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.

[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.

[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.