Integrate Curator instructions to the Crash example

[saikrishnanc-nv]

PhysicsNeMo Pull Request

Description

This PR integrates PhysicsNeMo-Curator instructions to the Crash example.

Checklist

• I am familiar with the Contributing Guidelines.
• New or existing tests cover these changes.
• The documentation is up to date with these changes.
• The CHANGELOG.md is up to date with these changes.
• An issue is linked to this pull request.

Dependencies

N/A

Review Process

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[greptile-apps]

Greptile Overview

Greptile Summary

This PR integrates PhysicsNeMo-Curator preprocessing instructions into the Crash example documentation and enhances the VTP reader to support additional point data fields (thickness, etc.).

Key Changes:

• Added comprehensive documentation section explaining how to use PhysicsNeMo-Curator to preprocess LS-DYNA d3plot files into VTP format
• Enhanced load_vtp_file() to return a third value point_data_dict containing non-displacement fields like thickness
• Updated process_vtp_data() to propagate point data through records using record.update(point_data_dict)
• Added comprehensive test suite with 8 test functions covering VTP loading, displacement application, connectivity extraction, and edge building

Issues Found:

• Critical dtype mismatch in test suite: uses np.uint8 for coordinates, displacements, and thickness, which will cause data truncation and type inconsistencies with production code (expects np.float64 for coords, np.float32 for features)

Confidence Score: 2/5

• This PR has critical dtype bugs in the test suite that will cause test failures and incorrect validation
• The documentation and vtp_reader.py changes are solid (5/5), but the test suite has systematic dtype errors using np.uint8 instead of np.float64/float32 throughout. This will cause data loss, type mismatches with production code expectations, and potential test failures. The logic is correct but the implementation has critical flaws that must be fixed before merge.
• examples/structural_mechanics/crash/tests/test_vtp_reader.py requires immediate attention - all dtype declarations need correction

Important Files Changed

File Analysis

Filename	Score	Overview
examples/structural_mechanics/crash/README.md	5/5	added comprehensive documentation for PhysicsNeMo-Curator integration, data preprocessing steps, input/output formats
examples/structural_mechanics/crash/vtp_reader.py	5/5	enhanced load_vtp_file to return additional point data (thickness, etc.), updated process_vtp_data to propagate point data through records
examples/structural_mechanics/crash/tests/test_vtp_reader.py	1/5	new comprehensive test suite for VTP reader, but uses incorrect np.uint8 dtypes causing data loss - should use np.float64 for coords/displacements and np.float32 for features

Sequence Diagram

sequenceDiagram
    participant User
    participant Curator as PhysicsNeMo-Curator
    participant VTPReader as vtp_reader.py
    participant Datapipe as datapipe.py
    participant Model as ML Model

    User->>Curator: physicsnemo-curator-etl<br/>(d3plot files)
    Curator->>Curator: Parse LS-DYNA d3plot<br/>Extract displacements<br/>Extract thickness from .k files
    Curator->>VTPReader: Generate .vtp files<br/>(displacement_t*, thickness)
    
    User->>VTPReader: load_vtp_file(vtp_path)
    VTPReader->>VTPReader: Read reference coords
    VTPReader->>VTPReader: Extract displacement_t* fields
    VTPReader->>VTPReader: Compute absolute positions<br/>(coords + displacement)
    VTPReader->>VTPReader: Extract mesh connectivity
    VTPReader->>VTPReader: Extract point_data_dict<br/>(thickness, etc.)
    VTPReader-->>Datapipe: Return (pos_raw, connectivity, point_data_dict)
    
    Datapipe->>Datapipe: Build records with<br/>coords + features
    Datapipe->>Datapipe: Normalize data
    Datapipe->>Datapipe: Create SimSample<br/>(x['coords'], x['features'], y)
    Datapipe-->>Model: Training-ready tensors

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[greptile-apps]

Greptile Overview

Greptile Summary

Adds comprehensive test suite for the Crash example's VTP reader module, addressing all critical dtype issues from previous review.

• Creates fixture-based tests using pyvista to generate synthetic VTP files
• Tests core functionality: file loading, displacement application, mesh connectivity extraction, and edge building
• Validates that displacement fields are correctly excluded from point_data_dict while other fields (like thickness) are included
• Includes edge case tests for missing displacement fields and empty connectivity
• All numpy arrays now use correct dtypes matching production code (float64 for coordinates/displacements, float32 for thickness)

Confidence Score: 5/5

• This PR is safe to merge with no remaining issues
• All critical dtype issues from previous review have been correctly addressed. The test suite is well-structured, comprehensive, and follows pytest best practices with proper fixtures and cleanup
• No files require special attention

Important Files Changed

File Analysis

Filename	Score	Overview
examples/structural_mechanics/crash/tests/test_vtp_reader.py	5/5	New comprehensive test suite for VTP reader functionality with corrected dtypes after addressing previous review feedback

Sequence Diagram

sequenceDiagram
    participant Test as Test Suite
    participant Fixture as simple_vtp_file fixture
    participant PyVista as PyVista
    participant VTPReader as vtp_reader module
    participant File as Temp VTP File

    Test->>Fixture: Request test fixture
    Fixture->>PyVista: Create PolyData with points (float64)
    Fixture->>PyVista: Add faces (quad cell)
    Fixture->>PyVista: Add displacement_t0.000 (float64)
    Fixture->>PyVista: Add displacement_t0.005 (float64)
    Fixture->>PyVista: Add displacement_t0.010 (float64)
    Fixture->>PyVista: Add thickness point data (float32)
    Fixture->>File: Save to temp .vtp file
    Fixture-->>Test: Return file path

