scine_chemoton.gears.elementary_steps.trial_generator

Classes

TrialGenerator()

Base class for elementary step trial generators

class scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator

Base class for elementary step trial generators

class Options(parent=None)

The options of the TrialGenerator

base_job_settings: ValueCollection

model: Model

unset_collections()

Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.

Return type:

None

abstract bimolecular_coordinates(structure_list, with_exact_settings_check=False)

Returns the reaction coordinates allowed for bimolecular reactions for the given structures based on the set options and filters. This method does not set up new calculations. The returned object is a list of dictionary. The keys are a tuple containing a reaction coordinates and the number of dissociations. The values hold a list of instructions. Each entry in this list allows to construct a reactive complex. Therefore, the number of reactive complexes per reaction coordinate can also be inferred.

Return type:

Dict[Tuple[List[Tuple[int, int]], int], List[Tuple[ndarray, ndarray, float, float]]]

Parameters:

structure_listList[db.Structure]

List of the two structures to be considered. The Structures have to be linked to a database.

with_exact_settings_checkbool

If True, more expensive queries are carried out to check if the settings of the calculations are exactly the same as the settings of the trial generator. This allows to add more inclusive additional reaction trials but the queries are less efficient, therefore this option should be only toggled if necessary.

Notes

The index basis (total system or separate systems) of the returned indices in the reaction coordinates varies between different implementations!

abstract bimolecular_reactions(structure_list, with_exact_settings_check=False)

Creates reactive complex calculations corresponding to the bimolecular reactions between the structures if there is not already a calculation to search for a reaction of the same structures with the same job order.

Return type:

None

Parameters:

structure_listList[db.Structure]

List of the two structures to be considered. The Structures have to be linked to a database.

with_exact_settings_checkbool

If True, more expensive queries are carried out to check if the settings of the calculations are exactly the same as the settings of the trial generator. This allows to add more inclusive additional reaction trials but the queries are less efficient, therefore this option should be only toggled if necessary.

abstract clear_cache()

abstract get_bimolecular_job_order()

Return type:

str

abstract get_unimolecular_job_order()

Return type:

str

initialize_collections(manager)

Return type:

None

static possible_attributes()

Return type:

List[str]

abstract unimolecular_coordinates(structure, with_exact_settings_check=False)

Returns the reaction coordinates allowed for unimolecular reactions for the given structure based on the set options and filters. This method does not set up new calculations. The returned object is a list of tuple. The first argument in the tuple is a list of reaction coordinates. The second argument in the tuple is the number of dissociations.

Return type:

List[Tuple[List[List[Tuple[int, int]]], int]]

Parameters:

structuredb.Structure

The structure to be considered. The Structure has to be linked to a database.

with_exact_settings_checkbool

If True, more expensive queries are carried out to check if the settings of the calculations are exactly the same as the settings of the trial generator. This allows to add more inclusive additional reaction trials but the queries are less efficient, therefore this option should be only toggled if necessary.

abstract unimolecular_reactions(structure, with_exact_settings_check=False)

Creates reactive complex calculations corresponding to the unimolecular reactions of the structure if there is not already a calculation to search for a reaction of the same structure with the same job order.

Return type:

None

Parameters:

structuredb.Structure

The structure to be considered. The Structure has to be linked to a database.

with_exact_settings_checkbool

If True, more expensive queries are carried out to check if the settings of the calculations are exactly the same as the settings of the trial generator. This allows to add more inclusive additional reaction trials but the queries are less efficient, therefore this option should be only toggled if necessary.

unset_collections()

Return type:

None

Modules

scine_chemoton.gears.elementary_steps.trial_generator.bond_based
scine_chemoton.gears.elementary_steps.trial_generator.connectivity_analyzer
scine_chemoton.gears.elementary_steps.trial_generator.fast_dissociations
scine_chemoton.gears.elementary_steps.trial_generator.fragment_based
scine_chemoton.gears.elementary_steps.trial_generator.template_based