREFIX="mpirun -np 4" PARA_POSTFIX="-npool 4" export OMP_NUM_THREADS=1 # how to run executables BANDS_COMMAND="$PARA_PREFIX $BIN_DIR/bands.x $PARA_POSTFIX" $BANDS_COMMAND bands.out $ECHO bands done I had tried to set the '-npool 1', but it did not work. At last I give my inputs for bands.x &inputpp prefix = 'BaNiAs' outdir = '/disk2/xgwan/tmp/' filband = 'bands.dat' / Thanks for helping me. Have a nice day! Pan Deng Najing University From vladan.stevanovic at epfl.ch Wed Feb 18 12:07:03 2009 From: vladan.stevanovic at epfl.ch (Vladan Stevanovic) Date: Wed, 18 Feb 2009 12:07:03 +0100 Subject: [Pw_forum] Question about postprocessing after the PBE0 calculation Message-ID: <499BEBD7.7090501@epfl.ch> Dear all, I would like to ask how does the postprocessing work after a hybrid calculation? Is the charge density, for example, that one reads with pp.x after the PBE0 calculation is finished really the PBE0 density? Thanks, Vladan Stevanovic From baris.malcioglu at gmail.com Wed Feb 18 12:18:33 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Wed, 18 Feb 2009 12:18:33 +0100 Subject: [Pw_forum] problem with the inputs of the 'bands.x' In-Reply-To: References: Message-ID: Dear ??, Try PARA_POSTFIX="" ? Or you can try wf_collect=.true. in pw.x and run bands.x in single processor... O. Baris Malcioglu SISSA CM sector. On Wed, Feb 18, 2009 at 12:02 PM, ?? wrote: > Dear All, > > It has the error massage while running the bands.x for plotting a band > structure.Please someone tell me where I was wrong. > > The error message are > > from bands : error # 4 > pools not implemented > > and I used this file to prosess the bands.x: > > PARA_PREFIX="mpirun -np 4" > PARA_POSTFIX="-npool 4" > export OMP_NUM_THREADS=1 > > # how to run executables > BANDS_COMMAND="$PARA_PREFIX $BIN_DIR/bands.x $PARA_POSTFIX" > > $BANDS_COMMAND bands.out > $ECHO bands done > > > I had tried to set the '-npool 1', but it did not work. > At last I give my inputs for bands.x > > &inputpp > prefix = 'BaNiAs' > outdir = '/disk2/xgwan/tmp/' > filband = 'bands.dat' > / > > Thanks for helping me. > > Have a nice day! > > Pan Deng > Najing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From elandry at andrew.cmu.edu Wed Feb 18 14:20:44 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Wed, 18 Feb 2009 08:20:44 -0500 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <499ACE44.3080706@democritos.it> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> Message-ID: <001201c991cb$b4de35a0$44390280@eLandry> Paolo, My make.sys file says this: MPIF90 = mpif90 #F90 = gfortran CC = gcc F77 = gfortran -Eric -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Tuesday, February 17, 2009 9:49 AM To: PWSCF Forum Subject: Re: [Pw_forum] Example 06 - problem with phonon calculation Eric Landry wrote: > I get an error message when running the phonon calculation (below) which compiler? the phonon code is miscompiled quite often Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Wed Feb 18 15:10:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Feb 2009 15:10:07 +0100 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <001201c991cb$b4de35a0$44390280@eLandry> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry> Message-ID: <499C16BF.6020902@democritos.it> Eric Landry wrote: > My make.sys file says this: > > MPIF90 = mpif90 > #F90 = gfortran > CC = gcc > F77 = gfortran most likely you have gfortran as underlying compiler in mpif90. Only recent versions of gfortran -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 18 15:18:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Feb 2009 15:18:10 +0100 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <499C16BF.6020902@democritos.it> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry> <499C16BF.6020902@democritos.it> Message-ID: <499C18A2.50107@democritos.it> Paolo Giannozzi wrote: > Eric Landry wrote: > >> My make.sys file says this: >> >> MPIF90 = mpif90 >> #F90 = gfortran >> CC = gcc >> F77 = gfortran > > most likely you have gfortran as underlying compiler in mpif90. > Only recent versions of gfortran ...produce executables that work, and maybe only part of them actually works (sorry for the previous truncated message) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 18 15:21:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Feb 2009 15:21:41 +0100 Subject: [Pw_forum] Question about postprocessing after the PBE0 calculation In-Reply-To: <499BEBD7.7090501@epfl.ch> References: <499BEBD7.7090501@epfl.ch> Message-ID: <499C1975.3080007@democritos.it> Vladan Stevanovic wrote: > Is the charge density, for example, that one reads with pp.x after > the PBE0 calculation is finished really the PBE0 density? I don't see any reason why it should be anything different. Since however hybrid functionals are still under development, carefully check what you get Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From saqib.javaid at ipcms.u-strasbg.fr Wed Feb 18 16:41:04 2009 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Wed, 18 Feb 2009 16:41:04 +0100 Subject: [Pw_forum] Trans.: problem with post processing code (paw routines) Message-ID: <1234971664.499c2c10bbd63@ipcms.u-strasbg.fr> ----- Message transf?r? de javaid at ipcms.u-strasbg.fr ----- Date?: Wed, 18 Feb 2009 15:08:40 +0100 De?: javaid at ipcms.u-strasbg.fr Adresse de retour?:javaid at ipcms.u-strasbg.fr Sujet?: problem with post processing code (paw routines) ??: pw_forum at pwscf.org Dear PWSCF users, I am trying to calculate the magnetization density of MnPc molecule using pp.x programe. While SCF run goes well with pw.x, when i use post processing code, i get the following error message %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from postproc : error # 1 post-processing paw routines not yet tested %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% i am using following pseudo potentials Mn 54.938049 Mn.pbe-paw_kj.UPF H 1.0079 H.pbe-paw_kj.UPF C 12.011 C.pbe-rrkjus.UPF N 14.007 N.pbe-rrkjus.UPF I would really appreciate if you can help me solve this problem Best regards Saqib JAVAID PhD student, university of Strasbourg, France ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fin du message transf?r? ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From paulatto at sissa.it Wed Feb 18 16:47:21 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 18 Feb 2009 16:47:21 +0100 Subject: [Pw_forum] Trans.: problem with post processing code (paw routines) In-Reply-To: <1234971664.499c2c10bbd63@ipcms.u-strasbg.fr> References: <1234971664.499c2c10bbd63@ipcms.u-strasbg.fr> Message-ID: On Wed, 18 Feb 2009 16:41:04 +0100, wrote: > I would really appreciate if you can help me solve this problem Just remove the check in PP/postproc.f90 at line 171-172 and recompile. Keep in mind that with PAW datasets the postprocessing has not yet been tested very much. BTW, why are you mixing PAW and Ultrasoft pseudopotentials? cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From nedward at MIT.EDU Wed Feb 18 18:20:46 2009 From: nedward at MIT.EDU (Nicholas E. Singh-Miller) Date: Wed, 18 Feb 2009 12:20:46 -0500 (EST) Subject: [Pw_forum] DCC correction to electrostatic potential In-Reply-To: References: Message-ID: Dear Hai-Ping, I am looking at espresso-4.1CVS. Looking at the subroutines in EE/, it looks like the DCC correction is currently only coded for isolated systems -- in which case the calculataion of BCs for a CNT would cut through the charge density. (but I could be missing something). Regads, Nick On Wed, 18 Feb 2009, lan haiping wrote: > Dear All, > > I did test calculations on DCC correction implemented in CVS version. > I came to problems when i examine the results of electrostatic potential. > Would you please give me some hints ? > My test calculation is a CNT (10,10) system, and the setting for > DCC correction is > which_compensation ='dcc', > ecutcoarse = 100.0, > n_charge_compensation= 5, > nlev = 4, > whichbc(1)= 0, whichbc(2)=0, > whichbc(3)=1, > But the final fermi energy i obtained is -3.99 eV, which is not consistent > with > previous report on workfunction of CNTs(about 4.6 eV ). > > Best, > Hai-Ping > > > ***************************************** Nicholas E. Singh-Miller Ph.D. Candidate Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From elandry at andrew.cmu.edu Wed Feb 18 19:03:44 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Wed, 18 Feb 2009 13:03:44 -0500 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <499C18A2.50107@democritos.it> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry><499C16BF.6020902@democritos.it> <499C18A2.50107@democritos.it> Message-ID: <001801c991f3$3d325900$44390280@eLandry> Paolo, I also have encountered a similar error message when I installed the code on a machine running Cygwin with the following compilers: MPIF90 = g95 #F90 = g95 CC = cc F77 = g95 Do you think the compiler might also be the issue here? Thanks, Eric -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Wednesday, February 18, 2009 9:18 AM To: PWSCF Forum Subject: Re: [Pw_forum] Example 06 - problem with phonon calculation Paolo Giannozzi wrote: > Eric Landry wrote: > >> My make.sys file says this: >> >> MPIF90 = mpif90 >> #F90 = gfortran >> CC = gcc >> F77 = gfortran > > most likely you have gfortran as underlying compiler in mpif90. > Only recent versions of gfortran ...produce executables that work, and maybe only part of them actually works (sorry for the previous truncated message) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Wed Feb 18 19:12:23 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 18 Feb 2009 13:12:23 -0500 (EST) Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <001801c991f3$3d325900$44390280@eLandry> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry><499C16BF.6020902@democritos.it> <499C18A2.50107@democritos.it> <001801c991f3$3d325900$44390280@eLandry> Message-ID: On Wed, 18 Feb 2009, Eric Landry wrote: EL> Paolo, EL> EL> I also have encountered a similar error message when I installed the code on EL> a machine running Cygwin with the following compilers: EL> EL> MPIF90 = g95 EL> #F90 = g95 EL> CC = cc EL> F77 = g95 EL> EL> Do you think the compiler might also be the issue here? the quality of g95 varies a lot with the individual binaries. the "stable" version seems quite reliable. even though i encountered a few quirks there as well. the "latest" version of g95 can be pretty good or pretty bad. mind you, the code that i am using g95 on, is using "modern" fortran 90/95 extensively, so it is exercising compilers hard, much, much more than Q-E does. gfortran currently doesn't stand a chance, PGI is a continuous catastrophe requiring many workarounds, and intel is a hit and miss (different compiler versions and patchlevels miscompile different parts of the code, however, most of the time only with full optimization). for this code, the stable g95 has the least problems. so i'd assume the same would hold for Q-E, unless there is some specific code construct used somewhere in Q-E, that g95 doesn't like (happens every once in a while). hope that helps (even though it is not very definite...), axel. EL> EL> Thanks, EL> Eric EL> EL> -----Original Message----- EL> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On EL> Behalf Of Paolo Giannozzi EL> Sent: Wednesday, February 18, 2009 9:18 AM EL> To: PWSCF Forum EL> Subject: Re: [Pw_forum] Example 06 - problem with phonon calculation EL> EL> Paolo Giannozzi wrote: EL> > Eric Landry wrote: EL> > EL> >> My make.sys file says this: EL> >> EL> >> MPIF90 = mpif90 EL> >> #F90 = gfortran EL> >> CC = gcc EL> >> F77 = gfortran EL> > EL> > most likely you have gfortran as underlying compiler in mpif90. EL> > Only recent versions of gfortran EL> EL> ...produce executables that work, and maybe only part of them actually works EL> (sorry for the previous truncated message) EL> EL> Paolo EL> -- EL> Paolo Giannozzi, Democritos and University of Udine, Italy EL> _______________________________________________ EL> Pw_forum mailing list EL> Pw_forum at pwscf.org EL> http://www.democritos.it/mailman/listinfo/pw_forum EL> EL> EL> _______________________________________________ EL> Pw_forum mailing list EL> Pw_forum at pwscf.org EL> http://www.democritos.it/mailman/listinfo/pw_forum EL> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Wed Feb 18 20:41:44 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 Feb 2009 20:41:44 +0100 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <001801c991f3$3d325900$44390280@eLandry> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry><499C16BF.6020902@democritos.it> <499C18A2.50107@democritos.it> <001801c991f3$3d325900$44390280@eLandry> Message-ID: <351BD1B6-8FB7-4940-8176-E7E9E72149D6@democritos.it> On Feb 18, 2009, at 19:03 , Eric Landry wrote: > I also have encountered a similar error message when I installed > the code on > a machine running Cygwin with the following compilers: > > MPIF90 = g95 > #F90 = g95 > CC = cc > F77 = g95 > > Do you think the compiler might also be the issue here? maybe your bad luck is an issue here :-) g95 is the most reliable fortran compiler I know. Why it doesn't work for you, I don't know. Did you also run the previous test with gfortran on cygwin? it could be a problem of cygwin. Example 06 has been tested before release on several machines and software and it works. It doesn't for v.4.1.2 of gfortran (the one I have on my PC) but it works for a more recent gfortran version on a Macintosh Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From elandry at andrew.cmu.edu Wed Feb 18 20:46:16 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Wed, 18 Feb 2009 14:46:16 -0500 Subject: [Pw_forum] Example 06 - problem with phonon calculation In-Reply-To: <351BD1B6-8FB7-4940-8176-E7E9E72149D6@democritos.it> References: <001301c9910b$3677abd0$44390280@eLandry> <499ACE44.3080706@democritos.it> <001201c991cb$b4de35a0$44390280@eLandry><499C16BF.6020902@democritos.it><499C18A2.50107@democritos.it><001801c991f3$3d325900$44390280@eLandry> <351BD1B6-8FB7-4940-8176-E7E9E72149D6@democritos.it> Message-ID: <002401c99201$90097010$44390280@eLandry> I JUST got it to work on Cygwin. I reinstalled g95 and everything worked fine. My previous installation of g95 was from a few years ago and maybe I didn't do it properly then. I should be able to figure out whats wrong with my other installation now. Thanks a lot for your help, Eric -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Wednesday, February 18, 2009 2:42 PM To: PWSCF Forum Subject: Re: [Pw_forum] Example 06 - problem with phonon calculation On Feb 18, 2009, at 19:03 , Eric Landry wrote: > I also have encountered a similar error message when I installed the > code on a machine running Cygwin with the following compilers: > > MPIF90 = g95 > #F90 = g95 > CC = cc > F77 = g95 > > Do you think the compiler might also be the issue here? maybe your bad luck is an issue here :-) g95 is the most reliable fortran compiler I know. Why it doesn't work for you, I don't know. Did you also run the previous test with gfortran on cygwin? it could be a problem of cygwin. Example 06 has been tested before release on several machines and software and it works. It doesn't for v.4.1.2 of gfortran (the one I have on my PC) but it works for a more recent gfortran version on a Macintosh Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From lanhaiping at gmail.com Thu Feb 19 03:12:28 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 19 Feb 2009 10:12:28 +0800 Subject: [Pw_forum] DCC correction to electrostatic potential In-Reply-To: References: Message-ID: Dear Nick, Thanks. Therefore, My problem is just due to wrong BC handling by QE. I found the settings for boundary conditions at $QE/Multigrid, and just thought it should be OK for all possible aperiodic situations. Would you mind to tell me which subroutine in $QE/EE accounts for boundary settings ? Regards, Hai-Ping On Thu, Feb 19, 2009 at 1:20 AM, Nicholas E. Singh-Miller wrote: > Dear Hai-Ping, > > I am looking at espresso-4.1CVS. > > Looking at the subroutines in EE/, it looks like the DCC correction is > currently only coded for isolated systems -- in which case the > calculataion of BCs for a CNT would cut through the charge density. (but I > could be missing something). > > Regads, > > Nick > > On Wed, 18 Feb 2009, lan haiping wrote: > > > Dear All, > > > > I did test calculations on DCC correction implemented in CVS version. > > I came to problems when i examine the results of electrostatic > potential. > > Would you please give me some hints ? > > My test calculation is a CNT (10,10) system, and the setting for > > DCC correction is > > which_compensation ='dcc', > > ecutcoarse = 100.0, > > n_charge_compensation= 5, > > nlev = 4, > > whichbc(1)= 0, whichbc(2)=0, > > whichbc(3)=1, > > But the final fermi energy i obtained is -3.99 eV, which is not > consistent > > with > > previous report on workfunction of CNTs(about 4.6 eV ). > > > > Best, > > Hai-Ping > > > > > > > > ***************************************** > Nicholas E. Singh-Miller > Ph.D. Candidate > Prof. Marzari Group (quasiamore.mit.edu) > Materials Science and Engineering > Massachusetts Institute of Technology > 13-4066 > (617)324-0372 > ***************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090219/03e48e26/attachment.htm From baroni at sissa.it Thu Feb 19 07:47:21 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 19 Feb 2009 07:47:21 +0100 Subject: [Pw_forum] Electronic structure school & Quantum ESPRESSO tutorial in sunny California References: <49983DB1.6040901@mit.edu> Message-ID: <4596D708-E3FB-41CD-9B97-5A0761FAA35B@sissa.it> NSF/ICMR Summer School on Materials Modeling from First Principles: Theory and Practice UC Santa Barbara, July 19 - Aug 1 2009 A summer school on "Materials Modeling from First Principles: Theory and Practice" will be held at the International Center for Materials Research in Santa Barbara from July 19 to August 1 2009. The school is supported by the National Science Foundation and the International Center for Materials Research, and is directed by S. Baroni, G. Galli, N. Marzari, and S. Narasimhan. The school will combine morning lectures with afternoon hands-on sessions based on the open-source Quantum-ESPRESSO codes. Evening keynote lectures will be delivered by some of the leading researchers in the field, including R. Car, W. Kohn (to be confirmed), S. Louie (to be confirmed), R. Martin, M. Scheffler, and N. Spaldin. The school is targeted at graduate students, postdocs, and senior researchers who would like to gain experience in materials modeling using state-of-the-art approaches based on density-functional theory. The school will cover basic concepts and recent advances and developments. The former include ground-state calculations for isolated molecules and extended systems, pseudopotential theory and plane-wave basis sets, forces, stresses, and geometry and reaction-path optimizations, linear-response theory and phonons, and ab-initio molecular dynamics. Advanced techniques include first-principles spectroscopies (IR, Raman, EPR and NMR), third-order electron-phonon and phonon-phonon response, time-dependent density-functional theory, Hubbard corrections and non-collinear magnetism, and Wannier functions and quantum transport. Full or partial support is available to cover participation expenses (travel, accommodation, and meals). Application forms can be downloaded from http://www.icmr.ucsb.edu/programs/firstprinciples.html and must be submitted by Mar 15th for applicants coming from outside the US and by Apr 15th for applicants based in the US. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090219/1d919572/attachment-0001.htm From eminekb at yahoo.com Thu Feb 19 16:39:39 2009 From: eminekb at yahoo.com (e kb) Date: Thu, 19 Feb 2009 07:39:39 -0800 (PST) Subject: [Pw_forum] DCC correction to electrostatic potential In-Reply-To: Message-ID: <540450.89408.qm@web34802.mail.mud.yahoo.com> Dear Hai-Ping Nick is right, DCC for partial periodicity is not in the cvs version of the code yet. The main issue is not the "whichbc" parameter that you've checked in the Multigrid directory. The way that the true potential is calculated?(add_boundary.f90)?and?Poisson equation that?is?solved should be modified accordingly (add_dcc_field.f90). Regards, ? Emine Kucukbenli, grad student, SISSA, Italy. --- On Thu, 2/19/09, lan haiping wrote: From: lan haiping Subject: Re: [Pw_forum] DCC correction to electrostatic potential To: "PWSCF Forum" Date: Thursday, February 19, 2009, 4:12 AM Dear Nick, Thanks.? Therefore, My problem is just due to wrong BC handling by QE. I found the settings for boundary conditions at $QE/Multigrid, and just thought it should be OK for all possible aperiodic situations. Would you mind to tell me which subroutine in $QE/EE accounts for boundary settings ? Regards, Hai-Ping On Thu, Feb 19, 2009 at 1:20 AM, Nicholas E. Singh-Miller wrote: Dear Hai-Ping, I am looking at espresso-4.1CVS. Looking at the subroutines in EE/, it looks like the DCC correction is currently only coded for isolated systems -- in which case the calculataion of BCs for a CNT would cut through the charge density. (but I could be missing something). Regads, Nick On Wed, 18 Feb 2009, lan haiping wrote: > Dear All, > > ?I did test calculations on DCC correction implemented in CVS version. > I came to ?problems when i examine the results of electrostatic potential. > Would you please give me some hints ? > My test calculation is a CNT (10,10) ?system, ?and the setting for > DCC correction is > ? ? ? ?which_compensation ='dcc', > ? ? ? ?ecutcoarse = 100.0, > ? ? ? ?n_charge_compensation= 5, > ? ? ? ?nlev = 4, > ? ? ? ?whichbc(1)= 0, whichbc(2)=0, > ? ? ? ?whichbc(3)=1, > But the final fermi energy i obtained is -3.99 eV, which is not consistent > with > previous report on workfunction of CNTs(about 4.6 eV ). > > Best, > Hai-Ping > > > ***************************************** Nicholas E. Singh-Miller Ph.D. Candidate Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090219/622f6901/attachment.htm From okunoyukihiro2000 at yahoo.co.jp Thu Feb 19 17:48:38 2009 From: okunoyukihiro2000 at yahoo.co.jp (Yukihiro Okuno) Date: Fri, 20 Feb 2009 01:48:38 +0900 Subject: [Pw_forum] Zn pseudopotential made by ld1.x Message-ID: Dear PWSCF Users. I want to compare the effects of different USPP pseudo potential for ZnO. The pseudopotential made by Vanderbilts's USPP program has orbital chage density weight around r=0 with l=1,l=2 pseudo wave function due to the augumentation chage's pseudize process. ( I confirmed it to Prof. Vanderbilt.) And , I want to use the Zn uspp (or NC) pseudo potential with correct orbital charge behavior because I want to test pseudo-SIC calculation. (now, I'm implementing.) So, If there are somebody who made Zn pseudo-potential by ld1.x, I want the input file for ld1.x for Zn, because I'm not accustomed to making pseudo potential. Sincerely. Yukihiro Okuno. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090220/ea5e9942/attachment.htm From eariel99 at gmail.com Fri Feb 20 03:48:11 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 19 Feb 2009 23:48:11 -0300 Subject: [Pw_forum] band and dos input files in xcrysden Message-ID: Hi Tone, Do you have plans to add the capability in PWGUI to generate inputs for bands.x and dos.x ? It would be goood to operate it in an easy way, i.e. inheriting outdir and prefix from the parent pw.x input and Emin=-10.0, Emax=25.0 from the pw.x output. Best regards -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090219/dbf95521/attachment.htm From saqib.javaid at ipcms.u-strasbg.fr Fri Feb 20 09:43:30 2009 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Fri, 20 Feb 2009 09:43:30 +0100 Subject: [Pw_forum] Trans.: problem with post processing code (paw routines) In-Reply-To: References: <1234971664.499c2c10bbd63@ipcms.u-strasbg.fr> Message-ID: <1235119410.499e6d321bbf8@ipcms.u-strasbg.fr> Dear Lorenzo Thanks a lot for your help and suggestions. It seems to woking fine for the time being. best regards Saqib Javaid phd student university of Strasbourg, France > On Wed, 18 Feb 2009 16:41:04 +0100, wrote: > > I would really appreciate if you can help me solve this problem > > Just remove the check in PP/postproc.f90 at line 171-172 and recompile. Keep > in mind that with PAW datasets the postprocessing has not yet been tested > very much. > > BTW, why are you mixing PAW and Ultrasoft pseudopotentials? > > cheers > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From lanhaiping at gmail.com Fri Feb 20 10:56:39 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 20 Feb 2009 17:56:39 +0800 Subject: [Pw_forum] DCC correction to electrostatic potential In-Reply-To: <540450.89408.qm@web34802.mail.mud.yahoo.com> References: <540450.89408.qm@web34802.mail.mud.yahoo.com> Message-ID: Dear Emine Thank you for this detailed description. Regards, Hai-Ping On Thu, Feb 19, 2009 at 11:39 PM, e kb wrote: > Dear Hai-Ping > Nick is right, DCC for partial periodicity is not in the cvs version of the > code yet. > The main issue is not the "whichbc" parameter that you've checked in the > Multigrid directory. The way that the true potential is > calculated (add_boundary.f90) and Poisson equation that is solved should be > modified accordingly (add_dcc_field.f90). > Regards, > > Emine Kucukbenli, > grad student, SISSA, Italy. > > --- On *Thu, 2/19/09, lan haiping * wrote: > > From: lan haiping > Subject: Re: [Pw_forum] DCC correction to electrostatic potential > To: "PWSCF Forum" > Date: Thursday, February 19, 2009, 4:12 AM > > > Dear Nick, > Thanks. > Therefore, My problem is just due to wrong BC handling by QE. I found the > settings for boundary conditions at $QE/Multigrid, and just thought it > should be OK for all possible aperiodic situations. > Would you mind to tell me > which subroutine in $QE/EE accounts for boundary settings ? > > Regards, > Hai-Ping > > On Thu, Feb 19, 2009 at 1:20 AM, Nicholas E. Singh-Miller > wrote: > >> Dear Hai-Ping, >> >> I am looking at espresso-4.1CVS. >> >> Looking at the subroutines in EE/, it looks like the DCC correction is >> currently only coded for isolated systems -- in which case the >> calculataion of BCs for a CNT would cut through the charge density. (but I >> could be missing something). >> >> Regads, >> >> Nick >> >> On Wed, 18 Feb 2009, lan haiping wrote: >> >> > Dear All, >> > >> > I did test calculations on DCC correction implemented in CVS version. >> > I came to problems when i examine the results of electrostatic >> potential. >> > Would you please give me some hints ? >> > My test calculation is a CNT (10,10) system, and the setting for >> > DCC correction is >> > which_compensation ='dcc', >> > ecutcoarse = 100.0, >> > n_charge_compensation= 5, >> > nlev = 4, >> > whichbc(1)= 0, whichbc(2)=0, >> > whichbc(3)=1, >> > But the final fermi energy i obtained is -3.99 eV, which is not >> consistent >> > with >> > previous report on workfunction of CNTs(about 4.6 eV ). >> > >> > Best, >> > Hai-Ping >> > >> > >> > >> >> ***************************************** >> Nicholas E. Singh-Miller >> Ph.D. Candidate >> Prof. Marzari Group (quasiamore.mit.edu) >> Materials Science and Engineering >> Massachusetts Institute of Technology >> 13-4066 >> (617)324-0372 >> ***************************************** >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090220/a5823560/attachment.htm From tone.kokalj at ijs.si Fri Feb 20 12:08:43 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Feb 2009 12:08:43 +0100 Subject: [Pw_forum] band and dos input files in xcrysden In-Reply-To: References: Message-ID: <1235128123.6067.11.camel@walk.ijs.si> On Thu, 2009-02-19 at 23:48 -0300, Eduardo Ariel Menendez Proupin wrote: > Hi Tone, > > Do you have plans to add the capability in PWGUI to generate inputs > for bands.x and dos.x ? Actually, I didn't have, but this can be easily done. Due to your request I will do so in the future. > It would be goood to operate it in an easy way, i.e. inheriting > outdir and prefix from the parent pw.x input and Emin=-10.0, Emax=25.0 > from the pw.x output. Don't know what exactly you mean for Emin and Emax, however, as far as the outdir and prefix are concerned, how should pwgui know which is the corresponding pw.x input file? (this would be needed for the inheritance). