[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/38d4a09f/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/9b2202ec/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/5f7d5890/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/5d06481e/attachment.htm
[Pw_forum] problems with vc-relax
Dear Xijun, Thanks very much for your advice. I will do the necessary changes and let you know how things go. Regards Elie > Date: Wed, 7 Sep 2011 15:58:37 -0400 > From: xijunw at gmail.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] problems with vc-relax > > On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes > wrote: > > Dear all, > > > > Dear Elie, > > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > > 4 days of execution and without reaching the desired force threshold. The > > following output was obtained : > > > > Please can anyone advice me on this? Shall I start with the new > > configuration and start relaxing again? > > > > I'm also doing some cell relaxation. As I understand, cell > optimization is not very easy, and it is common that it does not > converge after a very long run. > > Surely you should restart the calculation to achieve your convergence > criteria. You can just change the "restart_mod = 'from_scratch' " to > "restart_mode = 'restart' ", and submit the job again to continue from > where you stopped. Please be advised that pw.x will read cell > parameters / atomic positions, initial density, pseudopotentials from > the folder of GBphonon.save, so make sure you copy the folder to > computing-nodes. > > However, I highly suggest you do something to accelerate the > convergence. For example, if you do not expect the cell angle to > change (i.e. keep angles=90), you may add the following keywords to > the section. > >cell_dofree = xyz > > This will greatly reduce the uncertainty of the geometry optimization. > and reduce energy/force oscillation. > > Another great idea is to manually choose x, y and z, then do a > relaxation of atomic positions only. and plot the total energy changes > with x, y and z. However, be noted that different volume means > different numbers of PW basis function, and energy comparison in this > way could be a little confusing. Anyway, if volume change is not > large, still this would help a lot. > > Since I'm also a learner, any more comments or correction to my > comments are welcome. Thanks > > Xijun > > > > > Regards > > > > > > > > Elie Moujaes > > > > University of Nott > > > > University Park > > > > NGT 3RD > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Department of Chemistry and Biochemistry, Concordia University > 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 > Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 > ___ > 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/20110907/d18c2aa9/attachment.htm
[Pw_forum] QHA calculated error !
Hi, Recently,I want to calculated the partial_dos of phonon by QHA.Then,I have compiled it and run examples successfully.However,I run the ZnO.fc I calculated is failed. The step is followed: 1.Using ttrinp to generate K point by ./QHA/bin/tetra.x.../QHA/bin/tetra.x 2.Copy k point into matdy.in and then using .../bin/matdyn.xmatdyn.out to generate 'frequency' 3.Using ../QHA/bin/Partial_phonon_DOS.x < phdos1.in 4.Using ../QHA/bin/phonon_dos.x http://www.democritos.it/pipermail/pw_forum/attachments/20110907/e1cdeff2/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: ZnO.rar Type: application/rar Size: 102955 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110907/e1cdeff2/attachment-0001.rar
[Pw_forum] (no subject)
According to your input information, nat=48, I think you wanted to make 2x2x2
rutile-TiO2 supercell with a substitutional Nb. However, you setted celldm(1)
and ATOMIC_POSITIONS wrong.
You may set celldm(1)=1 and keep CELL_PARAMETERS; or keep celldm(1)=8.7 and set
CELL_PARAMETERS as
2.000 0.000 0.000
0.000 2.000 0.000
0.000 0.000 1.288
For ATOMIC_POSITIONS, you may set it as:
ATOMIC_POSITIONS {crystal}
O 0.1523998693948630 0.1523998693948630 0.
O 0.3476001306051368 0.3476001306051368 0.
O 0.0976001306051369 0.4023998693948629 0.2501
O 0.4023998693948629 0.0976001306051369 0.2501
O 0.6523998693948631 0.1523998693948630 0.
O 0.8476001306051368 0.3476001306051368 0.
O 0.5976001306051370 0.4023998693948629 0.2501
O 0.9023998693948629 0.0976001306051369 0.2501
O 0.1523998693948630 0.6523998693948631 0.
O 0.3476001306051368 0.8476001306051368 0.
O 0.0976001306051369 0.9023998693948629 0.2501
O 0.4023998693948629 0.5976001306051370 0.2501
O 0.6523998693948631 0.6523998693948631 0.
O 0.8476001306051368 0.8476001306051368 0.
