[Pw_forum] Graphene phonon calculations too slow
Dear all, I am running phonon calculations on graphene, and the calculations are taking days to complete! The calculations are run on a supercomputer and are running in parallel. I am using QE version 4.3.1, the amount of k-points that are calculated are 12x12x1 for an MP-grid which reduces down to 19 irreducible symmetry points. My phonon input is below: Phonon Dispersion of graphene &inputph recover=.true. tr2_ph=1.0d-16 ldisp=.true. nq1=12 nq2=12 nq3=1 prefix='graphene' amass(1)=12.01 fildyn='graphene.dyn' / and part of the output is shown here: Parallel version (MPI), running on48 processors K-points division: npool =3 R & G space division: proc/pool = 16 : : Computing dynamical matrix for q = ( 0.000 0.000 0.000 ) 25 Sym.Ops. (with q -> -q+G ) G cutoff = 245.0079 ( 16214 G-vectors) FFT grid: ( 32, 32,600) number of k points= 217 Methfessel-Paxton smearing, width (Ry)= 0.0100 : : There are 4 irreducible representations Representation 1 1 modes -B_2g To be done Representation 2 2 modes -E_2g To be done Representation 3 1 modes -A_2u To be done Representation 4 2 modes -E_1u To be done : : G cutoff = 245.0079 ( 259459 G-vectors) FFT grid: ( 32, 32,600) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 0.34 Mb ( 2220, 10) NL pseudopotentials 0.07 Mb ( 2220, 2) Each V/rho on FFT grid 0.59 Mb ( 38912) Each G-vector array 0.12 Mb ( 16224) G-vector shells 0.05 Mb ( 6856) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 1.35 Mb ( 2220, 40) Each subspace H/S matrix0.02 Mb ( 40, 40) Each matrix 0.00 Mb ( 2, 10) The potential is recalculated from file : ./_ph0/graphene.save/charge-density.dat Starting wfc are8 atomic +2 random wfc total cpu time spent up to now is 2.64 secs per-process dynamical memory:15.0 Mb Band Structure Calculation Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 1.25E-10, avg # of iterations = 63.7 total cpu time spent up to now is 4392.92 secs End of band structure calculation : : Any suggestions on how to speed up the process and if I am missing something?! Thank you in advance for all your kind help and time. Regards, Faris Imperial ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Graphene Phonons Not Working
Hi Paolo, On the supercomputer that I'm using, there is quantum-espresso/V.5.3.0 is that suitable? Or would you recommend using V.5.0.3 specifically? regards, Faris From: pw_forum-boun...@pwscf.org on behalf of Paolo Giannozzi Sent: 21 April 2016 20:12 To: PWSCF Forum Subject: Re: [Pw_forum] Graphene Phonons Not Working On Thu, Apr 21, 2016 at 5:42 PM, Abualnaja, Faris mailto:f.abualnaj...@imperial.ac.uk>> wrote: I've been having trouble lately trying to produce graphene phonon dispersion plots. I am currently using quantum-espresso/5.0.2<http://5.0.2.> V.5.0.2 has a nasty bug (fixed since v.5.0.3) that was leading to wrong phonons in some cases. Please try a more recent version Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Graphene Phonons Not Working
The k-points were chosen by observing the total energy and how it converges. At around 42 to 51 k-points, the total energy of the system converged. I have tried using a lower degauss (0.001) with the same mesh and the results at the gamma k and m points were not agreeable with literature. In fact at the K point there was a negative phonon! I should also mention that I have tried very similar calculations with other pseudopotentials (Ultrasoft GGA C.pbe-rrkjus.upf, Ultrasoft LDA C.pz-rrkjus, Norm Conserving Blyp C.blyp-mt.upf) the results were the same. The kpoints and ecutwfc were chosen by observing how the total energy converges with respect to changes in these parameters. Similarly the results were not reasonable, with negative values in some areas and even maximas and minimas at non-high symmetry points. Regards, Faris From: pw_forum-boun...