[Pw_forum] no scf started for huge system

Sat Jul 11 05:04:57 CEST 2015

No. 

stefano 
(sent from my phone)

> On 10 Jul 2015, at 16:42, Ludwig, Stephan <stephan.ludwig at pi1.physik.uni-stuttgart.de> wrote:
> 
> Hi Stefano,
> thank you for your reply. This means a grest improvement to my understanding.
> To improve it further:
> Consider a given cell with a given structure. Consider further I found a suitable planewave-cutoff. Now I disturb the structure by rearanging the atoms (no new atom) which leads to a loss in symetry (I produce chaos in my cell without enlarging the cell itself).
> For this less symetric structure do I need a larger cutoff (of course just for scf calculations)?
> 
> Thanks and Regards
> Stephan Ludwig
> -----Original message-----
> From: Stefano de Gironcoli <degironc at sissa.it>
> Sent: Friday 10th July 2015 16:28
> To: PWSCF Forum <pw_forum at pwscf.org>
> Subject: Re: [Pw_forum] no scf started for huge system
> 
> For a given cutoff as you increase the cell the number of basis functions increases automatically. The cutoff is mostly a property of the type of atoms (and type of pseudo) involved an can be reasonably estimated in simple cells... Take a simple molecule containing the same atoms and similar type of bonds. What is the energy criterion that you are using ? Might be too tight.
> Check convergence of forces and stress as well keeping in mind that 1d-4 is a very small force and 0.5 kbar is a small pressure ( for normally stiff materials) for organic crystals you may need to reduce this.  Estimate how much this would change in terms of lattice parameter and adapt to it.
> 
> stefano 
> (sent from my phone)
> 
>> On 10 Jul 2015, at 16:07, Ludwig, Stephan <stephan.ludwig at pi1.physik.uni-stuttgart.de> wrote:
>> 
>> Hello,
>> thank you for your reply and your help. 
>> Maybe I understood some basical concepts wrong:
>> The planewave cutoff defines the size of the planewave basis-set I use to approximate the real electron density (or to solve the KS-equations). The more complicated a system is the more basis functions I need in order to
>> get a suitable result. My unit cell shows little symetrie and contains an organic molecule with 236 atoms. Therefore I expected that I need for this material much more planewaves than for simple anorganic salts or elements.
>> Is this not right?
>> 
>> I check convergency with respect to the total energy.
>> Right or wrong?
>> 
>> I also tried to work with normconserving pseudos, but since I received no convergence with respect to the planewave-cutoff I changed to the ultrasofts (they need less planewaves).
>> Right or wrong?
>> 
>> I have no group! I'm a master student and I'm doing my thesis at an institute for experimental physics. No one here has an idea what I do.
>> My former supervisor left the institute two month after I started. 
>> 
>> Thanks and regards
>> 
>> Stephan
>> 
>> 
>> 
>> 
>> -----Original message-----
>> From: Axel Kohlmeyer <akohlmey at gmail.com>
>> Sent: Thursday 9th July 2015 16:24
>> To: PWSCF Forum <pw_forum at pwscf.org>
>> Subject: Re: [Pw_forum] no scf started for huge system
>> 
>> On Thu, Jul 9, 2015 at 9:28 AM, Ludwig, Stephan
>> <stephan.ludwig at pi1.physik.uni-stuttgart.de> wrote:
>> > Hello,
>> >
>> > I would like to check convergency but my scf calculations do not start...
>> >
>> > I need a huge cutoff because my cell contains 236 atoms and is pretty huge.
>> 
>> this is nonsense, the planewave cutoff is unrelated to the size of the system.
>> 
>> > On my own Pc (with just 4 procs) I found out that with cutoffs lower than
>> > 200 I'm far, far away from convergence.
>> 
>> then you may be doing something wrong. also, convergence with respect to what?
>> at such large planewave cutoffs you're likely better off with
>> normconserving pseudopotentials.
>> 
>> this all sounds a bit like you need to spend some time at a group that
>> is well experienced in doing QE calculations and get some proper
>> oversight and hands on training.
>> 
>> axel.
>> 
>> >
>> > Thanks and Regards
>> >
>> > Stephan
>> >
>> > -----Original message-----
>> > From: Gabriel Greene <gabriel.greene at tyndall.ie>
>> > Sent: Thursday 9th July 2015 12:53
>> > To: PWSCF Forum <pw_forum at pwscf.org>
>> > Subject: Re: [Pw_forum] no scf started for huge system
>> >
>> >
>> > Why do you need such a big wavefunction cutoff?
