This repository contains a library of Python classes for parsing LAMMPS density profiles and data files and specifically for post-processing of MD simulations of polymer brushes in equilibrium with solvent vapours.

Simply clone the repository using Git:

foo@bar:~$ git clone https://github.com/Compizfox/MDBrushAnalysis.git

or download a release and extract it. The Git approach has the advantage that updating is as easy as git pull.

MDBrushAnalysis requires at least Python 3.6. Numpy and Pandas are required by all scripts. Additionally, ProfileAnalyser also depends on SciPy, and DropletAnalyser depends on SciPy, Matplotlib, and OpenCV.

The dependencies can be installed in a virtualenv using Pipenv:

foo@bar:~$ pipenv install
foo@bar:~$ pipenv shell
(MDBrushAnalysis) foo@bar:~$ 

If you do not have Pipenv, you can install with pip install pipenv.

AveChunkParser defines a generic class for parsing data output by LAMMPS' ave/chunk fix. The method get_reshaped_data() provides a way to reshape the long format temporal frames to a new dimension. BrushDensityParser is a subclass of the former, specifically for density profiles.

LAMMPSDataParser defines a class that can parse LAMMPS data files. Using the method get_positions_by_type(), particles of a certain type can be selected and their coordinates returned. get_density_profile() computes N-dimensional density profiles by binning.

ProfileAnalyser defines a class for the post-processing of density profiles output by MD simulations of polymer brushes in equilibrium with solvent vapours. Density profiles of polymer and solvent are loaded using BrushDensityParser (described above). Unequilibrated temporal frames are trimmed from the beginning before temporal averaging and spatial interpolation. Temporally-averaged data is cached in files using pickle.

The class contains various methods for determining spatial limits of interest in the system and integrating density profiles to compute the amount and fraction of sorbed solvent.

DropletAnalyser defines a class for extracting contact angles from 2D density profiles (pixmaps) by fitting circles to the droplets. BrushDensityParser can be used to parse LAMMPS density profiles to pixmaps.

This project is free software licensed under the GPL. See LICENSE for details.