YAML Reference

Tip

Looking for the all end-to-end command? The all command consumes every section described on this page and forwards them to the appropriate subcommand. See all (in particular its “Subcommand → YAML Sections” mapping) for which sections are read by which stage.

Configuration precedence

Settings are resolved in the following order (later sources override earlier ones):

built-in defaults  <  --config (YAML)  <  CLI flags

1. Built-in defaults — hard-coded values in pdb2reaction/defaults.py.

2. --config — a YAML file that overrides defaults (e.g., --config my_settings.yaml).

3. CLI flags — explicit command-line options (e.g., -q -1, --thresh gau_loose). Only explicitly supplied flags override YAML; options left at their CLI default do not mask YAML values.

For example, if the YAML sets charge: 0 but the CLI passes -q -1, the charge will be -1.

This precedence applies uniformly to all, opt, tsopt, freq, irc, scan, scan2d, scan3d, path-opt, path-search, and dft. See also CLI Conventions: Configuration precedence.

Common CLI-to-YAML mapping

CLI flag	YAML key	Section
-q / --charge	charge	calc
-m / --multiplicity	spin	calc
-b / --backend	backend	calc
(YAML only)	model	calc
--solvent	solvent	calc
--device	device	calc
--thresh	thresh	opt
--max-cycles	max_cycles	opt
--dump	dump	opt
--opt-mode	opt_mode	opt (tsopt)
--freeze-atoms	freeze_atoms	geom
(YAML only)	coord_type	geom
--temperature (freq, all --freq-temperature)	temperature	thermo
--pressure (freq, all --freq-pressure)	pressure_atm	thermo
--engine (dft subcommand) / --dft-engine (all wrapper)	engine (CLI internal)	dft

Note

Name mismatch — --pressure vs pressure_atm. On the CLI the flag is --pressure (units implicit: atm); the matching YAML key under thermo: is pressure_atm with an explicit unit suffix. Both carry atm values and get converted to Pa internally.

Note

Name mismatch — --engine vs --dft-engine. The standalone dft subcommand exposes the backend selector as --engine (gpu / cpu). In pdb2reaction all, to avoid colliding with other engines, the same flag is renamed --dft-engine — see the –engine vs –dft-engine note in CLI Conventions.

Default --thresh per subcommand

--thresh defaults differ per subcommand because TS optimizers use a tighter “baker” preset while minimizers use the standard “gau” preset.

Subcommand	Default --thresh	Backing defaults block
opt	gau	OPT_BASE_KW (→ lbfgs / rfo)
tsopt (Hessian Dimer)	baker	HESSIAN_DIMER_KW, inner LBFGS_TS_KW
tsopt (RS-I-RFO)	baker	RSIRFO_KW
scan, scan2d, scan3d	gau	OPT_BASE_KW
path-search (per-step opt)	gau	OPT_BASE_KW
path-opt / StringOptimizer	gau_loose	STOPT_KW
all (pre-opt, post-opt min)	gau	OPT_BASE_KW
all (post-opt TS stage)	baker	HESSIAN_DIMER_KW / RSIRFO_KW

Accepted values: gau_loose, gau, gau_tight, gau_vtight, baker, never. Override per run with --thresh <preset> or under opt.thresh in YAML.

Note

Subcommands without --thresh. irc, freq, and dft do not expose --thresh:

• irc — convergence is governed by irc.rms_grad_thresh, irc.energy_thresh, and irc.max_cycles (see irc section). The optimizer preset family does not apply because IRC follows a predictor–corrector integrator, not a force-based minimizer.

• freq — there is no optimization step, so no --thresh. Numerical accuracy is governed by --hessian-calc-mode and the underlying MLIP precision.

• dft — SCF convergence uses dft.conv_tol (default 1e-9 hartree) and dft.max_cycle, not the gau/baker preset family. See the dft section.

