`pyqmmm.qm.charge_spin_extractor`¶

Extract charge and spin data for a given subset of atoms for graphing.

Module Contents¶

`get_files`(file_pattern)	Find all examples of a file type in the current directory.
`get_selection`(file)	Get the user's atom set.
`get_atoms`()
`get_spins`(atoms, file, selection)	Gets the charges for the atoms specified by the user and sums them.
`get_charges`(atoms, file, selection)	Gets the charge for the atoms specified by the user and sums them.
`write_data`(file, net_data)	Writes out the data for either the charge or spin.
`charge_spin_extractor`()

pyqmmm.qm.charge_spin_extractor.get_files(file_pattern)[source]¶

Find all examples of a file type in the current directory.

Parameters:: file_pattern (str) – The type of file the for which the user would like to search the current directory.
Returns:: xyz_filename_list – A list of files found matching the user’s pattern.
Return type:: list

pyqmmm.qm.charge_spin_extractor.get_selection(file)[source]¶: Get the user’s atom set. :returns: atoms – The index of the atom for which the user would like the spin and charge. :rtype: selection

pyqmmm.qm.charge_spin_extractor.get_spins(atoms, file, selection)[source]¶

Gets the charges for the atoms specified by the user and sums them.

Parameters:

atoms (list) – List of atoms indices.
file (str) – The name of the file that you would like to analyze.
selection (list) – The indices of the atoms for which the user would like the charge and spin.

Returns:

net_spins – List fo spins corresponding to each image in the scan.

Return type:

list

pyqmmm.qm.charge_spin_extractor.get_charges(atoms, file, selection)[source]¶

Gets the charge for the atoms specified by the user and sums them.

Parameters:

atoms (list) – List of atoms indices.
file (str) – The name of the file that you would like to analyze.
selection (list) – The atom indices for which the user would like the charge and spin.

Returns:

net_spins – List fo spins corresponding to each image in the scan.

Return type:

list

pyqmmm.qm.charge_spin_extractor.write_data(file, net_data)[source]¶

Writes out the data for either the charge or spin.

Parameters:

file (str) – The name of the file where we are going to write out the data.
net_data (list) – List of data extracted from either the spin or charge files.