pylimer-tools

Pylimer-Tools

A collection of utility python functions for handling LAMMPS output and polymers in Python.

This toolbox provides means to read LAMMPS output: be it data, dump or thermodynamic data files. Additionally, it provides various methods to calculate with the read data, such as computing the radius of gyration, mean end to end distance, or simply splitting a polymer network back up into its chains.

Installation

Use pip:

pip install pylimer-tools

Usage

NOTE: currently, this release's API is unstable and subject to change.

See the documentation for a current list of all available functions.

Example

Example useage can be found in the documentation, the tests, the CLI application or in the following code snippet:

import numpy as np

from pylimer_tools_cpp import UniverseSequence

filePath = "some_lammps_output_file.dat"
universeSequence = UniverseSequence()
universeSequence.initializeFromDataSequence([filePath])
universe = universeSequence.atIndex(0)
print("Size: {}. Volume: {} u^3".format(
    universe.getSize(), universe.getVolume()))
print("Mean bond length: {} u".format(
    np.mean([m.computeBondLengths().mean() for m in universe])))
print("Mean end to end distance: {} u".format(
    np.mean([m.computeEndToEndDistance() for m in universe])))