tangelo.algorithms.classical package

Subpackages

Submodules

tangelo.algorithms.classical.ccsd_solver module

Class performing electronic structure calculation employing the CCSD method.

class tangelo.algorithms.classical.ccsd_solver.CCSDSolver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Bases: ElectronicStructureSolver

Uses the Full CI method to solve the electronic structure problem.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in available_ccsd_solvers (from tangelo.algorithms.classical.ccsd_solver). Can also provide a user-defined CCSD implementation (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. lambdacc, fnocc), Convergence options etc.

solver

The backend specific CCSD solver

Type:

Type[ElectronicStructureSolver]

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If method “simulate” hasn’t been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total CCSD energy.

class tangelo.algorithms.classical.ccsd_solver.CCSDSolverPsi4(molecule: SecondQuantizedMolecule)

Bases: ElectronicStructureSolver

Uses the CCSD method to solve the electronic structure problem, through Psi4.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

ccwfn

The CCSD wavefunction (float64).

Type:

psi4.core.CCWavefunction

backend

The psi4 module

Type:

psi4

molecule

The molecule with symmetry=False

Type:

SecondQuantizedMolecule

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returning RDMS from a CCSD calculation in Psi4 is not implemented at this time.

It may be possible to obtain the one-rdm by running a psi4 CCSD gradient calculation (https://forum.psicode.org/t/saving-ccsd-density-for-read-in/2416/2) Another option to obtain the one-rdm is to use pycc (https://github.com/CrawfordGroup/pycc)

Raises:

NotImplementedError – Returning RDMs from Psi4 in Tangelo is not supported at this time.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total CCSD energy.

class tangelo.algorithms.classical.ccsd_solver.CCSDSolverPySCF(molecule)

Bases: ElectronicStructureSolver

Uses the CCSD method to solve the electronic structure problem, through pyscf.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

cc_fragment

The coupled-cluster object.

Type:

pyscf.cc.CCSD

mean_field

The mean field of the molecule.

Type:

pyscf.scf.RHF

frozen

Frozen molecular orbitals.

Type:

list or int

get_rdm()

Calculate the 1- and 2-particle reduced density matrices. The CCSD lambda equation will be solved for calculating the RDMs.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If no simulation has been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – CCSD energy.

tangelo.algorithms.classical.ccsd_solver.get_ccsd_solver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Return requested target CCSDSolverName object.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in ccsd_solver_dict (from tangelo.algorithms.classical.ccsd_solver). Can also provide a user-defined backend (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. lambdacc, fnocc), Convergence options etc.

tangelo.algorithms.classical.fci_solver module

Define electronic structure solver employing the full configuration interaction (CI) method.

class tangelo.algorithms.classical.fci_solver.FCISolver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Bases: ElectronicStructureSolver

Uses the Full CI method to solve the electronic structure problem.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in available_fci_solvers (from tangelo.algorithms.classical.fci_solver). Can also provide a user-defined FCI implementation (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. mcscf, fci), Convergence options etc.

solver

The solver that is used for obtaining the FCI solution.

Type:

Type[ElectronicStructureSolver]

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If method “simulate” hasn’t been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total FCI energy.

class tangelo.algorithms.classical.fci_solver.FCISolverPsi4(molecule: SecondQuantizedMolecule)

Bases: ElectronicStructureSolver

Uses the Full CI method to solve the electronic structure problem, through Psi4.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

ciwfn

The CI wavefunction (float64).

Type:

psi4.core.CIWavefunction

backend

The psi4 module

Type:

psi4

molecule

The molecule with symmetry=False

Type:

SecondQuantizedMolecule

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If method “simulate” hasn’t been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total FCI energy.

class tangelo.algorithms.classical.fci_solver.FCISolverPySCF(molecule)

Bases: ElectronicStructureSolver

Uses the Full CI method to solve the electronic structure problem, through pyscf.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

ci

The CI wavefunction (float64).

Type:

numpy.array

norb

The number of molecular orbitals.

Type:

int

nelec

The number of electrons.

Type:

int

cisolver

The Full CI object.

Type:

pyscf.fci.direct_spin0.FCI

mean_field

Mean field object.

Type:

pyscf.scf

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If method “simulate” hasn’t been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total FCI energy.

tangelo.algorithms.classical.fci_solver.get_fci_solver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Return requested target FCISolverName object.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in available_fci_solvers (from tangelo.algorithms.classical.fci_solver). Can also provide a user-defined FCI implementation (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. mcscf, fci), Convergence options etc.

tangelo.algorithms.classical.mp2_solver module

Define electronic structure solver employing the Moller-Plesset perturbation theory to second order (MP2) method.

class tangelo.algorithms.classical.mp2_solver.MP2Solver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Bases: ElectronicStructureSolver

Uses the MP2 method to solve the electronic structure problem.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in available_mp2_solvers (see mp2_solver.py). Can also provide a user-defined MP2 implementation (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. dfmp2, mp2), Convergence options etc.

solver

The solver that is used for obtaining the MP2 solution.

Type:

Type[ElectronicStructureSolver]

get_mp2_amplitudes()

Compute the double amplitudes from the MP2 perturbative method, and then reorder the elements into a dense list. The single (T1) amplitudes are set to a small non-zero value. The ordering is single, double (diagonal), double (non-diagonal).

