[Pw_forum] errors while executing ph.x in parallel computing mode
Professor Giannozzi, Thanks for the reply. I have figured it out. Elie > Subject: Re: [Pw_forum] errors while executing ph.x in parallel computing > mode > From: giannozz at democritos.it > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Date: Fri, 2 Mar 2012 18:05:53 +0100 > > On Fri, 2012-03-02 at 14:14 +, Elie M wrote: > > > is it a parallel computing problem or might be due to an error in the > > input? > > likely, none of the above, but some weird problem with the file > system. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/b05e0b40/attachment-0001.htm
[Pw_forum] Electronic structure calculation of graphene as a spintronic material using espresso-4.2)
Dear QE PWscf users,
I calculated scf, nscf,bands,plotband , dos and spin polarization of Graphene
as a spintronic material.
The band structure that I got is not desired as a semimetal(i.e. graphene) and
the spin polarization is
not desired(high %).
I am appreciate for any suggestion and comments.
"Please tell me where I was wrong or which detail I ignored."
I used the following PWscf code:
1. SCF code:
?
? calculation = 'scf'
? restart_mode='from_scratch'
? prefix='graphene'
? tstress=.true.
? tprnfor=.true.
? pseudo_dir = '/home/live/Desktop/pseudo/',
? outdir =
'/home/live/Desktop/testgraphene/'
? /
?
? ibrav=4
? celldm(1)=4.7243
? celldm(3)=3.92
? nat=2
? ntyp=1
? nspin=2
? starting_magnetization(1)=0.6
? ecutwfc=15.0
? ecutrho=350.0
? occupations='smearing'
? smearing='gaussian'
? nbnd = 8
? degauss=0.01
? /
?
? diagonalization='david'
? electron_maxstep = 100
? mixing_mode='plain'
? mixing_beta=0.1
? conv_thr = 1.0e-8
? /
? ATOMIC_SPECIES
? C 12.011 C.pz-rrkjus.UPF
?
?
? ATOMIC_POSITIONS (angstrom)
? C 0.0 0.0 0.0
? C 1.232850116 0.706423116 0.0
? K_POINTS {automatic}
? 16 16 1 0 0 0
2. NSCF code:
?
? calculation = 'nscf'
?
restart_mode='from_scratch'
? prefix='graphene'
? tstress=.true.
? tprnfor=.true.
? pseudo_dir = '/home/live/Desktop/pseudo/',
? outdir = '/home/live/Desktop/testgraphene/'
? /
?
? ibrav=4
? celldm(1)=4.7243
? celldm(3)=3.92
? nat=2
? ntyp=1
? nspin=2
? starting_magnetization(1)=0.6
? ecutwfc=15.0
? ecutrho=350.0
? occupations='smearing'
? smearing='gaussian'
? nbnd = 8
? degauss=0.01
? /
?
? diagonalization='david'
? electron_maxstep = 100
? mixing_mode='plain'
? mixing_beta=0.1
? conv_thr = 1.0e-8
? /
? ATOMIC_SPECIES
? C 12.011 C.pz-rrkjus.UPF
?
?
? ATOMIC_POSITIONS (angstrom)
? C 0.0 0.0 0.0
? C 1.232850116 0.706423116
0.0
? K_POINTS {automatic}
? 16 16 1 0 0 0
3.pw.x band code:
?
? calculation = 'bands'
? restart_mode='from_scratch'
? prefix='graphene'
? tstress=.true.
? tprnfor=.true.
? pseudo_dir = '/home/live/Desktop/pseudo/',
? outdir = '/home/live/Desktop/testgraphene/'
? /
?
? ibrav=4
? celldm(1)=4.7243
? celldm(3)=3.92
? nat=2
? ntyp=1
? nspin=2
? starting_magnetization(1)=0.6
? ecutwfc=15.0
? ecutrho=350.0
? occupations='smearing'
? smearing='gaussian'
? nbnd = 8
? degauss=0.01
? /
?
