States and processes

Inspect state and process records written by the AKMC and APE integrations. See Analyzing AKMC output for KMC transition histories and Analyzing APE output for exploration examples.

read_state_struct_array	Read one raw field from a state or process-delta record.
get_atomic_numbers_list	Read atomic numbers listed in the simulation components.
get_species_list	Read atomic numbers for the selected structure.
get_cell	Read the selected structure cell in ASE convention.
get_fixed_list	Read the fixed-atom mask for the selected structure.
get_pos	Read reconstructed atomic positions for the selected structure.
get_atoms	Build an ASE structure from stored coordinates and fixed-atom flags.
get_rsp_pos	Read positions for the reactant, saddle, and product.
get_rsp_atoms	Build ASE structures for the reactant, saddle, and product.
get_barrier	Read a process activation barrier in the selected direction.
get_barrier_list	Read forward and reverse process activation barriers.
get_prefactor	Read a process attempt frequency in the selected direction.
get_prefactor_list	Read forward and reverse process attempt frequencies.
get_rate	Calculate the Arrhenius rate from temperature, barrier, and prefactor.
get_energy	Read the stored energy of a process structure.
get_process_product_states_table	Read resolved process-to-product-state edges.
get_process_table	Read the process summary table for one state.
get_state_id_list	Return the sorted state identifiers present in the HDF5 file.
get_state_process_id_list	Return process identifiers available for one state.
structures_are_equivalent	Compare structures using species-aware minimum-image atom matching.
process_class	Inspect one AKMC/APE process and its reactant, saddle, and product.
state_class	Inspect one AKMC/APE state, its structures, and its process summaries.