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 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:
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 (look for the timing report or the ENDED AT line in the output).
During MD CP2K has generated various files named WATER-1.restart, WATER-pos-1.xyz, WATER-1.ener. These are a restart file for the MD (open this file in an editor to see that this is actually a regular input file), the trajectory of the MD, and a file summarizing the energies (potential, kinetic and conserved quantity). Before we analyze these files, we'll resubmit a job for the continuation of the MD.
modify the input to enable restarting:
&EXT_RESTART RESTART_FILE_NAME WATER-1.restart &END
If time permits, increase the WALLTIME (and the corresponding time limit in the job script), and run a longer job.
as soon as the job runs significantly longer than the time needed to perform the first few steps, restarting the job doesn't influence the efficiency. Your batch job system might have a convenient way to have chains of jobs, i.e. a simple way to enforce dependencies and automatic continuation. Look at the -w option of
bsub, or –dependency of sbatch
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.1425375431.txt.gz · Last modified: 2020/08/21 10:14 (external edit)