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From jwan at phy.cuhk.edu.hk Fri Feb 20 17:35:49 2009 From: jwan at phy.cuhk.edu.hk (Jones Tsz-Kai Wan) Date: Sat, 21 Feb 2009 00:35:49 +0800 Subject: [Pw_forum] Pseudopotential for Mg-PBE in upf file In-Reply-To: <610599.59614.qm@web31008.mail.mud.yahoo.com> References: <610599.59614.qm@web31008.mail.mud.yahoo.com> Message-ID: Dear Paolo and Nguyen, Just curious, I am wondering if this is a good PP, because PBE-PPs usually over-estimate lattice constants. -- Jones Wan On Tue, Feb 17, 2009 at 10:32 PM, Nguyen Ngoc Ha wrote: > Dear Paolo, > Thanks for your kindness. I'v just created a new PBE-PP from your input then > tested to calculate lattice parameters of MgO (cubic), k-points = 6x6x6, > Ecut = 25 ryd; here are results: > > Using PBE-PP: a = 4.144 angstroms > Using PBE-PP (modiffied from PW91-PP): a = 4.180 angstroms > Experimental data: a = 4.211 angstroms > > Best Regards, > Nguyen, Ngoc Ha > Hanoi National University of Education > Faculty of Chemistry > Department of Physical Chemistry > Tel: Office: 04/8330842 > Home: 04/7891674 > Mobile: 0989133436 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From vranjan at ncsu.edu Fri Feb 20 22:54:21 2009 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Fri, 20 Feb 2009 16:54:21 -0500 (EST) Subject: [Pw_forum] dielectric tensor Message-ID: <54930.152.14.74.117.1235166861.squirrel@webmail.ncsu.edu> Hello, I was wondering if PWSCF can calculate low frequency dielectric permittivity tensor. I would like to calculate dielectric constant in KHz frequency range. Thank you, Vivek Ranjan NCSU From niuli1978 at yahoo.com.cn Sat Feb 21 09:01:02 2009 From: niuli1978 at yahoo.com.cn (li niu) Date: Sat, 21 Feb 2009 16:01:02 +0800 (CST) Subject: [Pw_forum] Calculation for the neutron static structure factor Message-ID: <272321.83609.qm@web15004.mail.cnb.yahoo.com> Dear all, I want to calculate the neutron static structure factor based on the results of vibrational frequencies and eigenmodes obtained by the line-response method. The paper (Phys. Rev. B 2000, 61:3951-3959, Vibrational amplitudes in vitreous silica) gave the calculated formula. I tried to write a small code to calculate it, but the results are wrong. Is there is a small tool in QE to calculate it? Can anyone who successfully calculated the neutron static structure factor give me some help? ? Any help will be very appreciated. ? Best, ? Li Niu Ph.D. Candidate, Center for Composite Materials, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, People's Republic of China ? ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090221/326ca05e/attachment.htm From mpayami at aeoi.org.ir Sat Feb 21 13:06:32 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sat, 21 Feb 2009 15:36:32 +0330 Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 Message-ID: Hi All, I am trying to configure mpich2-1.0.8 for the best performance and perhaps comparison with openmpi-1.2.9 (openmpi-1.3 is still somehow unstable). In making mpich2, I used: FC=ifort F77=ifort F90=ifort ./configure --enable-fast --enable-sharedlibs=gcc Are these the right switches to make mpich2 performance as close as possible to that of openmpi? Any comment is highly appreciated. Best regards, Mahmoud Payami Phys. Group, Atomic Energy Org. of Iran From jdai3 at mail.ustc.edu.cn Sat Feb 21 14:18:33 2009 From: jdai3 at mail.ustc.edu.cn (Dai) Date: Sat, 21 Feb 2009 21:18:33 +0800 Subject: [Pw_forum] compile problem on IBM AIX61 Message-ID: <435222314.07439@ustc.edu.cn> Dear all, I encountered a problem when compile QE4.0.4 with gcc 4.0.0 and xlf V12.1, : ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; else make TLDEPS= all ; fi ) gcc -O3 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA -I../include -c cptimer.c /usr/include/unistd.h:923: error: parse error before '[' token /usr/include/unistd.h:924: error: parse error before 'rid_t' make: The error code from the last command is 1. Any idea on how to fix this problem? Thanks in advance. 2009-02-21 Best regards, Jun Dai ============================================================= Jun Dai Ph.D. Candidate, Hefei National Laboratory For Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China Tel.: 86-551-3606428 Fax.: 86-551-3602969 E-mail: jdai3 at mail.ustc.edu.cn ============================================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090221/aa3479c5/attachment.htm From eariel99 at gmail.com Sat Feb 21 17:05:04 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Sat, 21 Feb 2009 13:05:04 -0300 Subject: [Pw_forum] band and dos input files in xcrysden Message-ID: Dear Tone, Thanks for your interest in my request. >Don't know what exactly you mean for Emin and Emax, however, as far as >the outdir and prefix are concerned, how should pwgui know which is the >corresponding pw.x input file? (this would be needed for the >inheritance). Let me remind how is the process to obtain the DOS. It has three calculations and 3 input files pw.x < si.scf.in > si.scf.out # self consistent pw.x si.dos.out # non selfconsistent dense k-points mesh and a few options dos.x si.dos2.out # postprocessing At present, pwgui has a Menu File/New, where one can define the input files from the scratch. A typical input for dos.x looks like this &inputpp outdir='./temp', prefix='silicon' fildos='silicon.dos', Emin=-10.0, Emax=25.0, DeltaE=0.1 / One simple idea is to add a submenu to the menu "File/New from here" So, if I have an open pw.x input, when I select "File/New from here" it will make the new file inheriting all the properties: in this case outdir and prefix. I would also set by default fildos = prefix.dos. Emin and Emax are the minumum and maxima of the Kohn-Sham eigenvalues that can be taken from the pw.x outputs. pwgui may run an script to take these values from the pw.x output if this exists (I may want to run the files interactvely or just to make the input files and copy them to a server). We may ask Paolo to put Emin and Emax, and Efermi or HOMO in a single line of the output. NSCF calculation inherits many more fields from the SCF, so it makes more sense to generate the *.dos.in file from the .scf.in file. Let see the differences diff si.scf.in si.dos.in 2c2 < calculation = 'scf' , --- > calculation = 'nscf' , 15a16,17 > nbnd = 8, > occupations='tetrahedra', 29c31 < 5 5 5 1 1 1 --- > 20 20 20 0 0 0 This I make simply saving the si.scf.in with the name si.dos.in and changing the variables. However, it may be nice to make the changes automatically. The keywords nbnd, occupations, and the k-point mesh (20 20 20) are difficult to set automagically. I propose some maybe good default values nbnd can be searched in the output file. grep 'number of Kohn-Sham states' si.scf.out number of Kohn-Sham states= 4 and just double the number 4. It would be a different recipe if we deal with a metal, but let's keep simple and let the user to reduce it. I would set occupations='tetrahedra' by default. > 20 20 20 0 0 0 I would make a contest to select the winning idea. I have one recipe If I have in the scf input calculation K_POINTS automatic N1 N2 N3 1 1 1 or 'N1 N2 N3 0 0 0' then for the nscf calculation I would set N1n N2n N3n 0 0 0 such that N1n/N1 = N2n/N2 = N3n/N3 and N1n*N2n*N3n = (30^3)/nat (nat the number of atoms) A different strategy may be to have a menu Project and from the Project menu, select kinds of input fiiles or tasks. If one selects task DOS, for example, then pwgui can create the three input files and display a reminder of the sequence of calculations to be done. Best regards Eduardo > ---------- Mensaje reenviado ---------- > From: Tone Kokalj > To: PWSCF Forum > Date: Fri, 20 Feb 2009 12:08:43 +0100 > Subject: Re: [Pw_forum] band and dos input files in xcrysden > On Thu, 2009-02-19 at 23:48 -0300, Eduardo Ariel Menendez Proupin wrote: > > Hi Tone, > > > > Do you have plans to add the capability in PWGUI to generate inputs > > for bands.x and dos.x ? > > Actually, I didn't have, but this can be easily done. Due to your > request I will do so in the future. > > > It would be goood to operate it in an easy way, i.e. inheriting > > outdir and prefix from the parent pw.x input and Emin=-10.0, Emax=25.0 > > from the pw.x output. > > Don't know what exactly you mean for Emin and Emax, however, as far as > the outdir and prefix are concerned, how should pwgui know which is the > corresponding pw.x input file? (this would be needed for the > inheritance). > > Regards, Tone > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090221/e66cdff3/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Feb 21 17:51:11 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 21 Feb 2009 11:51:11 -0500 (EST) Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 In-Reply-To: References: Message-ID: On Sat, 21 Feb 2009, Mahmoud Payami Shabestari wrote: MP> Hi All, MP> I am trying to configure mpich2-1.0.8 for the best performance and perhaps MP> comparison with openmpi-1.2.9 (openmpi-1.3 is still somehow unstable). MP> In making mpich2, I used: MP> FC=ifort F77=ifort F90=ifort ./configure --enable-fast --enable-sharedlibs=gcc MP> MP> Are these the right switches to make mpich2 performance as close as MP> possible to that of openmpi? mahmoud, you should ask that the people developing MPICH2. this is not the right forum for this kind of question. one more remark. that might also help people here not to waste too much time on something pointless. in general, it is not a good idea to try an play with compiler optimization in the hope to make an MPI implementation (and thus communication) faster. if your application performance would depend so much on the optimization level use to compile your MPI library, then either you have a very crappy MPI implementation, or your application spends too much time in MPI calls. in the latter case, that usually corresponds to severe overload of your communication hardware and taking care of that would give you a much better performance increase than any compiler switches will. basically for almost _any_ system library (and that includes ATLAS and FFTW, btw) it is best to stick to a moderate optimization (-O) as aggressive optimization may interfere with the implemented algorithms and existing optimizations (e.g. both ATLAS and FFTW include optimizations on the C-language and algorithm level, higher compiler optimization can change the semantics of your code and thus negate the optimizations performed in the code). even more so, with many current compilers, aggressive optimization (-O3 or higher) incures a very high risk of the compiler miscompiling your library and thus leading to uncontrollable crashes or wrong results. that doesn't mean, that there may be a measurable benefit for singular cases, but from over 10 years of experience in management of HPC resources the overall effect is problematic. most of the time it is hard enough to chase down application bugs that are real or cause by compilers, you don't want to add having to track down problems in your libraries to that. cheers, axel. MP> Any comment is highly appreciated. MP> MP> Best regards, MP> Mahmoud Payami MP> Phys. Group, MP> Atomic Energy Org. of Iran MP> MP> _______________________________________________ MP> Pw_forum mailing list MP> Pw_forum at pwscf.org MP> http://www.democritos.it/mailman/listinfo/pw_forum MP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Feb 21 17:59:39 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 21 Feb 2009 11:59:39 -0500 (EST) Subject: [Pw_forum] compile problem on IBM AIX61 In-Reply-To: <435222314.07439@ustc.edu.cn> References: <435222314.07439@ustc.edu.cn> Message-ID: On Sat, 21 Feb 2009, Dai wrote: JD> Dear all, dear jun dai, JD> I encountered a problem when compile QE4.0.4 with gcc 4.0.0 and xlf V12.1, : JD> ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; else make TLDEPS= all ; fi ) JD> gcc -O3 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA -I../include -c cptimer.c JD> /usr/include/unistd.h:923: error: parse error before '[' token JD> /usr/include/unistd.h:924: error: parse error before 'rid_t' JD> make: The error code from the last command is 1. JD> JD> Any idea on how to fix this problem? Thanks in advance. this is either a bug in the unix headers of AIX or gcc-4.0.0 and _not_ a Q-E problem. most likely a combination of both. gcc-4.0.0 is a quite broken and long obsolete compiler version (it is a double zero release and that almost always spells trouble). i would recommend to either install a current gcc or use the system xlc (cc) instead. sometimes header conflicts on AIX can be resolved by adding -D__ALL_SOURCE to DFLAGS in make.sys cheers, axel. JD> JD> 2009-02-21 JD> JD> JD> JD> Best regards, JD> Jun Dai JD> JD> ============================================================= JD> Jun Dai JD> Ph.D. Candidate, JD> Hefei National Laboratory For Physical Sciences at the Microscale, JD> University of Science and Technology of China, JD> Hefei, Anhui, 230026, JD> People's Republic of China JD> Tel.: 86-551-3606428 JD> Fax.: 86-551-3602969 JD> E-mail: jdai3 at mail.ustc.edu.cn JD> ============================================================= JD> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mpayami at aeoi.org.ir Sat Feb 21 18:38:30 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sat, 21 Feb 2009 21:08:30 +0330 Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 In-Reply-To: References: Message-ID: Hi Axel, > you should ask that the people developing MPICH2. > this is not the right forum for this kind of question. > > one more remark. that might also help people here not > to waste too much time on something pointless [...]. It is the converse! I am trying to save the community's time. Here you are: ------------------------------------------------------------- mpich2_with_those_switches_that_I_mentioned: PWSCF : 9m46.25s CPU time, 12m 9.57s wall time --------------------------------------------------------------- openmpi-1.2.9 (default switches): PWSCF : 32m8.27s CPU time, 51m 23.38s wall time ---------------------------------------------------------------- These are the results of an scf calculation for 21-layered Al(110) slab with Ecut=22Ry, k_mesh=45x45x1, degauss=0.05 on a box with 2 x amd64 quad (8 cores). The memory used in mpich2 is less than half of that in (default switches)openmpi. Cheers, mahmoud > > in general, it is not a good idea to try an play with > compiler optimization in the hope to make an MPI implementation > (and thus communication) faster. > > if your application performance would depend so much on the > optimization level use to compile your MPI library, then either > you have a very crappy MPI implementation, or your application > spends too much time in MPI calls. in the latter case, that > usually corresponds to severe overload of your communication > hardware and taking care of that would give you a much better > performance increase than any compiler switches will. > > basically for almost _any_ system library (and that includes > ATLAS and FFTW, btw) it is best to stick to a moderate optimization > (-O) as aggressive optimization may interfere with the implemented > algorithms and existing optimizations (e.g. both ATLAS and FFTW > include optimizations on the C-language and algorithm level, higher > compiler optimization can change the semantics of your code and > thus negate the optimizations performed in the code). even more > so, with many current compilers, aggressive optimization (-O3 or > higher) incures a very high risk of the compiler miscompiling > your library and thus leading to uncontrollable crashes or wrong > results. that doesn't mean, that there may be a measurable benefit > for singular cases, but from over 10 years of experience in > management of HPC resources the overall effect is problematic. > most of the time it is hard enough to chase down application bugs > that are real or cause by compilers, you don't want to add having > to track down problems in your libraries to that. > > cheers, > axel. > > > MP> Any comment is highly appreciated. > MP> > MP> Best regards, > MP> Mahmoud Payami > MP> Phys. Group, > MP> Atomic Energy Org. of Iran > MP> > MP> _______________________________________________ > MP> Pw_forum mailing list > MP> Pw_forum at pwscf.org > MP> http://www.democritos.it/mailman/listinfo/pw_forum > MP> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Feb 21 20:08:16 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 21 Feb 2009 14:08:16 -0500 (EST) Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 In-Reply-To: References: Message-ID: On Sat, 21 Feb 2009, Mahmoud Payami Shabestari wrote: MP> MP> Hi Axel, MP> MP> > you should ask that the people developing MPICH2. MP> > this is not the right forum for this kind of question. MP> > MP> > one more remark. that might also help people here not MP> > to waste too much time on something pointless [...]. MP> MP> It is the converse! I am trying to save the community's time. Here you are: MP> ------------------------------------------------------------- MP> mpich2_with_those_switches_that_I_mentioned: MP> MP> PWSCF : 9m46.25s CPU time, 12m 9.57s wall time MP> --------------------------------------------------------------- MP> openmpi-1.2.9 (default switches): MP> MP> PWSCF : 32m8.27s CPU time, 51m 23.38s wall time MP> ---------------------------------------------------------------- mahmoud, as i already wrote to you in private e-mail. the huge discrepancy between wall and cpu time casts a severe doubt on the usefulness of these numbers. as i was stating in the previous mail. if the MPI library takes a significant time of the total time, there is a problem elsewhere that needs to be investigated first. you are obviously severely overloading your machine. MP> These are the results of an scf calculation for 21-layered Al(110) slab MP> with Ecut=22Ry, k_mesh=45x45x1, degauss=0.05 on a box with 2 x amd64 quad MP> (8 cores). MP> The memory used in mpich2 is less than half of that in (default MP> switches)openmpi. how did you determine that? you have to be careful to differentiate between memory being mapped into address space, physical memory used and virtual memory being in use. the respective columns in displayed in, e.g. top are: VIRT RES and CODE+DATA) cheers, axel. MP> MP> Cheers, MP> mahmoud MP> MP> MP> > MP> > in general, it is not a good idea to try an play with MP> > compiler optimization in the hope to make an MPI implementation MP> > (and thus communication) faster. MP> > MP> > if your application performance would depend so much on the MP> > optimization level use to compile your MPI library, then either MP> > you have a very crappy MPI implementation, or your application MP> > spends too much time in MPI calls. in the latter case, that MP> > usually corresponds to severe overload of your communication MP> > hardware and taking care of that would give you a much better MP> > performance increase than any compiler switches will. MP> > MP> > basically for almost _any_ system library (and that includes MP> > ATLAS and FFTW, btw) it is best to stick to a moderate optimization MP> > (-O) as aggressive optimization may interfere with the implemented MP> > algorithms and existing optimizations (e.g. both ATLAS and FFTW MP> > include optimizations on the C-language and algorithm level, higher MP> > compiler optimization can change the semantics of your code and MP> > thus negate the optimizations performed in the code). even more MP> > so, with many current compilers, aggressive optimization (-O3 or MP> > higher) incures a very high risk of the compiler miscompiling MP> > your library and thus leading to uncontrollable crashes or wrong MP> > results. that doesn't mean, that there may be a measurable benefit MP> > for singular cases, but from over 10 years of experience in MP> > management of HPC resources the overall effect is problematic. MP> > most of the time it is hard enough to chase down application bugs MP> > that are real or cause by compilers, you don't want to add having MP> > to track down problems in your libraries to that. MP> > MP> > cheers, MP> > axel. MP> > MP> > MP> > MP> Any comment is highly appreciated. MP> > MP> MP> > MP> Best regards, MP> > MP> Mahmoud Payami MP> > MP> Phys. Group, MP> > MP> Atomic Energy Org. of Iran MP> > MP> MP> > MP> _______________________________________________ MP> > MP> Pw_forum mailing list MP> > MP> Pw_forum at pwscf.org MP> > MP> http://www.democritos.it/mailman/listinfo/pw_forum MP> > MP> MP> > MP> > -- MP> > ======================================================================= MP> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu MP> > Center for Molecular Modeling -- University of Pennsylvania MP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 MP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 MP> > ======================================================================= MP> > If you make something idiot-proof, the universe creates a better idiot. MP> MP> _______________________________________________ MP> Pw_forum mailing list MP> Pw_forum at pwscf.org MP> http://www.democritos.it/mailman/listinfo/pw_forum MP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mpayami at aeoi.org.ir Sat Feb 21 20:18:22 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sat, 21 Feb 2009 22:48:22 +0330 Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 In-Reply-To: References: Message-ID: > > how are the timings if you don't use all 8 cores? > does the jobs get faster again? > N_core tot cputime for one iter ------- ----------------------- 1 398.89 sec 2 200.14 3 134.61 4 101.46 5 85.24 6 71.60 7 63.31 8 57.16 Is it surprising? > if you are still running the same "benchmark" that > you were running before. your comparisons are most > likely severely flawed. No, axel! It was a two-atom Au cluster with "relax" calculations ON pentium 4, 3.2GHz, dual core. Now it is SLAB. > you never could prove to me, > that you are running a correctly compiled executable > and mpi installation. so you may be comparing apples > and oranges. you openmpi timings are highly suspicious. > I do not want to prove anything. I just announce my experience. Everybody interested can verify by him/herself. > i was showing you, that openmpi _does_ behave properly > on an example that does specifically test MPI performance > and not depend on anything else (like NFS i/o). I agree with you. In that case you were comparing apple with orange! > > MP> > if you see these kinds of differences, then there is something > MP> > else causing problems. > MP> > > MP> > are you using processor and memory affinity with openmpi? > MP> > MP> I have no idea on these concepts. I just use (practice as a good(?) > MP> student) what you taught me during the hpc08. > > processor affinity is tying a process to a specific CP. > in multi-processor/multi-core environments, this has > severe performance implications, as it improves cpu > cache utilization. just stick those keyword into google > and you'll see. > > MP> > > MP> > what kind of processor is this exactly? > MP> It is 5420. > > ok. so that is intel quad-core. i have a bunch of 5430s > available to me. please redo those tests with the 32-water > cp.x input from example21 of the Q-E distribution. and > then we can start dicussing seriously. for as long as > nobody can reproduce your benchmarks, they are useless. I do not have any experience with CPMD. > > also you still have a huge difference between wall > clock and cpu clock. in short, you are trying to solve > the least important problem first. > > i'd kindly ask to not to make claims about mpi implementations > being "better" unless you can prove that the difference in > timings are really due to the mpi implementation and not due > to improper use of the machine or inadequate hardware. I just expressed my findings, and tried to share it. regards,mahmoud > > cheers, > axel. > > > > MP> > MP> regards,mahmoud > MP> > MP> > MP> > axel. > MP> > > MP> > MP> > MP> > MP> Cheers, > MP> > MP> mahmoud > MP> > MP> > MP> > MP> > MP> > > MP> > -- > MP> > > ======================================================================= > MP> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > MP> > Center for Molecular Modeling -- University of > Pennsylvania > MP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > MP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > MP> > > ======================================================================= > MP> > If you make something idiot-proof, the universe creates a better > idiot. > MP> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. From mpayami at aeoi.org.ir Sat Feb 21 20:23:19 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Sat, 21 Feb 2009 22:53:19 +0330 Subject: [Pw_forum] How to tune cputimes using mpich2-1.0.8 In-Reply-To: References: Message-ID: Dear Axel, > mahmoud, > > as i already wrote to you in private e-mail. the huge discrepancy > between wall and cpu time casts a severe doubt on the usefulness > of these numbers. > > as i was stating in the previous mail. if the MPI library takes > a significant time of the total time, there is a problem elsewhere > that needs to be investigated first. you are obviously severely > overloading your machine. > > MP> These are the results of an scf calculation for 21-layered Al(110) > slab > MP> with Ecut=22Ry, k_mesh=45x45x1, degauss=0.05 on a box with 2 x > amd64 quad > MP> (8 cores). > MP> The memory used in mpich2 is less than half of that in (default > MP> switches)openmpi. > > how did you determine that? > Using the "top" command and the fact that compiling with "shared" switch causes just one copy of lib be present in memory while without that the number of copies is the same as the number of processes. Bests, mahmoud > you have to be careful to differentiate between memory > being mapped into address space, physical memory used > and virtual memory being in use. the respective columns > in displayed in, e.g. top are: VIRT RES and CODE+DATA) > > cheers, > axel. > > > MP> > MP> Cheers, > MP> mahmoud > MP> > MP> > MP> > > MP> > in general, it is not a good idea to try an play with > MP> > compiler optimization in the hope to make an MPI implementation > MP> > (and thus communication) faster. > MP> > > MP> > if your application performance would depend so much on the > MP> > optimization level use to compile your MPI library, then either > MP> > you have a very crappy MPI implementation, or your application > MP> > spends too much time in MPI calls. in the latter case, that > MP> > usually corresponds to severe overload of your communication > MP> > hardware and taking care of that would give you a much better > MP> > performance increase than any compiler switches will. > MP> > > MP> > basically for almost _any_ system library (and that includes > MP> > ATLAS and FFTW, btw) it is best to stick to a moderate > optimization > MP> > (-O) as aggressive optimization may interfere with the > implemented > MP> > algorithms and existing optimizations (e.g. both ATLAS and FFTW > MP> > include optimizations on the C-language and algorithm level, > higher > MP> > compiler optimization can change the semantics of your code and > MP> > thus negate the optimizations performed in the code). even more > MP> > so, with many current compilers, aggressive optimization (-O3 or > MP> > higher) incures a very high risk of the compiler miscompiling > MP> > your library and thus leading to uncontrollable crashes or wrong > MP> > results. that doesn't mean, that there may be a measurable > benefit > MP> > for singular cases, but from over 10 years of experience in > MP> > management of HPC resources the overall effect is problematic. > MP> > most of the time it is hard enough to chase down application bugs > MP> > that are real or cause by compilers, you don't want to add having > MP> > to track down problems in your libraries to that. > MP> > > MP> > cheers, > MP> > axel. > MP> > > MP> > > MP> > MP> Any comment is highly appreciated. > MP> > MP> > MP> > MP> Best regards, > MP> > MP> Mahmoud Payami > MP> > MP> Phys. Group, > MP> > MP> Atomic Energy Org. of Iran > MP> > MP> > MP> > MP> _______________________________________________ > MP> > MP> Pw_forum mailing list > MP> > MP> Pw_forum at pwscf.org > MP> > MP> http://www.democritos.it/mailman/listinfo/pw_forum > MP> > MP> > MP> > > MP> > -- > MP> > > ======================================================================= > MP> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > MP> > Center for Molecular Modeling -- University of > Pennsylvania > MP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > MP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > MP> > > ======================================================================= > MP> > If you make something idiot-proof, the universe creates a better > idiot. > MP> > MP> _______________________________________________ > MP> Pw_forum mailing list > MP> Pw_forum at pwscf.org > MP> http://www.democritos.it/mailman/listinfo/pw_forum > MP> > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From panda.deng.pan at gmail.com Mon Feb 23 05:43:08 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 23 Feb 2009 12:43:08 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation Message-ID: Dear All, I was trying to do a Band calculation, and I got a error message like this : from card_kpoints : error # 1 error or end of file while reading tpiba k points The inputs is : &control calculation = 'bands' restart_mode='from_scratch' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' wf_collect=.true. / &system ibrav=7, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0 occupations= 'tetrahedra' / &electrons diagonalization = 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 56.00 Ba.pbe-nsp-van.UPF Ni 28.00 Ni.pbe-nd-rrkjus.UPF As 33.00 As.pbe-n-van.UPF ATOMIC_POSITIONS {crystal} Ba 0.0000 0.0000 0.0000 Ba 0.0000 0.0000 0.5000 Ni 0.5000 0.0000 0.2500 Ni 0.0000 0.5000 0.2500 Ni 0.5000 0.0000 0.7500 Ni 0.0000 0.5000 0.7500 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.0000 0.0000 0.8476 As 0.0000 0.0000 0.1524 K_POINTS 311 -0.500 0.500 0.500 1 -0.495 0.495 0.495 2 -0.490 0.490 0.490 3 -0.485 0.485 0.485 4 -0.480 0.480 0.480 5 ... ... I knew errors happened in the K_POINTS. And I have checked for many times, but I could not find where is the error.Would someone point it out for me ? Thanks a lot. Have nice day! Pan Deng Nanjing University From yccheng.nju at gmail.com Mon Feb 23 07:31:19 2009 From: yccheng.nju at gmail.com (yccheng.nju) Date: Mon, 23 Feb 2009 14:31:19 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation References: Message-ID: <200902231431180317037@gmail.com> K_POINTS 311 -0.500 0.500 0.500 1 -0.495 0.495 0.495 2 -0.490 0.490 0.490 3 -0.485 0.485 0.485 4 -0.480 0.480 0.480 5 You should change the k point set as follows: K_POINTS 311 -0.500 0.500 0.500 1 -0.495 0.495 0.495 1 -0.490 0.490 0.490 1 -0.485 0.485 0.485 1 -0.480 0.480 0.480 1 2009-02-23 yccheng.nju ???? ?? ????? 