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Auto_Polymerization Platform

Python 3.10 License: MIT

Automated, Robust, and Modular Polymer Synthesis and Characterization Platform

The Auto_Polymerization platform is a robust, modular, and fully automated system for polymer synthesis, monitoring, purification, and functionalization. It integrates NMR and UV-VIS spectroscopy, automated liquid handling, and comprehensive error-safe hardware control to provide end-to-end, reproducible polymer synthesis workflows. All modules are designed with DRY (Don't Repeat Yourself) principles, batch processing, and robust error handling for maximum reliability, maintainability, and extensibility. All hardware actions are logged, and all modules and functions include comprehensive, standardized docstrings.

📦 Required Packages and Setup

🔧 Hardware Drivers

Install drivers for the devices used in this project:

🐍 Python Environment

Python Version: 3.10

Install the linear actuator and valves control package from the local source in editable mode:

pip install -e src/linear_actuator_and_valves/

📚 Core Dependencies

pip install scipy numpy pandas matplotlib pyserial nmrglue requests pyyaml medusa-sdl pybaselines lmfit

🔬 MatterLab Packages

Install from MatterLab devices repository:

Easy Installation (if available):

pip install matterlab_hotplates
pip install matterlab_pumps
pip install matterlab_serial_device

Manual Installation:

Hotplates, Pumps, Serial Device:

https://gitlab.com/aspuru-guzik-group/self-driving-lab/devices

Spectrometers:

Note: If access is not public, contact Han Hao at University of Toronto.

⚙️ Configuration

User-Editable Configuration

All platform-wide settings (draw speeds, dispense speeds, default volumes, temperatures, etc.) are set in users/config/platform_config.py. Edit this file to change workflow parameters for your hardware and experiments.

Example:

draw_speeds = {
    "solvent": 5,
    "monomer": 5,
    "initiator": 5,
    "cta": 5,
    "modification": 5,
    "nmr": 3,
    "uv_vis": 2
}
dispense_speeds = {
    "solvent": 5,
    "monomer": 5,
    "initiator": 5,
    "cta": 5,
    "modification": 5,
    "nmr": 3,
    "uv_vis": 2
}
default_volumes = {
    "solvent": 10,
    "monomer": 4,
    "initiator": 3,
    "cta": 4,
    "modification": 2,
    "nmr": 3,
    "uv_vis": 2
}
polymerization_temp = 20
set_rpm = 600

The controller loads these values and passes them to all workflow modules. To change a speed or volume, simply edit users/config/platform_config.py:

draw_speeds['solvent'] = 8
default_volumes['monomer'] = 6

CSS200 Spectrometer DLL: Potentially you need to update the DLL_FILE value in ccs_spectrometer.py in the matterlab package: The correct file path is typically: DLL_FILE = Path(r"C:\Program Files\IVI Foundation\VISA\Win64\Bin\TLCCS_64.dll")

Arduino Setup:

  1. Install Arduino IDE on your PC
  2. Upload the Arduino code from users/setup/ to your Arduino board
  3. An overview of the hardware connections of the GPIO pins is given in "Arduino_contacts_overview_2025_06_27_bb.jpg"

⚠️ Important Notes

  • Physical Setup: For a successful experiment, correct hardware assembly is essential. See 🔧 Physical Setup & Hardware Guidance below for detailed instructions and diagrams.
  • Configuration: Always review and update users/config/platform_config.py to match your hardware and experimental needs before running workflows.
  • Device Safety: Double-check all connections and fluid paths before starting any automated run.

🔧 Physical Setup & Hardware Guidance

  • Setup Folder: All essential setup resources are in users/setup/.

    • Flow Paths:
      • Flow paths.pptx provides a comprehensive diagram of the fluidic connections between all pumps, valves, reactors, and analytical devices. Review this to ensure correct tubing and routing.
    • Arduino Wiring:
      • Arduino_contacts_overview_2025_06_27_bb.jpg shows the recommended GPIO pin assignments and wiring for relays, sensors, and actuators. Use this as a reference when connecting your Arduino and peripherals.
    • Firmware:
      • Linear_motor_and_relays.ino contains the Arduino sketch required for controlling the linear actuator and relay modules. Upload this to your Arduino using the Arduino IDE.

  • Before Running Experiments:

    • Double-check all tubing, electrical connections, and device addresses.
    • Ensure the Arduino firmware is uploaded and the correct COM port is set in your configuration.
    • Review the flow path diagram to avoid cross-contamination or incorrect routing.

