JSON Output Reference

This page lists the fields (keys) of the result.json and summary.json files written with --out-json, split into the fields every command shares and the fields of each command.

--out-json flag

opt, sp, tsopt, freq, irc, scan, scan2d, scan3d, path-opt, dft, extract, trj2fig, and energy-diagram support --out-json / --no-out-json (default: off). When enabled, result.json and summary.json are written beside the normal outputs; the two files have the same content, so read result.json.

pdb2reaction opt -i r.pdb -q -1 --out-json --out-dir result_opt
cat result_opt/result.json | python -m json.tool

Open result_opt/result.json and read execution_status and scientific_status first; opt, tsopt, and path-opt also record optimization_status. The summary.json that all and path-search write without an --out-json flag is a different file with its own structure.

Common fields

Every result file carries the fields below; fields marked optional appear only when the command has the corresponding data:

Field	Type	Description
schema_version	string	Schema version of the file; a new version signals a structural change.
command	string	Single commands record the subcommand name (e.g. "opt"); the all / path-search summaries record the full command line
pdb2reaction_version	string	Package version
execution_status	string	Execution completion: completed / failed.
scientific_status	string	Result usability: success / partial / failed.
run_id	string	Optional UUID of the current invocation; written in every all run, including its stages.
elapsed_seconds	float	Optional wall-clock time; omitted by commands that do not record timing
environment	object	Hardware info (see below)
mlip_backend	string | null	Optional backend identifier; null when a plot-only command did not evaluate a calculator
mlip_model	string | null	Optional exact model/checkpoint identifier, kept separate from the backend
mlip_model_label	string | null	Optional publication-facing model label derived from the exact identifier
mlip_task	string | null	Optional backend task used by a multi-domain model; mlip_model remains the exact identifier
mlip_precision	string | null	Effective public precision token (fp32 or fp64); null for a custom calculator whose dtype is controlled by user code

environment:

Field	Type	Example
device	string	"cuda" or "cpu"
gpu_name	string	"<gpu model>"
gpu_vram_gb	float	<vram in GB>
cuda_version	string	"<cuda version>"
cpu	string	"<cpu model>"
n_cpus	int	<int>
ram_gb	float	<ram in GB>

Execution and requested-stage completion

Every result reports execution_status and scientific_status; multi-stage and scan results also list the outcome of each stage in the fields below.

Field	Type	Description
execution_status	string	completed or failed. In all, an endpoint optimization after IRC that does not converge leaves it completed; one that stops on an error makes it failed.
scientific_status	string	success when every requested stage converged; otherwise partial or failed. In all --tsopt, a TS with n_imag ≥ 2 gives partial, and a TS with n_imag = 0 stops the run before IRC, so success means n_imag = 1. Standalone tsopt does not look at n_imag; read n_imaginary_modes.
scientific_status_reasons	string[]	Reasons for unusable or missing stages; omitted on clean success.
expected_item_ids / observed_item_ids	string[]	Expected and observed stage identifiers, used to detect missing work.
stage_outcomes	object[]	One entry per stage with stage, item_id, required, executed, converged, usable, reason, and artifacts.
point_outcomes	object[]	Scan points with point_id, executed, converged, energy_valid, artifact_written, seed_eligible, and reason.

Error fields (when a command stops on an exception)

Field	Type	Description
error	string	str(exc) of the original exception
error_type	string	Exception class name
error_class_chain	list[string]	Names of the exception class and all its parent classes, so agents can match the hierarchy without parsing text
error_module	string	Module the exception class was defined in
error_label	string	High-level CLI stage label

Error handling

When a run stops on an exception after the output directory is set up, result.json and summary.json are written even without --out-json, with "execution_status": "failed" and an "error_type"; for a failure before that point, see Notes.

When an optimization ends without converging, result.json records "optimization_status": "not_converged". Optimizer results include the final force/step or cycle fields that apply; DFT and Dimer omit the fields they do not have. For what to change before a retry, see Troubleshooting › Calculation / convergence.

An optimizer may also report "optimization_status": "stalled": the energy stopped decreasing over the configured window (an energy plateau) while the force/step convergence criteria remained unmet. A stall is a kind of non-convergence, never converged; stop_reason records why the run stopped.

