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.
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 waterRUN_TYPE MDBASIS_SET_FILE_NAME HFX_BASISMINIMIZER DIISABC [angstrom] 12.42 12.42 12.42COORD_FILE_NAME water.xyzBASIS_SET DZVP-GTH
Insert the following blocks in their respective sections:
&GLOBAL ! limit the runs to 5min WALLTIME 300 ! reduce the amount of IO IOLEVEL LOW &END GLOBAL
&SCF
! do not store the wfn during MD
&PRINT
&RESTART OFF
&END
&END
&END SCF
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 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exercises/2015_pitt/aimd.1425371742.txt.gz · Last modified: 2020/08/21 10:14 (external edit)