custodian.qchem package¶
Subpackages¶
Submodules¶
custodian.qchem.handlers module¶
custodian.qchem.jobs module¶
custodian.qchem.utils module¶
This module contains utility functions that are useful for Q-Chem jobs.
- perturb_coordinates(old_coords, negative_freq_vecs, molecule_perturb_scale, reversed_direction)[source]¶
Perturbs a structure along the imaginary mode vibrational frequency vectors
old_coords (np.ndarray): Initial molecule coordinates negative_freq_vecs (list of np.ndarray): Vibrational frequency vectors corresponding to
imaginary (negative) frequencies
- molecule_perturb_scale (float): Scaling factor for coordination modification. The perturbation
vector will be multiplied by this factor.
reversed_direction (bool): If True, then perturb in direction opposite of frequency modes.
- vector_list_diff(vecs1, vecs2)[source]¶
Calculates the summed difference of two vectors
Typically this function is used to compare between the different atom-wise components of a vibrational frequency mode vector.
- vecs1 (np.ndarray): Collection of vectors to be compared. Typical dimension
n x 3
- vecs2 (np.ndarray): Collection of vectors to be compared. Typical dimension
n x 3
Module contents¶
This package implements various QChem Jobs and Error Handlers.