Overview

Section	Description	Used by
geom	Geometry and coordinate settings	all, opt, scan, scan2d, scan3d, tsopt, freq, irc, path-opt, path-search
calc	MLIP backend configuration	all, opt, scan, scan2d, scan3d, tsopt, freq, irc, path-opt, path-search
opt	Shared optimizer settings	opt, scan, scan2d, scan3d, tsopt, path-opt, path-search
lbfgs	L-BFGS optimizer settings	opt, scan, scan2d, scan3d, path-search
rfo	RFO optimizer settings	opt, scan, scan2d, scan3d, path-search
gs	Growing String Method settings	path-opt, path-search
dmf	Direct Max Flux settings	path-opt, path-search
stopt	StringOptimizer settings	path-opt, path-search
irc	IRC integration settings	irc
freq	Vibrational analysis settings	freq
thermo	Thermochemistry settings	freq
dft	DFT calculation settings	dft
bias	Harmonic bias settings	scan, scan2d, scan3d
bond	Bond-change detection settings	scan, path-search
search	Recursive path search settings	path-search
hessian_dimer	Hessian Guided Dimer TS optimization	tsopt
rsirfo	RS-I-RFO TS optimization	tsopt, all

---

Shared Sections

geom

Geometry loading and coordinate handling.

geom:
 coord_type: cart # Coordinate type: "cart" (Cartesian) or "dlc" (delocalized internals)
 freeze_atoms: [] # 1-based indices of atoms to freeze; merged with CLI --freeze-links detection

Notes:

• freeze_atoms from YAML is merged with atoms detected via --freeze-links for PDB inputs

• Frozen atoms have zeroed forces; their Hessian columns are also zeroed

• For irc, geom.coord_type is forced to cart after YAML/CLI merging

---

calc

MLIP backend configuration. Supports multiple backends (UMA, ORB, MACE, AIMNet2) and optional xTB solvent corrections.

calc:
 backend: uma           # MLIP backend: "uma", "orb", "mace", or "aimnet2"
 charge: 0 # Total system charge (overridden by CLI -q)
 spin: 1 # Spin multiplicity 2S+1 (overridden by CLI -m)
 model: uma-s-1p1 # uma-s-1p1 | uma-m-1p1
 task_name: omol # Task tag recorded in UMA batches
 device: auto # Device: "cuda", "cpu", or "auto"
 max_neigh: null # Maximum neighbors for graph construction
 radius: null # Cutoff radius for neighbor search
 r_edges: false # Store radial edges
 workers: 1 # MLIP inference workers (workers>1 disables analytical Hessians; UMA backend only)
 workers_per_node: 1 # Workers per node for parallel predictor
 out_hess_torch: true # Return Hessian as torch.Tensor
 hessian_double: true # Assemble/return Hessian in float64
 # freeze_atoms: null # Inherited from geom.freeze_atoms; do not set directly
 hessian_calc_mode: FiniteDifference # Hessian mode: "Analytical" or "FiniteDifference"
 return_partial_hessian: true  # Return active-DOF block Hessian
 print_timing: true # Print Hessian timing breakdown
 print_vram: true # Print CUDA VRAM usage during Hessian (UMA backend only)
 # Solvent correction (xTB)
 solvent: none           # Implicit solvent name (e.g. "water", "methanol") or "none" to disable
 solvent_model: alpb     # xTB solvent model: "alpb" or "cpcmx"
 xtb_cmd: xtb            # Path to xTB executable
 xtb_acc: 0.2            # xTB accuracy parameter

Notes:

• backend selects the MLIP engine. All backends (UMA, ORB, MACE, AIMNet2) support both analytical (autograd) and finite-difference Hessians; multi-worker inference is UMA-only.

• workers / workers_per_node are effective with the UMA backend only.

• solvent enables xTB-based implicit solvent corrections (delta correction approach). Requires xtb to be installed.

