From mayankaditya at gmail.com Tue May 1 09:43:18 2012 From: mayankaditya at gmail.com (mayank gupta) Date: Tue, 1 May 2012 13:13:18 +0530 Subject: [Pw_forum] PP conversion from ABINIT format to UPF format Message-ID: how to convert abinit PP to UPF format. I tried fhi2upf.x utilitie for U but it doesn't work. I simply use fhi2upf.x out.UPF. I got lot of error massage like Input file > uranium, fhi98PP : Trouiller-Martins-type, GGA Perdew/Burke/Ernzerhof (1996), l= 1 local: file not found Input file > 92.000 6.000 011001 zatom,zion,pspdat: file not found Input file > 6 11 3 1 573 0 pspcod,pspxc,lmax,lloc,mmax,r2well: file not found Input file > 7.161 1.000 0.000 rchrg, fchrg, qchrg: file not found Input file > 5--- These two lines are available for giving more information, later: file not found Input file > 6: file not found Input file > 7-Here follows the cpi file from the fhi98pp code-: file not found Input file > 6.00000E+00 4: file not found Input file > 0.0000 0.0000 0.0000 0.0000: file not found .............. ............ Input file > ./fhi2upf.x: reading file name 0.78239361959522E+02 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cpmd2upf : error # 2 file: 0.78239361959522E+02 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00 not found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Please suggest me If I am doing any thing wrong. Gupta M K Mumbai From giannozz at democritos.it Tue May 1 11:21:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 1 May 2012 11:21:41 +0200 Subject: [Pw_forum] PP conversion from ABINIT format to UPF format In-Reply-To: References: Message-ID: On May 1, 2012, at 9:43 , mayank gupta wrote: > I simply use fhi2upf.x out.UPF you should simply use fhi2upf.x P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From himanshu at iopb.res.in Tue May 1 13:00:25 2012 From: himanshu at iopb.res.in (himanshu at iopb.res.in) Date: Tue, 1 May 2012 16:30:25 +0530 Subject: [Pw_forum] Regarding instillation problem in cluster system Message-ID: <3f2a544fd6747bc55e6dc917bd1e3dc8.squirrel@www.iopb.res.in> Respected PW_forum members, I am unable to install QUANTUM ESPRESSO-4.3 in our cluster(parallel) system. Since configuration file runs correctly; it recognise needed LIBRARY also, but when I put command 'make all' in terminal, I am getting following error:- configure: success [himanshu0 at anu1 espresso-4.3]$ make all test -d bin || mkdir bin if test -e extlibs/archive/iotk-1.2.beta.tar.gz ; then \ ( cd extlibs ; make libiotk) ; fi make[1]: Entering directory `/home1/himanshu0/espresso-4.3/extlibs' if test ! -d ../S3DE; then \ (gzip -dc archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ if test -e install/Makefile_iotk; then \ (cp install/Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ if test -e install/iotk_config.h; then \ (cp install/iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi cd ../S3DE/iotk/src; make lib+util; make[2]: Entering directory `/home1/himanshu0/espresso-4.3/S3DE/iotk/src' mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA -I../include -c iotk_dat+CHARACTER1_0.f90 iotk_dat.spp: In function ?iotk_write_dat_character1_0?: iotk_dat.spp:156: internal compiler error: in gfc_conv_function_call, at fortran/trans-expr.c:1105 Please submit a full bug report, with preprocessed source if appropriate. See for instructions. make[2]: *** [iotk_dat+CHARACTER1_0.o] Error 1 make[2]: Leaving directory `/home1/himanshu0/espresso-4.3/S3DE/iotk/src' make[1]: *** [libiotk] Error 2 make[1]: Leaving directory `/home1/himanshu0/espresso-4.3/extlibs' make: *** [libiotk] Error 2 [himanshu0 at anu1 espresso-4.3]$ Please give me appropriate guide lines to install it properly.I will remain really thankful to you. Looking forward to your response eagerly. Himanshu Lohani Doctoral Scholar Institute Of Physics Bhubaneswer(India) From akohlmey at gmail.com Tue May 1 14:33:21 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 1 May 2012 08:33:21 -0400 Subject: [Pw_forum] Regarding instillation problem in cluster system In-Reply-To: <3f2a544fd6747bc55e6dc917bd1e3dc8.squirrel@www.iopb.res.in> References: <3f2a544fd6747bc55e6dc917bd1e3dc8.squirrel@www.iopb.res.in> Message-ID: On Tue, May 1, 2012 at 7:00 AM, wrote: > Respected PW_forum members, > ? ? ? ? ? ? ? ? ? ? ? ? ? ?I am unable to install QUANTUM ESPRESSO-4.3 in > our cluster(parallel) system. Since > configuration file runs correctly; it > recognise needed LIBRARY also, but when I put > command 'make all' in terminal, I am getting > following error:- [...] > mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI > -D__PARA -I../include ?-c iotk_dat+CHARACTER1_0.f90 > iotk_dat.spp: In function ?iotk_write_dat_character1_0?: > iotk_dat.spp:156: internal compiler error: in gfc_conv_function_call, at > fortran/trans-expr.c:1105 > Please submit a full bug report, > with preprocessed source if appropriate. > See for instructions. > make[2]: *** [iotk_dat+CHARACTER1_0.o] Error 1 > make[2]: Leaving directory `/home1/himanshu0/espresso-4.3/S3DE/iotk/src' > make[1]: *** [libiotk] Error 2 > make[1]: Leaving directory `/home1/himanshu0/espresso-4.3/extlibs' > make: *** [libiotk] Error 2 > [himanshu0 at anu1 espresso-4.3]$ > > > ? ? ? ?Please give me appropriate guide lines to install it properly.I > will remain really thankful to you. internal compiler error means that you have a buggy compiler. the error message gives you detailed instructions of what to do in this case. have you considered just following them? is that too obvious? axel. > > ? ? ? Looking forward to your response eagerly. > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Himanshu Lohani > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Doctoral Scholar > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Institute Of Physics > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Bhubaneswer(India) > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From bfazi90 at gmail.com Tue May 1 18:35:24 2012 From: bfazi90 at gmail.com (bf azi) Date: Tue, 1 May 2012 21:05:24 +0430 Subject: [Pw_forum] absorption Message-ID: Dear all Which Bravais-lattice better for absorption hydrogen on BNNT "Hexagonal and Trigonal P" or "Tetragonal P (st)" ? thanks a lot Bani Adam Faculty of Science Egypt From degironc at sissa.it Tue May 1 19:55:36 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 01 May 2012 19:55:36 +0200 Subject: [Pw_forum] absorption In-Reply-To: References: Message-ID: <4FA02398.3090206@sissa.it> If the cell is large enough that the nanotube can be considered isolated then the result should not depend on the chosen Bravais lattice. An hexagonal BL may optimize better the minimum distance between images. stefano On 05/01/2012 06:35 PM, bf azi wrote: > Dear all > > Which Bravais-lattice better for absorption hydrogen on BNNT > "Hexagonal and Trigonal P" or "Tetragonal P (st)" ? > > thanks a lot > > Bani Adam > Faculty of Science > Egypt > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From reishme04 at gmail.com Wed May 2 04:53:56 2012 From: reishme04 at gmail.com (matt reish) Date: Wed, 2 May 2012 14:53:56 +1200 Subject: [Pw_forum] benzoic acid structure optimization Message-ID: Hi PW list, I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining Raman phonon frequencies of a benzoic acid crystal. I attained the optimized output geometry from a CASTEP calculation in the supplemental material of a paper. This geometry was used by the authors to calculate accurate IR phonon frequencies. I used a 'relax' calculation in Quantum Espresso on the optimized geometry but this led to large shifts in the atomic positions in the lattice and unreasonable structures for the molecules in the lattice after finding the optimized structure. My question is does anyone have a some experience calculating organic crystals in Quantum Espresso that could give me some tips? Here is my input file minus the atomic posititions: &CONTROL title = 'benzacidscftest' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/mreish/tmp/' , pseudo_dir = '/usr/share/espresso/pseudo/' , prefix = 'batest5' , disk_io = 'default' , nstep = 600 , / &SYSTEM ibrav = 12, A = 5.4996 , B = 5.1283 , C = 21.950 , cosAB = 0 , cosAC = -.128276341 , cosBC = 0 , nat = 60, ntyp = 3, ecutwfc = 5 , ecutrho = 40 , / &ELECTRONS electron_maxstep = 200, conv_thr = 1.0d-11 , / &IONS / ATOMIC_SPECIES C 12.01000 C.pbe-rrkjus.UPF O 16.00000 O.pbe-rrkjus.UPF H 1.00000 H.pbe-rrkjus.UPF ATOMIC_POSITIONS angstrom K_POINTS automatic 1 1 1 1 1 1 Cheers, Matthew Reish University of Otago Dunedin New Zealand -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120502/97d2631d/attachment.htm From akohlmey at gmail.com Wed May 2 05:02:07 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 1 May 2012 23:02:07 -0400 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: > Hi PW list, > > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining > Raman phonon frequencies of a benzoic acid crystal. I attained the optimized > output geometry from a CASTEP calculation in the supplemental material of a > paper. This geometry was used by the authors to calculate accurate IR phonon > frequencies. I used a 'relax' calculation in Quantum Espresso on the > optimized geometry but this led to large shifts in the atomic positions in > the lattice and unreasonable structures for the molecules in the lattice > after finding the optimized structure. My question is does anyone have a > some experience calculating organic crystals in Quantum Espresso that could > give me some tips? matt, you are using a *ridiculously* low wavefunction and density cutoff, that means your basis set is *far* too small. unphysical results are the logical consequence. axel. > > Here is my input file minus the atomic posititions: > > &CONTROL > ?????????????????????? title = 'benzacidscftest' , > ???????????????? calculation = 'relax' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????????? outdir = '/home/mreish/tmp/' , > ????????????????? pseudo_dir = '/usr/share/espresso/pseudo/' , > ????????????????????? prefix = 'batest5' , > ???????????????????? disk_io = 'default' , > ?????????????????????? nstep = 600 , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 12, > ?????????????????????????? A = 5.4996 , > ?????????????????????????? B = 5.1283 , > ?????????????????????????? C = 21.950 , > ?????????????????????? cosAB = 0 , > ?????????????????????? cosAC = -.128276341 , > ?????????????????????? cosBC = 0 , > ???????????????????????? nat = 60, > ??????????????????????? ntyp = 3, > ???????????????????? ecutwfc = 5 , > ???????????????????? ecutrho = 40 , > ?/ > ?&ELECTRONS > ??????????? electron_maxstep = 200, > ??????????????????? conv_thr = 1.0d-11 , > ?/ > ?&IONS > ?/ > ATOMIC_SPECIES > ??? C?? 12.01000? C.pbe-rrkjus.UPF > ??? O?? 16.00000? O.pbe-rrkjus.UPF > ??? H??? 1.00000? H.pbe-rrkjus.UPF > ATOMIC_POSITIONS angstrom > > K_POINTS automatic > ? 1 1 1?? 1 1 1 > > > Cheers, > > Matthew Reish > University of Otago > Dunedin > New Zealand > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From reishme04 at gmail.com Wed May 2 05:33:21 2012 From: reishme04 at gmail.com (matt reish) Date: Wed, 2 May 2012 15:33:21 +1200 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: Thanks for the reply, seemed to be going way too fast for what I had read I that I should expect. Any thoughts on what would be more reasonable cutoffs for wavefunction and density? Would it be reasonable to try to attain a useable result on a "cluster" using 8 processors? Cheers, Matt On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer wrote: > On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: > > Hi PW list, > > > > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining > > Raman phonon frequencies of a benzoic acid crystal. I attained the > optimized > > output geometry from a CASTEP calculation in the supplemental material > of a > > paper. This geometry was used by the authors to calculate accurate IR > phonon > > frequencies. I used a 'relax' calculation in Quantum Espresso on the > > optimized geometry but this led to large shifts in the atomic positions > in > > the lattice and unreasonable structures for the molecules in the lattice > > after finding the optimized structure. My question is does anyone have a > > some experience calculating organic crystals in Quantum Espresso that > could > > give me some tips? > > > matt, > > you are using a *ridiculously* low wavefunction > and density cutoff, that means your basis set > is *far* too small. unphysical results are the > logical consequence. > > axel. > > > > > > Here is my input file minus the atomic posititions: > > > > &CONTROL > > title = 'benzacidscftest' , > > calculation = 'relax' , > > restart_mode = 'from_scratch' , > > outdir = '/home/mreish/tmp/' , > > pseudo_dir = '/usr/share/espresso/pseudo/' , > > prefix = 'batest5' , > > disk_io = 'default' , > > nstep = 600 , > > / > > &SYSTEM > > ibrav = 12, > > A = 5.4996 , > > B = 5.1283 , > > C = 21.950 , > > cosAB = 0 , > > cosAC = -.128276341 , > > cosBC = 0 , > > nat = 60, > > ntyp = 3, > > ecutwfc = 5 , > > ecutrho = 40 , > > / > > &ELECTRONS > > electron_maxstep = 200, > > conv_thr = 1.0d-11 , > > / > > &IONS > > / > > ATOMIC_SPECIES > > C 12.01000 C.pbe-rrkjus.UPF > > O 16.00000 O.pbe-rrkjus.UPF > > H 1.00000 H.pbe-rrkjus.UPF > > ATOMIC_POSITIONS angstrom > > > > K_POINTS automatic > > 1 1 1 1 1 1 > > > > > > Cheers, > > > > Matthew Reish > > University of Otago > > Dunedin > > New Zealand > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Dr. Axel Kohlmeyer > akohlmey at gmail.com http://goo.gl/1wk0 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120502/04b0f844/attachment.htm From mohnish.iitk at gmail.com Wed May 2 05:51:45 2012 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 2 May 2012 09:21:45 +0530 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: 30 Rydberg at least for wavefunction cutoff and 240 for charge density. On Wed, May 2, 2012 at 9:03 AM, matt reish wrote: > Thanks for the reply, seemed to be going way too fast for what I had read I > that I should expect. Any thoughts on what would be more reasonable cutoffs > for wavefunction and density? Would it be reasonable to try to attain a > useable result on a "cluster" using 8 processors? > > Cheers, > > Matt > > > On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer wrote: >> >> On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: >> > Hi PW list, >> > >> > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining >> > Raman phonon frequencies of a benzoic acid crystal. I attained the >> > optimized >> > output geometry from a CASTEP calculation in the supplemental material >> > of a >> > paper. This geometry was used by the authors to calculate accurate IR >> > phonon >> > frequencies. I used a 'relax' calculation in Quantum Espresso on the >> > optimized geometry but this led to large shifts in the atomic positions >> > in >> > the lattice and unreasonable structures for the molecules in the lattice >> > after finding the optimized structure. My question is does anyone have a >> > some experience calculating organic crystals in Quantum Espresso that >> > could >> > give me some tips? >> >> >> matt, >> >> you are using a *ridiculously* low wavefunction >> and density cutoff, that means your basis set >> is *far* too small. unphysical results are the >> logical consequence. >> >> axel. >> >> >> > >> > Here is my input file minus the atomic posititions: >> > >> > &CONTROL >> > ?????????????????????? title = 'benzacidscftest' , >> > ???????????????? calculation = 'relax' , >> > ??????????????? restart_mode = 'from_scratch' , >> > ????????????????????? outdir = '/home/mreish/tmp/' , >> > ????????????????? pseudo_dir = '/usr/share/espresso/pseudo/' , >> > ????????????????????? prefix = 'batest5' , >> > ???????????????????? disk_io = 'default' , >> > ?????????????????????? nstep = 600 , >> > ?/ >> > ?&SYSTEM >> > ?????????????????????? ibrav = 12, >> > ?????????????????????????? A = 5.4996 , >> > ?????????????????????????? B = 5.1283 , >> > ?????????????????????????? C = 21.950 , >> > ?????????????????????? cosAB = 0 , >> > ?????????????????????? cosAC = -.128276341 , >> > ?????????????????????? cosBC = 0 , >> > ???????????????????????? nat = 60, >> > ??????????????????????? ntyp = 3, >> > ???????????????????? ecutwfc = 5 , >> > ???????????????????? ecutrho = 40 , >> > ?/ >> > ?&ELECTRONS >> > ??????????? electron_maxstep = 200, >> > ??????????????????? conv_thr = 1.0d-11 , >> > ?/ >> > ?&IONS >> > ?/ >> > ATOMIC_SPECIES >> > ??? C?? 12.01000? C.pbe-rrkjus.UPF >> > ??? O?? 16.00000? O.pbe-rrkjus.UPF >> > ??? H??? 1.00000? H.pbe-rrkjus.UPF >> > ATOMIC_POSITIONS angstrom >> > >> > K_POINTS automatic >> > ? 1 1 1?? 1 1 1 >> > >> > >> > Cheers, >> > >> > Matthew Reish >> > University of Otago >> > Dunedin >> > New Zealand >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer >> akohlmey at gmail.com ?http://goo.gl/1wk0 >> >> College of Science and Technology >> Temple University, Philadelphia PA, USA. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- From giuseppe.mattioli at ism.cnr.it Wed May 2 11:58:12 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 2 May 2012 11:58:12 +0200 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: <201205021158.12704.giuseppe.mattioli@ism.cnr.it> Dear Matt First, you should try to reach yourself convergence with respect to the wfc cutoff, even if the 30/240 Ry suggested should be fine for C, O ultrasoft pseudopotentials. I strongly recommend that you use some kind of dispersion correction (semiempirical or ab-initio, flick through the PW.x manual). Dispersion forces are quite relevant in organic crystals. As for the computational cost, you may only try and see... HTH Giuseppe On Wednesday 02 May 2012 05:33:21 matt reish wrote: > Thanks for the reply, seemed to be going way too fast for what I had read I > that I should expect. Any thoughts on what would be more reasonable cutoffs > for wavefunction and density? Would it be reasonable to try to attain a > useable result on a "cluster" using 8 processors? > > Cheers, > > Matt > > On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer wrote: > > On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: > > > Hi PW list, > > > > > > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining > > > Raman phonon frequencies of a benzoic acid crystal. I attained the > > > > optimized > > > > > output geometry from a CASTEP calculation in the supplemental material > > > > of a > > > > > paper. This geometry was used by the authors to calculate accurate IR > > > > phonon > > > > > frequencies. I used a 'relax' calculation in Quantum Espresso on the > > > optimized geometry but this led to large shifts in the atomic positions > > > > in > > > > > the lattice and unreasonable structures for the molecules in the > > > lattice after finding the optimized structure. My question is does > > > anyone have a some experience calculating organic crystals in Quantum > > > Espresso that > > > > could > > > > > give me some tips? > > > > matt, > > > > you are using a *ridiculously* low wavefunction > > and density cutoff, that means your basis set > > is *far* too small. unphysical results are the > > logical consequence. > > > > axel. > > > > > Here is my input file minus the atomic posititions: > > > > > > &CONTROL > > > > > > title = 'benzacidscftest' , > > > > > > calculation = 'relax' , > > > > > > restart_mode = 'from_scratch' , > > > > > > outdir = '/home/mreish/tmp/' , > > > > > > pseudo_dir = '/usr/share/espresso/pseudo/' , > > > > > > prefix = 'batest5' , > > > > > > disk_io = 'default' , > > > > > > nstep = 600 , > > > > > > / > > > &SYSTEM > > > > > > ibrav = 12, > > > > > > A = 5.4996 , > > > B = 5.1283 , > > > C = 21.950 , > > > > > > cosAB = 0 , > > > cosAC = -.128276341 , > > > cosBC = 0 , > > > > > > nat = 60, > > > > > > ntyp = 3, > > > > > > ecutwfc = 5 , > > > ecutrho = 40 , > > > > > > / > > > &ELECTRONS > > > > > > electron_maxstep = 200, > > > > > > conv_thr = 1.0d-11 , > > > > > > / > > > &IONS > > > / > > > > > > ATOMIC_SPECIES > > > > > > C 12.01000 C.pbe-rrkjus.UPF > > > O 16.00000 O.pbe-rrkjus.UPF > > > H 1.00000 H.pbe-rrkjus.UPF > > > > > > ATOMIC_POSITIONS angstrom > > > > > > K_POINTS automatic > > > > > > 1 1 1 1 1 1 > > > > > > Cheers, > > > > > > Matthew Reish > > > University of Otago > > > Dunedin > > > New Zealand > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > Dr. Axel Kohlmeyer > > akohlmey at gmail.com http://goo.gl/1wk0 > > > > College of Science and Technology > > Temple University, Philadelphia PA, USA. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From azadi at uni-mainz.de Wed May 2 13:36:07 2012 From: azadi at uni-mainz.de (Sam Azadi) Date: Wed, 2 May 2012 12:36:07 +0100 Subject: [Pw_forum] KZK functional Message-ID: <4FA11C27.5050605@uni-mainz.de> Dear QE developers, Using 'KZK' functional as 'input_dft' with K_POINTS input format of: K_POINTS (crystal) n xk(1,1) xk(2,1) xk(3,1) wk(1) ... ... gives me following error: --------- from set_finite_size_volume : error # 1 volume is not positive, check omega and/or nk1,nk2,nk3 --------- while no problem with same input file but changing K_POINTS input format to: K_POINTS (automatic) nk1 nk2 nk3 0 0 0 any comments would be appreciated Yours Sam ******************************************** Sam Azadi Institute of Physical Chemistry and Center of Computational Science Johannes Gutenberg University Mainz Staudinger Weg 9 D-55128 Mainz, Germnay ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120502/eb60ea5b/attachment.htm From akohlmey at gmail.com Wed May 2 15:01:58 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 2 May 2012 09:01:58 -0400 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: On Tue, May 1, 2012 at 11:33 PM, matt reish wrote: matt, > Thanks for the reply, seemed to be going way too fast for what I had read I > that I should expect. Any thoughts on what would be more reasonable cutoffs > for wavefunction and density? Would it be reasonable to try to attain a > useable result on a "cluster" using 8 processors? it is not the computational resources that you should worry about, but the fact that you are trying to use a tool without knowing how its fundamental principles work. quantum espresso has great tutorials and there are several good textbooks and papers to work through. working with plane waves and pseudopotentials is not overly difficult, but using them without knowing what you are doing, is like waving around a loaded sawn-off shotgun. simulation software is brutal: it will often run smoothly and produce "numbers", even if you feed it complete nonsense. cheers, axel. > > Cheers, > > Matt > > > On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer wrote: >> >> On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: >> > Hi PW list, >> > >> > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining >> > Raman phonon frequencies of a benzoic acid crystal. I attained the >> > optimized >> > output geometry from a CASTEP calculation in the supplemental material >> > of a >> > paper. This geometry was used by the authors to calculate accurate IR >> > phonon >> > frequencies. I used a 'relax' calculation in Quantum Espresso on the >> > optimized geometry but this led to large shifts in the atomic positions >> > in >> > the lattice and unreasonable structures for the molecules in the lattice >> > after finding the optimized structure. My question is does anyone have a >> > some experience calculating organic crystals in Quantum Espresso that >> > could >> > give me some tips? >> >> >> matt, >> >> you are using a *ridiculously* low wavefunction >> and density cutoff, that means your basis set >> is *far* too small. unphysical results are the >> logical consequence. >> >> axel. >> >> >> > >> > Here is my input file minus the atomic posititions: >> > >> > &CONTROL >> > ?????????????????????? title = 'benzacidscftest' , >> > ???????????????? calculation = 'relax' , >> > ??????????????? restart_mode = 'from_scratch' , >> > ????????????????????? outdir = '/home/mreish/tmp/' , >> > ????????????????? pseudo_dir = '/usr/share/espresso/pseudo/' , >> > ????????????????????? prefix = 'batest5' , >> > ???????????????????? disk_io = 'default' , >> > ?????????????????????? nstep = 600 , >> > ?/ >> > ?&SYSTEM >> > ?????????????????????? ibrav = 12, >> > ?????????????????????????? A = 5.4996 , >> > ?????????????????????????? B = 5.1283 , >> > ?????????????????????????? C = 21.950 , >> > ?????????????????????? cosAB = 0 , >> > ?????????????????????? cosAC = -.128276341 , >> > ?????????????????????? cosBC = 0 , >> > ???????????????????????? nat = 60, >> > ??????????????????????? ntyp = 3, >> > ???????????????????? ecutwfc = 5 , >> > ???????????????????? ecutrho = 40 , >> > ?/ >> > ?&ELECTRONS >> > ??????????? electron_maxstep = 200, >> > ??????????????????? conv_thr = 1.0d-11 , >> > ?/ >> > ?&IONS >> > ?/ >> > ATOMIC_SPECIES >> > ??? C?? 12.01000? C.pbe-rrkjus.UPF >> > ??? O?? 16.00000? O.pbe-rrkjus.UPF >> > ??? H??? 1.00000? H.pbe-rrkjus.UPF >> > ATOMIC_POSITIONS angstrom >> > >> > K_POINTS automatic >> > ? 1 1 1?? 1 1 1 >> > >> > >> > Cheers, >> > >> > Matthew Reish >> > University of Otago >> > Dunedin >> > New Zealand >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer >> akohlmey at gmail.com ?http://goo.gl/1wk0 >> >> College of Science and Technology >> Temple University, Philadelphia PA, USA. > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From victormengwa at gmail.com Wed May 2 16:43:15 2012 From: victormengwa at gmail.com (Victor Meng'wa) Date: Wed, 2 May 2012 17:43:15 +0300 Subject: [Pw_forum] Job Termination and convergence Message-ID: Dear QE users, i've a relax calculation job that has run for two weeks ,it has done 21 iterations but has not given me the final coordinates despite convergence threshold having been achieved. it has 86 atoms.The input file looks like this. it's organic polymer attached on SnO2. &CONTROL restart_mode='restart', calculation='relax', outdir='./', pseudo_dir='/mnt/m09nfshdd03/applications/espresso-PP/', prefix = 'SnOru_exc1', tstress = .t., tprnfor = .t., etot_conv_thr = 1.d-5, forc_conv_thr = 1.d-4, verbosity = 'high' / &SYSTEM ibrav=6, celldm(1)= 53.7129, celldm(3)=0.2242, nat= 86, ntyp= 5, ecutwfc =30,ecutrho = 280, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.005 / &ELECTRONS diagonalization = 'david' mixing_mode = 'local-TF', mixing_beta = 0.3, conv_thr = 1.0e-8, / &IONS ion_dynamics= 'damp', / ATOMIC_SPECIES Sn 50.011 Sn.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF C 12.0107 C.pw91-van_ak.UPF S 32.0650 S.pw91-van_ak.UPF H 1.0008 H.pw91-van_ak.UPF ATOMIC_POSITIONS {bohr} Sn 8.952203138 8.952203138 0.000000000 Sn 8.952203138 8.952203138 6.021425723 Sn 17.90421730 8.952203138 0.000000000 Sn 17.90421730 8.952203138 6.021425723 Sn 13.42821022 4.476007083 3.010712862 Sn 13.42821022 4.476007083 9.032138585 Sn 8.952203138 17.90421730 0.000000000 Sn 8.952203138 17.90421730 6.021425723 Sn 17.90421730 17.90421730 0.000000000 Sn 17.90421730 17.90421730 6.021425723 Sn 4.476007083 13.42821022 3.010712862 Sn 13.42821022 13.42821022 3.010712862 Sn 22.38041336 13.42821022 3.010712862 Sn 4.47007083 13.42821022 9.032138585 Sn 13.42821022 13.42821022 9.032138585 Sn 22.38041336 13.42821022 9.032138585 Sn 13.42821022 22.38041336 3.010712862 Sn 13.42821022 22.38041336 9.032138585 O 11.70043294 11.70043294 0.000000000 O 11.70043294 11.70043294 6.021425723 O 10.67998042 7.224425854 3.010712862 O 7.224425854 10.67998042 3.010712862 O 7.224425854 10.67998042 9.032138585 O 10.67998042 7.224425854 9.032138585 O 20.65263607 11.70043294 0.000000000 O 15.15598751 6.203784367 0.000000000 O 20.65263607 11.70043294 6.021425723 O 15.15598751 6.203784367 6.021425723 O 16.17644002 10.67998042 3.010712862 O 16.17644002 10.67998042 9.032138585 O 11.70043294 20.65263607 0.000000000 O 6.203784367 15.15598751 0.000000000 O 11.70043294 20.65263607 6.021425723 O 6.203784367 15.15598751 6.021425723 O 15.15598751 15.15598751 0.000000000 O 15.15598751 15.15598751 6.021425723 O 10.67998042 16.17644002 3.010712862 O 19.63199459 16.17644002 3.010712862 O 10.67998042 16.17644002 9.032138585 O 16.17644002 19.63199459 3.010712862 O 16.17644002 19.63199459 9.032138585 O 19.63199459 16.17644002 9.032138585 Sn 8.952203138 8.952203138 12.04285145 Sn 17.90421730 8.952203138 12.04285145 Sn 8.952203138 17.90421730 12.04285145 Sn 17.90421730 17.90421730 12.04285145 O 11.70043294 11.70043294 12.04285145 O 20.65263607 11.70043294 12.04285145 O 15.15598751 6.203784367 12.04285145 O 11.70043294 20.65263607 12.04285145 O 6.203784367 15.15598751 12.04285145 O 15.15598751 15.15598751 12.04285145 C 26.78442185 30.42290198 7.97086797 C 26.14985156 27.6053192 8.328404296 C 23.32357604 27.45565283 7.651126183 C 22.86059296 24.61142491 8.056472598 C 20.04074251 24.2931949 7.411697787 C 20.26902152 21.70615881 8.021701623 C 17.46069841 21.25886046 7.403382989 C 29.17076895 31.77556848 8.942754504 C 28.9379546 34.83106787 8.105227551 C 25.14394994 32.38235978 6.578517207 C 30.71259711 36.81206855 8.880771462 C 22.56863016 32.81000497 5.292558067 S 25.97032751 35.63741432 6.607996946 H 27.79750443 29.96067478 6.12668351 H 26.46468006 27.01742517 10.37686823 H 27.37344972 26.42064942 7.009185962 H 22.99306281 28.00575233 5.594725394 H 22.19862163 28.72498238 8.979604178 H 23.2290897 24.07341967 10.10984982 H 24.13842627 23.48117927 6.740844746 H 19.62670335 24.6184169 5.322793697 H 18.86287575 25.55931191 8.696523092 H 20.70498151 21.39492079 10.10833804 H 21.73658341 20.79209792 6.736309401 H 29.27999516 31.61267402 11.08797246 H 30.93747461 30.92027809 8.054582871 H 29.93516347 34.51208197 6.222492663 H 26.14229265 32.03861846 4.700695608 H 31.57865894 37.72480666 7.132207182 H 32.27370048 35.94581775 10.08660618 H 29.66549945 38.30589765 10.02670184 H 21.32840241 31.07126727 5.573182508 H 22.86550625 33.14788814 3.185701571 H 21.60600328 34.52757773 6.16674572 K_POINTS {automatic} 2 2 3 0 0 0 plz try to examine this input file and single out some parameters that are making this calcuation not to converge ,so that i can make corrections? is there a particular way in QE that you can terminate a job without necessarily killing it and provide the required output,in this case final coordinates since i feel convergence threshold has been achieved but it continues to run and whatever coordinates i get may be relaxed? cheers -- VICTOR KIRUI MENG'WA, POST GRADUATE STUDENT, CHEPKOILEL UNIVERSITY COLLEGE, DEPARTMENT OF PHYSICS, COMPUTATIONAL PHYSICS GROUP, P.O BOX 1125, ELDORET, KENYA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120502/70478d27/attachment-0001.htm From sbinnie at sissa.it Wed May 2 16:49:19 2012 From: sbinnie at sissa.it (Simon Binnie) Date: Wed, 02 May 2012 16:49:19 +0200 Subject: [Pw_forum] Job Termination and convergence In-Reply-To: References: Message-ID: On Wed, 02 May 2012 16:43:15 +0200, Victor Meng'wa wrote: >is there a particular way in QE that you can terminate a job without > necessarily killing it and provide the required output The max_seconds keyword allows you to have the job gracefully exit after a preset amount of time has elapsed. Also from what I understand you can force the job to end by creating a file prefix.EXIT in the outdir (where prefix is the job prefix you've set in the pwscf input file). Brgrds, Simon -- Simon Binnie | Post Doc, Condensed Matter Sector Scuola Internazionale di Studi Avanzati (SISSA) Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it From giannozz at democritos.it Wed May 2 17:02:52 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 2 May 2012 17:02:52 +0200 Subject: [Pw_forum] KZK functional In-Reply-To: <4FA11C27.5050605@uni-mainz.de> References: <4FA11C27.5050605@uni-mainz.de> Message-ID: <656B29D0-0750-4AFC-956C-99BA13BEF8B3@democritos.it> On May 2, 2012, at 13:36 , Sam Azadi wrote: > Using 'KZK' functional as 'input_dft' with K_POINTS input format of: > > K_POINTS (crystal) > n > xk(1,1) xk(2,1) xk(3,1) wk(1) > [...] gives me following error: > --------- > from set_finite_size_volume : error # 1 > volume is not positive, check omega and/or nk1,nk2,nk3 "grep set_finite_size_volume PW/*.f90" (or PW/src/*f90 in the SVN version) and you will understand. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From reishme04 at gmail.com Wed May 2 23:59:20 2012 From: reishme04 at gmail.com (matt reish) Date: Thu, 3 May 2012 09:59:20 +1200 Subject: [Pw_forum] benzoic acid structure optimization In-Reply-To: References: Message-ID: Axel, Thanks for the advice. I take your point and agree that my results would be much more meaningful with a better knowledge base. Hopefully I won't have any more questions until I can ask one worth asking. My initial goal was to see whether finding Raman phonon intensities on a system this size was feasible with the resources I have available and I think I've answered that question. It's definitely a testament to the software that a spectroscopist with no plane-wave experience could get the software "working" in just 3 days. I guess with ease comes black-box users. Thanks for your help, Matt On Thu, May 3, 2012 at 1:01 AM, Axel Kohlmeyer wrote: > On Tue, May 1, 2012 at 11:33 PM, matt reish wrote: > > matt, > > > Thanks for the reply, seemed to be going way too fast for what I had > read I > > that I should expect. Any thoughts on what would be more reasonable > cutoffs > > for wavefunction and density? Would it be reasonable to try to attain a > > useable result on a "cluster" using 8 processors? > > it is not the computational resources that you should worry about, > but the fact that you are trying to use a tool without knowing how > its fundamental principles work. quantum espresso has great > tutorials and there are several good textbooks and papers > to work through. working with plane waves and pseudopotentials > is not overly difficult, but using them without knowing what you > are doing, is like waving around a loaded sawn-off shotgun. > > simulation software is brutal: it will often run smoothly and > produce "numbers", even if you feed it complete nonsense. > > cheers, > axel. > > > > > Cheers, > > > > Matt > > > > > > On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer > wrote: > >> > >> On Tue, May 1, 2012 at 10:53 PM, matt reish > wrote: > >> > Hi PW list, > >> > > >> > I am working with Quantum Espresso (v4.3.2.1) in the hopes of > attaining > >> > Raman phonon frequencies of a benzoic acid crystal. I attained the > >> > optimized > >> > output geometry from a CASTEP calculation in the supplemental material > >> > of a > >> > paper. This geometry was used by the authors to calculate accurate IR > >> > phonon > >> > frequencies. I used a 'relax' calculation in Quantum Espresso on the > >> > optimized geometry but this led to large shifts in the atomic > positions > >> > in > >> > the lattice and unreasonable structures for the molecules in the > lattice > >> > after finding the optimized structure. My question is does anyone > have a > >> > some experience calculating organic crystals in Quantum Espresso that > >> > could > >> > give me some tips? > >> > >> > >> matt, > >> > >> you are using a *ridiculously* low wavefunction > >> and density cutoff, that means your basis set > >> is *far* too small. unphysical results are the > >> logical consequence. > >> > >> axel. > >> > >> > >> > > >> > Here is my input file minus the atomic posititions: > >> > > >> > &CONTROL > >> > title = 'benzacidscftest' , > >> > calculation = 'relax' , > >> > restart_mode = 'from_scratch' , > >> > outdir = '/home/mreish/tmp/' , > >> > pseudo_dir = '/usr/share/espresso/pseudo/' , > >> > prefix = 'batest5' , > >> > disk_io = 'default' , > >> > nstep = 600 , > >> > / > >> > &SYSTEM > >> > ibrav = 12, > >> > A = 5.4996 , > >> > B = 5.1283 , > >> > C = 21.950 , > >> > cosAB = 0 , > >> > cosAC = -.128276341 , > >> > cosBC = 0 , > >> > nat = 60, > >> > ntyp = 3, > >> > ecutwfc = 5 , > >> > ecutrho = 40 , > >> > / > >> > &ELECTRONS > >> > electron_maxstep = 200, > >> > conv_thr = 1.0d-11 , > >> > / > >> > &IONS > >> > / > >> > ATOMIC_SPECIES > >> > C 12.01000 C.pbe-rrkjus.UPF > >> > O 16.00000 O.pbe-rrkjus.UPF > >> > H 1.00000 H.pbe-rrkjus.UPF > >> > ATOMIC_POSITIONS angstrom > >> > > >> > K_POINTS automatic > >> > 1 1 1 1 1 1 > >> > > >> > > >> > Cheers, > >> > > >> > Matthew Reish > >> > University of Otago > >> > Dunedin > >> > New Zealand > >> > > >> > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > >> > >> > >> -- > >> Dr. Axel Kohlmeyer > >> akohlmey at gmail.com http://goo.gl/1wk0 > >> > >> College of Science and Technology > >> Temple University, Philadelphia PA, USA. > > > > > > > > -- > Dr. Axel Kohlmeyer > akohlmey at gmail.com http://goo.gl/1wk0 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120503/40e7414c/attachment.htm From divyasrivastava at jncasr.ac.in Thu May 3 13:28:41 2012 From: divyasrivastava at jncasr.ac.in (Divya Srivastava) Date: Thu, 03 May 2012 16:58:41 +0530 Subject: [Pw_forum] nk1,nk2,nk3 selection rule for HCP Message-ID: <1336044521.4fa26be9e886f@mercury.jncasr.ac.in> Dear QE Developers/Users I have used K_POINTS (automatic) 18 18 18 0 0 0 for HCP (hexagonal close packed) lattice in scf calculation. My lattice parameters are a= 4.0 a. u. and c/a = 1.59. I would like to know whether I can use nk1=nk2=nk3 for the HCP lattice or not. If not what is the criteria for choosing them in case of non cubic (HCP) lattices. Sincerely, Sincerely, Dr. Divya Srivastava Research Associate TSU, JNCASR Jakkur, Bangalore-64 Tel: +9122082834 From degironc at sissa.it Thu May 3 22:30:00 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 03 May 2012 22:30:00 +0200 Subject: [Pw_forum] nk1,nk2,nk3 selection rule for HCP In-Reply-To: <1336044521.4fa26be9e886f@mercury.jncasr.ac.in> References: <1336044521.4fa26be9e886f@mercury.jncasr.ac.in> Message-ID: <4FA2EAC8.80406@sissa.it> without additional knowledge of the electronic structure of the system I think a reasonable criterion is that the density of points in all directions is more or less the same. so I would say that in an hcp with c/a ~ 1.6 a more balanced grid could have been 18 18 12 (~18/1.6) 0 0 0. but how many points are needed depends on the dispersion of the band structure in the different directions. If on a given direction the band structure varies strongly and in another it is almost flat It is likely you'll need many more k-points in the former direction than in the latter. The golden rule is as usual to check convergence in your particular case and if the behavior of your convergence test does not agree with your expectation think which of the assumptions you based your expectation on does not apply. hope this helps, regards, stefano On 05/03/2012 01:28 PM, Divya Srivastava wrote: > Dear QE Developers/Users > > I have used K_POINTS (automatic) 18 18 18 0 0 0 for HCP (hexagonal close packed) lattice in scf calculation. My lattice parameters are a= 4.0 a. u. and c/a = 1.59. I would like to know whether I can use nk1=nk2=nk3 for the HCP lattice or not. If not what is the criteria for choosing them in case of non cubic (HCP) lattices. > > Sincerely, > Sincerely, > > Dr. Divya Srivastava > Research Associate > TSU, JNCASR > Jakkur, Bangalore-64 > > Tel: +9122082834 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giuseppe.mattioli at ism.cnr.it Thu May 3 22:46:03 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 3 May 2012 22:46:03 +0200 Subject: [Pw_forum] PAW pseudopotential with gipaw reconstruction Message-ID: <20120503224603.0rsz0vfj4kwow48s@webmail.sic.rm.cnr.it> Dear all I've generated a PAW pseudopotential with gipaw reconstruction, by following the template found in pslibrary.0.2.4. This is my PP &input title='C', prefix='C_paw_gipaw' zed=6, rel=0, config='1s2 2s2 2p2 3d-2', iswitch=3, dft='PBE' / &inputp upf_v1_format=.true., lpaw=.true., pseudotype=3, file_pseudopw='C.PBE-n-kjpaw-gipaw.UPF', author='GM following psl-0.2.4', lloc=2, which_augfun ='BESSEL', rmatch_augfun=1.1, nlcc=.true., new_core_ps=.true., rcore=0.8, tm=.true. lgipaw_reconstruction=.true., / 5 2S 1 0 2.00 0.00 1.00 1.30 0.0 2S 1 0 0.00 0.05 1.00 1.30 0.0 2P 2 1 2.00 0.00 1.00 1.45 0.0 2P 2 1 0.00 0.05 1.00 1.45 0.0 3D 3 2 -2.00 0.10 1.10 1.10 0.0 &test / 3 2S 1 0 2.00 0.00 1.00 1.30 0.0 2P 2 1 2.00 0.00 1.00 1.45 0.0 3D 3 2 -2.00 0.10 1.10 1.10 0.0 pw.x (QE 4.3.2) does not like the above PP... It stops complaining %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_pseudo_nl : error # 3 Reading pseudo file (QIJ) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... If I drop the following line from the input file (not suggested by the XSPECTRA manual...) upf_v1_format=.true., then pw.x crashes silently, and my cluster complains # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=-1) # ERROR IN: iotk_scan_begin (iotk_scan.f90:182) # CVS Revision: 1.23 # Tag not found namel=PP_GIPAW_ORBITALS Did I mess up with some of the properties of PAW PPs? You could say: why don't you try good old rrkjus PPs? I've tried this one &input title='C half1s', prefix='C-gipaw-1shalf', zed=6, rel=0, config='1s1.5 2s2 2p2 3d-2', iswitch=3, dft='PBE' / &inputp upf_v1_format=.true., pseudotype=3, file_pseudopw='C.pbe-n-rrkjus-half1s-gipaw.UPF', zval=4.5, author='GM', lloc=2, which_augfun ='PSQ', rmatch_augfun=0.9, nlcc=.true., new_core_ps=.true., rcore=0.8, tm=.true. lgipaw_reconstruction=.true., / 5 2S 1 0 2.00 0.00 1.00 1.30 0.0 2S 1 0 0.00 0.05 1.00 1.30 0.0 2P 2 1 2.00 0.00 1.00 1.45 0.0 2P 2 1 0.00 0.05 1.00 1.45 0.0 3D 3 2 -2.00 0.10 1.10 1.10 0.0 &test / 3 2S 1 0 2.00 0.00 1.00 1.30 0.0 2P 2 1 2.00 0.00 1.00 1.45 0.0 3D 3 2 -2.00 0.10 1.10 1.10 0.0 It contains half-core hole, which I need for XSPECTRA purposes, but it is roughly the same PP. The problem is that it is very hard to achieve convergence by using this one. Sometimes pw.x converges rather smoothly, sometimes diagonalization goes bananas (both cg and david, both with very tiny wfc mixing). I could suspect a ghost state, but I'm not able to deal with half-core ghosts... So I was looking for something different. Sorry for the long tale and thanks in advance for advice Giuseppe Giuseppe Mattioli ISM-CNR Italy From iyad.ne at gmail.com Thu May 3 23:18:18 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Thu, 3 May 2012 17:18:18 -0400 Subject: [Pw_forum] Polarization vectors and force constants file format Message-ID: Hello, I have few questions, It would be kind of you could answer: 1- How can I get the polarization vector correspond to each eigenvalue( phonon frequency). I know when I run ph.x for each q-vector, I get the phonon frequencies and the corresponding polarization vectors for each atom. But I want the polarization vectors also when I run matdyn.x, because I am calculating the frequencies for a large number of q-vectors ans it is not practical to run ph.x for a large mesh of q-vectors. 2- Anyone could explain to me the format of the force constants file *.fc Thank you very much. _______________________________ IYAD I. AL-QASIR, PhD Research Associate ORNL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120503/bd9edbea/attachment.htm From kirtinandan07 at gmail.com Fri May 4 06:21:54 2012 From: kirtinandan07 at gmail.com (vicky singh) Date: Fri, 4 May 2012 09:51:54 +0530 Subject: [Pw_forum] chemical potential of an element Message-ID: Dear all, I am calculating the substitutional formation energy of Ni- based system to study the partitioning behavior of the alloying elements. this just means that i need to find the preferential position of alloying element within the system based on the minimizing the total energy of the system. there i need to calculate the chemical potential of elements such as Ni, Al, W etc. can any body suggest how to calculate it or is it the same as energy per atom of the bulk structure. Also if i am studying FCC system then, for e.g. W, do i need to calculate the energy for stable BCC W or i should do calculation for FCC W. regards vicky singh Research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/c6663c15/attachment.htm From zdw2000 at gmail.com Fri May 4 08:13:21 2012 From: zdw2000 at gmail.com (Wei Zhou) Date: Fri, 4 May 2012 14:13:21 +0800 Subject: [Pw_forum] How can I get the Tc Hopfield parameter and the average of the squared phonon frequencies. Message-ID: When We anlaysi the Tc results ,we need the relatived parameteres about Hopfield parameter and the average of the squared phonon frequencies, is there a program which can extract the above paprameters from PWSCF during the electron-phonon coulping calculations? -- Any help will be appreciated ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/2635c289/attachment.htm From renpj at dicp.ac.cn Fri May 4 10:21:02 2012 From: renpj at dicp.ac.cn (PJ Ren) Date: Fri, 04 May 2012 16:21:02 +0800 Subject: [Pw_forum] V_tot potential curve of vdw-DF is not smooth away from nuclei Message-ID: <4FA3916E.5010508@dicp.ac.cn> Dear all, I have drawn the V_tot potential curve of vdw-DF and found that it is not smooth away from nuclei as expect. I also test LDA and PBE functional with same psudo potential and same parameters, no such phenomenon was found. I don't know whether it is a problem of vdw-DF or the method implemented in QE? The picture is attached which is V_tot and V_bare curve for carbon nanotube. Thanks. Pengju Ren -------------- next part -------------- A non-text attachment was scrubbed... Name: plot.png Type: image/png Size: 36487 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120504/ae4dc713/attachment-0001.png From giuseppe.mattioli at ism.cnr.it Fri May 4 14:11:29 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 4 May 2012 14:11:29 +0200 Subject: [Pw_forum] PAW pseudopotential with gipaw reconstruction In-Reply-To: References: <20120503225321.Horde.92ccIx8V4mxPovBBPsuHw7A@webmail.sissa.it> Message-ID: <201205041411.29621.giuseppe.mattioli@ism.cnr.it> Ciao Emine It is working fine, both with pw.x and xspectra.x Thank you very much Giuseppe On Thursday 03 May 2012 22:59:39 Kucukbenli Emine wrote: > Hello Giuseppe, > To make a paw pseudo with gipaw > add the following to the &inputp card: > > lgipaw_reconstruction=.true. > use_paw_as_gipaw=.true. > > and that should be all, > please let me know if it is not working for you. > > ciao > emine kucukbenli, postdoc, epfl, switzerland -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giuseppe.mattioli at ism.cnr.it Fri May 4 15:16:52 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 4 May 2012 15:16:52 +0200 Subject: [Pw_forum] PAW pseudopotential with gipaw reconstruction In-Reply-To: <201205041411.29621.giuseppe.mattioli@ism.cnr.it> References: <20120503225321.Horde.92ccIx8V4mxPovBBPsuHw7A@webmail.sissa.it> <201205041411.29621.giuseppe.mattioli@ism.cnr.it> Message-ID: <201205041516.52956.giuseppe.mattioli@ism.cnr.it> > It is working fine, both with pw.x and xspectra.x Not exactly... pw.x works fine, xspectra works fine till the lanczos chain is finished, but it is not able to calculate the spectrum. It says something very strange... Estimated error at iter 2350 is 2.773650816161815E-003 Estimated error at iter 2400 is 7.339432110204557E-003 Estimated error at iter 2450 is 3.915220430921537E-003 Estimated error at iter 2500 is 1.759769462142735E-003 Estimated error at iter 2550 is 1.609732607968768E-003 Estimated error at iter 2600 is 2.963442071041433E-003 Estimated error at iter 2650 is 3.196232925421465E-003 Estimated error at iter 2700 is 2.704414998145615E-003 Estimated error at iter 2750 is 2.510644989742356E-003 Estimated error at iter 2800 is 1.927644198666715E-003 Estimated error at iter 2850 is 2.702595324285325E-003 Estimated error at iter 2900 is 1.766250501508676E-003 CONVERGED at iter 2950 with error= 7.723753097511076E-004 Could not find the element C in the table of K edge energies! I've never seen that when using carbon NC or US gipaw PPs. Yours Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From pchen at ion.chem.utk.edu Fri May 4 15:31:48 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Fri, 4 May 2012 09:31:48 -0400 Subject: [Pw_forum] Conversion from conventional to primitive cell Message-ID: Dear All, Is there any tools (free) to convert a conventional unit cell to a primitive cell? Recently, I tried to convert atom positions from a face centered orthorhombic unit cell (space group cmca, basis vectors: a,b,c) to its primitive cell. I used basis vectors: 1/2(a,0,c), 1/2(a,b,0),1/2(0,b,c). But it looks they are not the correct ones because the chemical formula in this unit cell is not the same as that in conventional unit cell. -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/f7dda282/attachment.htm From fratesi at mater.unimib.it Fri May 4 15:51:50 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 04 May 2012 15:51:50 +0200 Subject: [Pw_forum] PAW pseudopotential with gipaw reconstruction In-Reply-To: <201205041516.52956.giuseppe.mattioli@ism.cnr.it> References: <20120503225321.Horde.92ccIx8V4mxPovBBPsuHw7A@webmail.sissa.it> <201205041411.29621.giuseppe.mattioli@ism.cnr.it> <201205041516.52956.giuseppe.mattioli@ism.cnr.it> Message-ID: <4FA3DEF6.8050108@mater.unimib.it> I found that error as well, when trying to play with a half core pseudopotential only few days ago. It depends on the way the element name is written in the UPF file: element=" C" rather than element="C " in the PP_HEADER section. Then the specific routine misses the core element. It seems that we are working towards similar goals... maybe we should get in touch. Let me write you privately as well. Best, Guido Fratesi On 05/04/2012 03:16 PM, Giuseppe Mattioli wrote: > >> It is working fine, both with pw.x and xspectra.x > > Not exactly... pw.x works fine, xspectra works fine till the lanczos chain is finished, but it is not > able to calculate the spectrum. It says something very strange... > > Estimated error at iter 2350 is 2.773650816161815E-003 > Estimated error at iter 2400 is 7.339432110204557E-003 > Estimated error at iter 2450 is 3.915220430921537E-003 > Estimated error at iter 2500 is 1.759769462142735E-003 > Estimated error at iter 2550 is 1.609732607968768E-003 > Estimated error at iter 2600 is 2.963442071041433E-003 > Estimated error at iter 2650 is 3.196232925421465E-003 > Estimated error at iter 2700 is 2.704414998145615E-003 > Estimated error at iter 2750 is 2.510644989742356E-003 > Estimated error at iter 2800 is 1.927644198666715E-003 > Estimated error at iter 2850 is 2.702595324285325E-003 > Estimated error at iter 2900 is 1.766250501508676E-003 > CONVERGED at iter 2950 with error= 7.723753097511076E-004 > Could not find the element C in the table of K edge energies! > > I've never seen that when using carbon NC or US gipaw PPs. > > Yours > > Giuseppe > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy Phone: +39 02 6448 5183 email: fratesi at mater.unimib.it From flux_ray12 at 163.com Fri May 4 15:41:44 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 4 May 2012 21:41:44 +0800 (CST) Subject: [Pw_forum] Conversion from conventional to primitive cell In-Reply-To: References: Message-ID: <5f729017.28f6a.1371815b464.Coremail.flux_ray12$163.com> How about trying the spacegroup code in Exciting or ELK package? At 2012-05-04 21:31:48,"Peng Chen" wrote: Dear All, Is there any tools (free) to convert a conventional unit cell to a primitive cell? Recently, I tried to convert atom positions from a face centered orthorhombic unit cell (space group cmca, basis vectors: a,b,c) to its primitive cell. I used basis vectors: 1/2(a,0,c), 1/2(a,b,0),1/2(0,b,c). But it looks they are not the correct ones because the chemical formula in this unit cell is not the same as that in conventional unit cell. -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/204bfc82/attachment.htm From giuseppe.mattioli at ism.cnr.it Fri May 4 17:05:45 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 4 May 2012 17:05:45 +0200 Subject: [Pw_forum] PAW pseudopotential with gipaw reconstruction Message-ID: <201205041705.45485.giuseppe.mattioli@ism.cnr.it> Dear Emine and Guido The problem is solved. The fix proposed by Guido works. Thanks G. On Friday 04 May 2012 16:04:12 you wrote: > Hi Guiseppe > I have no idea of the situation of xspectra with PAW pseudos. > perhaps someone involved in its development can tell more, or suggest a > quick fix. > > The recipe that I have given is valid for GIPAW , and pw of course. > ciao > emine > ________________________________________ > From: Giuseppe Mattioli [giuseppe.mattioli at ism.cnr.it] > Sent: Friday, May 04, 2012 3:16 PM > To: pw_forum at pwscf.org > Cc: Kucukbenli Emine > Subject: Re: [Pw_forum] PAW pseudopotential with gipaw reconstruction > > > It is working fine, both with pw.x and xspectra.x > > Not exactly... pw.x works fine, xspectra works fine till the lanczos chain > is finished, but it is not able to calculate the spectrum. It says > something very strange... > > Estimated error at iter 2350 is 2.773650816161815E-003 > Estimated error at iter 2400 is 7.339432110204557E-003 > Estimated error at iter 2450 is 3.915220430921537E-003 > Estimated error at iter 2500 is 1.759769462142735E-003 > Estimated error at iter 2550 is 1.609732607968768E-003 > Estimated error at iter 2600 is 2.963442071041433E-003 > Estimated error at iter 2650 is 3.196232925421465E-003 > Estimated error at iter 2700 is 2.704414998145615E-003 > Estimated error at iter 2750 is 2.510644989742356E-003 > Estimated error at iter 2800 is 1.927644198666715E-003 > Estimated error at iter 2850 is 2.702595324285325E-003 > Estimated error at iter 2900 is 1.766250501508676E-003 > CONVERGED at iter 2950 with error= 7.723753097511076E-004 > Could not find the element C in the table of K edge energies! > > I've never seen that when using carbon NC or US gipaw PPs. > > Yours > > Giuseppe > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From himanshu at iopb.res.in Fri May 4 17:34:41 2012 From: himanshu at iopb.res.in (himanshu at iopb.res.in) Date: Fri, 4 May 2012 21:04:41 +0530 Subject: [Pw_forum] regarding weight factor Message-ID: Respected QE users, Dos calculation with manual k grid which is dense at the point around, where energy band crosses the fermi level, I am confuse about the weight factor. Can I choose weight factor which is generated by the automatic k grid operation. I want to get better value of fermi energy . The value I got from automatic k grid operation is not giving good result in band structure calculation. HIMANSHU LOHANI Doctoral Scholar I.O.P Bhubaneswer From iyad.ne at gmail.com Fri May 4 23:26:24 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Fri, 4 May 2012 17:26:24 -0400 Subject: [Pw_forum] Force constants Message-ID: Dear All, I am trying to understand the format of the force constant file (*.fc) generated by running the executable q2r.x I hope someone could answer (or comment on) my questions below. Below is the part of q2r.f90 that prints force constants to *.fc DO j1=1,3 DO j2=1,3 DO na1=1,nat DO na2=1,nat WRITE (2,'(4i4)') j1,j2,na1,na2 nn=0 DO m3=1,nr3 DO m2=1,nr2 DO m1=1,nr1 nn=nn+1 WRITE (2,'(3i4,2x,1pe18.11)') & m1,m2,m3, DBLE(phid(nn,j1,j2,na1,na2)) ! why nn not END DO END DO END DO END DO END DO END DO END DO Here are my notes and questions: 1- j1 and j2 stands for x, y, and z directions? 