From fenghongjian at ss.buaa.edu.cn Thu Aug 2 05:49:14 2007 From: fenghongjian at ss.buaa.edu.cn (fenghongjian) Date: Thu, 2 Aug 2007 11:49:14 +0800 Subject: [Pw_forum] BiFeO3 problem Message-ID: <200708021149027344439@ss.buaa.edu.cn> Dear PWSCF users, I'm trying to calculate the electronic properties of rhombohedral BiFeO3 under R3C symmetry group. The wychoff position is Bi(2b)(0 0 0),Fe(2a)(0.221 0.221 0.221),O(6e)(0.538 0.933 0.395), hence under R3C group symmetry the atomic position should be Bi 0.00000 0.00000 0.00000 Bi 0.50000 0.50000 0.50000 Fe 0.22100 0.22100 0.22100 Fe 0.72100 0.72100 0.72100 O 0.53800 0.93300 0.39500 O 0.39500 0.53800 0.93300 O 0.93300 0.39500 0.53800 O 1.43300 1.03800 0.89500 O 1.03800 0.89500 1.43300 O 0.89500 1.43300 1.03800 When I set the ATOMIC_POSITIONS in alat unit the code gave no symmetry, and the code produced wrong symmertry ( not R3c group) with the ATOMIC_POSITIONS in crystal unit. Acturally in crystal unit the triplet coordinates should be less than 1, but in my case the 1.433 was obviously wrong, but O(6e)(0.538 0.933 0.395) under R3C will definitely produce the value above. I have encountered this problem for a long time, could anyone point the wrong place in my case? Any sugestions will be very appreciated. My input file was pasted below: &control calculation='scf' restart_mode='from_scratch', verbosity='high', prefix='bifo', pseudo_dir='./', outdir='./' / &system ibrav= 5, celldm(1)= 10.6427, celldm(4)= 0.5, nat= 10, ntyp= 3, ecutwfc=35.0 occupations = 'fixed' degauss=0.00 nbnd=100 lda_plus_u=.true. Hubbard_U(2)=5, nspin=2,multiplicity=5, / &electrons mixing_beta=0.3, diagonalization='cg' / ATOMIC_SPECIES Bi 208.98 Bi.pbe-d-mt.UPF Fe 55.847 Fe.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS {alat} Bi 0.00000 0.00000 0.00000 Bi 0.50000 0.50000 0.50000 Fe 0.22100 0.22100 0.22100 Fe 0.72100 0.72100 0.72100 O 0.53800 0.93300 0.39500 O 0.39500 0.53800 0.93300 O 0.93300 0.39500 0.53800 O 1.43300 1.03800 0.89500 O 1.03800 0.89500 1.43300 O 0.89500 1.43300 1.03800 K_POINTS {automatic} 8 8 8 0 0 0 Best Regards, Hongkien Feng Physics department, Beijing university of aeronautics and astronautics fenghongjian 2007-08-02 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070802/635b3441/attachment.htm From jameslipd at gmail.com Thu Aug 2 07:29:30 2007 From: jameslipd at gmail.com (Jiaye, Li) Date: Thu, 2 Aug 2007 13:29:30 +0800 Subject: [Pw_forum] Se pseudopotential Message-ID: Dear all I am seeking for a Se pseudopotential with PBE functional. And the core treatment and the relativity effect should be considered. Will anyone send me a copy? Thanks in advance. -- Sincerely J.Li ============================================== Li, Jiaye Graduate Student(China University of Geosciences, China) Interest and Field of Research: Computational Chemistry; Quantum Chemistry; Reserved mail Address: jameslibd at gmail.com QQ: 690559321 ============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070802/7bd0db8b/attachment.htm From ding at sissa.it Thu Aug 2 16:39:13 2007 From: ding at sissa.it (Xunlei Ding) Date: Thu, 02 Aug 2007 16:39:13 +0200 Subject: [Pw_forum] BiFeO3 problem In-Reply-To: <200708021149027344439@ss.buaa.edu.cn> References: <200708021149027344439@ss.buaa.edu.cn> Message-ID: <46B1EC91.5080608@sissa.it> Hi, Feng, In crystal unit, 1.433 equals to 0.433. So that's not the reason for your problem. And just setting the unit to "alat" is totally wrong. My suggestion is to use xcrysden to check the structure to see whether it is the same as you thought. Hope you will find the correct structure. Best regards, Ding fenghongjian wrote: > Dear PWSCF users, > I'm trying to calculate the electronic properties of rhombohedral > BiFeO3 under R3C > symmetry group. The wychoff position is Bi(2b)(0 0 0),Fe(2a)(0.221 > 0.221 0.221),O(6e)(0.538 > 0.933 0.395), hence under R3C group symmetry the atomic position should be > Bi 0.00000 0.00000 0.00000 > Bi 0.50000 0.50000 0.50000 > Fe 0.22100 0.22100 0.22100 > Fe 0.72100 0.72100 0.72100 > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 > When I set the ATOMIC_POSITIONS in alat unit the code gave no > symmetry, and the code > produced wrong symmertry ( not R3c group) with the ATOMIC_POSITIONS in > crystal unit. > Acturally in crystal unit the triplet coordinates should be less than > 1, but in my case the > 1.433 was obviously wrong, but O(6e)(0.538 0.933 0.395) under R3C will > definitely produce > the value above. I have encountered this problem for a long time, > could anyone point the > wrong place in my case? Any sugestions will be very appreciated. > My input file was pasted below: > &control > calculation='scf' > restart_mode='from_scratch', > verbosity='high', > prefix='bifo', > pseudo_dir='./', > outdir='./' > / > &system > ibrav= 5, celldm(1)= 10.6427, celldm(4)= 0.5, nat= 10, ntyp= 3, > ecutwfc=35.0 > occupations = 'fixed' > degauss=0.00 > nbnd=100 > lda_plus_u=.true. Hubbard_U(2)=5, > nspin=2,multiplicity=5, > / > &electrons > mixing_beta=0.3, > diagonalization='cg' > / > ATOMIC_SPECIES > Bi 208.98 Bi.pbe-d-mt.UPF > Fe 55.847 Fe.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS {alat} > Bi 0.00000 0.00000 0.00000 > Bi 0.50000 0.50000 0.50000 > Fe 0.22100 0.22100 0.22100 > Fe 0.72100 0.72100 0.72100 > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 > K_POINTS {automatic} > 8 8 8 0 0 0 > Best Regards, > > Hongkien Feng > Physics department, > Beijing university of > aeronautics and astronautics > ------------------------------------------------------------------------ > fenghongjian > 2007-08-02 > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at nest.sns.it Thu Aug 2 16:46:10 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 2 Aug 2007 16:46:10 +0200 Subject: [Pw_forum] BiFeO3 problem In-Reply-To: <200708021149027344439@ss.buaa.edu.cn> References: <200708021149027344439@ss.buaa.edu.cn> Message-ID: <3803BEF7-5CAB-455C-BA0E-369C17DC9BDD@nest.sns.it> On Aug 2, 2007, at 5:49 , fenghongjian wrote: > I'm trying to calculate the electronic properties of rhombohedral > BiFeO3 under R3C symmetry group. The wychoff position Wyckoff? these notes may be useful: http://www.vlab.msi.umn.edu/events/download/tutorial_wyckoff.pdf In crystallography books, atomic positions are typically given in crystal axis, but these may not be the same axis as those used by Q-E. The latter are described in detail in the INPUT_PW file. (anybody willing to convert crystal axis of Q-E to those used by the Wyckoff book is encouraged: a single routine, flib/latgen.f90, needs to be modified) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From fenghongjian at ss.buaa.edu.cn Fri Aug 3 06:50:11 2007 From: fenghongjian at ss.buaa.edu.cn (fenghongjian) Date: Fri, 3 Aug 2007 12:50:11 +0800 Subject: [Pw_forum] BiFeO3 problem References: <200708021149027344439@ss.buaa.edu.cn>, <46B1EC91.5080608@sissa.it> Message-ID: <200708031250027359905@ss.buaa.edu.cn> Dear Ding, Thank you very much, I have always visualized the structure using xcrsyden, the structure seems to be right. But the pwscf always could not find the right symmetry group(namely R3C), I am afraid that the input position is not appropriate in some place, unfortunately I couldn't find it so far. You mean the coordinates should subtract 1 from the original value when it's value exceed 1 in the crystal unit, that is to say the positon is displaced by one unit basis vector. So the same reason the 1.038 is equal to 0.038 in the crystal scheme. Am I right? Best regards Hongkien Feng Physics department, Beijing university of aeronautics and astronautics fenghongjian 2007-08-03 ???? Xunlei Ding ????? 2007-08-03 04:00:20 ???? PWSCF Forum ??? ??? Re: [Pw_forum] BiFeO3 problem Hi, Feng, In crystal unit, 1.433 equals to 0.433. So that's not the reason for your problem. And just setting the unit to "alat" is totally wrong. My suggestion is to use xcrysden to check the structure to see whether it is the same as you thought. Hope you will find the correct structure. Best regards, Ding fenghongjian wrote: > Dear PWSCF users, > I'm trying to calculate the electronic properties of rhombohedral > BiFeO3 under R3C > symmetry group. The wychoff position is Bi(2b)(0 0 0),Fe(2a)(0.221 > 0.221 0.221),O(6e)(0.538 > 0.933 0.395), hence under R3C group symmetry the atomic position should be > Bi 0.00000 0.00000 0.00000 > Bi 0.50000 0.50000 0.50000 > Fe 0.22100 0.22100 0.22100 > Fe 0.72100 0.72100 0.72100 > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 > When I set the ATOMIC_POSITIONS in alat unit the code gave no > symmetry, and the code > produced wrong symmertry ( not R3c group) with the ATOMIC_POSITIONS in > crystal unit. > Acturally in crystal unit the triplet coordinates should be less than > 1, but in my case the > 1.433 was obviously wrong, but O(6e)(0.538 0.933 0.395) under R3C will > definitely produce > the value above. I have encountered this problem for a long time, > could anyone point the > wrong place in my case? Any sugestions will be very appreciated. > My input file was pasted below: > &control > calculation='scf' > restart_mode='from_scratch', > verbosity='high', > prefix='bifo', > pseudo_dir='./', > outdir='./' > / > &system > ibrav= 5, celldm(1)= 10.6427, celldm(4)= 0.5, nat= 10, ntyp= 3, > ecutwfc=35.0 > occupations = 'fixed' > degauss=0.00 > nbnd=100 > lda_plus_u=.true. Hubbard_U(2)=5, > nspin=2,multiplicity=5, > / > &electrons > mixing_beta=0.3, > diagonalization='cg' > / > ATOMIC_SPECIES > Bi 208.98 Bi.pbe-d-mt.UPF > Fe 55.847 Fe.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS {alat} > Bi 0.00000 0.00000 0.00000 > Bi 0.50000 0.50000 0.50000 > Fe 0.22100 0.22100 0.22100 > Fe 0.72100 0.72100 0.72100 > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 > K_POINTS {automatic} > 8 8 8 0 0 0 > Best Regards, > > Hongkien Feng > Physics department, > Beijing university of > aeronautics and astronautics > ------------------------------------------------------------------------ > fenghongjian > 2007-08-02 > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070803/d047a02b/attachment.htm From ding at sissa.it Fri Aug 3 10:15:23 2007 From: ding at sissa.it (Xunlei Ding) Date: Fri, 03 Aug 2007 10:15:23 +0200 Subject: [Pw_forum] BiFeO3 problem In-Reply-To: <200708031250027359905@ss.buaa.edu.cn> References: <200708021149027344439@ss.buaa.edu.cn>, <46B1EC91.5080608@sissa.it> <200708031250027359905@ss.buaa.edu.cn> Message-ID: <46B2E41B.60109@sissa.it> Dear Feng, There is no difference whether you input 1.038 or 0.038. You can try it by using xcrysden to see the structure. Now your structrue is: > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 But why not: O 0.53800 0.93300 0.39500 O 0.39500 0.53800 0.93300 O 0.93300 0.39500 0.53800 O 1.03800 1.43300 0.89500 O 0.89500 1.03800 1.43300 O 1.43300 0.89500 1.03800 I am not familar with BiFeO3 and R3c. So I am not sure about that. Another question is: whether R3c symmetry is included in PWSCF, or whether "c" can be recognized by PWSCF. Best regards, Ding fenghongjian wrote: > Dear Ding, > Thank you very much, I have always visualized the structure using > xcrsyden, the structure seems to be right. But the pwscf always could > not find the right symmetry group(namely R3C), I am afraid that the > input position is not appropriate in some place, unfortunately I > couldn't find it so far. You mean the coordinates should subtract 1 > from the original value when it's value exceed 1 in the crystal unit, > that is to say the positon is displaced by one unit basis vector. So > the same reason the 1.038 is equal to 0.038 in the crystal scheme. Am > I right? > Best regards > Hongkien Feng > Physics department, > Beijing university of > aeronautics and astronautics > ------------------------------------------------------------------------ > fenghongjian > 2007-08-03 > ------------------------------------------------------------------------ > *????* Xunlei Ding > *?????* 2007-08-03 04:00:20 > *????* PWSCF Forum > *???* > *???* Re: [Pw_forum] BiFeO3 problem > Hi, Feng, > In crystal unit, 1.433 equals to 0.433. So that's not the reason for > your problem. > And just setting the unit to "alat" is totally wrong. > My suggestion is to use xcrysden to check the structure to see whether > it is the same as you thought. > Hope you will find the correct structure. > Best regards, > Ding > fenghongjian wrote: > > Dear PWSCF users, > > I'm trying to calculate the electronic properties of rhombohedral > > BiFeO3 under R3C > > symmetry group. The wychoff position is Bi(2b)(0 0 0),Fe(2a)(0.221 > > 0.221 0.221),O(6e)(0.538 > > 0.933 0.395), hence under R3C group symmetry the atomic position > should be > > Bi 0.00000 0.00000 0.00000 > > Bi 0.50000 0.50000 0.50000 > > Fe 0.22100 0.22100 0.22100 > > Fe 0.72100 0.72100 0.72100 > > O 0.53800 0.93300 0.39500 > > O 0.39500 0.53800 0.93300 > > O 0.93300 0.39500 0.53800 > > O 1.43300 1.03800 0.89500 > > O 1.03800 0.89500 1.43300 > > O 0.89500 1.43300 1.03800 > > When I set the ATOMIC_POSITIONS in alat unit the code gave no > > symmetry, and the code > > produced wrong symmertry ( not R3c group) with the ATOMIC_POSITIONS in > > crystal unit. > > Acturally in crystal unit the triplet coordinates should be less than > > 1, but in my case the > > 1.433 was obviously wrong, but O(6e)(0.538 0.933 0.395) under R3C will > > definitely produce > > the value above. I have encountered this problem for a long time, > > could anyone point the > > wrong place in my case? Any sugestions will be very appreciated. > > My input file was pasted below: > > &control > > calculation='scf' > > restart_mode='from_scratch', > > verbosity='high', > > prefix='bifo', > > pseudo_dir='./', > > outdir='./' > > / > > &system > > ibrav= 5, celldm(1)= 10.6427, celldm(4)= 0.5, nat= 10, ntyp= 3, > > ecutwfc=35.0 > > occupations = 'fixed' > > degauss=0.00 > > nbnd=100 > > lda_plus_u=.true. Hubbard_U(2)=5, > > nspin=2,multiplicity=5, > > / > > &electrons > > mixing_beta=0.3, > > diagonalization='cg' > > / > > ATOMIC_SPECIES > > Bi 208.98 Bi.pbe-d-mt.UPF > > Fe 55.847 Fe.pbe-sp-van_ak.UPF > > O 15.999 O.pbe-van_ak.UPF > > ATOMIC_POSITIONS {alat} > > Bi 0.00000 0.00000 0.00000 > > Bi 0.50000 0.50000 0.50000 > > Fe 0.22100 0.22100 0.22100 > > Fe 0.72100 0.72100 0.72100 > > O 0.53800 0.93300 0.39500 > > O 0.39500 0.53800 0.93300 > > O 0.93300 0.39500 0.53800 > > O 1.43300 1.03800 0.89500 > > O 1.03800 0.89500 1.43300 > > O 0.89500 1.43300 1.03800 > > K_POINTS {automatic} > > 8 8 8 0 0 0 > > Best Regards, > > > > Hongkien Feng > > Physics department, > > Beijing university of > > aeronautics and astronautics > > ------------------------------------------------------------------------ > > fenghongjian > > 2007-08-02 > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at nest.sns.it Fri Aug 3 11:20:43 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 3 Aug 2007 11:20:43 +0200 Subject: [Pw_forum] BiFeO3 problem In-Reply-To: <46B2E41B.60109@sissa.it> References: <200708021149027344439@ss.buaa.edu.cn>, <46B1EC91.5080608@sissa.it> <200708031250027359905@ss.buaa.edu.cn> <46B2E41B.60109@sissa.it> Message-ID: <5856BD20-B40D-4642-9173-780BC0C9C940@nest.sns.it> On Aug 3, 2007, at 10:15 , Xunlei Ding wrote: > Another question is: whether R3c symmetry is included in PWSCF, > or whether "c" can be recognized by PWSCF. ALL point symmetries that are relevant for periodic systems are included in PWscf. PWscf may not be able to recognize a given point group and to assign the correct label, but this has no effect on the final results. PWscf will find all point symmetries that are there. If it doesn't find them, it is because they are not there. BiFeO3 should have the same structure as LiNbO3: http://cst-www.nrl.navy.mil/lattice/struk/LiNbO3f.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From fenghongjian at ss.buaa.edu.cn Fri Aug 3 13:56:04 2007 From: fenghongjian at ss.buaa.edu.cn (fenghongjian) Date: Fri, 3 Aug 2007 19:56:04 +0800 Subject: [Pw_forum] BiFeO3 problem References: <200708021149027344439@ss.buaa.edu.cn>, <46B1EC91.5080608@sissa.it>, <200708031250027359905@ss.buaa.edu.cn>, <46B2E41B.60109@sissa.it> Message-ID: <200708031955509015392@ss.buaa.edu.cn> Dear Ding, Under R3c (x y z, z x y, y z x, y+1/2 x+1/2 z+1/2, x+1/2 z+1/2 y+1/2, z+1/2 y+1/2 x+1/2 with considering the 60 degree of rotation), Therefore the position {O(6e)(0.538 0.933 0.395) }should be > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 Thank you for your kindly discussion. Best regards Hongkien Feng fenghongjian 2007-08-03 ???? Xunlei Ding ????? 2007-08-03 16:39:48 ???? PWSCF Forum ??? ??? Re: [Pw_forum] BiFeO3 problem Dear Feng, There is no difference whether you input 1.038 or 0.038. You can try it by using xcrysden to see the structure. Now your structrue is: > O 0.53800 0.93300 0.39500 > O 0.39500 0.53800 0.93300 > O 0.93300 0.39500 0.53800 > O 1.43300 1.03800 0.89500 > O 1.03800 0.89500 1.43300 > O 0.89500 1.43300 1.03800 But why not: O 0.53800 0.93300 0.39500 O 0.39500 0.53800 0.93300 O 0.93300 0.39500 0.53800 O 1.03800 1.43300 0.89500 O 0.89500 1.03800 1.43300 O 1.43300 0.89500 1.03800 I am not familar with BiFeO3 and R3c. So I am not sure about that. Another question is: whether R3c symmetry is included in PWSCF, or whether "c" can be recognized by PWSCF. Best regards, Ding fenghongjian wrote: > Dear Ding, > Thank you very much, I have always visualized the structure using > xcrsyden, the structure seems to be right. But the pwscf always could > not find the right symmetry group(namely R3C), I am afraid that the > input position is not appropriate in some place, unfortunately I > couldn't find it so far. You mean the coordinates should subtract 1 > from the original value when it's value exceed 1 in the crystal unit, > that is to say the positon is displaced by one unit basis vector. So > the same reason the 1.038 is equal to 0.038 in the crystal scheme. Am > I right? > Best regards > Hongkien Feng > Physics department, > Beijing university of > aeronautics and astronautics > ------------------------------------------------------------------------ > fenghongjian > 2007-08-03 > ------------------------------------------------------------------------ > *????* Xunlei Ding > *?????* 2007-08-03 04:00:20 > *????* PWSCF Forum > *???* > *???* Re: [Pw_forum] BiFeO3 problem > Hi, Feng, > In crystal unit, 1.433 equals to 0.433. So that's not the reason for > your problem. > And just setting the unit to "alat" is totally wrong. > My suggestion is to use xcrysden to check the structure to see whether > it is the same as you thought. > Hope you will find the correct structure. > Best regards, > Ding > fenghongjian wrote: > > Dear PWSCF users, > > I'm trying to calculate the electronic properties of rhombohedral > > BiFeO3 under R3C > > symmetry group. The wychoff position is Bi(2b)(0 0 0),Fe(2a)(0.221 > > 0.221 0.221),O(6e)(0.538 > > 0.933 0.395), hence under R3C group symmetry the atomic position > should be > > Bi 0.00000 0.00000 0.00000 > > Bi 0.50000 0.50000 0.50000 > > Fe 0.22100 0.22100 0.22100 > > Fe 0.72100 0.72100 0.72100 > > O 0.53800 0.93300 0.39500 > > O 0.39500 0.53800 0.93300 > > O 0.93300 0.39500 0.53800 > > O 1.43300 1.03800 0.89500 > > O 1.03800 0.89500 1.43300 > > O 0.89500 1.43300 1.03800 > > When I set the ATOMIC_POSITIONS in alat unit the code gave no > > symmetry, and the code > > produced wrong symmertry ( not R3c group) with the ATOMIC_POSITIONS in > > crystal unit. > > Acturally in crystal unit the triplet coordinates should be less than > > 1, but in my case the > > 1.433 was obviously wrong, but O(6e)(0.538 0.933 0.395) under R3C will > > definitely produce > > the value above. I have encountered this problem for a long time, > > could anyone point the > > wrong place in my case? Any sugestions will be very appreciated. > > My input file was pasted below: > > &control > > calculation='scf' > > restart_mode='from_scratch', > > verbosity='high', > > prefix='bifo', > > pseudo_dir='./', > > outdir='./' > > / > > &system > > ibrav= 5, celldm(1)= 10.6427, celldm(4)= 0.5, nat= 10, ntyp= 3, > > ecutwfc=35.0 > > occupations = 'fixed' > > degauss=0.00 > > nbnd=100 > > lda_plus_u=.true. Hubbard_U(2)=5, > > nspin=2,multiplicity=5, > > / > > &electrons > > mixing_beta=0.3, > > diagonalization='cg' > > / > > ATOMIC_SPECIES > > Bi 208.98 Bi.pbe-d-mt.UPF > > Fe 55.847 Fe.pbe-sp-van_ak.UPF > > O 15.999 O.pbe-van_ak.UPF > > ATOMIC_POSITIONS {alat} > > Bi 0.00000 0.00000 0.00000 > > Bi 0.50000 0.50000 0.50000 > > Fe 0.22100 0.22100 0.22100 > > Fe 0.72100 0.72100 0.72100 > > O 0.53800 0.93300 0.39500 > > O 0.39500 0.53800 0.93300 > > O 0.93300 0.39500 0.53800 > > O 1.43300 1.03800 0.89500 > > O 1.03800 0.89500 1.43300 > > O 0.89500 1.43300 1.03800 > > K_POINTS {automatic} > > 8 8 8 0 0 0 > > Best Regards, > > > > Hongkien Feng > > Physics department, > > Beijing university of > > aeronautics and astronautics > > ------------------------------------------------------------------------ > > fenghongjian > > 2007-08-02 > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070803/f14d1bb0/attachment-0001.htm From fenghongjian at ss.buaa.edu.cn Fri Aug 3 14:07:30 2007 From: fenghongjian at ss.buaa.edu.cn (fenghongjian) Date: Fri, 3 Aug 2007 20:07:30 +0800 Subject: [Pw_forum] BiFeO3 problem References: <200708021149027344439@ss.buaa.edu.cn>, <46B1EC91.5080608@sissa.it>, <200708031250027359905@ss.buaa.edu.cn>, <46B2E41B.60109@sissa.it>, <5856BD20-B40D-4642-9173-780BC0C9C940@nest.sns.it> Message-ID: <200708032007216200691@ss.buaa.edu.cn> Dear Paolo Giannozzi, Thank you for your kindly reply, the information about wyckoff position is really helpful. You mean the point group might not be found by the Q-E with the right label, So we could disregard the label found in the output file, the program should give the right results as long as the atomic postion was created correctly under the specific point group. By the way,URL http://cst-www.nrl.navy.mil/lattice/struk/LiNbO3f.html could not be connected. Thank you again. Best regards Hongkien Feng fenghongjian 2007-08-03 ???? Paolo Giannozzi ????? 2007-08-03 17:39:42 ???? PWSCF Forum ??? ??? Re: [Pw_forum] BiFeO3 problem On Aug 3, 2007, at 10:15 , Xunlei Ding wrote: > Another question is: whether R3c symmetry is included in PWSCF, > or whether "c" can be recognized by PWSCF. ALL point symmetries that are relevant for periodic systems are included in PWscf. PWscf may not be able to recognize a given point group and to assign the correct label, but this has no effect on the final results. PWscf will find all point symmetries that are there. If it doesn't find them, it is because they are not there. BiFeO3 should have the same structure as LiNbO3: http://cst-www.nrl.navy.mil/lattice/struk/LiNbO3f.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070803/26a5f0ea/attachment.htm From ezadshojaee at hotmail.com Sat Aug 4 16:17:27 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Sat, 4 Aug 2007 14:17:27 +0000 Subject: [Pw_forum] problem with parallel ph.x Message-ID: Thanks for your time i want to know what may cause this problem? in the file you attached, the code generates for example 496 k_points for the second point in the grid, but in mine, it generates different #'s according to the # of npool, for example 276 for npool=2 (and also as you noticed, i get some anomalies). i have the same problem with other points in the grid, except Gamma. _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070804/aa5c7ec6/attachment.htm From giannozz at nest.sns.it Sat Aug 4 17:20:05 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 4 Aug 2007 17:20:05 +0200 Subject: [Pw_forum] problem with parallel ph.x In-Reply-To: References: Message-ID: <01356114-388F-4950-86A7-8E3D18545019@nest.sns.it> On Aug 4, 2007, at 16:17 , Ezad Shojaee wrote: > i want to know what may cause this problem? it is a known problem of version 3.2. There are two patches (*.diff files) on http://www.pwscf.org/download.htm that you should install. Assuming that espresso-3.2 is the root directory of the package: cd espresso-3.2/ patch -p1 < /path/to/the/diff/file/espresso-3.2.1.diff patch -p1 < /path/to/the/diff/file/espresso-3.2.2.diff (in this order!) I think you will need also the third one that is attached to this message. See ChangeLog.3.2.* . Of course you will have to recompile: "make ph" should take care of everything. -------------- next part -------------- A non-text attachment was scrubbed... Name: espresso-3.2.3.diff Type: application/octet-stream Size: 13672 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20070804/5dc539e7/attachment.obj -------------- next part -------------- Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From michaelv at Princeton.EDU Sun Aug 5 22:07:13 2007 From: michaelv at Princeton.EDU (Michael Vargas (michaelv@Princeton.EDU)) Date: Sun, 05 Aug 2007 16:07:13 -0400 Subject: [Pw_forum] Ultrasoft wavefunctions for all reference energies. Message-ID: Hello, I am trying to output the AE and US wavefunctions for all the reference energies. The file ld1.wfc only has the number of orbitals wavefunctions. Same thing with the US pseudo. If at all possible, I would like to have the wavefunctions for the first valence orbital, the first reference energy, the second reference energy, then the second valence orbital, the first reference energy.... and so on. i have tried printing them out right before the line "! For each angular momentum take the same integration point" in the file gener_pseudo.f90, but some of the functions seem to be unbound. I appreciate any help the group can give me. From kazempoor2000 at yahoo.com Mon Aug 6 17:01:34 2007 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Mon, 6 Aug 2007 08:01:34 -0700 (PDT) Subject: [Pw_forum] group Message-ID: <305861.12997.qm@web33108.mail.mud.yahoo.com> hi in starting for run the code take this error coset : error # 1 The order of the group is not a multiple of that of the subgroup. input file: &CONTROL title = MnAs , calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/scratch/akazempo/tmp/' , pseudo_dir = '/afs/ictp/home/a/akazempo/espresso-3.2/pseudo/' , prefix = MnAs , / &SYSTEM ibrav = 4, celldm(1) = 28.156 celldm(3)= 0.375337 nat = 8, ntyp = 2, ecutwfc = 30 , ecutrho = 400 , occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = 0.2, / &ELECTRONS electron_maxstep = 100, conv_thr = .00001 , / ATOMIC_SPECIES Mn 74.92000 Mn.PBE-VAN.UPF As 54.93000 As.pbe-n-van.UPF ATOMIC_POSITIONS crystal Mn 0.5 0.5 0.00000 Mn 0.5 0.5 0.5 As 0.583333 0.66666 0.25 As 0.583333 0.4166666 0.25 As 0.3333333 0.4166666 0.25 As 0.41666 0.5833333 0.75 As 0.66666 0.5833333 0.75 As 0.416666 0.3333333 0.75 K_POINTS automatic 2 2 6 1 1 1 ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz From giannozz at nest.sns.it Mon Aug 6 19:08:47 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 6 Aug 2007 19:08:47 +0200 Subject: [Pw_forum] group In-Reply-To: <305861.12997.qm@web33108.mail.mud.yahoo.com> References: <305861.12997.qm@web33108.mail.mud.yahoo.com> Message-ID: <2B54CFF2-B28A-4723-A055-69D10FEB2EE8@nest.sns.it> On Aug 6, 2007, at 17:01 , ali kazempoor wrote: > coset : error # 1 > The order of the group is not a multiple of that > of the subgroup. > input file: > > As 0.583333 0.66666 0.25 > As 0.583333 0.4166666 0.25 > As 0.3333333 0.4166666 0.25 > As 0.41666 0.5833333 0.75 > As 0.66666 0.5833333 0.75 > As 0.416666 0.3333333 0.75 use 6 significant digits everywhere: 0.66666=> 0.666666, 0.41666 = 0.416666 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From mitujoshi at gmail.com Fri Aug 10 08:21:17 2007 From: mitujoshi at gmail.com (Joshi Mitesh) Date: Fri, 10 Aug 2007 11:51:17 +0530 Subject: [Pw_forum] Charge density plot for AlAs Message-ID: Dear users, I am trying to learn how to plot the charge density in 2D and 3D, as given in exaple/example05/si example. I am using a simple example of AlAs, after scf calculation I run following PP.x input files, but output shows only one kind of atoms, How I can change that & how to visulize this in xcrysden cat > AlAs.pp_rho.in << EOF &inputpp prefix = 'AlAs' outdir = '/home/AlAs/Charge_Dens/' filplot = 'AlAscharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'AlAscharge' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'AlAs.rho.dat' e1(1) =0.0, e1(2)=1.0, e1(3) = 1.0, e2(1) =1.0, e2(2)=0.0, e2(3) = 0.0, nx=50, ny=30 / EOF $PW_ROOT/bin/pp.x < AlAs.pp_rho.in > AlAs.pp_rho.out ----------------------------------------------------------------------------------------------- Mitesh Joshi Department of Physics, S P University, Anand Gujarat India ------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070810/6a34c8bb/attachment.htm From fratesi at mater.unimib.it Fri Aug 10 10:14:55 2007 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Fri, 10 Aug 2007 10:14:55 +0200 (CEST) Subject: [Pw_forum] Charge density plot for AlAs In-Reply-To: References: Message-ID: Dear Joshi, you might want to specify the origin of the plane (vector x0). As it is now, the plane could possibly not intercept the other kind of atoms. (see Doc/INPUT_PP) I would suggest you to start with iflag=3 and output_format = 5 . This ignores all information about x0, e1, e2, e3, nx, ny, nz, and is quite fast. It generates an xcrysden file which you can see with xcrysden --xsf and you can then plot the charge along planes parallel to the cell faces. (see http://www.xcrysden.org/doc/density.html ) Then it should be even more easy to start playing and customizing. Have fun! Bye, Guido On Fri, 10 Aug 2007, Joshi Mitesh wrote: | Dear users, | I am trying to learn how to plot the charge density in 2D and 3D, as | given in exaple/example05/si example. | I am using a simple example of AlAs, after scf calculation I run following | PP.x input files, but output shows only one kind of atoms, | How I can change that & how to visulize this in xcrysden | | cat > AlAs.pp_rho.in << EOF | &inputpp | prefix = 'AlAs' | outdir = '/home/AlAs/Charge_Dens/' | filplot = 'AlAscharge' | plot_num= 0 | / | &plot | nfile = 1 | filepp(1) = 'AlAscharge' | weight(1) = 1.0 | iflag = 2 | output_format = 2 | fileout = 'AlAs.rho.dat' | e1(1) =0.0, e1(2)=1.0, e1(3) = 1.0, | e2(1) =1.0, e2(2)=0.0, e2(3) = 0.0, | nx=50, ny=30 | / | EOF | | $PW_ROOT/bin/pp.x < AlAs.pp_rho.in > AlAs.pp_rho.out | | ----------------------------------------------------------------------------------------------- | Mitesh Joshi | Department of Physics, | S P University, Anand Gujarat India | ------------------------------------------------------------------------------------------------ | -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From lawrence_lee_lee at yahoo.com.hk Fri Aug 10 15:28:13 2007 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Fri, 10 Aug 2007 21:28:13 +0800 (CST) Subject: [Pw_forum] Very large value of temperature at the beginning of a nose thrmostat run Message-ID: <493149.70972.qm@web54506.mail.re2.yahoo.com> Dear all, I am a newbie in using cp.x of the espresso package. I have a some problems concerning the use of nose thermostat in temperature control. First I do an electronic and ionic minimization on my system. And finally the output file said convergence has been achieved. Then I restart from this to make a 3000K run. Problem then emerge: when I looked at the cp.evp file, I found that the temperature has been so much higher than 3000K at some steps near the beginning (~0.079 ps to 0.089 ps, ie, 272 to 307 steps as I use dt =12), so high that the value is ****** (>10000K). However, after some 0.5 ps, the value stabilized, and fluctuating about 3000K with amplitude about a few hundred K. Other quantites after that about 0.5 ps all look fine, but that intermediate steps with very high temperature worries me. In fact, does it matter? Lawrence Lee Shun Hang MPhil student of the Chinese University of Hong Kong tel: 852-61094093 --------------------------------- ??Yahoo! Mail ???????????????????!???? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070810/a64ac275/attachment.htm From akohlmey at cmm.chem.upenn.edu Fri Aug 10 15:29:22 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 10 Aug 2007 09:29:22 -0400 (EDT) Subject: [Pw_forum] Very large value of temperature at the beginning of a nose thrmostat run In-Reply-To: <493149.70972.qm@web54506.mail.re2.yahoo.com> Message-ID: On Fri, 10 Aug 2007, Lawrence Lee wrote: LL> Dear all, dear lawrence, LL> I am a newbie in using cp.x of the espresso package. I have a some LL> problems concerning the use of nose thermostat in temperature LL> control. LL> First I do an electronic and ionic minimization on my system. And LL> finally the output file said convergence has been achieved. Then I LL> restart from this to make a 3000K run. LL> Problem then emerge: when I looked at the cp.evp file, I found that LL> the temperature has been so much higher than 3000K at some steps LL> near the beginning (~0.079 ps to 0.089 ps, ie, 272 to 307 steps as I LL> use dt =12), so high that the value is ****** (>10000K). However, LL> after some 0.5 ps, the value stabilized, and fluctuating about 3000K LL> with amplitude about a few hundred K. possibly you have started from a structure that was only a local minimum with respect to a 3000K system and/or seen a phase transition. it also is possible that your simulation has gone completely wrong. what are the values for the fictitious kinetic energy? what happens if you run born-oppenheimer (cg as electron dynamics)? does the structure look like what you would expect? does some published data from simulations on your system exist or for something similar? can you reproduce that? there are other possible sources of problems, that can only be seen from the input and relevant parts of the output. right now, all we can do is 'fish in the dark'. cheers, axel. LL> Other quantites after that about 0.5 ps all look fine, but that LL> intermediate steps with very high temperature worries me. In fact, LL> does it matter? LL> Lawrence Lee Shun Hang LL> MPhil student of the Chinese University of Hong Kong LL> tel: 852-61094093 LL> LL> LL> --------------------------------- LL> ????Yahoo! Mail ?L???q?l?x?s?q?A???o?U?h?A???A?L??????!???Y???? -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shruba at gmail.com Fri Aug 10 18:08:59 2007 From: shruba at gmail.com (shruba at gmail.com) Date: Fri, 10 Aug 2007 12:08:59 -0400 Subject: [Pw_forum] convergence not achived Message-ID: <822f4ec80708100908r17d9dc5asc8ea42aa4ecc854a@mail.gmail.com> Hi All, I am facing convergence problem, described in manual ''A typical sign of such behavior is that ,the self-consistency error goes down, down, down, than all of a sudden up again, and so on' it is a perovskite system SrCoO3 which is (2 x 2 x2) unit . I am using ultrasoft pseudopotential, I tried all the option described in manual, it was working for (1 x1 x1) unit before but for 2 x2x2 is is not converging , Here is my sample input, &CONTROL calculation = 'scf', restart_mode = 'from_scratch', tstress = .TRUE., tprnfor = .TRUE., prefix = '710d', pseudo_dir = outdir= / &SYSTEM ibrav = 1, celldm(1) = 14.2 nat =40, ntyp =3, ecutwfc = 45, ecutrho = 360, nspin=2, multiplicity=9, nbnd=364, occupations = 'smearing', smearing ='marzari-vanderbilt', degauss=0.04, / &ELECTRONS electron_maxstep =400, emass =1000.d0, emass_cutoff = 4.d0, orthogonalization = 'Gram-Schmidt', startingwfc ='atomic', n_inner = 8, tcg = .TRUE., passop=0.3, maxiter = 250, conv_thr=1.d-6, mixing_mode='local-TF' mixing_beta=0.1 / ATOMIC_SPECIES ......................................... ATOMIC_POSITIONS ................................. K_POINTS {automatic} 2 2 2 1 1 1 If anyone can give me hints to fix this problem, that will be great. Thanks in advance Shruba Gangopadhyay -- shruba gangopadhyay graduate student department of chemistry university of central florida orlando, FL-32826 'friendship doubles joys and reduces sorrows by half' (Francis Bacon). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070810/4878de1a/attachment.htm From xueyusally at hotmail.com Sat Aug 11 17:07:03 2007 From: xueyusally at hotmail.com (Yu Xue) Date: Sat, 11 Aug 2007 15:07:03 +0000 Subject: [Pw_forum] Hubbard U of Zn in ZnO Message-ID: Hello,all, I am trying to use LDA+U to do some calculations on ZnO. First,I need to decide Hubbard U of Zn in the scheme of Dr.Cococcioni,see PRB 71,035105(2005)-----(*) Everything looks good,just the result is unreasonable: d(alpha)/d(n)=-440.3838054 eV d(alpha_0)/d(n_0)= -2.2765143 eV U=(-d(alpha)/d(n))-(-d(alpha_0)/d(n_0))=2.2765143-440.3838054=-438.1072911 eV In Shujun Hu's paper,PRB 73, 245205(2006),he mentioned that "The method mentioned above is invalid to gain the Hubbard Uzn since diagonal elements indicating the Zn sites in Eq(19) of (*) are close to zero due to fully occupying of Zn 3d states. " So he uses Uzn as a fitting parameter.I don't quite understand that,and wonder,then we can't use constrained-density-functional and linear response scheme to calculate Hubbard U of Zn?Do we have some tricks to gain Uzn using this scheme? I appreciate any suggestions from you Thanks a lot Sally _________________________________________________________________ Puzzles, trivia teasers, word scrambles and more. Play for your chance to win! http://club.live.com/home.aspx?icid=CLUB_hotmailtextlink From matteo at umn.edu Sat Aug 11 19:28:37 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: Sat, 11 Aug 2007 12:28:37 -0500 Subject: [Pw_forum] Hubbard U of Zn in ZnO In-Reply-To: References: Message-ID: <46BDF1C5.2020704@umn.edu> Hi, Yu Xue wrote: > Hello,all, > > I am trying to use LDA+U to do some calculations on ZnO. > First,I need to decide Hubbard U of Zn in the scheme of Dr.Cococcioni,see > PRB 71,035105(2005)-----(*) > Everything looks good,just the result is unreasonable: > > what is that looks good then? > d(alpha)/d(n)=-440.3838054 eV > d(alpha_0)/d(n_0)= -2.2765143 eV > U=(-d(alpha)/d(n))-(-d(alpha_0)/d(n_0))=2.2765143-440.3838054=-438.1072911 > eV > > You seem to be inverting just two diagonal element of the response matrices dn^I/dalpha^J or dn_0^I/dalpha^J instead of taking the diagonal element of the difference between their inverses as the method above says. Also the difference between the two numbers is very large and sounds wrong to me. Are you sure: 1) your calculation is well converged (cut offs, smearing, k-points etc)? 2) you are using a big enough supercell? 3) when you run the perturbed calculations (with alpha =/= 0) you are setting diago_thr_init to a value close or smaller to the last ethr of the unperturbed scf calculation of which you read converged wavefunctions and potential? If you are sure of all this and your results still look unreasonable (because Zn has filled d bands) then you may try to use alpha values that are not centered in zero but around a small positive value x. This means you run a well converged scf calculation with the alpha on one Zn atom fixed at value of x then, starting from converged wfcs and potential you run perturbed calculations with Hubbard_alpha on the same Zn equal to x+0.01, x-0.01 x+0.02 x-0.02 x+0.05 x-0.05 etc etc. You should find a more stable number. Then maybe you can study the convergence of this number (the U) with x --> 0) > In Shujun Hu's paper,PRB 73, 245205(2006),he mentioned that "The method > mentioned above is invalid to gain the Hubbard Uzn since diagonal elements > indicating the Zn sites in Eq(19) of (*) are close to zero due to fully > occupying of Zn 3d states. " That U is close to 0 is not totally unreasonable because the d bands are full and you don't need to do much to encourage their occupation to be 1. > So he uses Uzn as a fitting parameter.I don't > quite understand that,and wonder,then we can't use > constrained-density-functional and linear response scheme to calculate > Hubbard U of Zn?Do we have some tricks to gain Uzn using this scheme? > > I don't understand either. In the sense that either you want to fit a value for U to a specific property and use it in your "non ab-initio" calculations, or you want to do everything "ab-initio". That was the reason why we tried to compute U. Probably it's not a perfect method, but it's not fitting. Also beware that U varies a lot when you change pseudopotential, if you distort the unit cell etc. So there is not a universal value to be used and keep in mind it is a correction whose strength depends on what you want to corerect. If you believe in the ab-initio way you should compare instead your results with experiments or more refined calculations. That will tell you about the quality of your calculations. Not the value of U itself, how close it is to 0 or to any other fitted value. Our linear response should be equivalent to a constraint DFT calculation. you could actually use the response matrices to learn how to constraint your system in such a way that only one atomic occupation changes. Hope this helps. Let us know. > I appreciate any suggestions from you > and the forum would appreciate to know more about you and your affiliation. Thanks. Matteo > Thanks a lot > > Sally > > _________________________________________________________________ > Puzzles, trivia teasers, word scrambles and more. Play for your chance to > win! http://club.live.com/home.aspx?icid=CLUB_hotmailtextlink > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... Name: matteo.vcf Type: text/x-vcard Size: 294 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20070811/d93a8584/attachment.vcf From brsahu at physics.utexas.edu Sun Aug 12 18:18:55 2007 From: brsahu at physics.utexas.edu (Bhagawan Sahu) Date: Sun, 12 Aug 2007 11:18:55 -0500 (CDT) Subject: [Pw_forum] restart problem Message-ID: Dear pwscfusers, I am getting the following error in a SCF restart run. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Forces acting on atoms (Ry/au): %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This happens when I restart the ionic relaxation calculation from a non-converged job (did not change anything in the input except restart_mode= 'restart'). The non-converged job had &control calculation='relax' restart_mode='from_scratch' which was changed to &control calculation='relax' restart_mode='restart', for restarting from the previous run. Is there a bug in the restart routine? Pl. note the same code compiled on POWER5 (IBM) machine do not have such restart problem. Sahu From brsahu at physics.utexas.edu Sun Aug 12 18:26:29 2007 From: brsahu at physics.utexas.edu (Bhagawan Sahu) Date: Sun, 12 Aug 2007 11:26:29 -0500 (CDT) Subject: [Pw_forum] restart problem (fwd) Message-ID: Dear pwscfusers, I forgot to tell you that the machine where the latest code (v.3.2) is compiled is a linux cluster running intel/9 fortran compiler and MKL/8.1.1 library. Also in the /tmp directory, the subdirctory file.save is created and the data files are written on to it. Sahu ---------- Forwarded message ---------- Date: Sun, 12 Aug 2007 11:18:55 -0500 (CDT) From: Bhagawan Sahu Reply-To: PWSCF Forum To: pw_forum at pwscf.org Subject: [Pw_forum] restart problem Dear pwscfusers, I am getting the following error in a SCF restart run. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Forces acting on atoms (Ry/au): %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 1 can't open a connected unit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This happens when I restart the ionic relaxation calculation from a non-converged job (did not change anything in the input except restart_mode= 'restart'). The non-converged job had &control calculation='relax' restart_mode='from_scratch' which was changed to &control calculation='relax' restart_mode='restart', for restarting from the previous run. Is there a bug in the restart routine? Pl. note the same code compiled on POWER5 (IBM) machine do not have such restart problem. Sahu _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From clie at aphy.iphy.ac.cn Mon Aug 13 05:42:11 2007 From: clie at aphy.iphy.ac.cn (clie) Date: Mon, 13 Aug 2007 03:42:11 GMT Subject: [Pw_forum] How to get the phonon frequency logarithmic average In-Reply-To: References: Message-ID: <20070813034211.22406.eqmail@aphy.iphy.ac.cn> Dear users, recently, i use pwscf to caliculate electron-phonon couple constance, but i want to get Tc and i need the phonon frequency logarithmic average. Could you tell me how to get the value? Thanks very much. From jhashemifar at gmail.com Mon Aug 13 09:47:59 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Mon, 13 Aug 2007 09:47:59 +0200 Subject: [Pw_forum] partial DOS Message-ID: <2fb18d9f0708130047pa8134f6nce450af52bf6a48b@mail.gmail.com> Dear PWscf users I am using program projwfc.x to calculate partial d DOS. This program splits orbital d according to the spherical quantum numbers m and generates five partial d DOS corresponding to m=+2 m=+1 .... m=-2 . But a more common way of splitting d (at least in solid state) is using the Cartesian components dz2 d(x2-y2) dxy dxz and dyz. Is it possible to calculate the Cartesian partial d DOS from the spherical components of d generated by projwfc.x ? The dz2 orbital obviously is equal to m=0 components of d but what about other Cartesian components. Thanks in advance Kind regards Javad Hashemifar ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From giannozz at nest.sns.it Mon Aug 13 10:13:11 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 13 Aug 2007 10:13:11 +0200 Subject: [Pw_forum] partial DOS In-Reply-To: <2fb18d9f0708130047pa8134f6nce450af52bf6a48b@mail.gmail.com> References: <2fb18d9f0708130047pa8134f6nce450af52bf6a48b@mail.gmail.com> Message-ID: <4C207AA0-DE18-402C-8242-8FF2097F3533@nest.sns.it> On Aug 13, 2007, at 9:47 , Javad hashemifar wrote: > I am using program projwfc.x to calculate partial d DOS. This program > splits orbital d according to the spherical quantum numbers m and > generates five partial d DOS corresponding to m=+2 m=+1 .... m=-2 . > But a more common way of splitting d (at least in solid state) is > using the Cartesian components dz2 d(x2-y2) dxy dxz and dyz. are you sure? real combinations of spherical harmonics are used everywhere. See the many answers to this same question, of variants of it, in the pw_forum archive, and here: http://www.quantum-espresso.org/wiki/index.php/ Frequently_Asked_Questions Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From kazempoor2000 at yahoo.com Mon Aug 13 12:41:35 2007 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Mon, 13 Aug 2007 03:41:35 -0700 (PDT) Subject: [Pw_forum] error Message-ID: <881811.36186.qm@web33112.mail.mud.yahoo.com> Dear users I done nscf calculation for hexagonal system MnAs ,but one error find: from efermig internal error, cannot braket Ef the input file is this: &CONTROL title = MnAs , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = '/scratch/akazempo/tmp/' , pseudo_dir = '/afs/ictp/home/a/akazempo/espresso-3.2/pseudo/' , prefix = MnAsf , / &SYSTEM ibrav = 4, celldm(1) = 7.039, celldm(3) = 1.5013, nat = 4, ntyp = 2, ecutwfc = 30 , ecutrho = 200 , nbnd = 16, occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = 0.1, / &ELECTRONS diagonalization='' mixing_mode = 'plain' electron_maxstep = 100, conv_thr = .00001 , / ATOMIC_SPECIES Mn 54.93000 Mn.PBE-VAN.UPF As 74.92000 As.pbe-n-van.UPF ATOMIC_POSITIONS Mn 0.000000000 0.000000000 0.000000000 Mn 0.000000000 0.000000000 0.500000000 As 0.333333333 0.666666666 0.250000000 As 0.666666666 0.333333333 0.750000000 K_POINTS tpiba 8 0.000000000 0.000000000 0.000000000 1.000000000 0.500000000 0.000000000 0.000000000 1.000000000 0.333333333 0.333333333 0.000000000 1.000000000 0.000000000 0.000000000 0.000000000 1.000000000 0.000000000 0.000000000 0.500000000 1.000000000 0.500000000 0.000000000 0.500000000 1.000000000 0.333333333 0.333333333 0.500000000 1.000000000 0.000000000 0.000000000 0.500000000 1.000000000 ____________________________________________________________________________________ Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting From kazempoor2000 at yahoo.com Mon Aug 13 12:43:06 2007 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Mon, 13 Aug 2007 03:43:06 -0700 (PDT) Subject: [Pw_forum] error Message-ID: <341469.94474.qm@web33111.mail.mud.yahoo.com> Dear users I done nscf calculation for hexagonal system MnAs ,but one error find: from efermig internal error, cannot braket Ef the input file is this: &CONTROL title = MnAs , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = '/scratch/akazempo/tmp/' , pseudo_dir = '/afs/ictp/home/a/akazempo/espresso-3.2/pseudo/' , prefix = MnAsf , / &SYSTEM ibrav = 4, celldm(1) = 7.039, celldm(3) = 1.5013, nat = 4, ntyp = 2, ecutwfc = 30 , ecutrho = 200 , nbnd = 16, occupations = 'smearing' , degauss = 0.02 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = 0.1, / &ELECTRONS diagonalization='' mixing_mode = 'plain' electron_maxstep = 100, conv_thr = .00001 , / ATOMIC_SPECIES Mn 54.93000 Mn.PBE-VAN.UPF As 74.92000 As.pbe-n-van.UPF ATOMIC_POSITIONS Mn 0.000000000 0.000000000 0.000000000 Mn 0.000000000 0.000000000 0.500000000 As 0.333333333 0.666666666 0.250000000 As 0.666666666 0.333333333 0.750000000 K_POINTS tpiba 8 0.000000000 0.000000000 0.000000000 1.000000000 0.500000000 0.000000000 0.000000000 1.000000000 0.333333333 0.333333333 0.000000000 1.000000000 0.000000000 0.000000000 0.000000000 1.000000000 0.000000000 0.000000000 0.500000000 1.000000000 0.500000000 0.000000000 0.500000000 1.000000000 0.333333333 0.333333333 0.500000000 1.000000000 0.000000000 0.000000000 0.500000000 1.000000000 ____________________________________________________________________________________Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. http://tv.yahoo.com/ From ding at sissa.it Mon Aug 13 12:57:48 2007 From: ding at sissa.it (Xunlei Ding) Date: Mon, 13 Aug 2007 12:57:48 +0200 Subject: [Pw_forum] error In-Reply-To: <341469.94474.qm@web33111.mail.mud.yahoo.com> References: <341469.94474.qm@web33111.mail.mud.yahoo.com> Message-ID: <46C0392C.2060406@sissa.it> Dear ali, How many electrons in your system? nbnd should be bigger than N_elec / 2. Best wishes, Ding ali kazempoor wrote: >Dear users >I done nscf calculation for hexagonal system MnAs ,but >one error find: >from efermig >internal error, cannot braket Ef > > >the input file is this: > &CONTROL > title = MnAs , > calculation = 'nscf' , > restart_mode = 'from_scratch' , > outdir = >'/scratch/akazempo/tmp/' , > pseudo_dir = >'/afs/ictp/home/a/akazempo/espresso-3.2/pseudo/' , > prefix = MnAsf , > / > &SYSTEM > ibrav = 4, > celldm(1) = 7.039, > celldm(3) = 1.5013, > nat = 4, > ntyp = 2, > ecutwfc = 30 , > ecutrho = 200 , > nbnd = 16, > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'methfessel-paxton' , > nspin = 2 , > starting_magnetization(1) = 1.0, > starting_magnetization(2) = 0.1, > / > &ELECTRONS > diagonalization='' > mixing_mode = 'plain' > electron_maxstep = 100, > conv_thr = .00001 , > / >ATOMIC_SPECIES > Mn 54.93000 Mn.PBE-VAN.UPF > As 74.92000 As.pbe-n-van.UPF >ATOMIC_POSITIONS > Mn 0.000000000 0.000000000 0.000000000 > > Mn 0.000000000 0.000000000 0.500000000 > > As 0.333333333 0.666666666 0.250000000 > > As 0.666666666 0.333333333 0.750000000 > >K_POINTS tpiba >8 > 0.000000000 0.000000000 0.000000000 >1.000000000 > 0.500000000 0.000000000 0.000000000 >1.000000000 > 0.333333333 0.333333333 0.000000000 >1.000000000 > 0.000000000 0.000000000 0.000000000 >1.000000000 > 0.000000000 0.000000000 0.500000000 >1.000000000 > 0.500000000 0.000000000 0.500000000 >1.000000000 > 0.333333333 0.333333333 0.500000000 >1.000000000 > 0.000000000 0.000000000 0.500000000 >1.000000000 > > > > > >____________________________________________________________________________________Ready for the edge of your seat? >Check out tonight's top picks on Yahoo! TV. >http://tv.yahoo.com/ >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > From giannozz at nest.sns.it Mon Aug 13 15:28:52 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 13 Aug 2007 15:28:52 +0200 Subject: [Pw_forum] error In-Reply-To: <341469.94474.qm@web33111.mail.mud.yahoo.com> References: <341469.94474.qm@web33111.mail.mud.yahoo.com> Message-ID: On Aug 13, 2007, at 12:43 , ali kazempoor wrote: > from efermig > internal error, cannot braket Ef use " calculation='bands' " if you are interested in eigenvalues only. If you use " calculation='nscf' ", the number of bands (nbnd) must be large enough to include all occupied or partially occupied bands. If your Mn PP has 15 e, you have 40 electrons; nbnd=16 will accommodate 32 electrons at most Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From paulatto at sissa.it Mon Aug 13 15:57:24 2007 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 13 Aug 2007 15:57:24 +0200 (CEST) Subject: [Pw_forum] Ultrasoft wavefunctions for all reference energies. In-Reply-To: References: Message-ID: <18883.82.52.175.146.1187013444.squirrel@webmail.sissa.it> On Sun, August 5, 2007 22:07, Michael Vargas (michaelv at Princeton.EDU) wrote: > i have tried printing them out right before the line "..." > but some of the functions seem to be unbound. I appreciate any help the > group can give me. Dear Michael, if the reference energy is greater than zero they actually *are* unbound. This is usually ok. For deeper details you should wait for the reply of someone more experienced than me. bye -- Lorenzo Paulatto +39 040 3787 312 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From giannozz at nest.sns.it Mon Aug 13 16:52:35 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 13 Aug 2007 16:52:35 +0200 Subject: [Pw_forum] How to get the phonon frequency logarithmic average In-Reply-To: <20070813034211.22406.eqmail@aphy.iphy.ac.cn> References: <20070813034211.22406.eqmail@aphy.iphy.ac.cn> Message-ID: <40FB3043-FB49-4DE9-A613-58F68FAEA099@nest.sns.it> On Aug 13, 2007, at 3:42 , clie wrote: > recently, i use pwscf to caliculate electron-phonon couple constance, > but i want to get Tc and i need the phonon frequency logarithmic > average. Could you tell me how to get the value? pwtools/lambda.f90 should calculate it. Unfortunately it has never been updated to read the new file formats produced by the electron-phonon calculation, so it will require some work Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From afloris at physik.fu-berlin.de Mon Aug 13 16:31:18 2007 From: afloris at physik.fu-berlin.de (Andrea Floris) Date: Mon, 13 Aug 2007 16:31:18 +0200 (CEST) Subject: [Pw_forum] How to get the phonon frequency logarithmic average In-Reply-To: <20070813034211.22406.eqmail@aphy.iphy.ac.cn> References: <20070813034211.22406.eqmail@aphy.iphy.ac.cn> Message-ID: Hi clie, if you run lambda.x (look at pwtools/lambda.f90), in the output you can find the phonon frequency logarithmic average values (one value for each degauss). In that output the quantity is called , cheers Andrea --------------- Dr. Andrea Floris Institut f"ur Theoretische Physik Freie Universit"at Berlin Arnimallee 14 D-14195 Berlin Germany Tel +49-30-838-53029 Fax +49-30-838-55258 e-mail: afloris at physik.fu-berlin.de On Mon, 13 Aug 2007, clie wrote: > Dear users, > recently, i use pwscf to caliculate electron-phonon couple constance, but i > want to get Tc and i need the phonon frequency logarithmic average. Could you > tell me how to get the value? Thanks very much. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at nest.sns.it Mon Aug 13 18:12:21 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 13 Aug 2007 18:12:21 +0200 Subject: [Pw_forum] convergence not achived In-Reply-To: <822f4ec80708100908r17d9dc5asc8ea42aa4ecc854a@mail.gmail.com> References: <822f4ec80708100908r17d9dc5asc8ea42aa4ecc854a@mail.gmail.com> Message-ID: <609CF1A3-E27E-44EC-9F2C-99BD1A9F2F63@nest.sns.it> On Aug 10, 2007, at 18:08 , shruba at gmail.com wrote: > I am facing convergence problem [....] Here is my sample input it looks like an entry in a contest for "most complicated input". Please remove everything that is either not needed or you do not know what it is about. The first step in any supercell calculation is to reproduce the data for the original cell. If you have the same physical system with a different description (i.e. same atomic positions, same cutoff, same k-point grid in the extended k-space etc) you should get exactly the same results, apart from minor numerical noise. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Aug 14 10:20:44 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 14 Aug 2007 10:20:44 +0200 Subject: [Pw_forum] restart problem In-Reply-To: References: Message-ID: <8010CD6F-9A3B-4B2D-A516-069CB3290B53@nest.sns.it> On Aug 12, 2007, at 18:18 , Bhagawan Sahu wrote: > Is there a bug in the restart routine? yes, there is one (in parallel execution, only for machines that do not initialize logical variables to 0, i.e. .false.; this is why it was working on ibm sp5, I think). The problem is that file access and I/O must be performed by a single process, while all other operations must be performed by all processes. The bug consisted in a setting of a variable that was done on a single process and not broadcast to the others. The correct routine (I hope) for both 3.2 and cvs version is attached. Thank you for bringing this to our attention Paolo -------------- next part -------------- A non-text attachment was scrubbed... Name: restart_from_file.f90 Type: application/octet-stream Size: 2638 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20070814/295e9b77/attachment.obj -------------- next part -------------- --- Paolo Giannozzi, Democritos and University of Udine, Italy From weiyong.mao at intel.com Tue Aug 14 11:18:22 2007 From: weiyong.mao at intel.com (Mao, Weiyong) Date: Tue, 14 Aug 2007 17:18:22 +0800 Subject: [Pw_forum] hpcc problem Message-ID: <82C666AA63DC75449C51EAD62E8B2BEC025A8D@pdsmsx412.ccr.corp.intel.com> Dear, When I use hpcc to test, is always a problem. The phenomenon is following: > rank 3 in job 1 n34_16977 caused > collective abort of all ranks exit status of rank 3: killed by signal 11 "Random crashes due to MPI errors have often been reported in Linux PC clusters. I just want to know what cause this problem , how to solve. Thanks in advance! Mao Weiyong Global Server Innovation Group -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070814/edf9cc1f/attachment.htm From giannozz at nest.sns.it Tue Aug 14 11:44:29 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 14 Aug 2007 11:44:29 +0200 Subject: [Pw_forum] hpcc problem In-Reply-To: <82C666AA63DC75449C51EAD62E8B2BEC025A8D@pdsmsx412.ccr.corp.intel.com> References: <82C666AA63DC75449C51EAD62E8B2BEC025A8D@pdsmsx412.ccr.corp.intel.com> Message-ID: On Aug 14, 2007, at 11:18 , Mao, Weiyong wrote: > When I use hpcc to test, is always a problem. hpcc = what? high-performance C compiler?? high-priced computer cluster??? P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From weiyong.mao at intel.com Wed Aug 15 09:51:00 2007 From: weiyong.mao at intel.com (Mao, Weiyong) Date: Wed, 15 Aug 2007 15:51:00 +0800 Subject: [Pw_forum] HPC [High Performance Computing] Test Problem Message-ID: <82C666AA63DC75449C51EAD62E8B2BEC025A93@pdsmsx412.ccr.corp.intel.com> Dear all I am sorry to tell you that I use HPC to test not HPCC. It''s my fault. When I finish compile step and use mpich2 to run this file There always exists a problem. The error information is following. ______________________________________________ > rank 3 in job 1 n34_16977 caused > collective abort of all ranks exit status of rank 3: killed by signal 11 ................................................... _______________________________________________________--- I want to know what cause this problem, how to solve it . Thanks in advance. Mao Weiyong Global Server Innovation Group -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070815/96a3a283/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Aug 15 17:43:31 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 15 Aug 2007 11:43:31 -0400 (EDT) Subject: [Pw_forum] HPC [High Performance Computing] Test Problem In-Reply-To: <82C666AA63DC75449C51EAD62E8B2BEC025A93@pdsmsx412.ccr.corp.intel.com> Message-ID: On Wed, 15 Aug 2007, Mao, Weiyong wrote: WM> Dear all dear mao weiyong, [...] WM> I want to know what cause this problem, how to solve it . ...and i want a pony for christmas. ;-) the best way to get help for your problem, is to post to the right forum and provide details of what you do and how you did it etc. in case you have not noticed, this is a forum about the quantum espresso package for electron structure calculations and you have failed to point out the connection to the 'HPC' test that you are referring to (if there is any at all). thanks, axel. p.s.: you may want to check out the followin, too: http://www.catb.org/~esr/faqs/smart-questions.html WM> WM> Thanks in advance. WM> WM> WM> WM> Mao Weiyong WM> WM> Global Server Innovation Group WM> WM> WM> WM> WM> WM> WM> WM> WM> WM> WM> WM> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lmoreira at fc.unesp.br Wed Aug 15 18:53:38 2007 From: lmoreira at fc.unesp.br (Leandro Moreira de Campos Pinto) Date: Wed, 15 Aug 2007 13:53:38 -0300 Subject: [Pw_forum] Compilation problem Message-ID: <20070815135338.afgtq4tskk404goo@webmail.fc.unesp.br> Dears, when I tried to compile the espresso-3.2 I found the following error. I'm using gfortran in a Fedora Core. (...) make[1]: Entering directory `/home/quimica/Download/espresso-3.2/CPV' test -n "" && ( cd .. ; make -w || exit 1) || : gfortran -O3 -x f95-cpp-input -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c cp_interfaces.f90 (...) gfortran -O3 -x f95-cpp-input -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c init.f90 gfortran -O3 -x f95-cpp-input -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c init_run.f90 In file init_run.f90:257 CALL readfile( 1, ndr, h, hold, nfi, c0, cm, taus, & 1 Error: Actual argument at (1) must be definable to match dummy INTENT = OUT/INOUT make[1]: *** [init_run.o] Error 1 make[1]: Leaving directory `/home/quimica/Download/espresso-3.2/CPV' make: *** [cp] Error 2 (...) Any suggestions? Thanks a lot. Leandro -- ************************************************** * Leandro Moreira de Campos Pinto * * Grupo de Eletrocat?lise e Rea??es Superficiais * * Departamento de Qu?mica * * Faculdades de Ci?ncias, UNESP, C.P. 473 * * Bauru, SP, CEP 17033-360, Brasil * * lmoreira at fc.unesp.br * * http://www.fc.unesp.br/grupo_dafc * ************************************************** ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From tsun at grad.physics.sunysb.edu Wed Aug 15 20:35:02 2007 From: tsun at grad.physics.sunysb.edu (Tao Sun) Date: Wed, 15 Aug 2007 14:35:02 -0400 (EDT) Subject: [Pw_forum] Error in divide_class ( with D_2 symmetry) Message-ID: Hi, When I tried to compute phonon at q=(-0.01000100010001, -1.000100010001, 0.5) in a shear-strained fcc primitive cell CELL_PARAMETERS (alat) -0.5 0.005 0.5 -0.005 0.5 0.5 -0.505 0.505 0.0 using espresso-3.2.2 I met the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from divide_class : error # 1 wrong axis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This error message comes from PW/divide_class.f90, in the D_2 symmetry part. between line 150-169: ----------------------------------------------------- ELSEIF (code_group==8) THEN ! ! D_2 ! ! versor find the rotation axis. ! is_axis(ax,ind) is true if ax the axis given by ind ! (1 asse x, 2 asse y, 3 asse z). ! DO iclass=2,nclass CALL versor(smat(1,1,elem(1,iclass)),ax) IF (is_axis(ax,3)) THEN which_irr(iclass)=2 ELSEIF (is_axis(ax,2)) THEN which_irr(iclass)=3 ELSEIF (is_axis(ax,2)) THEN which_irr(iclass)=4 ELSE CALL errore('divide_class','wrong axis',1) ENDIF ENDDO ----------------------------------------------------- The duplicated condition (is_axis(ax,2)) looks suspicious, but when I changed one of them into is_axis(ax,1), the error is still there. If I remove the CALL errore(... sentence, the code can compute the eigen-values, except gives weird symmetry label to each mode, as: --------------------------------------------------------- Mode symmetry, D_2 (222) point group: omega( 1 - 1) = 81.09814 [cm-1] --> ? omega( 1 - 1) = 81.09814 [cm-1] --> A omega( 1 - 1) = 81.09814 [cm-1] --> ? omega( 1 - 1) = 81.09814 [cm-1] --> B_1 omega( 2 - 2) = 111.55732 [cm-1] --> ? omega( 2 - 2) = 111.55732 [cm-1] --> B_2 omega( 2 - 2) = 111.55732 [cm-1] --> ? omega( 2 - 2) = 111.55732 [cm-1] --> B_3 omega( 3 - 3) = 124.59709 [cm-1] --> ? omega( 3 - 3) = 124.59709 [cm-1] --> B_2 omega( 3 - 3) = 124.59709 [cm-1] --> ? omega( 3 - 3) = 124.59709 [cm-1] --> B_3 ------------------------------------------------------ This error is independent of the system, we observe the same behavior in two different fcc crystals(MgO and Pt). BTW, similar problem exists in PW/divide_class_so.f90 while q points of other symmetry type(e.g. D_2h) seems OK. It will be great if somebody can help us fix the problem. Cheers. Tao Sun Graduate Student Dept. of Physics & Astronomy SUNY at Stony Brook From tgrassma at ucsd.edu Wed Aug 15 21:01:58 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Wed, 15 Aug 2007 12:01:58 -0700 Subject: [Pw_forum] Broken PP routines in espresso-3.2.2? Message-ID: <001301c7df6e$c1e4c360$6300a8c0@Crom> Hello. I've recently obtained and compiled the full Espresso package (v.3.2, patched to 3.2.2), although currently I'm only trying to work with the PW and PP components. As I'm new to this code, I've been working with the provided examples/tests (specifically, 1 and 8), and have run into a problem. I've found that the pw.x portions all work fine (serial and parallel), but the PP components (I've tested serial versions of bands.x, dos.x, and projwfc.x) all crash after a running for few seconds, and all in the exact same way, with no errors given... I get the standard introduction output: "Program POST-PROC v.3.2.2 starts ... Today is 15Aug2007 at 11: 1:30" and then after running a couple more seconds I get the segmentation fault. All the appropriate files appear to be in place, and the program is looking in the right place (if I move things around it'll complain that it can't find the tmp directory or the .save file). Unfortunately, my understanding of Fortran is rudimentary, at best, but I tried to trace down the issue by planting stdout write statements in the PP codes, and found that the routines do not seem to proceed beyond the read_file call (e.g. line 105 in dos.f90). And that's about where my debugging abilities end, I'm afraid. Has anyone else ran into this problem? My system and compilation setup is as follows... OS/Architecture = CentOS 4.3 (AMD64) on dual Opteron 2214 (dual-core) F90 = pgf90 (v.6.2-5) CC = gcc LAPACK/BLAS = acml (v.3.6) FFTW = internal I can give my optimizations and such if anyone wants them, but I've also tried turning off all optimizations (i.e. setting both CFLAGS and FFLAGS to -O0), and I get the same exact crashing, so I'm guessing that's not the issue. I've also tried compiling with pgf90 v.5.2-4, but pw.x itself segfaults, and I didn't think it was worth trying to figure that one out... But I'm not so sure that it's necessarily a compiler issue, since I've had plenty of suggess with pgf90 6.2-5 with pw.x, as well as other codes (such as VASP and CPMD). So, has anyone else run into these problems? Or does anyone have any ideas that I can do to try to remedy the situation? Thank you, Tyler Grassman Depts. of Materials Science, Chemistry/Biochemistry University of California, San Diego 9500 Gilman Dr. #0358 La Jolla, CA 92093-0358 From eyvaz_isaev at yahoo.com Wed Aug 15 21:28:38 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 15 Aug 2007 12:28:38 -0700 (PDT) Subject: [Pw_forum] Compilation problem In-Reply-To: <20070815135338.afgtq4tskk404goo@webmail.fc.unesp.br> Message-ID: <528522.78453.qm@web60317.mail.yahoo.com> Hi Leonardo, As far as I know gfortran is not able to compile QuantumEspresso code. Try g95, but Intel Fortran compiler which is free of charge is much better. You can try also Sun Fortran compiler. In the latter case see recent messages about Sun compiler. Bests, Eyvaz. --- Leandro Moreira de Campos Pinto wrote: > Dears, > > when I tried to compile the espresso-3.2 I found the > following error. > I'm using gfortran in a Fedora Core. > > > (...) > make[1]: Entering directory > `/home/quimica/Download/espresso-3.2/CPV' > test -n "" && ( cd .. ; make -w || exit 1) || : > gfortran -O3 -x f95-cpp-input -D__FFTW > -D__USE_INTERNAL_FFTW > -I../include -I./ -I../Modules -I../iotk/src > -I../PW -I../PH > -I../CPV -c cp_interfaces.f90 > (...) > gfortran -O3 -x f95-cpp-input -D__FFTW > -D__USE_INTERNAL_FFTW > -I../include -I./ -I../Modules -I../iotk/src > -I../PW -I../PH > -I../CPV -c init.f90 > gfortran -O3 -x f95-cpp-input -D__FFTW > -D__USE_INTERNAL_FFTW > -I../include -I./ -I../Modules -I../iotk/src > -I../PW -I../PH > -I../CPV -c init_run.f90 > In file init_run.f90:257 > > CALL readfile( 1, ndr, h, hold, nfi, c0, > cm, taus, & > 1 > Error: Actual argument at (1) must be definable to > match dummy INTENT > = OUT/INOUT > make[1]: *** [init_run.o] Error 1 > make[1]: Leaving directory > `/home/quimica/Download/espresso-3.2/CPV' > make: *** [cp] Error 2 > (...) > > Any suggestions? > > Thanks a lot. > > Leandro > > > -- > ************************************************** > * Leandro Moreira de Campos Pinto * > * Grupo de Eletrocat?lise e Rea??es Superficiais * > * Departamento de Qu?mica * > * Faculdades de Ci?ncias, UNESP, C.P. 473 * > * Bauru, SP, CEP 17033-360, Brasil * > * lmoreira at fc.unesp.br * > * http://www.fc.unesp.br/grupo_dafc * > ************************************************** > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet > Messaging Program. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow From akohlmey at cmm.chem.upenn.edu Wed Aug 15 20:29:13 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 15 Aug 2007 14:29:13 -0400 (EDT) Subject: [Pw_forum] Broken PP routines in espresso-3.2.2? In-Reply-To: <001301c7df6e$c1e4c360$6300a8c0@Crom> Message-ID: On Wed, 15 Aug 2007, Tyler Grassman wrote: hello tyler, TG> My system and compilation setup is as follows... TG> TG> OS/Architecture = CentOS 4.3 (AMD64) on dual Opteron 2214 (dual-core) TG> F90 = pgf90 (v.6.2-5) TG> CC = gcc TG> LAPACK/BLAS = acml (v.3.6) TG> FFTW = internal TG> TG> I can give my optimizations and such if anyone wants them, but I've also TG> tried turning off all optimizations (i.e. setting both CFLAGS and FFLAGS to TG> -O0), and I get the same exact crashing, so I'm guessing that's not the TG> issue. I've also tried compiling with pgf90 v.5.2-4, but pw.x itself TG> segfaults, and I didn't think it was worth trying to figure that one out... correct. see below. TG> But I'm not so sure that it's necessarily a compiler issue, since I've had TG> plenty of suggess with pgf90 6.2-5 with pw.x, as well as other codes (such TG> as VASP and CPMD). the pgi f90 compilers all have a number of (serious) issues with current standard complying fortran 90/95 code. btw, there are also some known issues with CPMD but they are mostly in harmless or rarely used places (e.g. the wavefunction guess, ultra-soft support). if you have access to the intel compilers (make sure you have updated versions there as well), it should work ok. or you may want to try g95 ( from www.g95.org, it is straightforward to try it out from the precompiled snapshots and to get rid of it, too). TG> So, has anyone else run into these problems? Or does anyone have any ideas TG> that I can do to try to remedy the situation? the i/o code based on iotk is a bit sensitive to compiler bugs, so switching compilers would be the best strategy to get a hint where the problem is coming from. sometimes code can be replaced with an equivalent less demanding implementation, sometimes there are features used that only work with certain compilers. cheers, axel. TG> TG> Thank you, TG> TG> Tyler Grassman TG> Depts. of Materials Science, Chemistry/Biochemistry TG> University of California, San Diego TG> 9500 Gilman Dr. #0358 TG> La Jolla, CA 92093-0358 TG> TG> _______________________________________________ TG> Pw_forum mailing list TG> Pw_forum at pwscf.org TG> http://www.democritos.it/mailman/listinfo/pw_forum TG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From tgrassma at ucsd.edu Thu Aug 16 02:04:34 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Wed, 15 Aug 2007 17:04:34 -0700 Subject: [Pw_forum] Broken PP routines in espresso-3.2.2? In-Reply-To: Message-ID: <002801c7df99$0827b9c0$6300a8c0@Crom> Axel, Thank you very much for your helpful response. I went ahead and recompiled using ifort 9.1.040 (FFLAGS = -O3 -xW -static) and acml 3.6 (ifort compiled), and it worked. It's a tiny bit slower than the PGI code, (2.5% on ni.scf.in from example08), so that's good. Thanks again! Regards, Tyler > -----Original Message----- > From: Axel Kohlmeyer [mailto:akohlmey at cmm.chem.upenn.edu] > Sent: Wednesday, August 15, 2007 11:29 AM > To: Tyler Grassman > Cc: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Broken PP routines in espresso-3.2.2? > > > On Wed, 15 Aug 2007, Tyler Grassman wrote: > > > hello tyler, > > > TG> My system and compilation setup is as follows... > TG> > TG> OS/Architecture = CentOS 4.3 (AMD64) on dual Opteron 2214 > TG> (dual-core) F90 = pgf90 (v.6.2-5) CC = gcc > TG> LAPACK/BLAS = acml (v.3.6) > TG> FFTW = internal > TG> > TG> I can give my optimizations and such if anyone wants > them, but I've > TG> also tried turning off all optimizations (i.e. setting > both CFLAGS > TG> and FFLAGS to -O0), and I get the same exact crashing, so I'm > TG> guessing that's not the issue. I've also tried compiling > with pgf90 > TG> v.5.2-4, but pw.x itself segfaults, and I didn't think it > was worth > TG> trying to figure that one out... > > correct. see below. > > TG> But I'm not so sure that it's necessarily a compiler issue, since > TG> I've had plenty of suggess with pgf90 6.2-5 with pw.x, as well as > TG> other codes (such as VASP and CPMD). > > the pgi f90 compilers all have a number of (serious) issues with > current standard complying fortran 90/95 code. btw, there are > also some known issues with CPMD but they are mostly in harmless or > rarely used places (e.g. the wavefunction guess, ultra-soft support). > > if you have access to the intel compilers (make sure you have > updated versions there as well), it should work ok. or you > may want to try g95 ( from www.g95.org, it is straightforward > to try it out from > the precompiled snapshots and to get rid of it, too). > > TG> So, has anyone else run into these problems? Or does anyone have > TG> any ideas that I can do to try to remedy the situation? > > the i/o code based on iotk is a bit sensitive to compiler bugs, > so switching compilers would be the best strategy to get a > hint where the problem is coming from. sometimes code can be > replaced with an equivalent less demanding implementation, > sometimes there are features used that only work with certain > compilers. > > cheers, > axel. > > TG> > TG> Thank you, > TG> > TG> Tyler Grassman > TG> Depts. of Materials Science, Chemistry/Biochemistry University of > TG> California, San Diego 9500 Gilman Dr. #0358 > TG> La Jolla, CA 92093-0358 > TG> > TG> _______________________________________________ > TG> Pw_forum mailing list > TG> Pw_forum at pwscf.org > TG> http://www.democritos.it/mailman/listinfo/pw_forum > TG> > > -- > ============================================================== > ========= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > ============================================================== > ========= > If you make something idiot-proof, the universe creates a > better idiot. > > Tyler Grassman Depts. of Materials Science, Chemistry/Biochemistry University of California, San Diego 9500 Gilman Dr. #0358 La Jolla, CA 92093-0358 From akohlmey at cmm.chem.upenn.edu Thu Aug 16 01:31:50 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 15 Aug 2007 19:31:50 -0400 (EDT) Subject: [Pw_forum] Broken PP routines in espresso-3.2.2? In-Reply-To: <002801c7df99$0827b9c0$6300a8c0@Crom> Message-ID: On Wed, 15 Aug 2007, Tyler Grassman wrote: TG> Axel, tyler, TG> Thank you very much for your helpful response. I went ahead and recompiled TG> using ifort 9.1.040 (FFLAGS = -O3 -xW -static) and acml 3.6 (ifort TG> compiled), and it worked. It's a tiny bit slower than the PGI code, (2.5% TG> on ni.scf.in from example08), so that's good. Thanks again! please try recompiling with: FFLAGS=-O2 -assume byterecl -tpp6 -pc64 -unroll and link with -i-static instead of -static the first should give you a better performance and the second will make your binaries more portable across machines. fully static linking is very bad these days on linux machines. cheers, axel. TG> TG> Regards, TG> Tyler TG> TG> TG> > -----Original Message----- TG> > From: Axel Kohlmeyer [mailto:akohlmey at cmm.chem.upenn.edu] TG> > Sent: Wednesday, August 15, 2007 11:29 AM TG> > To: Tyler Grassman TG> > Cc: pw_forum at pwscf.org TG> > Subject: Re: [Pw_forum] Broken PP routines in espresso-3.2.2? TG> > TG> > [...] -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From dalcorso at sissa.it Thu Aug 16 11:15:19 2007 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Thu, 16 Aug 2007 11:15:19 +0200 Subject: [Pw_forum] Error in divide_class ( with D_2 symmetry) In-Reply-To: References: Message-ID: <1187255719.3228.20.camel@dhpc-5-02.sissa.it> On Wed, 2007-08-15 at 14:35 -0400, Tao Sun wrote: > Hi, > > When I tried to compute phonon at q=(-0.01000100010001, -1.000100010001, > 0.5) in a shear-strained fcc primitive cell > > CELL_PARAMETERS (alat) > -0.5 0.005 0.5 > -0.005 0.5 0.5 > -0.505 0.505 0.0 > > using espresso-3.2.2 > > I met the following error message: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from divide_class : error # 1 > wrong axis > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > This error message comes from PW/divide_class.f90, in the D_2 > symmetry part. between line 150-169: > > ----------------------------------------------------- > ELSEIF (code_group==8) THEN > ! > ! D_2 > ! > ! versor find the rotation axis. > ! is_axis(ax,ind) is true if ax the axis given by ind > ! (1 asse x, 2 asse y, 3 asse z). > ! > DO iclass=2,nclass > CALL versor(smat(1,1,elem(1,iclass)),ax) > IF (is_axis(ax,3)) THEN > which_irr(iclass)=2 > ELSEIF (is_axis(ax,2)) THEN > which_irr(iclass)=3 > ELSEIF (is_axis(ax,2)) THEN > which_irr(iclass)=4 > ELSE > CALL errore('divide_class','wrong axis',1) > ENDIF > ENDDO > ----------------------------------------------------- > You are right, divide_class is wrong for D_2. Thank you for reporting this. Actually in your system two of the three C_2 axes are not parallel to x or y, so even correcting the bug will not solve the problem. One possibility is to take C_2 parallel to the axis of the first rotation, C_2' parallel to the axis of the second rotation, and C_2'' parallel to the axis of the third rotation. This can be done substituting the loop over classes with: DO iclass=2,nclass which_irr(iclass)=iclass ENDDO For divide_class_so we can do the same thing. The loop over the classes becomes: first=.true. DO iclass=2,nclass ts=tipo_sym(smat(1,1,elem(1,iclass))) IF (ts==1) THEN which_irr(iclass)=2 first=.false. ELSE if (first) then which_irr(iclass)=iclass+1 else which_irr(iclass)=iclass endif END IF ENDDO Hope this helps. Andrea > The duplicated condition (is_axis(ax,2)) looks suspicious, > but when I changed one of them into is_axis(ax,1), the > error is still there. > > If I remove the CALL errore(... sentence, the code can > compute the eigen-values, except gives weird symmetry > label to each mode, as: > > --------------------------------------------------------- > Mode symmetry, D_2 (222) point group: > > omega( 1 - 1) = 81.09814 [cm-1] --> ? > omega( 1 - 1) = 81.09814 [cm-1] --> A > omega( 1 - 1) = 81.09814 [cm-1] --> ? > omega( 1 - 1) = 81.09814 [cm-1] --> B_1 > omega( 2 - 2) = 111.55732 [cm-1] --> ? > omega( 2 - 2) = 111.55732 [cm-1] --> B_2 > omega( 2 - 2) = 111.55732 [cm-1] --> ? > omega( 2 - 2) = 111.55732 [cm-1] --> B_3 > omega( 3 - 3) = 124.59709 [cm-1] --> ? > omega( 3 - 3) = 124.59709 [cm-1] --> B_2 > omega( 3 - 3) = 124.59709 [cm-1] --> ? > omega( 3 - 3) = 124.59709 [cm-1] --> B_3 > ------------------------------------------------------ > > This error is independent of the system, we observe the > same behavior in two different fcc crystals(MgO and Pt). > > BTW, similar problem exists in PW/divide_class_so.f90 > while q points of other symmetry type(e.g. D_2h) seems OK. > > It will be great if somebody can help us fix the problem. > > Cheers. > > Tao Sun > > Graduate Student > Dept. of Physics & Astronomy > SUNY at Stony Brook > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From marzari at MIT.EDU Thu Aug 16 09:09:02 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 16 Aug 2007 03:09:02 -0400 Subject: [Pw_forum] Phonon Calculation error on AF system In-Reply-To: <7.0.1.0.2.20070815102722.0b737668@adm.njit.edu> References: <7.0.1.0.2.20070815102722.0b737668@adm.njit.edu> Message-ID: <46C3F80E.7090201@mit.edu> Dear Trevor, this is more appropriately posted to the pw_forum (also, I cannot really take individual questions). I'll do it for you. Your material is - I presume - an AF insulator, in your DFT-PBE calculations (if it is not, then you shouldn't try to calculate its dielectric constant, that is used to predict the correct LO-TO splitting). Still, you use smearing to aid convergence, so the code think your system is a metal (and it is, if unoccupied states are fractionally occupied), and it complains when you try to calculate the dielectric response. Now, you could turn off the smearing. Still, at least a few months ago, the code was still not set up to do the dielectric constant of spin-polarized insulators. It should be an easy modification (and following JCP 120,9934 (2004)) but we didn't try. It is my understanding that the phonons outside gamma would come out nevertheless correct, even with the code in the present status, provided you remove the dielec=.true. option (amybe someone else can confirm). So you would get everything right, but for the phonon at gamma, where you wouldn't have the LO-TO splitting (since it requires the calculation of effective charges and dielectric constant). nicola Trevor A. Tyson wrote: > Dear Dr. Nicola Marzari: > I have been trying to use PWScf to calculate the phonon modes (at > Gamma) for the oxide LaMnO3 (antiferromagnetic). The SCF computation > work fine but the phonon calculation fails. Below are the "run file" > and the output file "lmoAF.phG.out" indicating the error code. Thanks > in advance for your help. > Trevor A. Tyson > > ------------------------------------------------------------- > Trevor A. Tyson > Department of Physics > New Jersey Institute of Technology > Room 484, Tiernan Hall > 161 Warren Street > University Heights > Newark, New Jersey 07102-1982 > Tel: (973) 642-4681 > FAX: (973) 596-5794 > E-MAIL: TYSON at ADM.NJIT.EDU > WWW Page: http://web.njit.edu/~tyson/ > ---------------------------------------------------------------------------- > > > > > > > *************************************** > # how to run executables > PW_COMMAND='/home/tyson/PWSCF/espresso-3.2/bin/pw.x' > PH_COMMAND='/home/tyson/PWSCF/espresso-3.2/bin/ph.x' > $ECHO > $ECHO " running pw.x as: $PW_COMMAND" > $ECHO " running ph.x as: $PH_COMMAND" > $ECHO > # self-consistent calculation > cat > lmoAF.scf.in << EOF > &control > calculation='scf', > restart_mode='from_scratch', > prefix='lmoAF' > pseudo_dir = '/home/tyson/PWSCF/espresso-3.2/pseudo', > outdir='/home/tyson/PWSCF/espresso-3.2/tmp/' > / > &system > ibrav = 0, > celldm(1) = 10.8600, > nat= 20, ntyp= 5, ecutwfc = 25.0, ecutrho=250.0, > occupations='smearing', smearing='gauss', degauss=0.005, > nspin=2, > starting_magnetization(1)= 0.0, > starting_magnetization(2)= 0.5, > starting_magnetization(3)= -0.5, > starting_magnetization(4)= 0.0, > starting_magnetization(5)= 0.0, > > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > La1 138.91 La.pbe-nsp-van.UPF > Mn1 54.938 Mn.pbe-sp-van.UPF > Mn2 54.938 Mn.pbe-sp-van.UPF > O1 15.999 O.pbe-van_ak.UPF > O2 15.999 O.pbe-van_ak.UPF > > > CELL_PARAMETERS > 1.00 0.00 0.00 > 0.00 1.3385 0.00 > 0.00 0.00 0.96336 > > > ATOMIC_POSITIONS {crystal} > La1 0.049 0.25 0.9922 > La1 0.951 0.75 0.0078 > La1 0.549 0.25 0.5078 > La1 0.451 0.75 0.4922 > Mn1 0.0 0.0 0.5 > Mn1 0.5 0.0 0.0 > Mn2 0.5 0.5 0.0 > Mn2 0.0 0.5 0.5 > O1 0.4874 0.25 0.0745 > O1 0.9874 0.25 0.4255 > O1 0.0126 0.75 0.5745 > O1 0.5126 0.75 0.9255 > O2 0.3066 0.0384 0.7256 > O2 0.6934 0.9616 0.2744 > O2 0.3066 0.4616 0.7256 > O2 0.6934 0.5384 0.2744 > O2 0.1934 0.9616 0.2256 > O2 0.8066 0.0384 0.7744 > O2 0.1934 0.5384 0.2256 > O2 0.8066 0.4616 0.7744 > > K_POINTS automatic > 2 2 2 0 0 0 > > > EOF > $ECHO " running the scf calculation...\c" > $PW_COMMAND < lmoAF.scf.in > lmoAF.scf.out > $ECHO " done" > > # phonon calculation at Gamma > cat > lmoAF.phG.in << EOF > phonons of LaMnO3 AF at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='lmoAF', > epsil=.true., > amass(1) = 138.91, > amass(2) = 54.938, > amass(3) = 54.938, > amass(4) = 15.999, > amass(5) = 15.999, > outdir='/home/tyson/PWSCF/espresso-3.2/tmp', > fildyn='lmoAF.dynG', > / > 0.0 0.0 0.0 > EOF > $ECHO " running the phonon calculation at Gamma...\c" > $PH_COMMAND < lmoAF.phG.in > lmoAF.phG.out > $ECHO " done" > > > ************************************************************************** > lmoAF.phG.out > > > Program PHONON v.3.2 starts ... > Today is 15Aug2007 at 10: 2:42 > > Ultrasoft (Vanderbilt) Pseudopotentials > > nbndx = 106 nbnd = 106 natomwfc = 152 npwx = 3512 > nelec = 176.00 nkb = 240 ngl = 14863 > > Check: negative/imaginary core charge= -0.000002 0.000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from phq_readin : error # 1 > no elec. field with metals > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > stopping ... > > > > > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From tsun at grad.physics.sunysb.edu Fri Aug 17 00:10:53 2007 From: tsun at grad.physics.sunysb.edu (Tao Sun) Date: Thu, 16 Aug 2007 18:10:53 -0400 (EDT) Subject: [Pw_forum] Error in divide_class ( with D_2 symmetry) In-Reply-To: <1187255719.3228.20.camel@dhpc-5-02.sissa.it> Message-ID: Dear Andrea, Thanks. After your modification, the code ran smoothly and yielded the following: Mode symmetry, D_2 (222) point group: omega( 1 - 1) = 81.09814 [cm-1] --> B_1 omega( 2 - 2) = 111.55732 [cm-1] --> B_3 omega( 3 - 3) = 124.59709 [cm-1] --> B_2 I guess I need to look at the eigenvectors with respect to rotation axis to judge whether these symmetry assignments are correct. Anyway they are not very relevant to our current project and I hope you won't mind I didn't check this. Cheers. Tao On Thu, 16 Aug 2007, Dal Corso Andrea wrote: > On Wed, 2007-08-15 at 14:35 -0400, Tao Sun wrote: > > Hi, > > > > When I tried to compute phonon at q=(-0.01000100010001, -1.000100010001, > > 0.5) in a shear-strained fcc primitive cell > > > > CELL_PARAMETERS (alat) > > -0.5 0.005 0.5 > > -0.005 0.5 0.5 > > -0.505 0.505 0.0 > > > > using espresso-3.2.2 > > > > I met the following error message: > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from divide_class : error # 1 > > wrong axis > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > This error message comes from PW/divide_class.f90, in the D_2 > > symmetry part. between line 150-169: > > > > ----------------------------------------------------- > > ELSEIF (code_group==8) THEN > > ! > > ! D_2 > > ! > > ! versor find the rotation axis. > > ! is_axis(ax,ind) is true if ax the axis given by ind > > ! (1 asse x, 2 asse y, 3 asse z). > > ! > > DO iclass=2,nclass > > CALL versor(smat(1,1,elem(1,iclass)),ax) > > IF (is_axis(ax,3)) THEN > > which_irr(iclass)=2 > > ELSEIF (is_axis(ax,2)) THEN > > which_irr(iclass)=3 > > ELSEIF (is_axis(ax,2)) THEN > > which_irr(iclass)=4 > > ELSE > > CALL errore('divide_class','wrong axis',1) > > ENDIF > > ENDDO > > ----------------------------------------------------- > > > > You are right, divide_class is wrong for D_2. Thank you for reporting > this. Actually in your system two of the three C_2 axes are not parallel > to x or y, so even correcting the bug will not solve the problem. > > One possibility is to take C_2 parallel to the axis of > the first rotation, C_2' parallel to the axis of the > second rotation, and C_2'' parallel to the axis of the third rotation. > This can be done substituting the loop over classes with: > > DO iclass=2,nclass > which_irr(iclass)=iclass > ENDDO > > For divide_class_so we can do the same thing. The loop over the > classes becomes: > > > first=.true. > DO iclass=2,nclass > ts=tipo_sym(smat(1,1,elem(1,iclass))) > IF (ts==1) THEN > which_irr(iclass)=2 > first=.false. > ELSE > if (first) then > which_irr(iclass)=iclass+1 > else > which_irr(iclass)=iclass > endif > END IF > ENDDO > > > Hope this helps. > > Andrea > > > > > > > The duplicated condition (is_axis(ax,2)) looks suspicious, > > but when I changed one of them into is_axis(ax,1), the > > error is still there. > > > > If I remove the CALL errore(... sentence, the code can > > compute the eigen-values, except gives weird symmetry > > label to each mode, as: > > > > --------------------------------------------------------- > > Mode symmetry, D_2 (222) point group: > > > > omega( 1 - 1) = 81.09814 [cm-1] --> ? > > omega( 1 - 1) = 81.09814 [cm-1] --> A > > omega( 1 - 1) = 81.09814 [cm-1] --> ? > > omega( 1 - 1) = 81.09814 [cm-1] --> B_1 > > omega( 2 - 2) = 111.55732 [cm-1] --> ? > > omega( 2 - 2) = 111.55732 [cm-1] --> B_2 > > omega( 2 - 2) = 111.55732 [cm-1] --> ? > > omega( 2 - 2) = 111.55732 [cm-1] --> B_3 > > omega( 3 - 3) = 124.59709 [cm-1] --> ? > > omega( 3 - 3) = 124.59709 [cm-1] --> B_2 > > omega( 3 - 3) = 124.59709 [cm-1] --> ? > > omega( 3 - 3) = 124.59709 [cm-1] --> B_3 > > ------------------------------------------------------ > > > > This error is independent of the system, we observe the > > same behavior in two different fcc crystals(MgO and Pt). > > > > BTW, similar problem exists in PW/divide_class_so.f90 > > while q points of other symmetry type(e.g. D_2h) seems OK. > > > > It will be great if somebody can help us fix the problem. > > > > Cheers. > > > > Tao Sun > > > > Graduate Student > > Dept. of Physics & Astronomy > > SUNY at Stony Brook > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > From mmarques at staffmail.ed.ac.uk Fri Aug 17 13:46:50 2007 From: mmarques at staffmail.ed.ac.uk (Miriam Marques) Date: Fri, 17 Aug 2007 12:46:50 +0100 Subject: [Pw_forum] Phonon calculation crash in orthorhombic cell. Message-ID: <20070817124650.jhqpkahda0wkcg44@www.staffmail.ed.ac.uk> Dear PWSCF users, I am trying to perform a phonon calculation on a uniform grid of q-points for an orthorhombic metallic structure. First, I did the scf calculation for a 16x16x16 Monkhorst-Pack grid and tried to calculate phonons on a uniform (4x4x4) grid via ldisp, but the program phonon stopped with the error "end of self consistent calculation. No convergence has been achieved" in the representation 4 (mode 4) of the first q point different from gamma. (I am using tr2_ph=1.0d-12) Surprisingly, when I did the scf calculation for a 13x13x13 Monkhorst-Pack grid and then the phonon calculation via ldisp on a 4x4x2 grid, the program ran (it crashed again when I tried the 4X4x8 grid). I attached the input for the first case. # self-consistent calculation cat > pcmcm.