chemtools.wrappers.molecule.Molecule¶

class
chemtools.wrappers.molecule.
Molecule
(iodata)[source]¶ Molecule class from HORTON package.
Initialize class.
Parameters: iodata (horton.IOData) – An instance of horton.IOData object. 
classmethod
from_file
(fname)[source]¶ Initialize class given a file.
Parameters: fname (str) – Path to molecule”s files.

coordinates
¶ Cartesian coordinates of atomic centers.

numbers
¶ Atomic number of atomic centers.

ao
¶ Atomic orbital instance.

mo
¶ Molecular orbital instance.

compute_density_matrix
(spin='ab', index=None)[source]¶ Compute the density matrix array for the specified spin orbitals.
Parameters:  spin (str, optional) – The type of occupied spin orbitals. Options are “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_molecular_orbital
(points, spin='ab', index=None)[source]¶ Return molecular orbitals.
Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_density
(points, spin='ab', index=None)[source]¶ Return electron density.
Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_gradient
(points, spin='ab', index=None)[source]¶ Return gradient of the electron density.
Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_hessian
(points, spin='ab', index=None)[source]¶ Return hessian of the electron density.
Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_laplacian
(points, spin='ab', index=None)[source]¶ Return Laplacian of the electron density.
Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

compute_esp
(points, spin='ab', index=None, charges=None)[source]¶ Return molecular electrostatic potential.
The molecular electrostatic potential at point \(\mathbf{r}\) is caused by the electron density \(\rho\) of the specified spin orbitals and set of point charges \(\{q_A\}_{A=1}^{N_\text{atoms}}\) placed at the position of the nuclei. i.e,
\[V \left(\mathbf{r}\right) = \sum_{A=1}^{N_\text{atoms}} \frac{q_A}{\rvert \mathbf{R}_A  \mathbf{r} \lvert}  \int \frac{\rho \left(\mathbf{r}"\right)}{\rvert \mathbf{r}"  \mathbf{r} \lvert} d\mathbf{r}"\]Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.  charges (np.ndarray, optional) – Array with shape (n,) representing the point charges at the position of the nuclei.
When
None
, the pseudo numbers are used.

compute_ked
(points, spin='ab', index=None)[source]¶ Return positive definite or Lagrangian kinetic energy density.
\[\tau_\text{PD} \left(\mathbf{r}\right) = \tfrac{1}{2} \sum_i^N n_i \rvert \nabla \phi_i \left(\mathbf{r}\right) \lvert^2\]Parameters:  points (ndarray) – Cartesian coordinates of N points given as a 2Darray with (N, 3) shape.
 spin (str, optional) – Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), and “ab” (for alpha + beta).
 index (sequence of int, optional) – Sequence of integers representing the occupied spin orbitals which are indexed
from 1 to
nbasis
. IfNone
, all orbitals of the given spin(s) are included.

classmethod