irc

Overview

Summary: Runs EulerPC (Euler Predictor-Corrector)-based intrinsic reaction coordinate (IRC) integration from a transition state toward reactants and products. By default both forward and backward branches are computed. Setting --hessian-calc-mode Analytical is strongly recommended when VRAM permits.

At a glance

• Use when: Tracing the intrinsic reaction coordinate from an optimized TS (validated by tsopt) to confirm endpoint connectivity (R ↔ TS ↔ P).

• Method: EulerPC (Euler Predictor-Corrector) integration with an MLIP-backend Hessian (UMA by default; ORB/MACE/AIMNet2 also supported). Forward and backward branches run by default.

• Outputs: finished_irc_trj.xyz, forward_irc_trj.xyz, backward_irc_trj.xyz (and .pdb companions when a reference PDB is available).

• Defaults: --max-cycles 125, --step-size 0.10 Bohr, --root 0, --forward/--backward both on, --hessian-calc-mode FiniteDifference, backend uma. Hard overrides: IRC forces geom.coord_type = cart and calc.return_partial_hessian = true after YAML/CLI merging.

• Next step: Optimize IRC endpoints to true minima with opt, or pair with freq for thermochemistry. For Hessian evaluation modes, see Hessian evaluation mode.

pdb2reaction irc runs EulerPC-based IRC integrations with an MLIP backend (UMA by default; -b/--backend also supports ORB, MACE, and AIMNet2).

For XYZ/GJF inputs, --ref-pdb supplies a reference PDB topology while keeping XYZ coordinates, enabling format-aware PDB output conversion. A typical workflow is tsopt (which includes an imaginary-frequency check; confirm one imaginary frequency) → irc.

Minimal example

pdb2reaction irc -i ts.pdb -q 0 -m 1 --max-cycles 50 --out-dir ./result_irc

Output checklist

• result_irc/finished_irc_trj.xyz

• result_irc/forward_irc_trj.xyz

• result_irc/backward_irc_trj.xyz

Common examples

1. Run only the forward branch.

pdb2reaction irc -i ts.pdb -q 0 -m 1 --no-backward \
 --out-dir ./result_irc_forward

2. Increase step size and use analytical Hessians.

pdb2reaction irc -i ts.pdb -q 0 -m 1 --step-size 0.20 \
 --hessian-calc-mode Analytical --out-dir ./result_irc_analytical

3. Keep both branches and raise the step limit.

pdb2reaction irc -i ts.pdb -q 0 -m 1 --max-cycles 150 \
 --out-dir ./result_irc_long

Usage

pdb2reaction irc -i INPUT.{pdb|xyz|trj|...} [-q CHARGE] [-l, --ligand-charge <number|'RES:Q,...'>] \
 [-b/--backend uma|orb|mace|aimnet2] [--solvent SOLVENT] [--solvent-model alpb|cpcmx] \
 [--workers N] [--workers-per-node N] [-m 2S+1] \
 [--max-cycles N] [--step-size Δs] [--root k] \
 [--forward/--no-forward] [--backward/--no-backward] \
 [--freeze-links/--no-freeze-links] \
 [--out-dir DIR] [--config FILE] \
 [--convert-files/--no-convert-files] [--ref-pdb FILE] \
 [--hessian-calc-mode Analytical|FiniteDifference] \
 [--show-config] [--dry-run]

Examples

# Forward-only branch, finite-difference Hessian, larger step size
pdb2reaction irc -i ts.pdb -q 0 -m 1 --no-backward \
 --step-size 0.2 --hessian-calc-mode FiniteDifference --out-dir ./irc_fd/

# PDB input so finished and directional trajectories are also exported as PDB
pdb2reaction irc -i ts.pdb -q 0 -m 1 --max-cycles 50 --out-dir ./result_irc/

Workflow

1. Input preparation – Any format supported by geom_loader is accepted. When a reference PDB is available (input is .pdb or --ref-pdb is supplied), EulerPC trajectories are converted to PDB using that topology, and --freeze-links augments geom.freeze_atoms by freezing parents of link hydrogens for PDB inputs. Note: geom.coord_type is forced to cart (Cartesian) regardless of YAML/CLI settings, and calc.return_partial_hessian is forced to true (partial Hessian with active-DOF processing).

2. EulerPC integration – The EulerPC predictor-corrector integrator traces the IRC path from the transition state. Forward and/or backward branches are run according to --forward/--backward flags. Each step uses an energy-based predictor followed by a corrector step.

3. Trajectory output – Finished, forward, and backward IRC trajectories are written as XYZ files. When a reference PDB is available, PDB companions are also generated (--convert-files).

