Transition State Search (ORCA)

This page covers transition state optimization, NEB calculations, IRC calculations, and coordinate scanning using ORCA.

Transition State Search

Locate saddle points on the potential energy surface.

chemsmart sub [OPTIONS] orca [ORCA_OPTIONS] ts [SUBCMD_OPTIONS]

TS Options

Hessian Options
Option	Type	Description
`-i, --inhess/--no-inhess`	flag	Read Hessian file (default: disabled)
`-f, --inhess-filename`	string	Hessian filename
`--numhess/--no-numhess`	flag	Use numerical Hessian (default: disabled)
`-h, --hybrid-hess/--no-hybrid-hess`	flag	Use hybrid Hessian (default: disabled)
`-a, --hybrid-hess-atoms`	string	Atoms for hybrid Hessian (0-indexed)
`-s, --recalc-hess`	int	Hessian recalculation frequency (default: 5)

Search Options
Option	Type	Description
`-t, --trust-radius`	float	Trust radius for optimization
`-ts, --tssearch-type`	string	Search type: optts or scants (default: optts)
`-fs, --full-scan/--no-full-scan`	flag	Perform full scan (default: disabled)

Basic Usage

Standard TS search:

chemsmart sub orca -p project -f ts_guess.xyz ts

TS search with existing Hessian:

chemsmart sub orca -p project -f molecule.xyz ts -i -f hessian.hess

TS search with numerical Hessian:

chemsmart sub orca -p project -f molecule.xyz ts --numhess

ScanTS mode with full scan:

chemsmart sub orca -p project -f molecule.xyz ts -ts scants -fs

Nudged Elastic Band (NEB)

Find reaction pathways and transition states by optimizing a chain of molecular structures connecting reactant and product geometries.

chemsmart sub [OPTIONS] orca [ORCA_OPTIONS] neb [SUBCMD_OPTIONS]

NEB Options

General Options
Option	Type	Description
`-S, --skip-completed` / `-R, --no-skip-completed`	flag	Skip completed jobs (default) or rerun completed jobs.

Job Type Options
Option	Type	Description
`-j, --joboption`	choice	NEB calculation type: NEB, NEB-CI, NEB-TS, FAST-NEB-TS, TIGHT-NEB-TS, LOOSE-NEB, ZOOM-NEB, ZOOM-NEB-CI, ZOOM-NEB-TS, NEB-IDPP

Structure Options
Option	Type	Description
`-e, --ending-xyzfile`	string	Filename of ending geometry (product)
`-i, --intermediate-xyzfile`	string	Filename of intermediate geometry (TS guess)
`-r, --restarting-xyzfile`	string	Filename of geometry for restarting calculation

Optimization and Method Options
Option	Type	Description
`-o, --pre-optimization`	flag	Pre-optimize endpoint geometries before NEB calculation. [default: False]
`-s, --semiempirical`	choice	Semiempirical method for NEB calculation: XTB0, XTB1, XTB2
`-n, --nimages`	int	Number of images used for NEB calculation.

Basic Usage

Standard NEB calculation:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB-TS -e product.xyz -s XTB2

NEB with climbing image:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB-CI -e product.xyz -s XTB1

NEB with intermediate guess:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB-CI -e product.xyz -i ts_guess.xyz

Restart from previous calculation:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB -r restart.allxyz

NEB with geometry pre-optimization:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB-TS -e product.xyz -o -s XTB2

Advanced Usage

With custom number of images:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb -j NEB-CI -e product.xyz -n 16 -s XTB2

Using absolute paths for geometry files:

chemsmart sub orca -p project -f /path/to/reactant.xyz -c 0 -m 2 neb \
  -j NEB-CI -n 16 -e /path/to/product.xyz -o -s xtb0

With intermediate TS guess and pre-optimization:

chemsmart sub orca -p project -f reactant.xyz -c 0 -m 1 neb \
  -j NEB-TS -e product.xyz -i ts_initial_guess.xyz -o -s XTB2 -n 12

Running on specific server with scratch:

chemsmart sub -s my_server orca -p project -f reactant.xyz -c 0 -m 1 neb \
  -j NEB-CI -e product.xyz -s XTB1

