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exercises:2015_pitt:aimd

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Ab initio molecular dynamics

Once a standard GGA simulation has been set up, doing ab initio MD is easy. Here we prepare a simulation of bulk liquid water, a system that has been studied a lot with CP2K (e.g. 10.1063/1.1828433 or 10.1021/jp901990u). The second illustrates convincingly why dispersion corrections are essential.

The first goal is to setup a simulation in production mode by reducing output, and enabling restarting. The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD.

AIMD of water

For the sake of running this exercise quickly, we'll use the DZVP-GTH basis found in the HFX_BASIS file. This basis is smaller than what can be recommended, rather use TZV2P-GTH, TZV2P-MOLOPT-GTH, or cc-TZV2P or better basis sets for production runs.

Topics:

  • MD section (timestep)
  • Thermostat (NVE, NVT, NPT)

Start from the mode1.inp input file of the previous exercise, rename the file to water.inp. You'll also need a new file HFX_BASIS from the cp2k/data directory.

Change keywords to :

  • PROJECT WATER
  • RUN_TYPE MD
  • BASIS_SET_FILE_NAME HFX_BASIS
  • MINIMIZER DIIS
  • ABC [angstrom] 12.42 12.42 12.42
  • COORD_FILE_NAME water.xyz
  • BASIS_SET DZVP-GTH

Insert the following blocks in their respective sections:

Reduce output, and limit job time to 5min.

&GLOBAL
  ! limit the runs to 5min
  WALLTIME 300
  ! reduce the amount of IO
  IOLEVEL  LOW
&END GLOBAL

! do not write the wfn restart file every step, for large systems this is slow

    &SCF
      ! do not store the wfn during MD
      &PRINT
        &RESTART OFF
        &END
      &END
    &END SCF

! tune the output, switch off unneeded keywords ! only sample output of others.

    &PRINT
       ! at the end of the SCF procedure generate cube files of the density
       &E_DENSITY_CUBE OFF
       &END E_DENSITY_CUBE
       ! compute eigenvalues and homo-lumo gap each 10nd MD step
       &MO_CUBES
          ! compute 4 unoccupied orbital energies
          NLUMO 4
          NHOMO 4
          ! but don't write the cube files
          WRITE_CUBE .FALSE.
          ! do this every 10th MD step.
          &EACH
            MD 10
          &END
       &END
    &END

make sure trajectories and restart files are dumped as needed.

&MOTION
  &PRINT
   &TRAJECTORY
     &EACH
       MD 1
     &END EACH
   &END TRAJECTORY
   &VELOCITIES OFF
   &END VELOCITIES
   &FORCES OFF
   &END FORCES
   &RESTART_HISTORY
     &EACH
       MD 500
     &END EACH
   &END RESTART_HISTORY
   &RESTART
     BACKUP_COPIES 3
     &EACH
       MD 1
     &END EACH
   &END RESTART
  &END PRINT
&END MOTION

Now, run the input and check for successful completion of the job.

