🧬 Quantum Chemical Calculations Step Maker

A comprehensive Python application for automatically generating input files for quantum chemistry software packages (Gaussian and ORCA). Available as both a desktop GUI application and a web-based interface that works on iOS, Android, and desktop browsers.

✨ Features

🖥️ Desktop GUI Version

• Beautiful modern interface with tabbed navigation
• Dual software support: Gaussian (G16/G09) and ORCA
• Multiple input types:
  • .com files (Gaussian input format)
  • .log files (extract geometry from completed calculations)
  • .xyz files (XYZ coordinate format)
  • SMILES strings with ChemDraw SVG name extraction
• Full workflow generation (steps 1-7 for Gaussian, steps 1,2,4,7,9 for ORCA)
• PySOC integration for Spin-Orbit Coupling calculations
• Scheduler support: PBS, SLURM, and Local
• Advanced features:
  • TD-DFT with Singlet/Triplet/Mixed states
  • Solvent models (PCM, SMD)
  • Custom routes and keywords
  • Redundant coordinates
  • Geometry chaining

🌐 Web Version

• Cross-platform: Works on iOS Safari, Android Chrome, and desktop browsers
• No installation required: Just open in browser
• File upload/download: Easy file handling via web interface
• Same powerful features as desktop version
• Responsive design: Optimized for mobile and desktop

📋 Table of Contents

• Installation
• Quick Start
• Usage
• Features in Detail
• Web Version
• Contributing
• License
• Acknowledgments

🚀 Installation

Prerequisites

• Python 3.8 or higher
• RDKit (for SMILES processing) - optional but recommended

  # Using conda (recommended)
  conda install -c conda-forge rdkit
  
  # Or using pip (may have limitations)
  pip install rdkit-pypi

Desktop GUI Version

1. Clone the repository:

   git clone https://github.com/abedisyedaliabbas/Quantum-Chemistry-Software-Input-Generator.git
   cd Quantum-Chemistry-Software-Input-Generator

2. Install dependencies:

   pip install -r requirements.txt

3. Run the application:

   python quantum_steps_gui.py

Web Version

1. Install web dependencies:

   pip install -r requirements_web.txt

2. Start the web server:

   python quantum_steps_web.py

3. Open in browser:

   • Local: http://localhost:5000
   • Network: http://YOUR_IP:5000 (for sharing with friends on same WiFi)

See DEPLOYMENT_GUIDE.md for detailed deployment instructions.

🎯 Quick Start

Desktop GUI

1. Launch quantum_steps_gui.py
2. Select software (Gaussian or ORCA)
3. Choose input type (.com, .log, .xyz, or SMILES)
4. Configure settings in tabs:
   • Mode & IO: Select mode (Full/Single/Multiple) and input files
   • Method: Choose functional and basis set
   • Solvent: Configure solvent model
   • TD-DFT: Set excited state parameters
   • Resources: Set computational resources
   • Scheduler: Configure job submission
   • Advanced: Additional options
5. Click Generate to create all input files

Web Version

1. Start the server: python quantum_steps_web.py
2. Open http://localhost:5000 in your browser
3. Follow the same workflow as desktop version
4. Download generated files as ZIP archive

📖 Usage

Gaussian Workflow Steps

1. Step 1: Ground state geometry optimization
2. Step 2: Vertical excitation (Franck-Condon state)
3. Step 3: cLR correction of vertical excitation energy
4. Step 4: Excited state geometry optimization
5. Step 5: Density calculation at optimized excited state geometry
6. Step 6: cLR correction of excited state energy
7. Step 7: Ground state energy at excited state geometry

ORCA Workflow Steps

1. Step 1: Ground state optimization
2. Step 2: Vertical excitation (Franck-Condon state)
3. Step 4: Excited state optimization
4. Step 7: Ground state at excited state geometry
5. Step 9: Custom step (user-defined)

