`pychemiq.Molecules`#

Classes#

class Molecules(geometry=None, basis=None, multiplicity=None, charge=0, active=None, nfrozen=None)#

Initialize the electronic structure parameters of molecules, including charge, basis-set, atomic coordinates, spin multiplicity, etc.

Parameters:

geometry (str) – Enter the element symbol and coordinates of atoms in the molecule. It can be a string type or a string list. For example: geometry=”H 0 0 0, H 0 0 0.74” or geometry=[“H 0 0 0”, “H 0 0 0.74”].
basis (str) – Set the basis set level required for computation: [MINI / sto-3G / sto-6G / 3-21G / 6-31G / …]. Starting from version V1.1.0, pyChemiQ supports over 600 commonly used basis sets as well as user-defined basis sets. It supports most basis sets available on the Basis Set Exchange website (excluding a few excessively large ones), including but not limited to STO-nG basis sets, Pople series basis sets, Ahlrichs’ def-series basis sets, Dunning series basis sets, and pseudopotential basis sets. In previous versions, supported basis sets included: MINI, STO-3G, STO-6G, 3-21G, and 6-31G. Other basis sets can be directly entered by name. The specific string input rules for basis set names please refer to ./06API/Configs .
multiplicity (int) – Set the spin multiplicity (M=2S+1), with a default value of 1.
charge (int) – Set the number of charges in the system. When the number of charges is positive, there is no positive sign, and when it is negative, a negative sign is written. The default value is 0.
active (int,int) – Sets the active space, specified as two comma-separated integers. Default: not set. For example, textit{active = 4, 4} means 4 active spatial orbitals with 4 electrons in the active space.
nfrozen (int) – Sets the number of frozen orbitals. Default: 0. Note: active and nfrozen cannot be used simultaneously.

Returns:

None.

Attributes

n_atoms#: Obtaining the number of atoms in a molecular system.

n_electrons#: Obtaining the number of electrons in the molecular system.

n_orbitals#: Obtaining the total molecular orbital number of the molecular system.

n_qubits#: Obtaining the total number of quantum bits required for calculation (i.e. number of spin orbitals, 2 * number of molecular orbitals)

hf_energy#: Obtaining the Hartree-Fock energy(unit: Hartree).

nuclear_repulsion#: Obtaining the inter nuclear repulsion of the molecular system (unit: Hartree)

canonical_orbitals#: Obtaining the canonical orbital coefficients (i.e. molecular orbital coefficients) of the molecular system.

orbital_energies#: Obtaining the energy of each molecular orbital in the system.

overlap_integrals#: Obtaining overlapping integrals of a molecular system.

one_body_integrals#: Obtaining single electron integrals for a molecular system.

two_body_integrals#: Obtaining the double electron integral of a molecular system.

Methods

get_molecular_hamiltonian()#: Obtaining the Hamiltonian of the initialized molecular system.

Interface example:

from pychemiq import Molecules
multiplicity = 1
charge = 0
basis =  "sto-3g"
geom = "H 0 0 0,H 0 0 0.74"
mol = Molecules(
      geometry = geom,
      basis    = basis,
      multiplicity = multiplicity,
      charge = charge)

Call the following interface to obtain information about the molecular system:

print("The number of atoms is", mol.n_atoms)
print("The number of electrons is", mol.n_electrons)
print("The number of orbitals is", mol.n_orbitals)
print("The number of qubits is", mol.n_qubits)
print("The Hartree-Fock energy is", mol.hf_energy)
print("The nuclear repulsion is", mol.nuclear_repulsion)

The number of atoms is 2
The number of electrons is 2
The number of orbitals is 2
The number of qubits is 4
The Hartree-Fock energy is -1.1167593072992057
The nuclear repulsion is 0.7151043390810812

print("The canonical orbitals are\n", mol.canonical_orbitals)
print("The orbital energies are", mol.orbital_energies)
print("The overlap integrals are\n", mol.overlap_integrals)

The canonical orbitals are
 [[-0.54884228  1.21245192]
 [-0.54884228 -1.21245192]]

The orbital energies are [-0.57855386  0.67114349]

The overlap integrals are
 [[1.         0.65987312]
 [0.65987312 1.        ]]

print("The one body integrals are\n", mol.one_body_integrals)
print("The two body integrals are\n", mol.two_body_integrals)

The one body integrals are
 [[-1.25330979e+00  0.00000000e+00]
 [ 4.16333634e-17 -4.75068849e-01]]

The two body integrals are
 [[[[ 6.74755927e-01 -1.11022302e-16]
   [-8.32667268e-17  6.63711401e-01]]

  [[-3.46944695e-17  1.81210462e-01]
   [ 1.81210462e-01  0.00000000e+00]]]


 [[[-4.85722573e-17  1.81210462e-01]
   [ 1.81210462e-01 -2.22044605e-16]]

  [[ 6.63711401e-01 -2.22044605e-16]
   [-1.66533454e-16  6.97651504e-01]]]]

print("The molecular hamiltonian is", mol.get_molecular_hamiltonian())

The molecular hamiltonian is {
: 0.715104
0+ 0 : -1.253310
1+ 0+ 1 0 : -0.674756
1+ 0+ 3 2 : -0.181210
1+ 1 : -1.253310
2+ 0+ 2 0 : -0.482501
2+ 1+ 2 1 : -0.663711
2+ 1+ 3 0 : 0.181210
2+ 2 : -0.475069
3+ 0+ 2 1 : 0.181210
3+ 0+ 3 0 : -0.663711
3+ 1+ 3 1 : -0.482501
3+ 2+ 1 0 : -0.181210
3+ 2+ 3 2 : -0.697652
3+ 3 : -0.475069
}

pychemiq.Molecules#

Classes#

`pychemiq.Molecules`#