LAMMPS workflows

lammpsMD

The lammpsMD process runs a LAMMPS simulation is specified with an input file, and the set of auxiliary files. The process takes the params.lmp_cmd to specify the lammps binary, which can be specified during runtime or in nextflow.config.

Channels

Channel	Type	i/o[idx]	Note
name	val	`in[0]`	an id to identify the process
input	file	`in[1]`	LAMMPS input file
aux	file	`in[2]`	auxiliary files (force field, data, etc.)
name	val	`out[0]`	same as output
traj	file	`out[1]`	trajectory in `.dump` format
log	file	`out[2]`	LAMMPS log
restart	file	`out[3]`	LAMMPS restart files in `.restart`

Source code

nextflow.enable.dsl=2

params.lmp_cmd = 'lmp'
params.publish = 'lmp'

process lammpsMD {
  tag "$name"
  publishDir "$params.publish/$name"
  label 'lammps'

  input:
    tuple val(name), path(input), path(aux)

  output:
    tuple val(name), path('*.dump'), emit: traj
    tuple val(name), path('log.lammps'), emit: logs

  script:
    """
    #!/bin/bash
    $params.lmp_cmd -i $input
    """
}