Input Types

.com Files

• Standard Gaussian input files
• Automatically extracts geometry, charge, and multiplicity

.log Files

• Completed Gaussian calculations
• Extracts final optimized geometry
• Useful for continuing calculations

.xyz Files

• Standard XYZ coordinate format
• Simple coordinate input

SMILES Strings

• Chemical structure input using SMILES notation
• Supports ChemDraw SVG name extraction
• Automatic 3D coordinate generation using RDKit
• Format: name:SMILES or just SMILES

Example:

formaldehyde:CO
benzene:c1ccccc1
water:O

SMILES with ChemDraw Names

1. Copy SMILES from ChemDraw: Edit → Copy As → SMILES
2. Export structure names: File → Save As → SVG
3. Click "Load Names from SVG" in the GUI
4. Names are automatically matched with SMILES!

🔧 Features in Detail

Software Selection

• Gaussian: Full support for G16/G09 workflows
• ORCA: Complete ORCA input file generation

Modes

• Full Mode: Generate all steps (1-7 for Gaussian, 1,2,4,7,9 for ORCA)
• Single Mode: Generate one selected step
• Multiple Mode: Select specific steps to generate

TD-DFT Options

• Singlet: Standard closed-shell singlet states
• Triplet: Explicit triplet states (TD(Triplets, NStates=n))
• Mixed (50-50): Mixed singlet-triplet states for SOC calculations

Solvent Models

• PCM: Polarizable Continuum Model
• SMD: Solvation Model based on Density
• None: Gas phase calculations

PySOC Integration

• Automatic preparation for Spin-Orbit Coupling calculations
• Generates bash scripts for running PySOC
• Combines results into Excel files
• Requires: TD(50-50), %rwf, 6D 10F GFInput

Schedulers

• PBS: Portable Batch System
• SLURM: Simple Linux Utility for Resource Management
• Local: Local execution scripts

🌐 Web Version

The web version provides the same functionality as the desktop GUI but accessible through any web browser.

Sharing with Friends

Local Network (Same WiFi):

1. Start server: python quantum_steps_web.py
2. Share the URL shown (e.g., http://192.168.1.100:5000)
3. Friends can access from their devices

Cloud Deployment:

• Deploy to Railway, Render, or PythonAnywhere for public access
• See DEPLOYMENT_GUIDE.md for details

Web API Endpoints

• GET / - Main web interface
• GET /api/defaults/<software> - Get default settings
• POST /api/route-preview - Preview route for a step
• POST /api/smiles-to-coords - Convert SMILES to coordinates
• POST /api/extract-names-from-svg - Extract names from SVG
• POST /api/parse-log - Parse Gaussian log file
• POST /api/preview - Preview generated files
• POST /api/generate - Generate and download files
• GET /health - Health check

📁 Project Structure

Quantum-Chemistry-Software-Input-Generator/
├── quantum_steps_gui.py          # Main desktop GUI application
├── quantum_steps_web.py         # Flask web server
├── gaussian_steps_gui.py        # Gaussian backend logic
├── ORCA_Step_Maker.py           # ORCA backend logic (if separate)
├── templates/                    # Web UI templates
│   └── index.html
├── static/                       # Web static files
│   ├── css/
│   │   └── style.css
│   └── js/
│       └── app.js
├── requirements.txt             # Desktop dependencies
├── requirements_web.txt         # Web dependencies
├── README.md                     # This file
├── DEPLOYMENT_GUIDE.md          # Web deployment guide
├── LICENSE                       # MIT License
└── .gitignore                   # Git ignore rules

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

📝 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• Gaussian: For the powerful quantum chemistry software
• ORCA: For the open-source quantum chemistry package
• RDKit: For SMILES processing and 3D coordinate generation
• PySOC: For Spin-Orbit Coupling calculations
• ChemDraw: For structure drawing and SMILES export

📧 Contact

For questions, issues, or contributions, please open an issue on GitHub.

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Made with ❤️ for the quantum chemistry community