ComChemKit User Manual

ComChemKit is a high-performance, cluster-safe program designed to extract data from computational chemistry outputs and to create inputs. It runs in parallel with comprehensive safety features to prevent system overload and ensure stable operation in shared computing environments.

Overview

ComChemKit provides a comprehensive suite of tools for computational chemistry workflows:

• Parallel Processing: Efficiently processes multiple Gaussian output files simultaneously

• Job Management: Check and organize completed, failed, and problematic calculations

• Energy Calculations: Extract thermodynamic data and calculate high-level energies

• Coordinate Processing: Extract and organize molecular coordinates

• Input Generation: Create Gaussian input files from XYZ coordinate files

• Input prarameters template: Generate and reuse parameter templates for different calculation types

• Windows interactive mode: Windows users can use all features plus popular linux commands in the interactive mode

Key Features

Scientific Capabilities

• Extract thermodynamic properties (Gibbs free energy, enthalpy, entropy)

• Check and organize job statuses (completed, failed, errors)

• Calculate high-level energies combining different theory levels

• Process coordinates and generate input files

Performance & Safety

• Multi-threaded processing with automatic resource detection

• Cluster-aware operation (SLURM, PBS, SGE, LSF)

• Memory management with automatic limits

• Graceful shutdown handling

Workflow Integration

• Command-line interface with extensive options

• Configuration file support for defaults

• Template system for reproducible calculations

• Interactive mode for Windows users

Getting Started

New to ComChemKit? Start here:

1. Installation Guide - Install the software on your system

2. Usage Guide - Learn how to use all features with examples

3. api - Technical API documentation

Quick Start

# Basic usage - extract data from all .log files
cck

# Check job status and organize files
cck done     # Move completed jobs
cck errors   # Move failed jobs

# Generate input files from XYZ coordinates
cck ci --calc-type opt_freq

Contents

User Guide:

• Installation Guide
  • System Requirements
  • Supported Compilers
• Installation Methods
  • Pre-compiled Binary (Easiest)
  • Build from Source)
  • Cluster Installation
• Post-Installation Setup
  • Configuration File
  • Environment Setup
  • Verification
• Troubleshooting
  • Common Build Issues
  • Runtime Issues
  • Cluster-Specific Issues
• Performance Optimization
• Uninstallation
• Getting Help
• Usage Guide
  • Quick Start
  • Command Overview
• Core Commands
  • 1. Extract (Default Command)
  • 2. Job Status Commands
  • 3. High-Level Energy Calculations
  • 4. Coordinate Extraction
  • 5. Create Input Files (ci)
  • 6. Thermo Module (OpenThermo)
• Configuration and Customization
  • Configuration File
• Performance and Resource Management
  • Thread Management
  • Memory Management
  • File Size Handling
  • Batch Processing
• Safety Features
  • Cluster Environment Detection
  • Graceful Shutdown
  • Error Handling
• Advanced Workflows
  • Complete Computational Chemistry Workflow
  • High-Throughput Processing
  • Template-Based Automation
• Troubleshooting
  • Common Issues and Solutions
• Best Practices
• Command Reference
• Getting Help

Developer Guide:

• Developer Guide
• Project Overview
  • Architecture
  • New Modules in v0.5.0
  • Key Design Principles
• Development Setup
  • Prerequisites
  • Getting the Source Code
  • Building for Development
  • Testing
  • Code Quality Tools
  • Documentation
• Coding Standards
  • Code Style
  • Documentation Standards
  • Error Handling
  • Memory Management
  • Thread Safety
• Contributing
  • Development Workflow
  • Pull Request Guidelines
  • Code Review Process
• Testing Guidelines
  • Unit Testing
  • Integration Testing
  • Performance Testing
• Continuous Integration
  • CI/CD Pipeline
• Release Process
  • Version Numbering
• Support and Communication

API Reference:

• ComChemKit API
  • Class Hierarchy
  • File Hierarchy
  • Full API

Indices and Tables

• Index

• Module Index

• Search Page

Support & Contributing

For bug reports, feature requests, or safety concerns:

• • Issues: GitHub Issues

• Documentation: This user manual

• Help: Use cck --help for command-line help

License

ComChemKit is released under the MIT License. See the LICENSE file for details.

Version Information

Current Version: v0.000.6

• v0.000.1: Initial release featuring parallel data extraction, computational chemistry input generation, and thermo module for multi-program thermodynamic calculations

• v0.000.2: Updated version with new calculation types and improvements in create input functionality

• v0.000.3: Fix errors in create input functionality

• v0.000.4: Update concentration correction message

• v0.000.5: Thermal correction for high-level of theory

• v0.000.6: Print low-frequency vibrational treatment info in results

Note

This documentation is for ComChemKit v0.000.6. For older versions, please refer to the archived documentation.