2009-02-23 12:43:56 ???? pw_forum ??? ??? [Pw_forum] Help me with the Band Structure Calculation Dear All, I was trying to do a Band calculation, and I got a error message like this : from card_kpoints : error # 1 error or end of file while reading tpiba k points The inputs is : &control calculation = 'bands' restart_mode='from_scratch' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' wf_collect=.true. / &system ibrav=7, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0 occupations= 'tetrahedra' / &electrons diagonalization = 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 56.00 Ba.pbe-nsp-van.UPF Ni 28.00 Ni.pbe-nd-rrkjus.UPF As 33.00 As.pbe-n-van.UPF ATOMIC_POSITIONS {crystal} Ba 0.0000 0.0000 0.0000 Ba 0.0000 0.0000 0.5000 Ni 0.5000 0.0000 0.2500 Ni 0.0000 0.5000 0.2500 Ni 0.5000 0.0000 0.7500 Ni 0.0000 0.5000 0.7500 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.0000 0.0000 0.8476 As 0.0000 0.0000 0.1524 K_POINTS 311 -0.500 0.500 0.500 1 -0.495 0.495 0.495 2 -0.490 0.490 0.490 3 -0.485 0.485 0.485 4 -0.480 0.480 0.480 5 ... ... I knew errors happened in the K_POINTS. And I have checked for many times, but I could not find where is the error.Would someone point it out for me ? Thanks a lot. Have nice day! Pan Deng Nanjing 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/20090223/5ef5794a/attachment.htm From nazari at iasbs.ac.ir Mon Feb 23 11:10:05 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 23 Feb 2009 10:10:05 -0000 (UTC) Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <200902231431180317037@gmail.com> References: <200902231431180317037@gmail.com> Message-ID: <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> Also > > You should change the k point set as follows: > K_POINTS > 5 > -0.500 0.500 0.500 1 > -0.495 0.495 0.495 1 > -0.490 0.490 0.490 1 > -0.485 0.485 0.485 1 > -0.480 0.480 0.480 1 > From panda.deng.pan at gmail.com Mon Feb 23 08:13:24 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 23 Feb 2009 15:13:24 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> Message-ID: Dear yccheng.nju and nazari, I have tried to change to what you had suggested. But the error happens still, and the message unchange: from card_kpoints : error # 1 error or end of file while reading tpiba k points And for nazari, I did have 311 k points but I just gave five of them and ommitted the others. Thanks for two of you, but I do not know where the problem is. Please help me. Have a nice day Pan Deng Nanjing University From yccheng.nju at gmail.com Mon Feb 23 08:21:06 2009 From: yccheng.nju at gmail.com (yccheng.nju) Date: Mon, 23 Feb 2009 15:21:06 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation References: , <200902231431180317037@gmail.com>, <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir>, Message-ID: <200902231521044068026@gmail.com> You should set all number to "1" in the fourth column in kpoints. You have 311 K points, why you just give 5 in the input file. The error message have told you what your problem is ! 2009-02-23 yccheng.nju ???? ?? ????? 2009-02-23 15:14:13 ???? PWSCF Forum ??? ??? Re: [Pw_forum] Help me with the Band Structure Calculation Dear yccheng.nju and nazari, I have tried to change to what you had suggested. But the error happens still, and the message unchange: from card_kpoints : error # 1 error or end of file while reading tpiba k points And for nazari, I did have 311 k points but I just gave five of them and ommitted the others. Thanks for two of you, but I do not know where the problem is. Please help me. Have a nice day Pan Deng Nanjing 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/20090223/d4fd507a/attachment-0001.htm From lanhaiping at gmail.com Mon Feb 23 08:26:43 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 23 Feb 2009 15:26:43 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: Message-ID: Hi, Deng, this error is due to more or less lines you give in the input file. I checked the subroutine, and found that this error will be called for two situations , the one is wrong format, the other is wrong lines. Since your format for kpoints card is right, i think the most probability is wrong lines you gave . This situation may be due to transferring files from windows to linux. Regards, On Mon, Feb 23, 2009 at 12:43 PM, ?? wrote: > Dear All, > > I was trying to do a Band calculation, and I got a error message like this > : > > from card_kpoints : error # 1 > error or end of file while reading tpiba k points > > The inputs is : > > &control > calculation = 'bands' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > wf_collect=.true. > / > &system > ibrav=7, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0 > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 56.00 Ba.pbe-nsp-van.UPF > Ni 28.00 Ni.pbe-nd-rrkjus.UPF > As 33.00 As.pbe-n-van.UPF > ATOMIC_POSITIONS {crystal} > Ba 0.0000 0.0000 0.0000 > Ba 0.0000 0.0000 0.5000 > Ni 0.5000 0.0000 0.2500 > Ni 0.0000 0.5000 0.2500 > Ni 0.5000 0.0000 0.7500 > Ni 0.0000 0.5000 0.7500 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.0000 0.0000 0.8476 > As 0.0000 0.0000 0.1524 > K_POINTS > 311 > -0.500 0.500 0.500 1 > -0.495 0.495 0.495 2 > -0.490 0.490 0.490 3 > -0.485 0.485 0.485 4 > -0.480 0.480 0.480 5 > ... > ... > > I knew errors happened in the K_POINTS. And I have checked for many > times, but I could not find where is the error.Would someone point it > out for me ? Thanks a lot. > > Have nice day! > > Pan Deng > Nanjing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090223/eff7c2a8/attachment.htm From lanhaiping at gmail.com Mon Feb 23 08:29:27 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 23 Feb 2009 15:29:27 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <200902231521044068026@gmail.com> References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> Message-ID: Hi, the weights of kpoints can be set to any value as decribed in the Doc. On Mon, Feb 23, 2009 at 3:21 PM, yccheng.nju wrote: > You should set all number to "1" in the fourth column in kpoints. You > have 311 K points, why you just give 5 in the input file. The error message > have told you what your problem is ! > > > 2009-02-23 > ------------------------------ > yccheng.nju > ------------------------------ > *????* ?? > *?????* 2009-02-23 15:14:13 > *????* PWSCF Forum > *???* > *???* Re: [Pw_forum] Help me with the Band Structure Calculation > Dear yccheng.nju and nazari, > I have tried to change to what you had suggested. But the error > happens still, and the message unchange: > from card_kpoints : error # 1 > error or end of file while reading tpiba k points > And for nazari, I did have 311 k points but I just gave five of them > and ommitted the others. > > Thanks for two of you, but I do not know where the problem is. Please help me. > Have a nice day > Pan Deng > Nanjing University > _______________________________________________ > 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 > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090223/0bb7f043/attachment.htm From jdai3 at mail.ustc.edu.cn Mon Feb 23 08:31:23 2009 From: jdai3 at mail.ustc.edu.cn (Dai) Date: Mon, 23 Feb 2009 15:31:23 +0800 Subject: [Pw_forum] compile problem on IBM AIX61 References: <435222314.07439@ustc.edu.cn>, <435235960.32596@ustc.edu.cn> Message-ID: <435374285.03026@ustc.edu.cn> Dear Axel Kohlmeyer Thanks, with xlc and xlf, it works fine now. 2009-02-23 Best regards, Jun Dai ???? Axel Kohlmeyer ????? 2009-02-22 01:06:00 ???? Dai ??? PWSCF Forum ??? Re: [Pw_forum] compile problem on IBM AIX61 On Sat, 21 Feb 2009, Dai wrote: JD> Dear all, dear jun dai, JD> I encountered a problem when compile QE4.0.4 with gcc 4.0.0 and xlf V12.1, : JD> ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; else make TLDEPS= all ; fi ) JD> gcc -O3 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA -I../include -c cptimer.c JD> /usr/include/unistd.h:923: error: parse error before '[' token JD> /usr/include/unistd.h:924: error: parse error before 'rid_t' JD> make: The error code from the last command is 1. JD> JD> Any idea on how to fix this problem? Thanks in advance. this is either a bug in the unix headers of AIX or gcc-4.0.0 and _not_ a Q-E problem. most likely a combination of both. gcc-4.0.0 is a quite broken and long obsolete compiler version (it is a double zero release and that almost always spells trouble). i would recommend to either install a current gcc or use the system xlc (cc) instead. sometimes header conflicts on AIX can be resolved by adding -D__ALL_SOURCE to DFLAGS in make.sys cheers, axel. JD> JD> 2009-02-21 JD> JD> JD> JD> Best regards, JD> Jun Dai JD> JD> ============================================================= JD> Jun Dai JD> Ph.D. Candidate, JD> Hefei National Laboratory For Physical Sciences at the Microscale, JD> University of Science and Technology of China, JD> Hefei, Anhui, 230026, JD> People's Republic of China JD> Tel.: 86-551-3606428 JD> Fax.: 86-551-3602969 JD> E-mail: jdai3 at mail.ustc.edu.cn JD> ============================================================= JD> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090223/1844bf38/attachment-0001.htm From panda.deng.pan at gmail.com Mon Feb 23 08:31:36 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 23 Feb 2009 15:31:36 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <200902231521044068026@gmail.com> References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> Message-ID: Dear yccheng.nju > You should set all number to "1" in the fourth column in kpoints. You have I have set all the number to '1', > 311 K points, why you just give 5 in the input file. The error message have I ommit the other points in the email > told you what your problem is ! > I just know where the problem is. But I do not know what I have done wrong. It is not the problem you mentioned. Thank you all the same. From panda.deng.pan at gmail.com Mon Feb 23 08:35:10 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 23 Feb 2009 15:35:10 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> Message-ID: Thank you Haiping, I knew the weights can be set for any value.But it's still worth a shot. I have no idea what's wrong. thank you again.I will go for checking. From tone.kokalj at ijs.si Mon Feb 23 09:06:14 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 23 Feb 2009 09:06:14 +0100 Subject: [Pw_forum] band and dos input files in xcrysden In-Reply-To: References: Message-ID: <1235376374.13174.10.camel@walk.ijs.si> On Sat, 2009-02-21 at 13:05 -0300, Eduardo Ariel Menendez Proupin wrote: > One simple idea is to add a submenu to the menu "File/New from here" > So, if I have an open pw.x input, when I select "File/New from here" > it will make the new file inheriting all the properties: in this case > outdir and prefix. I would also set by default fildos = prefix.dos. What an excellent idea! > Emin and Emax are the minumum and maxima of the Kohn-Sham eigenvalues > that can be taken from the pw.x outputs. But this is the default (so why bother)!? > A different strategy may be to have a menu Project and from the > Project menu, select kinds of input fiiles or tasks. If one selects > task DOS, ... This is very good ideas as well. In such a task PWgui can produce three main pages: scf input, nscf input, and dos input. In the nscf input only those variables could be displayed that are of interest, and they can also be automatically set to some default values. > for example, then pwgui can create the three input files and display > a reminder of the sequence of calculations to be done. Instead of reminder, pwgui can actually offer to make all requested calculations. Thanks for your useful suggestions. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Mon Feb 23 09:48:31 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 23 Feb 2009 09:48:31 +0100 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> Message-ID: <49A262DF.8030905@democritos.it> ?? wrote: > I have tried to change to what you had suggested. But the error > happens still, and the message unchange: > > > from card_kpoints : error # 1 > error or end of file while reading tpiba k points > > And for nazari, I did have 311 k points but I just gave five of them > and ommitted the others. if you are ABSOLUTELY sure that you have 311 k-points and that the format of ALL of the 311 lines is correct: check for the presence of spurious line-feed characters in the input file. LF are typically present in files generated by Windows and are usually ignored on Linux machines, but on some other machines they produce mysterious errors like the one above Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Mon Feb 23 10:13:01 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 23 Feb 2009 10:13:01 +0100 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: Message-ID: <49A2689D.9040705@sissa.it> When you will have solved your reading issue and succeed in giving k-points on input, be careful that you'll be specifying the k-coordinates in units of 2pi/a, while maybe your input lines are meant for using with the keyword 'crystal' instead (at least this I can guess from your input file). Please have a look at the Doc/ files. GS > K_POINTS > 311 > -0.500 0.500 0.500 1 > -0.495 0.495 0.495 2 > -0.490 0.490 0.490 3 > -0.485 0.485 0.485 4 > -0.480 0.480 0.480 5 > ... > ... > > I knew errors happened in the K_POINTS. And I have checked for many > times, but I could not find where is the error.Would someone point it > out for me ? Thanks a lot. > > Have nice day! > > Pan Deng > Nanjing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Feb 23 10:16:37 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 23 Feb 2009 10:16:37 +0100 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> Message-ID: <49A26975.8060403@sissa.it> lan haiping wrote: > Hi, the weights of kpoints can be set to any value as decribed in the Doc. You're right, but for this type of calculation only. Please be careful that's not the case in nscf calculations that will be used for DOS like calculations, for instance (maybe that's obvious, but I just wanted to point it out). Regards, GS > > On Mon, Feb 23, 2009 at 3:21 PM, yccheng.nju > wrote: > > You should set all number to "1" in the fourth column in kpoints. > You have 311 K points, why you just give 5 in the input file. The > error message have told you what your problem is ! > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lanhaiping at gmail.com Mon Feb 23 12:13:22 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 23 Feb 2009 19:13:22 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <49A26975.8060403@sissa.it> References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> <49A26975.8060403@sissa.it> Message-ID: Hi , Gabriele, Thanks for this emphasis. I do wonder about any tricks to treat DOS or other nscf calculations with explicit kpoints set. In fact , my previous works of nscf calculations on DOS ,charge density and electrostaic potential et al were adopted MP grids. Regards, On Mon, Feb 23, 2009 at 5:16 PM, Gabriele Sclauzero wrote: > > lan haiping wrote: > > Hi, the weights of kpoints can be set to any value as decribed in the > Doc. > > You're right, but for this type of calculation only. Please be careful > that's not the case > in nscf calculations that will be used for DOS like calculations, for > instance (maybe > that's obvious, but I just wanted to point it out). > > Regards, > > GS > > > > > On Mon, Feb 23, 2009 at 3:21 PM, yccheng.nju > > wrote: > > > > You should set all number to "1" in the fourth column in kpoints. > > You have 311 K points, why you just give 5 in the input file. The > > error message have told you what your problem is ! > > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090223/d5f9b9a7/attachment.htm From sclauzer at sissa.it Mon Feb 23 12:28:36 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 23 Feb 2009 12:28:36 +0100 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> <49A26975.8060403@sissa.it> Message-ID: <49A28864.1090209@sissa.it> Dear Hai-Ping, lan haiping wrote: > Hi , Gabriele, > Thanks for this emphasis. > I do wonder about any tricks to treat DOS or > other nscf calculations with explicit kpoints set. What kind of tricks are you thinking of? I don't use any 'trick', but maybe there are. I usually do DOS/PDOS calculations starting from nscf k-point sets generated automatically (with or without offset, this should affect more or less convergency depending on the system, I think), so that weights are computed automatically and the hamiltonian is diagonlized only for points in the IBZ. In this way you can easily check convergence of the quantity you're interested in by simply increasing the grid size. > In fact , my previous works of nscf calculations on DOS ,charge density > and electrostaic potential et al were adopted MP grids. What are MP grids? Do you mean Monkhorst Pack grids? Maybe a more efficient way to converge faster DOS is to adopt the tetrahedra method, but I've never practiced with it (I don't know if it has been implemented for all cases, such as noncolinear, spin orbit, ...) GS > > Regards, > > On Mon, Feb 23, 2009 at 5:16 PM, Gabriele Sclauzero > wrote: > > > lan haiping wrote: > > Hi, the weights of kpoints can be set to any value as decribed > in the Doc. > > You're right, but for this type of calculation only. Please be > careful that's not the case > in nscf calculations that will be used for DOS like calculations, > for instance (maybe > that's obvious, but I just wanted to point it out). > > Regards, > > GS > > > > > On Mon, Feb 23, 2009 at 3:21 PM, yccheng.nju > > > >> wrote: > > > > You should set all number to "1" in the fourth column in kpoints. > > You have 311 K points, why you just give 5 in the input file. The > > error message have told you what your problem is ! > > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lanhaiping at gmail.com Mon Feb 23 13:37:22 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 23 Feb 2009 20:37:22 +0800 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: <49A28864.1090209@sissa.it> References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> <49A26975.8060403@sissa.it> <49A28864.1090209@sissa.it> Message-ID: On Mon, Feb 23, 2009 at 7:28 PM, Gabriele Sclauzero wrote: > Dear Hai-Ping, > > lan haiping wrote: > > Hi , Gabriele, > > Thanks for this emphasis. > > I do wonder about any tricks to treat DOS or > > other nscf calculations with explicit kpoints set. > > What kind of tricks are you thinking of? I don't use any 'trick', but maybe > there are. > I usually do DOS/PDOS calculations starting from nscf k-point sets > generated automatically > (with or without offset, this should affect more or less convergency > depending on the > system, I think), so that weights are computed automatically and the > hamiltonian is > diagonlized only for points in the IBZ. In this way you can easily check > convergence of > the quantity you're interested in by simply increasing the grid size. Thanks for sharing your experience . Due to my laziness, i havenot ever tried to use explicite kpoint sets but MP grids to sample BZ . This is why i do wonder about . > > In fact , my previous works of nscf calculations on DOS ,charge density > > and electrostaic potential et al were adopted MP grids. > > What are MP grids? Do you mean Monkhorst Pack grids? Yes, I do mean this scheme for BZ sampling. > > Maybe a more efficient way to converge faster DOS is to adopt the > tetrahedra method, but > I've never practiced with it (I don't know if it has been implemented for > all cases, such > as noncolinear, spin orbit, ...) > thanks again . > GS > > > > > Regards, > > > > On Mon, Feb 23, 2009 at 5:16 PM, Gabriele Sclauzero > > wrote: > > > > > > lan haiping wrote: > > > Hi, the weights of kpoints can be set to any value as decribed > > in the Doc. > > > > You're right, but for this type of calculation only. Please be > > careful that's not the case > > in nscf calculations that will be used for DOS like calculations, > > for instance (maybe > > that's obvious, but I just wanted to point it out). > > > > Regards, > > > > GS > > > > > > > > On Mon, Feb 23, 2009 at 3:21 PM, yccheng.nju > > > > > >> > wrote: > > > > > > You should set all number to "1" in the fourth column in > kpoints. > > > You have 311 K points, why you just give 5 in the input file. > The > > > error message have told you what your problem is ! > > > > > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it > > | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > Hai-Ping Lan > > Department of Electronics , > > Peking University , Bejing, 100871 > > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090223/fe2c5e8a/attachment-0001.htm From willykohn at gmail.com Mon Feb 23 15:24:03 2009 From: willykohn at gmail.com (willy kohn) Date: Mon, 23 Feb 2009 09:24:03 -0500 Subject: [Pw_forum] Help me with the Band Structure Calculation In-Reply-To: References: <200902231431180317037@gmail.com> <10937.213.176.122.17.1235383805.squirrel@mail.iasbs.ac.ir> <200902231521044068026@gmail.com> Message-ID: <8a1b6d820902230624m169695dfs46197eac390f47c1@mail.gmail.com> Hi, I met this problem before. It occurred when I used "<" to feed the input file to pw.x. I solved this problem by use "-inp" instead of "<" like the following: pw.x -inp xxx.in > xxx.out Hopefully, this information can help you. Best, Wei On Mon, Feb 23, 2009 at 2:31 AM, ?? wrote: > Dear yccheng.nju > > > You should set all number to "1" in the fourth column in kpoints. You > have > > I have set all the number to '1', > > > > 311 K points, why you just give 5 in the input file. The error message > have > > I ommit the other points in the email > > > told you what your problem is ! > > > > I just know where the problem is. But I do not know what I have done > wrong. It is not the problem you mentioned. Thank you all the same. > _______________________________________________ > 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/20090223/5fb41ce2/attachment.htm From jemmyhu at sharcnet.ca Mon Feb 23 15:41:34 2009 From: jemmyhu at sharcnet.ca (Jemmy Hu) Date: Mon, 23 Feb 2009 09:41:34 -0500 Subject: [Pw_forum] compile problem with PGI v6.1 compilers on AMD Opteron cluster In-Reply-To: References: <435222314.07439@ustc.edu.cn> Message-ID: <49A2B59E.8070806@sharcnet.ca> Dear All, Please help for this compile problem. Thanks. When compile PWSCF-4.0.4 using PGI v6.1 compilers, it gives errors in the make stage: Unknown flag -t Unknown flag -r Unknown flag -a Unknown flag -d Unknown flag -i Unknown flag -t Unknown flag -i Unknown flag -o Unknown flag -n Unknown flag -a Unknown flag -l Unknown flag -o PGF90-S-0034-Syntax error at or near (iotk_base.F90: 2) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 55) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 59) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 81) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 82) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 83) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 84) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 85) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 86) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 87) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 88) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 89) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 90) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 91) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 92) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 95) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 96) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 97) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 98) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 99) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 100) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 101) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 102) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 103) PGF90-S-0034-Syntax error at or near (iotk_base.F90: 104) PGF90-F-0008-Error limit exceeded (iotk_base.F90: 104) PGF90/any Linux/x86-64 6.1-6: compilation aborted make[2]: *** [iotk_base.o] Error 2 make[1]: *** [libiotk.a] Error 2 make: *** [libiotk] Error 2 On the wiki page, it says pgi v6.1 works (info from Paolo Cazzato) http://www.quantum-espresso.org/wiki/index.php/Main_Page but I cannot access to the contents. The wiki login page does not have the Create Account option http://www.quantum-espresso.org/wiki/index.php?title=Special:Userlogin&returnto=User_Guide Anyone has the idea to access the wiki page? Thanks. Jemmy From giannozz at democritos.it Mon Feb 23 15:49:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 23 Feb 2009 15:49:57 +0100 Subject: [Pw_forum] compile problem with PGI v6.1 compilers on AMD Opteron cluster In-Reply-To: <49A2B59E.8070806@sharcnet.ca> References: <435222314.07439@ustc.edu.cn> <49A2B59E.8070806@sharcnet.ca> Message-ID: <49A2B795.9090607@democritos.it> Jemmy Hu wrote: > On the wiki page, it says pgi v6.1 works (info from Paolo Cazzato) > http://www.quantum-espresso.org/wiki/index.php/Main_Page > but I cannot access to the contents. what do you mean by "access the content"? you cannot edit it, but you can visualize it Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Mon Feb 23 16:05:38 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 23 Feb 2009 10:05:38 -0500 (EST) Subject: [Pw_forum] compile problem with PGI v6.1 compilers on AMD Opteron cluster In-Reply-To: <49A2B59E.8070806@sharcnet.ca> References: <435222314.07439@ustc.edu.cn> <49A2B59E.8070806@sharcnet.ca> Message-ID: On Mon, 23 Feb 2009, Jemmy Hu wrote: JH> Dear All, JH> JH> Please help for this compile problem. Thanks. JH> When compile PWSCF-4.0.4 using PGI v6.1 compilers, it gives errors in JH> the make stage: JH> Unknown flag -t JH> Unknown flag -r JH> Unknown flag -a JH> Unknown flag -d JH> Unknown flag -i JH> Unknown flag -t JH> Unknown flag -i JH> Unknown flag -o JH> Unknown flag -n JH> Unknown flag -a JH> Unknown flag -l JH> Unknown flag -o this looks like you are trying to feed the pgi compiler flags that are meant for gcc preprocessor. thus there has to be something wrong in your make.sys file. [...] JH> On