[Pw_forum] Display of forces in a pure scf run
On Dec 7, 2011, at 4:23 PM, Cristian Degli Esposti Boschi wrote:
> Dear Stefano and Axel, thanks for your replies. Actually question can be
> rephrased as follows. Thanks to the Hellmann-Feynman theorem
> in order to compute the ionic forces I need only the partial
> derivatives of the total energy with respect to the ionic coordinates
this is not what you need, this is *the* definition of ionic force:
$\mathbf{F}_I=\frac{\partial E}{\partial\mathbf{R}_I}$, with obvious notation
and hopefully no LaTeX errors ...
> (see for instance 7.5 and 7.8 in Payne et al., RMP 64, p. 1045).
> If no real displacements of the atoms are needed to compute
> these derivatives, then I guess that they can be simply calculated
> as expectation values of the Hamiltonian on the current wavefunction
NO: they can be computed as expectation values of the derivative of the
external potential wrt ionic coordinates
> because they can written down once a (parametrized) expression of the
> ionic potential is chosen. Am I right?
I am afraid you aren't, but I am not sure because I could not quite understand
your last statement. There is nothing to choose in the parametric dependence of
the external potential on the ionic coordinates. It depends the way it must
[something like v(r-R), if the notation is clear enough ...], not the way we
choose ...
>
> Thanks for still devoting time to this...
you are most wlcome, as long as we can help ...
S.
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni
(skype)
La morale est une logique de l'action comme la logique est une morale de la
pens?e - Jean Piaget
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[Pw_forum] projwfc.x meet error
Dear Sclauzero: Thanks for remind me. The error message: from davcio : error #10 But how can i know what is ''error number 10?'' i 've set ''wf_collect = .true.'' many thanks!! jinxi State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry & Chemical Engineering, Xiamen University, Xiamen, 361005, P.R.China _ At 2011-12-07 16:57:24,"Gabriele Sclauzero" wrote: Dear Jinxi, please include your affiliation in your next posts. Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: Dear all: When I calculate PDOS using projwfc.x, I meet error like this: Calling projwave from davcio : error #10 error while reading from file % stopping ... This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives. how can i modify the file to pass reading wavefunctions? I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). HTH GS many thanks!! jinxi ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/6b334d6d/attachment-0001.htm
[Pw_forum] A minor mistype in INPUT_PW doc?
Dear QE developers, Today I find a word seems mistyped in Doc/INPUT_PW.html and INPUT_PW.txt in the k-points description part. Syntax: K_POINTS tpiba | crystal | tbiba_b | crystal_b Is the "tbiba_b" should be tpiba_b as used elsewhere? Thanks. -- Wu Feng Chemistry and Molecular Engineering, Peking University -- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/fd79a558/attachment.htm
[Pw_forum] Display of forces in a pure scf run
Dear Stefano and Axel, thanks for your replies. Actually question can be rephrased as follows. Thanks to the Hellmann-Feynman theorem in order to compute the ionic forces I need only the partial derivatives of the total energy with respect to the ionic coordinates (see for instance 7.5 and 7.8 in Payne et al., RMP 64, p. 1045). If no real displacements of the atoms are needed to compute these derivatives, then I guess that they can be simply calculated as expectation values of the Hamiltonian on the current wavefunction because they can written down once a (parametrized) expression of the ionic potential is chosen. Am I right? Thanks for still devoting time to this... -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 degliesposti -AT- bo.imm.cnr.it
[Pw_forum] projwfc.x meet error