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/', prefix='pcmcm' tprnfor = .true. tstress = .true. / &system ibrav= 9, celldm(1) =6.089228715122, celldm(2) =0.86757351, celldm(3)= 2.5838341, nat= 4, ntyp= 1, nbnd= 20, ecutwfc = 30.0, ecutrho=300, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons diagonalization='david' mixing_beta = 0.7 conv_thr = 1.0D-10 / ATOMIC_SPECIES P 30.973761 P.pw91-n-van.UPF ATOMIC_POSITIONS crystal P 0.0000000000 0.0000000000 0.00000000000 P 0.0000000000 0.0000000000 0.50000000000 P 0.0000000000 0.0000000000 0.25000000000 P 0.0000000000 0.0000000000 0.75000000000 K_POINTS {automatic} 16 16 16 0 0 0 EOF $ECHO " running the scf calculation for P...\c" $PW_COMMAND < pcmcm.scf.in > pcmcm.scf.out $ECHO " done" # phonon calculation on a (4 4 4) uniform grid of q-points cat > pcmcm.ph.in << EOF phonons of cmcm P &inputph tr2_ph=1.0d-12, prefix='pcmcm', ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=30.973761, outdir='$TMP_DIR/', fildyn='pcmcm.dyn', / EOF $ECHO " running the phonon calculation at Gamma...\c" $PH_COMMAND < pcmcm.ph.in > pcmcm.ph.out Thank you very much for your help, Miriam. ---------------------- Miriam Marques School of Physics University of Edinburgh ---------------------- From eyvaz_isaev at yahoo.com Fri Aug 17 14:52:49 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 17 Aug 2007 05:52:49 -0700 (PDT) Subject: [Pw_forum] Phonon calculation crash in orthorhombic cell. In-Reply-To: <20070817124650.jhqpkahda0wkcg44@www.staffmail.ed.ac.uk> Message-ID: <491074.93053.qm@web60316.mail.yahoo.com> Hi Miriam, Did you try reduce alpha_mix(1) parameter in your phonon calculations? By default it is 0.7. Bests, Eyvaz. --- Miriam Marques wrote: > > Dear PWSCF users, > > I am trying to perform a phonon calculation on a > uniform grid of > q-points for an orthorhombic metallic structure. > > First, I did the scf calculation for a 16x16x16 > Monkhorst-Pack grid > and tried to calculate phonons on a uniform (4x4x4) > grid via ldisp, > but the program phonon stopped with the error "end > of self consistent > calculation. No convergence has been achieved" in > the representation 4 > (mode 4) of the first q point different from gamma. > (I am using > tr2_ph=1.0d-12) > Surprisingly, when I did the scf calculation for a > 13x13x13 > Monkhorst-Pack grid and then the phonon calculation > via ldisp on a > 4x4x2 grid, the program ran (it crashed again when I > tried the 4X4x8 > grid). > > I attached the input for the first case. > > # self-consistent calculation > cat > pcmcm.scf.in << EOF > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/', > prefix='pcmcm' > tprnfor = .true. > tstress = .true. > / > &system > ibrav= 9, celldm(1) =6.089228715122, celldm(2) > =0.86757351, > celldm(3)= 2.5838341, nat= 4, ntyp= 1, nbnd= 20, > ecutwfc = 30.0, > ecutrho=300, occupations='smearing', > smearing='methfessel-paxton', > degauss=0.02 > / > &electrons > diagonalization='david' > mixing_beta = 0.7 > conv_thr = 1.0D-10 > / > ATOMIC_SPECIES > P 30.973761 P.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > P 0.0000000000 0.0000000000 0.00000000000 > P 0.0000000000 0.0000000000 0.50000000000 > P 0.0000000000 0.0000000000 0.25000000000 > P 0.0000000000 0.0000000000 0.75000000000 > K_POINTS {automatic} > 16 16 16 0 0 0 > EOF > $ECHO " running the scf calculation for > P...\c" > $PW_COMMAND < pcmcm.scf.in > pcmcm.scf.out > $ECHO " done" > > # phonon calculation on a (4 4 4) uniform grid of > q-points > cat > pcmcm.ph.in << EOF > phonons of cmcm P > &inputph > tr2_ph=1.0d-12, > prefix='pcmcm', > ldisp=.true., > nq1=4, nq2=4, nq3=4 > amass(1)=30.973761, > outdir='$TMP_DIR/', > fildyn='pcmcm.dyn', > / > EOF > $ECHO " running the phonon calculation at > Gamma...\c" > $PH_COMMAND < pcmcm.ph.in > pcmcm.ph.out > > > > Thank you very much for your help, > > Miriam. > > ---------------------- > Miriam Marques > School of Physics > University of Edinburgh > ---------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433 From mmarques at staffmail.ed.ac.uk Fri Aug 17 16:22:45 2007 From: mmarques at staffmail.ed.ac.uk (Miriam Marques) Date: Fri, 17 Aug 2007 15:22:45 +0100 Subject: [Pw_forum] Phonon calculation crash in orthorhombic cell. In-Reply-To: <491074.93053.qm@web60316.mail.yahoo.com> References: <491074.93053.qm@web60316.mail.yahoo.com> Message-ID: <20070817152245.1atds5wdoo404k40@www.staffmail.ed.ac.uk> Thank you very much Eyvaz. It has been a long time since I used this code and I had forgotten this parameter effects. I will reduce the alpha_mix(1) parameter as you suggested. Best regards, Miriam. ---------------------- Miriam Marques School of Physics University of Edinburgh ----------------------- Quoting Eyvaz Isaev : > Hi Miriam, > > Did you try reduce alpha_mix(1) parameter in your > phonon calculations? > By default it is 0.7. > > Bests, > Eyvaz. > > --- Miriam Marques > wrote: > >> >> Dear PWSCF users, >> >> I am trying to perform a phonon calculation on a >> uniform grid of >> q-points for an orthorhombic metallic structure. >> >> First, I did the scf calculation for a 16x16x16 >> Monkhorst-Pack grid >> and tried to calculate phonons on a uniform (4x4x4) >> grid via ldisp, >> but the program phonon stopped with the error "end >> of self consistent >> calculation. No convergence has been achieved" in >> the representation 4 >> (mode 4) of the first q point different from gamma. >> (I am using >> tr2_ph=1.0d-12) >> Surprisingly, when I did the scf calculation for a >> 13x13x13 >> Monkhorst-Pack grid and then the phonon calculation >> via ldisp on a >> 4x4x2 grid, the program ran (it crashed again when I >> tried the 4X4x8 >> grid). >> >> I attached the input for the first case. >> >> # self-consistent calculation >> cat > pcmcm.scf.in << EOF >> &control >> calculation='scf' >> restart_mode='from_scratch', >> pseudo_dir = '$PSEUDO_DIR/', >> outdir='$TMP_DIR/', >> prefix='pcmcm' >> tprnfor = .true. >> tstress = .true. >> / >> &system >> ibrav= 9, celldm(1) =6.089228715122, celldm(2) >> =0.86757351, >> celldm(3)= 2.5838341, nat= 4, ntyp= 1, nbnd= 20, >> ecutwfc = 30.0, >> ecutrho=300, occupations='smearing', >> smearing='methfessel-paxton', >> degauss=0.02 >> / >> &electrons >> diagonalization='david' >> mixing_beta = 0.7 >> conv_thr = 1.0D-10 >> / >> ATOMIC_SPECIES >> P 30.973761 P.pw91-n-van.UPF >> ATOMIC_POSITIONS crystal >> P 0.0000000000 0.0000000000 0.00000000000 >> P 0.0000000000 0.0000000000 0.50000000000 >> P 0.0000000000 0.0000000000 0.25000000000 >> P 0.0000000000 0.0000000000 0.75000000000 >> K_POINTS {automatic} >> 16 16 16 0 0 0 >> EOF >> $ECHO " running the scf calculation for >> P...\c" >> $PW_COMMAND < pcmcm.scf.in > pcmcm.scf.out >> $ECHO " done" >> >> # phonon calculation on a (4 4 4) uniform grid of >> q-points >> cat > pcmcm.ph.in << EOF >> phonons of cmcm P >> &inputph >> tr2_ph=1.0d-12, >> prefix='pcmcm', >> ldisp=.true., >> nq1=4, nq2=4, nq3=4 >> amass(1)=30.973761, >> outdir='$TMP_DIR/', >> fildyn='pcmcm.dyn', >> / >> EOF >> $ECHO " running the phonon calculation at >> Gamma...\c" >> $PH_COMMAND < pcmcm.ph.in > pcmcm.ph.out >> >> >> >> Thank you very much for your help, >> >> Miriam. >> >> ---------------------- >> Miriam Marques >> School of Physics >> University of Edinburgh >> ---------------------- >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & > Alloys, Russia, and > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com > > > > ____________________________________________________________________________________ > Be a better Heartthrob. Get better relationship answers from someone > who knows. Yahoo! Answers - Check it out. > http://answers.yahoo.com/dir/?link=list&sid=396545433 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From tgrassma at ucsd.edu Sun Aug 19 03:28:38 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Sat, 18 Aug 2007 18:28:38 -0700 Subject: [Pw_forum] EXX files I/O Message-ID: <000301c7e200$45f0b9f0$6300a8c0@Crom> Hello. I've been working with the EXX implementation in PWscf for a little bit now (just doing testing on bulk Si for the time being, getting to know the code a little bit, as I'm new to PWscf). I'm working on figuring out the optimal parallelization and disk I/O parameters. My cluster uses an NSF file system to share the /home directory (I know, everyone says not to with PWscf, but I don't see that I've much other choice). However, the compute nodes have large scratch disks, so setting the wfcdir tag to use the local node scratch disks helps reduce the NFS disk I/O. However, I find that the prefix.exx# files are still being written to the outdir, and they tend to be pretty big (each file is tens to hundreds of MBs, depending on the number of procs the job is being run on, even for this small bulk system). It looks like these files get rewritten every hybrid refinement loop (i.e. "NOW GO BACK TO REFINE HYBRID CALCULATION"). I'm guessing these files will get considerably larger once the system gets larger, too, in which case this I/O will really end up costing a lot in the wall time (and I plan on trying some considerably larger systems in the near future), yes? I looked in input.f90 source file and didn't see anything about it, but I was wondering if there was any way (or a plan to implement such a thing, if possible) to treat these files in the same way (some equivalent to wfcdir)? Or if not, does anyone have any suggestions? Thanks, Tyler Grassman Materials Science and Engineering University of California, San Diego From beyondstar2000 at gmail.com Sun Aug 19 05:07:39 2007 From: beyondstar2000 at gmail.com (david david) Date: Sun, 19 Aug 2007 11:07:39 +0800 Subject: [Pw_forum] EXX files I/O In-Reply-To: <000301c7e200$45f0b9f0$6300a8c0@Crom> References: <000301c7e200$45f0b9f0$6300a8c0@Crom> Message-ID: i want to know whethe the PW codes can calculate the maximally-localized Wannier functions of metal ,and whether it is a big memory job.thank you very much -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070819/dd3d05f6/attachment.htm From marzari at MIT.EDU Sun Aug 19 23:40:55 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 19 Aug 2007 17:40:55 -0400 Subject: [Pw_forum] EXX files I/O In-Reply-To: References: <000301c7e200$45f0b9f0$6300a8c0@Crom> Message-ID: <46C8B8E7.5040304@mit.edu> david david wrote: > > i want to know whethe the PW codes can calculate the > maximally-localized Wannier functions of metal ,and whether it is a big > memory job.thank you very much Yes. No. What's your affiliation ? nic --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From degironc at sissa.it Mon Aug 20 00:11:08 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 20 Aug 2007 00:11:08 +0200 (CEST) Subject: [Pw_forum] EXX files I/O In-Reply-To: <000301c7e200$45f0b9f0$6300a8c0@Crom> References: <000301c7e200$45f0b9f0$6300a8c0@Crom> Message-ID: Thank'you for noticing that... it will be changed. a simple temporary fix is to move the opening of the exx files into openfil.f90 #ifdef EXX exx_nwordwfc=2*nrxxs iunexx = find_free_unit() call diropn(iunexx,'exx', exx_nwordwfc, exst) #endif in this way they will be open in the same directory as wfc## files. Thank you, stefano de Gironcoli, SISSA and DEMOCRITOS On Sat, 18 Aug 2007, Tyler Grassman wrote: > Hello. I've been working with the EXX implementation in PWscf for a little > bit now (just doing testing on bulk Si for the time being, getting to know > the code a little bit, as I'm new to PWscf). I'm working on figuring out > the optimal parallelization and disk I/O parameters. My cluster uses an NSF > file system to share the /home directory (I know, everyone says not to with > PWscf, but I don't see that I've much other choice). However, the compute > nodes have large scratch disks, so setting the wfcdir tag to use the local > node scratch disks helps reduce the NFS disk I/O. However, I find that the > prefix.exx# files are still being written to the outdir, and they tend to be > pretty big (each file is tens to hundreds of MBs, depending on the number of > procs the job is being run on, even for this small bulk system). It looks > like these files get rewritten every hybrid refinement loop (i.e. "NOW GO > BACK TO REFINE HYBRID CALCULATION"). I'm guessing these files will get > considerably larger once the system gets larger, too, in which case this I/O > will really end up costing a lot in the wall time (and I plan on trying some > considerably larger systems in the near future), yes? I looked in input.f90 > source file and didn't see anything about it, but I was wondering if there > was any way (or a plan to implement such a thing, if possible) to treat > these files in the same way (some equivalent to wfcdir)? Or if not, does > anyone have any suggestions? > > Thanks, > > Tyler Grassman > Materials Science and Engineering > University of California, San Diego > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Mon Aug 20 00:06:28 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 19 Aug 2007 18:06:28 -0400 (EDT) Subject: [Pw_forum] how to ask. was Re: EXX files I/O In-Reply-To: Message-ID: On Sun, 19 Aug 2007, david david wrote: dear "david david beydondstar2000", to get a useful answer in this forum, it will be helpful if you understand a few things about how to send e-mails to mailing lists in general and particular this one. - _please_ use a meaningful subject line, however convenient it is to just reply to an existing e-mail. this is even more important, if you receive a digested version of the mailing list and quote everything. - many people in this forum prefer answering only to people that state their name and affiliation. it is not (yet) a strict rule, but adding, e.g., a short signature to all your e-mails is simple and will be much appriciated DD> i want to know whethe the PW codes can calculate the maximally-localized DD> Wannier functions of metal ,and whether it is a big memory job.thank you DD> very much - please always have a look at the manual and search the mailing list archives, before asking. all questions except the last one (which however can be inferred with a little bit of common sense) you could have answered yourself with very little effort. - in general, the quality of the answer you can get depends on the quality of the question you ask. since you didn't specify what you consider to be a big memory job (people's opinion on that depends a lot on what kind of hardware they have access to), it is very difficult to give a definite answer here. thanks and best regards, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jideson at gmail.com Mon Aug 20 03:25:58 2007 From: jideson at gmail.com (jideson) Date: Mon, 20 Aug 2007 09:25:58 +0800 Subject: [Pw_forum] questions about vc-relax or geomtry optimization Message-ID: <1187573159.4665.18.camel@amd.mm> Dear experts, I read some emails about vc-relax in this list, but still have some questions. It seems that geometry optimization (both cell and atomic postions) in pwscf is a diffcult job than other softwares such as CASTEP. Can you give me a step-by-step tutorial ? By the way , another question , are there differences between cp.x and cpmd(www.cpmd.org) code ? Thanks! Best regards Jideson From xylnew at gmail.com Mon Aug 20 03:40:06 2007 From: xylnew at gmail.com (Yuanliang Xie) Date: Mon, 20 Aug 2007 09:40:06 +0800 Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: <1187573159.4665.18.camel@amd.mm> References: <1187573159.4665.18.camel@amd.mm> Message-ID: <1187574006.5141.2.camel@amd.mm> Dear jideson, ? 2007-08-20?? 09:25 +0800?jideson??? > Dear experts, > I read some emails about vc-relax in this list, but still have > some questions. It seems that geometry optimization (both cell and > atomic postions) in pwscf is a diffcult job than other softwares such as > CASTEP. Can you give me a step-by-step tutorial ? Sorry. You must do_it_yourself. Because this is a GNU open source code. :) > By the way , another question , are there differences between cp.x > and cpmd(www.cpmd.org) code ? Thanks! > > > > > Best regards > > Jideson > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Yuanliang Xie From xylnew at gmail.com Mon Aug 20 03:44:24 2007 From: xylnew at gmail.com (Yuanliang Xie) Date: Mon, 20 Aug 2007 09:44:24 +0800 Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: <1187573159.4665.18.camel@amd.mm> References: <1187573159.4665.18.camel@amd.mm> Message-ID: <1187574264.5141.4.camel@amd.mm> Dear jideson, Please see this link , http://www.vlab.msi.umn.edu/events/download/VCS_tutorial.pdf ? 2007-08-20?? 09:25 +0800?jideson??? > Dear experts, > I read some emails about vc-relax in this list, but still have > some questions. It seems that geometry optimization (both cell and > atomic postions) in pwscf is a diffcult job than other softwares such as > CASTEP. Can you give me a step-by-step tutorial ? > By the way , another question , are there differences between cp.x > and cpmd(www.cpmd.org) code ? Thanks! > > > > Best regards > > Jideson > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Yuanliang Xie From akohlmey at cmm.chem.upenn.edu Mon Aug 20 02:44:06 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 19 Aug 2007 20:44:06 -0400 (EDT) Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: <1187573159.4665.18.camel@amd.mm> Message-ID: On Mon, 20 Aug 2007, jideson wrote: J> Dear experts, dear jideson, J> I read some emails about vc-relax in this list, but still have J> some questions. It seems that geometry optimization (both cell and J> atomic postions) in pwscf is a diffcult job than other softwares such as i disagree. it is not difficult, you just need to know what you are doing and particularly know what you can expect. the quantum espresso package allows you a lot of flexibility, but the price for that is that not everything works automatically right. usually, if something is not working easily, it is an indication, that you have not yet understood what you are doing (or else it would be obvious) or you have a problem that is not easy to start with or (which is rare) have found a bug in the code. J> CASTEP. Can you give me a step-by-step tutorial ? there are some input examples within the distribution and you may want to check out material from previous QE tutorials, e.g., the material at: http://www.vlab.msi.umn.edu/events/lecture.shtml J> By the way , another question , are there differences between cp.x J> and cpmd(www.cpmd.org) code ? Thanks! yes. both have the same origin, there have evolved into quite different species by now. cheers, axel. J> J> J> J> Best regards J> J> Jideson J> J> _______________________________________________ J> Pw_forum mailing list J> Pw_forum at pwscf.org J> http://www.democritos.it/mailman/listinfo/pw_forum J> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jideson at gmail.com Mon Aug 20 04:11:32 2007 From: jideson at gmail.com (jideson) Date: Mon, 20 Aug 2007 10:11:32 +0800 Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: References: Message-ID: <1187575892.5141.23.camel@amd.mm> Dear Dr. Axel, Thank you for your response quickly. Can you give me some details about BFGS in geometry optimization(which is used in CASTEP) ? I choose it in pwscf , it complains not implement. I want to predict a structure using pwscf . Can I get a reasonable result using vc-relax when my configure is far from equilibrium. ? 2007-08-19?? 20:44 -0400?Axel Kohlmeyer??? > On Mon, 20 Aug 2007, jideson wrote: > > J> Dear experts, > > dear jideson, > > J> I read some emails about vc-relax in this list, but still have > J> some questions. It seems that geometry optimization (both cell and > J> atomic postions) in pwscf is a diffcult job than other softwares such as > > i disagree. it is not difficult, you just need to know what you are > doing and particularly know what you can expect. the quantum espresso > package allows you a lot of flexibility, but the price for that is > that not everything works automatically right. usually, if something > is not working easily, it is an indication, that you have not yet > understood what you are doing (or else it would be obvious) or > you have a problem that is not easy to start with or (which is rare) > have found a bug in the code. > > J> CASTEP. Can you give me a step-by-step tutorial ? > > there are some input examples within the distribution > and you may want to check out material from previous QE > tutorials, e.g., the material at: > http://www.vlab.msi.umn.edu/events/lecture.shtml > > J> By the way , another question , are there differences between cp.x > J> and cpmd(www.cpmd.org) code ? Thanks! > > yes. both have the same origin, there have evolved into > quite different species by now. > > cheers, > axel. > > J> > J> > J> > J> Best regards > J> > J> Jideson > J> > J> _______________________________________________ > J> Pw_forum mailing list > J> Pw_forum at pwscf.org > J> http://www.democritos.it/mailman/listinfo/pw_forum > J> -- Best regards Jideson From tgrassma at ucsd.edu Mon Aug 20 04:10:29 2007 From: tgrassma at ucsd.edu (Tyler Grassman) Date: Sun, 19 Aug 2007 19:10:29 -0700 Subject: [Pw_forum] EXX files I/O Message-ID: <000001c7e2cf$486a9280$6300a8c0@Crom> Thank you very much for the response. I was only able to get everything to work right by putting iunexx and exx_nwordwfc into Modules/io_files.f90 and adding/removing the appropriate USE and INTEGER declarations in exx.f90 and openfil.f90 (as well as removing "iunexx = find_free_unit" and the diropn call from exx.f90). Results-wise... It doesn't really do much for the CPU time (as expected), but brings the wall times down to almost equal to the CPU times, with the biggest effect being for smaller #procs (where the .exx# files are quite large). I'm sure the effect will be even bigger with larger system sizes. So, thanks again! Regards, Tyler Grassman Materials Science and Engineering University of California, San Diego >Thank'you for noticing that... it will be changed. >a simple temporary fix is to move the opening of the exx files into >openfil.f90 > >#ifdef EXX > exx_nwordwfc=2*nrxxs > iunexx = find_free_unit() > call diropn(iunexx,'exx', exx_nwordwfc, exst) >#endif > >in this way they will be open in the same directory as wfc## files. >Thank you, > >stefano de Gironcoli, >SISSA and DEMOCRITOS > >On Sat, 18 Aug 2007, Tyler Grassman wrote: > >> Hello. I've been working with the EXX implementation in PWscf for a little >> bit now (just doing testing on bulk Si for the time being, getting to know >> the code a little bit, as I'm new to PWscf). I'm working on figuring out >> the optimal parallelization and disk I/O parameters. My cluster uses an NSF >> file system to share the /home directory (I know, everyone says not to with >> PWscf, but I don't see that I've much other choice). However, the compute >> nodes have large scratch disks, so setting the wfcdir tag to use the local >> node scratch disks helps reduce the NFS disk I/O. However, I find that the >> prefix.exx# files are still being written to the outdir, and they tend to be >> pretty big (each file is tens to hundreds of MBs, depending on the number of >> procs the job is being run on, even for this small bulk system). It looks >> like these files get rewritten every hybrid refinement loop (i.e. "NOW GO >> BACK TO REFINE HYBRID CALCULATION"). I'm guessing these files will get >> considerably larger once the system gets larger, too, in which case this I/O >> will really end up costing a lot in the wall time (and I plan on trying some >> considerably larger systems in the near future), yes? I looked in input.f90 >> source file and didn't see anything about it, but I was wondering if there >> was any way (or a plan to implement such a thing, if possible) to treat >> these files in the same way (some equivalent to wfcdir)? Or if not, does >> anyone have any suggestions? >> >> Thanks, >> >> Tyler Grassman >> Materials Science and Engineering >> University of California, San Diego >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> From akohlmey at cmm.chem.upenn.edu Mon Aug 20 04:12:30 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 19 Aug 2007 22:12:30 -0400 (EDT) Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: <1187575892.5141.23.camel@amd.mm> Message-ID: On Mon, 20 Aug 2007, jideson wrote: J> Dear Dr. Axel, J> Thank you for your response quickly. J> Can you give me some details about BFGS in geometry optimization(which J> is used in CASTEP) ? I choose it in pwscf , it complains not J> implement. i cannot comment on CASTEP. pw.x just does _exactly_ what one would expect after reading Doc/INPUT_PW! bfgs is only available for regular geometry optimization. J> I want to predict a structure using pwscf . Can I get a reasonable J> result using vc-relax when my configure is far from equilibrium. that depends on what you define as reasonable. nobody can tell you anything specific unless you provide more specific information. variable cell calculations need for sure more care than constant volume calculations as there are more ways to get wrong results. ...and while you're at it. please remember to provide name and affiliation. thanks, axel. [...] -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ihsanas at yahoo.com Mon Aug 20 10:22:41 2007 From: ihsanas at yahoo.com (ÇÍÓÇä ÚÑíÞÇÊ) Date: Mon, 20 Aug 2007 01:22:41 -0700 (PDT) Subject: [Pw_forum] delete step from neb Message-ID: <578563.27593.qm@web52310.mail.re2.yahoo.com> Hi neb was working fine but when electricity cutoff several times ,it seems as it stuck in same position and repeated it, can I delete the final path and then restart neb again ,if the answer is yes ,haw can I do so?when I delete the final path from temp it give me error ,please help me. best regard Ihsan ____________________________________________________________________________________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 From jideson at gmail.com Mon Aug 20 10:44:04 2007 From: jideson at gmail.com (jideson) Date: Mon, 20 Aug 2007 16:44:04 +0800 Subject: [Pw_forum] Why cannot download the old version of pwscf Message-ID: <1187599445.3029.7.camel@amd.mm> Dear pwscf team, I cannot download pwscf v1.0( write in f77) from http://www.pwscf.org/download.htm#previous. How can I get it? Thank you. -- Best regards Jideson From mitujoshi at gmail.com Mon Aug 20 11:35:00 2007 From: mitujoshi at gmail.com (Joshi Mitesh) Date: Mon, 20 Aug 2007 15:05:00 +0530 Subject: [Pw_forum] Phase transtion calculation Message-ID: Hi users, I am in a learning phase of pwscf and now trying to calculate phase transition, I take a simple example AlAs and calculate the total energies - volume for Zincblende (ZB) and Rocksalt (NaCl) Structures, but when I plot Enthalpy ( H = E +PV ) --> P curve after fitting EOS using ev.x. the curves crosses at 0 kbar. which is wrong. what shoud be the error ? am I doing a silly mistake ? Thanking you, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070820/5bc34836/attachment.htm From mitujoshi at gmail.com Mon Aug 20 11:37:21 2007 From: mitujoshi at gmail.com (Joshi Mitesh) Date: Mon, 20 Aug 2007 15:07:21 +0530 Subject: [Pw_forum] Fwd: Phase transtion calculation In-Reply-To: References: Message-ID: Hi users, I am in a learning phase of pwscf and now trying to calculate phase transition, I take a simple example AlAs and calculate the total energies - volume for Zincblende (ZB) and Rocksalt (NaCl) Structures, but when I plot Enthalpy ( H = E +PV ) --> P curve after fitting EOS using ev.x. the curves crosses at 0 kbar. which is wrong. what shoud be the error ? am I doing a silly mistake ? Thanking you, ----------------------------------------------------------------------------------------------- Mitesh Joshi Department of Physics, S P University, Anand Gujarat India ------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070820/8cf6172b/attachment.htm From jideson at gmail.com Mon Aug 20 12:02:18 2007 From: jideson at gmail.com (jideson) Date: Mon, 20 Aug 2007 18:02:18 +0800 Subject: [Pw_forum] Phase transtion calculation In-Reply-To: References: Message-ID: <1187604139.3029.16.camel@amd.mm> ? 2007-08-20?? 