? diagonalization='david'
? electron_maxstep = 100
? mixing_mode='plain'
? mixing_beta=0.1
? conv_thr = 1.0e-8
? /
? ATOMIC_SPECIES
? C
12.011 C.pz-rrkjus.UPF
?
?
? ATOMIC_POSITIONS (angstrom)
? C 0.0 0.0 0.0
? C 1.232850116 0.706423116 0.0
? K_POINTS {automatic}
? 16 16 1 0 0 0
4.band.x code:
?? prefix='graphene',
?? outdir='/home/live/Desktop/testgraphene/'
?? !filband='graphene.bands'
?? /
5.plotband.x code:
bands.out
-10.0 20.0
graphene.xmgr
graphene.ps
1.000
2.0 1.00
EOF
6. dos.x code:
?
? prefix='graphene'
? outdir=/home/live/Desktop/Graphenenbnd8/'
? fildos='graphene.dos',
? Emin=-25.0, Emax=20.0, DeltaE=0.1
Regards-
Rahen Badsha (Raihan)
A post graduate Thesis student
University of Rajshahi, Bangladesh
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20120302/67dfbd0e/attachment-0002.htm
[Pw_forum] Explanation of plotband program
Dear QE PWscf Users, I calculated the electronic structure of graphene. So I run scf, nscf, bands,plotband and dos program and got the output. But I could not understand the input code of plotband program and the output band structure. Have any person who will explain ? Please Please... help me. Best Wishes- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. Mobile:+8801710550252 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/b1dc1251/attachment.htm
[Pw_forum] Spin polarization of Graphene
Dear QE users, I am a researcher on graphene. I want to calculate the spin polarization of graphene. What will be the input code(i.e. scf, nscf, band, plotband and dos) of graphene as a spintronic material? How can I progress? What is the amount of percent of spin polarization of graphene? Please help me. Regards- Rahen Badsha (Raihan) A post graduate thesis student University of Rajshahi, Bangladesh. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/c8b5ee43/attachment.htm
[Pw_forum] errors while executing ph.x in parallel computing mode
On Fri, 2012-03-02 at 14:14 +, Elie M wrote: > is it a parallel computing problem or might be due to an error in the > input? likely, none of the above, but some weird problem with the file system. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] errors while executing ph.x in parallel computing mode
Dear all, I am running ph.x on the parallel computing version (on two nodes) and after 15 seconds I get the following errors: from create_directory: error: # 29/home_cluster/fis718/eliemouj//GB42_phresults/_ph0 : non existent or non writable from create_directory: error: # 29/home_cluster/fis718/eliemouj//GB42_phresults/_ph0 : non existent or non writable Since I got the same error twice, it might be related to nodes. I am doing phonon calculations so I ran a rather dense k gried for the scf calculations then I ran ph.x and I got this erroris it a parallel computing problem or might be due to an error in the input? Thanks Elie HoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/8b240860/attachment.htm
[Pw_forum] Convergene of Magnetic moment is very slow
Kamal, The scf will try to optimize the total energy. Once the energy is optimized, the magnetic moment should stop oscillating. Each step the program prints this line: "estimated scf accuracy: X". If X is becoming smaller over time, the calculation is converging. If not, then you can try other beta values, as discussed here: http://www.quantum-espresso.org/user_guide/node64.html#SECTION000137020 Just looking at the magnetization before the system gets self-consistent is pointless, since all kind of values will show up. A little idea that might help: be sure that you have enough kpoints. 