NPT simulations
tomfrigato
tomfr... at hotmail.com
Fri Oct 10 08:46:57 UTC 2008
ok thanks that was the info I needed
On Oct 8, 3:19 pm, Juerg Hutter <hut... at pci.uzh.ch> wrote:
> Hi
>
> in order to get a smooth energy-volume curve you should
> make use of the REFERENCE CELL concept. This way you
> keep the total number of plane waves in the calculation
> constant. However, you want also to keep the cutoff
> reasonably high during the whole calculation. Therefore
> I would suggest to use a higher cutoff (maybe 400 Ry,
> but you should check this) and have the reference cell
> larger than the expected range of cell sizes during the
> simulation.
>
> Do you have experience with NPT simulations using
> calssical potentials? If not, I would advice you to
> simulate your system first using classical potentials.
> This way you can test the barostat settings and you will
> get a feeling for the fluctuations you have to expect.
> This will also give you an estimate on the time-scale
> for converged averages.
>
> regards
>
> Juerg
>
> ----------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Physical Chemistry Institute FAX : ++41 44 635 6838
> University of Zurich E-mail: hut... at pci.uzh.ch
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> ----------------------------------------------------------
>
> On Wed, 8 Oct 2008, tomfrigato wrote:
>
> > Hi all,
>
> > I did a simulation on 128 H2O box applying both thermostat and
> > barostat, so NPT ensamble.
> > I am not using the latest cp2k (21 july 2008 version).
>
> > I have 2 questions: the first one is about the barostat. Although I
> > went through the discussion there was already in this group (under
> > "barostat"), and read the reference paper (Martyna et al, JCP 101,
> > 4177 (1994)), and used the suggested setup I found in the test file
> > cp2k/tests/Fist/H2O-32_NPT.inp
> > I see in my restart file run-1.restart at the end of the run that I
> > have 2 thermostat, one in the BAROSTAT section and one in the
> > THERMOSTAT section, with different coors, masses and velocities, and
> > honestly I still do not understand why one has 2 thermostats. My input
> > file is at the end of this post.
>
> > The second question is about some strange energy behaviour during the
> > run. I took the simulations coordinates and velocities from a previous
> > NVT simulations, and it looks like the setup I chose (BLYP, DZVP
> > basis) results in a more dense liquid. As the box shrinks there are
> > some large jumps in the total energy: for example this is a part of
> > the run-1.ener file:
>
> > 33 16.500 0.577002245
> > 317.150009889 -2199.101322770 -2198.365847076
> > 82.407300000
> > 34 17.000 0.579470429
> > 318.506650669 -2199.103374256 -2198.365814097
> > 93.484800000
> > 35 17.500 0.584554875
> > 321.301322756 -2199.107827624 -2198.365870421
> > 94.342100000
> > 36 18.000 0.591370574
> > 325.047580217 -2198.642282517 -2197.894050509
> > 101.114600000
> > 37 18.500 0.598376710
> > 328.898511501 -2198.649038164 -2197.894118726
> > 122.682700000
> > 38 19.000 0.604204462
> > 332.101743054 -2198.654572558 -2197.894131860
> > 111.490300000
>
> > as you see from step 35 to 36 the energy makes a huge jump.
> > I cannot attach the whole output files, but there are other jumps in
> > energies, and they always happen at given values of the cell size: if,
> > due to fluctuations, the cell size crosses again the value at which I
> > had seen an energy jump, the energy goes back to its previous value:
> > again from the energy file (see steps 1123-1124 and 1133-1134)
>
> > 1221 610.500 0.591046245
> > 324.869312116 -2198.746759475 -2197.893072489
> > 89.885600000
> > 1222 611.000 0.592657632
> > 325.755013337 -2198.748370081 -2197.893090644
> > 90.672400000
> > 1223 611.500 0.593445612
> > 326.188127577 -2198.749147687 -2197.893104641
> > 90.380400000
> > 1224 612.000 0.593277920
> > 326.095955187 -2198.455662880 -2197.599816140
> > 105.944200000
> > 1225 612.500 0.592358652
> > 325.590678712 -2198.454680205 -2197.599788503
> > 116.352000000
> > 1226 613.000 0.591168828
> > 324.936690356 -2198.453420020 -2197.599765859
> > 116.141900000
> > 1227 613.500 0.590088019
> > 324.342622042 -2198.452292381 -2197.599771406
> > 95.207900000
> > 1228 614.000 0.589119184
> > 323.810100872 -2198.451302027 -2197.599795642