the wiki page, it says pgi v6.1 works (info from Paolo Cazzato) JH> http://www.quantum-espresso.org/wiki/index.php/Main_Page how old is that information. the PGI compilers are notoriously bad at 'modern' fortran 95 code, and Q-E has a slowly increasing amout of them, so if this statement is not recent (which i assume), then it is probably not applicable anymore. i would strongly suggest to first try compiling with the latest g95 _release_ (_not_ snapshot!) version and then try and revisit pgi and see if there is a significant difference (in speed _and_ results). JH> but I cannot access to the contents. JH> The wiki login page does not have the Create Account option JH> http://www.quantum-espresso.org/wiki/index.php?title=Special:Userlogin&returnto=User_Guide JH> JH> JH> Anyone has the idea to access the wiki page? Thanks. what for?? cheers, axel. JH> JH> Jemmy JH> JH> JH> _______________________________________________ JH> Pw_forum mailing list JH> Pw_forum at pwscf.org JH> http://www.democritos.it/mailman/listinfo/pw_forum JH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From vranjan at ncsu.edu Mon Feb 23 16:05:03 2009 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Mon, 23 Feb 2009 10:05:03 -0500 (EST) Subject: [Pw_forum] [Fwd: dielectric tensor] Message-ID: <57404.152.14.74.117.1235401503.squirrel@webmail.ncsu.edu> ---------------------------- Original Message ---------------------------- Subject: dielectric tensor From: "Vivek Ranjan" Date: Fri, February 20, 2009 4:54 pm To: pw_forum at pwscf.org -------------------------------------------------------------------------- Hello, I was wondering if PWSCF can calculate low frequency dielectric permittivity tensor. I would like to calculate dielectric constant in KHz frequency range. Thank you, Vivek Ranjan NCSU __________________________________________________________________________ web : http://www.geocities.com/vivekranjanweb __________________________________________________________________________ Vivek Ranjan Email : vranjan at chips.ncsu.edu Center for High Performance Simulation : vranjan at ncsu.edu Department of Physics NC State University Phone : +1-919-513-0613 (Office) Campus Box 7518 Fax : +1-919-513-4804 Raleigh, NC 27695 -------------------------------------------------------------------------- From panda.deng.pan at gmail.com Tue Feb 24 06:49:14 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Tue, 24 Feb 2009 13:49:14 +0800 Subject: [Pw_forum] The inputs of "ph.x" Message-ID: Dear All Users, When I was try to running a phonon calculation,I have got this error message. from phq_readin : error # 1 reading inputph namelist Although I know I have some mistake in the inputs,I don't know which is.Here is the inputs of mine. &inputph tr2_ph=1.0d-10, prefix='BaNiAs', amass(1)=56.00, amass(2)=28.00, amass(3)=33.00, outdir='/disk2/xgwan/tmp/' fildyn='BaNiAs.dyn', ldisp=.true., nq1=8, nq2=8, nq3=8 / Perhaps the error is the missing of "xq(1)xq(2)xq(3)".But it not specified in the example06 either. If that is the problem, Please someone tell me how to set the value of these. Have nice day! Pan Deng Nanjing University From hqzhou at nju.edu.cn Tue Feb 24 07:45:23 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 24 Feb 2009 14:45:23 +0800 Subject: [Pw_forum] Use of pool Message-ID: <21B74D1AD49648479BDC1ABD309ED183@solarflare> Dear list users: I happened to test duration times of calculating the system I'm investigating against number of pools used. There are totally 36 k points. But the results surprised me quite a lot. no pool: 6m21.02s CPU time, 6m45.88s wall time 2 pools: 7m19.39s CPU time, 7m38.99s wall time 4 pools: 11m59.09s CPU time, 12m14.66s wall time 8 pools: 21m28.77s CPU time, 21m38.71s wall time The machine I'm using is an AMD box with 2 quad core shanghai. Is my understanding of usage of pool wrong? Huiqun Zhou @Nanjing University, China From sclauzer at sissa.it Tue Feb 24 10:02:27 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Feb 2009 10:02:27 +0100 Subject: [Pw_forum] The inputs of "ph.x" In-Reply-To: References: Message-ID: <49A3B7A3.3030806@sissa.it> Please read more carefully the input data description in Doc/INPUT_PH.txt or have just a look inside the phq_readin subroutine. From INPUT_PH: Structure of the input data: =============================================================================== title_line &INPUTPH ... / xq(1) xq(2) xq(3) [ irrep(1) irrep(2) ... irrep(nrapp) ] # if "nrapp" was specified [ atom(1) atom(2) ... atom(nat_todo) ] # if "nat_todo" was specified You'll see that the program expects a title line before reading the namelist, so add that line to your file and try again. Regards GS ?? wrote: > Dear All Users, > > When I was try to running a phonon calculation,I have got this error message. > > from phq_readin : error # 1 > reading inputph namelist > > Although I know I have some mistake in the inputs,I don't know which > is.Here is the inputs of mine. > > &inputph > tr2_ph=1.0d-10, > prefix='BaNiAs', > amass(1)=56.00, > amass(2)=28.00, > amass(3)=33.00, > outdir='/disk2/xgwan/tmp/' > fildyn='BaNiAs.dyn', > ldisp=.true., > nq1=8, nq2=8, nq3=8 > / > > > Perhaps the error is the missing of "xq(1)xq(2)xq(3)".But it not > specified in the example06 either. If that is the problem, Please > someone tell me how to set the value of these. > > Have nice day! > > Pan Deng > Nanjing University > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Tue Feb 24 10:16:02 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Feb 2009 10:16:02 +0100 Subject: [Pw_forum] Use of pool In-Reply-To: <21B74D1AD49648479BDC1ABD309ED183@solarflare> References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> Message-ID: <49A3BAD2.8080507@sissa.it> Contrary to what Axel usually says (but my experience is far little than his, so he is in the position to blame me) I do not believe that increasing the number of pools always gives a better timing for a given system. It depends on the system you are computing (of course...): how big is your supercell, how many electrons, how many k-points, how many bands... My experience is that, when working with big supercells is better try to use one pool until you have a decent scaling and THEN start using more pools. If you have a smaller cell (and consequently many more k-points) and not many electrons (like a slab geometry with small periodicity), then using pools would be more beneficial. However these timings may also depend on the configuration of your machine, i.e. how optimized are algebra and fft libraries and how fast are communications. To have a more precise idea of what's going on you should have a detailed look at the timings at the end of pw output. Last thing, you should be careful that increasing the number of pools you're increasing the memory request on your node (as well as the memory traffic on RAM and caches, I suppose), and that may also be a severe bottleneck to performance. Regards GS Huiqun Zhou wrote: > Dear list users: > > I happened to test duration times of calculating the system I'm > investigating against number of pools used. There are totally > 36 k points. But the results surprised me quite a lot. > > no pool: 6m21.02s CPU time, 6m45.88s wall time > 2 pools: 7m19.39s CPU time, 7m38.99s wall time > 4 pools: 11m59.09s CPU time, 12m14.66s wall time > 8 pools: 21m28.77s CPU time, 21m38.71s wall time > > The machine I'm using is an AMD box with 2 quad core shanghai. > > Is my understanding of usage of pool wrong? > > Huiqun Zhou > @Nanjing University, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lyu7 at ncsu.edu Tue Feb 24 14:49:28 2009 From: lyu7 at ncsu.edu (Liping Yu) Date: Tue, 24 Feb 2009 08:49:28 -0500 Subject: [Pw_forum] Use of pool In-Reply-To: <21B74D1AD49648479BDC1ABD309ED183@solarflare> References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> Message-ID: <49A3FAE8.5020603@ncsu.edu> Dear Huiqun, If your results are based on the same number of processes for different npools, they make sense to me. To my understanding, the almost linear time scaling of using npool means that the computer time is almost linear to npool (and also the total number of procs) only when we fix the number of the processors at each pool. Please correct me if I am wrong. Thanks! Liping Yu Department of Physics NC State University, USA Huiqun Zhou wrote: > Dear list users: > > I happened to test duration times of calculating the system I'm > investigating against number of pools used. There are totally > 36 k points. But the results surprised me quite a lot. > > no pool: 6m21.02s CPU time, 6m45.88s wall time > 2 pools: 7m19.39s CPU time, 7m38.99s wall time > 4 pools: 11m59.09s CPU time, 12m14.66s wall time > 8 pools: 21m28.77s CPU time, 21m38.71s wall time > > The machine I'm using is an AMD box with 2 quad core shanghai. > > Is my understanding of usage of pool wrong? > > Huiqun Zhou > @Nanjing University, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Tue Feb 24 15:46:03 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 24 Feb 2009 09:46:03 -0500 (EST) Subject: [Pw_forum] Use of pool In-Reply-To: <21B74D1AD49648479BDC1ABD309ED183@solarflare> References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> Message-ID: On Tue, 24 Feb 2009, Huiqun Zhou wrote: ZH> Dear list users: ZH> ZH> I happened to test duration times of calculating the system I'm ZH> investigating against number of pools used. There are totally ZH> 36 k points. But the results surprised me quite a lot. ZH> ZH> no pool: 6m21.02s CPU time, 6m45.88s wall time ZH> 2 pools: 7m19.39s CPU time, 7m38.99s wall time ZH> 4 pools: 11m59.09s CPU time, 12m14.66s wall time ZH> 8 pools: 21m28.77s CPU time, 21m38.71s wall time dear huiqun zhou, please note that benchmark numbers are useless without offering a way to reproduce them. so please provide the the input used for this test. also, this looks almost like you are running multiple copies of a serial binary. please check the top of the pw.x (you _are_ pw.x, right?) output and check whether there are the to be expected differences. finally, how does the job scale with just one pool? ZH> ZH> The machine I'm using is an AMD box with 2 quad core shanghai. ZH> ZH> Is my understanding of usage of pool wrong? impossible to tell. cheers, axel. ZH> ZH> Huiqun Zhou ZH> @Nanjing University, China ZH> _______________________________________________ ZH> Pw_forum mailing list ZH> Pw_forum at pwscf.org ZH> http://www.democritos.it/mailman/listinfo/pw_forum ZH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eariel99 at gmail.com Tue Feb 24 15:50:10 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 24 Feb 2009 11:50:10 -0300 Subject: [Pw_forum] [Fwd: dielectric tensor] Message-ID: Dear Vivek, I think you can calculate the low frequency dielectric tensor using the PHONON output and a formula. Please, see PHYSICAL REVIEW B 76, 245110 (2007), eq. (1). Maybe PHONON can calculate directly, but I don not find how. Best regards Eduardo -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez > > ---------- Mensaje reenviado ---------- > From: "Vivek Ranjan" > To: pw_forum at pwscf.org > Date: Mon, 23 Feb 2009 10:05:03 -0500 (EST) > Subject: [Pw_forum] [Fwd: dielectric tensor] > > > ---------------------------- Original Message ---------------------------- > Subject: dielectric tensor > From: "Vivek Ranjan" > Date: Fri, February 20, 2009 4:54 pm > To: pw_forum at pwscf.org > -------------------------------------------------------------------------- > > Hello, > > I was wondering if PWSCF can calculate low frequency dielectric > permittivity tensor. I would like to calculate dielectric constant in KHz > frequency range. > > Thank you, > > Vivek Ranjan > NCSU > > > __________________________________________________________________________ > web : http://www.geocities.com/vivekranjanweb > __________________________________________________________________________ > Vivek Ranjan Email : vranjan at chips.ncsu.edu > Center for High Performance Simulation : vranjan at ncsu.edu > Department of Physics > NC State University Phone : +1-919-513-0613 (Office) > Campus Box 7518 Fax : +1-919-513-4804 > Raleigh, NC 27695 > -------------------------------------------------------------------------- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090224/66374822/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Feb 24 16:20:11 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 24 Feb 2009 10:20:11 -0500 (EST) Subject: [Pw_forum] Use of pool In-Reply-To: <49A3BAD2.8080507@sissa.it> References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> <49A3BAD2.8080507@sissa.it> Message-ID: On Tue, 24 Feb 2009, Gabriele Sclauzero wrote: dear gabriele, GS> Contrary to what Axel usually says (but my experience is far little GS> than his, so he is in the position to blame me) I do not believe GS> that increasing the number of pools always gives a better timing for GS> a given system. It depends on the system you are computing (of GS> course...): how big is your supercell, how many electrons, how many GS> k-points, how many bands... there are _no_ absolute truths in benchmarking and optimizing performance. remember the saying: there are lies, damn lies, and benchmarks. ;) my experience is mostly based on using 2x single processor nodes. the recent change to multi-(soon many) core cpus with large caches but low memory bandwidth will change "the rules". i still remember the case of some benchmarks from eduardo, where the threading in MKL (and using no MPI) was more efficient than MPI with an unthreaded MKL. it will become more important to minimize memory and communication bandwidth and control channels of communication carefully. also, sometimes the more efficient algorithm in theory, may not be the best solution in practice, if it doesn't parallelize well or has the wrong scaling with system size. to give an example: at the last ICTP HPC school a few participants made some tests on multi-threading a simple classical MD code. here is some pseudo code (with f/force being vectors in x,y,z). do i=1,n-1 do j=i+,n force = compute_force(i,j) f(i) = f(i) + force f(j) = f(j) - force end do end do do i=1,n do j=1,n f(i) = f(i) + compute_force(i,j) end do end do the first version should be twice as efficicent, but once you use threading, you have problems with load imbalance (the amount of work in the innerloop changes) and overlapping data access to f(j), which require either using mutexes or caching of intermediate results and thus extra computations. once we went to >8 threads the second version wins, because it has less overhead and you can use static scheduling (which improves data locality and thus cache efficiency), despite it being in theory much less efficient. of course there are even better ways to handle this, but it is hopefully a simple enough example to see my point. GS> My experience is that, when working with big supercells is better GS> try to use one pool until you have a decent scaling and THEN start GS> using more pools. If you have a smaller cell (and consequently many GS> more k-points) and not many electrons (like a slab geometry with GS> small periodicity), then using pools would be more beneficial. lets put it this way. using pools should help the most when you scaling is determined by the communication. with pw.x you have to always consider a second important contribution to performance: disk i/o. one easy way to check this would be to run an equivalently sized input in cp.x, which does not write to the disk until a restart is written. with a multi/many core cpu node, concurrent disk access can be a big problem. using pools makes it worse, since you need more memory and this reduces the amount of memory available to the disk cache. experimenting with disk_io settings (e.g. 'low' or 'none') using a non-NFS scratch partition can have a significant impact. the rule of the thumb, that "npools are almost always better" is also based on the fact that using multiple nodes means multiple independent scratch partitions which is essentially equivalent to raid-0 scenario (actually even better as you have independent i/o busses, too). this is no longer true on a single node with quad-cores. a final remark on AMD cpus. those need special care for getting maximum performance. since you have a NUMA architecture and effectively each CPU has its _own_ memory that can be "borrowed" to the other, it is very important for good performance to enable both memory and processor affinity. but again, that also has implication of how much memory is available to jobs. ...and in some cases it may be even more efficient on quad-core cpus, to not use all cores, but only half of them. especially on intel core2 architecture since pairs of two cores share a L2 cache and with an overloaded memory bus, you gain more from doubling the cache than from doubling the number of (local) cpus. HTH, axel. GS> However these timings may also depend on the configuration of your machine, i.e. how GS> optimized are algebra and fft libraries and how fast are communications. GS> GS> To have a more precise idea of what's going on you should have a detailed look at the GS> timings at the end of pw output. GS> GS> Last thing, you should be careful that increasing the number of pools you're increasing GS> the memory request on your node (as well as the memory traffic on RAM and caches, I GS> suppose), and that may also be a severe bottleneck to performance. GS> GS> Regards GS> GS> GS GS> GS> Huiqun Zhou wrote: GS> > Dear list users: GS> > GS> > I happened to test duration times of calculating the system I'm GS> > investigating against number of pools used. There are totally GS> > 36 k points. But the results surprised me quite a lot. GS> > GS> > no pool: 6m21.02s CPU time, 6m45.88s wall time GS> > 2 pools: 7m19.39s CPU time, 7m38.99s wall time GS> > 4 pools: 11m59.09s CPU time, 12m14.66s wall time GS> > 8 pools: 21m28.77s CPU time, 21m38.71s wall time GS> > GS> > The machine I'm using is an AMD box with 2 quad core shanghai. GS> > GS> > Is my understanding of usage of pool wrong? GS> > GS> > Huiqun Zhou GS> > @Nanjing University, China GS> > _______________________________________________ GS> > Pw_forum mailing list GS> > Pw_forum at pwscf.org GS> > http://www.democritos.it/mailman/listinfo/pw_forum GS> > GS> GS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From vranjan at ncsu.edu Wed Feb 25 02:19:21 2009 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Tue, 24 Feb 2009 20:19:21 -0500 (EST) Subject: [Pw_forum] [Fwd: dielectric tensor] In-Reply-To: References: Message-ID: <47360.152.14.74.117.1235524761.squirrel@webmail.ncsu.edu> Thanks Eduardo, Yes, I am aware of the formalism..... but I was wondering if a utility has been created to analyze the derivative database and generate these numbers. It seems it is still not available. Perhaps I can code it and submit it to PWSCF. Thanks again, Vivek > Dear Vivek, > I think you can calculate the low frequency dielectric tensor using the > PHONON output and a formula. > Please, see PHYSICAL REVIEW B 76, 245110 (2007), eq. (1). > > Maybe PHONON can calculate directly, but I don not find how. > Best regards > Eduardo > > -- > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > > >> >> ---------- Mensaje reenviado ---------- >> From: "Vivek Ranjan" >> To: pw_forum at pwscf.org >> Date: Mon, 23 Feb 2009 10:05:03 -0500 (EST) >> Subject: [Pw_forum] [Fwd: dielectric tensor] >> >> >> ---------------------------- Original Message >> ---------------------------- >> Subject: dielectric tensor >> From: "Vivek Ranjan" >> Date: Fri, February 20, 2009 4:54 pm >> To: pw_forum at pwscf.org >> -------------------------------------------------------------------------- >> >> Hello, >> >> I was wondering if PWSCF can calculate low frequency dielectric >> permittivity tensor. I would like to calculate dielectric constant in >> KHz >> frequency range. >> >> Thank you, >> >> Vivek Ranjan >> NCSU >> >> >> __________________________________________________________________________ >> web : http://www.geocities.com/vivekranjanweb >> __________________________________________________________________________ >> Vivek Ranjan Email : vranjan at chips.ncsu.edu >> Center for High Performance Simulation : vranjan at ncsu.edu >> Department of Physics >> NC State University Phone : +1-919-513-0613 >> (Office) >> Campus Box 7518 Fax : +1-919-513-4804 >> Raleigh, NC 27695 >> -------------------------------------------------------------------------- >> >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________________________________________________ web : http://www.geocities.com/vivekranjanweb __________________________________________________________________________ Vivek Ranjan Email : vranjan at chips.ncsu.edu Center for High Performance Simulation : vranjan at ncsu.edu Department of Physics NC State University Phone : +1-919-513-0613 (Office) Campus Box 7518 Fax : +1-919-513-4804 Raleigh, NC 27695 -------------------------------------------------------------------------- From wyanchao at gmail.com Wed Feb 25 02:54:29 2009 From: wyanchao at gmail.com (wang yanchao) Date: Wed, 25 Feb 2009 09:54:29 +0800 Subject: [Pw_forum] the question of el-ph Message-ID: <55639d30902241754q63383381j1415ff6d636177a6@mail.gmail.com> Dear All, When I calculate the el-ph using the espresso-2.1.5, a very dense mesh is used to get goog convergence. I have changed the value of npk in parameters. I beleve it is enough big to our calculation. But when I calculate the q-point of no symmetry, the results were not saved to output file. The output follow: " ........ Atomic displacements: There are 6 irreducible representations Representation 1 1 modes - To be done Representation 2 1 modes - To be done Representation 3 1 modes - To be done Representation 4 1 modes - To be done Representation 5 1 modes - To be done Representation 6 1 modes - To be done PHONON : 10m 9.50s CPU time" The other content isn't shown in the file. So I want to know if there is some limitation of output file in espresso-2.1.5. Thanks in advance. Sincerely Yanchao -- Yanchao Wang National lab of Superhard Materials,JiLin Univ.Changchun 130012,P.R.China Email:wyanchao at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090225/aded90d6/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Feb 25 03:00:29 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 24 Feb 2009 21:00:29 -0500 (EST) Subject: [Pw_forum] the question of el-ph In-Reply-To: <55639d30902241754q63383381j1415ff6d636177a6@mail.gmail.com> References: <55639d30902241754q63383381j1415ff6d636177a6@mail.gmail.com> Message-ID: On Wed, 25 Feb 2009, wang yanchao wrote: YW> Dear All, YW> YW> When I calculate the el-ph using the espresso-2.1.5, a very dense mesh is quantum espresso version 2.1.5 was released three and a half years ago. i seriously doubt that anybody is even remotely interested in discussing any problems with that version. please check out the current version first. cheers, axel. YW> used to get goog convergence. I have changed the value of npk in parameters. YW> I beleve it is enough big to our calculation. But when I calculate the YW> q-point of no symmetry, the results were not saved to output file. YW> The output follow: YW> " ........ YW> Atomic displacements: YW> There are 6 irreducible representations YW> YW> Representation 1 1 modes - To be done YW> YW> Representation 2 1 modes - To be done YW> YW> Representation 3 1 modes - To be done YW> YW> Representation 4 1 modes - To be done YW> YW> Representation 5 1 modes - To be done YW> YW> Representation 6 1 modes - To be done YW> PHONON : 10m 9.50s CPU time" YW> YW> The other content isn't shown in the file. YW> YW> So I want to know if there is some limitation of output file in YW> espresso-2.1.5. YW> YW> Thanks in advance. YW> YW> Sincerely YW> YW> Yanchao YW> YW> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hushujun at mail.sdu.edu.cn Wed Feb 25 11:32:39 2009 From: hushujun at mail.sdu.edu.cn (Dr. Shu-jun Hu) Date: Wed, 25 Feb 2009 18:32:39 +0800 Subject: [Pw_forum] compile error on AIX 5.2 for Hitachi SR11000 Message-ID: <435557959.28285@mail.sdu.edu.cn> Dear All, I want to compile the QE-4.0.3 code on the Hitachi SR11000 system, and however get the error information: _________________________________________________________ checking build system type... powerpc-ibm-aix5.2 checking architecture... aix checking for Fortran 77 compiler default output file name... a.out checking whether the Fortran 77 compiler works... yes checking whether we are cross compiling... yes checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... no checking whether f90 accepts -g... yes checking for mpif90... mpif90 checking whether we are using the GNU Fortran 77 compiler... no checking whether mpif90 accepts -g... yes setting F90... f90 setting MPIF90... mpif90 checking whether we are using the GNU C compiler... no checking whether mpCC_r accepts -g... yes checking for mpCC_r option to accept ANSI C... none needed setting CC... mpCC_r checking how to run the C preprocessor... mpCC_r -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int *... yes checking size of int *... 4 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes checking for f90... f90 checking whether we are using the GNU Fortran 77 compiler... no checking whether f90 accepts -g... yes setting F77... f90 using F90... f90 setting FFLAGS... -Os -64 -precexp=4 -nompi -noparallel -qfree=f90 -cpp setting F90FLAGS... $(FFLAGS) setting FFLAGS_NOOPT... -O0 setting CFLAGS... -O3 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... mpif90 setting LDFLAGS... setting AR... ar setting ARFLAGS... -X64 ruv setting ARFLAGS_DYNAMIC...-X64 ruv checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... yes checking how to get verbose linking output from f90... -### checking for Fortran libraries of f90... -L/opt/hitachi/matmpp/lib -L/opt/hitachi/MSL2/lib -l/tmp/.200902251913551638458F90/conftest/conftest.L -L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90 -lfiexpmpi checking for dummy main to link with Fortran libraries... unknown configure: error: linking to Fortran libraries from C fails See `config.log' for more details. _________________________________________________________ As I trace the config.log, the following information tells me the souce of the error may be the link of libs: _________________________________________________________ configure:5050: mpCC_r -o conftest -g conftest.c -L/opt/hitachi/matmpp/lib -L/opt/hitachi/MSL2/lib -l/tmp/.200902251913551638458F90/conftest/conftest.L -L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90 -lfiexpmpi >&5 ld: 0706-006 Cannot find or open library file: -l /tmp/.200902251913551638458F90/conftest/conftest.L ld:open(): No such file or directory configure:5056: $? = 255 configure: failed program was: ... _________________________________________________________ The path: -l/tmp/.200902251913551638458F90/conftest/conftest.L is suspicious. How can I solve such problem? Any reply is appreciated. Best Shujun From giannozz at democritos.it Wed Feb 25 11:58:03 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Feb 2009 11:58:03 +0100 Subject: [Pw_forum] compile error on AIX 5.2 for Hitachi SR11000 In-Reply-To: <435557959.28285@mail.sdu.edu.cn> References: <435557959.28285@mail.sdu.edu.cn> Message-ID: <49A5243B.2050803@democritos.it> Dr. Shu-jun Hu wrote: > checking for dummy main to link with Fortran libraries... unknown > configure: error: linking to Fortran libraries from C fails I saw this on a cray xt3 a few days ago. Some supercomputers, and some supercomputing centers, seem to exist for the sole reason to make life hard to their users. Try first to run "autoconf" on your machine and then "configure" again. If it doesn't work: in configure.ac, comment (with a #) the line AC_F77_WRAPPERS run "autoconf" (on a machine that has a working autoconf), then configure again, then define F77_FUNC and F77_FUNC_ in include/c_defs.h following the instructions in include/defs.h.README Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From zxf888 at 163.com Wed Feb 25 13:33:25 2009 From: zxf888 at 163.com (Xiang-Feng Zhou) Date: Wed, 25 Feb 2009 20:33:25 +0800 (CST) Subject: [Pw_forum] quesition about gam.lines Message-ID: <2083754.446461235565205509.JavaMail.coremail@bj163app80.163.com> I know the numbers in the first column of the gam.lines are indexes for q-vectors along the directions which we defined. I want to ask the meaning of the next three columns in gam.lines of example07 (espresso-4.0). Thanks in advance. =============================================== Xiang-Feng ZHOU Ph.D candidate Physics Dept. of Nanjing University =============================================== ????