Abins mode intensities

A workflow to compute mode-resolved contributions to simulated inelastic neutron-scattering spectra.

Introduction

This workflow calls functions included in Mantid, that form part of the Abins algorithm. As these functions are an "implementation detail" subject to change, the workflow is intended to execute in a Conda environment that pins Mantid to version 6.10.

The steps of the workflow are:

• Call functions within Abins to produce intensities resolved by atom and mode and write these to an sqlite database along with nuclear cross-sections from Mantid
• Perform "normal" Abins runs to produce summed fundamental and multi-phonon spectra, writing the results to .csv files
• Query the sqlite database file to collect mode-resolved sums over atoms, weighted by nuclear cross-sections, writing the results to .csv files
• Plot from .csv files to verify that results are consistent with "normal" Abins results

Limitations

• Currently the workflow will only use a single q-point of the input phonon data.
• Mantid 6.10 is not built for ARM-based Mac; it should be possible to do something clever with a Rosetta/x86 conda environment, but this is not tested

Installation

To use this workflow, you need access to Conda (or Mamba) and Snakemake. For example, IDAaaS users should be able to create a suitable environment from a terminal with

mamba create -n snakemake -c bioconda -c conda-forge snakemake python=3.12

and activate it with

mamba activate snakemake

Running the workflow

Input files are configured in config/config.yaml. This workflow includes sample data for an ethanol molecule computed with GAUSSIAN16; to use your own data and modify other workflow parameters, either edit the config.yaml and run

snakemake -c 1 --sdm conda

or create a modified copy of config.yaml and point to it with

snakemake -c 1 --sdm conda --config /path/to/my/config.yaml