Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Support for GAFF and OPLS force fields via Foyer (#109).

  • A skip-interactive option to facilitate automated, high-throughput workflows (#113).

Changed

  • Refactored the core Workflow class to improve overall stability and maintainability (#115).

Fixed

  • Implemented timeouts for subprocess calls to prevent workflows from hanging indefinitely (#116).

[1.0.1] - 2026-09-29

Added

  • Support for direct dictionary inputs (including those containing Path objects) in the run function and ARXCLI class, enabling seamless integration with external APIs and tools.

  • Automatic serialization and saving of the input source (whether file or dictionary) to the output directory as input.json.

  • Add citations.bib generation alongside the output files.

Changed

  • Disabled vinyl radical coupling termination reactions in the vinyl polymers library.

  • Improved input data processing by recursively converting Path objects to strings for JSON compatibility.

  • Minor codebase maintenance including import ordering, formatting adjustments, and docstring updates.

Fixed

  • Fixed potential KeyError crashes in the reaction detector by safely retrieving the reference field using .get("reference", {}), making workflows more tolerant of missing input fields.

[1.0.0] - 2026-09-10

Added

  • Reaction progression workflow: Added iterative reaction-product generation so AutoREACTER can generate templates from products formed in earlier reaction steps. This improves support for multistage reactions, copolymerizations, and small-molecule systems where the initial monomers alone are not sufficient to generate all required polymerization templates.

  • Reaction iteration control: Added reaction_iteration_depth to control how many reaction-product iterations are attempted. The default value is 5, and the loop can be disabled by setting reaction_iteration_depth to false.

  • Index-based functional-group detection: Added index-based functional-group detection to track reactive atom positions more accurately during reaction progression.

  • Index-based reaction detection: Added index-based reaction detection so products generated in earlier reaction steps can be checked for additional valid reactions.

  • RDKit/NetworkX reaction deduplication: Added graph-based reaction deduplication to reduce redundant reaction pathways during reaction progression.

  • LAMMPS template deduplication: Added NetworkX-based LAMMPS template deduplication using generated pre-reaction templates, post-reaction templates, and map files.

  • Wildcard template support: Added support for LAMMPS wildcard map generation to reduce duplicate edge-template cases when using supported LAMMPS versions.

  • Expanded reaction libraries: Added and reorganized polymer reaction libraries for epoxy-amine, polyamide, polyester, polycarbonate, polysiloxane, polyurea, polyurethane, vinyl, and related polymerization chemistries.

  • Expanded functional-group libraries: Added modular functional-group libraries for nitrogen, oxygen, carboxyl/carbonyl, vinyl/alkene, sulfur, silicon, ring, active-center, and mixed AB-type groups.

  • TFE/vinyl support: Added support for tetrafluoroethylene and additional vinyl polymerization workflows.

  • Public API session access: Added arx.session() to expose the active AutoREACTER session for workflow inspection.

  • Unit tests: Added broader unit-test coverage for input parsing, ARX CLI behavior, reaction preparation, LUNAR client utilities, force-field wrapper components, walkers, and LAMMPS writers.

  • Documentation pages: Added new documentation pages for advanced options and template deduplication.

Changed

  • Input parser: Refactored input parsing and validation, including cleaner handling of workflow options, simulation setup fields, force-field aliases, and input schema checks.

  • Reaction-library organization: Refactored reaction libraries into dedicated modules and registries instead of relying on one monolithic reaction-library file.

  • Functional-group organization: Refactored functional-group definitions into modular registry-based libraries.

  • Reaction preparation: Refactored reaction preparation to support reaction progression, deduplication, inactive-template filtering, and clearer error handling.

  • REACTER file handling: Simplified REACTER file metadata storage by storing LAMMPS molecule paths directly on monomer entries and template/map paths directly on reaction metadata.

  • LAMMPS writers: Updated LAMMPS input writers to use the refactored REACTER metadata and filter inactive reaction templates.

  • 3D molecule preparation: Improved 3D embedding and repair handling for congested or difficult polymer structures.

  • Examples: Replaced older test-style example JSON files with cleaner v0.3 example inputs.

  • Documentation structure: Reorganized documentation into clearer user-facing and developer-facing pages.

Fixed

  • Fixed reaction progression issues where products from earlier steps were not correctly reused for later reaction detection.

  • Fixed index-alignment issues during functional-group and reaction detection.

  • Fixed radical handling for vinyl polymerization products and reaction deduplication.

  • Fixed duplicate-template detection behavior for both RDKit-level reaction metadata and LAMMPS-level template files.

