JSON Output Reference

pdb2reaction emits machine-readable JSON for programmatic use by scripts and agents.

--out-json flag

Most MLIP-based and reporting subcommands (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, authoritative result.json and its identical summary.json compatibility mirror are written beside the normal outputs.

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

The all and path-search commands write summary.json without an --out-json flag once execution reaches their summary writer. Early CLI/input validation can fail before the file exists.

summary.json mirror

write_result_json serializes each per-stage payload once, atomically publishes the summary.json mirror first, and publishes authoritative result.json last. A successful return means both files contain identical bytes. If an I/O failure interrupts publication, the writer raises instead of hiding mirror divergence; MCP consumers additionally require the current run identity.

Common envelope

The shared writer supplies the fields below; rows explicitly marked optional are present only when the producer supplies the corresponding data:

Field	Type	Description
schema_version	string	Envelope schema version; current value lives at pdb2reaction.core.utils.RESULT_JSON_SCHEMA_VERSION — pin against that constant rather than the literal in this doc. A version bump signals a structural change.
command	string	Leaf envelopes use the subcommand name (e.g. "opt"); aggregate all / path-search summaries record the full invocation string
pdb2reaction_version	string	Package version
status	string	Value depends on the subcommand (see each section below): e.g. converged / not_converged / stalled (opt, tsopt), completed (irc, freq), ok / partial / failed (bond-summary), success / partial / failed (all), success / partial (path-search), and error on failure
run_id	string	Optional current MCP invocation UUID. It is injected only when the product-specific run environment is active; a conflicting producer value is rejected.
elapsed_seconds	float	Optional wall-clock time; omitted by producers that do not pass timing to the shared writer
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

Leaf schemas also retain their local backend / model fields; consumers should prefer mlip_backend / mlip_model / mlip_precision for a uniform cross-command provenance contract.

Execution and scientific truth

Multi-stage and scan producers add the fields below when they can evaluate constituent work. These fields are additive and producer-dependent; the command-specific status remains for compatibility. Consumers should use scientific_status and the leaf outcomes when deciding whether a result is usable. Missing or ambiguous convergence is fail-closed and cannot promote a leaf to usable.

Field	Type	Description
execution_status	string	Normally completed or failed; reports whether required constituent commands executed.
scientific_status	string	success, partial, or failed; reports whether the produced scientific result is complete and usable.
scientific_status_reasons	string[]	Reasons for unusable or missing leaves; omitted on clean success. This is distinct from an aggregate workflow’s legacy status_reasons.
expected_item_ids / observed_item_ids	string[]	Expected and observed leaf identifiers used to detect missing aggregate work.
stage_outcomes	object[]	Stage leaves 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.

When present, run_id identifies the current invocation. The all aggregate summary also uses current_output_paths and key_output_files to report only artifacts claimed by that invocation; files left in a reused output directory are not current results.

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	Projection-kernel identifier
effective_rank	int	Number of rigid directions removed from the active Hessian
full_rigid_rank	int	Rank of the full-system rigid basis before frozen-anchor constraints
frozen_constraint_rank	int	Rank removed by the frozen-anchor constraints
svd_rtol	float	Relative SVD tolerance used for the rank decision
active_atom_count / frozen_atom_count	int	Active and frozen atom counts
active_atoms / frozen_atoms	int[]	0-based atom indices used by the projection kernel
hessian_space	string	"full" or "active" input Hessian space
hessian_source / source	string	Hessian provenance. freq/irc use hessian_source; 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.

constrained removes only full-system rigid motions that leave frozen anchors fixed. The treatment is fixed; stale non-constrained values fail explicitly. See Frozen Atoms.

Error envelope (when status == "error")

Field	Type	Description
error	string	str(exc) of the original exception
error_type	string	Exception class name
error_class_chain	list[string]	Full MRO class names 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

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>

Error handling

Caught runtime exceptions write a best-effort result.json with "status": "error" and an "error_type". Usage/validation exits and failures before the output directory is resolved may not create JSON, so a nonzero exit code or missing expected JSON is also a failure signal. Check stderr/job logs for the authoritative diagnostic.

