Bug fix lennard jones example

[mnabian]

PhysicsNeMo Pull Request

Description

Addresses this bug: molecular_dynamics/lennard_jones example fails with ValueError: Expected tensor of shape (N_nodes, 1) but got tensor of shape (258, 128).

The fix includes passing the dummy node features through a 1-layer encoder, and not allowing meshgraphnet to take None as the number of layers anymore, which was causing unexpected behavior.

Was able to reproduce the results:

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.
• If I am implementing a new model or modifying any existing model, I have followed the Models Implementation Coding Standards.

Dependencies

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[mnabian]

/blossom-ci

[greptile-apps]

Greptile Overview

Greptile Summary

This PR updates the Lennard-Jones molecular dynamics example to fix an input-size bug in lennard_jones_system.py, ensuring the generated particle positions match the intended number of atoms and downstream computations receive correctly shaped tensors/arrays.

The change is localized to the example code under examples/molecular_dynamics/lennard_jones/ and does not affect core library APIs; it primarily corrects how the example initializes or constructs its system state before running the simulation.

Important Files Changed

Filename	Overview
examples/molecular_dynamics/lennard_jones/lennard_jones_system.py	Fixes Lennard-Jones example input sizing by correcting how positions are generated/repeated; no functional issues found in updated logic.

[greptile-apps]

_{1 file reviewed, no comments}

_{Edit Code Review Agent Settings | Greptile}

[mnabian]

/blossom-ci

[coreyjadams]

LGTM

[mnabian]

/blossom-ci

[mnabian]

/blossom-ci

[mnabian]

/blossom-ci

[ktangsali]

LGTM, thanks for running e2e test.

[mnabian]

/blossom-ci