Merge pull request #1 from pyne/develop

Update from pnye/develop

CMakeLists.txt

@@ -10,6 +10,7 @@ project(pyne)
 include(PyneMacros)
 pyne_print_logo()  # Beware of dragons
 pyne_set_platform()
+pyne_set_asm_platform()
 pyne_set_build_spatial_solver()
 pyne_set_build_type()
 pyne_set_fast_compile()

cmake/DownloadAndExtract.cmake

@@ -0,0 +1,38 @@
+# Macros for downloading a tar file and extracting it if a sample file
+# doesn't already exist.
+
+macro(download_and_extract _url _checkfile)
+  if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_checkfile}")
+    # don't need to do anything
+    message(STATUS "${_checkfile} exists, no need to download or extract!")
+  else()
+    get_filename_component(_base "${_url}" NAME)
+    # download the file if we need to
+    if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_base}")
+      message(STATUS "Downloading ${_url} -> ${_base}")
+      file(DOWNLOAD "${_url}" "${CMAKE_CURRENT_SOURCE_DIR}/${_base}"
+           SHOW_PROGRESS STATUS _rtn TLS_VERIFY OFF)
+      list(GET _rtn 0 _rtncode)
+      if(NOT 0 EQUAL _rtncode)
+        message(FATAL_ERROR ${_rtn})
+      endif()
+    endif()
+    # extract the file
+    message(STATUS "Extracting ${_base}")
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf "${_base}"
+                    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+  endif()
+endmacro()
+
+
+macro(download_platform _base_url _base_name _ext_src _ext_plat)
+  # first download the src file
+  set(_url "${_base_url}/${_base_name}.tar.gz")
+  set(_checkfile "${_base_name}${_ext_src}")
+  download_and_extract("${_url}" "${_checkfile}")
+  # now download the platform specific file
+  set(_url "${_base_url}/${_base_name}-${PYNE_ASM_PLATFORM}.tar.gz")
+  set(_checkfile "${_base_name}-${PYNE_ASM_PLATFORM}${_ext_plat}")
+  download_and_extract("${_url}" "${_checkfile}")
+endmacro()
+

cmake/PyneMacros.cmake

@@ -1,3 +1,5 @@
+INCLUDE(DownloadAndExtract)
+
 # set platform preprocessor macro
 macro(pyne_set_platform)
   set(PYNE_PLATFORM "__${CMAKE_SYSTEM_NAME}__")
@@ -16,6 +18,28 @@ macro(pyne_set_platform)
   message("-- Pyne platform defined as: ${PYNE_PLATFORM}")
 endmacro()
 
+macro(pyne_set_asm_platform)
+  # first set OS
+  if (WIN32)
+    set(_plat "win")
+  elseif(APPLE)
+    set(_plat "apple")
+  else()
+    set(_plat "linux")
+  endif()
+  # next set compiler
+  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    set(_plat "${_plat}-gnu")
+  elseif (("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") OR
+    ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang"))
+    set(_plat "${_plat}-clang")
+  else()
+    set(_plat "${_plat}-NOTFOUND")
+  endif()
+  set(PYNE_ASM_PLATFORM "${_plat}")
+endmacro()
+
+
 # Fortran settings
 # FFLAGS depend on the compiler
 macro(pyne_setup_fortran)
@@ -169,6 +193,15 @@ macro(pyne_configure_rpath)
   MESSAGE("-- CMAKE_INSTALL_RPATH: ${CMAKE_INSTALL_RPATH}")
 endmacro()
 
+macro(pyne_download_platform)
+  # Download bateman solver from PyNE data
+  download_platform("https://raw.githubusercontent.com/pyne/data/master" "decay"
+                      ".cpp" ".s")
+
+  # Download CRAM solver from PyNE data
+  download_platform("http://raw.githubusercontent.com/pyne/data/master" "cram"
+                         ".c" ".s")
+endmacro()
 
 macro(pyne_set_fast_compile)
   if(NOT DEFINED PYNE_FAST_COMPILE)
@@ -182,10 +215,8 @@ endmacro()
 macro(fast_compile _srcname _gnuflags _clangflags _otherflags)
   get_filename_component(_base "${_srcname}" NAME_WE)  # get the base name, without the extension
   # get the assembly file name
-  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-    set(_asmname "${_base}-clang.s")
-  elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-    set(_asmname "${_base}-gnu.s")
+  if (PYNE_ASM_PLATFORM)
+    set(_asmname "${_base}-${PYNE_ASM_PLATFORM}.s")
   else()
     set(_asmname "${_base}-NOTFOUND")
   endif()
@@ -201,7 +232,7 @@ macro(fast_compile _srcname _gnuflags _clangflags _otherflags)
     message(STATUS "Compiling ${_srcname} fast from assembly ${_asmname}")
     set(_filename "${_asmname}")
   endif()
-  set(PYNE_SRCS "${PYNE_SRCS}" "${_filename}")
+    set(PYNE_SRCS "${_filename}" "${PYNE_SRCS}")
 
   # set some compile flags for the selected file
   if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")

news/Tag_shape_remove_unused_code.rst

@@ -0,0 +1,12 @@
+**Added:** None
+
+**Changed:** None
+
+**Deprecated:** None
+
+**Removed:** 
+* Code in mesh.py to reshpe a (N,1) to (N, ) array is no longer needed if PR #971 merged
+
+**Fixed:** None
+
+**Security:** None

news/change_ebounds_unit_to_MeV.rst

@@ -0,0 +1,11 @@
+**Added:** None
+
+**Changed:** Unit of e_bounds changed from eV to MeV
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:** None
+
+**Security:** None

news/r2s_change_loop_variables_name.rst

@@ -0,0 +1,13 @@
+**Added:** None
+
+**Changed:** 
+* Change loop variables to be v for volume elements and e for energy groups (instead of i & j)
+* Use bias_mode instead of mode to allow for additional mode types in future
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:** None
+
+**Security:** None

news/r2s_fix_wrong_mode_doc

@@ -0,0 +1,12 @@
+**Added:** None
+
+**Changed:** 
+* Correct the wrong mode description comment in pyne/src/source_sampling.h
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:** None
+
+**Security:** None

pyne/alara.py

@@ -620,7 +620,7 @@ def phtn_src_energy_bounds(input_file):
     Returns
     -------
     e_bounds : list of floats
-        The lower and upper energy bounds for the photon_source discretization.
+    The lower and upper energy bounds for the photon_source discretization. Unit: eV.
     """
     phtn_src_lines = ""
     with open(input_file, 'r') as f:

pyne/mesh.py

@@ -1252,11 +1252,6 @@ def tag_cell_fracs(self, cell_fracs):
             cell_largest_frac_number[i] = \
                     int(voxel_cell_number[i, largest_index])
 
-        # reshape the array
-        if max_num_cells == 1:
-            voxel_cell_number.shape = (num_vol_elements, )
-            voxel_cell_fracs.shape = (num_vol_elements, )
-
         # create the tags
         self.tag(name='cell_number', value=voxel_cell_number,
                  doc='cell numbers of the voxel, -1 used to fill vacancy',

scripts/r2s.py

@@ -180,6 +180,7 @@ def step2():
     e_bounds = phtn_src_energy_bounds("alara_geom")
     e_bounds_str = ""
     for e in e_bounds:
+        e = e/1e6 # convert unit to MeV
         e_bounds_str += "{0}\n".format(e)
     with open("e_bounds", 'w') as f:
         f.write(e_bounds_str)