NPT simulations

tomfrigato tomfr... at hotmail.com
Wed Oct 8 10:18:23 UTC 2008


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
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  O         9.8535094108       16.9874163628       13.4060698795
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  O        10.3123060431       17.0719806844       16.2233506657
  O         9.8875399229        6.3122085409       14.2337185454
  O         9.7703233972       10.9409484771       13.2129021307
  O         8.2080751767       12.0413221865        3.9749397633
  O         0.8748987915        9.0706634275        9.4369421231
  O         9.7608349953        8.0112227526        9.9772807880
  O         3.7242155574       14.6974927549       13.2272913945
  O         1.9926888232        3.5074552547       11.9259620015
  O         4.1829009711       10.2077465975       14.9018031455
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  H        13.7054340615       16.1299022439       16.4276662704
  H         9.9707814649       17.0174376849       14.3511516420
  H         9.2311503646       16.2722002004       13.3388368236
  H         3.3580618500       13.9382952946        4.7221758954
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  H         2.5432752625       12.7215723938        8.8988159750
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  H        11.3083480664        2.2769123881        4.2469976051
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  H        12.6374188891       13.8949498702       14.1849239236
  H         9.6493509817        5.6957183360        6.3297349807
  H        10.3813284930        6.8968760972        5.4992585581
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  H         9.7078079719       11.7995015270        6.8996463602
  H         9.6699113214       10.7719220204        8.0170215770
  H         6.9264078678        9.3582919463        4.2227757991
  H         6.2655585130        8.3624267957        3.0191902655
  H         7.1095096065        3.3692319057        6.6223144802
  H         5.7339436739        3.5684667877        5.6853559279
  H        13.0156648028       10.5990966838       12.2682211906
  H        12.8185645266        9.3666913713       13.2180109796
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  H        -1.1990149636       13.9974635866        3.5690953624
  H         6.1497613073       10.3270631601        9.6276668849
  H         6.6852317148        8.9691613929        8.9485884369
  H         6.1228319184       11.9089832593        6.1688539978
  H         5.5758286333       13.1242311441        5.3007181894
  H         7.0189228568       12.6526786347        9.5049072965
  H         6.7288533615       11.8311940343       10.9662575298
  H         4.5283851553       15.5863300529        8.4145889685
  H         3.9498826610       14.2813098955        9.2765298104
  H        11.4347728891       10.4241264607        3.4236968401
  H         9.9806715462       10.3765950805        4.0206174508
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  H        10.2343717962       16.2012252206        9.7273764265
  H        11.5256984259       15.5374278463        9.0522629419
  H         0.7272453859       16.0962957062       12.3821739599
  H         1.7233990496       17.3476618725       12.3872478468
  H         5.5847529905        7.8177207929       14.0185514923
  H         5.4041106549        8.0192436753       12.4600770731
  H         3.0339942563        6.6928825342       11.6907316349
  H         2.7361772801        5.9034098751       13.2436932884
  H         1.1138018452        6.4576976124        1.2654621955
  H         1.0200364710        5.0674245283        1.9882074698
  H         1.5690256328        3.9021134572        8.5163395406
  H         1.8231007347        5.4275848422        9.0228470199
  H         0.9475216888       16.3380966845        7.4204646605
  H         1.0566102267       16.5219788917        5.8400418313
  H        13.2495967204       11.7828936780        2.9486063893
  H        13.2679495253       10.9351507553        4.2893329537
  H        12.2119501222        5.8546881491       18.2735120759
  H        13.2224763754        7.0324420832       17.6741828036
  H         1.5018428218        1.9628673414        1.2340315379
  H         1.4092322920        1.3954284531        2.7431943046
  H        10.6954963499        4.2407768885       11.4513261115
  H        12.2164166058        4.1981847019       10.7516011968
  H        -1.9507549468        1.7691062171        2.7045305590
  H        -2.3059563594        2.3389163169        4.1133649718
  H        12.8681275162        7.3081616439       12.5744379329
  H        14.2750904007        7.8894377601       13.2154028753
