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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
202 stars 134 forks source link

fix: qe input blocks not seperated by empty lines #724

Closed wanghan-iapcm closed 2 months ago

wanghan-iapcm commented 2 months ago

the qe support only parse input file, in which cell blocks are separated by empty lines, like

ATOMIC_SPECIES
 Na  22.989769  Na_ONCV_PBE-1.0.upf

CELL_PARAMETERS {angstrom}
 7.171683039200000  0.000000000000000  0.000000000000000

however, the input file is valid when no empty line exists, like the following

ATOMIC_SPECIES
 Na  22.989769  Na_ONCV_PBE-1.0.upf  
CELL_PARAMETERS {angstrom} 
 7.171683039200000  0.000000000000000  0.000000000000000

This pr fixes the issue

Summary by CodeRabbit

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago
Walkthrough ## Walkthrough The changes enhance the `scf.py` module for improved handling of Quantum Espresso output data. A new list of keywords, `_QE_BLOCK_KEYWORDS`, is established to standardize block identification in output files. The `get_block` function is modified to utilize this list, while the `get_stress` function is updated to return `None` when no stress data is found. Additionally, a new test class `TestNa` is introduced to validate the functionality of the `dpdata.LabeledSystem` class with a specific Quantum Espresso output file, ensuring accurate atom and force data. ## Changes | Files | Change Summary | |-------------------------------------|----------------------------------------------------------------------------------------------------| | `dpdata/qe/scf.py` | Added `_QE_BLOCK_KEYWORDS` list; modified `get_block` to use this list; updated `get_stress` to return `None` instead of empty when no stress data is found. | | `tests/qe.scf/na.in` | Introduced configuration parameters for SCF calculation for sodium, including sections for control, system, and electron configurations. | | `tests/test_qe_pw_scf.py` | Added `TestNa` class with a `test` method to validate `dpdata.LabeledSystem` functionality for sodium atom configurations in a Quantum Espresso output file. | ## Sequence Diagram(s) ```mermaid sequenceDiagram participant User participant SCFModule as SCF Module participant OutputFile as Quantum Espresso Output File participant TestSuite as Test Suite User->>SCFModule: Request data extraction SCFModule->>OutputFile: Read output data SCFModule->>SCFModule: Identify blocks using _QE_BLOCK_KEYWORDS SCFModule->>OutputFile: Extract forces and stress data alt No stress data found SCFModule-->>User: Return None else Stress data found SCFModule-->>User: Return stress data end User->>TestSuite: Run tests TestSuite->>SCFModule: Validate LabeledSystem with output data TestSuite-->>User: Return test results ```
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 345aedd2ad5ed609344734f07d7937571708d5fe and 3b5033c740c364ce994208ee4d446784ea94d6c0.
Files ignored due to path filters (1) * `tests/qe.scf/na.out` is excluded by `!**/*.out`
Files selected for processing (3) * dpdata/qe/scf.py (2 hunks) * tests/qe.scf/na.in (1 hunks) * tests/test_qe_pw_scf.py (1 hunks)
Files skipped from review due to trivial changes (1) * tests/qe.scf/na.in
Files skipped from review as they are similar to previous changes (2) * dpdata/qe/scf.py * tests/test_qe_pw_scf.py
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codspeed-hq[bot] commented 2 months ago

CodSpeed Performance Report

Merging #724 will not alter performance

Comparing wanghan-iapcm:fix-qe-in (3b5033c) with devel (480242e)

Summary

✅ 2 untouched benchmarks

codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.53%. Comparing base (480242e) to head (3b5033c).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #724 +/- ## ========================================== + Coverage 84.51% 84.53% +0.01% ========================================== Files 81 81 Lines 7155 7156 +1 ========================================== + Hits 6047 6049 +2 + Misses 1108 1107 -1 ```

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