v0.2.21

[njzjz]

Summary by CodeRabbit

• New Features

  • Introduced a new BondOrderSystem class for managing chemical bond information.
  • Added magnetic data handling in the ABACUS plugin.
  • Enhanced SCF calculation configurations with new input parameters for various simulation types.

• Bug Fixes

  • Modified energy assertions in tests for relative equality checks.

• Documentation

  • Updated plugin documentation for clarity on adding the Format class.
  • Enhanced documentation for various system classes and input files.

• Tests

  • Added unit tests for ABACUS spin data handling and structure dumping functionalities.
  • Introduced tests for new input configurations and parsing methods.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

Walkthrough

This pull request encompasses a series of changes across multiple files, primarily focusing on updates to configuration files, enhancements to documentation, and the introduction of new functionalities in the dpdata library. Key modifications include version updates for pre-commit hooks, improvements in documentation clarity, the addition of new classes and methods to handle magnetic data, and refinements in existing functions to enhance their capabilities.

Changes

File(s)	Change Summary
.pre-commit-config.yaml	Updated Ruff pre-commit hook version from v0.6.3 to v0.6.5.
docs/plugin.md	Clarified documentation for adding the Format class to entry_points['dpdata.plugins'] in pyproject.toml.
docs/systems/bond_order_system.md	Introduced BondOrderSystem class for managing chemical bonds and formal charges, including a detailed sanitization procedure.
docs/systems/mixed.md	Corrected class reference syntax in documentation for deepmd/npy/mixed.
docs/systems/multi.md	Updated class and method references to use curly brace syntax for consistency.
docs/systems/system.md	Changed class reference formatting to curly brace syntax for System and LabeledSystem.
dpdata/abacus/md.py	Added get_mag_force function to retrieve magnetic moments and forces from outlines data.
dpdata/abacus/relax.py	Introduced get_mag_force function for magnetic data retrieval in relaxation calculations.
dpdata/abacus/scf.py	Added parse_stru_pos function for parsing atomic position data and updated several functions to handle new parameters related to atomic properties.
dpdata/data_type.py	Modified DataType class constructor to include an optional deepmd_name parameter.
dpdata/deepmd/comp.py	Removed handling of energy, force, and virial data from _load_set and to_system_data functions, simplifying data processing.
dpdata/deepmd/hdf5.py	Updated to_system_data and dump functions to dynamically handle data types without hardcoded entries.
dpdata/deepmd/raw.py	Simplified to_system_data and dump functions by removing energy, force, and virial data handling.
dpdata/plugins/abacus.py	Enhanced magnetic data handling with new function register_mag_data and updated methods to utilize it.
dpdata/plugins/ase.py	Modified stress calculation in to_labeled_system method to use structured array format.
dpdata/qe/scf.py	Updated import statements and logic in get_block and get_stress functions for improved clarity and functionality.
dpdata/system.py	Updated System and LabeledSystem classes to include deepmd_name attributes and modified the perturb method to include a new parameter for atom perturbation.
tests/...	Introduced various test files and methods for validating new functionalities, including tests for SCF calculations, relaxation, and molecular dynamics.

Possibly related PRs

• Feat: Support specifying proportion of atoms to be perturbed in System #716: Modifications to the perturb function in dpdata/system.py, introducing a new parameter for atom perturbation.
• feat: support spin for ABACUS #718: Enhancements in dpdata/plugins/abacus.py for registering magnetic data types, related to data handling updates.
• feat: support data type dumped to a different name #727: Introduction of an optional parameter to the DataType class for flexible naming conventions, similar to configuration updates in this PR.

Suggested reviewers

• wanghan-iapcm

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[codspeed-hq]

CodSpeed Performance Report

Merging #729 will not alter performance

_{Comparing njzjz:devel-0.2.21 (c1d6c73) with master (c685e62)}

Summary

✅ 2 untouched benchmarks