From 2bf5f3180d857fd7de47f016927bbab5e8bba6bc Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:29:02 +0600
Subject: [PATCH 01/32] find geant4 manual mode

---
 cmake/FindGeant4.cmake | 42 ++++++++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/cmake/FindGeant4.cmake b/cmake/FindGeant4.cmake
index b62365fbea..36c47b9ba8 100644
--- a/cmake/FindGeant4.cmake
+++ b/cmake/FindGeant4.cmake
@@ -1,25 +1,31 @@
 # Find Geant4 cmake config file
 set(Geant4_SEARCH_DIRS)
-# Is this line necessary?
-set(PACKAGE_FIND_VERSION ${Geant4_FIND_VERSION})
+set(Geant4_FIND_VERSION ${Geant4_FIND_VERSION})
 file(GLOB Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib*/Geant4-*")
 string(REPLACE "\n" ";" Geant4_SEARCH_DIRS ${Geant4_SEARCH_DIRS})
 
-find_path(Geant4_CMAKE_CONFIG_VERSION
-  NAMES Geant4ConfigVersion.cmake
-  PATHS ${Geant4_SEARCH_DIRS}
-  NO_DEFAULT_PATH
-  )
+# Extract the version number from the first directory in Geant4_SEARCH_DIRS
+if(Geant4_SEARCH_DIRS)
+    # Extract the version number from the directory name
+    list(GET Geant4_SEARCH_DIRS 0 Geant4_LIB_DIR)
+    file(RELATIVE_PATH Geant4_VERSION ${GEANT4_DIR} ${Geant4_LIB_DIR})
+    string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" Geant4_VERSION ${Geant4_VERSION})
 
-if (Geant4_CMAKE_CONFIG_VERSION)
-  set(Geant4_CMAKE_CONFIG_VERSION ${Geant4_CMAKE_CONFIG_VERSION}/Geant4ConfigVersion.cmake)
-  include(${Geant4_CMAKE_CONFIG_VERSION})
-  set(Geant4_VERSION ${PACKAGE_VERSION})
-  set(Geant4_VERSION_COMPATIBLE ${PACKAGE_VERSION_COMPATIBLE})
-  set(Geant4_VERSION_EXACT ${PACKAGE_VERSION_EXACT})
-else ()
-  message(FATAL_ERROR "Could not find Geant4")
-endif ()
+    if(Geant4_VERSION)
+        message("Found Geant4 version ${Geant4_VERSION}")
+        
+        # Compare the versions
+        if(Geant4_FIND_VERSION VERSION_GREATER Geant4_VERSION)
+            set(Geant4_VERSION_COMPATIBLE false)
+        else()
+            set(Geant4_VERSION_COMPATIBLE true)
+        endif()
+    else()
+        message(FATAL_ERROR "Failed to extract Geant4 version from directory name")
+    endif()
+else()
+    message(FATAL_ERROR "No Geant4 installation found")
+endif()
 
 find_path(Geant4_CMAKE_CONFIG
   NAMES Geant4Config.cmake
@@ -58,8 +64,8 @@ include(${Geant4_USE_FILE})
 set(CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS_SAVE})
 
 message(STATUS "Geant4 version: ${Geant4_VERSION}")
-message(STATUS "Geant4 version required: ${PACKAGE_FIND_VERSION}")
-message(STATUS "Geant4 version compatible: ${PACKAGE_VERSION_COMPATIBLE}")
+message(STATUS "Geant4 version required: ${Geant4_FIND_VERSION}")
+message(STATUS "Geant4 version compatible: ${Geant4_VERSION_COMPATIBLE}")
 message(STATUS "Geant4 version exact: ${PACKAGE_VERSION_EXACT}")
 message(STATUS "Geant4_INCLUDE_DIRS: ${Geant4_INCLUDE_DIRS}")
 message(STATUS "Geant4_LIBRARIES_SHARED: ${Geant4_LIBRARIES_SHARED}")

From 2b1fc2369c8bb48ef1864c13094aa2e94bc9a99c Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:33:04 +0600
Subject: [PATCH 02/32] remove moab condition

---
 src/dagmc/DagMC.cpp | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/src/dagmc/DagMC.cpp b/src/dagmc/DagMC.cpp
index c4e0494e41..c086c44027 100644
--- a/src/dagmc/DagMC.cpp
+++ b/src/dagmc/DagMC.cpp
@@ -811,15 +811,6 @@ ErrorCode DagMC::point_in_volume_slow(EntityHandle volume, const double xyz[3],
   return rval;
 }
 
-#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
-// find a which volume contains the current point
-ErrorCode DagMC::find_volume(const double xyz[3], EntityHandle& volume,
-                             const double* uvw) {
-  ErrorCode rval = ray_tracer->find_volume(xyz, volume, uvw);
-  return rval;
-}
-#endif
-
 // detemine distance to nearest surface
 ErrorCode DagMC::closest_to_location(EntityHandle volume,
                                      const double coords[3], double& result,
@@ -870,11 +861,11 @@ ErrorCode DagMC::next_vol(EntityHandle surface, EntityHandle old_volume,
 
 /* SECTION III: Indexing & Cross-referencing */
 
-EntityHandle DagMC::entity_by_id(int dimension, int id) const {
+EntityHandle DagMC::entity_by_id(int dimension, int id) {
   return GTT->entity_by_id(dimension, id);
 }
 
-int DagMC::id_by_index(int dimension, int index) const {
+int DagMC::id_by_index(int dimension, int index) {
   EntityHandle h = entity_by_index(dimension, index);
   if (!h) return 0;
 
@@ -883,7 +874,7 @@ int DagMC::id_by_index(int dimension, int index) const {
   return result;
 }
 
-int DagMC::get_entity_id(EntityHandle this_ent) const {
+int DagMC::get_entity_id(EntityHandle this_ent) {
   return GTT->global_id(this_ent);
 }
 

From 0c4a183dc184cee3625ff23dc85c225234b0ac49 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:34:02 +0600
Subject: [PATCH 03/32] remove moab version condition

---
 src/dagmc/DagMC.hpp | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/src/dagmc/DagMC.hpp b/src/dagmc/DagMC.hpp
index c4f28f2bcd..5ecce3c584 100644
--- a/src/dagmc/DagMC.hpp
+++ b/src/dagmc/DagMC.hpp
@@ -225,10 +225,6 @@ class DagMC {
 
   ErrorCode point_in_volume_slow(const EntityHandle volume, const double xyz[3],
                                  int& result);
-#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
-  ErrorCode find_volume(const double xyz[3], EntityHandle& volume,
-                        const double* uvw = NULL);
-#endif
 
   ErrorCode test_volume_boundary(const EntityHandle volume,
                                  const EntityHandle surface,
@@ -263,16 +259,16 @@ class DagMC {
    */
 