2- m1, m2, and m3 represents the integers for the position vector of a given unitcell? 3- Why in phid(nn, j1,j2,na1, na2) m1, m2 and m3 are mapped into nn? Where nn=m1*m2*m3 4- How can I build from the *.fc file a square force constants matrix where each element is 3x3. That is, to build the conventional matrix we see in text books? Thank you very much, IYAD Al-Qasir X-ray and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division ORNL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/074a9c57/attachment-0001.htm From pchen at ion.chem.utk.edu Sat May 5 00:12:45 2012 From: pchen at ion.chem.utk.edu (Peng Chen) Date: Fri, 4 May 2012 18:12:45 -0400 Subject: [Pw_forum] Conversion from conventional to primitive cell In-Reply-To: <4fa3e033.c168b40a.70ef.fffff39bSMTPIN_ADDED@mx.google.com> References: <4fa3e033.c168b40a.70ef.fffff39bSMTPIN_ADDED@mx.google.com> Message-ID: Hi Zhe, I tried Exciting. I used attribute primcell =true, but nothing happened. The result structure is still conventional unit cell in the geometry.OUT.xml. The input.xml is attached. On Fri, May 4, 2012 at 9:41 AM, GAO Zhe wrote: > How about trying the spacegroup code in Exciting or ELK package? > > > > At 2012-05-04 21:31:48,"Peng Chen" wrote: > > Dear All, > > Is there any tools (free) to convert a conventional unit cell to a > primitive cell? > > Recently, I tried to convert atom positions from a face centered > orthorhombic unit cell (space group cmca, basis vectors: a,b,c) > to its primitive cell. I used basis vectors: 1/2(a,0,c), > 1/2(a,b,0),1/2(0,b,c). But it looks they are not the correct ones because > the > chemical formula in this unit cell is not the same as that in conventional > unit cell. > > > -- > Best Regards. > Peng > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/15aad0db/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: input.xml Type: text/xml Size: 41100 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120504/15aad0db/attachment-0001.bin From dhruv.singh at gmail.com Sat May 5 00:24:36 2012 From: dhruv.singh at gmail.com (Dhruv Singh) Date: Fri, 4 May 2012 15:24:36 -0700 Subject: [Pw_forum] Force constants In-Reply-To: References: Message-ID: Please check this http://www.democritos.it/pipermail/pw_forum/2005-April/002408.html On Fri, May 4, 2012 at 2:26 PM, Iyad AL-QASIR wrote: > Dear All, > I am trying to understand the format of the force constant file (*.fc) > generated by running the executable q2r.x > > I hope someone could answer (or comment on) my questions below. > > Below is the part of q2r.f90 that prints force constants to *.fc > > ?DO j1=1,3 > ??????? DO j2=1,3 > ?????????? DO na1=1,nat > ????????????? DO na2=1,nat > ???????????????? WRITE (2,'(4i4)') j1,j2,na1,na2 > ???????????????? nn=0 > ???????????????? DO m3=1,nr3 > ??????????????????? DO m2=1,nr2 > ?????????????????????? DO m1=1,nr1 > ????????????????????????? nn=nn+1 > ????????????????????????? WRITE (2,'(3i4,2x,1pe18.11)')?? & > ?????????????????????????????? m1,m2,m3, > DBLE(phid(nn,j1,j2,na1,na2))???????????? ! why nn not > ?????????????????????? END DO > ??????????????????? END DO > ???????????????? END DO > ????????????? END DO > ?????????? END DO > ??????? END DO > ???? END DO > > Here are my notes and questions: > 1- j1 and j2 stands for x, y, and z directions? > 2- m1, m2, and m3 represents the integers for the position vector of a given > unitcell? > 3- Why in phid(nn, j1,j2,na1, na2) m1, m2 and m3 are mapped into nn? Where > nn=m1*m2*m3 > 4- How can I build from the? *.fc file a square force constants matrix where > each element is 3x3. That is, to build the conventional matrix we see in > text books? > > Thank you very much, > IYAD Al-Qasir > > X-ray and Neutron Scattering and Spectroscopy Group > Materials Science and Technology Division > ORNL > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dhruv From somayehfotohi at yahoo.com Sat May 5 06:27:57 2012 From: somayehfotohi at yahoo.com (somayeh fotohi) Date: Fri, 4 May 2012 21:27:57 -0700 (PDT) Subject: [Pw_forum] band structur In-Reply-To: Message-ID: <1336192077.97005.YahooMailClassic@web161402.mail.bf1.yahoo.com> Dear ?QE users, ? ? ? ? ? ? ? i calculate band structure??but i have many spike in E-K plot.?I appreciate if any one helpe me?for these spike? another question is, how can show?the band with different color ?do i change the input of band? ? somayeh fotoohi ? _______________________________________________ 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/20120504/ddaeb1e8/attachment.htm From mourad_fsm at yahoo.fr Sat May 5 11:23:10 2012 From: mourad_fsm at yahoo.fr (debbichi mourad) Date: Sat, 5 May 2012 10:23:10 +0100 (BST) Subject: [Pw_forum] HSE&PBE0 problem Message-ID: <1336209790.78739.YahooMailNeo@web29505.mail.ird.yahoo.com> Dear pwscf users, I performed some calculations by using PBE0 and HSE on the ZnO system. When I used a supercell with 4 atoms , I obtained a Fermi levels comparable to those calculate without hybrid functional (Ef= 7.68 eV) . ?Almost, the same result is obtained for a supercell with 16 atoms. But (for a supercell with 16 atoms) with PBE0 and HSE Ef becomes large (Ef~28,258 eV). Why such a problem occurs? Thanks a lot in advance Mourad ? DEBBICHI Mourad Unit? de Recherche Physique des Solides,99/UR/13-19, D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. t?l:+21697487042 mourad_fsm at yahoo.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120505/38d27371/attachment.htm From abmus007 at gmail.com Sat May 5 13:13:59 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Sat, 5 May 2012 12:13:59 +0100 Subject: [Pw_forum] QHA compilation Message-ID: Dear QE User, Pls l try to compile QHA on my laptop Intel pentium and am getting the following error: * need your assistance to be able to compile QHA suce*ssfully Thanks in anticipation of your favourable reply, ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [tetra] Error 1 ifort -O3 -c Debye.f90 ifort -O3 -c Debye_T.f ifort -O3 -c debye3.f ifort -O3 -c cheval.f ifort -O3 -c d1mach.f ifort -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [Debye_x] Error 1 ifort -FR -c Mean_square_displacement.f90 ifort -static -o Mean_square_displacement.x Mean_square_displacement.o ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [MSD] Error 1 Musari Abolore A Federal University of Agriculture Abeokuta Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120505/43c2ea3e/attachment.htm From vasudev.tcr at gmail.com Sun May 6 06:01:45 2012 From: vasudev.tcr at gmail.com (vasudevan m.v) Date: Sun, 6 May 2012 09:31:45 +0530 Subject: [Pw_forum] Work function calculation Message-ID: Dear all I was trying to calculate work function of * Au(111)* surface using Quantum Espresso 4.2.1. I used a 9 layer slab along with 22? vacuum. I first did a relax calculation and then post processing to extract potential (sum of Coulomb potential and Hartree part ) . Then took the planar average of this potential. I got a strange graph which I have attached with this mail. ** 1 Why shape of graph is coming like this ? 2 What is the need of excluding exchange correlation potential in calculating Work function ? I changed the pseudo potential and obtained same pattern of graph. Any help will be much appreciated. Vasudevan M V JNCASR Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120506/d1a9059e/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Graph.pdf Type: application/pdf Size: 3758 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120506/d1a9059e/attachment.pdf From bdslipun at gmail.com Sun May 6 08:19:42 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 6 May 2012 11:49:42 +0530 Subject: [Pw_forum] smearing and electronic temperture Message-ID: i want to find the dispersion curve at 300k how can be done because i have seen some paper related the value of electronic tempe. by using fermi dirac smearing is it possible in quantum espresso how can this be done? is there any physics of electronic temp and smearing value this is beacause many unstable phonon modes become stable by incrising smearing value what should be the calibaration of temp. and smearing in espresso suggetions highly thankful sahoo b reserch scholar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120506/01800eac/attachment.htm From abmus007 at gmail.com Sun May 6 09:29:35 2012 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 6 May 2012 08:29:35 +0100 Subject: [Pw_forum] QHA compilation In-Reply-To: References: Message-ID: Dear QE User, Pls l try to compile QHA on my laptop Intel pentium and am getting the following error: * need your assistance to be able to compile QHA suce*ssfully Thanks in anticipation of your favourable reply, ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [tetra] Error 1 ifort -O3 -c Debye.f90 ifort -O3 -c Debye_T.f ifort -O3 -c debye3.f ifort -O3 -c cheval.f ifort -O3 -c d1mach.f ifort -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [Debye_x] Error 1 ifort -FR -c Mean_square_displacement.f90 ifort -static -o Mean_square_displacement.x Mean_square_displacement.o ld: cannot find -lm ld: cannot find -lc ld: cannot find -ldl ld: cannot find -lc make: *** [MSD] Error 1 Musari Abolore A Federal University of Agriculture Abeokuta Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120506/7b018ee3/attachment.htm From baroni at sissa.it Sun May 6 12:08:30 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 6 May 2012 12:08:30 +0200 Subject: [Pw_forum] Work function calculation In-Reply-To: References: Message-ID: On May 6, 2012, at 6:01 AM, vasudevan m.v wrote: > Dear all > I was trying to calculate work function of Au(111) surface using Quantum Espresso 4.2.1. I used a 9 layer slab along with 22? vacuum. I first did a relax calculation and then post processing to extract potential (sum of Coulomb potential and Hartree part ) . Then took the planar average of this potential. I got a strange graph which I have attached with this mail. > > 1 Why shape of graph is coming like this ? why shouldn't it? what is wrong with that, according to your expectations? > 2 What is the need of excluding exchange correlation potential in calculating Work function ? because the exchange potential converges more slowly to the vacuum limit, due to its \rho^{1/3} behavior ... > I changed the pseudo potential and obtained same pattern of graph. I would be surprised if you didn't SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120506/22ee9158/attachment.htm From baroni at sissa.it Sun May 6 12:30:26 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 6 May 2012 12:30:26 +0200 Subject: [Pw_forum] smearing and electronic temperture In-Reply-To: References: Message-ID: <7F3DE372-DC4A-4303-8B65-251E18ABD42A@sissa.it> On May 6, 2012, at 8:19 AM, bhabya sahoo wrote: > i want to find the dispersion curve at 300k how can be done dispersion of what: electronic bands, or phonon bands? I would be surprised if 300 K made any difference in any electronic bands. Kohn anomalies in phonon dispersions may instead depend sensitively on temperature > because i have seen some paper related the value of electronic tempe. by using fermi dirac smearing > is it possible in quantum espresso > how can this be done? I think that you can specify "fermi-dirac" as a value for "smearing" variable > is there any physics of electronic temp and smearing value > this is beacause many unstable phonon modes become stable by incrising smearing value > what should be the calibaration of temp. and smearing in espresso look for "kohn anomaly" in the index of any good text in solid-state physics, study the relevant chapter, and revert to us if you need any further assistance. SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120506/8f2de6ab/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Sun May 6 12:30:50 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Sun, 06 May 2012 12:30:50 +0200 Subject: [Pw_forum] QHA compilation In-Reply-To: References: Message-ID: On Sun, 06 May 2012 09:29:35 +0200, Abolore Musari wrote: > Pls l try to compile QHA on my laptop Intel pentium and am getting the Dear Abolore, assuming you have downloaded the last version of QHA from here , you will need to edit the make.inc file to reflect your system configuration. If you are using an older version, you need to edit the Makefile in *every* subdirectory. In both cases, what you have to do is replace LD = $(FC) -static with LD = ifort best regards -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From ptao10b at imr.ac.cn Mon May 7 08:24:35 2012 From: ptao10b at imr.ac.cn (Peng Tao) Date: Mon, 7 May 2012 14:24:35 +0800 (CST) Subject: [Pw_forum] Magnetic susceptibility in GIPAW calculation Message-ID: <2280.188.13725f8904c.Coremail.ptao10b@imr.ac.cn> Dear all, I find it is difficult to understand the magnetic susceptibility in GIPAW output files. It is written like this: ? ? ?chi_bare pGv (HH) in 10^{-6} cm^3/mol: ? ? ? ? ? ?-17.5504 ? ? ? ? ?0.0000 ? ? ? ? ?0.0000 ? ? ? ? ? ? ?0.0000 ? ? ? ?-18.2449 ? ? ? ? ?0.0000 ? ? ? ? ? ? ?0.0000 ? ? ? ? ?0.0000 ? ? ? ?-24.3766 ? ? ?chi_bare vGv (VV) in 10^{-6} cm^3/mol: ? ? ? ? ? ?-17.8523 ? ? ? ? ?0.0000 ? ? ? ? ?0.0000 ? ? ? ? ? ? ?0.0000 ? ? ? ?-15.4914 ? ? ? ? ?0.0000 ? ? ? ? ? ? ?0.0000 ? ? ? ? ?0.0000 ? ? ? ?-25.0791 What is "pGv" or "vGv"? And, I want to investigate how the susceptibility varies with the time. Is it possible for GIPAW to realize this? Thank you very much and many regards. Plato Tao -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- From davide.ceresoli at istm.cnr.it Mon May 7 10:02:34 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Mon, 07 May 2012 10:02:34 +0200 Subject: [Pw_forum] Magnetic susceptibility in GIPAW calculation In-Reply-To: <2280.188.13725f8904c.Coremail.ptao10b@imr.ac.cn> References: <2280.188.13725f8904c.Coremail.ptao10b@imr.ac.cn> Message-ID: <4FA7819A.5050600@istm.cnr.it> Dear Peng Tao, let's take PRB 63, 245101 (the famous GIPAW paper by Pickard and Mauri). Eq. 65. is used to calculate the magnetic susceptibility, and the sequence of operators is: hence the name 'pGv'. However, the PAW contributions to the susceptibility are very complicated and have not been implemented, neither in QE-GIPAW nor in PARATEC. A good estimate is 'vGv', that is velocity*green's function*velocity. It is expected that the true susceptibility is bounded between the two values printed by the code (pGv and vGv). You can see that the difference in not huge. Regarding time evolution of susceptibility, I think you mean during a molecular dynamics run. Well, the only way is to extract snapshots from MD and computed the susceptibility for each of them. HTH. Best wishes, Davide On 05/07/2012 08:24 AM, Peng Tao wrote: > Dear all, > > I find it is difficult to understand the magnetic susceptibility in GIPAW output files. It is written like this: > > chi_bare pGv (HH) in 10^{-6} cm^3/mol: > -17.5504 0.0000 0.0000 > 0.0000 -18.2449 0.0000 > 0.0000 0.0000 -24.3766 > > > > > chi_bare vGv (VV) in 10^{-6} cm^3/mol: > -17.8523 0.0000 0.0000 > 0.0000 -15.4914 0.0000 > 0.0000 0.0000 -25.0791 > > > What is "pGv" or "vGv"? > > And, I want to investigate how the susceptibility varies with the time. Is it possible for GIPAW to realize this? > > Thank you very much and many regards. > > Plato Tao > > > -- > ------------------------------------------------------------------- > PH.D. candidate Peng Tao > Magnetism and Magnetic Materials Division > National Laboratory for Material Science > Institute of Metal Research, Chinese Academy of Sciences > Phone +86-024-83978751 > ------------------------------------------------------------------- From mourad_fsm at yahoo.fr Mon May 7 12:21:11 2012 From: mourad_fsm at yahoo.fr (debbichi mourad) Date: Mon, 7 May 2012 11:21:11 +0100 (BST) Subject: [Pw_forum] HSE&PBE0 problem In-Reply-To: <1336209790.78739.YahooMailNeo@web29505.mail.ird.yahoo.com> References: <1336209790.78739.YahooMailNeo@web29505.mail.ird.yahoo.com> Message-ID: <1336386071.42238.YahooMailNeo@web29502.mail.ird.yahoo.com> ? Dear pwscf users, I performed some calculations by using PBE0 and HSE on the ZnO system. When I used a supercell with 4 atoms , I obtained a Fermi levels comparable to those calculate without hybrid functional (Ef= 7.68 eV) . ?Almost, the same result is obtained for a supercell with 16 atoms. But (for a supercell with 16 atoms) with PBE0 and HSE Ef becomes large (Ef~28,258 eV). Why such a problem occurs? Thanks a lot in advance Mourad ? DEBBICHI Mourad Unit? de Recherche Physique des Solides,99/UR/13-19, D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. t?l:+21697487042 mourad_fsm at yahoo.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120507/d307202b/attachment.htm From lmartinsamos at gmail.com Mon May 7 12:57:23 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 7 May 2012 12:57:23 +0200 Subject: [Pw_forum] HSE&PBE0 problem In-Reply-To: <1336386071.42238.YahooMailNeo@web29502.mail.ird.yahoo.com> References: <1336209790.78739.YahooMailNeo@web29505.mail.ird.yahoo.com> <1336386071.42238.YahooMailNeo@web29502.mail.ird.yahoo.com> Message-ID: Dear mourad, in principle the exact exchange term is longer ranged than traditional DFT functionals. In any case you should converge your calculations with respect to the system size (or the kpoints and nqx1, nqx2 and nqx3 points). In the particular case of HSE, the screening parameter assumes a decay within the supercell (fixed from input). If the supercell is no big enough you could see strong oscillations with respect to the cell dimension for small cells. Look at the bibliography for more information. best regards Layla 2012/5/7 debbichi mourad > > Dear pwscf users, > > *I performed some calculations by using PBE0 and HSE on the ZnO system. When I used a supercell with 4 atoms , > I obtained a Fermi levels comparable to those calculate without hybrid functional (Ef= 7.68 eV) . > Almost, the same result is obtained for a supercell with 16 atoms. > But (for a supercell with 16 atoms) with PBE0 and HSE Ef becomes large (Ef~28,258 eV). > > Why such a problem occurs? > Thanks a lot in > advance** > Mourad > * > > > DEBBICHI Mourad > Unit? de Recherche Physique des Solides,99/UR/13-19, > D?partement de Physique, Facult? des Science de Monastir, > Avenue de l'Environnement 5019, Monastir Tunisie. > t?l:+21697487042 > mourad_fsm at yahoo.fr > > > > _______________________________________________ > 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/20120507/e83d0357/attachment.htm From joerg.buchwald at iom-leipzig.de Mon May 7 15:22:07 2012 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Mon, 7 May 2012 15:22:07 +0200 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties Message-ID: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> Hi, i tested a relaxed sapphire structure using a 10x10x10 k point set with a cutoff energy up to 250 Ry. Even at this Energy, a change of +/- 5 Ry in the cutoff lead to stresses of the order of 1 kbar. I used for Al and O pbe-n-van US pseudo potentials from the pseudo folder of quantum espresso. But also pbe-sp-van for Al and rrkjus for oxygen led to the same problem. I don't have a clue how high the cutoff must be, but 250 Ry seems to be far too high. Is that a problem of the pseudopotentials or does it have something to do with physical structure of sapphire? Thx for any hints, J?rg Buchwald -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr From joerg.buchwald at iom-leipzig.de Mon May 7 15:56:10 2012 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Mon, 7 May 2012 15:56:10 +0200 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> Message-ID: <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> that was also done. JB Am Mon, 7 May 2012 09:41:35 -0400 schrieb Iyad AL-QASIR : > Hello, > Try first to relax the atomic positions, then relax the structure. > > Thanks > > > On Mon, May 7, 2012 at 9:22 AM, J?rg Buchwald > > wrote: > > > Hi, > > i tested a relaxed sapphire structure using a 10x10x10 k point set > > with a cutoff energy up to 250 Ry. Even at this Energy, a change of > > +/- 5 Ry in the cutoff lead to stresses of the order of 1 kbar. > > I used for Al and O pbe-n-van US pseudo potentials from the pseudo > > folder of quantum espresso. But also pbe-sp-van for Al and rrkjus > > for oxygen led to the same problem. > > I don't have a clue how high the cutoff must be, but 250 Ry seems > > to be far too high. Is that a problem of the pseudopotentials or > > does it have something to do with physical structure of sapphire? > > Thx for any hints, > > J?rg Buchwald > > > > -- > > Leibniz-Institut fuer Oberflaechenmodifizierung e.V. > > > > Permoserstrasse 15 > > 04318 Leipzig > > GERMANY > > > > Phone: +49 341 / 235-3367 > > Web: http://www.uni-leipzig.de/~agmayr > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr From nicola.marzari at epfl.ch Mon May 7 16:07:52 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Mon, 07 May 2012 16:07:52 +0200 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> Message-ID: <4FA7D738.8000101@epfl.ch> Stress tensors tend to be very slow in their convergence - my understanding is that if one were to compare two approaches - minimum of the energy as a function of lattice parameter, or the zero of the trace of the strain, the latter would converge much more slowly with respect to cutoff. This slowly convergent contributions were, at least in III-V semiconductors, fairly independent of the local chemistry, so they really looked like something rigid (a better description of the part inside the core). How much does 1 kbar error translates into an error in lattice parameter? (keep atoms fixed, using relative coordinates, cutoff fixed, and expand celldm(1) by 0.3% - what's the change in stress? that change should be very well converged) I'd try to find the equilibrium celldm(1) from the minimum of the energy, for a given configuration of the ions (not relaxed, in relative coordinates), at different cutoffs, to get a sense of what it should be. Then, at the minimum celldm(1), monitor the stress tensor, to see if it converges at high cutoff to zero trace. nicola On 07/05/2012 15:56, J?rg Buchwald wrote: > that was also done. > JB > > Am Mon, 7 May 2012 09:41:35 -0400 > schrieb Iyad AL-QASIR: > >> Hello, >> Try first to relax the atomic positions, then relax the structure. >> >> Thanks >> >> >> On Mon, May 7, 2012 at 9:22 AM, J?rg Buchwald >> >> wrote: >> >>> Hi, >>> i tested a relaxed sapphire structure using a 10x10x10 k point set >>> with a cutoff energy up to 250 Ry. Even at this Energy, a change of >>> +/- 5 Ry in the cutoff lead to stresses of the order of 1 kbar. >>> I used for Al and O pbe-n-van US pseudo potentials from the pseudo >>> folder of quantum espresso. But also pbe-sp-van for Al and rrkjus >>> for oxygen led to the same problem. >>> I don't have a clue how high the cutoff must be, but 250 Ry seems >>> to be far too high. Is that a problem of the pseudopotentials or >>> does it have something to do with physical structure of sapphire? >>> Thx for any hints, >>> J?rg Buchwald >>> >>> -- >>> Leibniz-Institut fuer Oberflaechenmodifizierung e.V. >>> >>> Permoserstrasse 15 >>> 04318 Leipzig >>> GERMANY >>> >>> Phone: +49 341 / 235-3367 >>> Web: http://www.uni-leipzig.de/~agmayr >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> > > > -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From rcjhawk at gmail.com Mon May 7 20:22:58 2012 From: rcjhawk at gmail.com (Mike Mehl) Date: Mon, 7 May 2012 14:22:58 -0400 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: <4FA7D738.8000101@epfl.ch> References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> <4FA7D738.8000101@epfl.ch> Message-ID: To follow up on Nicola's point, the bulk modulus of sapphire is 240 GPa or 2400 kbar (http://www.mt-berlin.com/frames_cryst/descriptions/sapphire.htm). So a 1 kbar error corresponds to a very small change in volume. If we use the quick and dirty Birch equation of state: P(V) = 3/2 K0 [ (V0/V)^(7/3) - (V0/V)^(5/3)] with K0 = 2400 kbar and ask what volume will produce a 1 kbar change in pressure we get delta V/V0 = +/- 0.0004 Considering the normal errors in DFT, it's not worth trying to converge the stress to the 1 kbar accuracy you're trying to achieve. On Mon, May 7, 2012 at 10:07 AM, Nicola Marzari wrote: > > How much does 1 kbar error translates into an error in lattice > parameter? (keep atoms fixed, using relative coordinates, cutoff fixed, > and expand celldm(1) by 0.3% - what's the change in stress? that change > should be very well converged) > > -- Michael Mehl US Naval Research Laboratory Washington DC (Home email) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120507/96240df5/attachment-0001.htm From dyang2103 at gmail.com Tue May 8 08:07:56 2012 From: dyang2103 at gmail.com (david yang) Date: Tue, 8 May 2012 11:37:56 +0530 Subject: [Pw_forum] Regarding anharmonic IFCs Message-ID: Dear Users and developers of Quantum espresso, I have some question regarding D3 code . I am interested in Anharmonic properties of crystals and for that i am using D3 code of quantum espresso while going through the source code i figured out that present version of quantum espresso calculates Anharmonic IFCs only for q=0,q' and q" . So that mean that quantum espresso gives us anharmonic IFCs in reciprocal space something like phi(0,q',q') where phi denotes anharmonic IFC. I have two questions on this (1)--Whether my understanding is correct? (2)--For my work i need anharmonic IFCs in real space means phi(0,l,l') I known that this can be done by taking inverse Fourier transform of phi(0,q',-q') , but i am clue less after this . Can anyone give me hint that how to proceed for inverse Fourier transform ... I will be great-full to all of you. Awaiting for responses Thanks a lot With warm regards David yang NTU Singapore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120508/b6846ead/attachment.htm From bfazi90 at gmail.com Tue May 8 09:54:50 2012 From: bfazi90 at gmail.com (bf azi) Date: Tue, 8 May 2012 12:24:50 +0430 Subject: [Pw_forum] too many bands are not converged Message-ID: Dear all When I run "Relax" , after 12 iteration run stoped and show me : "from c_bands : error # 1 too many bands are not converged stopping ..." thanks a lot Bani Adam Faculty of Science Egypt From Heiles at cluster.pc.chemie.tu-darmstadt.de Tue May 8 11:43:22 2012 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Tue, 08 May 2012 11:43:22 +0200 Subject: [Pw_forum] Four Electron Pseudopotnetial for tin: US vs NC-PP Message-ID: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> Dear Quantum Espresso users. Our group is dealing with the global optimizations of clusters using Quantum Espresso. In the moment we investigate the Mn-Sn system for which it is known that a considerable charge transfer between Mn(positive) and Sn(negative) occurs. In order to model the clusters in a finite time it would be useful only to use a PP for the four valence electrons of tin while for Mn it is no problem to use 15 electrons (only one or two Mn are used). The Mn-PP is generated using the rrkjus fitting routine but the Sn-PP generation always fails if only four electrons are used for the ultra-soft PP. We tested to generate the 14 electron US-PP for tin in analogy to the Pb-US-PP found in the QE PP library and were able to generate a PP. Unfortunately, that many electrons are not of much use in our global optimization calculations. On the other hand the generation of a NC-PP with four electrons for tin is able to reproduce bulk and dimer properties but a similar procedure for Mn is not of much use. Does someone has an idea what the problem for the 4 electron US-PP for tin could be? Please find the generation parameters below. All the best Sven &input title='Sn', zed=50.0, rel=1, iswitch=3, config='[Kr] 4d10.0 5s2.0 5p2.0 6d-2.0', dft='LDA', / &inputp lloc=2, pseudotype=3, file_pseudopw='Sn.pz-rrkjus.UPF', author='', / 5 5S 1 0 2.00 0.00 2.50 2.50 5S 1 0 0.00 0.05 2.50 2.50 5P 2 1 2.00 0.00 2.70 2.90 5P 2 1 0.00 0.05 2.70 2.90 6D 3 2 -2.00 0.15 2.70 2.70 -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web:http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From Lorenzo.Paulatto at impmc.upmc.fr Tue May 8 12:10:43 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 08 May 2012 12:10:43 +0200 Subject: [Pw_forum] Regarding anharmonic IFCs In-Reply-To: References: Message-ID: On Tue, 08 May 2012 08:07:56 +0200, david yang wrote: > (1)--Whether my understanding is correct? Cross check with my post of February: http://www.democritos.it/pipermail/pw_forum/2012-February/023255.html > (2)--For my work i need anharmonic IFCs in real space means phi(0,l,l') > I known that this can be done by taking inverse Fourier transform of > phi(0,q',-q') , but i am clue less after this . > Can anyone give me hint that how to proceed for inverse Fourier transform Like in the q2r.x code (PH/q2r.f90) but with one more index bests -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From Lorenzo.Paulatto at impmc.upmc.fr Tue May 8 12:41:31 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 08 May 2012 12:41:31 +0200 Subject: [Pw_forum] Four Electron Pseudopotnetial for tin: US vs NC-PP In-Reply-To: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> References: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> Message-ID: On Tue, 08 May 2012 11:43:22 +0200, Sven Heiles wrote: > Does someone has an idea what the problem for the 4 electron > US-PP for tin could be? Please find the generation parameters below. Dear Sven, first of all have a look at the ps library http://qe-forge.org/frs/?group_id=35&release_id=109#pslibrary-pslibrary-0-2-4-title-content database by Dal Corso, it may already contain what you are looking for. If it does not, I have to admin that I got a bit lost in your message. What exactly do you want to do? An ultrasoft-pseudopotential for Sn with 4 valence electrons? bests -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From giannozz at democritos.it Tue May 8 13:58:11 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 08 May 2012 13:58:11 +0200 Subject: [Pw_forum] HSE&PBE0 problem In-Reply-To: <1336386071.42238.YahooMailNeo@web29502.mail.ird.yahoo.com> References: <1336209790.78739.YahooMailNeo@web29505.mail.ird.yahoo.com> <1336386071.42238.YahooMailNeo@web29502.mail.ird.yahoo.com> Message-ID: <1336478291.6587.61.camel@fe12lx.fisica.uniud.it> On Mon, 2012-05-07 at 11:21 +0100, debbichi mourad wrote: > Why such a problem occurs? which problem? absolute values of the Fermi energy are arbitrary. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue May 8 14:11:06 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 08 May 2012 14:11:06 +0200 Subject: [Pw_forum] regarding weight factor In-Reply-To: References: Message-ID: <1336479066.6587.74.camel@fe12lx.fisica.uniud.it> On Fri, 2012-05-04 at 21:04 +0530, himanshu at iopb.res.in wrote: > I am confused about the weight factor. the weight factor for manually supplied k-point grids is determined by the symmetry: it is proportional to the number of vectors in the star of each k-point P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From joerg.buchwald at iom-leipzig.de Tue May 8 18:42:34 2012 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Tue, 8 May 2012 18:42:34 +0200 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> <4FA7D738.8000101@epfl.ch> Message-ID: <20120508184234.2f8bef90@debian> Am Mon, 7 May 2012 14:22:58 -0400 schrieb Mike Mehl : > To follow up on Nicola's point, the bulk modulus of sapphire is 240 > GPa or 2400 kbar > (http://www.mt-berlin.com/frames_cryst/descriptions/sapphire.htm). So > a 1 kbar error corresponds to a very small change in volume. > > If we use the quick and dirty Birch equation of state: > > P(V) = 3/2 K0 [ (V0/V)^(7/3) - (V0/V)^(5/3)] > > with K0 = 2400 kbar and ask what volume will produce a 1 kbar change > in pressure we get > > delta V/V0 = +/- 0.0004 > > Considering the normal errors in DFT, it's not worth trying to > converge the stress to the 1 kbar accuracy you're trying to achieve. But to get the elastic constants in the elastic regime, i would like then apply strains of serveral per mill, which is of the same order of magnitude, i.e. also corresponds to changes of the stress tensor of the order of 1 kbar, which means that errors in the kbar range would be too high. An alternative could be the calculation of the elastic constants using the second derivative of the energy. But this won't work for big supercells due to the computation time and the number of measuring points needed. > > On Mon, May 7, 2012 at 10:07 AM, Nicola > Marzari wrote: > > > > > How much does 1 kbar error translates into an error in lattice > > parameter? (keep atoms fixed, using relative coordinates, cutoff > > fixed, and expand celldm(1) by 0.3% - what's the change in stress? > > that change should be very well converged) > > > > -- > Michael Mehl > US Naval Research Laboratory > Washington DC > (Home email) From nicola.marzari at epfl.ch Tue May 8 19:14:19 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Tue, 08 May 2012 19:14:19 +0200 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: <20120508184234.2f8bef90@debian> References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> <4FA7D738.8000101@epfl.ch> <20120508184234.2f8bef90@debian> Message-ID: <4FA9546B.9040606@epfl.ch> On 08/05/2012 18:42, J?rg Buchwald wrote: > But to get the elastic constants in the elastic regime, i would > like then apply strains of serveral per mill, which is of the same > order of magnitude, i.e. also corresponds to changes of the stress > tensor of the order of 1 kbar, which means that errors in the kbar > range would be too high. Hi Joerg, relative quantities (in this case, difference in stress upon change in strain) typically converge much faster than absolute quantities (the stress for a given strain), so you should be fine. Worth checking. > An alternative could be the calculation of the elastic constants using > the second derivative of the energy. But this won't work for big > supercells due to the computation time and the number of measuring > points needed. I think they would be comparable - for one elastic constant using the stress tensor I would probably do three calculations - one around equilibrium, and plus or minus 0.5% that . Using the energy, maybe five? +1 +0.5 0 -.5 -1? nicola ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From akohlmey at gmail.com Tue May 8 19:20:59 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 8 May 2012 13:20:59 -0400 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: <20120508184234.2f8bef90@debian> References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> <4FA7D738.8000101@epfl.ch> <20120508184234.2f8bef90@debian> Message-ID: On Tue, May 8, 2012 at 12:42 PM, J?rg Buchwald wrote: >> Considering the normal errors in DFT, it's not worth trying to >> converge the stress to the 1 kbar accuracy you're trying to achieve. > > But to get the elastic constants in the elastic regime, i would > like then apply strains of serveral per mill, which is of the same > order of magnitude, i.e. also corresponds to changes of the stress > tensor of the order of 1 kbar, which means that errors in the kbar > range would be too high. question is: do you have the same absolute error of the same magnitude and sign on all stress tensor computations, so that the *relative* error would be much smaller? remember, that when you do e.g. a geometry optimization you use forces (derivatives of the potential energy) that are converged long before your energy is converged, so by your argument, you would have to use a much higher cutoff for that as well. > An alternative could be the calculation of the elastic constants using > the second derivative of the energy. But this won't work for big > supercells due to the computation time and the number of measuring > points needed. see the comment about slow and fast converging properties. you probably don't need to converge the energy as tightly for this due to error cancellation, too. however, convergence and error cancellation is not always easily predictable. some careful experimentation is often better than using either brute force, guessing or faith in some random person's ramblings. ;-) cheers, axel. > > >> >> On Mon, May 7, 2012 at 10:07 AM, Nicola >> Marzari wrote: >> >> > >> > How much does 1 kbar error translates into an error in lattice >> > parameter? (keep atoms fixed, using relative coordinates, cutoff >> > fixed, and expand celldm(1) by 0.3% - what's the change in stress? >> > that change should be very well converged) >> > >> > -- >> Michael Mehl >> US Naval Research Laboratory >> Washington DC >> (Home email) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From faccin.giovani at gmail.com Tue May 8 19:45:38 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 8 May 2012 13:45:38 -0400 Subject: [Pw_forum] Four Electron Pseudopotnetial for tin: US vs NC-PP In-Reply-To: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> References: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> Message-ID: Dear Sven, I've built a few pseudopotentials in the past to study hybrid clusters. On those calculations I found that the TM pseudization succeeds at generating pseudopotentials much more often than the rrkj pseudization. Perhaps you could try it, and if it works, then use the cutoff parameters data that worked out with TM as a guide to try to generate a pseudo using rrkj, should you really have to stick to it. That said, a few ideas that might help: 1 - On the 6D line, why a negative number of electrons? Sorry if I'm mistaken, but shouldn't that number be positive? 2 - On this same line, why not use the reference energy (0.00), since it's a bound state, as done in 5S and 5P? 3 - If everything else is ok, the cutoff parameters (the 2.50 and 2.70 guys in the 6th and 7th columns) are usually to blame when generation fails. You'll have to explore those parameters in order to find a good combination. To aid in that, plot the all electron wavefunctions generated and look at them. That will give you an idea of reasonable values to use for the cutoff. Best, Giovani M. Faccin UFMS/Brazil 2012/5/8 Sven Heiles > Dear Quantum Espresso users. > > Our group is dealing with the global optimizations of clusters using > Quantum Espresso. In the moment we investigate > the Mn-Sn system for which it is known that a considerable charge > transfer between Mn(positive) and Sn(negative) occurs. In order to model > the clusters in a finite time it would be useful only to use a PP for > the four valence electrons of tin while for Mn it is no problem > to use 15 electrons (only one or two Mn are used). The Mn-PP is > generated using the rrkjus fitting routine but the Sn-PP generation > always fails if only four electrons > are used for the ultra-soft PP. We tested to generate the 14 electron > US-PP for tin in analogy to the Pb-US-PP found in the QE PP library and > were able to generate a PP. > Unfortunately, that many electrons are not of much use in our global > optimization calculations. > On the other hand the generation of a NC-PP with four electrons for tin > is able to reproduce bulk and > dimer properties but a similar procedure for Mn is not of much use. Does > someone has an idea what the problem for the 4 electron > US-PP for tin could be? Please find the generation parameters below. > > All the best > > Sven > > &input > title='Sn', > zed=50.0, > rel=1, > iswitch=3, > config='[Kr] 4d10.0 5s2.0 5p2.0 6d-2.0', > dft='LDA', > / > &inputp > lloc=2, > pseudotype=3, > file_pseudopw='Sn.pz-rrkjus.UPF', > author='', > / > 5 > 5S 1 0 2.00 0.00 2.50 2.50 > 5S 1 0 0.00 0.05 2.50 2.50 > 5P 2 1 2.00 0.00 2.70 2.90 > 5P 2 1 0.00 0.05 2.70 2.90 > 6D 3 2 -2.00 0.15 2.70 2.70 > > > -- > Dipl. Ing. Sven Heiles > Technische Universit?t Darmstadt > AK Sch?fer > Eduard-Zintl-Institut > Petersenstra?e 20 > D-64287 Darmstadt ? Germany > > Phone: ++49-(0)6151-164397 > Fax: ++49-(0)6151-166024 > Web:http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud > > _______________________________________________ > 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/20120508/787b8748/attachment-0001.htm From Lorenzo.Paulatto at impmc.upmc.fr Tue May 8 19:50:32 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 08 May 2012 19:50:32 +0200 Subject: [Pw_forum] Four Electron Pseudopotnetial for tin: US vs NC-PP In-Reply-To: References: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> Message-ID: On Tue, 08 May 2012 19:45:38 +0200, Giovani Faccin wrote: > 1 - On the 6D line, why a negative number of electrons? Sorry if I'm > mistaken, but shouldn't that number be positive? No, this is correct, it only means that the state label is reserved but not used in the all-electron calculation. However, I would rather use the 5D instead of the 6D, but I does not really make any difference for the pseudo-wavefunctions. > 2 - On this same line, why not use the reference energy (0.00), since > it's a bound state, as done in 5S and 5P? Because using a negative occupation number the eigenvalue is not computed :-) > > 3 - If everything else is ok, the cutoff parameters (the 2.50 and 2.70 > guys in the 6th and 7th columns) are usually to blame when generation > fails. Indeed, I think it is almost impossible to find a good cutoff radius for all the 5 reference wavefunctions, maybe one could start with a single-channel pseudopotential; then only add a second channel if necessary. However, 2 channels are required for ultrasoft, maybe Sven really want to make an USPP in the end. bests -- Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From faccin.giovani at gmail.com Tue May 8 19:53:23 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 8 May 2012 13:53:23 -0400 Subject: [Pw_forum] Four Electron Pseudopotnetial for tin: US vs NC-PP In-Reply-To: References: <4FA8EABA.5080800@cluster.pc.chemie.tu-darmstadt.de> Message-ID: Thank you Lorenzo! I realized what I'd written made no sense right after sending the email. Was typing another one to correct that, but you were faster. It's the after lunch sleepness :O) Giovani 2012/5/8 Lorenzo Paulatto > On Tue, 08 May 2012 19:45:38 +0200, Giovani Faccin > wrote: > > 1 - On the 6D line, why a negative number of electrons? Sorry if I'm > > mistaken, but shouldn't that number be positive? > > No, this is correct, it only means that the state label is reserved but > not used in the all-electron calculation. However, I would rather use the > 5D instead of the 6D, but I does not really make any difference for the > pseudo-wavefunctions. > > > 2 - On this same line, why not use the reference energy (0.00), since > > it's a bound state, as done in 5S and 5P? > > Because using a negative occupation number the eigenvalue is not computed > :-) > > > > > 3 - If everything else is ok, the cutoff parameters (the 2.50 and 2.70 > > guys in the 6th and 7th columns) are usually to blame when generation > > fails. > > Indeed, I think it is almost impossible to find a good cutoff radius for > all the 5 reference wavefunctions, maybe one could start with a > single-channel pseudopotential; then only add a second channel if > necessary. However, 2 channels are required for ultrasoft, maybe Sven > really want to make an USPP in the end. > > bests > > -- > Lorenzo Paulatto IdR CNRS @ IMPMC/UPMC - Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120508/a87ad1de/attachment.htm From zafartariq2003 at yahoo.com Wed May 9 14:54:02 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Wed, 9 May 2012 05:54:02 -0700 (PDT) Subject: [Pw_forum] About Elastic Constants ? Message-ID: <1336568042.76751.YahooMailClassic@web65408.mail.ac4.yahoo.com> Dear All I want to calculate elastic constants C11, C12, and other elastic constants. I got a link http://www.tfkp.physik.uni-erlangen.de/~oli/physics/downloads/elasthowto.pdf But unfortunately I can not found this file. If any body have this file or related material about "How to calculate Elastic constants" then please help me by sending this file or any other material. Best Regards Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120509/0561a74b/attachment.htm From parishok at gmail.com Wed May 9 15:40:11 2012 From: parishok at gmail.com (pari shok) Date: Wed, 9 May 2012 09:40:11 -0400 Subject: [Pw_forum] DOS per eV per volume Message-ID: Dear All, Hello. My question is: for calculating DOS per volume, whether I should divide it to unit cell volume that is given by scf output file or by unit cell/ 4(pi)^3. as you know the difference is a factor of 100. I appreciate your help. Yours P Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120509/1f2db7f9/attachment.htm From Michael.Mehl at nrl.navy.mil Wed May 9 16:04:59 2012 From: Michael.Mehl at nrl.navy.mil (Michael Mehl) Date: Wed, 09 May 2012 10:04:59 -0400 Subject: [Pw_forum] cutoff convergence of sapphire for elastic properties In-Reply-To: <20120508184234.2f8bef90@debian> References: <20120507152207.6fa9b3b3@PC-Mayr-Mitarb6.pc-flexi> <20120507155610.6f30a72a@PC-Mayr-Mitarb6.pc-flexi> <4FA7D738.8000101@epfl.ch> <20120508184234.2f8bef90@debian> Message-ID: <4FAA798B.7060705@nrl.navy.mil> The elastic constants of sapphire are all in the 100-500 GPa range (same reference as before). A 1 kbar error in your calculation, or even a 10 kbar (the pessimist in me says 100 kbar) is going to be small compared to DFT errors. In general, trying to get elastic constants accurate to 1 kbar (0.1 GPa) with current DFT functionals and techniques is futile. (Consider the change in the elastic constants due to volume, noting that DFT does not get the equilibrium volume correct to parts per thousand, much less parts per million.) In any case, Hooke's law usually works for strains up to a few percent, though I'm not sure what the range is for sapphire. My personal choice for doing elastic constant calculations is to take relatively large strains (1%, 2%, ... , even up to 10%) and see how long stress is proportional to strain. Then the effects of relatively small errors in stress are less important. (I should say I do this mostly with energy versus the strain squared, rather than stress versus strain, but the principle is the same.) On 05/08/2012 12:42 PM, J?rg Buchwald wrote: > Am Mon, 7 May 2012 14:22:58 -0400 > schrieb Mike Mehl: > > But to get the elastic constants in the elastic regime, i would > like then apply strains of serveral per mill, which is of the same > order of magnitude, i.e. also corresponds to changes of the stress > tensor of the order of 1 kbar, which means that errors in the kbar > range would be too high. > An alternative could be the calculation of the elastic constants using > the second derivative of the energy. But this won't work for big > supercells due to the computation time and the number of measuring > points needed. > > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From Michael.Mehl at nrl.navy.mil Wed May 9 16:14:06 2012 From: Michael.Mehl at nrl.navy.mil (Michael Mehl) Date: Wed, 09 May 2012 10:14:06 -0400 Subject: [Pw_forum] About Elastic Constants ? In-Reply-To: <1336568042.76751.YahooMailClassic@web65408.mail.ac4.yahoo.com> References: <1336568042.76751.YahooMailClassic@web65408.mail.ac4.yahoo.com> Message-ID: <4FAA7BAE.6080307@nrl.navy.mil> A shameless plug. The URL is to a preprint, but I'd appreciate the full reference being used in your papers :-) @InCollection{mehl94:fpcij, author = {M. J. Mehl and B. M. Klein and D. A. Papaconstantopoulos}, title = {First-Principles Calculation of Elastic Properties}, booktitle = {Intermetallic Compounds - Principles and Practice}, pages = {195-210}, publisher = {John Wiley and Sons}, year = 1994, editor = {J. H. Westbrook and R. L. Fleischer}, volume = 1, chapter = 9, address = {London}, url = {http://cst-www.nrl.navy.mil/users/mehl/papers/cij453.pdf}, } On 05/09/2012 08:54 AM, zafar rasheed wrote: > Dear All > I want to calculate elastic constants C11, C12, and other elastic > constants. I got a link > http://www.tfkp.physik.uni-erlangen.de/~oli/physics/downloads/elasthowto.pdf > But unfortunately I can not found this file. If any body have this > file or related material about "How to calculate Elastic constants" > then please help me by sending this file or any other material. > > Best Regards > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From nicola.marzari at epfl.ch Wed May 9 16:19:52 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Wed, 09 May 2012 16:19:52 +0200 Subject: [Pw_forum] About Elastic Constants ? In-Reply-To: <1336568042.76751.YahooMailClassic@web65408.mail.ac4.yahoo.com> References: <1336568042.76751.YahooMailClassic@web65408.mail.ac4.yahoo.com> Message-ID: <4FAA7D08.9010201@epfl.ch> Dear Zafar, see Lab2 from here - on elastic constants from quantum espresso: http://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/labs/ The homework has a pointer to Mike Mehl's page (and in turn to Mike's paper, that he just posted), on top of the now-broken Erlangen link. nicola On 09/05/2012 14:54, zafar rasheed wrote: > Dear All > I want to calculate elastic constants C11, C12, and other elastic > constants. I got a link > http://www.tfkp.physik.uni-erlangen.de/~oli/physics/downloads/elasthowto.pdf > But unfortunately I can not found this file. If any body have this file > or related material about "How to calculate Elastic constants" then > please help me by sending this file or any other material. > > Best Regards > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From fratesi at mater.unimib.it Wed May 9 16:34:23 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Wed, 09 May 2012 16:34:23 +0200 Subject: [Pw_forum] DOS per eV per volume In-Reply-To: References: Message-ID: <4FAA806F.9090203@mater.unimib.it> Dear Pari, from Doc/INPUT_PROJWFC: "All DOS(E) are in states/eV plotted vs E in eV" i.e., states/eV/cell; if you want them in states/eV/volume you should divide by volume/cell. To be sure, you can try once integrating numerically (histograms would be enough) the DOS up to the Fermi level to see you get the number of electrons (or the electron density) you expect for your system. HTH Guido On 05/09/2012 03:40 PM, pari shok wrote: > Dear All, > Hello. > My question is: for calculating DOS per volume, whether I should divide > it to unit cell volume that is given by scf output file or by unit cell/ > 4(pi)^3. as you know the difference is a factor of 100. > I appreciate your help. > Yours > P Shok > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From elie.moujaes at hotmail.co.uk Wed May 9 21:38:27 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 9 May 2012 20:38:27 +0100 Subject: [Pw_forum] quick question about the input file for phonon calculations at a point Message-ID: Dear all, I have a simple question about the coordinates of the point at which one would like to perform phonon calculations. It is just a quick check really. I am talking about the following input file for example: Phonon dispersion for monolayer grapheme at the gamma point &inputph tr2_ph=1.0d-14, prefix='phmonog', trans=.true., recover=.true., amass(1)=12.0107, outdir='/tmp/', fildyn='mgraph.dynG', / qx qy qz <------The point at which the phonon calculation is run. In what coordinate system must (qx,qy,qz) be expressed? Is it written in units of 2Pi/alat? and if so, should alat be in Angstroms or a.u.? Thanks Elie Moujhes University of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120509/5425bdb0/attachment.htm From avallabh at purdue.edu Wed May 9 21:56:18 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Wed, 9 May 2012 15:56:18 -0400 (EDT) Subject: [Pw_forum] quick question about the input file for phonon calculations at a point In-Reply-To: Message-ID: <1447552975.177534.1336593378575.JavaMail.root@mailhub016.itcs.purdue.edu> Elie, the coordinates should be in 2pi/alat units. You dont have to worry about ang or a.u, since the scf input will take care of this. Thanks Ajit From degironc at sissa.it Wed May 9 21:56:43 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 09 May 2012 21:56:43 +0200 Subject: [Pw_forum] quick question about the input file for phonon calculations at a point In-Reply-To: References: Message-ID: <4FAACBFB.8000709@sissa.it> qx, qy, qz are in unit of 2pi/alat which means that, for instance, in a simple cubic lattice the zone boundary along x has coordinates (0.5,0.0,0.0) because b1=(1,0,0)*2pi/a in an fcc lattice the zone boundary in the x direction is instead (1,0,0) because in fcc the smallest G vector in that direction is (2,0,0)*2pi/a stefano On 05/09/2012 09:38 PM, Elie M wrote: > Dear all, I have a simple question about the coordinates of the point at which one would like to perform phonon calculations. It is just a quick check really. I am talking about the following input file for example: > Phonon > dispersion for monolayer grapheme at the gamma point > > &inputph > > tr2_ph=1.0d-14, > > prefix='phmonog', > > trans=.true., > > > recover=.true., > > amass(1)=12.0107, > > outdir='/tmp/', > > fildyn='mgraph.dynG', > > / > > qx qy qz<------The point at which the phonon calculation is run. > In what coordinate system must (qx,qy,qz) be expressed? Is it written in units of 2Pi/alat? and if so, should alat be in Angstroms or a.u.? > Thanks > Elie Moujhes > University of NottinghamNG7 2RDUK > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120509/744c3caf/attachment-0001.htm From elie.moujaes at hotmail.co.uk Wed May 9 22:00:31 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 9 May 2012 21:00:31 +0100 Subject: [Pw_forum] quick question about the input file for phonon calculations at a point In-Reply-To: <1447552975.177534.1336593378575.JavaMail.root@mailhub016.itcs.purdue.edu> References: , <1447552975.177534.1336593378575.