Required files

water.xyz
192
water with unit cell: ABC [angstrom] 12.42 12.42 12.42
  O         3.8585873763       -4.7533175213        5.5091974759
  H         4.2109950951       -5.5568705259        5.9994585948
  H         3.0947084560       -4.3172663108        5.9135950646
  O        -3.5460761891        1.7456237131        4.2880212708
  H        -3.3572582677        0.8369944362        4.1529456220
  H        -3.6089143450        1.9436976972        5.2698392012
  O         4.5691359319        2.9343274990       -7.0999718127
  H         3.6785962350        3.2291072409       -6.8049831901
  H         4.4953665356        2.7845914189       -8.0458027314
  O        -2.5731801314       -0.1063102257       -3.4147140374
  H        -2.0386687011        0.4155234251       -2.8289645480
  H        -1.8891606976       -0.6148201666       -3.9280631618
  O        -3.7625034284       -7.7105940327        5.6279977389
  H        -4.6343536576       -7.4199803039        5.9874790347
  H        -3.8520633915       -7.6348492192        4.6607806353
  O        -6.7131259426       -0.0759204976        2.3176844292
  H        -6.0415850051       -0.4560400697        3.0079983076
  H        -6.2582643134        0.7343068494        1.9582947358
  O         4.0109535867       -5.5817692668       -0.4126912859
  H         3.3321311866       -5.6166906662        0.3076935926
  H         3.9051538355       -4.7533442556       -0.8369521875
  O        -2.6692626967       -3.0810510613       -1.2259349448
  H        -3.2486322997       -2.4491708867       -1.7386930105
  H        -2.1918958173       -2.5988518360       -0.5763067756
  O         5.4576244064       -3.1688044689        3.1002596795
  H         4.6854987571       -3.2457995297        3.6224179934
  H         5.2579372917       -3.0507495002        2.1311396222
  O         2.0078792352        3.8025888294       -6.6441198936
  H         1.3809036112        3.0702729257       -6.8038689306
  H         1.8366067800        4.0666291804       -5.7099975874
  O         4.0608830110       -3.8929207302       -3.0596772434
  H         3.2332712864       -3.7206669725       -3.6953758544
  H         4.3366899606       -2.9825098616       -2.9848217710
  O         1.9773593054       -1.8442291306        1.0225667179
  H         1.5650644885       -2.4713604568        1.6495937537
  H         1.6194813185       -1.9133123969        0.0656946095
  O         0.7338447631       -5.7432877136       -5.0100685957
  H         1.4795768454       -6.3299226862       -4.8189325814
  H         0.4491149358       -5.7095685669       -5.9473559749
  O        -7.5166459589       -8.6781062088       -3.2371569882
  H        -7.8737663294       -9.6027219294       -3.0814153209
  H        -7.1323941392       -8.5788960418       -2.3467663280
  O         3.0089956358       -1.6206934676        5.1704516391
  H         3.8547864750       -1.8022862145        5.6866350548
  H         3.1700832113       -0.8185381416        4.6102432456
  O        -0.0943492744        1.8634710749       -6.6861347029
  H         0.2389831969        1.0552334471       -6.3170377387
  H        -0.0534604238        1.7370469556       -7.6527831571
  O         1.3803001006       -3.0815472275        3.6598466091
  H         2.0052752091       -2.6793618758        4.3169228939
  H         1.0973942250       -3.9666380514        3.9813401483
  O        -2.3279129364        2.8060791527        2.2347417439
  H        -1.6230445751        2.1315230876        2.1866163236
  H        -2.7609234795        2.5819568350        3.0889511952
  O         0.8745131234       -0.6611187482       -5.6004046460
  H         1.7204015713       -0.8189656405       -6.1098612966
  H         1.1964117837       -0.2405057963       -4.7549061774
  O        -1.1866462102       -0.7164030048        0.2437849238
  H        -1.1340006348        0.2325710411       -0.0726156939
  H        -0.9335438317       -0.7854778370        1.2011335414
  O        -3.8861935106       -9.0129285534       -3.1318571683
  H        -4.4983492231       -8.2801255892       -3.2160220896
  H        -2.9183857578       -8.7301395642       -3.1224505015
  O         4.9784414381        4.5574106629        2.1605978288
