Command Line Interface Overview

CHEMSMART provides a comprehensive command-line interface for quantum chemistry calculations and molecular analysis. This guide covers the fundamental CLI structure, execution modes, and common options.

Basic Command Structure

CHEMSMART offers two main execution modes:

• Local execution: Use chemsmart run to execute tasks on the current terminal.

• HPC submission: Use chemsmart sub to submit jobs to high-performance computing clusters.

The basic command structure is:

chemsmart run/sub [OPTIONS] <CMD> [CMD_OPTIONS] <SUBCMD> [SUBCMD_OPTIONS]

Common Options for All Jobs

Server and Resource Options

Option	Type	Description
-s, --server	string	Server name from ~/.chemsmart/server/*.yaml (auto-detected if not specified)
-n, --num-cores	int	Number of cores per job
-g, --num-gpus	int	Number of GPUs per node (defaults to server configuration)
-m, --mem-gb	int	Memory allocation in gigabytes

Note

The -s option takes the server name without the .yaml extension. The -n, -g, and -m options override the server defaults.

Execution Control Options

Option	Type	Description
-S/-R, --skip-completed/--no-skip-completed	bool	Skip or rerun completed jobs (default: skip)
--fake/--no-fake	bool	Enable simulation mode with fake job runners (default: disabled)
--scratch/--no-scratch	bool	Run in scratch space or working directory (default: scratch)

Note

Use -R at the end of the command to rerun a completed job.

Debugging and Logging Options

Option	Type	Description
-d, --debug/--no-debug	bool	Enable debug logging (default: disabled)
--stream/--no-stream	bool	Enable logging to stdout (default: enabled)

Submission-Specific Options

These options are only available with chemsmart sub:

Option	Type	Description
-t, --time-hours	float	Maximum job runtime in hours
-q, --queue	string	HPC queue name
-v, --verbose/--no-verbose	bool	Enable verbose output and debug logging (default: disabled)
--test/--no-test	bool	Generate scripts without submitting (default: disabled)
--print-command/--no-print-command	bool	Print the generated command (default: disabled)

Available Commands

• gaussian: Run or submit Gaussian jobs

• orca: Run or submit ORCA jobs

• mol: Run PyMOL visualization and analysis jobs

• thermochemistry: Run thermochemistry analysis jobs

• grouper: Run structure grouping jobs

Next Steps

For specific job types, see the detailed tutorials:

• Gaussian CLI Options

• ORCA CLI Options

• PyMOL CLI Options

• Thermochemistry Analysis

• Grouper CLI Options

Note

CHEMSMART checks job name uniqueness. If a job with the same name is already running, submission will be blocked. Use -a (append label) or -l (label) options to create unique job names.