pyqmmm.qm.reaction_coordinate_collector

Extract RC against energy and generate CSV.

Module Contents

Functions

request_rc(rc_request)	Get the user's reaction coordinate definition.
get_distance(atoms, xyz_file)	Calculates the reaction coordinate at each step of the scan in the xyz file.
get_opt_energies(xyz_file)	Loop through the xyz file and collect optimized energies.
get_reaction_csv(xaxis_list, yaxis_list, extension)	Combine reaction coordinate and energy list and write them to a .csv file.
reaction_coordinate_collector()	Extract RC against energy and generate CSV.

pyqmmm.qm.reaction_coordinate_collector.request_rc(rc_request)

Get the user’s reaction coordinate definition.

Returns:

atoms – list of atoms indices

Return type:

list

pyqmmm.qm.reaction_coordinate_collector.get_distance(atoms, xyz_file)

Calculates the reaction coordinate at each step of the scan in the xyz file.

Parameters:

atoms (list) – List of two atoms defining a reaction coordiante distance.

Returns:

reaction_coordinates – List of values mapping to the distance that two atoms have moved.

Return type:

list

pyqmmm.qm.reaction_coordinate_collector.get_opt_energies(xyz_file)

Loop through the xyz file and collect optimized energies.

Returns:

• energy_df (dataframe) – The optimized energy from the current convergence line of the file.

• energy_list (list) – Returns a list of the energies extracted from the .out file.

pyqmmm.qm.reaction_coordinate_collector.get_reaction_csv(xaxis_list, yaxis_list, extension)

Combine reaction coordinate and energy list and write them to a .csv file.

Parameters:

• dist_list (list) – List of distances defining each step of the reaction coordinate.

• energy_list (list) – List of all energies mapping to each step of the reacitno coordinate.

pyqmmm.qm.reaction_coordinate_collector.reaction_coordinate_collector()

Extract RC against energy and generate CSV.

After performing a TeraChem PES, the coordinates are found in the xyz file. Using this file we can extract reaction coordinates against energies. This is can then be graphed in your plotter of choice such as XMGrace. The output is a .csv file with energies in column 1 and the RC in column 2.