YAML Reference

Overview

Section	Description	Used by
geom	Geometry and coordinate settings	all, opt, scan, scan2d, scan3d, tsopt, freq, irc, path-opt, path-search
calc	ML/MM calculator settings	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
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 Dimer TS optimization	tsopt
rsirfo	RS-I-RFO TS optimization	tsopt
stopt	String optimizer settings	path-opt, path-search
microiter	Micro-iteration (MM relaxation) settings	opt, tsopt

---

Shared Sections

geom

Geometry loading and coordinate handling.

geom:
 coord_type: cart # Coordinate type: "cart" (Cartesian) or "dlc" (delocalized internals)

Notes:

• 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 (section)

calc:
 # --- Input files ---
 input_pdb: null # Input PDB file path (usually set by CLI)
 real_parm7: null # Amber parm7 topology for the full (real) system
 model_pdb: null # PDB defining the ML (model) region atoms
 model_charge: 0 # Charge of the ML (model) region
 model_mult: 1 # Spin multiplicity of the ML (model) region
 link_mlmm: null # Link atom specification for ML/MM boundary
 link_atom_method: scaled    # Link atom placement: "scaled" (g-factor) or "fixed" (1.09/1.01 Å)

 # --- MLIP backend selection ---
 backend: uma # MLIP backend: "uma", "orb", "mace", or "aimnet2"

 # --- UMA backend settings ---
 uma_model: uma-s-1p1 # uma-s-1p1 | uma-m-1p1
 uma_task_name: omol # Task tag recorded in UMA batches (UMA backend only)

 # --- ORB backend settings ---
 orb_model: orb_v3_conservative_omol  # ORB model name (ORB backend only)
 orb_precision: float32  # ORB floating-point precision (ORB backend only)

 # --- MACE backend settings ---
 mace_model: MACE-OMOL-0 # MACE model name (MACE backend only)
 mace_dtype: float64      # MACE floating-point precision (MACE backend only)

 # --- AIMNet2 backend settings ---
 aimnet2_model: aimnet2   # AIMNet2 model name (AIMNet2 backend only)

 # --- ML device & Hessian ---
 ml_device: auto # Device for ML inference: "cuda", "cpu", or "auto"
 ml_cuda_idx: 0 # CUDA device index for ML inference
 hessian_calc_mode: FiniteDifference # ML Hessian mode: "Analytical" or "FiniteDifference"

 # --- xTB point-charge embedding ---
 embedcharge: false # Enable xTB point-charge embedding correction for MM->ML effects
 embedcharge_cutoff: 12.0 # Distance cutoff (Å) for MM point charges in xTB embedding
 embedcharge_step: 0.001 # Numerical Hessian step for embedding correction (Å)
 xtb_cmd: xtb # xTB executable command
 xtb_acc: 0.2 # xTB accuracy parameter
 xtb_workdir: tmp # xTB working directory
 xtb_keep_files: false # Keep xTB temporary files
 xtb_ncores: 4 # Number of cores for xTB

 # --- MM backend settings ---
 mm_backend: hessian_ff # MM backend: "hessian_ff" (analytical) | "openmm" (FD Hessian)
 use_cmap: false        # If true, include CMAP terms in model parm7. Default false (Gaussian ONIOM-compatible)
 mm_device: cpu # Device for MM calculation: "cuda" or "cpu" (hessian_ff is CPU-only)
 mm_cuda_idx: 0 # CUDA device index for MM calculation (OpenMM only)
 mm_threads: 16 # Number of threads for MM calculation
 mm_fd: true # Use finite-difference for MM Hessian
 mm_fd_dir: null # Directory for MM finite-difference scratch files
 mm_fd_delta: 0.001 # Finite-difference step size for MM Hessian

 # --- Hessian output settings ---
 out_hess_torch: true # Return Hessian as torch.Tensor
 H_double: true # Assemble/return Hessian in float64
 symmetrize_hessian: true # Symmetrize final Hessian as 0.5*(H+H^T)
 return_partial_hessian: true # Active-block partial Hessian (CLI wrappers default to true)

 # --- Layer configuration ---
 freeze_atoms: [] # 1-based indices of atoms to freeze (Frozen layer)
 hess_cutoff: null # Å; MM atoms within this distance of ML get Hessian (null = all movable)
 movable_cutoff: null # Å; MM atoms within this distance of ML are movable (null = use freeze_atoms)
 use_bfactor_layers: true # If true, read layer assignments from input PDB B-factors
 hess_mm_atoms: null # Explicit Hessian-target MM atom indices (1-based; overrides cutoffs)
 movable_mm_atoms: null # Explicit movable MM atom indices (1-based; overrides cutoffs)
 frozen_mm_atoms: null # Explicit frozen MM atom indices (1-based; overrides cutoffs)

 # --- Diagnostics ---
 print_timing: true # Print ML/MM Hessian timing breakdown
 print_vram: true # Print CUDA VRAM usage during Hessian

Notes:

• backend selects the MLIP backend: uma (default), orb, mace, or aimnet2. Alternative backends require optional dependencies (pip install "mlmm-toolkit[orb]", etc.)

