Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

Polyrate

Polyrate (with Gaussrate)

Version:

17 (20170808)

Dependencies:

Modules for Open MPI 2.1.1, GCC 6.2.0 and Gaussian 09 D.01 loaded.

URL for Polyrate:

https://comp.chem.umn.edu/polyrate/

URL for Gaussrate:

https://t1.chem.umn.edu/gaussrate/

Documentation for Polyrate:

https://comp.chem.umn.edu/polyrate/170808_Polyrate_Manual_v17.pdf

Documentation for Gaussrate:

https://comp.chem.umn.edu/gaussrate/170808_Gaussrate_17B_Manual.pdf

Quickstart Guide for Gaussrate:

https://comp.chem.umn.edu/gaussrate/GAUSSRATEQuickstartGuide.pdf

Polyrate 17: Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics. Gaussrate 17-B provides an interface between two other programs: Polyrate version 2017 and Gaussian 16 / 09. Note: Polyrate 17 and Gaussrate 17-B were compiled on ShARC to use the Reaction Path Variational Transition State Theory (RP-VTST) executables.

Usage

Polyrate 17 and Gaussrate 17-B can be activated using the module file:

module load apps/polyrate/17_20170808/gaussrate17-B/gcc-6.2-openmpi-2.1.1

The Polyrate/Gaussrate executable script is shuttle. All the Polyrate 17 and Gaussrate 17-B executables are in /usr/local/packages/apps/polyrate/17_20170808/gaussrate17-B/gcc-6.2-openmpi-2.1.1/polyrate17/exe.

Batch jobs

Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, which is submitted to the queue by typing qsub my_job.sh.

#!/bin/bash
#$ -cwd
#$ -l h_rt=00:30:00
#$ -l rmem=2G
#$ -pe smp 4

module load apps/polyrate/17_20170808/gaussrate17-B/gcc-6.2-openmpi-2.1.1

export GAUSS_SCRDIR=$TMPDIR
export scratchdir=$TMPDIR

./ch5tr1.jc

The script requests 4 cores using the shared memory parallel environment smp with a runtime of 30 mins and 2 GB of real memory per core. The Polyrate job control script is ch5tr1.jc and is for the test run example ch5tr1. Note: The Polyrate environment variables polydir and gausspath are set in the module file.

The ch5tr1 test run, an example calculation using Gaussrate, is described in the documentation and the input files and job control script can be found at /usr/local/packages/apps/polyrate/17_20170808/gaussrate17-B/gcc-6.2-openmpi-2.1.1/polyrate17/gaussrate17-B/testrun/ch5.

Installation notes

Polyrate 17 and Gaussrate 17-B were installed using the install_polyrate17.sh script; the module file is /usr/local/modulefiles/apps/polyrate/17_20170808/gaussrate17-B/gcc-6.2-openmpi-2.1.1. Polyrate 17 and Gaussrate 17-B were compiled on ShARC to use the Reaction Path Variational Transition State Theory (RP-VTST) executables.

The Polyrate 17 and Gaussrate 17-B installation was tested by running a batch job using the my_job.sh batch script, above, for the ch5tr1 test run.