15:05 +0530?Joshi Mitesh??? > Hi users, Dear joshi, Do you check the convergence? The "pulay stress" is also important when cell changes. > I am in a learning phase of pwscf and now trying to > calculate phase transition, > I take a simple example AlAs and calculate the total energies - volume > for Zincblende (ZB) and Rocksalt (NaCl) Structures, > but when I plot Enthalpy ( H = E +PV ) --> P curve after fitting EOS > using ev.x. the curves crosses at 0 kbar. which is wrong. > what shoud be the error ? am I doing a silly mistake ? > Thanking you, > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Best regards Jideson From baroni at sissa.it Mon Aug 20 12:26:37 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Aug 2007 12:26:37 +0200 Subject: [Pw_forum] Why cannot download the old version of pwscf In-Reply-To: <1187599445.3029.7.camel@amd.mm> References: <1187599445.3029.7.camel@amd.mm> Message-ID: <91BDB718-881F-4BAB-9D6A-A50C219F3AE3@sissa.it> Dear Jideson: > > Dear pwscf team, > I cannot download pwscf v1.0( write in f77) from > http://www.pwscf.org/download.htm#previous. How can I get it? > Thank you. I think it would be a very bad idea for you to use such an obsolete version of the code and for us to keep distributing it. Why, for God's sake, would you ever be interested in using such a version? fortran 90 compilers are easily available to anybody, these days ... > -- > Best regards > > Jideson please, do not forget to indicate sign with your full name and affiliation. Stefano Baroni --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070820/5679582c/attachment-0001.htm From baroni at sissa.it Mon Aug 20 12:54:05 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Aug 2007 12:54:05 +0200 Subject: [Pw_forum] Fwd: Phase transtion calculation In-Reply-To: References: Message-ID: <6CA1B142-A1EE-4D8B-A25F-140E94508433@sissa.it> On Aug 20, 2007, at 11:37 AM, Joshi Mitesh wrote: > > > > Hi users, > I am in a learning phase of pwscf and now trying to > calculate phase transition, > I take a simple example AlAs and calculate the total energies - > volume for Zincblende (ZB) and Rocksalt (NaCl) Structures, > but when I plot Enthalpy ( H = E +PV ) --> P curve after fitting > EOS using ev.x. the curves crosses at 0 kbar. which is wrong. > what shoud be the error ? am I doing a silly mistake ? Most probably. Have you tried to repproduce first the E vs. V data of, say, Mujica, Needs, and Munoz (PRB 52, 8881, 1995)? Have you paid attention to the fact that the NaCl phase is metallic and requires therefore a special care for the k-point integration? Cheers - SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070820/9f5b4578/attachment.htm From rudenko at dpt.ustu.ru Mon Aug 20 12:45:47 2007 From: rudenko at dpt.ustu.ru (Alexander Rudenko) Date: Mon, 20 Aug 2007 16:45:47 +0600 Subject: [Pw_forum] Angular moment in non-collinear spin-orbit calculations Message-ID: <20070820104547.GA29910@rudenko-desktop> Dear espresso users, I have some question about the possibility of estimating the angular component of magnetic moment in non-collinear spin-orbit case. How is it can to be done within espresso? Or is it not yet realized? As far I now, the PROJWFC utility gives only the total moment, projected onto atomic orbitals, but separation to spin and angular moment is absent there. Thank you in advance. -- Alexander Rudenko Department of Theoretical Physics and Applied Mathematics Ural State Technical University Ekaterinburg, Russia From baroni at sissa.it Mon Aug 20 13:35:40 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Aug 2007 13:35:40 +0200 Subject: [Pw_forum] Angular moment in non-collinear spin-orbit calculations In-Reply-To: <20070820104547.GA29910@rudenko-desktop> References: <20070820104547.GA29910@rudenko-desktop> Message-ID: Dera Sasha (?), the calculation of the orbital contribution to the total magnetization is not (yet) implemented in QE. Actually, the very concept of orbital magnetization in an infinite system is subject to intense theoretical research these days (say for instance Phys. Rev. Lett. 95, 137205 (2005), Phys. Rev. B 74, 024408 (2006), cond-mat 0705.3771). If you have a magnetic impurity in an extended system, a reasonable fix would be to calculate the projection of the dos onto localized orbitals (which, I think, can be done using PROJWFC), and to get from that an estimate of the orbital magnetization. Hope this helps SB On Aug 20, 2007, at 12:45 PM, Alexander Rudenko wrote: > Dear espresso users, > > I have some question about the possibility of estimating the angular > component of magnetic moment in non-collinear spin-orbit case. How > is it > can to be done within espresso? Or is it not yet realized? As far I > now, > the PROJWFC utility gives only the total moment, projected onto atomic > orbitals, but separation to spin and angular moment is absent there. > > Thank you in advance. > > -- > Alexander Rudenko > Department of Theoretical Physics and Applied Mathematics > Ural State Technical University > Ekaterinburg, Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070820/b85785a7/attachment-0001.htm From marcel at physik.tu-berlin.de Mon Aug 20 13:59:41 2007 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Mon, 20 Aug 2007 13:59:41 +0200 (CEST) Subject: [Pw_forum] questions about vc-relax or geomtry optimization In-Reply-To: <1187574264.5141.4.camel@amd.mm> References: <1187573159.4665.18.camel@amd.mm> <1187574264.5141.4.camel@amd.mm> Message-ID: <20070820135323.T17046@rosa.physik-pool.tu-berlin.de> Dear experts Now a question arises from myself: In the link below the parameter wmass is set as 0.0015 (amu) How is that chosen, as the default is the sum of the masses in the unit cell? That would be 2 times the mass of an As atom, \approx 150 amu . This would be 5 orders of magnitude larger? Thanks in advance Marcel On Mon, 20 Aug 2007, Yuanliang Xie wrote: > Dear jideson, > Please see this link , > http://www.vlab.msi.umn.edu/events/download/VCS_tutorial.pdf > > ?? 2007-08-20???? 09:25 +0800??jideson?????? >> Dear experts, >> I read some emails about vc-relax in this list, but still have >> some questions. It seems that geometry optimization (both cell and >> atomic postions) in pwscf is a diffcult job than other softwares such as >> CASTEP. Can you give me a step-by-step tutorial ? >> By the way , another question , are there differences between cp.x >> and cpmd(www.cpmd.org) code ? Thanks! >> >> >> >> Best regards >> >> Jideson >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > -- > Yuanliang Xie > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From emenendez at macul.ciencias.uchile.cl Mon Aug 20 18:34:05 2007 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Mon, 20 Aug 2007 12:34:05 -0400 (CLT) Subject: [Pw_forum] questions about vc-relax or geomtry Message-ID: Hi, I take the occasion to ask some clarifying on the variable-cell optimization. Maybe it seems difficult because is not well documented. After some laborious vc-relax calculations with small unit cells, the optimal values of wmass are still misterious for me. When I follows the the instructions in INPUT_PW wmass REAL ( default = sum of atomic masses in the cell ) fictitious cell mass [amu] for variable-cell simulations (both 'vc-md' and 'vc-relax') then I see that the cell varies extremely slowly. Then I have chosen "sum of atomic masses in the cell"/Factor using Factor as 100,1000,etc until I see and effective change in volume. When it happens I see the volume converges fast, but then the shape began to fluctuate for a long time (maybe this is the moment to use Factor=1). If wmass is not specified pw provides a value that is reported in the output and is much smaller than "sum of atomic masses in the cell". For example, a Pt in HCP structure, with two atoms per cell as "sum of atomic masses in the cell"=2x195.084=390.168 the default reported by pw when wmass is unset is "0.00300 AMU/(a.u.)^2" There is a factor of 130000, which I do not understand. ?What is a.u. in AMU/(a.u.)^2 ? The units of W seems to be E*T^2/V^2 (E=Energy,V=Volume,T=time) in the Andersen and Parrinello-Ramman Lagrangians. http://www.vlab.msi.umn.edu/events/download/vlab_lectures/renata/lecture1.pdf Is the factor related to the volume? In my case of Platinum el volumen es 203.4(a.u.)^3., so V^2=41371 which is near 130000/3. Hence, some relation is betwwen the mass in AMU, the volume, and maybe the time step. ?Can someone explain it? Second, it seems that one value is appropriate for volume relaxation, and other for shape relaxation, depending on the elastic constants. I welcome know-how sharing. Third. In damped dynamics, there should be some damping factor, but it seems to be fixed in PWSCF. Is it? Eduardo A. Menendez Proupin Department of Physics Faculty of Science University of Chile Las Palmeras 3425 ?u?oa, Santiago Chile Phone: (56)(2) 978 74 11 Fax : (56)(2) 271 29 73 http://fisica.ciencias.uchile.cl/~emenendez/ ? 2007-08-19?? 20:44 -0400?Axel Kohlmeyer??? > On Mon, 20 Aug 2007, jideson wrote: > > J> Dear experts, > > dear jideson, > > J> I read some emails about vc-relax in this list, but still have > J> some questions. It seems that geometry optimization (both cell and > J> atomic postions) in pwscf is a diffcult job than other softwares such as > > i disagree. it is not difficult, you just need to know what you are > doing and particularly know what you can expect. the quantum espresso > package allows you a lot of flexibility, but the price for that is > that not everything works automatically right. usually, if something > is not working easily, it is an indication, that you have not yet > understood what you are doing (or else it would be obvious) or > you have a problem that is not easy to start with or (which is rare) > have found a bug in the code. > > J> CASTEP. Can you give me a step-by-step tutorial ? > > there are some input examples within the distribution > and you may want to check out material from previous QE > tutorials, e.g., the material at: > http://www.vlab.msi.umn.edu/events/lecture.shtml > > J> By the way , another question , are there differences between cp.x > J> and cpmd(www.cpmd.org) code ? Thanks! > > yes. both have the same origin, there have evolved into > quite different species by now. > > cheers, > axel. From degironc at sissa.it Tue Aug 21 06:27:06 2007 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 21 Aug 2007 06:27:06 +0200 (CEST) Subject: [Pw_forum] questions about vc-relax or geomtry In-Reply-To: References: Message-ID: the variable cell shape MD part in PWscf is based on Renata Wentzcovitch's code, described in R.M. Wentzcovitch, PRB 44, 2358 (1991). Parrinello-Ramhan MD is also available from the same code. Notice however that the meaning of cell-mass in the two formulations is not the same. For a discussion of these issues one should look at the original references. The default value in PWscf are set to wmass=0.75*Tot_Mass/pi**2 for Parrinello Rahman MD and to wmass=0.75*Tot_Mass/pi**2/Omega**(2/3) for Wentzcovitch MD. Documentation should be corrected. I think that it is a good idea to start from the default value and possibly tweak a bit around it. I think it is a good idea to relax the internal coordinates before starting the variable cell-shape optimization. I think that it is good policy to set all atomic masses to the same value (for instance 1.0) if one is interested in relaxation so as to let Hydrogen and Uranium react in the same way to the forces, as the variation in interatomic forces is way less significant than (and uncorrelated with) the variation of atomic masses. I think that one should gain some idea what the proper time step should be with some short MD (undamped) run to estimate the period of free oscilaltions. Similar systems are likely to need similar time-steps. The damped dynamics performs a quickmin-style damping: at each step the velocity (of the internal coordinates or of the cell) is projected on the direction of the forces (and stress). When they happen to have a negative projection the corresponding velocity is stopped. No damping factor is needed. Hope this helps, stefano PS: the part of the code dealing with cell dynamincs is fairly independent from the rest of the code: only some information on the current and previous atomic&cell positions and forces&stress values are needed at each iteration. Whoever has the perfect, plug-and-play, easy-to-use, robust, efficient, well documented variable-cell-shape enthalpy minimizer is most welcome to provide it to the community. It will be relatively easy to add this functionality. thanks. On Mon, 20 Aug 2007, Eduardo Ariel Menendez P wrote: > > Hi, > I take the occasion to ask some clarifying on the variable-cell > optimization. Maybe it seems difficult because is not well documented. > After some laborious vc-relax calculations with small unit > cells, the optimal values of wmass are still misterious for me. > > When I follows the the instructions in INPUT_PW > > wmass REAL ( default = sum of atomic masses in the cell ) > fictitious cell mass [amu] for variable-cell simulations > (both 'vc-md' and 'vc-relax') > > then I see that the cell varies extremely slowly. Then I have chosen > "sum of atomic masses in the cell"/Factor using Factor as 100,1000,etc > until I see and effective change in volume. When it happens I see the volume > converges fast, but then the shape began to fluctuate for a long time > (maybe this is the moment to use Factor=1). > If wmass is not specified pw provides a value that > is reported in the output and is much smaller than "sum of atomic masses > in the cell". > > For example, a Pt in HCP structure, with two atoms per cell as > "sum of atomic masses in the cell"=2x195.084=390.168 > > the default reported by pw when wmass is unset is "0.00300 AMU/(a.u.)^2" > There is a factor of 130000, which I do not understand. ?What is a.u. in > AMU/(a.u.)^2 ? > > The units of W seems to be E*T^2/V^2 (E=Energy,V=Volume,T=time) in the > Andersen and Parrinello-Ramman Lagrangians. > http://www.vlab.msi.umn.edu/events/download/vlab_lectures/renata/lecture1.pdf > Is the factor related to the volume? > In my case of Platinum el volumen es 203.4(a.u.)^3., so V^2=41371 which is > near 130000/3. > > Hence, some relation is betwwen the mass in AMU, the volume, and maybe the > time step. ?Can someone explain it? > > Second, it seems that one value is appropriate for volume relaxation, and > other for shape relaxation, depending on the elastic constants. I > welcome know-how sharing. > > Third. In damped dynamics, there should be some damping factor, but it > seems to be fixed in PWSCF. Is it? > > Eduardo A. Menendez Proupin > Department of Physics > Faculty of Science > University of Chile > Las Palmeras 3425 > ?u?oa, Santiago > Chile > Phone: (56)(2) 978 74 11 > Fax : (56)(2) 271 29 73 > http://fisica.ciencias.uchile.cl/~emenendez/ > > > > > ? 2007-08-19?? 20:44 -0400?Axel Kohlmeyer??? >> On Mon, 20 Aug 2007, jideson wrote: >> >> J> Dear experts, >> >> dear jideson, >> >> J> I read some emails about vc-relax in this list, but still have >> J> some questions. It seems that geometry optimization (both cell and >> J> atomic postions) in pwscf is a diffcult job than other softwares such > as >> >> i disagree. it is not difficult, you just need to know what you are >> doing and particularly know what you can expect. the quantum espresso >> package allows you a lot of flexibility, but the price for that is >> that not everything works automatically right. usually, if something >> is not working easily, it is an indication, that you have not yet >> understood what you are doing (or else it would be obvious) or >> you have a problem that is not easy to start with or (which is rare) >> have found a bug in the code. >> >> J> CASTEP. Can you give me a step-by-step tutorial ? >> >> there are some input examples within the distribution >> and you may want to check out material from previous QE >> tutorials, e.g., the material at: >> http://www.vlab.msi.umn.edu/events/lecture.shtml >> >> J> By the way , another question , are there differences between cp.x >> J> and cpmd(www.cpmd.org) code ? Thanks! >> >> yes. both have the same origin, there have evolved into >> quite different species by now. >> >> cheers, >> axel. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sei.ou0722 at gmail.com Wed Aug 22 09:38:32 2007 From: sei.ou0722 at gmail.com (sei ou) Date: Wed, 22 Aug 2007 16:38:32 +0900 Subject: [Pw_forum] Interface geometry relaxation Message-ID: <161e5bd50708220038x361a3be9i4ca103816e4cef64@mail.gmail.com> Dear Forum, I am using PWscf for interface structural optimization. The geometry relaxation on interface (LiCoO2/sulfides) seems very difficult to converge so far. Can anyone give me help? Here is my input file: &CONTROL calculation = "relax", prefix = "intf66a_rlx" pseudo_dir = "./", outdir = "./", / &SYSTEM ibrav = 14, celldm(1) = 61.18796, celldm(2) = 0.18633, celldm(3) = 0.38711, celldm(4) = -0.22231431, celldm(5) = -0.39398, celldm(6) = 0.267793, nat = 66, ntyp = 5, ecutwfc = 42.D0, ecutrho = 320.D0, occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.05D0 / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.1D0, mixing_mode = "local-TF", / &IONS ion_dynamics = "bfgs", opt_scheme = "broyden", bfgs_ndim = 3, trust_radius_max = 0.8D0, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES P 30.9737 P.pbe-n-van.UPF Li 6.941 Li.pbe-n-van.UPF S 32.066 S.pbe-van_bm.UPF Co 58.9332 Co.pbe-nd-rrkjus.UPF O 15.9994 O.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} ........ K_POINTS crystal 1 0.2914500000 0.5294200000 -0.2781600000 1.0 =================================================== The output is as following: Total force = 1.677255 Total SCF correction = 0.001300 Total force = 0.607898 Total SCF correction = 0.002820 Total force = 0.448659 Total SCF correction = 0.002098 Total force = 0.352568 Total SCF correction = 0.001579 Total force = 0.291404 Total SCF correction = 0.001432 Total force = 0.254533 Total SCF correction = 0.001601 Total force = 0.233841 Total SCF correction = 0.001331 Total force = 0.223115 Total SCF correction = 0.001884 Total force = 0.222679 Total SCF correction = 0.001979 Total force = 0.230224 Total SCF correction = 0.001892 Total force = 0.241234 Total SCF correction = 0.001275 Total force = 0.252683 Total SCF correction = 0.001494 Total force = 0.266314 Total SCF correction = 0.001429 Total force = 0.284588 Total SCF correction = 0.001093 Total force = 0.309129 Total SCF correction = 0.001386 Total force = 0.312575 Total SCF correction = 0.001656 Total force = 0.306147 Total SCF correction = 0.001511 Total force = 0.280490 Total SCF correction = 0.001399 Total force = 0.261216 Total SCF correction = 0.000735 Total force = 0.244781 Total SCF correction = 0.001154 Total force = 0.230320 Total SCF correction = 0.001218 Thank you in advance Sei Ou Simulatio Co. Yokohama-shi, Japan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070822/102e4336/attachment.html From claudio.attaccalite at gmail.com Tue Aug 21 22:59:43 2007 From: claudio.attaccalite at gmail.com (Claudio Attaccalite) Date: Tue, 21 Aug 2007 22:59:43 +0200 Subject: [Pw_forum] Lecture notes on PWSCF Message-ID: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> Dear All in the last period I used PWSCF for different calculations and because the documentation is not so great, I searched on Internet and I found different lecture notes on PSWCF, I send the list if it can be useful to someone else: Vlab lecture notes: http://www.vlab.msi.umn.edu/events/lecture.shtml HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO* *: http://people.sissa.it/~degironc/QE-Tutorial/ Atomistic Computer Modeling of Materials: http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-320Spring-2005/CourseHome/index.htm Electronic Structure Calculations and Their Application in Material Science: http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ Tutorial on calculating phonons: http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/Tutorial_phonons_alfe.pdf?version=1 Modeling from the nanoscale to the macroscale: http://ermes.physics.ncsu.edu/MSE791K.htm Quantum Espresso Lab: http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab It should be nice if this list can appear in the pwscf webpage Best Regards Claudio Attaccalite -- ========================================================== Claudio Attaccalite Institute for Electronics, Microelectronics, and Nanotechnology Dept. ISEN B.P. 60069 59652 Villeneuve d'Ascq Cedex France Skype: claudioattaccalite web site: www.attaccalite.altervista.org =========================================================== Freely download scientific books from: www.freescience.info -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070821/c74c1da8/attachment.htm From baroni at sissa.it Wed Aug 22 11:17:09 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 22 Aug 2007 11:17:09 +0200 Subject: [Pw_forum] Lecture notes on PWSCF In-Reply-To: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> References: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> Message-ID: <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> Thank you very much, Claudio. This is a very good suggestion indeed. Is there anybody, out there, willing to help and try to distill from the material found by Claudio a self-contained documentation package? Thanks again - Stefano On Aug 21, 2007, at 10:59 PM, Claudio Attaccalite wrote: > Dear All > > in the last period I used PWSCF for different calculations and > because the documentation > is not so great, I searched on Internet and I found different > lecture notes on PSWCF, > I send the list if it can be useful to someone else: > > Vlab lecture notes: > http://www.vlab.msi.umn.edu/events/lecture.shtml > > HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO : > http://people.sissa.it/~degironc/QE-Tutorial/ > > Atomistic Computer Modeling of Materials: > http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/ > 3-320Spring-2005/CourseHome/index.htm > > Electronic Structure Calculations and Their Application in Material > Science: > http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ > > Tutorial on calculating phonons: > http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/ > Tutorial_phonons_alfe.pdf?version=1 > > Modeling from the nanoscale to the macroscale: > http://ermes.physics.ncsu.edu/MSE791K.htm > > Quantum Espresso Lab: > http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab > > It should be nice if this list can appear in the pwscf webpage > > Best Regards > Claudio Attaccalite > > -- > ========================================================== > Claudio Attaccalite > > Institute for Electronics, Microelectronics, and Nanotechnology > Dept. ISEN > B.P. 60069 > 59652 Villeneuve d'Ascq Cedex France > Skype: claudioattaccalite > web site: www.attaccalite.altervista.org > =========================================================== > > Freely download scientific books from: www.freescience.info > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070822/f3832e46/attachment.htm From baroni at sissa.it Wed Aug 22 11:22:50 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 22 Aug 2007 11:22:50 +0200 Subject: [Pw_forum] Interface geometry relaxation In-Reply-To: <161e5bd50708220038x361a3be9i4ca103816e4cef64@mail.gmail.com> References: <161e5bd50708220038x361a3be9i4ca103816e4cef64@mail.gmail.com> Message-ID: <544188F3-3C8B-469A-8340-E9B64202BC26@sissa.it> On Aug 22, 2007, at 9:38 AM, sei ou wrote: > Dear Forum, > > I am using PWscf for interface structural optimization. > The geometry relaxation on interface (LiCoO2/sulfides) seems very > difficult to converge so far. > Can anyone give me help? > > Here is my input file: > ... > ecutrho = 320.D0, > occupations = "smearing", > smearing = "methfessel-paxton", > degauss = 0.05D0 it seems you are treating the system as a metal ... > > / > &ELECTRONS > conv_thr = 1.D-6, > mixing_beta = 0.1D0, > mixing_mode = "local-TF", > / > ........ > K_POINTS crystal > 1 > 0.2914500000 0.5294200000 -0.2781600000 1.0 ... but then you are using only one k point to sample the Brillouin zone! what is probably happening is that two or more energy levels across the Homo-lumo (pseudo) gap keep oscillating ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070822/2569c028/attachment-0001.htm From w2agz at pacbell.net Tue Aug 21 18:12:56 2007 From: w2agz at pacbell.net (Paul M. Grant) Date: Tue, 21 Aug 2007 09:12:56 -0700 Subject: [Pw_forum] LDA+U for NiO Message-ID: <005d01c7e40e$24168840$0301a8c0@w2agz> To All Out There: Have any in the community done a PWscf LDA+U calculation for NiO (and/or CoO or CuO(tenorite)) as a "homework problem" or "exercise," similar to Example 25 (FeO, wustite)? If not, I'll try doing some by myself. I'm pretty familiar with the recent literature on NiO since the development of LDA+U methods, but if someone wants to point me to what they consider the "champion paper" on the electronic structure of NiO, that is, one that gets the Hubbard or Adler-Brooks gap right with the least amount of empirical futzing around, I'm all ears. -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070821/b1ddad61/attachment.htm From mgkrishn at ncsu.edu Wed Aug 22 20:35:32 2007 From: mgkrishn at ncsu.edu (mgkrishn at ncsu.edu) Date: Wed, 22 Aug 2007 14:35:32 -0400 (EDT) Subject: [Pw_forum] psuedo potentials for Bi and Te Message-ID: <2194.152.14.74.99.1187807732.squirrel@webmail.ncsu.edu> Dear All, I am trying to get LDA - psuedo potential for Bi and/or PBE - psuedo potential for Te. I am trying to run PW for Bi2Te3 and following is what is available on pwscf. Does anyone have hese or send me guidance to generate compatible psueopotentials Thanks Krishnan Name: Bismuth Symbol: Bi Atomic number: 83 Atomic configuration: [Xe+4f+5d] 6s2 6p2 Atomic mass: 208.98038(2) Available pseudopotentials: Bi.pbe-d-mt.UPF (details) Perdew-Burke-Ernzerhof (PBE) exch-corr semicore state d in valence Martins-Troullier Name: Tellurium Symbol: Te Atomic number: 52 Atomic configuration: [Kr+4d] 5s2 5p4 Atomic mass: 127.60 (3) Available pseudopotentials: Te.pz-bhs.UPF (details) Perdew-Zunger (LDA) exch-corr Bachelet-Hamann-Schlueter and derived From stewart at cnf.cornell.edu Wed Aug 22 21:43:06 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 22 Aug 2007 15:43:06 -0400 Subject: [Pw_forum] Lecture notes on PWSCF In-Reply-To: <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> References: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> Message-ID: <20070822194306.45966.qmail@mail.spidergraphics.com> Hi Stefano, This would be a good thing to include in the Quantum Espresso wiki. There is already a section for Tutorials and Examples. http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples I'll go ahead and add in some links. Best regards, Derek Stefano Baroni writes: > Thank you very much, Claudio. This is a very good suggestion indeed. > Is there anybody, out there, willing to help and try to distill from the > material found by Claudio a self-contained documentation package? > Thanks again - Stefano > > On Aug 21, 2007, at 10:59 PM, Claudio Attaccalite wrote: > >> Dear All >> >> in the last period I used PWSCF for different calculations and because >> the documentation >> is not so great, I searched on Internet and I found different lecture >> notes on PSWCF, >> I send the list if it can be useful to someone else: >> >> Vlab lecture notes: >> http://www.vlab.msi.umn.edu/events/lecture.shtml >> >> HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO : >> http://people.sissa.it/~degironc/QE-Tutorial/ >> >> Atomistic Computer Modeling of Materials: >> http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/ >> 3-320Spring-2005/CourseHome/index.htm >> >> Electronic Structure Calculations and Their Application in Material >> Science: >> http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ >> >> Tutorial on calculating phonons: >> http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/ >> Tutorial_phonons_alfe.pdf?version=1 >> >> Modeling from the nanoscale to the macroscale: >> http://ermes.physics.ncsu.edu/MSE791K.htm >> >> Quantum Espresso Lab: >> http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab >> >> It should be nice if this list can appear in the pwscf webpage >> >> Best Regards >> Claudio Attaccalite >> >> -- >> ========================================================== >> Claudio Attaccalite >> >> Institute for Electronics, Microelectronics, and Nanotechnology >> Dept. ISEN >> B.P. 60069 >> 59652 Villeneuve d'Ascq Cedex France >> Skype: claudioattaccalite >> web site: www.attaccalite.altervista.org >> =========================================================== >> >> Freely download scientific books from: www.freescience.info >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From brsahu at physics.utexas.edu Wed Aug 22 22:55:09 2007 From: brsahu at physics.utexas.edu (brsahu at physics.utexas.edu) Date: Wed, 22 Aug 2007 15:55:09 -0500 Subject: [Pw_forum] nstep, npool and FFT grid Message-ID: <20070822155509.retuwy3x450gcg4o@mail.ph.utexas.edu> Dear pwscf users, I have two questions regarding 1) FFT grid In a system where the FFT-grids along x-, y- and z-directions are not equal,which one of these decides the PW parallelization efficiency? I have a system with about 200 atoms. In the output, I get G cutoff = 164.2214 (2183159 G-vectors) FFT grid: ( 27,***,144) G cutoff = 43.7924 ( 301345 G-vectors) smooth grid: ( 15,625, 72) There are '***' printed for the y-dir FFT grid. This latest version of the pwscf code is compiled on a linux cluster (cvs version). Can something be changed (array declaration for FFT) so that it can print FFT grid for large systems so that I can tune the number of processors for G-vector and/or k-pt parallelization. 2) nstep and npool nstep (INPUT_PW file in Doc) says is the number of ionic+electronic steps which is 1 for scf, nscf, and bands and 0 for neb etc. and 50 for "relax" vc-relax etc by default. I have a run with "relax". I put nstep=250 does it mean it will do 250 ionic steps ? Is there a default for how about the electronic steps? I could not find a separate tag for electronic steps. Also How do one estimate whether k-point parallelization will be faster or G-vector(FFT) grid parallelization is faster for a given system. The suggestion for parallelization issues in the usersguide suggest that choose number of processors such that the third FFT grid is divisible by number of processors chosen. and choose number of pools of processors so that number of k-points are divisible by that. Is there a default for number of pools of processors that a running job assumes if not specified in the "job" submitting script or one has to specify it explicitly? Is number of pools of processors divides the number of processors specified in the "job" submitting and # of proc./# of pools = the number of processors that should be divisor of the third FFT grid? Bhagawan Sahu Microelectronics Research Center University of Texas at Austin 10100 Burnet Road, Bldg. 160 MER 1.606H, Mail code R9900, TX 78758-4445 e-mail: brsahu at physics.utexas.edu Phone: (512)-471-1344 FAX: (512)-471-8575 From naromero at gmail.com Thu Aug 23 02:12:33 2007 From: naromero at gmail.com (Nichols A. Romero) Date: Wed, 22 Aug 2007 20:12:33 -0400 Subject: [Pw_forum] psuedo potentials for Bi and Te In-Reply-To: <2194.152.14.74.99.1187807732.squirrel@webmail.ncsu.edu> References: <2194.152.14.74.99.1187807732.squirrel@webmail.ncsu.edu> Message-ID: <6ac064b60708221712u7f2c93c8g5e685f85f7b2a665@mail.gmail.com> Krishnan, For anything beyond the 2nd row + silicon, it is far better to generate your own pseudopotential (PP) with your particular problem in mind. For example, the Bi pseudopotential is designed for studying high pressure phases so it is quite hard and requires a large cutoff. You may not need such a PP for your application. PWSCF accepts both norm-conserving (NC) and ultrasoft (US) PP. Paolo Giannozzi has some good notes on generating the NC PP http://www.fisica.uniud.it/~giannozz/Atom/doc.pdf Also please check out the Quantum Espresso wiki there might be more notes there about generation PP thttp://www.quantum-espresso.org/wiki/index.php/Main_Page Also, the OPIUM software package generates NC PP compatible with PWSCF. There a good tutorial available http://opium.sourceforge.net/ I very much encourage you to sit down for several days to read the papers and work through some tutorials. Otherwise, you will be at the mercy of the PP experts. Good luck, P.S. Do the any of the developers mind if I make a minor contribution to http://www.quantum-espresso.org/wiki/index.php/Pseudopotentials Just want to add some additional references for the NC PP. On 8/22/07, mgkrishn at ncsu.edu wrote: > > Dear All, > > I am trying to get LDA - psuedo potential for Bi and/or PBE - psuedo > potential for Te. I am trying to run PW for Bi2Te3 and following is what > is available on pwscf. Does anyone have hese or send me guidance to > generate compatible psueopotentials > > Thanks > > Krishnan > > Name: Bismuth > Symbol: Bi > Atomic number: 83 > Atomic configuration: [Xe+4f+5d] 6s2 6p2 > Atomic mass: 208.98038(2) > > Available pseudopotentials: > > Bi.pbe-d-mt.UPF (details) > > Perdew-Burke-Ernzerhof (PBE) exch-corr > semicore state d in valence > Martins-Troullier > > > Name: Tellurium > Symbol: Te > Atomic number: 52 > Atomic configuration: [Kr+4d] 5s2 5p4 > Atomic mass: 127.60 (3) > > Available pseudopotentials: > > Te.pz-bhs.UPF (details) > > Perdew-Zunger (LDA) exch-corr > Bachelet-Hamann-Schlueter and derived > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. DoD User Productivity Enhancement and Technology Transfer (PET) Group High Performance Technologies, Inc. Reston, VA 443-567-8328 (C) 410-278-2692 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070822/d3d4a4fb/attachment.htm From jideson at gmail.com Thu Aug 23 04:05:09 2007 From: jideson at gmail.com (jideson) Date: Thu, 23 Aug 2007 10:05:09 +0800 Subject: [Pw_forum] Lecture notes on PWSCF In-Reply-To: <20070822194306.45966.qmail@mail.spidergraphics.com> References: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> <20070822194306.45966.qmail@mail.spidergraphics.com> Message-ID: <1187834710.9733.18.camel@amd.mm> Dear Derek, Please put this wiki link in somewhere of www.pwscf.org (such as http://www.pwscf.org/links.htm). It may help many new users. Thanks. -- Best regards Jideson http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples ? 