YAML 設定リファレンス¶
このドキュメントは、pdb2reaction の各コマンドで利用される YAML 設定の完全なリファレンスです。設定ファイルは --args-yaml で指定し、適用順序は デフォルト → CLI → YAML（YAMLが最優先）です。
概要¶
--args-yaml を受け付けるすべてのサブコマンドは共通の設定セクションを共有します:
セクション |
説明 |
使用されるコマンド |
|---|---|---|
ジオメトリと座標設定 |
all, opt, scan, scan2d, scan3d, tsopt, freq, irc, path-opt, path-search |
|
UMA 計算機の設定 |
all, opt, scan, scan2d, scan3d, tsopt, freq, irc, path-opt, path-search |
|
最適化の共通設定 |
opt, scan, scan2d, scan3d, tsopt, path-opt, path-search |
|
L-BFGSの設定 |
opt, scan, scan2d, scan3d, path-search |
|
RFOの設定 |
opt, scan, scan2d, scan3d, path-search |
|
GSM（Growing String Method）設定 |
path-opt, path-search |
|
DMF（Direct Max Flux）設定 |
path-opt, path-search |
|
IRC積分設定 |
irc |
|
振動数解析設定 |
freq |
|
熱化学設定 |
freq |
|
DFT計算設定 |
dft |
|
調和バイアス設定 |
scan, scan2d, scan3d |
|
結合変化検出設定 |
scan, path-search |
|
再帰的経路探索設定 |
path-search |
|
ヘシアン・ダイマーTS 最適化 |
tsopt |
|
RS-I-RFO TS 最適化 |
tsopt |
|
path-search用単一構造最適化 |
path-search |
共通セクション¶
geom¶
ジオメトリ読み込みと座標系の設定。
geom:
coord_type: cart # Coordinate type: "cart" (Cartesian) or "dlc" (delocalized internals)
freeze_atoms: [] # 0-based indices of atoms to freeze; merged with CLI --freeze-links detection
注記:
freeze_atomsは PDB 入力時の--freeze-links検出原子とマージされます。凍結原子は力がゼロ化され、ヘシアンの該当行/列もゼロ化されます。
ircではgeom.coord_typeが YAML/CLI マージ後にcartへ強制されます。
calc¶
UMA機械学習計算機の設定。
calc:
charge: 0 # Total system charge (overridden by CLI -q)
spin: 1 # Spin multiplicity 2S+1 (overridden by CLI -m)
model: uma-s-1p1 # UMA pretrained model name
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 # UMA inference workers (workers>1 disables analytical Hessians)
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 # geom.freeze_atoms から継承されるため直接指定しない
hessian_calc_mode: FiniteDifference # Hessian mode: "Analytical" or "FiniteDifference"
return_partial_hessian: false # Return only active-DOF Hessian block
注記:
VRAMが十分な場合は
hessian_calc_mode: Analyticalを推奨します。workers > 1の場合、解析ヘシアンは無効化されます。電荷/スピンは
.gjfテンプレートがあればそれを継承します。freqは既定でcalc.return_partial_hessian = true（PHVA）を設定します（YAML で上書き可能）。IRC は
geom.coord_type = cartとcalc.return_partial_hessian = falseを常に強制します（YAMLより優先）。ircではcalc.return_partial_hessianが YAML/CLI マージ後にfalseへ強制されます。
opt¶
L-BFGS/RFOで共通の最適化設定。
opt:
type: string # StringOptimizer 専用（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 専用：string が満たされたときの早期停止閾値
align: false # StringOptimizer 専用：alignment の有効/無効
scale_step: global # StringOptimizer 専用：step scaling モード
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
dump: false # Dump trajectory/restart data
dump_restart: false # Dump restart checkpoints
reparam_thresh: 0.0 # StringOptimizer 専用：再パラメータ化の閾値
coord_diff_thresh: 0.0 # StringOptimizer 専用：座標差分の閾値
prefix: "" # Filename prefix
out_dir: ./result_opt/ # Output directory
収束プリセット:
Preset |
Max Force |
RMS Force |
Max Step |
RMS Step |
|---|---|---|---|---|
|
2.5e-3 |
1.7e-3 |
1.0e-2 |
6.7e-3 |
|
4.5e-4 |
3.0e-4 |
1.8e-3 |
1.2e-3 |
|
1.5e-5 |
1.0e-5 |
6.0e-5 |
4.0e-5 |
|
2.0e-6 |
1.0e-6 |
6.0e-6 |
4.0e-6 |
|
3.0e-4 |
2.0e-4 |
3.0e-4 |
2.0e-4 |
lbfgs¶
L-BFGSの設定（opt を拡張）。
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¶
RFO（Rational Function Optimizer）の設定（opt を拡張）。
rfo:
# Inherits all opt settings, plus:
trust_radius: 0.1 # Trust-region radius
trust_update: true # Enable trust-region updates
trust_min: 0.0 # Minimum trust radius
trust_max: 0.1 # Maximum trust radius
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: 200 # 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
経路最適化セクション¶
gs¶
Growing String Method（GSM）の設定。
gs:
fix_first: true # Keep first endpoint fixed
fix_last: true # Keep last endpoint fixed
max_nodes: 10 # 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（DMF）によるMEP最適化。
dmf:
max_cycles: 300 # DMF/IPOPT の最大反復数（--max-cycles で上書き）
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
two_hop_mode: sparse # Neighbor traversal strategy
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
two_hop_mode: sparse # Neighbor traversal strategy
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¶
再帰的経路探索（path-searchのみ）。
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
rmsd_align: true # Legacy alignment flag (ignored)
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)
sopt¶
path-search向け単一構造最適化（HEI±1やkinkノード）。
sopt:
lbfgs:
# Same keys as lbfgs section above
thresh: gau
max_cycles: 10000
out_dir: ./result_path_search/
dump: false
# ... (see lbfgs section)
rfo:
# Same keys as rfo section above
thresh: gau
max_cycles: 10000
out_dir: ./result_path_search/
dump: false
# ... (see rfo section)
TS 最適化セクション¶
hessian_dimer¶
ヘシアン・ダイマーTS 最適化（tsopt –opt-mode light）。
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
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
rsirfo¶
RS-I-RFO TS 最適化（tsopt –opt-mode heavy）。
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_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
# Also inherits rfo-like settings: trust_radius, trust_update, etc.
IRCセクション¶
irc (section)¶
IRC積分設定。
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
振動解析セクション¶
freq (section)¶
振動数解析設定。
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"
thermo¶
熱化学設定。
thermo:
temperature: 298.15 # Thermochemistry temperature (K)
pressure_atm: 1.0 # Thermochemistry pressure (atm)
dump: false # Write thermoanalysis.yaml
DFTセクション¶
dft (section)¶
DFT計算設定。
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
スキャン関連セクション¶
bias¶
調和バイアス設定。
bias:
k: 300.0 # Harmonic bias strength (eV·Å⁻²)
bond¶
UMAベースの結合変化検出。
bond:
device: cuda # UMA 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
例: 設定ファイルの全体例¶
# pdb2reaction configuration example
# Use with: pdb2reaction all -i R.pdb P.pdb -c 'LIG' --args-yaml config.yaml
geom:
coord_type: cart
freeze_atoms: []
calc:
charge: 0
spin: 1
model: uma-s-1p1
device: auto
hessian_calc_mode: Analytical # Recommended when VRAM permits
gs:
max_nodes: 12
climb: true
climb_lanczos: true
opt:
thresh: gau
max_cycles: 300
dump: false
out_dir: ./result_all/
sopt:
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: wb97m-v
basis: def2-tzvpd
grid_level: 3