[CP2K-user] [CP2K:13033] AIMD for CO

Lucas Lodeiro eluni... at gmail.com
Sun Mar 29 05:11:17 UTC 2020


Hello Wanlu,

I think this a normal behaviour. Temperature is thermostatistical property,
then its significance is "real" when you use an average over time or
particles. When you run a MD with hundreds of particles, you have a
particle average at each frame, but when you use a single particle, the
temperature is not well defined for each frame, but the time average
temperature its better defined. As an example, a single particle harmonic
oscillator, you define an initial and conserved total energy, the particle
changes their potential and kinetic energy along the parabola, at the left
and the right "all" (forgot the zero point energy) the energy is potential
energy, and in the middle "all" is kinetic, the kinetic energy (and the
particle temperature) oscillate from total energy (the highest temperature)
to zero in an harmonic framework, and the time average gives you the
thermostatistic temperature. If you couple a thermostat to regulate the
temperature, you will add and subtract kinetic energy depending the time
local situation, and never achieve the equilibrium.
This is what happens in a single molecule MD (with some differences from
the previous picture, due to the oscillators are not totally harmonic, and
the time integration is not infinitesimal).
If you want to simulate a single molecule at a particular temperature T*, I
recommend to run a NVE MD, with an initial temperature of 2T*, and a
minimum energy geometry (at the same level of theory). In this framework,
from the equipartition principle, half of kinetic energy goes to the
potential energy (the average values) and the average temperature would T*,
or very near (due to the system and the simulation are not ideal or
perfect). This is like as running a harmonic MD with an initial geometry in
the bottom of the parabola, and giving some kinetic energy (where kinetic
energy is equal to total energy at the beginning).

Regards!

El sáb., 28 mar. 2020 a las 20:48, Wan-Lu Li (<wanlu... at gmail.com>)
escribió:

> Dear CP2K users,
>
> Now I'm running the AIMD simulation for CO molecule at 300K under NVT
> ensemble to calculate the time averaged energy. But I found the temperature
> fluctuation is very large (even for 2ps), while the energy seems quite
> converged. I attached part of my CO.ener file here and the end is my input
> file. Is this case normal and can I use the averaged energy from the fifth
> column? Thanks a lot for your help in advance.
>
> Best regards,
> Wanlu
>
> part of the CO.ener file:
> #     Step Nr.          Time[fs]        Kin.[a.u.]          Temp[K]
>      Pot.[a.u.]        Cons Qty[a.u.]        UsedTime[s]
>          0            0.000000         0.001425067       300.000000000
>   -21.617781192       -21.616356125         0.000000000
>          1            1.000000         0.000692729       145.830941811
>   -21.617837920       -21.616358277       194.412350386
>          2            2.000000         0.000839725       176.775929504
>   -21.617886447       -21.616360106        46.210681908
>          3            3.000000         0.001256199       264.450456994
>   -21.617967921       -21.616363102        57.633208051
>          4            4.000000         0.000374173        78.769638799
>   -21.617973412       -21.616363182        46.150063051
>          5            5.000000         0.000559107       117.701236643
>   -21.617953442       -21.616361844        59.398619272
>          6            6.000000         0.002482481       522.602979873
>   -21.617783307       -21.616353176       106.069239420
>          7            7.000000         0.001196440       251.870238012
>   -21.617652842       -21.616346215        58.390943444
>          8            8.000000         0.001901098       400.212437908
>   -21.617651021       -21.616345218        58.502904797
>          9            9.000000         0.000855354       180.066031924
>   -21.617744300       -21.616349141        31.228304488
>         10           10.000000         0.001273480       268.088528685
>   -21.618056502       -21.616361811        66.249216199
>         11           11.000000         0.001148365       241.749723441
>   -21.618101233       -21.616363020        65.788505557
>         12           12.000000         0.001337372       281.538780360
>   -21.618040656       -21.616360497        50.228434081
>         13           13.000000         0.001088173       229.078325293
>   -21.617815635       -21.616351586        65.527550608
>         14           14.000000         0.000638396       134.392771993
>   -21.617717647       -21.616347841        30.803143926
>         15           15.000000         0.001131299       238.157024534
>   -21.617750654       -21.616349105        30.703742482
>         16           16.000000         0.000882749       185.833161270
>   -21.618016211       -21.616359839        58.420952012
