Refactor REACTER file handling and simplify data storage

[janitha-mahanthe]

This pull request introduces several enhancements and refactorings to the vinyl and tetrafluoroethylene (TFE) polymerization reaction templates, input parsing, and simulation setup configuration in AutoREACTER. The main focus is on improving reaction template specificity, expanding configurability for simulation setup, and clarifying code structure and documentation. Below are the most important changes grouped by theme:

Vinyl and TFE Polymerization Reaction Templates

• Refactored and expanded the vinyl polymerization reaction templates in vinyl_polymers.py to clarify atom mapping, add detailed comments, and introduce new templates for copolymerization initiation and TFE (PTFE) polymerization. Some reactions (e.g., radical coupling termination) are now provided as commented-out options with thorough documentation for user control. [1] [2] [3]
• Updated TFE (PTFE) polymerization to distinguish between initiation, propagation, and termination steps, with clearer atom mapping and chain growth logic.

Input Parsing and Simulation Configuration

• Extended the SimulationSetup dataclass to support new configuration options: deep_search, reaction_iteration_depth, wildcards, deduplicate_reaction_templates, and write_second_reaction_stage, with sensible defaults and improved documentation. [1] [2]
• Enhanced input validation in InputParser to parse and validate the new simulation options, supporting multiple aliases for each option and setting up loop/iteration logic based on reaction_iteration_depth. [1] [2]

Monomer and File Handling

• Added a new optional field lmp_molecule_file to the MonomerEntry class to track the LAMMPS molecule file path, with updated docstrings to clarify file generation responsibilities.

CLI and Reaction Preparation

• Moved the generation of highlighted reaction template images from prepare_reactions to the main process method in arx_cli.py, ensuring images are only generated during the main workflow and not during preparation. [1] [2]

These changes improve the clarity, flexibility, and extensibility of reaction handling and simulation setup in AutoREACTER, making it easier for users to configure advanced polymerization workflows and maintain control over reaction selection and simulation stages.

[read-the-docs-community]

Documentation build overview

📚 AutoREACTER | 🛠️ Build #34109316 | 📁 Comparing 48b2114 against latest (14c029c)

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3 files changed

± change_log.html
± overview.html
± supported-reactions.html

[Copilot]

Pull request overview

Refactors reaction metadata/file storage, expands polymerization templates, and adds configurable reaction progression and simulation stages.

Changes:

• Stores generated files directly on monomer/reaction metadata.
• Adds workflow, deduplication, wildcard, and second-stage options.
• Expands vinyl, TFE, epoxy, styrene, and IPN examples.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
examples/test.json	Updates the default epoxy example.
examples/test_styrene.json	Adds varied styrene systems.
examples/test_ethelene.json	Replaces ethene with styrene data.
examples/test_epoxy.json	Updates the diepoxy structure.
examples/test_epoxy_dgeba_dds.json	Adds a DGEBA/DDS example.
examples/DGEBA_MMA_IPN.json	Adds an IPN example.
examples/DGEBA_MMA_IPN_homo2.json	Adds an MMA homopolymer example.
examples/DGEBA_MMA_IPN_homo1.json	Adds a TEGDMA homopolymer example.
AutoREACTER/sim_setup/writers/writer.py	Makes stage two optional.
AutoREACTER/sim_setup/writers/rxn_second_stage_writer.py	Refactors second-stage generation.
AutoREACTER/sim_setup/writers/rxn_first_stage_writer.py	Uses direct reaction file paths.
AutoREACTER/sim_setup/writers/post_eq_writer.py	Selects the final enabled stage.
AutoREACTER/sim_setup/writers/densification_writer.py	Uses direct monomer file paths.
AutoREACTER/session.py	Expands structured workflow state.
AutoREACTER/reaction_preparation/reaction_processor/reaction_progression.py	Uses configured iteration depth.
AutoREACTER/reaction_preparation/reaction_processor/prepare_reactions.py	Adds paths and active-template filtering.
AutoREACTER/reaction_preparation/ff_wrapper/REACTER_files_builder.py	Simplifies REACTER file storage.
AutoREACTER/reaction_preparation/deduplication_detector.py	Adds wildcard-aware deduplication.
AutoREACTER/input_parser.py	Parses new workflow options.
AutoREACTER/detectors/reactions_library/vinyl_polymers.py	Expands vinyl and TFE reactions.
AutoREACTER/arx_cli.py	Moves template image generation.

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