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

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [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 simulation 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.

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## [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.