>         17           17.000000         0.000704309       148.268604187
>   -21.618111383       -21.616364232        66.953019950
>         18           18.000000         0.000984427       207.238102770
>   -21.618056478       -21.616362640        65.433037204
>         19           19.000000         0.001300278       273.729917837
>   -21.617730686       -21.616349611        66.888907175
>         20           20.000000         0.001251339       263.427334256
>   -21.617350722       -21.616332279        57.671368687
>         21           21.000000         0.000071510        15.053991338
>   -21.617118557       -21.616320874        58.848506088
>         22           22.000000         0.000328659        69.188061889
>   -21.617273411       -21.616328474        50.358033484
>         23           23.000000         0.001961162       412.856931729
>   -21.617839418       -21.616354578        65.594630019
>         24           24.000000         0.003432034       722.499539826
>   -21.618087842       -21.616363528        65.576697189
>         25           25.000000         0.002137357       449.948804690
>   -21.617944687       -21.616356561        50.318810575
>         26           26.000000         0.000282373        59.444052481
>   -21.617674167       -21.616345681        50.183309429
>         27           27.000000         0.001428911       300.809318861
>   -21.617405859       -21.616335405        50.280129558
>         28           28.000000         0.001230288       258.995910868
>   -21.617190458       -21.616327303        60.631839060
>         29           29.000000         0.000778815       163.953411483
>   -21.617239252       -21.616329041        59.914822529
>         30           30.000000         0.001037451       218.400572007
>   -21.617555040       -21.616341263        58.026954871
>         31           31.000000         0.000257021        54.107232870
>   -21.617836485       -21.616352741        63.273706142
>         32           32.000000         0.000815204       171.613774933
>   -21.617983436       -21.616358974        51.766234757
>         33           33.000000         0.002147387       452.060254251
>   -21.618044023       -21.616365491        65.707532154
>         34           34.000000         0.001059117       222.961601928
>   -21.617875727       -21.616358444        42.327060248
>         35           35.000000         0.000556875       117.231265217
>   -21.617833972       -21.616356575        38.473901298
>         36           36.000000         0.002660563       560.092203650
>   -21.617900280       -21.616359371        38.686128197
>         37           37.000000         0.000306512        64.525842654
>   -21.618022387       -21.616364623        58.028456304
>         38           38.000000         0.001094222       230.351784002
>   -21.618059911       -21.616366229        30.907870563
>         39           39.000000         0.002375479       500.077458607
>   -21.618094890       -21.616365658        65.868519638
>         40           40.000000         0.001059975       223.142157446
>   -21.617922951       -21.616358024        66.814346387
>         41           41.000000         0.002150347       452.683436556
>   -21.617727451       -21.616350173        58.576830784
>         42           42.000000         0.000955871       201.226516876
>   -21.617573183       -21.616344211        58.266955604
>         43           43.000000         0.003461060       728.609943461
>   -21.617553106       -21.616343260        81.233679124
>         44           44.000000         0.003689339       776.666432065
>   -21.617708084       -21.616348597        59.117384726
>         45           45.000000         0.002945410       620.057281651
>   -21.617936220       -21.616357146        60.046403246
>         46           46.000000         0.004584184       965.046120081
>   -21.618135902       -21.616363905       119.776386127
>         47           47.000000         0.001211722       255.087403714
>   -21.618101005       -21.616362177        80.983581299
>         48           48.000000         0.003172557       667.875357276
>   -21.618027232       -21.616358757        57.963843688
>         49           49.000000         0.002787604       586.836497994
>   -21.617921379       -21.616353596        58.793182783
>         50           50.000000         0.001320236       277.931380619
>   -21.617895704       -21.616352103        58.655742473
>         51           51.000000         0.001349890       284.173930376
>   -21.617975899       -21.616356500        81.564031711
>         52           52.000000         0.004197290       883.598537868
>   -21.618093592       -21.616362967        93.771222658
>         53           53.000000         0.000804420       169.343569457
>   -21.618143900       -21.616365817        84.571369800
>         54           54.000000         0.001340079       282.108729947
