PyMatterSim 0.1.5

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]

Preparation: You need a C++compiler and cmake, which can be obtained from the source code installation section.

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

Install from source

• You need a C++compiler that supports at least the C++11 standard and cmake.

  Recommend using conda or mamba for installation.

  Linux: conda install gxx cmake or mamba install gxx cmake

  Mac OS.conda install clang cmake or mamba install clang cmake

  Windows: conda install gxx cmake or mamba install gxx cmake or Download visual studio installer from here and install the C++ compiler.

  A package manager is also a good choice, for example:

  ubuntu: sudo apt-get install g++ cmake

  centos: sudo yum install gcc-c++ cmake3

  macos: brew install gcc cmake

  Now that you have all the build tools, pip will help you complete everything for compilation.

git clone https://gitee.com/yuanchaohu/pymattersim  --recursive # get submodule
cd  pymattersim
pip install .

Confirm installation

Acceleration is enabled by default. You can determine whether to enable acceleration by importing the _acc module and checking the variables.

from PyMatterSim import _acc
print(_acc.ENABLE_ACC) # should be True

We also provide an environment variable DISABLE_ACC to disable acceleration code. Note that setting it to any non-zero value will result in disabling acceleration code.

export DISABLE_ACC=1 # will disable acceleration
# If you want to reactivate acceleration, do this.
unset(DISABLE_ACC) # will reactivate acceleration

Documentation

The documentation is now available online.

Requirements

• python 3.8-3.11 (recommend 3.10)
• numpy==1.26.4
• pandas==2.1.4
• freud-analysis==3.0.0
• scipy==1.15.2
• sympy==1.12
• 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 recommended 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

The activation of the acceleration code is slightly different for unit-test, and you need to manually compile the dynamic link library and place it in the _acc module.

# compile the dynamic link library
mkdir build
cd build
cmake ..
make
cp PyMatterSim/_acc/acc.cpython-313-x86_64-linux-gnu.so ../PyMatterSim/_acc/ # The dynamic library name varies depending on your platform.