pyqmmm.qm.plot_combined_nebs

Generalizable script for plotting the PES of an xyz trajectory with NEB boundaries.

Functions

collect_data()	Collect energies from the NEB xyz files and calculate NEB boundaries.
format_plot()	General plotting parameters.
get_trajectory_energies(filename, software)	Parse the energies from an xyz trajectory file.
get_xyz_files()	List all NEB xyz files in the current directory, sorted numerically.
identify_software(line)	Identify the software used for the calculation from a line.
parse_energy(line, software)	Parse the energy from a line based on the software used.
plot_data(total_energies_abs, ...)	Plot the collected energies with NEB boundaries.
plot_energies()	Main function that combines previous functions to generate the plot.
write_energies_to_csv(total_energies[, filename])	Write the energies to a CSV file.