snakemake-wrappers

This repository contains snakemake support scripts for using jams and common jams workflows. For configuring snakemake to run on the Leeds HPC clusters see: snakemake-gridengine.

To use this repository run snakemake with

snakemake --wrapper-prefix="https://github.com/stonerlab/snakemake-wrappers/raw/"

JAMS Snakemake wrapper

The wrapper allows easy execution of JAMS with some common parameters being configured as Snakemake params. And example input would be:

WRAPPER_PREFIX='https://github.com/stonerlab/snakemake-wrappers/raw'

rule test:
    input:
        'test.cfg'
    output: 
        'sim/{T}K/{prefix}_final.h5'
    log:
        'sim/{T}K/{prefix}.log'
    params:
        exe='jams-v2.3.1+3.97ac53b',
        name='{prefix}',
        temperature='{T}',
        alpha='0.1',
        settings='hamiltonians = ({ radius_cutoff = {r_cut}; });'
    wrapper:
        f"{WRAPPER_PREFIX}/0.1.5/phys/sim/jams"

Here we have used a variable WRAPPER_PREFIX instead of the command line argument --wrapper-prefix to make the work flow more portable.

The JAMS executable can be specified either as a path in input or a path or executable name in params.exe. If only the name is given then the wrapper will search PATH for the name. If neither input or params.exe work then it searches PATH for 'jams' anyway.

All input files ending .cfg are treated as JAMS config files. The first input file ending .h5 is treated as the initial spin input for the simulation.

The JAMS --output option will automatically be set by the path used for output.

The terminal output of JAMS is written to the log. If no log is given then the output will appear on the terminal where Snakemake is running.

Valid params are:

• exe: JAMS executable
• name: name to use for simulation (and basename of output files)
• size: a comma separated list inside a string of dimensions for the lattice (e.g. size="32,32,32")
• temperature: JAMS option physics.temperature
• alpha: a comma separated list inside a string of alpha for each material (e.g. alpha="0.1,0.1")
• cmc_constraint_theta: Constrained Monte Carlo theta constraint
• cmc_constraint_phi: Constrained Monte Carlo phi constraint
• settings: A string with any additional settings for JAMS.

NOTE: String settings in JAMS config files must use double quotes (") and so the string given to settings in the params must use single quotes for the python definition of the string so that you can use double quotes inside of the string.