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: Thanks very much for your help guys Elie > Date: Wed, 9 May 2012 15:56:18 -0400 > From: avallabh at purdue.edu > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] quick question about the input file for phonon calculations at a point > > Elie, > > > the coordinates should be in 2pi/alat units. You dont have to worry about ang or a.u, since the scf input will take care of this. > > Thanks > Ajit > _______________________________________________ > 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/20120509/65567748/attachment.htm From magda.birowska at gmail.com Thu May 10 12:57:06 2012 From: magda.birowska at gmail.com (Magdalena Birowska) Date: Thu, 10 May 2012 12:57:06 +0200 Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, very large estimated scf accuracy Message-ID: Dear All, I am trying to relax a surface slab of GaAs which has 72 atoms. I found strange behaviour of first cycle of scf convergence. The estimated scf convergence is huge. I terminated Ga surface using fractional charges H=1.25, which I downloaded from the quantum espresso official website. When I use H=1, I don't see such a behaviour. Can anyone kindly suggest the possible source of error on my part. First cycle of SCF convergence: estimated scf accuracy < 3906.28215610 Ry estimated scf accuracy < 39347.40892210 Ry estimated scf accuracy < 18170.90673442 Ry estimated scf accuracy < 15951.19730682 Ry estimated scf accuracy < 15662.52132268 Ry estimated scf accuracy < 12286.77018220 Ry estimated scf accuracy < 12233.77236956 Ry estimated scf accuracy < 11694.83354422 Ry estimated scf accuracy < 15271.15048386 Ry estimated scf accuracy < 15566.68838647 Ry estimated scf accuracy < 47265.52643459 Ry estimated scf accuracy < 22511.42062539 Ry estimated scf accuracy < 24008.31787289 Ry estimated scf accuracy < 12935.76752149 Ry estimated scf accuracy < 16811.33660587 Ry estimated scf accuracy < 10992.92010369 Ry estimated scf accuracy < 4144.02105761 Ry estimated scf accuracy < 30138.05735660 Ry estimated scf accuracy < 10240.01360270 Ry estimated scf accuracy < 16789.80502995 Ry estimated scf accuracy < 6254.96875173 Ry estimated scf accuracy < 5678.83239125 Ry estimated scf accuracy < 5653.94732457 Ry estimated scf accuracy < 4634.85427954 Ry estimated scf accuracy < 4748.33851037 Ry estimated scf accuracy < 4570.74005737 Ry estimated scf accuracy < 2807.69984889 Ry estimated scf accuracy < 5304.65877872 Ry estimated scf accuracy < 2066.38501462 Ry estimated scf accuracy < 17495.61285271 Ry estimated scf accuracy < 18676.38196709 Ry estimated scf accuracy < 10884.14492461 Ry estimated scf accuracy < 17200.92388789 Ry estimated scf accuracy < 1160.48758157 Ry estimated scf accuracy < 1080.24247591 Ry estimated scf accuracy < 399.14797137 Ry estimated scf accuracy < 122.19296219 Ry estimated scf accuracy < 99.50315590 Ry estimated scf accuracy < 55.04456371 Ry estimated scf accuracy < 9.17378773 Ry estimated scf accuracy < 1.52941820 Ry estimated scf accuracy < 4.24567233 Ry estimated scf accuracy < 31.40572065 Ry estimated scf accuracy < 0.15173499 Ry estimated scf accuracy < 0.25128323 Ry estimated scf accuracy < 0.08254494 Ry estimated scf accuracy < 0.04825066 Ry estimated scf accuracy < 0.02330525 Ry estimated scf accuracy < 0.01482943 Ry estimated scf accuracy < 0.00395579 Ry estimated scf accuracy < 0.00021627 Ry estimated scf accuracy < 0.00002718 Ry estimated scf accuracy < 0.00001596 Ry estimated scf accuracy < 0.00000423 Ry estimated scf accuracy < 0.00000096 Ry estimated scf accuracy < 0.00000049 Ry estimated scf accuracy < 0.00000040 Ry estimated scf accuracy < 0.00000004 Ry estimated scf accuracy < 8.2E-09 Ry My input file: &CONTROL calculation = "relax" , restart_mode = 'from_scratch' , outdir='/tmp/GaAs/' , pseudo_dir = './' , prefix='GaAs' disk_io = 'default' , ! verbosity = 'default' , tstress = .true. , tprnfor = .true. , nstep = 200 , etot_conv_thr = 1.0E-5 , forc_conv_thr = 1.0D-6 , ! iprint = 3 , max_seconds = 6000000 , dt = 1000000 , / &SYSTEM ibrav = 0 , celldm(1) =7.383383939, ! B = 3.70971016 , ! C = 3.70971016 , ! cosAB = 0.49517470 , ! cosAC = 0.49517470 , ! cosBC = 0.49517470 , nat = 72 , ntyp = 3 , ecutwfc = 40.0 , !ecutrho = 320.0 , occupations = 'smearing' , smearing = 'fd' , degauss = 0.005 , !nspin = 2 , lda_plus_u = .false. , !celldm(1) = 3.907118519, !celldm(3) = 10.D0, / &ELECTRONS electron_maxstep = 700 , conv_thr = 1.0d-8 , diagonalization = 'cg' , / &IONS bfgs_ndim =3, pot_extrapolation='atomic', / &CELL cell_dynamics = 'damp-w' , press = 0.00 , ! wmass = 0.00700000 , cell_dofree = 'xyz' , / CELL_PARAMETERS cubic 2.00000 0.000000 0.000000 0.00000 2.000000 0.000000 0.00000 0.000000 10.00000 ATOMIC_SPECIES Ga 69.723 Ga.rrkj3.UPF As 74.922 As.rrkj3.UPF H 1.00794 H-1.25.UPF ATOMIC_POSITIONS {alat} Ga 0.00000050 -0.00000025 0.00682815 Ga 0.49999874 0.49924596 0.70857798 As 0.50000024 0.00000000 0.35277077 As -0.00000050 0.49920484 1.06302457 Ga -0.00000075 1.00000049 0.00921110 Ga 0.50000024 1.50075426 0.70857948 As 0.49999949 1.00000074 0.35474173 As -0.00000050 1.50079488 1.06302507 Ga 0.00000000 0.00000050 1.42032605 Ga 0.49999974 0.50287293 2.12975309 As 0.49999999 0.00000025 1.77702420 As 0.00000000 0.50483913 2.48497829 Ga -0.00000025 0.99999948 1.41672691 Ga 0.49999949 1.49712679 2.12975209 As 0.49999974 0.99999923 1.77125600 As 0.00000000 1.49516135 2.48497904 Ga 0.00000025 -0.00000176 2.83068972 Ga 0.49999774 0.48620728 3.55158193 As 0.49999999 -0.00000125 3.18153191 As -0.00000075 0.47707341 3.90604332 Ga -0.00000050 0.99999798 2.85092365 Ga 0.49999849 1.51379294 3.55158244 As 0.50000100 0.99999923 3.21014318 As 0.00000000 1.52292731 3.90604307 Ga 0.00000000 0.00000025 4.30422216 Ga 0.49999974 0.55140319 4.97156294 As 0.49999974 0.00000075 4.67996164 As 0.00000000 0.69861686 5.30991586 Ga 0.00000000 0.99999948 4.21931590 Ga 0.49999949 1.44859754 4.97156219 As 0.50000024 1.00000024 4.55459604 As 0.00000000 1.30138387 5.30991436 H 0.00000025 0.29006390 -0.24872539 H 0.00000000 -0.29006290 -0.24872389 H -0.00000075 1.29045005 -0.24574939 H -0.00000075 0.70954892 -0.24574989 Ga 1.00000050 -0.00000025 0.00682815 Ga 1.49999874 0.49924596 0.70857798 As 1.50000024 0.00000000 0.35277077 As 0.99999950 0.49920484 1.06302457 Ga 0.99999925 1.00000049 0.00921110 Ga 1.50000024 1.50075426 0.70857948 As 1.49999949 1.00000074 0.35474173 As 0.99999950 1.50079488 1.06302507 Ga 1.00000000 0.00000050 1.42032605 Ga 1.49999974 0.50287293 2.12975309 As 1.49999999 0.00000025 1.77702420 As 1.00000000 0.50483913 2.48497829 Ga 0.99999975 0.99999948 1.41672691 Ga 1.49999949 1.49712679 2.12975209 As 1.49999974 0.99999923 1.77125600 As 1.00000000 1.49516135 2.48497904 Ga 1.00000025 -0.00000176 2.83068972 Ga 1.49999774 0.48620728 3.55158193 As 1.49999999 -0.00000125 3.18153191 As 0.99999925 0.47707341 3.90604332 Ga 0.99999950 0.99999798 2.85092365 Ga 1.49999849 1.51379294 3.55158244 As 1.50000100 0.99999923 3.21014318 As 1.00000000 1.52292731 3.90604307 Ga 1.00000000 0.00000025 4.30422216 Ga 1.49999974 0.55140319 4.97156294 As 1.49999974 0.00000075 4.67996164 As 1.00000000 0.69861686 5.30991586 Ga 1.00000000 0.99999948 4.21931590 Ga 1.49999949 1.44859754 4.97156219 As 1.50000024 1.00000024 4.55459604 As 1.00000000 1.30138387 5.30991436 H 1.00000025 0.29006390 -0.24872539 H 1.00000000 -0.29006290 -0.24872389 H 0.99999925 1.29045005 -0.24574939 H 0.99999925 0.70954892 -0.24574989 K_POINTS automatic 4 4 1 0 0 0 Best regards Magdalena Birowska -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/11bfa198/attachment.htm From manojnarayan86 at gmail.com Thu May 10 13:25:15 2012 From: manojnarayan86 at gmail.com (manoj narayanan) Date: Thu, 10 May 2012 16:55:15 +0530 Subject: [Pw_forum] Shift in K points Message-ID: Hello all Can any one tell in detail about shift in k point mesh, like what and why it is ? and off course any relevant reference regarding this will also be helpful. Thanking you in advance Manoj N -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/f07e563b/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu May 10 13:45:36 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 10 May 2012 13:45:36 +0200 Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, very large estimated scf accuracy In-Reply-To: References: Message-ID: <201205101345.37253.giuseppe.mattioli@ism.cnr.it> Dear Magdalena Why do you suspect that your calculation has something wrong if it reaches convergence in a not unusually large number of scf steps? How does the second bfgs step, starting from the previous wfc and density, perform the scf? Giuseppe On Thursday 10 May 2012 12:57:06 Magdalena Birowska wrote: > Dear All, > > I am trying to relax a surface slab of GaAs which has 72 atoms. > I found strange behaviour of first cycle of scf convergence. > The estimated scf convergence is huge. I terminated Ga surface using > fractional charges > H=1.25, which I downloaded from the quantum espresso official website. > When I use H=1, I don't see such a behaviour. > Can anyone kindly suggest the possible source of error on my part. > > First cycle of SCF convergence: > estimated scf accuracy < 3906.28215610 Ry > estimated scf accuracy < 39347.40892210 Ry > estimated scf accuracy < 18170.90673442 Ry > estimated scf accuracy < 15951.19730682 Ry > estimated scf accuracy < 15662.52132268 Ry > estimated scf accuracy < 12286.77018220 Ry > estimated scf accuracy < 12233.77236956 Ry > estimated scf accuracy < 11694.83354422 Ry > estimated scf accuracy < 15271.15048386 Ry > estimated scf accuracy < 15566.68838647 Ry > estimated scf accuracy < 47265.52643459 Ry > estimated scf accuracy < 22511.42062539 Ry > estimated scf accuracy < 24008.31787289 Ry > estimated scf accuracy < 12935.76752149 Ry > estimated scf accuracy < 16811.33660587 Ry > estimated scf accuracy < 10992.92010369 Ry > estimated scf accuracy < 4144.02105761 Ry > estimated scf accuracy < 30138.05735660 Ry > estimated scf accuracy < 10240.01360270 Ry > estimated scf accuracy < 16789.80502995 Ry > estimated scf accuracy < 6254.96875173 Ry > estimated scf accuracy < 5678.83239125 Ry > estimated scf accuracy < 5653.94732457 Ry > estimated scf accuracy < 4634.85427954 Ry > estimated scf accuracy < 4748.33851037 Ry > estimated scf accuracy < 4570.74005737 Ry > estimated scf accuracy < 2807.69984889 Ry > estimated scf accuracy < 5304.65877872 Ry > estimated scf accuracy < 2066.38501462 Ry > estimated scf accuracy < 17495.61285271 Ry > estimated scf accuracy < 18676.38196709 Ry > estimated scf accuracy < 10884.14492461 Ry > estimated scf accuracy < 17200.92388789 Ry > estimated scf accuracy < 1160.48758157 Ry > estimated scf accuracy < 1080.24247591 Ry > estimated scf accuracy < 399.14797137 Ry > estimated scf accuracy < 122.19296219 Ry > estimated scf accuracy < 99.50315590 Ry > estimated scf accuracy < 55.04456371 Ry > estimated scf accuracy < 9.17378773 Ry > estimated scf accuracy < 1.52941820 Ry > estimated scf accuracy < 4.24567233 Ry > estimated scf accuracy < 31.40572065 Ry > estimated scf accuracy < 0.15173499 Ry > estimated scf accuracy < 0.25128323 Ry > estimated scf accuracy < 0.08254494 Ry > estimated scf accuracy < 0.04825066 Ry > estimated scf accuracy < 0.02330525 Ry > estimated scf accuracy < 0.01482943 Ry > estimated scf accuracy < 0.00395579 Ry > estimated scf accuracy < 0.00021627 Ry > estimated scf accuracy < 0.00002718 Ry > estimated scf accuracy < 0.00001596 Ry > estimated scf accuracy < 0.00000423 Ry > estimated scf accuracy < 0.00000096 Ry > estimated scf accuracy < 0.00000049 Ry > estimated scf accuracy < 0.00000040 Ry > estimated scf accuracy < 0.00000004 Ry > estimated scf accuracy < 8.2E-09 Ry > > My input file: > > &CONTROL > calculation = "relax" , > restart_mode = 'from_scratch' , > outdir='/tmp/GaAs/' , > pseudo_dir = './' , > prefix='GaAs' > disk_io = 'default' , > ! verbosity = 'default' , > tstress = .true. , > tprnfor = .true. , > nstep = 200 , > etot_conv_thr = 1.0E-5 , > forc_conv_thr = 1.0D-6 , > ! iprint = 3 , > max_seconds = 6000000 , > dt = 1000000 , > / > &SYSTEM > ibrav = 0 , > celldm(1) =7.383383939, > ! B = 3.70971016 , > ! C = 3.70971016 , > ! cosAB = 0.49517470 , > ! cosAC = 0.49517470 , > ! cosBC = 0.49517470 , > nat = 72 , > ntyp = 3 , > ecutwfc = 40.0 , > !ecutrho = 320.0 , > occupations = 'smearing' , > smearing = 'fd' , > degauss = 0.005 , > !nspin = 2 , > lda_plus_u = .false. , > > !celldm(1) = 3.907118519, > !celldm(3) = 10.D0, > > / > &ELECTRONS > electron_maxstep = 700 , > conv_thr = 1.0d-8 , > diagonalization = 'cg' , > / > &IONS > bfgs_ndim =3, > pot_extrapolation='atomic', > / > &CELL > cell_dynamics = 'damp-w' , > press = 0.00 , > ! wmass = 0.00700000 , > cell_dofree = 'xyz' , > / > CELL_PARAMETERS cubic > 2.00000 0.000000 0.000000 > 0.00000 2.000000 0.000000 > 0.00000 0.000000 10.00000 > ATOMIC_SPECIES > Ga 69.723 Ga.rrkj3.UPF > As 74.922 As.rrkj3.UPF > H 1.00794 H-1.25.UPF > ATOMIC_POSITIONS {alat} > Ga 0.00000050 -0.00000025 0.00682815 > Ga 0.49999874 0.49924596 0.70857798 > As 0.50000024 0.00000000 0.35277077 > As -0.00000050 0.49920484 1.06302457 > Ga -0.00000075 1.00000049 0.00921110 > Ga 0.50000024 1.50075426 0.70857948 > As 0.49999949 1.00000074 0.35474173 > As -0.00000050 1.50079488 1.06302507 > Ga 0.00000000 0.00000050 1.42032605 > Ga 0.49999974 0.50287293 2.12975309 > As 0.49999999 0.00000025 1.77702420 > As 0.00000000 0.50483913 2.48497829 > Ga -0.00000025 0.99999948 1.41672691 > Ga 0.49999949 1.49712679 2.12975209 > As 0.49999974 0.99999923 1.77125600 > As 0.00000000 1.49516135 2.48497904 > Ga 0.00000025 -0.00000176 2.83068972 > Ga 0.49999774 0.48620728 3.55158193 > As 0.49999999 -0.00000125 3.18153191 > As -0.00000075 0.47707341 3.90604332 > Ga -0.00000050 0.99999798 2.85092365 > Ga 0.49999849 1.51379294 3.55158244 > As 0.50000100 0.99999923 3.21014318 > As 0.00000000 1.52292731 3.90604307 > Ga 0.00000000 0.00000025 4.30422216 > Ga 0.49999974 0.55140319 4.97156294 > As 0.49999974 0.00000075 4.67996164 > As 0.00000000 0.69861686 5.30991586 > Ga 0.00000000 0.99999948 4.21931590 > Ga 0.49999949 1.44859754 4.97156219 > As 0.50000024 1.00000024 4.55459604 > As 0.00000000 1.30138387 5.30991436 > H 0.00000025 0.29006390 -0.24872539 > H 0.00000000 -0.29006290 -0.24872389 > H -0.00000075 1.29045005 -0.24574939 > H -0.00000075 0.70954892 -0.24574989 > Ga 1.00000050 -0.00000025 0.00682815 > Ga 1.49999874 0.49924596 0.70857798 > As 1.50000024 0.00000000 0.35277077 > As 0.99999950 0.49920484 1.06302457 > Ga 0.99999925 1.00000049 0.00921110 > Ga 1.50000024 1.50075426 0.70857948 > As 1.49999949 1.00000074 0.35474173 > As 0.99999950 1.50079488 1.06302507 > Ga 1.00000000 0.00000050 1.42032605 > Ga 1.49999974 0.50287293 2.12975309 > As 1.49999999 0.00000025 1.77702420 > As 1.00000000 0.50483913 2.48497829 > Ga 0.99999975 0.99999948 1.41672691 > Ga 1.49999949 1.49712679 2.12975209 > As 1.49999974 0.99999923 1.77125600 > As 1.00000000 1.49516135 2.48497904 > Ga 1.00000025 -0.00000176 2.83068972 > Ga 1.49999774 0.48620728 3.55158193 > As 1.49999999 -0.00000125 3.18153191 > As 0.99999925 0.47707341 3.90604332 > Ga 0.99999950 0.99999798 2.85092365 > Ga 1.49999849 1.51379294 3.55158244 > As 1.50000100 0.99999923 3.21014318 > As 1.00000000 1.52292731 3.90604307 > Ga 1.00000000 0.00000025 4.30422216 > Ga 1.49999974 0.55140319 4.97156294 > As 1.49999974 0.00000075 4.67996164 > As 1.00000000 0.69861686 5.30991586 > Ga 1.00000000 0.99999948 4.21931590 > Ga 1.49999949 1.44859754 4.97156219 > As 1.50000024 1.00000024 4.55459604 > As 1.00000000 1.30138387 5.30991436 > H 1.00000025 0.29006390 -0.24872539 > H 1.00000000 -0.29006290 -0.24872389 > H 0.99999925 1.29045005 -0.24574939 > H 0.99999925 0.70954892 -0.24574989 > K_POINTS automatic > 4 4 1 0 0 0 > > Best regards > Magdalena Birowska -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From magda.birowska at gmail.com Thu May 10 14:03:09 2012 From: magda.birowska at gmail.com (Magdalena Birowska) Date: Thu, 10 May 2012 14:03:09 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 59, Issue 19 In-Reply-To: References: Message-ID: 2012/5/10 > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. GaAs surface with fractional charges H Zval=1.25, very large > estimated scf accuracy (Magdalena Birowska) > 2. Shift in K points (manoj narayanan) > 3. Re: GaAs surface with fractional charges H Zval=1.25, very > large estimated scf accuracy (Giuseppe Mattioli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 May 2012 12:57:06 +0200 > From: Magdalena Birowska > Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, > very large estimated scf accuracy > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > I am trying to relax a surface slab of GaAs which has 72 atoms. > I found strange behaviour of first cycle of scf convergence. > The estimated scf convergence is huge. I terminated Ga surface using > fractional charges > H=1.25, which I downloaded from the quantum espresso official website. > When I use H=1, I don't see such a behaviour. > Can anyone kindly suggest the possible source of error on my part. > > First cycle of SCF convergence: > estimated scf accuracy < 3906.28215610 Ry > estimated scf accuracy < 39347.40892210 Ry > estimated scf accuracy < 18170.90673442 Ry > estimated scf accuracy < 15951.19730682 Ry > estimated scf accuracy < 15662.52132268 Ry > estimated scf accuracy < 12286.77018220 Ry > estimated scf accuracy < 12233.77236956 Ry > estimated scf accuracy < 11694.83354422 Ry > estimated scf accuracy < 15271.15048386 Ry > estimated scf accuracy < 15566.68838647 Ry > estimated scf accuracy < 47265.52643459 Ry > estimated scf accuracy < 22511.42062539 Ry > estimated scf accuracy < 24008.31787289 Ry > estimated scf accuracy < 12935.76752149 Ry > estimated scf accuracy < 16811.33660587 Ry > estimated scf accuracy < 10992.92010369 Ry > estimated scf accuracy < 4144.02105761 Ry > estimated scf accuracy < 30138.05735660 Ry > estimated scf accuracy < 10240.01360270 Ry > estimated scf accuracy < 16789.80502995 Ry > estimated scf accuracy < 6254.96875173 Ry > estimated scf accuracy < 5678.83239125 Ry > estimated scf accuracy < 5653.94732457 Ry > estimated scf accuracy < 4634.85427954 Ry > estimated scf accuracy < 4748.33851037 Ry > estimated scf accuracy < 4570.74005737 Ry > estimated scf accuracy < 2807.69984889 Ry > estimated scf accuracy < 5304.65877872 Ry > estimated scf accuracy < 2066.38501462 Ry > estimated scf accuracy < 17495.61285271 Ry > estimated scf accuracy < 18676.38196709 Ry > estimated scf accuracy < 10884.14492461 Ry > estimated scf accuracy < 17200.92388789 Ry > estimated scf accuracy < 1160.48758157 Ry > estimated scf accuracy < 1080.24247591 Ry > estimated scf accuracy < 399.14797137 Ry > estimated scf accuracy < 122.19296219 Ry > estimated scf accuracy < 99.50315590 Ry > estimated scf accuracy < 55.04456371 Ry > estimated scf accuracy < 9.17378773 Ry > estimated scf accuracy < 1.52941820 Ry > estimated scf accuracy < 4.24567233 Ry > estimated scf accuracy < 31.40572065 Ry > estimated scf accuracy < 0.15173499 Ry > estimated scf accuracy < 0.25128323 Ry > estimated scf accuracy < 0.08254494 Ry > estimated scf accuracy < 0.04825066 Ry > estimated scf accuracy < 0.02330525 Ry > estimated scf accuracy < 0.01482943 Ry > estimated scf accuracy < 0.00395579 Ry > estimated scf accuracy < 0.00021627 Ry > estimated scf accuracy < 0.00002718 Ry > estimated scf accuracy < 0.00001596 Ry > estimated scf accuracy < 0.00000423 Ry > estimated scf accuracy < 0.00000096 Ry > estimated scf accuracy < 0.00000049 Ry > estimated scf accuracy < 0.00000040 Ry > estimated scf accuracy < 0.00000004 Ry > estimated scf accuracy < 8.2E-09 Ry > > My input file: > > &CONTROL > calculation = "relax" , > restart_mode = 'from_scratch' , > outdir='/tmp/GaAs/' , > pseudo_dir = './' , > prefix='GaAs' > disk_io = 'default' , > ! verbosity = 'default' , > tstress = .true. , > tprnfor = .true. , > nstep = 200 , > etot_conv_thr = 1.0E-5 , > forc_conv_thr = 1.0D-6 , > ! iprint = 3 , > max_seconds = 6000000 , > dt = 1000000 , > / > &SYSTEM > ibrav = 0 , > celldm(1) =7.383383939, > ! B = 3.70971016 , > ! C = 3.70971016 , > ! cosAB = 0.49517470 , > ! cosAC = 0.49517470 , > ! cosBC = 0.49517470 , > nat = 72 , > ntyp = 3 , > ecutwfc = 40.0 , > !ecutrho = 320.0 , > occupations = 'smearing' , > smearing = 'fd' , > degauss = 0.005 , > !nspin = 2 , > lda_plus_u = .false. , > > !celldm(1) = 3.907118519, > !celldm(3) = 10.D0, > > / > &ELECTRONS > electron_maxstep = 700 , > conv_thr = 1.0d-8 , > diagonalization = 'cg' , > / > &IONS > bfgs_ndim =3, > pot_extrapolation='atomic', > / > &CELL > cell_dynamics = 'damp-w' , > press = 0.00 , > ! wmass = 0.00700000 , > cell_dofree = 'xyz' , > / > CELL_PARAMETERS cubic > 2.00000 0.000000 0.000000 > 0.00000 2.000000 0.000000 > 0.00000 0.000000 10.00000 > ATOMIC_SPECIES > Ga 69.723 Ga.rrkj3.UPF > As 74.922 As.rrkj3.UPF > H 1.00794 H-1.25.UPF > ATOMIC_POSITIONS {alat} > Ga 0.00000050 -0.00000025 0.00682815 > Ga 0.49999874 0.49924596 0.70857798 > As 0.50000024 0.00000000 0.35277077 > As -0.00000050 0.49920484 1.06302457 > Ga -0.00000075 1.00000049 0.00921110 > Ga 0.50000024 1.50075426 0.70857948 > As 0.49999949 1.00000074 0.35474173 > As -0.00000050 1.50079488 1.06302507 > Ga 0.00000000 0.00000050 1.42032605 > Ga 0.49999974 0.50287293 2.12975309 > As 0.49999999 0.00000025 1.77702420 > As 0.00000000 0.50483913 2.48497829 > Ga -0.00000025 0.99999948 1.41672691 > Ga 0.49999949 1.49712679 2.12975209 > As 0.49999974 0.99999923 1.77125600 > As 0.00000000 1.49516135 2.48497904 > Ga 0.00000025 -0.00000176 2.83068972 > Ga 0.49999774 0.48620728 3.55158193 > As 0.49999999 -0.00000125 3.18153191 > As -0.00000075 0.47707341 3.90604332 > Ga -0.00000050 0.99999798 2.85092365 > Ga 0.49999849 1.51379294 3.55158244 > As 0.50000100 0.99999923 3.21014318 > As 0.00000000 1.52292731 3.90604307 > Ga 0.00000000 0.00000025 4.30422216 > Ga 0.49999974 0.55140319 4.97156294 > As 0.49999974 0.00000075 4.67996164 > As 0.00000000 0.69861686 5.30991586 > Ga 0.00000000 0.99999948 4.21931590 > Ga 0.49999949 1.44859754 4.97156219 > As 0.50000024 1.00000024 4.55459604 > As 0.00000000 1.30138387 5.30991436 > H 0.00000025 0.29006390 -0.24872539 > H 0.00000000 -0.29006290 -0.24872389 > H -0.00000075 1.29045005 -0.24574939 > H -0.00000075 0.70954892 -0.24574989 > Ga 1.00000050 -0.00000025 0.00682815 > Ga 1.49999874 0.49924596 0.70857798 > As 1.50000024 0.00000000 0.35277077 > As 0.99999950 0.49920484 1.06302457 > Ga 0.99999925 1.00000049 0.00921110 > Ga 1.50000024 1.50075426 0.70857948 > As 1.49999949 1.00000074 0.35474173 > As 0.99999950 1.50079488 1.06302507 > Ga 1.00000000 0.00000050 1.42032605 > Ga 1.49999974 0.50287293 2.12975309 > As 1.49999999 0.00000025 1.77702420 > As 1.00000000 0.50483913 2.48497829 > Ga 0.99999975 0.99999948 1.41672691 > Ga 1.49999949 1.49712679 2.12975209 > As 1.49999974 0.99999923 1.77125600 > As 1.00000000 1.49516135 2.48497904 > Ga 1.00000025 -0.00000176 2.83068972 > Ga 1.49999774 0.48620728 3.55158193 > As 1.49999999 -0.00000125 3.18153191 > As 0.99999925 0.47707341 3.90604332 > Ga 0.99999950 0.99999798 2.85092365 > Ga 1.49999849 1.51379294 3.55158244 > As 1.50000100 0.99999923 3.21014318 > As 1.00000000 1.52292731 3.90604307 > Ga 1.00000000 0.00000025 4.30422216 > Ga 1.49999974 0.55140319 4.97156294 > As 1.49999974 0.00000075 4.67996164 > As 1.00000000 0.69861686 5.30991586 > Ga 1.00000000 0.99999948 4.21931590 > Ga 1.49999949 1.44859754 4.97156219 > As 1.50000024 1.00000024 4.55459604 > As 1.00000000 1.30138387 5.30991436 > H 1.00000025 0.29006390 -0.24872539 > H 1.00000000 -0.29006290 -0.24872389 > H 0.99999925 1.29045005 -0.24574939 > H 0.99999925 0.70954892 -0.24574989 > K_POINTS automatic > 4 4 1 0 0 0 > > Best regards > Magdalena Birowska > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120510/11bfa198/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 10 May 2012 16:55:15 +0530 > From: manoj narayanan > Subject: [Pw_forum] Shift in K points > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all > Can any one tell in detail about shift in k point > mesh, like what and why it is ? and off course any relevant reference > regarding this will also be helpful. > > Thanking you in advance > Manoj N > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120510/f07e563b/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Thu, 10 May 2012 13:45:36 +0200 > From: Giuseppe Mattioli > Subject: Re: [Pw_forum] GaAs surface with fractional charges H > Zval=1.25, very large estimated scf accuracy > To: pw_forum at pwscf.org > Message-ID: <201205101345.37253.giuseppe.mattioli at ism.cnr.it> > Content-Type: Text/Plain; charset="iso-8859-15" > > > Dear Magdalena > Why do you suspect that your calculation has something wrong if it reaches > convergence in a not > unusually large number of scf steps? How does the second bfgs step, > starting from the previous wfc > and density, perform the scf? > Yes it starts from previous wfc and density and finally I got relaxed surface. But I was wondering why the scf estimated accuracy is so huge at the beginning of my calculations. Magda > Giuseppe > > On Thursday 10 May 2012 12:57:06 Magdalena Birowska wrote: > > Dear All, > > > > I am trying to relax a surface slab of GaAs which has 72 atoms. > > I found strange behaviour of first cycle of scf convergence. > > The estimated scf convergence is huge. I terminated Ga surface using > > fractional charges > > H=1.25, which I downloaded from the quantum espresso official website. > > When I use H=1, I don't see such a behaviour. > > Can anyone kindly suggest the possible source of error on my part. > > > > First cycle of SCF convergence: > > estimated scf accuracy < 3906.28215610 Ry > > estimated scf accuracy < 39347.40892210 Ry > > estimated scf accuracy < 18170.90673442 Ry > > estimated scf accuracy < 15951.19730682 Ry > > estimated scf accuracy < 15662.52132268 Ry > > estimated scf accuracy < 12286.77018220 Ry > > estimated scf accuracy < 12233.77236956 Ry > > estimated scf accuracy < 11694.83354422 Ry > > estimated scf accuracy < 15271.15048386 Ry > > estimated scf accuracy < 15566.68838647 Ry > > estimated scf accuracy < 47265.52643459 Ry > > estimated scf accuracy < 22511.42062539 Ry > > estimated scf accuracy < 24008.31787289 Ry > > estimated scf accuracy < 12935.76752149 Ry > > estimated scf accuracy < 16811.33660587 Ry > > estimated scf accuracy < 10992.92010369 Ry > > estimated scf accuracy < 4144.02105761 Ry > > estimated scf accuracy < 30138.05735660 Ry > > estimated scf accuracy < 10240.01360270 Ry > > estimated scf accuracy < 16789.80502995 Ry > > estimated scf accuracy < 6254.96875173 Ry > > estimated scf accuracy < 5678.83239125 Ry > > estimated scf accuracy < 5653.94732457 Ry > > estimated scf accuracy < 4634.85427954 Ry > > estimated scf accuracy < 4748.33851037 Ry > > estimated scf accuracy < 4570.74005737 Ry > > estimated scf accuracy < 2807.69984889 Ry > > estimated scf accuracy < 5304.65877872 Ry > > estimated scf accuracy < 2066.38501462 Ry > > estimated scf accuracy < 17495.61285271 Ry > > estimated scf accuracy < 18676.38196709 Ry > > estimated scf accuracy < 10884.14492461 Ry > > estimated scf accuracy < 17200.92388789 Ry > > estimated scf accuracy < 1160.48758157 Ry > > estimated scf accuracy < 1080.24247591 Ry > > estimated scf accuracy < 399.14797137 Ry > > estimated scf accuracy < 122.19296219 Ry > > estimated scf accuracy < 99.50315590 Ry > > estimated scf accuracy < 55.04456371 Ry > > estimated scf accuracy < 9.17378773 Ry > > estimated scf accuracy < 1.52941820 Ry > > estimated scf accuracy < 4.24567233 Ry > > estimated scf accuracy < 31.40572065 Ry > > estimated scf accuracy < 0.15173499 Ry > > estimated scf accuracy < 0.25128323 Ry > > estimated scf accuracy < 0.08254494 Ry > > estimated scf accuracy < 0.04825066 Ry > > estimated scf accuracy < 0.02330525 Ry > > estimated scf accuracy < 0.01482943 Ry > > estimated scf accuracy < 0.00395579 Ry > > estimated scf accuracy < 0.00021627 Ry > > estimated scf accuracy < 0.00002718 Ry > > estimated scf accuracy < 0.00001596 Ry > > estimated scf accuracy < 0.00000423 Ry > > estimated scf accuracy < 0.00000096 Ry > > estimated scf accuracy < 0.00000049 Ry > > estimated scf accuracy < 0.00000040 Ry > > estimated scf accuracy < 0.00000004 Ry > > estimated scf accuracy < 8.2E-09 Ry > > > > My input file: > > > > &CONTROL > > calculation = "relax" , > > restart_mode = 'from_scratch' , > > outdir='/tmp/GaAs/' , > > pseudo_dir = './' , > > prefix='GaAs' > > disk_io = 'default' , > > ! verbosity = 'default' , > > tstress = .true. , > > tprnfor = .true. , > > nstep = 200 , > > etot_conv_thr = 1.0E-5 , > > forc_conv_thr = 1.0D-6 , > > ! iprint = 3 , > > max_seconds = 6000000 , > > dt = 1000000 , > > / > > &SYSTEM > > ibrav = 0 , > > celldm(1) =7.383383939, > > ! B = 3.70971016 , > > ! C = 3.70971016 , > > ! cosAB = 0.49517470 , > > ! cosAC = 0.49517470 , > > ! cosBC = 0.49517470 , > > nat = 72 , > > ntyp = 3 , > > ecutwfc = 40.0 , > > !ecutrho = 320.0 , > > occupations = 'smearing' , > > smearing = 'fd' , > > degauss = 0.005 , > > !nspin = 2 , > > lda_plus_u = .false. , > > > > !celldm(1) = 3.907118519, > > !celldm(3) = 10.D0, > > > > / > > &ELECTRONS > > electron_maxstep = 700 , > > conv_thr = 1.0d-8 , > > diagonalization = 'cg' , > > / > > &IONS > > bfgs_ndim =3, > > pot_extrapolation='atomic', > > / > > &CELL > > cell_dynamics = 'damp-w' , > > press = 0.00 , > > ! wmass = 0.00700000 , > > cell_dofree = 'xyz' , > > / > > CELL_PARAMETERS cubic > > 2.00000 0.000000 0.000000 > > 0.00000 2.000000 0.000000 > > 0.00000 0.000000 10.00000 > > ATOMIC_SPECIES > > Ga 69.723 Ga.rrkj3.UPF > > As 74.922 As.rrkj3.UPF > > H 1.00794 H-1.25.UPF > > ATOMIC_POSITIONS {alat} > > Ga 0.00000050 -0.00000025 0.00682815 > > Ga 0.49999874 0.49924596 0.70857798 > > As 0.50000024 0.00000000 0.35277077 > > As -0.00000050 0.49920484 1.06302457 > > Ga -0.00000075 1.00000049 0.00921110 > > Ga 0.50000024 1.50075426 0.70857948 > > As 0.49999949 1.00000074 0.35474173 > > As -0.00000050 1.50079488 1.06302507 > > Ga 0.00000000 0.00000050 1.42032605 > > Ga 0.49999974 0.50287293 2.12975309 > > As 0.49999999 0.00000025 1.77702420 > > As 0.00000000 0.50483913 2.48497829 > > Ga -0.00000025 0.99999948 1.41672691 > > Ga 0.49999949 1.49712679 2.12975209 > > As 0.49999974 0.99999923 1.77125600 > > As 0.00000000 1.49516135 2.48497904 > > Ga 0.00000025 -0.00000176 2.83068972 > > Ga 0.49999774 0.48620728 3.55158193 > > As 0.49999999 -0.00000125 3.18153191 > > As -0.00000075 0.47707341 3.90604332 > > Ga -0.00000050 0.99999798 2.85092365 > > Ga 0.49999849 1.51379294 3.55158244 > > As 0.50000100 0.99999923 3.21014318 > > As 0.00000000 1.52292731 3.90604307 > > Ga 0.00000000 0.00000025 4.30422216 > > Ga 0.49999974 0.55140319 4.97156294 > > As 0.49999974 0.00000075 4.67996164 > > As 0.00000000 0.69861686 5.30991586 > > Ga 0.00000000 0.99999948 4.21931590 > > Ga 0.49999949 1.44859754 4.97156219 > > As 0.50000024 1.00000024 4.55459604 > > As 0.00000000 1.30138387 5.30991436 > > H 0.00000025 0.29006390 -0.24872539 > > H 0.00000000 -0.29006290 -0.24872389 > > H -0.00000075 1.29045005 -0.24574939 > > H -0.00000075 0.70954892 -0.24574989 > > Ga 1.00000050 -0.00000025 0.00682815 > > Ga 1.49999874 0.49924596 0.70857798 > > As 1.50000024 0.00000000 0.35277077 > > As 0.99999950 0.49920484 1.06302457 > > Ga 0.99999925 1.00000049 0.00921110 > > Ga 1.50000024 1.50075426 0.70857948 > > As 1.49999949 1.00000074 0.35474173 > > As 0.99999950 1.50079488 1.06302507 > > Ga 1.00000000 0.00000050 1.42032605 > > Ga 1.49999974 0.50287293 2.12975309 > > As 1.49999999 0.00000025 1.77702420 > > As 1.00000000 0.50483913 2.48497829 > > Ga 0.99999975 0.99999948 1.41672691 > > Ga 1.49999949 1.49712679 2.12975209 > > As 1.49999974 0.99999923 1.77125600 > > As 1.00000000 1.49516135 2.48497904 > > Ga 1.00000025 -0.00000176 2.83068972 > > Ga 1.49999774 0.48620728 3.55158193 > > As 1.49999999 -0.00000125 3.18153191 > > As 0.99999925 0.47707341 3.90604332 > > Ga 0.99999950 0.99999798 2.85092365 > > Ga 1.49999849 1.51379294 3.55158244 > > As 1.50000100 0.99999923 3.21014318 > > As 1.00000000 1.52292731 3.90604307 > > Ga 1.00000000 0.00000025 4.30422216 > > Ga 1.49999974 0.55140319 4.97156294 > > As 1.49999974 0.00000075 4.67996164 > > As 1.00000000 0.69861686 5.30991586 > > Ga 1.00000000 0.99999948 4.21931590 > > Ga 1.49999949 1.44859754 4.97156219 > > As 1.50000024 1.00000024 4.55459604 > > As 1.00000000 1.30138387 5.30991436 > > H 1.00000025 0.29006390 -0.24872539 > > H 1.00000000 -0.29006290 -0.24872389 > > H 0.99999925 1.29045005 -0.24574939 > > H 0.99999925 0.70954892 -0.24574989 > > K_POINTS automatic > > 4 4 1 0 0 0 > > > > Best regards > > Magdalena Birowska > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 59, Issue 19 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/10e04f5f/attachment-0001.htm From magda.birowska at gmail.com Thu May 10 14:10:49 2012 From: magda.birowska at gmail.com (Magdalena Birowska) Date: Thu, 10 May 2012 14:10:49 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 59, Issue 20 In-Reply-To: References: Message-ID: 2012/5/10 > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: Pw_forum Digest, Vol 59, Issue 19 (Magdalena Birowska) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 May 2012 14:03:09 +0200 > From: Magdalena Birowska > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 59, Issue 19 > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > 2012/5/10 > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/mailman/listinfo/pw_forum > > or, via email, send a message with subject or body 'help' to > > pw_forum-request at pwscf.org > > > > You can reach the person managing the list at > > pw_forum-owner at pwscf.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Pw_forum digest..." > > > > > > Today's Topics: > > > > 1. GaAs surface with fractional charges H Zval=1.25, very large > > estimated scf accuracy (Magdalena Birowska) > > 2. Shift in K points (manoj narayanan) > > 3. Re: GaAs surface with fractional charges H Zval=1.25, very > > large estimated scf accuracy (Giuseppe Mattioli) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 10 May 2012 12:57:06 +0200 > > From: Magdalena Birowska > > Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, > > very large estimated scf accuracy > > To: pw_forum at pwscf.org > > Message-ID: > > < > CA+H_66GKg7kWhg95McrDYX0OLBF8pRE0xKPOzkEBhsLxGUKoRQ at mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear All, > > > > I am trying to relax a surface slab of GaAs which has 72 atoms. > > I found strange behaviour of first cycle of scf convergence. > > The estimated scf convergence is huge. I terminated Ga surface using > > fractional charges > > H=1.25, which I downloaded from the quantum espresso official website. > > When I use H=1, I don't see such a behaviour. > > Can anyone kindly suggest the possible source of error on my part. > > > > First cycle of SCF convergence: > > estimated scf accuracy < 3906.28215610 Ry > > estimated scf accuracy < 39347.40892210 Ry > > estimated scf accuracy < 18170.90673442 Ry > > estimated scf accuracy < 15951.19730682 Ry > > estimated scf accuracy < 15662.52132268 Ry > > estimated scf accuracy < 12286.77018220 Ry > > estimated scf accuracy < 12233.77236956 Ry > > estimated scf accuracy < 11694.83354422 Ry > > estimated scf accuracy < 15271.15048386 Ry > > estimated scf accuracy < 15566.68838647 Ry > > estimated scf accuracy < 47265.52643459 Ry > > estimated scf accuracy < 22511.42062539 Ry > > estimated scf accuracy < 24008.31787289 Ry > > estimated scf accuracy < 12935.76752149 Ry > > estimated scf accuracy < 16811.33660587 Ry > > estimated scf accuracy < 10992.92010369 Ry > > estimated scf accuracy < 4144.02105761 Ry > > estimated scf accuracy < 30138.05735660 Ry > > estimated scf accuracy < 10240.01360270 Ry > > estimated scf accuracy < 16789.80502995 Ry > > estimated scf accuracy < 6254.96875173 Ry > > estimated scf accuracy < 5678.83239125 Ry > > estimated scf accuracy < 5653.94732457 Ry > > estimated scf accuracy < 4634.85427954 Ry > > estimated scf accuracy < 4748.33851037 Ry > > estimated scf accuracy < 4570.74005737 Ry > > estimated scf accuracy < 2807.69984889 Ry > > estimated scf accuracy < 5304.65877872 Ry > > estimated scf accuracy < 2066.38501462 Ry > > estimated scf accuracy < 17495.61285271 Ry > > estimated scf accuracy < 18676.38196709 Ry > > estimated scf accuracy < 10884.14492461 Ry > > estimated scf accuracy < 17200.92388789 Ry > > estimated scf accuracy < 1160.48758157 Ry > > estimated scf accuracy < 1080.24247591 Ry > > estimated scf accuracy < 399.14797137 Ry > > estimated scf accuracy < 122.19296219 Ry > > estimated scf accuracy < 99.50315590 Ry > > estimated scf accuracy < 55.04456371 Ry > > estimated scf accuracy < 9.17378773 Ry > > estimated scf accuracy < 1.52941820 Ry > > estimated scf accuracy < 4.24567233 Ry > > estimated scf accuracy < 31.40572065 Ry > > estimated scf accuracy < 0.15173499 Ry > > estimated scf accuracy < 0.25128323 Ry > > estimated scf accuracy < 0.08254494 Ry > > estimated scf accuracy < 0.04825066 Ry > > estimated scf accuracy < 0.02330525 Ry > > estimated scf accuracy < 0.01482943 Ry > > estimated scf accuracy < 0.00395579 Ry > > estimated scf accuracy < 0.00021627 Ry > > estimated scf accuracy < 0.00002718 Ry > > estimated scf accuracy < 0.00001596 Ry > > estimated scf accuracy < 0.00000423 Ry > > estimated scf accuracy < 0.00000096 Ry > > estimated scf accuracy < 0.00000049 Ry > > estimated scf accuracy < 0.00000040 Ry > > estimated scf accuracy < 0.00000004 Ry > > estimated scf accuracy < 8.2E-09 Ry > > > > My input file: > > > > &CONTROL > > calculation = "relax" , > > restart_mode = 'from_scratch' , > > outdir='/tmp/GaAs/' , > > pseudo_dir = './' , > > prefix='GaAs' > > disk_io = 'default' , > > ! verbosity = 'default' , > > tstress = .true. , > > tprnfor = .true. , > > nstep = 200 , > > etot_conv_thr = 1.0E-5 , > > forc_conv_thr = 1.0D-6 , > > ! iprint = 3 , > > max_seconds = 6000000 , > > dt = 1000000 , > > / > > &SYSTEM > > ibrav = 0 , > > celldm(1) =7.383383939, > > ! B = 3.70971016 , > > ! C = 3.70971016 , > > ! cosAB = 0.49517470 , > > ! cosAC = 0.49517470 , > > ! cosBC = 0.49517470 , > > nat = 72 , > > ntyp = 3 , > > ecutwfc = 40.0 , > > !ecutrho = 320.0 , > > occupations = 'smearing' , > > smearing = 'fd' , > > degauss = 0.005 , > > !nspin = 2 , > > lda_plus_u = .false. , > > > > !celldm(1) = 3.907118519, > > !celldm(3) = 10.D0, > > > > / > > &ELECTRONS > > electron_maxstep = 700 , > > conv_thr = 1.0d-8 , > > diagonalization = 'cg' , > > / > > &IONS > > bfgs_ndim =3, > > pot_extrapolation='atomic', > > / > > &CELL > > cell_dynamics = 'damp-w' , > > press = 0.00 , > > ! wmass = 0.00700000 , > > cell_dofree = 'xyz' , > > / > > CELL_PARAMETERS cubic > > 2.00000 0.000000 0.000000 > > 0.00000 2.000000 0.000000 > > 0.00000 0.000000 10.00000 > > ATOMIC_SPECIES > > Ga 69.723 Ga.rrkj3.UPF > > As 74.922 As.rrkj3.UPF > > H 1.00794 H-1.25.UPF > > ATOMIC_POSITIONS {alat} > > Ga 0.00000050 -0.00000025 0.00682815 > > Ga 0.49999874 0.49924596 0.70857798 > > As 0.50000024 0.00000000 0.35277077 > > As -0.00000050 0.49920484 1.06302457 > > Ga -0.00000075 1.00000049 0.00921110 > > Ga 0.50000024 1.50075426 0.70857948 > > As 0.49999949 1.00000074 0.35474173 > > As -0.00000050 1.50079488 1.06302507 > > Ga 0.00000000 0.00000050 1.42032605 > > Ga 0.49999974 0.50287293 2.12975309 > > As 0.49999999 0.00000025 1.77702420 > > As 0.00000000 0.50483913 2.48497829 > > Ga -0.00000025 0.99999948 1.41672691 > > Ga 0.49999949 1.49712679 2.12975209 > > As 0.49999974 0.99999923 1.77125600 > > As 0.00000000 1.49516135 2.48497904 > > Ga 0.00000025 -0.00000176 2.83068972 > > Ga 0.49999774 0.48620728 3.55158193 > > As 0.49999999 -0.00000125 3.18153191 > > As -0.00000075 0.47707341 3.90604332 > > Ga -0.00000050 0.99999798 2.85092365 > > Ga 0.49999849 1.51379294 3.55158244 > > As 0.50000100 0.99999923 3.21014318 > > As 0.00000000 1.52292731 3.90604307 > > Ga 0.00000000 0.00000025 4.30422216 > > Ga 0.49999974 0.55140319 4.97156294 > > As 0.49999974 0.00000075 4.67996164 > > As 0.00000000 0.69861686 5.30991586 > > Ga 0.00000000 0.99999948 4.21931590 > > Ga 0.49999949 1.44859754 4.97156219 > > As 0.50000024 1.00000024 4.55459604 > > As 0.00000000 1.30138387 5.30991436 > > H 0.00000025 0.29006390 -0.24872539 > > H 0.00000000 -0.29006290 -0.24872389 > > H -0.00000075 1.29045005 -0.24574939 > > H -0.00000075 0.70954892 -0.24574989 > > Ga 1.00000050 -0.00000025 0.00682815 > > Ga 1.49999874 0.49924596 0.70857798 > > As 1.50000024 0.00000000 0.35277077 > > As 0.99999950 0.49920484 1.06302457 > > Ga 0.99999925 1.00000049 0.00921110 > > Ga 1.50000024 1.50075426 0.70857948 > > As 1.49999949 1.00000074 0.35474173 > > As 0.99999950 1.50079488 1.06302507 > > Ga 1.00000000 0.00000050 1.42032605 > > Ga 1.49999974 0.50287293 2.12975309 > > As 1.49999999 0.00000025 1.77702420 > > As 1.00000000 0.50483913 2.48497829 > > Ga 0.99999975 0.99999948 1.41672691 > > Ga 1.49999949 1.49712679 2.12975209 > > As 1.49999974 0.99999923 1.77125600 > > As 1.00000000 1.49516135 2.48497904 > > Ga 1.00000025 -0.00000176 2.83068972 > > Ga 1.49999774 0.48620728 3.55158193 > > As 1.49999999 -0.00000125 3.18153191 > > As 0.99999925 0.47707341 3.90604332 > > Ga 0.99999950 0.99999798 2.85092365 > > Ga 1.49999849 1.51379294 3.55158244 > > As 1.50000100 0.99999923 3.21014318 > > As 1.00000000 1.52292731 3.90604307 > > Ga 1.00000000 0.00000025 4.30422216 > > Ga 1.49999974 0.55140319 4.97156294 > > As 1.49999974 0.00000075 4.67996164 > > As 1.00000000 0.69861686 5.30991586 > > Ga 1.00000000 0.99999948 4.21931590 > > Ga 1.49999949 1.44859754 4.97156219 > > As 1.50000024 1.00000024 4.55459604 > > As 1.00000000 1.30138387 5.30991436 > > H 1.00000025 0.29006390 -0.24872539 > > H 1.00000000 -0.29006290 -0.24872389 > > H 0.99999925 1.29045005 -0.24574939 > > H 0.99999925 0.70954892 -0.24574989 > > K_POINTS automatic > > 4 4 1 0 0 0 > > > > Best regards > > Magdalena Birowska > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20120510/11bfa198/attachment-0001.htm > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 10 May 2012 16:55:15 +0530 > > From: manoj narayanan > > Subject: [Pw_forum] Shift in K points > > To: pw_forum at pwscf.org > > Message-ID: > > 5AgHqA6ustmtKovWH6qA at mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello all > > Can any one tell in detail about shift in k > point > > mesh, like what and why it is ? and off course any relevant reference > > regarding this will also be helpful. > > > > Thanking you in advance > > Manoj N > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://www.democritos.it/pipermail/pw_forum/attachments/20120510/f07e563b/attachment-0001.htm > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 10 May 2012 13:45:36 +0200 > > From: Giuseppe Mattioli > > Subject: Re: [Pw_forum] GaAs surface with fractional charges H > > Zval=1.25, very large estimated scf accuracy > > To: pw_forum at pwscf.org > > Message-ID: <201205101345.37253.giuseppe.mattioli at ism.cnr.it> > > Content-Type: Text/Plain; charset="iso-8859-15" > > > > > > Dear Magdalena > > Why do you suspect that your calculation has something wrong if it > reaches > > convergence in a not > > unusually large number of scf steps? How does the second bfgs step, > > starting from the previous wfc > > and density, perform the scf? > > > > From the output I got : starting charge 263.92728, renormalised to 266.00000 negative rho (up, down): 0.236E-02 0.000E+00 Starting wfc are 264 randomized atomic wfcs, Why 264 atomic wfcs, shouldn't be 266 or fractional electron don't count? > Yes it starts from previous wfc and density and finally I got relaxed > surface. > But I was wondering why the scf estimated accuracy is so huge at the > beginning of my calculations. > > Magda > > > Giuseppe > > > > On Thursday 10 May 2012 12:57:06 Magdalena Birowska wrote: > > > Dear All, > > > > > > I am trying to relax a surface slab of GaAs which has 72 atoms. > > > I found strange behaviour of first cycle of scf convergence. > > > The estimated scf convergence is huge. I terminated Ga surface using > > > fractional charges > > > H=1.25, which I downloaded from the quantum espresso official website. > > > When I use H=1, I don't see such a behaviour. > > > Can anyone kindly suggest the possible source of error on my part. > > > > > > First cycle of SCF convergence: > > > estimated scf accuracy < 3906.28215610 Ry > > > estimated scf accuracy < 39347.40892210 Ry > > > estimated scf accuracy < 18170.90673442 Ry > > > estimated scf accuracy < 15951.19730682 Ry > > > estimated scf accuracy < 15662.52132268 Ry > > > estimated scf accuracy < 12286.77018220 Ry > > > estimated scf accuracy < 12233.77236956 Ry > > > estimated scf accuracy < 11694.83354422 Ry > > > estimated scf accuracy < 15271.15048386 Ry > > > estimated scf accuracy < 15566.68838647 Ry > > > estimated scf accuracy < 47265.52643459 Ry > > > estimated scf accuracy < 22511.42062539 Ry > > > estimated scf accuracy < 24008.31787289 Ry > > > estimated scf accuracy < 12935.76752149 Ry > > > estimated scf accuracy < 16811.33660587 Ry > > > estimated scf accuracy < 10992.92010369 Ry > > > estimated scf accuracy < 4144.02105761 Ry > > > estimated scf accuracy < 30138.05735660 Ry > > > estimated scf accuracy < 10240.01360270 Ry > > > estimated scf accuracy < 16789.80502995 Ry > > > estimated scf accuracy < 6254.96875173 Ry > > > estimated scf accuracy < 5678.83239125 Ry > > > estimated scf accuracy < 5653.94732457 Ry > > > estimated scf accuracy < 4634.85427954 Ry > > > estimated scf accuracy < 4748.33851037 Ry > > > estimated scf accuracy < 4570.74005737 Ry > > > estimated scf accuracy < 2807.69984889 Ry > > > estimated scf accuracy < 5304.65877872 Ry > > > estimated scf accuracy < 2066.38501462 Ry > > > estimated scf accuracy < 17495.61285271 Ry > > > estimated scf accuracy < 18676.38196709 Ry > > > estimated scf accuracy < 10884.14492461 Ry > > > estimated scf accuracy < 17200.92388789 Ry > > > estimated scf accuracy < 1160.48758157 Ry > > > estimated scf accuracy < 1080.24247591 Ry > > > estimated scf accuracy < 399.14797137 Ry > > > estimated scf accuracy < 122.19296219 Ry > > > estimated scf accuracy < 99.50315590 Ry > > > estimated scf accuracy < 55.04456371 Ry > > > estimated scf accuracy < 9.17378773 Ry > > > estimated scf accuracy < 1.52941820 Ry > > > estimated scf accuracy < 4.24567233 Ry > > > estimated scf accuracy < 31.40572065 Ry > > > estimated scf accuracy < 0.15173499 Ry > > > estimated scf accuracy < 0.25128323 Ry > > > estimated scf accuracy < 0.08254494 Ry > > > estimated scf accuracy < 0.04825066 Ry > > > estimated scf accuracy < 0.02330525 Ry > > > estimated scf accuracy < 0.01482943 Ry > > > estimated scf accuracy < 0.00395579 Ry > > > estimated scf accuracy < 0.00021627 Ry > > > estimated scf accuracy < 0.00002718 Ry > > > estimated scf accuracy < 0.00001596 Ry > > > estimated scf accuracy < 0.00000423 Ry > > > estimated scf accuracy < 0.00000096 Ry > > > estimated scf accuracy < 0.00000049 Ry > > > estimated scf accuracy < 0.00000040 Ry > > > estimated scf accuracy < 0.00000004 Ry > > > estimated scf accuracy < 8.2E-09 Ry > > > > > > My input file: > > > > > > &CONTROL > > > calculation = "relax" , > > > restart_mode = 'from_scratch' , > > > outdir='/tmp/GaAs/' , > > > pseudo_dir = './' , > > > prefix='GaAs' > > > disk_io = 'default' , > > > ! verbosity = 'default' , > > > tstress = .true. , > > > tprnfor = .true. , > > > nstep = 200 , > > > etot_conv_thr = 1.0E-5 , > > > forc_conv_thr = 1.0D-6 , > > > ! iprint = 3 , > > > max_seconds = 6000000 , > > > dt = 1000000 , > > > / > > > &SYSTEM > > > ibrav = 0 , > > > celldm(1) =7.383383939, > > > ! B = 3.70971016 , > > > ! C = 3.70971016 , > > > ! cosAB = 0.49517470 , > > > ! cosAC = 0.49517470 , > > > ! cosBC = 0.49517470 , > > > nat = 72 , > > > ntyp = 3 , > > > ecutwfc = 40.0 , > > > !ecutrho = 320.0 , > > > occupations = 'smearing' , > > > smearing = 'fd' , > > > degauss = 0.005 , > > > !nspin = 2 , > > > lda_plus_u = .false. , > > > > > > !celldm(1) = 3.907118519, > > > !celldm(3) = 10.D0, > > > > > > / > > > &ELECTRONS > > > electron_maxstep = 700 , > > > conv_thr = 1.0d-8 , > > > diagonalization = 'cg' , > > > / > > > &IONS > > > bfgs_ndim =3, > > > pot_extrapolation='atomic', > > > / > > > &CELL > > > cell_dynamics = 'damp-w' , > > > press = 0.00 , > > > ! wmass = 0.00700000 , > > > cell_dofree = 'xyz' , > > > / > > > CELL_PARAMETERS cubic > > > 2.00000 0.000000 0.000000 > > > 0.00000 2.000000 0.000000 > > > 0.00000 0.000000 10.00000 > > > ATOMIC_SPECIES > > > Ga 69.723 Ga.rrkj3.UPF > > > As 74.922 As.rrkj3.UPF > > > H 1.00794 H-1.25.UPF > > > ATOMIC_POSITIONS {alat} > > > Ga 0.00000050 -0.00000025 0.00682815 > > > Ga 0.49999874 0.49924596 0.70857798 > > > As 0.50000024 0.00000000 0.35277077 > > > As -0.00000050 0.49920484 1.06302457 > > > Ga -0.00000075 1.00000049 0.00921110 > > > Ga 0.50000024 1.50075426 0.70857948 > > > As 0.49999949 1.00000074 0.35474173 > > > As -0.00000050 1.50079488 1.06302507 > > > Ga 0.00000000 0.00000050 1.42032605 > > > Ga 0.49999974 0.50287293 2.12975309 > > > As 0.49999999 0.00000025 1.77702420 > > > As 0.00000000 0.50483913 2.48497829 > > > Ga -0.00000025 0.99999948 1.41672691 > > > Ga 0.49999949 1.49712679 2.12975209 > > > As 0.49999974 0.99999923 1.77125600 > > > As 0.00000000 1.49516135 2.48497904 > > > Ga 0.00000025 -0.00000176 2.83068972 > > > Ga 0.49999774 0.48620728 3.55158193 > > > As 0.49999999 -0.00000125 3.18153191 > > > As -0.00000075 0.47707341 3.90604332 > > > Ga -0.00000050 0.99999798 2.85092365 > > > Ga 0.49999849 1.51379294 3.55158244 > > > As 0.50000100 0.99999923 3.21014318 > > > As 0.00000000 1.52292731 3.90604307 > > > Ga 0.00000000 0.00000025 4.30422216 > > > Ga 0.49999974 0.55140319 4.97156294 > > > As 0.49999974 0.00000075 4.67996164 > > > As 0.00000000 0.69861686 5.30991586 > > > Ga 0.00000000 0.99999948 4.21931590 > > > Ga 0.49999949 1.44859754 4.97156219 > > > As 0.50000024 1.00000024 4.55459604 > > > As 0.00000000 1.30138387 5.30991436 > > > H 0.00000025 0.29006390 -0.24872539 > > > H 0.00000000 -0.29006290 -0.24872389 > > > H -0.00000075 1.29045005 -0.24574939 > > > H -0.00000075 0.70954892 -0.24574989 > > > Ga 1.00000050 -0.00000025 0.00682815 > > > Ga 1.49999874 0.49924596 0.70857798 > > > As 1.50000024 0.00000000 0.35277077 > > > As 0.99999950 0.49920484 1.06302457 > > > Ga 0.99999925 1.00000049 0.00921110 > > > Ga 1.50000024 1.50075426 0.70857948 > > > As 1.49999949 1.00000074 0.35474173 > > > As 0.99999950 1.50079488 1.06302507 > > > Ga 1.00000000 0.00000050 1.42032605 > > > Ga 1.49999974 0.50287293 2.12975309 > > > As 1.49999999 0.00000025 1.77702420 > > > As 1.00000000 0.50483913 2.48497829 > > > Ga 0.99999975 0.99999948 1.41672691 > > > Ga 1.49999949 1.49712679 2.12975209 > > > As 1.49999974 0.99999923 1.77125600 > > > As 1.00000000 1.49516135 2.48497904 > > > Ga 1.00000025 -0.00000176 2.83068972 > > > Ga 1.49999774 0.48620728 3.55158193 > > > As 1.49999999 -0.00000125 3.18153191 > > > As 0.99999925 0.47707341 3.90604332 > > > Ga 0.99999950 0.99999798 2.85092365 > > > Ga 1.49999849 1.51379294 3.55158244 > > > As 1.50000100 0.99999923 3.21014318 > > > As 1.00000000 1.52292731 3.90604307 > > > Ga 1.00000000 0.00000025 4.30422216 > > > Ga 1.49999974 0.55140319 4.97156294 > > > As 1.49999974 0.00000075 4.67996164 > > > As 1.00000000 0.69861686 5.30991586 > > > Ga 1.00000000 0.99999948 4.21931590 > > > Ga 1.49999949 1.44859754 4.97156219 > > > As 1.50000024 1.00000024 4.55459604 > > > As 1.00000000 1.30138387 5.30991436 > > > H 1.00000025 0.29006390 -0.24872539 > > > H 1.00000000 -0.29006290 -0.24872389 > > > H 0.99999925 1.29045005 -0.24574939 > > > H 0.99999925 0.70954892 -0.24574989 > > > K_POINTS automatic > > > 4 4 1 0 0 0 > > > > > > Best regards > > > Magdalena Birowska > > > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00015 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 59, Issue 19 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120510/10e04f5f/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 59, Issue 20 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/f8e2db32/attachment-0001.htm From izaakw89 at yahoo.com Thu May 10 17:03:17 2012 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 10 May 2012 08:03:17 -0700 (PDT) Subject: [Pw_forum] Choosing awin for planar average calculations Message-ID: <1336662197.11502.YahooMailNeo@web43411.mail.sp1.yahoo.com> Dear All, I want to calculate the planar average of potential along a certain direction for a bulk supercell. Could anyone tell me how to choose the value for awin (window size for macroscopic averages)? Thank you. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/ab14583e/attachment.htm From bfazi90 at gmail.com Thu May 10 17:11:45 2012 From: bfazi90 at gmail.com (bf azi) Date: Thu, 10 May 2012 19:41:45 +0430 Subject: [Pw_forum] occupations Message-ID: Dear all Which "occupations" better for "BNNT"? ("smearing" or "fixed") thanks a lot Bani Adam Faculty of Science Egypt From lorenzo.paulatto at impmc.upmc.fr Thu May 10 17:37:40 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 10 May 2012 17:37:40 +0200 Subject: [Pw_forum] occupations In-Reply-To: References: Message-ID: On Thu, 10 May 2012 17:11:45 +0200, bf azi wrote: > Which "occupations" better for "BNNT"? > ("smearing" or "fixed") Dear Bani, it depends, what is a BNNT? -- Lorenzo Paulatto -- Paris From alex.kutana at gmail.com Thu May 10 18:53:56 2012 From: alex.kutana at gmail.com (Alex Kutana) Date: Thu, 10 May 2012 12:53:56 -0400 Subject: [Pw_forum] symmetry of the electron-phonon coupling coefficients Message-ID: Dear PW forum users and developers: Could please somebody with the knowledge of inner workings of the electron-phonon code help me with this issue: I am looking at the symmetry of the electron-phonon coupling coefficients with respect to displacement patterns. In particular, if one displacement pattern is the negative of the other, the coefficients should be identical but with opposite signs. However, when I look at these coefficients in, an e.g. a CO molecule, there is no such symmetry. I have a C atom at the origin, and an O atom on the x axis at 1.133999556 0.0 0.0 A. The first displacement pattern is -1.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 and the second one is -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -1.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 -0.000000000000000E+000,-0.000000000000000E+000 i.e. the second is the negative of the first. However, the electron-phonon matrix elements for these patterns differ by more than just a sign. Below is a list of matrix elements for transitions among 9 electronic bands. As expected, the diagonal elements are same and of opposite signs, but the off-diagonal elements are very different. Is there an explanation of this that I was missing? Thank you. Alex Kutana Naval Research Laboratory displacement pattern #1: 0->0 0.286566684793000 -0.000000000000000 |g|^2= 0.082120464833251 1->0 -0.034559192981500 0.000031395207500 |g|^2= 0.001194338805192 2->0 -0.000000009558500 0.000000000406000 |g|^2= 0.000000000000000 3->0 0.000000003843000 -0.000000000408500 |g|^2= 0.000000000000000 4->0 0.209537778542500 0.001560705053000 |g|^2= 0.043908516436788 5->0 -0.000000245218500 0.000000483888500 |g|^2= 0.000000000000294 6->0 -0.000000151028000 -0.000000094130500 |g|^2= 0.000000000000032 7->0 0.015210336449500 0.009035433075000 |g|^2= 0.000312993385760 8->0 -0.018916187765500 0.000692293887500 |g|^2= 0.000358301430406 0->1 -0.065753284810500 -0.000059732881500 |g|^2= 0.004323498031388 1->1 -0.010470695547000 0.000000000000000 |g|^2= 0.000109635465238 2->1 0.000000003980500 0.000000000330000 |g|^2= 0.000000000000000 3->1 -0.000000001742000 0.000000000782000 |g|^2= 0.000000000000000 4->1 -0.116488042493500 -0.000973469004500 |g|^2= 0.013570411685870 5->1 0.000000058681500 -0.000000183316500 |g|^2= 0.000000000000037 6->1 0.000000093539000 0.000000028930500 |g|^2= 0.000000000000010 7->1 -0.007170125204000 -0.004268243132000 |g|^2= 0.000069628594875 8->1 0.006675139863000 -0.000242290788500 |g|^2= 0.000044616197017 0->2 -0.000000006649000 -0.000000000795500 |g|^2= 0.000000000000000 1->2 0.000000003757500 -0.000000000281000 |g|^2= 0.000000000000000 2->2 0.172144600342000 -0.000000000000000 |g|^2= 0.029633763426907 3->2 -0.000000007757000 0.000000000424000 |g|^2= 0.000000000000000 4->2 -0.000000007901500 -0.000000000563000 |g|^2= 0.000000000000000 5->2 0.030940253556500 -0.030452295289500 |g|^2= 0.001884641578539 6->2 -0.001917560140000 0.001237350092000 |g|^2= 0.000005208072141 7->2 -0.000005383433500 -0.000006566545000 |g|^2= 0.000000000072101 8->2 0.001206036691000 0.000501228329000 |g|^2= 0.000001705754338 0->3 0.000000002888000 -0.000000000118000 |g|^2= 0.000000000000000 1->3 -0.000000001701000 -0.000000000735000 |g|^2= 0.000000000000000 2->3 -0.000000007757000 -0.000000000424000 |g|^2= 0.000000000000000 3->3 0.172144582271500 -0.000000000000000 |g|^2= 0.029633757205429 4->3 0.000000004962500 0.000000000048500 |g|^2= 0.000000000000000 5->3 -0.002270121070500 0.000239348528500 |g|^2= 0.000005210737393 6->3 -0.043196420568000 -0.004313967793500 |g|^2= 0.001884541068011 7->3 -0.000000730034000 -0.000003790831000 |g|^2= 0.000000000014903 8->3 -0.000008416957500 0.000059829663500 |g|^2= 0.000000003650434 0->4 0.214778021593500 -0.001599735961000 |g|^2= 0.046132157714763 1->4 -0.124602739906000 0.001041282029500 |g|^2= 0.015526927060347 2->4 -0.000000007138000 0.000000000629000 |g|^2= 0.000000000000000 3->4 0.000000004680500 0.000000000120000 |g|^2= 0.000000000000000 4->4 -0.044695925543000 -0.000000000000000 |g|^2= 0.001997725760145 5->4 -0.000000242546000 0.000000487089500 |g|^2= 0.000000000000296 6->4 -0.000000143113500 -0.000000102335000 |g|^2= 0.000000000000031 7->4 -0.004399490592000 -0.002570431486500 |g|^2= 0.000025962635496 8->4 -0.042523842474500 0.001638507220500 |g|^2= 0.001810961884708 0->5 -0.000000167311000 -0.000000343222500 |g|^2= 0.000000000000146 1->5 0.000000058893000 0.000000158656000 |g|^2= 0.000000000000029 2->5 0.032613474298500 0.032099121156000 |g|^2= 0.002093992284806 3->5 -0.002392872109500 -0.000252279387500 |g|^2= 0.000005789481822 4->5 -0.000000180652000 -0.000000410655000 |g|^2= 0.000000000000201 5->5 -0.185897249768000 0.000000000000000 |g|^2= 0.034557787471306 6->5 -0.000000087123000 -0.000000071728500 |g|^2= 0.000000000000013 7->5 0.000000490662500 -0.000011219521500 |g|^2= 0.000000000126118 8->5 0.000649413466000 0.001510073388500 |g|^2= 0.000002702059488 0->6 -0.000000102127000 0.000000060209500 |g|^2= 0.000000000000014 1->6 0.000000074069000 -0.000000025468000 |g|^2= 0.000000000000006 2->6 -0.002021278101500 -0.001304265009000 |g|^2= 0.000005786672377 3->6 -0.045532542731000 0.004547271821500 |g|^2= 0.002093890128569 4->6 -0.000000144484000 0.000000080179500 |g|^2= 0.000000000000027 5->6 -0.000000087123000 0.000000071728500 |g|^2= 0.000000000000013 6->6 -0.185898399888000 -0.000000000000000 |g|^2= 0.034558215080919 7->6 0.000000984953000 0.000004942462000 |g|^2= 0.000000000025398 8->6 -0.000038006325000 -0.000142788293500 |g|^2= 0.000000021832978 0->7 0.015372187389000 -0.009132041345000 |g|^2= 0.000319698324249 1->7 -0.009727469332000 0.005790740403500 |g|^2= 0.000128156334026 2->7 -0.000004934450500 0.000006008964000 |g|^2= 0.000000000060456 3->7 -0.000000667739000 0.000003460446000 |g|^2= 0.000000000012421 4->7 -0.009877533487000 0.005769648051000 |g|^2= 0.000130854506419 5->7 0.000000496943500 0.000011202097500 |g|^2= 0.000000000125734 6->7 0.000000981650000 -0.000004929340500 |g|^2= 0.000000000025262 7->7 -0.000633793442000 0.000000000000000 |g|^2= 0.000000401694127 8->7 0.000030518449500 -0.000027055324500 |g|^2= 0.000000001663366 0->8 -0.013941745790500 -0.000533958928500 |g|^2= 0.000194657387824 1->8 0.004172651103000 0.000183619549500 |g|^2= 0.000017444733366 2->8 0.001106454865000 -0.000459738505500 |g|^2= 0.000001435601862 3->8 -0.000007736827500 -0.000054991042000 |g|^2= 0.000000003083873 4->8 -0.042832546265500 -0.001607772328500 |g|^2= 0.001837211951446 5->8 0.000648997548500 -0.001509835303000 |g|^2= 0.000002700800460 6->8 -0.000038017739500 0.000142907934000 |g|^2= 0.000000021868026 7->8 0.000025705638000 0.000024838755500 |g|^2= 0.000000001277744 8->8 -0.003734049495500 0.000000000000000 |g|^2= 0.000013943125635 displacement pattern #2: 0->0 -0.286565847377500 -0.000000000000000 |g|^2= 0.082119984883185 1->0 0.379851516091000 -0.000345068730000 |g|^2= 0.144287293349060 2->0 0.000000006163500 -0.000000002258000 |g|^2= 0.000000000000000 3->0 0.000000001618500 -0.000000001134500 |g|^2= 0.000000000000000 4->0 -0.133458411497500 -0.000994042731000 |g|^2= 0.017812135720387 5->0 0.000000190857000 -0.000000051579000 |g|^2= 0.000000000000039 6->0 -0.000000069523000 -0.000000017790500 |g|^2= 0.000000000000005 7->0 -0.019890115224000 -0.011817220800500 |g|^2= 0.000535263391072 8->0 -0.039430161288000 0.001065942700500 |g|^2= 0.001555873853038 0->1 0.462246877696500 0.000419919480500 |g|^2= 0.213672352272533 1->1 0.010494926539500 0.000000000000000 |g|^2= 0.000110143483070 2->1 -0.000000003602000 -0.000000000104000 |g|^2= 0.000000000000000 3->1 -0.000000004409500 0.000000001875500 |g|^2= 0.000000000000000 4->1 0.065269015154500 0.000545440362000 |g|^2= 0.004260341844427 5->1 -0.000000404569000 0.000000095724000 |g|^2= 0.000000000000173 6->1 0.000000304352500 -0.000000014508500 |g|^2= 0.000000000000093 7->1 0.018784573101500 0.011183159264000 |g|^2= 0.000477923237730 8->1 0.042649049483000 -0.001095308735500 |g|^2= 0.001820141123029 0->2 0.000000009800000 0.000000002671000 |g|^2= 0.000000000000000 1->2 -0.000000003294500 0.000000000339500 |g|^2= 0.000000000000000 2->2 -0.172141736923500 0.000000000000000 |g|^2= 0.029632777591039 3->2 0.000000095818500 -0.000000007298000 |g|^2= 0.000000000000009 4->2 0.000000001027500 0.000000000264500 |g|^2= 0.000000000000000 5->2 0.058175921580500 -0.057258304602500 |g|^2= 0.006662951297693 6->2 -0.003606567884000 0.002326495942500 |g|^2= 0.000018419915272 7->2 0.000017034603500 0.000020332543000 |g|^2= 0.000000000703590 8->2 -0.003455200640000 -0.001431532813500 |g|^2= 0.000013987697659 0->3 0.000000001244500 0.000000000964500 |g|^2= 0.000000000000000 1->3 -0.000000004262500 -0.000000001807000 |g|^2= 0.000000000000000 2->3 0.000000095818500 0.000000007298000 |g|^2= 0.000000000000009 3->3 -0.172141573131500 0.000000000000000 |g|^2= 0.029632721200188 4->3 0.000000002276500 -0.000000000110500 |g|^2= 0.000000000000000 5->3 -0.004267707540000 0.000449461611500 |g|^2= 0.000018415343387 6->3 -0.081224513696500 -0.008111670337000 |g|^2= 0.006663220820889 7->3 0.000001861979500 0.000010745158500 |g|^2= 0.000000000118925 8->3 0.000028586479000 -0.000167502870000 |g|^2= 0.000000028874398 0->4 -0.231003310734000 0.001720588928000 |g|^2= 0.053365489996328 1->4 0.047001759819500 -0.000392784013500 |g|^2= 0.002209319705411 2->4 0.000000001059500 -0.000000000150500 |g|^2= 0.000000000000000 3->4 0.000000002186000 0.000000000118000 |g|^2= 0.000000000000000 4->4 0.044659534793500 0.000000000000000 |g|^2= 0.001994474047972 5->4 0.000000150192500 0.000000032648000 |g|^2= 0.000000000000024 6->4 -0.000000156776000 -0.000000002718000 |g|^2= 0.000000000000025 7->4 -0.001310064441500 -0.000765519326000 |g|^2= 0.000002302288679 8->4 -0.020407897616500 0.000742934507000 |g|^2= 0.000417034236807 0->5 0.000000235769000 0.000000210453500 |g|^2= 0.000000000000100 1->5 -0.000000265807500 -0.000000046707500 |g|^2= 0.000000000000073 2->5 0.056219406513000 0.055332648710500 |g|^2= 0.006222323681994 3->5 -0.004124172441500 -0.000434330422000 |g|^2= 0.000017197441243 4->5 0.000000122701500 -0.000000029810500 |g|^2= 0.000000000000016 5->5 0.185880014452500 0.000000000000000 |g|^2= 0.034551379772862 6->5 0.000000140947000 0.000000125297000 |g|^2= 0.000000000000036 7->5 -0.000000941527500 0.000011971521000 |g|^2= 0.000000000144204 8->5 -0.000798785488000 -0.001869578039500 |g|^2= 0.000004133380302 0->6 0.000000026588500 0.000000024247000 |g|^2= 0.000000000000001 1->6 0.000000266009000 0.000000033201000 |g|^2= 0.000000000000072 2->6 -0.003485291586500 -0.002248257310000 |g|^2= 0.000017201918375 3->6 -0.078492855467500 0.007838873909000 |g|^2= 0.006222576303603 4->6 -0.000000139482000 -0.000000000856000 |g|^2= 0.000000000000019 5->6 0.000000140947000 -0.000000125297000 |g|^2= 0.000000000000036 6->6 0.185880943275000 -0.000000000000000 |g|^2= 0.034551725072804 7->6 -0.000001321611500 -0.000005771953000 |g|^2= 0.000000000035062 8->6 0.000048260043000 0.000176321833000 |g|^2= 0.000000033418421 0->7 -0.026071694374000 0.015489281608000 |g|^2= 0.000919651092263 1->7 0.001697741814000 -0.001010730029500 |g|^2= 0.000003903902460 2->7 0.000015106160500 -0.000018083799000 |g|^2= 0.000000000555220 3->7 0.000001672337500 -0.000009663610500 |g|^2= 0.000000000096182 4->7 0.002315940634500 -0.001352389584500 |g|^2= 0.000007192538611 5->7 -0.000000927570500 -0.000011708792000 |g|^2= 0.000000000137956 6->7 -0.000001291943000 0.000005661201000 |g|^2= 0.000000000033718 7->7 0.000818543483500 -0.000000000000000 |g|^2= 0.000000670013434 8->7 -0.000425351836000 0.000280356039500 |g|^2= 0.000000259523693 0->8 -0.026410868906000 -0.000617126400500 |g|^2= 0.000697914841364 1->8 0.008979264003000 0.000226470303000 |g|^2= 0.000080678470834 2->8 -0.003085839551500 0.001279050530500 |g|^2= 0.000011158375997 3->8 0.000025569678000 0.000149732451000 |g|^2= 0.000000023073615 4->8 -0.010002857794000 -0.000375228864000 |g|^2= 0.000100197960747 5->8 -0.000775808756500 0.001816292782500 |g|^2= 0.000003900798698 6->8 0.000046818670500 -0.000171407224000 |g|^2= 0.000000031572424 7->8 -0.000239755938500 -0.000163419629500 |g|^2= 0.000000084188885 8->8 0.003793073996500 0.000000000000000 |g|^2= 0.000014387410343 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/1fb36a0f/attachment-0001.htm From giannozz at democritos.it Thu May 10 22:15:16 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 May 2012 22:15:16 +0200 Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, very large estimated scf accuracy In-Reply-To: References: Message-ID: <22B3717B-9A10-48C5-9015-11E35AFF00CE@democritos.it> On May 10, 2012, at 12:57 , Magdalena Birowska wrote: > I found strange behaviour of first cycle of scf convergence. it is quite normal to have a large error in the first iteration and an even larger one in the second for surfaces. Typically the scf error decays quite quickly afterwards. In this case it is rather slow, although it seem to converge nicely at the end > When I use H=1, I don't see such a behaviour. you might start with H=1 and continue with H=1.25 > etot_conv_thr = 1.0E-5 default (very tight) > forc_conv_thr = 1.0D-6 too tight: relaxation will never converge > smearing = 'fd' , very inefficient, should not be normally used > degauss = 0.005 , likely too small to have effect > conv_thr = 1.0d-8 in structural relaxation it is usually convenient to start with a larger threshold, 1.0d-6 or so; it will be automatically reduced during relaxation > diagonalization = 'cg' don't use this unless 'david' fails P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Thu May 10 22:56:49 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 10 May 2012 22:56:49 +0200 Subject: [Pw_forum] symmetry of the electron-phonon coupling coefficients In-Reply-To: References: Message-ID: <4FAC2B91.4060103@sissa.it> dear Alex I don't think that the two matrix element should be equal and opposite. suppose you apply both displacement together which means you displace the molecule as a whole. the eigenvalue will not change, hence < i | dV | i > = 0 but the new eigen-wavefunctions | i' > will be the translated of the original ones, hence different from them. to first order |i'> = |i> + sum |j> /delta e_IJ since |i'> =/= |i> no reason to believe that < j | d V | i > = 0. stefano On 05/10/2012 06:53 PM, Alex Kutana wrote: > Dear PW forum users and developers: > > Could please somebody with the knowledge of inner workings of the > electron-phonon code help me with this issue: > I am looking at the symmetry of the electron-phonon coupling coefficients > with respect to displacement patterns. > In particular, if one displacement pattern is the negative of the other, > the coefficients should be identical but with opposite signs. > However, when I look at these coefficients in, an e.g. a CO molecule, there > is no such symmetry. > I have a C atom at the origin, and an O atom on the x axis at 1.133999556 > 0.0 0.0 A. > The first displacement pattern is > -1.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > > and the second one is > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -1.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > -0.000000000000000E+000,-0.000000000000000E+000 > > i.e. the second is the negative of the first. > > However, the electron-phonon matrix elements for these patterns differ by > more than just a sign. Below is a list of matrix elements for transitions > among 9 electronic bands. As expected, the diagonal elements > are same and of opposite signs, but the off-diagonal elements are very > different. Is there an explanation of this that I was missing? > Thank you. > > Alex Kutana > Naval Research Laboratory > > > displacement pattern #1: > 0->0 0.286566684793000 -0.000000000000000 |g|^2= 0.082120464833251 > 1->0 -0.034559192981500 0.000031395207500 |g|^2= 0.001194338805192 > 2->0 -0.000000009558500 0.000000000406000 |g|^2= 0.000000000000000 > 3->0 0.000000003843000 -0.000000000408500 |g|^2= 0.000000000000000 > 4->0 0.209537778542500 0.001560705053000 |g|^2= 0.043908516436788 > 5->0 -0.000000245218500 0.000000483888500 |g|^2= 0.000000000000294 > 6->0 -0.000000151028000 -0.000000094130500 |g|^2= 0.000000000000032 > 7->0 0.015210336449500 0.009035433075000 |g|^2= 0.000312993385760 > 8->0 -0.018916187765500 0.000692293887500 |g|^2= 0.000358301430406 > 0->1 -0.065753284810500 -0.000059732881500 |g|^2= 0.004323498031388 > 1->1 -0.010470695547000 0.000000000000000 |g|^2= 0.000109635465238 > 2->1 0.000000003980500 0.000000000330000 |g|^2= 0.000000000000000 > 3->1 -0.000000001742000 0.000000000782000 |g|^2= 0.000000000000000 > 4->1 -0.116488042493500 -0.000973469004500 |g|^2= 0.013570411685870 > 5->1 0.000000058681500 -0.000000183316500 |g|^2= 0.000000000000037 > 6->1 0.000000093539000 0.000000028930500 |g|^2= 0.000000000000010 > 7->1 -0.007170125204000 -0.004268243132000 |g|^2= 0.000069628594875 > 8->1 0.006675139863000 -0.000242290788500 |g|^2= 0.000044616197017 > 0->2 -0.000000006649000 -0.000000000795500 |g|^2= 0.000000000000000 > 1->2 0.000000003757500 -0.000000000281000 |g|^2= 0.000000000000000 > 2->2 0.172144600342000 -0.000000000000000 |g|^2= 0.029633763426907 > 3->2 -0.000000007757000 0.000000000424000 |g|^2= 0.000000000000000 > 4->2 -0.000000007901500 -0.000000000563000 |g|^2= 0.000000000000000 > 5->2 0.030940253556500 -0.030452295289500 |g|^2= 0.001884641578539 > 6->2 -0.001917560140000 0.001237350092000 |g|^2= 0.000005208072141 > 7->2 -0.000005383433500 -0.000006566545000 |g|^2= 0.000000000072101 > 8->2 0.001206036691000 0.000501228329000 |g|^2= 0.000001705754338 > 0->3 0.000000002888000 -0.000000000118000 |g|^2= 0.000000000000000 > 1->3 -0.000000001701000 -0.000000000735000 |g|^2= 0.000000000000000 > 2->3 -0.000000007757000 -0.000000000424000 |g|^2= 0.000000000000000 > 3->3 0.172144582271500 -0.000000000000000 |g|^2= 0.029633757205429 > 4->3 0.000000004962500 0.000000000048500 |g|^2= 0.000000000000000 > 5->3 -0.002270121070500 0.000239348528500 |g|^2= 0.000005210737393 > 6->3 -0.043196420568000 -0.004313967793500 |g|^2= 0.001884541068011 > 7->3 -0.000000730034000 -0.000003790831000 |g|^2= 0.000000000014903 > 8->3 -0.000008416957500 0.000059829663500 |g|^2= 0.000000003650434 > 0->4 0.214778021593500 -0.001599735961000 |g|^2= 0.046132157714763 > 1->4 -0.124602739906000 0.001041282029500 |g|^2= 0.015526927060347 > 2->4 -0.000000007138000 0.000000000629000 |g|^2= 0.000000000000000 > 3->4 0.000000004680500 0.000000000120000 |g|^2= 0.000000000000000 > 4->4 -0.044695925543000 -0.000000000000000 |g|^2= 0.001997725760145 > 5->4 -0.000000242546000 0.000000487089500 |g|^2= 0.000000000000296 > 6->4 -0.000000143113500 -0.000000102335000 |g|^2= 0.000000000000031 > 7->4 -0.004399490592000 -0.002570431486500 |g|^2= 0.000025962635496 > 8->4 -0.042523842474500 0.001638507220500 |g|^2= 0.001810961884708 > 0->5 -0.000000167311000 -0.000000343222500 |g|^2= 0.000000000000146 > 1->5 0.000000058893000 0.000000158656000 |g|^2= 0.000000000000029 > 2->5 0.032613474298500 0.032099121156000 |g|^2= 0.002093992284806 > 3->5 -0.002392872109500 -0.000252279387500 |g|^2= 0.000005789481822 > 4->5 -0.000000180652000 -0.000000410655000 |g|^2= 0.000000000000201 > 5->5 -0.185897249768000 0.000000000000000 |g|^2= 0.034557787471306 > 6->5 -0.000000087123000 -0.000000071728500 |g|^2= 0.000000000000013 > 7->5 0.000000490662500 -0.000011219521500 |g|^2= 0.000000000126118 > 8->5 0.000649413466000 0.001510073388500 |g|^2= 0.000002702059488 > 0->6 -0.000000102127000 0.000000060209500 |g|^2= 0.000000000000014 > 1->6 0.000000074069000 -0.000000025468000 |g|^2= 0.000000000000006 > 2->6 -0.002021278101500 -0.001304265009000 |g|^2= 0.000005786672377 > 3->6 -0.045532542731000 0.004547271821500 |g|^2= 0.002093890128569 > 4->6 -0.000000144484000 0.000000080179500 |g|^2= 0.000000000000027 > 5->6 -0.000000087123000 0.000000071728500 |g|^2= 0.000000000000013 > 6->6 -0.185898399888000 -0.000000000000000 |g|^2= 0.034558215080919 > 7->6 0.000000984953000 0.000004942462000 |g|^2= 0.000000000025398 > 8->6 -0.000038006325000 -0.000142788293500 |g|^2= 0.000000021832978 > 0->7 0.015372187389000 -0.009132041345000 |g|^2= 0.000319698324249 > 1->7 -0.009727469332000 0.005790740403500 |g|^2= 0.000128156334026 > 2->7 -0.000004934450500 0.000006008964000 |g|^2= 0.000000000060456 > 3->7 -0.000000667739000 0.000003460446000 |g|^2= 0.000000000012421 > 4->7 -0.009877533487000 0.005769648051000 |g|^2= 0.000130854506419 > 5->7 0.000000496943500 0.000011202097500 |g|^2= 0.000000000125734 > 6->7 0.000000981650000 -0.000004929340500 |g|^2= 0.000000000025262 > 7->7 -0.000633793442000 0.000000000000000 |g|^2= 0.000000401694127 > 8->7 0.000030518449500 -0.000027055324500 |g|^2= 0.000000001663366 > 0->8 -0.013941745790500 -0.000533958928500 |g|^2= 0.000194657387824 > 1->8 0.004172651103000 0.000183619549500 |g|^2= 0.000017444733366 > 2->8 0.001106454865000 -0.000459738505500 |g|^2= 0.000001435601862 > 3->8 -0.000007736827500 -0.000054991042000 |g|^2= 0.000000003083873 > 4->8 -0.042832546265500 -0.001607772328500 |g|^2= 0.001837211951446 > 5->8 0.000648997548500 -0.001509835303000 |g|^2= 0.000002700800460 > 6->8 -0.000038017739500 0.000142907934000 |g|^2= 0.000000021868026 > 7->8 0.000025705638000 0.000024838755500 |g|^2= 0.000000001277744 > 8->8 -0.003734049495500 0.000000000000000 |g|^2= 0.000013943125635 > > displacement pattern #2: > 0->0 -0.286565847377500 -0.000000000000000 |g|^2= 0.082119984883185 > 1->0 0.379851516091000 -0.000345068730000 |g|^2= 0.144287293349060 > 2->0 0.000000006163500 -0.000000002258000 |g|^2= 0.000000000000000 > 3->0 0.000000001618500 -0.000000001134500 |g|^2= 0.000000000000000 > 4->0 -0.133458411497500 -0.000994042731000 |g|^2= 0.017812135720387 > 5->0 0.000000190857000 -0.000000051579000 |g|^2= 0.000000000000039 > 6->0 -0.000000069523000 -0.000000017790500 |g|^2= 0.000000000000005 > 7->0 -0.019890115224000 -0.011817220800500 |g|^2= 0.000535263391072 > 8->0 -0.039430161288000 0.001065942700500 |g|^2= 0.001555873853038 > 0->1 0.462246877696500 0.000419919480500 |g|^2= 0.213672352272533 > 1->1 0.010494926539500 0.000000000000000 |g|^2= 0.000110143483070 > 2->1 -0.000000003602000 -0.000000000104000 |g|^2= 0.000000000000000 > 3->1 -0.000000004409500 0.000000001875500 |g|^2= 0.000000000000000 > 4->1 0.065269015154500 0.000545440362000 |g|^2= 0.004260341844427 > 5->1 -0.000000404569000 0.000000095724000 |g|^2= 0.000000000000173 > 6->1 0.000000304352500 -0.000000014508500 |g|^2= 0.000000000000093 > 7->1 0.018784573101500 0.011183159264000 |g|^2= 0.000477923237730 > 8->1 0.042649049483000 -0.001095308735500 |g|^2= 0.001820141123029 > 0->2 0.000000009800000 0.000000002671000 |g|^2= 0.000000000000000 > 1->2 -0.000000003294500 0.000000000339500 |g|^2= 0.000000000000000 > 2->2 -0.172141736923500 0.000000000000000 |g|^2= 0.029632777591039 > 3->2 0.000000095818500 -0.000000007298000 |g|^2= 0.000000000000009 > 4->2 0.000000001027500 0.000000000264500 |g|^2= 0.000000000000000 > 5->2 0.058175921580500 -0.057258304602500 |g|^2= 0.006662951297693 > 6->2 -0.003606567884000 0.002326495942500 |g|^2= 0.000018419915272 > 7->2 0.000017034603500 0.000020332543000 |g|^2= 0.000000000703590 > 8->2 -0.003455200640000 -0.001431532813500 |g|^2= 0.000013987697659 > 0->3 0.000000001244500 0.000000000964500 |g|^2= 0.000000000000000 > 1->3 -0.000000004262500 -0.000000001807000 |g|^2= 0.000000000000000 > 2->3 0.000000095818500 0.000000007298000 |g|^2= 0.000000000000009 > 3->3 -0.172141573131500 0.000000000000000 |g|^2= 0.029632721200188 > 4->3 0.000000002276500 -0.000000000110500 |g|^2= 0.000000000000000 > 5->3 -0.004267707540000 0.000449461611500 |g|^2= 0.000018415343387 > 6->3 -0.081224513696500 -0.008111670337000 |g|^2= 0.006663220820889 > 7->3 0.000001861979500 0.000010745158500 |g|^2= 0.000000000118925 > 8->3 0.000028586479000 -0.000167502870000 |g|^2= 0.000000028874398 > 0->4 -0.231003310734000 0.001720588928000 |g|^2= 0.053365489996328 > 1->4 0.047001759819500 -0.000392784013500 |g|^2= 0.002209319705411 > 2->4 0.000000001059500 -0.000000000150500 |g|^2= 0.000000000000000 > 3->4 0.000000002186000 0.000000000118000 |g|^2= 0.000000000000000 > 4->4 0.044659534793500 0.000000000000000 |g|^2= 0.001994474047972 > 5->4 0.000000150192500 0.000000032648000 |g|^2= 0.000000000000024 > 6->4 -0.000000156776000 -0.000000002718000 |g|^2= 0.000000000000025 > 7->4 -0.001310064441500 -0.000765519326000 |g|^2= 0.000002302288679 > 8->4 -0.020407897616500 0.000742934507000 |g|^2= 0.000417034236807 > 0->5 0.000000235769000 0.000000210453500 |g|^2= 0.000000000000100 > 1->5 -0.000000265807500 -0.000000046707500 |g|^2= 0.000000000000073 > 2->5 0.056219406513000 0.055332648710500 |g|^2= 0.006222323681994 > 3->5 -0.004124172441500 -0.000434330422000 |g|^2= 0.000017197441243 > 4->5 0.000000122701500 -0.000000029810500 |g|^2= 0.000000000000016 > 5->5 0.185880014452500 0.000000000000000 |g|^2= 0.034551379772862 > 6->5 0.000000140947000 0.000000125297000 |g|^2= 0.000000000000036 > 7->5 -0.000000941527500 0.000011971521000 |g|^2= 0.000000000144204 > 8->5 -0.000798785488000 -0.001869578039500 |g|^2= 0.000004133380302 > 0->6 0.000000026588500 0.000000024247000 |g|^2= 0.000000000000001 > 1->6 0.000000266009000 0.000000033201000 |g|^2= 0.000000000000072 > 2->6 -0.003485291586500 -0.002248257310000 |g|^2= 0.000017201918375 > 3->6 -0.078492855467500 0.007838873909000 |g|^2= 0.006222576303603 > 4->6 -0.000000139482000 -0.000000000856000 |g|^2= 0.000000000000019 > 5->6 0.000000140947000 -0.000000125297000 |g|^2= 0.000000000000036 > 6->6 0.185880943275000 -0.000000000000000 |g|^2= 0.034551725072804 > 7->6 -0.000001321611500 -0.000005771953000 |g|^2= 0.000000000035062 > 8->6 0.000048260043000 0.000176321833000 |g|^2= 0.000000033418421 > 0->7 -0.026071694374000 0.015489281608000 |g|^2= 0.000919651092263 > 1->7 0.001697741814000 -0.001010730029500 |g|^2= 0.000003903902460 > 2->7 0.000015106160500 -0.000018083799000 |g|^2= 0.000000000555220 > 3->7 0.000001672337500 -0.000009663610500 |g|^2= 0.000000000096182 > 4->7 0.002315940634500 -0.001352389584500 |g|^2= 0.000007192538611 > 5->7 -0.000000927570500 -0.000011708792000 |g|^2= 0.000000000137956 > 6->7 -0.000001291943000 0.000005661201000 |g|^2= 0.000000000033718 > 7->7 0.000818543483500 -0.000000000000000 |g|^2= 0.000000670013434 > 8->7 -0.000425351836000 0.000280356039500 |g|^2= 0.000000259523693 > 0->8 -0.026410868906000 -0.000617126400500 |g|^2= 0.000697914841364 > 1->8 0.008979264003000 0.000226470303000 |g|^2= 0.000080678470834 > 2->8 -0.003085839551500 0.001279050530500 |g|^2= 0.000011158375997 > 3->8 0.000025569678000 0.000149732451000 |g|^2= 0.000000023073615 > 4->8 -0.010002857794000 -0.000375228864000 |g|^2= 0.000100197960747 > 5->8 -0.000775808756500 0.001816292782500 |g|^2= 0.000003900798698 > 6->8 0.000046818670500 -0.000171407224000 |g|^2= 0.000000031572424 > 7->8 -0.000239755938500 -0.000163419629500 |g|^2= 0.000000084188885 > 8->8 0.003793073996500 0.000000000000000 |g|^2= 0.000014387410343 > > > > _______________________________________________ > 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/20120510/56ea76ba/attachment-0001.htm From alex.kutana at gmail.com Fri May 11 00:10:31 2012 From: alex.kutana at gmail.com (Alex Kutana) Date: Thu, 10 May 2012 18:10:31 -0400 Subject: [Pw_forum] symmetry of the electron-phonon coupling coefficients In-Reply-To: <4FAC2B91.4060103@sissa.it> References: <4FAC2B91.4060103@sissa.it> Message-ID: Dear Stefano, Thank you for your explanation. I incorrectly assumed that translation should leave the matrix element invariant, which is false, since wavefunctions actually stay fixed. Thanks again for your help. Alex On Thu, May 10, 2012 at 4:56 PM, Stefano de Gironcoli wrote: > ** > dear Alex > > I don't think that the two matrix element should be equal and opposite. > suppose you apply both displacement together which means you displace > the molecule as a whole. > > the eigenvalue will not change, hence < i | dV | i > = 0 > but the new eigen-wavefunctions | i' > will be the translated of the > original ones, hence different from them. > to first order |i'> = |i> + sum |j> /delta e_IJ > since |i'> =/= |i> no reason to believe that < j | d V | i > = 0. > > stefano > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120510/08cb0669/attachment.htm From jiachen at princeton.edu Fri May 11 06:12:33 2012 From: jiachen at princeton.edu (jia chen) Date: Fri, 11 May 2012 00:12:33 -0400 Subject: [Pw_forum] Errors in PS-KS equation Message-ID: Hello Everyone, I am trying to make a norm-conserving pseudopotential of Ti with sp semicore. But I kept getting "Errors in PS-KS equation" from ld1.x. I played around cutoffs a lot, but failed to find a way out. Following is my input file, any idea or comment will be appreciated. &input title='Ti', zed=22, rel=1, config='[ne] 3s2.0 3p6.0 3d2.0 4s2.0 4p0.0', iswitch=3, dft='pbe' / &inputp pseudotype=2, file_pseudopw='Ti.pbe-nc-tm.UPF', author='TM', lloc=2, nlcc=.true., tm=.true. / 5 3S 1 0 2.00 0.00 1.00 1.00 3P 2 1 6.00 0.00 1.20 1.20 4S 4 0 2.00 0.00 1.30 1.30 4P 5 1 0.00 0.00 1.80 1.80 3D 3 2 1.00 0.00 1.30 1.30 -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120511/0ac21e90/attachment.htm From jiachen at princeton.edu Fri May 11 06:17:37 2012 From: jiachen at princeton.edu (jia chen) Date: Fri, 11 May 2012 00:17:37 -0400 Subject: [Pw_forum] Errors in PS-KS equation In-Reply-To: References: Message-ID: Sorry, there is a mistake in the input in last email. The last line should be 3D 3 2 2.00 0.00 1.30 1.30 Without this mistake, I am still not able to make a pseudopotential without Errors in PS-KS equation. On Fri, May 11, 2012 at 12:12 AM, jia chen wrote: > Hello Everyone, > > I am trying to make a norm-conserving pseudopotential of Ti with sp > semicore. But I kept getting "Errors in PS-KS equation" from ld1.x. I > played around cutoffs a lot, but failed to find a way out. Following is my > input file, any idea or comment will be appreciated. > > &input > title='Ti', > zed=22, > rel=1, > config='[ne] 3s2.0 3p6.0 3d2.0 4s2.0 4p0.0', > iswitch=3, > dft='pbe' > / > &inputp > pseudotype=2, > file_pseudopw='Ti.pbe-nc-tm.UPF', > author='TM', > lloc=2, > nlcc=.true., > tm=.true. > / > 5 > 3S 1 0 2.00 0.00 1.00 1.00 > 3P 2 1 6.00 0.00 1.20 1.20 > 4S 4 0 2.00 0.00 1.30 1.30 > 4P 5 1 0.00 0.00 1.80 1.80 > 3D 3 2 1.00 0.00 1.30 1.30 > > > -- > Jia Chen > > > -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120511/1a26b3b6/attachment.htm From gabriele.sclauzero at epfl.ch Fri May 11 09:48:09 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Fri, 11 May 2012 09:48:09 +0200 Subject: [Pw_forum] occupations In-Reply-To: References: Message-ID: <76A44FBB-4812-4B0B-88D6-AE33DC956782@epfl.ch> Boron nitride nanotube, peut-?tre? These beasts have a pretty large band gap, so that you should be able to used fixed occupations without any problem. For instance, by googling I've found this: http://iopscience.iop.org/0295-5075/28/5/007 HTH GS Il giorno 10/mag/2012, alle ore 17.37, Lorenzo Paulatto ha scritto: > On Thu, 10 May 2012 17:11:45 +0200, bf azi wrote: >> Which "occupations" better for "BNNT"? >> ("smearing" or "fixed") > > Dear Bani, > it depends, what is a BNNT? > > > -- > Lorenzo Paulatto -- Paris > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120511/d12b578c/attachment.htm From giuseppe.mattioli at ism.cnr.it Fri May 11 11:40:00 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 11 May 2012 11:40:00 +0200 Subject: [Pw_forum] Errors in PS-KS equation In-Reply-To: References: Message-ID: <201205111140.00368.giuseppe.mattioli@ism.cnr.it> Dear jia chen Please look carefully at this file YourQE/atomic_doc/pseudo-gen.pdf HTH Giuseppe On Friday 11 May 2012 06:17:37 jia chen wrote: > Sorry, there is a mistake in the input in last email. The last line should > be > 3D 3 2 2.00 0.00 1.30 1.30 > Without this mistake, I am still not able to make a pseudopotential without > Errors in PS-KS equation. > > On Fri, May 11, 2012 at 12:12 AM, jia chen wrote: > > Hello Everyone, > > > > I am trying to make a norm-conserving pseudopotential of Ti with sp > > semicore. But I kept getting "Errors in PS-KS equation" from ld1.x. I > > played around cutoffs a lot, but failed to find a way out. Following is > > my input file, any idea or comment will be appreciated. > > > > &input > > > > title='Ti', > > zed=22, > > rel=1, > > config='[ne] 3s2.0 3p6.0 3d2.0 4s2.0 4p0.0', > > iswitch=3, > > dft='pbe' > > > > / > > &inputp > > > > pseudotype=2, > > file_pseudopw='Ti.pbe-nc-tm.UPF', > > author='TM', > > lloc=2, > > nlcc=.true., > > tm=.true. > > > > / > > > > 5 > > 3S 1 0 2.00 0.00 1.00 1.00 > > 3P 2 1 6.00 0.00 1.20 1.20 > > 4S 4 0 2.00 0.00 1.30 1.30 > > 4P 5 1 0.00 0.00 1.80 1.80 > > 3D 3 2 1.00 0.00 1.30 1.30 > > > > > > -- > > Jia Chen -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From parishok at gmail.com Fri May 11 16:07:08 2012 From: parishok at gmail.com (pari shok) Date: Fri, 11 May 2012 10:07:08 -0400 Subject: [Pw_forum] DOS per eV/volume Message-ID: *Dear Guido, Thank you very much for your reply to my question on calculating DOS per eV per volume. As far as I remember, there is a factor of 4(pi)^3 for calculating the DOS per volume. Even the following post mentions it. So, I was wondering whether I should divide DOS just to unit cell or unit cell/ 4(pi)^3. As I wrote, there is a factor of 100. I appreciate your help. Yours P Shok Usually:*>* DOS(E) dE = number of energy levels in the energy range from E and E+dE*>**>* and according to this definition*>* \int_E0^E1 DOS(E) dE = total number of states between E0 and E1*>* (adimensional).*>**>* This is what the dos.x executable included in Quantum-ESPRESSO computes.*>**>* According to the above definition:*>**>* DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z *V / (4*>* \pi^3)*>**>* If you carefully read the chapter 8 of Ashcroft-Mermin, it says:*>* "....one can define a density of levels per unit volume (or "density of*>* levels" for short)....."*>* and Eq. (8.57) (provided we're looking to the same edition!) is exactly*>* the definition you gave*>* (so, "per-unit-of-volume" definition).*>**>* Giovanni* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120511/810accd9/attachment.htm From giannozz at democritos.it Fri May 11 16:21:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 May 2012 16:21:41 +0200 Subject: [Pw_forum] Errors in PS-KS equation In-Reply-To: References: Message-ID: <1336746101.11859.2.camel@fe12lx.fisica.uniud.it> On Fri, 2012-05-11 at 00:12 -0400, jia chen wrote: > > I am trying to make a norm-conserving pseudopotential of Ti with sp > semicore. But I kept getting "Errors in PS-KS equation" from ld1.x. the generation of multiple-projector norm-conserving PPs is actually NOT properly implemented. You should try to generate single-projector PPs instead P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 11 16:22:42 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 May 2012 16:22:42 +0200 Subject: [Pw_forum] Choosing awin for planar average calculations In-Reply-To: <1336662197.11502.YahooMailNeo@web43411.mail.sp1.yahoo.com> References: <1336662197.11502.YahooMailNeo@web43411.mail.sp1.yahoo.com> Message-ID: <1336746162.11859.4.camel@fe12lx.fisica.uniud.it> On Thu, 2012-05-10 at 08:03 -0700, Izaak Williamson wrote: > > I want to calculate the planar average of potential along a certain > direction for a bulk supercell. Could anyone tell me how to choose the > value for awin (window size for macroscopic averages)? a lattice parameter of the original cell? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 11 16:24:46 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 May 2012 16:24:46 +0200 Subject: [Pw_forum] Shift in K points In-Reply-To: References: Message-ID: <1336746286.11859.7.camel@fe12lx.fisica.uniud.it> On Thu, 2012-05-10 at 16:55 +0530, manoj narayanan wrote: > Can any one tell in detail about shift in k point mesh, > like what and why it is ? and off course any relevant > reference regarding this will also be helpful. any "historic" reference on k-points (Chadi and Cohen, Monkhorst and Pack) will be helpful P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From amrit.abhilash at yahoo.com Sat May 12 08:13:39 2012 From: amrit.abhilash at yahoo.com (Amrit Abhilash) Date: Fri, 11 May 2012 23:13:39 -0700 (PDT) Subject: [Pw_forum] error while installing QE Message-ID: <1336803219.64592.YahooMailNeo@web121805.mail.ne1.yahoo.com> sir, while i have fortran 95 installed in my system. but when i tried to install QE in ubuntu , it couldn't identify the fortran 95 compiler and thus refused to run as expected. pls ?help me over this problem. Amrit -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120511/db799224/attachment.htm From giannozz at democritos.it Sat May 12 08:57:44 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 12 May 2012 08:57:44 +0200 Subject: [Pw_forum] GaAs surface with fractional charges H Zval=1.25, very large estimated scf accuracy In-Reply-To: References: Message-ID: On May 10, 2012, at 12:57 , Magdalena Birowska wrote: > I am trying to relax a surface slab of GaAs which has 72 atoms. mixing_mode='local-TF' should yield the best performances for surfaces P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From akohlmey at gmail.com Sat May 12 17:34:04 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sat, 12 May 2012 11:34:04 -0400 Subject: [Pw_forum] error while installing QE In-Reply-To: <1336803219.64592.YahooMailNeo@web121805.mail.ne1.yahoo.com> References: <1336803219.64592.YahooMailNeo@web121805.mail.ne1.yahoo.com> Message-ID: On Sat, May 12, 2012 at 2:13 AM, Amrit Abhilash wrote: > sir, > while i have fortran 95 installed in my system. but when i tried to install > QE in ubuntu , it couldn't identify the fortran 95 compiler and thus refused > to run as expected. pls ?help me over this problem. then you have to tell it. read the installation instructions. it describes how to do it. axel. > > Amrit > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From zafartariq2003 at yahoo.com Sat May 12 23:22:21 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Sat, 12 May 2012 14:22:21 -0700 (PDT) Subject: [Pw_forum] Calculation of lattic constants and bulk modulus od w-ZnO Message-ID: <1336857741.95398.YahooMailClassic@web65411.mail.ac4.yahoo.com> Dear All I want to calculate lattice constants a, and c and bulk modulus of w-ZnO. For this purpose: I take experimental lattice constants (a= 3.25 Ang. and c = 5.206 Ang. and by changing these values into bohr.) and first take different values above and below a and do scf calculations to optimize a. As in case of W ZnO (Hexagonal and Trigonal P) ibrav= 4 and celldm(3) =c/a is used. So when I change a (celldm (1))I have to change celldm (3). In this way I get lattice constant a which is nearly same as experimental with 2 percent error. Then I fix this lattice constant a (celldm (1)) and change lattice constant c (By taking different values above and below experimental value of c). As c changes celldm (3) also changes. In this way I get lattice constant c which is very close to experimental lattice constant with a little error of 2 percent. The output data for the calculation of c by fixing a I use to calculate BULK modulus for ZnO. Again these results are comparable with experimental and already calculated results by different techniques . Now I want to know that, Is my calculation procedure is right? Best Regards Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120512/09ca677a/attachment.htm From mohnish.iitk at gmail.com Sun May 13 08:35:38 2012 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sun, 13 May 2012 12:05:38 +0530 Subject: [Pw_forum] Calculation of lattic constants and bulk modulus od w-ZnO In-Reply-To: <1336857741.95398.YahooMailClassic@web65411.mail.ac4.yahoo.com> References: <1336857741.95398.YahooMailClassic@web65411.mail.ac4.yahoo.com> Message-ID: Dear Muhammad, Their is an easier way to calculate the optimized the lattice constant which is based on calculation of stress and forces on the system. In the flag "calculation" put "vc-relax" and in "ion_dynamics" put "bfgs" (there are other options too) and in the "cell_dynamics" put "bfgs" (again there are other options also) and run the job. When the calculation is over the code will print the final lattice vectors by which you can calculate the optimized lattice constant. For further details look into /quantum-espresso-folder/Doc/INPUT_PW.html On Sun, May 13, 2012 at 2:52 AM, zafar rasheed wrote: > Dear All > > I want to calculate lattice constants a, and c and bulk modulus of w-ZnO. > For this purpose: > > 1. > > I take experimental lattice constants (a= 3.25 Ang. and c = 5.206 Ang. > and by changing these values into bohr.) and first take different values > above and below a and do scf calculations to optimize a. As in case of W > ZnO (Hexagonal and Trigonal P) ibrav= 4 and celldm(3) =c/a is used. So when > I change a (celldm (1))I have to change celldm (3). In this way I get > lattice constant a which is nearly same as experimental with 2 percent > error. > 2. > > Then I fix this lattice constant a (celldm (1)) and change lattice > constant c (By taking different values above and below experimental value > of c). As c changes celldm (3) also changes. In this way I get lattice > constant c which is very close to experimental lattice constant with a > little error of 2 percent. > 3. > > The output data for the calculation of c by fixing a I use to > calculate BULK modulus for ZnO. Again these results are comparable with > experimental and already calculated results by different techniques . > 4. > > Now I want to know that, Is my calculation procedure is right? > > Best Regards > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120513/b914f805/attachment.htm From nicola.marzari at epfl.ch Sun May 13 12:16:03 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Sun, 13 May 2012 12:16:03 +0200 Subject: [Pw_forum] Calculation of lattic constants and bulk modulus od w-ZnO In-Reply-To: References: <1336857741.95398.YahooMailClassic@web65411.mail.ac4.yahoo.com> Message-ID: <4FAF89E3.3050604@epfl.ch> Dear Zavar, both your approach and the one suggested by Mohnish are good - vc_relax is more straightforward, but the one you have chosen requires you to think a bit more about the problem (and it's good for that). While you are learning, try both, and see if they give you the same results. As a side notice, you typically need a larger cutoffo to converge well the stress tensor, used by vc_relax - hence your approach of minimizing the energy can be more accurate, at usual cutoffs. nicola On 13/05/2012 08:35, mohnish pandey wrote: > Dear Muhammad, > > Their is an easier way to calculate the optimized the lattice constant > which is based on calculation of stress and forces on the system. In the > flag "calculation" put "vc-relax" and in "ion_dynamics" put "bfgs" > (there are other options too) and in the "cell_dynamics" put "bfgs" > (again there are other options also) and run the job. When the > calculation is over the code will print the final lattice vectors by > which you can calculate the optimized lattice constant. For further > details look into /quantum-espresso-folder/Doc/INPUT_PW.html > > > On Sun, May 13, 2012 at 2:52 AM, zafar rasheed > wrote: > > Dear All > > I want to calculate lattice constants a, and c and bulk modulus of > w-ZnO. For this purpose: > > 1. > > I take experimental lattice constants (a= 3.25 Ang. and c = > 5.206 Ang. and by changing these values into bohr.) and first > take different values above and below a and do scf calculations > to optimize a. As in case of W ZnO (Hexagonal and Trigonal P) > ibrav= 4 and celldm(3) =c/a is used. So when I change a (celldm > (1))I have to change celldm (3). In this way I get lattice > constant a which is nearly same as experimental with 2 percent > error. > > 2. > > Then I fix this lattice constant a (celldm (1)) and change > lattice constant c (By taking different values above and below > experimental value of c). As c changes celldm (3) also changes. > In this way I get lattice constant c which is very close to > experimental lattice constant with a little error of 2 percent. > > 3. > > The output data for the calculation of c by fixing a I use to > calculate BULK modulus for ZnO. Again these results are > comparable with experimental and already calculated results by > different techniques . > > 4. > > Now I want to know that, Is my calculation procedure is right? > > Best Regards > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > > ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From bfazi90 at gmail.com Sun May 13 22:25:25 2012 From: bfazi90 at gmail.com (bf azi) Date: Mon, 14 May 2012 00:55:25 +0430 Subject: [Pw_forum] Harris-Foulkes estimate Message-ID: Dear all What is "Harris-Foulkes estimate"? What a difference between "total energy" and "Harris-Foulkes estimate" in scf.out? thanks Bani Adam Faculty of Science Egypt From giannozz at democritos.it Sun May 13 22:45:11 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 13 May 2012 22:45:11 +0200 Subject: [Pw_forum] Harris-Foulkes estimate In-Reply-To: References: Message-ID: <4EECA900-370C-43A7-9886-9A3E5AE380AC@democritos.it> On May 13, 2012, at 22:25 , bf azi wrote: > What is "Harris-Foulkes estimate"? http://en.wikipedia.org/wiki/Harris_functional P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elie.moujaes at hotmail.co.uk Mon May 14 04:07:12 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 14 May 2012 03:07:12 +0100 Subject: [Pw_forum] Irreps and vibrational modes Message-ID: Dear all, I am calculating the phonon modes at Gamma=0 for a 42 Carbon atom supercell. If N=42 then one has 3N= 3*42 modes= 128 modes. Just to confirm: (1) Are all the modes vibrational? (2) Are any modes missing from the calculation like optical or accoustical modes? (3) i did the calculation and got two of the modes negative which means either threshold is high or the ecutwav must be at least eight times ecutrho. Is a threshold of 10^(-15) still too high for such a system? Thanks ElieUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120514/3f5a2b63/attachment.htm From lmartinsamos at gmail.com Mon May 14 11:06:37 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 14 May 2012 11:06:37 +0200 Subject: [Pw_forum] Quantum ESPRESSO release 5.0 Message-ID: Version 5.0 of the Quantum ESPRESSO distribution is available for download from the website http://www.quantum-espresso.org . This release contains the following improvements over previous versions: * More ways of calculating electron-phonon coefficients. * Full DFT+U scheme (with J and additional parameters) implemented. Should work also for fully-relativistic calculations. * band parallelization for Green function sum in EXX (memory replication). Note the following major changes: * The directory structure has been re-organized to better reflect the division into packages. As a consequence, almost nothing is in the same directory where it used to be * It is no longer needed to download the entire distribution: the base package will download the required packages at compile time * compilation with -DEXX no longer required for hybrid functionals and the following incompatibilities: * Postprocessing codes dos.x, bands.x, projwfc.x, now use namelist &dos, &bands, &projwfc respectively, instead of &inputpp * Options 'cubic'/'hexagonal' to CELL_PARAMETERS removed: it is no longer useful, the code will anyway find the correct sym.ops. * Options 'bohr'/'angstrom'/'alat' to CELL_PARAMETERS implemented * PHonon: input variable 'elph' replaced by 'electron_phonon' For other minor improvements, changes, bug fixes, see file Doc/release-notes Everybody who is using the Quantum ESPRESSO distribution is encouraged to upgrade and to report problems to the mailing list. The Quantum ESPRESSO group -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120514/26101fe0/attachment.htm From tone.kokalj at ijs.si Mon May 14 12:39:20 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 14 May 2012 12:39:20 +0200 Subject: [Pw_forum] Quantum ESPRESSO release 5.0 In-Reply-To: References: Message-ID: <1336991960.5739.9.camel@catalyst.ijs.si> On Mon, 2012-05-14 at 11:06 +0200, Layla Martin-Samos wrote: > Version 5.0 of the Quantum ESPRESSO distribution is available for > download from the website http://www.quantum-espresso.org . This > release contains the following improvements over previous versions: Layla, the PWgui tarball is wrong! It should be created with "make tar-gui" from espresso's root directory and not simply by tar-gzing the GUI directory. By doing the latter, the GUI will be neither functional nor its directory structure intuitive. Please also name the GUi's tarball as PWgui-5.0 and not GUI-5.0 (change this also in the plugins_list file) > * Options 'cubic'/'hexagonal' to CELL_PARAMETERS removed: it is no > longer useful, the code will anyway find the correct sym.ops. > * Options 'bohr'/'angstrom'/'alat' to CELL_PARAMETERS implemented Ups. This escaped my detection. I will change the PWgui immediately to cope with this and after you can remake the PWgui-05.0 tarbal and put it on qe-forge.org download page. As for INPUW_PW.def|html|txt I believe the way the new CELL_PARAMETERS options are specified now is not very intuitive as 'alat' is only implicit, e.g.: CELL_PARAMETERS { bohr | angstrom } I suggest changing it to CELL_PARAMETERS { alat | bohr | angstrom } although 'alat' will be silently ignored but nevertheless in effect, i.e.: IF ( matches( "BOHR", input_line ) ) THEN cell_units = 'bohr' ELSEIF ( matches( "ANGSTROM", input_line ) ) THEN cell_units = 'angstrom' ELSE cell_units = 'alat' ENDIF 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 May 14 17:35:26 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 May 2012 17:35:26 +0200 Subject: [Pw_forum] Irreps and vibrational modes In-Reply-To: References: Message-ID: <1337009726.9680.41.camel@fe12lx.fisica.uniud.it> On Mon, 2012-05-14 at 03:07 +0100, Elie M wrote: > (1) Are all the modes vibrational? there are always three translational modes > (2) Are any modes missing from the calculation there shouldn't be anything missing > (3) i did the calculation and got two of the modes negative if they go to zero when you apply the acoustic sum rule, with all other modes unchanged or litle affected, it is not a problem P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From elie.moujaes at hotmail.co.uk Mon May 14 20:43:08 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 14 May 2012 19:43:08 +0100 Subject: [Pw_forum] Irreps and vibrational modes In-Reply-To: <1337009726.9680.41.camel@fe12lx.fisica.uniud.it> References: , <1337009726.9680.41.camel@fe12lx.fisica.uniud.it> Message-ID: Thanks for the information, Prof. Giannozzi. Elie > Subject: Re: [Pw_forum] Irreps and vibrational modes > From: giannozz at democritos.it > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Date: Mon, 14 May 2012 17:35:26 +0200 > > On Mon, 2012-05-14 at 03:07 +0100, Elie M wrote: > > > (1) Are all the modes vibrational? > > there are always three translational modes > > > (2) Are any modes missing from the calculation > > there shouldn't be anything missing > > > (3) i did the calculation and got two of the modes negative > > if they go to zero when you apply the acoustic sum rule, with all > other modes unchanged or litle affected, it is not a problem > > P. > > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120514/e80a3ca4/attachment.htm From rdong at ncsu.edu Mon May 14 23:26:36 2012 From: rdong at ncsu.edu (DONG Rui) Date: Mon, 14 May 2012 17:26:36 -0400 Subject: [Pw_forum] radius of the "core" in pseudopotential Message-ID: Hi, all I was trying to determine the effective radius of the core in a given pseudopotential, core meaning the actual *atomic core* + *core electrons.