COGITOico

Icohp / COHP integration and chemical bonding analysis utilities.

class COGITO_dft.COGITOico.COGITO_ICO(directory: str, verbose: int = 0, file_suffix: str = '', orbs_orth: bool = False, spin_polar: bool = False)[source]

Bases: object

read_input(file: str = 'tb_input.txt') → None[source]

Reads the tb_input.txt for information about the unit cell, atoms, orbitals, fermi energy, energy shift, and spin polarization.

read_overlaps(file: str = 'overlaps.txt') → None[source]

Reads in the orbital overlaps from a file formatted like wannier90_hr.dat. Only neccesary for plotting the bond densities.

Parameters:

file (str) – The file name for the overlaps.

read_ICOHP(file: str = 'ICOHP.txt') → None[source]
read_ICOOP(file: str = 'ICOOP.txt') → None[source]
read_bond_occup(file: str = 'bond_occup.txt') → None[source]
read_orbitals(file: str = 'orbitals.npy') → None[source]

This function reads in the orbitals as coefficents for a gaussian expansion. The information in ‘orbitals.npy’ is combined with the orbital data in ‘tb_input.txt’.

Parameters:

file (str) – Orbital file.

save_ICOnpy()[source]
static get_neighbors(self) → list[source]

This sorts the matrix of TB parameters into terms which are 1NN, 2NN, etc. Relevant for labeling bonds.

get_bonds_figure(energy_cutoff: float = 0.1, elem_colors: list = [], atom_colors: list = [], atom_labels: list = [], plot_atom: int = None, one_atom: bool = False, bond_max: float = 3.0, fovy: float = 10, return_fig: bool = False) → None[source]

This is deprecated. This will plot the crystal structure atoms with line weighted by iCOHP. Each line should also be hoverable to reveal the number and amounts that are s-s,s-p, and p-p.

Parameters:

  • energy_cutoff (float) – This is the minimum bond magnitude that will be plotted.

  • elem_colors (list) – Colors for the elements based on order in tb_input. Length of list should be the number of unique elements. Can either be integer list to reference the default colors or list of plotly compatable colors.

  • atom_colors (list) – Colors for the atoms based on order in tb_input. Length of list should be the number of atoms in the primitive cell. Can either be integer list to reference the default colors or list of plotly compatable colors. If not set defaults to elem_colors.

  • atom_labels (list) – List of atom labels as a string.

  • plot_atom (int) – Set with one_atom=True, plots only one atom and it’s bonds, this passes the atom number to plot.

  • one_atom (bool) – Whether only the atom defined in plot_atom should be plotted; default is False.

  • bond_max (float) – The maximum bond distance that will be plotted outside the primitive cell.

  • fovy (float) – Field of view in the vertical direction. Use this tag to adjust depth perception in crystal. Set between 3 (for close to orthographic) and 30 (for good perspective depth).

Returns:

Nothing

Return type:

None

get_bonds_charge_figure(energy_cutoff: float = 0.1, bond_max: float = 3.0, elem_colors: list = [], atom_colors: list = [], atom_labels: list = [], auto_label: str = '', plot_atom: int = None, one_atom: bool = False, fovy: float = 10, return_fig: bool = False) → None[source]

This will plot the crystal structure atoms with line weighted by iCOHP. Each line should also be hoverable to reveal the number and amounts that are s-s,s-p, and p-p.

Parameters:

  • energy_cutoff (float) – This is the minimum bond magnitude that will be plotted

  • bond_max (float) – Atoms are plotted outside the primitive cell only if they have a bond with a primitive cell atom that is shorter than this amount. This does not filter bonds between atoms that are already plotted.

  • elem_colors (list) – Colors for the elements based on order in tb_input. Length of list should be the number of unique elements. Can either be integer list to reference the default colors or list of plotly compatable colors.

