Merge remote-tracking branch 'upstream/develop' into dagmc_decoupling

.github/workflows/ci.yml

@@ -96,7 +96,6 @@ jobs:
 
       - name: Environment Variables
         run: |
-          echo "DAGMC_ROOT=$HOME/DAGMC"
           echo "OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml" >> $GITHUB_ENV
           echo "OPENMC_ENDF_DATA=$HOME/endf-b-vii.1" >> $GITHUB_ENV
 
@@ -131,6 +130,11 @@ jobs:
           echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
 
+      - name: display-config
+        shell: bash
+        run: |
+          openmc -v
+
       - name: cache-xs
         uses: actions/cache@v4
         with:

CMakeLists.txt

@@ -510,6 +510,14 @@ endif()
 if(OPENMC_USE_DAGMC)
   target_compile_definitions(libopenmc PRIVATE DAGMC)
   target_link_libraries(libopenmc dagmc-shared)
+
+  if(OPENMC_USE_UWUW)
+    target_compile_definitions(libopenmc PRIVATE OPENMC_UWUW)
+    target_link_libraries(libopenmc uwuw-shared)
+  endif()
+elseif(OPENMC_USE_UWUW)
+  set(OPENMC_USE_UWUW OFF)
+  message(FATAL_ERROR "DAGMC must be enabled when UWUW is enabled.")
 endif()
 
 if(OPENMC_USE_LIBMESH)
@@ -546,11 +554,6 @@ if(OPENMC_USE_NCRYSTAL)
   target_link_libraries(libopenmc NCrystal::NCrystal)
 endif()
 
-if (OPENMC_USE_UWUW)
-  target_compile_definitions(libopenmc PRIVATE UWUW)
-  target_link_libraries(libopenmc uwuw-shared)
-endif()
-
 #===============================================================================
 # Log build info that this executable can report later
 #===============================================================================

cmake/Modules/FindLIBMESH.cmake

@@ -15,7 +15,7 @@ if(DEFINED ENV{METHOD})
 endif()
 
 find_package(PkgConfig REQUIRED)
-set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}:${LIBMESH_PC}")
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
+
+set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH TRUE)
 pkg_check_modules(LIBMESH REQUIRED ${LIBMESH_PC_FILE}>=1.7.0 IMPORTED_TARGET)
 pkg_get_variable(LIBMESH_PREFIX ${LIBMESH_PC_FILE} prefix)

cmake/OpenMCConfig.cmake.in

@@ -39,6 +39,6 @@ if(@OPENMC_USE_MCPL@)
   find_package(MCPL REQUIRED)
 endif()
 
-if(@OPENMC_USE_UWUW@)
-  find_package(UWUW REQUIRED)
-endif()
+if(@OPENMC_USE_UWUW@ AND NOT ${DAGMC_BUILD_UWUW})
+  message(FATAL_ERROR "UWUW is enabled in OpenMC but the DAGMC installation discovered was not configured with UWUW.")
+endif()

docs/source/pythonapi/model.rst

@@ -22,6 +22,7 @@ Composite Surfaces
    :nosignatures:
    :template: myclass.rst
 
+   openmc.model.ConicalFrustum
    openmc.model.CruciformPrism
    openmc.model.CylinderSector
    openmc.model.HexagonalPrism

docs/source/usersguide/geometry.rst

@@ -474,7 +474,7 @@ applied as universes in the OpenMC geometry file. A geometry represented
 entirely by a DAGMC geometry will contain only the DAGMC universe. Using a
 :class:`openmc.DAGMCUniverse` looks like the following::
 
-   dag_univ = openmc.DAGMCUniverse(filename='dagmc.h5m')
+   dag_univ = openmc.DAGMCUniverse('dagmc.h5m')
    geometry = openmc.Geometry(dag_univ)
    geometry.export_to_xml()
 
@@ -495,13 +495,22 @@ It is important in these cases to understand the DAGMC model's position
 with respect to the CSG geometry. DAGMC geometries can be plotted with
 OpenMC to verify that the model matches one's expectations.
 
-**Note:** DAGMC geometries used in OpenMC are currently required to be clean,
-meaning that all surfaces have been `imprinted and merged
-<https://svalinn.github.io/DAGMC/usersguide/cubit_basics.html>`_ successfully
-and that the model is `watertight
-<https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_.
-Future implementations of DAGMC geometry will support small volume overlaps and
-un-merged surfaces.
+By default, when you specify a .h5m file for a :class:`~openmc.DAGMCUniverse`
+instance, it will store the absolute path to the .h5m file. If you prefer to
+store the relative path, you can set the ``'resolve_paths'`` configuration
+variable::
+
+  openmc.config['resolve_paths'] = False
+  dag_univ = openmc.DAGMCUniverse('dagmc.h5m')
+
+.. note::
+    DAGMC geometries used in OpenMC are currently required to be clean,
+    meaning that all surfaces have been `imprinted and merged
+    <https://svalinn.github.io/DAGMC/usersguide/cubit_basics.html>`_ successfully
+    and that the model is `watertight
+    <https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_.
+    Future implementations of DAGMC geometry will support small volume overlaps and
+    un-merged surfaces.
 