2007-08-22?? 15:43 -0400?stewart at cnf.cornell.edu??? > Hi Stefano, > > This would be a good thing to include in the Quantum Espresso wiki. There > is already a section for Tutorials and Examples. > > http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples > > I'll go ahead and add in some links. > > Best regards, > > Derek > > > Stefano Baroni writes: > > > Thank you very much, Claudio. This is a very good suggestion indeed. > > Is there anybody, out there, willing to help and try to distill from the > > material found by Claudio a self-contained documentation package? > > Thanks again - Stefano > > > > On Aug 21, 2007, at 10:59 PM, Claudio Attaccalite wrote: > > > >> Dear All > >> > >> in the last period I used PWSCF for different calculations and because > >> the documentation > >> is not so great, I searched on Internet and I found different lecture > >> notes on PSWCF, > >> I send the list if it can be useful to someone else: > >> > >> Vlab lecture notes: > >> http://www.vlab.msi.umn.edu/events/lecture.shtml > >> > >> HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO : > >> http://people.sissa.it/~degironc/QE-Tutorial/ > >> > >> Atomistic Computer Modeling of Materials: > >> http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/ > >> 3-320Spring-2005/CourseHome/index.htm > >> > >> Electronic Structure Calculations and Their Application in Material > >> Science: > >> http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ > >> > >> Tutorial on calculating phonons: > >> http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/ > >> Tutorial_phonons_alfe.pdf?version=1 > >> > >> Modeling from the nanoscale to the macroscale: > >> http://ermes.physics.ncsu.edu/MSE791K.htm > >> > >> Quantum Espresso Lab: > >> http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab > >> > >> It should be nice if this list can appear in the pwscf webpage > >> > >> Best Regards > >> Claudio Attaccalite > >> > >> -- > >> ========================================================== > >> Claudio Attaccalite > >> > >> Institute for Electronics, Microelectronics, and Nanotechnology > >> Dept. ISEN > >> B.P. 60069 > >> 59652 Villeneuve d'Ascq Cedex France > >> Skype: claudioattaccalite > >> web site: www.attaccalite.altervista.org > >> =========================================================== > >> > >> Freely download scientific books from: www.freescience.info > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > > Trieste > > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From marzari at MIT.EDU Thu Aug 23 05:31:27 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 22 Aug 2007 23:31:27 -0400 Subject: [Pw_forum] psuedo potentials for Bi and Te In-Reply-To: <6ac064b60708221712u7f2c93c8g5e685f85f7b2a665@mail.gmail.com> References: <2194.152.14.74.99.1187807732.squirrel@webmail.ncsu.edu> <6ac064b60708221712u7f2c93c8g5e685f85f7b2a665@mail.gmail.com> Message-ID: <46CCFF8F.2060907@mit.edu> Nichols A. Romero wrote: > P.S. Do the any of the developers mind if I make a minor contribution to > http://www.quantum-espresso.org/wiki/index.php/Pseudopotentials > Just want to add some additional references for the NC PP. Not at all - always very welcome. The wiki is not meant to be a developers' domain, but it's actually how the community contributes back. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From stewart at cnf.cornell.edu Thu Aug 23 15:34:18 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Thu, 23 Aug 2007 09:34:18 -0400 Subject: [Pw_forum] Lecture notes on PWSCF In-Reply-To: <1187834710.9733.18.camel@amd.mm> References: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> <20070822194306.45966.qmail@mail.spidergraphics.com> <1187834710.9733.18.camel@amd.mm> Message-ID: <20070823133418.94288.qmail@mail.spidergraphics.com> Hi Jideson, I have an account set up to changes things on the Quantum Espresso wiki. However, I don't have access to changes things on the PWscf webpage. This would be have to be done by one of the core developers. Best regards, Derek jideson writes: > Dear Derek, > Please put this wiki link in somewhere of www.pwscf.org (such as > http://www.pwscf.org/links.htm). It may help many new users. Thanks. > > -- > Best regards > > Jideson > http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples > > ? 2007-08-22?? 15:43 -0400?stewart at cnf.cornell.edu??? >> Hi Stefano, >> >> This would be a good thing to include in the Quantum Espresso wiki. There >> is already a section for Tutorials and Examples. >> >> http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples >> >> I'll go ahead and add in some links. >> >> Best regards, >> >> Derek >> >> >> Stefano Baroni writes: >> >> > Thank you very much, Claudio. This is a very good suggestion indeed. >> > Is there anybody, out there, willing to help and try to distill from the >> > material found by Claudio a self-contained documentation package? >> > Thanks again - Stefano >> > >> > On Aug 21, 2007, at 10:59 PM, Claudio Attaccalite wrote: >> > >> >> Dear All >> >> >> >> in the last period I used PWSCF for different calculations and because >> >> the documentation >> >> is not so great, I searched on Internet and I found different lecture >> >> notes on PSWCF, >> >> I send the list if it can be useful to someone else: >> >> >> >> Vlab lecture notes: >> >> http://www.vlab.msi.umn.edu/events/lecture.shtml >> >> >> >> HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO : >> >> http://people.sissa.it/~degironc/QE-Tutorial/ >> >> >> >> Atomistic Computer Modeling of Materials: >> >> http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/ >> >> 3-320Spring-2005/CourseHome/index.htm >> >> >> >> Electronic Structure Calculations and Their Application in Material >> >> Science: >> >> http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ >> >> >> >> Tutorial on calculating phonons: >> >> http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/ >> >> Tutorial_phonons_alfe.pdf?version=1 >> >> >> >> Modeling from the nanoscale to the macroscale: >> >> http://ermes.physics.ncsu.edu/MSE791K.htm >> >> >> >> Quantum Espresso Lab: >> >> http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab >> >> >> >> It should be nice if this list can appear in the pwscf webpage >> >> >> >> Best Regards >> >> Claudio Attaccalite >> >> >> >> -- >> >> ========================================================== >> >> Claudio Attaccalite >> >> >> >> Institute for Electronics, Microelectronics, and Nanotechnology >> >> Dept. ISEN >> >> B.P. 60069 >> >> 59652 Villeneuve d'Ascq Cedex France >> >> Skype: claudioattaccalite >> >> web site: www.attaccalite.altervista.org >> >> =========================================================== >> >> >> >> Freely download scientific books from: www.freescience.info >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > --- >> > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - >> > Trieste >> > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) >> > >> > Please, if possible, don't send me MS Word or PowerPoint attachments >> > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html >> > >> > >> > >> >> >> >> ################################ >> Derek Stewart, Ph. D. >> Scientific Computation Associate >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From brsahu at physics.utexas.edu Sat Aug 25 23:06:08 2007 From: brsahu at physics.utexas.edu (brsahu at physics.utexas.edu) Date: Sat, 25 Aug 2007 16:06:08 -0500 Subject: [Pw_forum] Fwd: nstep, npool and FFT grid Message-ID: <20070825160608.5bniad1nglwoggck@mail.ph.utexas.edu> Dear PWSCF users, I submitted a query few days ago. If you have any suggestions pl. let me know Bhagawan ----- Forwarded message from brsahu at physics.utexas.edu ----- Date: Wed, 22 Aug 2007 15:55:09 -0500 From: brsahu at physics.utexas.edu Reply-To: brsahu at physics.utexas.edu Subject: nstep, npool and FFT grid To: pw_forum at pwscf.org Dear pwscf users, I have two questions regarding 1) FFT grid In a system where the FFT-grids along x-, y- and z-directions are not equal,which one of these decides the PW parallelization efficiency? I have a system with about 200 atoms. In the output, I get G cutoff = 164.2214 (2183159 G-vectors) FFT grid: ( 27,***,144) G cutoff = 43.7924 ( 301345 G-vectors) smooth grid: ( 15,625, 72) There are '***' printed for the y-dir FFT grid. This latest version of the pwscf code is compiled on a linux cluster (cvs version). Can something be changed (array declaration for FFT) so that it can print FFT grid for large systems so that I can tune the number of processors for G-vector and/or k-pt parallelization. 2) nstep and npool nstep (INPUT_PW file in Doc) says is the number of ionic+electronic steps which is 1 for scf, nscf, and bands and 0 for neb etc. and 50 for "relax" vc-relax etc by default. I have a run with "relax". I put nstep=250 does it mean it will do 250 ionic steps ? Is there a default for how about the electronic steps? I could not find a separate tag for electronic steps. Also How do one estimate whether k-point parallelization will be faster or G-vector(FFT) grid parallelization is faster for a given system. The suggestion for parallelization issues in the usersguide suggest that choose number of processors such that the third FFT grid is divisible by number of processors chosen. and choose number of pools of processors so that number of k-points are divisible by that. Is there a default for number of pools of processors that a running job assumes if not specified in the "job" submitting script or one has to specify it explicitly? Is number of pools of processors divides the number of processors specified in the "job" submitting and # of proc./# of pools = the number of processors that should be divisor of the third FFT grid? Bhagawan Sahu Microelectronics Research Center University of Texas at Austin 10100 Burnet Road, Bldg. 160 MER 1.606H, Mail code R9900, TX 78758-4445 e-mail: brsahu at physics.utexas.edu Phone: (512)-471-1344 FAX: (512)-471-8575 ----- End forwarded message ----- Bhagawan Sahu Microelectronics Research Center University of Texas at Austin 10100 Burnet Road, Bldg. 160 MER 1.606H, Mail code R9900, TX 78758-4445 e-mail: brsahu at physics.utexas.edu Phone: (512)-471-1344 FAX: (512)-471-8575 From marzari at MIT.EDU Sat Aug 25 23:35:35 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 25 Aug 2007 17:35:35 -0400 Subject: [Pw_forum] Fwd: nstep, npool and FFT grid In-Reply-To: <20070825160608.5bniad1nglwoggck@mail.ph.utexas.edu> References: <20070825160608.5bniad1nglwoggck@mail.ph.utexas.edu> Message-ID: <46D0A0A7.4030202@mit.edu> Dear Bhagawan, you raise several relevant questions - hopefully someone can help as well. Testing your specific system, on your clusterwith your communication devices, is in any case the most important strategy. 1) the "***" come from a format declaration (i3, likely). We should switch to i4, but you should be able to fish in pw where that line is printed, and change the format output. I'm not sure about about the fine details of FFT parallelization. Stefano de Gironcoli would probably be the person, but I think he is currently on travel. 2) this is easily answered by looking at INPUT_PW. Electronic minimizations (at fixed ions) are controlled by electron_maxstep INTEGER ( default = 100 ) maximum number of iterations in a scf step conv_thr REAL ( default = 1.D-6 ) Convergence threshold for selfconsistency: estimated energy error < conv_thr For ionic relaxations, at each ionic step the electrons are relaxed as above, and the ionic relaxations are controlled by etot_conv_thr REAL ( default = 1.0D-4 ) convergence threshold on total energy (a.u) for ionic minimization: the convergence criterion is satisfied when the total energy changes less than etot_conv_thr between two consecutive scf steps. See also forc_conv_thr - both criteria must be satisfied forc_conv_thr REAL ( default = 1.0D-3 ) convergence threshold on forces (a.u) for ionic minimization: the convergence criterion is satisfied when all components of all forces are smaller than forc_conv_thr. See also etot_conv_thr - both criteria must be satisfied The code will do a maximum of "nstep" ionic steps. 3) npools partitioning doesn't decrease the size of the memory each processor needs, so it is usefull for small systems with many kpoints. It is also very good for low communications. If you have 12 k-points, run on 1, 2, 3, 4, 6, or 12 processors. G-parallelization is a tad faster if your communications are excellent, but for larger and larger systems it's difficult to keep perfect scaling. But a g-parallel job is partitioned in smaller chuncks, so this parallelization is necessary if you study systems that do not fit on 1 processor alone. Not sure about the other questions on fft performance etc. nicola brsahu at physics.utexas.edu wrote: > Dear PWSCF users, > > I submitted a query few days ago. If you have any suggestions pl. let me know > > Bhagawan > > ----- Forwarded message from brsahu at physics.utexas.edu ----- > Date: Wed, 22 Aug 2007 15:55:09 -0500 > From: brsahu at physics.utexas.edu > Reply-To: brsahu at physics.utexas.edu > Subject: nstep, npool and FFT grid > To: pw_forum at pwscf.org > > Dear pwscf users, > > I have two questions regarding > > 1) FFT grid > > In a system where the FFT-grids along x-, y- and z-directions are not > equal,which one of these decides the PW parallelization efficiency? > > I have a system with about 200 atoms. In the output, I get > > G cutoff = 164.2214 (2183159 G-vectors) FFT grid: ( 27,***,144) > G cutoff = 43.7924 ( 301345 G-vectors) smooth grid: ( 15,625, 72) > > There are '***' printed for the y-dir FFT grid. > > This latest version of the pwscf code is compiled on a linux cluster > (cvs version). > > Can something be changed (array declaration for FFT) so that it can > print FFT grid for large systems so that I can tune the number of > processors for > G-vector and/or k-pt parallelization. > > 2) nstep and npool > > nstep (INPUT_PW file in Doc) says is the number of ionic+electronic > steps which is > 1 for scf, nscf, and bands and 0 for neb etc. and 50 for "relax" > vc-relax etc by default. > > I have a run with "relax". I put nstep=250 does it mean it will do 250 > ionic steps > ? Is there a default for how about the electronic steps? I could not > find a separate tag > for electronic steps. > > Also How do one estimate whether k-point parallelization will be > faster or G-vector(FFT) > grid parallelization is faster for a given system. The suggestion for > parallelization > issues in the usersguide suggest that choose number of processors such > that the third FFT > grid is divisible by number of processors chosen. and choose number of > pools of > processors so that number of k-points are divisible by that. Is there > a default for > number of pools of processors that a running job assumes if not > specified in the "job" > submitting script or one has to specify it explicitly? > > Is number of pools of processors divides the number of processors > specified in the "job" > submitting and # of proc./# of pools = the number of processors that > should be divisor of > the third FFT grid? -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From eyvaz_isaev at yahoo.com Mon Aug 27 10:21:50 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 27 Aug 2007 01:21:50 -0700 (PDT) Subject: [Pw_forum] psuedo potentials for Bi and Te In-Reply-To: <2194.152.14.74.99.1187807732.squirrel@webmail.ncsu.edu> Message-ID: <631822.20839.qm@web60324.mail.yahoo.com> Hi Krishnan, I have all you need in PBE. They gave pressure around 1GPa within experimental lattice parameters and, so, seem to be reasonable. Besides, definitly, Be2Ti3 is a semiconductor, but do not ask me about the bang gap. If you can tell me about the macroscopic dielectric constant, then I can decide whether post them to the website or not. Bests, Eyvaz. --- mgkrishn at ncsu.edu wrote: > Dear All, > > I am trying to get LDA - psuedo potential for Bi > and/or PBE - psuedo > potential for Te. I am trying to run PW for Bi2Te3 > and following is what > is available on pwscf. Does anyone have hese or send > me guidance to > generate compatible psueopotentials > > Thanks > > Krishnan > > Name: Bismuth > Symbol: Bi > Atomic number: 83 > Atomic configuration: [Xe+4f+5d] 6s2 6p2 > Atomic mass: 208.98038(2) > > Available pseudopotentials: > > Bi.pbe-d-mt.UPF (details) > > Perdew-Burke-Ernzerhof (PBE) exch-corr > semicore state d in valence > Martins-Troullier > > > Name: Tellurium > Symbol: Te > Atomic number: 52 > Atomic configuration: [Kr+4d] 5s2 5p4 > Atomic mass: 127.60 (3) > > Available pseudopotentials: > > Te.pz-bhs.UPF (details) > > Perdew-Zunger (LDA) exch-corr > Bachelet-Hamann-Schlueter and derived > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 From baroni at sissa.it Mon Aug 27 12:18:56 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 27 Aug 2007 12:18:56 +0200 Subject: [Pw_forum] Lecture notes on PWSCF In-Reply-To: <20070823133418.94288.qmail@mail.spidergraphics.com> References: <6b6a635f0708211359g5713cd18t2cb6eb46d59523bb@mail.gmail.com> <464B62FF-9912-4D8A-9AC7-72878B777A00@sissa.it> <20070822194306.45966.qmail@mail.spidergraphics.com> <1187834710.9733.18.camel@amd.mm> <20070823133418.94288.qmail@mail.spidergraphics.com> Message-ID: Dear Derek, Jideson, et al. We have modified the home page of PWscf with some links pointing to the Quantum ESPRESSO home page, and some other pointing to the wiki directly. Please, feel free to suggest other changes, additions, etc. Cheers - SB On Aug 23, 2007, at 3:34 PM, stewart at cnf.cornell.edu wrote: > Hi Jideson, > > I have an account set up to changes things on the Quantum Espresso > wiki. > However, I don't have access to changes things on the PWscf > webpage. This > would be have to be done by one of the core developers. > > Best regards, > > Derek > > > > jideson writes: > >> Dear Derek, >> Please put this wiki link in somewhere of www.pwscf.org (such as >> http://www.pwscf.org/links.htm). It may help many new users. Thanks. >> >> -- >> Best regards >> >> Jideson >> http://www.quantum-espresso.org/wiki/index.php/Tutorials_and_Examples >> >> ? 2007-08-22?? 15:43 -0400?stewart at cnf.cornell.edu??? >>> Hi Stefano, >>> >>> This would be a good thing to include in the Quantum Espresso >>> wiki. There >>> is already a section for Tutorials and Examples. >>> >>> http://www.quantum-espresso.org/wiki/index.php/ >>> Tutorials_and_Examples >>> >>> I'll go ahead and add in some links. >>> >>> Best regards, >>> >>> Derek >>> >>> >>> Stefano Baroni writes: >>> >>>> Thank you very much, Claudio. This is a very good suggestion >>>> indeed. >>>> Is there anybody, out there, willing to help and try to distill >>>> from the >>>> material found by Claudio a self-contained documentation package? >>>> Thanks again - Stefano >>>> >>>> On Aug 21, 2007, at 10:59 PM, Claudio Attaccalite wrote: >>>> >>>>> Dear All >>>>> >>>>> in the last period I used PWSCF for different calculations and >>>>> because >>>>> the documentation >>>>> is not so great, I searched on Internet and I found different >>>>> lecture >>>>> notes on PSWCF, >>>>> I send the list if it can be useful to someone else: >>>>> >>>>> Vlab lecture notes: >>>>> http://www.vlab.msi.umn.edu/events/lecture.shtml >>>>> >>>>> HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO : >>>>> http://people.sissa.it/~degironc/QE-Tutorial/ >>>>> >>>>> Atomistic Computer Modeling of Materials: >>>>> http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/ >>>>> 3-320Spring-2005/CourseHome/index.htm >>>>> >>>>> Electronic Structure Calculations and Their Application in >>>>> Material >>>>> Science: >>>>> http://cdsagenda5.ictp.trieste.it/html_trees_links/1590597488/ >>>>> >>>>> Tutorial on calculating phonons: >>>>> http://cms.mcc.uiuc.edu/wiki/download/attachments/5800018/ >>>>> Tutorial_phonons_alfe.pdf?version=1 >>>>> >>>>> Modeling from the nanoscale to the macroscale: >>>>> http://ermes.physics.ncsu.edu/MSE791K.htm >>>>> >>>>> Quantum Espresso Lab: >>>>> http://cms.mcc.uiuc.edu/wiki/display/ss2006/Quantum+Espresso+Lab >>>>> >>>>> It should be nice if this list can appear in the pwscf webpage >>>>> >>>>> Best Regards >>>>> Claudio Attaccalite >>>>> >>>>> -- >>>>> ========================================================== >>>>> Claudio Attaccalite >>>>> >>>>> Institute for Electronics, Microelectronics, and Nanotechnology >>>>> Dept. ISEN >>>>> B.P. 60069 >>>>> 59652 Villeneuve d'Ascq Cedex France >>>>> Skype: claudioattaccalite >>>>> web site: www.attaccalite.altervista.org >>>>> =========================================================== >>>>> >>>>> Freely download scientific books from: www.freescience.info >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> --- >>>> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - >>>> Trieste >>>> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) >>>> >>>> Please, if possible, don't send me MS Word or PowerPoint >>>> attachments >>>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html >>>> >>>> >>>> >>> >>> >>> >>> ################################ >>> Derek Stewart, Ph. D. >>> Scientific Computation Associate >>> 250 Duffield Hall >>> Cornell Nanoscale Facility (CNF) >>> Ithaca, NY 14853 >>> stewart (at) cnf.cornell.edu >>> (607) 255-2856 >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070827/4daaefab/attachment-0001.htm From hande at newton.physics.metu.edu.tr Mon Aug 27 14:16:59 2007 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Mon, 27 Aug 2007 15:16:59 +0300 (EEST) Subject: [Pw_forum] C pseudo regeneration Message-ID: Dear forum members, I have a problem concerning the reproduction of one of the C pseudopotentials. I'm trying to reproduce the C.pz-rrkjus.UPF pseudopotential as best I can using the input provided below. Although I get excellent agreement with the log derivatives and test cases (pls see below), even with cutoffs of 40/400 Ryd, I get a diamond lattice constant that is 1.2% too little and a rather bumpy E vs a curve. I've tried a rather exhaustive set of different parameters but I haven't been able to generate a smooth enough curve. The C.pz-rrkjus.UPF from the web site on the other hand gives a very nice smooth curve with an error of only 0.9% for the same calculation parameters. I've posted both curves here. http://www.physics.metu.edu.tr/~hande/curves I guess the errors are not terribly different but should I be worried about the bumpiness? If yes, it would be really helpful if anyone could spot the difference between my input and the pseudo online. If not, any suggestion on improving my pseudo would be more than welcome. Thank you very much in advance. Best regards, Hande PS : I'm using version 3.2. Input : ------- &input atom='C', rlderiv=3.0, eminld=-4.0, emaxld= 4.0, deld = 0.02, nld = 3, config=' 1s2 2s2 2p2 3d0.00', iswitch=3, prefix='c' dft='pz', / &inputp pseudotype=3, lloc=2, tm=.false., nlcc=.false., file_pseudopw='C.pz.uspp-rrkj.UPF', / 5 2S 1 0 2 0.00 1.3 1.6 2S 1 0 0 -0.4 1.3 1.6 2P 2 1 2 0.00 1.6 1.6 2P 2 1 0 -0.1 1.6 1.6 3D 3 2 -2.0 2.00 1.3 1.3 &test nconf=1, configts(1)='2s2 2p2 ', / Test results : -------------- Atomic configuration : s2 p2 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 2S 1( 2.00) -1.00195 -1.00210 0.00015 2 1 2P 1( 2.00) -0.39860 -0.39861 0.00002 Test case 1 : s2 p1.75 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 2S 1( 2.00) -1.20025 -1.20038 0.00012 2 1 2P 1( 1.75) -0.58967 -0.58941 -0.00026 Test case 2 : s1.00 p1.50 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 Test case 3 : s1.00 p1.50 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From dalcorso at sissa.it Mon Aug 27 15:02:24 2007 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Mon, 27 Aug 2007 15:02:24 +0200 Subject: [Pw_forum] C pseudo regeneration In-Reply-To: References: Message-ID: <1188219744.3385.9.camel@dhpc-5-02.sissa.it> On Mon, 2007-08-27 at 15:16 +0300, Hande Ustunel wrote: > Dear forum members, > > I have a problem concerning the reproduction of one of the C > pseudopotentials. I'm trying to reproduce the C.pz-rrkjus.UPF > pseudopotential as best I can using the input provided below. Although I > get excellent agreement with the log derivatives and test cases (pls see > below), even with cutoffs of 40/400 Ryd, I get a diamond lattice constant > that is 1.2% too little and a rather bumpy E vs a curve. I've tried a > rather exhaustive set of different parameters but I haven't been able to > generate a smooth enough curve. The C.pz-rrkjus.UPF from the web site on > the other hand gives a very nice smooth curve with an error of only 0.9% > for the same calculation parameters. I've posted both curves here. > > http://www.physics.metu.edu.tr/~hande/curves > > I guess the errors are not terribly different but should I be worried about > the bumpiness? If yes, it would be really helpful if anyone could spot the > difference between my input and the pseudo online. If not, any suggestion > on improving my pseudo would be more than welcome. Thank you very much in > advance. > > Best regards, > Hande > > PS : I'm using version 3.2. > > Input : > ------- > > &input > atom='C', > rlderiv=3.0, > eminld=-4.0, > emaxld= 4.0, > deld = 0.02, > nld = 3, > config=' 1s2 2s2 2p2 3d0.00', > iswitch=3, > prefix='c' > dft='pz', > / > &inputp > pseudotype=3, > lloc=2, > tm=.false., > nlcc=.false., > file_pseudopw='C.pz.uspp-rrkj.UPF', > / > 5 > 2S 1 0 2 0.00 1.3 1.6 > 2S 1 0 0 -0.4 1.3 1.6 > 2P 2 1 2 0.00 1.6 1.6 > 2P 2 1 0 -0.1 1.6 1.6 The core radii of the 2P wavefunctions seem strange to me. This is a norm conserving pseudopotential for the 2P functions. 1.3 1.6 usually work. Andrea > 3D 3 2 -2.0 2.00 1.3 1.3 > &test > nconf=1, > configts(1)='2s2 2p2 ', > / > > > > Test results : > -------------- > Atomic configuration : s2 p2 > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > 1 0 2S 1( 2.00) -1.00195 -1.00210 0.00015 > 2 1 2P 1( 2.00) -0.39860 -0.39861 0.00002 > > Test case 1 : s2 p1.75 > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > 1 0 2S 1( 2.00) -1.20025 -1.20038 0.00012 > 2 1 2P 1( 1.75) -0.58967 -0.58941 -0.00026 > > Test case 2 : s1.00 p1.50 > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 > 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 > > Test case 3 : s1.00 p1.50 > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 > 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 > > > -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From hande at newton.physics.metu.edu.tr Mon Aug 27 15:25:45 2007 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Mon, 27 Aug 2007 16:25:45 +0300 (EEST) Subject: [Pw_forum] C pseudo regeneration In-Reply-To: <1188219744.3385.9.camel@dhpc-5-02.sissa.it> Message-ID: Dear Andrea, Many thanks. That fixed the problem. I had indeed intended it to be 1.3 but had an error in my automatized script. Best regards, Hande On Mon, 27 Aug 2007, Dal Corso Andrea wrote: > On Mon, 2007-08-27 at 15:16 +0300, Hande Ustunel wrote: > > Dear forum members, > > > > I have a problem concerning the reproduction of one of the C > > pseudopotentials. I'm trying to reproduce the C.pz-rrkjus.UPF > > pseudopotential as best I can using the input provided below. Although I > > get excellent agreement with the log derivatives and test cases (pls see > > below), even with cutoffs of 40/400 Ryd, I get a diamond lattice constant > > that is 1.2% too little and a rather bumpy E vs a curve. I've tried a > > rather exhaustive set of different parameters but I haven't been able to > > generate a smooth enough curve. The C.pz-rrkjus.UPF from the web site on > > the other hand gives a very nice smooth curve with an error of only 0.9% > > for the same calculation parameters. I've posted both curves here. > > > > http://www.physics.metu.edu.tr/~hande/curves > > > > I guess the errors are not terribly different but should I be worried about > > the bumpiness? If yes, it would be really helpful if anyone could spot the > > difference between my input and the pseudo online. If not, any suggestion > > on improving my pseudo would be more than welcome. Thank you very much in > > advance. > > > > Best regards, > > Hande > > > > PS : I'm using version 3.2. > > > > Input : > > ------- > > > > &input > > atom='C', > > rlderiv=3.0, > > eminld=-4.0, > > emaxld= 4.0, > > deld = 0.02, > > nld = 3, > > config=' 1s2 2s2 2p2 3d0.00', > > iswitch=3, > > prefix='c' > > dft='pz', > > / > > &inputp > > pseudotype=3, > > lloc=2, > > tm=.false., > > nlcc=.false., > > file_pseudopw='C.pz.uspp-rrkj.UPF', > > / > > 5 > > 2S 1 0 2 0.00 1.3 1.6 > > 2S 1 0 0 -0.4 1.3 1.6 > > 2P 2 1 2 0.00 1.6 1.6 > > 2P 2 1 0 -0.1 1.6 1.6 > > The core radii of the 2P wavefunctions seem strange to me. This is a > norm conserving pseudopotential for the 2P functions. 