  H         4.5742506248        4.0690251974        1.4375040342
  H         4.2106782789        4.9079438424        2.6736093641
  O         4.2074812608        1.0294752439       -3.2134938111
  H         4.6250866171        0.8524308220       -4.0648666086
  H         4.4221519308        0.1920392568       -2.7364360799
  O        -5.2106345443       -6.3463699492       -2.6806456410
  H        -5.3801630197       -6.0861826108       -1.7737611737
  H        -5.9985546753       -6.0894306119       -3.1521879087
  O         4.8272006144       -2.1493089974        0.6957555837
  H         5.1698114049       -1.3843105780        1.1680731517
  H         3.8731403616       -2.0152767607        0.7901517878
  O         2.1084974235        0.9406557281        1.6964699575
  H         2.7635704789        1.5106519967        1.2582480434
  H         2.3138417141        0.0791504768        1.2943222699
  O        -5.7579045611       -5.0935991816       -0.3613728277
  H        -6.6922016300       -5.4438912590       -0.2434456391
  H        -5.9339541154       -4.1852263482       -0.6893230982
  O        -4.8501183696        4.6347512586        2.6323657871
  H        -5.8186923573        4.7291496971        2.3648078237
  H        -4.7686962808        3.6685062675        2.2489112658
  O         5.5123889390        0.8523825517       -5.5927914459
  H         6.4009274201        1.1961666201       -5.3454982775
  H         5.0326268549        1.4571097750       -6.2820870000
  O         0.7365184732       -1.9176950430       -1.2724577473
  H         0.4366627686       -2.6685959517       -1.8452499204
  H        -0.0280723827       -1.6346960324       -0.7323636982
  O         3.9005939808        2.6221972296        0.0824981180
  H         4.6603628952        2.4136405159       -0.4885023274
  H         3.3619307241        3.2465911837       -0.4599512808
  O        -1.0991624885       -1.3693412589        2.9498880034
  H        -0.3354058556       -2.0369012425        3.1075024163
  H        -1.8473458549       -1.9916364646        3.2032143743
  O         2.0718451094       -5.6501678174        1.3629079156
  H         1.2043618452       -6.1369822674        1.2560686630
  H         2.4507495844       -5.8859092245        2.2558212721
  O        -0.6280310316       -3.8273493362       -2.8460859716
  H        -1.5583639221       -3.7769636412       -2.5811140145
  H        -0.5112292363       -4.5879523025       -3.3982225959
  O        -5.2918433010        2.0621670074        1.4353011132
  H        -4.4549447831        1.8776050679        1.9014549175
  H        -5.1335936869        1.9198214761        0.4197228743
  O         1.9599719653       -3.4245632717       -5.2673604360
  H         1.3225562775       -4.2123092010       -5.0388832852
  H         1.2999292168       -2.7711468268       -5.4986783863
  O        -1.1933205846        3.9368513830       -3.3737465077
  H        -1.2003012694        3.9803649971       -4.3582935942
  H        -0.7402505311        4.6500956055       -2.9405594580
  O        -5.4243979802       -5.0029807582        4.2784625506
  H        -6.1164034705       -4.5127003053        3.7817315683
  H        -4.7403199519       -5.3498607764        3.6920944114
  O         2.9732984993        5.7937546317        3.6041830736
  H         3.4176710045        6.4726708296        4.1695014822
  H         2.4485201643        5.2041088060        4.2250869218
  O        -4.0511295134        1.5445925671       -5.0626498585
  H        -3.5387103609        0.7974835831       -4.6210546124
  H        -4.0333821170        2.3518494025       -4.4301366268
  O         3.4847726839        0.5997692637        4.0091486817
  H         2.7896502362        0.5375110591        3.2686671028
  H         4.3189983631        0.4153324309        3.4395276451
  O        -4.6207476869       -1.0117618538        4.0048952776
  H        -5.3477593066       -1.2443059233        4.6253237945
  H        -4.2163881176       -1.8844792105        3.8428058821
  O        -0.2165387154        1.2751467697        3.1167167744
  H         0.6371782887        1.4136801810        2.7286969429
  H        -0.3894124526        0.3225841245        3.0508790291
