Class for storing molecule data from a fixed basis set at a fixed
openfermion.chem.MolecularData(
geometry=None,
basis=None,
multiplicity=None,
charge=0,
description='',
filename='',
data_directory=None
)
Used in the notebooks
geometry that is obtained from classical electronic structure
packages. Not every field is filled in every calculation. All data
that can (for some instance) exceed 10 MB should be saved
separately. Data saved in HDF5 format.
Args |
|---|
geometry
|
A list of tuples giving the coordinates of each atom.
An example is [('H', (0, 0, 0)), ('H', (0, 0, 0.7414))].
Distances in angstrom. Use atomic symbols to
specify atoms. Only optional if loading from file.
|
basis
|
A string giving the basis set. An example is 'cc-pvtz'.
Only optional if loading from file.
|
charge
|
An integer giving the total molecular charge. Defaults
to 0. Only optional if loading from file.
|
multiplicity
|
An integer giving the spin multiplicity. Only
optional if loading from file.
|
description
|
A optional string giving a description. As an
example, for dimers a likely description is the bond length
(e.g. 0.7414).
|
filename
|
An optional string giving name of file.
If filename is not provided, one is generated automatically.
|
data_directory
|
Optional data directory to change from default
data directory specified in config file.
|
Attributes |
|---|
geometry
|
A list of tuples giving the coordinates of each atom. An
example is [('H', (0, 0, 0)), ('H', (0, 0, 0.7414))]. Distances
in angstrom. Use atomic symbols to specify atoms.
|
basis
|
A string giving the basis set. An example is 'cc-pvtz'.
|
charge
|
An integer giving the total molecular charge. Defaults to 0.
|
multiplicity
|
An integer giving the spin multiplicity.
|
description
|
An optional string giving a description. As an example,
for dimers a likely description is the bond length (e.g. 0.7414).
|
name
|
A string giving a characteristic name for the instance.
|
filename
|
The name of the file where the molecule data is saved.
|
n_atoms
|
Integer giving the number of atoms in the molecule.
|
n_electrons
|
Integer giving the number of electrons in the molecule.
|
atoms
|
List of the atoms in molecule sorted by atomic number.
|
protons
|
List of atomic charges in molecule sorted by atomic number.
|
hf_energy
|
Energy from open or closed shell Hartree-Fock.
|
nuclear_repulsion
|
Energy from nuclei-nuclei interaction.
|
canonical_orbitals
|
numpy array giving canonical orbital coefficients.
|
n_orbitals
|
Integer giving total number of spatial orbitals.
|
n_qubits
|
Integer giving total number of qubits that would be needed.
|
orbital_energies
|
Numpy array giving the canonical orbital energies.
|
fock_matrix
|
Numpy array giving the Fock matrix.
|
overlap_integrals
|
Numpy array of AO overlap integrals
|
one_body_integrals
|
Numpy array of one-electron integrals
|
two_body_integrals
|
Numpy array of two-electron integrals
|
mp2_energy
|
Energy from MP2 perturbation theory.
|
cisd_energy
|
Energy from configuration interaction singles + doubles.
|
cisd_one_rdm
|
Numpy array giving 1-RDM from CISD calculation.
|
cisd_two_rdm
|
Numpy array giving 2-RDM from CISD calculation.
|
fci_energy
|
Exact energy of molecule within given basis.
|
fci_one_rdm
|
Numpy array giving 1-RDM from FCI calculation.
|
fci_two_rdm
|
Numpy array giving 2-RDM from FCI calculation.
|
ccsd_energy
|
Energy from coupled cluster singles + doubles.
|
ccsd_single_amps
|
Numpy array holding single amplitudes
|
ccsd_double_amps
|
Numpy array holding double amplitudes
|
general_calculations
|
A dictionary storing general calculation results
for this system annotated by the key.
