Protocol buffer implementation

.gitignore

@@ -34,11 +34,3 @@ html/
 latex/
 build/
 test_data/
-
-# For ggtags
-GPATH
-GRTAGS
-GTAGS
-
-# For emacs users
-.dir-locals.el

CMakeLists.txt

@@ -52,10 +52,14 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
 set(GTEST_ROOT "/usr")
 find_package(GTest REQUIRED 1.8.0)
 find_package(GMock REQUIRED)
-#set(GTEST_INCLUDE_DIRS "/usr/include")
-#set(GTEST_BOTH_LIBRARIES "/usr/lib/libgtest_main.so;/usr/lib/libgtest.so")
-#set(GMOCK_BOTH_LIBRARIES "/usr/lib/libgmock.a;/usr/lib/libgmock_main.a")
 
+### PROTOCOL BUFFERS #################################################
+
+#include(FindProtobuf)
+find_package(Protobuf REQUIRED)
+protobuf_generate_cpp(PROTO_SRCS PROTO_HDRS
+  "${CMAKE_SOURCE_DIR}/protobuf/material.proto")
+get_filename_component(PROTO_INC_DIR ${PROTO_HDRS} DIRECTORY)
 ### COMPILE AND LINKER FLAGS #########################################
 
 SET(DEAL_II_CXX_FLAGS_DEBUG "${DEAL_II_CXX_FLAGS_DEBUG} -g -O0 --coverage")
@@ -73,6 +77,7 @@ ENABLE_TESTING()
 # Recursively find source files
 
 file(GLOB_RECURSE sources "src/*.cpp" "src/*.cc")
+list(APPEND sources ${PROTO_SRCS} ${PROTO_HDRS})
 set(testing_sources ${sources})
 list(FILTER sources EXCLUDE REGEX ".*/tests/.*")
 list(FILTER sources EXCLUDE REGEX ".*/test_helpers/.*")
@@ -81,7 +86,8 @@ list(FILTER testing_sources EXCLUDE REGEX ".*/main.cc$")
 
 # Include directories
 include_directories(${GTEST_INCLUDE_DIRS}
-  ${CMAKE_SOURCE_DIR}/inc)
+  ${CMAKE_SOURCE_DIR}/inc
+  ${PROTO_INC_DIR})
 
 # Add xtrans executables
 ADD_EXECUTABLE(xtrans ${sources})
@@ -90,8 +96,10 @@ ADD_EXECUTABLE(xtrans_test ${testing_sources})
 # Add testing definition and library to xtrans_test
 target_compile_definitions(xtrans_test PUBLIC -DTEST)
 
+
+target_link_libraries(xtrans ${Protobuf_LIBRARIES})
 target_link_libraries(xtrans_test ${GTEST_BOTH_LIBRARIES}
-  ${GMOCK_BOTH_LIBRARIES})
+  ${GMOCK_BOTH_LIBRARIES} ${Protobuf_LIBRARIES})
 
 # Add subdirectory builds to build libraries for CTEST
 ADD_SUBDIRECTORY(${CMAKE_SOURCE_DIR}/src/mesh)
@@ -133,3 +141,8 @@ foreach(test_file ${ctest_files})
     COMMAND ${CMAKE_COMMAND} -E copy ${test_file} ${file_name})
 endforeach()
 add_dependencies(xtrans_test copy_ctest_output_files)
+
+# Create copies of material protocol buffer data
+add_custom_target(copy_protoc_files ALL)
+file(COPY "./src/material/tests/data/" DESTINATION "./test_data/material")
+add_dependencies(xtrans_test copy_protoc_files)

README.md

@@ -1,4 +1,8 @@
-[![Build Status](https://travis-ci.org/SlaybaughLab/BART.svg?branch=master)](https://travis-ci.org/SlaybaughLab/BART)
+| `master` | `dev` | `restart` |
+|----------|-------|-----------|
+|[![Build Status](https://travis-ci.org/SlaybaughLab/BART.svg?branch=master)](https://travis-ci.org/SlaybaughLab/BART)|[![Build Status](https://travis-ci.org/SlaybaughLab/BART.svg?branch=dev)](https://travis-ci.org/SlaybaughLab/BART)|[![Build Status](https://travis-ci.org/SlaybaughLab/BART.svg?branch=restart)](https://travis-ci.org/SlaybaughLab/BART)  [![Codecov](https://codecov.io/gh/SlaybaughLab/BART/branch/restart/graph/badge.svg)](https://codecov.io/gh/SlaybaughLab/BART/branch/restart)|
+
+
 