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090225/a26b04ea/attachment.htm From baroni at sissa.it Wed Feb 25 13:57:24 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 25 Feb 2009 13:57:24 +0100 Subject: [Pw_forum] dielectric tensor In-Reply-To: <54930.152.14.74.117.1235166861.squirrel@webmail.ncsu.edu> References: <54930.152.14.74.117.1235166861.squirrel@webmail.ncsu.edu> Message-ID: <7C4479A5-82CC-4436-84D4-08E412DB0224@sissa.it> not quite pwscf. the PHONON code, also included in the QE distribution, does this. SB On Feb 20, 2009, at 10:54 PM, Vivek Ranjan wrote: > Hello, > > I was wondering if PWSCF can calculate low frequency dielectric > permittivity tensor. I would like to calculate dielectric constant > in KHz > frequency range. > > Thank you, > > Vivek Ranjan > NCSU > _______________________________________________ > 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 [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090225/715691b8/attachment.htm From baroni at sissa.it Wed Feb 25 14:01:34 2009 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 25 Feb 2009 14:01:34 +0100 Subject: [Pw_forum] [Fwd: dielectric tensor] In-Reply-To: <47360.152.14.74.117.1235524761.squirrel@webmail.ncsu.edu> References: <47360.152.14.74.117.1235524761.squirrel@webmail.ncsu.edu> Message-ID: <2BCF0198-CCAE-47F8-8A38-14550A09FF74@sissa.it> On Feb 25, 2009, at 2:19 AM, Vivek Ranjan wrote: > Thanks Eduardo, > > Yes, I am aware of the formalism..... but I was wondering if a > utility has > been created to analyze the derivative database and generate these > numbers. > It seems it is still not available. Perhaps I can code it and submit > it to > PWSCF. great! we are all looking forward to it Stefano > --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090225/2965d6b2/attachment.htm From giannozz at democritos.it Wed Feb 25 14:42:25 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Feb 2009 14:42:25 +0100 Subject: [Pw_forum] quesition about gam.lines In-Reply-To: <2083754.446461235565205509.JavaMail.coremail@bj163app80.163.com> References: <2083754.446461235565205509.JavaMail.coremail@bj163app80.163.com> Message-ID: <49A54AC1.80304@democritos.it> Xiang-Feng Zhou wrote: > I know the numbers in the first column of the gam.lines are indexes for > q-vectors along the directions which we defined. I want to ask the > meaning of the next three columns in gam.lines of example07 gamma(i) (phonon linewidth), where i=1,..,3*number of atoms P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Wed Feb 25 15:28:59 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 25 Feb 2009 09:28:59 -0500 (EST) Subject: [Pw_forum] compile error on AIX 5.2 for Hitachi SR11000 In-Reply-To: <435557959.28285@mail.sdu.edu.cn> References: <435557959.28285@mail.sdu.edu.cn> Message-ID: On Wed, 25 Feb 2009, Dr. Shu-jun Hu wrote: SH> SH> Dear All, SH> SH> I want to compile the QE-4.0.3 code on the Hitachi SR11000 system, and however get SH> the error information: a word of caution: are you really, really, _really_ sure you want to do that??? don't you have access to a decent linux cluster instead? i can tell you from my experiences with CPMD that you are in for a lot of trouble and getting the code compiled is only the least of it. the CPMD code is full of hacks and workarounds to get stuff working correctly on these monsters. ...and - unlike CPMD - Q-E doesn't have a "sancto mauro" watching over it. cheers, axel. SH> SH> _________________________________________________________ SH> checking build system type... powerpc-ibm-aix5.2 SH> checking architecture... aix SH> checking for Fortran 77 compiler default output file name... a.out SH> checking whether the Fortran 77 compiler works... yes SH> checking whether we are cross compiling... yes SH> checking for suffix of executables... SH> checking for suffix of object files... o SH> checking whether we are using the GNU Fortran 77 compiler... no SH> checking whether f90 accepts -g... yes SH> checking for mpif90... mpif90 SH> checking whether we are using the GNU Fortran 77 compiler... no SH> checking whether mpif90 accepts -g... yes SH> setting F90... f90 SH> setting MPIF90... mpif90 SH> checking whether we are using the GNU C compiler... no SH> checking whether mpCC_r accepts -g... yes SH> checking for mpCC_r option to accept ANSI C... none needed SH> setting CC... mpCC_r SH> checking how to run the C preprocessor... mpCC_r -E SH> checking for egrep... grep -E SH> checking for ANSI C header files... yes SH> checking for sys/types.h... yes SH> checking for sys/stat.h... yes SH> checking for stdlib.h... yes SH> checking for string.h... yes SH> checking for memory.h... yes SH> checking for strings.h... yes SH> checking for inttypes.h... yes SH> checking for stdint.h... yes SH> checking for unistd.h... yes SH> checking for int *... yes SH> checking size of int *... 4 SH> checking malloc.h usability... yes SH> checking malloc.h presence... yes SH> checking for malloc.h... yes SH> checking for struct mallinfo.arena... yes SH> checking for f90... f90 SH> checking whether we are using the GNU Fortran 77 compiler... no SH> checking whether f90 accepts -g... yes SH> setting F77... f90 SH> using F90... f90 SH> setting FFLAGS... -Os -64 -precexp=4 -nompi -noparallel -qfree=f90 -cpp SH> setting F90FLAGS... $(FFLAGS) SH> setting FFLAGS_NOOPT... -O0 SH> setting CFLAGS... -O3 SH> setting CPP... cpp SH> setting CPPFLAGS... -P -traditional SH> setting LD... mpif90 SH> setting LDFLAGS... SH> setting AR... ar SH> setting ARFLAGS... -X64 ruv SH> setting ARFLAGS_DYNAMIC...-X64 ruv SH> checking whether make sets $(MAKE)... yes SH> checking whether Fortran files must be preprocessed... yes SH> checking how to get verbose linking output from f90... -### SH> checking for Fortran libraries of f90... -L/opt/hitachi/matmpp/lib SH> -L/opt/hitachi/MSL2/lib -l/tmp/.200902251913551638458F90/conftest/conftest.L SH> -L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90 -lfiexpmpi SH> checking for dummy main to link with Fortran libraries... unknown SH> configure: error: linking to Fortran libraries from C fails SH> See `config.log' for more details. SH> _________________________________________________________ SH> SH> SH> As I trace the config.log, the following information tells me the souce of the SH> error may be the link of libs: SH> SH> _________________________________________________________ SH> configure:5050: mpCC_r -o conftest -g conftest.c -L/opt/hitachi/matmpp/lib SH> -L/opt/hitachi/MSL2/lib -l/tmp/.200902251913551638458F90/conftest/conftest.L SH> -L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90 -lfiexpmpi >&5 SH> ld: 0706-006 Cannot find or open library file: -l SH> /tmp/.200902251913551638458F90/conftest/conftest.L SH> ld:open(): No such file or directory SH> configure:5056: $? = 255 SH> configure: failed program was: SH> ... SH> _________________________________________________________ SH> SH> The path: SH> SH> -l/tmp/.200902251913551638458F90/conftest/conftest.L SH> SH> is suspicious. How can I solve such problem? SH> SH> Any reply is appreciated. SH> SH> Best SH> SH> Shujun SH> SH> SH> SH> SH> SH> SH> SH> SH> SH> _______________________________________________ SH> Pw_forum mailing list SH> Pw_forum at pwscf.org SH> http://www.democritos.it/mailman/listinfo/pw_forum SH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From stewart at cnf.cornell.edu Wed Feb 25 20:14:15 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 25 Feb 2009 14:14:15 -0500 Subject: [Pw_forum] segmentation faults in pwcond.x Message-ID: <20090225191415.5074.qmail@mail.spidergraphics.com> Hi everyone, I am trying to do some calculations with pwcond to determine the complex band structure for a fairly large unit cell structure (22 atoms). I am using QE version 4.0.4 compiled with the intel compilers (ifort & icc v10.1, mkl 10.0.4) in parallel with lam-mpi 7.1.4. I have no problem running the scf calculation. However, my pwcond calculation crashes after printing out the atomic positions and the following lines: k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 ngper, shell number = 951 256 ngper, n2d = 951 212 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source Stack trace terminated abnormally. forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source The run was done in parallel over 10 processors. I have set the stack as unlimited. Looking back through the pwscf archive, it appears that other people have run into segmenation faults at a similar point in their calculation. It was mentioned that pwcond performs a diagonilization over a non-symmetric matrix that occasionally crashes. Has this issue been resolved? Also, are there problems with larger systems for pwcond and total RAM required? All my parameters for the pwcond input file are similar to those used in example12. Any suggestions would be greatly appreciated! Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From lex at phys.ufl.edu Wed Feb 25 20:23:51 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Wed, 25 Feb 2009 14:23:51 -0500 Subject: [Pw_forum] segmentation faults in pwcond.x In-Reply-To: <20090225191415.5074.qmail@mail.spidergraphics.com> References: <20090225191415.5074.qmail@mail.spidergraphics.com> Message-ID: <49A59AC7.7020502@phys.ufl.edu> Hey everyone, To address one part of this question, I kept track of the memory used by pwcond while working on a large system. The error below (assuming it's the same one I have) is not RAM related, or at least was not in my case. I've tried different compilers/libraries, including the ones Dr. Stewart used. Lex Kemper Ph. D. student Department of Physics University of Florida Derek Stewart wrote: > Hi everyone, > > I am trying to do some calculations with pwcond to determine the complex > band structure for a fairly large unit cell structure (22 atoms). I am > using QE version 4.0.4 compiled with the intel compilers (ifort & icc v10.1, > mkl 10.0.4) in parallel with lam-mpi 7.1.4. I have no problem running the > scf calculation. > > However, my pwcond calculation crashes after printing out the atomic > positions and the following lines: > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > ngper, shell number = 951 256 > ngper, n2d = 951 212 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > Stack trace terminated abnormally. > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > > The run was done in parallel over 10 processors. I have set the stack as > unlimited. > > Looking back through the pwscf archive, it appears that other people have > run into segmenation faults at a similar point in their calculation. It was > mentioned that pwcond performs a diagonilization over a non-symmetric matrix > that occasionally crashes. Has this issue been resolved? Also, are there > problems with larger systems for pwcond and total RAM required? > > All my parameters for the pwcond input file are similar to those used in > example12. > > Any suggestions would be greatly appreciated! > > Thanks, > > Derek > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From zxf888 at 163.com Thu Feb 26 03:45:15 2009 From: zxf888 at 163.com (Xiang-Feng Zhou) Date: Thu, 26 Feb 2009 10:45:15 +0800 (CST) Subject: [Pw_forum] quesition about gam.lines (Paolo Giannozzi) In-Reply-To: References: Message-ID: <27037741.628021235616315812.JavaMail.coremail@bj163app80.163.com> >Xiang-Feng Zhou wrote: > >> I know the numbers in the first column of the gam.lines are indexes for >> q-vectors along the directions which we defined. I want to ask the >> meaning of the next three columns in gam.lines of example07 >gamma(i) (phonon linewidth), where i=1,..,3*number of atoms >Paolo Giannozzi, Democritos and University of Udine, Italy Dear Giannozzi: I will read more references, thanks a lot! =============================================== Xiang-Feng ZHOU Ph.D candidate Physics Dept. of Nanjing University National Lab. of Solid State Microstructures 22 Hankou Road, Gulou District Nanjing, Jiangsu Province 210093 China =============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/26b2f841/attachment.htm From niuli1978 at yahoo.com.cn Thu Feb 26 03:45:33 2009 From: niuli1978 at yahoo.com.cn (li niu) Date: Thu, 26 Feb 2009 10:45:33 +0800 (CST) Subject: [Pw_forum] the neutron static structure factor Message-ID: <963790.68121.qm@web15001.mail.cnb.yahoo.com> Dear all, I want to calculate the neutron static structure factor based on the results of vibrational frequencies and eigenmodes obtained by the line-response method. The paper (Phys. Rev. B 2000, 61:3951-3959, Vibrational amplitudes in vitreous silica) and Paolo Umari's thesis gave the calculated formula. I tried to code it, but the results are wrong. I was wondering if there is a code in QE to calculate it. Can anyone who successfully calculated the neutron static structure factor give me some help? ? Thanks again, ? Best, ? Li Niu Ph.D. Candidate, Center for Composite Materials, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, People's Republic of China ? ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/813461e1/attachment.htm From hqzhou at nju.edu.cn Thu Feb 26 05:43:01 2009 From: hqzhou at nju.edu.cn (hqzhou) Date: Thu, 26 Feb 2009 12:43:01 +0800 (CST) Subject: [Pw_forum] Use of pool Message-ID: Axel, Thank you very much for your response! > please note that benchmark numbers are useless without > offering a way to reproduce them. so please provide the > the input used for this test. > Sorry, I'm out of town right now, I'll send the input file to you directly as soon as I return home. > also, this looks almost like you are running multiple > copies of a serial binary. please check the top of the > pw.x (you _are_ pw.x, right?) output and check whether > there are the to be expected differences. > No, it's a parallel version compiled with intel MPI 3.1 and sequential MKL (libmkl_intel_lp64, libmkl_sequential and libmkl_core). The header part of my pw output indicates definitly that it's a parallel run. > finally, how does the job scale with just one pool? > The job scales quite well with just one pool, with efficiency from 92% on two cores to 74% on 8 cores, same tendency coincident with Intel's nehalem beta version. Huiqun Zhou @Nanjing University From ziba.zand at gmail.com Thu Feb 26 06:57:54 2009 From: ziba.zand at gmail.com (ziba zand) Date: Thu, 26 Feb 2009 09:27:54 +0330 Subject: [Pw_forum] how to plot pseudopotential and real and pseudo wavefunction? Message-ID: <55fa970e0902252157qef6e0c0kd04261326a28700f@mail.gmail.com> Dear every one, I am trying to plot pseudopotential and wavefunction by information which are existed in the xx.upf & xx.pwfn.data files. Unfortunately I can't do it. Would you please help me? Thanks in advance. Yours, Ziba -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/7803e32a/attachment.htm From smogunov at sissa.it Thu Feb 26 08:56:29 2009 From: smogunov at sissa.it (Alexander Smogunov) Date: Thu, 26 Feb 2009 08:56:29 +0100 Subject: [Pw_forum] segmentation faults in pwcond.x In-Reply-To: <20090225191415.5074.qmail@mail.spidergraphics.com> References: <20090225191415.5074.qmail@mail.spidergraphics.com> Message-ID: <200902260856.29514.smogunov@sissa.it> Dear Derek Try to use 8 or 16 CPUs, unfortunately the pwcond is supposed to run with 2^n (n integer) CPUs, we should put the check of that ... Regards, Alexander On Wednesday 25 February 2009 20:14, Derek Stewart wrote: > Hi everyone, > > I am trying to do some calculations with pwcond to determine the complex > band structure for a fairly large unit cell structure (22 atoms). I am > using QE version 4.0.4 compiled with the intel compilers (ifort & icc > v10.1, mkl 10.0.4) in parallel with lam-mpi 7.1.4. I have no problem > running the scf calculation. > > However, my pwcond calculation crashes after printing out the atomic > positions and the following lines: > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > ngper, shell number = 951 256 > ngper, n2d = 951 212 > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > Stack trace terminated abnormally. > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > > The run was done in parallel over 10 processors. I have set the stack as > unlimited. > > Looking back through the pwscf archive, it appears that other people have > run into segmenation faults at a similar point in their calculation. It > was mentioned that pwcond performs a diagonilization over a non-symmetric > matrix that occasionally crashes. Has this issue been resolved? Also, are > there problems with larger systems for pwcond and total RAM required? > > All my parameters for the pwcond input file are similar to those used in > example12. > > Any suggestions would be greatly appreciated! > > Thanks, > > Derek > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Thu Feb 26 09:31:22 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 26 Feb 2009 09:31:22 +0100 Subject: [Pw_forum] how to plot pseudopotential and real and pseudo wavefunction? In-Reply-To: <55fa970e0902252157qef6e0c0kd04261326a28700f@mail.gmail.com> References: <55fa970e0902252157qef6e0c0kd04261326a28700f@mail.gmail.com> Message-ID: <49A6535A.8070105@sissa.it> Dear Ziba ziba zand wrote: > Dear every one, > > I am trying to plot pseudopotential and wavefunction by information > which are existed in the xx.upf & xx.pwfn.data files. You can do a pseudopotential test calculation (iswitch.eq.2) with ld1.x (source code is in atomic/ directory). After the PP has been read by the program you can access all relevant data of the PP through internal variables of ld1 (see ld1inc module for the description). If you simply need wfcs, maybe they will be put in the .wfc .pwfc files, though not sure of that (please see files in atomic_doc/ for more precise information). HTH GS > Unfortunately I can't do it. > Would you please help me? > Thanks in advance. > > Yours, > Ziba Please specify your affiliation, thanks. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Thu Feb 26 10:34:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Feb 2009 10:34:30 +0100 Subject: [Pw_forum] band and dos input files in xcrysden In-Reply-To: References: Message-ID: <55EE491D-3505-4986-A914-7D6158F23F79@democritos.it> On Feb 21, 2009, at 17:05 , Eduardo Ariel Menendez Proupin wrote: > Let me remind how is the process to obtain the DOS. It has three > calculations > and 3 input files > > pw.x < si.scf.in > si.scf.out # self consistent > pw.x si.dos.out # non selfconsistent dense k-points > mesh and a few options > dos.x si.dos2.out # postprocessing Hi Eduardo, the issue you raise is a serious one and requires some though. Right now several standard calculations in q-e are clumsy because they require separate steps. While I think that it is a good idea to keep separate steps separate, I also think that at least the most common calculations might be streamlined. I am not convinced that the PWGui is the right tool for this, though, at least not in the present form (a tool to produce input data). The ideal solution would be the usage of a high-level scripting language like python to "glue" the various pieces together, but this is highly nontrivial (at least for me and for 99% of q-e users). A simpler option could be to collapse some calculations into the same executable: for instance - add a call to dos after a nscf calculation in pw.x, add a call to bands after a bands calculation in pw.x or - prepend a nscf calculation to dos.x, prepend a band calculation to bands.x Suggestions are welcome Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From baris.malcioglu at gmail.com Thu Feb 26 11:09:08 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Thu, 26 Feb 2009 11:09:08 +0100 Subject: [Pw_forum] band and dos input files in xcrysden In-Reply-To: <55EE491D-3505-4986-A914-7D6158F23F79@democritos.it> References: <55EE491D-3505-4986-A914-7D6158F23F79@democritos.it> Message-ID: Dear Paolo, I, being a script-happy person, like the "seperate steps" approach of pw.x very very much. Although not as high level as a python one, please find a script written in TCL which I use for preparing DOS and PDOS plots. Use this at your own risk! Being a script I modify it constantly for my needs, and I am not sure this is the "most corrected" version. Basically you use it like this : makedosgraph.tcl "pw.x input file" "pw.x output file for latest coordinates or -- to use coordinates in input file" -i "mpi related things + directory" run the script without parameters to see available options. some examples: Prepare the pdos showing atoms 1 3 5 with a degauss of 0.002 from a pwscf result makedosgraph.tcl in.grapheneO -- -i "/home/obm/Progs/pwscf/bin/" -plot_dg 0.002 -fermi_at_zero -atoms "1 3 5" Prepare a nscf file using the latest coordinates from a output file of a relaxation run makedosgraph.tcl in.grapheneO out.grapheneO -s 1 Prepare gnuplot files for an already run projwfc.x/dos.x makedosgraph.tcl in.grapheneO -- -s 4 -fermi_at_zero -atoms "1 3 5" (I also remember having something for bands and workfunctions somewhere) Best, Baris Malcioglu SISSA . makedosgraph.tcl #!/bin/sh # the next line restarts using tclsh \ exec tclsh8.4 "$0" "$@" ########################### # this script will # 1) read an input file for prefix and outdir # 2) read an output file for latest coordinates # 2) do a nscf calculation according to above data # 3) do a dos.x calculation according to above data # 4) do a projwfc.x calculation according to above data # 5) prepare gnuplot files # # Osman Baris Malcioglu 2007 v.1 alpha # ########################## proc ::main {argc argv} { global pw_input_file global pw_output_file global plot_dg global stag global spref global plotlist global nspin set plot_dg 0 set stag 0 set spref "" set plotlist "" get_commandline $argc $argv do_calcs } ########################## #A procedure to read commandline ########################## proc ::get_commandline {argc argv} { global pw_input_file global pw_output_file global plot_dg global stag global spref global plotlist global fatzero set fatzero 0 if { $argc < 2} { puts stderr "Usage: makedosgraph \[parameters\]" puts stderr "Parameters:" puts stderr "-s : set calculation stage " puts stderr " 1 : prepare nscf files and exit" puts stderr " 2 : use present files and run nscf, and quit" puts stderr " 3 : prepare for and run dos.x and projwfc.x" puts stderr " 4 : prepare gnuplot baches for pdos output only" puts stderr "-plot_dg : set the plotting degauss in dos.x" puts stderr "-i <\"prefix to pwscf\"> : the prefix to be appended to runs" puts stderr "-atoms <\"space seperated list of atoms\">: will draw these atoms only" puts stderr "-fermi_at_zero move the graphs such that Ef is at 0" exit 1 } if { $argc > 0 } { set state first foreach arg $argv { switch -- $state { first { set state second #check if the infile exists set pw_input_file $arg if { [file exists $pw_input_file] } { puts "using input file $pw_input_file" } else { puts stderr "Input file $pw_input_file does not exits" exit 1 } } second { set state flag #check if the outfile exists set pw_output_file $arg if { [file exists $pw_output_file] || $pw_output_file == "--"} { puts "using output file $pw_output_file" } else { puts stderr "Output file $pw_output_file does not exist" exit 1 } } flag { switch -glob -- $arg { -plot_dg { set state p_dg } -s { set state sstag } -i { set state sspref } -atoms {set state splotlist} -fermi_at_zero {set fatzero 1} default { puts stderr "unknown flag $arg" exit 2 } } } p_dg { if { [ regexp -- {-?[0-9]+\.?[0-9]*} $arg plot_dg ] } { puts "using plot degauss = $plot_dg" set state flag } else { puts stderr " I didn't understand $arg after -plot_dg " exit 2 } } sstag { if { [ regexp -- {[1-4]} $arg stag ] } { puts "Calculation stage set to $stag" set state flag } else { puts stderr " I didn't understand $arg after -s " exit 2 } } sspref { set spref $arg puts "run prefix is $spref" set state flag } splotlist { set plotlist $arg puts "Plotlist is $plotlist" set state flag } } } } if {![file exists [file join $spref "pw.x"]]} { puts "Warning: I can not find [file join $spref pw.x ]" } if {![file exists [file join $spref "dos.x"]]} { puts "Warning: I can not find [file join $spref dos.x ]" } if {![file exists [file join $spref "projwfc.x"]]} { puts "Warning: I can not find [file join $spref projwfc.x ]" } } ####################### #This procedure reads the input file, prepares input files for nscf dos.x projwfc.x #and runs them ###################### proc ::do_calcs {} { global pw_input_file global pw_output_file global pw_outdir global n_at global pw_prefix global lc_pos global lc_posin global stag global spref global nspin global e_fermi global plotlist global plot_dg global fatzero if [catch {open $pw_input_file r} fileId] { puts stderr "Cannot open $pw_input_file: $fileId" exit 1 } set tmpfile [read $fileId] close $fileId if { ! [regexp -linestop -- {outdir\s*=\s*'?"?(.*?)[!',]*} $tmpfile match pw_outdir] } { puts stderr "outdir not found !" exit 1 } else { puts "The outdir is : $pw_outdir" } if { ! [regexp -linestop -- {prefix\s*=\s*'?"?(.*?)[!',]*} $tmpfile match pw_prefix] } { puts stderr "prefix not found !" exit 1 } else { puts "The prefix is : $pw_prefix" } # read number of atoms if {![regexp -linestop -- {nat\s*=\s*([0-9]+)} $tmpfile match n_at]} { puts "Error reading n_at, exiting" exit 2 } puts "nat=$n_at" # read nspin if {![regexp -linestop -- {nspin\s*=\s*([1-2])} $tmpfile match nspin]} { puts "no nspin line found, setting nspin to 1" set nspin 1 } puts "nspin=$nspin" # do this only if stage is 0 or 1 if {$stag<2} { regsub -nocase -linestop -- {calculation.*} $tmpfile {calculation = 'nscf'} tmpfile2 regsub -nocase -linestop -- {restart_mode.*} $tmpfile2 {} tmpfile2 if { $pw_output_file != "--" } { if [catch {open $pw_output_file r} fileId] { puts stderr "Cannot open $pw_output_file: $fileId" exit 1 } set tmpoutfile [read $fileId] close $fileId if {[regexp -all -indices -nocase -- {ATOMIC_POSITIONS\s*\([a-z]+\)\s*} $tmpoutfile lc_pos] == 0 } { puts stderr "Error locating latest coordinates in $pw_output_file " exit 1 } set lc_pos [lindex [split $lc_pos] 1] puts "Latest coordinates at index:$lc_pos in output file" if {[regexp -all -indices -nocase -- {ATOMIC_POSITIONS\s*\{?\(?[a-z]+\)?\}?\s*} $tmpfile2 lc_posin] == 0 } { puts stderr "Error locating latest coordinates in $pw_input_file " exit 1 } set lc_posin [lindex [split $lc_posin] 1] puts "Coordinates at index:$lc_posin in input file" for {set i 0} {$i<$n_at} {incr i 1} { set search "regexp -start $lc_pos -linestop -nocase -- {\[a-z\]+\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*} \$tmpoutfile match" #puts "$search" eval $search set search "regexp -start $lc_posin -linestop -nocase -- {\[a-z\]+\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*} \$tmpfile2 match2" #puts "$search" eval $search puts "replacing $match2 with $match" puts "[regsub -linestop "$match2" $tmpfile2 "$match" tmpfile2] replacements was made" set search "regexp -start $lc_pos -linestop -nocase -indices -- {\[a-z\]+\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s*} \$tmpoutfile match" #puts $search eval $search set lc_pos [lindex [split $match] 1] set search "regexp -start $lc_posin -linestop -nocase -indices -- {\[a-z\]+\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s+-?\[0-9\]+\\.?\[0-9\]*\\s*} \$tmpfile2 match2" #puts $search eval $search set lc_posin [lindex [split $match2] 1] } unset tmpoutfile } else { puts "using input coordinates" } if {![regexp -nocase -linestop -- {diagonalization} $tmpfile2]} { puts "The diagonalization method is now set to cg" regsub -- {\&electrons} $tmpfile2 "\\&electrons\n diagonalization='cg'" tmpfile2 } puts "Preparing nscf input in.$pw_prefix.nscf" if [catch {open in.$pw_prefix.nscf w} fileId] { puts stderr "Cannot open in.$pw_prefix.nscf: $fileId" exit 1 } puts $fileId $tmpfile2 close $fileId } # do this only if stage is 2 or 0 if {$stag == 2 || $stag == 0} { puts "Running nscf calculation" exec [file join $spref pw.x ] < in.$pw_prefix.nscf > out.$pw_prefix.nscf } #do this if stage is anyhing but 4 if {$stag < 4 } { puts "preparing DOS input : in.$pw_prefix.dosx" if [catch {open in.$pw_prefix.dosx w} fileId] { puts stderr "Cannot open in.$pw_prefix.dosx: $fileId" exit 1 } puts $fileId "&inputpp" puts $fileId " outdir='$pw_outdir'" puts $fileId " prefix='$pw_prefix'" if {$plot_dg > 0} { puts $fileId " degauss = $plot_dg" } puts $fileId "/" close $fileId puts "Running Dos.x" exec [file join $spref dos.x ] out.