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deepmodeling / dpdata

A Python package for manipulating atomistic data of software in computational science
https://docs.deepmodeling.com/projects/dpdata/
GNU Lesser General Public License v3.0
203 stars 134 forks source link

v0.2.21 #729

Closed njzjz closed 2 months ago

njzjz commented 2 months ago

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago

[!CAUTION]

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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 - **#716**: Modifications to the `perturb` function in `dpdata/system.py`, introducing a new parameter for atom perturbation. - **#718**: Enhancements in `dpdata/plugins/abacus.py` for registering magnetic data types, related to data handling updates. - **#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[bot] commented 2 months ago

CodSpeed Performance Report

Merging #729 will not alter performance

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

Summary

✅ 2 untouched benchmarks