From 62c61b02f41640b744286c89e8143f674fe21b65 Mon Sep 17 00:00:00 2001
From: Andrew Davis <andrew.davis@ukaea.uk>
Date: Fri, 15 May 2020 15:14:02 +0100
Subject: [PATCH] Fixed to reflect FLUKA-CERN

---
 cmake/FindFluka.cmake        |  6 +++---
 src/fluka/app/mainFluDAG.cpp | 40 ++++++++++++++++++------------------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/cmake/FindFluka.cmake b/cmake/FindFluka.cmake
index 2b28f5a60f..532530ec25 100644
--- a/cmake/FindFluka.cmake
+++ b/cmake/FindFluka.cmake
@@ -1,6 +1,6 @@
 find_path(FLUKA_LIBRARIES
-  NAMES libflukahp.a
-  HINTS ${FLUKA_DIR}
+  NAMES libfluka.a
+  HINTS ${FLUKA_DIR} ${FLUKA_DIR}/lib
   PATHS ENV FLUKA_DIR
   NO_DEFAULT_PATH
 )
@@ -8,7 +8,7 @@ if (FLUKA_LIBRARIES)
   get_filename_component(FLUKA_LIBRARIES ${FLUKA_LIBRARIES} ABSOLUTE)
 endif ()
 
-set(FLUKA_LIBRARIES ${FLUKA_LIBRARIES}/libflukahp.a gfortran)
+set(FLUKA_LIBRARIES ${FLUKA_LIBRARIES}/libfluka.a gfortran)
 
 message(STATUS "FLUKA_LIBRARIES: ${FLUKA_LIBRARIES}")
 
diff --git a/src/fluka/app/mainFluDAG.cpp b/src/fluka/app/mainFluDAG.cpp
index 61ab95c05d..a011244088 100644
--- a/src/fluka/app/mainFluDAG.cpp
+++ b/src/fluka/app/mainFluDAG.cpp
@@ -11,6 +11,7 @@
 
 #include "DagMC.hpp"
 #include "dagmcmetadata.hpp"
+#include "moab/ProgOptions.hpp"
 
 #include <cstring>
 #include <fstream>
@@ -39,37 +40,37 @@ int main(int argc, char* argv[]) {
 
   // Default h5m filename is for fluka runs
   std::string infile = "dagmc.h5m";
+  std::string dagmc_file = "";
 
-  if (argc == 1) {   // then its a fluka run
-    // fluka creates a run dir one lvl higher
-    infile = "../" + infile;
+  // form the inputs and determine if this is a true calculation or a preprocess run
+  ProgOptions po("mainfludag: a DAGMC enabled version of FLUKA-CERN");
+  po.addOpt<std::string>("dagmc", "Path to h5m DAGMC file to proccess", &dagmc_file);
+  po.addOptionalArgs<std::string>(0,"","");
+  po.parseCommandLine(argc, argv);
+
+  // if no string has been provided, dagmc command not applied
+  // we assume that its a FLUKA run
+  if (dagmc_file.empty()) {
     flukarun = true;
-  } else if (argc > 2) {
-    std::cout << "run as main_fludag <facet_file>  to produce"
-              << " material assignments" << std::endl;
-    std::cout << "too many arguments provided" << std::endl;
-    exit(1);
-  } else { // its a pre process run
-    infile = argv[1]; // must be the 2nd argument
+    // fluka creates a run dir one lvl higher than cwd
+    infile = "../" + infile;
+  } else {
+    // dagmc command has been set do the its a process run
+    infile = dagmc_file;
   }
 
-
+  // test to see if the file exists
   std::ifstream h5mfile(infile.c_str());  // filestream for mesh geom
   if (!h5mfile.good()) {
     std::cout << "h5m file does not exist" << std::endl;
     exit(1);
   }
 
-  int max_pbl = 1;
-
   // get the current time
   time(&time_before);  /* get current time; same as: timer = time(NULL)  */
 
-
   // DAG call to load the file
-  std::cout << "Loading the faceted geometry file " << infile << "..." << std::endl;
   error = DAG->load_file(infile.c_str()); // load the dag file takeing the faceting from h5m
-
   if (error != moab::MB_SUCCESS) {
     std::cerr << "DAGMC failed to read input file: " << infile << std::endl;
     exit(EXIT_FAILURE);
@@ -78,9 +79,7 @@ int main(int argc, char* argv[]) {
   time(&time_after);
 
   double seconds = difftime(time_after, time_before); //get the time in seconds to load file
-
   time_before = time_after; // reset time to now for the next call
-
   std::cout << "Time to load the h5m file = " << seconds << " seconds" << std::endl;
 
   // DAG call to initialize geometry
@@ -90,20 +89,21 @@ int main(int argc, char* argv[]) {
     error = DAG->init_OBBTree();
   } else {
     // otherwise this is a preprocess run
-    // no need to build the tree
+    // no need to build the tree - its faster
     error = DAG->setup_impl_compl();
     error = DAG->setup_indices();
   }
 
+  // check
   if (error != moab::MB_SUCCESS) {
     std::cerr << "DAGMC failed to initialize geometry and create OBB tree" <<  std::endl;
     exit(EXIT_FAILURE);
   }
 
   time(&time_after);
-
   seconds = difftime(time_after, time_before);
   std::cout << "Time to initialise the geometry" << seconds << std::endl;
+
   // if fluka preprocess run then create mat file to paste into input deck
   if (!flukarun) {
     std::string lcad = "mat.inp";