Resolving merge conflicts.

makeclean · May 12, 2014 · 035ff53 · 035ff53
2 parents 4665ee3 + a94f01e
commit 035ff53
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Showing 219 changed files with 19,853 additions and 18,703 deletions.
diff --git a/.gitignore b/.gitignore
@@ -31,5 +31,5 @@ tests/test.file
 tests/test.txt
 tests/U235.txt
 tests/Ni59.txt
-
+docs/rxname_listing
 .ipynb_checkpoints
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -33,6 +33,9 @@ message("-- PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
 # Check for MOAB library
 find_package(MOAB)
 message("-- MOAB Found: ${MOAB_FOUND}")
+if(${MOAB_FOUND})
+ include_directories(${MOAB_INCLUDE_DIR})
+endif(${MOAB_FOUND})
 
 # Include the CMake script UseCython.cmake. This defines add_cython_module().
 # Instruction for use can be found at the top of cmake/UseCython.cmake.
@@ -60,7 +63,8 @@ set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 if(APPLE)
  # I think that this is the right thing to do for MacOSX 10.5+ --Anthony
- set(CMAKE_INSTALL_RPATH "@rpath/lib")
+ set(CMAKE_MACOSX_RPATH 1)
+ set(CMAKE_INSTALL_RPATH "@loader_path/lib")
 elseif(WIN32)
  if(MSVC)
  # ??? Who knows what to do here?! --Anthony
@@ -97,7 +101,7 @@ add_subdirectory(pyne/xs)
 
 # Print include dir
 get_property(inc_dirs DIRECTORY PROPERTY INCLUDE_DIRECTORIES)
-message("-- C_INCLUDE_PATH for ${CMAKE_CURRENT_SOURCE_DIR}: ${inc_dirs}")
+message("-- Include paths for ${CMAKE_CURRENT_SOURCE_DIR}: ${inc_dirs}")
 
 message("-- Copying C/C++ header files.")
 file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/cpp/" DESTINATION

diff --git a/cmake/FindPythonLibsNew.cmake b/cmake/FindPythonLibsNew.cmake
@@ -146,7 +146,7 @@ find_library(PYTHON_LIBRARY
  "Python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}m"
  "Python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}mu"
  "Python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}dm"
- PATHS ${_PYTHON_LIBS_SEARCH}
+ HINTS ${_PYTHON_LIBS_SEARCH}
  NO_SYSTEM_ENVIRONMENT_PATH)
 #endif()
 

diff --git a/configure.py b/configure.py
@@ -90,7 +90,7 @@ def setup():
  scripts = [s for s in scripts if (os.name == 'nt' and s.endswith('.bat')) or 
  (os.name != 'nt' and not s.endswith('.bat'))]
  packages = ['pyne', 'pyne.lib', 'pyne.dbgen', 'pyne.apigen', 'pyne.xs', 
- 'pyne.simplesim', 'pyne.transmute', 'pyne.gui', 'pyne.cli']
+ 'pyne.transmute', 'pyne.gui', 'pyne.cli']
  pack_dir = {
  'pyne': 'pyne',
  'pyne.xs': 'pyne/xs',
@@ -99,7 +99,6 @@ def setup():
  'pyne.cli': 'pyne/cli',
  'pyne.dbgen': 'pyne/dbgen',
  'pyne.apigen': 'pyne/apigen',
- 'pyne.simplesim': 'pyne/simplesim',
  'pyne.transmute': 'pyne/transmute',
  }
  extpttn = ['*.dll', '*.so', '*.dylib', '*.pyd', '*.pyo']

diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -26,7 +26,7 @@ install_lib(pyne_rxname)
 add_library(pyne_data data.cpp)
 set_target_properties(pyne_data PROPERTIES 
  LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/pyne/lib")
-target_link_libraries(pyne_data pyne_nucname pyne hdf5)
+target_link_libraries(pyne_data pyne_nucname pyne_rxname pyne hdf5)
 install_lib(pyne_data)
 
 # pyne_material
@@ -44,9 +44,16 @@ set_target_properties(pyne_enrichment PROPERTIES
 target_link_libraries(pyne_enrichment pyne_material)
 install_lib(pyne_enrichment)
 