5x5x5 can be too few for many purposes. I'd give it a try with, say, 11x11x11 to see if the final magnetization (after the scf is concluded) changes. Best regards, Giovani M. Faccin CPPP / UFMS - Brazil 2012/3/2 > Dear Users, > > I am running scf-iterations of a ferrimagnetic yttrium iron garnet (bcc > primitive cell with 80 atoms) system and find that the convergence of > magnetic moment is very slow. Can you any suggest me how to accelerate the > overall convergence? Please see the last a few steps of magmom of the > 100-scf steps: > > total magnetization =78.61 Bohr mag/cell > total magnetization =78.79 Bohr mag/cell > total magnetization =78.78 Bohr mag/cell > total magnetization =78.91 Bohr mag/cell > total magnetization =79.25 Bohr mag/cell > total magnetization =79.17 Bohr mag/cell > total magnetization =79.22 Bohr mag/cell > total magnetization =79.06 Bohr mag/cell > total magnetization =79.08 Bohr mag/cell > total magnetization =79.10 Bohr mag/cell > total magnetization =79.12 Bohr mag/cell > total magnetization =79.09 Bohr mag/cell > total magnetization =79.15 Bohr mag/cell > total magnetization =79.23 Bohr mag/cell > total magnetization =79.17 Bohr mag/cell > total magnetization =79.47 Bohr mag/cell > total magnetization =79.45 Bohr mag/cell > total magnetization =79.15 Bohr mag/cell > total magnetization =81.33 Bohr mag/cell > total magnetization =82.16 Bohr mag/cell > total magnetization =82.24 Bohr mag/cell > total magnetization =82.32 Bohr mag/cell > total magnetization =82.53 Bohr mag/cell > total magnetization =84.89 Bohr mag/cell > total magnetization =82.93 Bohr mag/cell > total magnetization =78.05 Bohr mag/cell > total magnetization =84.82 Bohr mag/cell > total magnetization =84.32 Bohr mag/cell > total magnetization =84.69 Bohr mag/cell > total magnetization =85.38 Bohr mag/cell > total magnetization =87.34 Bohr mag/cell > > Also, here is the part of the script which you may want to look at: > > >ibrav = 3, >celldm(1) = 23.24362966, ! = a, in Bohr >nat= 80, >ntyp= 3, >nspin=2, >starting_magnetization(1)=0.0, >starting_magnetization(2)=2.60, >starting_magnetization(3)=0.0, >occupations='smearing', >smearing='mp', >degauss=0.02, >ecutwfc =30, >ecutrho =240 > / > >electron_maxstep = 400, >diagonalization='david', >conv_thr = 1.0e-6, >mixing_beta = 0.05, >!mixing_ndim = 6 >mixing_ndim = 10 > / > ATOMIC_SPECIES > Y 88.90585Y.pbe-nsp-van.UPF > Fe 55.84500Fe.pbe-sp-van_mit.UPF > O 15.99940O.pbe-van_ak.UPF > . > . > . > K_POINTS automatic > 5 5 5 1 1 1 > > Many thanks for your comments and suggestions, > > Regards, > Kamal > > == > Kamal K. Saha > Department of Physics and Astronomy > University of Delaware > Newark, DE 19716-2570 > Phone: (302) 831-8519, Fax: (302) 831-1637 > > http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha > == > > > ___ > 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/20120302/9e98cd7b/attachment.htm
[Pw_forum] Error in using bands_FS.x to get Fermi surface,
I checked the code of bands_FS.f90, and found like this: open(12,file='input_FS') read(12,*) n_start, n_last read(12,*) E_fermi read(12,*) sysname read(12,*) na,nb, nc read(12,*) x(1),x(2),x(3) read(12,*) y(1),y(2),y(3) read(12,*) z(1),z(2),z(3) So I am just wondering whether it can work well, if you change your input file name as "input_FS", and run only by the command bands_FS.x < CWrium.fs.in > CWrium.fs.out, where CWrium.fs.in is a nscf calculation input file with the K_Points obtained by kvec_FS.x. The more ditailed process is in example 08. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 11:08:12,"Chan-Woo Lee" wrote: Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies?. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 12 12 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc?ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo --- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/ddc3f215/attachment.htm
[Pw_forum] Convergene of Magnetic moment is very slow
