[Pw_forum] usage of recover=.true.
If you are afraid of losing files, you can copy the corresponding files out as backup before restarting. I just tried restart DFPT once, about 2 months ago. I remember just recover = .t. was needed and everything was fine~ How about the error message in your new output file? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:27:33,"Elie Moujaes" wrote: Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual: /..././ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks again Elie Date: Mon, 22 Aug 2011 22:21:25 +0800 From:flux_ray12 at 163.com To:pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK ___ Pw_forum mailing listPw_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/20110822/88d00709/attachment.htm
[Pw_forum] Phonon Calculations: partial results
Dear Antonio: There is a small code that is capable of calculating the partial contribution of each atom in each phonon mode. Link: http://blog.sciencenet.cn/home.php?mod=space&uid=345795&do=blog&quickforward=1&id=422819 Best Wishes! Yours Sincerely L. F. Huang > Date: Mon, 22 Aug 2011 11:03:48 -0300 > From: Antonio > Subject: [Pw_forum] Phonon Calculations: partial results > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear QE's users. > > I'm carrying out some phonon calculations using the Espresso4.1. I > would like to ask if I can check the partial results, such as the > first normal mode calculated. > > Best regards! > > -- > Doutorando Ant?nio M. Da Silva Jr. > NEQC: Nucleo de Estudos em Quimica Computacional > Departamento de Quimica - ICE > Universidade Federal de Juiz de Fora > Campus Universitario S/N 36.036-330 > Juiz de Fora - MG - Brasil > http://lattes.cnpq.br/0895213089855328 > -- == L.F.Huang(???) DFT and phonon physics == Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 == -- next part ------ An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/36e54423/attachment.htm
[Pw_forum] usage of recover=.true.
If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/ca0a9564/attachment.htm
[Pw_forum] partial band structure
hallo i am doing calculation of band structure in DOS there is no option of getting partial density of states can i calculate that plesase give me suggetions b d sahoo, reserch scolar barc mmbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a73a6984/attachment.htm
[Pw_forum] usage of recover=.true.
No. What I suggested is exactly what you want. In the first calculation, set recover to false, the code will compute the first 105 modes for you. When it is working on the 106th mode, it stops as you said. Then you modify the input file, turn "recover" to true, run the calculation again and the code is able to recover what you have done and start from the 106th mode. I would suggest you to write to another output. In the output, you will see: ? Representation1 1 modes - Done ? Representation105 1 modes - Done Representation106 1 modes - To be done ? HTH Changru On 22 Aug, 2011, at 16:23, Elie Moujaes wrote: > Thanks a lot for the answer. The problem is I started calculating the phonons > at the Gamma point. In my system there are 180 modes and something went wrong > with the server so it stopped at the 106.I am doing the 180 in one go! Is > there a way to save the 106 ones already done! or u suggest that I calculate > each one of them in a separate fie and use recover=.true.? > > > Thanks > Elie > > From: crma at sissa.it > Date: Mon, 22 Aug 2011 16:17:17 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] usage of recover=.true. > > Dear Elie, > > In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: > >Variable: recover > >Type: LOGICAL >Default:.false. >Description:If .true. restart from an interrupted run. > > So set it to false in your first run and true in the second and the following > runs. > > HTH, > Changru > > On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have > 180 irreducible representations (modes) to work out). The server was shut for > a day. I have used in my input file recover=.true. I have reached > representation 106 before the server broke down. Does it mean that If I > executed the command ph.x again, the calculations will start from where it > was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > > ___ 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 --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/52bdda15/attachment.htm
[Pw_forum] usage of recover=.true.
Il giorno 22/ago/2011, alle ore 16.27, Elie Moujaes ha scritto: > Thank you.I hope it works as I definitely do not want to lose the 105 > modes..It took 7 days to do that. But how to re execute the ph.x command..I > tried doing the usual: > /..././ph.x GB60.phG.out but it exited. Could you be more specific? Have you tried to read the output to understand why it did not complete the calculation? HTH GS > Is there another way to restart the command? > > Thanks again > Elie > > Date: Mon, 22 Aug 2011 22:21:25 +0800 > From: flux_ray12 at 163.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] usage of recover=.true. > > If you specify the right outdir path and prefix name, then the restarted one > will definitely begin from 106th mode, since 105 modes have been finished. > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-08-22 22:06:49,"Elie Moujaes" wrote: > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have > 180 irreducible representations (modes) to work out). The server was shut for > a day. I have used in my input file recover=.true. I have reached > representation 106 before the server broke down. Does it mean that If I > executed the command ph.x again, the calculations will start from where it > was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > > > ___ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? 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/20110822/5277e6cc/attachment-0001.htm
[Pw_forum] usage of recover=.true.
Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default:.false. Description:If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH, Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have > 180 irreducible representations (modes) to work out). The server was shut for > a day. I have used in my input file recover=.true. I have reached > representation 106 before the server broke down. Does it mean that If I > executed the command ph.x again, the calculations will start from where it > was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/b461a2f8/attachment-0001.htm
[Pw_forum] usage of recover=.true. (solved)
Guys, Thanks a lot for your help. I just checked the output file now and the calculations are running normally. I am at mode 139. Thanks once again for all the suggestions Elie -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/8374aa8f/attachment-0001.htm
[Pw_forum] usage of recover=.true.
Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual:/..././ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks againElie Date: Mon, 22 Aug 2011 22:21:25 +0800 From: flux_ra...@163.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a3c78cb1/attachment.htm
[Pw_forum] usage of recover=.true.
Thanks a lot for the answer. The problem is I started calculating the phonons at the Gamma point. In my system there are 180 modes and something went wrong with the server so it stopped at the 106.I am doing the 180 in one go! Is there a way to save the 106 ones already done! or u suggest that I calculate each one of them in a separate fie and use recover=.true.? ThanksElie From: c...@sissa.it Date: Mon, 22 Aug 2011 16:17:17 +0200 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default:.false. Description:If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH,Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote:Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- ___ 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/20110822/d55d7b8b/attachment.htm
[Pw_forum] usage of recover=.true.
Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/72337054/attachment.htm
[Pw_forum] Re : Thermal conductivity and Gruneisen parameters
6 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/14828414/attachment.htm
[Pw_forum] Phonon Calculations: partial results
Dear QE's users. I'm carrying out some phonon calculations using the Espresso4.1. I would like to ask if I can check the partial results, such as the first normal mode calculated. Best regards! -- Doutorando Ant?nio M. Da Silva Jr. NEQC: Nucleo de Estudos em Quimica Computacional Departamento de Quimica - ICE Universidade Federal de Juiz de Fora Campus Universitario S/N 36.036-330 Juiz de Fora - MG - Brasil http://lattes.cnpq.br/0895213089855328
[Pw_forum] Can not find minimum free energy by QHA
Dear QE Developer and Users
I am using DFPT+QHA to predict model's properties at high temperature.
According to the paper,Ab initio lattice dynamics and phase transformations of
ZrO2, Phy Rev B 71, 064301, free energyv.s. volume figure can be plotted at
certain temperature for EOS-fitting and so on.
Having determined the equlibrium lattice parameter, 8.18 a.u. , of TiC(FCC) by
both EOS-fitting and vc-relax, I chose 20 different lattice paramters
(7.98~8.38a.u.) and calculated phonon dispersion and thermodynamic properties.
However, the free energy kept decreasing as a monotone decreasing function of
lattice parameter, even when imaginary frequency began to occur at 8.88a.u..
My DFPT calculation script shows below:
cat >TiC_${INT}.scf.in <TiC_${INT}.scf.out
cat >TiC_${INT}.ph.in <TiC_${INT}.ph.out
QHA is calculated by Prof. Isaev's code which released with QE package.
Any suggestion will be welcome.
Thanks.