@pwscf.org on behalf of stefano de gironcoli Sent: 21 April 2016 19:51 To: PWSCF Forum Subject: Re: [Pw_forum] Graphene Phonons Not Working Dear Abualnaja , how did you chose the smearing and k-point combination ? your degauss (0.1 Ry =1.36 eV) looks huge to me, while your k-point grid looks very dense. mp smearing is a good choice for *real* metals (with a significant dos(e_F)) even if someone would favor mv smearing. I think that in the case of graphene with vanishing dos(e_F) the simpler gaussian broadening should be fine and possibly preferable. stefano On 21/04/2016 20:32, Abualnaja, Faris wrote: Apologies all in the q2r and matdyn files zasr and asr should both be 'simple' and NOT 'crystal' From: pw_forum-boun...@pwscf.org<mailto:pw_forum-boun...@pwscf.org> <mailto:pw_forum-boun...@pwscf.org> on behalf of Abualnaja, Faris <mailto:f.abualnaj...@imperial.ac.uk> Sent: 21 April 2016 16:42 To: pw_forum@pwscf.org<mailto:pw_forum@pwscf.org> Subject: [Pw_forum] Graphene Phonons Not Working To whom it may concern, I've been having trouble lately trying to produce graphene phonon dispersion plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation using an LDA norm conserving pseudo potential (C.pz-vbc.UPF). I found an optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I then ran an scf with the optimised lattice parameter and ecutwfc. I then proceeded onto producing a band structure with the following k-points in units of 2pi/a (Gamma (0,0,0) - K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). The band structure agrees with literature, where the dirac points meet at the K point. I then moved on to calculating the phonon at each k (or q) point. I ran the scf calculation once again in a new directory, I ran the phonon at gamma, K, and M. the results seemed to agree with literature. However, when I ran the phonon dispersion calculation, the results go all over the place. The gamma k and m points are the same but the curve is not expected. Obviously, after running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. To be clear I checked my k-points, I checked the k-path, the mp grid I used was 12x12x1 when calculating the phonon dispersion and 48x48x1 when running an scf calculation. Also, to clarify I did the tutorial for Al and Si and produced correct plots. Below are my input files: SCF - &CONTROL prefix = 'graphene' pseudo_dir = '/home/fa2215/bin/upf_files' calculation= 'scf' restart_mode = 'from_scratch' verbosity = 'high' tprnfor= .TRUE. tstress= .TRUE. etot_conv_thr = 1.0D-4 forc_conv_thr = 1.0D-3 nstep = 5 wf_collect = .TRUE. / &SYSTEM ibrav= 4 celldm(1)= 4.698 celldm(3)= 18.616 nat = 2 ntyp = 1 nbnd = 10 ecutwfc = 110 ecutrho = 440 occupations = 'smearing' smearing = 'mp' degauss = 0.1 / &ELECTRONS diagonalization = 'david' electron_maxstep = 1000 conv_thr = 1.0e-8 mixing_beta = 0.3 / ATOMIC_SPECIES C 12.01 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C
Re: [Pw_forum] Graphene Phonons Not Working
Apologies all in the q2r and matdyn files zasr and asr should both be 'simple' and NOT 'crystal' From: pw_forum-boun...@pwscf.org on behalf of Abualnaja, Faris Sent: 21 April 2016 16:42 To: pw_forum@pwscf.org Subject: [Pw_forum] Graphene Phonons Not Working To whom it may concern, I've been having trouble lately trying to produce graphene phonon dispersion plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation using an LDA norm conserving pseudo potential (C.pz-vbc.UPF). I found an optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I then ran an scf with the optimised lattice parameter and ecutwfc. I then proceeded onto producing a band structure with the following k-points in units of 2pi/a (Gamma (0,0,0) - K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). The band structure agrees with literature, where the dirac points meet at the K point. I then moved on to calculating the phonon at each k (or q) point. I ran the scf calculation once again in a new directory, I ran the phonon at gamma, K, and M. the results seemed to