CrySF (Crystallography Sites Finder) is a specialized Python software designed to analize molecular dynamics trajectories of crystalline solid-state ionic conductors. This tool not only identifies and characterizes the crystallographic sites occupied by diffusive atoms but also examines the transitions of these atoms between sites. Such analyses provide crucial insights for researchers studying advanced materials.
The software operates through two distinct commands. The first command, DensityMap, processes the atomic trajectories into data that the second command, CrySF, can further analyze. For a comprehensive understanding of the theoretical foundations and functionalities of CrySF, readers are encouraged to consult the examples and manuscript titled "####" authored by Henry A. Cortés, Mauricio R. Bonilla, and Elena Akhmatskaya. This document includes numerous examples that demonstrate the practical applications of the software.
CrySF can be requiers minimal prior knowledge about the material's and soports different trajectory formats (XTC, TRR, LAMMPSDUMP and XDATCAR).
- Python (>=3.8) https://www.python.org/downloads/
- MDanalysis https://www.mdanalysis.org/
- scikit-learn https://scikit-learn.org/stable/
- Matplotlib https://matplotlib.org/
- SciPy https://scipy.org/
- Seaborn https://seaborn.pydata.org/
To install and use the CrySF software in a Linux-like system. The user can obtain the code by cloning the following repository:
git clone https://gitlab.bcamath.org/hacortes/crysf
The command will create the crysf/ folder with the source files. For the CrySF package installation, execute the following command (in a UNIX-like terminal):
cd crysf/
pip install .
Copy the files densitymap.py and crysf.py scripts into the same folder as your simulation data.
- Execute DensityMap to create the density map:
python densitymap.py -to "topology file" -tr "trajectory file" -f "format" -ts "time interval [ps]" -a "atom name or type" -v "voxel size [Å]"
- After generating the density map, run crysf.py with the command:
python crysf.py -nts "time interval between frames [ps]"
Details of the settings to be used in the DensityMap and CrySF commands can be found in the examples folder.
- Dr. Henry Andres Cortes, BCAM - Basque Center for Applied Mathematics, Spain
- Dr. Mauricio Rincon Bonilla, BCAM - Basque Center for Applied Mathematics, Spain
- Prof. Elena Akhmatskaya, BCAM - Basque Center for Applied Mathematics, Spain