   /** map from dimension & global ID to EntityHandle */
-  EntityHandle entity_by_id(int dimension, int id) const;
+  EntityHandle entity_by_id(int dimension, int id);
   /** map from dimension & base-1 ordinal index to EntityHandle */
-  EntityHandle entity_by_index(int dimension, int index) const;
+  EntityHandle entity_by_index(int dimension, int index);
   /** map from dimension & base-1 ordinal index to global ID */
-  int id_by_index(int dimension, int index) const;
+  int id_by_index(int dimension, int index);
   /** PPHW: Missing dim & global ID ==> base-1 ordinal index */
   /** map from EntityHandle to base-1 ordinal index */
-  int index_by_handle(EntityHandle handle) const;
+  int index_by_handle(EntityHandle handle);
   /** map from EntityHandle to global ID */
-  int get_entity_id(EntityHandle this_ent) const;
+  int get_entity_id(EntityHandle this_ent);
 
   /**\brief get number of geometric sets corresponding to geometry of specified
    *dimension
@@ -282,7 +278,7 @@ class DagMC {
    *the dimensionality of the entities in question \return integer number of
    *entities of that dimension
    */
-  unsigned int num_entities(int dimension) const;
+  unsigned int num_entities(int dimension);
 
  private:
   /** get all group sets on the model */
@@ -564,18 +560,18 @@ class DagMC {
 
 };  // end DagMC
 
-inline EntityHandle DagMC::entity_by_index(int dimension, int index) const {
+inline EntityHandle DagMC::entity_by_index(int dimension, int index) {
   assert(2 <= dimension && 3 >= dimension &&
          (unsigned)index < entHandles[dimension].size());
   return entHandles[dimension][index];
 }
 
-inline int DagMC::index_by_handle(EntityHandle handle) const {
+inline int DagMC::index_by_handle(EntityHandle handle) {
   assert(handle - setOffset < entIndices.size());
   return entIndices[handle - setOffset];
 }
 
-inline unsigned int DagMC::num_entities(int dimension) const {
+inline unsigned int DagMC::num_entities(int dimension) {
   assert(vertex_handle_idx <= dimension && groups_handle_idx >= dimension);
   return entHandles[dimension].size() - 1;
 }

From 8a6af96580333896e992f7483c42b83f862d3722 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:36:12 +0600
Subject: [PATCH 04/32] rearrange logger, then require_density

---
 src/dagmc/dagmcmetadata.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/dagmc/dagmcmetadata.cpp b/src/dagmc/dagmcmetadata.cpp
index b2753cf2f8..3392901011 100644
--- a/src/dagmc/dagmcmetadata.cpp
+++ b/src/dagmc/dagmcmetadata.cpp
@@ -12,8 +12,8 @@
 dagmcMetaData::dagmcMetaData(moab::DagMC* dag_ptr, bool verbosity,
                              bool require_density_present)
     : DAG(dag_ptr),
-      require_density(require_density_present),
-      logger(verbosity) {
+      logger(verbosity),
+      require_density(require_density_present) {
   // these are the keywords that dagmc will understand
   // from groups if you need to process more
   // they should be added here

From c1629505c15765b49e6a89051ee552359a5c67a5 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:37:32 +0600
Subject: [PATCH 05/32] remove moab conditions

---
 src/dagmc/tests/dagmc_simple_test.cpp | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/src/dagmc/tests/dagmc_simple_test.cpp b/src/dagmc/tests/dagmc_simple_test.cpp
index ee1525a524..9d46f47fb9 100644
--- a/src/dagmc/tests/dagmc_simple_test.cpp
+++ b/src/dagmc/tests/dagmc_simple_test.cpp
@@ -156,19 +156,6 @@ TEST_F(DagmcSimpleTest, dagmc_point_in) {
   EXPECT_EQ(expect_result, result);
 }
 
-#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
-TEST_F(DagmcSimpleTest, dagmc_find_volume) {
-  int vol_idx = 1;
-  int vol_dim = 3;
-  double xyz[3] = {0.0, 0.0, 0.0};
-  EntityHandle vol_h;
-  EntityHandle expected_vol_h = DAG->entity_by_index(vol_dim, vol_idx);
-  ErrorCode rval = DAG->find_volume(xyz, vol_h);
-  EXPECT_EQ(rval, MB_SUCCESS);
-  EXPECT_EQ(expected_vol_h, vol_h);
-}
-#endif
-
 TEST_F(DagmcSimpleTest, dagmc_test_obb_retreval_rayfire) {
   // make new dagmc
   std::cout << "test_obb_retreval and ray_fire" << std::endl;

From 47cd28bc5a09ed0e3e4b973c3cfb33df2baa0766 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:38:46 +0600
Subject: [PATCH 06/32] new condition Geant4_VERSION GREATER_EQUAL 11.0

---
 src/geant4/CMakeLists.txt | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/geant4/CMakeLists.txt b/src/geant4/CMakeLists.txt
index d203d00ced..7599946d9b 100644
--- a/src/geant4/CMakeLists.txt
+++ b/src/geant4/CMakeLists.txt
@@ -2,7 +2,11 @@ message("")
 
 find_package(Geant4 10.4.2 REQUIRED)
 
-if ( Geant4_VERSION GREATER_EQUAL 10.6 )
+if ( Geant4_VERSION GREATER_EQUAL 11.0 )
+  message(STATUS "Configuring DAGMC for Geant4 version >= 11.0")
+  add_compile_definitions(GEANT4_GT_10_6=1)
+  add_compile_definitions(GEANT4_GT_11=1)
+  elseif( Geant4_VERSION GREATER_EQUAL 10.6 )
   message(STATUS "Configuring DAGMC for Geant4 version >= 10.6")
   add_compile_definitions(GEANT4_GT_10_6=1)
 endif()

From 71a17633ae35fc039cdd617a0e24a0d4520dc8e7 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:40:32 +0600
Subject: [PATCH 07/32] removed itaps and added PyNE's dagmc by @gonuke

---
 src/geant4/generate_geant4 | 83 +++++++++-----------------------------
 1 file changed, 18 insertions(+), 65 deletions(-)

diff --git a/src/geant4/generate_geant4 b/src/geant4/generate_geant4
index 524b312394..182c29c55b 100755
--- a/src/geant4/generate_geant4
+++ b/src/geant4/generate_geant4
@@ -2,11 +2,13 @@
 
 from optparse import OptionParser
 import os,errno
-from itaps import iMesh,iBase
+import sys
 # for material handling
-from pyne.material import Material,MaterialLibrary
+from pyne.material import Material
+from pyne.material_library import MaterialLibrary
 from pyne.nucname import name, znum, anum, id, alara
 from pyne.data import atomic_mass
+from pyne import dagmc
 
