soda_lib_class¶

class soda_analyzer.soda_lib_class(h5_path, workflow='auto', state_load=True, proc_load=False, structure_load=True, storesummariesinfile=True, env_load=False, nebscape_load=True, ezga_load=True)¶

Open SODA HDF5 output and expose views for its independently developed workflows.

Parameters:

h5_path (str or pathlib.Path) – Path to the SODA HDF5 output; opened read-only.
workflow (str, optional) – Workflow selector: auto, ape, ezga, nebscape, or akmc. Automatic detection uses the groups present in the file. Default: 'auto'.
state_load (bool, optional) – Populate state_list while opening the database. Default: True.
proc_load (bool, optional) – Populate process objects while loading states. Default: False.
structure_load (bool, optional) – Construct ASE structure objects during loading rather than on a later request. Default: True.
storesummariesinfile (bool, optional) – Read stored per-state search summaries when true; skip those summaries when false. Default: True.
env_load (bool, optional) – Populate the environment object list during loading. Default: False.
nebscape_load (bool, optional) – Create the NEBScape view if its group is present. Default: True.
ezga_load (bool, optional) – Create the EZGA view if its group is present. Default: True.

h5¶

Read-only HDF5 handle owned by this library.

Type:: h5py.File

workflow¶

Detected or requested workflow; mixed files report mixed.

Type:: str

state_id_list¶

State IDs as strings in numeric order.

Type:: numpy.ndarray

state_list¶

Loaded state views; empty if state loading is disabled.

Type:: list of state_class

state_num¶

Number of stored states.

Type:: int

environment_lib¶

Environment view, populated when requested.

Type:: environment_lib_class or None

ezga¶

EZGA view if its group exists and loading is enabled.

Type:: ezga_lib_class or None

nebscape¶

NEBScape view if its group exists and loading is enabled.

Type:: nebscape_lib_class or None

Notes

Available under the public name SodaLibrary; soda_lib_class remains a compatible name.

Call close() when finished. The explicit loading options above show the effective defaults; internal sentinels retain compatibility with the older positional constructor.

Examples

>>> from soda_analyzer import SodaLibrary
>>> db = SodaLibrary("output/output.h5", state_load=False)
>>> print(db.workflow)
>>> db.close()

Methods¶

`analyze_process_product_states`	Validate resolved process-to-product-state edges against process summaries.
`check_ape_cluster_member_distances`	Scan clustering-member embedded descriptors for cross-cluster distances.
`check_duplicate_processes`	Check process duplicates within each state using saddle and product equivalence.
`check_duplicate_states`	Check each state against earlier state IDs for duplicate structures.
`check_nebscape_minhop_history_equivalence`	Check MinHop result equivalence in a NEBScape SODA HDF5 source.
`close`	Close the HDF5 file owned by this library view.
`compare_nebscape_fairchem_native_outputs`	Compare Fairchem-backed SODA NEBScape evidence with native outputs.
`compare_nebscape_native_downstream_outputs`	Compare SODA downstream NEBScape endpoints with native staged artifacts.
`compare_nebscape_optimize_only_native_outputs`	Compare SODA optimize-only MinHop outputs with native minhop.xyz files.
`detect_workflow`	Detect the workflow from the requested selector and stored HDF5 groups.
`get_final_results`	Collect available NEBScape bands and optional refinement outputs.
`get_nebscape_workflow_progress_diagnostics`	Summarize persisted NEBScape workflow progress and dependencies.
`read_dynamics`	Read recorded AKMC state-to-state transitions.
`read_environmentlib`	Create and cache the APE environment library.
`read_ezga`	Create and cache the EZGA analysis view.
`read_meta`	Reload state identifiers and simulation metadata.
`read_nebscape`	Create and cache the NEBScape analysis view.
`read_process_product_states`	Read process-to-product-state edges.
`read_state`	Read one AKMC/APE state view.
`read_statelist`	Load and cache all state views.
`summarize_descriptor_registry_provenance`	Return counts for descriptor registry update/assignment cycle provenance.
`summarize_descriptor_sampling_flags`	Return counts for descriptor sampling flags, including alias-blocked rows.
`summarize_nebscape_fairchem_hdf5_numeric_sanity`	Check persisted NEBScape calculator-output fields for finite values.
`summarize_nebscape_fairchem_runtime`	Summarize Fairchem UMA runtime and calculate-metrics evidence from logs.
`summarize_nebscape_geometry_pair_preparation_logs`	Summarize split NEBScape geometry-pair preparation diagnostics from logs.
`summarize_nebscape_hpc_acceptance`	Return a mechanical acceptance report for a NEBScape multi-node run.
`summarize_nebscape_minhop_rejections`	Summarize the rejected MinHop result fraction in a NEBScape HDF5 source.
`summarize_nebscape_minhop_run_modes`	Summarize NEBScape search history and optimize-only finalization outcomes.
`summarize_nebscape_workflow_progress`	Summarize NEBScape workflow progress, partial rows, and dependencies.