starpolymers

starpolymers is a Python Library used for generating LAMMPS input files and analysing LAMMPS output files, in dump formats and other formats. Additionally, there are scripts used for interacting with Colvars input/output files.

The package is used to generate molecules and LAMMPS configuration files that follow the atom_style full convention. User-defined molecules can be added if the package is installed manually

Features

• Create LAMMPS system containing 'molecules'
• Molecules include salt, linear polyelectrolytes, star polymers
• Use a template LAMMPS input file and change the variables
• Generate a Colvars input file for free energy calculations
• Import LAMMPS dump files

Upcoming

• Analysis on dump files
• Plotting tools
• Custom molecules without manual installation

Installation

pip

Star Polymers is available on PyPi and can be installed using:

pip install starpolymers

conda

From v1.1.3 it will be possible to install starpolymers using anaconda, via conda-forge:

conda install starpolymers -c conda-forge

manual installation

To install the package manually run the following commands:

git clone https://github.com/debeshmandal/starpolymers.git
cd starpolymers
pip install . -vv

Alternatively, since the package is written entirely in Python, one can clone the package and append the path to the $PYTHONPATH environment variable.

Usage

A variety of examples can be found in the ./test folder which contains tests for generating files. Notably the config and input_files subfolders contain examples of generating files needed to create LAMMPS systems and run simulations.

Example

import starpolymers
lammps_system = starpolymers.generators.System(50)
molecules = starpolymers.generators.MoleculeFactory([
        {
            'molecule' : 'salt', 
            'concentration' : 100, 
            'anion' : 1, 
            'cation' : 1
        }
    ])
lammps_system.add_molecules(molecules)
config_file = starpolymers.generators.ConfigFile(system)
config_file.write('config.dat')