process_class¶

class soda_analyzer.process_class(h5_lib, stateID, procID=0, structure_load=False)¶

Inspect one AKMC/APE process and its reactant, saddle, and product.

Parameters:

h5_lib (h5py.File) – Open SODA HDF5 file. Keep it open while using views derived from it.
stateID (int) – State identifier in /States.
procID (int, optional) – Process identifier within the selected state. Default: 0.
structure_load (bool, optional) – Construct ASE structure objects during loading rather than on a later request. Default: False.

stateID¶

Parent state identifier.

procID¶

Process identifier within the state.

fixed_list¶

Reactant fixed-atom boolean mask.

rsp_pos¶

Reconstructed reactant, saddle, and product coordinates in angstrom.

rsp_atoms¶

ASE structures, or an empty list when structure_load=False.

barrier_list¶

Forward and reverse barriers in eV.

prefactor_list¶

Forward and reverse attempt frequencies in inverse seconds.

energies¶

Reactant, saddle, and product energies in eV.

Notes

Available under the public name AkmcApeProcess; process_class remains a compatible name.

This record borrows its HDF5 handle. Keep the owning library open while accessing related records or lazily loaded data.

Methods¶

`get_atoms`	Build an ASE structure from stored coordinates and fixed-atom flags.
`get_barrier`	Read a process activation barrier in the selected direction.
`get_barrier_list`	Read forward and reverse process activation barriers.
`get_cell`	Read the selected structure cell in ASE convention.
`get_count`	Read the reactant delta atom-count field.
`get_energies`	Read energies of the reactant, saddle, and product.
`get_energy`	Read the stored energy of a process structure.
`get_fixed_list`	Read the fixed-atom mask for the selected structure.
`get_pos`	Read reconstructed atomic positions for the selected structure.
`get_prefactor`	Read a process attempt frequency in the selected direction.
`get_prefactor_list`	Read forward and reverse process attempt frequencies.
`get_rates`	Calculate forward and reverse rates from this process summary.
`get_refst`	Read the reactant delta reference-state field.
`get_rsp_atoms`	Build ASE structures for the reactant, saddle, and product.
`get_rsp_count`	Read delta counts through the process compatibility wrapper.
`get_rsp_pos`	Read positions for the reactant, saddle, and product.
`get_rsp_refst`	Read the reference-state fields through the process compatibility wrapper.
`get_species_list`	Read atomic numbers for the selected structure.
`get_stat_repeats`	Read the number of times this process was rediscovered.