1.3 1.6 usually > work. > > Andrea > > > > 3D 3 2 -2.0 2.00 1.3 1.3 > > &test > > nconf=1, > > configts(1)='2s2 2p2 ', > > / > > > > > > > > Test results : > > -------------- > > Atomic configuration : s2 p2 > > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > > 1 0 2S 1( 2.00) -1.00195 -1.00210 0.00015 > > 2 1 2P 1( 2.00) -0.39860 -0.39861 0.00002 > > > > Test case 1 : s2 p1.75 > > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > > 1 0 2S 1( 2.00) -1.20025 -1.20038 0.00012 > > 2 1 2P 1( 1.75) -0.58967 -0.58941 -0.00026 > > > > Test case 2 : s1.00 p1.50 > > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > > 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 > > 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 > > > > Test case 3 : s1.00 p1.50 > > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > > 1 0 2S 1( 1.00) -2.38716 -2.38539 -0.00178 > > 2 1 2P 1( 1.50) -1.76433 -1.76042 -0.00391 > > > > > > > -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From shaposh at isp.nsc.ru Tue Aug 28 11:16:31 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Tue, 28 Aug 2007 16:16:31 +0700 Subject: [Pw_forum] About "crystal" coordinates Message-ID: <200708281616.31328.shaposh@isp.nsc.ru> Hello All, i have been trying to figure out how to set up monoclinic base-centered cell for Ta2O5 and have some difficulty in determining the right format . My question is, in what exactly vectors the coordinates in "crystal" format are entered? Are they initial a,b,c vectors or transformed a1,b1,c1 ? (notations from the "input_pw" doc file ). Best Regards, A. Shaposhnikov From amosleffler at sbcglobal.net Tue Aug 28 17:48:04 2007 From: amosleffler at sbcglobal.net (Amos Leffler) Date: Tue, 28 Aug 2007 08:48:04 -0700 Subject: [Pw_forum] Compilation Problem Message-ID: <46D443B4.6070002@sbcglobal.net> Dear Forum, I have run into a compilation problem using SuSE Linux 10.2, gcc-4.2.1, and Intel 10.0.023 fortran. It is shown in the attached files which come from espresso-3.2.sav (!) which shows that it hangs up in input_parameters.f90 in the "Module" directory. I have been able to compile espresso earlier using a similar setup. Hopefully someone will see the problem. Any help would be much appreciated. Amos Leffler -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: temp.4_bug Url: http://www.democritos.it/pipermail/pw_forum/attachments/20070828/11f36ff3/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: espresso.err Url: http://www.democritos.it/pipermail/pw_forum/attachments/20070828/11f36ff3/attachment-0001.txt From paulatto at sissa.it Tue Aug 28 19:43:59 2007 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 28 Aug 2007 19:43:59 +0200 (CEST) Subject: [Pw_forum] Compilation Problem In-Reply-To: <46D443B4.6070002@sbcglobal.net> References: <46D443B4.6070002@sbcglobal.net> Message-ID: <11872.79.6.238.217.1188323039.squirrel@webmail.sissa.it> On Tue, August 28, 2007 17:48, Amos Leffler wrote: > Intel 10.0.023 fortran. Hi Amos, from the error message it is clear that you are not using ifort but gfortran. The latter cannot compile QE. In order to use the right compiler you have to set the variable F90=ifort before running configure. My advice is to run "./configure --help" and to read README.install for more details. bye -- Lorenzo Paulatto +39 040 3787 312 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From konstantin_kudin at yahoo.com Wed Aug 29 04:11:56 2007 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Tue, 28 Aug 2007 19:11:56 -0700 (PDT) Subject: [Pw_forum] PH error: k-points are odd In-Reply-To: <11872.79.6.238.217.1188323039.squirrel@webmail.sissa.it> Message-ID: <318172.44343.qm@web57714.mail.re3.yahoo.com> All, I am trying to get phonons at a non-Gamma point, but the code is crashing with the message: from phq_readin : error # 1 k-points are odd Could anyone check what is happening here? These are the input/output files: https://kiev.princeton.edu/grapu2w.zip Thanks in advance! Kostya ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz From fenghongjian at ss.buaa.edu.cn Wed Aug 29 14:09:45 2007 From: fenghongjian at ss.buaa.edu.cn (hongkien) Date: Wed, 29 Aug 2007 20:09:45 +0800 Subject: [Pw_forum] error in finite electric field Message-ID: <1188389385.3828.14.camel@node0> Dear all, I have beening calculating the ferroelectic properties of BaTiO3 under finite electric field, but in the scf cycle the code always crashed without giving any suggestions.I found the related error in the output file like this: iteration # 1 ecut= 35.00 Ry beta=0.30 Davidson diagonalization with overlap error hepsiher: translated G= 0.291666666666667 0.583333333333333 0.000000000000000E+000 with crystal coordinates 0 1 0 corresponds to ng= 6 but G(ng)= 0.000000000000000E+000 1.00000000000000 0.000000000000000E+000 probably because G_par is NOT a reciprocal lattice vector Possible choices as smallest G_par: i= 1 G= 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 i= 2 G= 0.000000000000000E+000 0.000000000000000E+000 -0.986981711228891 i= 3 G= 0.000000000000000E+000 0.000000000000000E+000 0.986981711228891 ....... I have tried different Kponts structure and the diagonalization methods,but failed. Is it a pseudopotential problem? It will be very appreciated for any suggestion about this. Thank you in advance. My input file was pasted here: &control calculation='scf' restart_mode='restart' prefix='bto', verbosity='high', pseudo_dir='./', outdir='./', gdir=3, nppstr=7, lelfield=.true., nberrycyc=3, / &system ibrav= 6, celldm(1)= 7.6153, celldm(3)= 1.01319, nat= 5, ntyp= 3, lda_plus_u=.true. Hubbard_U(2)=4.3 ecutwfc= 35.0, nosym=.true / &electrons mixing_beta=0.3, conv_thr= 1e-8, efield=0.001, startingwfc='random' / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.88 Ti.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} Ba 0.00000 0.00000 0.00000 Ti 0.50000 0.50000 0.50000 O 0.50000 0.50000 0.00000 O 0.00000 0.50000 0.50000 O 0.50000 0.00000 0.50000 K_POINTS 16 0.0 0.0 0.0 1 0.0 0.25 0.0 1 0.0 0.50 0.0 1 0.0 0.75 0.0 1 0.25 0.0 0.0 1 0.25 0.25 0.0 1 0.25 0.50 0.0 1 0.25 0.75 0.0 1 0.50 0.0 0.0 1 0.50 0.25 0.0 1 0.50 0.50 0.0 1 0.50 0.75 0.0 1 0.75 0.0 0.0 1 0.75 0.25 0.0 1 0.75 0.50 0.0 1 0.75 0.75 0.0 1 Hongkien Feng physcis department, Beijing University of aeronautics & astronautics From vparkash at mtu.edu Wed Aug 29 07:42:10 2007 From: vparkash at mtu.edu (vparkash at mtu.edu) Date: Wed, 29 Aug 2007 01:42:10 -0400 (EDT) Subject: [Pw_forum] Convergence problem Message-ID: <33668.141.219.80.101.1188366130.squirrel@huskymail.mtu.edu> Hi Everyone... This may be a bit newbie type question, but I can seem to figure it out, so please help me out I'm trying to do a scf type calculation, and the output first converges, and the all of a sudden, the error shoots up.I checked up the manual and the reason this happens is that apparently my system is metallic, which may indeed be the case. The remedy that was suggested was to include broadening and increase the number of bands. I'm using PWgui for creating the input file....apparently I cant figure out how do you do either of these using PWgui Thanks Vidur From umari at democritos.it Wed Aug 29 09:07:09 2007 From: umari at democritos.it (umari at democritos.it) Date: Wed, 29 Aug 2007 09:07:09 +0200 Subject: [Pw_forum] error in finite electric field Message-ID: <20070829090709.kxey97bq8g88go0w@mail.democritos.it> Dear Hongkien, > I have beening calculating the ferroelectic properties of BaTiO3 > under finite electric field, but in the scf cycle the code always > crashed without giving any suggestions.I found the related error in the > output file like this: > > iteration # 1 ecut= 35.00 Ry beta=0.30 > Davidson diagonalization with overlap > error hepsiher: translated G= 0.291666666666667 > 0.583333333333333 0.000000000000000E+000 with crystal > coordinates 0 > 1 > 0 corresponds to ng= 6 but G(ng)= > 0.000000000000000E+000 > 1.00000000000000 0.000000000000000E+000 > probably because G_par is NOT a reciprocal lattice vector > Possible choices as smallest G_par: > i= 1 G= 0.000000000000000E+000 0.000000000000000E+000 > 0.000000000000000E+000 > i= 2 G= 0.000000000000000E+000 0.000000000000000E+000 > -0.986981711228891 i= 3 G= 0.000000000000000E+000 > 0.000000000000000E+000 > 0.986981711228891 ....... > I have tried different Kponts structure and the diagonalization > methods,but failed. Is it a pseudopotential problem? It will be very > appreciated for any suggestion about this. Thank you in advance. As explained in the README of example 31 the direction of the electric field is given by gdir, note that till now only orthorombic cells have been tested and gdir==3 is the only choice working for parallel calculations, then nppstr gives the number of equally spaced k-point along the direction gdir, which must be give in appropriate order. In your case you have a mesh of 4 k-points along the second direction but in the input file nppstr is 7 instead of 4 and gdir is 3 instead of 2 Best regards, Paolo Umari, DEMOCRITOS, Italy > My input file was pasted here: > &control > calculation='scf' > restart_mode='restart' > prefix='bto', > verbosity='high', > pseudo_dir='./', > outdir='./', > gdir=3, > nppstr=7, > lelfield=.true., > nberrycyc=3, > / > &system > ibrav= 6, > celldm(1)= 7.6153, > celldm(3)= 1.01319, > nat= 5, > ntyp= 3, > lda_plus_u=.true. > Hubbard_U(2)=4.3 > ecutwfc= 35.0, > nosym=.true > / > &electrons > mixing_beta=0.3, > conv_thr= 1e-8, > efield=0.001, > startingwfc='random' > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ti 47.88 Ti.pbe-sp-van_ak.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS {crystal} > Ba 0.00000 0.00000 0.00000 > Ti 0.50000 0.50000 0.50000 > O 0.50000 0.50000 0.00000 > O 0.00000 0.50000 0.50000 > O 0.50000 0.00000 0.50000 > K_POINTS 16 > 0.0 0.0 0.0 1 > 0.0 0.25 0.0 1 > 0.0 0.50 0.0 1 > 0.0 0.75 0.0 1 > 0.25 0.0 0.0 1 > 0.25 0.25 0.0 1 > 0.25 0.50 0.0 1 > 0.25 0.75 0.0 1 > 0.50 0.0 0.0 1 > 0.50 0.25 0.0 1 > 0.50 0.50 0.0 1 > 0.50 0.75 0.0 1 > 0.75 0.0 0.0 1 > 0.75 0.25 0.0 1 > 0.75 0.50 0.0 1 > 0.75 0.75 0.0 1 > Hongkien Feng > physcis department, > Beijing University of aeronautics & astronautics ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From dalcorso at sissa.it Wed Aug 29 10:03:30 2007 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Wed, 29 Aug 2007 10:03:30 +0200 Subject: [Pw_forum] PH error: k-points are odd In-Reply-To: <318172.44343.qm@web57714.mail.re3.yahoo.com> References: <318172.44343.qm@web57714.mail.re3.yahoo.com> Message-ID: <1188374610.3405.4.camel@dhpc-5-02.sissa.it> On Tue, 2007-08-28 at 19:11 -0700, Konstantin Kudin wrote: > All, > > I am trying to get phonons at a non-Gamma point, but the code is > crashing with the message: > from phq_readin : error # 1 > k-points are odd > > Could anyone check what is happening here? Did you run a 'phonon' band calculation before ph.x? Andrea > > These are the input/output files: > https://kiev.princeton.edu/grapu2w.zip > > Thanks in advance! > > Kostya > > > > > ____________________________________________________________________________________ > Got a little couch potato? > Check out fun summer activities for kids. > http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From fenghongjian at ss.buaa.edu.cn Wed Aug 29 20:45:33 2007 From: fenghongjian at ss.buaa.edu.cn (hongkien) Date: Thu, 30 Aug 2007 02:45:33 +0800 Subject: [Pw_forum] error in finite electric field In-Reply-To: <20070829090709.kxey97bq8g88go0w@mail.democritos.it> References: <20070829090709.kxey97bq8g88go0w@mail.democritos.it> Message-ID: <1188413133.3004.4.camel@node0> ? 2007-08-29?? 09:07 +0200?umari at democritos.it??? > Dear Hongkien, > > > I have beening calculating the ferroelectic properties of BaTiO3 > > under finite electric field, but in the scf cycle the code always > > crashed without giving any suggestions.I found the related error in the > > output file like this: > > > > iteration # 1 ecut= 35.00 Ry beta=0.30 > > Davidson diagonalization with overlap > > error hepsiher: translated G= 0.291666666666667 > > 0.583333333333333 0.000000000000000E+000 with crystal > > coordinates 0 > > 1 > > 0 corresponds to ng= 6 but G(ng)= > > 0.000000000000000E+000 > > 1.00000000000000 0.000000000000000E+000 > > probably because G_par is NOT a reciprocal lattice vector > > Possible choices as smallest G_par: > > i= 1 G= 0.000000000000000E+000 0.000000000000000E+000 > > 0.000000000000000E+000 > > i= 2 G= 0.000000000000000E+000 0.000000000000000E+000 > > -0.986981711228891 i= 3 G= 0.000000000000000E+000 > > 0.000000000000000E+000 > > 0.986981711228891 ....... > > > I have tried different Kponts structure and the diagonalization > > methods,but failed. Is it a pseudopotential problem? It will be very > > appreciated for any suggestion about this. Thank you in advance. > > As explained in the README of example 31 the direction of the electric > field is given by gdir, note that till now > only orthorombic cells have been tested and gdir==3 is the only choice > working for parallel calculations, > then nppstr gives the number of equally spaced k-point along the direction > gdir, which must be give in appropriate order. > > In your case you have a mesh of 4 k-points along the second direction > but in the input file nppstr is 7 instead of 4 and gdir is 3 instead of 2 > > Best regards, > Paolo Umari, > > DEMOCRITOS, Italy Dear Paolo , I have already tried the following kpoints structure (along the third direction divided by 7), it still produced the same error.I do not know how to solve this problem. &control calculation='scf' restart_mode='restart' prefix='bto', verbosity='high', pseudo_dir='./', outdir='./', gdir=3, nppstr=7, lelfield=.true., nberrycyc=3, / &system ibrav= 6, celldm(1)= 7.6153, celldm(3)= 1.01319, nat= 5, ntyp= 3, lda_plus_u=.true. Hubbard_U(2)=4.3 ecutwfc= 35.0, nosym=.true / &electrons mixing_beta=0.3, conv_thr= 1e-8, efield=0.001, startingwfc='random' / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.88 Ti.pbe-sp-van_ak.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS {crystal} Ba 0.00000 0.00000 0.00000 Ti 0.50000 0.50000 0.50000 O 0.50000 0.50000 0.00000 O 0.00000 0.50000 0.50000 O 0.50000 0.00000 0.50000 K_POINTS 63 0. 0. 0. 1 0. 0. 0.142857143 1 0. 0. 0.285714286 1 0. 0. 0.428571429 1 0. 0. 0.571428571 1 0. 0. 0.714285714 1 0. 0. 0.857142857 1 0. 0.333333333 0. 1 0. 0.333333333 0.142857143 1 0. 0.333333333 0.285714286 1 0. 0.333333333 0.428571429 1 0. 0.333333333 0.571428571 1 0. 0.333333333 0.714285714 1 0. 0.333333333 0.857142857 1 0. 0.666666667 0. 1 0. 0.666666667 0.142857143 1 0. 0.666666667 0.285714286 1 0. 0.666666667 0.428571429 1 0. 0.666666667 0.571428571 1 0. 0.666666667 0.714285714 1 0. 0.666666667 0.857142857 1 0.333333333 0. 0. 1 0.333333333 0. 0.142857143 1 0.333333333 0. 0.285714286 1 0.333333333 0. 0.428571429 1 0.333333333 0. 0.571428571 1 0.333333333 0. 0.714285714 1 0.333333333 0. 0.857142857 1 0.333333333 0.333333333 0. 1 0.333333333 0.333333333 0.142857143 1 0.333333333 0.333333333 0.285714286 1 0.333333333 0.333333333 0.428571429 1 0.333333333 0.333333333 0.571428571 1 0.333333333 0.333333333 0.714285714 1 0.333333333 0.333333333 0.857142857 1 0.333333333 0.666666667 0. 1 0.333333333 0.666666667 0.142857143 1 0.333333333 0.666666667 0.285714286 1 0.333333333 0.666666667 0.428571429 1 0.333333333 0.666666667 0.571428571 1 0.333333333 0.666666667 0.714285714 1 0.333333333 0.666666667 0.857142857 1 0.666666667 0. 0. 1 0.666666667 0. 0.142857143 1 0.666666667 0. 0.285714286 1 0.666666667 0. 0.428571429 1 0.666666667 0. 0.571428571 1 0.666666667 0. 0.714285714 1 0.666666667 0. 0.857142857 1 0.666666667 0.333333333 0. 1 0.666666667 0.333333333 0.142857143 1 0.666666667 0.333333333 0.285714286 1 0.666666667 0.333333333 0.428571429 1 0.666666667 0.333333333 0.571428571 1 0.666666667 0.333333333 0.714285714 1 0.666666667 0.333333333 0.857142857 1 0.666666667 0.666666667 0. 1 0.666666667 0.666666667 0.142857143 1 0.666666667 0.666666667 0.285714286 1 0.666666667 0.666666667 0.428571429 1 0.666666667 0.666666667 0.571428571 1 0.666666667 0.666666667 0.714285714 1 0.666666667 0.666666667 0.857142857 1 Best regards Hongkien Feng physics department Beijing University of aeronautics &astronautics > > > My input file was pasted here: > > &control > > calculation='scf' > > restart_mode='restart' > > prefix='bto', > > verbosity='high', > > pseudo_dir='./', > > outdir='./', > > gdir=3, > > nppstr=7, > > lelfield=.true., > > nberrycyc=3, > > / > > &system > > ibrav= 6, > > celldm(1)= 7.6153, > > celldm(3)= 1.01319, > > nat= 5, > > ntyp= 3, > > lda_plus_u=.true. > > Hubbard_U(2)=4.3 > > ecutwfc= 35.0, > > nosym=.true > > / > > &electrons > > mixing_beta=0.3, > > conv_thr= 1e-8, > > efield=0.001, > > startingwfc='random' > > / > > ATOMIC_SPECIES > > Ba 137.327 Ba.pbe-nsp-van.UPF > > Ti 47.88 Ti.pbe-sp-van_ak.UPF > > O 15.999 O.pbe-van_ak.UPF > > ATOMIC_POSITIONS {crystal} > > Ba 0.00000 0.00000 0.00000 > > Ti 0.50000 0.50000 0.50000 > > O 0.50000 0.50000 0.00000 > > O 0.00000 0.50000 0.50000 > > O 0.50000 0.00000 0.50000 > > K_POINTS 16 > > 0.0 0.0 0.0 1 > > 0.0 0.25 0.0 1 > > 0.0 0.50 0.0 1 > > 0.0 0.75 0.0 1 > > 0.25 0.0 0.0 1 > > 0.25 0.25 0.0 1 > > 0.25 0.50 0.0 1 > > 0.25 0.75 0.0 1 > > 0.50 0.0 0.0 1 > > 0.50 0.25 0.0 1 > > 0.50 0.50 0.0 1 > > 0.50 0.75 0.0 1 > > 0.75 0.0 0.0 1 > > 0.75 0.25 0.0 1 > > 0.75 0.50 0.0 1 > > 0.75 0.75 0.0 1 > > > > Hongkien Feng > > > physcis department, > > Beijing University of aeronautics & astronautics > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Wed Aug 29 13:20:10 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 29 Aug 2007 13:20:10 +0200 Subject: [Pw_forum] Fwd: nstep, npool and FFT grid In-Reply-To: <20070825160608.5bniad1nglwoggck@mail.ph.utexas.edu> References: <20070825160608.5bniad1nglwoggck@mail.ph.utexas.edu> Message-ID: <400790D1-50A7-412A-A0E0-4332B27C8B6D@nest.sns.it> On Aug 25, 2007, at 23:06 , brsahu at physics.utexas.edu wrote: > In a system where the FFT-grids along x-, y- and z-directions are not > equal,which one of these decides the PW parallelization efficiency? as mentioned, but not in a clear way, in the user guide, the FFT arrays are "sliced" in real space along z. The most effective choice of axis depends on the specific case: if you want to run on as many processors as possible, it is typically convenient to have the largest FFT grid along z. > Is there a default for number of pools of processors that a running > job > assumes if not specified in the "job" submitting script a single pool, i.e. no k-point parallelization Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Aug 29 14:45:06 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 29 Aug 2007 14:45:06 +0200 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: <200708281616.31328.shaposh@isp.nsc.ru> References: <200708281616.31328.shaposh@isp.nsc.ru> Message-ID: On Aug 28, 2007, at 11:16 , Alexander Shaposhnikov wrote: > i have been trying to figure out how to set up monoclinic base- > centered cell > for Ta2O5 and have some difficulty in determining the right format . > > My question is, in what exactly vectors the coordinates in > "crystal" format > are entered? Are they initial a,b,c vectors or transformed a1,b1,c1 ? > (notations from the "input_pw" doc file the latter, i.e. what is printed in output. Note that the monoclinic base-centered cell (ibrav=13) was incorrect in all versions preceding 18-oct-2006. See: http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/flib/latgen.f90 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From zdw2000 at gmail.com Wed Aug 29 14:47:58 2007 From: zdw2000 at gmail.com (Wei Zhou) Date: Wed, 29 Aug 2007 20:47:58 +0800 Subject: [Pw_forum] maximally localized wannier function and k points generated Message-ID: <3e36a8fc0708290547r6e130c1dodb85a8fe3c19d377@mail.gmail.com> Dear all I am a newe pwscf user , I want to calcalate the maximally localized wannier function use pwscf together with Want, I have two question . I want to user molececlar dynamics to simulate different strcure at temperature and pressure ,and calcualate the maximally localized wannier function of the differet structure and to see it's changs .my system is metal, I wonder if I can use pwscf and Want to achieve this aims-simulating different strcure and calculating maximally localized wannier function .I know If my system is not metal ,then CP method is encough ,but if I use BODM molecular dynamics,then how I can calculate the maximally localized wannier function,this is the first question. Second question, I have searched the pwsfc maillist for calculating maximally localized wannier function , the first step is scf calculation ,second is nscf calculation, then run want calculation ,I feel puzzle the k points generation of three procedure ,are these is the same.all along the standard symmetry lines ? Thanks in advance. **Best regards, ZhouDaWei -- 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/20070829/2f1b6e2c/attachment.htm From ferretti.andrea at unimore.it Wed Aug 29 16:25:02 2007 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Wed, 29 Aug 2007 16:25:02 +0200 (CEST) Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: <3e36a8fc0708290547r6e130c1dodb85a8fe3c19d377@mail.gmail.com> References: <3e36a8fc0708290547r6e130c1dodb85a8fe3c19d377@mail.gmail.com> Message-ID: Hi Zhou, > I am a newe pwscf user , I want to calcalate the maximally localized > wannier function use pwscf together with Want, > I have two question . (note that, due to technical problems with the web site, want-2.1 is there only since few days ago; consider to update to this version if the case) > I want to user molececalr dynamics to simulate different strcure at > temperature and pressure ,and calcualate > the maximally localized wannier function of the differet structure > and to see it's changs .my system is metal, > I wonder if I can use pwscf and Want to achieve this aims-simulating > different strcure and calculating maximally localized > wannier function. yes, you can; maximally localized Wannier funcitons for metals are computed following the framework of Souza, Marzari and Vanderbilt. > I know If my system is not metal ,then CP method is > encough ,but if I use BODM molecular dynamics,then how > I can calculate the maximally localized wannier function,this is the > first question. whatever method you use to compute the electronic structure of your system, espresso will export dft data in the same way (i.e. with the same format), so you can compute WFs on top of any configuration you have computed... see below for the technical aspects (input vars, etc) > Second question, I have searched the pwsfc maillist for calculating > maximally localized wannier function , the first step is scf calculation > ,second is nscf calculation, then run want calculation ,I feel puzzle the k > points generation of three procedure ,are these is the same.all along the > standard symmetry lines ? WanT needs DFT data (the "electronic structure") on a regular (i.e. equally spaced) mesh of k-points in the *full* BZ; where full means not reduced by symmetry (the possibility of using kpt symmetrization is under development at the moment, but not yet available for production). a way to do a WF calculation using pwscf is the following: * perform a scf calculation (whatever kpt mesh which gives you a converged charge density) * perform a nscf calculation providing a regular kpt mesh over the whole Brillouin zone. Such mesh can be generated with the kgrid.x utility of WanT * do not forget to use wf_collect = .TRUE. in the nscf calculation, or to run pw_export.x after the nscf calculation to export dft data note that *all* these calculations aim to sample the full BZ, and therefore there is no reference to any "standard symmetry line" > Thanks in advance. > **Best regards, > ZhouDaWei > hope it helps andrea -- Andrea Ferretti National Research Center S3, CNR-INFM ( http://s3.infm.it ) Dip. Fisica, Univ. di Modena e Reggio E. (Italy) Tel: +39 059 2055301; Fax: +39 059 374794; Skype: andrea_ferretti URL: http://www.nanoscience.unimo.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From zdw2000 at gmail.com Wed Aug 29 16:53:24 2007 From: zdw2000 at gmail.com (Wei Zhou) Date: Wed, 29 Aug 2007 22:53:24 +0800 Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: References: <3e36a8fc0708290547r6e130c1dodb85a8fe3c19d377@mail.gmail.com> Message-ID: <3e36a8fc0708290753y5b5c1623wd1e4935b0729b878@mail.gmail.com> thank you very much ,your answer is so clearly, now I know what to do ! 2007/8/29, Andrea Ferretti : > > > Hi Zhou, > > > I am a newe pwscf user , I want to calcalate the maximally localized > > wannier function use pwscf together with Want, > > I have two question . > > (note that, due to technical problems with the web site, want-2.1 is > there only since few days ago; consider to update to this version if the > case) > > > I want to user molececalr dynamics to simulate different strcure at > > temperature and pressure ,and calcualate > > the maximally localized wannier function of the differet structure > > and to see it's changs .my system is metal, > > I wonder if I can use pwscf and Want to achieve this aims-simulating > > different strcure and calculating maximally localized > > wannier function. > > yes, you can; maximally localized Wannier funcitons for metals are > computed following the framework of Souza, Marzari and Vanderbilt. > > > I know If my system is not metal ,then CP method is > > encough ,but if I use BODM molecular dynamics,then how > > I can calculate the maximally localized wannier function,this is the > > first question. > > whatever method you use to compute the electronic structure of > your system, espresso will export dft data in the same way (i.e. with > the same format), > so you can compute WFs on top of any configuration you have computed... > see below for the technical aspects (input vars, etc) > > > Second question, I have searched the pwsfc maillist for calculating > > maximally localized wannier function , the first step is scf calculation > > ,second is nscf calculation, then run want calculation ,I feel puzzle > the k > > points generation of three procedure ,are these is the same.all along > the > > standard symmetry lines ? > > WanT needs DFT data (the "electronic structure") on a regular (i.e. > equally spaced) mesh of k-points in the *full* BZ; > where full means not reduced by symmetry (the possibility of using kpt > symmetrization is under development at the moment, but not yet available > for production). > > a way to do a WF calculation using pwscf is the following: > > * perform a scf calculation (whatever kpt mesh which gives you a > converged charge density) > > * perform a nscf calculation providing a regular kpt mesh over the whole > Brillouin zone. Such mesh can be generated > with the kgrid.x utility of WanT > > * do not forget to use wf_collect = .TRUE. in the nscf calculation, > or to run pw_export.x after the nscf calculation to export dft data > > note that *all* these calculations aim to sample the full BZ, and > therefore there is no reference to any "standard symmetry line" > > > > Thanks in advance. > > **Best regards, > > ZhouDaWei > > > > hope it helps > andrea > > -- > Andrea Ferretti > National Research Center S3, CNR-INFM ( http://s3.infm.it ) > Dip. Fisica, Univ. di Modena e Reggio E. (Italy) > Tel: +39 059 2055301; Fax: +39 059 374794; Skype: andrea_ferretti > URL: http://www.nanoscience.unimo.it > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20070829/3a50d203/attachment-0001.htm From konstantin_kudin at yahoo.com Wed Aug 29 23:42:22 2007 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Wed, 29 Aug 2007 14:42:22 -0700 (PDT) Subject: [Pw_forum] PH error: k-points are odd In-Reply-To: <1188374610.3405.4.camel@dhpc-5-02.sissa.it> Message-ID: <447988.53338.qm@web57704.mail.re3.yahoo.com> Andrea, thanks! Indeed, I was not aware of the need to run PW with 'phonon' before PH for a general k point. I patched a little the PH code in the CVS such that if the desired k point can be found on a regular k space grid, one can set the input for the dispersion calculation with some mesh and then specify that just one k point from the mesh is of interest. The significant advantage of this option is that the need for the prior PW run with 'phonon' disappears - thus the job script can be shorter :-) Kostya --- Dal Corso Andrea wrote: > On Tue, 2007-08-28 at 19:11 -0700, Konstantin Kudin wrote: > > All, > > > > I am trying to get phonons at a non-Gamma point, but the code is > > crashing with the message: > > from phq_readin : error # 1 > > k-points are odd > > > > Could anyone check what is happening here? > > Did you run a 'phonon' band calculation before ph.x? > > > Andrea > > > > > > These are the input/output files: > > https://kiev.princeton.edu/grapu2w.zip > > > > Thanks in advance! > > > > Kostya > > > > > > > > > > > ____________________________________________________________________________________ > > Got a little couch potato? > > Check out fun summer activities for kids. > > > http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > -- > Andrea Dal Corso Tel. 0039-040-3787428 > SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 > 34014 Trieste (Italy) e-mail: dalcorso at sissa.it > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________________________________________ Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 From eyvaz_isaev at yahoo.com Wed Aug 29 23:46:12 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 29 Aug 2007 14:46:12 -0700 (PDT) Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: Message-ID: <464953.68630.qm@web60316.mail.yahoo.com> Hi Andrea, --- Andrea Ferretti wrote: > (note that, due to technical problems with the web > site, want-2.1 is there only since few days ago; > consider to update to this version if the case) But what I see on the website (www.wannier.org): Download Wannier90 is now available for download! Wannier90 (v1.0.2), released 04-DEC-2006: Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 From marzari at MIT.EDU Wed Aug 29 23:51:27 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 29 Aug 2007 17:51:27 -0400 Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: <464953.68630.qm@web60316.mail.yahoo.com> References: <464953.68630.qm@web60316.mail.yahoo.com> Message-ID: <46D5EA5F.4050509@mit.edu> Hi Eyvaz, these are two separate projects: www.wannier.org and www.wannier-transport.org . Admittedly, they do similar things, but, as Xavier Gonze once said, biodiversity is good for the environment. nicola > --- Andrea Ferretti > wrote: > >> (note that, due to technical problems with the web >> site, want-2.1 is there only since few days ago; >> consider to update to this version if the case) > > But what I see on the website (www.wannier.org): > > Download > Wannier90 is now available for download! > Wannier90 (v1.0.2), released 04-DEC-2006: > > > Bests, > Eyvaz. -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From eyvaz_isaev at yahoo.com Thu Aug 30 