Dear all: When I calculate PDOS using projwfc.x, I meet error like this: Calling projwave from davcio : error #10 error while reading from file % stopping ... But example08 and example16 are OK, I guess there's something wrong with my pseudopotential file. I attached the pp file (from the psilibrary), here's the first few lines: Generated using "atomic" code by A. Dal Corso (Quantum ESPRESSO distribution) Author: TM Generation date: 17Oct2011 Pseudopotential type: NC Element: Si Functional: PBE Suggested minimum cutoff for wavefunctions: 0. Ry Suggested minimum cutoff for charge density: 0. Ry The Pseudo was generated with a Scalar-Relativistic Calculation L component and cutoff radius for Local Potential: 2 1.8000 Valence configuration: nl pn l occ RcutRcut US E pseu 3S 1 0 2.00 1.800 1.800-0.794728 3P 2 1 2.00 1.800 1.800-0.299963 Generation configuration: 3S 1 0 2.00 1.800 1.800-0.794724 3P 2 1 2.00 1.800 1.800-0.299964 3D 3 2 0.00 1.800 1.800 0.10 Pseudization used: troullier-martins functional="PBE" z_valence="4.000E+000" total_psenergy="-9.286635279439430E+000" wfc_cutoff="0.000E+000" rho_cutoff="0.000E+000" l_max="2" l_max_rho="4" l_local="2" mesh_size="1141" number_of_wfc="2" number_of_proj="2"/> 6.513442611103688E-005 6.595371633350159E-005 6.678331195832729E-005 6.762334261151813E-005 ... how can i modify the file to pass reading wavefunctions? many thanks!! jinxi -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/cf7f4705/attachment.htm
[Pw_forum] projwfc.x meet error
Dear Jinxi, davcio is the subroutine dedicated to input/output of restart files. The error code is related to the value of some internal variable when the code crashed and sometimes it might be useful to identify better at which point it stopped, but you shouldn't attach any special meaning to that number. Just check that your files are not corrupted and that you do things properly. Regards, GS Il giorno 07/dic/2011, alle ore 10.29, jinxi ha scritto: > Dear Sclauzero: >Thanks for remind me. >The error message: > from davcio : error #10 >But how can i know what is ''error number 10?'' >i 've set ''wf_collect = .true.'' > many thanks!! > > jinxi > State Key Laboratory of Physical Chemistry of Solid Surfaces, > Department of Chemistry, College of Chemistry & Chemical Engineering, > Xiamen University, Xiamen, 361005, P.R.China > _ > > At 2011-12-07 16:57:24,"Gabriele Sclauzero" > wrote: > Dear Jinxi, > > please include your affiliation in your next posts. > > Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: > >> >> Dear all: >> When I calculate PDOS using projwfc.x, I meet error like this: >> Calling projwave >> >> from davcio : error #10 >> error while reading from file >> % >> stopping ... > > > This is pretty self explanatory: there has been an error while reading from > file (in this case the wavefunctions, *.wfc* files), probably because the > file(s) is (are) corrupted or because you ran the postprocessing on a > different number of processors than for the previous pw.x calculation. > >> But example08 and example16 are OK, I guess there's something wrong with my >> pseudopotential file. > > I don't think you can blame your PP file. I think you should search for > possible reasons giving this error in the user guide, the FAQ, and in the > forum archives. > >> >> how can i modify the file to pass reading wavefunctions? > > I don't understand completely what you meant here. The wavefunctions are > needed by projwfc.x, you can't run this calculation if you don't have them. > The wavefunctions are automatically written by pw.x at the end of the run. In > some cases, you may need to use the wf_collect option (see input description > in Doc/). > > > HTH > > > GS > >> many thanks!! >> jinxi >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA >PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/73f988d3/attachment.htm
[Pw_forum] projwfc.x meet error
On Dec 7, 2011, at 10:29 , jinxi wrote: >But how can i know what is ''error number 10?'' by searching the documentation and the archives of the mailing list? P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] study the phase transition with vc-md or vc-cp
