qrunch.chemistry.reaction_path_problem.builders.even_handed_reaction_path_problem_builders

Module containing builder for reaction path problems using the even-handed subsystem selection method.

Functions

`compare`(old_point_data, new_point_data)	Compare two lists of integers and return the new and missing values.
`log_preliminary_data_change`(new_data, data)	Print the data.

Classes

`EvenHandedReactionPathProblemBuilder`	Reaction path problem builder which uses the even-handed subsystem selection method.
`EvenHandedRestrictedReactionPathProblemBuilder`	Restricted reaction path problem builder which uses the even-handed subsystem selection method.
`EvenHandedUnrestrictedReactionPathProblemBuilder`	Unrestricted reaction path problem builder which uses the even-handed subsystem selection method.

class EvenHandedReactionPathProblemBuilder

Bases: ReactionPathProblemBuilder

Reaction path problem builder which uses the even-handed subsystem selection method.

The Even-handed subsystem selection is described in https://doi.org/10.1063/1.5050533.

__init__(full_system_solver: MeanFieldCalculator, embedded_orbital_calculator: MolecularOrbitalCalculator, localizer: OrbitalLocalizer, orbital_assigner: OrbitalAssigner, projector_builder: ManbysLevelShiftProjectorBuilder, data_persister_manager: DataPersisterManager | None = None, problem_modifiers: list[GroundStateProblemModifier] | None = None, cube_generator: ProjectiveEmbeddingCubeGenerator | None = None, repulsion_integral_builder: TwoBodyElectronRepulsionIntegralBuilderProtocol | None = None) → None

Initialize an even-handed reaction path problem builder.

Parameters:

full_system_solver (MeanFieldCalculator) – Mean field solver used to find orbitals for the whole system.
embedded_orbital_calculator (MolecularOrbitalCalculator) – Solver used to find orbitals for the embedded system.
localizer (OrbitalLocalizer) – Localizer used to localize orbitals before embedding.
orbital_assigner (OrbitalAssigner) – Orbital assigner used to assign localized orbitals to the embedded region.
projector_builder (ManbysLevelShiftProjectorBuilder) – Projector used separate the embedded and environment regions while solving.
data_persister_manager (DataPersisterManager | None) – Manager to handle saving and loading heavy full system calculations.
problem_modifiers (list[GroundStateProblemModifier] | None) – A list of problem modifiers
cube_generator (ProjectiveEmbeddingCubeGenerator | None) – An Optional Cube Generator
repulsion_integral_builder (TwoBodyElectronRepulsionIntegralBuilderProtocol | None) – The object that can build two electron repulsion integrals. TwoBodyElectronRepulsionIntegralBuilder is used as default.

Return type:

None

build_restricted(reaction_configuration: ReactionConfiguration) → RestrictedReactionPathProblem

Build the restricted even-handed reaction path problem.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: RestrictedReactionPathProblem

build_restricted_cube_files(reaction_configuration: ReactionConfiguration) → None

Build restricted cube files.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: None

build_unrestricted(reaction_configuration: ReactionConfiguration) → UnrestrictedReactionPathProblem

Build the unrestricted even-handed reaction path problem.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: UnrestrictedReactionPathProblem

build_unrestricted_cube_files(reaction_configuration: ReactionConfiguration) → None

Build unrestricted cube files.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: None

classmethod persistence_checkpoints() → list[str]

Define the persistence checkpoints used during the embedding process.

These checkpoints specify computational stages where intermediate results can be saved and loaded to optimize computations and ensure reproducibility.

Return type:: list[str]

class EvenHandedRestrictedReactionPathProblemBuilder

Bases: object

Restricted reaction path problem builder which uses the even-handed subsystem selection method.

The Even-handed subsystem selection is described in https://doi.org/10.1063/1.5050533.

__init__(full_system_solver: MeanFieldCalculator, embedded_orbital_calculator: MolecularOrbitalCalculator, localizer: OrbitalLocalizer, orbital_assigner: OrbitalAssigner, projector_builder: ManbysLevelShiftProjectorBuilder, data_persister_manager: DataPersisterManager | None = None, problem_modifiers: list[GroundStateProblemModifier] | None = None, cube_generator: ProjectiveEmbeddingCubeGenerator | None = None, repulsion_integral_builder: TwoBodyElectronRepulsionIntegralBuilderProtocol | None = None) → None

Initialize an even-handed reaction path problem builder.

