[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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