00:06:46 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 29 Aug 2007 15:06:46 -0700 (PDT) Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: <46D5EA5F.4050509@mit.edu> Message-ID: <836250.23085.qm@web60314.mail.yahoo.com> Hi Nicola, Thanks, and my apologies. I am upset very much mixing such a kind different biodiversity, indeed. Of course, everything is OK on the right website. Bests, Eyvaz. --- Nicola Marzari wrote: > > > Hi Eyvaz, > > these are two separate projects: > > www.wannier.org and www.wannier-transport.org . > > Admittedly, they do similar things, but, as Xavier > Gonze once said, biodiversity is good for the > environment. > > nicola > > > > > --- Andrea Ferretti > > wrote: > > > >> (note that, due to technical problems with the > web > >> site, want-2.1 is there only since few days ago; > > >> consider to update to this version if the case) > > > > But what I see on the website (www.wannier.org): > > > > Download > > Wannier90 is now available for download! > > Wannier90 (v1.0.2), released 04-DEC-2006: > > > > > > Bests, > > Eyvaz. > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials > Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge > MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu > http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC From nakhmanson at anl.gov Wed Aug 29 23:52:28 2007 From: nakhmanson at anl.gov (Serge Nakhmanson) Date: Wed, 29 Aug 2007 16:52:28 -0500 Subject: [Pw_forum] maximally localized wannier function and k points generated In-Reply-To: <464953.68630.qm@web60316.mail.yahoo.com> References: <464953.68630.qm@web60316.mail.yahoo.com> Message-ID: <46D5EA9C.1000203@anl.gov> You are confusing Wannier90: http://wannier.org/ and WanT: http://www.wannier-transport.org/ These are two different codes. Cheers, S. Eyvaz Isaev wrote: > Hi Andrea, > > --- Andrea Ferretti > wrote: > >> (note that, due to technical problems with the web >> site, want-2.1 is there only since few days ago; >> consider to update to this version if the case) > > But what I see on the website (www.wannier.org): > > Download > Wannier90 is now available for download! > Wannier90 (v1.0.2), released 04-DEC-2006: > > > Bests, > Eyvaz. > -- ********************************************************* Serge M. Nakhmanson phone: (630) 252-5205 Assistant Scientist fax: (630) 252-4798 MSD-212, Rm. C-224 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From giannozz at nest.sns.it Thu Aug 30 10:11:27 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 30 Aug 2007 10:11:27 +0200 Subject: [Pw_forum] PH error: k-points are odd In-Reply-To: <447988.53338.qm@web57704.mail.re3.yahoo.com> References: <447988.53338.qm@web57704.mail.re3.yahoo.com> Message-ID: On Aug 29, 2007, at 23:42 , Konstantin Kudin wrote: > Indeed, I was not aware of the need to run PW with 'phonon' before PH > for a general k point. it is clearly stated in the documentation > I patched a little the PH code in the CVS such that if the desired k > point can be found on a regular k space grid, one can set the input > for > the dispersion calculation with some mesh and then specify that just > one k point from the mesh is of interest. The significant advantage of > this option is that the need for the prior PW run with 'phonon' > disappears - thus the job script can be shorter :-) the significant disadvantage is that option 'lnscf' does exacty what you wanted in a much more straightforward way Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From stirling at chemres.hu Thu Aug 30 10:21:26 2007 From: stirling at chemres.hu (stirling andras) Date: Thu, 30 Aug 2007 10:21:26 +0200 Subject: [Pw_forum] ESR g-tensor calculation Message-ID: <1188462086.4748.10.camel@geronimo.mta-kk> Dear espresso users, I would like to ask if it is possible to calculate g-tensor for ESR spectra, using the espresso package? The mailing list has one note from last year about the implementation of the Pickard-Mauri method. I would like to know if it works and if yes, what are the keywords to obtain the g-tensor for a system containing unpaired spin(s)? Thank you for your attention, Andras Stirling Department of Theoretical Chemistry, Chemical Research Center, Budapest, Hungary -- stirling andras From ari.p.seitsonen at iki.fi Thu Aug 30 12:29:13 2007 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 30 Aug 2007 12:29:13 +0200 (CEST) Subject: [Pw_forum] ESR g-tensor calculation In-Reply-To: <1188462086.4748.10.camel@geronimo.mta-kk> References: <1188462086.4748.10.camel@geronimo.mta-kk> Message-ID: Dear Andras, We are about to finish an implementation of the g tensor; we are currently testing and cleaning up the code (the first test cases work pretty satisfactorily, but we have not tested the robustness etc). We hope to be ready for a release in 4-8 weeks, the latest. Greetings from Sunny Paris, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ IMPMC, CNRS & Universit? Pierre et Marie Curie Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 On Thu, 30 Aug 2007, stirling andras wrote: > > Dear espresso users, > > I would like to ask if it is possible to > calculate g-tensor for ESR spectra, using the espresso package? > > The mailing list has one note from last year about the implementation > of the Pickard-Mauri method. I would like to know > if it works and if yes, what are the keywords to obtain > the g-tensor for a system containing unpaired spin(s)? > > Thank you for your attention, > > Andras Stirling > Department of Theoretical Chemistry, > Chemical Research Center, Budapest, Hungary > > > -- > stirling andras > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From konstantin_kudin at yahoo.com Thu Aug 30 17:00:59 2007 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Thu, 30 Aug 2007 08:00:59 -0700 (PDT) Subject: [Pw_forum] PH error: k-points are odd In-Reply-To: Message-ID: <561107.62260.qm@web57712.mail.re3.yahoo.com> --- Paolo Giannozzi wrote: > > On Aug 29, 2007, at 23:42 , Konstantin Kudin wrote: > > > Indeed, I was not aware of the need to run PW with 'phonon' before > PH > > for a general k point. > > it is clearly stated in the documentation > > I patched a little the PH code in the CVS such that if the desired > k > > point can be found on a regular k space grid, one can set the input > > > for > > the dispersion calculation with some mesh and then specify that > just > > one k point from the mesh is of interest. The significant advantage > of > > this option is that the need for the prior PW run with 'phonon' > > disappears - thus the job script can be shorter :-) > > the significant disadvantage is that option 'lnscf' does exacty what > you wanted in a much more straightforward way Then this is quite confusing. If 'lnscf' *is* working, why advise people to run PW with 'phonon' first where 'lnscf' in PH by itself would work just fine? I also did try 'lnscf' with a CVS version from a couple of months ago, and it did not work there, since the failing case I posted previously did have lnscf=.true. . The recent version works, so it must have been fixed in the meantime. I could not find which specific commit addressed the issue recently, that is why I thought the older version was just as good. Finally, in the "clear" documentation there are 2 different options - 'nscf' and 'phonon' for PW. The manual says to run 'phonon' before PH, at the same time lnscf=.true. in PH promises to run 'nscf' first. This does not seem to be that particularly clear ... Kostya ____________________________________________________________________________________ Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 From Zahraa.Ibrahim at uoit.ca Thu Aug 30 19:21:11 2007 From: Zahraa.Ibrahim at uoit.ca (Zahraa Ibrahim) Date: Thu, 30 Aug 2007 13:21:11 -0400 Subject: [Pw_forum] Temperature extraction from PW Message-ID: Hello PWSCF users I recently changed from the democritus version of PW to the espresso version. I noticed that the temperature in the espresso version is calculated from T = 2 * (kinetic energy - center of mass energy) / (3N-3) [I am not setting any constraints] while in the democritus version it was calculated by dividing the numerator by (3N). (N being the number of particles). I was wondering what exactly this extra 3 stands for. Another, probably related, question is about the effect of periodic boundary conditions on the temperature. I am simulating thermal motion in a solid with a relatively small number of atoms. Do the periodic boundary conditions change the degrees of freedom of the solid in any ways, that need to be taken into account in the temperature estimation. Greetings Zahraa Ibrahim This message has been scanned by F-Secure Anti-Virus for Microsoft Exchange. For more information, connect to http://www.f-secure.com/ From shaposh at isp.nsc.ru Fri Aug 31 06:32:31 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 31 Aug 2007 11:32:31 +0700 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: References: <200708281616.31328.shaposh@isp.nsc.ru> Message-ID: <200708311132.31759.shaposh@isp.nsc.ru> Thank you for clarification. Thats what i thought myself. I have found that Xcrysden displays structure incorrectly if i open the input file, but the output file looks like it should. What could be the explanation for this phenomena? Best Regards, A. Shaposhnikov On Wednesday 29 August 2007 19:45, Paolo Giannozzi wrote: > On Aug 28, 2007, at 11:16 , Alexander Shaposhnikov wrote: > > i have been trying to figure out how to set up monoclinic base- > > centered cell > > for Ta2O5 and have some difficulty in determining the right format . > > > > My question is, in what exactly vectors the coordinates in > > "crystal" format > > are entered? Are they initial a,b,c vectors or transformed a1,b1,c1 ? > > (notations from the "input_pw" doc file > > the latter, i.e. what is printed in output. > > Note that the monoclinic base-centered cell (ibrav=13) was incorrect > in all > versions preceding 18-oct-2006. See: > http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/flib/latgen.f90 > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Fri Aug 31 07:14:26 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 31 Aug 2007 01:14:26 -0400 (EDT) Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: <200708311132.31759.shaposh@isp.nsc.ru> Message-ID: On Fri, 31 Aug 2007, Alexander Shaposhnikov wrote: AS> Thank you for clarification. Thats what i thought myself. AS> AS> I have found that Xcrysden displays structure incorrectly if i open the input AS> file, but the output file looks like it should. What could be the explanation AS> for this phenomena? please check, whether you are not victim of some locale related issues. i.e. do "setenv LC_ALL C" or "export LC_ALL=C" (depending on whether you are using c-shell or bourne shell, respectively) and try again. cheers, axel. AS> AS> Best Regards, AS> A. Shaposhnikov AS> AS> On Wednesday 29 August 2007 19:45, Paolo Giannozzi wrote: AS> > On Aug 28, 2007, at 11:16 , Alexander Shaposhnikov wrote: AS> > > i have been trying to figure out how to set up monoclinic base- AS> > > centered cell AS> > > for Ta2O5 and have some difficulty in determining the right format . AS> > > AS> > > My question is, in what exactly vectors the coordinates in AS> > > "crystal" format AS> > > are entered? Are they initial a,b,c vectors or transformed a1,b1,c1 ? AS> > > (notations from the "input_pw" doc file AS> > AS> > the latter, i.e. what is printed in output. AS> > AS> > Note that the monoclinic base-centered cell (ibrav=13) was incorrect AS> > in all AS> > versions preceding 18-oct-2006. See: AS> > http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/flib/latgen.f90 AS> > AS> > Paolo AS> > --- AS> > Paolo Giannozzi, Democritos and University of Udine, Italy AS> > AS> > AS> > _______________________________________________ AS> > Pw_forum mailing list AS> > Pw_forum at pwscf.org AS> > http://www.democritos.it/mailman/listinfo/pw_forum AS> _______________________________________________ AS> Pw_forum mailing list AS> Pw_forum at pwscf.org AS> http://www.democritos.it/mailman/listinfo/pw_forum AS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shaposh at isp.nsc.ru Fri Aug 31 09:22:26 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 31 Aug 2007 14:22:26 +0700 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: References: Message-ID: <200708311422.26824.shaposh@isp.nsc.ru> Could you explain what it does? Anyway, i dont think this has anything to do with locale. I have english SuSe 10.2. Probably this is error in Xcrysden with monoclinic base centered (celldm 13) cell? Best Regards, A. Shaoshnikov On Friday 31 August 2007 12:14, Axel Kohlmeyer wrote: > On Fri, 31 Aug 2007, Alexander Shaposhnikov wrote: > > AS> Thank you for clarification. Thats what i thought myself. > AS> > AS> I have found that Xcrysden displays structure incorrectly if i open the > input AS> file, but the output file looks like it should. What could be > the explanation AS> for this phenomena? > > please check, whether you are not victim of some locale related > issues. i.e. do "setenv LC_ALL C" or "export LC_ALL=C" (depending > on whether you are using c-shell or bourne shell, respectively) > and try again. > cheers, > axel. > > > AS> > AS> Best Regards, > AS> A. Shaposhnikov > AS> > AS> On Wednesday 29 August 2007 19:45, Paolo Giannozzi wrote: > AS> > On Aug 28, 2007, at 11:16 , Alexander Shaposhnikov wrote: > AS> > > i have been trying to figure out how to set up monoclinic base- > AS> > > centered cell > AS> > > for Ta2O5 and have some difficulty in determining the right format > . AS> > > > AS> > > My question is, in what exactly vectors the coordinates in > AS> > > "crystal" format > AS> > > are entered? Are they initial a,b,c vectors or transformed a1,b1,c1 > ? AS> > > (notations from the "input_pw" doc file > AS> > > AS> > the latter, i.e. what is printed in output. > AS> > > AS> > Note that the monoclinic base-centered cell (ibrav=13) was incorrect > AS> > in all > AS> > versions preceding 18-oct-2006. See: > AS> > > http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/flib/latgen.f90 AS> > > > AS> > Paolo > AS> > --- > AS> > Paolo Giannozzi, Democritos and University of Udine, Italy > AS> > > AS> > > AS> > _______________________________________________ > AS> > Pw_forum mailing list > AS> > Pw_forum at pwscf.org > AS> > http://www.democritos.it/mailman/listinfo/pw_forum > AS> _______________________________________________ > AS> Pw_forum mailing list > AS> Pw_forum at pwscf.org > AS> http://www.democritos.it/mailman/listinfo/pw_forum > AS> From tone.kokalj at ijs.si Fri Aug 31 10:03:10 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 31 Aug 2007 10:03:10 +0200 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: <200708311422.26824.shaposh@isp.nsc.ru> References: <200708311422.26824.shaposh@isp.nsc.ru> Message-ID: <1188547390.2576.5.camel@localhost.localdomain> On Fri, 2007-08-31 at 14:22 +0700, Alexander Shaposhnikov wrote: > Could you explain what it does? > > Anyway, i dont think this has anything to do with locale. > I have english SuSe 10.2. > Probably this is error in Xcrysden with monoclinic base centered (celldm 13) . > cell? You are right, it is a bug. I just found a bug in the pwi2xsf filter (which transforms the pwscf input to xsf file). I attach the fix (pwi2xsf.tgz). There are three fotran files + makefile. Compile the "pwi2xsf" program and copy it to: $XCRSYDEN_TOPDIR/bin Then try your case. Let me know if the fix works. Regards, Tone -------------- next part -------------- A non-text attachment was scrubbed... Name: pwi2xsf.tgz Type: application/x-compressed-tar Size: 6371 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20070831/4d5fb37c/attachment.bin From shaposh at isp.nsc.ru Fri Aug 31 10:20:33 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 31 Aug 2007 15:20:33 +0700 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: <1188547390.2576.5.camel@localhost.localdomain> References: <200708311422.26824.shaposh@isp.nsc.ru> <1188547390.2576.5.camel@localhost.localdomain> Message-ID: <200708311520.33959.shaposh@isp.nsc.ru> Compiled it (with ifort) and swaped, but the things become worse :) The distances are now on the order of magnitude more than should be. Regards, Alex On Friday 31 August 2007 15:03, Tone Kokalj wrote: > On Fri, 2007-08-31 at 14:22 +0700, Alexander Shaposhnikov wrote: > > Could you explain what it does? > > > > Anyway, i dont think this has anything to do with locale. > > I have english SuSe 10.2. > > Probably this is error in Xcrysden with monoclinic base centered (celldm > > 13) . cell? > > You are right, it is a bug. I just found a bug in the pwi2xsf filter > (which transforms the pwscf input to xsf file). > > I attach the fix (pwi2xsf.tgz). There are three fotran files + makefile. > Compile the "pwi2xsf" program and copy it to: $XCRSYDEN_TOPDIR/bin > > Then try your case. Let me know if the fix works. > > Regards, Tone From tone.kokalj at ijs.si Fri Aug 31 11:37:02 2007 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 31 Aug 2007 11:37:02 +0200 Subject: [Pw_forum] About "crystal" coordinates In-Reply-To: <200708311520.33959.shaposh@isp.nsc.ru> References: <200708311422.26824.shaposh@isp.nsc.ru> <1188547390.2576.5.camel@localhost.localdomain> <200708311520.33959.shaposh@isp.nsc.ru> Message-ID: <1188553023.2576.9.camel@localhost.localdomain> On Fri, 2007-08-31 at 15:20 +0700, Alexander Shaposhnikov wrote: > Compiled it (with ifort) and swaped, but the things become worse :) > The distances are now on the order of magnitude more than should be. I was too fast with the fix. Can you retry with this. Tone -------------- next part -------------- A non-text attachment was scrubbed... Name: pwi2xsf.tgz Type: application/x-compressed-tar Size: 6244 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20070831/794b4f8f/attachment-0001.bin From uccaati at ucl.ac.uk Fri Aug 31 13:10:34 2007 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Fri, 31 Aug 2007 12:10:34 +0100 (BST) Subject: [Pw_forum] Temperature extraction from PW In-Reply-To: References: Message-ID: I think the extra 3 takes into account the translational (center of mass) degrees of freedom: if the center of mass is fixed, the total number of degrees of freedom decreases by 3. At the same time, the c.o.m. kinetic energy will be zero, so there is probably no need to subtract it from the total kinetic energy in the numerator. Antonio Tilocca UCL Message: 5 Date: Thu, 30 Aug 2007 13:21:11 -0400 From: "Zahraa Ibrahim" Subject: [Pw_forum] Temperature extraction from PW I noticed that the temperature in the espresso version is calculated from T = 2 * (kinetic energy - center of mass energy) / (3N-3) [I am not setting any constraints] while in the democritus version it was calculated by dividing the numerator by (3N). (N being the number of particles). I was wondering what exactly this extra 3 stands for. Another, probably related, question is about the effect of periodic boundary conditions on the temperature. I am simulating thermal motion in a solid with a relatively small number of atoms. Do the periodic boundary conditions change the degrees of freedom of the solid in any ways, that need to be taken into account in the temperature estimation. Greetings Zahraa Ibrahim From brsahu at physics.utexas.edu Fri Aug 31 21:15:36 2007 From: brsahu at physics.utexas.edu (Bhagawan Sahu) Date: Fri, 31 Aug 2007 14:15:36 -0500 (CDT) Subject: [Pw_forum] Max. no. of processors Message-ID: Dear PWSCF users, For a 288 processors jog on a linux cluster), I got the error message as %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 140 from startup : error # 288 too many processors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 99 from startup : error # 288 too many processors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% In PW/para.f90 MODULE para_const !---------------------------------------------------------------------------- ! SAVE ! INTEGER, PARAMETER :: & #if defined(__QK_USER__) maxproc = 2048 ! maximum number of processors. ! make it big for 'big iron'. #else maxproc = 128 ! maximum number of processors #endif END MODULE para_const Do I have to change #else maxproc = 128 ! maximum number of processors to a large number (say 1000 or anything greater than I need) and recompile the code again and this will take care of the error. Bhagawan Sahu Microelectronics Research Center University of Texas at Austin Austin TX 78758 From naromero at gmail.com Fri Aug 31 21:51:16 2007 From: naromero at gmail.com (Nichols A. Romero) Date: Fri, 31 Aug 2007 15:51:16 -0400 Subject: [Pw_forum] Max. no. of processors In-Reply-To: References: Message-ID: <6ac064b60708311251l1627b4b4l9c4f24e09b4f7970@mail.gmail.com> Give that a try. Depending on the nature of the problem, it may not easily parallelize to that many processors. On 8/31/07, Bhagawan Sahu wrote: > > > Dear PWSCF users, > > For a 288 processors jog on a linux cluster), I got the error message > as > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 140 from startup : error # 288 > too many processors > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 99 > from startup : error # 288 > too many processors > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > In PW/para.f90 > > MODULE para_const > > > !---------------------------------------------------------------------------- > ! > SAVE > ! > INTEGER, PARAMETER :: & > #if defined(__QK_USER__) > maxproc = 2048 ! maximum number of processors. > ! make it big for 'big iron'. > #else > maxproc = 128 ! maximum number of processors > #endif > END MODULE para_const > > > Do I have to change > > #else > maxproc = 128 ! maximum number of processors > > to a large number (say 1000 or anything greater than I need) and recompile > the code again and this will take care of the error. > > Bhagawan Sahu > Microelectronics Research Center > University of Texas at Austin > Austin TX 78758 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. DoD User Productivity Enhancement and Technology Transfer (PET) Group High Performance Technologies, Inc. Reston, VA 443-567-8328 (C) 410-278-2692 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20070831/fdc00d1a/attachment.htm From bogus@does.not.exist.com Wed Aug 22 09:38:52 2007 From: bogus@does.not.exist.com () Date: Wed, 22 Aug 2007 07:38:52 -0000 Subject: No subject Message-ID: using copper. Marcel And could you please post your affiliation On Mon, 22 Oct 2007, oulihui666 wrote: > > Dear pwscf users: > Because of the need of research, I tried to calculate the properties of free OH with pwscf, however,when calculating, error information was found, it displayed: > ============================================== > from electrons : error # 1 > charge is wrong > ============================================== > I am really newbie in this thing, sorry about these naive questions... > Can you please suggest some solutions? > And this is the input file: > Thanks a lot > best regards > Lihui Ou > > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = '/home/olh/tmp/' , > pseudo_dir = '/home/olh/pseudo/' , > prefix = 'OH' , > forc_conv_thr = 1.0D-4 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 14, > A = 10.000 , > B = 10.000 , > C = 10.000 , > cosAB = 0 , > cosAC = 0 , > cosBC = 0 , > nat = 2, > ntyp = 2, > ecutwfc = 60 , > ecutrho = 240 , > / > &ELECTRONS > conv_thr = 1.D-7 , > mixing_beta = 0.7D0 , > / > &IONS > ion_dynamics = 'bfgs' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > / > ATOMIC_SPECIES > O 16.00000 O.pz-rrkjus.UPF > H 1.00000 Cu.pz-d-rrkjus.UPF > ATOMIC_POSITIONS angstrom > O 5.000000000 5.000000000 5.000000000 > H 5.000000000 5.000000000 6.000000000 > K_POINTS automatic > 3 3 1 1 1 1 > From bogus@does.not.exist.com Wed Aug 22 09:38:52 2007 From: bogus@does.not.exist.com () Date: Wed, 22 Aug 2007 07:38:52 -0000 Subject: No subject Message-ID: that should be equivalent by translational symmetry (although even then there seem to be other issuses with the coordinates). A quick and easy way to check these things would be with Xcrysden (esp for pwscf) http://www.xcrysden.org/ -Nick On Wed, 7 Nov 2007, oulihui666 wrote: > Dear pwscf users: > I am now doing a large job of 'relax' calculation. The unit cell contains 20 atoms and vacuum. The job has been running for seven days. While the total energy is decreasing, the amount it decreases is approximately a constant. We calculated the Pt(111) surface with pwscf, we use a five-layer slab containing 20 Pt atoms, the atoms in the bottom three layers are fixed, and the others are allowed to relax. The input file and structure can be found in below. However, calculated results indicated, the atoms in the top two layers are not inward or outward relaxation, but upward or downward relaxation, Could you tell me whether the input file is correct or not? and the final structure is correct or not please? > Thanks a lot > Best wishes > Lihui Ou > > > > &CONTROL > > calculation = 'relax' , > > restart_mode = 'from_scratch' , > > outdir = '/home/olh/tmp/' , > > pseudo_dir = '/home/olh/pseudo/' , > > prefix = 'Pt111_20' , > > tstress = .true. , > > tprnfor = .true. , > > / > > &SYSTEM > > ibrav = 4, > > A = 5.549 , > > B = 5.549 , > > C = 21.062 , > > cosAB = -0.5 , > > cosAC = 0 , > > cosBC = 0 , > > nat = 20, > > ntyp = 1, > > ecutwfc = 70 , > > ecutrho = 0 , > > occupations = 'smearing' , > > degauss = 0.02 , > > smearing = 'gaussian' , > > / > > &ELECTRONS > > conv_thr = 1.0D-8 , > > mixing_beta = 0.7D0 , > > diagonalization = 'david' , > > / > > &IONS > > / > > ATOMIC_SPECIES > > Pt 195.09000 Pt.pz-rrkjus.linux.UPF > > ATOMIC_POSITIONS angstrom > > Pt -0.000000000 0.000000000 -9.062000000 0 0 0 > > Pt -0.000000000 2.775000000 -9.062000000 0 0 0 > > Pt 2.403000000 -1.387000000 -9.062000000 0 0 0 > > Pt 2.403000000 1.387000000 -9.062000000 0 0 0 > > Pt -0.000000000 -0.000000000 -2.265000000 1 1 1 > > Pt -0.000000000 2.775000000 -2.265000000 1 1 1 > > Pt 2.403000000 -1.387000000 -2.265000000 1 1 1 > > Pt 2.403000000 1.387000000 -2.265000000 1 1 1 > > Pt 1.602000000 0.000000000 -4.531000000 0 0 0 > > Pt 1.602000000 2.775000000 -4.531000000 0 0 0 > > Pt 4.005000000 -1.387000000 -4.531000000 0 0 0 > > Pt 4.005000000 1.387000000 -4.531000000 0 0 0 > > Pt 0.801000000 1.387000000 -6.796000000 0 0 0 > > Pt 0.801000000 4.162000000 -6.796000000 0 0 0 > > Pt 3.204000000 0.000000000 -6.796000000 0 0 0 > > Pt 3.204000000 2.775000000 -6.796000000 0 0 0 > > Pt 0.801000000 1.387000000 -0.000000000 1 1 1 > > Pt 0.801000000 4.162000000 -0.000000000 1 1 1 > > Pt 3.204000000 -0.000000000 -0.000000000 1 1 1 > > Pt 3.204000000 2.775000000 -0.000000000 1 1 1 > > K_POINTS automatic > > 3 3 1 1 1 1 > > > > -- > > ====================================== > Lihui Ou > PH.D Candidate in Electrochemistry > College of Chemistry and Molecular Science > Wuhan University,430072,Hubei Province,China > E-mail:oulihui666 at 126.com > ====================================== ***************************************** Nicholas E. Singh-Miller Ph.D. Candidate Prof. Marzari Group (quasiamore.mit.edu) Materials Science and Engineering Massachusetts Institute of Technology 13-4066 (617)324-0372 ***************************************** From bogus@does.not.exist.com Wed Aug 22 09:38:52 2007 From: bogus@does.not.exist.com () Date: Wed, 22 Aug 2007 07:38:52 -0000 Subject: No subject Message-ID: temporary directory for your calculation; in other words your outdir is set to some place, probably in you home directory, which is not local to nodes but stays on a server and is shared via NFS (network file system). If this is your case, every time wavefunctions are written the data has to pass trough the network, it is somehow equivalent to collect_wfc=.true. but done externally by the operating system. Furthermore if you are using the same network for NFS and mpi when the traffic from NFS suddenly bursts it is likely to conflict with mpi and slow it down a lot. To avoid this problem you must use a local directory as outdir (like /tmp), but you to have to remember that if you want to restart a job you have to use exactly the same node you used before in order for them to find their wavefunctions. Otherwise you may have to recollect the data by hand, which is probably not trivial (I have never tried). I hope what I wrote was not already known to you, goodbye. -- Lorenzo Paulatto +39 040 3787 511 http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From bogus@does.not.exist.com Wed Aug 22 09:38:52 2007 From: bogus@does.not.exist.com () Date: Wed, 22 Aug 2007 07:38:52 -0000 Subject: No subject Message-ID: calculate the charge density or not. It might be something went in wrong way in your tests and you got no CHDENS file. Please have a look at your output files. >TK4GUIPWscf Even Google knows nothing about this search tag, but it is aware of TkGUI4PWscf, which is supplied to the QE distribution. Bests, Eyvaz --- Souraya Goumri-Said wrote: > Dear PWSCF user's, > > I am new user of PWSCF and I have 2 questions : > > 1- I am trying to run some examples under the > graphical interface of > PWSCF, but I have the following error message " > > can't read "::pwscf::settings(CHDENS)": no such > element in array > can't read "::pwscf::settings(CHDENS)": no such > element in array > while executing > "::tclu::newset run(CHDENS,$moduleObj) > $::pwscf::settings(CHDENS)" > (procedure "_init" line 16) > invoked from within > "_init $guiObj" > (procedure "::pwscf::run::run" line 7) > invoked from within > "::pwscf::run::run ::gUI0" > invoked from within > ".gui0.shellchildsite.menubar.menubar.run.menu > invoke active" > ("uplevel" body line 1) > invoked from within > "uplevel #0 [list $w invoke active]" > (procedure "tk::MenuInvoke" line 47) > invoked from within > "tk::MenuInvoke > .gui0.shellchildsite.menubar.menubar.run.menu 1" > (command bound to event > > *2. *I a searching for the user guide related to the > graphical interface > of PWSCF : TK4GUIPWscf. Where I can find it, please? > > > Sincerely yours, > > * > *-- > > Dr. Souraya Goumri-Said > Laboratoire de Physique de l'Etat Condens?, UMR CNRS > 6087 > Institut de Recherche en Ing?nierie Mol?culaire et > Mat?riaux Fonctionnels, FR CNRS 2575 > Universit? du Maine. Avenue Olivier Messiaen > 72085 LE MANS Cedex 9 (France). > Email : Souraya.Goumri-Said at univ-lemans.fr > web : http://geocities.com/saidsouraya/ > Tel : (+33) (0) 2 43 83 26 26 / > Fax : (+33) (0) 2 02 43 83 35 18 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, IFM, Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping