PyMatterSim 0.0.1

A python data analysis library for computer simulations

pymattersim

Summary

Physics-driven data analyis of computer simulations for materials science, chemistry, physics, and beyond.

Installation

Requirements

• python 3.6 or higher
• numpy
• pandas
• freud-analysis
• scipy
• sympy
• gsd (optional)
• mdtraj (optional)
• voro++ (optional, standalone binary)

Usage

Please refer to the /docs/ for documentation and examples. Some examples are provided from the unittest modules (tests/)

Types of computer simulations

1. LAMMPS
   1. atom type & molecular type such as patchy particle, rigid body, molecules et al.
   2. x, xs, xu type particle positions
   3. orthagonal / triclinic box
2. Hoomd-blue
   1. GSD for structure analysis (need gsd==3.2.0)
   2. GSD + DCD for dynamics analysis (need gsd==3.2.0 and mdtraj==1.9.9)
3. VASP (to be added)
4. Any type of simulators as long as the input were formatted well, modifying the reader module to use the computational modules.

Notes

Voro++ is recommend to install separately for specific Voronoi analysis. Some of the analysis from the original voro++ is maintained from the freud-analysis package developed by the Glozter group.

Citation

UnitTest

Please run the bash scripts available from shell/ for unittests. As follows are test statistics:

Test	# Tests and Runtime	Status
test_dynamics	Ran 15 tests in 10.303s	OK
test_neighbors	Ran 11 tests in 91.711s	OK
test_reader	Ran 11 tests in 0.270s	OK
test_static	Ran 28 tests in 298.248s	OK
test_utils	Ran 30 tests in 4.997s	OK
test_writer	Ran 3 tests in 0.005s	OK