 # Bay Area Radiation Transport (BART)
 ## What is BART for?

coverage.sh

@@ -7,3 +7,8 @@ lcov --remove coverage.info '/usr/*' \
      '/home/dealii/libs/*' \
      --output-file coverage.info # filter out system and includes
 lcov --list coverage.info #debug info
+if [ $1 = "-r" ]
+then
+    genhtml coverage.info --branch-coverage --output-directory ./code_coverage_report/
+fi
+rm *.gcda *.gcno

doxygen_config

@@ -790,7 +790,14 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT=./src/aqdata ./src/equation ./src/common ./src/iteration ./src/mesh ./src/material ./src/test_helpers ./src/utility
+INPUT=	./src/aqdata \
+	./src/equation \
+	./src/common \
+	./src/iteration \
+	./src/mesh \
+	./src/material \
+	./src/test_helpers \
+	./src/utility
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

protobuf/material.proto

@@ -0,0 +1,53 @@
+syntax = "proto3";
+
+message Material {
+  string full_name = 1;
+  string abbreviation = 2;
+  string id = 3;
+
+  uint32 number_of_groups = 4;
+  uint32 thermal_groups = 5;
+
+  repeated ScalarProperty scalar_property = 6;
+  repeated VectorProperty vector_property = 7;
+  repeated MatrixProperty matrix_property = 8;
+
+  enum ScalarId {
+    UNKNOWN_SCALAR = 0;
+    DENSITY = 1;
+  }
+
+  enum VectorId {
+    UNKNOWN_VECTOR = 0;
+    ENERGY_GROUPS = 1; // edges of energy groups in eV
+    CHI = 2;
+    SIGMA_T = 3; // group homogenized cross sections in 1/cm
+    SIGMA_A = 4;
+    NU_SIG_F = 5;
+    KAPPA_SIG_F = 6;
+    Q = 7;
+  }
+
+  enum MatrixId {
+    UNKNOWN_MATRIX = 0;
+    SIGMA_S = 1; // element r*number_of_groups + c represents scattering from group r+1 to group c+1
+  }
+
+
+  message ScalarProperty {
+    ScalarId id = 1;
+    double value = 2;
+  }
+
+  message VectorProperty {
+    VectorId id = 1;
+    repeated double value = 2 [packed=true];
+  }
+
+  message MatrixProperty {
+    MatrixId id = 1;
+    uint32 rows = 2;
+    uint32 cols = 3;
+    repeated double value = 4 [packed=true];
+  }
+}

src/common/bart_builder.cc

@@ -90,16 +90,6 @@ void BuildAQ (const dealii::ParameterHandler &prm,
   }
 }
 
-void BuildMaterial (dealii::ParameterHandler &prm,
-    std::unique_ptr<Materials> &mat_ptr) {
-  mat_ptr = std::unique_ptr<Materials> (new Materials(prm));
-}
-
-std::unique_ptr<Materials> BuildMaterial (
-    dealii::ParameterHandler &prm) {
-  return std::unique_ptr<Materials> (new Materials(prm));
-}
-
 template <int dim>
 void BuildMesh (dealii::ParameterHandler &prm,
     std::unique_ptr<MeshGenerator<dim>> &msh_ptr) {

src/common/bart_builder.h

@@ -3,7 +3,6 @@
 
 #include "../aqdata/aq_base.h"
 #include "../mesh/mesh_generator.h"
-#include "../material/materials.h"
 #include "../equation/equation_base.h"
 #include "../iteration/eigen_base.h"
 #include "../iteration/mg_base.h"
@@ -51,28 +50,6 @@ namespace bbuilders {
   void BuildAQ (const dealii::ParameterHandler &prm,
       std::unique_ptr<AQBase<dim>> &aq_ptr);
 