  • atom_colors (list) – Colors for the atoms based on order in tb_input. Length of list should be the number of atoms in the primitive cell. Can either be integer list to reference the default colors or list of plotly compatable colors. If not set defaults to elem_colors.

  • atom_labels (list) – List of atom labels as a string.

  • auto_label (str) – Different options for plotting includes: (can include multiple in the string) “mulliken” - Plots the onsite charge and mag (if spin_polar) on atoms by mulliken population (overrides atom_labels). “full” - Plots the charge and magnetics moments (if spin_polar) on atoms and bonds (overrides atom_labels). “color” - Colors the atoms and bonds based on their charge (overrides atom_colors or elem_colors). “color mag” - Colors the atoms and bonds based on their magnetic moments (overrides atom_colors or elem_colors). NOTE: Only use “mulliken” OR “full”, NOT both.

  • plot_atom (int) – Set with one_atom=True, plots only one atom and it’s bonds, this passes the atom number to plot.

  • one_atom (bool) – Whether only the atom defined in plot_atom should be plotted; default is False.

  • fovy (float) – Field of view in the vertical direction. Use this tag to adjust depth perception in crystal. Set between 3 (for close to orthographic) and 30 (for good perspective depth).

  • return_fig (bool) – If False, this function saves figure to crystal_bonds.html. If True, this function will return the plotly figure object

Returns:

Depend on return_fig parameter.

Return type:

None

make_bond(atmind1, atmind2, center1, center2, orbCOOP, cartXYZ)[source]

This is a function which will generate populate the cartXYZ grid with values for the bond density between the atoms given using the orbCOOP provided.

Parameters:

  • atmind1 (unknown) – The atom number for the first atom.

  • atmind2 (unknown) – The atom number for the second atom.

  • center1 (unknown) – The center of the first atom (not using self.primATOMs).

  • center2 (unknown) – The center of the second atom (not using self.primATOMs).

  • orbCOOP (unknown) – The orbCOOP which reveals how much of each orbital combo that is included in the bond. Dimension nxm where n is the # of orbitals for atom 1 and m is # of orbitals for atom 2.

  • cartXYZ (unknown) – The 3D flattened grid that the bond density is calculated on.

Returns:

A 1D array (3D flattened) of the bond density.

Return type:

unknown

get_bond_density_figure(energy_cutoff: float = 0.1, iso_max: float = 0.03, iso_min: float = 0.003, elem_colors: list = [], atom_colors: list = [], atom_labels: list = [], auto_label: str = '', plot_atom: int = None, one_atom: bool = False, bond_max: float = 3.0, fovy: float = 10, return_fig: bool = False) → None[source]

Plots the crystal structure atoms with bonds plotted based on iCOHP. Each line should also be hoverable to reveal the number and amounts that are s-s,s-p, and p-p. The charge and magnetic moment will also be plotted acording to auto_label.

Parameters:

  • energy_cutoff (float) – This is the minimum bond magnitude that will be plotted.

  • iso_max (float) – The positive isosurface for plotting the bonds.

  • iso_min (float) – The negative isosurface for plotting the bonds.

  • elem_colors (list) – Colors for the elements based on order in tb_input. Length of list should be the number of unique elements. Can either be integer list to reference the default colors or list of plotly compatable colors.

  • atom_colors (list) – Colors for the atoms based on order in tb_input. Length of list should be the number of atoms in the primitive cell. Can either be integer list to reference the default colors or list of plotly compatable colors. If not set defaults to elem_colors.

  • atom_labels (list) – List of atom labels as a string.

  • auto_label (str) – Different options for plotting includes: (can include multiple in the string) “mulliken” - Plots the onsite charge and mag (if spin_polar) on atoms by mulliken population (overrides atom_labels). “full” - Plots the charge and magnetics moments (if spin_polar) on atoms and bonds (overrides atom_labels). “color” - Colors the atoms and bonds based on their charge (overrides atom_colors or elem_colors). “color mag” - Colors the atoms and bonds based on their magnetic moments (overrides atom_colors or elem_colors). NOTE: Only use “mulliken” OR “full”, NOT both.