• hessian_calc_mode: Analytical is recommended when sufficient VRAM is available

• workers > 1 disables analytical Hessians — when workers > 1, analytical Hessian is silently downgraded to finite difference (no warning is issued) even if hessian_calc_mode: Analytical is set. Since FiniteDifference is the default anyway, this usually only matters when you explicitly opted into Analytical. See the MLIP Calculator hessian-evaluation note for details.

• Charge/spin inherit .gjf template metadata when available

• freq sets calc.return_partial_hessian = true by default (PHVA); YAML can override.

• IRC forces geom.coord_type = cart and calc.return_partial_hessian = true regardless of YAML (partial Hessian with active-DOF processing).

---

opt

Shared single-structure optimizer controls used by both L-BFGS and RFO.

opt:
 thresh: gau # Convergence preset: gau_loose, gau, gau_tight, gau_vtight, baker, never
 max_cycles: 10000 # Maximum optimizer iterations
 print_every: 100 # Logging stride
 min_step_norm: 1.0e-08 # Minimum step norm for acceptance
 assert_min_step: true # Stop if steps fall below threshold
 rms_force: null # Explicit RMS force target
 rms_force_only: false # Rely only on RMS force convergence
 max_force_only: false # Rely only on max force convergence
 force_only: false # Skip displacement checks
 converge_to_geom_rms_thresh: 0.05 # RMS threshold when converging to reference geometry
 overachieve_factor: 0.0 # Factor to tighten thresholds
 check_eigval_structure: false # Validate Hessian eigenstructure
 line_search: true # Enable line search
 energy_plateau: true # Declare convergence when the energy range flattens (see note below)
 energy_plateau_thresh: 1.0e-04 # au (~0.06 kcal/mol); fallback convergence threshold for the plateau check
 energy_plateau_window: 50 # Number of most recent steps inspected for the plateau check
 dump: false # Dump trajectory/restart data
 dump_restart: false # Dump restart checkpoints
 prefix: "" # Filename prefix
 out_dir: ./result_opt/ # Output directory

Energy plateau fallback (new in v0.3.5): When energy_plateau: true, the optimizer declares convergence if the energy range (max − min) over the last energy_plateau_window steps falls below energy_plateau_thresh (default 1e-4 au ≈ 0.06 kcal/mol over 50 steps). This prevents wasted cycles when the MLIP force noise floor (typically ~4×10⁻⁴ au) exceeds the force-based convergence threshold (e.g. baker max_force = 3×10⁻⁴ au), so the force criterion can never be satisfied even though the energy has clearly flattened. The fallback is skipped for chain-of-states (COS) optimizers such as stopt, gs, and DMF, because those store per-image energy arrays rather than a single scalar trace.

Convergence Presets:

Preset	Max Force	RMS Force	Max Step	RMS Step
gau_loose	2.5e-3	1.7e-3	1.0e-2	6.7e-3
gau	4.5e-4	3.0e-4	1.8e-3	1.2e-3
gau_tight	1.5e-5	1.0e-5	6.0e-5	4.0e-5
gau_vtight	2.0e-6	1.0e-6	6.0e-6	4.0e-6
baker	3.0e-4	2.0e-4	3.0e-4	2.0e-4

---

lbfgs

L-BFGS optimizer settings (extends opt).

lbfgs:
  # Inherits all opt settings, plus:
 keep_last: 7 # History size for L-BFGS buffers
 beta: 1.0 # Initial damping beta
 gamma_mult: false # Multiplicative gamma update toggle
 max_step: 0.3 # Maximum step length
 control_step: true # Control step length adaptively
 double_damp: true # Double damping safeguard
 mu_reg: null # Regularization strength
 max_mu_reg_adaptions: 10 # Cap on mu adaptations

---

rfo

Rational Function Optimizer settings (extends opt).