  O        -1.9915351632        5.0697083632        0.6000194332
  H        -2.3376502958        4.2340876605        1.0013898546
  H        -2.6520248188        5.7471163392        0.8506616742
  O        -1.3075474036       -1.8956122645       -4.9542920356
  H        -0.8701251561       -2.4028189929       -4.2563741889
  H        -0.5949693850       -1.3532124979       -5.4532434800
  O        -5.1373452268        1.8062068789       -1.2867681226
  H        -4.6981592560        2.4597481938       -1.8505668997
  H        -5.4245526684        1.1256927260       -1.8633945543
  O        -7.3836561358       -1.2119873462       -1.9506599575
  H        -6.4212881329       -1.0371432188       -2.1463799566
  H        -7.4808782211       -1.5310477918       -1.0339482458
  O        -0.4639445925        1.4048471789       -1.7228637494
  H        -0.7867348868        2.1866499220       -2.1962304023
  H         0.2743927320        0.9864157199       -2.2215845685
  O        -0.0298107043       -6.5210921839       -1.0933643185
  H         0.0021424143       -5.5311453888       -1.1226646288
  H        -0.8031132631       -6.7435142146       -0.4648562320
  O         5.7090935537       -1.6927086580        6.0185486672
  H         6.0227718591       -2.5102376528        6.4195407580
  H         5.6793497711       -0.9012395738        6.6521961143
  O        -2.5962982991       -5.7683972037       -4.2195771395
  H        -2.6049028140       -6.7077669400       -4.4728336739
  H        -3.4354537463       -5.5645841736       -3.8483514813
  O        -4.9449687319       -1.4086720170       -3.2473392351
  H        -4.8913021653       -2.2217322989       -3.7674224672
  H        -3.9689548003       -1.0964857745       -3.2341980948
  O         2.2983754229       -8.0809494482       -1.2132412662
  H         1.3003681505       -8.0636283692       -1.1143923954
  H         2.5161940132       -7.1053673603       -1.1768519202
  O         6.7754357543       -3.8965331032       -5.3359261145
  H         7.5499418595       -4.1003001805       -5.8213622687
  H         6.0430158524       -4.4328146397       -5.6479610986
  O        -0.3424844631        4.9658112476        2.9508285728
  H        -0.6418240309        4.1672557959        3.4716379980
  H        -0.6759740908        4.8699377537        2.0551376194
  O        -2.8056288807       -4.0048234272        6.2239057927
  H        -2.3850599469       -4.6322887909        6.8455564859
  H        -2.3797353004       -3.1498233269        6.4330163166
  O        -2.7925113864       -3.4732237158        3.4612331596
  H        -3.1129543056       -3.8620641144        4.2746132111
  H        -3.2856093678       -4.0271447136        2.8274407488
  O         2.4867711476        4.6803618907       -3.9511208166
  H         3.3971373036        4.5081635205       -3.6298163906
  H         1.9790712168        4.6240682409       -3.1152437525
  O         1.6590765104        0.0523137912       -3.1069189687
  H         1.5113564742       -0.5996769003       -2.3563690233
  H         2.5068721250        0.5264194699       -3.0661523880
  O        -1.2023048654       -8.1603479212       -6.3670700282
  H        -0.9055157967       -9.0690551157       -6.5705273597
  H        -2.1798096138       -8.0740016376       -6.5464905196
  O        -0.4761071273        8.3851620636        0.5987466087
  H         0.3632441731        8.3096547993        1.1058350782
  H        -1.2852386123        8.0753854402        1.0587255936
  O         5.9065449362       -6.7989771803       -6.6004398209
  H         5.4130154976       -7.6233171741       -6.9137876216
  H         6.2177506878       -6.2344541440       -7.3198720135
  O        -0.3594330297       -5.2622440761        4.6704297767
  H        -0.4156127476       -6.0988819305        4.1367481919
  H        -1.2931127588       -5.1547968831        4.9497584977
  O        -3.8273131578       -5.5279235466        1.7633664403
  H        -4.1388543582       -6.3621998573        2.1513804320
  H        -4.3955669691       -5.3216936959        1.0405948547
exercises/2015_pitt/aimd.1425373010.txt.gz · Last modified: 2020/08/21 10:14 (external edit)