PyMatterSim 0.1.0

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 [in a virtual environment]

• python3.10 -m venv .venv
• source .venv/bin/activate
• pip install PyMatterSim
• version upgrade pip install --upgrade pymattersim

Documentation

The documentation is now available online.

Requirements

• python 3.6-3.11 (recommend 3.10)
• numpy
• pandas
• freud-analysis (3.1.0, 3.2.0)
• 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

@article{hu2024pymattersimpythondataanalysis,
      title={PyMatterSim: a Python Data Analysis Library for Computer Simulations of Materials Science, Physics, Chemistry, and Beyond}, 
      author={Y. -C. Hu and J. Tian},
      year={2024},
      eprint={2411.17970},
      archivePrefix={arXiv},
      primaryClass={cond-mat.mtrl-sci},
      url={https://arxiv.org/abs/2411.17970}, 
}

References

• Y.-C. Hu et al. Origin of the boson peak in amorphous solids. Nature Physics, 18(6), 669-677 (2022)
• Y.-C. Hu et al. Revealing the role of liquid preordering in crystallisation of supercooled liquids. Nature Communications, 13(1), 4519 (2022)
• Y.-C. Hu et al. Physical origin of glass formation from multicomponent systems. Science Advances 6 (50), eabd2928 (2020)
• Y.-C. Hu et al. Configuration correlation governs slow dynamics of supercooled metallic liquids. Proceedings of the National Academy of Sciences U.S.A., 115(25), 6375-6380 (2018)
• Y.-C. Hu et al. Five-fold symmetry as indicator of dynamic arrest in metallic glass-forming liquids. Nature Communications, 6(1), 8310 (2015)

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