v1.0.1

Recent Changes

Documentation Updates

• 007432c - Update documentation with new deployment guide and GitHub workflows
  • Added CI/CD workflows for automated testing and documentation deployment
  • Added comprehensive deployment guide (DEPLOYMENT_GUIDE.md)
  • Updated documentation structure and improved formatting

Code Formatting and Cleanup

• 8ffb0dd - Code formatting improvements
  • Updated formatting in LAMMPS plugin files
  • Consistent code style across C++ files

Testing Infrastructure

• a1496d8 - Added batch test script for LAMMPS

  • New run_all_tests.sh script for automated testing
  • Improved test organization with proper gitignore files

• 45f48f1 - Cleaned up test structure for verlet split dplr

  • Reorganized test files and directories
  • Removed redundant test output files
  • Improved test consistency checking

• 589bb99 - Additional formatting improvements

  • Updated pre-commit configuration
  • Code style consistency across multiple files

Major Feature Developments

LAMMPS Integration Improvements

• 7514da1 - Major reconstruction of verlet/split for dplr

  • Complete refactoring of verlet split implementation
  • New modular architecture with separate kspace handling
  • Improved code organization and maintainability

• c90a21e - Extended verlet/split/dplr compatibility

  • Made verlet/split/dplr applicable to more kspace styles
  • Enhanced flexibility for different simulation configurations
  • Improved installation and build process

Bug Fixes and Enhancements

• 64a7f74 - Added support for pppm/dplr with verlet/split/dplr

  • Corrected self-energy computation for non-pppm/dplr k-space styles
  • Enhanced compatibility with various kspace methods

• 986c6a6 - Fixed bugs in LAMMPS plugin

  • Resolved issues in plugin initialization and execution
  • Improved stability and reliability

Examples and Testing

• c665e6a - Added comprehensive tests for verlet_split_dplr

  • New bulk water test case with reference data
  • Automated consistency checking between reference and test outputs
  • Complete test infrastructure with input files and expected results

• 5541f3c - Updated electrode example

  • Added complete electrode simulation example
  • Included system data and configuration files

Code Organization

• 3caa204 - Reorganized project files
  • Moved example files to appropriate directories
  • Improved project structure and organization
  • Enhanced maintainability

Documentation

• 35e4383 - Updated README and documentation
  • Improved project documentation
  • Enhanced user guides and API documentation

Dependency Management

• f69c5ee - Added version requirement for numpy
  • Specified numpy<2.0 requirement for compatibility
  • Updated pyproject.toml with dependency constraints

Project Configuration Updates

Build System

• 1ae9213 - Fixed format bug in LAMMPS version number in CMakeLists.txt
• 6d47527 - Format improvements in CMakeLists.txt

Project Metadata

• b4e5629 - Updated README and pyproject.toml
  • Enhanced project description
  • Updated version information and dependencies

Code Quality Improvements

Cleanup and Optimization

• c99eb9b - Removed commented-out code

  • Cleaned up legacy code in verlet_split_dplr.cpp
  • Improved code readability

• 057e2bc - Removed redundant code in verlet/split/dplr

  • Streamlined implementation
  • Reduced code complexity

Testing Examples

• 2c8b6ea - Added comprehensive examples for verlet/split

  • New reference and test examples
  • Complete input/output data for validation

• 2f91847 - Updated existing examples

  • Improved example configurations
  • Enhanced test coverage

• fd2c20f - Minor example updates

  • Refined input parameters
  • Improved output formatting

Technical Details

Commit Statistics

• Total Commits: 27
• Time Span: 6 months ago to 2025-11-25
• Primary Contributors: Jia-Xin Zhu, hans
• Files Changed: 100+ files across the project
• Lines Added: ~150,000+ (including test data)
• Lines Removed: ~120,000+ (mostly redundant test outputs)

Most Frequently Modified Files

1. src/lmp/verlet_split_dplr.cpp - Modified in 8+ commits
2. src/lmp/ecmlpplugin.cpp - Modified in 5+ commits
3. README.md - Modified in 4+ commits
4. .pre-commit-config.yaml - Modified in 3+ commits
5. src/lmp/CMakeLists.txt - Modified in 3+ commits

New Files Added

• .github/workflows/ci.yml
• .github/workflows/deploy-docs-ghpages.yml
• .github/workflows/deploy-docs.yml
• DEPLOYMENT_GUIDE.md
• tests/lmp/run_all_tests.sh
• src/lmp/verlet_split_kspace.cpp
• src/lmp/verlet_split_kspace.h

Files Removed

• src/lmp/mylmpplugin.cpp
• Various test output files (dump.lammpstrj, log.lammps, etc.)

Summary

The v1.0.1 release includes significant improvements to the ec-MLP project since v1.0.0, including:

1. Major Architecture Refactoring: Complete reconstruction of the verlet/split implementation for better modularity and maintainability.
2. Enhanced LAMMPS Integration: Improved compatibility with various kspace styles and better plugin stability.
3. Comprehensive Testing: Added extensive test infrastructure with automated validation and consistency checking.
4. Documentation Improvements: Enhanced documentation with deployment guides and automated workflows.
5. Code Quality: Significant cleanup, formatting improvements, and removal of redundant code.
6. Example Enhancements: Added new examples and improved existing ones for better user guidance.

These changes collectively improve the reliability, usability, and maintainability of the ec-MLP project while maintaining backward compatibility with existing workflows.

Migration Notes

Breaking Changes

• None explicitly identified, but users should verify their LAMMPS plugin configurations

Compatibility

• Maintained backward compatibility with existing workflows
• Enhanced compatibility with more kspace styles

Recommended Actions

1. Update LAMMPS plugin installations
2. Review new documentation for deployment procedures
3. Utilize new automated testing infrastructure for validation