  • Support: If you encounter issues with the hardware setup, consult the diagrams and images in users/setup/ first. For further help, please open an issue or contact the project maintainers.

📁 Project Structure

Auto_Polymerization/
├── 📂 demo/                          # Demo and minimal workflow test scripts
│   └── 🧪 test_minimal_workflow.py    # Minimal workflow and device test
├── 📂 tests/                         # Test scripts
│   ├── 🧪 test_minimal_workflow.py    # Minimal workflow and device test
│   ├── 🧪 test_modification_workflow.py # Modification workflow unit tests
│   └── 🧪 test_uv_vis_utils.py        # UV-VIS utilities unit tests
├── 📂 src/                           # Source code modules
│   ├── 🔬 UV_VIS/                    # UV-VIS spectroscopy utilities
│   │   ├── uv_vis_utils.py           # UV-VIS data acquisition and analysis
│   │   └── ERROR_SUMMARY.md          # Error handling documentation
│   ├── 💧 liquid_transfers/          # Liquid transfer modules
│   │   └── liquid_transfers_utils.py # Error-safe transfer functions
│   ├── 🧲 NMR/                       # NMR analysis utilities and example data
│   │   ├── nmr_utils.py              # NMR spectrum analysis and processing
│   │   ├── examples/                 # Example NMR analysis scripts
│   │   └── example_data_*/           # Example NMR data sets
│   └── ⚙️ linear_actuator_and_valves/ # Hardware control modules
├── 📂 workflow_steps/                # Workflow step modules
│   ├── _0_preparation.py             # Hardware setup and NMR shimming
│   ├── _1_polymerization_module.py   # Polymerization reaction setup
│   ├── _2_polymerization_monitoring.py # NMR-based reaction monitoring
│   ├── _3_dialysis_module.py         # Polymer purification
│   ├── _4_modification_module.py     # UV-VIS-based functionalization
│   ├── _5_precipitation_module.py    # Polymer precipitation (placeholder)
│   └── _6_cleaning_module.py         # System cleaning (placeholder)
├── 📂 users/                         # User configuration and data
│   ├── ⚙️ config/                    # Configuration files
│   │   ├── platform_config.py        # User-editable platform configuration
│   │   ├── fluidic_design_autopoly.json # Hardware layout configuration
│   │   └── old_designs/              # Previous hardware configurations
│   ├── 📊 data/                      # Data storage
│   ├── 📚 docs/                      # Documentation
│   └── 🔧 setup/                     # Setup files
│       ├── Arduino_contacts_overview_2025_06_27_bb.jpg
│       ├── Flow paths.pptx
│       ├── Linear_motor_and_relays.ino
│       └── medusa_designer_setup.py
├── 🎮 platform_controller.py         # Main workflow controller
├── 🔄 controler_fallback.py          # Legacy controller with pseudo-code
└── 📄 setup.py                       # Package setup

🚦 Complete Workflow Overview

The Auto_Polymerization platform provides a complete automated workflow for polymer synthesis:

Workflow Steps:

  1. Preparation (_0_preparation.py)

    • Hardware initialization and setup
    • NMR shimming with deuterated solvent
    • System priming and cleaning

  2. Polymerization (_1_polymerization_module.py)

    • Component transfer (solvent, monomer, CTA, initiator)
    • Active deoxygenation with argon gas
    • Pre-polymerization NMR t0 measurements
    • Reaction initiation with temperature control

  3. Monitoring (_2_polymerization_monitoring.py)

    • NMR-based conversion tracking
    • Automated shimming at regular intervals
    • Real-time conversion calculation
    • Stopping criteria based on conversion threshold

  4. Dialysis (_3_dialysis_module.py)

    • Polymer purification using peristaltic pumps
    • NMR-based purification monitoring
    • Configurable stopping (noise-based or time-based)
    • Automated system cleanup

  5. Modification (_4_modification_module.py)

    • UV-VIS-based functionalization reaction
    • Reference and t0 spectrum acquisition
    • Hotplate temperature and vial position control (actuator)
    • Absorbance monitoring for reaction completion (stability-based at 520 nm)
    • Final argon push to UV/VIS cell for safe clearing
    • Post-modification dialysis

  6. Post-Modification Dialysis (Platform Controller)

    • Additional purification after modification
    • Time-based stopping only
    • System preparation for next run

Key Features:

  • Error-Safe Transfers: All liquid and gas transfers use robust error handling with COM port conflict resolution and exponential backoff.
  • Absorbance Stability Monitoring: Functionalization completion is detected by monitoring absorbance stability at 520 nm.
  • Final Argon Push: After modification, the UV/VIS cell is cleared with a controlled argon push.
  • Config-Driven & DRY: All parameters are set in platform_config.py and all code follows DRY principles.
  • Comprehensive Logging & Docstrings: All hardware actions and errors are logged; all modules and functions have standardized docstrings.
  • Batch Processing: UV-VIS and NMR data are processed in batch with duplicate protection and robust file handling.
  • Modular Design: Each workflow step is a separate, testable module for easy extension and maintenance.
  • Robust Error Handling: All modules include error handling and logging for safe unattended operation.