  • Fixed handling of inactive or duplicate reaction templates so they are skipped in later workflow stages.

  • Fixed empty-reaction cases so AutoREACTER raises clearer errors when no valid reaction instances are found.

  • Fixed LAMMPS molecule/template file path handling after the REACTER metadata refactor.

  • Fixed cache staging behavior during output directory preparation.

  • Fixed documentation heading and toctree issues for cleaner Sphinx builds.

Removed

  • Removed legacy compatibility shims.

  • Removed unused placeholder detector, fragment-comparison, and legacy library files.

  • Removed older cluttered example JSON files in favor of focused v0.3 examples.

[0.2.3] - [2026-06-24]

Added

  • Added a new Session class to centralize session-based input/output handling across the entire package.

  • Added a new ARXCLI module to provide a streamlined Command-Line Interface for running the AutoREACTER workflow with a single command.

    • The CLI supports input file parsing, session management, and orchestrating the end-to-end workflow.

Changed

  • Centralized state management across the entire package. The Session object is now the single source of truth. All modules and functions have been refactored to use the Session for accessing inputs, outputs, and configuration.

  • Centralized the versioning system to dynamically pull from the package’s __version__ attribute.

  • Updated all documentation, examples, and CI configuration to reflect the new API and workflow changes.

[0.2.2] - 2026-06-09

Added

  • Added a new PyPI-ready version of AutoREACTER.

  • Added new reactions to the reaction library.

  • Added the ARXSession module for centralized session-based input/output handling.

  • Added unit tests for the LUNAR API wrapper.

  • Added MANIFEST.in to support packaging of required non-Python files.

  • Added outputs save direction same as the input file directory.

Changed

  • Refactored cache and staging logic to use temporary/session-based directories instead of manually managed base_dir paths.

  • Updated .frc file handling to use package-included force field files.

  • Moved frc_files inside the AutoREACTER package for more reliable access after installation.

  • Improved PCFF .frc directory discovery to be more robust against repository layout changes.

  • Updated prepare_reactions.py, molecule_3d_preparation.py, REACTER_files_builder.py, and lunar_api_wrapper.py to use session-based inputs.

  • Updated documentation, examples, CI configuration, and getting-started instructions.

Deprecated

  • Deprecated direct base_dir-style path handling in favor of ARXSession-based workflow management.

Removed

  • Removed older manual cache directory resolution logic.

  • Removed temporary/editor backup files from the repository.

  • Removed outdated path-resolution behavior that depended on repository-relative assumptions.

  • Removed the old dated folder output method.

Fixed

  • Fixed .frc file path resolution issues when running AutoREACTER from different locations.

  • Improved error messages for missing or unresolved .frc files.

Security

  • No security-related changes in this release.

[0.2.1] - 2026-05-04

Fixed

  • Fixed issue where cache/00_cache was not cleared when initiating a new AutoREACTER run.

  • Improved cache handling to prevent bugs caused by deleting cache files in the middle of a run.

  • Added a warning message when the --cleanup command is used to delete all cached runs, to prevent accidental data loss.

[0.2.0] - 2026-05-01

Breaking

  • Migrated to a class-based architecture (not backward compatible).

  • Updated input schema: explicit density and temperature per replica required.

  • Replaced RDKit atom map numbers with isotope-based tracking.

  • Changed output structure to dated run directories.

  • Introduced library-driven workflow for reactions and functional groups.

Added

  • CLI interface (AutoREACTER.py) with –help and –cleanup support.

  • Jupyter-based interactive visualization tools.

  • Support for string-based LAMMPS atom types (e.g., PCFF).

  • Force field selection via input.json.

  • Retention cleanup utility for managing old runs.

  • Modular detectors and libraries for workflow stages.

  • Control over non-reactive species retention.

Changed

  • Refactored core workflow into modular classes.

  • Improved atom mapping robustness using isotopes.

  • Optimized input generation to reduce unnecessary LAMMPS files.

Fixed

  • Enforced strict validation of external tool paths.

[0.1.0] - 2026-02-17

Added

  • Initial release of AutoREACTER as a script-based workflow for polymer simulation preparation.

  • Support for Jupyter Notebook–based interactive execution.

  • Functional group detection using SMARTS-based pattern matching (step-growth monomers only).

  • Library-driven workflow with structured definitions for functional groups and reactions.

  • Deterministic reindexing for consistent reaction templates and mapping files.

  • Generation of REACTER-compatible LAMMPS input files using integer-based atom typing.

  • Unified input parsing via a single structured input file for simulation configuration.