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 wavefunction file.
Parameters: fname (str) – Path to molecule’s wavefunction 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 2darray 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 2darray 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
. IfNone
, 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 2darray 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
. IfNone
, 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 isosurface 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 isosurface 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.

classmethod