> > 95.125000000
> > 1229 614.500 0.588046292
> > 323.220384100 -2198.450211148 -2197.599804872
> > 95.287500000
> > 1230 615.000 0.586837735
> > 322.556099316 -2198.448987597 -2197.599789891
> > 94.607400000
> > 1231 615.500 0.585740577
> > 321.953045182 -2198.447906730 -2197.599776478
> > 84.758700000
> > 1232 616.000 0.584965082
> > 321.526793185 -2198.447193178 -2197.599783531
> > 84.078000000
> > 1233 616.500 0.584434830
> > 321.235339807 -2198.446749014 -2197.599799740
> > 84.934900000
> > 1234 617.000 0.583845770
> > 320.911562132 -2198.739006343 -2197.892564477
> > 113.249800000
> > 1235 617.500 0.582981114
> > 320.436302633 -2198.738224089 -2197.892561054
> > 124.694600000
> > 1236 618.000 0.581865190
> > 319.822934015 -2198.737172705 -2197.892552522
> > 124.378000000
> > 1237 618.500 0.580530383
> > 319.089255611 -2198.735891778 -2197.892549785
> > 101.654300000
>
> > Finally, my input file:
>
> > &GLOBAL
> > PREFERRED_FFT_LIBRARY FFTSG
> > PROJECT run
> > RUN_TYPE MD # # MD ## GEO_OPT ## ENERGY ----------
> > PRINT_LEVEL LOW
> > &END GLOBAL
> > &FORCE_EVAL
> > STRESS_TENSOR ANALYTICAL
> > &DFT
> > #UKS
> > #CHARGE -1
> > BASIS_SET_FILE_NAME /home/cocktail/frigato/tools/data/cp2k/
> > GTH_BASIS_SETS
> > POTENTIAL_FILE_NAME /home/cocktail/frigato/tools/data/cp2k/
> > POTENTIAL
> > &MGRID
> > CUTOFF 280
> > &END MGRID
> > &QS
> > EPS_DEFAULT 1.0E-12
> > EXTRAPOLATION PS
> > EXTRAPOLATION_ORDER 3
> > &END QS
> > &SCF
> > SCF_GUESS ATOMIC
> > MIXING 0.1
> > MAX_SCF 200
> > EPS_SCF 1.0E-6
> > &OT
> > MINIMIZER DIIS
> > &END OT
> > &END SCF
> > &XC
> > &XC_FUNCTIONAL BLYP
> > &END XC_FUNCTIONAL
> > &XC_GRID
> > XC_DERIV SPLINE2_SMOOTH
> > XC_SMOOTH_RHO NN10
> > &END XC_GRID
> > &END XC
> > &END DFT
> > &SUBSYS
> > &CELL
> > PERIODIC XYZ
> > ABC 15.6404 15.6404 15.6404
> > UNIT ANGSTROM
> > &END CELL
> > &COORD
> > O 5.0690777924 10.7617066505 6.9842780865
> > O 6.6632674135 13.4028906181 14.3663821388
> > O 13.0606048650 16.2596326055 17.2529079177
> > O 9.8535094108 16.9874163628 13.4060698795
> > O 4.3158371962 14.3480431308 4.8332685572
> > O 2.8829801460 13.2512395390 9.7337791051
> > O 14.5126869096 17.8407022987 8.7488705410
> > O 12.8821690135 13.3200872468 2.2368493548
> > O 11.9423768892 1.7954282633 4.8433506817
> > O 7.4949024969 17.0825867083 4.0557252122
> > O 13.3039677456 14.2904933244 13.5401773352
> > O 9.5601769959 6.3256441702 5.5613662781
> > O 8.2084422415 9.1412385973 5.8782616117
> > O 9.9011943423 10.8576262887 7.0377195711
> > O 6.4728649627 9.2831553535 3.3533770389
> > O 6.7343524385 3.4279558791 5.6954782777
> > O 12.7409535892 10.3730460422 13.2254554721
> > O -0.4800696680 14.2457146076 4.2278673414
> > O 5.8136695984 9.4109476867 9.3433537260
> > O 6.3969214937 12.8252363109 5.8271264396
> > O 7.2313702050 11.8135017452 10.1218920349
> > O 4.7139313982 15.0376434536 9.2214597784
> > O 10.6021550149 9.8737149601 3.5131596295
> > O 0.3382092079 7.9727144486 13.2733944065
> > O 8.5253441357 16.6317803956 9.8006760972
> > O 11.2210080416 16.3914510070 9.5897465499
> > O 1.4358882591 16.4966251666 12.9170987698
> > O 6.0652315916 7.7438591033 13.1836350909
> > O 2.5597578973 6.6551598623 12.5742667955
> > O 1.2860404843 5.5263933091 1.1299760644
> > O 1.3933913303 4.5550282657 9.2714768567
> > O 1.5902674866 16.5924459760 6.7015594793
> > O 13.1159458907 10.7688067716 3.2855634813
> > O 13.0889908347 6.3512556663 18.4522685453
> > O 2.0464308337 1.6907217189 2.0129429100
> > O 11.2935943536 4.6255278453 10.6821726498
> > O -1.8432194814 2.6299364315 3.2885038108
> > O 13.3369191444 7.6866000496 13.4138852363
> > O 4.7685382008 3.5119874150 11.7585219019
> > O 5.5929165058 6.8959573979 2.4897720618
> > O 6.1268429404 16.6219893583 11.1171549523
> > O -0.9715543907 15.5849194282 15.3863626873
> > O 9.3051988584 11.7999184526 15.8570649035
> > O 0.9266612927 8.0143063412 4.9677279750
> > O 4.6925948734 7.2689938899 15.4883712206
> > O 7.3470597478 4.6775970296 0.3528372523
> > O 2.1030938217 10.9152916936 2.9411362036
> > O 1.7106479127 3.6288881153 6.7470461198
> > O 13.6642783284 11.0910726270 5.9786873176
> > O 14.1133073800 13.6376064048 6.6508934235
> > O 11.9251912556 7.8114835770 4.9976409797
> > O 6.8934791238
>
> ...
>
> read more »
More information about the CP2K-user
mailing list