sovapy 0.6.0

SOVA (Structural Order Visualization and Analysis) with python

SOVApy (Structural Order Viaualization and Analysis with Python)

SOVA can be installed in Windows, MacOS and Linux.
(The package name to be imported is "sovapy".)

Install from PyPI

pip install sovapy

Build and Install sovapy

1. Clone the SOVA repo

git clone https://github.com/MotokiShiga/sova-cui.git

And move to the downloaded directory

cd sova-cui

2. To compile and to generate so or dll files, run
   for macos and linux

bash run_install_mac_linux.sh

For windows, use "x64 Native Tools Command Prompt for Visual Studio 2022" to run

install_win.bat

3. To install SOVA, run

pip install .  

For the usage, see example codes in the directory 'examples'.

Environment

Major packages used for our development

Package	Version
Python	3.10.0
ase	3.22.1
h5py	3.7.0
igraph	0.11.3
matplotlib	3.6.3
networkx	3.1
numpy	1.23.5
PyCifRW	4.4.5
scipy	1.8.1
spglib	2.0.2

The versions of other packages can be found in requirements.txt.

You can make the virtual environment for sova by

python -m venv sova-cui
source sova-cui/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

Acknowledgements

SOVA reuses source codes of the following package:

• pyMolDyn
• cif2cell

Examples

0_all_analysis  : All analysis and saving results in a hdf5
1_pdf_xyz       : PDF analysis from xyz file (amorphous SiO2)
2_pdf_cif       : PDF analysis from xyz file (beta-cristobalite)
3_pdf_cfg       : PDF analysis from cfg file generated by RMC++ (amorphous SiO2)
4_coordination  : Coordination number analysis (amorphous SiO2)
5_bond_angle    : Bond angle analysis (amorphous SiO2)
6_polyhedra     : Polyhedral symmetry analysis (q-value) (amorphous SiO2)
7_ring          : Ring analysis  (beta-cristobalite)
8_cavity        : Cavity analysis (amorphous SiO2)
9_save_result   : Save and load calculated results

Citation

We are preaparing a manuscript for this package. Before the publication, you should cite this url and the following papers. If you have implemented ring analysis, please cite the original papers of ring definitions (Guttman, King, and Primitive) and our paper:
[1] M. Shiga, A. Hirata, Y. Onodera, H. Masai, Ring-originated anisotropy of local structural ordering in amorphous and crystalline silicon dioxide. Commun. Mater. 4, 91 (2023). https://doi.org/10.1038/s43246-023-00416-w

For cavity analysis, please cite
[2] I. Meyer, F. Rhiem, F. Beule, D. Knodt, J. Heinen, R. O. Jones, pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter, J. Comput. Chem., 38, 389–394 (2017). https://doi.org/10.1002/jcc.24697