-  //! Function used to build material
-  /*!
-   The main functionality is to build pointer to object of Materials
-   based on parameters specified in prm.
-
-   \param prm dealii::ParameterHandler object.
-   \param mat_ptr Materials object pointer.
-   \return Void.
-   */
-  void BuildMaterial (dealii::ParameterHandler &prm,
-      std::unique_ptr<Materials> &mat_ptr);
-
-  //! Function used to build material
-  /*!
-   The same as previous function but returning pointer to material.
-
-   \param prm dealii::ParameterHandler object.
-   \return Materials object pointer.
-   */
-  std::unique_ptr<Materials> BuildMaterial (
-      dealii::ParameterHandler &prm);
-
   //! Function used to build mesh
   /*!
    The main functionality is to build pointer to object of MeshGenerator<dim>

src/common/computing_data.cc

@@ -3,32 +3,47 @@
 
 #include <deal.II/fe/fe_update_flags.h>
 
-XSections::XSections (Materials& material)
+// XSections::XSections (Materials& material)
+//     :
+//     sigt(material.GetSigT()),
+//     inv_sigt(material.GetInvSigT()),
+//     q(material.GetQ()),
+//     q_per_ster(material.GetQPerSter()),
+//     is_material_fissile(material.GetFissileIDMap()),
+//     nu_sigf(material.GetNuSigf()),
+//     sigs(material.GetSigS()),
+//     sigs_per_ster(material.GetSigSPerSter()),
+//     fiss_transfer(material.GetFissTransfer()),
+//     fiss_transfer_per_ster(material.GetFissTransferPerSter()) {}
+
+XSections::XSections (MaterialBase& material)
     :
     sigt(material.GetSigT()),
     inv_sigt(material.GetInvSigT()),
     q(material.GetQ()),
     q_per_ster(material.GetQPerSter()),
     is_material_fissile(material.GetFissileIDMap()),
-    nu_sigf(material.GetNuSigf()),
+    nu_sigf(material.GetNuSigF()),
     sigs(material.GetSigS()),
     sigs_per_ster(material.GetSigSPerSter()),
-    fiss_transfer(material.GetFissTransfer()),
-    fiss_transfer_per_ster(material.GetFissTransferPerSter()) {}
+    fiss_transfer(material.GetChiNuSigF()),
+    fiss_transfer_per_ster(material.GetChiNuSigFPerSter())
+{}
 
 template <int dim>
 FundamentalData<dim>::FundamentalData (dealii::ParameterHandler &prm,
     dealii::Triangulation<dim> &tria)
     :
     pcout(std::cout,
         (dealii::Utilities::MPI::this_mpi_process(MPI_COMM_WORLD)==0)),
-    material(prm),
+    //material(prm),
     mesh(prm),
     mat_vec(std::shared_ptr<MatrixVector> (new MatrixVector())),
     //xsec(std::shared_ptr<XSections> (new XSections(material))),
     fe_data(prm),
     dof_handler(tria) {
-  xsec = std::shared_ptr<XSections> (new XSections(material));
+  MaterialProtobuf material{prm};
+  xsec = std::make_shared<XSections>(material);
   bbuilders::BuildAQ<dim>(prm, aq);
   aq->MakeAQ();
 }

src/common/computing_data.h

@@ -1,7 +1,8 @@
 #ifndef BART_SRC_COMMON_COMPUTING_DATA_H_
 #define BART_SRC_COMMON_COMPUTING_DATA_H_
 
-#include "../material/materials.h"
+#include "../material/material_base.h"
+#include "../material/material_protobuf.h"
 #include "../aqdata/aq_base.h"
 #include "../mesh/mesh_generator.h"
 
@@ -36,7 +37,7 @@ struct MatrixVector {
 };
 
 struct XSections {
-  XSections (Materials &material);
+  XSections (MaterialBase &material_properties);
 
   //! \f$\sigma_\mathrm{t}\f$ of all groups for all materials.
   const std::unordered_map<int, std::vector<double>> sigt;
@@ -133,7 +134,8 @@ struct FundamentalData {
 
   std::unique_ptr<AQBase<dim>> aq;//!< Pointer to aq data
   MeshGenerator<dim> mesh;//!< Pointer to mesh generator
-  Materials material;//!< Pointer to material properties
+  //Materials material;//!< Pointer to material properties
+  //std::unique_ptr<MaterialPropertiesI> material_properties;
 
   std::shared_ptr<MatrixVector> mat_vec;
   std::shared_ptr<XSections> xsec;//!< Pointer to access all cross sections.