O 0.5976001306051370 0.9023998693948629 0.2501
O 0.9023998693948629 0.5976001306051370 0.2501
O 0.1523998693948630 0.1523998693948630 0.5000
O 0.3476001306051368 0.3476001306051368 0.5000
O 0.0976001306051369 0.4023998693948629 0.7501
O 0.4023998693948629 0.0976001306051369 0.7501
O 0.6523998693948631 0.1523998693948630 0.5000
O 0.8476001306051368 0.3476001306051368 0.5000
O 0.5976001306051370 0.4023998693948629 0.7501
O 0.9023998693948629 0.0976001306051369 0.7501
O 0.1523998693948630 0.6523998693948631 0.5000
O 0.3476001306051368 0.8476001306051368 0.5000
O 0.0976001306051369 0.9023998693948629 0.7501
O 0.4023998693948629 0.5976001306051370 0.7501
O 0.6523998693948631 0.6523998693948631 0.5000
O 0.8476001306051368 0.8476001306051368 0.5000
O 0.5976001306051370 0.9023998693948629 0.7501
O 0.9023998693948629 0.5976001306051370 0.7501
Ti -0. -0. 0.
Ti 0.2498 0.2498 0.2501
Ti 0.5000 -0. 0.
Ti 0.7498 0.2498 0.2501
Ti -0. 0.5000 0.
Ti 0.2498 0.7498 0.2501
Ti 0.5000 0.5000 0.
Ti 0.7498 0.7498 0.2501
Ti -0. -0. 0.5000
Ti 0.2498 0.2498 0.7501
Ti 0.5000 -0. 0.5000
Ti 0.7498 0.2498 0.7501
Ti -0. 0.5000 0.5000
Ti 0.2498 0.7498 0.7501
Ti 0.5000 0.5000 0.5000
Ti 0.7498 0.7498 0.7501
--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
At 2011-09-07 20:22:30,"Winfred Mulwa" wrote:
Dear all
I have tried doing a vc-relax on the attached TiO2 rutile supercell,
the calculations stop after a few minutes without giving any error.
What might be the problem?
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[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate =-676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0 .. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie Moujaes University of Nott University Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/17335ac0/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/467de01e/attachment.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/df4a8543/attachment-0001.htm
[Pw_forum] problems with vc-relax
Dear all, I am relaxing a 60 atom supercell (graphene grain boundary) to make the total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after 4 days of execution and without reaching the desired force threshold. The following output was obtained : 1st relaxation process: Total force 0.091 Pressure =- 114.1 kbar 2nd relaxation process: total force 0.1 Pressure = -55 kbar (new enthalpy < old enthalpy) 3rd process: total force = 0.058 pressure = -11 kbar Then in the 4th process, calculations stopped. Here are the last few lines of the output: iteration # 2 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 4 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 5 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged ethr = 2.90E-04, avg # of iterations = 17.6 negative rho (up, down): 0.132E-01 0.000E+00 total cpu time spent up to now is 382283.13 secs total energy =-676.77947904 Ry Harris-Foulkes estimate = -676.82846513 Ry estimated scf accuracy< 0.17363554 Ry iteration # 3 ecut=36.75 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged The input of the vc-relax is: prefix='GBphonon', calculation='vc-relax', restart_mode='from_scratch', tstress=.true., tprnfor=.true, pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', / ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, occupations='smearing', smearing='mp',degauss=0.01 / conv_thr=1.D-6, mixing_beta=0.3D0, diago_david_ndim=2, / ion_dynamics='bfgs' / $cell cell_dynamics='bfgs', / CELL_PARAMETERS (alat) 24.064488464 0.000772242 0.0 0.0 6.503051170 0.0 0.0 0.0 8.470514812 ATOMIC_SPECIES C 12.0107 C.blyp-mt.UPF ATOMIC_POSITIONS (angstrom) C -11.330758616 -3.527803203 0.0 C -10.659793092 -1.160339161 0.0 C -12.039843315 -7.112619698 0.0 C -12.041158182 -5.732701936 0.0 C -10.941089654 -4.881442842 0.0.. Please can anyone advice me on this? Shall I start with the new configuration and start relaxing again? Regards Elie MoujaesUniversity of NottUniversity Park NGT 3RD -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/eec0853b/attachment.htm
[Pw_forum] (no subject)
On Sep 7, 2011, at 18:12 , Xijun Wang wrote
:
> (2) Your K_POINTS card should be: K_POINTS {automatic}
> But you use: K_POINTS (automatic)
this should not be a problem: the code actually looks for "automatic",
not for "(" or "{". Also ignored: blank lines and inappropriate options
pot_extrapolation = 'second order', wfc_extrapolation = 'second order'
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] All electron calculation