  • plot_atom (int) – Set with one_atom=True, plots only one atom and it’s bonds, this passes the atom number to plot.

  • one_atom (bool) – Whether only the atom defined in plot_atom should be plotted; default is False.

  • bond_max (float) – The maximum bond distance that will be plotted outside the primitive cell.

  • fovy (float) – Field of view in the vertical direction. Use this tag to adjust depth perception in crystal. Set between 3 (for close to orthographic) and 30 (for good perspective depth).

Returns:

Nothing, but saves plotly figure to ‘crystal_bonds.html’.

Return type:

None

static get_COHP(self: object, orbs: dict, NN: int = None, include_onsite: bool = False, just_one: bool = False) → ndarray[tuple[Any, ...], dtype[_ScalarT]][source]

Calculates the COHP for the given orbitals and nearest neighbors.

Parameters:

  • self (object) – An object of the class COGITO_BAND or COGITO_UNIFORM.

  • orbs (dict) – Either a list of two dictionaries giving elements as keys and orbital types as items (eg [{“Pb”:[“s”,”d”],”O”:[“s”,”p”]},{“Pb”:[“s”]”O”:[“p”]}]) or give list of orb numbers [[1,2,3,5,6,7],[1,2,3,4,5,6,7,8]].

  • NN (int) – An integer for which nearest neighbor number to include (eg 1 for 1NN) or None or “All” for all nearest neighbors.

  • include_onsite (bool) – Includes atomic orbital energy terms (H_ab(R) where R=0 and a=b) instead of just bonding terms.

Returns:

Returns COHP values in a [kpt,band] dimension.

Return type:

npt.NDArray

static get_COOP(self: object, orbs: dict, NN: int = None, include_onsite: bool = False, spin: int = 0) → ndarray[tuple[Any, ...], dtype[_ScalarT]][source]

Calculates the COHP for the given orbitals and nearest neighbors.

Parameters:

  • self (object) – An object of the class COGITO_BAND or COGITO_UNIFORM.

  • orbs (dict) – Either a list of two dictionaries giving elements as keys and orbital types as items (eg [{“Pb”:[“s”,”d”],”O”:[“s”,”p”]},{“Pb”:[“s”]”O”:[“p”]}]) or give list of orb numbers [[1,2,3,5,6,7],[1,2,3,4,5,6,7,8]].

  • NN (int) – An integer for which nearest neighbor number to include (eg 1 for 1NN) or None or “All” for all nearest neighbors.

  • include_onsite (bool) – Includes atomic orbital energy terms (H_ab(R) where R=0 and a=b) instead of just bonding terms.

Returns:

Returns COHP values in a [kpt,band] dimension.

Return type:

npt.NDArray

static get_mulliken_charge(self: object, elem: str, only_onsite=False) → float[source]

Returns the atomic partial charge by Mulliken partitioning. If the calculation is spin polarized, also returns the atomic magnetization by Mulliken. If the element label (str) is used, the code returns the average charge/magnetization for the element type.

Parameters:

  • elem (str or int) – Either the element label (e.g. “Pb”) or the index of the atom in the list of atoms (as seen in tb_input.txt). When is the element label, the function will return a value for each atom of that type.

  • only_onsite (bool) – Default False. If True, don’t actually do the Mulliken repartitioning from bonds, only include onsite charges. Note if True: Summing only atoms with onsite charge will not be charge neutral, need to include bond charge for neutrality.

Returns:

Atomic partial charge or if spin polarized, (partial charge, atomic magnetic moment).

If elem is element label (e.g. “Pb”), returns a list for charge and magmom.

Return type:

(float or tuple)

COGITO_dft.COGITOico.func_for_rad(x, a, b, c, d, e, f, g, h, l)[source]
COGITO_dft.COGITOico.complex128funs(phi, theta, sphharm_key)[source]