CPMD

From CC Doc
Jump to navigation Jump to search
Other languages:

CPMD is a plane wave/pseudo-potential DFT code for ab initio molecular dynamics simulations.

License limitations

Before you can start using CPMD, you have to register and accept the CPMD license terms and then send us a support request stating that you have in fact registered and accepted the CPMD license terms. Afterwards, we will get in touch with the CPMD admins to confirm your registration, and you will be granted access to the CPMD software.

Module

You can access CPMD by loading a module.

module load intel/2020.1.217 openmpi/4.0.3 cpmd/4.3

Local installation of CPMD

Recently it has been our experience that a response from CPMD admins can unfortunately take weeks or even months. If you are a registered CPMD user, you have access to the CPMD source files and can therefore build the software yourself in your home directory using our software build environment called EasyBuild, using the exact same recipe that we would use for a central installation.

Below are instructions on how to build CPMD 4.3 under your account on the cluster of your choice:

Create a local directory, first, like so

$ mkdir -p ~/.local/easybuild/sources/c/CPMD

Place all the CPMD source tarballs and patches into that directory

$ ls -al ~/.local/easybuild/sources/c/CPMD
cpmd2cube.tar.gz
cpmd2xyz-scripts.tar.gz
cpmd-v4.3.tar.gz
fourier.tar.gz
patch.to.4612
patch.to.4615
patch.to.4616
patch.to.4621
patch.to.4624
patch.to.4627

Then run the EasyBuild command

$ eb CPMD-4.3-iomkl-2020a.eb --rebuild

The --rebuild option forces EasyBuild to ignore CPMD 4.3 installed in a central location and proceed instead with the installation in your home directory.

Once the software is installed, log out and log back in.

Now, when you type module load cpmd, the software installed in your home directory will get picked up.

$ module load cpmd
$ which cpmd.x
~/.local/easybuild/software/2020/avx2/MPI/intel2020/openmpi4/cpmd/4.3/bin/cpmd.x

You can use it now as usual in your submission script.

Example of job script

To run a job, you will need to set an input file and access to the pseudo-potentials available for download from the CPMD website after authentication (only for registered users).

If the input file and the pseudo-potentials are in the same directory, the command to run the program in parallel is:

srun cpmd.x <input files> > <output file> (as in the script 1)

It is also possible to put the pseudo-potentials in another directory and run the code as follows:

srun cpmd.x <input files> <path to pseudo potentials location> > <output file> (as in the script 2)

File : 1-h2-wave.inp

&INFO
isolated hydrogen molecule.
single point calculation.
&END

&CPMD
 OPTIMIZE WAVEFUNCTION
 CONVERGENCE ORBITALS
  1.0d-7
 CENTER MOLECULE ON
 PRINT FORCES ON
&END
  
&SYSTEM
 SYMMETRY
  1
 ANGSTROM
 CELL
  8.00 1.0 1.0  0.0  0.0  0.0
 CUTOFF
  70.0
&END 

&DFT
 FUNCTIONAL LDA
&END  

&ATOMS
*H_MT_LDA.psp
 LMAX=S
  2
 4.371   4.000   4.000
 3.629   4.000   4.000
&END


File : run-cpmd.sh

#!/bin/bash

#SBATCH --account=def-someacct
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=2500M
#SBATCH --time=0-1:00

# Load the modules:

module load intel/2020.1.217 openmpi/4.0.3 cpmd/4.3

echo "Starting run at: `date`"

CPMD_INPUT="1-h2-wave.inp"
CPMD_OUTPUT="1-h2-wave_output.txt"

srun cpmd.x ${CPMD_INPUT} > ${CPMD_OUTPUT}

echo "Program finished with exit code $? at: `date`"


File : run-cpmd.sh

#!/bin/bash

#SBATCH --account=def-someacct
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=2500M
#SBATCH --time=0-1:00

# Load the modules:

module load intel/2020.1.217 openmpi/4.0.3 cpmd/4.3

echo "Starting run at: `date`"

CPMD_INPUT="1-h2-wave.inp"
CPMD_OUTPUT="1-h2-wave_output.txt"
PP_PATH=<path to the location of pseudo-potentials>

srun cpmd.x ${CPMD_INPUT} ${PP_PATH} > ${CPMD_OUTPUT}

echo "Program finished with exit code $? at: `date`"


Related links