Usage

python cp2k_to_extxyz.py path=<path> coordinates=<coordinates_filename> \
                         sp_output=<output_filename> from=<start_folder> \
                         to=<end_folder> step=<folder_step>

Arguments

path : Base directory path containing subdirectories with input files. Each subdirectory will be processed.

coordinates : Name of the coordinates file (e.g., 'coordinates.xyz') in each subdirectory.

sp_output : Name of the output file (e.g., 'output') in each subdirectory, which contains total energy and force data.

from : Starting number for the subdirectory loop. For example, 'from=1' starts processing from folder '1'.

to : Ending number for the subdirectory loop. For example, 'to=100' processes up to folder '100'.

step : Step size for incrementing through subdirectories. For example, 'step=5' processes every 5th folder in the specified range.

Example

python cp2k_to_extxyz.py path=/data/simulations \
                         coordinates=coordinates.xyz \
                         sp_output=output from=1 to=100 step=5

This example processes folders /data/simulations/1, /data/simulations/6, /data/simulations/11, ..., /data/simulations/96. Each processed folder's data is appended to a single output file named combined_coordinates_forces.xyz created in the base path.