 # for coloring the volumes
 import colorsys
@@ -70,7 +72,7 @@ def parse_arguments():
             try:
                 fh = open(options.dag_file, "r")
             except IOError:
-                print "Error: can\'t find DAG file"
+                print("Error: can't find DAG file")
             else:
                 fh.close()
         if not options.directory:
@@ -90,69 +92,17 @@ dag_filename : h5m filename
 
 Returns
 ---------
-dag_volnames : dictionary of volume names
-
+dag_vol_names : list of volume names
+dag_materials : dictionary of material assignments
 """
 
 def _get_dag_info(dag_filename):
-    dag_vol_names = [] # list of dag volume names (Cubit id)
-    dag_materials = {} # list of material assignments from group
-
-    # create imesh instance
-    dag_geom = iMesh.Mesh()
-    # load the file
-    dag_geom.load(dag_filename)
-
-    # get all entities
-    ents = dag_geom.getEntities()
-
-    # create a  mesh set
-    mesh_set = dag_geom.getEntSets()
-    # list of volume ent handles
-
-    mat_list = []
-    # get all geom_dimension ents
-    geom_list = []
-
-    cat_list = []
-
-    vol_tag = dag_geom.getTagHandle('GEOM_DIMENSION')
 
-    name_tag = dag_geom.getTagHandle('GLOBAL_ID')
+    dag_materials = dagmc.cell_material_assignments(dag_filename)
 
-    mat_tag = dag_geom.getTagHandle('NAME')
+    dag_vol_names = [dag_materials.keys()]
 
-    cat_tag = dag_geom.getTagHandle('CATEGORY')
-
-    # get the list we need
-    for i in mesh_set:
-        tags = dag_geom.getAllTags(i)
-        for tag in tags:
-            if tag == vol_tag:
-                geom_list.append(i)
-            if tag == mat_tag:
-                mat_list.append(i)
-            if tag == cat_tag:
-                cat_list.append(i)
-
-    # for the 3d entities
-    for entity in geom_list:
-        if vol_tag[entity] == 3:
-             dag_vol_names.append(str(name_tag[entity]))          
-
-
-    # loop over all the volumes
-    for entity in geom_list:
-        # loop over the material sets
-        for meshset in mat_list:
-            # if volume in set
-            if meshset.contains(entity):
-                mat_name = mat_tag[meshset]
-                volume_name = name_tag[entity]
-                dag_materials[volume_name]="".join( chr( val ) for val in mat_name )
-
-
-    return dag_vol_names,dag_materials
+    return dag_vol_names, dag_materials
 
 """
 Function to pull out the pyne materials from the h5m file
@@ -179,8 +129,8 @@ def _get_material_info(dag_file):
         mat_lib.from_hdf5(dag_file)
         materials =  mat_lib.keys()
     except:
-        print "!! There are no materials in the h5m file !!"
-        print " Assuming all volumes contain vacuum "
+        print("There are no materials in the h5m file!!")
+        print("Assuming all volumes contain vacuum")
         materials = {}
     
     nuclides = set()
@@ -534,7 +484,7 @@ dag_volume_names : list or dictionary of volume names
 def _setup_dagspecific_headers(dag_volume_names, tallies_needed):
 
     if not dag_volume_names:
-        print "dag volume names not assigned", sys.exc_info()[0]
+        print("dag volume names not assigned", sys.exc_info()[0])
         raise
 
     headers = {}
@@ -1680,7 +1630,7 @@ def _write_files(path, dictionary_files):
         try:
             fh = open(path+'/'+key, "w")
         except IOError:
-                print "Error: "+file+" file exists"
+                print("Error: "+key+" file exists")
         else:
             for line in dictionary_files[key]:
                 fh.write(line)
@@ -1707,9 +1657,12 @@ def _create_directory_structure(directory):
     _mkdir_p(directory+'/src')
     return
 
+# Fix: Don't know what it does
+"""
 def _dagmc_volume_material(dagmc_h5m, index):
 
     return material_name
+ """
 
 """
 Function from http://stackoverflow.com/questions
@@ -1724,7 +1677,7 @@ def _mkdir_p(path):
     try:
         os.makedirs(path)
     except OSError:     
-        print "Error: can\'t create directory, "+path
+        print("Error: can't create directory, "+path)
         raise
 
 

From 627be18de999a55c5099df798ed4a8bc53313844 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:40:58 +0600
Subject: [PATCH 08/32] GEANT4_GT_11

---
 src/geant4/app/include/ExN01Analysis.hh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/geant4/app/include/ExN01Analysis.hh b/src/geant4/app/include/ExN01Analysis.hh
index 15618704ce..530d274df5 100644
--- a/src/geant4/app/include/ExN01Analysis.hh
+++ b/src/geant4/app/include/ExN01Analysis.hh
@@ -7,6 +7,10 @@
 #ifndef ExN01Analysis_h
 #define ExN01Analysis_h 1
 
+#ifdef GEANT4_GT_11
+#include "G4AnalysisManager.hh"
+#else
 #include "g4root.hh"
+#endif
 
 #endif

From 0e17740cbc0b12b5b5fb5305793bde19671c4ddd Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:41:12 +0600
Subject: [PATCH 09/32] GEANT4_GT_11

---
 src/geant4/app/src/ExN01DetectorConstruction.cc | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/geant4/app/src/ExN01DetectorConstruction.cc b/src/geant4/app/src/ExN01DetectorConstruction.cc
index 23b6e91dc1..bf9236bee0 100644
--- a/src/geant4/app/src/ExN01DetectorConstruction.cc
+++ b/src/geant4/app/src/ExN01DetectorConstruction.cc
@@ -51,8 +51,11 @@ G4VPhysicalVolume* ExN01DetectorConstruction::Construct() {
   // load the material from the UW^2 library
   std::map<std::string, G4Material*> material_lib;
   material_lib = load_uwuw_materials(workflow_data);
-
+#ifdef GEANT4_GT_11
+  G4VisAttributes* invis = new G4VisAttributes(G4VisAttributes::GetInvisible());
+#else
   G4VisAttributes* invis = new G4VisAttributes(G4VisAttributes::Invisible);
+#endif
 
   //------------------------------------------------------ volumes
   // -- World Volume in which we place other volumes

From 55292f7601b2813f28ad8057c8290afc71691e49 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:41:51 +0600
Subject: [PATCH 10/32] GEANT4_GT_10_6 uill use MeshScoreMap

---
 src/geant4/app/src/ExN01UserScoreWriter.cc | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/geant4/app/src/ExN01UserScoreWriter.cc b/src/geant4/app/src/ExN01UserScoreWriter.cc
index 4fe0f8e9bc..b18f0ec94c 100644
--- a/src/geant4/app/src/ExN01UserScoreWriter.cc
+++ b/src/geant4/app/src/ExN01UserScoreWriter.cc
@@ -30,7 +30,11 @@ void ExN01UserScoreWriter::DumpAllQuantitiesToFile(const G4String& fileName,
   G4cout << "Dumping mesh " << fScoringMesh->GetWorldName() << " to file"
          << G4endl;
 
