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
- 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
- Analysis on dump files
- Plotting tools
- Custom molecules without manual installation
Star Polymers is available on PyPi and can be installed using:
pip install starpolymers
From v1.1.3 it will be possible to install starpolymers using anaconda, via conda-forge:
conda install starpolymers -c conda-forge
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.
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.
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')