Subcommand schemas

sp

Field	Type	Description
stage	string	"sp"
input	string	Input path used for the calculation
backend / model	string / string | null	MLIP backend and model; the same values appear in the common mlip_* fields
custom_calculator	string | null	filename:factory for --calc-file, otherwise null
charge / spin	int / int	Total charge and multiplicity
n_atoms	int	Atom count
energy_au	float	Single-point energy (Hartree)
forces_path	string	Path to forces.npy
hessian_path	string | null	Path to hessian.npy, or null without --hess
elapsed	string	Human-readable elapsed-time text

opt

Field	Type	Description
optimization_status	string	"converged", "not_converged", or "stalled" (energy plateau; see above)
stop_reason	string	Present only when the optimizer stopped early without converging (stalled or not_converged); records why, e.g. the energy-plateau range/window and the failed criteria
energy_hartree	float	Final energy (Hartree)
n_opt_cycles	int	Optimization cycles completed
opt_mode	string	"grad", "hess", "lbfgs", or "rfo"
backend	string	Calculator backend ("uma", "orb", "mace", "aimnet2", "dft", or "custom" with --calc-file); for dft, model is FUNCTIONAL/BASIS, the engine is recorded separately, and MLIP precision is null
charge	int	System charge
spin	int	Spin multiplicity
model	string	MLIP model identifier, or FUNCTIONAL/BASIS for dft
n_atoms	int	Total atoms
n_freeze_atoms	int	Frozen atoms
solvent	string	Implicit solvent or "none"
thresh	string	Convergence threshold preset
max_cycles	int	Maximum allowed cycles
input_file	string	Input filename
final_max_force	float	Last max gradient (Hartree/Bohr)
final_rms_force	float	Last RMS gradient
final_max_step	float	Last max displacement (Bohr)
final_rms_step	float	Last RMS displacement
convergence_thresholds	object	{max_force_thresh, rms_force_thresh, max_step_thresh, rms_step_thresh}. Force/step units: Hartree/Bohr and Bohr (Cartesian), Hartree/rad and rad (angular).
files	object	Output file map
rigid_projection	object	Optional; present when --flatten runs. See projection provenance.

tsopt

All fields from opt, plus:

Field	Type	Description
optimization_status	string	Numerical optimizer outcome: "converged", "not_converged", or "stalled"; independent of saddle order
saddle_validation	string	"first_order", "higher_order", "no_imaginary", or "unavailable" from terminal exact PHVA (partial Hessian vibrational analysis)
hessian_status	string	"completed", "failed", "skipped", or "unavailable"; hessian_error gives the failure reason
reaction_mode_index	int|null	0-based index, in the PHVA frequency list, of the imaginary mode that all follows in IRC: the mode tracked by the optimizer when it is imaginary, otherwise the lowest imaginary mode. reaction_mode_source records which ("mep-reference-overlap" or "lowest-imaginary"); null when there is no imaginary mode
n_imaginary_modes	int|null	Number of imaginary frequencies; null if PHVA was not run
n_negative_modes	int|null	Number of negative frequencies of any size, including those within the cutoff; a diagnostic next to n_imaginary_modes, null if PHVA was not run
imaginary_frequencies_cm	float[]|null	Imaginary frequencies (cm⁻¹, negative); null or [] when PHVA was not run
frequency_zero_cutoff_cm	float	Cutoff in cm⁻¹ (default 5.0); with the default, only ν < −5.00 cm⁻¹ counts as imaginary
imaginary_mode_criterion	string	Name of the counting rule; the value is "frequency_cutoff_cm"
imaginary_frequency_threshold_cm	float	The same cutoff with a negative sign (default -5.0)
opt_mode	string	"rsprfo" (default), "rsirfo", "trim", or "dimer"
opt_mode_requested	string	Requested CLI preset (grad, hess, or an explicit algorithm)
optimizer	string	Effective optimizer algorithm used by the run
reference_mode_file	string|null	Advanced path-mode file supplied through --ref-mode; normally generated and passed by all
safeguards	object	Hessian-TS diagnostics, including exact saddle checks, final target-mode identity/overlap, stop reason, and any explicitly enabled mode-loss/recovery activity. These recovery paths are inactive by default.
rigid_projection	object	Rigid-mode and exact-Hessian provenance; see projection provenance

