cuby_scan

This module runs cuby calculation on a series of geometries. The geometries can be prepared by script geometry_scan.

Input file should contain definition of the calculation, including the keyword job.

The default format of the series of geometries (a trajectory) is .xyz file. If the information in .xyz file is not enough for the calculation (example: calculation uses atom types that are stored in PDB format only), a template geometry in any format supported by cuby can be provided using commandline option -g. This template geometry is the updated with coordinates from the trajectory.