• Backend-specific model keys are only relevant when the corresponding backend is selected:

  • uma_model, uma_task_name — UMA backend only

  • orb_model, orb_precision — ORB backend only

  • mace_model, mace_dtype — MACE backend only

  • aimnet2_model — AIMNet2 backend only

• embedcharge: true enables xTB point-charge embedding, which models MM-to-ML electrostatic polarization effects. Default is false. Requires an xtb executable on $PATH.

• xtb_cmd, xtb_acc, xtb_ncores, xtb_workdir, xtb_keep_files configure the xTB subprocess when embedcharge is enabled.

• hessian_calc_mode: Analytical is recommended when sufficient VRAM is available for the ML region (24 GB+ for 300+ ML atoms). Only available for the UMA backend; other backends use FiniteDifference automatically.

• mm_fd: true uses finite-difference for MM Hessian; set to false to use analytical MM Hessian from hessian_ff

• use_cmap: false (default) excludes CMAP (backbone cross-map dihedral correction) from the model parm7, consistent with Gaussian ONIOM behavior. Set true to include CMAP in the model region (CMAP remains in the real system in both cases).

• real_parm7 and model_pdb are required for ML/MM calculations

• model_charge and model_mult override -q and -m for the ML region specifically

• opt, tsopt, irc, and freq use partial Hessian by default when calc.return_partial_hessian is not explicitly set in YAML.

• To force full Hessian output in those commands, set calc.return_partial_hessian: false explicitly.

• irc forces geom.coord_type = cart regardless of YAML.

opt

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

opt:
 type: string # StringOptimizer-only (path-opt/path-search): optimizer type label
 thresh: gau # Convergence preset: gau_loose, gau, gau_tight, gau_vtight, baker, never
 stop_in_when_full: 300 # StringOptimizer-only: early stop threshold when string is full
 align: false # StringOptimizer-only: alignment toggle
 scale_step: global # StringOptimizer-only: step scaling mode
 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
 energy_plateau: true # Fallback: declare convergence when the energy stops evolving
 energy_plateau_thresh: 1.0e-4 # Energy range tolerance in au (~0.06 kcal/mol)
 energy_plateau_window: 50 # Number of trailing steps used for plateau detection
 line_search: true # Enable line search
 dump: false # Dump trajectory/restart data
 dump_restart: false # Dump restart checkpoints
 reparam_thresh: 0.0 # StringOptimizer-only: reparameterization threshold
 coord_diff_thresh: 0.0 # StringOptimizer-only: coordinate difference threshold
 prefix: "" # Filename prefix
 out_dir: ./result_opt/ # Output directory

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

Energy plateau fallback:

When energy_plateau: true (default), the optimizer declares convergence if the energy range max(E) - min(E) over the last energy_plateau_window steps (default 50) falls below energy_plateau_thresh (default 1.0e-4 au, ~0.06 kcal/mol).

This is a safety net for ML/MM optimizations where the MLIP force noise floor can exceed the standard gradient-based convergence thresholds, causing the optimizer to wander indefinitely. Once the energy itself has plateaued within the MLIP’s numerical precision, further cycles cannot reduce the residual force below the noise floor, so the plateau trigger stops the run cleanly.

Set energy_plateau: false to disable the fallback (the optimizer will then rely solely on the thresh preset). The plateau check is automatically skipped for chain-of-states (COS) optimizers (e.g., GS, DMF string optimizers).

---

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 (tightened in v0.2.8 for ML/MM stability)
 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)
 perp_thresh: 0.005 # Perpendicular displacement threshold
 reparam_check: rms # Reparametrization check metric
 reparam_every: 1 # Reparametrization stride
 reparam_every_full: 1 # Full reparametrization stride
 param: equi # Parametrization 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

---

dmf

Direct Max Flux settings for MEP optimization.

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

String optimizer settings for path-opt and path-search. Controls the GS/DMF string optimization (not individual node optimization).

stopt:
 type: string           # Optimizer type label (used by StringOptimizer)
 thresh: gau_loose      # Convergence preset for string optimization
 stop_in_when_full: 300 # Early stop threshold when string is full
 align: false           # Alignment toggle
 scale_step: global     # Step scaling mode
 max_cycles: 300        # Maximum string optimizer iterations
 dump: false            # Dump trajectory/restart data
 dump_restart: false    # Dump restart checkpoints
 reparam_thresh: 0.0    # Reparametrization threshold
 coord_diff_thresh: 0.0 # Coordinate difference threshold
 out_dir: ./result_path_opt/  # Output directory
 print_every: 10        # Logging stride
 lbfgs:
   # Same keys as lbfgs section (for single-structure optimizer)
   thresh: gau
   max_cycles: 10000
   #... (see lbfgs section)
 rfo:
   # Same keys as rfo section (for single-structure optimizer)
   thresh: gau
   max_cycles: 10000
   #... (see rfo section)