Returns:

list of float – The electronic excitation amplitudes.

get_rdm()

Compute the Full CI 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total MP2 energy.

class tangelo.algorithms.classical.mp2_solver.MP2SolverPsi4(molecule: SecondQuantizedMolecule)

Bases: ElectronicStructureSolver

Uses the MP2 method to solve the electronic structure problem, through Psi4.

Only supports frozen core (active) orbitals sequentially from bottom (top) of energy ordering.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

mp2wfn

The Psi4 Wavefunction returned from an mp2 calculation.

Type:

psi4.core.Wavefunction

backend

The psi4 module

Type:

psi4

molecule

The molecule with symmetry=False

Type:

SecondQuantizedMolecule

get_mp2_amplitudes()

Compute the double amplitudes from the MP2 perturbative method, and then reorder the elements into a dense list. The single (T1) amplitudes are set to a small non-zero value. The ordering is single, double (diagonal), double (non-diagonal).

Returning MP2 amplitudes from Psi4 is not currently supported in Tangelo

Using https://github.com/psi4/psi4numpy/blob/master/Tutorials/10_Orbital_Optimized_Methods/10a_orbital-optimized-mp2.ipynb should return appropriate amplitudes for a closed shell RHF reference.

Raises:

NotImplementedError – Not implemented at this time

get_rdm()

Calculate the 1- and 2-particle reduced density matrices.

Obtaining MP2 rdms from Psi4 is not currently supported in Tangelo.

Using https://github.com/psi4/psi4numpy/blob/master/Tutorials/10_Orbital_Optimized_Methods/10a_orbital-optimized-mp2.ipynb should return appropriate RDMs for a closed shell RHF reference.

Raises:

NotImplementedError – Not implemented at this time

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – Total MP2 energy.

class tangelo.algorithms.classical.mp2_solver.MP2SolverPySCF(molecule)

Bases: ElectronicStructureSolver

Uses the Second-order Moller-Plesset perturbation theory (MP2) method to solve the electronic structure problem, through pyscf.

Parameters:

molecule (SecondQuantizedMolecule) – The molecule to simulate.

mp2_fragment

The coupled-cluster object.

Type:

pyscf.mp.MP2

mean_field

The mean field of the molecule.

Type:

pyscf.scf.RHF

frozen

Frozen molecular orbitals.

Type:

list or int

get_mp2_amplitudes()

Compute the double amplitudes from the MP2 perturbative method, and then reorder the elements into a dense list. The single (T1) amplitudes are set to a small non-zero value. The ordering is single, double (diagonal), double (non-diagonal).

Returns:

list of float – The electronic excitation amplitudes.

get_rdm()

Calculate the 1- and 2-particle reduced density matrices.

Returns:

• numpy.array – One-particle RDM.

• numpy.array – Two-particle RDM.

Raises:

RuntimeError – If no simulation has been run.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – MP2 energy.

tangelo.algorithms.classical.mp2_solver.get_mp2_solver(molecule: SecondQuantizedMolecule, solver: None | str | Type[ElectronicStructureSolver] = 'pyscf', **solver_kwargs)

Return requested target MP2SolverName object.

Parameters:

• molecule (SecondQuantizedMolecule) – Molecule

• solver (string or Type[ElectronicStructureSolver] or None) – Supported string identifiers can be found in available_mp2_solvers (see mp2_solver.py). Can also provide a user-defined MP2 implementation (child to ElectronicStructureSolver class)

• solver_kwargs – Other arguments that could be passed to a target. Examples are solver type (e.g. mcscf, mp2), Convergence options etc.

Raises:

• ModuleNoyFoundError – No solver is specified and a user defined IntegralSolver was used in molecule.

• ValueError – The specified solver str is not one of the available_mp2_solvers (see mp2_solver.py)

• TypeError – The specified solver was not a string or sub class of ElectronicStructureSolver.

tangelo.algorithms.classical.semi_empirical_solver module

Class performing electronic structure calculation employing the semi-empirical methods. At first, semi-empirical methods are ways of computing the total energy of a molecule in a very fast way to optimize its geometry. Those methods are not ab initio as they employ empirical parameters, as stated in the name “semi-empirical”. They are in fact related to simplified Hartree-Fock versions with empirical corrections. Differences between them come from the process chosen to compute the empirical parameters. For example, MINDO3 inventors used atomization energies to fit their mathematical models.

They have been introduced in this package for the purpose of computing an environment energy and inducing constraints on atomic positions. As stand-alone solvers, they are however a poor choice, as they do not provide an accurate approximation of energies.

Here are the semi-empirical method(s) implemented:

• MINDO3

class tangelo.algorithms.classical.semi_empirical_solver.MINDO3Solver(molecule)

Bases: ElectronicStructureSolver

Uses the MINDO3 method to solve the electronic structure problem, through pyscf. Only the restricted (RMINDO3) flavor is implemented.

Parameters:

molecule (Molecule or SecondQuantizedMolecule) – The molecule to simulate.

Refs:

• 18. 3. Bingham, M. J. Dewar, D. H. Lo, J. Am. Chem. Soc., 97, 1285

  (1975).

• 4. 6. Lewis, Chem. Rev. 86, 1111 (1986).

get_rdm()

Method must be defined (ElectronicStructureSolver). For semi-empirical methods, it is not relevant nor defined.

simulate()

Perform the simulation (energy calculation) for the molecule.

Returns:

float – RMINDO3 energy.

Module contents