For jobs that reach a controlled non-convergence writer, result.json uses "status": "not_converged". Optimizer-family payloads expose the applicable final force/step or cycle fields; DFT and Dimer omit fields they do not own. Consult the command-specific schema before deciding whether to retry.

An optimizer may also report "status": "stalled": the energy stopped decreasing over the configured window (an energy plateau) while the configured force/step convergence criteria remained unmet. A stall is a distinct, non-converged outcome — it is never reported as converged. In tsopt it also stops the flatten/retry loop rather than repeating a non-progressing search; opt --flatten still runs its flatten loop, which exists to displace along the remaining imaginary modes and leave the plateau. When present, a stop_reason string records the energy range, window, and the failed criteria. A stall may be retried (e.g. from a perturbed geometry or with tighter step control); it is not an alias for max_cycles exhaustion or a generic failure.

Subcommand schemas

sp

Field	Type	Description
status	string	"ok"
stage	string	"sp"
input	string	Prepared public input path
backend / model	string / string | null	Local MLIP provenance, mirrored to 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
status	string	"converged", "not_converged", or "stalled" (energy plateau; see above)
stop_reason	string	Present only for a non-converged stop (stalled/stopped); records the energy plateau range/window and 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	MLIP backend ("uma", "orb", "mace", "aimnet2", or "custom" with --calc-file)
charge	int	System charge
spin	int	Spin multiplicity
model	string	MLIP model identifier
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} (Hartree/Bohr)
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
hessian_status	string	"completed", "failed", "skipped", or "unavailable"; hessian_error gives the failure reason
reaction_mode_index	int|null	Selected negative exact-PHVA root for downstream IRC; fallback root 0 is explicitly labelled and does not verify reaction identity
n_imaginary_modes	int|null	Number of imaginary frequencies; null if PHVA was not run
imaginary_frequencies_cm	float[]|null	Imaginary frequencies (cm⁻¹, negative); null when PHVA was not run
opt_mode	string	"rsprfo" (default), "rsirfo", "trim", or "dimer"
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). Terminal PHVA runs only after numerical convergence. A non-converged or stalled run retains the terminal geometry and records PHVA as skipped; a PHVA calculation failure is recorded as hessian_status: "failed" without discarding the structure or fabricating frequencies. status/optimization_status describe numerical optimization, while saddle_validation describes exact-PHVA order. A numerically converged higher-order stationary point remains optimization_status: "converged" with saddle_validation: "higher_order"; it is not a certified first-order TS. all may use a validated negative root for warning-labelled diagnostic IRC. Numerical non-convergence, zero imaginary modes, missing/failed PHVA, or no valid negative root stops all after TS artifact registration and before IRC. Dimer uses the same additive terminal fields but still omits Hessian-family per-cycle force/step convergence details and the safeguards object.

freq

Field	Type	Description
status	string	"completed"
n_modes	int	Total normal modes
n_imaginary	int	Imaginary frequency count
frequencies_cm	float[]	All frequencies (cm⁻¹)
imaginary_frequencies_cm	float[]	Negative frequencies only
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"}
rigid_projection	object	Rigid-mode and Hessian provenance; also written to thermoanalysis.yaml with --dump

thermochemistry (null if thermoanalysis unavailable):

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

Field	Type	Description
status	string	"completed"
n_frames_forward	int	Forward IRC frames
n_frames_backward	int	Backward IRC frames
n_frames_total	int	Total frames
energy_first_hartree	float	Energy of the first stitched-path endpoint; standalone IRC does not assign chemical identity
energy_ts_hartree	float	TS energy
energy_last_hartree	float	Energy of the last stitched-path endpoint; standalone IRC does not assign chemical identity
endpoint_energy_orientation	string	"finished_first_to_finished_last"
energy_reactant_hartree / energy_product_hartree	float	Legacy aliases for first / last, respectively; do not infer chemical R/P identity from these names
forward_converged	bool | null	Forward IRC converged? null when the integrator did not expose the flag
backward_converged	bool | null	Backward IRC converged? null when the integrator did not expose the flag
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 available PDB/CIF companions)
rigid_projection	object	Rigid-mode and initial-Hessian provenance; see projection provenance

scan

Field	Type	Description
status	string	"completed"
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} from has_bond_change (free-text summary; null/"" when the comparison did not run).

