Merge pull request #390 from sandialabs/add_ejoin_assemblies

gsjaardema · web-flow · commit 7db697baee32 · 2023-05-26T12:15:17.000-06:00
Add ejoin assemblies
diff --git a/packages/seacas/applications/ejoin/EJ_SystemInterface.C b/packages/seacas/applications/ejoin/EJ_SystemInterface.C
@@ -55,7 +55,7 @@ void SystemInterface::enroll_options()
   options_.enroll("version", GetLongOption::NoValue, "Print version and exit", nullptr);
 
   options_.enroll("output", GetLongOption::MandatoryValue, "Name of output file to create",
-                  "ejoin-out.e");
+                  "ejoin-out.e", nullptr, true);
 
   options_.enroll(
       "extract_blocks", GetLongOption::MandatoryValue,
@@ -75,6 +75,19 @@ void SystemInterface::enroll_options()
                   "\t\t\t '-omit_blocks p1:1:3:4,p2:2:3:4,p5:8'",
                   nullptr);
 
+  options_.enroll("omit_assemblies", GetLongOption::MandatoryValue,
+                  "If no value, then don't transfer any assemblies to output file.\n"
+                  "\t\tIf just p#,p#,... specified, then omit assemblies on specified parts\n"
+                  "\t\tIf p#:id1:id2,p#:id2,id4... then omit the assemblies with the specified\n"
+                  "\t\tid in the specified parts.",
+                  nullptr, "ALL");
+
+  options_.enroll(
+      "omit_part_assemblies", GetLongOption::NoValue,
+      "Do not create an assembly for each input part containing the blocks in that part.\n"
+      "\t\tDefault is to create the part assemblies.",
+      nullptr);
+
   options_.enroll("omit_nodesets", GetLongOption::OptionalValue,
                   "If no value, then don't transfer any nodesets to output file.\n"
                   "\t\tIf just p#,p#,... specified, then omit sets on specified parts\n"
@@ -94,7 +107,7 @@ void SystemInterface::enroll_options()
                   "\t\tcreate a nodeset containing the nodes of that part\n"
                   "\t\tand output the nodal fields as nodeset fields instead of nodal fields.\n"
                   "\t\tFormat is comma-separated list of parts (1-based), or ALL",
-                  nullptr);
+                  nullptr, nullptr, true);
 
   options_.enroll("match_node_ids", GetLongOption::NoValue,
                   "Combine nodes if their global ids match.", nullptr);
@@ -115,19 +128,20 @@ void SystemInterface::enroll_options()
 #endif
 
   options_.enroll("tolerance", GetLongOption::MandatoryValue,
-                  "Maximum distance between two nodes to be considered colocated.", nullptr);
+                  "Maximum distance between two nodes to be considered colocated.", nullptr,
+                  nullptr, true);
 
   options_.enroll(
       "block_prefix", GetLongOption::MandatoryValue,
       "Prefix used on the input block names of second and subsequent meshes to make them\n"
-      "\t\tunique.  Default is 'p'.  Example: block1, p1_block1, p2_block1.",
+      "\t\tunique.  Default is 'p'.  Example: block1, p2_block1, p3_block1.",
       "p");
 
   options_.enroll("offset", GetLongOption::MandatoryValue,
                   "Comma-separated x,y,z offset for coordinates of second and subsequent meshes.\n"
                   "\t\tThe offset will be multiplied by the part number-1 so:\n"
                   "\t\tP1: no offset; P2: 1x, 1y, 1z; P3: 2x, 2y, 2z; P(n+1): nx, ny, nz",
-                  nullptr);
+                  nullptr, nullptr, true);
 
   options_.enroll("steps", GetLongOption::MandatoryValue,
                   "Specify subset of timesteps to transfer to output file.\n"
@@ -171,7 +185,7 @@ void SystemInterface::enroll_options()
                   "Ignore the element id maps on the input database and just use a 1..#elements id "
                   "map on output.\n"
                   "\t\tMuch faster for large models if do not need specific element global ids",
-                  nullptr);
+                  nullptr, nullptr, true);
 
   options_.enroll("netcdf4", GetLongOption::NoValue,
                   "Create output database using the HDF5-based "
@@ -249,6 +263,7 @@ bool SystemInterface::parse_options(int argc, char **argv)
   blockInclusions_.resize(part_count);
   nsetOmissions_.resize(part_count);
   ssetOmissions_.resize(part_count);
+  assemblyOmissions_.resize(part_count);
 
   // Get options from environment variable also...
   char *options = getenv("EJOIN_OPTIONS");
@@ -303,6 +318,17 @@ bool SystemInterface::parse_options(int argc, char **argv)
     }
   }
 
