lammps_tools

A collection of tools for interacting with LAMMPS

install-lammps.sh

A script for installing LAMMPS.

Usage:

sh install-lammps.sh

read_lammps_log.py

A script for plotting variables from the thermo output of LAMMPS.

Usage:

python read_lammps_log.py log.lammps

Notes

• The script makes certain assumptions on what variables to plot.

read_lammps_data.py

A script for reading topology information from LAMMPS data files.

Usage:

python read_lammps_data.py system.data

Notes

• This script will attempt to write a GROMACS .gro file with the system coordinates.
• It will probably be more useful to modify the script to suit your needs, e.g. if you want to investigate bonds, angles etc.

read_lammpstrj.py

A script for reading frames from a LAMMPS trajectory file.

Usage:

python read_lammpstrj.py dump.lammpstrj

average_lammps_profile.py

A script for averaging profiles created by LAMMPS.

Usage:

python average_lammps_profile.py -f temp1.txt -p

Notes

• The profiles are assumed to be written by LAMMPS using a command like:

  fix out_temp1 all ave/chunk 5 1000 5000 cc1 temp file temp1.txt
  

average_lammps_rdf.py

A script for averaging RDFs created by LAMMPS.

Usage:

python average_lammps_profile.py -f rdf-X-Y.txt -p

Notes

• The RDFs are assumed to be written by LAMMPS using a command like:

  fix fix_rdf_X_Y all ave/time 100 1 100 c_rdf_X_Y[*] file rdf-X-Y.txt mode vector
  

skip_lammpstrj.py

A script for reducing the size of .lammpstrj files. It will write a new file with every N'th frame.

Usage:

python skip_lammpstrj.py infile.lammpstrj 100

This will produce a new file infile-skip-100.lammpstrj with every 100th frame from infile.lammpstrj.