+# pyne_tally
+add_library(pyne_tally tally.cpp)
+set_target_properties(pyne_tally PROPERTIES 
+ LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/pyne/lib")
+install_lib(pyne_tally)
+
+
 # Print include dir
 get_property(inc_dirs DIRECTORY PROPERTY INCLUDE_DIRECTORIES)
-message("-- C_INCLUDE_PATH for ${CMAKE_CURRENT_SOURCE_DIR}: ${inc_dirs}")
+message("-- Include paths for ${CMAKE_CURRENT_SOURCE_DIR}: ${inc_dirs}")
 
 #file(COPY "${CMAKE_CURRENT_SOURCE_DIR}" DESTINATION 
 # "${CMAKE_BINARY_DIR}/pyne/includes/" FILES_MATCHING PATTERN "*.h")
diff --git a/cpp/dagmc_bridge.cpp b/cpp/dagmc_bridge.cpp
@@ -18,23 +18,23 @@ using moab::EntityHandle;
 
 namespace pyne {
 
-float dag_version(void){
+float dag_version(void) {
  return DagMC::version();
 }
 
-unsigned dag_rev_version(void){
+unsigned dag_rev_version(void) {
  return DagMC::interface_revision();
 }
 
-int dag_ent_handle_size(void){
+int dag_ent_handle_size(void) {
  return sizeof(EntityHandle);
 }
 
 static std::vector<int> surfList;
 static std::vector<int> volList;
 
-const int* geom_id_list(int dimension, int* number_of_items){
- switch(dimension){
+const int* geom_id_list(int dimension, int* number_of_items) {
+ switch(dimension) {
  case 2:
  *number_of_items = surfList.size();
  return &(surfList.front());
@@ -47,11 +47,11 @@ const int* geom_id_list(int dimension, int* number_of_items){
  }
 }
 
-EntityHandle handle_from_id(int dimension, int id){
+EntityHandle handle_from_id(int dimension, int id) {
  return DagMC::instance()->entity_by_id(dimension, id);
 }
 
-int id_from_handle(EntityHandle eh){
+int id_from_handle(EntityHandle eh) {
  return DagMC::instance()->get_entity_id(eh);
 }
 
@@ -80,31 +80,31 @@ ErrorCode dag_load(const char* filename){
 
  int num_surfs = dag->num_entities(2);
  surfList.reserve(num_surfs);
- for(int i = 1; i <= num_surfs; ++i){
+ for(int i = 1; i <= num_surfs; ++i) {
  surfList.push_back(dag->id_by_index(2, i));
  }
 
  int num_vols = dag->num_entities(3);
  volList.reserve(num_vols);
- for(int i = 1; i <= num_vols; ++i){
+ for(int i = 1; i <= num_vols; ++i) {
  volList.push_back(dag->id_by_index(3, i));
  }
 
  return err;
 }
 
 
-void* dag_alloc_ray_history(void){
+void* dag_alloc_ray_history(void) {
  return new DagMC::RayHistory();
 }
 
-void dag_dealloc_ray_history(void* r){
+void dag_dealloc_ray_history(void* r) {
  delete (static_cast<DagMC::RayHistory*>(r));
 }
 
 ErrorCode dag_ray_fire(EntityHandle vol, vec3 ray_start, vec3 ray_dir, 
  EntityHandle* next_surf_ent, double* next_surf_dist,
- void* history, double distance_limit){
+ void* history, double distance_limit) {
  ErrorCode err;
 
  DagMC* dag = DagMC::instance();
@@ -116,7 +116,7 @@ ErrorCode dag_ray_fire(EntityHandle vol, vec3 ray_start, vec3 ray_dir,
  return err;
 }
 
-class ray_buffers{
+class ray_buffers {
 
  public:
  DagMC::RayHistory history;
@@ -144,12 +144,12 @@ ErrorCode dag_ray_follow(EntityHandle firstvol, vec3 ray_start, vec3 ray_dir,
  CartVect uvw(ray_dir);
 
  // iterate over the ray until no more intersections are available
- while(vol){
+ while(vol) {
  err = dag->ray_fire(vol, ray_point.array(), ray_dir, 
  next_surf, next_surf_dist, &(buf->history), dlimit);
  CHECKERR(err);
 
