Usage

python cp2k2extxyz.py path=<path> coordinates=<coordinates_filename> \
                         sp_output=<output_filename> lattice=<a b c>

Arguments

• path (Required):
  Base directory containing subdirectories with input files to process.

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

• sp_output (Required):
  Output file name in each subdirectory containing total energy and force data.

• lattice (Required):
  Lattice parameters in the form "a b c" (e.g., "15.0 15.0 15.0").

• from (Optional):
  Starting index for subdirectory processing. If omitted, all subdirs are processed.

• to (Optional):
  Ending index for subdirectory processing. If omitted, all subdirs are processed.

• step (Optional):
  Step size between subdirectories. Only used if from and to are provided.

• convert_energy (Optional):
  Convert energy values. Supported: au2eV.

• convert_forces (Optional):
  Convert force values. Supported: au2eVA.

Example

python cp2k2extxyz.py path=/data/simulations \
                         coordinates=coordinates.xyz \
                         sp_output=output from=1 to=100 step=5 \
                         lattice="15.0 15.0 15.0" convert_energy=au2eV \
                         convert_forces=au2eVA

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. The forces and energies will be converted accordingly. If 'from' and 'to' are omitted, all subdirectories under 'path' will be processed.