If you want to do all-electron atomic calculations (in spherical symmetry), then you should use ld1.x, not pw.x HTH GS Il giorno 07/set/2011, alle ore 18.45, Tram Bui ha scritto: > Dear Everyone, > I'm trying to run a quick all electron calculation for Cs. where I have > the input file(cs.in) as below: > > title='Cs', > zed=55.0, > iswitch=1, > dft='PBE', > config='[Xe] 6s1 5d0 6p0 ' > / > then I run bin/pw.x < cs.in > cs.out. I got an error message saying > "from read_namelists : error # 1 > reading namelist control" > what might have been wrong in my code? is pw.x is the right command for all > electron calculation? > > > Thank you very much, > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > ___ > 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/20110907/dd14cfe3/attachment-0001.htm
[Pw_forum] ATOMIC_POSITIONS after 'final coordinates'
Most likely the damped dynamics algorithm updates the atomic positions one last time before printing them 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] Pseudopotential for Terbium in upf file
Dear Users I'm trying to find the pseudopotential for Terbium but it seems like there is no upf file about Terbium. Does any one can share the codes or give me some advice? Thank you. Chengyang Li Department of Physics Western Michigan Univerisity
[Pw_forum] (no subject)
On Sep 7, 2011, at 16:34 , Phillip Nyawere wrote:
> Your file has no directory for output data.
not a big problem, though: the code will write to
either ESPRESSO_TMPDIR or to the current
directory ("./")
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] (no subject)
Your file has no directory for output data. On Wed, Sep 7, 2011 at 1:57 PM, Winfred Mulwa wrote: > Dear all, > > I have tried doing a vc-relax on the attached TiO*2 *rutile > supercell, but the calculations stop after a few seconds without > giving any error. What might be the problem? > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Phillip W. Otieno Nyawere, The Abdus Salam International Center for Theoretical Physics, Enrico Fermi Building Associate Office 18, Strada Costiera 11, 34014 Trieste, Italy Tel +393382213805, or +39 040 2240 567 pnyawere at gmail.com, pnyawere at ictp.it, God raises the meek from the ground and sits them with Kings. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/50278601/attachment.htm
[Pw_forum] problems with vc-relax
Hi, Elie, Please do not repeat sending the same message to the mail list. Also, people will be more happy to help you if you keep your mail neat by removing all the unnecessary blank lines in the input file. Regards, Xijun On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > Dear all, > > > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > 4 days of execution and without reaching the desired force threshold. The > following output was obtained : > > > > 1st relaxation process: > > > > Total force 0.091 ? Pressure =- 114.1 kbar > > > > 2nd relaxation process: > > > > total force 0.1 ? Pressure = -55 kbar > > > > (new enthalpy < old enthalpy) > > > > 3rd process: > > > > total force = 0.058 ? pressure = -11 kbar > > > > Then in the 4th process, calculations stopped. Here are the last few lines > of the output: > > > > iteration #??2?ecut=36.75 Ry?beta=0.30 > ?Davidson diagonalization with overlap > ?c_bands:??5 eigenvalues not converged > ?c_bands:??1 eigenvalues not converged > ?c_bands:??3 eigenvalues not converged > ?c_bands:??1 eigenvalues not converged > ?c_bands:??4 eigenvalues not converged > ?c_bands:??4 eigenvalues not converged > ?c_bands:??4 eigenvalues not converged > ?c_bands:??4 eigenvalues not converged > ?c_bands:??5 eigenvalues not converged > ?c_bands:??5 eigenvalues not converged > ?c_bands:??2 eigenvalues not converged > ?c_bands:??2 eigenvalues not converged > ?ethr =??2.90E-04,??avg # of iterations = 17.6 > > ?negative rho (up, down):??0.132E-01 0.000E+00 > > ?total cpu time spent up to now is 382283.13 secs > > ?total energy??=-676.77947904 Ry > ?Harris-Foulkes estimate???=-676.82846513 Ry > ?estimated scf accuracy > ?iteration #??3?ecut=36.75 Ry?beta=0.30 > ?Davidson diagonalization with overlap > ?c_bands:??1 eigenvalues not converged > ?c_bands:??1 eigenvalues not converged > ?c_bands:??2 eigenvalues not converged > ?c_bands:??3 eigenvalues not converged > > > > The input of the vc-relax is: > > > > > > prefix='GBphonon', > > calculation='vc-relax', > > restart_mode='from_scratch', > > tstress=.true., > > tprnfor=.true, > > pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.3/Pseudo/', > > outdir='/exp/home/caiapo/emoujaes/espresso/Moujaes-Results/', > > > > ?/ > > ? > > ibrav= 0, celldm(1) =1.889725989, nat=60, ntyp= 1, ecutwfc =36.749309, > occupations='smearing', smearing='mp',degauss=0.01 > > / > > ? > > conv_thr=1.D-6, > > mixing_beta=0.3D0, > > diago_david_ndim=2, > > > > ?/ > > > > > > ?ion_dynamics='bfgs' > > > > / > > $cell > > cell_dynamics='bfgs', > > > > / > > > > CELL_PARAMETERS (alat) > > ??24.064488464???0.000772242???0.0 > > ???0.0???6.503051170???0.0 > > ???0.0???0.0???8.470514812 > > > > > > ATOMIC_SPECIES > > ?C??12.0107??C.blyp-mt.UPF > > > > ATOMIC_POSITIONS (angstrom) > > C??-11.330758616??-3.527803203???0.0 > > C??-10.659793092??-1.160339161???0.0 > > C??-12.039843315??-7.112619698???0.0 > > C??-12.041158182??-5.732701936???0.0 > > C??-10.941089654??-4.881442842???0.0 > > .. > > > > Please can anyone advice me on this? Shall I start with the new > configuration and start relaxing again? > > > > Regards > > > > Elie Moujaes > > University of Nott > > University Park > > NGT 3RD > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dept. of Chem and Biochem, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23