-  // retrieve the map
+// retrieve the map
+#ifdef GEANT4_GT_10_6
+  using MeshScoreMap = G4VScoringMesh::MeshScoreMap;
+#endif
+
   MeshScoreMap scMap = fScoringMesh->GetScoreMap();
 
   // get the number of bins

From a1d03629e9519c8085864f1421c9420ac4031bcb Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:45:21 +0600
Subject: [PATCH 11/32] geant4 v11 support

---
 doc/CHANGELOG.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/CHANGELOG.rst b/doc/CHANGELOG.rst
index 46b49d1fe5..00ca380195 100644
--- a/doc/CHANGELOG.rst
+++ b/doc/CHANGELOG.rst
@@ -29,7 +29,7 @@ Next version
    * Adding const identifier to cross-reference methods (#906)
 
 **Fixed:**
-   * Patch to compile with Geant4 10.6 (#803)
+   * Patch to compile with Geant4 10.6 (#803 #860)
    * Patched cmake-search paths for double-down and MOAB (#878)
    * Patch to compile with gcc-13 (#882)
    * Tweak conda environment for Windows build to avoid conflicting gtest headers (#888)

From 0f5239dca9656e5f292c728cdfb2fe38d3ade010 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 18 Sep 2023 23:55:26 +0600
Subject: [PATCH 12/32] Patch to compile with Geant4 11.x

---
 doc/CHANGELOG.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/CHANGELOG.rst b/doc/CHANGELOG.rst
index 00ca380195..62c86101d9 100644
--- a/doc/CHANGELOG.rst
+++ b/doc/CHANGELOG.rst
@@ -29,7 +29,7 @@ Next version
    * Adding const identifier to cross-reference methods (#906)
 
 **Fixed:**
-   * Patch to compile with Geant4 10.6 (#803 #860)
+   * Patch to compile with Geant4 11.x (#803 #907)
    * Patched cmake-search paths for double-down and MOAB (#878)
    * Patch to compile with gcc-13 (#882)
    * Tweak conda environment for Windows build to avoid conflicting gtest headers (#888)

From f7c4acff5393c86bde2c357d8bfe0003ec9e2aa5 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Tue, 19 Sep 2023 08:16:06 +0600
Subject: [PATCH 13/32] Geant4ConfigVersion

---
 cmake/FindGeant4.cmake | 44 ++++++++++++++++++------------------------
 1 file changed, 19 insertions(+), 25 deletions(-)

diff --git a/cmake/FindGeant4.cmake b/cmake/FindGeant4.cmake
index 36c47b9ba8..098f28573c 100644
--- a/cmake/FindGeant4.cmake
+++ b/cmake/FindGeant4.cmake
@@ -1,37 +1,31 @@
 # Find Geant4 cmake config file
 set(Geant4_SEARCH_DIRS)
-set(Geant4_FIND_VERSION ${Geant4_FIND_VERSION})
+
 file(GLOB Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib*/Geant4-*")
 string(REPLACE "\n" ";" Geant4_SEARCH_DIRS ${Geant4_SEARCH_DIRS})
 
-# Extract the version number from the first directory in Geant4_SEARCH_DIRS
-if(Geant4_SEARCH_DIRS)
-    # Extract the version number from the directory name
-    list(GET Geant4_SEARCH_DIRS 0 Geant4_LIB_DIR)
-    file(RELATIVE_PATH Geant4_VERSION ${GEANT4_DIR} ${Geant4_LIB_DIR})
-    string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" Geant4_VERSION ${Geant4_VERSION})
-
-    if(Geant4_VERSION)
-        message("Found Geant4 version ${Geant4_VERSION}")
-        
-        # Compare the versions
-        if(Geant4_FIND_VERSION VERSION_GREATER Geant4_VERSION)
-            set(Geant4_VERSION_COMPATIBLE false)
-        else()
-            set(Geant4_VERSION_COMPATIBLE true)
-        endif()
-    else()
-        message(FATAL_ERROR "Failed to extract Geant4 version from directory name")
-    endif()
-else()
-    message(FATAL_ERROR "No Geant4 installation found")
-endif()
-
 find_path(Geant4_CMAKE_CONFIG
   NAMES Geant4Config.cmake
   PATHS ${Geant4_SEARCH_DIRS}
   NO_DEFAULT_PATH
 )
+
+find_path(Geant4_CMAKE_CONFIG_VERSION
+  NAMES Geant4ConfigVersion.cmake
+  PATHS ${Geant4_CMAKE_CONFIG}
+  NO_DEFAULT_PATH
+  )
+
+if (Geant4_CMAKE_CONFIG_VERSION)
+  set(Geant4_CMAKE_CONFIG_VERSION ${Geant4_CMAKE_CONFIG_VERSION}/Geant4ConfigVersion.cmake)
+  include(${Geant4_CMAKE_CONFIG_VERSION})
+  set(Geant4_VERSION ${PACKAGE_VERSION})
+  set(Geant4_VERSION_COMPATIBLE ${PACKAGE_VERSION_COMPATIBLE})
+  set(Geant4_VERSION_EXACT ${PACKAGE_VERSION_EXACT})
+else ()
+  message(FATAL_ERROR "Could not find Geant4")
+endif ()
+
 if (Geant4_CMAKE_CONFIG)
   set(Geant4_CMAKE_CONFIG ${Geant4_CMAKE_CONFIG}/Geant4Config.cmake)
   message(STATUS "Geant4_CMAKE_CONFIG: ${Geant4_CMAKE_CONFIG}")
@@ -65,7 +59,7 @@ set(CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS_SAVE})
 
 message(STATUS "Geant4 version: ${Geant4_VERSION}")
 message(STATUS "Geant4 version required: ${Geant4_FIND_VERSION}")
-message(STATUS "Geant4 version compatible: ${Geant4_VERSION_COMPATIBLE}")
+message(STATUS "Geant4 version compatible: ${PACKAGE_VERSION_COMPATIBLE}")
 message(STATUS "Geant4 version exact: ${PACKAGE_VERSION_EXACT}")
 message(STATUS "Geant4_INCLUDE_DIRS: ${Geant4_INCLUDE_DIRS}")
 message(STATUS "Geant4_LIBRARIES_SHARED: ${Geant4_LIBRARIES_SHARED}")

From 4c0302e5e9e168d2a1a28c55eea45ee0ef1e0d26 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 2 Oct 2023 19:04:18 +0600
Subject: [PATCH 14/32] find a volume in a DAGMC instance if moab >5.2

