This protocol automates repeating calculations along a series of geometries (geometry keyword should point to .xyz file with multiple entries).
Scan modes
Two different scan modes are available:
- Parallel - All the calculations are prepared separately and then run using Cuby's internal queue system. Only after all calculations finish, the results are printed. The points can be calculated in parallel using the ::cuby_threads:: keyword.
- Serial - One calculation is set up and then called repeatedly while updating the geometry. Therefore, it can use the previous result as a starting point (if the interface supports that). The results are printed to the output one by one as they are calculated. Additionally, if a calculation fails in this mode, a message is printed and the program continues moves to the next point.
Geometry file
The geometry file should be an .xyz wile with multiple entries. A following extension is implemented: if the comment (second line) in the .xyz file starts with "scan:", the rest of the line is printed in the cuby output before each result. If the value of the scanned coordinate is used, the output then becomes a nice table ready for processing / plotting.
Scan generators
Optionally, the scan can be generated by Cuby. The generator is called using keyword ::scan_generator:: and set up using keyword ::scan_generator_setup::. Following generators are avilable:
- grid_xyz - the selected part of the geometry is moved to points on a cartesian grid (the center of the selection is positioned at the new coordinates). Moreover, the points are filtered by van der Waals distance, points with contact between the moved part and the rest of the system shorter than rvdw_min and longer than rvdw_max are removed (these values are relative to the vdW equilibrium distance).
- z-matrix - allows simultaneous setting or scaling of internal coordinates. The geometry has to be in z-matrix format with named variables.
- interpolate_zm - Interpolate between two z-matrices (geometry and geometry2).
Examples are provided below for each generator.