[Pw_forum] problems with vc-relax
On Wed, Sep 7, 2011 at 3:28 PM, Elie Moujaes wrote: > Dear all, > Dear Elie, > > I am relaxing a 60 atom supercell (graphene grain boundary) to make the > total force on atoms mainly 0.001 Ry/au. However the vc-relax stopped after > 4 days of execution and without reaching the desired force threshold. The > following output was obtained : > > Please can anyone advice me on this? Shall I start with the new > configuration and start relaxing again? > I'm also doing some cell relaxation. As I understand, cell optimization is not very easy, and it is common that it does not converge after a very long run. Surely you should restart the calculation to achieve your convergence criteria. You can just change the "restart_mod = 'from_scratch' " to "restart_mode = 'restart' ", and submit the job again to continue from where you stopped. Please be advised that pw.x will read cell parameters / atomic positions, initial density, pseudopotentials from the folder of GBphonon.save, so make sure you copy the folder to computing-nodes. However, I highly suggest you do something to accelerate the convergence. For example, if you do not expect the cell angle to change (i.e. keep angles=90), you may add the following keywords to the section. cell_dofree = xyz This will greatly reduce the uncertainty of the geometry optimization. and reduce energy/force oscillation. Another great idea is to manually choose x, y and z, then do a relaxation of atomic positions only. and plot the total energy changes with x, y and z. However, be noted that different volume means different numbers of PW basis function, and energy comparison in this way could be a little confusing. Anyway, if volume change is not large, still this would help a lot. Since I'm also a learner, any more comments or correction to my comments are welcome. Thanks Xijun > > Regards > > > > Elie Moujaes > > University of Nott > > University Park > > NGT 3RD > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23
[Pw_forum] (no subject)
On Sep 7, 2011, at 15:16 , GAO Zhe wrote: > Oh, my mistake, I forgot that bohr is used in QE. So, if you wanna > keep > CELL_PARAMETERS, you have to set celldm(1) = 1.889725989. while this is possible and legitimate, I do not think it is a wise move to fill "celldm(1)" (or "a") with strange numbers instead of the lattice parameter 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] (no subject)
Dear all, I have tried doing a vc-relax on the attached TiO*2 *rutile supercell, but the calculations stop after a few seconds without giving any error. What might be the problem? -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/7239ed27/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: TiOsc.scf.in1 Type: application/octet-stream Size: 3618 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110907/7239ed27/attachment.obj
[Pw_forum] (no subject)
Dear Winfred, I just have a look at the input you provided. Are you sure this is TiO2 rutile? Please visualize the structure with a software like Xcrysden first. HTH, Changru On 7 Sep, 2011, at 14:22, Winfred Mulwa wrote: > Dear all > >I have tried doing a vc-relax on the attached TiO2 rutile supercell, > the calculations stop after a few minutes without giving any error. > What might be the problem? > ___ > 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/20110907/0f1b7804/attachment.htm
[Pw_forum] [SUSPECTED SPAM-Ironport] (no subject)
Dear Winfred I suspect that nobody will help you if you do not: a) choose a meaningful subject for your post (e.g., tio2 supercell unexpected pw.x crash) b) sign your post (with your scientific affiliation) c) provide more details (e.g., QE version, pw.x output, ...) Yours Giuseppe On Wednesday 07 September 2011 14:22:30 Winfred Mulwa wrote: > Dear all > > ?? I have tried doing a vc-relax on the attached TiO2 rutile supercell, > the calculations stop after a few minutes without giving any error. > > What might be the problem? -- - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail:
