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

CMakeLists.txt

@@ -9,6 +9,11 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 # Set module path
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
 
+# Allow user to specify <project>_ROOT variables
+if (NOT (CMAKE_VERSION VERSION_LESS 3.12))
+  cmake_policy(SET CMP0074 NEW)
+endif()
+
 #===============================================================================
 # Command line options
 #===============================================================================
@@ -35,18 +40,18 @@ endif()
 #===============================================================================
 if(dagmc)
   find_package(DAGMC REQUIRED)
+  add_library(dagmc-imported INTERFACE IMPORTED)
   link_directories(${DAGMC_LIBRARY_DIRS})
+  target_link_libraries(dagmc-imported INTERFACE ${DAGMC_LIBRARIES})
+  target_include_directories(dagmc-imported INTERFACE ${DAGMC_INCLUDE_DIRS})
+else()
+  set(DAGMC_FOUND false)
 endif()
 
 #===============================================================================
 # HDF5 for binary output
 #===============================================================================
 
-# Allow user to specify HDF5_ROOT
-if (NOT (CMAKE_VERSION VERSION_LESS 3.12))
-  cmake_policy(SET CMP0074 NEW)
-endif()
-
 # Unfortunately FindHDF5.cmake will always prefer a serial HDF5 installation
 # over a parallel installation if both appear on the user's PATH. To get around
 # this, we check for the environment variable HDF5_ROOT and if it exists, use it
@@ -357,8 +362,7 @@ target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES
 
 if(dagmc)
   target_compile_definitions(libopenmc PRIVATE DAGMC)
-  target_link_libraries(libopenmc ${DAGMC_LIBRARIES})
-  target_include_directories(libopenmc PRIVATE ${DAGMC_INCLUDE_DIRS})
+  target_link_libraries(libopenmc dagmc-imported)
 endif()
 
 #===============================================================================
@@ -388,6 +392,8 @@ add_custom_command(TARGET libopenmc POST_BUILD
 # Install executable, scripts, manpage, license
 #===============================================================================
 
+configure_file(cmake/OpenMCConfig.cmake.in "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake" @ONLY)
+
 set(INSTALL_CONFIGDIR ${CMAKE_INSTALL_LIBDIR}/cmake/OpenMC)
 install(TARGETS openmc libopenmc faddeeva
   EXPORT openmc-targets
@@ -401,7 +407,7 @@ install(EXPORT openmc-targets
   DESTINATION ${INSTALL_CONFIGDIR})
 
 install(DIRECTORY src/relaxng DESTINATION ${CMAKE_INSTALL_DATADIR}/openmc)
-install(FILES cmake/OpenMCConfig.cmake DESTINATION ${INSTALL_CONFIGDIR})
+install(FILES "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake" DESTINATION ${INSTALL_CONFIGDIR})
 install(FILES man/man1/openmc.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 install(FILES LICENSE DESTINATION "${CMAKE_INSTALL_DOCDIR}" RENAME copyright)
 install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})

cmake/Modules/FindDAGMC.cmake

@@ -12,7 +12,9 @@ find_path(DAGMC_CMAKE_CONFIG NAMES DAGMCConfig.cmake
           PATHS ENV LD_LIBRARY_PATH
           PATH_SUFFIXES lib Lib cmake lib/cmake
           NO_DEFAULT_PATH)
-
-message(STATUS "Found DAGMC in ${DAGMC_CMAKE_CONFIG}")
-
-include(${DAGMC_CMAKE_CONFIG}/DAGMCConfig.cmake)
+if(DAGMC_CMAKE_CONFIG)
+  message(STATUS "Found DAGMC in ${DAGMC_CMAKE_CONFIG}")
+  include(${DAGMC_CMAKE_CONFIG}/DAGMCConfig.cmake)
+else()
+  message(WARNING "Cound not find DAGMC")
+endif()

