mcse

The Molecular Crystal Simulation Environment (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures. mcse provides a practical and parallel set of tools to efficiently analyze thousands of geometries. Included is a unique Structure class for representing molecular crystals that allows users to easily and automatically obtain the molecules that make up the crystal. The molecules are found automatically by computing the covalent bonds from the periodic atomic geometry. Any typical geometry file format is accepted, through wrappers to ase and pymatgen.

Installation

To start installing and using mcse, it's highly recommended to start from an Anaconda distribution of Python, which can be downloaded for free here.

Then download the library from Github. A zip file can be downloaded using the green download code button. Alternatively, this repository can be obtained using the following command.

$ git clone https://github.com/manny405/mcse.git

After navigating to the mcse directory, installation is completed with the following commands.

$ python -m pip install -r requirements.txt
$ python setup.py install

All requirements and dependencies will be installed automatically. Please be patient as this may take a while if multiple significant dependencies are missing.

Examples

The examples folder provides an introduction to the mcse library. Included are details about the current features and analysis methods that are implemented. Geometry files are included for running every example in each respective folder. Provided is a short description of the topics that are covered:

• 1_Introduction: Covers the input and output (IO) of geometry files, the features of the mcse.Structure object including automatically finding molecules, and converting to and from ase, Pymatgen, and mcse.
• 2_Standardize: Covers the standardization of molecules and crystal geometries. Standardization of crystals is to ensure that the covalent bonds of molecules are not split across periodic boundary conditions. Standardization of molecules places their center of mass and principal axis at the origin.
• 3_Analysis_Drivers: Covers the Driver class for performing complex analysis of molecular crystals through a standardized API. Covers the PairwiseDriver class for comparing crystal geometries. All currently available analysis methods in mcse are described. Lastly, covers how analysis can be automatically parallelization libmpi.
• 4_Visualize: Covers rendering of images for molecules and crystals provided in mcse. These capabilities automate the creation of excellent images for hundreds or thousands of geometries.

Features

Currently provided is a pre-release version of mcse. Given below is a visual representation of the features of the pre-release library. Each feature is covered in more detail with examples in the examples directory.

Credits

I have been the sole developer of this library during my PhD. The use of this library by others within my research group and by external collaborators has provided a catalyst for the implementation of many features and API changes. Thank you to everyone that has used the library prior to this initial release.