AiiDA ChemShell

An AiiDA plugin for the ChemShell multiscale computational chemistry software package.

Installation

This plugin is available through PyPI and should be installed using pip python package manager.

pip install aiida-chemshell 

Requirements

To use this plugin a configured AiiDA profile and computer configuration are required, see the AiiDa documentation for instructions on how to install and configure AiiDA.

Setup

To configure the ChemShell plugin an AiiDA code instance needs to be configured for the ChemShell executable. The following is an example of a basic YAML configuration file:

label: chemsh
description: ChemShell 
computer: localhost 
filepath_executable: /absolute/path/to/chemsh
default_calc_job_plugin: chemshell
use_double_quotes: false 
with_mpi: false 
prepend_text: '' 
append_text: '' 

Write this to a file named chemshell.yml ensuring the value for computer matches the label of your computer configured in the previous step. The code can then be configured by running:

verdi code create core.code.installed --config chemshell.yml -n 

If successful this will have created a code with the label chemsh which can then be used to run ChemShell jobs within the AiiDA workflow.

ChemShell with MPI

It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses the chemsh or chemsh.x executable. If you have a parallel (MPI enabled) build of ChemShell but are using the chemsh wrapper executable please set with_mpi: false as the underlying plugin will handle how to call the mpi runtime. If you are calling the chemsh.x executable directly then with_mpi: true is required to run parallel jobs.

Examples

QM Based Single Point Energy

The following is a python script that will run a Quantum Mechanics based single point energy calculation using the NWChem ChemShell interface. The associated structure file can be found in the tests/data/ folder.

from aiida.engine import run
from aiida.orm import load_code, SinglefileData, Dict
from aiida import load_profile

# This is not required if running in a verdi shell environment
load_profile("user_profile")

builder = load_code("chemsh").get_builder()
builder.structure = SinglefileData(file="/absolute/path/to/water.cjson")
builder.qm_parameters = Dict({"theory": "NWChem", "method": "HF", "basis": "3-21G"})
builder.calculation_parameters = Dict({"gradients": False, "hessian": False})

results, node = run.get_node(builder)

print("Final Energy = ", results.get("energy"))

This can either be run as a script or as directly within a verdi shell python environment.

QM/MM Based Geometry Optimisation

The following is a python script that will run a combined QM/MM based geometry optimisation using the NWChem and DL_POLY ChemShell interfaces. The associated structure and force field files can be found in the tests/data/ folder.

from aiida.engine import run
from aiida.orm import load_code, SinglefileData, Dict
from aiida import load_profile

# This is not required if running in a verdi shell environment
load_profile("user_profile")

builder = load_code("chemsh").get_builder()
builder.structure = SinglefileData(file="/absolute/path/to/h2o_dimer.cjson")
builder.qm_parameters = Dict({"theory": "NWChem", "method": "DFT", "basis": "6-31G"})
builder.mm_parameters = Dict({"theory": "DL_POLY"})
builder.force_field_file = SinglefileData(file="/absolute/path/to/h2o_dimer.ff")
builder.optimisation_parameters = Dict({"algorithm": "lbfgs", "maxcyle": 100})

results, node = run.get_node(builder)

print("Final Energy = ", result.get("energy"))

This can either be run as a script or as directly within a verdi shell python environment.