* Or, if I can get the charge distribution of the core, it will also work. Does anyone have idea what should I do? Thank you for help! -- Sincerely, Rui DONG -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120514/b8330055/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue May 15 09:22:09 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 15 May 2012 09:22:09 +0200 Subject: [Pw_forum] radius of the "core" in pseudopotential In-Reply-To: References: Message-ID: On Mon, May 14, 2012 at 11:26 PM, DONG Rui wrote: > I was trying to determine the effective radius of the core in a given > pseudopotential, core meaning the actual *atomic core* + *core electrons.* Or, > if I can get the charge distribution of the core, it will also work. > Dear Rui Dong, in a pseudopotential the core electrons are, by construction, exactly the same as in an all-electron calculation of the spherical-symmetric ground state for the isolated atom. You can do such an all-electron calculation with ld1.x fro the QE distribution. It can also write out the core charge on a radial grid. Notice however that there is no cutoff radius for the core, as it is assumed to be rigid, not to be limited. best regards -- Lorenzo Paulatto - Paris -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120515/8097f1ab/attachment.htm From ramzialaya at hotmail.fr Tue May 15 12:43:37 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Tue, 15 May 2012 11:43:37 +0100 Subject: [Pw_forum] (no subject) Message-ID: Dear all; I checked the Pwscf for US Ga PZ Non relativitic pseudopotential but could not find or generate it myself . Thus could you please send me Ga US pseudopotential with PZ approximation. Thank you.Regards. ********************************************************************************* Ramzi AlayaE-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120515/124e1fe5/attachment-0001.htm From trambui at u.boisestate.edu Tue May 15 18:51:57 2012 From: trambui at u.boisestate.edu (Tram Bui) Date: Tue, 15 May 2012 10:51:57 -0600 Subject: [Pw_forum] Questions on the warning message from relax calculation Message-ID: Dear QE users, I ran a relax calculation of Cs substitution silicon atom in grain boundary SiC and when I looked at the output file, I saw the message below WARNING: integrated charge= 1020.00000000, expected= 1021.00000000 My question is, will it effect the calculated total energy values? Can this be neglected? if not, what should I do to fix it, should I add charge_tot=+1 to make it 1021? Best Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120515/ff17f53a/attachment.htm From ruimao20 at gmail.com Tue May 15 23:19:51 2012 From: ruimao20 at gmail.com (Rui Mao) Date: Tue, 15 May 2012 17:19:51 -0400 Subject: [Pw_forum] Splitting phonon calculation over q point and irr Message-ID: Hi all! I had some trouble implementing the grid calculation for phonon calculation, which splits the calculation over q and representations. I have spend last few days try to do the splitting following the run_example script in GRID_example folder. I am running the QE V4.3 on HPC machine (IBM Blade Center Linux Cluster, henry2, 981 dual Xeon compute nodes with Intel Xeon Processors (mix of single-, dual-, quad-, and six- core), 2-4GB per core distributed memory, dual gigabit Ethernet interconnects) 8-16 cpus are assigned to each splitted jobs After some calculations, I found that the splitting is actually not feasible on HPC! Before you can split the job over q points and representations, you have to copy PREFIX.save (which is generated by scf calculation) to each sub directories where you want to do the ph calculation separately. If the system is slightly large (more 20 atoms in unit cell), the PREFIX.save will be several GBs, then let's say if you want to split over 3 q points and 48 representations, you have to copy the PREFIX.save files 3x48=144 times! (144x 3GB + 144 X 5GB > 1TB) I had a script doing this job, but it quickly used up the disk space (it used more 1TB )! which made this approach unusable on HPC machine! Is there anyway to do the splitting phonon calculation without copying the PREFIX.save generated by scf to each sub directories? Can we let all the splitted phonon calculations look for the same input directory for PREFIX.save so that we do not need to copy files around? Any comment on how to do the splitting job without using up the disk space will be greatly appreciated! Thank you, Rui Mao Part of the script that copy the PREFIX.save files generated by scf to each sub directories: mkdir $TMP_DIR/$q.$irr cp -r $TMP_DIR/$PREFIX.save $TMP_DIR/$q.$irr mkdir -p $TMP_DIR/$q.$irr/_ph0/$PREFIX.phsave cp -r $TMP_DIR/_ph0/$PREFIX.phsave/* $TMP_DIR/$q.$irr/_ph0/$PREFIX.phsave Scf putfile: &control calculation = 'scf', restart_mode='from_scratch', wf_collect=.true., prefix='graphite', tstress = .true., tprnfor = .true., forc_conv_thr = 1.0D-3, etot_conv_thr = 1.0D-4, pseudo_dir = '/home/rmao/Pseudo/', outdir='/share2/Ray/grid_graphite/scf', / &system ibrav=4, celldm(1) =9.2961, celldm(3)=1.3579, nat=16, ntyp= 1, ecutwfc =70, ecutrho=700, occupations='smearing', smearing='mp', degauss=0.003, / &electrons diagonalization='cg', mixing_mode = 'plain', mixing_beta = 0.5, conv_thr = 1.0d-8, / ATOMIC_SPECIES C 12.01070 C.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 1.183416184 0.709967199 -3.339999736 C 1.183397032 2.130056591 -3.339999831 C 2.413378375 2.839955863 -3.339999742 C -0.046321206 2.840033775 -3.339999742 C 2.413196667 4.260044397 -3.339999829 C -0.046512842 4.260108061 -3.339999831 C 1.183461168 4.970022576 -3.339999741 C 3.643012948 2.129829924 -3.339999823 C 0.000008073 -0.000036198 -0.000000172 C -0.000009822 1.420051269 -0.000000260 C 1.229970973 2.129951526 -0.000000171 C -1.229729485 2.130029208 -0.000000172 C 1.229791025 3.550039979 -0.000000260 C -1.229918926 3.550102386 -0.000000260 C 0.000053606 4.260017465 -0.000000171 C 2.459606230 1.419825978 -0.000000260 K_POINTS {automatic} 8 8 16 0 0 0 Ph inputfile phonons of Graphite_2x2 &inputph tr2_ph=1.0d-16, alpha_mix(1)=0.5, prefix='graphite', ldisp=.true., epsil=.false., recover=.false., reduce_io=.false., amass(1)=12.01070, start_irr=0, last_irr=0, nq1=1, nq2=1, nq3=4, outdir='/share2/Ray/grid_graphite/scf', fildyn='graphite.dyn' / -- Rui Mao ============================================================ Department of Electrical and Computer Engineering (ECE) North Carolina State University (NCSU) Raleigh, NC, 27606 Email: rmao at ncsu.edu Email: ruimao20 at gmail.com ============================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120515/d44aa498/attachment.htm From bdslipun at gmail.com Wed May 16 06:36:11 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 16 May 2012 10:06:11 +0530 Subject: [Pw_forum] electron phonon Message-ID: i want to calculate lambda (elph coefficients) i calculated scf by 16.16.16 kpoint grid and phonon by 4.4.4 grid for my TaC (TANTALUM CARBIDE ) but at q2r.x output shows the error q-space grid ok, #points = 64 fft-check success (sum of imaginary terms < 10^-12) Preparing gamma for a2F %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from init : error # 1 nc already filled: wrong q grid or wrong nr %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... 2 what is the problem ? is there i have to increse kpoint or decrese qpoint grid thanks in advance b sahoo reserch scolar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/4811a636/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed May 16 08:47:36 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 16 May 2012 08:47:36 +0200 Subject: [Pw_forum] electron phonon In-Reply-To: References: Message-ID: On Wed, May 16, 2012 at 6:36 AM, bhabya sahoo wrote: > > what is the problem ? is there i have to increse kpoint or decrese qpoint > grid > Neither, there is a problem in your q2r.x input. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/49428de0/attachment.htm From iyad.ne at gmail.com Wed May 16 17:10:05 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Wed, 16 May 2012 11:10:05 -0400 Subject: [Pw_forum] el-ph calculations Message-ID: Dear QE users, I am trying to study the el-ph interaction in NbC, in particular I want to calculate the phonon line widths along high symmetry directions in the BZ. My input files work properly ( following example07). I am asking how can I accelerate the calculations. I am using 32 processors. What make things slow is I can not use npool >1. since this is not implemented yet for el-ph calculations. (Note that: in scf calculations when I set -np 32 and -npool 32 I speed up the calculations by ~25 times, but this is not the case when I set npool 1). My question: is there away to make these calculation with less time, such as can I in elph calculations using ph,x run each q- point separately and then collect them.In order to do so what do I need to specify in my input files (*.elph.in, and q2r.in)? Kindest Regards, IYAD X-ray and Neutron Scattering Group Materials Science and Technology division ORNL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/d2c3272b/attachment.htm From dyang2103 at gmail.com Wed May 16 17:51:38 2012 From: dyang2103 at gmail.com (david yang) Date: Wed, 16 May 2012 21:21:38 +0530 Subject: [Pw_forum] some help on D3 code Message-ID: Hi all , I am using D3 code for anharmonic terms calcualtion for ZnO. But during final step (while executing D3.x command ) it showing me error ======================================== task # 0 from d3_readin : error # 1 US not implemented ======================================= My input file looks as &control calculation='scf' restart_mode='from_scratch', !pseudo_dir='directory where ps !outdir='directory where large files are written/' pseudo_dir='./', outdir='./' prefix='ZnO', !ldisp=.true. / &system ibrav=4, celldm(1)=9.826575141,celldm(3)=1.625,nat=4, ntyp=2, ecutwfc =16.0 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.39 Zn.pbe-van.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS Zn 0.3333 0.6667 0.0000 Zn 0.6667 0.3333 0.5000 O 0.3333 0.6667 0.3750 O 0.6667 0.3333 0.8750 K_POINTS {automatic} 3 3 3 0 0 0 and D3 file is Anharm at Q1 &inputph prefix = 'ZnO', fildrho = 'ZnO.drho_Q1', fild0rho = 'ZnO.drho_Q1', amass(1) = 65.39, amass(2) = 15.9994, outdir = './', fildyn = 'ZnO.anh_Q1', / 0.0 0.0 0.0 I believe that this error is related to pseudo potential and i tried changing pseudo potential but nothing is working . Can any give me quick suggestion on this matter. Thanks in advance regards David Yang NTU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/7623b382/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed May 16 17:55:03 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 16 May 2012 17:55:03 +0200 Subject: [Pw_forum] some help on D3 code In-Reply-To: References: Message-ID: On Wed, May 16, 2012 at 5:51 PM, david yang wrote: > But during final step (while executing D3.x command ) it showing me error > ======================================== > task # 0 > from d3_readin : error # 1 > US not implemented > ======================================= > > US means Ultrasoft, the error means that the code does not support ultrasoft pseudopotentials. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/a0ca96c9/attachment.htm From konda.physics at gmail.com Wed May 16 19:27:56 2012 From: konda.physics at gmail.com (Kondaiah Samudrala) Date: Wed, 16 May 2012 22:57:56 +0530 Subject: [Pw_forum] requesting for thermodynamical properties Message-ID: Dear All, I am new to pwscf. I want to calculate thermodynamical properties using PWSCF. will you please any one. Thanks in advance with regards S.Appalakondaiah research scholar University of Hyderabad India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/832b3597/attachment.htm From bdslipun at gmail.com Wed May 16 20:08:38 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 16 May 2012 23:38:38 +0530 Subject: [Pw_forum] Fwd: electron phonon In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Wed, May 16, 2012 at 6:19 PM Subject: Re: [Pw_forum] electron phonon To: Lorenzo Paulatto my q2r.x input is given is there any problem &input zasr='simple', fildyn='tac.dyn', flfrc='tac0444.fc', la2F=.true. / On Wed, May 16, 2012 at 12:17 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > On Wed, May 16, 2012 at 6:36 AM, bhabya sahoo wrote: > >> >> what is the problem ? is there i have to increse kpoint or decrese qpoint >> grid >> > > > Neither, there is a problem in your q2r.x input. > > best regards > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/a5de0748/attachment.htm From giannozz at democritos.it Wed May 16 21:51:04 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 May 2012 21:51:04 +0200 Subject: [Pw_forum] el-ph calculations In-Reply-To: References: Message-ID: <2AEE90A0-1B62-487B-A5EC-D0B0188AB07C@democritos.it> On May 16, 2012, at 17:10 , Iyad AL-QASIR wrote: > What make things slow is I can not use npool >1. since this is not > implemented yet for el-ph calculations I vaguely remember that k-point parallelization was implemented some time ago. In any case, if you run the example for the electron-phonon case (PHonon/examples/example03 in the new directory structure) it seems to work with -npool 2 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed May 16 21:58:24 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 May 2012 21:58:24 +0200 Subject: [Pw_forum] Splitting phonon calculation over q point and irr In-Reply-To: References: Message-ID: On May 15, 2012, at 23:19 , Rui Mao wrote: > Before you can split the job over q points and representations, > you have to copy PREFIX.save (which is generated by scf calculation) > to each sub directories where you want to do the ph calculation > separately. > If the system is slightly large (more 20 atoms in unit cell), the > PREFIX.save > will be several GBs if you have a parallel file system (i.e. one that is visible to all processors), it might be sufficient to create symlinks. I don't know how this stuff is working now: just guessing P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed May 16 22:00:59 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 May 2012 22:00:59 +0200 Subject: [Pw_forum] Questions on the warning message from relax calculation In-Reply-To: References: Message-ID: On May 15, 2012, at 18:51 , Tram Bui wrote: > I saw the message below > WARNING: integrated charge= 1020.00000000, expected= > 1021.00000000 if there is one electron missing during self-consistency, the code stops. if the code didn't stop, everything should be fine. Maybe you have seen it in exrapolation between optimization steps. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From iyad.ne at gmail.com Wed May 16 23:22:33 2012 From: iyad.ne at gmail.com (Iyad AL-QASIR) Date: Wed, 16 May 2012 17:22:33 -0400 Subject: [Pw_forum] el-ph calculations In-Reply-To: <2AEE90A0-1B62-487B-A5EC-D0B0188AB07C@democritos.it> References: <2AEE90A0-1B62-487B-A5EC-D0B0188AB07C@democritos.it> Message-ID: Actually, I have no problem with k-points parallelization in case of scf calculations. The problem is when running *.ph.in using ph.x ( with elph=.true.,)- in this case I have to set npool =1 so the calculations will continue-. I will try the Al example in the new version and let you know. Actually I was running this example ( example07 in espresso example directory) using espresso-4.0.3 and I had the same problem of using more than pool. Many Thanks IYAD On Wed, May 16, 2012 at 3:51 PM, Paolo Giannozzi wrote: > > On May 16, 2012, at 17:10 , Iyad AL-QASIR wrote: > > What make things slow is I can not use npool >1. since this is not >> implemented yet for el-ph calculations >> > > I vaguely remember that k-point parallelization was implemented > some time ago. In any case, if you run the example for the > electron-phonon case (PHonon/examples/example03 in the > new directory structure) it seems to work with -npool 2 > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > - -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120516/0cef2c39/attachment-0001.htm From daijiayu at nudt.edu.cn Thu May 17 09:23:03 2012 From: daijiayu at nudt.edu.cn (jiayudai) Date: Thu, 17 May 2012 15:23:03 +0800 Subject: [Pw_forum] Reduced density gradient In-Reply-To: <537068217.29054@eyou.net> References: <537068217.29054@eyou.net> Message-ID: <120517152303cc1b1c5e5eaec2d93caf26a5c2db125a@nudt.edu.cn> Dear users, It's so pleased that the new version of QE code is released, and thanks a lot. In the new version, i found that the "Reduced density gradient" (J. Chem. Theory Comput. 7, 625 (2011)) can be postprocessed using plot_num=9. So, is there any example on this new implemention? Thanks a lot. Jiayu Dai ---------------- ------------------------------------------- Jiayu Dai Department of PhysicsNational University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120517/b618ce3c/attachment.htm From davide.ceresoli at istm.cnr.it Thu May 17 10:03:04 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Thu, 17 May 2012 10:03:04 +0200 Subject: [Pw_forum] Reduced density gradient In-Reply-To: <120517152303cc1b1c5e5eaec2d93caf26a5c2db125a@nudt.edu.cn> References: <537068217.29054@eyou.net> <120517152303cc1b1c5e5eaec2d93caf26a5c2db125a@nudt.edu.cn> Message-ID: <4FB4B0B8.9020906@istm.cnr.it> Dear Jiayu Dai, I haven't included any example of RDG but I successfully reproduced all pictures of the JCTC. It works like plot_num=0 (charge density) and you can produce an XSF file. Then open it with XCrysden and set the isovalue as suggested in the JCTC paper and in the documentation. You should see a 'lenticular shape surface' for each non-bonded interaction. Davide On 05/17/2012 09:23 AM, jiayudai wrote: > Dear users, > > It's so pleased that the new version of QE code is released, and thanks a lot. > > In the new version, i found that the "Reduced density gradient" (J. Chem. Theory > Comput. 7, 625 (2011)) can be postprocessed using plot_num=9. So, is there any > example on this new implemention? > > Thanks a lot. > > Jiayu Dai > > > > ---------------- > ------------------------------------------- > Jiayu Dai > Department of PhysicsNational University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- -- +--------------------------------------------------------------+ Davide Ceresoli CNR Institute of Molecular Science and Technology (CNR-ISTM) c/o University of Milan, via Golgi 19, 20133 Milan, Italy Email: davide.ceresoli at istm.cnr.it Phone: +39-02-50314276, +39-347-1001570 (mobile) Skype: dceresoli +--------------------------------------------------------------+ From lorenzo.paulatto at impmc.upmc.fr Thu May 17 10:38:47 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 17 May 2012 10:38:47 +0200 Subject: [Pw_forum] Splitting phonon calculation over q point and irr In-Reply-To: References: Message-ID: On Wed, May 16, 2012 at 9:58 PM, Paolo Giannozzi wrote: > > On May 15, 2012, at 23:19 , Rui Mao wrote: > > > Before you can split the job over q points and representations, > > you have to copy PREFIX.save (which is generated by scf calculation) > > to each sub directories where you want to do the ph calculation > > separately. > > If the system is slightly large (more 20 atoms in unit cell), the > > PREFIX.save > > will be several GBs > > if you have a parallel file system (i.e. one that is visible to all > processors), it > might be sufficient to create symlinks. I don't know how this stuff > is working > now: just guessing > The phonon calculation should not modify the prefix.save directory, except when running at Gamma AND not in a grid calculation. I have a slightly modified version of the phonon code that works in a subdirectory whose name depends on the q-point, and never writes anything in prefix,save, not even for Gamma. With it you can run several different instances with the same prefix and outdir as long as the q points are different. If you want to test it, I should be able to send you the patch tomorrow (today is holiday here) bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120517/2af4651a/attachment.htm From ruimao20 at gmail.com Thu May 17 17:27:58 2012 From: ruimao20 at gmail.com (Rui Mao) Date: Thu, 17 May 2012 11:27:58 -0400 Subject: [Pw_forum] Splitting phonon calculation over q point and irr In-Reply-To: References: Message-ID: Hi Dr. Lorenzo Paulatto, Thank you for your reply. I am glad to run some tests on the modified version of phonon code. Please let me know how to compile it when you send me the patch. Thank you, Rui On Thu, May 17, 2012 at 4:38 AM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > On Wed, May 16, 2012 at 9:58 PM, Paolo Giannozzi > wrote: > >> >> On May 15, 2012, at 23:19 , Rui Mao wrote: >> >> > Before you can split the job over q points and representations, >> > you have to copy PREFIX.save (which is generated by scf calculation) >> > to each sub directories where you want to do the ph calculation >> > separately. >> > If the system is slightly large (more 20 atoms in unit cell), the >> > PREFIX.save >> > will be several GBs >> >> if you have a parallel file system (i.e. one that is visible to all >> processors), it >> might be sufficient to create symlinks. I don't know how this stuff >> is working >> now: just guessing >> > The phonon calculation should not modify the prefix.save directory, except > when running at Gamma AND not in a grid calculation. > > I have a slightly modified version of the phonon code that works in a > subdirectory whose name depends on the q-point, and never writes anything > in prefix,save, not even for Gamma. With it you can run several different > instances with the same prefix and outdir as long as the q points are > different. > > If you want to test it, I should be able to send you the patch tomorrow > (today is holiday here) > > bests > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Rui Mao ============================================================ Department of Electrical and Computer Engineering (ECE) North Carolina State University (NCSU) Raleigh, NC, 27606 Email: rmao at ncsu.edu Email: ruimao20 at gmail.com ============================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120517/d02e9192/attachment.htm From ruimao20 at gmail.com Thu May 17 17:30:27 2012 From: ruimao20 at gmail.com (Rui Mao) Date: Thu, 17 May 2012 11:30:27 -0400 Subject: [Pw_forum] Splitting phonon calculation over q point and irr In-Reply-To: References: Message-ID: Hi Dr. Paolo Giannozzi The symbolic link works well, and I do not need to copy PREFIX.save around now. Thank you for your help! Best, Rui On Wed, May 16, 2012 at 3:58 PM, Paolo Giannozzi wrote: > > On May 15, 2012, at 23:19 , Rui Mao wrote: > > Before you can split the job over q points and representations, >> you have to copy PREFIX.save (which is generated by scf calculation) >> to each sub directories where you want to do the ph calculation >> separately. >> If the system is slightly large (more 20 atoms in unit cell), the >> PREFIX.save >> will be several GBs >> > > if you have a parallel file system (i.e. one that is visible to all > processors), it > might be sufficient to create symlinks. I don't know how this stuff is > working > now: just guessing > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > -- Rui Mao ============================================================ Department of Electrical and Computer Engineering (ECE) North Carolina State University (NCSU) Raleigh, NC, 27606 Email: rmao at ncsu.edu Email: ruimao20 at gmail.com ============================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120517/68ec3d14/attachment.htm From pmoreira at ifi.unicamp.br Thu May 17 20:07:39 2012 From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira) Date: Thu, 17 May 2012 15:07:39 -0300 Subject: [Pw_forum] A long relaxation Message-ID: <4FB53E6B.3080909@ifi.unicamp.br> Dear all, I am doing a relaxation which is consuming a very long time. My input is below, but I think it is OK, because there is nothing wrong with my output and the system energies are decreasing . However, I have noted that the total forces and the forces acting on each atoms have oscillated a lot. I summarized below the total forces, which are showed in the end of each SC calculation. Is it right? Or could the program find a local minimum and cannot get out of it (or anything similar)? Thanks a lot, Pedro ####Total forces##### Total force = 0.162129 Total SCF correction = 0.000046 Total force = 0.131410 Total SCF correction = 0.039799 Total force = 0.199885 Total SCF correction = 0.004809 Total force = 0.254130 Total SCF correction = 0.004143 Total force = 0.285538 Total SCF correction = 0.003092 Total force = 0.339246 Total SCF correction = 0.001453 Total force = 0.419218 Total SCF correction = 0.000630 Total force = 0.509140 Total SCF correction = 0.000243 Total force = 0.593476 Total SCF correction = 0.000133 Total force = 0.534968 Total SCF correction = 0.000206 Total force = 0.431853 Total SCF correction = 0.004582 Total force = 0.308932 Total SCF correction = 0.000404 #####Input######## &control calculation='relax', restart_mode='from_scratch', pseudo_dir = '/quantum-espresso/espresso/pseudo/', outdir='/quantum-espresso/espresso/tmp/', prefix='ap5', tprnfor = .true., nstep = 1000, / &system ibrav = 4, celldm(1) = 17.8749, celldm(3) = 0.7241, nat = 42, ntyp = 4, ecutwfc = 52.0, ecutrho = 900.0, / &electrons electron_maxstep = 500 mixing_beta = 0.1, / &ions ion_dynamics='bfgs', / ATOMIC_SPECIES Ca 40.0780 Ca.pz-n-vbc.UPF P 30.9738 P.pz-van_ak.UPF O 15.9994 O.pz-van_ak.UPF F 18.99840 F.pz-van_asa.UPF ATOMIC_POSITIONS angstrom . . . ############################## -- Pedro Moreira IFGW - Unicamp - Brazil From izaakw89 at yahoo.com Thu May 17 23:43:45 2012 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 17 May 2012 14:43:45 -0700 (PDT) Subject: [Pw_forum] Determining Bandgap with DOS In-Reply-To: References: Message-ID: <1337291025.95774.YahooMailNeo@web43415.mail.sp1.yahoo.com> Hello all, I am trying to calculate the electronic bandgap for wurtzite ZnO using the attached plot of?DoS (E), where the Fermi level is represented by a vertical dashed-line and EV represents the valence band maximum. My question is, should I use EC1 or EC2 as my conduction band minimum? If I use EC1, the bandgap is ~0.5eV but if I consider those states at that point negligible and use EC2 then the bandgap is ~1.5eV. (NOTE: the experimental bandgap is 3.36eV.) Thanks for the help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120517/b7b34cf0/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: bandgap-pdos.png Type: image/png Size: 32553 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120517/b7b34cf0/attachment-0001.png From huazhorg at 163.com Fri May 18 03:58:31 2012 From: huazhorg at 163.com (Huazhong Liu) Date: Fri, 18 May 2012 09:58:31 +0800 (CST) Subject: [Pw_forum] Help: About spin-polarization Message-ID: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> Dear all, I have got a problem of spin-polarization calculation. I put one H atom onto the stoichiometric TiO2 surface. I think that is must have magnetic properties after I optimized the adsorption system. But I didn't find the magnetism in the system after the calculation. Here are the parameters which set for spin-polarization calculation: ................... / &system ibrav=.......... nat=49 , ntyp=3, nspin=2, starting_magnetization(1)= 0.5 starting_magnetization(2)= 0.5 starting_magnetization(3)= 0.5 ecutwfc=30.0, ecutrho=300.0, occupations='smearing', smearing='gauss', degauss=0.02, / ATOMIC_SPECIES Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.9994 O.pbe-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF ........................... I got the result as below: The total energy is the sum of the following terms: one-electron contribution = -12795.07240972 Ry hartree contribution = 6472.21004247 Ry xc contribution = -456.66736582 Ry ewald contribution = 3879.97911645 Ry smearing contrib. (-TS) = -0.01329486 Ry total magnetization = 0.00 Bohr mag/cell absolute magnetization = 0.00 Bohr mag/cell convergence has been achieved in 10 iterations .................................. Will you please find any problem in my parameters? Why I can not get the magnetism of the system? Thank you! regards, Huazhong Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/151cfedb/attachment.htm From bdslipun at gmail.com Fri May 18 05:35:02 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 18 May 2012 09:05:02 +0530 Subject: [Pw_forum] Fwd: electron phonon In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Wed, May 16, 2012 at 11:38 PM Subject: Fwd: [Pw_forum] electron phonon To: PWSCF Forum ---------- Forwarded message ---------- From: bhabya sahoo Date: Wed, May 16, 2012 at 6:19 PM Subject: Re: [Pw_forum] electron phonon To: Lorenzo Paulatto my q2r.x input is given is there any problem &input zasr='simple', fildyn='tac.dyn', flfrc='tac0444.fc', la2F=.true. / On Wed, May 16, 2012 at 12:17 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > On Wed, May 16, 2012 at 6:36 AM, bhabya sahoo wrote: > >> >> what is the problem ? is there i have to increse kpoint or decrese qpoint >> grid >> > > > Neither, there is a problem in your q2r.x input. > > best regards > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/7325be3b/attachment.htm From jiachenchem at gmail.com Fri May 18 08:53:24 2012 From: jiachenchem at gmail.com (Jia Chen) Date: Fri, 18 May 2012 02:53:24 -0400 Subject: [Pw_forum] Help: About spin-polarization In-Reply-To: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> References: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> Message-ID: Hi Huazhong, Only problem I can spot is that the smearing is a little bit too large. Room temperature is only 23meV, degauss = 0.002Ry would be more reasonable. I guess the situation is that the single electron should be a d state of Ti, but PBE functional makes it a delocalized state and the system becomes metallic, then big smearing completely eliminates magnetization... Just my guess... On Thu, May 17, 2012 at 9:58 PM, Huazhong Liu wrote: > Dear all, > I have got a problem of spin-polarization calculation. I put one H > atom onto the stoichiometric TiO2 surface. I think that is must have > magnetic properties after I optimized the adsorption system. But I didn't > find the magnetism in the system after the calculation. Here are the > parameters which set for spin-polarization calculation: > ................... > / > &system > ibrav=.......... > nat=49 , ntyp=3, > nspin=2, > starting_magnetization(1)= 0.5 > starting_magnetization(2)= 0.5 > starting_magnetization(3)= 0.5 > ecutwfc=30.0, > ecutrho=300.0, > occupations='smearing', smearing='gauss', degauss=0.02, > / > ATOMIC_SPECIES > Ti 47.867 Ti.pbe-sp-van_ak.UPF > O 15.9994 O.pbe-van_ak.UPF > H 1.00794 H.pbe-van_ak.UPF > ........................... > > I got the result as below: > The total energy is the sum of the following terms: > > one-electron contribution = -12795.07240972 Ry > hartree contribution = 6472.21004247 Ry > xc contribution = -456.66736582 Ry > ewald contribution = 3879.97911645 Ry > smearing contrib. (-TS) = -0.01329486 Ry > > total magnetization = 0.00 Bohr mag/cell > absolute magnetization = 0.00 Bohr mag/cell > > convergence has been achieved in 10 iterations > .................................. > > Will you please find any problem in my parameters? Why I can not get the > magnetism of the system? Thank you! > > regards, > Huazhong Liu > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/ff38a13f/attachment.htm From lmartinsamos at gmail.com Fri May 18 08:58:08 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 18 May 2012 08:58:08 +0200 Subject: [Pw_forum] Change in the number of qe-forge users Message-ID: Dear all, we are thinking in moving qe-forge from fusionforge to gforge. Unfortunately it seems that gforge ask for a commercial License which pro-year prince will depends on the number of users. As all of you know, nor Quantum ESPRESSO nor qe-forge have any direct financial support, so we can not afford big expenses. In order to reduce potential costs of the gforge commercial License, our system administrator has eliminated all the qe-forge users that are not bound to any qe-forge project. Depending on the License price then or we move to gforge or we stay with fusionforge. In any case we will let you know in order to rationalize the qe-forge users. Sorry for the inconvenience, best regards Layla -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/1abef484/attachment.htm From lmartinsamos at gmail.com Fri May 18 09:08:25 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 18 May 2012 09:08:25 +0200 Subject: [Pw_forum] Quantum ESPRESSO Highlights 2011, thank s to all contributors Message-ID: Dear all, as you have probably noticed in our new HOME page we have introduced 4 immages that correspond to the "call for immages and quantum ESPRESSO highlights 2011" that we sent to pw_forum some months ago. We would like to thank all the participants for their kind contribution. At the end of the year we will renew the call for Quantum ESPRESSO highlights 2012! good work and "May the GIMP be with you" ;-) Layla -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/2a6b476c/attachment.htm From lmartinsamos at gmail.com Fri May 18 09:27:11 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 18 May 2012 09:27:11 +0200 Subject: [Pw_forum] [Q-e-developers] [Pw_users] Change in the number of qe-forge users In-Reply-To: <67C89F8F-070D-439E-A405-DE8AE0F78171@epfl.ch> References: <67C89F8F-070D-439E-A405-DE8AE0F78171@epfl.ch> Message-ID: Dear Giovanni, if I am not wrong github is for git version management. Most of the projects on qe-forge use svn or cvs. When we decide to move from cvs to svn we also have considered the possibility of moving to git. However, as we say in italianish "we know our chickens", and the "unlimited" freedom that gives git could have introduced many coordination issues in the quantum ESPRESSO global management. thank you for your suggestion Layla 2012/5/18 Giovanni Cangiani > what about github ? > > best, > > Giovanni > > -- > Giovanni Cangiani > > On May 18, 2012, at 8:58, Layla Martin-Samos > wrote: > > > Dear all, we are thinking in moving qe-forge from fusionforge to gforge. > Unfortunately it seems that gforge ask for a commercial License which > pro-year prince will depends on the number of users. As all of you know, > nor Quantum ESPRESSO nor qe-forge have any direct financial support, so we > can not afford big expenses. In order to reduce potential costs of the > gforge commercial License, our system administrator has eliminated all the > qe-forge users that are not bound to any qe-forge project. Depending on the > License price then or we move to gforge or we stay with fusionforge. In any > case we will let you know in order to rationalize the qe-forge users. > > > > Sorry for the inconvenience, best regards > > > > Layla > > _______________________________________________ > > Pw_users mailing list > > Pw_users at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_users > _______________________________________________ > Q-e-developers mailing list > Q-e-developers at qe-forge.org > http://qe-forge.org/mailman/listinfo/q-e-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/e2e5531e/attachment-0001.htm From fratesi at mater.unimib.it Fri May 18 09:37:08 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 18 May 2012 09:37:08 +0200 Subject: [Pw_forum] Determining Bandgap with DOS In-Reply-To: <1337291025.95774.YahooMailNeo@web43415.mail.sp1.yahoo.com> References: <1337291025.95774.YahooMailNeo@web43415.mail.sp1.yahoo.com> Message-ID: <4FB5FC24.1020107@mater.unimib.it> Dear Izaak, a few preliminary questions you might find helpful answering before going on: - have you used a sufficient number of k points? - have you used a sufficiently dense energy grid in the plot? - how is it possible that the curve "without smearing" is more smeared than the one "with smearing"? Check what default values are. - why do you indicate by arrows not the state found in the DOS, but the energy point at which your gaussian (of arbitrary width indeed) looks different from zero? - why not looking at eigenvalues printed by pw.x on output to get the real (computed) numbers? (Yet the DOS plot is helpful to get an overview) Hope this helps. Guido On 05/17/2012 11:43 PM, Izaak Williamson wrote: > Hello all, > > I am trying to calculate the electronic bandgap for wurtzite ZnO using > the attached plot of DoS (E), where the Fermi level is represented by a > vertical > dashed-line and EV represents the valence band maximum. > > My question is, should I use EC1 or EC2 as my conduction band minimum? > If I use EC1, the bandgap is ~0.5eV but if I consider those states at > that point negligible and use EC2 then the bandgap is ~1.5eV. (NOTE: > the experimental bandgap is 3.36eV.) > > Thanks for the help. -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From fratesi at mater.unimib.it Fri May 18 09:44:24 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 18 May 2012 09:44:24 +0200 Subject: [Pw_forum] A long relaxation In-Reply-To: <4FB53E6B.3080909@ifi.unicamp.br> References: <4FB53E6B.3080909@ifi.unicamp.br> Message-ID: <4FB5FDD8.2030304@mater.unimib.it> Dear Pedro, if the energy is decreasing you are not trapped in a local minimum (not yet, at least: maybe you are approaching it). From the extract you sent us, forces are rather increasing than oscillating, and if the energy is instead decreasing that suggests me that your system started close to some saddle point or energy maximum, then after some relaxation steps it found some stronger energy gradient and started following it. Are atoms moving considerably, meanwhile? PS do you really need so large ecutrho and small mixing_beta? Best, Guido On 05/17/2012 08:07 PM, Pedro Augusto F. P. Moreira wrote: > Dear all, > > I am doing a relaxation which is consuming a very long time. My input > is below, but I think it is OK, because there is nothing wrong with my > output and the system energies are decreasing . > However, I have noted that the total forces and the forces acting on > each atoms have oscillated a lot. I summarized below the total forces, > which are showed in the end of each SC calculation. > Is it right? Or could the program find a local minimum and cannot get > out of it (or anything similar)? > > Thanks a lot, > > Pedro > > ####Total forces##### > Total force = 0.162129 Total SCF correction = 0.000046 > Total force = 0.131410 Total SCF correction = 0.039799 > Total force = 0.199885 Total SCF correction = 0.004809 > Total force = 0.254130 Total SCF correction = 0.004143 > Total force = 0.285538 Total SCF correction = 0.003092 > Total force = 0.339246 Total SCF correction = 0.001453 > Total force = 0.419218 Total SCF correction = 0.000630 > Total force = 0.509140 Total SCF correction = 0.000243 > Total force = 0.593476 Total SCF correction = 0.000133 > Total force = 0.534968 Total SCF correction = 0.000206 > Total force = 0.431853 Total SCF correction = 0.004582 > Total force = 0.308932 Total SCF correction = 0.000404 > > #####Input######## > &control > calculation='relax', > restart_mode='from_scratch', > pseudo_dir = '/quantum-espresso/espresso/pseudo/', > outdir='/quantum-espresso/espresso/tmp/', > prefix='ap5', > tprnfor = .true., > nstep = 1000, > / > &system > ibrav = 4, celldm(1) = 17.8749, celldm(3) = 0.7241, > nat = 42, ntyp = 4, > ecutwfc = 52.0, ecutrho = 900.0, > / > &electrons > electron_maxstep = 500 > mixing_beta = 0.1, > / > &ions > ion_dynamics='bfgs', > / > ATOMIC_SPECIES > Ca 40.0780 Ca.pz-n-vbc.UPF > P 30.9738 P.pz-van_ak.UPF > O 15.9994 O.pz-van_ak.UPF > F 18.99840 F.pz-van_asa.UPF > ATOMIC_POSITIONS angstrom > . > . > . > ############################## > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From giuseppe.mattioli at ism.cnr.it Fri May 18 11:53:45 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 18 May 2012 11:53:45 +0200 Subject: [Pw_forum] Determining Bandgap with DOS In-Reply-To: <1337291025.95774.YahooMailNeo@web43415.mail.sp1.yahoo.com> References: <1337291025.95774.YahooMailNeo@web43415.mail.sp1.yahoo.com> Message-ID: <201205181153.45748.giuseppe.mattioli@ism.cnr.it> Dear Izaak Wurtzite ZnO is a very (VERY) nasty semiconductor... I find a PBE band gap of 0.8 eV, in agreement with previous investigations. Hybrid functionals, as HSE with alpha=0.25, do not heal the whole of it; you find something around 2.2 eV (If you are interested, I can cite several papers). This is due to the very narrow Zn 3d band which is very strongly affected by delocalisation (aka self- interaction) errors. The conduction band minimum (CBM) appears as a tiny feature (the 0.5 eV one, I suppose) in your DOS because the CB is sharply peaked around Gamma, so that even if your calculation is well converged wrt energy, forces, stress, ..., you do not achieve a good sampling around the CBM. How can you cure it? It depends on your final purpose, which I suppose is not the band structure of a 4-atoms cell... You mat write directly to me if you are going to look for further advice. HTH Giuseppe On Thursday 17 May 2012 23:43:45 Izaak Williamson wrote: > Hello all, > > I am trying to calculate the electronic bandgap for wurtzite ZnO using > the attached plot of DoS (E), where the Fermi level is represented by a > vertical > > dashed-line and EV represents the valence band maximum. > > My question is, should I use EC1 or EC2 as my conduction band minimum? > If I use EC1, the bandgap is ~0.5eV but if I consider those states at > that point negligible and use EC2 then the bandgap is ~1.5eV. (NOTE: > > the experimental bandgap is 3.36eV.) > > Thanks for the help. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giuseppe.mattioli at ism.cnr.it Fri May 18 12:01:07 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 18 May 2012 12:01:07 +0200 Subject: [Pw_forum] Help: About spin-polarization In-Reply-To: References: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> Message-ID: <201205181201.07546.giuseppe.mattioli@ism.cnr.it> Dear Huazhong Liu Flicking through some literature...? Excess electrons in TiO2 (bulk, surface, nanostructures, ...) are one of the most investigated issues in theoretical (and experimental) condensed matter, physical chemistry, surface chemistry, environmental science, ..., papers. I avoid to cite papers of mine (noblesse oblige), but you can find many papers by Annabella Selloni and Elio Pacchioni which should be quite interesting... HTH Giuseppe On Friday 18 May 2012 08:53:24 Jia Chen wrote: > Hi Huazhong, > > Only problem I can spot is that the smearing is a little bit too large. > Room temperature is only 23meV, degauss = 0.002Ry would be more reasonable. > I guess the situation is that the single electron should be a d state of > Ti, but PBE functional makes it a delocalized state and the system becomes > metallic, then big smearing completely eliminates magnetization... Just my > guess... > > On Thu, May 17, 2012 at 9:58 PM, Huazhong Liu wrote: > > Dear all, > > > > I have got a problem of spin-polarization calculation. I put one H > > > > atom onto the stoichiometric TiO2 surface. I think that is must have > > magnetic properties after I optimized the adsorption system. But I didn't > > find the magnetism in the system after the calculation. Here are the > > parameters which set for spin-polarization calculation: > > ................... > > > > / > > &system > > > > ibrav=.......... > > nat=49 , ntyp=3, > > nspin=2, > > starting_magnetization(1)= 0.5 > > starting_magnetization(2)= 0.5 > > starting_magnetization(3)= 0.5 > > ecutwfc=30.0, > > ecutrho=300.0, > > occupations='smearing', smearing='gauss', degauss=0.02, > > > > / > > > > ATOMIC_SPECIES > > > > Ti 47.867 Ti.pbe-sp-van_ak.UPF > > O 15.9994 O.pbe-van_ak.UPF > > H 1.00794 H.pbe-van_ak.UPF > > > > ........................... > > > > I got the result as below: > > The total energy is the sum of the following terms: > > one-electron contribution = -12795.07240972 Ry > > hartree contribution = 6472.21004247 Ry > > xc contribution = -456.66736582 Ry > > ewald contribution = 3879.97911645 Ry > > smearing contrib. (-TS) = -0.01329486 Ry > > > > total magnetization = 0.00 Bohr mag/cell > > absolute magnetization = 0.00 Bohr mag/cell > > > > convergence has been achieved in 10 iterations > > > > .................................. > > > > Will you please find any problem in my parameters? Why I can not get the > > magnetism of the system? Thank you! > > > > regards, > > Huazhong Liu > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giannozz at democritos.it Fri May 18 12:10:22 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 May 2012 12:10:22 +0200 Subject: [Pw_forum] Help: About spin-polarization In-Reply-To: <201205181201.07546.giuseppe.mattioli@ism.cnr.it> References: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> <201205181201.07546.giuseppe.mattioli@ism.cnr.it> Message-ID: <1337335822.22765.37.camel@fe12lx.fisica.uniud.it> On Fri, 2012-05-18 at 12:01 +0200, Giuseppe Mattioli wrote: > Elio Pacchioni "Elio" (i.e. Helium in English) would be a very appropriate name for a quantum chemist, but his name is actually Gianfranco P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri May 18 12:25:23 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 May 2012 12:25:23 +0200 Subject: [Pw_forum] Change in the behavior of "Reply" Message-ID: <1337336723.22765.52.camel@fe12lx.fisica.uniud.it> Please note that the behavior of this mailing list with respect to the "Reply" command has been reverted to the previous "Reply-to munging" option, that is: if you hit "Reply", the message will go to the mailing list, not to the poster. So please THINK before hitting "Reply" (think EVEN MORE before hitting "Send"), avoid unnecessary or inappropriate traffic in this mailing list. Here is a reminder of the guidelines for posting: Before posting, please: browse or search the archives ? links are available in the Contacts page of the quantum ESPRESSO web site. Most questions are asked over and over again. Also: make an attempt to search the available documentation, notably the FAQ, the User Guide, and the Input Data Description. The answer to most questions is already there. * Sign your post with your name and affiliation. * Choose a meaningful subject. Do not use ?Reply? to start a new thread: it will confuse the ordering of messages into threads that most mailers can do. In particular, NEVER use ?Reply? to a Digest!!! * Be short: no need to send 128 copies of the same error message just because this is what came out of your 128-processor run. No need to send the entire compilation log for a single error appearing at the end. * Avoid excessive or irrelevant quoting of previous messages. Your message must be immediately visible and easily readable, not hidden into a sea of quoted text. * Remember that even experts cannot guess where a problem lies in the absence of sufficient information. One piece of information that must always be provided is the version number you are using. * Remember that the mailing list is a voluntary endeavour: nobody is entitled to an answer, even less to an immediate answer. Please check in the archive if your e-mails have gone through before thinking or even worse complaining that nobody is answering my questions. * Finally, please note that the mailing list is not a replacement for your own work, nor is it a replacement for your thesis director?s work. Reporting BUGS * Problems should be reported to the pw_forum mailing list, NOT to a single developer * Before reporting an unexpected behavior as a problem, * check your input data: most problems originate from there * if you have a problem with examples, look for the error message printed by the code in the output file: few things irritate developers like messages saying "I got error 137 in example 24", or "What does error # 1924 mean?" * carefully read the error message issued by the code, if present: sometimes it explains everything. For the provided examples, you must look inside the output files. * trust the code if it says "this doesn?t exist" or "this is wrong"! * check if a similar or same problem hasn?t already been reported * Before deciding that a problem is due to a bug in the codes, verify if it is reproducible on different machines/architectures/phases of the moon: erratic or irreproducible problems, especially in parallel execution, are often an indication of buggy compilers or libraries * Bug reports should preferably be filed using the bug tracking facility of qe-forge.org: http://qe-forge.org/tracker/?group_id=10 * Bug reports should include enough information to be reproduced, e.g. version number (mandatory!), hardware/software combination(s) for which the problem arises, whether it happens in serial or parallel execution or both, and, most important, an input and output exhibiting such behavior (fast to execute if possible). The error message alone is usually not a sufficient piece of information. Segmentation violation or obscure MPI error messages are NEVER a sufficient piece of information. