chemtools.toolbox.motbased.MOTBasedTool

class chemtools.toolbox.motbased.MOTBasedTool(molecule)[source]

Molecular Orbital Theory Based Descriptive Tools.

Initialize class from Molecule instance.

Parameters:molecule (Molecule) – An instance of Molecule class.
classmethod from_molecule(molecule)[source]

Initialize class from Molecule instance.

Parameters:molecule (Molecule) – An instance of Molecule class.
classmethod from_file(fname)[source]

Initialize class from wave-function file.

Parameters:fname (str) – Path to molecule’s wave-function file.
coordinates

Cartesian coordinates of atomic centers.

numbers

Atomic number of atomic centers.

nbasis

Number of basis functions.

nelectrons

Number of alpha and beta electrons.

homo_index

Index of alpha and beta HOMO orbital.

lumo_index

Index of alpha and beta LUMO orbital.

homo_energy

Energy of alpha and beta HOMO orbital.

lumo_energy

Energy of alpha and beta LUMO orbital.

orbital_occupation

Orbital occupation of alpha and beta electrons.

orbital_energy

Orbital energy of alpha and beta electrons.

orbital_coefficient

Orbital coefficient of alpha and beta electrons.

The alpha and beta orbital coefficients are each storied in a 2d-array in which the columns represent the basis coefficients of each molecular orbital.

orbital_overlap

Return the overlap matrix of molecular orbitals.

compute_density_matrix(spin='ab')[source]

Return the density matrix array for the specified spin orbitals.

compute_orbital_expression(points, spin='ab', index=None)[source]

Return molecular orbitals evaluated on the given points for the spin orbitals.

Parameters:
  • points (ndarray) – The 2d-array containing the cartesian coordinates of points on which density is evaluated. It has a shape (n, 3) where n is the number of points.
  • spin (str) –

    The type of occupied spin orbitals.

    • ”a” or “alpha”: consider alpha electrons
    • ”b” or “beta”: consider beta electrons
  • index (sequence, default=None) – Sequence of integers representing the index of spin orbitals. Alpha and beta spin orbitals are each indexed from 1 to nbasis. If None, all occupied spin orbitals are included.
  • output (np.ndarray, default=None) – Array with shape (n, m) to store the output, where n in the number of points and m is the number of molecular orbitals. When None the array is allocated.
compute_density(points, spin='ab', index=None)[source]

Return electron density evaluated on the given points for the spin orbitals.

Parameters:
  • points (ndarray) – The 2d-array containing the cartesian coordinates of points on which density is evaluated. It has a shape (n, 3) where n is the number of points.
  • spin (str) –

    The type of occupied spin orbitals. By default, the alpha and beta electrons (i.e. alpha and beta occupied spin orbitals) are used for computing the electron density.

    • ”a” or “alpha”: consider alpha electrons
    • ”b” or “beta”: consider beta electrons
    • ”ab”: consider alpha and beta electrons
  • index (sequence) – Sequence of integers representing the index of spin orbitals. Alpha and beta spin orbitals are each indexed from 1 to nbasis. If None, all occupied spin orbitals are included.
  • output (np.ndarray) – Array with shape (n,) to store the output, where n in the number of points. When None the array is allocated.
generate_scripts(fname, spin='a', index=None, isosurf=0.05, grid=None)[source]

Generate VMD script(s) and cube file(s) to visualize MO iso-surface of given orbitals.

Parameters:
  • fname (str) – A string representing the path to a fname of generated files. The VMD script and cube file will be named fname_mo{index}.vmd and fname_mo{index}.cube, respectively.
  • spin (str, optional) – The type of occupied spin orbitals. Choose either ‘a’ or ‘b’.
  • index (int, optional) – Integer representing the index of spin orbital to visualize. Spin orbitals are each indexed from 1 to nbasis. If None, files for visualizing all orbitals are generated.
  • isosurf (float, optional) – Value of MO iso-surface used in VMD script.
  • grid (UniformGrid, optional) – Instance of UniformGrid used for computation and generating cube file(s). If None, a cubic grid is constructed from molecule with spacing=0.2 & extension=5.0.