agree with literature. However, when I ran the phonon dispersion calculation, the results go all over the place. The gamma k and m points are the same but the curve is not expected. Obviously, after running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. To be clear I checked my k-points, I checked the k-path, the mp grid I used was 12x12x1 when calculating the phonon dispersion and 48x48x1 when running an scf calculation. Also, to clarify I did the tutorial for Al and Si and produced correct plots. Below are my input files: SCF - &CONTROL prefix = 'graphene' pseudo_dir = '/home/fa2215/bin/upf_files' calculation= 'scf' restart_mode = 'from_scratch' verbosity = 'high' tprnfor= .TRUE. tstress= .TRUE. etot_conv_thr = 1.0D-4 forc_conv_thr = 1.0D-3 nstep = 5 wf_collect = .TRUE. / &SYSTEM ibrav= 4 celldm(1)= 4.698 celldm(3)= 18.616 nat = 2 ntyp = 1 nbnd = 10 ecutwfc = 110 ecutrho = 440 occupations = 'smearing' smearing = 'mp' degauss = 0.1 / &ELECTRONS diagonalization = 'david' electron_maxstep = 1000 conv_thr = 1.0e-8 mixing_beta = 0.3 / ATOMIC_SPECIES C 12.01 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.66 0.33 0.00 C 0.33 0.66 0.00 K_POINTS (automatic) 48 48 1 0 0 0 -- PHONON - Phonon Dispersion of graphene &inputph tr2_ph=1.0d-12 ldisp=.true. nq1=12 nq2=12 nq3=1 prefix='graphene' amass(1)=12.01 outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2' fildyn='graphene.dyn' / --- Q2R &input fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc' / MATDYN -
[Pw_forum] Graphene Phonons Not Working
To whom it may concern, I've been having trouble lately trying to produce graphene phonon dispersion plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation using an LDA norm conserving pseudo potential (C.pz-vbc.UPF). I found an optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I then ran an scf with the optimised lattice parameter and ecutwfc. I then proceeded onto producing a band structure with the following k-points in units of 2pi/a (Gamma (0,0,0) - K (0.3, 0.57735027, 0) - M (0.5, 0.28867513, 0)). The band structure agrees with literature, where the dirac points meet at the K point. I then moved on to calculating the phonon at each k (or q) point. I ran the scf calculation once again in a new directory, I ran the phonon at gamma, K, and M. the results seemed to agree with literature. However, when I ran the phonon dispersion calculation, the results go all over the place. The gamma k and m points are the same but the curve is not expected. Obviously, after running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. To be clear I checked my k-points, I checked the k-path, the mp grid I used was 12x12x1 when calculating the phonon dispersion and 48x48x1 when running an scf calculation. Also, to clarify I did the tutorial for Al and Si and produced correct plots. Below are my input files: SCF - &CONTROL prefix = 'graphene' pseudo_dir = '/home/fa2215/bin/upf_files' calculation= 'scf' restart_mode = 'from_scratch' verbosity = 'high' tprnfor= .TRUE. tstress= .TRUE. etot_conv_thr = 1.0D-4 forc_conv_thr = 1.0D-3 nstep = 5 wf_collect = .TRUE. / &SYSTEM ibrav= 4 celldm(1)= 4.698 celldm(3)= 18.616 nat = 2 ntyp = 1 nbnd = 10 ecutwfc = 110 ecutrho = 440 occupations = 'smearing' smearing = 'mp' degauss = 0.1 / &ELECTRONS diagonalization = 'david' electron_maxstep = 1000 conv_thr = 1.0e-8 mixing_beta = 0.3 / ATOMIC_SPECIES C 12.01 C.pz-vbc.UPF ATOMIC_POSITIONS crystal C 0.66 0.33 0.00 C 0.33 0.66 0.00 K_POINTS (automatic) 48 48 1 0 0 0 -- PHONON - Phonon Dispersion of graphene &inputph tr2_ph=1.0d-12 ldisp=.true. nq1=12 nq2=12 nq3=1 prefix='graphene' amass(1)=12.01 outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2' fildyn='graphene.dyn' / --- Q2R &input fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc' / MATDYN --- &input asr='crystal' amass(1)=12.01 flfrc='graphene.fc' flfrq='graphene.freq' / 219 0.000.000.00 1.0 :::: So to recap my procedure wa