+  {
+    const char *temp = options_.retrieve("omit_assemblies");
+    if (temp != nullptr) {
+      parse_omissions(temp, &assemblyOmissions_, "assembly", true);
+    }
+  }
+
+  if (options_.retrieve("omit_part_assemblies") != nullptr) {
+    createAssemblies_ = false;
+  }
+
   {
     const char *temp = options_.retrieve("extract_blocks");
     if (temp != nullptr) {
diff --git a/packages/seacas/applications/ejoin/EJ_SystemInterface.h b/packages/seacas/applications/ejoin/EJ_SystemInterface.h
@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2022 National Technology & Engineering Solutions
+// Copyright(C) 1999-, 20232023 National Technology & Engineering Solutions
 // of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 // NTESS, the U.S. Government retains certain rights in this software.
 //
@@ -29,10 +29,12 @@ class SystemInterface
   bool   omit_nodesets() const { return omitNodesets_; }
   bool   omit_sidesets() const { return omitSidesets_; }
   bool   convert_nodes_to_nodesets(int part_number) const;
-  bool   disable_field_recognition() const { return disableFieldRecognition_; }
-  bool   ints64bit() const { return ints64bit_; }
-  bool   use_netcdf4() const { return useNetcdf4_; }
-  bool   ignore_element_ids() const { return ignoreElementIds_; }
+  bool   create_assemblies() const { return createAssemblies_; }
+
+  bool disable_field_recognition() const { return disableFieldRecognition_; }
+  bool ints64bit() const { return ints64bit_; }
+  bool use_netcdf4() const { return useNetcdf4_; }
+  bool ignore_element_ids() const { return ignoreElementIds_; }
 
   int  compression_level() const { return compressionLevel_; }
   bool zlib() const { return zlib_; }
@@ -53,6 +55,7 @@ class SystemInterface
   const Omissions &block_omissions() const { return blockOmissions_; }
   const Omissions &nset_omissions() const { return nsetOmissions_; }
   const Omissions &sset_omissions() const { return ssetOmissions_; }
+  const Omissions &assembly_omissions() const { return assemblyOmissions_; }
 
   const std::string &block_prefix() const { return blockPrefix_; }
 
@@ -96,6 +99,7 @@ class SystemInterface
   bool ignoreElementIds_{false};
   bool zlib_{true};
   bool szip_{false};
+  bool createAssemblies_{true};
 
   std::string blockPrefix_{"p"};
 
@@ -104,6 +108,7 @@ class SystemInterface
 
   Omissions blockInclusions_;
   Omissions blockOmissions_;
+  Omissions assemblyOmissions_;
   Omissions nsetOmissions_;
   Omissions ssetOmissions_;
 
diff --git a/packages/seacas/applications/ejoin/EJ_Version.h b/packages/seacas/applications/ejoin/EJ_Version.h
@@ -9,6 +9,6 @@
 
 static std::array<std::string, 3> qainfo{
     "ejoin",
-    "2022/01/24",
-    "1.5.7",
+    "2023/05/26",
+    "1.6.0",
 };
diff --git a/packages/seacas/applications/ejoin/EJoin.C b/packages/seacas/applications/ejoin/EJoin.C
@@ -80,6 +80,7 @@ namespace {
                               const std::vector<INT> &local_node_map, SystemInterface &interFace);
   void process_nset_omissions(RegionVector &part_mesh, const Omissions &omit);
   void process_sset_omissions(RegionVector &part_mesh, const Omissions &omit);
+  void process_assembly_omissions(RegionVector &part_mesh, const Omissions &omit);
 
   int count_omissions(Ioss::Region *region)
   {
@@ -123,7 +124,9 @@ namespace {
 } // namespace
 
 namespace {
-  void transfer_elementblock(Ioss::Region &region, Ioss::Region &output_region, bool debug);
+  void transfer_elementblock(Ioss::Region &region, Ioss::Region &output_region,
+                             bool create_assemblies, bool debug);
+  void transfer_assembly(Ioss::Region &region, Ioss::Region &output_region, bool debug);
   void transfer_nodesets(Ioss::Region &region, Ioss::Region &output_region, bool debug);
   void transfer_sidesets(Ioss::Region &region, Ioss::Region &output_region, bool debug);
   void create_nodal_nodeset(Ioss::Region &region, Ioss::Region &output_region, bool debug);
@@ -240,6 +243,7 @@ int main(int argc, char *argv[])
 
     process_nset_omissions(part_mesh, interFace.nset_omissions());
     process_sset_omissions(part_mesh, interFace.sset_omissions());
+    process_assembly_omissions(part_mesh, interFace.assembly_omissions());
 
     double time = 0.0;
 
@@ -404,7 +408,7 @@ double ejoin(SystemInterface &interFace, std::vector<Ioss::Region *> &part_mesh,
 
   // Add element blocks, nodesets, sidesets
   for (size_t p = 0; p < part_count; p++) {
-    transfer_elementblock(*part_mesh[p], output_region, false);
+    transfer_elementblock(*part_mesh[p], output_region, interFace.create_assemblies(), false);
     if (interFace.convert_nodes_to_nodesets(p + 1)) {
       create_nodal_nodeset(*part_mesh[p], output_region, false);
     }
@@ -414,6 +418,7 @@ double ejoin(SystemInterface &interFace, std::vector<Ioss::Region *> &part_mesh,
     if (!interFace.omit_sidesets()) {
       transfer_sidesets(*part_mesh[p], output_region, false);
     }
+    transfer_assembly(*part_mesh[p], output_region, false);
   }
 
   if (!interFace.information_record_parts().empty()) {
@@ -565,11 +570,19 @@ namespace {
     return omitted;
   }
 