scan2d / scan3d

Field	Type	Description
status	string	"completed"
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 used by interactive Results viewers
current_output_paths	string[]	Current-run CSV/HTML/PNG and grid geometries; consumers can exclude stale files without filename inference
grid_shape	int[]	Grid dimensions (only when running fresh; absent under scan3d --csv)
pair1, pair2 (,pair3)	object	{i, j, low, high} with optional label_i, label_j. 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
status	string	"converged" / "not_converged" / "completed"
converged	bool	Convergence flag
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. Once execution reaches its summary writer it writes summary.json with the shared envelope (command, pdb2reaction_version, environment) plus the fields below; early CLI/input validation can fail before the file exists.

Field	Type	Description
status	string	"success" / "partial"
n_segments	int	Recursive MEP segment count
segments	object[]	Per-segment index, tag, kind, barrier_kcal, delta_kcal, bond_changes (list of {title: [entries]} dicts; bridge segments emit "").
energy_diagrams	object[]	Per-segment labeled energy profiles (kcal/mol)
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

See also the extended summary.json section for the additional fields that all layers on top.

dft

Note: dft writes result.json and summary.json for both converged and non-converged SCF attempts. Non-convergence records status: "not_converged" and converged: false, then exits with code 3. An unhandled exception writes the standard error envelope.

Field	Type	Description
status	string	"converged" or "not_converged"
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	gpu4pyscf.dft.rks_lowmem.RKS actually used? (False on open-shell, CPU, --no-lowmem, or pre-rks_lowmem GPU4PySCF)
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
status	string	"ok"
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
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
status	string	"ok"
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"
energy_provenance	string[]	Per-frame energy source provenance
energy_unit	string	Stored energy unit (hartree)
backend	string or null	MLIP backend only when frame energies were recomputed; null in comment-energy mode
charge / multiplicity	int or null	Resolved recomputation state, otherwise null
solvent / solvent_model	string or 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	Legacy basename-to-path map; retained for compatibility and therefore lossy when basenames collide

energy-diagram

Field	Type	Description
status	string	"ok"
n_points	int	Number of energy data points
files	object	Output diagram files

bond-summary

When --json is enabled, bond-summary prints JSON to stdout (no result.json file is written; redirect stdout if you need to persist it). This is unlike the MLIP-based subcommands above, which all write a result.json file into out_dir:

Field	Type	Description
status	string	"ok" (every pair compared without error), "partial" (some pairs failed), or "failed" (no pair compared successfully)
comparisons	object[]	Per-pair comparison with structure_a (string), structure_b (string), bonds_formed (int count), bonds_broken (int count).

summary.json (path-search / all)

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

Field	Type	Description
status	string	"success" / "partial" / "failed" (all); "success" / "partial" (path-search)
execution_status / scientific_status	string / string	Execution completeness and scientific usability; evaluate these separately from legacy status.
scientific_status_reasons	string[]	Reasons for incomplete or unusable science; omitted on clean success.
expected_item_ids / observed_item_ids	string[]	Expected and observed aggregate leaves.
n_segments	int	Segment count
segments	object[]	Per-segment index, tag, kind, barrier_kcal, delta_kcal, bond_changes (list of {title: [entries]} dicts produced by _bond_changes_block; bridge segments emit "").
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 resolved workflow, 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
rate_limiting_step	object	Legacy key for the highest independently referenced local barrier at the highest method complete across every reactive 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[].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

import json

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

status = result["status"]
if status == "error":
    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 '.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

See Also

• CLI Conventions — --out-json / --no-out-json flag conventions and exit codes

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

• all, path-search — subcommands that always emit summary.json

• opt, tsopt, freq, irc, scan, path-opt, dft, extract — subcommands that emit result.json only under --out-json