NWChem

• General Information
• Usage on Vilje
  • Sample NWChem Job Script
• Test case: Water Molecule geometry optimization
• Further Information

General Information

Home page	Version	Module dependencies
		Compiler	MPT
www.nwchem-sw.org	6.5	intelcomp/15.0.1	mpt/2.10
	6.6	intelcomp/16.0.1	mpt/2.13

NWChem is an ab initio computational chemistry software package that provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of force fields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

Usage on Vilje

Load one of the nwchem, and the corresponding intel compiler and mpt modules to use NWChem on Vilje, e.g.:

$ module load intelcomp/16.0.1 mpt/2.13 nwchem/6.6

Important!   Since compute nodes on Vilje are diskless, to reduce the file I/O, NWChem must be run in 'semidirect' (or 'direct') mode.

The 'semidirect' directive is used to define the memory size and disk space per process for storing integrals. When running 16 processes per compute node on Vilje, specify in the input file, e.g. for SCF calculations:

scf
  semidirect memsize 100000000 filesize 0
  ...etc.
end

For fully direct calculation with recomputation of the integrals at each iteration, specify:

scf
  direct
  ...etc.
end

Sample NWChem Job Script

#!/bin/bash
###################################################
#
#  NWChem job
#
###################################################
#
#PBS -N test
#PBS -A nn1234k
#PBS -l select=2:ncpus=32:mpiprocs=16
#PBS -l walltime=24:00:00
#
 
module load intelcomp/16.0.1
module load mpt/2.13
module load nwchem/6.6
 
case=$PBS_JOBNAME
 
cd $PBS_O_WORKDIR
 
# Create (if necessary) the working directory
w=/work/$PBS_O_LOGNAME/nwchem/$case
if [ ! -d $w ]; then mkdir -p $w/tmp; fi

export SCRATCH_DIR=$w/tmp

# Copy inputfiles and move to working directory
cp $case.nw $w
cd $w

export MPI_BUFS_PER_PROC=512

mpiexec_mpt nwchem $case.nw

Test case: Water Molecule geometry optimization

This example shows an SCF geometry optimization of a positively charged water molecule using second-order Møller-Plesset perturbation theory (MP2), followed by a computation of frequencies at the optimized geometry.

See the NWChem Getting Started web page for a description of the input file.

1.Unpack the test case files

$ tar xf /sw/sdev/Modules/nwchem/nwchem-6.6/share/water.tar

2. Replace nn1234k with your project account number in the nwchem.pbs job script, and submit the job to the queuing system

$ qsub nwchem.pbs

3. When the job has finished, check the output file and compare with the output water.out included in test case.

Further Information

• NWChem User Documentation