Updated 2022-02-14

Run CP2K on the Cluster

Overview

  • CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
  • This guide will cover how to run CP2K with a batch script on the cluster.
  • Here is a link to CP2K's homepage that can provide more information.

Tips

  • Here is a link to the manual provided by CP2K to give more information on different functions.
  • You can find more exercises and examples other than the one covered in this guide here.

Walkthrough: Run CP2K on the Cluster

  • In this example, we will illustrate how to relax the structure of a system (without changing the cell dimensions) using the relaxation of a water molecule as an example.
  • This example is directly taken from an exercise posted on CP2K's website. You can visit the link for more information about what each section in the input file means.
  • Some of the files needed for this example are stored inside the cp2k module. You can copy those files to your current directory with the following command after first loading the cp2k module:
module load cp2k
cp $(dirname $(which cp2k.popt))/../share/data/{BASIS_SET,POTENTIAL} .
  • Create a basic H2O.inp input file with this content:
&GLOBAL
  PROJECT H2O
  RUN_TYPE GEO_OPT
  PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
  METHOD QS
  &SUBSYS
    &CELL
      ABC 12.4138 12.4138 12.4138
    &END CELL
    &COORD
      O      12.235322       1.376642      10.869880
      H      12.415139       2.233125      11.257611
      H      11.922476       1.573799       9.986994
    &END COORD
    &KIND H
      BASIS_SET DZVP-GTH-PADE
      POTENTIAL GTH-PADE-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-GTH-PADE
      POTENTIAL GTH-PADE-q6
    &END KIND
  &END SUBSYS
  &DFT
    BASIS_SET_FILE_NAME ./BASIS_SET
    POTENTIAL_FILE_NAME ./POTENTIAL
    &QS
      EPS_DEFAULT 1.0E-7
    &END QS
    &MGRID
      CUTOFF 200
      NGRIDS 4
      REL_CUTOFF 30
    &END MGRID
    &SCF
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-05
      MAX_SCF 200
      &DIAGONALIZATION T
        ALGORITHM STANDARD
      &END DIAGONALIZATION
      &MIXING T
        ALPHA 0.5
        METHOD PULAY_MIXING
        NPULAY 5
      &END MIXING
      &PRINT
        &RESTART OFF
        &END RESTART
      &END PRINT
    &END SCF
    &XC
      &XC_FUNCTIONAL PADE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
&END FORCE_EVAL
&MOTION
  &GEO_OPT
    TYPE MINIMIZATION
    MAX_DR    1.0E-03
    MAX_FORCE 1.0E-03
    RMS_DR    1.0E-03
    RMS_FORCE 1.0E-03
    MAX_ITER 200
    OPTIMIZER CG
    &CG
      MAX_STEEP_STEPS  0
      RESTART_LIMIT 9.0E-01
    &END CG
  &END GEO_OPT
  &CONSTRAINT
    &FIXED_ATOMS
      COMPONENTS_TO_FIX XYZ
      LIST 1
    &END FIXED_ATOMS
  &END CONSTRAINT
&END MOTION
  • The PBS Script can be found below.
  • You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part 1: The PBS Script

#!/bin/bash
#PBS -N cp2kTest
#PBS -A [Account] 
#PBS -l nodes=1:ppn=24
#PBS -l walltime=15:00
#PBS -q hive-all
#PBS -j oe
#PBS -o cp2kTest.out

cd $PBS_O_WORKDIR

module load cp2k/6.1-mva2

mpirun cp2k.popt -o H2O.out H2O.inp
  • The #PBS directives request 15 minutes of walltime with 1 node and 24 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.
  • Output Files will also show up in this directory as well.
  • module load cp2k/6.1-mva2 loads the 6.1 version of CP2K. To see what CP2K versions are available, run module spider cp2k, and load the one you want. The other modules are dependencies for the cp2k module and must be loaded prior to loading the cp2k module.
  • cp2k.popt -o H2O.out H2O.inp & passes the H2O.inp input file to the cp2k.popt function to run the program.

Part 2: Submit Job and Check Status

  • Make sure you're in the dir that contains the PBS Script as well as the CP2K program
  • Submit as normal, with qsub <pbs script name>. In this case qsub cp2kTest.pbs
  • Check job status with qstat -t 22182721, replacing the number with the job id returned after running qsub.
  • You can delete the job with qdel 22182721, again replacing the number with the jobid returned after running qsub.

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see the following files generated from the job:

    • H2O.out
    • H2O-pos-1.xyz
    • H2O-1.restart
    • H2O-1.restart.bak-1
    • H2O-1.restart.bak-2
    • H2O-1.restart.bak-3

  • Use cat or open the file in a text editor to take a look.

  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran CP2K on the cluster.