src/common/tests/computing_data_test.cc

@@ -1,13 +1,29 @@
 #include "../computing_data.h"
+
+#include <unordered_map>
+#include <vector>
+
+#include <gtest/gtest.h>
+#include <deal.II/lac/full_matrix.h>
+
 #include "../problem_definition.h"
+#include "../../material/tests/mock_material.h"
 #include "../../test_helpers/bart_test_helper.h"
+#include "../../test_helpers/gmock_wrapper.h"
+#include "../../test_helpers/test_helper_functions.h"
+
+class XSectionsTest : public ::testing::Test {
+ protected:
+  using id_vector_map = std::unordered_map<int, std::vector<double>>;
+  using id_matrix_map = std::unordered_map<int, dealii::FullMatrix<double>>;
+  btest::MockMaterial mock_material_properties;
+};
 
 class ComputingDataTestMPI
     :
     public btest::BARTParallelEnvironment {
  public:
-  void SetUp ();
-
+  void SetUp (); 
   dealii::ParameterHandler prm_;
 };
 
@@ -25,3 +41,51 @@ void ComputingDataTestMPI::SetUp() {
 TEST_F (ComputingDataTestMPI, 2DFundamentalDataTest) {
   dealii::parallel::distributed::Triangulation<2> tria_2d(MPI_COMM_WORLD);
 }
+
+TEST_F(XSectionsTest, XSectionsConstructor) {
+
+  id_vector_map sigma_t_map = btest::RandomIntVectorMap();
+  id_vector_map sigma_t_inv_map = btest::RandomIntVectorMap();
+  id_vector_map q_map = btest::RandomIntVectorMap();
+  id_vector_map q_per_ster_map = btest::RandomIntVectorMap();
+  id_vector_map nu_sigf_map = btest::RandomIntVectorMap();
+  id_matrix_map sig_s_map = btest::RandomIntMatrixMap();
+  id_matrix_map sig_s_per_ster_map = btest::RandomIntMatrixMap();
+  id_matrix_map chi_nu_sig_f_map = btest::RandomIntMatrixMap();
+  id_matrix_map chi_nu_sig_f_per_ster_map = btest::RandomIntMatrixMap();
+  std::unordered_map<int, bool> fissile_id_map{{1, true}, {2, false}};
+
+  EXPECT_CALL(mock_material_properties, GetSigT())
+      .WillOnce(::testing::Return(sigma_t_map));
+  EXPECT_CALL(mock_material_properties, GetInvSigT())
+      .WillOnce(::testing::Return(sigma_t_inv_map));
+  EXPECT_CALL(mock_material_properties, GetQ())
+      .WillOnce(::testing::Return(q_map));
+  EXPECT_CALL(mock_material_properties, GetQPerSter())
+      .WillOnce(::testing::Return(q_per_ster_map));
+  EXPECT_CALL(mock_material_properties, GetNuSigF())
+      .WillOnce(::testing::Return(nu_sigf_map));
+  EXPECT_CALL(mock_material_properties, GetSigS())
+      .WillOnce(::testing::Return(sig_s_map));
+  EXPECT_CALL(mock_material_properties, GetSigSPerSter())
+      .WillOnce(::testing::Return(sig_s_per_ster_map));
+  EXPECT_CALL(mock_material_properties, GetChiNuSigF())
+      .WillOnce(::testing::Return(chi_nu_sig_f_map));
+  EXPECT_CALL(mock_material_properties, GetChiNuSigFPerSter())
+      .WillOnce(::testing::Return(chi_nu_sig_f_per_ster_map));
+  EXPECT_CALL(mock_material_properties, GetFissileIDMap())
+      .WillOnce(::testing::Return(fissile_id_map));
+
+  XSections test_xsections(mock_material_properties);
+
+  EXPECT_EQ(test_xsections.sigt, sigma_t_map);
+  EXPECT_EQ(test_xsections.inv_sigt, sigma_t_inv_map);
+  EXPECT_EQ(test_xsections.q, q_map);
+  EXPECT_EQ(test_xsections.q_per_ster, q_per_ster_map);
+  EXPECT_EQ(test_xsections.nu_sigf, nu_sigf_map);
+  EXPECT_EQ(test_xsections.sigs, sig_s_map);
+  EXPECT_EQ(test_xsections.sigs_per_ster, sig_s_per_ster_map);
+  EXPECT_EQ(test_xsections.fiss_transfer, chi_nu_sig_f_map);
+  EXPECT_EQ(test_xsections.fiss_transfer_per_ster, chi_nu_sig_f_per_ster_map);
+  EXPECT_EQ(test_xsections.is_material_fissile, fissile_id_map);
+}