add spin for lammps

[pxlxingliang]

Reference #728 to add the spin information for lammps.

Summary by CodeRabbit

• New Features

  • Introduced functions to extract and normalize spin data from LAMMPS dump files.
  • Added support for registering spin data types in the system.
  • Created new simulation input and output files for LAMMPS.
  • Added new compute and dump commands for calculating and outputting spin properties in LAMMPS.

• Tests

  • Implemented unit tests for verifying the handling of spin configurations in LAMMPS files, including scenarios with zero spin values and incomplete data.

[coderabbitai[bot]]

📝 Walkthrough

## Walkthrough This pull request introduces several new functions and modifies existing ones to enhance the handling of spin data in LAMMPS dump files. A new function `get_spin_keys` is added to extract spin-related keys from a LAMMPS dump file, while `get_spin` retrieves spin data from the "ATOMS" block. The `get_spins` function processes atom lines for spin values. The `system_data` function is updated in both `dump.py` and `lmp.py` to include spin data in the returned system dictionary. Additionally, a new function `register_spin` is created to register spin data types, and new test files are added to validate these functionalities. ## Changes | File | Change Summary | |----------------------------------|----------------------------------------------------------------------------------------------------| | `dpdata/lammps/dump.py` | - Added `get_spin_keys(inputfile)` and `get_spin(lines, spin_keys)` functions.
- Updated `system_data` to include spins and modified its signature to include `input_file`. | | `dpdata/lammps/lmp.py` | - Added `get_spins(lines)` to extract and normalize spin values.
- Updated `system_data` and `from_system_data` to handle spins. | | `dpdata/plugins/lammps.py` | - Added `register_spin(data)` to register spin data types with `dpdata.System`.
- Updated `from_system` methods to include `input_file`. | | `tests/lammps/in.lmp` | - Added a new compute command for spin properties and a dump command for outputting spin data. | | `tests/lammps/spin.lmp` | - New file created to define a simulation setup with spin data. | | `tests/lammps/traj.dump` | - New file created containing simulation data formatted for LAMMPS. | | `tests/test_lammps_spin.py` | - Added unit tests for LAMMPS spin configurations, including methods in `TestLmp` and `TestDump`. | ## Possibly related PRs - #718: The changes in this PR involve the registration of spin data types and modifications to methods handling spin information, which aligns with the main PR's focus on introducing new functions for extracting and processing spin data in LAMMPS dump files. ## Suggested reviewers - wanghan-iapcm - njzjz

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[codspeed-hq[bot]]

CodSpeed Performance Report

Merging #738 will not alter performance

_{Comparing pxlxingliang:lmp-spin (ef386da) with devel (cdbbe1b)}

Summary

✅ 2 untouched benchmarks

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 96.55172% with 3 lines in your changes missing coverage. Please review.

Project coverage is 84.92%. Comparing base (74bfccc) to head (ef386da). Report is 3 commits behind head on devel.

Files with missing lines	Patch %	Lines
dpdata/lammps/dump.py	94.23%	3 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #738 +/- ## ========================================== + Coverage 84.80% 84.92% +0.12% ========================================== Files 81 81 Lines 7336 7418 +82 ========================================== + Hits 6221 6300 +79 - Misses 1115 1118 +3 ```

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