Skip to content

ChemShell

ChemShell is a script-based chemistry code focusing on hybrid QM/MM calculations with support for standard quantum chemical or force field calculations. There are two versions: an older Tcl-based version Tcl-ChemShell and a more recent python-based version Py-ChemShell.

The advice from https://www.chemshell.org/licence on the difference is:

We regard Py-ChemShell 21.0 as suitable for production calculations on materials systems, and would encourage materials modellers to consider switching from Tcl-ChemShell to Py-ChemShell if they haven't already done so.

Py-ChemShell 21.0 is the first beta release to include support for calculations on biomolecular systems, including a guided protein solvation workflow and automated import of CHARMM and AMBER forcefields for biomolecular QM/MM calculations. We encourage experienced ChemShell users to try the new functionality and send us feedback on your experience. For new users, we would currently still recommend using Tcl-ChemShell for biomolecular calculations until the next beta release of Py-ChemShell, which is anticipated for summer 2022.

Using Py-ChemShell on ARCHER2

The python-based version of ChemShell is open-source and is freely available to all users on ARCHER2. The version of Py-ChemShell pre-installed on ARCHER2 is compiled with NWChem and GULP as libraries.

Warning

Py-ChemShell on ARCHER2 is compiled with GULP 6.0. This is a licenced software that is free to use for academics. If you are not an academic user (or if you are using Py-ChemShell for non-academic work), please ensure that you have the correct GULP licence before using GULP functionalities in py-ChemShell or make sure that you are not using any of the GULP functionalities in your code (i.e., do not set theory=GULP in your calculations).

Running parallel Py-ChemShell jobs

Unlike most other ARCHER2 software packages, the Py-ChemShell module is built in such a way as to enable users to create and submit jobs to the compute nodes by running a chemsh script from the login node rather than by creating and submitting a Slurm submission script. Below is an example command for submitting a pure MPI Py-ChemShell job running on 8 nodes (128x8 cores) with the chemsh command:

    # Run this from the login node
    module load py-chemshell

    # Replace [budget code] below with your project code (e.g. t01)
    chemsh --submit               \
           --jobname pychmsh      \
           --account [budget code] \
           --partition standard   \
           --qos standard         \
           --walltime 0:10:0      \
           --nnodes 8             \
           --nprocs 1024          \ 
           py-chemshell-job.py

Using Tcl-ChemShell on ARCHER2

The older version of Tcl-based ChemShell requires a license. Users with a valid license should request access via the ARCHER2 SAFE.

Running parallel Tcl-ChemShell jobs

The following script will run a pure MPI Tcl-based ChemShell job using 8 nodes (128x8 cores).

    #!/bin/bash

    #SBATCH --job-name=lammps_test
    #SBATCH --nodes=8
    #SBATCH --ntasks-per-node=128
    #SBATCH --cpus-per-task=1
    #SBATCH --time=00:20:00

    # Replace [budget code] below with your project code (e.g. t01)
    #SBATCH --account=[budget code] 
    #SBATCH --partition=standard
    #SBATCH --qos=standard

    module load tcl-chemshell/3.7.1

    srun --distribution=block:block --hint=nomultithread chemsh.x input.chm