scine_chemoton.gears.elementary_steps¶
Classes
Base class for elementary step reaction generators |
- class scine_chemoton.gears.elementary_steps.ElementaryStepGear[source]¶
Base class for elementary step reaction generators
- class Options(_parent=None)[source]¶
The options for an ElementarySteps Gear.
-
base_job_settings:
ValueCollection¶ - ValueCollection
The base settings for the jobs. Duplicate keys are overwritten by the settings of the TrialGenerator.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- enable_bimolecular_trials¶
- bool
If True, enables the exploration of bimolecular reactions.
- enable_unimolecular_trials¶
- bool
If True, enables the exploration of unimolecular reactions.
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model:
Model¶ - db.Model
The model the Gear is working with.
- run_one_cycle_with_settings_enhancement¶
- bool
If True, enables the enhancement of the settings for the next cycle.
-
structure_model:
Model¶ - Optional[db.Model]
If not None, calculations are only started for structures with the given model.
-
base_job_settings:
- bimolecular_coordinates(credentials, observer=None)[source]¶
Returns the reaction coordinates allowed for bimolecular reactions for the whole database based on the set options and filters. This method does not set up new calculations. The returned object is a dictionary of dictionaries containing a dictionary specifying the coordinates. The dictionary holds the aggregate IDs, the next dictionary holds then the structures of each aggregate with the reaction coordinate information. 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[str,Dict[str,Dict[Tuple[List[Tuple[int,int]],int],List[Tuple[ndarray,ndarray,float,float]]]]]- Parameters:
- credentialsdb.Credentials
The credentials of the database.
- observerOptional[Callable[[], None]]
A function that is called after each aggregate to count the number of aggregates processed.
Notes
The index basis (total system or separate systems) of the returned indices in the reaction coordinates varies between different TrialGenerator implementations!
- unimolecular_coordinates(credentials, observer=None)[source]¶
Returns the reaction coordinates allowed for unimolecular reactions for the whole database based on the set options and filters. This method does not set up new calculations. The returned object is a dictionary of dictionaries containing list of tuple. The dictionary holds the aggregate IDs, the next dictionary holds then the structures of each aggregate with the reaction coordinate information. The first argument in the tuple is a list of reaction coordinates. The second argument in the tuple is the number of dissociations.
Modules
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