Job Types

Job Type	Description
`NEB`	Standard nudged elastic band calculation
`NEB-CI`	NEB with climbing image to find exact saddle point
`NEB-TS`	NEB calculation optimized for transition state search
`FAST-NEB-TS`	Fast convergence NEB for TS search with loose criteria
`TIGHT-NEB-TS`	Tight convergence NEB for accurate TS search
`LOOSE-NEB`	NEB calculation with loose convergence criteria
`ZOOM-NEB`	Variable density NEB with focus on important regions
`ZOOM-NEB-CI`	ZOOM-NEB with climbing image
`ZOOM-NEB-TS`	ZOOM-NEB optimized for TS search
`NEB-IDPP`	NEB with image-dependent pair potential interpolation

Requirements

Starting geometry (-f option): reactant structure
Ending geometry (-e option): product structure
At minimum, NEB requires reactant and product geometries
For TS searches, use NEB-TS or NEB-CI job types
Semiempirical methods (XTB) are recommended for initial exploration

Important Notes

File Paths

All XYZ file paths (-f, -e, -i, -r) can be specified as absolute or relative paths
Relative paths are resolved relative to the job folder
Files are automatically copied to scratch directory when scratch execution is enabled
File references in the ORCA input use basenames only for portability

Scratch Directory Execution

When running with scratch enabled (default for most servers), all geometry files are automatically copied to the scratch directory
This ensures ORCA can find all required files during execution
After job completion, all output files are copied back to the job folder
No manual file management is required

Pre-optimization Flag

Use -o flag alone to enable pre-optimization (no True/False value needed)
Example: neb -j NEB-TS -e product.xyz -o will pre-optimize endpoint geometries
Omit the -o flag to skip pre-optimization (default behavior)

Modred Jobs

Constrained geometry optimization using modified redundant coordinates.

chemsmart sub [OPTIONS] orca [ORCA_OPTIONS] modred [SUBCMD_OPTIONS]

Intrinsic Reaction Coordinate (IRC)

Trace the minimum energy pathway from a transition state.

chemsmart sub [OPTIONS] orca [ORCA_OPTIONS] irc [SUBCMD_OPTIONS]

IRC Options

General Options
Option	Type	Description
`--maxiter`	int	Maximum iterations
`-p, --printlevel`	int	Print level
`-d, --direction`	choice	Direction: both, forward, backward, down

Hessian Options
Option	Type	Description
`-i, --inithess`	choice	Initial Hessian: read, calc_anfreq, calc_numfreq
`-f, --hess-filename`	string	Initial Hessian filename
`-m, --hessmode`	int	Hessian mode for initial displacement (default: 0)

Displacement Options
Option	Type	Description
`--init-displ`	choice	Initial displacement: DE or length
`--scale-init-displ`	float	Step size from TS (default: 0.1 a.u.)
`--de-init-displ`	float	Energy difference for displacement (default: 2 mEh)

Convergence Options
Option	Type	Description
`--tolrmsg`	float	RMS gradient tolerance (default: 5e-4)
`--tolmaxg`	float	Max gradient tolerance (default: 2e-3)
`-M, --monitor-internals/--no-monitor-internals`	flag	Monitor internal coordinates
`-I, --internal-modred`	string	Internal coordinates to monitor

Basic Usage

Standard IRC calculation:

chemsmart sub orca -p project -f ts.xyz irc

IRC in both directions:

chemsmart sub orca -p project -f ts.xyz irc -d both

IRC with existing Hessian:

chemsmart sub orca -p project -f ts.xyz irc -i read -f hessian.hess

Coordinate Scanning

Explore potential energy surfaces by varying specific coordinates.

chemsmart sub [OPTIONS] orca [ORCA_OPTIONS] scan [SUBCMD_OPTIONS]

Scan Options

Option	Type	Description
`-j, --jobtype`	string	Job type: opt, ts, modred, scan, sp
`-c, --coordinates`	string	Coordinates to scan (1-indexed)
`-x, --dist-start`	string	Starting distance/angle
`-y, --dist-end`	string	Ending distance/angle
`-n, --num-steps`	string	Number of scan steps
`-cc, --constrained-coordinates`	string	Coordinates to keep fixed

Basic Usage

Scan a bond distance:

chemsmart sub orca -p project -f molecule.xyz scan -j scan -c [[1,2]] -x 1.0 -y 3.0 -n 20

Scan with constraints:

chemsmart sub orca -p project -f molecule.xyz scan -j scan -c [[1,2]] -x 1.0 -y 3.0 -n 20 -cc [[5,8]]

Multi-coordinate scan:

chemsmart sub orca -p project -f molecule.xyz scan -j scan -c [[1,2],[3,4,5]] -x [1.5,70.0] -y [3.5,85.0] -n [10,15]