---
 src/dagmc/DagMC.cpp                   |  9 +++++++++
 src/dagmc/tests/dagmc_simple_test.cpp | 13 +++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/src/dagmc/DagMC.cpp b/src/dagmc/DagMC.cpp
index c086c44027..8f92ca8672 100644
--- a/src/dagmc/DagMC.cpp
+++ b/src/dagmc/DagMC.cpp
@@ -811,6 +811,15 @@ ErrorCode DagMC::point_in_volume_slow(EntityHandle volume, const double xyz[3],
   return rval;
 }
 
+#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
+// find a which volume contains the current point
+ErrorCode DagMC::find_volume(const double xyz[3], EntityHandle& volume,
+                             const double* uvw) {
+  ErrorCode rval = ray_tracer->find_volume(xyz, volume, uvw);
+  return rval;
+}
+#endif
+
 // detemine distance to nearest surface
 ErrorCode DagMC::closest_to_location(EntityHandle volume,
                                      const double coords[3], double& result,
diff --git a/src/dagmc/tests/dagmc_simple_test.cpp b/src/dagmc/tests/dagmc_simple_test.cpp
index 9d46f47fb9..ee1525a524 100644
--- a/src/dagmc/tests/dagmc_simple_test.cpp
+++ b/src/dagmc/tests/dagmc_simple_test.cpp
@@ -156,6 +156,19 @@ TEST_F(DagmcSimpleTest, dagmc_point_in) {
   EXPECT_EQ(expect_result, result);
 }
 
+#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
+TEST_F(DagmcSimpleTest, dagmc_find_volume) {
+  int vol_idx = 1;
+  int vol_dim = 3;
+  double xyz[3] = {0.0, 0.0, 0.0};
+  EntityHandle vol_h;
+  EntityHandle expected_vol_h = DAG->entity_by_index(vol_dim, vol_idx);
+  ErrorCode rval = DAG->find_volume(xyz, vol_h);
+  EXPECT_EQ(rval, MB_SUCCESS);
+  EXPECT_EQ(expected_vol_h, vol_h);
+}
+#endif
+
 TEST_F(DagmcSimpleTest, dagmc_test_obb_retreval_rayfire) {
   // make new dagmc
   std::cout << "test_obb_retreval and ray_fire" << std::endl;

From 5737e4563beccae7f099a37323ab1a36ce25066d Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 2 Oct 2023 21:00:44 +0600
Subject: [PATCH 15/32] geant4 11.1.2 added

---
 .github/workflows/docker_publish.yml | 59 +++++++---------------------
 1 file changed, 15 insertions(+), 44 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index c8d84031f4..a7687c2f69 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -5,8 +5,8 @@ on:
   workflow_dispatch:
   push:
     paths:
-      - 'CI/Dockerfile'
-      - '.github/workflows/docker_publish.yml'
+      - "CI/Dockerfile"
+      - ".github/workflows/docker_publish.yml"
 
 jobs:
   build-dependency-and-test-img:
@@ -14,26 +14,12 @@ jobs:
 
     strategy:
       matrix:
-        ubuntu_versions : [
-          20.04,
-          22.04,
-          ]
-        compiler : [
-          gcc,
-          clang,
-          ]
-        hdf5_versions : [
-         1.10.4,
-        ]
-        moab_versions : [
-         5.3.0,
-        ]
-        double_down : [
-          OFF,
-        ]
-        geant_version : [
-          10.7.4,
-        ]
+        ubuntu_versions: [20.04, 22.04]
+        compiler: [gcc, clang]
+        hdf5_versions: [1.10.4]
+        moab_versions: [5.3.0, 5.4.0]
+        double_down: [OFF]
+        geant_version: [10.7.4, 11.1.2]
 
     name: Installing Dependencies, Building DAGMC and running tests
     steps:
@@ -68,36 +54,21 @@ jobs:
           dockerfile: CI/Dockerfile
           build-args: double_down=${{ matrix.double_down}}, geant4_version=${{ matrix.geant_version }}, COMPILER=${{ matrix.compiler }}, UBUNTU_VERSION=${{ matrix.ubuntu_versions }}, HDF5_VERSION=${{ matrix.hdf5_versions }}, MOAB_BRANCH=${{ matrix.moab_versions }}
 
-
   push_stable_ci_img:
     needs: [build-dependency-and-test-img]
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        ubuntu_versions : [
-          20.04,
-          22.04,
-          ]
-        compiler : [
-          gcc,
-          clang,
-          ]
-        hdf5_versions : [
-         1.10.4,
-        ]
-        moab_versions : [
-         5.3.0,
-        ]
-        double_down : [
-          OFF,
-        ]
-        geant_version : [
-          10.7.4,
-        ]
+        ubuntu_versions: [20.04, 22.04]
+        compiler: [gcc, clang]
+        hdf5_versions: [1.10.4]
+        moab_versions: [5.3.0, 5.4.0]
+        double_down: [OFF]
+        geant_version: [10.7.4, 11.1.2]
 
     name: Pushing final images
-    steps:       
+    steps:
       - name: Log in to the Container registry
         if: ${{ github.repository_owner == 'svalinn' }}
         uses: docker/login-action@v2

From 968f6f763d9d5c2c4b2f9aab012a3c8eafde5a16 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Mon, 2 Oct 2023 22:26:18 +0600
Subject: [PATCH 16/32] geant4_version=11.1.2

---
 CI/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CI/Dockerfile b/CI/Dockerfile
index 5eba2cfe5d..434d43a767 100644
--- a/CI/Dockerfile
+++ b/CI/Dockerfile
@@ -5,7 +5,7 @@
 
 # Global ARGS set before the first build stage are accessable by all build stages
 ARG EMBREE_BRANCH='v3.6.1'
-ARG geant4_version=10.7.4
+ARG geant4_version=11.1.2
 ARG UBUNTU_VERSION=20.04
 ARG MOAB_BRANCH=5.3.0
 ARG double_down=OFF

From 6d8c89df680b6c2cdb3a09ff5c5c5c1af622a740 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 19 Oct 2023 19:45:03 +0600
Subject: [PATCH 17/32] follow dagmc format

