pyqmmm.qm.plot_combined_nebs

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

Module Contents

Functions

get_xyz_files()

List all NEB xyz files in the current directory, sorted numerically.

write_energies_to_csv(total_energies[, filename])

Write the energies to a CSV file.

parse_energy(line, software)

Parse the energy from a line based on the software used.

get_trajectory_energies(filename, software)

Parse the energies from an xyz trajectory file.

identify_software(line)

Identify the software used for the calculation from a line.

format_plot(→ None)

General plotting parameters.

collect_data()

Collect energies from the NEB xyz files and calculate NEB boundaries.

plot_data(total_energies_abs, ...)

Plot the collected energies with NEB boundaries.

plot_energies()

Main function that combines previous functions to generate the plot.

Attributes

HARTREE_TO_KCAL

pyqmmm.qm.plot_combined_nebs.HARTREE_TO_KCAL = 627.509
pyqmmm.qm.plot_combined_nebs.get_xyz_files()[source]

List all NEB xyz files in the current directory, sorted numerically.

pyqmmm.qm.plot_combined_nebs.write_energies_to_csv(total_energies, filename='energy_plot_data.csv')[source]

Write the energies to a CSV file.

Parameters:

  • total_energies (list) – List of concatenated energies for all NEBs in kcal/mol.

  • filename (str) – The name of the output CSV file.

pyqmmm.qm.plot_combined_nebs.parse_energy(line, software)[source]

Parse the energy from a line based on the software used.

Parameters:

  • line (str) – Line from the file containing energy information.

  • software (str) – The software used for the calculation.

Returns:

The energy extracted from the line, in Hartrees.

Return type:

float

pyqmmm.qm.plot_combined_nebs.get_trajectory_energies(filename, software)[source]

Parse the energies from an xyz trajectory file.

Parameters:

  • filename (str) – Path to the trajectory file.

  • software (str) – Software used for the calculation.

Returns:

First value is a list of absolute energies for each frame, in kcal/mol. Second value is the first frame energy in kcal/mol. Third value is a list of absolute energies in Hartrees.

Return type:

tuple

pyqmmm.qm.plot_combined_nebs.identify_software(line)[source]

Identify the software used for the calculation from a line.

Parameters:

line (str) – Line from the file.

Returns:

Identifier of the software used for the calculation.

Return type:

str

pyqmmm.qm.plot_combined_nebs.format_plot() → None[source]

General plotting parameters.

pyqmmm.qm.plot_combined_nebs.collect_data()[source]

Collect energies from the NEB xyz files and calculate NEB boundaries.

Returns:

  • list – A list of concatenated absolute energies for all NEBs in kcal/mol.

  • float – The first frame energy of the first NEB in kcal/mol.

  • list – A list of cumulative frame counts where each NEB ends.

pyqmmm.qm.plot_combined_nebs.plot_data(total_energies_abs, first_energy_kcal_of_first_neb, dim_list, neb_boundaries)[source]

Plot the collected energies with NEB boundaries.

Parameters:

  • total_energies_abs (list) – List of concatenated absolute energies for all NEBs in kcal/mol.

  • first_energy_kcal_of_first_neb (float) – The first frame energy of the first NEB in kcal/mol.

  • dim_list (list) – Dimensions for the plot.

  • neb_boundaries (list) – List of cumulative frame counts where each NEB ends.

pyqmmm.qm.plot_combined_nebs.plot_energies()[source]

Main function that combines previous functions to generate the plot.