dagmc-h5m-file-inspector 0.7.2

Extracts information from DAGMC h5m files including volumes number, material tags

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

Finding volume IDs

import dagmc_h5m_file_inspector as di

di.get_volumes("dagmc.h5m")

>>> [1, 2]

Finding material tags

import dagmc_h5m_file_inspector as di

di.get_materials("dagmc.h5m")

>>> ['big_box', 'small_box']

Finding volume IDs with their materials

import dagmc_h5m_file_inspector as di

di.get_volumes_and_materials("dagmc.h5m")

>>> {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

di.get_cell_ids_by_group_name("dagmc.h5m")

>>> {'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

di.get_groups_by_cell_id("dagmc.h5m")

>>> {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

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

Finding surface IDs

import dagmc_h5m_file_inspector as di

di.get_surface_ids("dagmc.h5m")

>>> [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

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

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

Finding surface IDs by material name

import dagmc_h5m_file_inspector as di

di.get_surface_ids_by_material_name("dagmc.h5m", 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

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

>>> 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
18000.0

>>> 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:

# 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
bbox_intersection = bbox1 & bbox2
bbox_union = bbox1 | bbox2

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

import dagmc_h5m_file_inspector as di

# Bounding box for a single material
bbox = di.get_bounding_box("dagmc.h5m", 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 = di.get_bounding_box("dagmc.h5m", 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

di.get_volumes_by_cell_id("dagmc.h5m")

>>> {1: 1000.0, 2: 8000.0}

Getting geometric volume sizes by material name

import dagmc_h5m_file_inspector as di

di.get_volumes_by_material_name("dagmc.h5m")

>>> {'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

di.get_volumes_by_cell_id_and_material_name("dagmc.h5m")

>>> {(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

di.get_surface_area_by_cell_id("dagmc.h5m", 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

di.get_surface_area_by_material_name("dagmc.h5m", 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

di.get_surface_area_by_surface_id("dagmc.h5m")

>>> {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

di.get_surface_shared_status("dagmc.h5m")

>>> {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 function 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
di.set_openmc_material_volumes(materials, "dagmc.h5m")

>>> small_box.volume
1000.0

>>> big_box.volume
8000.0

Getting triangle connectivity and coordinates for each volume

This function 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

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

>>> data
{1: (array([[0, 1, 2], [0, 2, 3], ...]), array([[0., 0., 0.], [10., 0., 0.], ...])),
 2: (array([[0, 1, 2], [0, 2, 3], ...]), array([[-5., -10., -10.], [25., -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
di.convert_h5m_to_vtkhdf(h5m_filename='dagmc.h5m', vtkhdf_filename= '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

di.get_materials("dagmc.h5m")

>>> ['big_box', 'small_box']

# Remove a single material
di.remove_materials(
    input_filename="dagmc.h5m",
    output_filename="dagmc_reduced.h5m",
    materials_to_remove="small_box",
)

di.get_materials("dagmc_reduced.h5m")

>>> ['big_box']

import dagmc_h5m_file_inspector as di

di.get_materials("reactor.h5m")

>>> ['blanket', 'first_wall', 'shield']

# Remove multiple materials
di.remove_materials(
    input_filename="reactor.h5m",
    output_filename="reactor_reduced.h5m",
    materials_to_remove=["blanket", "shield"],
)

di.get_materials("reactor_reduced.h5m")

>>> ['first_wall']

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

di.rotate_around_axis(
    filename="dagmc.h5m",
    axis="z",
    degrees=90,
    output="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

di.move(
    filename="dagmc.h5m",
    x=10.0,
    y=0.0,
    z=0.0,
    output="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

# Find surface IDs and their areas
areas = di.get_surface_area_by_surface_id("dagmc.h5m")

>>> {1: 50.0, 2: 80.0}

# Set the larger surface to vacuum (e.g. outer surface of a shell)
di.set_boundary_condition(
    input_filename="dagmc.h5m",
    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

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

di.get_volumes("combined.h5m")

>>> [1, 2]

di.get_materials("combined.h5m")

>>> ['mat_a', 'mat_b']

Using the pymoab backend

All functions support an optional backend parameter. The default is "h5py", but "pymoab" can be used if pymoab is installed:

import dagmc_h5m_file_inspector as di

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

>>> [1, 2]