The Kohn Sham matrix is not 100% occupied

Claudio marg... at gmail.com
Tue Nov 17 12:29:05 CET 2009


Dear Manuel,
thanks again for providing some guidance on this calculation. I did
what you suggested, and the HF run appears to converge

 1 OT CG       0.15E+00 1241.8     0.00004886     -6103.3087142795
-6.10E+03

however cube files for orbitals are full on NaN, not the density cube
though. Furthermore I get at the end of the output something that I
hadn't seen before on any dft calculations. Part of the output
follows:



 
-------------------------------------------------------------------------------
 
-
-
 -                                T I M I N
G                                  -
 
-
-
 
-------------------------------------------------------------------------------
 SUBROUTINE                       CALLS  ASD         SELF TIME
TOTAL TIME
                                              AVERAGE  MAXIMUM
AVERAGE  MAXIMUM
 CP2K                                 1  1.0    0.223    0.325
1305.554 1305.638
 qs_energies_scf                      1  2.0    0.000    0.001
1301.807 1301.899
 scf_env_do_scf                       1  3.0    0.000    0.000
1243.079 1243.128
 init_scf_loop                        1  4.0    0.000    0.000
1241.378 1241.400
 qs_ks_update_qs_env                  2  5.0    0.000    0.000
1240.934 1240.956
 qs_ks_build_kohn_sham_matrix         1  6.0    0.004    0.017
1240.932 1240.954
 integrate_four_center                1  7.0  143.888  246.392
1238.092 1238.114
 integrate_four_center_main           1  8.0    0.000    0.001
1068.609 1211.585
 integrate_four_center_bin           64  9.0 1068.608 1211.585
1068.608 1211.585
 scf_post_calculation_gpw             1  3.0    0.047    0.049
55.556   55.600
 ot_eigensolver                       1  4.0    0.010    0.012
43.961   43.963
 dbcsr_sm_fm_multiply               304  5.0    0.031    0.036
43.093   43.389
 dbcsr_sm_sm_multiply               304  6.0    0.038    0.045
41.428   41.557
 dbcsr_mult_e_ec_m_rma              304  7.0   38.174   38.293
38.197   38.306
 
-------------------------------------------------------------------------------

  **** **** ******  **  PROGRAM ENDED AT                 2009-11-17
05:26:51.494
 ***** ** ***  *** **   PROGRAM RAN
ON                                   node014
 **    ****   ******    PROGRAM RAN
BY                                  claudiom
 ***** **    ** ** **   PROGRAM PROCESS
ID                                 11756
  **** **  *******  **  PROGRAM STOPPED IN /home/claudiom/snapshots/
cp2k/mmim-cl
                                           /b3lyp/neutral
Remaining memory: 80 bytes at 00000000375ad338 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at Remaining memory: 80 bytes at
0000000035dd0d98 allocated at line 1806 of /raid/home/claudiom/src/
cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000359e0eb8 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
0000000034c0f9a8Remaining memory: 80 bytes at 0000000034853078
allocated at line 1808 of /raid/home/claudiom/src/cp2k/makefiles/../
src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000347705e8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000003466da98 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000036afd98 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000344fc578 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000000472d9c8 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000047211d8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000000469c168 allocated at line
allocated at line 1808 of /raid/home/claudiom/src/cp2k/makefiles/../
src/dbcsr_util.F1806 of /raid/home/claudiom/src/cp2k/makefiles/../src/
dbcs\
r_util.F
Remaining memory: 80 bytes at 00000000046ab708 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000048116f8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80
 bytes at 00000000047d4938 allocated at line 1806 of /raid/home/
claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: Remaining memory: 80 bytes at 00000000047d4308
allocated at line 1808 of /raid/home/claudiom/src/cp2k/makefiles/../
src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000047d0158 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
80Remaining memory: 80 bytes at 0000000004812368 allocated at line
1808 of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000004813718 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory:  bytes at 80 bytes at 000000000484e8d8 allocated at
line 1806 of /raid/home/claudiom/src/cp2k/makefiles/../src/
dbcsr_util.F
Remaining memory: 80 bytes at 0000000004819838 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/
dbcsr_util.F00000000346ce238
Remaining memory: 80 bytes at 00000000048184a8 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000048146e8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000344fc278 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
allocated at line
Remaining memory: 80 bytes at 000000003455bbd8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000345270e8 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000034527f18 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
 ... More segments remain
1806 of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000003469e8b8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000000490fea8 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000004897f28 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000004890c18 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 000000000473b218 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 00000000031fe748 allocated at line 1808
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000004712328 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F
Remaining memory: 80 bytes at 0000000004719fd8 allocated at line 1806
of /raid/home/claudiom/src/cp2k/makefiles/../src/dbcsr_util.F


and many more lines of memory complaints...  Any ideas on how to
overcome this are really welcome.

Thanks,
Claudio




On Nov 16, 9:14 am, Claudio <marg... at gmail.com> wrote:
> Thanks Manuel, I just read the paper.
> I will try some of this and will report back.
>
> Cheers,
> Claudio
>
> On Nov 16, 8:13 am, mguidon <manuel... at gmail.com> wrote:
>
>
>
> > Hi Claudio.
>
> > There are several issues that could cause troubles in a periodic HFX
> > calculation:
>
> > 1. Always use the truncated Coulomb operator, otherwise your results
> > might converge to an unphysical wavefunction (i.e. total energies a
> > far lower than what you would expect)
> > 2. The sparsity-patterns of the Fock- and Kohn-Sham matrice are not
> > the same. This issue can be solved by putting EPS_PGF_ORB to 1.0E-32
> > or similar. (But usually, a 90 % occupied Kohn-Sham matrix is good
> > enough, especially when you apply the truncated potential)
> > 3. By putting a threshold on all the integrals (EPS_SCHWARZ) you
> > introduce some random errors of the same order. As a rule of thumb,
> > eps_schwarz should be roughly equal to the inverse square of the
> > condition number of the overlap matrix. For example: If the condition
> > number of the overlap matrix is 1.0E4, then you should put eps_schwarz
> > to 1.0E-8 (but this is a worst case estimate!) Keep in mind, that the
> > amount of work roughly doubles by decreasing eps_schwarz by one order
> > of magnitude. It might be better to decrease the condition number of
> > the overlap matrix by choosing a less diffuse basis set.
> > 4. Always add the keyword EPS_STORAGE_SCALING 1.0E-1 in order to avoid
> > suppress noise in the compression/decompression routines.
>
> > For more details see
>
> > J. Chem. Theory Comput., 2009, 5 (11), pp 3010-3021
>
> > Hope that helps
>
> > Manuel
>
> > On Nov 16, 1:56 pm, Claudio <marg... at gmail.com> wrote:
>
> > > Dear all, when I try to run a periodic HF calculation or a mixed HF
> > > DFT run (b3lyp) for example. I always get
>
> > >  *** 06:49:15 WARNING in
> > > hfx_energy_potential:integrate_four_center         ***
> > >  *** err=-300  The Kohn Sham matrix is not 100% occupied. This may
> > > result   ***
> > >  *** in uncorrect Hartree-Fock results. Try to decrease EPS_PGF_ORB in
> > > the  ***
> > >  *** QS
> > > section.
> > > ***
>
> > > Same system converges without problem without HF using for example
> > > PBE. I tried decreasing EPS_PGF_ORB and EPS_DEFAULT without much
> > > success. I also tried decreasing basis set size. I am not using a
> > > truncated potential.
>
> > > Is this warning relevant? I am having a very hard time converging the
> > > b3lyp calculation.
>
> > > Thanks,
> > > Claudio



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