[Pw_forum] no scf started for huge system

Wed Jul 15 12:07:54 CEST 2015

Short and precise. Thank you 

-----Original message-----
From: Stefano de Gironcoli <degironc at sissa.it>
Sent: Saturday 11th July 2015 5:08
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] no scf started for huge system

No. 

stefano 
(sent from my phone)

On 10 Jul 2015, at 16:42, Ludwig, Stephan <stephan.ludwig at pi1.physik.uni-stuttgart.de <mailto: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 <mailto:degironc at sissa.it> >
Sent: Friday 10th July 2015 16:28
To: PWSCF Forum <pw_forum at pwscf.org <mailto: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 <mailto: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 <mailto:akohlmey at gmail.com> >
Sent: Thursday 9th July 2015 16:24
To: PWSCF Forum <pw_forum at pwscf.org <mailto: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 <mailto: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 <mailto:gabriel.greene at tyndall.ie> >
> Sent: Thursday 9th July 2015 12:53
> To: PWSCF Forum <pw_forum at pwscf.org <mailto: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 <mailto:pw_forum-bounces at pwscf.org>  [pw_forum-bounces at pwscf.org <mailto:pw_forum-bounces at pwscf.org> ] on behalf of
> Ludwig, Stephan [stephan.ludwig at pi1.physik.uni-stuttgart.de <mailto: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 <mailto:stephan.ludwig at pi1.physik.uni-stuttgart.de> >
> Sent: Thursday 9th July 2015 12:42
> To: Forum, PWSCF (pw_forum at pwscf.org <mailto:pw_forum at pwscf.org> ) <pw_forum at pwscf.org <mailto: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
>
>
> _______________________________________________
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-- 
Dr. Axel Kohlmeyer  akohlmey at gmail.com <mailto:akohlmey at gmail.com>   http://goo.gl/1wk0 <http://goo.gl/1wk0> 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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