Pseudooptimization?
Ilya
ikupc... at gmail.com
Wed Nov 18 01:14:48 UTC 2009
Thanks for your remark, Axel!
I made some tests. Fortunately, in my case the difference between
centered and non-centered molecules is only +/- 1 kj/mole which is ok.
What I'd like to do is to calculate/fit MM potential parameters that
would
adequately describe both overall molecule-surface interactions and
reproduce differences between adsorption sites.
So I want to describe short and long-range pairwise Molecule Atoms -
Surface Atoms interactions by empirical MM potentials, some kind of LJ
and Coulomb.
Using MM fields I could run really long MD trajectories (~2-3*10^3 ps)
Hence, I need to estimate atom-atom interactions somehow.
Do you(or any one) know how can I get pairwise atom-atom interaction
energies and forces in cp2k?
With this I could really break through!
Sincerely,
Ilya
On 17 ноя, 23:56, Axel <akoh... at gmail.com> wrote:
> On Nov 17, 12:22 pm, Teodoro Laino <teodor... at gmail.com> wrote:
>
> > Centering coordinates after each restart is slightly moving your system.
> > This creates spurious forces (because of the presence of the grid ->
> > see old messages) and the optimization may go on over forever..
>
> > Take out the CENTER_COORDINATES and everything should go in the way you
> > think it should.
>
> this will get you consistently into the same minimum, but
> perhaps, one should add to this, that because of theses "ripples"
> there is a limit to the accuracy of the energy of a geometry
> optimization. this is a limitation of using plane waves and
> does not only affect CP2k with QS.
> this doesn't matter for MD, but if you are after very small
> differences, it should be taken under consideration
> as well as the inherent other accuracy limitations (e.g.
> using DFT, basis set, BSSE, and so on). at some point small
> differences are just random noise.
>
> cheers,
> axel.
>
> > Teo
>
> > Ilya wrote:
> > > Dear CP2K users.
>
> > > I run into a problem few days ago.
>
> > > I have performed a small (60 atoms) piece of hydrated quartz QS DFT
> > > relaxation.
>
> > > Cp2k could not find energy minimum at a time.
>
> > > If I take optimized coordinates, put them in the input file again and
> > > restart the optimization with the SCF_GUESS ATOMIC, cp2k will continue
> > > optimization and will find some lower minimum.
>
> > > The amount of opt steps needed to reach the minimum is much fewer. The
> > > energy may differ by ~0.01 but in my case it really matters.
>
> > > Launching 2-3 sequential optimizations I managed to find the exact
> > > minimum value.
>
> > > Anyway it looks suspicious. As it makes up a new wave function
> > > approximation for an "optimized" coords the whole optimization goes in
> > > a slightly different way each restart. As I got.
>
> > > I tried to apply different optmizers - CG, BFGS, LBFGS. I also tried
> > > to use OT, Mixing/Diag, changing SCF optimizers CG, DIIS. All those
> > > influenced slightly. Still it does new optimization each restart,
> > > instead of saing "nothing to do everything is optimized".
>
> > > Now trying to change CUTOFF value, may be this could help.
> > > The question might be stupid, I feel that the answer is simple, just
> > > can't get it.
>
> > > If someone have some ideas, I will appreciate you advice.
>
> > > Input
>
> > > &GLOBAL
> > > PRINT_LEVEL LOW
> > > PROJECT_NAME ps-t-11
> > > RUN_TYPE GEO_OPT
> > > PREFERRED_FFT_LIBRARY FFTW
> > > &END GLOBAL
> > > &MOTION
> > > &GEO_OPT
> > > OPTIMIZER CG
> > > MAX_DR 3.00000000E-04
> > > MAX_FORCE 4.50000000E-05
> > > RMS_DR 1.50000000E-04
> > > RMS_FORCE 3.00000000E-05
> > > MAX_ITER 1000
> > > &END GEO_OPT
> > > &END MOTION
> > > &FORCE_EVAL
> > > METHOD QS
> > > &DFT
> > > BASIS_SET_FILE_NAME GTH_BASIS_SETS
> > > &SCF
> > > SCF_GUESS ATOMIC
> > > MAX_SCF 1000
> > > &END SCF
> > > &XC
> > > &XC_FUNCTIONAL PBE
> > > &END XC_FUNCTIONAL
