nonrad.ccd module

Convenience utilities for nonrad.

This module contains various convenience utilities for working with and preparing input for nonrad.

nonrad.ccd.get_PES_from_vaspruns(ground: Structure, excited: Structure, vasprun_paths: list[str], tol: float = 0.001) → tuple[ndarray, ndarray][source]

Extract the potential energy surface (PES) from vasprun.xml files.

This function reads in vasprun.xml files to extract the energy and Q value of each calculation and then returns it as a list.

Parameters:

  • ground (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the ground (final) state

  • excited (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the excited (initial) state

  • vasprun_paths (list(strings)) – a list of paths to each of the vasprun.xml files that make up the PES. Note that the minimum (0% displacement) should be included in the list, and each path should end in ‘vasprun.xml’ (e.g. /path/to/vasprun.xml)

  • tol (float) – tolerance to pass to get_Q_from_struct

Returns:

  • Q (np.array(float)) – array of Q values (amu^{1/2} Angstrom) corresponding to each vasprun

  • energy (np.array(float)) – array of energies (eV) corresponding to each vasprun

nonrad.ccd.get_Q_from_struct(ground: Structure, excited: Structure, struct: Structure | str, tol: float = 0.0001, nround: int = 5) → float[source]

Calculate the Q value for a given structure.

This function calculates the Q value for a given structure, knowing the endpoints and assuming linear interpolation.

Parameters:

  • ground (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the ground (final) state

  • excited (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the excited (initial) state

  • struct (pymatgen.core.structure.Structure or str) – pymatgen structure corresponding to the structure we want to calculate the Q value for (may also be a path to a file containing a structure)

  • tol (float) – distance cutoff to throw away coordinates for determining Q (sites that don’t move very far could introduce numerical noise)

  • nround (int) – number of decimal places to round to in determining Q value

Returns:

the Q value (amu^{1/2} Angstrom) of the structure

Return type:

float

nonrad.ccd.get_barrier_harmonic(dQ: float, dE: float, wi: float, wf: float) → float | None[source]

Calculate the barrier height within the Harmonic approximation.

Parameters:

  • dQ (float) – displacement between harmonic oscillators in amu^{1/2} Angstrom

  • dE (float) – energy offset between the two harmonic oscillators

  • wi (float) – frequencies of the harmonic oscillators in eV

  • wf (float) – frequencies of the harmonic oscillators in eV

Returns:

barrier energy in eV or None if no crossing found

Return type:

float, None

nonrad.ccd.get_cc_structures(ground: Structure, excited: Structure, displacements: ndarray, remove_zero: bool = True) → tuple[list, list][source]

Generate the structures for a CC diagram.

Parameters:

  • ground (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the ground (final) state

  • excited (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the excited (initial) state

  • displacements (list(float)) – list of displacements to compute the perturbed structures. Note: the displacements are for only one potential energy surface and will be applied to both (e.g. displacements=np.linspace(-0.1, 0.1, 5)) will return 10 structures 5 of the ground state displaced at +-10%, +-5%, and 0% and 5 of the excited state displaced similarly)

  • remove_zero (bool) – remove 0% displacement from list (default is True)

Returns:

  • ground_structs = list(pymatgen.core.structure.Struture) – a list of structures corresponding to the displaced ground state

  • excited_structs = list(pymatgen.core.structure.Structure) – a list of structures corresponding to the displaced excited state

nonrad.ccd.get_dQ(ground: Structure, excited: Structure) → float[source]

Calculate dQ from the initial and final structures.

Parameters:

  • ground (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the ground (final) state

  • excited (pymatgen.core.structure.Structure) – pymatgen structure corresponding to the excited (initial) state

Returns:

the dQ value (amu^{1/2} Angstrom)

Return type:

float

nonrad.ccd.get_omega_from_PES(Q: ndarray, energy: ndarray, Q0: float | None = None, ax=None, q: ndarray | None = None) → float[source]

Calculate the harmonic phonon frequency for the given PES.

Parameters:

  • Q (np.array(float)) – array of Q values (amu^{1/2} Angstrom) corresponding to each vasprun

  • energy (np.array(float)) – array of energies (eV) corresponding to each vasprun

  • Q0 (float) – fix the minimum of the parabola (default is None)

  • ax (matplotlib.axes.Axes) – optional axis object to plot the resulting fit (default is None)

  • q (np.array(float)) – array of Q values to evaluate the fitting function at

Returns:

harmonic phonon frequency from the PES in eV

Return type:

float