The files object may include imaginary_mode_files (list of vib file paths) and hessian_npy (absolute path of the --dump-hess file). A successful TS optimization gives one imaginary mode along the reaction coordinate: saddle_validation: "first_order" with n_imaginary_modes: 1. The final PHVA runs after the optimizer converges or stops on an energy plateau (stalled); otherwise it is recorded as skipped. optimization_status and saddle_validation are independent, so a converged run can end with saddle_validation: "higher_order"; it is not a first-order TS. For when all goes on to IRC, see tsopt › Reading the TS result. Dimer results have the same TS fields but no per-cycle force/step details and no safeguards object.

freq

Field	Type	Description
n_modes	int	Total normal modes
n_imaginary	int	Imaginary frequency count (n_imag): frequencies below −freq.zero_cutoff_cm
n_negative_modes	int	Number of negative frequencies of any size, including those within the cutoff
frequencies_cm	float[]	All frequencies (cm⁻¹)
imaginary_frequencies_cm	float[]	The frequencies counted in n_imaginary
thermochemistry	object|null	Thermodynamic data (see below)
backend	string	MLIP backend
charge	int	System charge
spin	int	Spin multiplicity
model	string	Model identifier
n_atoms	int	Total atoms
n_freeze_atoms	int	Frozen atoms
solvent	string	Implicit solvent or "none"
temperature_K	float	Temperature (K)
pressure_atm	float	Pressure (atm)
input_file	string	Input filename
files	object	{"frequencies_txt": "frequencies_cm-1.txt"}; includes hessian_npy (absolute path) when --dump-hess wrote a file
rigid_projection	object	Rigid-mode and Hessian provenance; also written to thermoanalysis.yaml with --dump

thermochemistry:

Field	Type	Unit
point_group	string	Automatically detected molecular point group
point_group_source	string	"auto" or conservative "auto-fallback"
symmetry_number	int	External rotational symmetry number
symmetry_number_source	string	"auto", "auto-fallback", "config", or "override"
electronic_energy_ha	float	Hartree
zpe_correction_ha	float	Hartree
thermal_correction_energy_ha	float	Hartree
thermal_correction_enthalpy_ha	float	Hartree
thermal_correction_free_energy_ha	float	Hartree
sum_EE_and_ZPE_ha	float	Hartree
sum_EE_and_thermal_energy_ha	float	Hartree
sum_EE_and_thermal_enthalpy_ha	float	Hartree
sum_EE_and_thermal_free_energy_ha	float	Hartree
E_thermal_cal_per_mol	float	cal/mol
Cv_cal_per_mol_K	float	cal/(mol K)
S_cal_per_mol_K	float	cal/(mol K)

irc

IRC reports execution_status and scientific_status and keeps the stop reason and trajectory of each direction; all reports the endpoint optimizations that follow under endpoint_opt. The stitched path runs from finished_first (the forward end) through the TS to finished_last (the backward end); which end is R and which is P is not decided by the order.

Field	Type	Description
n_frames_forward	int	Forward IRC frames
forward_short_branch / backward_short_branch	bool	Branch produced at most three frames without reaching the cycle cap; diagnostic only
n_frames_backward	int	Backward IRC frames
n_frames_total	int	Total frames
energy_first_hartree	float	Energy of finished_first
energy_ts_hartree	float	TS energy
energy_last_hartree	float	Energy of finished_last
endpoint_energy_orientation	string	"finished_first_to_finished_last"
forward_requested / backward_requested	bool	Whether each direction was requested
forward_integration_converged / backward_integration_converged	bool | null	Whether the direction stopped because the RMS-gradient stationarity criterion fired; diagnostic only, and always false under --never-stop, which bypasses that criterion. Combine it with *_downhill_departure_valid to check that the branch both left the TS downhill and met that criterion.
forward_downhill_departure_valid / backward_downhill_departure_valid	bool | null	Whether the branch established a downhill departure from the TS
forward_integration_stop_reason / backward_integration_stop_reason	string | null	Non-empty only for a numerical propagation failure
forward_energy_increased	bool | null	Final forward step exceeded irc.energy_increase_thresh (default 0 Hartree: any rise)
backward_energy_increased	bool | null	Final backward step exceeded irc.energy_increase_thresh (default 0 Hartree: any rise)
backend	string	MLIP backend
charge	int	System charge
spin	int	Spin multiplicity
model	string	Model identifier
never_stop	bool	Whether opt-in physical endpoint-stop bypass mode was enabled
never_stop_energy_bypasses	int	Number of energy-rise or one-step energy-change stop events actually bypassed
n_freeze_atoms	int	Frozen atoms
solvent	string	Implicit solvent or "none"
bond_changes	object	Directed first→last {formed: [...], broken: [...]} of element-prefixed 1-based atom-pair strings (e.g. "C7-O12"); key is omitted when the comparison fails or finished_first.xyz/finished_last.xyz are absent.
bond_changes_direction	string	"finished_first_to_finished_last" when bond_changes is present
step_length	float	IRC step length (Bohr)
max_cycles	int	Maximum IRC steps
input_file	string	Input filename
files	object	Trajectory files (XYZ, plus PDB/CIF versions when available)
rigid_projection	object	Rigid-mode and initial-Hessian provenance; see projection provenance