rfo:
  # Inherits all opt settings, plus:
 trust_radius: 0.10 # Trust-region radius
 trust_update: true # Enable trust-region updates
 trust_min: 0.0001 # Minimum trust radius
 trust_max: 0.10 # Maximum trust radius (bohr); reduced from 0.20 in v0.3.5
 max_energy_incr: null # Allowed energy increase per step
 hessian_update: bfgs # Hessian update scheme: bfgs, bofill, etc.
 hessian_init: calc # Hessian initialization: calc, unit, etc.
 hessian_recalc: 500 # Rebuild Hessian every N steps
 hessian_recalc_adapt: null # Adaptive Hessian rebuild factor
 small_eigval_thresh: 1.0e-08 # Eigenvalue threshold for stability
 alpha0: 1.0 # Initial micro step
 max_micro_cycles: 50 # Micro-iteration limit
 rfo_overlaps: false # Enable RFO overlaps
 gediis: false # Enable GEDIIS
 gdiis: true # Enable GDIIS
 gdiis_thresh: 0.0025 # GDIIS acceptance threshold
 gediis_thresh: 0.01 # GEDIIS acceptance threshold
 gdiis_test_direction: true # Test descent direction before DIIS
 adapt_step_func: true # Adaptive step scaling

---

Path Optimization Sections

gs

Growing String Method settings.

gs:
 fix_first: true # Keep first endpoint fixed
 fix_last: true # Keep last endpoint fixed
 max_nodes: 20 # Maximum string nodes (internal images); for GSM the total path has +2 endpoints
 perp_thresh: 0.005 # Perpendicular displacement threshold
 reparam_check: rms # Reparameterization check metric
 reparam_every: 1 # Reparameterization stride
 reparam_every_full: 1 # Full reparameterization stride
 param: equi # Parameterization scheme
 max_micro_cycles: 10 # Micro-iteration limit
 reset_dlc: true # Rebuild delocalized coordinates each step
 climb: true # Enable climbing image
 climb_rms: 0.0005 # Climbing RMS threshold
 climb_lanczos: true # Lanczos refinement for climbing
 climb_lanczos_rms: 0.0005 # Lanczos RMS threshold
 climb_fixed: false # Keep climbing image fixed
 scheduler: null # Optional scheduler backend

Note

max_nodes semantics differ between GSM and DMF. For GSM (mep-mode gs), gs.max_nodes is the number of internal images — the total path length is max_nodes + 2 because the two endpoints are fixed. For DMF (mep-mode dmf), the CLI flag --max-nodes instead counts the number of movable images with no implicit endpoint expansion. See path-opt for per-method details.

---

dmf

Direct Max Flux settings for MEP optimization.

Note

--max-nodes for DMF means “number of movable images” — unlike GSM, DMF does not add +2 for fixed endpoints. See the gs.max_nodes note above for the contrast.

dmf:
 max_cycles: 300 # Maximum DMF/IPOPT iterations (overridden by --max-cycles)
 correlated: true # Correlated DMF propagation
 sequential: true # Sequential DMF execution
 fbenm_only_endpoints: false # Run FB-ENM beyond endpoints
 fbenm_options:
   delta_scale: 0.2 # FB-ENM displacement scaling
   bond_scale: 1.25 # Bond cutoff scaling
   fix_planes: true # Enforce planar constraints
 cfbenm_options:
   bond_scale: 1.25 # CFB-ENM bond cutoff scaling
   corr0_scale: 1.1 # Correlation scale for corr0
   corr1_scale: 1.5 # Correlation scale for corr1
   corr2_scale: 1.6 # Correlation scale for corr2
   eps: 0.05 # Correlation epsilon
   pivotal: true # Pivotal residue handling
   single: true # Single-atom pivots
   remove_fourmembered: true # Prune four-membered rings
 dmf_options:
   remove_rotation_and_translation: false # Keep rigid-body motions
   mass_weighted: false # Toggle mass weighting
   parallel: false # Enable parallel DMF
   eps_vel: 0.01 # Velocity tolerance
   eps_rot: 0.01 # Rotational tolerance
   beta: 10.0 # Beta parameter for DMF
   update_teval: false # Update transition evaluation
   k_fix: 300.0 # Harmonic constant for restraints