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Dear Gregor, gipaw is based on paw, as long as it stays so it will always require paw description of the atom.. if you are using a traditional norm conserving or ultrasoft pseudopotential that means you need this description to be calculated and written, which will make it a 'gipaw pseudopotential' If you are using a paw pseudopotential however, everything is already calculated. unfortunately it has not been the default to write down this necessary information. in the future i would like to make it default, such that every paw pseudopotential file already is gipaw-suitable. it is just that there are some details to work out,like,you may want the pw.x to use a different set of projectors (possibly cheaper ones) than gipaw.x part..so we should keep this freedom etc. about not having the paw set for the atoms you are not interested in..what would you propose? the induced magnetic field at a point depends on the induced current in all space..do you suggest a space cut off? or calculating the current response of these atoms we are not interested in without paw constructions? instead there is the 'converse approach' you may want to look at, that sounds more efficient if you are interested in nmr parameters of one atom in huge molecule, for example.. we can hear more from Davide about it. emine kucukbenli, phd student, sissa, italy SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Dear Davide, does the code still require that pseudopotentials for all the species contain the GIPAW reconstruction part. Is it (or will it be) possible that one uses 'non-gipaw' pseudopotentials for the atomic species if one is not interested in NMR shifts or EPR parameters of these species (or if one does not have a proper gipaw pseudopotential for that atomic species)? Best regards. Gregor Gregor Mali Kemijski institut/National Institute of Chemistry Hajdrihova 19 SI-1001 Ljubljana tel. +386 1 47 60 412 fax +386 1 47 60 300 > -Original Message- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Davide Ceresoli > Sent: 7. september 2011 11:40 > To: PWSCF Forum > Subject: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 > (unit = 14, file = '') > > Dear Daniel, > this is a fallback situation. When GIPAW > pseudopotentials are not available, the code will try to read > the 'Paratec reconstruction file'. We did this in the > beginning in order to debug the code and make sure we > obtained the same results of Paratec. This feature will be > removed soon and a clearer error message will be printed. > > Cheers, > Davide > > > On 01/-10/-28163 08:59 PM, Daniel Lima wrote: > > Hi, > > My name is Daniel Aguiar, and I'm a beginner in Theoretical > Calculations. > > I'm having some troubles with the gipaw.x calculations. > > The pw.x was sucessed (JOB DONE!!). > > But in gipaw.x the following mensage appear: > > > > At line 174 of file paw_gipaw.f90 (unit = 14, file = '') Fortran > > runtime error: File '' does not exist > > > > > > I verified in paw_gipaw.f90 and the line is: > > > > OPEN ( 14, FILE = filerec_sp ) > > > > What's wrong? > > > > My nmr input is following below: > > > > > > job = 'nmr' > > prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' > > tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' > > isolve = 0 > > iverbosity = 1 > > q_gipaw = 0.01 > > spline_ps = .true. > > use_nmr_macroscopic_shape = .false. > > / > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] ATOMIC_POSITIONS after 'final coordinates'
Thanks Paolo. If this is true, then the 'final coordinates' is not actually final. -Xijun On Wed, Sep 7, 2011 at 11:45 AM, Paolo Giannozzi wrote: > Most likely the damped dynamics algorithm updates the > atomic positions one last time before printing them > > 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 mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23
[Pw_forum] ATOMIC_POSITIONS after 'final coordinates'
On Wed, Sep 7, 2011 at 4:54 AM, Paolo Giannozzi wrote: > > On Sep 7, 2011, at 1:35 , Xijun Wang wrote: > >> There is an extra "ATOMIC_POSITIONS" section after the "final >> coordinates". It is neither the final coordinates > > why are you saying this? P. Because they are different. -XJ > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Department of Chemistry and Biochemistry, Concordia University 7141 Sherbrooke Ouest, Montreal, QC H4B 1R6 Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23
[Pw_forum] about PWscf PP generation
On Sep 7, 2011, at 4:45 , Robin H wrote: > I 'm not good at PP generation nobody is. Did you read atomic_doc/pseudo-gen.tex? it is incomplete but better than nothing 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] ATOMIC_POSITIONS after 'final coordinates'
On Sep 7, 2011, at 1:35 , Xijun Wang wrote: > There is an extra "ATOMIC_POSITIONS" section after the "final > coordinates". It is neither the final coordinates why are you saying this? 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] How to speed up gipaw?
