TransitionPath

class TransitionPath(configurations, filename, object_id, image_distance=None, preoptimization=None, assumed_prefactor=None, log_filename_prefix=None, number_of_processes_per_task=None, optimize_geometry_parameters=None)

Constructor for the TransitionPath object.

Parameters:
  • configurations (List of BulkConfiguration) – List of configurations for the transition path. The initial image to be used for the nudged elastic band configuration (first on list) should have an attached calculator. The following configurations will be intermediate states in the path. The last configuration will be final image to be used for the nudged elastic band configuration.
  • filename (str) – The full or relative filename path the Study object should be saved to. See nlsave().
  • object_id (str) – The name of the study that the Study object should be saved to within the file. This needs to be a unique name in this file. See nlsave().
  • image_distance (PhysicalQuantity of type length) – Distance between the coordinates of successive configurations for generating the nudged elastic band configuration.
    Default: 0.5 * Angstrom
  • preoptimization (bool) – Whether to optimize the end-point configurations before the start of the nudged elastic band optimization.
    Default: False
  • assumed_prefactor (PhysicalQuantity of type frequency) – A fixed value for the prefactors (both forward and reverse).
    Default: The prefactors are calculated from the vibrational frequencies at the minima and saddle point.
  • log_filename_prefix (str | LogToStdOut) – Filename prefix for the logging output of the transition path calculations. If LogToStdOut, all logging will instead be sent to standard output.
    Default: 'transitionpath'
  • number_of_processes_per_task (int) – The number of processes that will be used to execute each task. If this value is greater than or equal to the total number of available processes, each single task will be executed collaboratively over all processes. Otherwise, a delegator-worker scheme is used; in this case, one process will be set aside as the delegator, and the remaining ones will be grouped into workers and execute tasks concurrently.
    Default: All available processes execute each task collaboratively.
  • optimize_geometry_parameters (OptimizeGeometryParameters) – The parameters to use for optimizing the geometry. Note that constraints, pre_step_hook and```post_step_hook`` must be left unset.
    Default: OptimizeGeometryParameters()
assumedPrefactor()
Returns:The fixed value for the prefactors, if specified.
Return type:PhysicalQuantity of type frequency | None
calculator()
Returns:The calculator used for optimizing the nudged elastic band configuration.
Return type:Calculator
filename()
Returns:The filename where the study object is stored.
Return type:str
finalConfiguration()
Returns:The final image used for the nudged elastic band configuration.
Return type:BulkConfiguration
htstEvent()

Retrieve the HTSTEvent object with the calculated reaction rates.

Returns:The HTSTEvent object. If there was an error in the calculation, the error message is returned instead. If not available, returns None.
Return type:HTSTEvent | str | None
initialConfiguration()
Returns:The initial image used for the nudged elastic band configuration.
Return type:BulkConfiguration
isConverged()

Method for determining the convergence status of this transition path calculation. Successful convergence requires that (i) the NEB optimization has converged and (ii) the HTST event calculation was performed without errors.

Returns:The convergence status of this transition path.
Return type:bool | None
logFilenamePrefix()
Returns:The filename prefix for the logging output of the study.
Return type:str | LogToStdOut
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 should execute each task collaboratively.
Return type:int | None
objectId()
Returns:The name of the study object in the file.
Return type:str
optimizeGeometryParameters()
Returns:Parameters required to optimize the geometry.
Return type:OptimizeGeometryParameters
optimizedNudgedElasticBand()

Retrieve the optimized nudged elastic band configuration.

Returns:The optimized nudged elastic band configuration. If not available, returns None.
Return type:NudgedElasticBand | None
preoptimization()
Returns:Whether the end-point configurations are optimized before the start of the nudged elastic band optimization.
Return type:bool
update()

Run the calculations for the study object.