MolecularReactionPath¶

class MolecularReactionPath(reaction_path, filename, object_id, calculator=None, fuzz_factor=None, log_filename_prefix=None, number_of_processes_per_task=None, optimize_geometry_parameters=None, dynamical_matrix_parameters=None)¶

Class for estimating the reactant, transition and product states of a NudgedElasticBand. The product state can only be bimolecular.

Parameters:

reaction_path (NudgedElasticBand) – The reaction path to investigate the best transition state estimate on. The reaction path can only contain MoleculeConfigurations.
filename (str) – The full or relative path to save the results to. See nlsave().
object_id (str) – The object id to use when saving. See nlsave().
calculator (Calculator | None) – A calculator to attach.
Default: Use the calculator on the reaction path.
fuzz_factor (float) – The factor by which the covalent radii are multiplied to determine the cutoff distance for a bond.
Default: 1.2
log_filename_prefix (str | LogToStdOut) – Filename prefix for the logging output of magnetic anisotropy energy calculations. If LogToStdOut, all logging will instead be sent to standard output.
Default: 'molecular_reaction_path_'.
number_of_processes_per_task (int | None | ProcessesPerNode) – The number of processes that will be used to execute each task. If the total number of process does not divide evenly into the tasks, some tasks may have less than this number of processes. If None, all available processes execute each task collaboratively.
optimize_geometry_parameters (OptimizeGeometryParameters) – The parameters for the geometry optimization.
dynamical_matrix_parameters (DynamicalMatrixParameters) – The parameters for the DynamicalMatrix.

dependentStudies()¶

Returns:: The list of dependent studies.
Return type:: list of Study

dynamicalMatrixParameters()¶

Returns:: The parameters for the dynamical matrix.
Return type:: DynamicalMatrixParameters

filename()¶

Returns:: The filename where the study object is stored.
Return type:: str

firstProductMolecule()¶

Returns:: The first reaction product state.
Return type:: IdealGasThermoChemistry

fuzzFactor()¶

Returns:: The factor by which the covalent radii are multiplied to determine the cutoff distance for a bond.
Return type:: float

hasTightBarrier()¶

Returns:: None if the study has not been updated, True if a tight barrier was found.
Return type:: None | bool

logFilenamePrefix()¶

Returns:: The filename prefix for the logging output of the study.
Return type:: str | LogToStdOut

nlinfo()¶

Returns:: Structured information about the DynamicalMatrix.
Return type:: dict

nlprint(stream=None)¶

Print a string containing an ASCII table useful for plotting the Study object.

Parameters:: stream (python stream) – The stream the table should be written to.
Default: NLPrintLogger()

numberOfProcessesPerTask()¶

Returns:: The number of processes to be used to execute each task. If None, all available processes execute each task collaboratively.
Return type:: int | None | ProcessesPerNode

numberOfProcessesPerTaskResolved()¶

Returns:: The number of processes to be used to execute each task. Default values are resolved based on the current execution settings.
Return type:: int

objectId()¶

Returns:: The name of the study object in the file.
Return type:: str

optimizeGeometryParameters()¶

Returns:: The parameters for the geometry optimization.
Return type:: OptimizeGeometryParameters

products()¶

Returns:: The product states.
Return type:: list (size 2) of IdealGasThermoChemistry

reactant()¶

Returns:: The reactant state.
Return type:: IdealGasThermoChemistry

reactionPath()¶

Returns:: The reaction path.
Return type:: NudgedElasticBand

saveToFileAfterUpdate()¶

Returns:: Whether the study is automatically saved after it is updated.
Return type:: bool

secondProductMolecule()¶

Returns:: The second reaction product state.
Return type:: IdealGasThermoChemistry

transitionState()¶

Returns:: The transition state at the given temperature.
Return type:: IdealGasThermoChemistry

uniqueString()¶: Return a unique string representing the state of the object.

update()¶: Perform the update