---

search

Recursive path search settings (path-search only).

search:
 max_depth: 10 # Recursion depth limit
 stitch_rmsd_thresh: 0.0001 # RMSD threshold for stitching segments
 bridge_rmsd_thresh: 0.0001 # RMSD threshold for bridging nodes
 max_nodes_segment: 10 # Max nodes per segment
 max_nodes_bridge: 5 # Max nodes per bridge
 kink_max_nodes: 3 # Max nodes for kink optimizations
 max_seq_kink: 2 # Max sequential kinks
 refine_mode: null # Refinement strategy: peak, minima, or null (auto)

---

stopt

StringOptimizer settings for chain-of-states path optimization (path-opt, path-search).

stopt:
 type: string # Optimizer type label
 thresh: gau_loose # StringOptimizer convergence preset
 stop_in_when_full: 300 # Early stop threshold when the string is full
 align: false # Alignment toggle (forced to False in path-opt/path-search; external Kabsch alignment is used instead)
 scale_step: global # Step scaling mode
 max_cycles: 300 # Maximum StringOptimizer iterations
 dump: false # Dump trajectory/restart data
 dump_restart: false # Dump restart checkpoints
 reparam_thresh: 0.0 # Reparameterization threshold
 coord_diff_thresh: 0.0 # Coordinate-difference threshold
 out_dir: ./result_path_opt/ # Output directory
 print_every: 10 # Logging stride

---

TS Optimization Sections

TS optimization uses two mutually exclusive algorithm sections, selected by --opt-mode:

• --opt-mode dimer (or grad) → uses hessian_dimer section

• --opt-mode rsirfo (or hess, default) → uses rsirfo section

Shared optimizer settings (thresh, max_cycles, dump) are read from the opt section above.

hessian_dimer

Hessian Guided Dimer TS optimization settings (tsopt –opt-mode grad).

hessian_dimer:
 thresh_loose: gau_loose # Loose convergence preset
 thresh: baker # Main convergence preset
 update_interval_hessian: 500 # Hessian rebuild cadence
 neg_freq_thresh_cm: 5.0 # Imaginary-frequency detection threshold (cm⁻¹)
 flatten_amp_ang: 0.1 # Flattening amplitude (Å)
 flatten_max_iter: 50 # Flattening iteration cap (see note below)
 flatten_sep_cutoff: 0.0 # Minimum distance between representative atoms
 flatten_k: 10 # Representative atoms sampled per mode
 flatten_loop_bofill: false # Bofill update for flatten displacements
 mem: 100000 # Memory limit for solver
 device: auto # Device selection for eigensolver
 root: 0 # Targeted TS root index
 dimer:
   length: 0.0189 # Dimer separation (Bohr)
   rotation_max_cycles: 15 # Max rotation iterations
   rotation_method: fourier # Rotation optimizer method
   rotation_thresh: 0.0001 # Rotation convergence threshold
   rotation_tol: 1 # Rotation tolerance factor
   rotation_max_element: 0.001 # Max rotation matrix element
   rotation_interpolate: true # Interpolate rotation steps
   rotation_disable: false # Disable rotations entirely
   rotation_disable_pos_curv: true # Disable when positive curvature detected
   rotation_remove_trans: true # Remove translational components
   trans_force_f_perp: true # Project forces perpendicular to translation
   bonds: null # Bond list for constraints
   N_hessian: null # Hessian size override
   bias_rotation: false # Bias rotational search
   bias_translation: false # Bias translational search
   bias_gaussian_dot: 0.1 # Gaussian bias dot product
   seed: null # RNG seed for rotations
   write_orientations: true # Write rotation orientations
   forward_hessian: true # Propagate Hessian forward
   lbfgs:
     # Same keys as lbfgs section
     thresh: baker
     max_cycles: 10000

Note

flatten_max_iter CLI precedence exception. The YAML value hessian_dimer.flatten_max_iter: 50 (and the analogous rsirfo.flatten_max_iter override) is overridden to 0 by the CLI unless --flatten is explicitly passed, regardless of the normal defaults < YAML < CLI ordering. See --flatten precedence caveat for the full behavior table.