scan

Field	Type	Description
scan_opt_mode	string	Optimizer preset used for the constrained relaxations
scan_optimizer	string	Effective optimizer identity (lbfgs or rfo)
charge	int	System charge
spin	int	Spin multiplicity
backend	string	MLIP backend
model	string	Model identifier
solvent	string	Implicit solvent or "none"
preopt	bool	Pre-optimization performed?
max_step_size_angstrom	float	Max bond-length step per increment (Å)
n_stages	int	Number of scan stages
stages	object[]	Per-stage data (see below)
files	object	Output files

stages[]:

Field	Type	Description
index	int	1-based stage index
n_steps	int	Steps in this stage
converged	bool	Constrained optimization converged?
pairs_1based	list	Atom pairs (1-based)
initial_distances_angstrom	list	Starting distances
target_distances_angstrom	list	Target distances
final_energy_hartree	float	Energy at last step
energies_hartree	float[]	Per-step energies
bond_changes	object	{"changed": bool | null, "summary": str} (free-text summary; null/"" when the comparison did not run).

scan2d / scan3d

Field	Type	Description
charge	int | null	System charge; null for plot-only scan3d --csv
spin	int | null	Spin multiplicity; null for plot-only scan3d --csv
backend	string | null	MLIP backend; null for plot-only scan3d --csv
model	string | null	Model identifier; null for plot-only scan3d --csv
solvent	string | null	Implicit solvent or "none"; null for plot-only scan3d --csv because imported energies have no calculator provenance
max_step_size_angstrom	float	Max bond-length step per increment (Å, scan2d only)
n_grid_points	int	Grid rows excluding is_preopt=true
execution_status	string	Execution-level completion state
n_points_attempted	int	Fresh-run grid points attempted, excluding preoptimization
n_points_usable	int	Fresh-run points eligible for scientific reuse
point_outcomes	object[]	Per-point convergence, energy, artifact, and eligibility data
grid_points	object[]	Explicit grid-index, distances, energy, convergence, and geometry_file mapping
current_output_paths	string[]	CSV/HTML/PNG files and grid geometries written by this run; files left from an earlier run are not listed
grid_shape	int[]	Grid dimensions (only when running fresh; absent under scan3d --csv)
pair1, pair2 (,pair3)	object	{kind, atoms_1based, unit, low, high} (distance axes also carry i, j) with optional atom_labels. scan3d: present only when running fresh; absent under --csv re-plot
min_energy_hartree	float	Surface minimum energy
files	object	CSV + plot files

The outcome-count fields are emitted by fresh scans. Plot-only scan3d --csv does not report an attempted count and may omit usable count when the imported CSV lacks complete provenance.

path-opt

Field	Type	Description
optimization_status	string	"converged" / "not_converged" / "completed"
converged	bool | null	Convergence flag: true / false from the engine’s own convergence signal, null when it exposed none (optimization_status is then "completed", never a success claim)
mep_mode	string	"dmf" or "gsm"
backend	string	MLIP backend
charge	int	System charge
spin	int	Spin multiplicity
model	string	Model identifier
solvent	string	Implicit solvent or "none"
preopt	bool	Whether endpoint pre-optimization was enabled
reactant_energy_hartree	float	First-image energy (Hartree)
product_energy_hartree	float	Last-image energy (Hartree)
image_energies_hartree	float[]	All image energies
n_images	int	Image count
hei_index	int	Highest-energy image index
hei_energy_hartree	float	HEI energy (Hartree)
barrier_kcal	float	Forward barrier (kcal/mol)
delta_kcal	float	Reaction energy (kcal/mol)
files	object	Trajectory + HEI files

path-search

path-search has no --out-json flag. It writes summary.json; its fields are listed in summary.json (path-search / all).

dft

Note: With --out-json, dft writes result.json and summary.json for both converged and non-converged SCF attempts, recording scientific_status: "failed" and converged: false on non-convergence. A non-converged SCF exits with code 1.