>> >
>> > ecutwfc=200 is pretty big (400 is extreme)...have you checked convergence?
>> >
>> > ________________________________
>> > From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf of
>> > Ludwig, Stephan [stephan.ludwig at pi1.physik.uni-stuttgart.de]
>> > Sent: Thursday, July 09, 2015 11:48 AM
>> > To: PWSCF Forum
>> > Subject: Re: [Pw_forum] no scf started for huge system
>> >
>> > Hello,
>> >
>> > I tried found out that when I increase ecutwfc to 400 I receive an error
>> > message:
>> >
>> >
>> > Initial potential from superposition of free atoms
>> >
>> > starting charge 875.99411, renormalised to 876.00000
>> >
>> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> > Error in routine diropn (3):
>> > wrong record length
>> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >
>> > stopping ...
>> > --------------------------------------------------------------------------
>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> > with errorcode 1.
>> >
>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> > You may or may not see output from other processes, depending on
>> > exactly when Open MPI kills them.
>> > ------------------------------------------------------------
>> >
>> > 
>> >
>> > Does anybody know what this means?
>> >
>> >
>> > Thanks and Regards
>> >
>> >
>> > Stephan
>> >
>> >
>> > -----Original message-----
>> > From: Ludwig, Stephan <stephan.ludwig at pi1.physik.uni-stuttgart.de>
>> > Sent: Thursday 9th July 2015 12:42
>> > To: Forum, PWSCF (pw_forum at pwscf.org) <pw_forum at pwscf.org>
>> > Subject: [Pw_forum] no scf started for huge system
>> >
>> > Hello
>> >
>> > I try to do scf calculation for an organic salt with 236 atoms in a unit
>> > cell.
>> >
>> > I'm working on a cluster using 45 procs for the calculation.
>> >
>> > Within the allowed time span (2 days) these procs do not even start the scf
>> > cycles.
>> >
>> > The last part of the output data is:
>> >
>> >
>> > Largest allocated arrays est. size (Mb) dimensions
>> > Kohn-Sham Wavefunctions 7508.34 Mb ( 935488, 526)
>> > NL pseudopotentials 20098.38 Mb ( 935488, 1408)
>> > Each V/rho on FFT grid 243.00 Mb (15925248)
>> > Each G-vector array 57.08 Mb ( 7481721)
>> > G-vector shells 14.43 Mb ( 1891088)
>> > Largest temporary arrays est. size (Mb) dimensions
>> > Auxiliary wavefunctions 30033.37 Mb ( 935488, 2104)
>> > Each subspace H/S matrix 67.55 Mb ( 2104, 2104)
>> > Each <psi_i|beta_j> matrix 11.30 Mb ( 1408, 526)
>> > Arrays for rho mixing 1944.00 Mb (15925248, 8)
>> >
>> > Check: negative/imaginary core charge= -0.000001 0.000000
>> >
>> > Initial potential from superposition of free atoms
>> >
>> > 
>> >
>> > starting charge 875.99411, renormalised to 876.00000
>> > Starting wfc are 704 randomized atomic wfcs
>> >
>> > 
>> >
>> > Then the job cancels due to time limit.
>> >
>> > I want to be sure that this happens just because of the fact that the system
>> > is too huge and not because I made some bad mistake.