---

rsirfo

RS-I-RFO TS optimization settings (tsopt –opt-mode hess).

rsirfo:
 thresh: baker # RS-IRFO convergence preset
 max_cycles: 10000 # Iteration cap
 print_every: 100 # Logging stride
 min_step_norm: 1.0e-08 # Minimum accepted step norm
 assert_min_step: true # Assert when steps stagnate
 roots: [0] # Target root indices
 hessian_ref: null # Reference Hessian
 rx_modes: null # Reaction-mode definitions
 prim_coord: null # Primary coordinates to monitor
 rx_coords: null # Reaction coordinates to monitor
 hessian_update: bofill # Hessian update scheme
 hessian_recalc: 500 # Rebuild exact Hessian every N macro steps (inherited from rfo)
 hessian_recalc_reset: true # Reset recalc counter after exact Hessian
 max_micro_cycles: 50 # Micro-iterations per macro cycle
 augment_bonds: false # Augment reaction path based on bond analysis
 min_line_search: true # Enforce minimum line-search step
 max_line_search: true # Enforce maximum line-search step
 assert_neg_eigval: false # Require negative eigenvalue at convergence
 track_mode_by_overlap: false # Track the selected TS mode by overlap with the previous Hessian
 # Also inherits rfo-like settings: trust_radius, trust_update, etc.

Note

--flatten precedence. The flatten loop for both Hessian-Dimer and RS-I-RFO paths is configured under the hessian_dimer: YAML section (key flatten_max_iter, default 50); rsirfo: does not define its own flatten counter. The CLI overrides flatten_max_iter to 0 unless --flatten is explicitly passed on the command line. See --flatten precedence caveat.

---

IRC Section

irc (section)

IRC integration settings.

irc:
 step_length: 0.1 # Integration step length
 max_cycles: 125 # Maximum steps along IRC
 downhill: false # Follow downhill direction only
 forward: true # Propagate in forward direction
 backward: true # Propagate in backward direction
 root: 0 # Normal-mode root index
 hessian_init: calc # Hessian initialization source
 hessian_update: bofill # Hessian update scheme
 hessian_recalc: null # Hessian rebuild cadence
 displ: energy # Displacement construction method
 displ_energy: 0.001 # Energy-based displacement scaling
 displ_length: 0.1 # Length-based displacement fallback
 rms_grad_thresh: 0.001 # RMS gradient convergence threshold
 hard_rms_grad_thresh: null # Hard RMS gradient stop
 energy_thresh: 0.000001 # Energy change threshold
 imag_below: 0.0 # Imaginary frequency cutoff
 force_inflection: true # Enforce inflection detection
 check_bonds: false # Check bonds during propagation
 out_dir: ./result_irc/ # Output directory
 prefix: "" # Filename prefix
 max_pred_steps: 500 # Predictor-corrector max steps
 loose_cycles: 3 # Loose cycles before tightening
 corr_func: mbs # EulerPC corrector function: "mbs" (modified Bulirsch–Stoer, default) or "rk4"

The corr_func key selects the corrector step used by the predictor–corrector IRC integrator (EulerPC). "mbs" is the pysisyphus-native modified Bulirsch–Stoer implementation (default) and "rk4" requests a classical fourth-order Runge–Kutta corrector. Change this only if the default integrator is numerically unstable on your system; most users should leave it at mbs.