Field	Type	Description
converged	bool	SCF converged?
charge	int	System charge
spin	int	Spin multiplicity
n_atoms	int	Atom count
grid_level	int	DFT grid level
conv_tol	float	SCF convergence tolerance
max_cycle	int	Maximum SCF cycles
input_file	string	Input filename
energy_hartree	float	DFT energy
energy_kcal_per_mol	float	DFT energy (kcal/mol)
xc_functional	string	XC functional
basis_set	string	Basis set
engine	string	Effective engine label ("gpu4pyscf(rks_lowmem)", "gpu4pyscf", or "pyscf(cpu)")
used_gpu	bool	GPU acceleration used?
used_lowmem	bool	Low-memory GPU4PySCF solver actually used? (False on open-shell, CPU, or --no-dft-low-memory)
lowmem_requested	bool	Whether low-memory mode was requested
dft_settings / dft_resources	object	Canonical scientific settings and effective host resources
effective_ecp	string/object | null	Effective ECP passed to PySCF
solvent / solvent_model	string	Effective native implicit-solvent settings
charges	object	{mulliken, lowdin, iao} per-atom arrays
spin_densities	object	{mulliken, lowdin, iao} per-atom arrays
files	object	{"result_yaml": "result.yaml", "input_geometry_xyz": "input_geometry.xyz"}

extract

Field	Type	Description
n_atoms_raw	int	Atoms in selected residues before backbone/truncation filtering (not the whole input structure)
n_atoms_extracted	int	Selected atoms kept after truncation, before cap-H addition
total_charge	float	Computed total charge
protein_charge	float	Protein charge
ligand_total_charge	float	Ligand charge sum
ion_total_charge	float	Ion charge sum
ion_charges	list	[[name, charge], ...]
unknown_residue_charges	object	{resname: charge}
n_link_hydrogens	int	Cap hydrogens added at carbon-parent truncation bonds; the model has n_atoms_extracted + n_link_hydrogens atoms
exclude_backbone	bool	Whether backbone atoms were excluded
include_h2o	bool	Whether crystallographic waters were included
ligand_charge_input	string | null	User-supplied mapping, or null when omitted
center	string	Center residue
radius	float	Extraction radius (angstrom)
input_files	string[]	Original input PDB/mmCIF paths
files	object	Output PDB / cluster filenames

trj2fig

Field	Type	Description
n_frames	int	Number of trajectory frames
min_energy_hartree	float	Minimum energy across frames
max_energy_hartree	float	Maximum energy across frames
energy_source	string	"trajectory_comment" or "mlip_recomputed"
mlip_backend / mlip_model / mlip_model_label / mlip_task / mlip_precision	string | null	Effective recomputation provenance; all are null in trajectory-comment mode
energy_provenance	string[]	Per-frame energy source provenance
energy_unit	string	Stored energy unit (hartree)
backend	string | null	MLIP backend only when frame energies were recomputed; null in comment-energy mode
charge / multiplicity	int | null	Charge and multiplicity used when energies were recomputed, otherwise null
solvent / solvent_model	string | null	Recomputed-calculator solvent settings, otherwise null
output_files	string[]	Canonical ordered paths for every output; preserves files with the same basename in different directories
files	object	Basename-to-path map; when two outputs share a basename only one is kept, so prefer output_files

energy-diagram

Field	Type	Description
n_points	int	Number of energy data points
files	object	Output diagram files

bond-summary

With --json, bond-summary prints JSON to stdout and, unlike the subcommands above, writes no result.json file:

Field	Type	Description
execution_status / scientific_status	string / string	completed / success when every pair was compared. If any pair could not be compared, execution_status is failed and scientific_status is partial or failed.
comparisons	object[]	Per-pair comparison with structure_a (string), structure_b (string), bonds_formed (int count), bonds_broken (int count).

Rigid projection provenance

freq, irc, and tsopt results include a rigid_projection object; opt includes it when --flatten runs. freq --dump also writes the same object to thermoanalysis.yaml.

