Gaussian CLI Options

This page documents the CLI options available for all Gaussian jobs. Use chemsmart sub gaussian --help for the complete list.

Basic Command Structure

chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] <SUBCMD> [SUBCMD_OPTIONS]

Gaussian Options

Project and File Options

Option	Type	Description
`-p, --project`	string	Project settings from `~/.chemsmart/gaussian/*.yaml`
`-f, --filename`	string	Input file for job preparation
`-l, --label`	string	Custom output filename (without extension)
`-a, --append-label`	string	String to append to the base filename
`-i, --index`	string	Structure index (1-based, default: last structure)
`-t, --title`	string	Gaussian job title
`-P, --pubchem`	string	Query structure from PubChem (name, SMILES, CID)

Note

-p uses the project name without the .yaml extension.
-f accepts various formats: .xyz, .com, .gjf, .log, .inp, or .out.

Specifying Output Filenames

Use -l to set a custom filename:

chemsmart sub gaussian -p test -f test.com -l custom_name opt

This creates custom_name.com instead of test_opt.com.

Use -a to append a string to the base filename:

chemsmart sub gaussian -p test -f test.com -a suffix ts

This creates test_suffix.com instead of test_ts.com.

Selecting Structures

Use -i to select a specific structure from multi-structure files:

chemsmart sub gaussian -p test -f molecules.db -i 5 -c 0 -m 1 opt

This uses the 5th structure (1-indexed) from the ASE database file.

Warning

CHEMSMART uses 1-based indexing to match most molecular visualization software.

Using PubChem

Fetch structures directly from PubChem:

chemsmart sub gaussian -p test -P 962 -c 0 -m 1 -l water opt

This fetches water (CID 962) and creates water.com.

Molecular Properties Options

Option	Type	Description
`-c, --charge`	int	Molecular charge
`-m, --multiplicity`	int	Molecular multiplicity

Warning

If the input file lacks charge/multiplicity information, you must specify them with -c and -m.

Examples:

# Modify charge to +1
chemsmart sub gaussian -p test -f molecule.com -c 1 opt

# Modify multiplicity to 3 (triplet)
chemsmart sub gaussian -p test -f molecule.com -m 3 opt

# Modify both charge (-1) and multiplicity (2)
chemsmart sub gaussian -p test -f molecule.com -c -1 -m 2 opt

Tip

This is useful when using an optimized neutral closed-shell structure to run calculations on a charged radical ion.

Method and Basis Set Options

Option	Type	Description
`-x, --functional`	string	DFT functional
`-b, --basis`	string	Basis set
`-s, --semiempirical`	string	Semiempirical method (PM6, AM1, etc.)

Examples:

# Use a different functional
chemsmart sub gaussian -p test -f molecule.com -x b3lyp opt

# Use a different basis set
chemsmart sub gaussian -p test -f molecule.com -b "6-31G*" opt

# Use semiempirical method for TS search
chemsmart sub gaussian -p test -f molecule.com -s pm6 ts

Route and Calculation Options

Option	Type	Description
`-o, --additional-opt-options`	string	Additional optimization options
`-r, --additional-route-parameters`	string	Additional route parameters
`-A, --append-additional-info`	string	Information appended after coordinates
`-C, --custom-solvent`	string	Custom solvent parameters
`-d, --dieze-tag`	string	Route prefix: “n”, “p”, or “t” for #n, #p, #t
`--forces/--no-forces`	bool	Calculate forces (default: disabled)

Examples:

# Add optimization options
chemsmart sub gaussian -p test -f molecule.com -o maxstep=8,maxsize=12 opt

# Add route parameters
chemsmart sub gaussian -p test -f molecule.com -r nosymm opt

Solvent Options

Solvent settings can be specified at the Gaussian group level, which means they apply to any subcommand (opt, td, sp, ts, etc.). This is useful when the project settings define a gas-phase calculation but you want to add solvation for a particular run without modifying the project file.

Option	Type	Description
`--remove-solvent/--no-remove-solvent`	bool	Remove solvent from the job, overriding project settings (default: disabled)
`-sm, --solvent-model`	string	Implicit solvent model (e.g. `smd`, `cpcm`, `iefpcm`)
`-si, --solvent-id`	string	Solvent identifier (e.g. `water`, `toluene`, `dichloromethane`)
`-so, --solvent-options`	string	Additional options appended inside the `scrf=()` keyword (e.g. `iterative`)

Note

Both -sm and -si must be provided together; specifying only one will raise an error when Gaussian processes the input file. -so is only applied when solvent is active — it is ignored when --remove-solvent is used.

Examples:

# Gas phase optimization (project default)
chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -a no_solv opt

# Solvated optimization with SMD/water (overrides project gas-phase settings)
chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -sm smd -si water -a solv opt

# Solvated optimization with additional iterative SCRF option
chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -sm smd -si water -so iterative -a solv opt

# Solvated TD-DFT calculation
chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -sm smd -si water -so iterative -a solv_td td

# Remove solvent when project settings include one
chemsmart sub gaussian -p solv_project -f molecule.xyz -c 0 -m 1 --remove-solvent opt

The solvated opt example above produces a route line of the form:

# opt freq b3lyp def2svp scrf=(smd,solvent=water,iterative)

and the solvated TD-DFT example gives:

# freq cam-b3lyp def2svp scrf=(smd,solvent=water,iterative) TD(singlets,nstates=3,root=1)

Available Subcommands

Conformational Sampling & Dynamics

Subcommand	Description
`crest`	CREST conformational search jobs
`traj`	Trajectory analysis jobs

Structure Optimization

Subcommand	Description
`opt`	Geometry optimization

Transition State Search

Subcommand	Description
`ts`	Transition state optimization
`modred`	Modified redundant coordinate optimization
`irc`	Intrinsic reaction coordinate calculations
`scan`	Potential energy surface scanning

Electronic Structure Properties

Subcommand	Description
`sp`	Single point energy calculation
`nci`	Non-covalent interaction analysis
`dias`	Distortion-Interaction/Activation-Strain analysis
`resp`	RESP charge fitting
`td`	Time-dependent DFT calculations
`wbi`	Wiberg Bond Index analysis

Other Jobs

Subcommand	Description
`com`	Run Gaussian input file as-is
`link`	Multi-step link jobs
`userjob`	Custom user-defined jobs

Next Steps

For detailed information on each job type: