`pyqmmm.qm.mechanism_plotter`¶

Module Contents¶

`read_energy_from_xyz`(filename)	Extract energy values from an xyz file.
`format_plot`(→ None)	General plotting parameters for the Kulik Lab.
`plot_group_energies`(group_files, ref_energy, offset, color)	Process a group of related intermediate files and plot their energies.
`read_files`()	Read xyz files and group them by base name.
`process_xyz_files`()	Process xyz files and generate plot data.
`generate_plot`(color_scheme)	Generate plot using processed data.

`HARTREE_TO_KCAL`
`color_scheme`

pyqmmm.qm.mechanism_plotter.read_energy_from_xyz(filename)[source]¶

Extract energy values from an xyz file.

Parameters:: filename (str) – The name of the xyz file.
Returns:: energies – A list of energy values from each frame in the file.
Return type:: list

pyqmmm.qm.mechanism_plotter.format_plot() → None[source]¶: General plotting parameters for the Kulik Lab.

pyqmmm.qm.mechanism_plotter.plot_group_energies(group_files, ref_energy, offset, color)[source]¶

Process a group of related intermediate files and plot their energies.

Parameters:

group_files (list) – A list of filenames related to a single intermediate step.
ref_energy (float) – The reference energy value to which other energies are compared.
offset (int) – The current frame offset for the x-axis.
color (str) – The color to use when plotting this group’s energies.

Returns:

offset – The updated frame offset for the x-axis.

Return type:

int

pyqmmm.qm.mechanism_plotter.read_files()[source]¶: Read xyz files and group them by base name.

pyqmmm.qm.mechanism_plotter.process_xyz_files()[source]¶: Process xyz files and generate plot data.

pyqmmm.qm.mechanism_plotter.generate_plot(color_scheme)[source]¶: Generate plot using processed data.