cmake/OpenMCConfig.cmake.in

@@ -5,6 +5,15 @@ find_package(gsl-lite REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../gsl-lite)
 find_package(pugixml REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../pugixml)
 find_package(xtl REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtl)
 find_package(xtensor REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtensor)
+if(@DAGMC_FOUND@)
+  find_package(DAGMC REQUIRED HINTS @DAGMC_LIBRARY_DIRS@)
+  add_library(dagmc-imported INTERFACE IMPORTED)
+  target_link_libraries(dagmc-imported INTERFACE ${DAGMC_LIBRARIES})
+  foreach(dir ${DAGMC_LIBRARY_DIRS})
+    target_link_libraries(dagmc-imported INTERFACE "-L${dir}")
+  endforeach()
+  target_include_directories(dagmc-imported INTERFACE ${DAGMC_INCLUDE_DIRS})
+endif()
 
 if(NOT TARGET OpenMC::libopenmc)
   include("${OpenMC_CMAKE_DIR}/OpenMCTargets.cmake")

openmc/data/photon.py

@@ -784,8 +784,9 @@ class IncidentPhoton(EqualityMixin):
                 sub_group = shell_group.create_group(key)
 
                 # Write atomic relaxation
-                if key in self.atomic_relaxation.subshells:
-                    self.atomic_relaxation.to_hdf5(sub_group, key)
+                if self.atomic_relaxation is not None:
+                    if key in self.atomic_relaxation.subshells:
+                        self.atomic_relaxation.to_hdf5(sub_group, key)
             else:
                 continue
 

src/cell.cpp

@@ -377,7 +377,7 @@ CSGCell::CSGCell(pugi::xml_node cell_node)
         throw std::runtime_error{"Invalid surface ID " + std::to_string(abs(r))
           + " specified in region for cell " + std::to_string(id_) + "."};
       }
-      r = copysign(it->second + 1, r);
+      r = (r > 0) ? it->second + 1 : -(it->second + 1);
     }
   }
 
@@ -536,8 +536,8 @@ CSGCell::to_hdf5(hid_t cell_group) const
         region_spec << " |";
       } else {
         // Note the off-by-one indexing
-        region_spec << " "
-             << copysign(model::surfaces[abs(token)-1]->id_, token);
+        auto surf_id = model::surfaces[abs(token)-1]->id_;
+        region_spec << " " << ((token > 0) ? surf_id : -surf_id);
       }
     }
     write_string(group, "region", region_spec.str(), false);

src/output.cpp

@@ -192,7 +192,7 @@ extern "C" void print_particle(Particle* p)
   // Display miscellaneous info.
   if (p->surface_ != 0) {
     const Surface& surf {*model::surfaces[std::abs(p->surface_)-1]};
-    fmt::print("  Surface = {}\n", std::copysign(surf.id_, p->surface_));
+    fmt::print("  Surface = {}\n", (p->surface_ > 0) ? surf.id_ : -surf.id_);
   }
   fmt::print("  Weight = {}\n", p->wgt_);
   if (settings::run_CE) {

src/particle.cpp

@@ -1,7 +1,7 @@
 #include "openmc/particle.h"
 
 #include <algorithm> // copy, min
-#include <cmath>     // log, abs, copysign
+#include <cmath>     // log, abs
 
 #include <fmt/core.h>
 
@@ -539,7 +539,7 @@ Particle::cross_surface()
     // TODO: off-by-one
     surface_ = rotational ?
       surf_p->i_periodic_ + 1 :
-      std::copysign(surf_p->i_periodic_ + 1, surface_);
+      ((surface_ > 0) ? surf_p->i_periodic_ + 1 : -(surf_p->i_periodic_ + 1));
 
     // Figure out what cell particle is in now
     n_coord_ = 1;

tests/unit_tests/test_data_photon.py

@@ -2,6 +2,7 @@
 
 from collections.abc import Mapping, Callable
 import os
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -144,3 +145,9 @@ def test_export_to_hdf5(tmpdir, element):
            element2.bremsstrahlung['electron_energy']).all()
     # Export to hdf5 again
     element2.export_to_hdf5(filename, 'w')
+
+def test_photodat_only(run_in_tmpdir):
+    endf_dir = Path(os.environ['OPENMC_ENDF_DATA'])
+    photoatomic_file = endf_dir / 'photoat' / 'photoat-001_H_000.endf'
+    data = openmc.data.IncidentPhoton.from_endf(photoatomic_file)
+    data.export_to_hdf5('tmp.h5', 'w')