dagmc-h5m-file-inspector

A minimal Python package that inspects DAGMC h5m files to extract volume IDs, surface IDs, material tags, bounding boxes, geometric volumes, and surface areas.

Installation

pip install dagmc-h5m-file-inspector

The package uses h5py as the default backend. Optionally, pymoab can be used as an alternative backend if installed.

Python API Usage

Loading once for multiple queries

Use DAGMCFile for queries and edits. Geometry and material data are loaded once and reused by the in-memory methods.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")

volume_ids = dagmc.get_volumes()
materials = dagmc.get_materials()
volumes_and_materials = dagmc.get_volumes_and_materials()
bounding_box = dagmc.get_bounding_box()

Edits are applied in memory, so several operations can be performed after one load and then written once:

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.remove_volumes(1)
dagmc.remove_materials("big_box")
dagmc.move(x=10.0)
dagmc.rotate_around_axis(axis="z", degrees=45)
dagmc.write("modified.h5m")

Finding volume IDs

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_volumes()

# [1, 2]

Finding material tags

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_materials()

# ['big_box', 'small_box']

Finding volume IDs with their materials

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_volumes_and_materials()

# {1: 'small_box', 2: 'big_box'}

Finding cell IDs by group name

Besides the mat: material groups, a DAGMC h5m file can contain other groups (for example component: groups tagging individual components). These readers surface that non-material group membership so you can map groups onto cell (volume) IDs, which is handy for building an openmc.CellFilter. Material (mat:) groups are excluded as they are already available via get_volumes_and_materials.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_cell_ids_by_group_name()

# {'component:small_box': [1], 'component:big_box': [2], 'assembly:all': [1, 2]}

The inverse mapping (cell ID to the groups it belongs to) is also available:

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_groups_by_cell_id()

# {1: ['assembly:all', 'component:small_box'],
#  2: ['assembly:all', 'component:big_box']}

These can be combined with OpenMC to tally on a component rather than duplicating material definitions:

import openmc
import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
cell_ids = dagmc.get_cell_ids_by_group_name()["component:small_box"]
cell_filter = openmc.CellFilter(cell_ids)

Finding surface IDs

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_ids()

# [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]

Finding surface IDs by cell ID

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_ids_by_cell_id(cell_id=1)

# [1, 2, 3, 4, 5, 6]

Finding surface IDs by material name

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_ids_by_material_name(material="small_box")

# [1, 2, 3, 4, 5, 6]

Getting the bounding box

Returns a BoundingBox object that is API compatible with OpenMC's openmc.BoundingBox.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
bbox = dagmc.get_bounding_box()

# bbox == BoundingBox((-5.0, -10.0, -10.0), (25.0, 10.0, 10.0))
bbox.lower_left  # (-5.0, -10.0, -10.0)
bbox.upper_right  # (25.0, 10.0, 10.0)
bbox.center  # (10.0, 0.0, 0.0)
bbox.volume  # 12000.0
bbox.width  # (30.0, 20.0, 20.0)
bbox.extent
# {'xy': (-5.0, 25.0, -10.0, 10.0),
#  'xz': (-5.0, 25.0, -10.0, 10.0),
#  'yz': (-10.0, 10.0, -10.0, 10.0)}

The BoundingBox supports indexing, unpacking, containment checks, and set operations:

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
bbox = dagmc.get_bounding_box()

# Unpacking
lower_left, upper_right = bbox

# Indexing
bbox[0]  # (-5.0, -10.0, -10.0)

# Point containment
(0.0, 0.0, 0.0) in bbox  # True

# Intersection and union of two bounding boxes
small_box_bbox = dagmc.get_bounding_box(materials="small_box")
bbox_intersection = bbox & small_box_bbox
bbox_union = bbox | small_box_bbox

Optionally filter by material tag to get the bounding box for specific materials:

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")

# Bounding box for a single material
bbox = dagmc.get_bounding_box(materials="small_box")

bbox.lower_left  # (-5.0, -5.0, -5.0)
bbox.upper_right  # (5.0, 5.0, 5.0)

# Bounding box for multiple materials (combined)
bbox = dagmc.get_bounding_box(materials=["small_box", "big_box"])

bbox.lower_left  # (-5.0, -10.0, -10.0)
bbox.upper_right  # (25.0, 10.0, 10.0)

Getting geometric volume sizes by cell ID

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_volumes_by_cell_id()

# {1: 1000.0, 2: 8000.0}

Getting geometric volume sizes by material name

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_volumes_by_material_name()

# {'small_box': 1000.0, 'big_box': 8000.0}

Getting geometric volume sizes by cell ID and material name

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_volumes_by_cell_id_and_material_name()

# {(1, 'small_box'): 1000.0, (2, 'big_box'): 8000.0}

Getting surface areas by cell ID

Returns a list of surface areas, one per DAGMC surface bounding the volume.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_area_by_cell_id(cell_id=1)

# [100.0, 100.0, 100.0, 100.0, 100.0, 100.0]

Getting surface areas by material name

Returns a list of surface areas for all DAGMC surfaces bounding volumes with the given material.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_area_by_material_name(material="small_box")

# [100.0, 100.0, 100.0, 100.0, 100.0, 100.0]

Getting surface areas by surface ID

Returns a dictionary mapping each surface ID to its area. Useful for computing wall loading when combined with surface current tallies.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_area_by_surface_id()

