Welcome to the SPECI Documentation!

This site contains documentation for the Python-based SPECI code scripts.

SPECI (A Computational Tool for Speciation Study)

SPECI is a graph-theory-based tool designed for speciation studies in coordination chemistry. By integrating 2D graph enumeration, 3D embedding, and automated microkinetic modeling, SPECI enables the exploration of diverse assemblies—including coordinating solvents, oligomers, and interacting ion pairs—without relying on predefined bonding templates.

If you use this software or any function originated from this software please cite it as below in your work. Mu, M., Sommer, T., & García-Melchor, M. (2025). SPECI (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.16823094

Getting Started

• Installation
  • Setting Up Your Environment
  • Dependencies
  • Troubleshooting
• General Input Files
  • Input File Types
  • Example: Component Data CSV
  • Tips for Creating Input Files
  • Location of Input Files
• Input Settings
  • Graph Generation Parameters
• Additional Settings for Advanced Users
  • 2D to 3D Structure Embedding Settings
  • XYZ Structure Optimization and Gaussian Input
  • Gaussian Output Interpretation & Data Export
  • Interacting Ion Pair (IIP) Generation
  • Important Notes
• General Output Files
  • Output File Types
  • Output File Locations
  • Interpreting Output Files
  • Typical Workflow Example
  • Troubleshooting and Tips

Examples

• Solvent Coordination: Example Case Study (LiTMP/THF)
  • Directory Overview
  • Input Preparation
  • Running the Workflow
  • Analyzing Output
  • Tips & Best Practices
  • References & Further Reading
• Actinide Complexes: Example Case Study
  • Directory Overview
  • Input Preparation
  • Running the Workflow
  • Analyzing Output
  • Tips & Best Practices
  • References & Further Reading
• Bimetallic IIP: Example Case Study
  • Overview & Workflow
  • Example Directory Structure
  • Customization & Expansion
  • Best Practices & Tips
  • References & Further Reading

Automated Microkinetic Modelling

• AUTOCOPASI: Installation & Setup
  • Obtaining AUTOCOPASI
  • Python Environment Setup
  • Usage & Integration
  • Best Practices
  • Troubleshooting & Support
  • References & Related Links
• Example Usage: SPECI-AUTOCOPASI Integration
  • Automated Input Preparation from SPECI
  • Running the SPECI-AUTOCOPASI Workflow
  • COPASI Script Execution & Output
  • Troubleshooting
  • References & Links

Indices and Tables

• Index

• Module Index

• Search Page