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giuseppe.mattioli at ism.cnr.it Fri May 18 12:37:54 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 18 May 2012 12:37:54 +0200 Subject: [Pw_forum] Help: About spin-polarization In-Reply-To: <1337335822.22765.37.camel@fe12lx.fisica.uniud.it> References: <54e05eba.2022c.1375daaeabb.Coremail.huazhorg@163.com> <201205181201.07546.giuseppe.mattioli@ism.cnr.it> <1337335822.22765.37.camel@fe12lx.fisica.uniud.it> Message-ID: <201205181237.54764.giuseppe.mattioli@ism.cnr.it> Sorry, Elio Pacchioni is a friend of mine whom I confused with professor Gianfranco Pacchioni...:-) G. On Friday 18 May 2012 12:10:22 Paolo Giannozzi wrote: > On Fri, 2012-05-18 at 12:01 +0200, Giuseppe Mattioli wrote: > > Elio Pacchioni > > "Elio" (i.e. Helium in English) would be a very appropriate name > for a quantum chemist, but his name is actually Gianfranco > > P. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From victormengwa at gmail.com Fri May 18 13:09:39 2012 From: victormengwa at gmail.com (Victor Meng'wa) Date: Fri, 18 May 2012 14:09:39 +0300 Subject: [Pw_forum] Surface Band structure calculation Message-ID: Dear QE users, i've done bands calculation,when i check my output on every kpoint there's this message after computation, that implies a significant number of eigenvalues in the c_bands have not converged. Computing kpt #: 9 c_bands: 4 eigenvalues not converged total cpu time spent up to now is 6412.1 secs Computing kpt #: 10 c_bands: 4 eigenvalues not converged total cpu time spent up to now is 7113.1 secs this is almost repetitive almost for every kpoint when i do the plotband.x ,i can't get the bands since theres an error message Reading 72 bands at 73 k-points Error reading k-point # 1 then it stops. part of my input looks like: &CONTROL restart_mode='from_scratch', calculation='bands', outdir='./', pseudo_dir='/home/mikeat/Applications/espresso-4.3.2/pseudo/', prefix = 'SnOru_exc1', tstress = .t., tprnfor = .t., etot_conv_thr = 1.d-5, forc_conv_thr = 1.d-4 verbosity = 'high' / &SYSTEM ibrav=6, celldm(1)= 53.7129, celldm(3)=0.2242, nat= 53, ntyp= 2, nbnd=72, ecutwfc =30,ecutrho = 280, occupations='smearing', smearing='Gaussian', degauss=0.005 / &ELECTRONS diagonalization = 'david' mixing_mode = 'local-TF', mixing_beta = 0.3, conv_thr = 1.0e-8, / ATOMIC_SPECIES Sn 50.011 Sn.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF ATOMIC_POSITIONS {bohr} please i've been unable to i dentify why eigenvalues in the C_bands do not converge and could this be reason why i get the error in reading the k-points and how can i correct this? please assist -- VICTOR KIRUI MENG'WA, POST GRADUATE STUDENT, CHEPKOILEL UNIVERSITY COLLEGE, DEPARTMENT OF PHYSICS, COMPUTATIONAL PHYSICS GROUP, P.O BOX 1125, ELDORET, KENYA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/85994ce1/attachment-0001.htm From karandeepster at gmail.com Fri May 18 15:39:22 2012 From: karandeepster at gmail.com (karan deep) Date: Fri, 18 May 2012 19:09:22 +0530 Subject: [Pw_forum] symmetry operation not allowed Message-ID: i am trying to relax monoclinic lattice (space group no. 14) with 20 atoms in unit cell. pwscf is not detecting symmetry with warning warning: symmetry operation # 2 not allowed. fractional translation: 0.4988459 0.4999973 -0.5000000 in crystal coordinates after some search i come to now i have to specify nr1 nr2 nr3 manually to achive abs (ft1 - nint (ft1) ) / nr1 < 1.0d-5 for all three translations. but i am getting very high values(10000) of nr1 and nr3 to achieve this but nr2=100,110 works well but high values of nr1, nr3 are not spotted.how can i get rid of this error. Secondly my system has four symmetry operations E, C2 , i, Sh while system is only detecting E no warnings for i, Sh are given any help will be greatly appreciated Karandeep Research Scholar Physics Department, IIT, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/40f25fc4/attachment.htm From naromero at gmail.com Fri May 18 16:28:56 2012 From: naromero at gmail.com (Nichols A. Romero) Date: Fri, 18 May 2012 09:28:56 -0500 Subject: [Pw_forum] [Q-e-developers] [Pw_users] Change in the number of qe-forge users In-Reply-To: References: <67C89F8F-070D-439E-A405-DE8AE0F78171@epfl.ch> Message-ID: You may also want to take a look at assembla.com to see if the pricing is cheaper. I use it for another project, but it has much fewer developers. Lastly, googlecode is free. On Fri, May 18, 2012 at 2:27 AM, Layla Martin-Samos wrote: > Dear Giovanni, if I am not wrong github is for git version management. Most > of the projects on qe-forge use svn or cvs. When we decide to move from cvs > to svn we also have considered the possibility of moving to git. However, as > we say in italianish "we know our chickens", and the "unlimited" freedom > that gives git could have introduced many coordination issues in the quantum > ESPRESSO global management. > > thank you for your suggestion > > Layla > > 2012/5/18 Giovanni Cangiani >> >> what about github ? >> >> best, >> >> Giovanni >> >> -- >> Giovanni Cangiani >> >> >> On May 18, 2012, at 8:58, Layla Martin-Samos >> wrote: >> >> > Dear all, we are thinking in moving qe-forge from fusionforge to gforge. >> > Unfortunately it seems that gforge ask for a commercial License which >> > pro-year prince will depends on the number of users. As all of you know, nor >> > Quantum ESPRESSO nor qe-forge have any direct financial support, so we can >> > not afford big expenses. In order to reduce potential costs of the gforge >> > commercial License, our system administrator has eliminated all the qe-forge >> > users that are not bound to any qe-forge project. Depending on the License >> > price then or we move to gforge or we stay with fusionforge. In any case we >> > will let you know in order to rationalize the qe-forge users. >> > >> > Sorry for the inconvenience, best regards >> > >> > Layla >> > _______________________________________________ >> > Pw_users mailing list >> > Pw_users at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_users >> _______________________________________________ >> Q-e-developers mailing list >> Q-e-developers at qe-forge.org >> http://qe-forge.org/mailman/listinfo/q-e-developers > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne, IL 60490 (630) 447-9793 From spiga.filippo at gmail.com Fri May 18 17:33:45 2012 From: spiga.filippo at gmail.com (Filippo Spiga) Date: Fri, 18 May 2012 08:33:45 -0700 Subject: [Pw_forum] [Q-e-developers] Change in the number of qe-forge users In-Reply-To: References: Message-ID: <377B3006-BE18-4921-B303-260D5200F1A2@gmail.com> Dear Layla, why moving from fusionforge to gforge? What about Trac (http://trac.edgewall.org/)? I mean, the point is? what exactly gforge has that we do need? And what if we will not use some of those advanced and fancy features that gforge will provide? You mention a "pro-year price" that depends by the number of users. Just for curiosity, can you tell us with the current number of users how much is this license? Filippo -- Mr. Filippo SPIGA, HPC and GPU Technologist website: http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert On May 17, 2012, at 11:58 PM, Layla Martin-Samos wrote: > Dear all, we are thinking in moving qe-forge from fusionforge to gforge. Unfortunately it seems that gforge ask for a commercial License which pro-year prince will depends on the number of users. As all of you know, nor Quantum ESPRESSO nor qe-forge have any direct financial support, so we can not afford big expenses. In order to reduce potential costs of the gforge commercial License, our system administrator has eliminated all the qe-forge users that are not bound to any qe-forge project. Depending on the License price then or we move to gforge or we stay with fusionforge. In any case we will let you know in order to rationalize the qe-forge users. > > Sorry for the inconvenience, best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/d222411f/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Fri May 18 17:55:54 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 18 May 2012 17:55:54 +0200 Subject: [Pw_forum] Splitting phonon calculation over q point and irr In-Reply-To: References: Message-ID: On Thu, May 17, 2012 at 5:30 PM, Rui Mao wrote: > The symbolic link works well, and I do not need to copy PREFIX.save around > now. > Thank you for your help! > > in case you still need it in the future, I've attached the modified files for using separate directories, they only apply to QE 5.0 good work -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/a98e86ad/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: ph-separate-dirs.tgz Type: application/x-gzip Size: 11860 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120518/a98e86ad/attachment-0001.bin From pmoreira at ifi.unicamp.br Fri May 18 19:02:10 2012 From: pmoreira at ifi.unicamp.br (Pedro Augusto F. P. Moreira) Date: Fri, 18 May 2012 14:02:10 -0300 Subject: [Pw_forum] Fwd: Re: A long relaxation In-Reply-To: <4FB5FDD8.2030304@mater.unimib.it> References: <4FB5FDD8.2030304@mater.unimib.it> Message-ID: <4FB68092.5070907@ifi.unicamp.br> Thanks, Guido. Are atoms moving considerably, meanwhile? Yes, they are. do you really need so large ecutrho and small mixing_beta? There is no necessity about a large ecutrho. Which value do you think is more suitable? For mixing_beta, I tried the default value, but the program always stopped with some error, which I do not remember anymore. Then, I followed the suggestion of FAQs to try a value between 0.1 and 0.3.. Pedro Moreira IFGW-Unicamp-Brazil -------- Mensagem original -------- Assunto: Re: [Pw_forum] A long relaxation Data: Fri, 18 May 2012 09:44:24 +0200 De: Guido Fratesi Para: pw_forum at pwscf.org Dear Pedro, if the energy is decreasing you are not trapped in a local minimum (not yet, at least: maybe you are approaching it). From the extract you sent us, forces are rather increasing than oscillating, and if the energy is instead decreasing that suggests me that your system started close to some saddle point or energy maximum, then after some relaxation steps it found some stronger energy gradient and started following it. Are atoms moving considerably, meanwhile? PS do you really need so large ecutrho and small mixing_beta? Best, Guido On 05/17/2012 08:07 PM, Pedro Augusto F. P. Moreira wrote: > Dear all, > > I am doing a relaxation which is consuming a very long time. My input > is below, but I think it is OK, because there is nothing wrong with my > output and the system energies are decreasing . > However, I have noted that the total forces and the forces acting on > each atoms have oscillated a lot. I summarized below the total forces, > which are showed in the end of each SC calculation. > Is it right? Or could the program find a local minimum and cannot get > out of it (or anything similar)? > > Thanks a lot, > > Pedro > > ####Total forces##### > Total force = 0.162129 Total SCF correction = 0.000046 > Total force = 0.131410 Total SCF correction = 0.039799 > Total force = 0.199885 Total SCF correction = 0.004809 > Total force = 0.254130 Total SCF correction = 0.004143 > Total force = 0.285538 Total SCF correction = 0.003092 > Total force = 0.339246 Total SCF correction = 0.001453 > Total force = 0.419218 Total SCF correction = 0.000630 > Total force = 0.509140 Total SCF correction = 0.000243 > Total force = 0.593476 Total SCF correction = 0.000133 > Total force = 0.534968 Total SCF correction = 0.000206 > Total force = 0.431853 Total SCF correction = 0.004582 > Total force = 0.308932 Total SCF correction = 0.000404 > > #####Input######## > &control > calculation='relax', > restart_mode='from_scratch', > pseudo_dir = '/quantum-espresso/espresso/pseudo/', > outdir='/quantum-espresso/espresso/tmp/', > prefix='ap5', > tprnfor = .true., > nstep = 1000, > / > &system > ibrav = 4, celldm(1) = 17.8749, celldm(3) = 0.7241, > nat = 42, ntyp = 4, > ecutwfc = 52.0, ecutrho = 900.0, > / > &electrons > electron_maxstep = 500 > mixing_beta = 0.1, > / > &ions > ion_dynamics='bfgs', > / > ATOMIC_SPECIES > Ca 40.0780 Ca.pz-n-vbc.UPF > P 30.9738 P.pz-van_ak.UPF > O 15.9994 O.pz-van_ak.UPF > F 18.99840 F.pz-van_asa.UPF > ATOMIC_POSITIONS angstrom > . > . > . > ############################## > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120518/e4f40270/attachment.htm From daijiayu at nudt.edu.cn Fri May 18 19:28:18 2012 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sat, 19 May 2012 01:28:18 +0800 Subject: [Pw_forum] Reduced density gradient In-Reply-To: <537290977.17453@eyou.net> References: <537290977.17453@eyou.net> Message-ID: <12051901281873b44fd7f9232250ec2138168da001b7@nudt.edu.cn> Dear Davide, Thanks for your reply. So, the technique is depended on the choosing the range of the density, and we should try different values to get the rquired information. By the way, for the isofurface, it means that only when the density is lower than the isofurface value, the contour line will be plotted. Is it correct? Thanks Jiayu ---------------------------------------------------------------------- Message: 1 Date: Thu, 17 May 2012 10:03:04 +0200 From: Davide Ceresoli Subject: Re: [Pw_forum] Reduced density gradient To: jiayudai Cc: pw_forum at pwscf.org Message-ID: <4FB4B0B8.9020906 at istm.cnr.it> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear Jiayu Dai, I haven't included any example of RDG but I successfully reproduced all pictures of the JCTC. It works like plot_num=0 (charge density) and you can produce an XSF file. Then open it with XCrysden and set the isovalue as suggested in the JCTC paper and in the documentation. You should see a 'lenticular shape surface' for each non-bonded interaction. Davide On 05/17/2012 09:23 AM, jiayudai wrote: > Dear users, > > It's so pleased that the new version of QE code is released, and thanks a lot. > > In the new version, i found that the "Reduced density gradient" (J. Chem. Theory > Comput. 7, 625 (2011)) can be postprocessed using plot_num=9. So, is there any > example on this new implemention? > > Thanks a lot. > > Jiayu Dai > > > > ---------------- > ------------------------------------------- > Jiayu Dai > Department of PhysicsNational University of Defense Technology, > Changsha, 410073, P R China > ----------------------------------------- -- +--------------------------------------------------------------+ Davide Ceresoli CNR Institute of Molecular Science and Technology (CNR-ISTM) c/o University of Milan, via Golgi 19, 20133 Milan, Italy Email: davide.ceresoli at istm.cnr.it Phone: +39-02-50314276, +39-347-1001570 (mobile) Skype: dceresoli +--------------------------------------------------------------+ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120519/a9ab19be/attachment.htm From davide.ceresoli at istm.cnr.it Sat May 19 10:35:05 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Sat, 19 May 2012 10:35:05 +0200 Subject: [Pw_forum] Reduced density gradient In-Reply-To: <12051901281873b44fd7f9232250ec2138168da001b7@nudt.edu.cn> References: <537290977.17453@eyou.net> <12051901281873b44fd7f9232250ec2138168da001b7@nudt.edu.cn> Message-ID: <4FB75B39.4000205@istm.cnr.it> On 05/18/2012 07:28 PM, jiayudai wrote: > Dear Davide, > > Thanks for your reply. So, the technique is depended on the choosing the range > of the density, and we should try different values to get the rquired information. Dear Jiayu, yes it does. An isovalue of 0.5-0.6 au (bohr^-3) is believed to show dispersion interaction. A lower isovalue, 0.3-0.4 au is for ionic polarized bonds. Right now this technique will give you a qualitative description but there is work in progress to make it quantitative. > By the way, for the isofurface, it means that only when the density is lower > than the isofurface value, the contour line will be plotted. Is it correct? Actually, only points which have the same value as the isovalue will be plotted. The density can be larger inside the isosurface. > > Thanks > > Jiayu > Best regards, Davide From zucco at dipteris.unige.it Sat May 19 17:52:43 2012 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Sat, 19 May 2012 17:52:43 +0200 Subject: [Pw_forum] ld1.x and virtual.x compatibility Message-ID: <126C3ADE-2BFA-467E-816F-7F66CDBEBE92@dipteris.unige.it> Hello to all, I would like to mix some species (i.e. Al-Si) trying to create (if necessary) some modified PP starting form input files distributed in pslibrary. I generated the Al PP with the input below with ld1.x of 5.0 release (but the same happens in 4.3.2) and I used it in virtual.x, but after an error I compared the new one Al PP file with one distributed with espresso (and converted from Vanderbilt format). The structure of the sections are clearly different. Thus the question is, virtual.x is usable with the PP generated by ld1.x and with these keywords? Do I must convert it in an old format (less probable, I think)? Thanks in advance m. &input title='Al', zed=13.0, rel=1, config='[Ne] 3s2 3p1 3d-2.0 4f-2.0', iswitch=3, dft='PW91', rlderiv=2.9, eminld=-2, emaxld=4.0, deld=0.02, nld=3 / &inputp pseudotype=3, file_pseudopw='Al.pw91-n-rrkjus.UPF', author='ADC', lloc=2, which_augfun='PSQ', rmatch_augfun=1.8, nlcc=.true., tm=.true. / 5 3S 1 0 2.00 0.00 2.00 2.20 0.0 3S 1 0 0.00 6.20 1.40 2.20 0.0 3P 2 1 1.00 0.00 2.00 2.10 0.0 3P 2 1 0.00 6.20 1.40 2.10 0.0 3D 3 2 -2.00 -0.30 1.90 1.90 0.0 ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From elie.moujaes at hotmail.co.uk Sat May 19 18:54:02 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 19 May 2012 17:54:02 +0100 Subject: [Pw_forum] Irreps and vibrational modes In-Reply-To: References: , Message-ID: A final question about that! Is there a way to check the frequencies of the Irreducible representations once each one is done or one has just to wait for the whole vibrational modes calculations to finish; The reason i am asking this is that since one might get negativefrequencies , I was wondering if I can check that before the whole calculation terminates (which takes 25 days) so I then can see what the problem is and lower the threshold if it is what is going wrong. Are those frequencies written to a file other than the output one? Thanks Elie Date: Mon, 14 May 2012 09:45:53 +0200 Subject: Re: [Pw_forum] Irreps and vibrational modes From: lorenzo.paulatto at impmc.upmc.fr To: elie.moujaes at hotmail.co.uk On Mon, May 14, 2012 at 4:07 AM, Elie M wrote: (1) Are all the modes vibrational? No, at Gamma you always have 3 translational modes of zero energy (2) Are any modes missing from the calculation like optical or accoustical modes? No (3) i did the calculation and got two of the modes negative which means either threshold is high or the ecutwav must be at least eight times ecutrho. Is a threshold of 10^(-15) still too high for such a system? This is FAQ2 for phonon calculations: http://www.quantum-espresso.org/?page_id=366#7.2 Thanks ElieUniversity of NottinghamNG7 2RDUK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6phone: +33 (0)1 44275 084 / skype: paulatzwww: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120519/d32f97cc/attachment.htm From elie.moujaes at hotmail.co.uk Sat May 19 22:55:50 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sat, 19 May 2012 21:55:50 +0100 Subject: [Pw_forum] g77 compiler specification Message-ID: Dear all, I am installing QE on a network that has the g77 compiler...in what subdirectory, configure script and lines of QE do i have to specify the type of the compiler g77 so that it succeeds in creating executables using ./configure? Thanks Elie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120519/608f51a6/attachment.htm From wxpurw at wm.edu Sat May 19 23:59:50 2012 From: wxpurw at wm.edu (wxpurw at wm.edu) Date: Sat, 19 May 2012 17:59:50 -0400 (EDT) Subject: [Pw_forum] g77 compiler specification In-Reply-To: References: Message-ID: QE is a f90/95+ code so it won't compile with g77. Wirawan On Sat, 19 May 2012, Elie M wrote: > Dear all, > I am installing QE on a network that has the g77 compiler...in what subdirectory, configure script and lines of QE do i have to specify the type of the compiler g77 so that > it succeeds in creating executables using ./configure? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > From giannozz at democritos.it Sun May 20 18:20:55 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 20 May 2012 18:20:55 +0200 Subject: [Pw_forum] ld1.x and virtual.x compatibility In-Reply-To: <126C3ADE-2BFA-467E-816F-7F66CDBEBE92@dipteris.unige.it> References: <126C3ADE-2BFA-467E-816F-7F66CDBEBE92@dipteris.unige.it> Message-ID: <016D7FC9-F86A-453A-BB88-EF56CB3B68FD@democritos.it> On May 19, 2012, at 17:52 , Marino Vetuschi Zuccolini wrote: > I generated the Al PP with the input below with ld1.x [...] and I > used it in virtual.x, > but after an error an error where? in virtual.x? > I compared the new one Al PP file with one distributed with > espresso [...] > The structure of the sections are clearly different. IIRC newer PP are written to a different version of the file format (there is a tag or something like this) that virtual.x cannot read. You can force the PP file to be in the old format using option "upf_v1_format" in ld1.x, though P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From permeakra at gmail.com Mon May 21 01:04:28 2012 From: permeakra at gmail.com (=?UTF-8?B?0JXQstCz0LXQvdC40Lkg0J/QtdGA0LzRj9C60L7Qsg==?=) Date: Mon, 21 May 2012 03:04:28 +0400 Subject: [Pw_forum] Problem with NEB run Message-ID: <4FB9787C.9020307@gmail.com> Hello! When I tries to run neb.x, I get error with text At line 275 of file compute_scf.f90 Fortran runtime error: Bad unit number in OPEN statement parsing_file_name: neb.in I found, that statement in consideration is file open statement, but all directories and files does exist, so I have no idea what else to check. What can I do? Input attached -------------- next part -------------- BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 80, ds = 2.D0, opt_scheme = "broyden", num_of_images = 8, k_max = 0.3D0, k_min = 0.2D0, path_thr = 0.2D0, use_freezing = true / END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL outdir = "/home/permeakra/calc/rel-pbe/ribbons/MoS2.4.50/Mo-edge-sulfidized-H2-da/neb-anti-MoH-lSH--lSHH/out/" , prefix = "run1" , pseudo_dir = "/home/permeakra/pseudo/pslibrary.0.2.3/rel-pbe/PSEUDOPOTENTIALS/" , tstress = .true. , tprnfor = .true. , nstep = 80 , etot_conv_thr = 1.0E-3 , forc_conv_thr = 1.0E-3 , iprint = 1 , max_seconds = 172800 , dt = 150 , / &SYSTEM ibrav = 0 , celldm(1) = 1.8867924528301885 , nat = 54 , ntyp = 3 , ecutwfc = 50 , ecutrho = 200 , nbnd = 190 , occupations = 'smearing' , smearing = 'gauss' , degauss = 1.0E-02 , / &ELECTRONS conv_thr = 1.0E-4 , mixing_mode = 'local-TF' , mixing_beta = 0.3 , diagonalization = 'cg', / &IONS / &CELL press = 0.00 , wmass = 0.000010 , cell_dofree = 'x' , / CELL_PARAMETERS { cubic } 12.640 0 0 0 20.0 0 0 0 12.6 K_POINTS { Gamma } ATOMIC_SPECIES Mo 1.0 Mo.rel-pbe-nc.UPF S 1.0 S.rel-pbe-nc.UPF H 1.0 H.rel-pbe-nc.UPF BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS { alat } S 0.000000000 0.000000000 1.598000000 0 0 0 S 0.000000000 0.000000000 -1.598000000 0 0 0 S 3.160000000 0.000000000 1.598000000 0 0 0 S 3.160000000 0.000000000 -1.598000000 0 0 0 S 6.320000000 0.000000000 1.598000000 0 0 0 S 6.320000000 0.000000000 -1.598000000 0 0 0 S 9.480000000 0.000000000 1.598000000 0 0 0 S 9.480000000 0.000000000 -1.598000000 0 0 0 Mo 1.580000000 0.912000000 0.000000000 0 0 0 Mo 4.740000000 0.912000000 0.000000000 0 0 0 Mo 7.900000000 0.912000000 0.000000000 0 0 0 Mo 11.060000000 0.912000000 0.000000000 0 0 0 S 1.580000000 2.736500000 1.598000000 0 0 0 S 1.580000000 2.736500000 -1.598000000 0 0 0 S 4.740000000 2.736500000 1.598000000 0 0 0 S 4.740000000 2.736500000 -1.598000000 0 0 0 S 7.900000000 2.736500000 1.598000000 0 0 0 S 7.900000000 2.736500000 -1.598000000 0 0 0 S 11.060000000 2.736500000 1.598000000 0 0 0 S 11.060000000 2.736500000 -1.598000000 0 0 0 Mo 0.000000000 3.649000000 0.000000000 0 0 0 Mo 3.160000000 3.649000000 0.000000000 0 0 0 Mo 6.320000000 3.649000000 0.000000000 0 0 0 Mo 9.480000000 3.649000000 0.000000000 0 0 0 S 0.004893561 5.504936162 1.616867431 S -0.001154334 5.516755229 -1.606532079 S 3.165794212 5.543839664 1.600595710 S 3.166293041 5.547240584 -1.594977210 S 6.309788232 5.551160840 1.595661934 S 6.301554983 5.546096178 -1.601717825 S 9.475633253 5.510136327 1.612206835 S 9.490147138 5.512073200 -1.610871839 Mo 1.562914779 6.475577474 0.001658323 Mo 4.729321823 6.522894918 0.004246911 Mo 7.913017926 6.468936257 -0.013931807 Mo 11.063765772 6.454969331 0.016631382 S 1.501447810 8.342435940 1.661758537 S 1.521847937 8.339455031 -1.657440933 S 4.683010795 8.478848666 1.565263396 S 4.693691026 8.505928531 -1.509495688 S 7.979911807 8.324350924 1.627927979 S 7.969498483 8.327307217 -1.642836205 S 11.084450317 8.317362749 1.681866959 S 11.079021714 8.341079688 -1.627200330 Mo -0.062259041 9.305399486 0.016731104 Mo 2.881570841 9.367630378 0.013921130 Mo 6.511656892 9.328641294 0.022566614 Mo 9.574789291 9.279650099 -0.003987319 S 1.510459269 11.236465893 -0.172082024 S 4.702013515 11.172972647 0.119367656 S 8.078116311 11.115154277 -0.504390134 S 11.080708674 11.156418633 0.361718502 H 6.714306541 10.391591309 1.381015110 H 4.612568668 11.559805523 -1.186948923 LAST_IMAGE ATOMIC_POSITIONS { alat } S 0.000000000 0.000000000 1.598000000 0 0 0 S 0.000000000 0.000000000 -1.598000000 0 0 0 S 3.160000000 0.000000000 1.598000000 0 0 0 S 3.160000000 0.000000000 -1.598000000 0 0 0 S 6.320000000 0.000000000 1.598000000 0 0 0 S 6.320000000 0.000000000 -1.598000000 0 0 0 S 9.480000000 0.000000000 1.598000000 0 0 0 S 9.480000000 0.000000000 -1.598000000 0 0 0 Mo 1.580000000 0.912000000 0.000000000 0 0 0 Mo 4.740000000 0.912000000 0.000000000 0 0 0 Mo 7.900000000 0.912000000 0.000000000 0 0 0 Mo 11.060000000 0.912000000 0.000000000 0 0 0 S 1.580000000 2.736500000 1.598000000 0 0 0 S 1.580000000 2.736500000 -1.598000000 0 0 0 S 4.740000000 2.736500000 1.598000000 0 0 0 S 4.740000000 2.736500000 -1.598000000 0 0 0 S 7.900000000 2.736500000 1.598000000 0 0 0 S 7.900000000 2.736500000 -1.598000000 0 0 0 S 11.060000000 2.736500000 1.598000000 0 0 0 S 11.060000000 2.736500000 -1.598000000 0 0 0 Mo 0.000000000 3.649000000 0.000000000 0 0 0 Mo 3.160000000 3.649000000 0.000000000 0 0 0 Mo 6.320000000 3.649000000 0.000000000 0 0 0 Mo 9.480000000 3.649000000 0.000000000 0 0 0 S -0.003489958 5.517919721 1.609916471 S -0.003489958 5.517919721 -1.609916471 S 3.173080535 5.536258983 1.598045077 S 3.173080535 5.536258983 -1.598045077 S 6.305207900 5.536268007 1.598047127 S 6.305207900 5.536268007 -1.598047127 S 9.482175139 5.517757023 1.610031791 S 9.482175139 5.517757023 -1.610031791 Mo 1.577198183 6.472018407 0.000000000 Mo 4.738164491 6.506406371 0.000000000 Mo 7.899826132 6.471561827 0.000000000 Mo 11.058323527 6.457081114 0.000000000 S 1.548231961 8.286501445 1.692460866 S 1.548231961 8.286501445 -1.692460866 S 4.732398862 8.503872291 1.542183168 S 4.732398862 8.503872291 -1.542183168 S 7.919896470 8.285774594 1.692911043 S 7.919896470 8.285774594 -1.692911043 S 11.053367248 8.378812225 1.553281290 S 11.053367248 8.378812225 -1.553281290 Mo 0.129659186 9.290731031 0.000000000 Mo 2.901462078 9.317715219 0.000000000 Mo 6.564484423 9.315500686 0.000000000 Mo 9.336656286 9.290594167 0.000000000 S 1.554148501 11.244563724 0.000000000 S 4.732722430 11.105240168 0.000000000 S 7.906336523 11.243704687 0.000000000 S 11.050367665 11.012367265 0.000000000 H 4.736859386 12.029754521 1.008523460 H 4.736859386 12.029754521 -1.008523460 END_POSITIONS END_ENGINE_INPUT END From giannozz at democritos.it Mon May 21 07:45:27 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 May 2012 07:45:27 +0200 Subject: [Pw_forum] Problem with NEB run In-Reply-To: <4FB9787C.9020307@gmail.com> References: <4FB9787C.9020307@gmail.com> Message-ID: <8893FB07-E3D7-4ECC-831B-97EA8F655A06@democritos.it> On May 21, 2012, at 1:04 , ??????? ???????? wrote: > At line 275 of file compute_scf.f90 > Fortran runtime error: Bad unit number in OPEN statement > > parsing_file_name: neb.in code version? serial or parallel execution? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From permeakra at gmail.com Mon May 21 07:50:58 2012 From: permeakra at gmail.com (=?UTF-8?B?0JXQstCz0LXQvdC40Lkg0J/QtdGA0LzRj9C60L7Qsg==?=) Date: Mon, 21 May 2012 09:50:58 +0400 Subject: [Pw_forum] Problem with NEB run In-Reply-To: <8893FB07-E3D7-4ECC-831B-97EA8F655A06@democritos.it> References: <4FB9787C.9020307@gmail.com> <8893FB07-E3D7-4ECC-831B-97EA8F655A06@democritos.it> Message-ID: <4FB9D7C2.3040202@gmail.com> On 05/21/2012 09:45 AM, Paolo Giannozzi wrote: > On May 21, 2012, at 1:04 , ??????? ???????? wrote: > >> At line 275 of file compute_scf.f90 >> Fortran runtime error: Bad unit number in OPEN statement >> >> parsing_file_name: neb.in > code version? serial or parallel execution? > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum 4.3.2 problem traced to name of out dir ("--" part is somehow problematic and had to be changed to "-2-") AND position of extra pw.x cards. Error reporting facilites really need improvement From pankajsahota at gmail.com Mon May 21 09:30:34 2012 From: pankajsahota at gmail.com (pankaj sahota) Date: Mon, 21 May 2012 13:00:34 +0530 Subject: [Pw_forum] Error in getting the transmission results. Message-ID: Hello Everybody, I am trying to reproduce the results of a paper by X. Qian (PHYSICAL REVIEW B 82, 195442 2010). But in the result i am getting ******* in the transmission files. I am pasting the input files for the scattering, lead and the input file for pwcond.x. Can any one have a look on where I am going wrong. I have checked the compilers and ran all the examples in the code. They are all running fine. * Scattering region:* &CONTROL calculation = 'scf' , outdir = './tmp' , pseudo_dir = '/usr/local/src/espresso_potentials/' , prefix = 'c7-al' , etot_conv_thr = 1D-7 , verbosity = 'high', / &SYSTEM ibrav = 6, celldm(1) = 26.46, celldm(3) = 1.57771, nat = 39, ntyp = 2, occupations='smearing' , smearing = 'mp' , degauss = 0.01 , ecutwfc = 27 , ecutrho = 300 , / &ELECTRONS conv_thr = 1.D-6, startingpot = 'file' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.7 , / ATOMIC_SPECIES Al 26.981539 Al.pbe-rrkj.UPF C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal Al 0.289286 0.433929 0.0000000 Al 0.433929 0.289286 0.0000000 Al 0.578571 0.433929 0.0000000 Al 0.433929 0.578571 0.0000000 Al 0.289286 0.289286 0.0916787 Al 0.289286 0.578571 0.0916787 Al 0.578571 0.289286 0.0916787 Al 0.578571 0.578571 0.0916787 Al 0.433929 0.433929 0.0916787 Al 0.289286 0.433929 0.183357 Al 0.433929 0.289286 0.183357 Al 0.578571 0.433929 0.183357 Al 0.433929 0.578571 0.183357 Al 0.289286 0.289286 0.275036 Al 0.289286 0.578571 0.275036 Al 0.578571 0.289286 0.275036 Al 0.578571 0.578571 0.275036 Al 0.433929 0.433929 0.275036 C 0.433929 0.433929 0.3203100 C 0.433929 0.433929 0.380206 C 0.433929 0.433929 0.440103 C 0.433929 0.433929 0.500000 C 0.433929 0.433929 0.559897 C 0.433929 0.433929 0.619794 C 0.433929 0.433929 0.67969 Al 0.289286 0.289286 0.724964 Al 0.289286 0.578571 0.724964 Al 0.578571 0.289286 0.724964 Al 0.578571 0.578571 0.724964 Al 0.433929 0.433929 0.724964 Al 0.289286 0.433929 0.816643 Al 0.433929 0.289286 0.816643 Al 0.578571 0.433929 0.816643 Al 0.433929 0.578571 0.816643 Al 0.289286 0.289286 0.908321 Al 0.289286 0.578571 0.908321 Al 0.578571 0.289286 0.908321 Al 0.578571 0.578571 0.908321 Al 0.433929 0.433929 0.908321 K_POINTS gamma *Lead Region:* &CONTROL calculation = 'scf' , outdir = './tmp' , pseudo_dir = '/home/pankajkumar/potentials/quantum_es/' , prefix = 'lead2' , etot_conv_thr = 1D-7 , verbosity = 'high', / &SYSTEM ibrav = 6, celldm(1) = 26.46, celldm(3) = 0.289285, nat = 9, ntyp = 1, occupations='smearing' , smearing = 'mp' , degauss = 0.01 , ecutwfc = 27 , ecutrho = 300 , / &ELECTRONS conv_thr = 1.D-6, startingpot = 'file' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.7 , / ATOMIC_SPECIES Al 26.981539 Al.pbe-rrkj.UPF ATOMIC_POSITIONS crystal Al 0.289285 0.289285 0.0 Al 0.289285 0.578571 0.0 Al 0.578571 0.289285 0.0 Al 0.578571 0.578571 0.0 Al 0.433928 0.433928 0.0 Al 0.289285 0.433928 0.5 Al 0.433928 0.289285 0.5 Al 0.578571 0.433928 0.5 Al 0.433928 0.578571 0.5 K_POINTS gamma Input file for calculating the conduction: &inputcond outdir='./tmp' prefixl='lead2', prefixs='c7-al', ikind=1, energy0=1.0d0, denergy=-0.05d0, ewind=1.0d0, tran_file='spin_con_up', nz1 = 1, epsproj = 1.d-3, / 1 0.0 0.0 1.0 41 *output file for transmission:* # E-Ef, T 1.000000********** 0.950000********** 0.900000412.340267 0.850000497.711187 0.800000802.461207 0.750000440.526889 0.700000958.543158 0.650000389.683665 0.600000908.336839 0.550000586.578929 0.500000362.790961 0.450000268.789968 0.400000174.116786 0.350000265.822178 0.300000********** 0.250000171.305651 0.200000********** 0.150000559.105443 0.100000********** 0.050000********** 0.000000********** -0.050000********** -0.100000********** -0.150000866.786899 -0.200000********** -0.250000********** -0.300000378.547020 -0.350000268.718613 -0.400000162.547897 -0.450000131.448607 -0.500000199.233657 -0.550000532.739318 -0.600000145.867531 -0.650000********** -0.700000915.016527 -0.750000376.695715 -0.800000********** -0.850000********** -0.900000********** -0.950000********** -1.000000********** Thanks and regards. Pankaj. -- Pankaj Kumar DST Project Fellow(Ph.D.) Department of Physics The LNM IIT Jaipur Mob. No. +91 9736694726 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120521/b09cb42b/attachment-0001.htm From carlo.nervi at unito.it Mon May 21 10:22:16 2012 From: carlo.nervi at unito.it (Carlo Nervi) Date: Mon, 21 May 2012 10:22:16 +0200 Subject: [Pw_forum] [Q-e-developers] Change in the number of qe-forge users In-Reply-To: <377B3006-BE18-4921-B303-260D5200F1A2@gmail.com> References: <377B3006-BE18-4921-B303-260D5200F1A2@gmail.com> Message-ID: <4FB9FB38.2060004@unito.it> Hello, I do not have great experience in the field, however a lot of very good free public code is developed on http://sourceforge.net/ I have no idea is this is acceptable for the development, but I would give to it a try. Cheers, Carlo Il 18/05/2012 17.33, Filippo Spiga ha scritto: > Dear Layla, > > why moving from fusionforge to gforge? What about Trac > (http://trac.edgewall.org/)? I mean, the point is? what exactly gforge > has that we do need? And what if we will not use some of those advanced > and fancy features that gforge will provide? > > You mention a "pro-year price" that depends by the number of users. Just > for curiosity, can you tell us with the current number of users how much > is this license? > > Filippo > > -- > Mr. Filippo SPIGA, HPC and GPU Technologist > website: http://filippospiga.me ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > > On May 17, 2012, at 11:58 PM, Layla Martin-Samos wrote: >> Dear all, we are thinking in moving qe-forge from fusionforge to >> gforge. Unfortunately it seems that gforge ask for a commercial >> License which pro-year prince will depends on the number of users. As >> all of you know, nor Quantum ESPRESSO nor qe-forge have any direct >> financial support, so we can not afford big expenses. In order to >> reduce potential costs of the gforge commercial License, our system >> administrator has eliminated all the qe-forge users that are not bound >> to any qe-forge project. Depending on the License price then or we >> move to gforge or we stay with fusionforge. In any case we will let >> you know in order to rationalize the qe-forge users. >> >> Sorry for the inconvenience, best regards > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ------------------------------------------------------------ Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ From gabriele.sclauzero at epfl.ch Mon May 21 10:55:31 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 21 May 2012 10:55:31 +0200 Subject: [Pw_forum] Error in getting the transmission results. In-Reply-To: References: Message-ID: <449C8DC4-9F05-4F14-BE47-E38EB08421FB@epfl.ch> Dear Pankaj, you already posted for a similar problem about one month ago. The reply is the same. Have you ever stopped a minute to think how much should be the transmission values that one could expect for this system? I see at least one or two additional problems in your input files: 1. the lead region needs some k-point sampling along z, gamma is not sufficient! 2. eps_proj looks way too large for me, while nz1 seems too small. Generally you should check convergence of your results w.r.t to these (and other) parameters. ... but there might be other errors that I could not spot... I suggest you to practice with smaller examples in order to understand the method (just running the examples provided is not enough, d?sol?...) HTH GS Il giorno 21/mag/2012, alle ore 09.30, pankaj sahota ha scritto: > Hello Everybody, > > I am trying to reproduce the results of a paper by X. Qian (PHYSICAL REVIEW B 82, 195442 2010). But in the result i am getting ******* in the transmission files. I am pasting the input files for the scattering, lead and the input file for pwcond.x. Can any one have a look on where I am going wrong. I have checked the compilers and ran all the examples in the code. They are all running fine. > > > Scattering region: > > &CONTROL > calculation = 'scf' , > outdir = './tmp' , > pseudo_dir = '/usr/local/src/espresso_potentials/' , > prefix = 'c7-al' , > etot_conv_thr = 1D-7 , > verbosity = 'high', > / > &SYSTEM > ibrav = 6, > celldm(1) = 26.46, > celldm(3) = 1.57771, > nat = 39, > ntyp = 2, > occupations='smearing' , > smearing = 'mp' , > degauss = 0.01 , > ecutwfc = 27 , > ecutrho = 300 , > / > &ELECTRONS > conv_thr = 1.D-6, > startingpot = 'file' , > startingwfc = 'atomic' , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > Al 26.981539 Al.pbe-rrkj.UPF > C 12.0107 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS crystal > Al 0.289286 0.433929 0.0000000 > Al 0.433929 0.289286 0.0000000 > Al 0.578571 0.433929 0.0000000 > Al 0.433929 0.578571 0.0000000 > Al 0.289286 0.289286 0.0916787 > Al 0.289286 0.578571 0.0916787 > Al 0.578571 0.289286 0.0916787 > Al 0.578571 0.578571 0.0916787 > Al 0.433929 0.433929 0.0916787 > Al 0.289286 0.433929 0.183357 > Al 0.433929 0.289286 0.183357 > Al 0.578571 0.433929 0.183357 > Al 0.433929 0.578571 0.183357 > Al 0.289286 0.289286 0.275036 > Al 0.289286 0.578571 0.275036 > Al 0.578571 0.289286 0.275036 > Al 0.578571 0.578571 0.275036 > Al 0.433929 0.433929 0.275036 > C 0.433929 0.433929 0.3203100 > C 0.433929 0.433929 0.380206 > C 0.433929 0.433929 0.440103 > C 0.433929 0.433929 0.500000 > C 0.433929 0.433929 0.559897 > C 0.433929 0.433929 0.619794 > C 0.433929 0.433929 0.67969 > Al 0.289286 0.289286 0.724964 > Al 0.289286 0.578571 0.724964 > Al 0.578571 0.289286 0.724964 > Al 0.578571 0.578571 0.724964 > Al 0.433929 0.433929 0.724964 > Al 0.289286 0.433929 0.816643 > Al 0.433929 0.289286 0.816643 > Al 0.578571 0.433929 0.816643 > Al 0.433929 0.578571 0.816643 > Al 0.289286 0.289286 0.908321 > Al 0.289286 0.578571 0.908321 > Al 0.578571 0.289286 0.908321 > Al 0.578571 0.578571 0.908321 > Al 0.433929 0.433929 0.908321 > K_POINTS gamma > > Lead Region: > > &CONTROL > calculation = 'scf' , > outdir = './tmp' , > pseudo_dir = '/home/pankajkumar/potentials/quantum_es/' , > prefix = 'lead2' , > etot_conv_thr = 1D-7 , > verbosity = 'high', > / > &SYSTEM > ibrav = 6, > celldm(1) = 26.46, > celldm(3) = 0.289285, > nat = 9, > ntyp = 1, > occupations='smearing' , > smearing = 'mp' , > degauss = 0.01 , > ecutwfc = 27 , > ecutrho = 300 , > / > &ELECTRONS > conv_thr = 1.D-6, > startingpot = 'file' , > startingwfc = 'atomic' , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > Al 26.981539 Al.pbe-rrkj.UPF > ATOMIC_POSITIONS crystal > Al 0.289285 0.289285 0.0 > Al 0.289285 0.578571 0.0 > Al 0.578571 0.289285 0.0 > Al 0.578571 0.578571 0.0 > Al 0.433928 0.433928 0.0 > Al 0.289285 0.433928 0.5 > Al 0.433928 0.289285 0.5 > Al 0.578571 0.433928 0.5 > Al 0.433928 0.578571 0.5 > K_POINTS gamma > > Input file for calculating the conduction: > > &inputcond > outdir='./tmp' > prefixl='lead2', > prefixs='c7-al', > ikind=1, > energy0=1.0d0, > denergy=-0.05d0, > ewind=1.0d0, > tran_file='spin_con_up', > nz1 = 1, > epsproj = 1.d-3, > / > 1 > 0.0 0.0 1.0 > 41 > > output file for transmission: > > # E-Ef, T > 1.000000********** > 0.950000********** > 0.900000412.340267 > 0.850000497.711187 > 0.800000802.461207 > 0.750000440.526889 > 0.700000958.543158 > 0.650000389.683665 > 0.600000908.336839 > 0.550000586.578929 > 0.500000362.790961 > 0.450000268.789968 > 0.400000174.116786 > 0.350000265.822178 > 0.300000********** > 0.250000171.305651 > 0.200000********** > 0.150000559.105443 > 0.100000********** > 0.050000********** > 0.000000********** > -0.050000********** > -0.100000********** > -0.150000866.786899 > -0.200000********** > -0.250000********** > -0.300000378.547020 > -0.350000268.718613 > -0.400000162.547897 > -0.450000131.448607 > -0.500000199.233657 > -0.550000532.739318 > -0.600000145.867531 > -0.650000********** > -0.700000915.016527 > -0.750000376.695715 > -0.800000********** > -0.850000********** > -0.900000********** > -0.950000********** > -1.000000********** > > Thanks and regards. > Pankaj. > > > -- > Pankaj Kumar > DST Project Fellow(Ph.D.) > Department of Physics > The LNM IIT Jaipur > Mob. No. +91 9736694726 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120521/1a432262/attachment-0001.htm From zucco at dipteris.unige.it Mon May 21 11:01:25 2012 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Mon, 21 May 2012 11:01:25 +0200 Subject: [Pw_forum] ld1.x and virtual.x compatibility In-Reply-To: <016D7FC9-F86A-453A-BB88-EF56CB3B68FD@democritos.it> References: <126C3ADE-2BFA-467E-816F-7F66CDBEBE92@dipteris.unige.it> <016D7FC9-F86A-453A-BB88-EF56CB3B68FD@democritos.it> Message-ID: <36A28019-8ABB-4453-B8B1-F45D48C394AD@dipteris.unige.it> Dear Paolo, On 20 May 2012, at 18:20, Paolo Giannozzi wrote: > > On May 19, 2012, at 17:52 , Marino Vetuschi Zuccolini wrote: > >> I generated the Al PP with the input below with ld1.x [...] and I >> used it in virtual.x, >> but after an error > > an error where? in virtual.x? the "error" was an error message by the fact that virtual.x was unable to read upf_v1_format, as you said. I understand why browsing files upf_v*_format. > >> I compared the new one Al PP file with one distributed with >> espresso [...] >> The structure of the sections are clearly different. > > IIRC newer PP are written to a different version of the file format > (there is a tag or something like this) > that virtual.x cannot read. You can force the PP file to be > in the old format using option "upf_v1_format" in ld1.x, though > That's what I need, and next time I will spend more time to read the *.x manual. The problem is solved fully changing which_augfun='PSQ' to which_augfun='AE' Thanks m. ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From ramzialaya at hotmail.fr Mon May 21 12:42:39 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Mon, 21 May 2012 11:42:39 +0100 Subject: [Pw_forum] (no subject) Message-ID: Dear all; I need a Ga Non-relativistic pseudo-potential with PZ approximation.Is that someone can help me please? Thank you.Regards. ********************************************************************************* Ramzi AlayaE-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120521/52904bcf/attachment.htm From giuseppe.mattioli at ism.cnr.it Mon May 21 14:01:56 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Mon, 21 May 2012 14:01:56 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <201205211401.56578.giuseppe.mattioli@ism.cnr.it> Dear Ramzi Look at http://qe-forge.org/projects/pslibrary HTH Giuseppe On Monday 21 May 2012 12:42:39 ramzi alaya wrote: > Dear all; I need a Ga Non-relativistic pseudo-potential with PZ > approximation.Is that someone can help me please? Thank you.Regards. > > > > *************************************************************************** > ****** Ramzi AlayaE-mail : ramzialaya at hotmail.fr > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From tfcao at theory.issp.ac.cn Mon May 21 14:13:54 2012 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Mon, 21 May 2012 20:13:54 +0800 Subject: [Pw_forum] =?utf-8?q?A_little_energy_gap_=28=7E_0=2E2_eV=29_for_g?= =?utf-8?q?raphene?= Message-ID: <20120521121354.16813.qmail@ms.hfcas.ac.cn> Dear QE users, I have calculated the density of states (DOS) of pure graphene. The supercell used in my work is a rectangular cell containing 60 carbon atoms. But something has puzzled me greatly. There is always a little energy gap (~0.2 eV) in the DOS, which contracts with the fact that graphene is zero gap semiconductor. Although I have change many parameters. This problem has not been solved. Here I give the input file and I will be greatly appreciated if you can give me some suggestions. For scf.in &CONTROL title = 'graphene layer' , calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '~pseudo' , prefix = 'graphene' , / &SYSTEM ibrav = 8 , a = 12.31 , b = 12.79312342 , c = 12.000 , nat = 60 , ntyp = 1 , occupations = 'smearing' , tot_charge = 0.0, degauss = 0.02 , smearing = 'mp' , nspin = 2 , starting_magnetization(1) = 0.5 , ecutwfc = 30.0 , ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_mode = 'local-TF' , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.0000000 0.0000000 0.50000000 C 0.10000000 5.55555671E-02 0.50000000 C 0.10000000 0.16666667 0.50000000 C 0.0000000 0.22222224 0.50000000 C 0.0000000 0.33333334 0.50000000 C 0.10000000 0.38888890 0.50000000 C 0.10000000 0.50000000 0.50000000 C 0.0000000 0.55555558 0.50000000 C 0.0000000 0.66666669 0.50000000 C 0.10000000 0.72222227 0.50000000 C 0.10000000 0.83333337 0.50000000 C 0.0000000 0.88888896 0.50000000 C 0.20000000 0.0000000 0.50000000 C 0.30000001 5.55555671E-02 0.50000000 C 0.30000001 0.16666667 0.50000000 C 0.20000000 0.22222224 0.50000000 C 0.20000000 0.33333334 0.50000000 C 0.30000001 0.38888890 0.50000000 C 0.30000001 0.50000000 0.50000000 C 0.20000000 0.55555558 0.50000000 C 0.20000000 0.66666669 0.50000000 C 0.30000001 0.72222227 0.50000000 C 0.30000001 0.83333337 0.50000000 C 0.20000000 0.88888896 0.50000000 C 0.40000001 0.0000000 0.50000000 C 0.50000000 5.55555671E-02 0.50000000 C 0.50000000 0.16666667 0.50000000 C 0.40000001 0.22222224 0.50000000 C 0.40000001 0.33333334 0.50000000 C 0.50000000 0.38888890 0.50000000 C 0.50000000 0.50000000 0.50000000 C 0.40000001 0.55555558 0.50000000 C 0.40000001 0.66666669 0.50000000 C 0.50000000 0.72222227 0.50000000 C 0.50000000 0.83333337 0.50000000 C 0.40000001 0.88888896 0.50000000 C 0.60000002 0.0000000 0.50000000 C 0.70000005 5.55555671E-02 0.50000000 C 0.70000005 0.16666667 0.50000000 C 0.60000002 0.22222224 0.50000000 C 0.60000002 0.33333334 0.50000000 C 0.70000005 0.38888890 0.50000000 C 0.70000005 0.50000000 0.50000000 C 0.60000002 0.55555558 0.50000000 C 0.60000002 0.66666669 0.50000000 C 0.70000005 0.72222227 0.50000000 C 0.70000005 0.83333337 0.50000000 C 0.60000002 0.88888896 0.50000000 C 0.80000001 0.0000000 0.50000000 C 0.90000004 5.55555671E-02 0.50000000 C 0.90000004 0.16666667 0.50000000 C 0.80000001 0.22222224 0.50000000 C 0.80000001 0.33333334 0.50000000 C 0.90000004 0.38888890 0.50000000 C 0.90000004 0.50000000 0.50000000 C 0.80000001 0.55555558 0.50000000 C 0.80000001 0.66666669 0.50000000 C 0.90000004 0.72222227 0.50000000 C 0.90000004 0.83333337 0.50000000 C 0.80000001 0.88888896 0.50000000 K_POINTS automatic 8 8 1 0 0 0 For nscf.in &CONTROL title = 'graphene layer' , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , prefix = 'graphene' , / &SYSTEM ibrav = 8 , a = 12.31 , b = 12.79312342 , c = 12.000 , nat = 60 , ntyp = 1 , occupations = 'tetrahedra' , tot_charge = 0.0, nspin = 2 , starting_magnetization(1) = 0.5 , ecutwfc = 30.0 , ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_mode = 'local-TF' , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF For dos.in &inputpp prefix = 'graphene' , outdir = './tmp' , Emin = -4.0 , Emax = 4.0 , DeltaE = 0.01 , fildos = graphene.dos , / The accessory is the DOS I have got. I am sorry for such a long file. I hope that you can give some suggestions. ====================================================================== Tengfei Cao, Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, ====================================================================== 93,2 ?? 