Dear Lily, the answer, as it often is, is "it depends". Different crystal structures are usually separated by an enthalpy barrier, whose crossing is a "rare event" if its height is sufficiently high. In order to observe the transition in an actual MD run, you have to either overheat or overload the system, or to bias the dynamics using one of the many available techniques, the most powerful and popular one probably being metadyamics. I am no expert in this field, but I think that the problem has been extensively treated in the literature. References that naturally occur to me are the original paper by Parrinello and Raman, or the more recent one by Parrinello and Laio on metadynamics (as well as others coauthored by R. Martonak, specifically on crystal-structure sampling), as well as the literature citing these articles. HTH - SB On Dec 6, 2011, at 9:24 AM, Lily Anh wrote: > Hi all, > > Is it possible to observe the spontaneous phase transitions by the vc-md > (PW.X) or vc-cp (CP.X) simulations staring from the initial structure input? > If possible, what should we do? > > Any discussion is helpful? > > Regards & Thank you > Lily > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/545b63b5/attachment.htm
[Pw_forum] projwfc.x meet error
Dear Jinxi, please include your affiliation in your next posts. Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: > > Dear all: > When I calculate PDOS using projwfc.x, I meet error like this: > Calling projwave > > from davcio : error #10 > error while reading from file > % > stopping ... This is pretty self explanatory: there has been an error while reading from file (in this case the wavefunctions, *.wfc* files), probably because the file(s) is (are) corrupted or because you ran the postprocessing on a different number of processors than for the previous pw.x calculation. > But example08 and example16 are OK, I guess there's something wrong with my > pseudopotential file. I don't think you can blame your PP file. I think you should search for possible reasons giving this error in the user guide, the FAQ, and in the forum archives. > > how can i modify the file to pass reading wavefunctions? I don't understand completely what you meant here. The wavefunctions are needed by projwfc.x, you can't run this calculation if you don't have them. The wavefunctions are automatically written by pw.x at the end of the run. In some cases, you may need to use the wf_collect option (see input description in Doc/). HTH GS > many thanks!! > jinxi > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/4a6bc855/attachment.htm
[Pw_forum] projwfc.x meet error
On Dec 7, 2011, at 9:20 , jinxi wrote: > I guess there's something wrong with my pseudopotential file. there is nothing wrong in your pseudopotential file P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] neb calculation
Dear all,
I am using neb.x in QE-4.3.2 to do neb calculations. However, unlike
the older versions, I do not see the PW.out (containing the outputs of
the scf calculations for each image) file for each of the images in
the directories containing the wavefunction files for the images of
the path.
Do I need to set some parameters in the input file ?
My neb input file is:
BEGIN
BEGIN_PATH_INPUT
! restart_mode = 'restart'
string_method = 'neb'
nstep_path= 50
num_of_images=5
use_freezing=.true.
opt_scheme='broyden'
first_last_opt=.false.
!CI_scheme='auto'
!ds=0.7
k_max=0.6169
k_min=0.6169
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
outdir='/gpfs/scratch/userexternal/pghosh00/Rhn-MgO/Rh3/neb-walk-1',
pseudo_dir = '/gpfs/scratch/userexternal/pghosh00/pseudo',
!max_seconds = 18000,
!restart_mode='restart'
nstep = 100
wf_collect=.true.
prefix='Rh2_rot_neb_1'
wf_collect=.true.
/
ibrav= 0, celldm(1) =5.68,
nat= 131, ntyp= 3,
ecutwfc =30.0, ecutrho=240,
occupations='smearing', smearing='gaussian',
degauss=0.002, starting_magnetization(3)=0.5,
nspin=2,
/
mixing_mode = 'local-TF'
mixing_beta = 0.2
conv_thr = 1.0d-7
electron_maxstep=150
! startingpot='file'
! startingwfc='file'
/
/
ATOMIC_SPECIES
Mg 24.305 Mg.pbe-n-rrkjus.UPF
O 15.999 O.pbe-rrkjus.UPF
Rh 102.90550 Rh.pbe-nd-rrkjus.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS crystal
Mg 0.0 0.0 0.00 0 0
Mg 0.0 0.25000 0.00 0 0
Mg 0.0 0.5 0.00 0 0
Mg 0.0 0.75000 0.00 0 0
Mg 0.25000 0.0 0.00 0 0
..
LAST_IMAGE
ATOMIC_POSITIONS crystal
Mg 0.0 0.0 0.00 0 0
Mg 0.0 0.25000 0.00 0 0
Mg 0.0 0.5 0.00 0 0
Mg 0.0 0.75000 0.00 0 0
Mg 0.25000 0.0 0.00 0 0
Mg 0.25000 0.25000 0.00 0 0
Mg 0.25000 0.5 0.00 0 0
Mg 0.25000 0.75000 0.00 0 0
Mg 0.5 0.0 0.00 0 0
...
END_POSITIONS
CELL_PARAMETERS {cubic}
4.0 0.0 0.0
0.0 4.0 0.0
0.0 0.0 7.77682129982394366197
K_POINTS {automatic}
2 2 1 1 1 1
END_ENGINE_INPUT
END
With regards,
Prasenjit
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India
Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
[Pw_forum] A minor mistype in INPUT_PW doc?