>> >
>> > My input file looks like this:
>> >
>> >
>> > &CONTROL
>> > title = 'etot_vs_ecutwfc' ,
>> > calculation = 'scf' ,
>> > wf_collect = .FALSE.,
>> > outdir = './' ,
>> > wfcdir = './' ,
>> > pseudo_dir = '/home/st/st_st/st_phy72394/pseudo/' ,
>> > prefix = 'MeDH-TTPetot_vs_ecutwfc' ,
>> > /
>> > &SYSTEM
>> > ibrav = -12,
>> > A = 32.783 ,
>> > B = 7.995 ,
>> > C = 11.170 ,
>> > cosAB = 0 ,
>> > cosAC = -0.132602381688 ,
>> > cosBC = 0 ,
>> > nat = 236,
>> > ntyp = 5,
>> > ecutwfc = 200,
>> > occupations = 'smearing' ,
>> > degauss = 0.02 ,
>> > smearing = 'gaussian' ,
>> > exxdiv_treatment = 'gygi-baldereschi' ,
>> > /
>> > &ELECTRONS
>> > conv_thr = 1.0D-8
>> > /
>> > ATOMIC_SPECIES
>> > H 1.00790 H.pz-rrkjus_psl.0.1.UPF
>> > C 12.01100 C.pz-n-rrkjus_psl.0.1.UPF
>> > F 18.98800 F.pz-n-rrkjus_psl.0.1.UPF
>> > S 32.06500 S.pz-n-rrkjus_psl.0.1.UPF
>> > As 74.92200 As.pz-n-rrkjus_psl.0.2.UPF
>> > ATOMIC_POSITIONS angstroms
>> > S 5.52835 0.29521 2.16999
>> > S 21.91985 4.29246 2.16999
>> > S 4.78777 7.69929 7.70567
>> > S 21.17927 3.70204 7.70567
>> > S 8.91117 6.37745 3.91040
>> > S 25.30267 2.38020 3.91040
>> > S 8.17058 1.61705 9.44608
>> > S 24.56208 5.61430 9.44608
>> > S 8.53628 0.30838 1.68728
>> > S 24.92778 4.30563 1.68728
>> > S 7.79569 7.68612 7.22296
>> > S 24.18719 3.68887 7.22296
>> > S 5.91488 6.35256 4.41083
>> > S 22.30638 2.35531 4.41083
>> > S 5.17429 1.64194 9.94651
>> > S 21.56579 5.63919 9.94651
>> > As 31.25307 7.42312 4.40640
>> > As 14.86156 3.42587 4.40640
>> > As 30.51248 0.57138 9.94208
>> > As 14.12098 4.56863 9.94208
>> > S 22.77175 0.24544 7.42335
>> > S 6.38025 4.24269 7.42335
>> > S 23.51233 7.74906 1.88767
>> > S 7.12083 3.75181 1.88767
>> > S 22.41272 6.31548 5.17143
>> > S 6.02122 2.31823 5.17143
>> > S 21.67213 1.67902 10.70711
>> > S 5.28063 5.67627 10.70711
>> > S 19.75130 0.27959 7.86510
>> > S 3.35980 4.27684 7.86510
>> > S 20.49188 7.71491 2.32941
>> > S 4.10038 3.71766 2.32941
>> > S 19.39879 6.33792 5.62425
>> > S 3.00729 2.34067 5.62425
>> > S 20.13937 1.65658 0.08857
>> > S 3.74787 5.65383 0.08857
>> > S 25.96310 0.08881 6.99046
>> > S 9.57160 4.08606 6.99046
>> > S 26.70368 7.90569 1.45478
>> > S 10.31218 3.90844 1.45478
>> > S 25.56056 6.28376 4.68983
>> > S 9.16906 2.28651 4.68983
>> > S 24.81997 1.71074 10.22551
>> > S 8.42848 5.70799 10.22551
>> > S 12.08748 6.57702 3.54505
>> > S 28.47898 2.57977 3.54505
>> > S 11.34689 1.41748 9.08073
>> > S 27.73839 5.41473 9.08073
>> > S 11.74373 0.68898 1.53781
>> > S 28.13523 4.68623 1.53781
>> > S 11.00315 7.30552 7.07349
>> > S 27.39465 3.30827 7.07349
>> > C 2.50124 7.97352 2.72134
>> > C 18.89274 3.97627 2.72134
>> > C 1.76066 0.02098 8.25702
>> > C 18.15215 4.01823 8.25702
>> > H 2.98979 0.63970 2.22534
>> > H 19.38129 4.63695 2.22534
>> > H 2.24920 7.35480 7.76102
>> > H 18.64071 3.35755 7.76102
>> > H 1.85588 0.41427 3.28266
>> > H 18.24738 4.41152 3.28266
>> > H 1.11530 7.58023 8.81834
>> > H 17.50680 3.58298 8.81834
>> > H 2.05231 7.38359 2.11352
>> > H 18.44381 3.38634 2.11352
>> > H 1.31173 0.61091 7.64920
>> > H 17.70323 4.60816 7.64920
>> > F 32.09159 6.20228 3.55280
>> > F 15.70009 2.20503 3.55280