|
Methods
get_active_space_integrals
View source
get_active_space_integrals(
occupied_indices=None, active_indices=None
)
Restricts a molecule at a spatial orbital level to an active space
This active space may be defined by a list of active indices and
doubly occupied indices. Note that one_body_integrals and
two_body_integrals must be defined
n an orthonormal basis set.
| Args |
|---|
occupied_indices
|
A list of spatial orbital indices
indicating which orbitals should be considered doubly occupied.
|
active_indices
|
A list of spatial orbital indices indicating
which orbitals should be considered active.
|
| Returns |
|---|
tuple
|
Tuple with the following entries:
core_constant: Adjustment to constant shift in Hamiltonian
from integrating out core orbitals
one_body_integrals_new: one-electron integrals over active
space.
two_body_integrals_new: two-electron integrals over active
space.
|
get_antisym
View source
get_antisym()
Method to return anti-symmetrized integrals in spin-orbital basis.
| Returns |
|---|
antisymints
|
Numpy array of anti-symmetrized integrals in spin-
orbital basis = - (physicist ordering)
|
| Raises |
|---|
MissingCalculationError
|
If integrals are not calculated.
|
get_from_file
View source
get_from_file(
property_name
)
Helper routine to re-open HDF5 file and pull out single property
| Args |
|---|
property_name
|
Property name to load from self.filename
|
| Returns |
|---|
|
The data located at file[property_name] for the HDF5 file at
self.filename. Returns None if the key is not found in the
file.
|
get_integrals
View source
get_integrals()
Method to return 1-electron and 2-electron integrals in MO basis.
| Returns |
|---|
one_body_integrals
|
An array of the one-electron integrals having
shape of (n_orbitals, n_orbitals).
|
two_body_integrals
|
An array of the two-electron integrals having
shape of (n_orbitals, n_orbitals, n_orbitals, n_orbitals).
|
| Raises |
|---|
MissingCalculationError
|
If integrals are not calculated.
|
get_j
View source
get_j()
Method to return coulomb matrix.
| Returns |
|---|
k_matr
|
Numpy array of the coulomb integrals J_{p,q} = (pp|qq)
(in chemist notation).
|
| Raises |
|---|
MissingCalculationError
|
If integrals are not calculated.
|
get_k
View source
get_k()
Method to return exchange matrix.
| Returns |
|---|
k_matr
|
Numpy array of the coulomb integrals K_{p,q} = (pq|qp)
(in chemist notation).
|
| Raises |
|---|
MissingCalculationError
|
If integrals are not calculated.
|
get_molecular_hamiltonian
View source
get_molecular_hamiltonian(
occupied_indices=None, active_indices=None
)
Output arrays of the second quantized Hamiltonian coefficients.
| Args |
|---|
|
occupied_indices(list): A list of spatial orbital indices
indicating which orbitals should be considered doubly occupied.
active_indices(list): A list of spatial orbital indices indicating
which orbitals should be considered active.
|
| Returns |
|---|
molecular_hamiltonian
|
An instance of the MolecularOperator class.
|
Note:
The indexing convention used is that even indices correspond to
spin-up (alpha) modes and odd indices correspond to spin-down
(beta) modes.
get_molecular_rdm
View source
get_molecular_rdm(
use_fci=False
)
Method to return 1-RDM and 2-RDMs from CISD or FCI.
| Args |
|---|
use_fci
|
Boolean indicating whether to use RDM from FCI
calculation.
|
| Returns |
|---|
rdm
|
An instance of the MolecularRDM class.
|
| Raises |
|---|
MisissingCalculationError
|
If the CI calculation has not been
performed.
|
get_n_alpha_electrons
View source
get_n_alpha_electrons()
Return number of alpha electrons.
get_n_beta_electrons
View source
get_n_beta_electrons()
Return number of beta electrons.
init_lazy_properties
View source
init_lazy_properties()
Initializes properties loaded on demand to None
load
View source
load()
save
View source
save()
Method to save the class under a systematic name.
View source on GitHub