docs: add CALYPSO model deviation arginfo

[njzjz-bot]

Summary

• Add CALYPSO-specific model_devi_engine argument metadata for generated configuration docs.
• Normalize single-item list values used by the existing CALYPSO examples before generating input.dat.
• Allow scalar PSTRESS values by normalizing them to the pressure list used for CALYPSO work directories.

Context

This follows up on #1795. While reviewing that PR, I found two issues:

• pre-commit failed on formatting/trailing whitespace;
• several documented single-item list forms (for example PopSize: [5] and fmax: [0.01]) were not normalized before reaching make_calypso_input(), which expects scalar values.

Tests

• uvx pre-commit run --files dpgen/generator/arginfo.py dpgen/generator/lib/make_calypso.py dpgen/generator/run.py tests/generator/test_calypso.py
• uv run --with pytest pytest tests/generator/test_calypso.py -q

Authored by OpenClaw (version: 2026.5.28, model: custom-chat-jinzhezeng-group/gpt-5.5)

Summary by CodeRabbit

• New Features

  • Enhanced CALYPSO model-deviation engine with comprehensive configuration options for structure generation, optimization parameters, and convergence criteria.
  • Improved input parameter handling with automatic normalization for more flexible configuration formats.

• Tests

  • Added validation test for parameter normalization in model-deviation workflows.

[codecov]

Codecov Report

❌ Patch coverage is 91.11111% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 50.10%. Comparing base (7af5246) to head (fada1ca).

Files with missing lines	Patch %	Lines
dpgen/generator/lib/make_calypso.py	84.21%	3 Missing ⚠️
dpgen/generator/run.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1887      +/-   ##
==========================================
+ Coverage   49.80%   50.10%   +0.29%     
==========================================
  Files          83       83              
  Lines       14986    15023      +37     
==========================================
+ Hits         7464     7527      +63     
+ Misses       7522     7496      -26     

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[coderabbitai]

Caution

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📝 Walkthrough

Walkthrough

Adds a complete model_devi_calypso_args() argument schema for the CALYPSO engine and wires it into model_devi_args(). Introduces two normalization helpers—_normalize_calypso_scalar and _normalize_calypso_pressures—applied inside _make_model_devi_native_calypso and run.py to standardize scalar/list input shapes. A new test validates single-item list acceptance.

Changes

CALYPSO Engine Schema and Input Normalization

Layer / File(s)	Summary
CALYPSO arginfo schema and engine wiring dpgen/generator/arginfo.py	Introduces model_devi_calypso_args() with a repeatable model_devi_jobs list schema covering species/composition, distance constraints, PSO/optimization controls, VSC options, and convergence targets, plus top-level calypso_input_path, model_devi_max_iter, and vsc fields. Wires it into the calypso variant of model_devi_engine in model_devi_args(), replacing the previous empty placeholder.
Normalization helpers, application, and test dpgen/generator/lib/make_calypso.py, dpgen/generator/run.py, tests/generator/test_calypso.py	Adds _normalize_calypso_scalar (raises on multi-item lists, unwraps single-item lists) and _normalize_calypso_pressures (wraps non-list values into a list). Applies the scalar normalizer to Volume, PsoRatio, PopSize, MaxStep, ICode, MaxNumAtom, and fmax inside _make_model_devi_native_calypso, and the pressure normalizer to PSTRESS there and in run.py before per-pressure subdirectory generation. New test asserts correct input.dat output when job fields are single-element lists.

Sequence Diagram(s)

sequenceDiagram
  participant run.py
  participant _normalize_calypso_pressures
  participant _make_model_devi_native_calypso
  participant _normalize_calypso_scalar

  run.py->>_normalize_calypso_pressures: cur_job.get("PSTRESS", [0.0001])
  _normalize_calypso_pressures-->>run.py: normalized pressure list
  run.py->>_make_model_devi_native_calypso: job dict, work path per pressure
  _make_model_devi_native_calypso->>_normalize_calypso_scalar: scalar fields (PsoRatio, PopSize, etc.)
  _normalize_calypso_scalar-->>_make_model_devi_native_calypso: unwrapped scalar
  _make_model_devi_native_calypso->>_normalize_calypso_pressures: PSTRESS field
  _normalize_calypso_pressures-->>_make_model_devi_native_calypso: pressure list
  _make_model_devi_native_calypso-->>run.py: writes input.dat

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Title check	⚠️ Warning	The PR title 'docs: add CALYPSO model deviation arginfo' is misleading; the changeset primarily implements normalization logic for single-item list values and pressure handling, with documentation metadata being only one aspect.	Consider a more comprehensive title like 'Add CALYPSO model deviation arginfo and normalize input values' that reflects both documentation and functional changes.
Docstring Coverage	⚠️ Warning	Docstring coverage is 18.18% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[njzjz-bot]

Verdict: Two blocking issues remain; do not merge yet. Because this PR was opened by the active njzjz-bot account, GitHub does not allow the author to submit a REQUEST_CHANGES review, so this COMMENT review records the blocking findings. The scalar/singleton-list normalization is a good direction and the targeted CALYPSO tests pass, but the schema omits runtime-required fields and external-input mode lacks conditional validation.

Note: The Codex quota is about to reset, so I am using the remaining tokens to review all open PRs in this repository.

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

[Blocking] The CALYPSO variant ends here, but the labeling stage still unconditionally reads model_devi_skip, model_devi_f_trust_lo, and model_devi_f_trust_hi in the FP configuration path. A minimal configuration generated from this arginfo can pass schema validation and then fail with KeyError during FP selection. Please add the common model-deviation post-processing fields (including applicable clean/adaptive/virial settings and defaults), preferably via a shared LAMMPS/CALYPSO helper, and add a regression test that reaches FP using only schema-required fields.

[njzjz-bot]

[Blocking] The documentation says model_devi_max_iter is required in calypso_input_path mode, but this still allows it to be omitted. The runtime uses jdata.get("model_devi_max_iter"); a missing value does not trigger the existing except KeyError and instead fails at iter_index > None with TypeError. Add explicit conditional validation before iteration and a missing-value test. Making the field globally required would not be correct because native-job mode does not need it.