$pw_prefix.dosx puts "Preparing gnuplot batch for DOS: $pw_prefix.dosx.gnu" if [catch {open $pw_prefix.dosx.gnu w} gnufile] { puts stderr "Cannot open in.$pw_prefix.dosx: $gnufile" exit 1 } puts $gnufile "set term jpeg size 1024,768" puts $gnufile "set output '$pw_prefix-dos.jpg'" puts $gnufile "set key below" puts $gnufile "set title '$pw_prefix'" puts $gnufile "set xlabel 'Energy in (eV)'" puts $gnufile "set ylabel 'DOS'" if {$nspin == 2} { puts $gnufile "plot '$pw_prefix.dos' using 1:2 w l title 'Spin up','$pw_prefix.dos' using 1:3 w l title 'Spin down'" } else { puts $gnufile "unset key" puts $gnufile "plot '$pw_prefix.dos' using 1:2 w l " } close $gnufile puts "Running PDOS" exec [file join $spref projwfc.x ] out.$pw_prefix.pdosx } # do anyhow, preparation for further stages if {$stag < 5 } { puts "preparing gnuplot file for pdos : $pw_prefix-pdos.gnu" if [catch {open out.$pw_prefix.nscf r} fileId] { puts "Warning : Cannot open out.$pw_prefix.nscf: $fileId , setting Fermi Energy to zero" set e_fermi 0 } else { set tmpoutfile [read $fileId] close $fileId if {[regexp -linestop -- {the Fermi energy is\s+(-?[0-9]+\.?[0-9]*)} $tmpoutfile match e_fermi]} { puts "NSCF calculation yields an Efermi of $e_fermi" } else { puts "Error reading E_fermi, set to 0" set e_fermi 0 } } if [catch {open $pw_prefix-pdos.gnu w} gnufile] { puts stderr "Cannot open in.$pw_prefix.dosx: $gnufile" exit 1 } puts $gnufile "set term jpeg size 1024,768" puts $gnufile "set output '$pw_prefix-pdos.jpg'" puts $gnufile "set key below" puts $gnufile "set title '$pw_prefix'" puts $gnufile "set xlabel 'Energy in (eV)'" puts $gnufile "unset ylabel" puts $gnufile "unset ytics" puts $gnufile "set yrange \[0:[expr {[llength $plotlist]*1.5 + 2}]\]" if {[llength $plotlist]==0} { if {$nspin == 2} { puts $gnufile "plot '$pw_prefix.pdos_tot' using 1:4 w l title 'Spin up','$pw_prefix.pdos_tot' using 1:5 w l title 'Spin down'" } else { puts $gnufile "unset key" puts $gnufile "plot '$pw_prefix.pdos_tot' using 1:3 w l " } } else { puts $gnufile "unset key" if {$nspin == 2} { if { $fatzero == 0 } { puts $gnufile "set label \"Ef=$e_fermi\" at [expr {$e_fermi+0.2}],0.6 front rotate" } else { puts $gnufile "set label \"Ef\" at 0.2,0.6 front rotate" } puts $gnufile "set label \"S\" at graph 0,1.02 point lt 1" puts $gnufile "set label \"Pz\" at graph 0.1,1.02 point lt 2" puts $gnufile "set label \"Px\" at graph 0.2,1.02 point lt 3" puts $gnufile "set label \"Py\" at graph 0.3,1.02 point lt 4" set plot_incr 0 foreach atom_no $plotlist { puts $gnufile "set label \"Atom $atom_no\" at graph -0.01,first [expr {$plot_incr+0.6}] rotate" set plot_incr [ expr {$plot_incr + 1.5} ] } puts $gnufile "set label \"Tot Pdos\" at graph -0.01, first [expr {[llength $plotlist]*1.5 + 0.7}] rotate" puts -nonewline $gnufile "plot " set plot_incr 0 foreach atom_no $plotlist { foreach file [glob -nocomplain $pw_prefix.pdos_atm#$atom_no* ] { if {[regexp "$pw_prefix.pdos_atm#$atom_no\\(.+?\\)_wfc#1\\(s\\)" $file match]} { if { $fatzero == 0 } { puts -nonewline $gnufile "'$match' using 1:($plot_incr+\$4) w l lt 1," } else { puts -nonewline $gnufile "'$match' using (\$1-$e_fermi):($plot_incr+\$4) w l lt 1," } } if {[regexp "$pw_prefix.pdos_atm#$atom_no\\(.+?\\)_wfc#2\\(p\\)" $file match]} { if { $fatzero == 0 } { puts -nonewline $gnufile "'$match' u 1:($plot_incr+\$4) w l lt 2,'$match' u 1:($plot_incr+\$6) w l lt 3,'$match' u 1:($plot_incr+\$8) w l lt 4," } else { puts -nonewline $gnufile "'$match' u (\$1-$e_fermi):($plot_incr+\$4) w l lt 2,'$match' u (\$1-$e_fermi):($plot_incr+\$6) w l lt 3,'$match' u (\$1-$e_fermi):($plot_incr+\$8) w l lt 4," } } } set plot_incr [expr {$plot_incr + 1.5}] } if { $fatzero == 0 } { puts $gnufile "'$pw_prefix.pdos_tot' using 1:(\$2/4+$plot_incr) w l lt 1,'-' w l lt 8" puts $gnufile "$e_fermi 0" puts $gnufile "$e_fermi [expr {$plot_incr+10}]" puts $gnufile "e" } else { puts $gnufile "'$pw_prefix.pdos_tot' using (\$1-$e_fermi):(\$2/4+$plot_incr) w l lt 1,'-' w l lt 8" puts $gnufile "0 0" puts $gnufile "0 [expr {$plot_incr+10}]" puts $gnufile "e" } } else { if { $fatzero == 0 } { puts $gnufile "set label \"Ef=$e_fermi\" at [expr {$e_fermi+0.2}],0.6 front rotate" } else { puts $gnufile "set label \"Ef\" at 0.2,0.6 front rotate" } puts $gnufile "set label \"S\" at graph 0,1.02 point lt 1" puts $gnufile "set label \"Pz\" at graph 0.1,1.02 point lt 2" puts $gnufile "set label \"Px\" at graph 0.2,1.02 point lt 3" puts $gnufile "set label \"Py\" at graph 0.3,1.02 point lt 4" set plot_incr 0 foreach atom_no $plotlist { puts $gnufile "set label \"Atom $atom_no\" at graph -0.01,first [expr {$plot_incr+0.6}] rotate" set plot_incr [ expr {$plot_incr + 1.5} ] } puts $gnufile "set label \"Tot Pdos\" at graph -0.01, first [expr {[llength $plotlist]*1.5 + 0.7}] rotate" puts -nonewline $gnufile "plot " set plot_incr 0 foreach atom_no $plotlist { foreach file [glob -nocomplain $pw_prefix.pdos_atm#$atom_no* ] { if {[regexp "$pw_prefix.pdos_atm#$atom_no\\(.+?\\)_wfc#1\\(s\\)" $file match]} { if { $fatzero == 0 } { puts -nonewline $gnufile "'$match' using 1:($plot_incr+\$3) w l lt 1," } else { puts -nonewline $gnufile "'$match' using (\$1-$e_fermi):($plot_incr+\$3) w l lt 1," } } if {[regexp "$pw_prefix.pdos_atm#$atom_no\\(.+?\\)_wfc#2\\(p\\)" $file match]} { if { $fatzero == 0 } { puts -nonewline $gnufile "'$match' u 1:($plot_incr+\$3) w l lt 2,'$match' u 1:($plot_incr+\$4) w l lt 3,'$match' u 1:($plot_incr+\$5) w l lt 4," } else { puts -nonewline $gnufile "'$match' u (\$1-$e_fermi):($plot_incr+\$3) w l lt 2,'$match' u (\$1-$e_fermi):($plot_incr+\$4) w l lt 3,'$match' u (\$1-$e_fermi):($plot_incr+\$5) w l lt 4," } } } set plot_incr [expr {$plot_incr + 1.5}] } if { $fatzero == 0 } { puts $gnufile "'$pw_prefix.pdos_tot' using 1:(\$2/4+$plot_incr) w l lt 1,'-' w l lt 8" puts $gnufile "$e_fermi 0" puts $gnufile "$e_fermi [expr {$plot_incr+10}]" puts $gnufile "e" } else { puts $gnufile "'$pw_prefix.pdos_tot' using (\$1-$e_fermi):(\$2/4+$plot_incr) w l lt 1,'-' w l lt 8" puts $gnufile "0 0" puts $gnufile "0 [expr {$plot_incr+10}]" puts $gnufile "e" } } } close $gnufile } } main $argc $argv On Thu, Feb 26, 2009 at 10:34 AM, Paolo Giannozzi wrote: > > On Feb 21, 2009, at 17:05 , Eduardo Ariel Menendez Proupin wrote: > >> Let me remind how is the process to obtain the DOS. It has three >> calculations >> and 3 input files >> >> pw.x < si.scf.in > si.scf.out ? # self consistent >> pw.x si.dos.out ?# non selfconsistent dense k-points >> mesh and a few options >> dos.x ?si.dos2.out ?# postprocessing > > Hi Eduardo, ?the issue you raise is a serious one and requires some > though. > Right now several standard calculations in q-e are clumsy because they > require separate steps. While I think that it is a good idea to keep > separate > steps separate, I also think that at least the most common > calculations might > be streamlined. I am not convinced that the PWGui is the right tool > for this, > though, at least not in the present form (a tool to produce input data). > The ideal ?solution would be the usage of a high-level scripting > language like > python to "glue" the various pieces together, but this is highly > nontrivial > (at least for me and for 99% of q-e users). > A simpler option could be to collapse some calculations into the same > executable: > for instance > - add a call to dos after a nscf calculation in pw.x, > ? add a call to bands after a bands calculation in pw.x > or > - prepend a nscf calculation to dos.x, > ? prepend a band calculation to bands.x > Suggestions are welcome > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zhuli at email.jlu.edu.cn Thu Feb 26 13:16:59 2009 From: zhuli at email.jlu.edu.cn (Li Zhu) Date: Thu, 26 Feb 2009 20:16:59 +0800 Subject: [Pw_forum] How can I get Hamiltonian matrix ? Message-ID: <49A6883B.8080904@email.jlu.edu.cn> Dear users and developers, I want to calculate the electron-phonon interaction by Wannier-Fourier interpolation (PRB 76,165108). And I should get Hamiltonian matrix form pwscf (Eq.[26],PRB 76,165108). But I haven't found the variable that store the Hamiltonian matrix. Who can help me to get the Hamiltonian matrix in pwscf ? Thanks. Sincerely, Li Zhu From giannozz at democritos.it Thu Feb 26 14:00:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Feb 2009 14:00:27 +0100 Subject: [Pw_forum] How can I get Hamiltonian matrix ? In-Reply-To: <49A6883B.8080904@email.jlu.edu.cn> References: <49A6883B.8080904@email.jlu.edu.cn> Message-ID: <747F24B3-71FC-4C65-8A3D-34ECC4B6953B@democritos.it> On Feb 26, 2009, at 13:16 , Li Zhu wrote: > Who can help me to get the Hamiltonian matrix in pwscf ? there is no such thing as "the Hamiltonian matrix" in pwscf. The operator H is defined via its action on a vector \psi: see routine "h_psi" Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Thu Feb 26 14:05:22 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 26 Feb 2009 14:05:22 +0100 Subject: [Pw_forum] How can I get Hamiltonian matrix ? In-Reply-To: <49A6883B.8080904@email.jlu.edu.cn> References: <49A6883B.8080904@email.jlu.edu.cn> Message-ID: On Thu, 26 Feb 2009 13:16:59 +0100, Li Zhu wrote: > Who can help me to get the Hamiltonian matrix in pwscf ? dear Li Zhu, it may not be as simple as you expect; as Paolo says in pw.x there is no hamiltonian matrix at all... yet since 4.0.0 version, QE distribution includes the Wannier90 code, in the W90 subdirectory. Inside it you will find the routines to get the hamiltonian on a Wannier-basis representation. Furthermore W90 can be used as a library, allowing you to implement Wannier-function-based with relative ease. I have no idea (anymore) of how it works in detail, but you can find a user manual in W90/doc that also has a developer-oriented section. good luck! -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From baroni at sissa.it Thu Feb 26 16:13:40 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 26 Feb 2009 16:13:40 +0100 Subject: [Pw_forum] How can I get Hamiltonian matrix ? In-Reply-To: <747F24B3-71FC-4C65-8A3D-34ECC4B6953B@democritos.it> References: <49A6883B.8080904@email.jlu.edu.cn> <747F24B3-71FC-4C65-8A3D-34ECC4B6953B@democritos.it> Message-ID: On Feb 26, 2009, at 2:00 PM, Paolo Giannozzi wrote: > > On Feb 26, 2009, at 13:16 , Li Zhu wrote: > >> Who can help me to get the Hamiltonian matrix in pwscf ? > > there is no such thing as "the Hamiltonian matrix" in pwscf. > The operator H is defined via its action on a vector \psi: > see routine "h_psi" this being said, you can still calculate matrix elements if you really want to. h_psi calculates (guess what?) H*psi, say psi' if you want to calculate the matrix element: , just calculate Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/eb3198a9/attachment.htm From lanhaiping at gmail.com Thu Feb 26 19:17:11 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 27 Feb 2009 02:17:11 +0800 Subject: [Pw_forum] ELF .vs. Charge difference Message-ID: Dear All, I came to a problem to analyze bond type for an interface. I wonder about the difference between electron localization function and charge difference with respect to understanding bonding interaction. In fact , I just read a work of PhysRevLett.89.106403, it seems ELF and charge difference give the same feature with respect to bonds. I appreciate any hint and help. Thanks Regards, Hai-Ping LAN -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090227/4120e3f9/attachment.htm From trinh.vo at jpl.nasa.gov Thu Feb 26 21:23:12 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 26 Feb 2009 12:23:12 -0800 Subject: [Pw_forum] Insufficient Virtual Memory Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> Dear PWSCF users, I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: "forrtl: severe (41): insufficient virtual memory". I do not know how to deal with this. Any help or suggestion is appreciated. For other cases, the runs were fine. Below are the specifications of my cluster: Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) For compilation, I used the following: QE ver. 4.0.3 ifort 10.1015, MKL 10.0.3.020, impi 3.1 internal fftw I also attach here the output file. Thank you, Trinh Vo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/0fc122f9/attachment.htm From sandabotis at gmail.com Thu Feb 26 21:47:12 2009 From: sandabotis at gmail.com (Sanda Botis) Date: Thu, 26 Feb 2009 14:47:12 -0600 Subject: [Pw_forum] paramagnetic defects in solids Message-ID: <98e923e50902261247k6d565933v4d80672eb4dc423e@mail.gmail.com> Hi everyone, I would like to know if anyone has experience working on paramagnetic defects in solids and using QE. I know that the 4.0 version is supposed to be able to calculate g-tensors and hyperfine constants but I am not sure how well it works for solids and how computationally demanding this type of calculations are. Maybe you can give me a few suggestions based on your experience with QE. Thank you, Sanda -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090226/d882f7ee/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Feb 26 22:03:54 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 26 Feb 2009 16:03:54 -0500 (EST) Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear PWSCF users, TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> I do not know how to deal with this. Any help or suggestion is TV> appreciated. For other cases, the runs were fine. have you _read_ the README file in that directory??? axel. TV> TV> Below are the specifications of my cluster: TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> For compilation, I used the following: TV> QE ver. 4.0.3 TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> internal fftw TV> TV> I also attach here the output file. TV> TV> TV> Thank you, TV> TV> Trinh Vo TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From paulatto at sissa.it Thu Feb 26 23:04:10 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 26 Feb 2009 23:04:10 +0100 (CET) Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.J PL> References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: <41960.78.12.161.122.1235685850.squirrel@webmail.sissa.it> On Gio, Febbraio 26, 2009 21:23, Vo, Trinh wrote: > 512 H2O with 4cores/node, Dear Trinh Vo, to be honest, I don't think you have much chance to run a system with ~3500 electrons on 78 processors with only 1GB of RAM/processor. You may try using half the processors and 2GB each (leaving half of them idle), but this will probably take a painfully long time. My suggestion is to have a look at two recent threads from the mailing list archives: "PW taskgroups and a large run on a BG/P" and "Trying to find reasonable parallelization parameters" where the problem of computing large systems have been discussed extensively. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From trinh.vo at jpl.nasa.gov Thu Feb 26 23:50:14 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 26 Feb 2009 14:50:14 -0800 Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153696859F5@ALTPHYEMBEVSP10.RES.AD.JPL> Dear Axel, Yes, I read the README file. I first just run "run_example" to get the input files (I wanted to see what they are). I then run each job individually. Since I saw in one of previous emails, you mentioned the following link, which is related to the benchmark of the 8cores: http://cp2k.googlegroups.com/web/cp2k-water-bench-cmm.png?gda=cZtL20oAAABKcjB2R2-kyOTBNGr0GXCNfKm1opB3ppoZQi3FVKdigwDOq5Mi_ip_cCKVysjiE_BA1utot6QxKJxvVe1Mw7MU_e3Wg0GnqfdKOwDqUih1tA In the plot, I saw the result for 512 H2O and 4core/nodes. Thus, I tried to repeat all the calculations to compare, but I could not run that case. Thank you, Trinh -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Thursday, February 26, 2009 1:04 PM To: PWSCF Forum Subject: Re: [Pw_forum] Insufficient Virtual Memory On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear PWSCF users, TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> I do not know how to deal with this. Any help or suggestion is TV> appreciated. For other cases, the runs were fine. have you _read_ the README file in that directory??? axel. TV> TV> Below are the specifications of my cluster: TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> For compilation, I used the following: TV> QE ver. 4.0.3 TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> internal fftw TV> TV> I also attach here the output file. TV> TV> TV> Thank you, TV> TV> Trinh Vo TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From trinh.vo at jpl.nasa.gov Thu Feb 26 23:52:19 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 26 Feb 2009 14:52:19 -0800 Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: <41960.78.12.161.122.1235685850.squirrel@webmail.sissa.it> References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> <41960.78.12.161.122.1235685850.squirrel@webmail.sissa.it> Message-ID: <63E24D720DCE7246ABAA722B52D23CDF0153696859F8@ALTPHYEMBEVSP10.RES.AD.JPL> Dear Lorenzo, Thanks for your comments. I will go and have a look at it. If I have any further questions, I'll post it to PWSCF forum again. Trinh -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Lorenzo Paulatto Sent: Thursday, February 26, 2009 2:04 PM To: PWSCF Forum Subject: Re: [Pw_forum] Insufficient Virtual Memory On Gio, Febbraio 26, 2009 21:23, Vo, Trinh wrote: > 512 H2O with 4cores/node, Dear Trinh Vo, to be honest, I don't think you have much chance to run a system with ~3500 electrons on 78 processors with only 1GB of RAM/processor. You may try using half the processors and 2GB each (leaving half of them idle), but this will probably take a painfully long time. My suggestion is to have a look at two recent threads from the mailing list archives: "PW taskgroups and a large run on a BG/P" and "Trying to find reasonable parallelization parameters" where the problem of computing large systems have been discussed extensively. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Fri Feb 27 00:22:59 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 26 Feb 2009 18:22:59 -0500 (EST) Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF0153696859F5@ALTPHYEMBEVSP10.RES.AD.JPL> References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> <63E24D720DCE7246ABAA722B52D23CDF0153696859F5@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear Axel, TV> TV> Yes, I read the README file. I first just run "run_example" to get TV> the input files (I wanted to see what they are). I then run each TV> job individually. Since I saw in one of previous emails, you TV> mentioned the following link, which is related to the benchmark of TV> the 8cores: TV> http://cp2k.googlegroups.com/web/cp2k-water-bench-cmm.png?gda=cZtL20oAAABKcjB2R2-kyOTBNGr0GXCNfKm1opB3ppoZQi3FVKdigwDOq5Mi_ip_cCKVysjiE_BA1utot6QxKJxvVe1Mw7MU_e3Wg0GnqfdKOwDqUih1tA TV> In the plot, I saw the result for 512 H2O and 4core/nodes. Thus, I TV> tried to repeat all the calculations to compare, but I could not run TV> that case. this graph was done with a _very_ different code, cp2k, that uses a method (quickstep) different from the CP in cp.x and has therefore different memory requirements and system size scaling. the README of example21 explicitly warns you about running out of memory. give the current difference in speed between hard drives and main memory, every calculation where you run into using swap is not worth the effort (unlike 10 years ago). just for reference: because of the difference in methods cp.x should scale better with the number of processors, whereas cp2k should scale better with the problem set size than cp.x with the same number of processors. that being said, cp2k demonstrates the problem of overloading memory and communication channels very nicely and thus the graphs are a nice point of reference to showcase how bad it can get and that the not so obvious choice of not using all cpus actually gives you the better performance. cheers, axel. TV> TV> Thank you, TV> TV> Trinh TV> TV> TV> TV> -----Original Message----- TV> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer TV> Sent: Thursday, February 26, 2009 1:04 PM TV> To: PWSCF Forum TV> Subject: Re: [Pw_forum] Insufficient Virtual Memory TV> TV> On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> TV> TV> Dear PWSCF users, TV> TV> TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> TV> TV> TV> I do not know how to deal with this. Any help or suggestion is TV> TV> appreciated. For other cases, the runs were fine. TV> TV> have you _read_ the README file in that directory??? TV> TV> axel. TV> TV> TV> TV> TV> TV> Below are the specifications of my cluster: TV> TV> TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> TV> TV> For compilation, I used the following: TV> TV> QE ver. 4.0.3 TV> TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> TV> internal fftw TV> TV> TV> TV> I also attach here the output file. TV> TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> Trinh Vo TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From trinh.vo at jpl.nasa.gov Fri Feb 27 00:48:40 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Thu, 26 Feb 2009 15:48:40 -0800 Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> <63E24D720DCE7246ABAA722B52D23CDF0153696859F5@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: <63E24D720DCE7246ABAA722B52D23CDF015369685A13@ALTPHYEMBEVSP10.RES.AD.JPL> Dear Axel, I am sorry. I may be out of date. Is the cp2k code included in QE package, or in some other codes? I saw the word "cp2k" in the title of the plot, but I thought that it might be the same cp code of QE. Actually, the benchmark plot that I obtained does not look as good as the posted plot. I will send it to you in the next email. I need to make a better plot before I send it. Thanks, Trinh -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer Sent: Thursday, February 26, 2009 3:23 PM To: PWSCF Forum Subject: Re: [Pw_forum] Insufficient Virtual Memory On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear Axel, TV> TV> Yes, I read the README file. I first just run "run_example" to get TV> the input files (I wanted to see what they are). I then run each TV> job individually. Since I saw in one of previous emails, you TV> mentioned the following link, which is related to the benchmark of TV> the 8cores: TV> http://cp2k.googlegroups.com/web/cp2k-water-bench-cmm.png?gda=cZtL20oAAABKcjB2R2-kyOTBNGr0GXCNfKm1opB3ppoZQi3FVKdigwDOq5Mi_ip_cCKVysjiE_BA1utot6QxKJxvVe1Mw7MU_e3Wg0GnqfdKOwDqUih1tA TV> In the plot, I saw the result for 512 H2O and 4core/nodes. Thus, I TV> tried to repeat all the calculations to compare, but I could not run TV> that case. this graph was done with a _very_ different code, cp2k, that uses a method (quickstep) different from the CP in cp.x and has therefore different memory requirements and system size scaling. the README of example21 explicitly warns you about running out of memory. give the current difference in speed between hard drives and main memory, every calculation where you run into using swap is not worth the effort (unlike 10 years ago). just for reference: because of the difference in methods cp.x should scale better with the number of processors, whereas cp2k should scale better with the problem set size than cp.x with the same number of processors. that being said, cp2k demonstrates the problem of overloading memory and communication channels very nicely and thus the graphs are a nice point of reference to showcase how bad it can get and that the not so obvious choice of not using all cpus actually gives you the better performance. cheers, axel. TV> TV> Thank you, TV> TV> Trinh TV> TV> TV> TV> -----Original Message----- TV> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer TV> Sent: Thursday, February 26, 2009 1:04 PM TV> To: PWSCF Forum TV> Subject: Re: [Pw_forum] Insufficient Virtual Memory TV> TV> On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> TV> TV> Dear PWSCF users, TV> TV> TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> TV> TV> TV> I do not know how to deal with this. Any help or suggestion is TV> TV> appreciated. For other cases, the runs were fine. TV> TV> have you _read_ the README file in that directory??? TV> TV> axel. TV> TV> TV> TV> TV> TV> Below are the specifications of my cluster: TV> TV> TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> TV> TV> For compilation, I used the following: TV> TV> QE ver. 4.0.3 TV> TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> TV> internal fftw TV> TV> TV> TV> I also attach here the output file. TV> TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> Trinh Vo TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Fri Feb 27 01:34:51 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 26 Feb 2009 19:34:51 -0500 (EST) Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: <63E24D720DCE7246ABAA722B52D23CDF015369685A13@ALTPHYEMBEVSP10.RES.AD.JPL> References: <63E24D720DCE7246ABAA722B52D23CDF0153696859A1@ALTPHYEMBEVSP10.RES.AD.JPL> <63E24D720DCE7246ABAA722B52D23CDF0153696859F5@ALTPHYEMBEVSP10.RES.AD.JPL> <63E24D720DCE7246ABAA722B52D23CDF015369685A13@ALTPHYEMBEVSP10.RES.AD.JPL> Message-ID: On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear Axel, TV> TV> I am sorry. I may be out of date. Is the cp2k code included in QE TV> package, or in some other codes? I saw the word "cp2k" in the title perhaps i was not clear enough. cp2k is a completely different project and has not much else to do with Q-E outside of the fact that both have a DFT module and that i and a few others are using both codes. TV> of the plot, but I thought that it might be the same cp code of QE. no. i already wrote that. in fact, "there is no CP in CP2k". i suggested this phase as a subtitle to the project, but people found it to negative. ;) TV> Actually, the benchmark plot that I obtained does not look as good TV> as the posted plot. I will send it to you in the next email. I need TV> to make a better plot before I send it. benchmark in terms of scaling or in terms of problem set size? there should be a post in the cp2k google group referring to the benchmark graph and describing the exact system setup. cheers, axel. TV> TV> Thanks, TV> TV> Trinh TV> TV> TV> TV> tried to repeat all the calculations to compare, but I could not run TV> TV> that case. TV> TV> this graph was done with a _very_ different code, cp2k, that TV> uses a method (quickstep) different from the CP in cp.x and has TV> therefore different memory requirements and system size scaling. TV> the README of example21 explicitly warns you about running out TV> of memory. give the current difference in speed between hard TV> drives and main memory, every calculation where you run into TV> using swap is not worth the effort (unlike 10 years ago). TV> TV> just for reference: because of the difference in methods cp.x TV> should scale better with the number of processors, whereas TV> cp2k should scale better with the problem set size than cp.x TV> with the same number of processors. TV> TV> that being said, cp2k demonstrates the problem of overloading TV> memory and communication channels very nicely and thus the TV> graphs are a nice point of reference to showcase how bad it TV> can get and that the not so obvious choice of not using all TV> cpus actually gives you the better performance. TV> TV> cheers, TV> axel. TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> Trinh TV> TV> TV> TV> TV> TV> TV> TV> -----Original Message----- TV> TV> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer TV> TV> Sent: Thursday, February 26, 2009 1:04 PM TV> TV> To: PWSCF Forum TV> TV> Subject: Re: [Pw_forum] Insufficient Virtual Memory TV> TV> TV> TV> On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> TV> TV> TV> TV> Dear PWSCF users, TV> TV> TV> TV> TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> TV> TV> TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> TV> TV> TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> TV> TV> TV> TV> TV> TV> I do not know how to deal with this. Any help or suggestion is TV> TV> TV> appreciated. For other cases, the runs were fine. TV> TV> TV> TV> have you _read_ the README file in that directory??? TV> TV> TV> TV> axel. TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> Below are the specifications of my cluster: TV> TV> TV> TV> TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> TV> TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> TV> TV> TV> TV> For compilation, I used the following: TV> TV> TV> QE