>> > F 31.35101 1.79222 9.08848
>> > F 14.95951 5.78947 9.08848
>> > F 31.99917 0.61481 3.45094
>> > F 15.60767 4.61206 3.45094
>> > F 31.25859 7.37969 8.98662
>> > F 14.86709 3.38244 8.98662
>> > F 30.39326 0.65482 5.22458
>> > F 14.00176 4.65207 5.22458
>> > F 29.65268 7.33968 10.76026
>> > F 13.26118 3.34243 10.76026
>> > F 30.47339 6.23106 5.35854
>> > F 14.08189 2.23381 5.35854
>> > F 29.73280 1.76344 10.89422
>> > F 13.34130 5.76069 10.89422
>> > F 29.96030 7.30601 3.28598
>> > F 13.56880 3.30876 3.28598
>> > F 29.21972 0.68849 8.82166
>> > F 12.82821 4.68574 8.82166
>> > F -0.26088 7.52461 5.52461
>> > F 16.13062 3.52736 5.52461
>> > F -1.00147 0.46989 11.06029
>> > F 15.39003 4.46714 11.06029
>> > C 4.77264 7.25965 3.40666
>> > C 21.16414 3.26240 3.40666
>> > C 4.03205 0.73485 8.94234
>> > C 20.42355 4.73210 8.94234
>> > C 7.12868 7.79932 2.56191
>> > C 23.52018 3.80207 2.56191
>> > C 6.38809 0.19518 8.09759
>> > C 22.77959 4.19243 8.09759
>> > C 24.86295 7.22306 5.97079
>> > C 8.47145 3.22581 5.97079
>> > C 25.60353 0.77144 0.43510
>> > C 9.21203 4.76869 0.43510
>> > C 18.61690 7.45190 6.77235
>> > C 2.22540 3.45465 6.77235
>> > C 19.35749 0.54260 1.23667
>> > C 2.96599 4.53985 1.23667
>> > C 11.00638 7.55584 2.60731
>> > C 27.39788 3.55859 2.60731
>> > C 10.26580 0.43866 8.14299
>> > C 26.65730 4.43591 8.14299
>> > C 9.65436 7.44215 2.72245
>> > C 26.04587 3.44490 2.72245
>> > C 8.91378 0.55235 8.25813
>> > C 25.30528 4.54960 8.25813
>> > C 16.66566 0.56358 7.82192
>> > C 0.27416 4.56083 7.82192
>> > C 17.40624 7.43092 2.28624
>> > C 1.01474 3.43367 2.28624
>> > H 17.33387 0.90270 8.42088
>> > H 0.94237 4.89995 8.42088
>> > H 18.07446 7.09180 2.88520
>> > H 1.68295 3.09455 2.88520
>> > H 15.99844 0.08734 8.32234
>> > H -0.39307 4.08459 8.32234
>> > H 16.73902 7.90716 2.78666
>> > H 0.34752 3.90991 2.78666
>> > H 16.25380 1.29452 7.35581
>> > H -0.13770 5.29177 7.35581
>> > H 16.99438 6.69998 1.82013
>> > H 0.60288 2.70273 1.82013
>> > C 2.84149 6.31548 4.62008
>> > C 19.23299 2.31823 4.62008
>> > C 2.10091 1.67902 10.15576
>> > C 18.49241 5.67627 10.15576
>> > H 3.50975 5.72019 4.96440
>> > H 19.90125 1.72294 4.96440
>> > H 2.76917 2.27431 10.50008
>> > H 19.16067 6.27156 10.50008
>> > H 2.12009 5.80314 4.23922
>> > H 18.51159 1.80589 4.23922
>> > H 1.37951 2.19136 9.77491
>> > H 17.77101 6.18861 9.77491
>> > H 2.49999 6.86149 5.33308
>> > H 18.89149 2.86424 5.33308
>> > H 1.75941 1.13301 10.86876
>> > H 18.15091 5.13026 10.86876
>> > C 16.35379 6.90785 5.93536
>> > C -0.03771 2.91060 5.93536
>> > C 17.09438 1.08665 0.39968
>> > C 0.70288 5.08390 0.39968
>> > H 16.84589 6.32182 5.35300
>> > H 0.45439 2.32457 5.35300
>> > H 16.10531 1.67268 10.88868
>> > H -0.28619 5.66993 10.88868
>> > H 15.86389 7.54510 5.40947
>> > H -0.52761 3.54785 5.40947
>> > H 15.12331 0.44940 10.94515
>> > H -1.26819 4.44665 10.94515
>> > H 15.74245 6.39404 6.46678
>> > H -0.64905 2.39679 6.46678
>> > H 16.48303 1.60046 0.93110
>> > H 0.09153 5.59771 0.93110
>> > C 17.30660 7.62854 6.82992
>> > C 0.91510 3.63129 6.82992
>> > C 18.04719 0.36596 1.29424
>> > C 1.65569 4.36321 1.29424
>> > C 3.44486 7.19037 3.56498
>> > C 19.83636 3.19312 3.56498