> > > &END XC
> > > &POISSON
> > > PERIODIC XZ
> > > POISSON_SOLVER WAVELET
> > > &END POISSON
> > > &END DFT
> > > &SUBSYS
> > > &CELL
> > > ABC 9.8724 25.0 10.08094
> > > UNITS ANGSTROM
> > > PERIODIC XZ
> > > &END CELL
> > > &KIND Si
> > > BASIS_SET TZVP-GTH
> > > POTENTIAL GTH-PBE-q4
> > > &END KIND
> > > &KIND O
> > > BASIS_SET TZVP-GTH
> > > POTENTIAL GTH-PBE-q6
> > > &END KIND
> > > &KIND C
> > > BASIS_SET TZVP-GTH
> > > POTENTIAL GTH-PBE-q4
> > > &END KIND
> > > &KIND B
> > > BASIS_SET TZVPP-GTH
> > > POTENTIAL GTH-PBE-q3
> > > &END KIND
> > > &KIND H
> > > BASIS_SET TZVP-GTH
> > > POTENTIAL GTH-PBE-q1
> > > &END KIND
> > > &TOPOLOGY
> > > COORD_FILE_FORMAT XYZ
> > > COORD_FILE_NAME /home/kupchenko/job/ps/t/ps.xyz
> > > CENTER_COORDINATES T
> > > &END TOPOLOGY
> > > &END SUBSYS
> > > &END FORCE_EVAL
>
> > > Coordinate file ps.xyz:
>
> > > 60
> > > i = 1, E = -570.7446060489
> > > H 1.2164405235 15.4842136302 0.4143744831
> > > H 6.1121896899 15.5038087647 0.4144334876
> > > H 1.2707602262 15.3655789278 5.4048093021
> > > H 6.1271079554 15.4026946050 5.4235580700
> > > O 0.4551586659 15.1183862048 0.9207263709
> > > O 5.3651001781 15.1154121407 0.9229189539
> > > O 0.5077183637 15.1235599574 5.9915222988
> > > O 5.3762635138 15.1158339064 6.0005346429
> > > H 3.8570937184 15.1545145022 5.1023747623
> > > H 8.8344418767 15.1584752804 5.0833260666
> > > H 3.8786236331 15.1947700953 10.3189982581
> > > H 8.8423420430 15.2102731172 10.2764809174
> > > O 3.0957286169 14.9472184410 4.5045744980
> > > O 8.0582595943 14.9554451515 4.5037182386
> > > O 3.0983543419 14.9962628173 9.7165567981
> > > O 8.0637432247 15.0292909929 9.6668423665
> > > O 2.4682398721 13.9468761359 2.1126453081
> > > O 7.4016859412 13.9535260868 2.1076981879
> > > O 2.4331459358 13.9452444285 7.4094370497
> > > O 7.3474209604 13.9487720010 7.3996943622
> > > Si 0.9174823157 13.6452453328 1.6331964708
> > > Si 5.8506776815 13.6460140438 1.6312922823
> > > Si 0.8945731285 13.7654223514 6.8801727781
> > > Si 5.8090768385 13.7639843442 6.8815442106
> > > Si 3.3445442865 13.6624717732 3.4584593898
> > > Si 8.2735277184 13.6625861281 3.4589630814
> > > Si 3.3211393429 13.6848373669 8.7566224332
> > > Si 8.2481557358 13.6840992310 8.7402594584
> > > O 4.9261822520 13.4850120463 3.0058435744
> > > O 9.8492612051 13.4823424700 2.9989183455
> > > O 4.8578563490 13.4964580997 8.1955274091
> > > O 9.7798690555 13.4911169759 8.1692673736
> > > O 0.8797033120 12.3830946804 0.6001141356
> > > O 5.7933420692 12.3831395817 0.6001632671
> > > O 0.8817757579 12.3795984391 6.0019735587
> > > O 5.7953154313 12.3796068132 6.0019844251
> > > O 2.7873912363 12.2645536217 4.1156930416
> > > O 7.7011498729 12.2647096129 4.1156209075
> > > O 2.8124720845 12.2891736146 9.5066763280
> > > O 7.7263380707 12.2894528459 9.5065558302
> > > Si 1.8767330997 11.4234259421 -0.2249206571
> > > Si 6.7904244881 11.4233716970 -0.2249530592
> > > Si 1.8906925923 11.4346717365 5.1661113227
> > > Si 6.8044045172 11.4346717256 5.1660918387
> > > O 2.8683800441 10.6886833092 0.8130047883
> > > O 7.7820554561 10.6886976079 0.8130092380
> > > O 2.8661225434 10.6907181430 6.2154513092
> > > O 7.7798155302 10.6907252061 6.2154563221
> > > O 0.9993480464 10.3826593668 4.3304611630
> > > O 5.9130553067 10.3826768100 4.3304808739
> > > O 0.9879650764 10.3694140533 9.7308331231
> > > O 5.9016086863 10.3694428080 9.7308465605
> > > H 2.5220936594 9.9015909978 1.2556566675
> > > H 7.4361354814 9.8984291273 1.2500346062
> > > H 3.8152371223 10.6874649056 5.9934984006
> > > H 8.7297691935 10.6932243995 5.9965260796
> > > H 1.3674986990 9.4962228514 4.1919909263
> > > H 6.2998681174 9.5107427878 4.1552631113
> > > H 0.0234329886 10.3965414804 9.7770309728
> > > H 4.9370093473 10.3979787214 9.7924189287
>
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>
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