DAGMC Cell Override Updates

[pshriwise]

Description

This takes a different approach to material overrides by reusing the current XML cell specification. The goal is to provide better support for not only material overrides but other cell properties as well (e.g. temperatures, densities). Later, with support for lattice/universe fills of DAGMC cells additional properties like translation and rotation will become useful as well.

Things to consider:

• I've made a hard transition here, removing support for the old override format right away as it hasn't been with us long. Old XML files using that format can still be read into Python or C++, however.
• I've refactored some code for reading temperatures and materials from an XML cell node, which may be a little overkill in terms of indirection to reduce duplicate code.

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Claude's PR Description

Summary

This PR replaces the ad-hoc <material_overrides> XML schema for DAGMC universes with a
generalized <cell> sub-element approach that reuses OpenMC's standard cell XML schema.
The new format supports material, temperature, density, and volume overrides on a per-cell
basis, with full parity between the Python and C++ interfaces.

Motivation

The previous <material_overrides> schema was limited to material assignment only and used
a bespoke XML structure not shared with the rest of OpenMC's geometry input. This PR:

• Aligns DAGMC cell overrides with the standard <cell> XML schema
• Adds support for temperature, density, and volume overrides
• Consolidates duplicated XML parsing logic into shared free functions
• Provides backward compatibility for existing inputs using the old format
• Removes the deprecated material_overrides property, replace_material_assignment
  method, and related internal state from DAGMCUniverse

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<cell> Sub-element Specification

A <cell> element nested inside a <dagmc_universe> overrides properties of the DAGMC
volume with the matching id.

Supported Attributes

Attribute	Required	Type	Description
id	Yes	integer	DAGMC cell/volume ID to override
name	No	string	Optional label for the cell
material	Yes	string or space-separated list	Material ID(s). Use void for vacuum. Multiple IDs specify a distribmat fill. May also be a <material> child element.
temperature	No	float or space-separated list	Temperature(s) in Kelvin. Must be ≥ 0. May also be a <temperature> child element.
density	No	float or space-separated list	Density in g/cm³. Must be > 0. Requires a non-void material fill. May also be a <density> child element.
volume	No	float	Cell volume in cm³. Note: DAGMC can compute volumes exactly from the triangulated mesh. Specifying a manual volume overrides that capability and risks inconsistency.

Unsupported Attributes

The following standard <cell> attributes are not valid inside <dagmc_universe> and will
raise an error:

Attribute	Reason
region	DAGMC cells have no CSG region definition
fill	Only material fills are supported (universe fills are not)
universe	Cannot specify a containing universe
translation	Not yet supported
rotation	Not yet supported

Example

<dagmc_universe id="1" filename="model.h5m">
  <!-- Single material + temperature override -->
  <cell id="3" material="10" temperature="900.0"/>

  <!-- Distribmat override (two materials) -->
  <cell id="5">
    <material>20 21</material>
  </cell>

  <!-- Void fill -->
  <cell id="7" material="void"/>

  <!-- Density + volume override (use volume with caution) -->
  <cell id="9" material="10" density="10.5" volume="42.0"/>
</dagmc_universe>

Backward Compatibility

The old <material_overrides> format is deprecated but still accepted in both Python
and C++. A DeprecationWarning (Python) or warning() (C++) is emitted, and the overrides
are converted to the new <cell> representation at parse time. It is an error to mix both
formats on the same universe.

<!-- DEPRECATED — use <cell> sub-elements instead -->
<dagmc_universe id="1" filename="model.h5m">
  <material_overrides>
    <cell_override id="3"><material_ids>10</material_ids></cell_override>
  </material_overrides>
</dagmc_universe>

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Implementation Details

C++ (src/cell.cpp, include/openmc/cell.h)

Three free functions are added to centralize <cell> XML parsing, shared by both
CSGCell::CSGCell and DAGUniverse:

• parse_cell_material_xml(node, cell_id) — parses material attribute/element, handles "void"
• parse_cell_temperature_xml(node, cell_id) — parses temperature, validates ≥ 0
• parse_cell_density_xml(node, cell_id) — parses density, validates > 0

DAGUniverse uses intermediate maps (MaterialOverrides, TemperatureOverrides,
DensityOverrides) rather than applying values directly, because DAGMC Cell objects do
not exist until the .h5m file is loaded during init_geometry().

Python (openmc/dagmc.py)

• DAGMCCell.from_xml_element is added as a classmethod that delegates to
  Cell.from_xml_element via super(). It accepts an optional universe parameter; when
  called from _parse_cell_overrides the owning DAGMCUniverse is passed directly so the
  cell is registered in one step without a separate add_cell call.
• DAGMCUniverse._parse_legacy_material_overrides handles the deprecated XML format.
• The material_overrides property is retained but both the getter and setter now raise
  AttributeError with a message directing users to the DAGMCCell-based API.
• The replace_material_assignment method, _get_cell_material_overrides helper, and
  the _material_overrides internal attribute are removed entirely.

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Tests

• tests/unit_tests/test_cell.py — test_dagmccell_from_xml_element: round-trip of
  material, temperature, density, and volume; rejection of forbidden attributes; missing
  material error.
• tests/unit_tests/dagmc/test_model.py:
  • test_dagmc_xml_legacy_single_material_compat — old format, single material
  • test_dagmc_xml_legacy_distribmat_compat — old format, multiple material IDs
  • test_dagmc_xml_legacy_void_compat — old format, void material
  • test_dagmc_xml_legacy_both_raises — error when both formats present on same universe
  • test_dagmc_xml_legacy_deprecation_warning — confirms DeprecationWarning is emitted
  • test_dagmc_xml_legacy_roundtrip — old format parsed → new <cell> format emitted

Checklist

• I have performed a self-review of my own code
• I have run clang-format (version 18) on any C++ source files (if applicable)
• I have followed the style guidelines for Python source files (if applicable)
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works (if applicable)

[pshriwise]

@bam241 I'd especially like to hear your thoughts on this one if you have the time.