---
 .github/workflows/docker_publish.yml | 60 +++++++++++++++++++++-------
 1 file changed, 45 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index a7687c2f69..65d59ec798 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -5,8 +5,8 @@ on:
   workflow_dispatch:
   push:
     paths:
-      - "CI/Dockerfile"
-      - ".github/workflows/docker_publish.yml"
+      - 'CI/Dockerfile'
+      - '.github/workflows/docker_publish.yml'
 
 jobs:
   build-dependency-and-test-img:
@@ -14,12 +14,26 @@ jobs:
 
     strategy:
       matrix:
-        ubuntu_versions: [20.04, 22.04]
-        compiler: [gcc, clang]
-        hdf5_versions: [1.10.4]
-        moab_versions: [5.3.0, 5.4.0]
-        double_down: [OFF]
-        geant_version: [10.7.4, 11.1.2]
+        ubuntu_versions : [
+          20.04,
+          22.04,
+          ]
+        compiler : [
+          gcc,
+          clang,
+          ]
+        hdf5_versions : [
+         1.10.4,
+        ]
+        moab_versions : [
+         5.3.0,
+        ]
+        double_down : [
+          OFF,
+        ]
+        geant_version : [
+          10.7.4,
+        ]
 
     name: Installing Dependencies, Building DAGMC and running tests
     steps:
@@ -54,21 +68,37 @@ jobs:
           dockerfile: CI/Dockerfile
           build-args: double_down=${{ matrix.double_down}}, geant4_version=${{ matrix.geant_version }}, COMPILER=${{ matrix.compiler }}, UBUNTU_VERSION=${{ matrix.ubuntu_versions }}, HDF5_VERSION=${{ matrix.hdf5_versions }}, MOAB_BRANCH=${{ matrix.moab_versions }}
 
+
   push_stable_ci_img:
     needs: [build-dependency-and-test-img]
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        ubuntu_versions: [20.04, 22.04]
-        compiler: [gcc, clang]
-        hdf5_versions: [1.10.4]
-        moab_versions: [5.3.0, 5.4.0]
-        double_down: [OFF]
-        geant_version: [10.7.4, 11.1.2]
+        ubuntu_versions : [
+          20.04,
+          22.04,
+          ]
+        compiler : [
+          gcc,
+          clang,
+          ]
+        hdf5_versions : [
+         1.10.4,
+        ]
+        moab_versions : [
+         5.3.0,
+        ]
+        double_down : [
+          OFF,
+        ]
+        geant_version : [
+          10.7.4,
+          11.1.2
+        ]
 
     name: Pushing final images
-    steps:
+    steps:       
       - name: Log in to the Container registry
         if: ${{ github.repository_owner == 'svalinn' }}
         uses: docker/login-action@v2

From 8f583c6907b787f7fca58efabb46fdd9aed235c0 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 19 Oct 2023 20:57:02 +0600
Subject: [PATCH 18/32] add const

---
 src/dagmc/DagMC.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/dagmc/DagMC.cpp b/src/dagmc/DagMC.cpp
index 8f92ca8672..c4e0494e41 100644
--- a/src/dagmc/DagMC.cpp
+++ b/src/dagmc/DagMC.cpp
@@ -870,11 +870,11 @@ ErrorCode DagMC::next_vol(EntityHandle surface, EntityHandle old_volume,
 
 /* SECTION III: Indexing & Cross-referencing */
 
-EntityHandle DagMC::entity_by_id(int dimension, int id) {
+EntityHandle DagMC::entity_by_id(int dimension, int id) const {
   return GTT->entity_by_id(dimension, id);
 }
 
-int DagMC::id_by_index(int dimension, int index) {
+int DagMC::id_by_index(int dimension, int index) const {
   EntityHandle h = entity_by_index(dimension, index);
   if (!h) return 0;
 
@@ -883,7 +883,7 @@ int DagMC::id_by_index(int dimension, int index) {
   return result;
 }
 
-int DagMC::get_entity_id(EntityHandle this_ent) {
+int DagMC::get_entity_id(EntityHandle this_ent) const {
   return GTT->global_id(this_ent);
 }
 

From 8ce9f3b3099a6909ce3d651c52746026b8c44d7f Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 19 Oct 2023 22:45:39 +0600
Subject: [PATCH 19/32] add const

---
 src/dagmc/DagMC.hpp | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/dagmc/DagMC.hpp b/src/dagmc/DagMC.hpp
index 5ecce3c584..c4f28f2bcd 100644
--- a/src/dagmc/DagMC.hpp
+++ b/src/dagmc/DagMC.hpp
@@ -225,6 +225,10 @@ class DagMC {
 
   ErrorCode point_in_volume_slow(const EntityHandle volume, const double xyz[3],
                                  int& result);
+#if MOAB_VERSION_MAJOR == 5 && MOAB_VERSION_MINOR > 2
+  ErrorCode find_volume(const double xyz[3], EntityHandle& volume,
+                        const double* uvw = NULL);
+#endif
 
   ErrorCode test_volume_boundary(const EntityHandle volume,
                                  const EntityHandle surface,
@@ -259,16 +263,16 @@ class DagMC {
    */
 
   /** map from dimension & global ID to EntityHandle */
-  EntityHandle entity_by_id(int dimension, int id);
+  EntityHandle entity_by_id(int dimension, int id) const;
   /** map from dimension & base-1 ordinal index to EntityHandle */
-  EntityHandle entity_by_index(int dimension, int index);
+  EntityHandle entity_by_index(int dimension, int index) const;
   /** map from dimension & base-1 ordinal index to global ID */
-  int id_by_index(int dimension, int index);
+  int id_by_index(int dimension, int index) const;
   /** PPHW: Missing dim & global ID ==> base-1 ordinal index */
   /** map from EntityHandle to base-1 ordinal index */
-  int index_by_handle(EntityHandle handle);
+  int index_by_handle(EntityHandle handle) const;
   /** map from EntityHandle to global ID */
-  int get_entity_id(EntityHandle this_ent);
+  int get_entity_id(EntityHandle this_ent) const;
 
   /**\brief get number of geometric sets corresponding to geometry of specified
    *dimension
@@ -278,7 +282,7 @@ class DagMC {
    *the dimensionality of the entities in question \return integer number of
    *entities of that dimension
    */
-  unsigned int num_entities(int dimension);
+  unsigned int num_entities(int dimension) const;
 
  private:
   /** get all group sets on the model */
@@ -560,18 +564,18 @@ class DagMC {
 
 };  // end DagMC
 
-inline EntityHandle DagMC::entity_by_index(int dimension, int index) {
+inline EntityHandle DagMC::entity_by_index(int dimension, int index) const {
   assert(2 <= dimension && 3 >= dimension &&
          (unsigned)index < entHandles[dimension].size());
   return entHandles[dimension][index];
 }
 
-inline int DagMC::index_by_handle(EntityHandle handle) {
+inline int DagMC::index_by_handle(EntityHandle handle) const {
   assert(handle - setOffset < entIndices.size());
   return entIndices[handle - setOffset];
 }
 
-inline unsigned int DagMC::num_entities(int dimension) {
+inline unsigned int DagMC::num_entities(int dimension) const {
   assert(vertex_handle_idx <= dimension && groups_handle_idx >= dimension);
   return entHandles[dimension].size() - 1;
 }

From 61f28e5c88a4efb4d9f0b835cad38192c611cc18 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 19 Oct 2023 22:53:33 +0600
Subject: [PATCH 20/32] soft reset