1,2 ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120521/17eee2aa/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: graphene.dos Type: application/octet-stream Size: 35290 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120521/17eee2aa/attachment-0001.obj From nkxirainbow at gmail.com Mon May 21 17:11:58 2012 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 21 May 2012 23:11:58 +0800 Subject: [Pw_forum] A little energy gap (~ 0.2 eV) for graphene In-Reply-To: <20120521121354.16813.qmail@ms.hfcas.ac.cn> References: <20120521121354.16813.qmail@ms.hfcas.ac.cn> Message-ID: Please make sure that the Kpoint of the primitive grephene unit cell is included in your kmesh. On Mon, May 21, 2012 at 8:13 PM, Cao TF wrote: > ** > Dear QE users, > I have calculated the density of states (DOS) of pure graphene. The > supercell used in my work is a rectangular cell containing 60 carbon atoms. > But something has puzzled me greatly. There is always a little energy gap > (~0.2 eV) in the DOS, which contracts with the fact that graphene is zero > gap semiconductor. Although I have change many parameters. This problem has > not been solved. Here I give the input file and I will be greatly > appreciated if you can give me some suggestions. > For scf.in > &CONTROL > title = 'graphene layer' , > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = './tmp' , > pseudo_dir = '~pseudo' , > prefix = 'graphene' , > / > &SYSTEM > ibrav = 8 , > a = 12.31 , b = 12.79312342 , c = 12.000 , > nat = 60 , > ntyp = 1 , > occupations = 'smearing' , > tot_charge = 0.0, > degauss = 0.02 , > smearing = 'mp' , > nspin = 2 , > starting_magnetization(1) = 0.5 , > ecutwfc = 30.0 , > ecutrho = 300.0 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS crystal > C 0.0000000 0.0000000 0.50000000 > C 0.10000000 5.55555671E-02 0.50000000 > C 0.10000000 0.16666667 0.50000000 > C 0.0000000 0.22222224 0.50000000 > C 0.0000000 0.33333334 0.50000000 > C 0.10000000 0.38888890 0.50000000 > C 0.10000000 0.50000000 0.50000000 > C 0.0000000 0.55555558 0.50000000 > C 0.0000000 0.66666669 0.50000000 > C 0.10000000 0.72222227 0.50000000 > C 0.10000000 0.83333337 0.50000000 > C 0.0000000 0.88888896 0.50000000 > C 0.20000000 0.0000000 0.50000000 > C 0.30000001 5.55555671E-02 0.50000000 > C 0.30000001 0.16666667 0.50000000 > C 0.20000000 0.22222224 0.50000000 > C 0.20000000 0.33333334 0.50000000 > C 0.30000001 0.38888890 0.50000000 > C 0.30000001 0.50000000 0.50000000 > C 0.20000000 0.55555558 0.50000000 > C 0.20000000 0.66666669 0.50000000 > C 0.30000001 0.72222227 0.50000000 > C 0.30000001 0.83333337 0.50000000 > C 0.20000000 0.88888896 0.50000000 > C 0.40000001 0.0000000 0.50000000 > C 0.50000000 5.55555671E-02 0.50000000 > C 0.50000000 0.16666667 0.50000000 > C 0.40000001 0.22222224 0.50000000 > C 0.40000001 0.33333334 0.50000000 > C 0.50000000 0.38888890 0.50000000 > C 0.50000000 0.50000000 0.50000000 > C 0.40000001 0.55555558 0.50000000 > C 0.40000001 0.66666669 0.50000000 > C 0.50000000 0.72222227 0.50000000 > C 0.50000000 0.83333337 0.50000000 > C 0.40000001 0.88888896 0.50000000 > C 0.60000002 0.0000000 0.50000000 > C 0.70000005 5.55555671E-02 0.50000000 > C 0.70000005 0.16666667 0.50000000 > C 0.60000002 0.22222224 0.50000000 > C 0.60000002 0.33333334 0.50000000 > C 0.70000005 0.38888890 0.50000000 > C 0.70000005 0.50000000 0.50000000 > C 0.60000002 0.55555558 0.50000000 > C 0.60000002 0.66666669 0.50000000 > C 0.70000005 0.72222227 0.50000000 > C 0.70000005 0.83333337 0.50000000 > C 0.60000002 0.88888896 0.50000000 > C 0.80000001 0.0000000 0.50000000 > C 0.90000004 5.55555671E-02 0.50000000 > C 0.90000004 0.16666667 0.50000000 > C 0.80000001 0.22222224 0.50000000 > C 0.80000001 0.33333334 0.50000000 > C 0.90000004 0.38888890 0.50000000 > C 0.90000004 0.50000000 0.50000000 > C 0.80000001 0.55555558 0.50000000 > C 0.80000001 0.66666669 0.50000000 > C 0.90000004 0.72222227 0.50000000 > C 0.90000004 0.83333337 0.50000000 > C 0.80000001 0.88888896 0.50000000 > K_POINTS automatic > 8 8 1 0 0 0 > For nscf.in > &CONTROL > title = 'graphene layer' , > calculation = 'nscf' , > restart_mode = 'from_scratch' , > outdir = './tmp' , > pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , > prefix = 'graphene' , > / > &SYSTEM > ibrav = 8 , > a = 12.31 , b = 12.79312342 , c = 12.000 , > nat = 60 , > ntyp = 1 , > occupations = 'tetrahedra' , > tot_charge = 0.0, > nspin = 2 , > starting_magnetization(1) = 0.5 , > ecutwfc = 30.0 , > ecutrho = 300.0 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > For dos.in > &inputpp > prefix = 'graphene' , > outdir = './tmp' , > Emin = -4.0 , > Emax = 4.0 , > DeltaE = 0.01 , > fildos = graphene.dos , > / > The accessory is the DOS I have got. > I am sorry for such a long file. I hope that you can give some > suggestions. > ====================================================================== > Tengfei Cao, Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > > ====================================================================== > > > > > > > 93,2 ?? > 1,2 ?? > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120521/42f4374c/attachment.htm From renpj at dicp.ac.cn Tue May 22 04:02:15 2012 From: renpj at dicp.ac.cn (PJ Ren) Date: Tue, 22 May 2012 10:02:15 +0800 Subject: [Pw_forum] A little energy gap (~ 0.2 eV) for graphene In-Reply-To: <20120521121354.16813.qmail@ms.hfcas.ac.cn> References: <20120521121354.16813.qmail@ms.hfcas.ac.cn> Message-ID: <4FBAF3A7.8010009@dicp.ac.cn> Dear Cao, I am new to graphene calculation, and there is some questions about your input files. First, why do you use rectangular cell, not a trigonal primary cell? Second, is it necessary to consider the magnetization of graphene? Can you share some paper on this? Thanks very much. Pengju Ren Dalian Institute of Chemical Physics, CAS On 05/21/2012 08:13 PM, Cao TF wrote: > Dear QE users, > I have calculated the density of states (DOS) of pure graphene. The > supercell used in my work is a rectangular cell containing 60 carbon > atoms. But something has puzzled me greatly. There is always a little > energy gap (~0.2 eV) in the DOS, which contracts with the fact that > graphene is zero gap semiconductor. Although I have change many > parameters. This problem has not been solved. Here I give the input > file and I will be greatly appreciated if you can give me some > suggestions. > For scf.in > &CONTROL > title = 'graphene layer' , > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = './tmp' , > pseudo_dir = '~pseudo' , > prefix = 'graphene' , > / > &SYSTEM > ibrav = 8 , > a = 12.31 , b = 12.79312342 , c = 12.000 , > nat = 60 , > ntyp = 1 , > occupations = 'smearing' , > tot_charge = 0.0, > degauss = 0.02 , > smearing = 'mp' , > nspin = 2 , > starting_magnetization(1) = 0.5 , > ecutwfc = 30.0 , > ecutrho = 300.0 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS crystal > C 0.0000000 0.0000000 0.50000000 > C 0.10000000 5.55555671E-02 0.50000000 > C 0.10000000 0.16666667 0.50000000 > C 0.0000000 0.22222224 0.50000000 > C 0.0000000 0.33333334 0.50000000 > C 0.10000000 0.38888890 0.50000000 > C 0.10000000 0.50000000 0.50000000 > C 0.0000000 0.55555558 0.50000000 > C 0.0000000 0.66666669 0.50000000 > C 0.10000000 0.72222227 0.50000000 > C 0.10000000 0.83333337 0.50000000 > C 0.0000000 0.88888896 0.50000000 > C 0.20000000 0.0000000 0.50000000 > C 0.30000001 5.55555671E-02 0.50000000 > C 0.30000001 0.16666667 0.50000000 > C 0.20000000 0.22222224 0.50000000 > C 0.20000000 0.33333334 0.50000000 > C 0.30000001 0.38888890 0.50000000 > C 0.30000001 0.50000000 0.50000000 > C 0.20000000 0.55555558 0.50000000 > C 0.20000000 0.66666669 0.50000000 > C 0.30000001 0.72222227 0.50000000 > C 0.30000001 0.83333337 0.50000000 > C 0.20000000 0.88888896 0.50000000 > C 0.40000001 0.0000000 0.50000000 > C 0.50000000 5.55555671E-02 0.50000000 > C 0.50000000 0.16666667 0.50000000 > C 0.40000001 0.22222224 0.50000000 > C 0.40000001 0.33333334 0.50000000 > C 0.50000000 0.38888890 0.50000000 > C 0.50000000 0.50000000 0.50000000 > C 0.40000001 0.55555558 0.50000000 > C 0.40000001 0.66666669 0.50000000 > C 0.50000000 0.72222227 0.50000000 > C 0.50000000 0.83333337 0.50000000 > C 0.40000001 0.88888896 0.50000000 > C 0.60000002 0.0000000 0.50000000 > C 0.70000005 5.55555671E-02 0.50000000 > C 0.70000005 0.16666667 0.50000000 > C 0.60000002 0.22222224 0.50000000 > C 0.60000002 0.33333334 0.50000000 > C 0.70000005 0.38888890 0.50000000 > C 0.70000005 0.50000000 0.50000000 > C 0.60000002 0.55555558 0.50000000 > C 0.60000002 0.66666669 0.50000000 > C 0.70000005 0.72222227 0.50000000 > C 0.70000005 0.83333337 0.50000000 > C 0.60000002 0.88888896 0.50000000 > C 0.80000001 0.0000000 0.50000000 > C 0.90000004 5.55555671E-02 0.50000000 > C 0.90000004 0.16666667 0.50000000 > C 0.80000001 0.22222224 0.50000000 > C 0.80000001 0.33333334 0.50000000 > C 0.90000004 0.38888890 0.50000000 > C 0.90000004 0.50000000 0.50000000 > C 0.80000001 0.55555558 0.50000000 > C 0.80000001 0.66666669 0.50000000 > C 0.90000004 0.72222227 0.50000000 > C 0.90000004 0.83333337 0.50000000 > C 0.80000001 0.88888896 0.50000000 > K_POINTS automatic > 8 8 1 0 0 0 > For nscf.in > &CONTROL > title = 'graphene layer' , > calculation = 'nscf' , > restart_mode = 'from_scratch' , > outdir = './tmp' , > pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , > prefix = 'graphene' , > / > &SYSTEM > ibrav = 8 , > a = 12.31 , b = 12.79312342 , c = 12.000 , > nat = 60 , > ntyp = 1 , > occupations = 'tetrahedra' , > tot_charge = 0.0, > nspin = 2 , > starting_magnetization(1) = 0.5 , > ecutwfc = 30.0 , > ecutrho = 300.0 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C 12.0107 C.pbe-rrkjus.UPF > For dos.in > &inputpp > prefix = 'graphene' , > outdir = './tmp' , > Emin = -4.0 , > Emax = 4.0 , > DeltaE = 0.01 , > fildos = graphene.dos , > / > The accessory is the DOS I have got. > I am sorry for such a long file. I hope that you can give some > suggestions. > ====================================================================== > Tengfei Cao, Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > > ====================================================================== > > > > > > > 93,2 ?? > 1,2 ?? > > > _______________________________________________ > 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/20120522/5c84671b/attachment-0001.htm From flux_ray12 at 163.com Tue May 22 05:20:31 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 22 May 2012 11:20:31 +0800 (CST) Subject: [Pw_forum] The phonon frequency unit in matdyn.x v5.0 Message-ID: <71f128cf.1c4bb.137728f6e71.Coremail.flux_ray12@163.com> Dear QE developer and users: I am using QE 5.0 now. I am not sure whether I did not read the manual carefully. But when I use the matdyn.x as in QE 4.3.2, the output unit became different. Detail: In matdyn.x v4.x, one did not have to set the parameters amass(i) and the element mass can be read from IFCs file. The output frequency was in cm^(-1) unit. Now, in matdyn.x v5.0, if I did not set amass(i), the output frequency would be in some other unit. I though it was THz, but I compared it with the output from matdyn.x v4.3.2 by the same IFCs, the arbitrary value was a little bit higher than when unit in THz. The same issue was found when calculate phonon DOS. However, if I added amass(i) parameters, all of the result would be in cm^(-1) unit. The comparason for with and without amass(i) in matdyn.x v5.0 is shown as the accessory, which was from the example of Fe_AFM in PlotPhon. By the way, when I used 'crystal' method for ASR in matdyn.x v4.3, the results from with and without amass(i) has some different in low frequency acoustics bratches as: With amass(i): 0.010000 0.000000 0.000000 6.5359 3.0829 3.2829 155.3803 173.4756 173.4207 232.7133 232.7937 237.6018 280.0328 280.1047 283.2520 .... 0.020000 0.000000 0.000000 13.0533 6.1661 6.5649 155.4117 173.5031 173.2838 232.4662 232.7895 237.6108 279.8124 280.0984 283.2260 .... Without amass(i): 0.010000 0.000000 0.000000 3.0829 3.2829 6.5359 155.3803 173.4207 173.4756 232.7133 232.7937 237.6018 280.0328 280.1047 283.2520 .... 0.020000 0.000000 0.000000 6.1661 6.5649 13.0533 155.4117 173.2838 173.5031 232.4662 232.7895 237.6108 279.8124 280.0984 283.2260 .... -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/2fa09642/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Fe_AFM.Thz.png Type: image/png Size: 75739 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120522/2fa09642/attachment-0001.png From flux_ray12 at 163.com Tue May 22 05:23:26 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 22 May 2012 11:23:26 +0800 (CST) Subject: [Pw_forum] The phonon frequency unit in matdyn.x v5.0 (sorry for the wrong Fig in last one) Message-ID: <7591abe.1c5e8.13772921821.Coremail.flux_ray12@163.com> Dear QE developer and users: I am so sorry that I attached the wrong Fig in last email~~~~~ This is the right comparason~~~~~ -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/e458b15e/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Compare.png Type: image/png Size: 69768 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120522/e458b15e/attachment-0001.png From tfcao at theory.issp.ac.cn Tue May 22 11:07:33 2012 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Tue, 22 May 2012 17:07:33 +0800 Subject: [Pw_forum] =?utf-8?q?A_little_energy_gap_=28=7E_0=2E2_eV=29_for_g?= =?utf-8?q?raphene?= Message-ID: <20120522090733.7734.qmail@ms.hfcas.ac.cn> Dear Ren I use the rectangular cell because I want to simulate STM image of hydrogen clusters on graphene. And I want to compare the DOS of graphene with hydrogenated graphene. I set the magnetic moment to graphene in order to separate the spin-up and spin-down DOS. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/816c43e3/attachment.htm From victor.bermudez at nrl.navy.mil Tue May 22 11:38:05 2012 From: victor.bermudez at nrl.navy.mil (Vic Bermudez) Date: Tue, 22 May 2012 05:38:05 -0400 Subject: [Pw_forum] Pseudopotentials for Pseudo-Hydrogens Message-ID: Hello, I'm setting up a slab calculation for the GaSb (100) surface using PW91 USPP's for Ga and Sb. I want to passivate the "bottom" (Ga-terminated) surface with pseudo-hydrogens, which will require two Z=5/4 pseudo-H's per Ga. However, the QE website gives only PZ pseudopotentials for pseudo-H's. Here's my question. I know that it's problematic to mix different kinds of PP's in the same calculation, and, of course, pw.scf gives a fatal error when I try. Will I get into trouble if I override this by using input_dft='pw91', so that I can use the PZ PP's for the pseudo-H's ? I'm interested mainly in adsorption energies, which are the differences in energies between bare and adsorbate-covered slabs. Will any errors incurred by mixing PP's cancel in the difference. As always, thanks for your help and advice. Victor M. Bermudez Code 6876 U.S. Naval Research Laboratory 4555 Overlook Ave., S.W. Washington, DC 20375-5347 Phone: 202-767-6728 FAX: 202-767-1165 E-mail: victor.bermudez at nrl.navy.mil From gabriele.sclauzero at epfl.ch Tue May 22 12:02:17 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 22 May 2012 12:02:17 +0200 Subject: [Pw_forum] A little energy gap (~ 0.2 eV) for graphene In-Reply-To: <20120521121354.16813.qmail@ms.hfcas.ac.cn> References: <20120521121354.16813.qmail@ms.hfcas.ac.cn> Message-ID: Dear Cao, I'm pretty sure that at the DFT level (without SO) the DOS of graphene has to be linear close to the Dirac point (which corresponds to the Fermi energy for pristine graphene). You can easily understand this by looking at the band structure studied with the primitive unit cell. The gap that you see is due to the discrete k-point sampling and the peculiar band structure of graphene. I also think that the effect is amplified by the fact that you use the tetrahedron method, which was devised for three-dimensional systems (though it seems to work fine also for graphene). Most probably, for your k-point mesh the two closest eigenvalues across the Dirac point are spaced by about 0.2eV. I don't think this is a real problem for your application. HTH GS Il giorno 21/mag/2012, alle ore 14.13, Cao TF ha scritto: > Dear QE users, > I have calculated the density of states (DOS) of pure graphene. The supercell used in my work is a rectangular cell containing 60 carbon atoms. But something has puzzled me greatly. There is always a little energy gap (~0.2 eV) in the DOS, which contracts with the fact that graphene is zero gap semiconductor. Although I have change many parameters. This problem has not been solved. Here I give the input file and I will be greatly appreciated if you can give me some suggestions. > For nscf.in > &CONTROL > title = 'graphene layer' , > calculation = 'nscf' , > restart_mode = 'from_scratch' , > outdir = './tmp' , > pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , > prefix = 'graphene' , > / > &SYSTEM > ibrav = 8 , > a = 12.31 , b = 12.79312342 , c = 12.000 , > nat = 60 , > ntyp = 1 , > occupations = 'tetrahedra' , > tot_charge = 0.0, > nspin = 2 , > starting_magnetization(1) = 0.5 , > ecutwfc = 30.0 , > ecutrho = 300.0 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_mode = 'local-TF' , > mixing_beta = 0.7 , > diagonalization = 'david' , > / ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/b42e965d/attachment.htm From giannozz at democritos.it Tue May 22 12:05:47 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 May 2012 12:05:47 +0200 Subject: [Pw_forum] Pseudopotentials for Pseudo-Hydrogens In-Reply-To: References: Message-ID: <1337681147.8699.2.camel@fe12lx.fisica.uniud.it> On Tue, 2012-05-22 at 05:38 -0400, Vic Bermudez wrote: > Will I get into trouble if I override this by using input_dft='pw91' > so that I can use the PZ PP's for the pseudo-H's ? I don't expect any problem, since we are talking about bogus PPs anyway, used only to saturate the surface P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From gabriele.sclauzero at epfl.ch Tue May 22 12:12:03 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 22 May 2012 12:12:03 +0200 Subject: [Pw_forum] Pseudopotentials for Pseudo-Hydrogens In-Reply-To: References: Message-ID: > Here's my question. I know that it's problematic to mix different kinds of > PP's in the same calculation, What do you mean by different kinds? You can safely mix ultrasoft and norm-conserving PPs, for instance. You cannot mix different exchange-correlation functionals, obviously. > and, of course, pw.scf gives a fatal error > when I try. Of course it does, but just because it is wrong (not just "problematic") to mix PPs made for different XC functionals. > Will I get into trouble if I override this by using > input_dft='pw91', so that I can use the PZ PP's for the pseudo-H's ? This would be "incautious", to use an euphemism... > I'm > interested mainly in adsorption energies, which are the differences in > energies between bare and adsorbate-covered slabs. Will any errors incurred > by mixing PP's cancel in the difference. There are no additional errors from "mixing" PPs of same XC functional other than those coming from the intrinsic PP approximations. HTH GS > As always, thanks for your help and advice. > > Victor M. Bermudez > Code 6876 > U.S. Naval Research Laboratory > 4555 Overlook Ave., S.W. > Washington, DC 20375-5347 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/91bd31f7/attachment-0001.htm From gabriele.sclauzero at epfl.ch Tue May 22 12:17:12 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 22 May 2012 12:17:12 +0200 Subject: [Pw_forum] Pseudopotentials for Pseudo-Hydrogens In-Reply-To: References: Message-ID: <5EF9C22B-C302-4AB4-A766-5AB8BD1C9E43@epfl.ch> I think I've misunderstood your statements, probably I've told you things that you already know... About the specific case of bogus PPs and the tricks of the trade, I would trust Paolo, of course. GS >> Here's my question. I know that it's problematic to mix different kinds of >> PP's in the same calculation, > > What do you mean by different kinds? You can safely mix ultrasoft and norm-conserving PPs, for instance. > > You cannot mix different exchange-correlation functionals, obviously. > >> and, of course, pw.scf gives a fatal error >> when I try. > > Of course it does, but just because it is wrong (not just "problematic") to mix PPs made for different XC functionals. > >> Will I get into trouble if I override this by using >> input_dft='pw91', so that I can use the PZ PP's for the pseudo-H's ? > > This would be "incautious", to use an euphemism... > >> I'm >> interested mainly in adsorption energies, which are the differences in >> energies between bare and adsorbate-covered slabs. Will any errors incurred >> by mixing PP's cancel in the difference. > > There are no additional errors from "mixing" PPs of same XC functional other than those coming from the intrinsic PP approximations. > > HTH > > GS > >> As always, thanks for your help and advice. >> >> Victor M. Bermudez >> Code 6876 >> U.S. Naval Research Laboratory >> 4555 Overlook Ave., S.W. >> Washington, DC 20375-5347 > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/8dd3f140/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue May 22 12:40:31 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 22 May 2012 12:40:31 +0200 Subject: [Pw_forum] A little energy gap (~ 0.2 eV) for graphene In-Reply-To: <20120521121354.16813.qmail@ms.hfcas.ac.cn> References: <20120521121354.16813.qmail@ms.hfcas.ac.cn> Message-ID: On Mon, May 21, 2012 at 2:13 PM, Cao TF wrote: > ** > occupations = 'tetrahedra' , > Dear Tengfei Cao, I could not spot any obvious problem in your file. All I can suggest is to try a normal smearing instead of tetrahedra for the nscf calculation: I'm not sure tetrahedras are suitable for 2-dimensional systems. In particular I got some funny graphics using tetrahedras to integrate the *phonon* dos of graphene. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/8c2d62ce/attachment.htm From ramzialaya at hotmail.fr Tue May 22 13:00:13 2012 From: ramzialaya at hotmail.fr (ramzi alaya) Date: Tue, 22 May 2012 12:00:13 +0100 Subject: [Pw_forum] Pseudopotentials for Ga Message-ID: Dear all; I need a Ga Non-relativistic pseudo-potential with PZ approximation.Is that someone can help me please? Thank you. Regards.********************************************************************************* Ramzi AlayaE-mail : ramzialaya at hotmail.fr Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/d5600893/attachment.htm From mayankaditya at gmail.com Tue May 22 13:39:44 2012 From: mayankaditya at gmail.com (mayank gupta) Date: Tue, 22 May 2012 17:09:44 +0530 Subject: [Pw_forum] Dielectric constant of metal oxides Message-ID: Dear All Users I want to calculate the dielectric constant of metal oxide for LO -TO calculation of PHONON. Since it has odd no. of electrons it is treated like conductor even its a insulator. Please suggest some methods in which I can calculate the dielectric constant. Thanks Mayank PhD HBNI MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/dacca343/attachment.htm From carlo.nervi at unito.it Tue May 22 13:52:03 2012 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 22 May 2012 13:52:03 +0200 Subject: [Pw_forum] GIPAW and nosymm Message-ID: <4FBB7DE3.2030406@unito.it> Dear PW community, using GIPAW, up to now, I always added 'nosym= .true.' to preliminar scf calculations with Quantum espresso 4.3.2 Is the limitation still necessary for GIPAW calculations? I'm doing calculations on a rather large system and symmetry could help a lot. BTW, the new version QE 5.0 includes some improvements in this respect? Thanks, Carlo -- ------------------------------------------------------------ Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ From giuseppe.mattioli at ism.cnr.it Tue May 22 13:53:13 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Tue, 22 May 2012 13:53:13 +0200 Subject: [Pw_forum] Pseudopotentials for Ga In-Reply-To: References: Message-ID: <201205221353.14117.giuseppe.mattioli@ism.cnr.it> Same question, same answer... Download and look into the new pseudopotential library. It contains plenty of input files for building every kind of pseudopotential with the ld1.x program. http://qe-forge.org/projects/pslibrary Giuseppe On Tuesday 22 May 2012 13:00:13 ramzi alaya wrote: > Dear all; I need a Ga Non-relativistic pseudo-potential with PZ > approximation.Is that someone can help me please? Thank you. > Regards.******************************************************************* > ************** Ramzi AlayaE-mail : ramzialaya at hotmail.fr > Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie > Unit? de Recherche sur les H?t?ro-Epitaxies et Applications -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From davide.ceresoli at istm.cnr.it Tue May 22 14:02:06 2012 From: davide.ceresoli at istm.cnr.it (Davide Ceresoli) Date: Tue, 22 May 2012 14:02:06 +0200 Subject: [Pw_forum] GIPAW and nosymm In-Reply-To: <4FBB7DE3.2030406@unito.it> References: <4FBB7DE3.2030406@unito.it> Message-ID: <4FBB803E.1020101@istm.cnr.it> Dear Carlo, can you rotate your cell parameters (using ibrav=0) such that symmetry operations map cartesian axes into themselves, like in the quartz example? In that case you can still exploit symmetry. Otherwise... not with the current implementation. Davide On 05/22/2012 01:52 PM, Carlo Nervi wrote: > Dear PW community, > using GIPAW, up to now, I always added 'nosym= .true.' to preliminar scf > calculations with Quantum espresso 4.3.2 > Is the limitation still necessary for GIPAW calculations? > I'm doing calculations on a rather large system and symmetry could help a lot. > BTW, the new version QE 5.0 includes some improvements in this respect? > Thanks, > Carlo From giannozz at democritos.it Tue May 22 18:45:57 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 May 2012 18:45:57 +0200 Subject: [Pw_forum] The phonon frequency unit in matdyn.x v5.0 In-Reply-To: <71f128cf.1c4bb.137728f6e71.Coremail.flux_ray12@163.com> References: <71f128cf.1c4bb.137728f6e71.Coremail.flux_ray12@163.com> Message-ID: <1337705157.10226.18.camel@fe12lx.fisica.uniud.it> On Tue, 2012-05-22 at 11:20 +0800, GAO Zhe wrote: > Now, in matdyn.x v5.0, if I did not set amass(i), the output frequency > would be in some other unit. output frequencies are in the same units, but maybe the mass is not what you expect, or what should have been. There have been some changes in the internal units of mass. From Doc/release-notes: * atomic masses in the code are in amu unless otherwise stated This might have some unexpected consequences. P. Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From jdeslip at gmail.com Tue May 22 19:38:13 2012 From: jdeslip at gmail.com (Jack Deslippe) Date: Tue, 22 May 2012 10:38:13 -0700 Subject: [Pw_forum] Using scalapack in PW/tests causes failures Message-ID: Hi, I apologize ahead of time if this is a duplicate of a previous report (I searched for recent matches and didn't find any). I am trying to build ESPRESSO 5.0 for a couple different parallel machines but am having trouble verifying the build. In particular, for builds with scalapack, the PW/tests fail pretty substantially when using more than 1 processor. Here is the output using PGI Compilers + Cray LibSci using 4 processors. hecking atom...passed Checking atom-lsda...passed Checking atom-pbe...discrepancy in number of scf iterations detected Reference: 7, You got: 5 discrepancy in pressure detected Reference: -14.46, You got: 94.93 Checking atom-sigmapbe...discrepancy in number of scf iterations detected Reference: 11, You got: 15 discrepancy in pressure detected Reference: -14.98, You got: 104.92 I get the same result using GNU Compilers + LibSci and using various levels of optimization include -O0. I also see the same problem using my own scalapack build as well as using MKL scalapack on another machine. When using only one processor, these tests pass as well as with 4 processors and scalapack disabled. It is possible I am missing something obvious (like these tests only being intended to be run in serial), but I want to make sure the code is behaving as expected. Sincerely, Jack Deslippe -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/da829bb7/attachment.htm From bahadira at buffalo.edu Tue May 22 20:54:55 2012 From: bahadira at buffalo.edu (Bahadir Altintas) Date: Tue, 22 May 2012 14:54:55 -0400 Subject: [Pw_forum] Construction of PtH structure, wrong pointgroup problem Message-ID: <4FBBE0FF.90701@buffalo.edu> Hi, I have a problem in constructing the PtH structure. I have prepared the input with following data from J. Phys. Chem. C, 2012, 116 (2), pp 1995--2000 (http://http://pubs.acs.org/doi/abs/10.1021%2Fjp210780m) for hexagonal PtH. Spacegroup : 194 - P63/mmc Point group : D_6h a=2.795 c=7.769 Pt: 2c (1/3 2/3 0.25) H: 2a ( 0 0 0 ) Point group of this input gives D_3d (-3m) instead of D_6h (6/mmm). I am not sure what am i missing. here is my input for vc-relax under 100GPa (Espresso-4.3.2): &CONTROL calculation = "vc-relax" , restart_mode = 'from_scratch' , outdir='/tmp' , pseudo_dir ='/home/pseudos/espresso/' , etot_conv_thr = 1.0D-14 , forc_conv_thr = 1.0D-5 , prefix='PtH_sp194_100GPa.opt', tstress=.true., verbosity='high' / &SYSTEM ibrav= 4, celldm(1)=5.2817842823, celldm(3)=1.706261153, nat= 4, ntyp= 2, ecutwfc=37 ecutrho = 222 , occupations = 'smearing' , smearing = 'mp' , degauss = 0.02 , / &ELECTRONS conv_thr = 1.0d-7, diagonalization='david' / &IONS ion_dynamics = 'bfgs', / &CELL cell_dynamics = 'bfgs' , cell_factor=1.2, press= 1000.00 / ATOMIC_SPECIES Pt 195.08 Pt.pbe-n-van.UPF H 1.00794 H.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Pt 0.333333343 0.666666687 0.250000438 Pt 0.666666627 0.333333313 0.749999562 H 0.000000000 0.000000000 0.000000000 H 0.000000000 0.000000000 0.500000000 K_POINTS automatic 4 4 4 1 1 1 Thanks, Bahadir Altintas University at Buffalo Dept of Chemistry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/e519d3f8/attachment.htm From bahadira at buffalo.edu Tue May 22 20:59:49 2012 From: bahadira at buffalo.edu (Bahadir Altintas) Date: Tue, 22 May 2012 14:59:49 -0400 Subject: [Pw_forum] Construction of PtH structure, wrong pointgroup problem In-Reply-To: <4FBBE0FF.90701@buffalo.edu> References: <4FBBE0FF.90701@buffalo.edu> Message-ID: <4FBBE225.6000701@buffalo.edu> c should be 4.749 instead of 7.769. i wrote wrong literature value. so ignore the previous c value in the mail. bahadir On 05/22/2012 02:54 PM, Bahadir Altintas wrote: > Hi, > I have a problem in constructing the PtH structure. > I have prepared the input with following data from J. Phys. Chem. C, > 2012, 116 (2), pp 1995--2000 > (http://http://pubs.acs.org/doi/abs/10.1021%2Fjp210780m) for hexagonal > PtH. > > Spacegroup : 194 - P63/mmc > Point group : D_6h > a=2.795 > c=7.769 Pt: 2c (1/3 2/3 0.25) > H: 2a ( 0 0 0 ) > > Point group of this input gives D_3d (-3m) instead of D_6h (6/mmm). > I am not sure what am i missing. > > here is my input for vc-relax under 100GPa (Espresso-4.3.2): > > &CONTROL > calculation = "vc-relax" , > restart_mode = 'from_scratch' , > outdir='/tmp' , > pseudo_dir ='/home/pseudos/espresso/' , > etot_conv_thr = 1.0D-14 , > forc_conv_thr = 1.0D-5 , > prefix='PtH_sp194_100GPa.opt', > tstress=.true., > verbosity='high' > / > &SYSTEM > ibrav= 4, > celldm(1)=5.2817842823, > celldm(3)=1.706261153, > nat= 4, > ntyp= 2, > ecutwfc=37 > ecutrho = 222 , > occupations = 'smearing' , > smearing = 'mp' , > degauss = 0.02 , > / > &ELECTRONS > conv_thr = 1.0d-7, > diagonalization='david' > / > &IONS > ion_dynamics = 'bfgs', > / > &CELL > cell_dynamics = 'bfgs' , > cell_factor=1.2, > press= 1000.00 > / > > ATOMIC_SPECIES > Pt 195.08 Pt.pbe-n-van.UPF > H 1.00794 H.pbe-van_ak.UPF > > ATOMIC_POSITIONS (crystal) > Pt 0.333333343 0.666666687 0.250000438 > Pt 0.666666627 0.333333313 0.749999562 > H 0.000000000 0.000000000 0.000000000 > H 0.000000000 0.000000000 0.500000000 > > K_POINTS automatic > 4 4 4 1 1 1 > > > > > > Thanks, > > Bahadir Altintas > University at Buffalo > Dept of Chemistry > > > _______________________________________________ > 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/20120522/a583a4c0/attachment-0001.htm From giannozz at democritos.it Tue May 22 21:54:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 May 2012 21:54:35 +0200 Subject: [Pw_forum] Construction of PtH structure, wrong pointgroup problem In-Reply-To: <4FBBE0FF.90701@buffalo.edu> References: <4FBBE0FF.90701@buffalo.edu> Message-ID: <0C108285-488F-4DBD-BECE-565CD7754441@democritos.it> On May 22, 2012, at 20:54 , Bahadir Altintas wrote: > Point group of this input gives D_3d (-3m) instead of D_6h (6/mmm). > I am not sure what am i missing. you are missing this message (the misspell will be fixed in next release): 12 Sym. Ops., with inversion, found (note: 12 additional sym.ops. were found but ignored their fractional transations are incommensurate with FFT grid) If you do not need to perform phonon calculations, you may try option use_all_frac=.true. in namelist &system P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bahadira at buffalo.edu Tue May 22 21:59:03 2012 From: bahadira at buffalo.edu (Bahadir Altintas) Date: Tue, 22 May 2012 15:59:03 -0400 Subject: [Pw_forum] Construction of PtH structure, wrong pointgroup problem In-Reply-To: <0C108285-488F-4DBD-BECE-565CD7754441@democritos.it> References: <4FBBE0FF.90701@buffalo.edu> <0C108285-488F-4DBD-BECE-565CD7754441@democritos.it> Message-ID: <4FBBF007.9000406@buffalo.edu> thanks for quick reply. infact, i am going to perform phonon calculation for this structure. what should i do to get correct pointgroup? bahadir On 05/22/2012 03:54 PM, Paolo Giannozzi wrote: > On May 22, 2012, at 20:54 , Bahadir Altintas wrote: > >> Point group of this input gives D_3d (-3m) instead of D_6h (6/mmm). >> I am not sure what am i missing. > you are missing this message (the misspell will be fixed in next > release): > > 12 Sym. Ops., with inversion, found > (note: 12 additional sym.ops. were found but ignored > their fractional transations are incommensurate with FFT > grid) > > If you do not need to perform phonon calculations, you may try option > use_all_frac=.true. in namelist&system > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue May 22 22:03:00 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 May 2012 22:03:00 +0200 Subject: [Pw_forum] Construction of PtH structure, wrong pointgroup problem In-Reply-To: <4FBBF007.9000406@buffalo.edu> References: <4FBBE0FF.90701@buffalo.edu> <0C108285-488F-4DBD-BECE-565CD7754441@democritos.it> <4FBBF007.9000406@buffalo.edu> Message-ID: On May 22, 2012, at 21:59 , Bahadir Altintas wrote: > infact, i am going to perform phonon calculation for this structure. > what should i do to get correct pointgroup? use a FFT grid that is commensurate with the fractional translation. The alternative is to implement symmetrization in G-space for the phonon code. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From smirshamsi at phys.ufl.edu Tue May 22 22:09:24 2012 From: smirshamsi at phys.ufl.edu (Sahar Mirshamsi) Date: Tue, 22 May 2012 16:09:24 -0400 (EDT) Subject: [Pw_forum] Is spin polarized vdW-DF implemented in QE 5.0? Message-ID: Hi QE users and developers, I just want to know if spin polarized vdW-DF is implemented in QE 5.0? and if not, is it going to be implemented sometime soon? Thanks, Sahar Mirshamsi Department of Physics University of Florida From flux_ray12 at 163.com Wed May 23 04:41:42 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 23 May 2012 10:41:42 +0800 (CST) Subject: [Pw_forum] The phonon frequency unit in matdyn.x v5.0 In-Reply-To: <1337705157.10226.18.camel@fe12lx.fisica.uniud.it> References: <71f128cf.1c4bb.137728f6e71.Coremail.flux_ray12@163.com> <1337705157.10226.18.camel@fe12lx.fisica.uniud.it> Message-ID: <5462b22d.4865.13777923f66.Coremail.flux_ray12@163.com> Thank you very much Prof. Giannozzi, I think I caught your idea. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-05-23 00:45:57,"Paolo Giannozzi" wrote: >On Tue, 2012-05-22 at 11:20 +0800, GAO Zhe wrote: > >> Now, in matdyn.x v5.0, if I did not set amass(i), the output frequency >> would be in some other unit. > >output frequencies are in the same units, but maybe the mass is not >what you expect, or what should have been. There have been some >changes in the internal units of mass. From Doc/release-notes: > * atomic masses in the code are in amu unless otherwise stated >This might have some unexpected consequences. > >P. > >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120523/52bad8d3/attachment.htm From giuseppe.mattioli at ism.cnr.it Wed May 23 11:03:01 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 23 May 2012 11:03:01 +0200 Subject: [Pw_forum] Is spin polarized vdW-DF implemented in QE 5.0? In-Reply-To: References: Message-ID: <201205231103.02285.giuseppe.mattioli@ism.cnr.it> Dear Sahar vdwDF itself is not defined in a open shell framework (or I suppose so... You should read the references printed at standard output by pw.x when you enforce the vdwDF functional). If you need some dispersion correction and nspin=2, you may try with the semi-empirical DFTD2 approach (london=.true. in pw.x input). HTH Giuseppe On Tuesday 22 May 2012 22:09:24 Sahar Mirshamsi wrote: > Hi QE users and developers, > > I just want to know if spin polarized vdW-DF is implemented in QE 5.0? and > if not, is it going to be implemented sometime soon? > > Thanks, > > Sahar Mirshamsi > Department of Physics > University of Florida > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giacsport at libero.it Thu May 24 04:45:14 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 24 May 2012 04:45:14 +0200 (CEST) Subject: [Pw_forum] HSE vs PBE Message-ID: <19527450.558661337827514835.JavaMail.defaultUser@defaultHost> Dear All, I am using the development version of PWscf. I would like to ask you this question. I want to make HSE hybrid calculations (vc-relax) using pseudopotential at PBE level. I want indeed test the impact of the hybrid functional in the lattice parameter (this is the case of Copper) I mean is it a correct procedure to optimize the system with such initial settings / &system ibrav= 2, celldm(1) = 6.830792531 nat= 4, ntyp= 1, nspin=2, ecutwfc = 95., nbnd = 80, occupations='smearing', degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 / and then use the same for HSE (same pseudopotentials at PBE, taken from the PwSCF website) / &system ibrav= 2, celldm(1) = 6.830792531 nat= 4, ntyp= 1, nspin=2, ecutwfc = 95., nbnd = 80, occupations='smearing', degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2, x_gamma_extrapolation = .TRUE. / is it OK? can I do it? I.e., using PBE psudopotential for HSE calculations? Thanks in advance for any suggestion! Best, Giacomo -- Giacomo GIORGI Assistant Professor Research Center for Advanced Science and Technology (RCAST), The University of Tokyo 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan tel./fax: +81 3 5452 5448 From pandey.bramha at gmail.com Thu May 24 07:59:49 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 24 May 2012 11:29:49 +0530 Subject: [Pw_forum] Problem...saw tooth like band structure for ZB GaN Message-ID: Dear All QE users I am trying to plot the band structure of ZB GaN but after running the plotband.x, i am obtaining the saw tooth like wave for the bands which is obviously not currect. As i have increased the the k-point in nscf calculation zigzag nature was more dominant in band plot. Please someone has help me in this regard. Thanks in advanced for your kind attention. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120524/df5773a1/attachment.htm From giannozz at democritos.it Thu May 24 08:18:43 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 May 2012 08:18:43 +0200 Subject: [Pw_forum] Using scalapack in PW/tests causes failures In-Reply-To: References: Message-ID: <9223B98D-5026-43EA-80D3-249EF9B114D8@democritos.it> On May 22, 2012, at 19:38 , Jack Deslippe wrote: > discrepancy in pressure detected > Reference: -14.46, You got: 94.93 oops ... there is a serious error in the calculation of the stress in the Gamma-only case, in parallel. I don't think it is directly related to Scalapack, though P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mayankaditya at gmail.com Thu May 24 11:03:13 2012 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 24 May 2012 14:33:13 +0530 Subject: [Pw_forum] zone boundary is not coming out correctly Message-ID: Dear User's I am doing phonon calculation of a primitive Hexagonal system. From symmetry analysis the zone boundary along 110 direction is at (1/2 1/2 0), while I am getting it at (1 1 0) in our calculation. I have taken 2x2x2 q points for dynamical matrix calculation. The c/a ratio is about 2.30 for this system. Is it the problem for small mesh of q point or some thing else. Please give your comments. Mayank PhD BARC MUMBAI INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120524/02340d8c/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu May 24 11:27:04 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 24 May 2012 11:27:04 +0200 Subject: [Pw_forum] HSE vs PBE In-Reply-To: <19527450.558661337827514835.JavaMail.defaultUser@defaultHost> References: <19527450.558661337827514835.JavaMail.defaultUser@defaultHost> Message-ID: <201205241127.04840.giuseppe.mattioli@ism.cnr.it> Dear Giacomo > is it OK? can I do it? I.e., using PBE psudopotential for HSE calculations? A the present time, there is no other way to perform hybrid calculations but with GGA (norm conserving) pseudopotentials. In this regard, I suppose that a 95 Ry wfc cutoff may be poor for copper (with semicore 3s and 3p). You should test the convergence of your PBE results before attempting HSE calculations. > and then use the same for HSE (same pseudopotentials at PBE, taken from the > PwSCF website) I'm quite puzzled... There is no NC pseudopotential for copper in the website. Do you mean the pslibrary? > input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2, You should check the convergence of your results wrt the blend of k points and q points, and this is the most painful task when using hybrid functionals (and metals are very sensitive to k points...). In practice, be sure to the convergence of k points in the PBE calculation, and starting from nqx1= 1, nqx2= 1, nqx3= 1, try to reach convergence (or reach the most bloody-cpu-consuming grid you can afford) wrt the q points. > nspin=2 Copper is nonmagnetic, and you have an even number of atoms. Save (a lot of) time with nspin=1. > nbnd = 80 > occupations='smearing' The latter provide already a fair number of unoccupied states, you do not need to use the former. HTH Giuseppe On Thursday 24 May 2012 04:45:14 giacsport at libero.it wrote: > Dear All, > I am using the development version of PWscf. > > I would like to ask you this question. > > I want to make HSE hybrid calculations (vc-relax) using pseudopotential at > PBE level. > I want indeed test the impact of the hybrid functional in the lattice > parameter (this is the case of Copper) > > I mean is it a correct procedure to optimize the system with such initial > settings > > / > &system > ibrav= 2, celldm(1) = 6.830792531 > nat= 4, ntyp= 1, nspin=2, > ecutwfc = 95., nbnd = 80, occupations='smearing', > degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 > / > > and then use the same for HSE (same pseudopotentials at PBE, taken from the > PwSCF website) > > / > &system > ibrav= 2, celldm(1) = 6.830792531 > nat= 4, ntyp= 1, nspin=2, > ecutwfc = 95., nbnd = 80, occupations='smearing', > degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 > input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2, > x_gamma_extrapolation = .TRUE. > / > > is it OK? can I do it? I.e., using PBE psudopotential for HSE calculations? > > > Thanks in advance for any suggestion! > > Best, > Giacomo -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From mbanck at debian.org Thu May 24 15:51:32 2012 From: mbanck at debian.org (Michael Banck) Date: Thu, 24 May 2012 15:51:32 +0200 Subject: [Pw_forum] Change in the number of qe-forge users In-Reply-To: References: Message-ID: <20120524135132.GH8883@nighthawk.chemicalconnection.dyndns.org> Hi, On Fri, May 18, 2012 at 08:58:08AM +0200, Layla Martin-Samos wrote: > Dear all, we are thinking in moving qe-forge from fusionforge to gforge. What are the reasons for this? The Debian project is running on FusionForge (http://alioth.debian.org/) and as far as I know, there are no big issues with this; Alioth hosts almost 1000 projects and has more than 10000 registered users. > Unfortunately it seems that gforge ask for a commercial License which > pro-year prince will depends on the number of users. There seems to be a community edition available; unless, of course, you require one of the features only available in the Advanced Server product? > As all of you know, nor Quantum ESPRESSO nor qe-forge have any direct > financial support, so we can not afford big expenses. In order to > reduce potential costs of the gforge commercial License, our system > administrator has eliminated all the qe-forge users that are not bound > to any qe-forge project. Depending on the License price then or we > move to gforge or we stay with fusionforge. In any case we will let > you know in order to rationalize the qe-forge users. This looks like a bad decision if you want to create an inclusive community. Users who want to submit bug reports or patches should be able to register and get an account without negative influence on the project's finances. Some of those users might become developers later on. Cheers, Michael From giacsport at libero.it Thu May 24 16:16:27 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 24 May 2012 16:16:27 +0200 (CEST) Subject: [Pw_forum] R: Re: HSE vs PBE Message-ID: <21190978.860841337868987599.JavaMail.defaultUser@defaultHost> Dear Giuseppe, really thanks for the very clear and helpful reply. But let me ask you this. From giuseppe.mattioli at ism.cnr.it Thu May 24 17:41:28 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 24 May 2012 17:41:28 +0200 Subject: [Pw_forum] R: Re: HSE vs PBE In-Reply-To: <21190978.860841337868987599.JavaMail.defaultUser@defaultHost> References: <21190978.860841337868987599.JavaMail.defaultUser@defaultHost> Message-ID: <201205241741.29171.giuseppe.mattioli@ism.cnr.it> > Do you mean that hybrid calcs can be performed only with Norm Conserving > ones? Yes, absolutely...:-( On Thursday 24 May 2012 16:16:27 giacsport at libero.it wrote: > Dear Giuseppe, > really thanks for the very clear and helpful > reply. > > But let me ask you this. > > From the psesudo library of PWSCF I took the > > Cu.pbe-n-van.UPF (hard to say...I dont find it anymore in the > database....has the database been changed recently?...anyway the header of > the pseudo is reported below) > > pseudo that is a USPP one. > > Do you mean that hybrid calcs can be performed only with Norm Conserving > ones? > > :'( > > Thanks once more! > > Best, > Giacomo > > > the pseudo header > > > Generated using Vanderbilt code, version 7 3 > 4 > Author: unknown Generation date: 4 3 > 5 > Automatically converted from original > format > 1 The Pseudo was generated with a Scalar-Relativistic > Calculation 2.00000000000E+00 Local Potential cutoff radius > nl pn l occ Rcut Rcut US E pseu > 3D 3 2 9.50 10.00000000000 2.00000000000 -0.60492460120 > 4S 4 0 1.00 10.00000000000 2.10000000000 -0.43710222811 > 4P 4 1 0.50 10.00000000000 2.20000000000 -0.10740671642 > > > > > 0 Version Number > Cu Element > US Ultrasoft pseudopotential > T Nonlinear Core Correction > SLA PW PBE PBE PBE Exchange-Correlation functional > 11.00000000000 Z valence > -121.01063523375 Total energy > 0.0000000 0.0000000 Suggested cutoff for wfc and rho > 2 Max angular momentum component > 867 Number of points in mesh > 3 6 Number of Wavefunctions, Number of Projectors > Wavefunctions nl l occ > 3D 2 9.50 > 4S 0 1.00 > 4P 1 0.50 > > > >----Messaggio originale---- > >Da: giuseppe.mattioli at ism.cnr.it > >Data: 24/05/2012 11.27 > >A: "giacsport at libero.it", "PWSCF > >Forum" > org> > > >Ogg: Re: [Pw_forum] HSE vs PBE > > > > > >Dear Giacomo > > > >> is it OK? can I do it? I.e., using PBE psudopotential for HSE > >> calculations? > > > >A the present time, there is no other way to perform hybrid calculations > >but > > with GGA (norm > > >conserving) pseudopotentials. In this regard, I suppose that a 95 Ry wfc > > cutoff may be poor for > > >copper (with semicore 3s and 3p). You should test the convergence of your > >PBE > > results before > > >attempting HSE calculations. > > > >> and then use the same for HSE (same pseudopotentials at PBE, taken from > >> the PwSCF website) > > > >I'm quite puzzled... There is no NC pseudopotential for copper in the > > website. Do you mean the > > >pslibrary? > > > >> input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2, > > > >You should check the convergence of your results wrt the blend of k points > > and q points, and this is > > >the most painful task when using hybrid functionals (and metals are very > > sensitive to k points...). > > >In practice, be sure to the convergence of k points in the PBE > >calculation, > > and starting from > > >nqx1= 1, nqx2= 1, nqx3= 1, > > > >try to reach convergence (or reach the most bloody-cpu-consuming grid you > >can > > afford) wrt the q > > >points. > > > >> nspin=2 > > > >Copper is nonmagnetic, and you have an even number of atoms. Save (a lot > >of) > > time with nspin=1. > > >> nbnd = 80 > >> occupations='smearing' > > > >The latter provide already a fair number of unoccupied states, you do not > > need to use the former. > > >HTH > > > >Giuseppe > > > >On Thursday 24 May 2012 04:45:14 giacsport at libero.it wrote: > >> Dear All, > >> > >> I am using the development version of PWscf. > >> > >> I would like to ask you this question. > >> > >> I want to make HSE hybrid calculations (vc-relax) using pseudopotential > >> at PBE level. > >> I want indeed test the impact of the hybrid functional in the lattice > >> parameter (this is the case of Copper) > >> > >> I mean is it a correct procedure to optimize the system with such > >> initial settings > >> > >> / > >> &system > >> > >> ibrav= 2, celldm(1) = 6.830792531 > >> nat= 4, ntyp= 1, nspin=2, > >> ecutwfc = 95., nbnd = 80, occupations='smearing', > >> degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 > >> > >> / > >> > >> and then use the same for HSE (same pseudopotentials at PBE, taken from > >> the PwSCF website) > >> > >> / > >> &system > >> > >> ibrav= 2, celldm(1) = 6.830792531 > >> nat= 4, ntyp= 1, nspin=2, > >> ecutwfc = 95., nbnd = 80, occupations='smearing', > >> degauss=0.01,smearing='gaussian', starting_magnetization(1)=1 > >> input_dft='hse', nqx1= 2, nqx2= 2, nqx3= 2, > >> x_gamma_extrapolation = .TRUE. > >> > >> / > >> > >> is it OK? can I do it? I.e., using PBE psudopotential for HSE > >> calculations? > >> > >> > >> Thanks in advance for any suggestion! > >> > >> Best, > >> Giacomo > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From giannozz at democritos.it Fri May 25 09:55:02 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 May 2012 09:55:02 +0200 Subject: [Pw_forum] Using scalapack in PW/tests causes failures In-Reply-To: References: Message-ID: <1337932502.3527.6.camel@fe12lx.fisica.uniud.it> Please try the attached version of PW/src/stres_us.f90 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- A non-text attachment was scrubbed... Name: stres_us.f90 Type: text/x-fortran Size: 24363 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120525/8cb0b41d/attachment.bin From giuseppe.mattioli at ism.cnr.it Fri May 25 11:19:35 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 25 May 2012 11:19:35 +0200 Subject: [Pw_forum] virtual states in TDDFT (turbo_lanczos.x) calculations Message-ID: <201205251119.35822.giuseppe.mattioli@ism.cnr.it> Dear all I've performed a TDDFT calculation of the absorption spectrum of a molecule, and I am playing around with the new (QE 5.0) "stage 2" calculations, which should indicate the contribution of virtual states to the absorption coefficients, as explained in my_Espresso/5.0/TDDFPT/Examples/CH4-BOND The "stage 2" calculation has been pointed on the first absorption band found by turbo_spectrum.x; my molecule has 98 occupied states, and 10 unoccupied have been calculated by pw.x (nband=108) and I suppose to be quite satisfied (for all I know of this molecule) with these lines 98 1 0.28374685E+04 -0.82400471E+04 2.33588 98 2 0.27984762E+04 -0.82731097E+04 2.34525 98 3 -0.52066456E-05 0.13245374E-04 0.00000 98 4 -0.93634066E-05 0.23337916E-04 0.00000 98 5 0.52748267E-05 -0.14618050E-04 0.00000 98 6 -0.78431969E+01 0.20124113E+02 -0.00570 98 7 -0.78379694E+01 0.20102365E+02 -0.00570 98 8 -0.10283141E-04 0.18715947E-04 0.00000 98 9 -0.29200741E-04 0.36618310E-04 0.00000 98 10 0.38666959E-05 -0.12074233E-04 0.00000 which seem to indicate that the onset of the absorption spectum can be attributed to single-particle transitions involving the highest occupied state and the first and second virtual states (I daresay HOMO connected with LUMO and LUMO+1...). But what about these lines? 