ver. 4.0.3 TV> TV> TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> TV> TV> internal fftw TV> TV> TV> TV> TV> TV> I also attach here the output file. TV> TV> TV> TV> TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> TV> TV> Trinh Vo TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yukihiro_okuno at fujifilm.co.jp Fri Feb 27 09:22:39 2009 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Fri, 27 Feb 2009 17:22:39 +0900 Subject: [Pw_forum] range of plotting area for charge density --- definition of e1, e2 Message-ID: Dear PWSCF Users. I want to plot 2D charge density by pp.x and plotrho.x. In the input file for pp.x for charge density calculation, what is the unit of e1, e2, which specifies the plotting area of charge density ? Do e1 and e2 have Bohr length (au) or the unit of alat ? Is the results of plotting charge has e1 * e2 length^{2} ? &inputpp prefic = 'testSample' outdir = './' filplot = 'testSample' plot_num = 0 / &plot nfile = 1 filepp(1)='testSamplecharge' weight = 2 iflag = 2 output_format=2 fileout = 'testSampe.rho.dat' e1(1)=0.0,e1(2)=1.0,e1(3)=0.0, e2(1)=0.0,e2(2)=0.0,e2(3)=0.0 x0(1) = 0.0, x0(2)=0.0,x0(3)=0.0 nx = 56, ny = 56 / From ari.p.seitsonen at iki.fi Fri Feb 27 09:30:08 2009 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 27 Feb 2009 09:30:08 +0100 (CET) Subject: [Pw_forum] paramagnetic defects in solids In-Reply-To: <98e923e50902261247k6d565933v4d80672eb4dc423e@mail.gmail.com> References: <98e923e50902261247k6d565933v4d80672eb4dc423e@mail.gmail.com> Message-ID: Dear Sanda, We do not yet have extensive experience on the implementation, but it should work, in particular for solids (the GIPAW method, needed for the g tensor, was designed in particular for this purpose). The computational cost of hyper-fine constants is vanishing after you have obtained the optimised wave functions (and geometry, if you did optimise it), it is simple post-processing tool. The calculation of the g tensor is more time-consuming, maybe a about ten times the calculation of the self-consistent electronic structure. If you do use the code, please let us know about your experiences, so that we can further develop the code. And please do not forget that you need the pseudo potentials with the GIPAW reconstruction data; some are given at http://www.impmc.jussieu.fr/~software/gipaw/ together with (very basic) information on how to generate the projectors for the reconstruction. Greetings from Paris, apsi On Thu, 26 Feb 2009, Sanda Botis wrote: > Hi everyone, > > I would like to know if anyone has experience working on paramagnetic > defects in solids and using QE. I know that the 4.0 version is supposed to > be able to calculate g-tensors and hyperfine constants but I am not sure how > well it works for solids and how computationally demanding this type of > calculations are. > > Maybe you can give me a few suggestions based on your experience with QE. > > Thank you, > Sanda > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ IMPMC, CNRS & Universit? Pierre et Marie Curie Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 From degironc at sissa.it Fri Feb 27 09:47:36 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 27 Feb 2009 09:47:36 +0100 Subject: [Pw_forum] ELF .vs. Charge difference In-Reply-To: References: Message-ID: <49A7A8A8.9070102@sissa.it> Dear Hai-Ping LAN, my understanding of ELF is that it gives you an indication of whether the occupied electronic manifold in a given region of space is associated with a single main wavefunction (in the Wannier function sense) which is typical of covalent bonds or associated with many such states which is more the case in metallic bonds. Total density difference are what they are... they tell where charge accumulates upon formation of bonds... The two indicators may (hopefully should) give consistent indications when applied to a given system but they measure two different things. Hope this helps, stefano de Gironcoli - SISSA and DEMOCRITOS lan haiping wrote: > Dear All, > > I came to a problem to analyze bond type for an interface. > I wonder about the difference between electron localization function and > charge difference with respect to understanding bonding interaction. > In fact , I just read a work of PhysRevLett.89.106403, it seems ELF and > charge difference give the same feature with respect to bonds. > I appreciate any hint and help. > Thanks > Regards, > Hai-Ping LAN > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Fri Feb 27 10:20:36 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 27 Feb 2009 10:20:36 +0100 Subject: [Pw_forum] range of plotting area for charge density --- definition of e1, e2 In-Reply-To: References: Message-ID: <49A7B064.3010907@sissa.it> yukihiro_okuno at fujifilm.co.jp wrote: > Dear PWSCF Users. > > I want to plot 2D charge density by pp.x and plotrho.x. > > In the input file for pp.x for charge density calculation, what is > the unit of e1, e2, which specifies the plotting area of charge density ? > > Do e1 and e2 have Bohr length (au) or the unit of alat ? Please read more carefully Doc/INPUT_PP.txt, it is written there: !!! x0, e1, e2, e3 are in alat units !!! > > Is the results of plotting charge has e1 * e2 length^{2} ? Sorry, I don't understand this question... You will simply get the charge density (or better twice the charge, since you put weight = 2; BTW be careful, that's a vector, you should write weight(1), weight(2),... ) in the (portion of) plane which is defined by the two vectors x0+e1, x0+e2. > > > &inputpp > prefic = 'testSample' prefix = > outdir = './' > filplot = 'testSample' > plot_num = 0 > / > &plot > nfile = 1 > filepp(1)='testSamplecharge' > weight = 2 > iflag = 2 > output_format=2 I usually use output_format=0, since I use gnuplot directly, but I think that =2 should do the equivalent jjob passing through a plotrho processing step. > fileout = 'testSampe.rho.dat' > e1(1)=0.0,e1(2)=1.0,e1(3)=0.0, > e2(1)=0.0,e2(2)=0.0,e2(3)=0.0 This values for e2 are meaningless, you need a non-null vector. > x0(1) = 0.0, x0(2)=0.0,x0(3)=0.0 > nx = 56, ny = 56 > / Please sign your e-mail and provide affiliation, thanks. HTH GS > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From stewart at cnf.cornell.edu Fri Feb 27 19:40:15 2009 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Fri, 27 Feb 2009 13:40:15 -0500 Subject: [Pw_forum] follow up on segmentation faults in pwcond.x In-Reply-To: <200902260856.29514.smogunov@sissa.it> References: <20090225191415.5074.qmail@mail.spidergraphics.com> <200902260856.29514.smogunov@sissa.it> Message-ID: <20090227184015.6112.qmail@mail.spidergraphics.com> Hi everyone, I just wanted to follow up on my segmentation fault issue I was having with pwcond.x. In previous discussions, I saw that the bravais lattice defined could lead to issues. I was originally using ibrav=0 so I switched this to ibrav=8 (orthorhombic). Following Alexander's suggestion, I also ran it using 16 processors instead of just 10. With these changes, I have been able to run without problems. Thanks! Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From sandabotis at gmail.com Fri Feb 27 21:05:54 2009 From: sandabotis at gmail.com (Sanda Botis) Date: Fri, 27 Feb 2009 12:05:54 -0800 Subject: [Pw_forum] paramagnetic defects in solids In-Reply-To: References: <98e923e50902261247k6d565933v4d80672eb4dc423e@mail.gmail.com> Message-ID: <98e923e50902271205h34af790dv27d96430e112522d@mail.gmail.com> Dear Ari, Thank you for the reply. I tried to access the GIPAW pseudo-potentials but it looks like "The page cannot be found". A more specific question about the pseudo-potentials: Do I need to do all the calculations (scf, geometry optimisation of my system, hyperfine structure, g tensors) with the GIPAW pp, or could it be done in 2 steps scf and geom optimisation with a set of pp and hyperfine structure + g tensor calculations with GIPAW pp. My guess is that I would have to use the GIPAW pp for the entire process which means that I really need to generate my own GIPAW pp (since I see there there are a limited no. of GIPAW pp available). I am really determined to use the code (since one of my committee members think that is so much better that another code that I have been using).:) I'll let you know how things progress. Cheers, Sanda On Fri, Feb 27, 2009 at 12:30 AM, Ari P Seitsonen wrote: > > Dear Sanda, > > We do not yet have extensive experience on the implementation, but it > should work, in particular for solids (the GIPAW method, needed for the g > tensor, was designed in particular for this purpose). The computational cost > of hyper-fine constants is vanishing after you have obtained the optimised > wave functions (and geometry, if you did optimise it), it is simple > post-processing tool. The calculation of the g tensor is more > time-consuming, maybe a about ten times the calculation of the > self-consistent electronic structure. > > If you do use the code, please let us know about your experiences, so that > we can further develop the code. And please do not forget that you need the > pseudo potentials with the GIPAW reconstruction data; some are given at > http://www.impmc.jussieu.fr/~software/gipaw/ > together with (very basic) information on how to generate the projectors > for the reconstruction. > > Greetings from Paris, > > apsi > > > > On Thu, 26 Feb 2009, Sanda Botis wrote: > > Hi everyone, >> >> I would like to know if anyone has experience working on paramagnetic >> defects in solids and using QE. I know that the 4.0 version is supposed to >> be able to calculate g-tensors and hyperfine constants but I am not sure >> how >> well it works for solids and how computationally demanding this type of >> calculations are. >> >> Maybe you can give me a few suggestions based on your experience with QE. >> >> Thank you, >> Sanda >> >> > -- > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > IMPMC, CNRS & Universit? Pierre et Marie Curie > Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 > _______________________________________________ > 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/20090227/6fde4651/attachment.htm From gbilalbegovic at gmail.com Fri Feb 27 22:48:51 2009 From: gbilalbegovic at gmail.com (Goranka Bilalbegovic) Date: Fri, 27 Feb 2009 22:48:51 +0100 Subject: [Pw_forum] paramagnetic defects in solids In-Reply-To: <98e923e50902271205h34af790dv27d96430e112522d@mail.gmail.com> References: <98e923e50902261247k6d565933v4d80672eb4dc423e@mail.gmail.com> <98e923e50902271205h34af790dv27d96430e112522d@mail.gmail.com> Message-ID: <7332fead0902271348i639e31b3jaf30c23c7b3e9579@mail.gmail.com> On Fri, Feb 27, 2009 at 9:05 PM, Sanda Botis wrote: > Dear Ari, > > Thank you for the reply. I will try to answer some questions because I am not sure that Ari will answer this weekend and it looks that you will like to continue immediately. >I tried to access the GIPAW pseudo-potentials but > it looks like "The page cannot be found". Yes, something is wrong with these links, but it is possible to see the GIPAW pseudopotentials on Ari's page: http://www-ext.impmc.jussieu.fr/~software/gipaw/PP_LIBRARY/ > A more specific question about the pseudo-potentials: Do I need to do all > the calculations (scf, geometry optimisation of my system, hyperfine > structure, g tensors) with the GIPAW pp, or could it be done in 2 steps scf > and geom optimisation with a set of pp and hyperfine structure + g tensor > calculations with GIPAW pp. My guess is that I would have to use the GIPAW > pp for the entire process which means that I really need to generate my own > GIPAW pp (since I see there there are a limited no. of GIPAW pp available). Yes, I think you are right: the GIPAW pseudopotentials are used for the entire process. But perhaps, if the first steps are already done in the Quantum Espresso (pwscf) with other pseudopotentials, then output geometries are not very far from GIPAW ones. > I am really determined to use the code (since one of my committee members > think that is so much better that another code that I have been using).:) I agree with your committee member.:) Best regards, Goranka Bilalbegovic, Department of Physics, Faculty of Science, University of Zagreb, Croatia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090227/a11ec691/attachment-0001.htm From trinh.vo at jpl.nasa.gov Sat Feb 28 00:34:11 2009 From: trinh.vo at jpl.nasa.gov (Vo, Trinh) Date: Fri, 27 Feb 2009 15:34:11 -0800 Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: Message-ID: Dear Axel, Thanks for clarification. About the benchmarks, I just simply to see how well is the performance of the cluster we bought in term of scaling with QE. I sent some plots to you, but the email did not go thru because of the restriction of the size (larger than 40K). Currently, I am not happy at the fact that the difference in CPU time and wall time is too large. When I run a longer job, which took ~2h CPU time long, the wall time was ~7h when I run from the head node, and ~4h when I run from another node, which is not the head node. The reason why I avoided running from the head node was that other users might use the head node to do their work, causing the long wall time. Even when I did the test runs (short runs), when no one used the cluster, the difference was still up to 25%, depending on how many nodes I used. I do not know what I should do to improve this difference. According to you, what should I look at to fix the problem. (I also need to read the forum discussion as Lorenzo said in his email). Thanks, Trinh On 2/26/09 4:34 PM, "Axel Kohlmeyer" wrote: On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> Dear Axel, TV> TV> I am sorry. I may be out of date. Is the cp2k code included in QE TV> package, or in some other codes? I saw the word "cp2k" in the title perhaps i was not clear enough. cp2k is a completely different project and has not much else to do with Q-E outside of the fact that both have a DFT module and that i and a few others are using both codes. TV> of the plot, but I thought that it might be the same cp code of QE. no. i already wrote that. in fact, "there is no CP in CP2k". i suggested this phase as a subtitle to the project, but people found it to negative. ;) TV> Actually, the benchmark plot that I obtained does not look as good TV> as the posted plot. I will send it to you in the next email. I need TV> to make a better plot before I send it. benchmark in terms of scaling or in terms of problem set size? there should be a post in the cp2k google group referring to the benchmark graph and describing the exact system setup. cheers, axel. TV> TV> Thanks, TV> TV> Trinh TV> TV> TV> TV> tried to repeat all the calculations to compare, but I could not run TV> TV> that case. TV> TV> this graph was done with a _very_ different code, cp2k, that TV> uses a method (quickstep) different from the CP in cp.x and has TV> therefore different memory requirements and system size scaling. TV> the README of example21 explicitly warns you about running out TV> of memory. give the current difference in speed between hard TV> drives and main memory, every calculation where you run into TV> using swap is not worth the effort (unlike 10 years ago). TV> TV> just for reference: because of the difference in methods cp.x TV> should scale better with the number of processors, whereas TV> cp2k should scale better with the problem set size than cp.x TV> with the same number of processors. TV> TV> that being said, cp2k demonstrates the problem of overloading TV> memory and communication channels very nicely and thus the TV> graphs are a nice point of reference to showcase how bad it TV> can get and that the not so obvious choice of not using all TV> cpus actually gives you the better performance. TV> TV> cheers, TV> axel. TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> Trinh TV> TV> TV> TV> TV> TV> TV> TV> -----Original Message----- TV> TV> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Axel Kohlmeyer TV> TV> Sent: Thursday, February 26, 2009 1:04 PM TV> TV> To: PWSCF Forum TV> TV> Subject: Re: [Pw_forum] Insufficient Virtual Memory TV> TV> TV> TV> On Thu, 26 Feb 2009, Vo, Trinh wrote: TV> TV> TV> TV> TV> Dear PWSCF users, TV> TV> TV> TV> TV> TV> I was running a benchmark (using example21 in QE) for my computer cluster (total 18 nodes) to compare the results with those posted on web link that was mentioned by Axel in some previous forum emails.. TV> TV> TV> TV> TV> TV> When I performed the calculation for the case of 512 H2O with 4cores/node, the job crashed with the error: TV> TV> TV> TV> TV> TV> "forrtl: severe (41): insufficient virtual memory". TV> TV> TV> TV> TV> TV> TV> TV> I do not know how to deal with this. Any help or suggestion is TV> TV> TV> appreciated. For other cases, the runs were fine. TV> TV> TV> TV> have you _read_ the README file in that directory??? TV> TV> TV> TV> axel. TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> Below are the specifications of my cluster: TV> TV> TV> TV> TV> TV> Intel CPU Xeon X5450 Quad Core 3.0GHz with 12M cache 133MHz FSB TV> TV> TV> DDRII667 4GB RAM FBD ECC (D-667D2D4F5/4GB) TV> TV> TV> TV> TV> TV> For compilation, I used the following: TV> TV> TV> QE ver. 4.0.3 TV> TV> TV> ifort 10.1015, MKL 10.0.3.020, impi 3.1 TV> TV> TV> internal fftw TV> TV> TV> TV> TV> TV> I also attach here the output file. TV> TV> TV> TV> TV> TV> TV> TV> TV> Thank you, TV> TV> TV> TV> TV> TV> Trinh Vo TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> TV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ 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/20090227/2764d071/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Feb 28 01:53:49 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Feb 2009 19:53:49 -0500 (EST) Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: References: Message-ID: On Fri, 27 Feb 2009, Vo, Trinh wrote: VT> Dear Axel, VT> VT> Thanks for clarification. VT> VT> About the benchmarks, I just simply to see how well is the VT> performance of the cluster we bought in term of scaling with QE. I VT> sent some plots to you, but the email did not go thru because of the VT> restriction of the size (larger than 40K). please send it to me personally. VT> Currently, I am not happy at the fact that the difference in CPU VT> time and wall time is too large. When I run a longer job, which what kind of hardware do you have, how much memory, and what kind of interconnect do you have? VT> took ~2h CPU time long, the wall time was ~7h when I run from the VT> head node, and ~4h when I run from another node, which is not the VT> head node. The reason why I avoided running from the head node was VT> that other users might use the head node to do their work, causing VT> the long wall time. Even when I did the test runs (short runs), VT> when no one used the cluster, the difference was still up to 25%, VT> depending on how many nodes I used. I do not know what I should do VT> to improve this difference. According to you, what should I look at VT> to fix the problem. (I also need to read the forum discussion as VT> Lorenzo said in his email). how should the number of users on the machine affect the performance? don't you use a batch system to regulate access to the nodes? cheers, axel. VT> VT> Thanks, VT> VT> Trinh VT> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From chenhanghuipwscf at gmail.com Sat Feb 28 04:07:21 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Fri, 27 Feb 2009 22:07:21 -0500 Subject: [Pw_forum] Restart calculation of LSDA Message-ID: <22ae3ca40902271907r18018d55v89f4782a0d7bc34d@mail.gmail.com> Dear PWSCF users, I have a question of how to efficiently restart the calculation of LSDA. It is a little bit complicated. The system I study is always metallic. When I relax a system using LDA, usually I can first relax it at a 'high temperature' (a wider broading width for smearing) and a coarse k grid. Then I use the relaxed atomic positions and the charge density (charge-density.dat) to restart the relaxation at a 'lower temperature' and a more dense k grid. However if I run a spin-polarized calculation (LSDA), I find that a system could be paramagnetic at "high temperature" and ferromagnetic at 'low temperature'. However if I relax a big system using very small broading width and a very dense k grid, it is too computationally intensive. But if I first relax it using a wider broading width and a coarse k grid, the system will relax to a paramagnetic state. Then if I restart it, the system will always be in the paramagnetic state. So is there a clear trick so that I can restart the calculation using the previous charge density but make a new initial guess for the magnetization rather than reading from the file "spin-polarization.dat'? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090227/544a5984/attachment.htm From bali.6666 at gmail.com Sat Feb 28 11:05:55 2009 From: bali.6666 at gmail.com (dr baliram lone) Date: Sat, 28 Feb 2009 15:35:55 +0530 Subject: [Pw_forum] forum Message-ID: <9dc405a30902280205t67f7b030g337e54054e01b555@mail.gmail.com> sent -- Dr.Baliram G Lone Principal Investigator Head,Nanomaterials Research Laboratory Dept. of Physics, V P Mahavidyalaya Vaijapur-423701 Dist.Aurangabad M.S.,India E-mail:bali.6666 at gmail.com,drbglone at gmail.com Cell:+91-9960755296 Vigited countries:Germany,Poland From ziba.zand at gmail.com Sat Feb 28 13:57:54 2009 From: ziba.zand at gmail.com (ziba zand) Date: Sat, 28 Feb 2009 16:27:54 +0330 Subject: [Pw_forum] how to plot pseudopotential and real and pseudo wavefunction? In-Reply-To: <49A6535A.8070105@sissa.it> References: <55fa970e0902252157qef6e0c0kd04261326a28700f@mail.gmail.com> <49A6535A.8070105@sissa.it> Message-ID: <55fa970e0902280457q23cc2e60w5428deac2f7e801c@mail.gmail.com> Dear all, I attempted to make an input file for ld1.x, but I wasn't successful. Would you please send me an example of input file for it? Thanks in advance, Ziba On Thu, Feb 26, 2009 at 12:01 PM, Gabriele Sclauzero wrote: > Dear Ziba > > ziba zand wrote: > > Dear every one, > > > > I am trying to plot pseudopotential and wavefunction by information > > which are existed in the xx.upf & xx.pwfn.data files. > > You can do a pseudopotential test calculation (iswitch.eq.2) with ld1.x > (source code is in > atomic/ directory). After the PP has been read by the program you can > access all relevant > data of the PP through internal variables of ld1 (see ld1inc module for the > description). > If you simply need wfcs, maybe they will be put in the .wfc .pwfc files, > though not sure > of that (please see files in atomic_doc/ for more precise information). > > HTH > > GS > > > > Unfortunately I can't do it. > > Would you please help me? > > Thanks in advance. > > > > Yours, > > Ziba > > Please specify your affiliation, thanks. > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090228/da69d083/attachment.htm From lanhaiping at gmail.com Sat Feb 28 14:45:52 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 28 Feb 2009 21:45:52 +0800 Subject: [Pw_forum] how to plot pseudopotential and real and pseudo wavefunction? In-Reply-To: <55fa970e0902280457q23cc2e60w5428deac2f7e801c@mail.gmail.com> References: <55fa970e0902252157qef6e0c0kd04261326a28700f@mail.gmail.com> <49A6535A.8070105@sissa.it> <55fa970e0902280457q23cc2e60w5428deac2f7e801c@mail.gmail.com> Message-ID: Hi, Take a look at $QE/atomic_doc/pseudo**, there are documents and examples for ld1.x On Sat, Feb 28, 2009 at 8:57 PM, ziba zand wrote: > Dear all, > > I attempted to make an input file for ld1.x, but I wasn't successful. > Would you please send me an example of input file for it? > > Thanks in advance, > > Ziba > > > > > On Thu, Feb 26, 2009 at 12:01 PM, Gabriele Sclauzero wrote: > >> Dear Ziba >> >> ziba zand wrote: >> > Dear every one, >> > >> > I am trying to plot pseudopotential and wavefunction by information >> > which are existed in the xx.upf & xx.pwfn.data files. >> >> You can do a pseudopotential test calculation (iswitch.eq.2) with ld1.x >> (source code is in >> atomic/ directory). After the PP has been read by the program you can >> access all relevant >> data of the PP through internal variables of ld1 (see ld1inc module for >> the description). >> If you simply need wfcs, maybe they will be put in the .wfc .pwfc files, >> though not sure >> of that (please see files in atomic_doc/ for more precise information). >> >> HTH >> >> GS >> >> >> > Unfortunately I can't do it. >> > Would you please help me? >> > Thanks in advance. >> > >> > Yours, >> > Ziba >> >> Please specify your affiliation, thanks. >> >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090228/6928bffd/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Feb 28 19:23:35 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 28 Feb 2009 13:23:35 -0500 Subject: [Pw_forum] Insufficient Virtual Memory In-Reply-To: References: Message-ID: <7b6913e90902281023v6f821794ud83cf3349424b96b@mail.gmail.com> On Fri, Feb 27, 2009 at 6:34 PM, Vo, Trinh wrote: > Dear Axel, > > Thanks for clarification. > > About the benchmarks, I just simply to see how well is the performance of > the cluster we bought in term of scaling with QE. I sent some plots to > you, but the email did not go thru because of the restriction of the size > (larger than 40K). > > Currently, I am not happy at the fact that the difference in CPU time and > wall time is too large. When I run a longer job, which took ~2h CPU time > long, the wall time was ~7h when I run from the head node, and ~4h when I that probably means you ran a job that was too big in the machine and thus swapping all the time. for your reference, here are some numbers from one of our local clusters. the machine has: 2x Intel Xeon E5430 @ 2.66GHz and 8GB per node and a 2xDDR infiniband interconnect. this first block are runs with four nodes and different -npernode numbers: h2o-32-4x2.out: CP : 18.33s CPU time, 18.79s wall time h2o-32-4x4.out: CP : 16.75s CPU time, 17.50s wall time h2o-32-4x8.out: CP : 25.31s CPU time, 25.94s wall time h2o-64-4x1.out: CP : 2m50.18s CPU time, 3m18.88s wall time h2o-64-4x2.out: CP : 1m29.72s CPU time, 1m33.60s wall time h2o-64-4x4.out: CP : 1m12.42s CPU time, 1m13.70s wall time h2o-64-4x8.out: CP : 1m19.53s CPU time, 1m20.86s wall time as you can see, same as with cp2k, using 8 cores per node is hurting performance, especially for smaller jobs, and using 4 cores per node is a much better choice. and here the corresponding single node times (run on the frontend): h2o-32-np1.out: CP : 2m24.38s CPU time, 2m39.38s wall time h2o-32-np2.out: CP : 1m24.22s CPU time, 1m42.09s wall time h2o-32-np4.out: CP : 48.92s CPU time, 51.58s wall time h2o-32-np8.out: CP : 41.89s CPU time, 42.72s wall time h2o-64-np2.out: CP : 6m39.17s CPU time, 7m49.54s wall time h2o-64-np4.out: CP : 4m19.69s CPU time, 5m14.73s wall time h2o-64-np8.out: CP : 4m12.16s CPU time, 4m24.57s wall time the saturation of the memory bandwidth becomes apparent (little gain going from 4 mpi tasks to 8 mpi tasks). you have to keep in mind on the intel quad cores, the difference between using 4 cores and 8 cores is especially drastic, as the cpus share caches between two cores, so with 4 cores i have effectively double the L2-cache as with 8 cores. it would be interesting to see somebody do a similar test with AMD quad cores, since those are true quad cores. you should also note, that those timings contain some non-parallel overhead that happens when starting a job. for testing production speed you should run a 20 step and a 10 step job and then subtract the time for the 10 step job from the 20 step job to get the timing for 10 steps. HTH, axel. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From bogus@does.not.exist.com Tue Feb 17 11:48:01 2009 From: bogus@does.not.exist.com () Date: Tue, 17 Feb 2009 10:48:01 -0000 Subject: No subject Message-ID: the final bands are showed as surface projected bulk bands, distinctively pointing out the surface states and the surface resonance states. How can I separate the surface state and surface resonance state from the bulk state using PWSCF package? or additional codes are required ? Could anyone give me suggestion? Thanks a million. Wenmei Ming Institue of Physics, Chinese Academy of Sciences Beijing 100190 People's Republic of China _________________________________________________________________ MSN????????????????????????????????????MSN?????? http://im.live.cn/safe/ --_61ef5d4b-4ccd-421b-81d8-248ba71edc75_ Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: 8bit
Dear all,
 
