Merge pull request #1258 from paulromano/gsl

Add guidelines support library and fix a bug

CMakeLists.txt

@@ -124,6 +124,16 @@ add_subdirectory(vendor/xtl)
 add_subdirectory(vendor/xtensor)
 target_link_libraries(xtensor INTERFACE xtl)
 
+#===============================================================================
+# GSL header-only library
+#===============================================================================
+
+add_library(gsl INTERFACE)
+target_include_directories(gsl INTERFACE vendor/gsl/include)
+
+# Make sure contract violations throw exceptions
+target_compile_definitions(gsl INTERFACE GSL_THROW_ON_CONTRACT_VIOLATION)
+
 #===============================================================================
 # RPATH information
 #===============================================================================
@@ -292,7 +302,7 @@ endif()
 # target_link_libraries treats any arguments starting with - but not -l as
 # linker flags. Thus, we can pass both linker flags and libraries together.
 target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES}
-                      pugixml faddeeva xtensor)
+                      pugixml faddeeva xtensor gsl)
 
 if(dagmc)
   target_compile_definitions(libopenmc PRIVATE DAGMC)

src/material.cpp

@@ -1169,7 +1169,7 @@ openmc_material_add_nuclide(int32_t index, const char* name, double density)
       // Create copy of atom_density_ array with one extra entry
       xt::xtensor<double, 1> atom_density = xt::zeros<double>({n});
       xt::view(atom_density, xt::range(0, n-1)) = m->atom_density_;
-      atom_density(n) = density;
+      atom_density(n-1) = density;
       m->atom_density_ = atom_density;
 
       m->density_ += density;

tests/unit_tests/test_capi.py

@@ -124,6 +124,13 @@ def test_material(capi_init):
     assert m.density == pytest.approx(0.1)
 
 
+def test_material_add_nuclide(capi_init):
+    m = openmc.capi.materials[3]
+    m.add_nuclide('Xe135', 1e-12)
+    assert m.nuclides[-1] == 'Xe135'
+    assert m.densities[-1] == 1e-12
+
+
 def test_new_material(capi_init):
     with pytest.raises(exc.AllocationError):
         openmc.capi.Material(1)
@@ -135,7 +142,7 @@ def test_new_material(capi_init):
 def test_nuclide_mapping(capi_init):
     nucs = openmc.capi.nuclides
     assert isinstance(nucs, Mapping)
-    assert len(nucs) == 12
+    assert len(nucs) == 13
     for name, nuc in nucs.items():
         assert isinstance(nuc, openmc.capi.Nuclide)
         assert name == nuc.name

vendor/gsl/include/gsl/gsl

@@ -0,0 +1,27 @@
+//
+// gsl-lite is based on GSL: Guidelines Support Library.
+// For more information see https://github.com/martinmoene/gsl-lite
+//
+// Copyright (c) 2015 Martin Moene
+// Copyright (c) 2015 Microsoft Corporation. All rights reserved. 
+// 
+// This code is licensed under the MIT License (MIT). 
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+// THE SOFTWARE. 
+
+// mimic MS include hierarchy
+
+#pragma once
+
+#ifndef GSL_GSL_H_INCLUDED
+#define GSL_GSL_H_INCLUDED
+
+#include "gsl-lite.hpp"
+
+#endif // GSL_GSL_H_INCLUDED