embedding the uwuw preprocessing in the plugin

buid_plugin.sh

@@ -0,0 +1,101 @@
+#!/bin/bash
+
+sudo apt-get install autogen autoconf libtool libeigen3-dev libhdf5-dev patchelf gfortran
+
+# Setup
+CURRENT=$(pwd)
+SCRIPTPATH=`dirname $(realpath $0)`
+
+PLUGIN_DIR="plugin-build"
+
+mkdir ${PLUGIN_DIR}
+PLUGIN_ABS_PATH=${CURRENT}/${PLUGIN_DIR}
+
+echo "Building the Trelis plugin in ${CURRENT}\\${PLUGIN_DIR}"
+
+unset LD_LIBRARY_PATH
+
+cd ${PLUGIN_ABS_PATH}
+ln -s $SCRIPTPATH ./
+
+mkdir -pv moab/bld
+cd moab
+git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
+cd moab
+autoreconf -fi
+cd ../bld
+../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+                  --disable-blaslapack \
+                  --enable-shared \
+                  --enable-optimize \
+                  --disable-debug \
+                  --disable-blaslapack \
+                  --with-eigen3=/usr/include/eigen3 \
+                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
+                  --prefix=${PLUGIN_ABS_PATH}/moab
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv DAGMC/bld
+cd DAGMC
+git clone https://github.com/svalinn/DAGMC -b develop
+cd bld
+cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+               -DMOAB_DIR=${PLUGIN_ABS_PATH}/moab \
+               -DBUILD_UWUW=ON \
+               -DBUILD_TALLY=OFF \
+               -DBUILD_BUILD_OBB=OFF \
+               -DBUILD_MAKE_WATERTIGHT=ON \
+               -DBUILD_SHARED_LIBS=ON \
+               -DBUILD_STATIC_LIBS=OFF \
+               -DCMAKE_BUILD_TYPE=Release \
+               -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}/DAGMC
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+
+cd ${PLUGIN_ABS_PATH}/Trelis-plugin
+git submodule update --init
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv bld
+cd bld
+cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
+                       -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
+                       -DCMAKE_BUILD_TYPE=Release \
+                       -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -p pack/bin/plugins/svalinn
+cd pack/bin/plugins/svalinn
+
+# Copy all needed libraries into current directory
+cp -pPv ${PLUGIN_ABS_PATH}/lib/* .
+cp -pPv ${PLUGIN_ABS_PATH}/moab/lib/libMOAB.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libdagmc.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libmakeWatertight.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libpyne_dagmc.so .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libuwuw.so .
+cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
+chmod 644 *
+
+# Set the RPATH to be the current directory for the DAGMC libraries
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
+
+# Create the Svalinn plugin tarball
+cd ..
+ln -sv svalinn/libsvalinn_plugin.so .
+cd ../..
+tar --sort=name -czvf svalinn-plugin.tgz bin
+mv -v svalinn-plugin.tgz ..
+cd ..
+rm -rf pack bld DAGMC lib moab
+rm Trelis-plugin

export_dagmc_cmd/DAGMCExportCommand.cpp

@@ -25,6 +25,9 @@
 #include "moab/Interface.hpp"
 #include "moab/GeomTopoTool.hpp"
 
+// DAGMC includes
+#include "uwuw_preprocessor.hpp"
+
 #define CHK_MB_ERR_RET(A,B)  if (moab::MB_SUCCESS != (B)) { \
   message << (A) << (B) << std::endl;                                   \
   CubitInterface::get_cubit_message_handler()->print_message(message.str().c_str()); \
@@ -46,6 +49,9 @@ DAGMCExportCommand::DAGMCExportCommand() :
   verbose_warnings = false;
   fatal_on_curves = false;
 
+  pyne_mat_lib = "";
+  hdf5_path = "/materials";
+
   CubitMessageHandler *console = CubitInterface::get_cubit_message_handler();
   if (console) {
     std::ostringstream load_message;
@@ -70,6 +76,8 @@ std::vector<std::string> DAGMCExportCommand::get_syntax()
       "[length_tolerance <value:label='length_tolerance',help='<length tolerance>'>] "
       "[normal_tolerance <value:label='normal_tolerance',help='<normal tolerance>'>] "
       "[make_watertight]"
+      "[pyne_mat_lib <string:label='pyne_mat_lib',help='<pyne_mat_lib>'>]"
+      "[hdf5_path <string:label='hdf5_path',help='<hdf5_path>'>]"
       "[verbose] [fatal_on_curves]";
 
   std::vector<std::string> syntax_list;
@@ -159,6 +167,24 @@ bool DAGMCExportCommand::execute(CubitCommandData &data)
   rval = teardown();
   CHK_MB_ERR_RET("Error tearing down export command.",rval);
 
+  // if a PyNE material library is provided then try to process the mats
+  if(pyne_mat_lib != "") {
+    bool fatal_errors = false;
+
+    uwuw_preprocessor* uwuw_preproc = new uwuw_preprocessor(pyne_mat_lib, filename, filename, hdf5_path, verbose_warnings, fatal_errors);
+    // process the materials
+    uwuw_preproc->process_materials();
+
+    // process the tallies
+    uwuw_preproc->process_tallies();
+
+    // write the material data
+    uwuw_preproc->write_uwuw_materials();
+
+    // write the tally data
+    uwuw_preproc->write_uwuw_tallies();
+  }
+
   return result;
 }
 
@@ -191,7 +217,20 @@ moab::ErrorCode DAGMCExportCommand::parse_options(CubitCommandData &data, moab::
   verbose_warnings = data.find_keyword("verbose");
   fatal_on_curves = data.find_keyword("fatal_on_curves");
   make_watertight = data.find_keyword("make_watertight");
-
+
+  // read parsed command for normal tolerance
+  data.get_string("pyne_mat_lib", pyne_mat_lib);
+  if (pyne_mat_lib != "") {
+    message << "Looking for the PyNE material Lib in " << pyne_mat_lib << std::endl;
+    data.get_string("hdf5_path",hdf5_path);
+    message << "hdf5 path set to " << hdf5_path << std::endl;
+  }
+  else {
+    message
+        << "No Material Library set, material assignments will not be processed"
+        << std::endl;
+  }
+
   if (verbose_warnings && fatal_on_curves)
     message << "This export will fail if curves fail to facet" << std::endl;
 

export_dagmc_cmd/DAGMCExportCommand.hpp

@@ -70,7 +70,10 @@ class DAGMCExportCommand: public CubitCommand
   bool verbose_warnings;
   bool fatal_on_curves;
   bool make_watertight;
-
+  std::string pyne_mat_lib;
+  std::string hdf5_path;
+
+
   int failed_curve_count;
   std::vector<int> failed_curves;