Field	Type	Description
treatment	string	Fixed rigid-mode treatment: "constrained"
algorithm	string	Name of the projection method
effective_rank	int	Number of rigid directions removed from the Hessian of the movable atoms
full_rigid_rank	int	Rank of the rigid motions of the whole system before the frozen atoms are taken into account
frozen_constraint_rank	int	Rank removed because the frozen atoms must stay in place
svd_rtol	float	Relative SVD tolerance used for the rank decision
active_atom_count / frozen_atom_count	int	Movable and frozen atom counts
active_atoms / frozen_atoms	int[]	0-based indices of the movable and frozen atoms
hessian_space	string	"full" or "active" input Hessian space
hessian_source / source	string	Hessian provenance. freq/irc use hessian_source: "file" (--read-hess), "cache" (earlier stage in the same run), or "fresh"; opt/tsopt use source.
hessian_shape / raw_hessian_shape	int[2]	Input Hessian shape. freq/irc use hessian_shape; opt/tsopt use raw_hessian_shape.
near_zero_mode_count / near_zero_frequencies_cm	int / float[]	Number and values of the modes within ±frequency_zero_cutoff_cm (5.00 cm⁻¹ by default); these modes are also in the full frequency list

constrained removes only the rigid motions of the whole system that keep the frozen atoms in place; see freq.

summary.json (path-search / all)

The all and path-search commands write summary.json with a richer structure:

Field	Type	Description
execution_status / scientific_status	string / string	Execution completeness and completion of requested numerical/calculation stages.
scientific_status_reasons	string[]	Reasons for missing or unusable requested results; omitted on success.
pipeline_stop	object | absent	Present only on an early stop. stage is post (reason no_segments / no_reactive_segment), before_irc (a TSOPT reason, plus segment and tsopt_result), or endpoint_opt (endpoint_execution_failed and endpoint-specific failures). Rendered in summary.log as Pipeline stop.
expected_item_ids / observed_item_ids	string[]	Expected and observed stage identifiers.
scan	object | absent	Preliminary scan status, stage outcomes and diagnostics in scan-seeded all runs.
n_segments	int	Segment count
search_max_depth	int	Effective recursion cap; 0 means subdivision was disabled
path_optimizers	string[]	Single-structure optimizers actually used during path preparation/refinement (lbfgs, rfo); includes scan and alignment work in all. Also present in path-opt result.json
preopt_requested / preopt_converged	bool / bool | null	Whether endpoint preoptimization ran, and whether every endpoint converged; null when any endpoint reported no readable signal. In all, preopt_converged counts toward scientific_status; with --tsopt, it no longer counts once the TS and both endpoint optimizations have converged for every reactive segment
segments	object[]	Per-segment index (1-based; all writes segment 1 to segments/seg_01/), tag (a label; its number can differ from index), kind ("seg" for a reactive segment, "kink" for a kink with no covalent bond change, "bridge" for a bridge segment, "tsopt" in TS-only mode), converged (whether every optimization that built the segment converged; null when no convergence signal was readable), barrier_kcal, delta_kcal, bond_changes (list of {title: [entries]} dicts; bridge segments emit ""). barrier_kcal is the barrier on the MEP before TS optimization (null for a kink); in TS-only mode it is TS − R, where R is the higher-energy IRC endpoint (a name for the direction, not the chemical direction of the reaction; see all › Notes).
energy_diagrams	object[]	Energy profiles with labels and kcal/mol values
mlip_backend	string	Backend identifier
mlip_model	string | null	Model identifier, recorded separately from the backend
mlip_model_label	string | null	Publication-facing model label
mlip_task	string | null	Backend task for a multi-domain model
mlip_precision	string | null	Effective fp32 / fp64 token; null for custom calculators
charge	int	System charge
spin	int	Spin multiplicity
environment	object	Hardware info
references	object[]	Methods actually used by the run, as {method, citation, doi} records. The same reference set is grouped at the end of summary.log and final stdout immediately before elapsed time.