On Dec 7, 2011, at 9:28 , WF wrote: >Is the ?tbiba_b? should be tpiba_b as used elsewhere? > yes. It is fixed in the next version. Thank you P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] projwfc.x meet error
Dear Jinxi, I got the same problem few days back, and fortunately it is solved now. The thing is davcio is for reading from input and writing to the output, now if you scf calculation is done in different number of processor than your Projwfc.x than it get problem while reading from input. So please check if your pw.x calculation and projwfc.x caculation have same number of processor or not. Thank you. Alamgir Kabir PhD Student University of Central Florida U.S.A From: Gabriele Sclauzero To: PWSCF Forum Sent: Wednesday, December 7, 2011 8:33 AM Subject: Re: [Pw_forum] projwfc.x meet error Dear Jinxi, ? ? davcio is the subroutine dedicated to input/output of restart files. The error code is related to the value of some internal variable when the code crashed and sometimes it might be useful to identify better at which point it stopped, but you shouldn't attach any special meaning to that number. Just check that your files are not corrupted and that you do things properly. Regards, GS Il giorno 07/dic/2011, alle ore 10.29, jinxi ha scritto: Dear Sclauzero: >?? Thanks for remind me. >?? The error message: > from davcio : error #??? 10 >???But how can i know what is ''error number 10?'' >???i?'ve set?''wf_collect = .true.''? >many thanks!! > >jinxi >State Key Laboratory of Physical Chemistry of Solid Surfaces, >Department of Chemistry, College of Chemistry & Chemical Engineering, >Xiamen University, Xiamen, 361005,?P.R.China >_ > >At 2011-12-07 16:57:24,"Gabriele?Sclauzero"? >wrote: > >Dear Jinxi, >> >> >>? ? please include your affiliation in your next posts.? >> >> >>Il giorno 07/dic/2011, alle ore 09.20, jinxi ha scritto: >> >>?Dear all: >>>When I calculate PDOS using projwfc.x, I meet error like this: >>>? Calling projwave >>>? >>> from davcio : error #??? 10 >>> error while reading from file >>>?% >>> stopping ... >>> >> >> >> >> >>This is pretty self explanatory: there has been an error while reading from >>file (in this case the wavefunctions, *.wfc* files), probably because the >>file(s) is (are) corrupted or because you ran the postprocessing on a >>different number of processors than for the previous pw.x calculation. >> >>But example08 and example16 are OK, I?guess there's something wrong with my >>pseudopotential file. >> >> >>I don't think you can blame your PP file. I think you should search for >>possible reasons giving this error in the user guide, the FAQ, and in the >>forum archives.? >> >>? >>>how can i modify the file to pass reading wavefunctions? >> >> >>I don't understand completely what you meant here. The wavefunctions are >>needed by projwfc.x, you can't run this calculation if you don't have them. >>The wavefunctions are automatically written by pw.x at the end of the run. In >>some cases, you may need to use the wf_collect option (see input description >>in Doc/). >> >> >> >> >>HTH >> >> >> >> >>GS >> >>many thanks!! >>>jinxi >>>? >>>? >>> >>>___ >>>Pw_forum mailing list >>>Pw_forum at pwscf.org >>>http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >>? Gabriele Sclauzero,?EPFL SB ITP CSEA >>?? PH H2 462, Station 3,?CH-1015 Lausanne >> >> >> >> >> >> >> > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > ? Gabriele Sclauzero,?EPFL SB ITP CSEA ?? PH H2 462, Station 3,?CH-1015 Lausanne ___ 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/20111207/d81aee2b/attachment-0001.htm
[Pw_forum] Hexagonal lattice equivalent of fcc(rocksalt-like) phase change Ge2Sb2Te5 (GST)
Hello everyone, ? The face-centered-cubic (fcc) structure of the phase-change material Ge2Sb2Te5 (GST) can be approximated by an equivalent hexagonal structure. May somebody assist me with or direct me to where I can find the atomic coordinates for?this equivalent hexagonal structure for GST. ? Regards, Henry Otunga. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111207/b2a7ad4e/attachment.htm