92 1 -0.67396365E+03 0.17328962E+04 -0.49124 92 2 -0.68404352E+03 0.17306015E+04 -0.49059 92 3 0.94419011E-05 -0.60010033E-04 0.00000 92 4 -0.18274042E-04 0.26892556E-04 0.00000 92 5 -0.51970803E-04 0.11972278E-03 0.00000 92 6 -0.38956134E+01 0.48423966E+01 -0.00137 92 7 -0.38946693E+01 0.48428589E+01 -0.00137 92 8 -0.20625070E-01 -0.59183925E-04 0.00000 92 9 -0.17290402E-02 -0.34538054E-04 0.00000 92 10 0.59116529E-05 -0.18839515E-04 0.00000 That is, what do negative (and not so small) coefficients means? Thank you in advance Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From daijiayu at nudt.edu.cn Sat May 26 08:49:43 2012 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sat, 26 May 2012 14:49:43 +0800 Subject: [Pw_forum] band parallelization in QE In-Reply-To: <537932287.11903@eyou.net> References: <537932287.11903@eyou.net> Message-ID: <120526144943d8d2589fa776dd42a61cca64c2b7c538@nudt.edu.cn> Dear developers and users, It's really a good news that there is band parallelization for EXX calculations. Does this function work for the other models in QE? I mean, can we use the same way to accelerate the calculations especially we have large number of bands. Besides, is there any difference between EXX and hybrid functional? It is a little puzzled for me because i thought they are difference theories before. Thanks a lot. Jiayu ---------------- ------------------------------------------- Jiayu Dai Department of PhysicsNational University of Defense Technology, Changsha, 410073, P R China ----------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120526/bcd8e07d/attachment.htm From baroni at sissa.it Sat May 26 13:10:46 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 26 May 2012 13:10:46 +0200 Subject: [Pw_forum] band parallelization in QE In-Reply-To: <120526144943d8d2589fa776dd42a61cca64c2b7c538@nudt.edu.cn> References: <537932287.11903@eyou.net> <120526144943d8d2589fa776dd42a61cca64c2b7c538@nudt.edu.cn> Message-ID: <1646D911-87B2-4C8D-B7EB-061739F12916@sissa.it> On May 26, 2012, at 8:49 AM, jiayudai wrote: > Dear developers and users, > > It's really a good news that there is band parallelization for EXX calculations. Does this function work for the other models in QE? I mean, can we use the same way to accelerate the calculations especially we have large number of bands. EXX/hybrids require a double loop over bands. (the action of the Fock exchange over a single band requires a number of FFTs equal to the number of occupied bands) > Besides, is there any difference between EXX and hybrid functional? It is a little puzzled for me because i thought they are difference theories before. different theories, but essentially identical technical/algorithmic details, as an even superficial study of the theories would indicate. SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120526/b075bcbe/attachment.htm From samsonovserg at gmail.com Sat May 26 22:13:26 2012 From: samsonovserg at gmail.com (Sergey Samsonov) Date: Sat, 26 May 2012 22:13:26 +0200 Subject: [Pw_forum] iotk error References: 4E9D9AC6.5010406@gucas.ac.cn Message-ID: <4FC13966.5050101@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120526/70cee6aa/attachment.htm From hamid.rasekhoon at gmail.com Sun May 27 15:36:02 2012 From: hamid.rasekhoon at gmail.com (hamid hasanzadeh) Date: Sun, 27 May 2012 18:06:02 +0430 Subject: [Pw_forum] piezoelectricity Message-ID: hello dear all I am working on piezoelectricity properties of materials I runed example 10 in quantum espresso but i am not Purpose of some parameters in input and output files. i look to "INPUT_PW.html" for meaninigs of this parameters but i was not Realized to the Real Concept of this parameters ?.please introduce papers or books in this case.please help me. INPUT FILE: &control calculation = 'nscf' pseudo_dir = '$PSEUDO_DIR/' outdir = '$TMP_DIR/' lberry = .true. PROBLEM 1.WHAT IS THE MEANINIG OF "lberry"? gdir = 2 PROBLEM 2.WHAT IS THE MEANINIG OF "gdir "? nppstr = 7 PROBLEM 3.WHAT IS THE MEANINIG OF " nppstr "? ibrav = 1 celldm(1) = 7.3699 nat = 5 ntyp = 3 nbnd = 22 ecutwfc = 30.0 occupations = 'fixed' degauss = 0.00 / &electrons conv_thr = 1e-5 mixing_beta = 0.3 / ATOMIC_SPECIES Pb 207.2 Pb.pz-d-van.UPF Ti 47.867 Ti.pz-sp-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS Pb 0.000 0.000 0.010 Ti 0.500 0.500 0.500 O 0.000 0.500 0.500 O 0.500 0.500 0.000 O 0.500 0.000 0.500 K_POINTS {automatic} 4 4 7 1 1 1 HAMID HASSANZADEH M.Sc STUDENT OF FERDOWSI UNIVERCITY From masoudnahali at gmail.com Sun May 27 15:49:57 2012 From: masoudnahali at gmail.com (m) Date: Sun, 27 May 2012 15:49:57 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 Message-ID: Hi Are there any changes implemented in QE 5.0 concerning how to link to math libraries ? On an AMD system with gfortran 4.6.3-1, MKL 10.3.4.191, and openmpi 1.6 we have compiled QE 4.2, 4.2.1, 4.3, and 4.3.2 successfully and the code functions. But the QE 5.0 stops during compilation with an error concerning linking to math libraries. libmkl_core.so : undefined reference to . . . . *** [generate_vwd_kernel_table.x] error 1 any comment ? thank you in advance. Best Wishes Ciao, m ---------------------------------------- Masoud Nahali, International School for Advanced Studies (SISSA) Sharif University of Technology masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120527/453ab99f/attachment.htm From giannozz at democritos.it Sun May 27 16:04:02 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 May 2012 16:04:02 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 In-Reply-To: References: Message-ID: On May 27, 2012, at 15:49 , m wrote: > Are there any changes implemented in QE 5.0 concerning how to link > to math libraries ? nothing relevant > QE 5.0 stops during compilation with an error concerning linking to > math libraries. > libmkl_core.so : undefined reference to . . . . ... to what? > *** [generate_vwd_kernel_table.x] error 1 > any comment ? does it produce a pw.x executable? the auxiliary executable generate_vwd_kernel_table.x is linked after pw.x and is needed only if you plan to use vdw-DF nonlocal functionals P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From masoudnahali at gmail.com Sun May 27 16:29:56 2012 From: masoudnahali at gmail.com (m) Date: Sun, 27 May 2012 16:29:56 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 Message-ID: *on Sun May 27 16:04:02 2012 Paolo wrote :* * * > ... to what? /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dsyr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_get_proc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlaed0' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_sgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zpotrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_cswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_cgeru' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dormlq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zhptrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_ssytrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_pre_cgs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_zswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslv1_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blklu_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_cgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_dswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_pre_cgs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_cswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_clabrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sormrq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dormrq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zhemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sormql' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dsyr2k' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_isamax' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlasyf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_pre_cgs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dormql' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_invs_perm_mod_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkldlslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sgeqrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_psol_fwgath_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ctrmm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_pre_cgs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_cgemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dgttrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blklu_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlaspf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ladj_mod_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cunmlq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sgbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_cpotf2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_psol_fwgath_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blklu_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlasr3' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zgemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_dger' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlaspf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_claev2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgghrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_metis_mlevelnesteddissection_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zpptrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_sgemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_cgs_b' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dpotrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_cher' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_dgetrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_cgs_i' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_cgs_a' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_metis_mlevelnesteddissection_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_psol_fwgath_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sgetrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_spptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv1_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlabrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_zsyr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_zlaev2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_csytrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_sscal' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_spbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_zgeru' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkldlslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dgetrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ladj_mod_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_psol_bwscat_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zsptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cpptrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_psol_bwscat_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cgbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_zscal' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dpptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_cscal' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dpbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zhetrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blklu_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dsptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_ch_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlaed0' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cgghrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_cgs_b' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_clatrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkslv1_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dtrsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_dgemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zhptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_psol_bwscat_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_cgs_i' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_cgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zpptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_sgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlasyf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_chetrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_spotrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv_unsym_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_psol_bwscat_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blklu_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ssyr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_cgs_a' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cpotrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zswap' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_ztrsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zpbtrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_serv_mkl_get_max_threads' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_strsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_zgemm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zherk' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blklu_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blklu_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dgeqrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlaeh2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_clacgv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlahef' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_get_dynamic_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_dgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zhgeqz_applycr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_dlaswp' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_slasyf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_slaed0' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blklu_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dsptrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgghrd_applycr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_crot' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zrot' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lnnt_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_get_proc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_chetrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dsyrk' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_psol_fwgath_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ssyr2k' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_csyr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sgbtrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_amuxy_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_slaeh2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_cgs_b' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blklu_unsym_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_invs_perm_mod_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_csscal' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkldl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkldlslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslv1_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkl_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlaeh2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cgghrd_applycr' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zlatrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_lnnt_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_zher2k' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_diag_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslv_unsym_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_dtrsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_ssptrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_cgs_b' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_claed0' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_crot' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_psol_fwgath_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_c_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blklu_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sormlq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_ch_blkldlslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_sgttrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blkslvs_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_dgemv' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_cpttrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zsytrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ztrsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkslv_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkldlslvs_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zunmql' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_idamax' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blklu_ooc_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_ch_blkldl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_slaswp' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_c_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_serv_progress' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zunmlq' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_claswp' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_c_blkslv_unsym_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_izamax' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_sp_blkslv_unsym_ooc_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgbtrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dsytrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_chgeqz' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_strsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blkslv1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_c_blklu_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_dlatrd' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zpttrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ssymm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_blkldlslvs1_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_zpotf2' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_ztrmm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_lp64_ctrsm' /lib/../lib/libmkl_core.so: undefined reference to `mkl_blas_cher2k' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_ch_blkl_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_ssptrs' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslv1_unsym_omp_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_lp64_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_lp64_zlacgv' does it produce a pw.x executable? the auxiliary executable > generate_vwd_kernel_table.x is linked after pw.x and is needed > only if you plan to use vdw-DF nonlocal functionals Yes, just pw.x (size 9.3 MB) and iotk.x were compiled. But other binary files like pp.x, neb.x, projwfc.x, dos.x, and . . . were not compiled. Concerning compilation of QE 4.2, 4.2.1, 4.3, and 4.3.2 all the binary files were made successfully in QE/bin directory. Many Thanks, m ---------------------------------------- Masoud Nahali, International School for Advanced Studies (SISSA) Sharif University of Technology masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120527/0b5ee7fa/attachment-0001.htm From giannozz at democritos.it Sun May 27 16:47:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 May 2012 16:47:28 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 In-Reply-To: References: Message-ID: <33C03266-6BB2-43F0-969D-AAC21E053887@democritos.it> On May 27, 2012, at 16:29 , m wrote: > Yes, just pw.x (size 9.3 MB) and iotk.x were compiled. > But other binary files like pp.x, neb.x, projwfc.x, dos.x, and . . . > were not compiled. they were not "linked"; they were "compiled". The linking procedure is the same for all executables. Look at the line where linking is performed. It is something like: mpif90 -o pw.x \ pwscf.o libpw.a ../../Modules/libqemod.a ../../flib/ ptools.a ../../flib/flib.a ../../clib/clib.a ../../iotk/src/ libiotk.a -llapack /Users/giannozz/trunk/espresso/lapack-3.2/ lapack.a -lfftw3 -latlas Compare what is done in v.4.3.2 with what is done in v.5.0; compare what is done for pw.x and what is done for all other codes. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From masoudnahali at gmail.com Sun May 27 21:47:42 2012 From: masoudnahali at gmail.com (m) Date: Sun, 27 May 2012 21:47:42 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 Message-ID: *on Sun May 27 16:47:28 CEST 2012 Paolo wrote :* * * > Compare what is done in v.4.3.2 with what is done in v.5.0; > compare what is done for pw.x and what is done for all other codes. * * * * In the below* *lines the compilation of pw.x and generate_vdW_kernel_table.f90 for QE-5.0 and QE-4.3.2 is compared. At this point the error appears for QE-5.0 but everything is OK for QE- 4.2 - QE 4.3.2. QE- 5.0 : mpif90 -g -o pw.x \ pwscf.o libpw.a ../../Modules/libqemod.a ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core ( cd ../../bin; ln -fs ../PW/src/pw.x . ) mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA -D__SCALAPACK -I../include -I../../iotk/src -I../../Modules -I. -c generate_vdW_kernel_table.f90 mpif90 -g -o generate_vdW_kernel_table.x \ generate_vdW_kernel_table.o ../../Modules/libqemod.a libpw.a ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core /lib/../lib/libmkl_core.so: undefined reference to `mkl_pds_sp_blkslv_pardiso' /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgetrf' /lib/../lib/libmkl_core.so: undefined reference to `mkl_serv_xerbla' . . . . . . . . . *** [generate_vwd_kernel_table.x] error 1 QE- 4.3.2 : mpif90 -g -o pw.x \ pwscf.o libpw.a ../Modules/libqemod.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_intel_lp64 -lmkl_sequential -lmkl_core ( cd ../bin; ln -fs ../PW/pw.x . ) mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA -I../include -I../iotk/src -I../Modules -I. -c generate_vdW_kernel_table.f90 mpif90 -g -o generate_vdW_kernel_table.x \ generate_vdW_kernel_table.o ../Modules/libqemod.a libpw.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -lmkl_intel_lp64 -lmkl_sequential -lmkl_core ( cd ../bin; ln -fs ../PW/generate_vdW_kernel_table.x . ) make[1]: Leaving directory `/home/luca/QE4.3.2/espresso-4.3.2/PW' the same error happens for QE-5.0 when I make neb or pp. Many Thanks Ciao, m ---------------------------------------- Masoud Nahali, International School for Advanced Studies (SISSA) Sharif University of Technology masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120527/29975f3d/attachment.htm From akohlmey at gmail.com Sun May 27 22:01:26 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sun, 27 May 2012 16:01:26 -0400 Subject: [Pw_forum] linking to math libraries in QE 5.0 In-Reply-To: References: Message-ID: On Sun, May 27, 2012 at 3:47 PM, m wrote: > on Sun May 27 16:47:28 CEST 2012 Paolo wrote : > >> Compare what is done in v.4.3.2 with what is done in v.5.0; >> compare what is done for pw.x and what is done for all other codes. > > > ? In the below?lines the compilation of pw.x and > generate_vdW_kernel_table.f90 for QE-5.0 and QE-4.3.2 is compared. At this > point the error appears for QE-5.0 but everything is OK for QE- 4.2 - QE > 4.3.2. > > > ? QE- 5.0 : > > ??mpif90 -g -o pw.x \ > ? pwscf.o ?libpw.a ../../Modules/libqemod.a ../../flib/ptools.a > ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a > -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 ? -lmkl_intel_lp64 > ?-lmkl_sequential -lmkl_core > ( cd ../../bin; ln -fs ../PW/src/pw.x . ) > mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI > -D__PARA -D__SCALAPACK -I../include -I../../iotk/src -I../../Modules -I. -c > generate_vdW_kernel_table.f90 > mpif90 -g -o generate_vdW_kernel_table.x \ > generate_vdW_kernel_table.o ../../Modules/libqemod.a libpw.a > ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a > ../../iotk/src/libiotk.a -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 > -lmkl_intel_lp64 ?-lmkl_sequential -lmkl_core > /lib/../lib/libmkl_core.so: undefined reference to > `mkl_pds_sp_blkslv_pardiso' > /lib/../lib/libmkl_core.so: undefined reference to `mkl_lapack_zgetrf' > /lib/../lib/libmkl_core.so: undefined reference to `mkl_serv_xerbla' > . . . > . . . > . . . > > *** [generate_vwd_kernel_table.x] error 1 > > > QE- 4.3.2 : > > mpif90 -g -o pw.x \ > ? pwscf.o ?libpw.a ../Modules/libqemod.a ../flib/ptools.a ../flib/flib.a > ../clib/clib.a ../iotk/src/libiotk.a ? ? -lmkl_intel_lp64 ?-lmkl_sequential > -lmkl_core > ( cd ../bin; ln -fs ../PW/pw.x . ) > mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI > -D__PARA -I../include -I../iotk/src -I../Modules -I. -c > generate_vdW_kernel_table.f90 > mpif90 -g -o generate_vdW_kernel_table.x \ > generate_vdW_kernel_table.o ../Modules/libqemod.a libpw.a ../flib/ptools.a > ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a ? ? -lmkl_intel_lp64 > ?-lmkl_sequential -lmkl_core > ( cd ../bin; ln -fs ../PW/generate_vdW_kernel_table.x . ) > make[1]: Leaving directory `/home/luca/QE4.3.2/espresso-4.3.2/PW' > > the same error happens for QE-5.0 when I make neb or pp. well, if you look closely, you are not compiling both packages the same way. QE-5.0 you request the inclusion of ScaLAPACK and in QE-4.3.2 you don't. the errors you see are a result of that. the scalapack issue is a result of changes in the GNU linker to only satisfy undefined references "to the left". you might be able to work around this with some GNU linker magic, if you change the MKL related parts with: -Wl,--start-group -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group there also is an error in your older linker line by including the intel startup code instead of the gfortran startup code. finally, it may be more convenient to link mkl statically and this can be done with: -Wl,--start-group,-Bstatic -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group,-Bdynamic axel. > > Many Thanks > > > > > Ciao, m > > > > > ---------------------------------------- > Masoud Nahali, > International School for Advanced Studies (SISSA) > Sharif University of Technology > masoud.nahali at gmail.com > alum.sharif.edu/~m_nahali > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From giannozz at democritos.it Sun May 27 22:02:35 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 27 May 2012 22:02:35 +0200 Subject: [Pw_forum] linking to math libraries in QE 5.0 In-Reply-To: References: Message-ID: <5ACF6C2C-EE2B-4168-9F58-8A6C837BF0C7@democritos.it> On May 27, 2012, at 21:47 , m wrote: > In the below lines the compilation of pw.x and > generate_vdW_kernel_table.f90 for QE-5.0 and QE-4.3.2 is compared. > At this point the error appears for QE-5.0 but everything is OK for > QE- 4.2 - QE 4.3.2. > the only difference is the presence of scalapack libraries. Try to compile without them: ./configure --with-scalapack=no (or --without-scalapack, I don't remember), make clean, make ... I do not see anything wrong, though P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ptao10b at imr.ac.cn Mon May 28 05:11:36 2012 From: ptao10b at imr.ac.cn (Peng Tao) Date: Mon, 28 May 2012 11:11:36 +0800 (CST) Subject: [Pw_forum] starting and expecting charges are differ when using ph.x Message-ID: <43df91.7ed4.137916d6da0.Coremail.ptao10b@imr.ac.cn> Dear all, I'm trying to calculate the phonon dispersion of charged system. I set tot_charge=0.5, and phonon calculation is executed after scf run. And an error occurs as follows: Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.04 Mb ( 286, 10) NL pseudopotentials 0.10 Mb ( 286, 24) Each V/rho on FFT grid 0.61 Mb ( 40000) Each G-vector array 0.06 Mb ( 8439) G-vector shells 0.03 Mb ( 3989) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 0.17 Mb ( 286, 40) Each subspace H/S matrix 0.02 Mb ( 40, 40) Each matrix 0.00 Mb ( 24, 10) The potential is recalculated from file : ./trat/_ph0/e_q2/e.save/charge-density.dat %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from potinit : error # 1 starting and expected charges differ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... What's wrong with it? Here are my scf and phonon input files: &CONTROL prefix='e', calculation = "scf", tstress=.true. wf_collect=.true. tprnfor=.true. forc_conv_thr=1.0D-5, pseudo_dir = "./", outdir = "./trat/", / &SYSTEM ibrav = 6, celldm(1)=35, celldm(3)=0.153, nat = 6, ntyp = 2, ecutwfc = 30.80 ecutrho = 300.0 occupations = "smearing", smearing = "gaussian", degauss = 0.03D0, tot_charge = 0.5 / &ELECTRONS mixing_beta = 0.3D0, conv_thr = 1.D-10, / ATOMIC_SPECIES ...... ATOMIC_POSITIONS crystal ...... K_POINTS AUTOMATIC 1 1 80 0 0 0 ------------------------------------------------- ------------------------------------------------- phonon for ** &inputph tr2_ph=1.0d-14, prefix='e', fildvscf='edv', outdir='./trat/', fildyn='e.dyn', trans=.true., ldisp=.true., nq1=1, nq2=1, nq3=5 / Thank you very much! Warmest regards, Plato Tao From baris.malcioglu at gmail.com Mon May 28 18:33:00 2012 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Mon, 28 May 2012 18:33:00 +0200 Subject: [Pw_forum] virtual states in TDDFT (turbo_lanczos.x) calculations In-Reply-To: <201205251119.35822.giuseppe.mattioli@ism.cnr.it> References: <201205251119.35822.giuseppe.mattioli@ism.cnr.it> Message-ID: Dear Giuseppe, Understanding the negative values is quite simple actually. Imagine two compatible Hilbert spaces. Let's say Cartesian coordinates and spherical coordinates. Let's be in 2D to make things simple. Transforming a coordinate like d=135 degrees and r=1 cm (which are both positive numbers) will give you 0.707107y, -0.707107x so it is possible to have a transformation that gives you negative values, although you start with positive values. Mathematically speaking, as long as you are dealing with spaces that obey closure/completeness you can choose whatever to represent your results. The KS states constitute a complete set (assuming you have infinite/enough virtual orbitals calculated), so you can choose it to describe your results, but it is very important to remember that the interpretation should be adapted to new situation. O.k. This part needs a risky allegory. Imagine a particle that can move only in a line. The Hilbert space spanned by the corresponding Hamiltonian will then be on a line as well, say it consists of +X and -X When you add a perturbation to the system, say a slight perturbation in the Y direction, the new Hilbert space is +X,-X,+Y and -Y Since this is a perturbation, the magnitude of the Y component is negligible in comparison to magnitude of X component. The result is almost exactly equivalent to re-adjusting the length of the X in the previous calculation. So let's assume your Hilbert space remains the same in both cases. When you want to represent the perturbed result using +X and -X Hilbert space, irrespective if you have a constraint in the system that restricts the particle to move only in +X direction, when you "project" the +Y or -Y component in your perturbed system to the vectors spanning the unperturbed Hilbert space, you will see a -X. So what can be the values that will serve our best interest in our case? After a lengthy discussion, and I totally agree with it, the most physically useful value we come up with are the oscillator strengths. So, those values are to be interpreted as corrections to the oscillator strengths due to transitions that "look like" mentioned elements. (In a vaguely similar manner how a movement in Y direction looks like -X, but since we are talking about a Hilbert space that obeys closure and can span both Hamiltonians, this time the resemblance is more "exact") and I would advise you to use more virtual states, otherwise you will have too much spilling (i.e. error due to not satisfying closure) Baris On Fri, May 25, 2012 at 11:19 AM, Giuseppe Mattioli wrote: > > Dear all > I've performed a TDDFT calculation of the absorption spectrum of a molecule, and I am playing around > with the new (QE 5.0) "stage 2" calculations, which should indicate the contribution of virtual > states to the absorption coefficients, as explained in > > my_Espresso/5.0/TDDFPT/Examples/CH4-BOND > > The "stage 2" calculation has been pointed on the first absorption band found by turbo_spectrum.x; my > molecule has 98 occupied states, and 10 unoccupied have been calculated by pw.x (nband=108) and I > suppose to be quite satisfied (for all I know of this molecule) with these lines > > ? ? ?98 ? 1 ? ? 0.28374685E+04 ? -0.82400471E+04 ? 2.33588 > ? ? ?98 ? 2 ? ? 0.27984762E+04 ? -0.82731097E+04 ? 2.34525 > ? ? ?98 ? 3 ? ?-0.52066456E-05 ? ?0.13245374E-04 ? 0.00000 > ? ? ?98 ? 4 ? ?-0.93634066E-05 ? ?0.23337916E-04 ? 0.00000 > ? ? ?98 ? 5 ? ? 0.52748267E-05 ? -0.14618050E-04 ? 0.00000 > ? ? ?98 ? 6 ? ?-0.78431969E+01 ? ?0.20124113E+02 ?-0.00570 > ? ? ?98 ? 7 ? ?-0.78379694E+01 ? ?0.20102365E+02 ?-0.00570 > ? ? ?98 ? 8 ? ?-0.10283141E-04 ? ?0.18715947E-04 ? 0.00000 > ? ? ?98 ? 9 ? ?-0.29200741E-04 ? ?0.36618310E-04 ? 0.00000 > ? ? ?98 ?10 ? ? 0.38666959E-05 ? -0.12074233E-04 ? 0.00000 > > which seem to indicate that the onset of the absorption spectum can be attributed to single-particle > transitions involving the highest occupied state and the first and second virtual states (I daresay > HOMO connected with LUMO and LUMO+1...). > > But what about these lines? > > ? ? ?92 ? 1 ? ?-0.67396365E+03 ? ?0.17328962E+04 ?-0.49124 > ? ? ?92 ? 2 ? ?-0.68404352E+03 ? ?0.17306015E+04 ?-0.49059 > ? ? ?92 ? 3 ? ? 0.94419011E-05 ? -0.60010033E-04 ? 0.00000 > ? ? ?92 ? 4 ? ?-0.18274042E-04 ? ?0.26892556E-04 ? 0.00000 > ? ? ?92 ? 5 ? ?-0.51970803E-04 ? ?0.11972278E-03 ? 0.00000 > ? ? ?92 ? 6 ? ?-0.38956134E+01 ? ?0.48423966E+01 ?-0.00137 > ? ? ?92 ? 7 ? ?-0.38946693E+01 ? ?0.48428589E+01 ?-0.00137 > ? ? ?92 ? 8 ? ?-0.20625070E-01 ? -0.59183925E-04 ? 0.00000 > ? ? ?92 ? 9 ? ?-0.17290402E-02 ? -0.34538054E-04 ? 0.00000 > ? ? ?92 ?10 ? ? 0.59116529E-05 ? -0.18839515E-04 ? 0.00000 > > That is, what do negative (and not so small) coefficients means? > > Thank you in advance > > Giuseppe > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > ? Giuseppe Mattioli > ? CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > ? v. Salaria Km 29,300 - C.P. 10 > ? I 00015 - Monterotondo Stazione (RM) > ? Tel + 39 06 90672836 - Fax +39 06 90672316 > ? E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sohailphysics at yahoo.co.in Mon May 28 23:02:31 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Tue, 29 May 2012 05:02:31 +0800 (SGT) Subject: [Pw_forum] publication Message-ID: <1338238951.38573.YahooMailClassic@web192202.mail.sg3.yahoo.com> Dear All Where can i find the list of publication resulting from QE The? website????? http://www.quantum-espresso.org/wiki/index.php/Main_Page doesnot work Thanks Sohail Saudi Arabia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120529/a5f3f873/attachment.htm From giannozz at democritos.it Tue May 29 08:46:03 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 May 2012 08:46:03 +0200 Subject: [Pw_forum] publication In-Reply-To: <1338238951.38573.YahooMailClassic@web192202.mail.sg3.yahoo.com> References: <1338238951.38573.YahooMailClassic@web192202.mail.sg3.yahoo.com> Message-ID: <47757941-F857-494A-AFEB-319A2E8AD000@democritos.it> On May 28, 2012, at 23:02 , Sohail Ahmad wrote: > Where can i find the list of publication resulting from QE > > The website http://www.quantum-espresso.org/wiki/index.php/ > Main_Page > does not work the old site is still accessible under http://testwp.qe-forge.it P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lmartinsamos at gmail.com Tue May 29 08:49:48 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 29 May 2012 08:49:48 +0200 Subject: [Pw_forum] publication In-Reply-To: <1338238951.38573.YahooMailClassic@web192202.mail.sg3.yahoo.com> References: <1338238951.38573.YahooMailClassic@web192202.mail.sg3.yahoo.com> Message-ID: Dear Sohail, you can use webofscience and search for QE paper Title: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials Author(s): Giannozzi Paolo; Baroni Stefano; Bonini Nicola; et al. Source: JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 21 Issue: 39 Article Number: 395502 DOI: 10.1088/0953-8984/21/39/395502 Published: SEP 30 2009 Times Cited: 1,038(from Web of Science) you can click on the citation number and you will get the list of publications. best regards Layla 2012/5/28 Sohail Ahmad > Dear All > > Where can i find the list of publication resulting from QE > > The website http://www.quantum-espresso.org/wiki/index.php/Main_Page > doesnot work > > Thanks > > Sohail > Saudi Arabia > > _______________________________________________ > 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/20120529/689ec3a4/attachment.htm From giuseppe.mattioli at ism.cnr.it Tue May 29 11:10:58 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Tue, 29 May 2012 11:10:58 +0200 Subject: [Pw_forum] virtual states in TDDFT (turbo_lanczos.x) calculations In-Reply-To: References: <201205251119.35822.giuseppe.mattioli@ism.cnr.it> Message-ID: <201205291110.59055.giuseppe.mattioli@ism.cnr.it> Dear Baris Thank you. I should read the answer another couple o' times, and then I may possibly post further questions...:-) Giuseppe On Monday 28 May 2012 18:33:00 O. Baris Malcioglu wrote: > Dear Giuseppe, > > Understanding the negative values is quite simple actually. > > Imagine two compatible Hilbert spaces. Let's say Cartesian coordinates > and spherical coordinates. Let's be in 2D to make things simple. > > Transforming a coordinate like d=135 degrees and r=1 cm (which are > both positive numbers) will give you 0.707107y, -0.707107x > > so it is possible to have a transformation that gives you negative > values, although you start with positive values. > > Mathematically speaking, as long as you are dealing with spaces that > obey closure/completeness you can choose whatever to represent your > results. The KS states constitute a complete set (assuming you have > infinite/enough virtual orbitals calculated), so you can choose it to > describe your results, but it is very important to remember that the > interpretation should be adapted to new situation. > > > O.k. This part needs a risky allegory. > > Imagine a particle that can move only in a line. The Hilbert space > spanned by the corresponding Hamiltonian will then be on a line as > well, say it consists of +X and -X > > When you add a perturbation to the system, say a slight perturbation > in the Y direction, the new Hilbert space is +X,-X,+Y and -Y > > Since this is a perturbation, the magnitude of the Y component is > negligible in comparison to magnitude of X component. The result is > almost exactly equivalent to re-adjusting the length of the X in the > previous calculation. So let's assume your Hilbert space remains the > same in both cases. > > When you want to represent the perturbed result using +X and -X > Hilbert space, irrespective if you have a constraint in the system > that restricts the particle to move only in +X direction, when you > "project" the +Y or -Y component in your perturbed system to the > vectors spanning the unperturbed Hilbert space, you will see a -X. > > > So what can be the values that will serve our best interest in our case? > > After a lengthy discussion, and I totally agree with it, the most > physically useful value we come up with are the oscillator strengths. > So, those values are to be interpreted as corrections to the > oscillator strengths due to transitions that "look like" mentioned > elements. (In a vaguely similar manner how a movement in Y direction > looks like -X, but since we are talking about a Hilbert space that > obeys closure and can span both Hamiltonians, this time the > resemblance is more "exact") > > > and I would advise you to use more virtual states, otherwise you will > have too much spilling (i.e. error due to not satisfying closure) > > > Baris > > > > > > > > On Fri, May 25, 2012 at 11:19 AM, Giuseppe Mattioli > > wrote: > > Dear all > > I've performed a TDDFT calculation of the absorption spectrum of a > > molecule, and I am playing around with the new (QE 5.0) "stage 2" > > calculations, which should indicate the contribution of virtual states > > to the absorption coefficients, as explained in > > > > my_Espresso/5.0/TDDFPT/Examples/CH4-BOND > > > > The "stage 2" calculation has been pointed on the first absorption band > > found by turbo_spectrum.x; my molecule has 98 occupied states, and 10 > > unoccupied have been calculated by pw.x (nband=108) and I suppose to be > > quite satisfied (for all I know of this molecule) with these lines > > > > 98 1 0.28374685E+04 -0.82400471E+04 2.33588 > > 98 2 0.27984762E+04 -0.82731097E+04 2.34525 > > 98 3 -0.52066456E-05 0.13245374E-04 0.00000 > > 98 4 -0.93634066E-05 0.23337916E-04 0.00000 > > 98 5 0.52748267E-05 -0.14618050E-04 0.00000 > > 98 6 -0.78431969E+01 0.20124113E+02 -0.00570 > > 98 7 -0.78379694E+01 0.20102365E+02 -0.00570 > > 98 8 -0.10283141E-04 0.18715947E-04 0.00000 > > 98 9 -0.29200741E-04 0.36618310E-04 0.00000 > > 98 10 0.38666959E-05 -0.12074233E-04 0.00000 > > > > which seem to indicate that the onset of the absorption spectum can be > > attributed to single-particle transitions involving the highest occupied > > state and the first and second virtual states (I daresay HOMO connected > > with LUMO and LUMO+1...). > > > > But what about these lines? > > > > 92 1 -0.67396365E+03 0.17328962E+04 -0.49124 > > 92 2 -0.68404352E+03 0.17306015E+04 -0.49059 > > 92 3 0.94419011E-05 -0.60010033E-04 0.00000 > > 92 4 -0.18274042E-04 0.26892556E-04 0.00000 > > 92 5 -0.51970803E-04 0.11972278E-03 0.00000 > > 92 6 -0.38956134E+01 0.48423966E+01 -0.00137 > > 92 7 -0.38946693E+01 0.48428589E+01 -0.00137 > > 92 8 -0.20625070E-01 -0.59183925E-04 0.00000 > > 92 9 -0.17290402E-02 -0.34538054E-04 0.00000 > > 92 10 0.59116529E-05 -0.18839515E-04 0.00000 > > > > That is, what do negative (and not so small) coefficients means? > > > > Thank you in advance > > > > Giuseppe > > > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00015 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: From amirhosseinba67 at gmail.com Tue May 29 22:51:45 2012 From: amirhosseinba67 at gmail.com (Amir hosseini) Date: Tue, 29 May 2012 13:51:45 -0700 Subject: [Pw_forum] Do not match Message-ID: Dear all I calculated DOS and Transmission of Boron Nitrogen nanotube and plot them but graph of them not match and need to shift. Why this happened and what am I do? Thanks Amir hossein Bayani M.S.C student of Ferdowsi university of Mashhad-Iran From lorenzo.paulatto at impmc.upmc.fr Tue May 29 23:54:33 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 29 May 2012 23:54:33 +0200 Subject: [Pw_forum] Do not match In-Reply-To: References: Message-ID: On Tue, May 29, 2012 at 10:51 PM, Amir hosseini wrote: > I calculated DOS and Transmission of Boron Nitrogen nanotube and plot > them but graph of them not match and need to shift. > > Dear Amir, the choice of the energy for the energy bands, and consequently for the dos, is arbitrary. It is customary to choose the Fermi energy as zero, but it is not done automatically by the dos.x code. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120529/05eeec16/attachment.htm From fratesi at mater.unimib.it Wed May 30 12:10:30 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Wed, 30 May 2012 12:10:30 +0200 Subject: [Pw_forum] problem with chdens with ibrav=0 Message-ID: <4FC5F216.1030409@mater.unimib.it> Dear all, I noticed a problem when running pp.x with ibrav=0, namely the program stops with "incompatible celldm". This is a code check that the celldm of all files to plot in the run are compatible with each other, but it occurs also when plotting from a single file, which of course is compatible with itself. Actually, with ibrav=0, celldm(1) is defined to |a1| by latgen and stored in the variable "celldm" (see chdens.f90), but no similar definition is done for variable "celldms" which is left to 0, hence the stop. I am using QE-5.0, but the same would happen with earlier versions. I enclose a test case (atomic H) for a quick run. NB By removing the check the code produces the results expected, yet this is not *the* solution. Guido PS Of course you might ask why am I using ibrav=0... -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy -------------- next part -------------- A non-text attachment was scrubbed... Name: chdens-ibrav0.tgz Type: application/x-compressed-tar Size: 3859 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120530/883fbde5/attachment.bin From t.p.hoang at iup.edu Wed May 30 16:09:16 2012 From: t.p.hoang at iup.edu (Tony Phuc Hoang) Date: Wed, 30 May 2012 10:09:16 -0400 Subject: [Pw_forum] pwscf question- R-halide comparison Message-ID: I am trying to compare R-Br and R-Cl systems. For the chlorine, I've used Cl.pbe-n-van.UPF and for the bromine Br.pbe-van_mit.UPF I know that bromine reacts faster than chlorine, so it should have a lower barrier. But when I compared the neb using the above pseudopotentials, the bromine has a higher barrier. The atoms in the R-groups all use ultrasoft. My question is, is it because the pseudopotentials of the bromine and chlorine different that is causing the mix up (sort of like comparing apples to oranges)? Do you have any recommendations? Thanks. From dyang2103 at gmail.com Thu May 31 10:58:39 2012 From: dyang2103 at gmail.com (david yang) Date: Thu, 31 May 2012 14:28:39 +0530 Subject: [Pw_forum] slow speed of D3 code Message-ID: Hi all, I am calculating anharmonic IFCS for Si on a 3x3x3 supercell on 32 processor. But the calculation seems to be very slow ,it takes 250 hours for calculating IFCs at a particular point(e.g on X,L,or any arbitrary point). If there is any trick by which I can speed up my calculation . thanking you with regards David -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120531/bd7a68c6/attachment.htm From meghdad_saeedian at yahoo.com Thu May 31 11:08:26 2012 From: meghdad_saeedian at yahoo.com (meghdad saeedian) Date: Thu, 31 May 2012 02:08:26 -0700 (PDT) Subject: [Pw_forum] erroe in compilation Espresso-5.0 Message-ID: <1338455306.17612.YahooMailClassic@web140604.mail.bf1.yahoo.com> Dear all I want to instal the newest version of QE (5) on a machine of type X86_64 with operating system CentOS-4.7 fortran compiler Version 11.0 and math libraries Version 11.0 ? I have used this command to configure it parrallel and configuration was successful: ./configure MPIF90=mpif77 F77=mpif77 CC=mpicc --enable-parallel ? but in the compilation it give an error as below : /opt/intel/Compiler/11.0/081/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(sys2blacs_handle_.oo)(.text+0x1d2): In function `Csys2blacs_handle': : undefined reference to `ompi_mpi_comm_world' /opt/intel/Compiler/11.0/081/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(BI_MPI_F77_to_c_trans_comm.o)(.text+0x6): In function `BI_MPI_F77_to_c_trans_comm': : undefined reference to `MPI_Comm_f2c' make[2]: *** [pw.x] Error 1 make[2]: Leaving directory `/home/user41/espresso-5.0/PW/src' make[1]: *** [pw] Error 2 make[1]: Leaving directory `/home/user41/espresso-5.0/PW' make: *** [pw] Error 2 [user41 at ce espresso-5.0]$ ? I was wondering if anyone could help me. Tanks in advance ? Meghdad Saeedian MSc graduated from the University Of Tehran, Departemant Of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120531/94ec6c7c/attachment.htm From giacsport at libero.it Thu May 31 11:17:29 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 31 May 2012 11:17:29 +0200 (CEST) Subject: [Pw_forum] NOSYM tag Message-ID: <27994441.3925691338455849514.JavaMail.defaultUser@defaultHost> Dear All, I would like to calculate the GS energy of Al atom (and similarly of other elements). In order to do this I set this input file &control calculation = 'scf', restart_mode='from_scratch', pseudo_dir = './' outdir='./', prefix='Aluminium_1atom', tprnfor = .true., tstress = .true., wf_collect=.true., / &system ibrav= 1, celldm(1)= 17. nat= 1, ntyp= 1, nspin=2, nosym= 'true', ecutwfc = 65., occupations='smearing', degauss=0.01, smearing='gaussian', starting_magnetization(1)= 1 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS / &CELL cell_dynamics='none' / ATOMIC_SPECIES Al 26.982 Al.pbe-rrkj.UPF ATOMIC_POSITIONS crystal Al 0.50000 0.50000 0.50000 K_POINTS automatic 1 1 1 0 0 0 and I get an error message Program PWSCF v.4.1.3 starts ... Today is 31May2012 at 18: 6:42 Parallel version (MPI) Number of processors in use: 8 R & G space division: proc/pool = 8 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 64 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% but when I remove the tag nosym='true' the calculation successfully ends. Could you kindly tell me what is wrog in my input file? Thanks in advance for the kind cooperation. With best regards, Giacomo --------- Giacomo GIORGI Assistant Professor Research Center for Advanced Science and Technology (RCAST), The University of Tokyo 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan From lorenzo.paulatto at impmc.upmc.fr Thu May 31 11:37:34 2012 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 31 May 2012 11:37:34 +0200 Subject: [Pw_forum] NOSYM tag In-Reply-To: <27994441.3925691338455849514.JavaMail.defaultUser@defaultHost> References: <27994441.3925691338455849514.JavaMail.defaultUser@defaultHost> Message-ID: On Thu, May 31, 2012 at 11:17 AM, giacsport at libero.it wrote: > nosym= 'true', > Dear Giacomo, nosym=.true. is not the same as nosym='true' best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120531/d5f10447/attachment.htm From giacsport at libero.it Thu May 31 12:59:31 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 31 May 2012 12:59:31 +0200 (CEST) Subject: [Pw_forum] R: Re: NOSYM tag + atomization energy Message-ID: <22004421.4006831338461971984.JavaMail.defaultUser@defaultHost> got the point.... thanks, Lorenzo! By the way, to complete my post, I would like to understand where is the source of my error....I am trying to calculate the atomization energy for C....I always get a value (11.14 eV/atom) well above the experimental one (7.37 eV/atom) and also above other values still calculated at PBE level. I have tried "adjusting" all the possible parameters (cutoff, vacuum, kpoint sampling), but at the end I am not able to further reduce such value.Has anybody any suggestion for me? The pseudo I use has 2e in 2s and 1.5e in 2p. Here I attach the two input files for the bulk (8atoms) calculation and for the single atom calculation. Any hint is very appreciated BULK_8 ATOM CELL calculation = 'vc-relax', restart_mode='from_scratch', pseudo_dir = './' nstep=300 outdir='./', prefix='Carbon', tprnfor = .true., tstress = .true., wf_collect=.true., / &system ibrav= 1, celldm(1) = 6.740274656 nat= 8, ntyp= 1, nspin=2, ecutwfc = 80., occupations='smearing', degauss=0.01, smearing='gaussian', starting_magnetization(1)=1 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-7 / &CELL cell_dynamics='bfgs' / ATOMIC_SPECIES C 12.011 C.pbe-mt_gipaw.UPF ATOMIC_POSITIONS (crystal) C 0.00000 0.00000 0.00000 C 0.25000 0.25000 0.25000 C 0.00000 0.50000 0.50000 C 0.25000 0.75000 0.75000 C 0.50000 0.00000 0.50000 C 0.75000 0.25000 0.75000 C 0.50000 0.50000 0.00000 C 0.75000 0.75000 0.25000 K_POINTS (automatic) 9 9 9 0 0 0 AND the ATOMIC CASE &control calculation = 'scf', restart_mode='from_scratch', pseudo_dir = './' outdir='./', prefix='Carbon.1atom', wf_collect=.true., / &system ibrav= 1, celldm(1) = 18., nat= 1, ntyp= 1, nspin=2, ecutwfc = 80., occupations='smearing', nosym=.true., degauss=0.01, smearing='gaussian', / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES C 12.011 C.pbe-mt_gipaw.UPF ATOMIC_POSITIONS (crystal) C 0.50000 0.50000 0.50000 K_POINTS (automatic) 1 1 1 0 0 0 Thanks in advance!G ----Messaggio originale---- Da: lorenzo.paulatto at impmc.upmc.fr Data: 31/05/2012 11.37 A: "giacsport at libero.it", "PWSCF Forum" Ogg: Re: [Pw_forum] NOSYM tag On Thu, May 31, 2012 at 11:17 AM, giacsport at libero.it wrote: nosym= 'true', Dear Giacomo,nosym=.true. is not the same as nosym='true' best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatzwww: http://www-int.impmc.upmc.fr/~paulatto/mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120531/8a43ff05/attachment.htm From giannozz at democritos.it Thu May 31 16:09:54 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 31 May 2012 16:09:54 +0200 Subject: [Pw_forum] R: Re: NOSYM tag + atomization energy In-Reply-To: <22004421.4006831338461971984.JavaMail.defaultUser@defaultHost> References: <22004421.4006831338461971984.JavaMail.defaultUser@defaultHost> Message-ID: <1338473394.26664.1.camel@fe12lx.fisica.uniud.it> The atom should be spin-polarized. You should either set the occupancies or break the symmetry with starting_magnetization P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 31 16:18:36 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 31 May 2012 16:18:36 +0200 Subject: [Pw_forum] erroe in compilation Espresso-5.0 In-Reply-To: <1338455306.17612.YahooMailClassic@web140604.mail.bf1.yahoo.com> References: <1338455306.17612.YahooMailClassic@web140604.mail.bf1.yahoo.com> Message-ID: <1338473916.26664.9.camel@fe12lx.fisica.uniud.it> The error you have is NOT a compilation error: it is an error at the linking stage, apparently related to openmpi and blacs. The following comment in configure.ac may be useful: # If you want to use the version of scalapack distributed with MKL # you should be careful about: # 1) the size of the integer variable when calling MKL subroutine, # QE (up to now) uses integer*4, so you should link version with # the suffix: lp64 and NOT ilp64 . # 2) you should link the appropriate blacs for your MPI library: # INTEL MPI -> libmkl_blacs_intelmpi_lp64.a # OpenMPI -> libmkl_blacs_openmpi_lp64.a # SGI MPI -> libmkl_blacs_sgimpt_lp64.a P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu May 31 22:05:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 31 May 2012 22:05:39 +0200 Subject: [Pw_forum] problem with chdens with ibrav=0 In-Reply-To: <4FC5F216.1030409@mater.unimib.it> References: <4FC5F216.1030409@mater.unimib.it> Message-ID: <7BF3D4AA-145F-46C7-AB7F-F9F9E953405E@democritos.it> On May 30, 2012, at 12:10 , Guido Fratesi wrote: > By removing the check the code produces the results expected, > yet this is not *the* solution. "the" solution is a little bit complex to implement; an approximate solution is to remove the check if ibrav=0 (done in development version). Thank you for reporting this P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222