Dear Users, I am running scf-iterations of a ferrimagnetic yttrium iron garnet (bcc primitive cell with 80 atoms) system and find that the convergence of magnetic moment is very slow. Can you any suggest me how to accelerate the overall convergence? Please see the last a few steps of magmom of the 100-scf steps: total magnetization =78.61 Bohr mag/cell total magnetization =78.79 Bohr mag/cell total magnetization =78.78 Bohr mag/cell total magnetization =78.91 Bohr mag/cell total magnetization =79.25 Bohr mag/cell total magnetization =79.17 Bohr mag/cell total magnetization =79.22 Bohr mag/cell total magnetization =79.06 Bohr mag/cell total magnetization =79.08 Bohr mag/cell total magnetization =79.10 Bohr mag/cell total magnetization =79.12 Bohr mag/cell total magnetization =79.09 Bohr mag/cell total magnetization =79.15 Bohr mag/cell total magnetization =79.23 Bohr mag/cell total magnetization =79.17 Bohr mag/cell total magnetization =79.47 Bohr mag/cell total magnetization =79.45 Bohr mag/cell total magnetization =79.15 Bohr mag/cell total magnetization =81.33 Bohr mag/cell total magnetization =82.16 Bohr mag/cell total magnetization =82.24 Bohr mag/cell total magnetization =82.32 Bohr mag/cell total magnetization =82.53 Bohr mag/cell total magnetization =84.89 Bohr mag/cell total magnetization =82.93 Bohr mag/cell total magnetization =78.05 Bohr mag/cell total magnetization =84.82 Bohr mag/cell total magnetization =84.32 Bohr mag/cell total magnetization =84.69 Bohr mag/cell total magnetization =85.38 Bohr mag/cell total magnetization =87.34 Bohr mag/cell Also, here is the part of the script which you may want to look at: ibrav = 3, celldm(1) = 23.24362966, ! = a, in Bohr nat= 80, ntyp= 3, nspin=2, starting_magnetization(1)=0.0, starting_magnetization(2)=2.60, starting_magnetization(3)=0.0, occupations='smearing', smearing='mp', degauss=0.02, ecutwfc =30, ecutrho =240 / electron_maxstep = 400, diagonalization='david', conv_thr = 1.0e-6, mixing_beta = 0.05, !mixing_ndim = 6 mixing_ndim = 10 / ATOMIC_SPECIES Y 88.90585Y.pbe-nsp-van.UPF Fe 55.84500Fe.pbe-sp-van_mit.UPF O 15.99940O.pbe-van_ak.UPF . . . K_POINTS automatic 5 5 5 1 1 1 Many thanks for your comments and suggestions, Regards, Kamal == Kamal K. Saha Department of Physics and Astronomy University of Delaware Newark, DE 19716-2570 Phone: (302) 831-8519, Fax: (302) 831-1637 http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha ==
[Pw_forum] Hartree calculations for small molecules
Dear Giuseppe and Paolo Thank you very much for your kind answers. I will use the classroom codes of Paolo to provide some Hartree calculations on Helium atom. Kind regards SJ Hashemifar == Seyed Javad Hashemifar Department of Physics, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel: +98 311 391 2375 Fax:+98 311 3912376 Email: hashemifar at cc.iut.ac.ir Group Homepage: http://cmsgroup.iut.ac.ir Personal Homepage: http://hashemifar.iut.ac.ir --- On Wed, Feb 29, 2012 at 9:00 PM, Paolo Giannozzi wrote: > On Wed, 2012-02-29 at 17:26 +0330, Seyed Javad Hashemifar wrote: > > > For educational purpose, I am looking for some Hartree calculations > > on small molecules such as H2. > > not sure QE is the right tool for such a simple problem. Here some > simpler tools: > http://www.fisica.uniud.it/~giannozz/Corsi/MQ/mq.html > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/1912aa69/attachment.htm
[Pw_forum] scf cslculation
Dear all, I performed scf cslculation but? end of the output file of scf appears this massage: End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping . . . JOB DONE. what do I change in input file? for obtaining correct answer? Many thanks for your comments and suggestions, Regards, Somayeh Fotoohi ? -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/6c2df899/attachment.htm
[Pw_forum] Eyvaz Isaev
Hi everyone, I was very saddened to hear that Eyvaz passed away. Although I never had a chance to meet him in person, we exchanged emails on several research topics and I feel lucky to have met him through this forum. He was always ready to provide advice and encouragement to anyone working with Quantum Espresso. For my own research, his contributions to QE on phonon properties and Fermi surface visualization have been extremely helpful. He will definitely be missed. Derek Derek Stewart, Ph. D. Senior Research Associate http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 3/2/2012 2:44 AM, Paolo Giannozzi wrote: > I have the regret to announce that Prof. Dr. Eyvaz Isaev, > author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > > P.