The all command additionally includes:

Field	Type	Description
config	object	Effective settings. mep_mode identifies GSM/DMF; ts_opt_mode and endpoint_opt_mode identify the configured post-processing presets. Generic opt_mode* keys record the effective CLI values. path_opt_mode is the single-structure optimizer used for endpoint preoptimization (see preopt), not the MEP path algorithm.
rate_limiting_step	object	Highest local barrier among the reactive segments, taken at the highest-level method available for every segment (DFT//MLIP_Gibbs > DFT > MLIP_Gibbs > MLIP > MEP), with explicit method and raw mep_barrier_kcal. It is not a microkinetic rate-limiting-step assignment.
overall_reaction_energy_kcal	float	Overall reaction energy
overall_reaction_energy_method	string	Method of the overall reaction energy (MEP, MLIP, MLIP_Gibbs, DFT, or DFT//MLIP_Gibbs)
post_segments	list	Per-segment TS/IRC/freq/DFT results
post_segments[].tsopt.n_imaginary_modes / .imaginary_frequencies_cm	int / float[]	n_imag of the optimized TS and its imaginary frequencies (cm⁻¹, negative)
post_segments[].mlip / .gibbs_mlip / .dft / .gibbs_dft_mlip	object	R, TS, and P energies at one level, with barrier_kcal, delta_kcal, and energies_kcal: MLIP electronic energies (--tsopt), MLIP Gibbs energies (--thermo), DFT energies (--dft), and DFT//MLIP Gibbs energies (--thermo with --dft)
post_segments[].tsopt.energy_valid / .structure_valid	bool	energy_valid: the final TS energy is a finite number. structure_valid: the final TS structure file exists and its coordinates are finite
post_segments[].tsopt.n_opt_cycles / .max_cycles	int / int|null	TS optimization cycles executed and configured limit. These are reported for both converged and normally non-converged runs.
post_segments[].irc / .endpoint_assignment / .endpoint_opt	object	IRC stop diagnostics, endpoint orientation, and endpoint-OPT convergence, respectively. endpoint_opt.reactant and .product report optimization_status, n_opt_cycles, max_cycles, and any stop_reason. How the IRC stopped and whether the bond changes match do not enter scientific_status; whether the optimized endpoints are the intended R and P is for you to check.
post_segments[].thermo_symmetry	object	Child-reported point-group and rotational-symmetry provenance by state. Only R/TS/P states with valid symmetry-number provenance are included; missing states are omitted, and the field is absent only when no state has valid provenance.
current_output_paths	string[]	Sorted paths relative to --out-dir, limited to artifacts claimed by the current invocation.
key_output_files	object	Current-run output index: root filename → description; each seg_NN entry is {description, files} with paths relative to that segment directory.

Usage examples

Python

The script reads result_opt/result.json, which opt --out-json writes.

import json

with open("result_opt/result.json") as f:
    result = json.load(f)

status = result.get("optimization_status")
if result["execution_status"] == "failed":
    raise RuntimeError(f"{result['error_type']}: {result['error']}")
elif status == "converged":
    print(f"Energy: {result['energy_hartree']:.6f} Hartree")
elif status in {"not_converged", "stalled"}:
    print(f"Not converged after {result['n_opt_cycles']} cycles")
    print(f"Max force: {result['final_max_force']:.6f}")
else:
    print(f"Status: {status}")

jq

# Check convergence
jq '{execution_status, scientific_status}' result.json

# Get barrier from path-opt
jq '.barrier_kcal' result.json

# List imaginary frequencies from tsopt
jq '.imaginary_frequencies_cm' result.json

# Get thermochemistry from freq
jq '.thermochemistry.sum_EE_and_thermal_free_energy_ha' result.json

# Get each segment's barrier from all (after --tsopt)
jq '.post_segments[] | {index, barrier_kcal: .mlip.barrier_kcal}' result_all/summary.json

Notes

• A run that fails while the CLI options or the input are being checked (before the output directory is set up) can stop without writing any JSON. Treat a nonzero exit code as a failure, and read stderr or the job log for the message.

• all and path-search write summary.json only once the run reaches its summary step, so an early input error leaves no file.

• The per-command sections also have their own backend / model fields. Scripts that read several commands should use mlip_backend / mlip_model / mlip_precision, which mean the same thing in every command.

• How the IRC stopped does not enter scientific_status: a standalone irc reports success when the integration finishes, also at --max-cycles, and all judges the TS and endpoint optimizations.

See Also

• Exit codes — what each exit code means

• Output layout — where result.json and summary.json are written

• Troubleshooting — what to change after a failed or non-converged run

• YAML Reference — configuration inputs whose values surface in these schemas

• all, path-search — subcommands that write summary.json without --out-json

• opt, sp, tsopt, freq, irc, scan, scan2d, scan3d, path-opt, dft, extract, trj2fig, energy-diagram — subcommands that emit result.json only under --out-json