Notes:

• stopt.lbfgs and stopt.rfo configure the single-structure optimizer used for HEI+/-1 endpoint optimization and kink node optimization within path-search

• The outer stopt keys control the string optimizer (GS or DMF wrapper)

---

TS Optimization Sections

hessian_dimer

Hessian 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 # Negative frequency threshold (cm-1)
 flatten_amp_ang: 0.1 # Flattening amplitude (Å)
 flatten_max_iter: 50 # Flattening iteration cap (default 50; --no-flatten sets to 0)
 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
 partial_hessian_flatten: true # Use partial Hessian for imaginary mode detection
 ml_only_hessian_dimer: false # Use only ML-region atoms for Dimer rotation
 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

Notes:

• flatten_max_iter controls the maximum number of imaginary-mode flattening iterations. The default value is 50.

• The CLI flags --flatten / --no-flatten (in tsopt and all) interact with this setting: --flatten enables the flattening loop with the default flatten_max_iter (50); --no-flatten forces flatten_max_iter to 0, effectively disabling the loop. An explicit YAML value for flatten_max_iter takes precedence when provided alongside --flatten.

---

rsirfo

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

rsirfo:
 thresh: baker # RS-I-RFO 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 (pysisyphus default; not set by mlmm)
 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_init: calc # Hessian initialization
 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: false # Line search along imaginary mode (pysisyphus default)
 max_line_search: false # Line search in minimized subspace (pysisyphus default)
 assert_neg_eigval: false # Require negative eigenvalue at convergence
 trust_radius: 0.10 # Trust region radius
 trust_update: true # Trust region update
 trust_min: 0.0001 # Minimum trust radius
 trust_max: 0.10 # Maximum trust radius (tightened in v0.2.8 for ML/MM stability)
 hessian_recalc: 500 # Hessian rebuild cadence
 small_eigval_thresh: 1.0e-08 # Eigenvalue threshold for stability
 out_dir: ./result_tsopt/ # Output directory

---

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
 dump_fn: irc_data.h5 # IRC data filename
 dump_every: 5 # Dump stride
 max_pred_steps: 500 # Predictor-corrector max steps
 loose_cycles: 3 # Loose cycles before tightening
 corr_func: mbs # Correlation function choice

---

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

---

microiter

Micro-iteration settings for ML/MM optimization. When --microiter is enabled, the MM region is relaxed (with frozen ML atoms) between each macro-step of the ML-region optimizer. This can dramatically reduce the number of expensive ML Hessian evaluations needed.

microiter:
 micro_thresh: null       # Convergence preset for MM relaxation (L-BFGS); null → same as macro thresh
 micro_max_cycles: 10000  # Maximum L-BFGS iterations per micro-iteration

Notes:

• Enabled via --microiter / --no-microiter CLI flag (default: on)

• Available in opt (with --opt-mode hess) and tsopt (with --opt-mode hess)

• Uses L-BFGS to minimize MM-region forces while ML atoms are frozen

• micro_thresh accepts the same presets as opt.thresh (gau_loose, gau, gau_tight, etc.); when null or omitted, defaults to the same threshold as the macro step

---

DFT Section

dft (section)

DFT calculation settings.

dft:
 func_basis: wb97m-v/def2-tzvpd # Combined "FUNC/BASIS" string
 conv_tol: 1.0e-09 # SCF convergence tolerance (Hartree)
 max_cycle: 100 # Maximum SCF iterations
 grid_level: 3 # PySCF grid level
 lowmem: true # Use gpu4pyscf rks_lowmem.RKS for closed-shell GPU runs
 verbose: 4 # PySCF verbosity level
 out_dir: ./result_dft/ # Output directory

---

Scan Sections

bias

Harmonic bias settings for scans.

bias:
 k: 300.0 # Harmonic bias strength (eV/Ų)

---

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 full example combining multiple sections:

# mlmm configuration example

geom:
 coord_type: cart
 freeze_atoms: []

calc:
 model_charge: 0
 model_mult: 1
 backend: uma                  # MLIP backend: "uma", "orb", "mace", or "aimnet2"
 embedcharge: false            # xTB point-charge embedding correction
 uma_model: uma-s-1p1          # uma-s-1p1 | uma-m-1p1
 ml_device: auto
 hessian_calc_mode: Analytical   # Recommended when VRAM permits
 mm_device: cpu
 mm_fd: true
 use_bfactor_layers: true # Read layers from PDB B-factors

gs:
 max_nodes: 12
 climb: true
 climb_lanczos: true

opt:
 thresh: gau
 max_cycles: 300
 dump: false
 out_dir: ./result_all/

stopt:
 thresh: gau_loose
 max_cycles: 300
 lbfgs:
   thresh: gau
   max_cycles: 10000
 rfo:
   thresh: gau
   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_basis: wb97m-v/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

• Concepts – ML/MM 3-layer system and ONIOM energy decomposition