CHEMSMART Documentation

CHEMSMART is a Python-based toolkit for automating quantum chemistry workflows. It provides tools for creating input files, submitting jobs to HPC clusters, and analyzing simulation results from Gaussian, ORCA, and other computational chemistry software.

Getting Started

• Introduction
  • Citation
  • Additional Citations
• Installation for Linux and macOS
  • Create Environment
  • Make Installation
  • Configure CHEMSMART
• Installation for Windows Using WSL/Ubuntu
  • Prerequisites
  • Installation
• Installation for Windows Using Git Bash
  • Create Environment
  • Make Installation
  • Configure CHEMSMART
• Installation for Windows Using Anaconda PowerShell
  • Create Environment
  • Make Installation
  • Configure CHEMSMART
  • Troubleshooting
• Installation for HPC Cluster
  • Prerequisites
  • Installation

Configuration

• Configuration Overview
  • For Linux, macOS, Ubuntu, and Clusters
  • For Windows Users
• Test Installation and Configuration
  • Verify Installation
• User Settings
  • User Settings File
• Server Settings
  • Server Configuration
• Project Settings
  • Gaussian Project Settings
  • ORCA Project Settings
  • Scratch Directory

CLI Reference

• Command Line Interface Overview
  • Basic Command Structure
  • Common Options for All Jobs
  • Submission-Specific Options
  • Available Commands
  • Next Steps
• Molecule Input Formats
  • Workflow Overview
  • Supported File Formats
  • Molecular Databases
  • Python Object Integration
  • Best Practices
  • See Also
• ChemDraw Organometallic Complex Files
  • Why
  • Supported Organometallic Inputs
  • Requirements
  • How It Works
  • Extracting Ring-Ligand Structures
  • Current Restrictions
  • Examples
  • See Also

Gaussian Jobs

• Gaussian CLI Options
  • Basic Command Structure
  • Gaussian Options
  • Available Subcommands
  • Next Steps
• Structure Optimization (Gaussian)
  • Geometry Optimization
• Transition State Search (Gaussian)
  • Transition State Optimization
  • Modified Redundant Coordinate (Modred) Jobs
  • Intrinsic Reaction Coordinate (IRC) Calculations
  • Potential Energy Surface Scanning
• Conformational Sampling & Dynamics (Gaussian)
  • CREST Jobs
  • Trajectory Analysis
  • Grouper Options for CREST/Trajectory Jobs
• Quick Reaction Coordinate (QRC) Jobs
  • Introduction
  • QRC Options
  • Workflow Overview
  • Basic Usage
  • Extended QRC Applications
  • Summary
• Electronic Structure Properties & Analyses (Gaussian)
  • Single Point Jobs
  • DI-AS Analysis
  • RESP Jobs
  • NCI Jobs
  • TD-DFT Jobs
  • WBI Jobs
• Gaussian QM/MM ONIOM Calculations Guide
  • Overview
  • Basic QM/MM Command
  • QM/MM-Specific Options
  • Usage Examples
  • GaussianQMMMJobSettings Reference
  • Configuration Methods
  • Troubleshooting
• Other Gaussian Jobs
  • Link Jobs
  • Custom User Jobs
  • Direct Input File Execution

ORCA Jobs

• ORCA CLI Options
  • Basic Command Structure
  • ORCA Options
  • Available Subcommands
  • Next Steps
• Structure Optimization (ORCA)
  • Geometry Optimization
  • Single Point Calculations
• Transition State Search (ORCA)
  • Transition State Search
  • Nudged Elastic Band (NEB)
  • Modred Jobs
  • Intrinsic Reaction Coordinate (IRC)
  • Coordinate Scanning
• Direct ORCA Input
  • Direct Input File Execution
• ORCA QM/MM Multiscale Calculations Guide
  • Overview
  • Basic QM/MM Command
  • QM/MM-Specific Options
  • Usage Examples
  • Project Configuration
  • Next Steps
  • Quick Reference
  • ORCAQMMMJobSettings Reference
  • Troubleshooting

Thermochemistry

• Thermochemistry Analysis
  • Thermochemistry Analysis Jobs
  • Boltzmann Weighted Averaging Jobs

PyMOL Visualization

• PyMOL CLI Options
  • Basic Command Structure
  • MOL Options
  • Available Subcommands
  • Next Steps
• Basic Visualization (PyMOL)
  • Visualization Jobs
  • Movie Jobs
  • Hybrid Visualization
  • Align Jobs
• Reaction Analysis (PyMOL)
  • IRC Jobs
• Electronic Structure Analysis (PyMOL)
  • Molecular Orbital (MO) Jobs
  • Spin Density Jobs
• Interaction Analysis (PyMOL)
  • NCI Jobs

NCIPLOT

• NCIPLOT Tutorial
  • Overview
  • Input File Types and Density Calculations
  • Usage Examples
  • Custom Job Labels
  • Multiple Input Files
  • Additional NCIPLOT Options

Auxiliary Scripts

• Auxiliary Scripts Overview
• File Management
  • File Organization Script
  • File Conversion Script
• Electronic Structure Analysis
  • FMO Analysis Script
  • Mulliken Population Analysis Script
  • Hirshfeld Population Analysis Script
  • Wiberg Bond Index Analysis Script

API Reference

• CHEMSMART Modules
  • chemsmart package
  • tests package

Indices and Tables

• Index

• Module Index

• Search Page