Dear Pengju, on possibility is to use pools, in order to distribute k-points on more CPUs. I always set iverbosity=1 to see some output as the calculation is running (I suffer of empty-output-phobia). To get an idea of the computational cost: I have calculated a complicated silicate mineral with 88 atoms in the unit cell. 4 special k-points. The calculation took 1 day on 16 CPUs. Davide On 01/-10/-28163 08:59 PM, Ren PJ wrote: > Dear all, > I'm using gipaw to calculate NMR of a system contain more than 100 > atoms, but the first k point haven't been done after more than 40 > hours. It's so slow for me. > Here is my input: > > job =nmr' > prefix =pw' > tmp_dir =./tmp/' > isolve = > conv_threshold -10 > iverbosity = > q_gipaw = .01 > spline_ps =true. > use_nmr_macroscopic_shape =true. > nmr_macroscopic_shape =.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.6667 > / > Can anyone figure me out how to improve this? > PS. My computer is 8 core cpu, and gipaw and QE is compiled with intel > mkl lib. > Thanks very much! > > Pengju Ren > > Dalian Institute of Chemical Physics, > Chinese Academy of Science >
[Pw_forum] All electron calculation
Dear Everyone, * I'm trying to run a quick all electron calculation for Cs. where I have the input file(cs.in) as below: * title='Cs', zed=55.0, iswitch=1, dft='PBE', config='[Xe] 6s1 5d0 6p0 ' / *then I run bin/pw.x < cs.in > cs.out. I got an error message saying * "from read_namelists : error # 1 reading namelist control" *what might have been wrong in my code? is pw.x is the right command for all electron calculation? * Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/98986cd8/attachment.htm
[Pw_forum] about PWscf PP generation
thank you for your tips,I'm so careless to make such a stupid mistake.After trying for many times I 'm encountered the only problem is how to choose a perfect rc.When I set rc=1.9,in the pseudo_run there is a warning like this: WARNING! Expected number of nodes: 1= 3- 1- 1, number of nodes found: 0. Setting wfc to zero for this iteration. (This warning will only be printed once per wavefunction) Zero norm: self consistency problem; state: 5 (l= 1, j=0.0) and the generated PP is not very well: n l nl e AE (Ry)e PS (Ry)De AE-PS (Ry) 1 0 5S 1( 2.00) -2.85985 -3.283550.42370 2 1 5P 1( 6.00) -1.64629 -1.991380.34509 2 0 6S 1( 2.00) -0.26736 -0.300230.03286 3 2 5D 1( 1.00) -0.22479 -0.440030.21524 3 1 6P 1( 0.00) -0.09835 -0.098350.0 this is my input file : title='La' zed=57. rel=1, config='[Xe] 6s2.00 5d1.00 6p0.00', iswitch=3, dft='revPBE' / lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5D 3 2 1.000.00 2.00 2.20 5D 3 2 0.000.50 2.00 2.20 5S 1 0 2.000.00 2.00 2.20 5S 1 0 0.000.50 2.00 2.20 5P 2 1 6.000.00 1.90 1.90 configts(1)='5s2 5p6 6s2 5d1 6p0', I 'm not good at PP generation.And maybe I choose an unproper rc,so I can't get a good result for calculation.You're so kind and so experienced in solving this kind of problem,hope for your advice. ? 2011?9?4? ??9:55?GAO Zhe ??? > Of course, since the element Xe already has 5s2 and 5p2~ you can change > parameter "config" like: '[Xe] 5d1 6s1.5 6p0.5' > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-09-04 20:37:09,"Robin H" wrote: > > Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for > the first time I met a mistake like this > Program LD1 v.4.3.1starts on 4Sep2011 at 19:53:36 > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org;, > in publications or presentations arising from this work. More details > at > > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > Parallel version (MPI), running on 1 processors > > > %% > from el_config : error #12 > wavefunction 5S found too many times > > > %% > stopping ... > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > since the input is like this > > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', > iswitch=3, > dft='revPBE' > / > >lloc=1, >pseudotype=3, >nlcc=.true., >tm=.true., >file_pseudopw='La.revPBE.UPF', > / > 5 > 5D 3 2 1.00 0.00 2.20 2.20 > 5D 3 2 0.00 0.05 2.20 2.20 > 6S 1 0 2.00 0.00 2.20 2.20 > 6S 1 0 0.00 0.05 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.00 > Is there anything wrong in my electric configuration of La? > as I changed like this : > > title='La' > zed=57. > rel=1, > config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', > iswitch=3, > dft='revPBE' > / > >lloc=1, >pseudotype=3, >nlcc=.true., >tm=.true., >file_pseudopw='La.revPBE.UPF', > / > 5 > 5S 1 0 2.00 0.00 2.20 2.20 > 5P 2 1 6.00 0.00 2.20 2.20 > 5D 3 2 1.00 0.00 2.20 2.20 > 6S 1 0 1.50 0.00 2.20 2.20 > 6P 2 1 0.50 0.00 2.20 2.00 > the error is still exist like the fomer.what's the error suggest ?I'm > wondered that how to write the list of states following the namelist of > tried to find some information in the reference of PWscf to make > me clear,but this part seemed hard to understand,hope everyone who is > sophisticated at PP generation to give me some tips, I'm appreciated. > > > > > ___ > 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/20110907/5b5ec167/attachment.htm
[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')
Dear Daniel, this is a fallback situation. When GIPAW pseudopotentials are not available, the code will try to read the 'Paratec reconstruction file'. We did this in the beginning in order to debug the code and make sure we obtained the same results of Paratec. This feature will be removed soon and a clearer error message will be printed. Cheers, Davide On 01/-10/-28163 08:59 PM, Daniel Lima wrote: > Hi, > My name is Daniel Aguiar, and I'm a beginner in Theoretical Calculations. > I'm having some troubles with the gipaw.x calculations. > The pw.x was sucessed (JOB DONE!!). > But in gipaw.x the following mensage appear: > > At line 174 of file paw_gipaw.f90 (unit = 14, file = '') > Fortran runtime error: File '' does not exist > > > I verified in paw_gipaw.f90 and the line is: > > OPEN ( 14, FILE = filerec_sp ) > > What's wrong? > > My nmr input is following below: > > > job = 'nmr' > prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' > tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' > isolve = 0 > iverbosity = 1 > q_gipaw = 0.01 > spline_ps = .true. > use_nmr_macroscopic_shape = .false. > /
[Pw_forum] How to speed up gipaw?
Dear all, I'm using gipaw to calculate NMR of a system contain more than 100 atoms, but the first k point haven't been done after more than 40 hours. It's so slow for me. Here is my input: job = 'nmr' prefix = 'pw' tmp_dir = './tmp/' isolve = 0 conv_threshold=1e-10 iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. use_nmr_macroscopic_shape = .true. nmr_macroscopic_shape = 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.6667 / Can anyone figure me out how to improve this? PS. My computer is 8 core cpu, and gipaw and QE is compiled with intel mkl lib. Thanks very much! Pengju Ren Dalian Institute of Chemical Physics, Chinese Academy of Science
[Pw_forum] (no subject)
Dear all ?? I have tried doing a vc-relax on the attached TiO2 rutile supercell, the calculations stop after a few minutes without giving any error. What might be the problem? -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/63d5859b/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: TiOsc.scf.in1 Type: application/octet-stream Size: 3619 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110907/63d5859b/attachment-0001.obj