>   -21.618089714       -21.616364198        86.971021005
>         55           55.000000         0.001111101       233.904941648
>   -21.618038691       -21.616362607        65.827716856
>         56           56.000000         0.001635646       344.330302044
>   -21.618001500       -21.616361434        38.540800519
>         57           57.000000         0.000383350        80.701385444
>   -21.617996052       -21.616361311        65.489763892
>         58           58.000000         0.000581642       122.445243901
>   -21.618027478       -21.616362320        57.710738976
>         59           59.000000         0.000637017       134.102594542
>   -21.618072549       -21.616363699        57.981170168
>         60           60.000000         0.000256226        53.939856452
>   -21.618106586       -21.616364617        58.548539240
>         61           61.000000         0.000276851        58.281711503
>   -21.618134608       -21.616365048        58.458087666
>         62           62.000000         0.001327029       279.361436939
>   -21.618142721       -21.616364759        58.208439551
>         63           63.000000         0.000305662        64.346965320
>   -21.618138401       -21.616363258        57.932972059
>         64           64.000000         0.000792654       166.866636174
>   -21.618141563       -21.616362838        46.120169683
>         65           65.000000         0.000968894       203.968166349
>   -21.618163658       -21.616363286        30.770339062
>         66           66.000000         0.001585392       333.751027453
>   -21.618228272       -21.616365914        81.433016635
>         67           67.000000         0.003230830       680.142887167
>   -21.618248138       -21.616366576        57.805929371
>         68           68.000000         0.004550695       957.996018285
>   -21.618173297       -21.616364727        85.084943491
>         69           69.000000         0.001315308       276.894023628
>   -21.618119388       -21.616363118        38.600684694
>         70           70.000000         0.002560177       538.959267435
>   -21.618098609       -21.616362903        40.223963304
>         71           71.000000         0.001819033       382.936419195
>   -21.618079845       -21.616362398        90.782305011
>         72           72.000000         0.000517145       108.867468032
>   -21.618072415       -21.616363269        59.907460252
>         73           73.000000         0.000564062       118.744295312
>   -21.618059739       -21.616363893        59.481724930
>         74           74.000000         0.000521309       109.744026596
>   -21.618038633       -21.616363840        59.628348131
>         75           75.000000         0.002132719       448.972441454
>   -21.618004901       -21.616363063        61.541181826
>         76           76.000000         0.000535457       112.722531882
>   -21.617998466       -21.616362945        25.172890818
>         77           77.000000         0.000791883       166.704365624
>   -21.617996265       -21.616363155        40.223652923
>         78           78.000000         0.001431101       301.270260395
>   -21.618006814       -21.616363694        40.042347613
>         79           79.000000         0.001260725       265.403370341
>   -21.618019664       -21.616364007        39.697757854
>         80           80.000000         0.000110691        23.302251401
>   -21.618026769       -21.616364035        41.031351849
>         81           81.000000         0.001271648       267.702757536
>   -21.618039910       -21.616364022        40.622016474
>         82           82.000000         0.001943523       409.143432763
>   -21.618051808       -21.616363856        40.130044182
>         83           83.000000         0.002089133       439.796797555
>   -21.618072968       -21.616363811        59.343040636
>         84           84.000000         0.002634760       554.660284803
>   -21.618104400       -21.616364023        60.067878875
>         85           85.000000         0.002369065       498.727210926
>   -21.618147035       -21.616364725        85.188466185
>         86           86.000000         0.000799557       168.319960767
>   -21.618169688       -21.616364951        60.087728120
>         87           87.000000         0.001556181       327.601699012
>   -21.618191051       -21.616365285        59.620458533
>         88           88.000000         0.001500868       315.957459040
>   -21.618206771       -21.616365513        59.495860192
>         89           89.000000         0.000521386       109.760310787
>   -21.618210141       -21.616365465        60.615616803
>         90           90.000000         0.000642020       135.155667286
>   -21.618194752       -21.616364400        60.373461886
>         91           91.000000         0.000287061        60.431151866
>   -21.618191018       -21.616364295        24.119875298
