Feat/enhance post fp cp2k

[SchrodingersCattt]

Summary by CodeRabbit

• New Features

  • Automatic determination of spin multiplicity in CP2K input files based on chemical composition and system charge.

• Bug Fixes

  • Improved mapping of pseudopotential and orbital files to atomic types for better alignment in input generation.
  • Enhanced robustness in reading model deviation files and prevented empty systems from being counted as successful in post-processing.

• Chores

  • Updated Python linter version in pre-commit configuration.
  • Cleaned up redundant entries in example configuration files.

• Tests

  • Removed unnecessary test data setup related to pseudopotential files.

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📝 Walkthrough

Walkthrough

This update introduces changes across several modules: it improves pseudopotential and orbital file mapping in ABACUS SCF generation, adds automatic spin multiplicity calculation for CP2K input generation, adjusts perturbation loops in VASP MD data collection, refines model deviation file reading and system counting logic, updates a JSON example configuration, removes a test data line, and bumps the ruff linter version.

Changes

Cohort / File(s)	Change Summary
Pre-commit Linter Version .pre-commit-config.yaml	Updated the ruff Python linter version from v0.9.6 to v0.12.5.
VASP MD Perturbation Loop dpgen/data/gen.py	Changed the perturbation index loop in coll_vasp_md from range(pert_numb) to range(pert_numb + 1), increasing the number of processed perturbations per scale by one.
ABACUS SCF Pseudopotential/Orbital Mapping dpgen/generator/lib/abacus_scf.py	Enhanced make_abacus_scf_stru to use a type_map for explicit mapping of atom types to pseudopotential and orbital files, ensuring correct file alignment with atom ordering.
CP2K Multiplicity Calculation dpgen/generator/lib/cp2k.py	Added an element-to-atomic-number dictionary and a calculate_multiplicity function. Modified make_cp2k_input to compute and insert spin multiplicity based on system composition and charge if not provided.
Generator Run Logic Adjustments dpgen/generator/run.py	Replaced direct file loading with a helper function for model deviation reading and added a check to only count and append non-empty systems in post_fp_cp2k.
Example Configuration Cleanup examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json	Removed two redundant entries from the sys_batch_size array, reducing it from four to two elements.
Test Data Simplification tests/data/test_gen_bulk_abacus.py	Removed the line assigning the "potcars" key in the testSTRU method, eliminating a redundant test data entry.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant make_cp2k_input
    participant calculate_multiplicity

    User->>make_cp2k_input: Provide sys_data, fp_params
    make_cp2k_input->>make_cp2k_input: Extract atom_names, atom_types, charge
    make_cp2k_input->>calculate_multiplicity: If multiplicity not in fp_params, compute using atom_names/types and charge
    calculate_multiplicity-->>make_cp2k_input: Return computed multiplicity
    make_cp2k_input->>make_cp2k_input: Merge multiplicity into input config
    make_cp2k_input-->>User: Return input string with correct multiplicity

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~15–20 minutes

Possibly related PRs

• abacus: fix bug in make_abacus_scf_stru #1755: Both PRs modify make_abacus_scf_stru to improve pseudopotential and orbital file mapping for atom types in ABACUS SCF generation.
• Update param-ch4.json #1752: Both PRs update examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json by removing redundant entries from the sys_batch_size array.
• fix bug in reading abacus stru #1714: Both PRs refactor and enhance make_abacus_scf_stru in dpgen/generator/lib/abacus_scf.py for better ABACUS structure handling and file mapping.

Suggested reviewers

• wanghan-iapcm

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 9b5fab4 and aa4d225.

📒 Files selected for processing (7)

• .pre-commit-config.yaml (1 hunks)
• dpgen/data/gen.py (1 hunks)
• dpgen/generator/lib/abacus_scf.py (1 hunks)
• dpgen/generator/lib/cp2k.py (3 hunks)
• dpgen/generator/run.py (1 hunks)
• examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json (0 hunks)
• tests/data/test_gen_bulk_abacus.py (0 hunks)

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