 Cell, Surface, and Material IDs
 -------------------------------

openmc/config.py

@@ -1,4 +1,5 @@
 from collections.abc import MutableMapping
+from contextlib import contextmanager
 import os
 from pathlib import Path
 import warnings
@@ -11,7 +12,7 @@
 
 class _Config(MutableMapping):
     def __init__(self, data=()):
-        self._mapping = {}
+        self._mapping = {'resolve_paths': True}
         self.update(data)
 
     def __getitem__(self, key):
@@ -42,10 +43,12 @@ def __setitem__(self, key, value):
             # Reset photon source data since it relies on chain file
             _DECAY_PHOTON_ENERGY.clear()
             _DECAY_ENERGY.clear()
+        elif key == 'resolve_paths':
+            self._mapping[key] = value
         else:
             raise KeyError(f'Unrecognized config key: {key}. Acceptable keys '
-                           'are "cross_sections", "mg_cross_sections" and '
-                           '"chain_file"')
+                           'are "cross_sections", "mg_cross_sections", '
+                           '"chain_file", and "resolve_paths".')
 
     def __iter__(self):
         return iter(self._mapping)
@@ -61,6 +64,24 @@ def _set_path(self, key, value):
         if not p.exists():
             warnings.warn(f"'{value}' does not exist.")
 
+    @contextmanager
+    def patch(self, key, value):
+        """Temporarily change a value in the configuration.
+
+        Parameters
+        ----------
+        key : str
+            Key to change
+        value : object
+            New value
+        """
+        previous_value = self.get(key)
+        self[key] = value
+        yield
+        if previous_value is None:
+            del self[key]
+        else:
+            self[key] = previous_value
 
 def _default_config():
     """Return default configuration"""

openmc/dagmc.py

@@ -86,9 +86,9 @@ class DAGMCUniverse(openmc.UniverseBase):
         material name is found in the DAGMC file, the material will be replaced
         with the openmc.Material object in the value.
     """
-
+    
     def __init__(self,
-                 filename,
+                 filename: cv.PathLike,
                  universe_id=None,
                  name='',
                  auto_geom_ids=False,
@@ -179,9 +179,9 @@ def add_material_override(self, mat_name=None, cell_id=None, overrides=None):
         self.material_overrides[mat_name] = overrides
 
     @filename.setter
-    def filename(self, val):
-        cv.check_type('DAGMC filename', val, (Path, str))
-        self._filename = val
+    def filename(self, val: cv.PathLike):
+        cv.check_type('DAGMC filename', val, cv.PathLike)
+        self._filename = input_path(val)
 
     @property
     def auto_geom_ids(self):
@@ -241,8 +241,7 @@ def _n_geom_elements(self, geom_type):
         def decode_str_tag(tag_val):
             return tag_val.tobytes().decode().replace('\x00', '')
 
-        dagmc_filepath = Path(self.filename).resolve()
-        with h5py.File(dagmc_filepath) as dagmc_file:
+        with h5py.File(self.filename) as dagmc_file:
             category_data = dagmc_file['tstt/tags/CATEGORY/values']
             category_strs = map(decode_str_tag, category_data)
             n = sum([v == geom_type.capitalize() for v in category_strs])
@@ -580,7 +579,7 @@ def boundingbox(self):
         warnings.warn("Bounding box is not available for cells in a DAGMC "
                       "universe", Warning)
         return BoundingBox.infinite()
-        
+
     def get_all_cells(self, memo=None):
         warnings.warn("get_all_cells is not available for cells in a DAGMC "
                       "universe", Warning)