# {1: 100.0, 2: 100.0, 3: 100.0, 4: 100.0, 5: 100.0, 6: 100.0,
#  7: 100.0, 8: 400.0, 9: 400.0, 10: 400.0, 11: 400.0, 12: 400.0}

Getting surface shared status

Returns a dictionary mapping each surface ID to the cell IDs and materials that share it. Useful for identifying interfaces between volumes.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_surface_shared_status()

# {1: {'materials': ['small_box'], 'cell_ids': [1]},
#  2: {'materials': ['small_box'], 'cell_ids': [1]},
#  ...
#  7: {'materials': ['small_box', 'big_box'], 'cell_ids': [1, 2]},
#  ...}

Setting OpenMC material volumes from DAGMC geometry

This method reads the DAGMC file, matches materials by name, and sets the volume attribute on the corresponding OpenMC Material objects.

import openmc
import dagmc_h5m_file_inspector as di

# Create OpenMC materials with names matching the DAGMC file
small_box = openmc.Material(name="small_box")
big_box = openmc.Material(name="big_box")
materials = openmc.Materials([small_box, big_box])

# Set volumes from DAGMC geometry
dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.set_openmc_material_volumes(materials)

small_box.volume  # 1000.0
big_box.volume  # 8000.0

Getting triangle connectivity and coordinates for each volume

This method extracts the triangle mesh data for each volume, returning the connectivity (vertex indices) and coordinates (3D points) needed for visualization or mesh processing.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
data = dagmc.get_triangle_conn_and_coords_by_volume()

# {1: (array([[0, 1, 2], ...]), array([[0., 0., 0.], ...])),
#  2: (array([[0, 1, 2], ...]), array([[-5., -10., -10.], ...]))}

# Access data for a specific volume
connectivity, coordinates = data[1]
connectivity.shape  # (12, 3): 12 triangles, each with 3 vertex indices
coordinates.shape  # (8, 3): 8 unique vertices, each with x, y, z coordinates

Convert h5m file to vtkhdf

Convert DAGMC h5m files to vtkhdf which can be directly opened in Paraview 5.13+.

The resulting Paraview files have color for cell IDs and material tags present within the h5m file.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.convert_to_vtkhdf("dagmc.vtkhdf")

Removing materials from h5m files

Remove one or more materials (and their associated volumes) from a DAGMC h5m file, writing the result to a new file.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.get_materials()

# ['big_box', 'small_box']

# Remove a single material
dagmc.remove_materials("small_box")
dagmc.write("dagmc_reduced.h5m")

reduced = di.DAGMCFile("dagmc_reduced.h5m")
reduced.get_materials()

# ['big_box']

import dagmc_h5m_file_inspector as di

reactor = di.DAGMCFile("reactor.h5m")
reactor.get_materials()

# ['blanket', 'first_wall', 'shield']

# Remove multiple materials
reactor.remove_materials(["blanket", "shield"])
reactor.write("reactor_reduced.h5m")

reduced = di.DAGMCFile("reactor_reduced.h5m")
reduced.get_materials()

# ['first_wall']

Removing volumes from h5m files

Remove one or more volumes by ID while retaining all other volumes. Material tags remain when they are also used by a surviving volume.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("volume_removal.h5m")
dagmc.get_volumes_and_materials()

# {1: 'steel', 2: 'steel', 3: 'water'}

dagmc.remove_volumes(1)
dagmc.write("dagmc_reduced.h5m")

reduced = di.DAGMCFile("dagmc_reduced.h5m")
reduced.get_volumes_and_materials()

# {2: 'steel', 3: 'water'}

Rotating a DAGMC geometry around an axis

Rotate the mesh coordinates around a coordinate axis and write a new h5m file.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.rotate_around_axis(axis="z", degrees=90)
dagmc.write("dagmc_rotated.h5m")

Moving a DAGMC geometry

Translate (move) the mesh coordinates by an offset and write a new h5m file.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")
dagmc.move(x=10.0, y=0.0, z=0.0)
dagmc.write("dagmc_moved.h5m")

Setting boundary conditions on surfaces

Set a boundary condition (e.g. vacuum, reflective) on a DAGMC surface. This creates a Group entity in the h5m file that OpenMC reads to apply the boundary condition during transport.

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m")

# Find surface IDs and their areas
areas = dagmc.get_surface_area_by_surface_id()

# {1: 50.0, 2: 80.0, ...}

# Set the larger surface to vacuum (e.g. outer surface of a shell)
dagmc.set_boundary_condition(
    surface_id=2,
    boundary_condition="vacuum",
    output_filename="dagmc_with_bc.h5m",
)

Supported boundary conditions: "vacuum", "reflective". If output_filename is omitted the input file is modified in place.

Combining multiple DAGMC h5m files

Merge multiple DAGMC h5m files into a single file. Volumes are renumbered sequentially in the output. It is the caller's responsibility to ensure the geometries do not overlap.

import dagmc_h5m_file_inspector as di

combined = di.DAGMCFile.combine_h5m_files(
    input_files=["file_a.h5m", "file_b.h5m"],
    output_file="combined.h5m",
)

combined.get_volumes()

# [1, 2]

combined.get_materials()

# ['mat_a', 'mat_b']

Using the pymoab backend

The backend is selected when constructing a DAGMCFile. The default is "h5py", but "pymoab" can be used if pymoab is installed:

import dagmc_h5m_file_inspector as di

dagmc = di.DAGMCFile("dagmc.h5m", backend="pymoab")
dagmc.get_volumes()

# [1, 2]