Parameters:

full_system_solver (MeanFieldCalculator) – Mean field solver used to find orbitals for the whole system.
embedded_orbital_calculator (MolecularOrbitalCalculator) – Solver used to find orbitals for the embedded system.
localizer (OrbitalLocalizer) – Localizer used to localize orbitals before embedding.
orbital_assigner (OrbitalAssigner) – Orbital assigner used to assign localized orbitals to the embedded region.
projector_builder (ManbysLevelShiftProjectorBuilder) – Projector used separate the embedded and environment regions while solving.
data_persister_manager (DataPersisterManager | None) – Manager to handle saving and loading heavy full system calculations.
problem_modifiers (list[GroundStateProblemModifier] | None) – A list of problem modifiers
cube_generator (ProjectiveEmbeddingCubeGenerator | None) – An Optional Cube Generator
repulsion_integral_builder (TwoBodyElectronRepulsionIntegralBuilderProtocol | None) – The object that can build two electron repulsion integrals. TwoBodyElectronRepulsionIntegralBuilder is used as default.

Return type:

None

build(reaction_configuration: ReactionConfiguration) → RestrictedReactionPathProblem

Build the reaction path problem.

This method uses the Even-handed subsystem selection as described in https://doi.org/10.1063/1.5050533.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: RestrictedReactionPathProblem

build_cube_files(reaction_configuration: ReactionConfiguration) → None

Build cube files.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: None

classmethod persistence_checkpoints() → list[str]

Define the persistence checkpoints used during the embedding process.

These checkpoints specify computational stages where intermediate results can be saved and loaded to optimize computations and ensure reproducibility.

Return type:: list[str]

class EvenHandedUnrestrictedReactionPathProblemBuilder

Bases: object

Unrestricted reaction path problem builder which uses the even-handed subsystem selection method.

The Even-handed subsystem selection is described in https://doi.org/10.1063/1.5050533.

__init__(full_system_solver: MeanFieldCalculator, embedded_orbital_calculator: MolecularOrbitalCalculator, localizer: OrbitalLocalizer, orbital_assigner: OrbitalAssigner, projector_builder: ManbysLevelShiftProjectorBuilder, data_persister_manager: DataPersisterManager | None = None, problem_modifiers: list[GroundStateProblemModifier] | None = None, cube_generator: ProjectiveEmbeddingCubeGenerator | None = None, repulsion_integral_builder: TwoBodyElectronRepulsionIntegralBuilderProtocol | None = None) → None

Initialize an even-handed reaction path problem builder.

Parameters:

full_system_solver (MeanFieldCalculator) – Mean field solver used to find orbitals for the whole system.
embedded_orbital_calculator (MolecularOrbitalCalculator) – Solver used to find orbitals for the embedded system.
localizer (OrbitalLocalizer) – Localizer used to localize orbitals before embedding.
orbital_assigner (OrbitalAssigner) – Orbital assigner used to assign localized orbitals to the embedded region.
projector_builder (ManbysLevelShiftProjectorBuilder) – Projector used separate the embedded and environment regions while solving.
data_persister_manager (DataPersisterManager | None) – Manager to handle saving and loading heavy full system calculations.
problem_modifiers (list[GroundStateProblemModifier] | None) – A list of problem modifiers
cube_generator (ProjectiveEmbeddingCubeGenerator | None) – An Optional Cube Generator
repulsion_integral_builder (TwoBodyElectronRepulsionIntegralBuilderProtocol | None) – The object that can build two electron repulsion integrals. TwoBodyElectronRepulsionIntegralBuilder is used as default.

Return type:

None

build(reaction_configuration: ReactionConfiguration) → UnrestrictedReactionPathProblem

Build the reaction path problem.

This method uses the Even-handed subsystem selection as described in https://doi.org/10.1063/1.5050533.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: UnrestrictedReactionPathProblem

build_cube_files(reaction_configuration: ReactionConfiguration) → None

Build cube files.

Parameters:: reaction_configuration (ReactionConfiguration) – The reaction configuration object.
Return type:: None

classmethod persistence_checkpoints() → list[str]

Define the persistence checkpoints used during the embedding process.

These checkpoints specify computational stages where intermediate results can be saved and loaded to optimize computations and ensure reproducibility.

Return type:: list[str]

compare(old_point_data: list[int], new_point_data: list[int]) → tuple[list[int], list[int]]

Compare two lists of integers and return the new and missing values.

Parameters:

old_point_data (list[int]) – The old list of integers.
new_point_data (list[int]) – The new list of integers.

Return type:

tuple[list[int], list[int]]

log_preliminary_data_change(new_data: list[PreliminaryRestrictedData] | list[PreliminaryUnrestrictedData], data: list[PreliminaryRestrictedData] | list[PreliminaryUnrestrictedData]) → None

Print the data.

Parameters:

new_data (list[PreliminaryRestrictedData] | list[PreliminaryUnrestrictedData]) – The list of orbital data for each configuration.
data (list[PreliminaryRestrictedData] | list[PreliminaryUnrestrictedData]) – The list of orbital data for each configuration.

Return type:

None