🚀 Getting Started

Recommended Workflow:

  1. Install dependencies as described in the 📦 Required Packages and Setup section
  2. Configure your hardware using the setup files in users/setup/
  3. Edit users/config/platform_config.py to set your workflow parameters (speeds, volumes, etc.)
  4. Test your devices and workflow using test_minimal_workflow.py in tests/
  5. Run experiments using platform_controller.py

Quick Start:

To quickly check your hardware and workflow integration, use the minimal workflow test:

cd Auto_Polymerization/tests
python test_minimal_workflow.py

This script will:

  • Test heat/stir and temperature/RPM readout
  • Perform a simple volumetric pump transfer
  • Test all syringe and peristaltic pumps with a volumetric transfer
  • Test UV-VIS spectrometer (reference spectrum)
  • Test SerialDevice commands (gas valve, precipitation valve, linear actuator)

You can also run this script from the demo/ folder.

🧩 Main Components

Component Description Location
🎮 Platform Controller Main workflow orchestration platform_controller.py
🧪 Minimal Workflow Test End-to-end device and workflow test tests/test_minimal_workflow.py
🔬 UV-VIS Utilities Spectroscopy data acquisition, batch processing, absorbance stability, and analysis src/UV_VIS/uv_vis_utils.py
🧲 NMR Utilities NMR spectrum analysis and batch processing src/NMR/nmr_utils.py
💧 Liquid Transfer Utils Error-safe, config-driven transfer functions src/liquid_transfers/liquid_transfers_utils.py
⚙️ Workflow Modules Individual workflow steps (modular, testable) workflow_steps/
⚙️ Configuration User-editable parameters users/config/platform_config.py

📚 Documentation

Topic Location Description
🔬 UV-VIS Utilities src/UV_VIS/uv_vis_utils.py UV-VIS data acquisition, batch processing, absorbance stability, and analysis
🧲 NMR Utilities src/NMR/nmr_utils.py NMR spectrum analysis and processing
💧 Liquid Transfers src/liquid_transfers/liquid_transfers_utils.py Error-safe, config-driven transfer functions
⚙️ Workflow Steps workflow_steps/ Individual workflow modules
🎮 Platform Controller platform_controller.py Main workflow orchestration
⚙️ Configuration users/config/platform_config.py User-editable parameters

🔧 Development

If you want to develop the package further, use the development mode:

pip install -e .

Changes to the source code will be picked up immediately.

Testing:

Run unit tests for individual components:

# Test modification workflow
python -m pytest tests/test_modification_workflow.py

# Test UV-VIS utilities
python -m pytest tests/test_uv_vis_utils.py

# Test minimal workflow
python tests/test_minimal_workflow.py

Code Quality:

  • All modules and functions include comprehensive, standardized docstrings
  • Error-safe transfer functions with retry logic and exponential backoff
  • Modular, DRY, and config-driven design for easy testing, extension, and maintenance
  • Batch processing and duplicate protection for all spectroscopy data
  • Robust error handling and logging throughout

📄 License

MIT License - see the LICENSE.txt file for details.

🧪 NMR Analysis Utilities

The main NMR analysis utilities are located in src/NMR/nmr_utils.py.

  • Example data for NMR analysis is provided in src/NMR/example_data_MMA_and_standard/ and related folders.
  • To batch analyze NMR spectra or test the analysis workflow, you can run the main/test block in nmr_utils.py:
cd Auto_Polymerization
python -m src.NMR.nmr_utils

This will process all spectra in the example data folder and output integration results and plots.

🆘 Support

For issues and questions:

  1. Run the minimal workflow test in tests/ or demo/
  2. Check the troubleshooting sections in the README
  3. Verify hardware connections and configuration
  4. Run the full test suite to ensure all modules are working as expected
  5. Open an issue on GitHub or contact the maintainers

❓ Questions or issues?
Please open an issue on GitHub or contact the maintainers.

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Code for the orchestration of an automated polymerization workflow

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