CLI options

Option	Description	Default
-i, --input PATH	Transition-state structure accepted by geom_loader.	Required
-q, --charge INT	Total charge; used unless YAML sets calc.charge. Required unless a .gjf template or --ligand-charge/-l (PDB inputs or XYZ/GJF with --ref-pdb) supplies it. Explicit -q still overrides --ligand-charge/-l when both are set.	Required unless template/derivation applies
-l, --ligand-charge TEXT	Per-residue charge mapping (e.g., GPP:-3,SAM:1). Automatically derives the total system charge from PDB residue charges — no manual counting needed. Used when -q is omitted (PDB inputs or XYZ/GJF with --ref-pdb).	None
--workers INT	MLIP predictor parallelism (workers > 1 disables analytic Hessians). See workers > 1 silent FD downgrade for diagnostic notes.	1
--workers-per-node INT	Workers per node, forwarded to the parallel predictor.	1
-m, --multiplicity INT	Spin multiplicity (2S+1); used unless YAML sets calc.spin.	.gjf template value or 1
--max-cycles INT	Maximum IRC steps; used unless YAML sets irc.max_cycles.	125
--step-size FLOAT	Step length in unweighted Cartesian coordinates (Bohr); used unless YAML sets irc.step_length.	0.10
--root INT	0-based index into the projected Hessian’s eigenvalues sorted in ascending order (most-negative first), used to pick the mode for the initial IRC displacement. For a validated TS with exactly one imaginary mode, leave --root 0 (the sole negative eigenvalue). Use --root 1, --root 2, … only if you know the active imaginary mode is ranked above more-negative spurious modes. Used unless YAML sets irc.root.	0
--forward/--no-forward	Run forward branch (irc.forward), used unless YAML sets irc.forward.	True
--backward/--no-backward	Run backward branch (irc.backward), used unless YAML sets irc.backward.	True
--freeze-links/--no-freeze-links	For PDB inputs, freeze link-H parents (merged with geom.freeze_atoms). See extract for link-hydrogen details.	True
--freeze-atoms TEXT	Comma-separated 1-based atom indices to freeze explicitly (e.g., '1,3,5'). Complements --freeze-links; applies to any input format.	None
-o, --out-dir TEXT	Output directory (irc.out_dir), used unless YAML sets irc.out_dir.	./result_irc/
--convert-files/--no-convert-files	Toggle XYZ/TRJ → PDB companions when a reference PDB is available.	True
--ref-pdb FILE	Reference PDB topology to use when the input is XYZ/GJF (keeps XYZ coordinates).	None
--hessian-calc-mode CHOICE	MLIP Hessian mode (calc.hessian_calc_mode), used unless YAML sets calc.hessian_calc_mode.	FiniteDifference
--config FILE	Base YAML configuration applied before explicit CLI options.	None
--show-config/--no-show-config	Print resolved YAML layers/config and continue.	False
--out-json/--no-out-json	Write a machine-readable result.json to out_dir. See JSON Output Schema for the schema.	False
-b, --backend {uma,orb,mace,aimnet2}	MLIP backend.	uma
--solvent TEXT	Implicit solvent name for xTB correction (e.g. water). none to disable.	none
--solvent-model {alpb,cpcmx}	xTB solvent model.	alpb
--dry-run/--no-dry-run	Validate and print execution plan without running IRC.	False

Outputs

out_dir/ (default:./result_irc/)
├─ <prefix>finished_irc_trj.xyz # Complete IRC trajectory
├─ <prefix>forward_irc_trj.xyz # Present when the forward branch runs
├─ <prefix>backward_irc_trj.xyz # Present when the backward branch runs
└─ *.pdb # Trajectory companions when a reference PDB is available (conversion enabled)

• Console summaries of resolved geom, calc, and irc configurations plus wall-clock timing.

Exit codes

See Exit codes in CLI Conventions.

Notes

• For symptom-first diagnosis, start with Common Error Recipes, then use Troubleshooting for detailed fixes.

• The MLIP backend (UMA by default) is reused throughout the IRC; aggressive step_length values can destabilize EulerPC.

• For Hessian evaluation modes, see Hessian evaluation mode.

• When --freeze-links is active, link-hydrogen parent atoms are automatically frozen (see Link hydrogen and frozen atoms).

See CLI Conventions: Configuration precedence for the full resolution order.

The geom, calc, and irc sections are unchanged from the canonical definitions in YAML Reference: see geom, calc, and irc. --freeze-links augments geom.freeze_atoms for PDB inputs, and --hessian-calc-mode plus CLI charge/spin values supplement the merged calc block.

irc-specific hard overrides (applied after YAML/CLI merging, regardless of YAML values):

geom:
 coord_type: cart # forced to cart for irc (YAML value ignored)
calc:
 return_partial_hessian: true # forced true for irc (partial Hessian with active-DOF processing)

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See Also

• Common Error Recipes – Symptom-first failure routing

• tsopt — Optimize the TS before running IRC

• freq — Full vibrational analysis and thermochemistry (imaginary-frequency check is already included in tsopt)

• opt — Optimize IRC endpoints to true minima

• all — End-to-end workflow that runs IRC after tsopt

• YAML Reference — Full irc configuration options

• Glossary — Definition of IRC (Intrinsic Reaction Coordinate)