User guide to Metalquicha

This is the user guide to Metalquicha, a Fortran program for quantum chemistry calculations. It is designed to be modular and extensible, allowing users to easily add new features and methods.

The API docs for the code itself can be found here: https://jorgeg94.github.io/metalquicha/

Contents:

• History
  • Origin of Metalquicha
• Installation
  • Obtaining Metalquicha
  • Building Metalquicha
  • Building with the Fortran Package Manager (fpm)
  • Running Metalquicha
• Getting Started
  • What is Metalquicha?
  • Quick Start
  • Directory Structure
  • Key Concepts
  • Code Flow: How a Calculation Works
  • Understanding the Modules
  • Where to Start Reading
  • Running Examples
  • Adding New Features
  • Testing
  • Common Patterns in the Code
  • Glossary
  • Additional Resources
  • Getting Help
  • Next Steps
• Capabilities
  • Fragmentation Methods
  • Quantum Chemistry Methods
  • Calculation Types
  • Hydrogen Capping
  • Input/Output
  • Parallelization
  • Configuration Options
  • System Requirements
  • Limitations and Future Work
  • Performance Notes
• Input File Formats
  • Overview
  • Generating .mqc Files
  • JSON Input Format
  • .mqc File Format
  • Running Calculations
  • Examples
  • Best Practices
  • Troubleshooting
• JSON Output Format
  • Overview
  • Common Fields
  • Unfragmented Calculations
  • MBE Detailed Breakdown
  • GMBE Output
  • GMBE PIE Output
  • Vibrational Analysis
  • Number Format
• Physics Validation Testing
  • Overview
  • Directory Structure
  • Workflow
  • Running the Validation Suite
  • Test Types
  • Energy Extraction
  • Tolerance Configuration
  • Validation Test Examples
  • CI Integration
  • Troubleshooting
  • Best Practices
  • Generating Reference Energies
  • Validation Test Manifest Schema
  • Contributing New Tests
• Vibrational Analysis and Thermochemistry
  • From Hessian to Vibrational Frequencies
  • IR Intensities from Dipole Derivatives
  • Thermochemistry (RRHO Approximation)
  • Implementation Notes
  • References

Developer Guide:

• Adding New Input File Parameters
  • Overview
  • Step-by-Step Guide
  • Example: Adding a New Section
  • Input File Format Reference
  • Testing Your Changes
• Adding New JSON Output Fields
  • Overview
  • Step-by-Step Guide
  • Example: Adding Orbital Energies
  • Architecture Notes
• Method Configuration Architecture
  • Design Philosophy
  • Configuration Type Hierarchy
  • Method Type Constants
  • The Factory Pattern
  • Adding a New Method
  • Example: Method Configuration in Practice
  • Design Rationale
  • File Locations