    Test->>VTPReader: load_vtp_file(path)
    VTPReader->>PyVista: pv.read(vtp_path)
    PyVista-->>VTPReader: Return PolyData
    VTPReader->>VTPReader: Extract coords (float64)
    VTPReader->>VTPReader: Find displacement fields
    VTPReader->>VTPReader: Apply displacements to coords
    VTPReader->>VTPReader: extract_mesh_connectivity_from_polydata()
    VTPReader->>VTPReader: Extract non-displacement point data
    VTPReader-->>Test: Return (pos_raw, connectivity, point_data_dict)

    Test->>Test: Assert shapes and values
    Test->>VTPReader: extract_mesh_connectivity_from_polydata()
    VTPReader-->>Test: Return connectivity list
    Test->>VTPReader: build_edges_from_mesh_connectivity()
    VTPReader-->>Test: Return edge set

    Test->>Fixture: Cleanup
    Fixture->>File: Delete temp file

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[mnabian]

Thanks Sai for the PR! It looks good to me, although I suggest we hold this until the other curator PR is also reviewed. We need to also think about whether we should keep the current d3plot reader or not, a discussion we should probably have with Ram.

[saikrishnanc-nv]

Thanks Sai for the PR! It looks good to me, although I suggest we hold this until the other curator PR is also reviewed. We need to also think about whether we should keep the current d3plot reader or not, a discussion we should probably have with Ram.

@mnabian Thanks for the review Mohammad! The PR in Curator has been merged. Can you approve this PR, and then we can remove the d3plot reader if Ram feels so? It should be easy to remove, since it's supported by default in Curator now.

[saikrishnanc-nv]

/blossom-ci

[greptile-apps]

Greptile Overview

Greptile Summary

Integrates PhysicsNeMo-Curator preprocessing workflow into the Crash example by adding comprehensive documentation and enhancing the VTP reader to extract additional point data fields (thickness, etc.).

Key changes:

• Added detailed Curator documentation to README covering installation, data structure requirements, and VTP format specifications
• Enhanced load_vtp_file to return a point_data_dict containing non-displacement fields like thickness
• Updated process_vtp_data to propagate point data fields to output records for use by the datapipe
• Added comprehensive test coverage for VTP reader functionality

Note: The test fixture uses np.uint8 dtype for test data, which has already been flagged in previous comments as causing potential data loss and dtype mismatches with production code expectations.

Confidence Score: 4/5

• Safe to merge with minor test data quality issues already flagged
• The core functionality changes are well-implemented and backward-compatible. Documentation additions are helpful and accurate. The only concern is the test fixture dtype issue (np.uint8) which has been thoroughly documented in previous comments and should be addressed separately to ensure tests accurately reflect production data characteristics.
• The test file examples/structural_mechanics/crash/tests/test_vtp_reader.py requires dtype corrections (already flagged in previous comments) to ensure test data matches production expectations

Important Files Changed

File Analysis

Filename	Score	Overview
examples/structural_mechanics/crash/README.md	5/5	Added comprehensive PhysicsNeMo-Curator documentation with installation instructions, data structure requirements, and VTP format details - purely documentation changes with no code impact
examples/structural_mechanics/crash/vtp_reader.py	5/5	Enhanced load_vtp_file to return point data dictionary (e.g., thickness) and updated process_vtp_data to include this data in output records - clean implementation that preserves backward compatibility
examples/structural_mechanics/crash/tests/test_vtp_reader.py	3/5	New test file with comprehensive coverage for VTP reader functionality - however, fixture uses np.uint8 dtype which causes data inconsistencies (already flagged in previous comments)

Sequence Diagram

sequenceDiagram
    participant User
    participant Curator as PhysicsNeMo-Curator
    participant VTPReader as vtp_reader.py
    participant DataPipe as datapipe.py
    participant Model as Training/Inference

    User->>Curator: Run physicsnemo-curator-etl
    Note over Curator: Process d3plot files
    Curator->>Curator: Extract mesh coordinates
    Curator->>Curator: Extract displacement fields per timestep
    Curator->>Curator: Extract thickness from .k files
    Curator-->>User: Generate VTP files with:<br/>- Reference coords<br/>- displacement_t* fields<br/>- thickness data

    User->>VTPReader: Load VTP file via Reader()
    VTPReader->>VTPReader: load_vtp_file(vtp_path)
    VTPReader->>VTPReader: Read poly.points as coords (float64)
    VTPReader->>VTPReader: Sort displacement_t* fields
    VTPReader->>VTPReader: Compute pos_raw = coords + displacements
    VTPReader->>VTPReader: Extract mesh_connectivity from faces
    VTPReader->>VTPReader: Extract point_data_dict (thickness, etc.)
    VTPReader-->>DataPipe: Return (srcs, dsts, point_data)<br/>point_data = {"coords": [T,N,3], "thickness": [N]}

    DataPipe->>DataPipe: Convert coords to float32 tensors
    DataPipe->>DataPipe: Concatenate features (thickness, etc.) as float32
    DataPipe->>DataPipe: Normalize positions and features
    DataPipe-->>Model: Provide x={'coords': [N,3], 'features': [N,F]}<br/>and targets y: [N,(T-1)*3]

    Model->>Model: Train or infer on crash dynamics

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[greptile-apps]

_{3 files reviewed, no comments}

_{Edit Code Review Agent Settings | Greptile}

[mnabian]

/blossom-ci

[greptile-apps]

_{3 files reviewed, no comments}

_{Edit Code Review Agent Settings | Greptile}

[saikrishnanc-nv]

/blossom-ci

[greptile-apps]

_{3 files reviewed, no comments}

_{Edit Code Review Agent Settings | Greptile}

[mnabian]

/blossom-ci

[mnabian]

LGTM!