>         92           92.000000         0.000548709       115.512238254
>   -21.618190786       -21.616364325        23.668599707
>         93           93.000000         0.001219521       256.729274925
>   -21.618195472       -21.616364513        40.134158431
>         94           94.000000         0.002274151       478.746167486
>   -21.618202538       -21.616364616        41.108107413
>         95           95.000000         0.002352777       495.298222687
>   -21.618207847       -21.616364591        40.475635013
>         96           96.000000         0.000042770         9.003762756
>   -21.618210327       -21.616364411        40.231778402
>         97           97.000000         0.000644745       135.729403123
>   -21.618213635       -21.616364382        23.213505859
>         98           98.000000         0.000375875        79.127780711
>   -21.618227316       -21.616364562        58.810299742
>         99           99.000000         0.002188839       460.786546096
>   -21.618248055       -21.616364869        60.821353728
>        100          100.000000         0.000810643       170.653709364
>   -21.618263919       -21.616365060        59.688553417
> ... ... (the phenomenon looks unchanged even upon 2ps)
>
> Here is the input:
>
> &FORCE_EVAL
>         METHOD QS
>         &PRINT
>                 &FORCES ON
>                 &END
>         &END
>         &DFT
>                 BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL
>                 POTENTIAL_FILE_NAME GTH_POTENTIALS
>                 &MGRID
>                         CUTOFF 400
>                         REL_CUTOFF 60
>                 &END MGRID
>                 &QS
>                         EPS_DEFAULT 1.0E-12
>                         WF_INTERPOLATION ASPC
>                 &END QS
>                 &SCF
>                   SCF_GUESS RESTART
>                   MAX_SCF 500
>
>                   ADDED_MOS 500
>
>                   CHOLESKY INVERSE
>
>                   &SMEAR ON
>
>                   METHOD FERMI_DIRAC
>
>                   ELECTRONIC_TEMPERATURE [K] 300
>
>                   &END SMEAR
>
>                   &DIAGONALIZATION
>
>                   ALGORITHM STANDARD
>
>                   &END DIAGONALIZATION
>
>                   &MIXING
>
>                   METHOD BROYDEN_MIXING
>
>                   ALPHA 0.1
>
>                   BETA 1.5
>
>                   NBROYDEN 8
>
>                   &END MIXING
>                   &PRINT
>                     &RESTART
>                        ADD_LAST NUMERIC
>                         &EACH
>                            QS_SCF 0
>                         &END EACH
>                     &END RESTART
>                   &END PRINT
>                   &END SCF
>                 &XC
>                         &XC_FUNCTIONAL
>                                 &LIBXC
>                                         FUNCTIONAL XC_MGGA_XC_B97M_V
>                                 &END LIBXC
>                         &END XC_FUNCTIONAL
>                         &vdW_POTENTIAL
>                                 DISPERSION_FUNCTIONAL NON_LOCAL
>                                 &NON_LOCAL
>                                         TYPE RVV10
>                                         PARAMETERS 6.0 0.01
>                                         KERNEL_FILE_NAME
> /usr/common/usg/cp2k/6.1/data/rVV10_kernel_table.dat
>                                 &END NON_LOCAL
>                         &END vdW_POTENTIAL
>                         &XC_GRID
>                                 XC_DERIV NN50_SMOOTH
>                         &END XC_GRID
>                  &END XC
>         &END DFT
>         &SUBSYS
>                 &CELL
>                         ABC 15.363 15.363 43.902
>                         ALPHA_BETA_GAMMA 90.0  90.0 120.
>                 &END CELL
>                 &COORD
>                         @INCLUDE 'CO.xyz'
>                 &END COORD
>                 &KIND C
>                         BASIS_SET TZVP-MOLOPT-GTH
>                         POTENTIAL GTH-PBE-q4
>                 &END KIND
>                 &KIND O
>                         BASIS_SET TZVP-MOLOPT-GTH
>                         POTENTIAL GTH-PBE-q6
>                 &END KIND
>          &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>         PROJECT MD_CO
>         RUN_TYPE MD
>         PRINT_LEVEL LOW
> &END GLOBAL
> &MD
>             ENSEMBLE NVT
>             STEPS 100000
>             TIMESTEP 1.0
>             TEMPERATURE 300.0
>          &THERMOSTAT
>           REGION GLOBAL
>           TYPE CSVR
>           &CSVR
>           TIMECON [fs] 1.
>          &END CSVR
>         &END THERMOSTAT
>     &END MD
>     &PRINT
>      &TRAJECTORY
>        &EACH
>         MD 10
>        &END EACH
>      &END TRAJECTORY
>      &RESTART
>      &EACH
>        MD 1
>      &END EACH
>    &END RESTART
>     &END PRINT
> &END MOTION
>
>
>
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