--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
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[Pw_forum] Invitation to connect on LinkedIn
Stop this, Please. SKG On Mon, Aug 22, 2011 at 8:51 AM, Thaneshwor Kaloni via LinkedIn < member at linkedin.com> wrote: > LinkedIn > Thaneshwor Kaloni requested to add you as a connection on LinkedIn: > > veronica, > > I'd like to add you to my professional network on LinkedIn. > > - Thaneshwor > > > Accept<http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvczkSc3gPcPB9bSxckj4Ps6V7bPsPcjwNdz4TdPcLrCBxbOYWrSlI/EML_comm_afe/> > View invitation from Thaneshwor > Kaloni<http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/0MdBYOdjoMd3cPekALqnpPbOYWrSlI/S2_svi/> > > > *WHY MIGHT CONNECTING WITH THANESHWOR KALONI BE A GOOD IDEA?* > > *Have a question? Thaneshwor Kaloni's network will probably have an answer > * > You can use LinkedIn > Answers<http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/ash/inv19_ayn/>to > distribute your professional questions to Thaneshwor Kaloni and your > extended network. You can get high-quality answers from experienced > professionals. > > > ? 2011, LinkedIn Corporation > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a30b0507/attachment.htm
[Pw_forum] Re : Thermal conductivity and Gruneisen parameters
Dear all, After Prof. Stefano's comments, I will like to indicate that my aim was just to give a contribution, hoping that it will help. If I am wrong in any of my statements, please kindly suggest. Furthermore, everything in my answer has been given with reference and the reader should get acquainted with in order to solve his own problem. Sorry! B. SITAMTZE --- En date de?: Dim 21.8.11, Stefano Baroni a ?crit?: De: Stefano Baroni Objet: Re: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters ?: "PWSCF Forum" Date: Dimanche 21 ao?t 2011, 9h23 On Aug 20, 2011, at 11:45 AM, Bertrand SITAMTZE wrote: Thermal conductivity could be obtained through velocity autocorrelation function? after running molecular dynamics (CP in QE).( See the book of Frenkel and Smith on page 90). I do not have Frenkel & Smith's book handy, but I would be surprised if it stated what you say. The calculation of the thermal conductivity through MD requires a proper definition of the energy current which is well known for classical systems (though it involves something more complicated than just velocities), but not yet available, to the best of my knowledge, in DFT. If I am wring, please correct me. As for Gruneisen parameters, one could calculate the specific heat through QHA and the bulk modulus with PW, then use the relationship between them. (See the book of L. Anderson on equations of state, starting from page 6). Here, I beg to differ as well. First, the calculation of the constant-volume specific heat does not involve any Gruneisen parameters (gamma). The constant-pressure specific heat (Cp) certainly does, but in the sense that you need them in the first place in order to calculate it. Second, It would seem rather innatural to calculate Cp just to estimate some of the parameters used to obtain it! In any case, the expression for Cp in terms of the gammas is an integral from which it would be impossible to obtain back their individual values.? All in all, before asking what QE (or any other code, for that matter) can or cannot do, one should stop for a while and ask oneself what are the most elementary pieces of information needed to compute what we are interested in, and only then ask if any specific code can compute those specific pieces of information. This may take some time, but it is much more instructive than hoping that computer codes can ever be a substitute for our own understanding. In the specific case of the thermal conductivity, one has the choice to follow the quasi-harmonic or the Kubo-Greenwood routes. Nicola Marzari has already given some hints on the former. Dr. Simatze's comments (and my present reply) apply to the latter. As for Gruneisen parameters, you just have just to inspect their definition (gamma = v/omega d (omega) / d (v)), and realize that any code able to compute vibrational frequencies can with little effort calculate them ... QE can calculate phonon frequencies, I will leave the final conclusion to you ... Hope this helpsStefano B ---Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Triestehttp://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 Please, if possible, don't??send me MS Word or PowerPoint attachmentsWhy? See:??http://www.gnu.org/philosophy/no-word-attachments.html -La pi?ce jointe associ?e suit- ___ 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/20110822/f9d64226/attachment-0001.htm
[Pw_forum] Invitation to connect on LinkedIn
LinkedIn Thaneshwor Kaloni requested to add you as a connection on LinkedIn: -- veronica, I'd like to add you to my professional network on LinkedIn. - Thaneshwor Accept invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvczkSc3gPcPB9bSxckj4Ps6V7bPsPcjwNdz4TdPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/0MdBYOdjoMd3cPekALqnpPbOYWrSlI/svi/ -- Why might connecting with Thaneshwor Kaloni be a good idea? Have a question? Thaneshwor Kaloni's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Thaneshwor Kaloni and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/22b2b82b/attachment.htm
