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 »


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