A collection of utility python functions for handling LAMMPS output and polymers in Python
Project description
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
An example useage can be found in the documentation, 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])))
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