---
 src/dagmc/dagmcmetadata.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/dagmc/dagmcmetadata.cpp b/src/dagmc/dagmcmetadata.cpp
index 3392901011..b2753cf2f8 100644
--- a/src/dagmc/dagmcmetadata.cpp
+++ b/src/dagmc/dagmcmetadata.cpp
@@ -12,8 +12,8 @@
 dagmcMetaData::dagmcMetaData(moab::DagMC* dag_ptr, bool verbosity,
                              bool require_density_present)
     : DAG(dag_ptr),
-      logger(verbosity),
-      require_density(require_density_present) {
+      require_density(require_density_present),
+      logger(verbosity) {
   // these are the keywords that dagmc will understand
   // from groups if you need to process more
   // they should be added here

From 0769e844b37cfacbe951aed6c8ed02b9850cf5ea Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 19 Oct 2023 23:10:13 +0600
Subject: [PATCH 21/32] geant4 11.1.2

---
 .github/workflows/docker_publish.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 65d59ec798..902a9703f9 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -33,6 +33,7 @@ jobs:
         ]
         geant_version : [
           10.7.4,
+          11.1.2
         ]
 
     name: Installing Dependencies, Building DAGMC and running tests

From b4b5a7dc5b34137fbd7b36798a29884cd5fffa31 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 20 Oct 2023 09:42:23 +0600
Subject: [PATCH 22/32] sefault geant4 11.1.2

---
 .github/actions/upstream-test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/upstream-test/action.yml b/.github/actions/upstream-test/action.yml
index 0cb8182274..68064d160b 100644
--- a/.github/actions/upstream-test/action.yml
+++ b/.github/actions/upstream-test/action.yml
@@ -8,7 +8,7 @@ inputs:
   geant_version:
     description: Version of Geant4
     required: false
-    default: 10.7.4
+    default: 11.1.2
   ubuntu_version:
     description: Underlying OS version
     required: false

From fc1507cf0d361def4b9193d002f5dbaeb73f121f Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 20 Oct 2023 09:42:39 +0600
Subject: [PATCH 23/32] new stage geant4

---
 .github/workflows/docker_publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 902a9703f9..70d12dd5a4 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -61,7 +61,7 @@ jobs:
         uses: firehed/multistage-docker-build-action@v1
         with:
           repository: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-geant4_${{ matrix.geant_version }}-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}
-          stages: base, external_deps, hdf5, moab, dagmc
+          stages: base, external_deps, hdf5, moab, geant4, dagmc
           server-stage: dagmc_test
           quiet: false
           parallel: true

From 510445f116cbbf12a257518ab238720619de96c2 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 20 Oct 2023 09:42:56 +0600
Subject: [PATCH 24/32] add 11.1.2 geant4

---
 .github/workflows/linux_build_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/linux_build_test.yml b/.github/workflows/linux_build_test.yml
index e17b2b36c7..1902f36817 100644
--- a/.github/workflows/linux_build_test.yml
+++ b/.github/workflows/linux_build_test.yml
@@ -55,6 +55,7 @@ jobs:
         ]
         geant_version : [
           10.7.4,
+          11.1.2
         ]
 
     container:

From 928b9f07f6d58c020682c702725a62636fcc2dca Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 20 Oct 2023 09:43:09 +0600
Subject: [PATCH 25/32] geant4 11.1.2

---
 .github/workflows/linux_upstream_test_geant4.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linux_upstream_test_geant4.yml b/.github/workflows/linux_upstream_test_geant4.yml
index d5871a4907..3e09d0161a 100644
--- a/.github/workflows/linux_upstream_test_geant4.yml
+++ b/.github/workflows/linux_upstream_test_geant4.yml
@@ -27,5 +27,5 @@ jobs:
         uses: ./.github/actions/upstream-test
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          geant_version: 11.1.1
+          geant_version: 11.1.2
             

From ee0b75b3f23303a9af48a19d1eff2e200519010b Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 20 Oct 2023 09:46:20 +0600
Subject: [PATCH 26/32] soft reset

---
 .github/workflows/docker_publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_publish.yml b/.github/workflows/docker_publish.yml
index 70d12dd5a4..902a9703f9 100644
--- a/.github/workflows/docker_publish.yml
+++ b/.github/workflows/docker_publish.yml
@@ -61,7 +61,7 @@ jobs:
         uses: firehed/multistage-docker-build-action@v1
         with:
           repository: ghcr.io/${{ github.repository_owner }}/dagmc-ci-ubuntu-${{ matrix.ubuntu_versions }}-${{ matrix.compiler}}-geant4_${{ matrix.geant_version }}-hdf5_${{ matrix.hdf5_versions}}-moab_${{ matrix.moab_versions }}
-          stages: base, external_deps, hdf5, moab, geant4, dagmc
+          stages: base, external_deps, hdf5, moab, dagmc
           server-stage: dagmc_test
           quiet: false
           parallel: true

From c0fc92ca6d8c01f5d1f31f4c48ee1ca233512677 Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Thu, 30 Nov 2023 20:30:05 +0600
Subject: [PATCH 27/32] Update cmake/FindGeant4.cmake

Co-authored-by: Paul Wilson <paul.wilson@wisc.edu>
---
 cmake/FindGeant4.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/FindGeant4.cmake b/cmake/FindGeant4.cmake
index 098f28573c..c8a0fda751 100644
--- a/cmake/FindGeant4.cmake
+++ b/cmake/FindGeant4.cmake
@@ -1,7 +1,7 @@
 # Find Geant4 cmake config file
 set(Geant4_SEARCH_DIRS)
 
-file(GLOB Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib*/Geant4-*")
+file(GLOB Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib*/Geant4*")
 string(REPLACE "\n" ";" Geant4_SEARCH_DIRS ${Geant4_SEARCH_DIRS})
 
 find_path(Geant4_CMAKE_CONFIG

From fa54fff6c90505281c444df719080ab3b364b73f Mon Sep 17 00:00:00 2001
From: Ahnaf Tahmid Chowdhury <ahnaf-tahmid@outlook.com>
Date: Fri, 1 Dec 2023 00:07:26 +0600
Subject: [PATCH 28/32] find path for geant4 11+

---
 cmake/FindGeant4.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cmake/FindGeant4.cmake b/cmake/FindGeant4.cmake
index c8a0fda751..f22f19b60b 100644
--- a/cmake/FindGeant4.cmake
+++ b/cmake/FindGeant4.cmake
@@ -3,6 +3,7 @@ set(Geant4_SEARCH_DIRS)
 
 file(GLOB Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib*/Geant4*")
 string(REPLACE "\n" ";" Geant4_SEARCH_DIRS ${Geant4_SEARCH_DIRS})
+list(APPEND Geant4_SEARCH_DIRS "${GEANT4_DIR}/lib/cmake/Geant4")
 
 find_path(Geant4_CMAKE_CONFIG
   NAMES Geant4Config.cmake

From 6b761f1d9b8992cc3f527ede578dd5ca44fd56df Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Thu, 30 Nov 2023 17:24:16 -0600
Subject: [PATCH 29/32] remove build test until we have a working docker
 container