I am simulating the Be(0001) surface through N-layer slab construction.
But how can I decompose the calculated bands into surface states and bulk states.
From a few publications concerning DFT calculation of surface structure,
the final bands are showed as surface projected bulk bands, distinctively pointing out
the surface states and the surface resonance states.
 
How can I separate the surface state and surface resonance state from the bulk state
using PWSCF package? or additional codes are required ?
 
Could anyone give me suggestion?
Thanks a million.
 
Wenmei Ming
 
Institue of Physics,
Chinese Academy of Sciences
Beijing 100190
People's Republic of China

?????????? Windows Live Messenger ???????????????? ?????????? --_61ef5d4b-4ccd-421b-81d8-248ba71edc75_-- From bogus@does.not.exist.com Tue Feb 17 11:48:01 2009 From: bogus@does.not.exist.com () Date: Tue, 17 Feb 2009 10:48:01 -0000 Subject: No subject Message-ID: Chemistry viewpoint, certain atomic structure could result in different hybrid styles of molecular orbitals. The feature I identified may have a favorable shape of hybrid orbitals for water approaching and dissociating. I wonder whether QE has a function for ploting the shape of hybrid molecular orbitals near the surface. thank you for reading best, vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** --001636163d19c830c60466ccc604 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,

I'm studying the water splitting behavior on certain s= urfaces. And I have identified a special structural features of the surface= for water dissociation.
But I can't tell why that kin= d of feature did a positive effect on water dissociation. One visitor to ou= r group thought this behavior has a strong dependence of molecular hybrid o= rbitals of atoms near the surface. From a = Structural Chemistry viewpoint, certain atomic structure could resul= t in different hybrid styles of molecular orbitals. The feature I identifie= d may have a favorable shape of hybrid orbitals for water approaching and d= issociating.

I wonder whether QE has a function for ploting the shape of hybrid mole= cular orbitals near the surface.

thank you for reading

best,<= br>
vega

--
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Vega Lew ( weijia liu)
PH.D Candidate in Chemical Engineering
State K= ey Laboratory of Materials-oriented Chemical Engineering
College of Chem= istry and Chemical Engineering
Nanjing University of Technology, 210009,= Nanjing, Jiangsu, China
***************************************************************************= ***************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovatio= n Building, Xinmofan Road 5#, Nanjing, Jiangsu, China =A0
***************************************************************************= ***************************************
--001636163d19c830c60466ccc604-- From bogus@does.not.exist.com Tue Feb 17 11:48:01 2009 From: bogus@does.not.exist.com () Date: Tue, 17 Feb 2009 10:48:01 -0000 Subject: No subject Message-ID: ! Then, if (.not.dos) : ! nq number of q-points ! (q(i,n), i=1,3) nq q-points in 2pi/a units ! If q = 0, the direction qhat (q=>0) for the non-analytic part ! is extracted from the sequence of q-points as follows: ! qhat = q(n) - q(n-1) or qhat = q(n) - q(n+1) ! depending on which one is available and nonzero. ! For low-symmetry crystals, specify twice q = 0 in the list ! if you want to have q = 0 results for two different directions ! Anyway, you should specify 2 directions like x(1) y(1) z(1) ........ x(N-1) y(N) z(N) 0 0 0 !!!!! Gamma point x(N)=0 y(N)=0 z(N)=0 x(N+1) y(N+1) z(N+1) ......... x(M) y(M) z(M) For a hexagonal lattice you could try A (00z) --> G(000) --> K(-1/3,2/3,0), as example. Hope this helps. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 4/16/09, Li YL wrote: > From: Li YL > Subject: [Pw_forum] propagation direction in the input file for dynmat.x > To: "pw_forum" > Date: Thursday, April 16, 2009, 4:05 PM > Dear all users, > > Now I've a question on the polar materials. In order to > get LO-TO splitting, you know, we need to use dynmat.x. In > the input file for dynmat.x, we need input q(1), q(2), and > q(3), that is, the propagation direction. I don't know > how to choose this direction. My system has hexagonal > symmetry and its primitive cell is rhombohedral. > Any suggestions are welcome. Thanks in advance. > > Bests, > > Yanling Li, > > Institute of Solid states physics, CAS, P. R. China. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From bogus@does.not.exist.com Tue Feb 17 11:48:01 2009 From: bogus@does.not.exist.com () Date: Tue, 17 Feb 2009 10:48:01 -0000 Subject: No subject Message-ID: This execute the PWscf code on 4096 processors, to simulate a system with 8 images, each of which is distributed across 512 processors. K-points are distributed across 2 pools of 256 processors each, 3D FFT is performed using 8 task groups (64 processors each, so the 3D real-space grid is cut into 64 slices), and the diagonalization of the subspace Hamiltonian is distributed to a square grid of 144 processors (12x12). Default values are: -nimage 1 -npool 1 -ntg 1 ; ndiag is chosen by the code as the fastest n^2 (n integer) that fits into the size of each pool. *Massively parallel calculations*: For very large jobs (i.e. O(1000) atoms or so) or for very long jobs to be run on massively parallel machines (e.g. IBM BlueGene) it is crucial to use in an effective way both the "task group" and the "ortho group" parallelization. Without a judicious choice of parameters, large jobs will find a stumbling block in either memory or CPU requirements. In particular, the "ortho group" parallelization is used in the diagonalization of matrices in the subspace of Kohn-Sham states (whose dimension is as a strict minumum equal to the number of occupied states). These are stored as block-distributed matrixes (distributed across processors) and diagonalized using custom-taylored diagonalization algorithms that work on block-distributed matrixes. Thanks -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez --001e680f0a54ca5bfb046868120d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi, I found in the new, or maybe not so new, users guide, that 1000 atom= s or so can be calculated, and new ways to paralelize.=A0

The example= in the manual is 

 mpirun -np 4096 ./pw.x -ni=
mage 8 -npool 2 -ntg 8 -ndiag 144 -input myin=
put.in

I have played a bit, but not with a massive computer, and I have found t= hat the default options are always better than my unexpert=A0 choices.

<= p>So, I would like to see some hints, in addition to what=A0 is reproduced = below (from the users guide), about the good choices of -ntg and -ndiag. Ma= ybe=A0 some examples is enough to understand it.


From the users guide:

This execute the PWscf co= de on 4096 processors, to simulate a system with 8 images, each of which is distributed across 512 processors. K-points are distributed across 2 pools of 256 processors each,=20 3D FFT is performed using 8 task groups (64 processors each, so the 3D real-space grid is cut into 64 slices), and the diagonalization of the subspace Hamiltonian is distributed to a square grid of 144 processors (12x12).

Default values are: -nimage 1 -npool 1 -ntg 1=A0; ndiag is chosen by the code as the fastest n^2 (n integer) that fits into the size of each pool.

Massively parallel calculations: For very large jobs (i.e. O(1000) atoms or so) or for very long jobs to be = run on massively=20 parallel machines (e.g. IBM BlueGene) it is crucial to use in an effective= way both the "task group" and the "ortho group" parallelization. Wit= hout a judicious choice of parameters, large jobs will find a stumbling block in either memory or=20 CPU requirements. In particular, the "ortho group" parallelizatio= n is used in the diagonalization=20 of matrices in the subspace of Kohn-Sham states (whose dimension is as a st= rict minumum equal to=20 the number of occupied states). These are stored as block-distributed matri= xes (distributed across processors) and diagonalized using custom-taylored diagonalization a= lgorithms=20 that work on block-distributed matrixes.

Thanks

--
Eduardo Menendez
Departamento de = Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)978= 7439
URL: http:/= /fisica.ciencias.uchile.cl/~emenendez
--001e680f0a54ca5bfb046868120d--