tcutility.analysis.vibration package

Submodules

tcutility.analysis.vibration.ts_vibration module

avg_relative_bond_length_delta(base, pos, neg, atom1, atom2)

Function to calculate relative atom distance change in vibrational mode

Parameters:

• base (Molecule) – plams.Molecule object containing the coordinates before applying vibration

• pos (Molecule) – plams.Molecule object with the vibrational mode added

• neg (Molecule) – plams.Molecule object with the vibrational mode subtracted

• atom1 (int) – label for the first atom

• atom2 (int) – label for the second atom

Return type:

float

Returns:

Average relative difference from the baseline distance between selected atoms in this vibrational mode (as percentage).

determine_ts_reactioncoordinate(data, mode_index=0, bond_tolerance=1.28, min_delta_dist=0.0)

Function to retrieve reaction coordinate from a given transitionstate, using the first imaginary frequency.

Parameters:

• data (Result) – TCutility.results.Result object containing calculation data

• mode_index (int) – vibrational mode index to analyze

• bond_tolerance (float) – parameter for plams.Molecule.guess_bonds() function

• min_delta_dist (float) – minimum relative bond length change before qualifying as active atom. If 0, all bond changes are counted

Return type:

ndarray

Returns:

Array containing all the obtained reaction coordinates. Reaction coordinate format is [active_atom1, active_atom2, sign], using Distance reactioncoordinate Symmetry elements are ignored, by convention the atom labels are increasing (atom1 < atom2)

validate_transitionstate(calc_dir, rcatoms=None, analyze_modes=1, **kwargs)

Function to determine whether a transition state calculation yielded the expected transition state. Checks the reaction coordinates provided by the user (or in the .rkf file User Input section) and compares

this against the reaction coordinates found in the imaginary modes of the transitionstate. If the transitionstate has multiple imaginary frequencies, it is possible to check multiple modes for the expected reaction coordinate.

Parameters:

• calc_dir (str) – path pointing to the desired calculation.

• rcatoms (list) – list or array containing expected reaction coordinates, to check against the transition state. If not defined, it is obtained from the ams.rkf user input. Only uses ‘Distance’ reaction coordinate. Format should be [atomlabel1, atomlabel2, (optional) sign]

• analyze_modes (int) – Number of imaginary modes to analyze, default only the first mode. Modes are ordered lowest frequency first. If 0 or negative value is provided, analyze all modes with imaginary frequency.

• **kwargs – keyword arguments for use in determine_ts_reactioncoordinate().

Return type:

bool

Returns:

Boolean value, True if the found transition state reaction coordinates contain the expected reaction coordinates, False otherwise. If multiple modes are analyzed, returns True if at least one mode contains the expected reaction coordinates.

Module contents