---
 .github/workflows/linux_build_test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/linux_build_test.yml b/.github/workflows/linux_build_test.yml
index 0e866db731..5e8bbc30d0 100644
--- a/.github/workflows/linux_build_test.yml
+++ b/.github/workflows/linux_build_test.yml
@@ -55,7 +55,6 @@ jobs:
         ]
         geant_version : [
           10.7.4,
-          11.1.2
         ]
 
     container:

From 4ec7aa6d6c92621db3b34189d7740e8db937c56c Mon Sep 17 00:00:00 2001
From: Paul Wilson <paul.wilson@wisc.edu>
Date: Fri, 1 Dec 2023 09:07:53 -0600
Subject: [PATCH 30/32] remove explicit gcc install in mac_build_test.yml

---
 .github/workflows/mac_build_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/mac_build_test.yml b/.github/workflows/mac_build_test.yml
index 59678ce08e..a959052f76 100644
--- a/.github/workflows/mac_build_test.yml
+++ b/.github/workflows/mac_build_test.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Initial setup
         shell: bash -l {0}
         run: |
-          brew install eigen gcc@6 hdf5
+          brew install eigen hdf5
 
       - name: Environment Variables
         shell: bash -l {0}

From 1f137ffffaa2f8a78f7e182d12705929f32e9dee Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Wed, 6 Dec 2023 20:45:00 -0600
Subject: [PATCH 31/32] address review comments

---
 src/geant4/app/src/ExN01UserScoreWriter.cc |  6 +----
 src/geant4/generate_geant4                 | 27 ++++++++--------------
 2 files changed, 10 insertions(+), 23 deletions(-)

diff --git a/src/geant4/app/src/ExN01UserScoreWriter.cc b/src/geant4/app/src/ExN01UserScoreWriter.cc
index b18f0ec94c..b2dfb6018c 100644
--- a/src/geant4/app/src/ExN01UserScoreWriter.cc
+++ b/src/geant4/app/src/ExN01UserScoreWriter.cc
@@ -30,11 +30,7 @@ void ExN01UserScoreWriter::DumpAllQuantitiesToFile(const G4String& fileName,
   G4cout << "Dumping mesh " << fScoringMesh->GetWorldName() << " to file"
          << G4endl;
 
-// retrieve the map
-#ifdef GEANT4_GT_10_6
-  using MeshScoreMap = G4VScoringMesh::MeshScoreMap;
-#endif
-
+  x// retrieve the map
   MeshScoreMap scMap = fScoringMesh->GetScoreMap();
 
   // get the number of bins
diff --git a/src/geant4/generate_geant4 b/src/geant4/generate_geant4
index 182c29c55b..af7b3c64af 100755
--- a/src/geant4/generate_geant4
+++ b/src/geant4/generate_geant4
@@ -71,10 +71,9 @@ def parse_arguments():
         if options.dag_file:
             try:
                 fh = open(options.dag_file, "r")
-            except IOError:
-                print("Error: can't find DAG file")
-            else:
                 fh.close()
+            except IOError:
+                print("Error: can't find DAG file: '{} ".format(options.dag_file))
         if not options.directory:
             options.directory = os.getcwd()
     else:
@@ -100,7 +99,7 @@ def _get_dag_info(dag_filename):
 
     dag_materials = dagmc.cell_material_assignments(dag_filename)
 
-    dag_vol_names = [dag_materials.keys()]
+    dag_vol_names = list(dag_materials.keys())
 
     return dag_vol_names, dag_materials
 
@@ -129,8 +128,8 @@ def _get_material_info(dag_file):
         mat_lib.from_hdf5(dag_file)
         materials =  mat_lib.keys()
     except:
-        print("There are no materials in the h5m file!!")
-        print("Assuming all volumes contain vacuum")
+        print("There are no materials in the h5m file.\n"
+              "Assuming all volumes contain vacuum")
         materials = {}
     
     nuclides = set()
@@ -484,7 +483,7 @@ dag_volume_names : list or dictionary of volume names
 def _setup_dagspecific_headers(dag_volume_names, tallies_needed):
 
     if not dag_volume_names:
-        print("dag volume names not assigned", sys.exc_info()[0])
+        print("DAGMC volume names are not assigned", sys.exc_info()[0])
         raise
 
     headers = {}
@@ -1629,12 +1628,11 @@ def _write_files(path, dictionary_files):
     for key in dictionary_files:
         try:
             fh = open(path+'/'+key, "w")
-        except IOError:
-                print("Error: "+key+" file exists")
-        else:
             for line in dictionary_files[key]:
                 fh.write(line)
                 fh.close
+        except IOError:
+                print("Error: '{}' file exists".format(key))
 
 
 """ 
@@ -1657,13 +1655,6 @@ def _create_directory_structure(directory):
     _mkdir_p(directory+'/src')
     return
 
-# Fix: Don't know what it does
-"""
-def _dagmc_volume_material(dagmc_h5m, index):
-
-    return material_name
- """
-
 """
 Function from http://stackoverflow.com/questions
 /600268/mkdir-p-functionality-in-python, to create 
@@ -1677,7 +1668,7 @@ def _mkdir_p(path):
     try:
         os.makedirs(path)
     except OSError:     
-        print("Error: can't create directory, "+path)
+        print("Error: can't create directory '{}' ".format(path))
         raise
 
 

From b1e00914e54971f89f88343eef4c124e823807cd Mon Sep 17 00:00:00 2001
From: "Paul P.H. Wilson" <paul.wilson@wisc.edu>
Date: Wed, 6 Dec 2023 20:47:02 -0600
Subject: [PATCH 32/32] random typo

---
 src/geant4/app/src/ExN01UserScoreWriter.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/geant4/app/src/ExN01UserScoreWriter.cc b/src/geant4/app/src/ExN01UserScoreWriter.cc
index b2dfb6018c..4fe0f8e9bc 100644
--- a/src/geant4/app/src/ExN01UserScoreWriter.cc
+++ b/src/geant4/app/src/ExN01UserScoreWriter.cc
@@ -30,7 +30,7 @@ void ExN01UserScoreWriter::DumpAllQuantitiesToFile(const G4String& fileName,
   G4cout << "Dumping mesh " << fScoringMesh->GetWorldName() << " to file"
          << G4endl;
 
-  x// retrieve the map
+  // retrieve the map
   MeshScoreMap scMap = fScoringMesh->GetScoreMap();
 
   // get the number of bins