  H         5.4434281830        4.1464479944       12.2166349234
  H         5.3303831428        2.6470000389       11.8039133295
  H         6.2501272456        6.3805581614        3.0221801046
  H         4.7708272946        6.8854452276        3.0181226373
  H         5.4125565970       16.0235096902       10.6874983444
  H         6.6665861949       15.9392252626       11.6727591197
  H        -0.2133831181       16.1940034663       15.1990398126
  H        -1.4638486449       15.3157296896       14.4997676937
  H         8.9821935298       11.2202326552       16.5654150541
  H         9.2960348021       11.3492976836       14.9812493444
  H         0.4254768412        8.4012109999        4.1927204178
  H         0.3175896944        7.3164075872        5.4262075158
  H         5.2947738035        7.0484800344       16.2858681483
  H         4.3668675149        8.1887922641       15.5287349531
  H         6.4650532450        4.2435937084        0.3401559493
  H         7.8757228701        4.0571912261        0.8560363095
  H         2.8592709676       10.5663730339        3.4822351475
  H         1.4144224070       10.2355678739        2.8702006073
  H         1.0392232259        4.3556677304        6.5404899316
  H         1.3713747410        2.7469923435        6.9335908310
  H        13.1201161643       10.9507003744        6.8130987722
  H        14.6320656914       10.8453283532        6.2069322399
  H        13.2175783879       13.9017516471        7.0106337023
  H        14.0550994975       12.6343644316        6.5605493651
  H        12.4003031000        7.3509605028        4.2289951655
  H        11.4559756627        8.5793919848        4.5887654864
  H         6.1779908418       14.4686321016        8.9439930626
  H         6.5977799711       13.5354021047        7.6497207751
  H         2.8208168834        7.1559483413        4.7992951288
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        -0.0001256093        0.0007753490        0.0000404585
        -0.0000643365       -0.0000429437        0.0005392108
        -0.0000085557        0.0006851354       -0.0001253411
         0.0008988832       -0.0002842097        0.0021022182
        -0.0006597173        0.0001419525       -0.0004343161
         0.0004890521       -0.0006018432        0.0004103716
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        -0.0001840742       -0.0014064098        0.0009873768
        -0.0007421603       -0.0003873652       -0.0010365434
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         0.0000869418        0.0003549072       -0.0006759036
         0.0001409361       -0.0003918870       -0.0007182293
         0.0014643318        0.0001198285        0.0014833106
        -0.0003455558       -0.0005464685        0.0005691375
        -0.0000951769        0.0005769488       -0.0009694491
        -0.0019850731        0.0000833627        0.0014011041
        -0.0002243268        0.0000071686        0.0001978542
        -0.0000140946        0.0008803605        0.0003467160
         0.0009180453       -0.0000205805        0.0001921299
         0.0002326215        0.0004720817        0.0008967664
         0.0009061050       -0.0008771595       -0.0005406529
         0.0000296826       -0.0003165455        0.0016032775
         0.0005653023       -0.0004270476        0.0016209415
         0.0015923803        0.0018508712        0.0003735631
         0.0011122442       -0.0000906278        0.0007790221
         0.0001349027       -0.0010413688        0.0005172572
        -0.0002512011       -0.0002185301       -0.0009096043
        -0.0004609907       -0.0008471012        0.0005954164
         0.0004049408       -0.0002540121       -0.0003031137
        -0.0013334284        0.0002904444       -0.0000427043
        -0.0000901368        0.0007974882        0.0006323092
         0.0003344009        0.0003963514       -0.0000919052
  &END VELOCITY
   &KIND H
     BASIS_SET DZVP-GTH
     POTENTIAL GTH-BLYP-q1
   &END KIND
   &KIND O
     BASIS_SET DZVP-GTH
     POTENTIAL GTH-BLYP-q6
   &END KIND
 &END SUBSYS
&END FORCE_EVAL
&MOTION
  &MD
   ENSEMBLE NPT_I
   STEPS 4000
   TIMESTEP 0.5
   TEMPERATURE 300.0
   &BAROSTAT
      PRESSURE 1.0132
      TIMECON 100
   &END BAROSTAT
   &THERMOSTAT
       &NOSE
         LENGTH               3
         YOSHIDA               3
         TIMECON   100
         MTS               2
       &END NOSE
   &END THERMOSTAT
   &END MD
    &PRINT
        &TRAJECTORY
            &EACH
                MD 1
            &END EACH
        &END TRAJECTORY
        &VELOCITIES
            &EACH
                MD 1
            &END EACH
        &END VELOCITIES
    &END PRINT
&END MOTION

Hope this is enough to get some help.
thanks
tomaso





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