CREST CLI Options

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

Basic Command Structure

chemsmart sub [OPTIONS] crest [CREST_OPTIONS] <SUBCMD> [SUBCMD_OPTIONS]

CREST Options

Project and File Options

Option

Type

Description

-p, --project

string

Project settings from ~/.chemsmart/crest/*.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)

-P, --pubchem

string

Query structure from PubChem (name, SMILES, CID)

--ri, --record-index

int

Select a record from a CHEMSMART database by its 1-based index

--rid, --record-id

string

Select a record from a CHEMSMART database by its ID

--sid, --structure-id

string

Select a structure from a CHEMSMART database by its ID

Note

  • -p uses the project name without the .yaml extension.

  • -f accepts various formats: .xyz, .com, .gjf, .log, .inp, .out, or a CHEMSMART database .db file.

Specifying Output Filenames

Use -l to set a custom label:

chemsmart sub -s server crest -p test -f molecule.xyz -l custom_name conformers

This creates a job folder labeled custom_name instead of the default molecule_conformers.

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

chemsmart sub -s server crest -p test2 -f molecule.xyz -a solv conformers

This creates molecule_solv instead of molecule_conformers.

Selecting Structures

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

chemsmart sub -s server crest -p test -f molecules.xyz -i 5 -c 0 -m 1 conformers

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

Using PubChem

Fetch structures directly from PubChem:

chemsmart sub -s server crest -p test -P 356 -c 0 -m 1 -l octane conformers

This fetches octane (CID 356) and runs CREST labeled octane.

Molecular Properties Options

Option

Type

Description

-c, --charge

int

Molecular charge

-m, --multiplicity

int

Molecular spin multiplicity, this is the actual spin multiplicity (2S+1) and it will be converted automatically by CHEMSMART to uhf in CREST, which is the number of unpaired electrons.

Note

If the input lacks charge/multiplicity, specify them with -c and -m for charge and spin multiplicity. CHEMSMART automatically converts the supplied charge and multiplicity into --chrg and unpaired electrons --uhf (= multiplicity - 1), respectively, required by CREST.

Examples:

# Anion doublet
chemsmart sub -s server crest -p test -f molecule.xyz -c -1 -m 2 conformers

# Triplet
chemsmart sub -s server crest -p test -f molecule.xyz -c 0 -m 3 conformers

Method Options

Option

Type

Description

-g, --gfn-version

choice

GFN method: gfn1, gfn2, gfnff, or the gfn2//gfnff composite protocol. If not specified, defaults to the CREST default (gfn2).

-O, --optimization-level

choice

Optimization level: crude, sloppy, loose, lax, normal, tight, vtight, extreme. If not specified, defaults to the CREST default (vtight).

Examples:

# GFN2-xTB conformational search with very tight optimization level
chemsmart sub -s server crest -p test -f molecule.xyz -g gfn2 -O vtight conformers

# GFN-FF method
chemsmart sub -s server crest -p test -f molecule.xyz -g gfnff conformers

# GFN2-xTB//GFN-FF composite method
chemsmart sub -s server crest -p test -f molecule.xyz -g gfn2//gfnff conformers

Calculation Options

Option

Type

Description

-r, --additional-flags

string

Extra CREST CLI flags appended to the generated command

--nci/--no-nci

bool

Enable or disable non-covalent interaction mode. If not specified, defaults to the CREST default (disable NCI).

-w, --energy-window

float

Energy window in kcal/mol for conformer selection. If not specified, defaults to the CREST default (6.0 kcal/mol).

Examples:

# Append extra CREST flags (whitespace-separated)
chemsmart sub -s server crest -p test -f molecule.xyz -r "--norotmd --niceprint" conformers

# Non-covalent interaction mode
chemsmart sub -s server crest -p test -f molecule.xyz --nci conformers

# Energy window for conformer selection
chemsmart sub -s server crest -p test -f molecule.xyz -w 6.0 conformers

Solvent Options

Solvent options are specified at the CREST group level and apply to all job types.

Option

Type

Description

-sm, --solvent-model

string

Implicit solvent model (e.g. alpb, gbsa)

-si, --solvent-id

string

Solvent name recognized by CREST (e.g. water, toluene)

--remove-solvent/--no-remove-solvent

bool

Remove solvent settings inherited from the project YAML

Important

CHEMSMART renders solvent flags only when both solvent_model and solvent_id are set. Specifying only one of them leaves the calculation in the gas phase.

Note

CREST uses the xTB backend for implicit solvation. The list of parameterized solvents and which solvation models support them is maintained in the xTB documentation on parameterized solvents.

CHEMSMART does not verify model-specific compatibility at job-setup time. Please check the official xTB documentation before choosing a solvent_model / solvent_id combination.

Examples:

# ALPB(water) conformational search
chemsmart sub -s server crest -p test -f molecule.xyz -sm alpb -si water conformers

# Override a solvated project to gas phase
chemsmart sub -s server crest -p solv_project -f molecule.xyz --remove-solvent conformers

Database Input

CREST jobs can take geometries from a CHEMSMART .db file using the selectors:

# By record index (last structure of that record by default)
chemsmart sub -s server crest -p test -f results.db --ri 3 -c 0 -m 1 conformers

# By structure ID
chemsmart sub -s server crest -p test -f results.db --sid c4d5e6f78a9b -c 0 -m 1 conformers

From Other Program Outputs

CREST can also start from Gaussian, ORCA, or xTB outputs:

# From Gaussian log
chemsmart sub -s server crest -p test -f water_opt.log conformers

# From ORCA output
chemsmart sub -s server crest -p test -f molecule.out conformers

# From xTB main output
chemsmart sub -s server crest -p test -f water_ohess/water_ohess.out conformers

See Molecule Input Formats for the full list of supported geometry sources.

How Commands Are Built

For a typical CREST conformational search, CHEMSMART builds a command like:

crest molecule.xyz --gfn2 --chrg 0 --uhf 0

Solvent (when both model and id are set) adds --<model> <id>, for example --alpb water. Additional command-line arguments provided via -r are appended at the end.

For constrained searches, CHEMSMART additionally generates a constraints.inp file containing the specified distance, angle, and/or dihedral constraints and, if specified, the requested force constant.

Next Steps