- if(next_surf){
+ if(next_surf) {
  ray_point += uvw * next_surf_dist;
  buf->surfs.push_back(next_surf);
  buf->dists.push_back(next_surf_dist);
@@ -173,12 +173,12 @@ ErrorCode dag_ray_follow(EntityHandle firstvol, vec3 ray_start, vec3 ray_dir,
  return err;
 }
 
-void dag_dealloc_ray_buffer(void* data_buffers){
+void dag_dealloc_ray_buffer(void* data_buffers) {
  ray_buffers* b = static_cast<ray_buffers*>(data_buffers);
  delete b;
 }
 
-ErrorCode dag_pt_in_vol(EntityHandle vol, vec3 pt, int* result, vec3 dir, const void* history){
+ErrorCode dag_pt_in_vol(EntityHandle vol, vec3 pt, int* result, vec3 dir, const void* history) {
 
  ErrorCode err;
 
@@ -189,7 +189,7 @@ ErrorCode dag_pt_in_vol(EntityHandle vol, vec3 pt, int* result, vec3 dir, const
  return err;
 }
 
-ErrorCode dag_next_vol(EntityHandle surface, EntityHandle volume, EntityHandle* next_vol){
+ErrorCode dag_next_vol(EntityHandle surface, EntityHandle volume, EntityHandle* next_vol) {
 
  ErrorCode err;
  DagMC* dag = DagMC::instance();
@@ -199,7 +199,7 @@ ErrorCode dag_next_vol(EntityHandle surface, EntityHandle volume, EntityHandle*
  return err;
 }
 
-int vol_is_graveyard(EntityHandle vol){
+int vol_is_graveyard(EntityHandle vol) {
  return DagMC::instance()->has_prop(vol, "graveyard");
 }
 
@@ -210,7 +210,7 @@ int vol_is_implicit_complement(EntityHandle vol){
  return DagMC::instance()->is_implicit_complement(vol);
 }
 
-ErrorCode get_volume_metadata(EntityHandle vol, int* material, double* density, double* importance){
+ErrorCode get_volume_metadata(EntityHandle vol, int* material, double* density, double* importance) {
  ErrorCode err;
  DagMC* dag = DagMC::instance();
 
@@ -220,28 +220,28 @@ ErrorCode get_volume_metadata(EntityHandle vol, int* material, double* density,
 
  std::string str;
  err = dag->prop_value(vol, "mat", str);
- if(err == moab::MB_SUCCESS){
+ if(err == moab::MB_SUCCESS) {
  mat_id = strtol(str.c_str(), NULL, 10);
  }
- else if(err != moab::MB_TAG_NOT_FOUND){
+ else if(err != moab::MB_TAG_NOT_FOUND) {
  // TAG_NOT_FOUND should not be returned as an error; it just means
  // the default value of mat_id needs to be used.
  CHECKERR(err);
  }
 
  err = dag->prop_value(vol, "rho", str);
- if(err == moab::MB_SUCCESS){
+ if(err == moab::MB_SUCCESS) {
  rho = strtod(str.c_str(), NULL);
  }
- else if(err != moab::MB_TAG_NOT_FOUND){
+ else if(err != moab::MB_TAG_NOT_FOUND) {
  CHECKERR(err);
  }
 
  err = dag->prop_value(vol, "imp", str);
- if(err == moab::MB_SUCCESS){
+ if(err == moab::MB_SUCCESS) {
  imp = strtod(str.c_str(), NULL);
  }
- else if(err != moab::MB_TAG_NOT_FOUND){
+ else if(err != moab::MB_TAG_NOT_FOUND) {
  CHECKERR(err);
  }
 
@@ -252,7 +252,7 @@ ErrorCode get_volume_metadata(EntityHandle vol, int* material, double* density,
  return moab::MB_SUCCESS;
 }
 
-ErrorCode get_volume_boundary(EntityHandle vol, vec3 minPt, vec3 maxPt){
+ErrorCode get_volume_boundary(EntityHandle vol, vec3 minPt, vec3 maxPt) {
  return DagMC::instance()->getobb(vol, minPt, maxPt);
 }