[Pw_forum] [LDA+U] elements in occupation matrix are real number?
Dear Chan-Woo.
The n matrix is always hermitian, it is clear from definition. In the case
of
collinear LSDA there is always psi_sigma --> psi_sigma* symmetry, due
to hermicity of Hamiltonians for each spin, which can be considered as the
time-reversal operation. This is why you always have k --> -k symmetry
even if you do not have inversion operation. Because of this time-reversal
symmetry one can readily see that the n matrix should be real.
It is not anymore the case in general noncollinear calculation where the
occupation matrix is in general complex (and hermitian).
Concerning negative eigenvalues, I think they are just small numbers,
probably due to computational errors, which should be thought of as 0.
regards,
Alexander
Le 1 mars 2012 20:56, Chan-Woo Lee a ?crit :
> Dear QE developers and users,
>
> ** **
>
> I have a question in understanding occupation matrix from LDA+U output
> file.
>
> ** **
>
> 1) Definition of occupation matrix, n is:
>
> ** **
>
> n= \sum{f<psi|phi_i>}, where psi is KS eigenstates, phi_i is
> atomic orbital of i orbital, f is scaling factor. As i and j from phi_i and
> phi_j don?t have to be identical, I think it?s not guaranteed that elements
> in n matrix are always real? However, in the QE output, they are all shown
> as real numbers. In new_ns.f90, I can find that n (nr and ns) are defined
> as real numbers but I can?t find any restrictions other than this.
>
> ** **
>
> 2) While elements in the matrix are real, some of them are ?negative?. How
> can I understand this? I found one paper about multiconfigurational
> character of wave functions (
> http://jcp.aip.org/resource/1/jcpsa6/v110/i9/p4199_s1 ) but it?s beyond
> my scope.
>
> ** **
>
> Did I miss something? Any suggestions and advices will truly be
> appreciated?
>
> ** **
>
> Sincerely,
>
> ** **
>
> Chan-Woo
>
> ** **
>
> ** **
>
> *---
> Chan-Woo Lee, Ph.D.*
>
> *Postdoctoral Research Associate*
>
> * *
>
> *Department of Chemistry
> University of Pennsylvania
> 231 South 34th Street
> Philadelphia, PA 19104-6323
> Phone: 1-215-898-3564 (Office)
> *Email: leechanw at sas.upenn.edu / cwandtj at gmail.com
>
> ** **
>
> ** **
>
> ** **
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20120302/90853a47/attachment.htm
[Pw_forum] Eyvaz Isaev
I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] Dr. Eyvaz Isaev
Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo --- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/ddc3f215/attachment-0001.htm -- Message: 3 Date: Fri, 02 Mar 2012 08:44:11 +0100 From: Paolo Giannozzi <giann...@democritos.it> Subject: [Pw_forum] Eyvaz Isaev To: PWSCF Forum Message-ID: <1330674251.26056.5.camel at fe12lx.fisica.uniud.it> Content-Type: text/plain I have the regret to announce that Prof. Dr. Eyvaz Isaev, author of QHA and PlotPhon packages, passed away on Sept.11, 2011 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -- Message: 4 Date: Fri, 2 Mar 2012 12:06:27 +0330 From: Seyed Javad Hashemifar <hashemi...@cc.iut.ac.ir> Subject: Re: [Pw_forum] Hartree calculations for small molecules To: PWSCF Forum Message-ID: ???
