exma 0.2.0

extendable molecular dynamics analyzer

exma

exma is an extendable molecular analyzer.

This project is mainly developed with the objective of analyzing molecular dynamics trajectories using different tools that characterize both the configurational properties and the dynamics of the system. It is intended to analyze monatomic materials or alloys.

Features

With exma you can:

• Read and write MD trajectory frames in .xyz and .lammpstrj format (including charges, image of the particles or some other property).
• Write input file for LAMMPS.
• Estimate errors with the block average method.
• Initializate positions of atoms in:
  • SC, BCC, FCC, DCC crystals,
  • spherical nanoparticles.
  • replicate crystal structures.
• Apply PBC.
• Calculate:
  • clusterization (dbscan),
  • the coordination number (CN), the ligancy or in a shell, for monoatomic or diatomic systems,
  • effective neighbors (EN),
  • mean square displacement (MSD),
  • short range order, an amorphous parameter, defined here,
  • the radial distribution function (RDF) of monoatomic or diatomic systems.

Requirements

exma requires Python 3.8 to run, the others specific requirements are provided during installation. gcc 9.3 is necesary to compile the shared libreries if you are going to run tox.

Installation

Stable release

To install the most recent stable release of exma with pip, run the following command in your termninal:

pip3 install exma

From sources

To installing exma from sources you can clone this GitHub repo

git clone https://github.com/fernandezfran/exma.git

and inside your local directory install it in the following way

pip3 install .

or

python3 setup.py install

Usage

To use the extendable molecular analyzer in a project:

import exma

There are different examples in the documentation tutorials.

Release History

HISTORY

License

MIT License

TODO

TODO List

Contributing

Contributing