Getting started

After performing an atomistic simulation, CrySF can be used for analysis via the following steps:

1. Prepare the Simulation Data:

   1. Store the atomistic trajectory in a dedicated folder. Include the following files based on the simulation software used:

      • XDATCAR from VASP.

      • For LAMMPS or GROMACS, include the topology and trajectory files.

2. Set Up the Analysis Scripts:

   • Copy the files densitymap.py and crysf.py into the same folder as your simulation data.

3. Execute `DensityMap` to Create a Density Map:

   • Run the following command to execute densitymap.py:

     ` python densitymap.py -to 'str' -tr 'str' -f 'str' -ts float -v float -a int or 'str' -tts int -verb int -clus int `

4. Execute `CrySF` to Analyze the Density Map:

   • After generating the density map, run crysf.py with the command:

     ` python crysf.py -nts float -minv float -maxv float -clus int -dop int -verb int -deltf int -scaler 'str' `

The settings to use the DensityMap and CrySF commands are detailed in the Settings section.

The time it takes to analyze a trajectory depends on the simulation’s number of atoms and the frequency with which the trajectory is printed. Usually, the analysis takes a few minutes.