>> > C 2.70427 0.80413 9.10066
>> > C 19.09577 4.80138 9.10066
>> > C 7.30907 6.93029 3.56166
>> > C 23.70057 2.93304 3.56166
>> > C 6.56849 1.06421 9.09734
>> > C 22.95999 5.06146 9.09734
>> > C 23.51465 7.25282 6.17782
>> > C 7.12315 3.25557 6.17782
>> > C 24.25523 0.74168 0.64214
>> > C 7.86373 4.73893 0.64214
>> > C 21.16001 7.74028 6.99710
>> > C 4.76851 3.74303 6.99710
>> > C 21.90060 0.25422 1.46142
>> > C 5.50910 4.25147 1.46142
>> > C 21.00252 6.87857 5.99071
>> > C 4.61102 2.88132 5.99071
>> > C 21.74310 1.11593 0.45503
>> > C 5.35160 5.11318 0.45503
>> > C 27.41664 7.76370 5.98186
>> > C 11.02514 3.76645 5.98186
>> > C 28.15722 0.23080 0.44618
>> > C 11.76572 4.22805 0.44618
>> > H 27.59489 0.54455 5.42718
>> > H 11.20339 4.54180 5.42718
>> > H 26.85431 7.44995 10.96286
>> > H 10.46280 3.45270 10.96286
>> > H 28.18126 7.63147 6.56310
>> > H 11.78976 3.63422 6.56310
>> > H 28.92184 0.36303 1.02742
>> > H 12.53034 4.36028 1.02742
>> > C 27.26323 6.60922 5.13933
>> > C 10.87173 2.61197 5.13933
>> > C 26.52265 1.38528 10.67501
>> > C 10.13115 5.38253 10.67501
>> > H 27.61795 5.83339 5.59879
>> > H 11.22645 1.83614 5.59879
>> > H 28.35854 2.16111 0.06311
>> > H 11.96704 6.15836 0.06311
>> > H 27.78169 6.73853 4.33001
>> > H 11.39019 2.74128 4.33001
>> > H 27.04111 1.25597 9.86569
>> > H 10.64961 5.25322 9.86569
>> > C 13.44202 0.18298 1.85556
>> > C 29.83352 4.18023 1.85556
>> > C 12.70144 7.81152 7.39124
>> > C 29.09294 3.81427 7.39124
>> > H 13.72839 7.55876 1.16581
>> > H 30.11989 3.56151 1.16581
>> > H 12.98780 0.43574 6.70150
>> > H 29.37930 4.43299 6.70150
>> > H 14.02273 0.95930 1.82235
>> > H 30.41423 4.95655 1.82235
>> > H 13.28214 7.03520 7.35803
>> > H 29.67364 3.03795 7.35803
>> > C 13.55775 7.53144 3.17416
>> > C 29.94925 3.53419 3.17416
>> > C 12.81716 0.46306 8.70984
>> > C 29.20866 4.46031 8.70984
>> > H 13.68661 0.21518 3.85616
>> > H 30.07811 4.21243 3.85616
>> > H 12.94602 7.77932 9.39184
>> > H 29.33752 3.78207 9.39184
>> > H 14.33307 6.94883 3.18191
>> > H 30.72457 2.95158 3.18191
>> > H 13.59248 1.04567 8.71759
>> > H 29.98398 5.04292 8.71759
>> > K_POINTS automatic
>> > 1 2 2 0 0 0
>> >
>> >
>> > Has anybody made similar experiences? Any ideas how to come at least to a
>> > scf calculation?
>> >
>> > Does anybody know any tricks and hints for huge systems?
>> >
>> >
>> > Thanks and regards
>> >
>> >
>> > Stephan
>> >
>> >
>> > _______________________________________________
>> >
>> > Pw_forum mailing list
>> >
>> > Pw_forum at pwscf.org
>> >
>> > http://pwscf.org/mailman/listinfo/pw_forum
>> >
>> > _______________________________________________
>> >
>> > Pw_forum mailing list
>> >
>> > Pw_forum at pwscf.org
>> >
>> > http://pwscf.org/mailman/listinfo/pw_forum
>> >
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://pwscf.org/mailman/listinfo/pw_forum
>> 
>> 
>> 
>> -- 
>> Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
> 
> _______________________________________________
> 
> Pw_forum mailing list
> 
> Pw_forum at pwscf.org
> 
> http://pwscf.org/mailman/listinfo/pw_forum
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20150711/808dce30/attachment.html>