ADF on Lisa

Introduction

ADF, the Amsterdam Density Functional program package, is available on the national compute cluster Lisa. To use ADF, your login must be added to the "adf" group. Contact hic@surfsara.nl.

The ADF environment is defined with:

module load adf

ADF example batch job

# ADF example batch job on Lisa.
#
# Water Geometry Optimization with Delocalized Coordinates.
# cf. http://www.scm.com/Doc/Doc2006.01/ADF/Examples/page6.html
#
#PBS -S /bin/bash
#PBS -lnodes=2:ppn=8
#PBS -lwalltime=0:05:00
#PBS -j oe

if [ -z "$PBS_NODEFILE" ]
then
        >&2 echo ERROR: ADF should not be run interactively.
        >&2 echo ERROR: Please use \"qsub $0 \" to submit this script as a batch job.
        exit 1
fi

# Load the appropriate modules for running ADF 2006.
# paffinity is to ensure that processes are bound to cores

module load adf
module load paffinity

# set the stacksize limit to 1 GB

ulimit -s 1048576

# Compute the number of cores from the PBS nodefile
# Set the ADF dependent environment variable NSCM to the number of tasks

export NSCM=`wc -l < $PBS_NODEFILE`

# ADF specific environment:
export SCM_MACHINEFILE=$PBS_NODEFILE
export SCM_TMPDIR="$TMPDIR"
export SCM_USETMPDIR=yes

# for the MPI environment:
export NETWORK=ib
export MPIVERS=hpmpi

# Change the current directory to where the batch job was submitted.
cd $PBS_O_WORKDIR

# Remove previous intermediate and output files.
rm -f TAPE21 t21.O t21.H t21.H2O

# ADF example run.

adf <<eor
Title WATER Geometry Optimization with Delocalized Coordinates

Atoms
 O     0.000000     0.000000     0.000000
 H     0.000000    -0.689440    -0.578509
 H     0.000000     0.689440    -0.578509
End

Basis
 Type TZP
 Core Small
End

Geometry
  Optim Deloc
End

End Input
eor

# Rename the output file.

mv TAPE21 t21.H2O

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