openmc/data/effective_dose/dose.py

@@ -2,40 +2,61 @@
 
 import numpy as np
 
-_FILES = (
-    ('electron', 'electrons.txt'),
-    ('helium', 'helium_ions.txt'),
-    ('mu-', 'negative_muons.txt'),
-    ('pi-', 'negative_pions.txt'),
-    ('neutron', 'neutrons.txt'),
-    ('photon', 'photons.txt'),
-    ('photon kerma', 'photons_kerma.txt'),
-    ('mu+', 'positive_muons.txt'),
-    ('pi+', 'positive_pions.txt'),
-    ('positron', 'positrons.txt'),
-    ('proton', 'protons.txt')
-)
-
-_DOSE_ICRP116 = {}
-
-
-def _load_dose_icrp116():
-    """Load effective dose tables from text files"""
-    for particle, filename in _FILES:
-        path = Path(__file__).parent / filename
-        data = np.loadtxt(path, skiprows=3, encoding='utf-8')
-        data[:, 0] *= 1e6   # Change energies to eV
-        _DOSE_ICRP116[particle] = data
-
-
-def dose_coefficients(particle, geometry='AP'):
-    """Return effective dose conversion coefficients from ICRP-116
-
-    This function provides fluence (and air kerma) to effective dose conversion
-    coefficients for various types of external exposures based on values in
-    `ICRP Publication 116 <https://doi.org/10.1016/j.icrp.2011.10.001>`_.
-    Corrected values found in a correigendum are used rather than the values in
-    theoriginal report.
+import openmc.checkvalue as cv
+
+_FILES = {
+    ('icrp74', 'neutron'): Path('icrp74') / 'neutrons.txt',
+    ('icrp74', 'photon'): Path('icrp74') / 'photons.txt',
+    ('icrp116', 'electron'): Path('icrp116') / 'electrons.txt',
+    ('icrp116', 'helium'): Path('icrp116') / 'helium_ions.txt',
+    ('icrp116', 'mu-'): Path('icrp116') / 'negative_muons.txt',
+    ('icrp116', 'pi-'): Path('icrp116') / 'negative_pions.txt',
+    ('icrp116', 'neutron'): Path('icrp116') / 'neutrons.txt',
+    ('icrp116', 'photon'): Path('icrp116') / 'photons.txt',
+    ('icrp116', 'photon kerma'): Path('icrp116') / 'photons_kerma.txt',
+    ('icrp116', 'mu+'): Path('icrp116') / 'positive_muons.txt',
+    ('icrp116', 'pi+'): Path('icrp116') / 'positive_pions.txt',
+    ('icrp116', 'positron'): Path('icrp116') / 'positrons.txt',
+    ('icrp116', 'proton'): Path('icrp116') / 'protons.txt',
+}
+
+_DOSE_TABLES = {}
+
+
+def _load_dose_icrp(data_source: str, particle: str):
+    """Load effective dose tables from text files.
+
+    Parameters
+    ----------
+    data_source : {'icrp74', 'icrp116'}
+        The dose conversion data source to use
+    particle : {'neutron', 'photon', 'photon kerma', 'electron', 'positron'}
+        Incident particle
+
+    """
+    path = Path(__file__).parent / _FILES[data_source, particle]
+    data = np.loadtxt(path, skiprows=3, encoding='utf-8')
+    data[:, 0] *= 1e6   # Change energies to eV
+    _DOSE_TABLES[data_source, particle] = data
+
+
+def dose_coefficients(particle, geometry='AP', data_source='icrp116'):
+    """Return effective dose conversion coefficients.
+
+    This function provides fluence (and air kerma) to effective or ambient dose
+    (H*(10)) conversion coefficients for various types of external exposures
+    based on values in ICRP publications. Corrected values found in a
+    corrigendum are used rather than the values in the original report.
+    Available libraries include `ICRP Publication 74
+    <https://doi.org/10.1016/S0146-6453(96)90010-X>` and `ICRP Publication 116
+    <https://doi.org/10.1016/j.icrp.2011.10.001>`.
+
+    For ICRP 74 data, the photon effective dose per fluence is determined by
+    multiplying the air kerma per fluence values (Table A.1) by the effective
+    dose per air kerma (Table A.17). The neutron effective dose per fluence is
+    found in Table A.41. For ICRP 116 data, the photon effective dose per
+    fluence is found in Table A.1 and the neutron effective dose per fluence is
+    found in Table A.5.
 
     Parameters
     ----------
@@ -44,6 +65,8 @@ def dose_coefficients(particle, geometry='AP'):
     geometry : {'AP', 'PA', 'LLAT', 'RLAT', 'ROT', 'ISO'}
         Irradiation geometry assumed. Refer to ICRP-116 (Section 3.2) for the
         meaning of the options here.
+    data_source : {'icrp74', 'icrp116'}
+        The data source for the effective dose conversion coefficients.
 
     Returns
     -------
@@ -54,19 +77,24 @@ def dose_coefficients(particle, geometry='AP'):
         'photon kerma', the coefficients are given in [Sv/Gy].
 
     """
-    if not _DOSE_ICRP116:
-        _load_dose_icrp116()
+
+    cv.check_value('geometry', geometry, {'AP', 'PA', 'LLAT', 'RLAT', 'ROT', 'ISO'})
+    cv.check_value('data_source', data_source, {'icrp74', 'icrp116'})
+
+    if (data_source, particle) not in _FILES:
+        raise ValueError(f"{particle} has no dose data in data source {data_source}.")
+    elif (data_source, particle) not in _DOSE_TABLES:
+        _load_dose_icrp(data_source, particle)
 
     # Get all data for selected particle
-    data = _DOSE_ICRP116.get(particle)
-    if data is None:
-        raise ValueError(f"{particle} has no effective dose data")
+    data = _DOSE_TABLES[data_source, particle]
 
     # Determine index for selected geometry
     if particle in ('neutron', 'photon', 'proton', 'photon kerma'):
-        index = ('AP', 'PA', 'LLAT', 'RLAT', 'ROT', 'ISO').index(geometry)
+        columns = ('AP', 'PA', 'LLAT', 'RLAT', 'ROT', 'ISO')
     else:
-        index = ('AP', 'PA', 'ISO').index(geometry)
+        columns = ('AP', 'PA', 'ISO')
+    index = columns.index(geometry)
 
     # Pull out energy and dose from table
     energy = data[:, 0].copy()