---

Vibrational Analysis Sections

freq (section)

Vibrational frequency analysis settings.

freq:
 amplitude_ang: 0.8 # Displacement amplitude for modes (Å)
 n_frames: 20 # Number of frames per mode animation
 max_write: 10 # Maximum number of modes to write
 sort: value # Sort order: "value" or "abs"
 out_dir: ./result_freq/ # Output directory

---

thermo

Thermochemistry settings.

thermo:
 temperature: 298.15 # Thermochemistry temperature (K)
 pressure_atm: 1.0 # Thermochemistry pressure (atm)
 dump: false # Write thermoanalysis.yaml

---

DFT Section

dft (section)

DFT calculation settings.

dft:
 func: wb97m-v # Exchange-correlation functional
 basis: def2-tzvpd # Basis set name
 func_basis: null # Combined "FUNC/BASIS" string (overrides func/basis)
 conv_tol: 1.0e-09 # SCF convergence tolerance (hartree)
 max_cycle: 100 # Maximum SCF iterations
 grid_level: 3 # PySCF grid level
 verbose: 0 # PySCF verbosity (0-9)
 out_dir: ./result_dft/ # Output directory root

---

Scan Sections

Scan coordinates are specified via --scan-lists/-s (inline or YAML file), not in the main YAML config. See Quickstart: scan workflow for scan coordinate syntax (PDB selectors, multi-stage).

bias

Harmonic bias settings for scans and restraint-based optimizations.

bias:
 k: 300.0 # Harmonic bias strength (eV·Å⁻²)

Shared spring constant across subcommands. The same physical harmonic penalty (k, in eV·Å⁻²) appears in three places with the same default of 300.0:

YAML key	Used by	CLI flag
bias.k	opt (--bias-k applied to --dist-freeze pairs), scan, scan2d, scan3d	--bias-k
dmf.dmf_options.k_fix	path-opt / path-search when mep_mode: dmf	— (YAML only)

Override any of these to tune how stiff the harmonic restraint is. A smaller value (e.g. 20.0) is appropriate when the geometry should relax against a soft guidance term; the default 300.0 enforces near-rigid pinning.

---

bond

MLIP-based bond-change detection.

bond:
 device: auto # MLIP device for bond analysis
 bond_factor: 1.2 # Covalent-radius scaling for cutoff
 margin_fraction: 0.05 # Fractional tolerance for comparisons
 delta_fraction: 0.05 # Minimum relative change to flag bond formation/breaking

---

Example: Complete Configuration File

Below is a complete example combining multiple sections:

# pdb2reaction configuration example

geom:
 coord_type: cart
 freeze_atoms: []

calc:
 backend: uma
 charge: 0
 spin: 1
 model: uma-s-1p1 # uma-s-1p1 | uma-m-1p1
 device: auto
 hessian_calc_mode: Analytical # Recommended when VRAM permits
 solvent: none                 # Set to e.g. "water" for implicit solvent

gs:
 max_nodes: 12
 climb: true
 climb_lanczos: true

stopt:
 thresh: gau_loose
 max_cycles: 300
 dump: false
 out_dir: ./result_all/

opt:
 thresh: gau
 lbfgs:                     # also accepted at top-level as `lbfgs:`
   max_cycles: 10000
 rfo:                       # also accepted at top-level as `rfo:`
   max_cycles: 10000

bond:
 bond_factor: 1.2
 delta_fraction: 0.05

search:
 max_depth: 10
 max_nodes_segment: 10

freq:
 max_write: 10
 amplitude_ang: 0.8

thermo:
 temperature: 298.15
 pressure_atm: 1.0

dft:
 func: wb97m-v
 basis: def2-tzvpd
 grid_level: 3

---

See Also

• all - End-to-end workflow

• opt - Single-structure optimization

• tsopt - Transition state optimization

• path-search - Recursive MEP search

• freq - Vibrational analysis

• dft - DFT calculations

• uma-pysis - MLIP backend details