-  void transfer_elementblock(Ioss::Region &region, Ioss::Region &output_region, bool debug)
+  void transfer_elementblock(Ioss::Region &region, Ioss::Region &output_region,
+                             bool create_assemblies, bool debug)
   {
     static int         used_blocks = 0;
     const std::string &prefix      = region.name();
 
+    Ioss::Assembly *assem = nullptr;
+    if (create_assemblies) {
+      assem = new Ioss::Assembly(output_region.get_database(), region.name());
+      output_region.add(assem);
+      assem->property_add(Ioss::Property("name_in_output", region.name()));
+    }
+
     const Ioss::ElementBlockContainer &ebs = region.get_element_blocks();
     for (const auto &eb : ebs) {
       if (!entity_is_omitted(eb)) {
@@ -581,6 +594,8 @@ namespace {
             exit(EXIT_FAILURE);
           }
         }
+        eb->property_add(Ioss::Property("name_in_output", name));
+
         if (debug) {
           fmt::print(stderr, "{}, ", name);
         }
@@ -601,6 +616,54 @@ namespace {
             // Set the new property
             ebn->property_add(Ioss::Property("original_topology_type", oes));
           }
+
+          if (create_assemblies) {
+            assem->add(ebn);
+          }
+        }
+      }
+    }
+  }
+
+  void transfer_assembly(Ioss::Region &region, Ioss::Region &output_region, bool debug)
+  {
+    // All assemblies on the input parts will be transferred to the output mesh
+    // Possibly renamed if a name conflict
+    // Also need to update names of the entities in the assembly since they were possibly
+    // renamed on the output...
+    // TODO: handle renamed nested assemblies...
+    const std::string &prefix = region.name();
+
+    const Ioss::AssemblyContainer &assems = region.get_assemblies();
+    for (const auto &as : assems) {
+      if (!entity_is_omitted(as)) {
+        std::string name = as->name();
+        if (output_region.get_assembly(name) != nullptr) {
+          name = prefix + "_" + as->name();
+          if (output_region.get_assembly(name) != nullptr) {
+            fmt::print(stderr, "ERROR: Duplicate assemblies named '{}'\n", name);
+            exit(EXIT_FAILURE);
+          }
+        }
+        as->property_add(Ioss::Property("name_in_output", name));
+
+        if (debug) {
+          fmt::print(stderr, "{}, ", name);
+        }
+        size_t num_members = as->entity_count();
+        if (num_members > 0) {
+          auto member_type = as->get_member_type();
+          auto asn         = new Ioss::Assembly(output_region.get_database(), name);
+          output_region.add(asn);
+
+          const auto &members = as->get_members();
+          for (const auto &member : members) {
+            auto output_name = member->get_property("name_in_output").get_string();
+
+            auto *entity = output_region.get_entity(output_name, member_type);
+            assert(entity != nullptr);
+            asn->add(entity);
+          }
         }
       }
     }
@@ -621,6 +684,7 @@ namespace {
             exit(EXIT_FAILURE);
           }
         }
+        fs->property_add(Ioss::Property("name_in_output", name));
         if (debug) {
           fmt::print(stderr, "{}, ", name);
         }
@@ -633,6 +697,7 @@ namespace {
           if (debug) {
             fmt::print(stderr, "{}, ", fbname);
           }
+          fb->property_add(Ioss::Property("name_in_output", fbname));
           std::string fbtype   = fb->topology()->name();
           std::string partype  = fb->parent_element_topology()->name();
           size_t      num_side = fb->entity_count();
@@ -747,6 +812,7 @@ namespace {
             exit(EXIT_FAILURE);
           }
         }
+        ns->property_add(Ioss::Property("name_in_output", name));
         if (debug) {
           fmt::print(stderr, "{}, ", name);
         }
@@ -1493,4 +1559,28 @@ namespace {
       }
     }
   }
+
+  void process_assembly_omissions(RegionVector &part_mesh, const Omissions &omit)
+  {
+    size_t part_count = part_mesh.size();
+    for (size_t p = 0; p < part_count; p++) {
+      if (!omit[p].empty()) {
+        // Get the assemblies for this part and set the "omitted" property on the assembly
+        if (omit[p][0] == "ALL") {
+          const auto &assemblies = part_mesh[p]->get_assemblies();
+          for (auto &as : assemblies) {
+            as->property_add(Ioss::Property(std::string("omitted"), 1));
+          }
+        }
+        else {
+          for (const auto &omitted : omit[p]) {
+            auto *as = part_mesh[p]->get_assembly(omitted);
+            if (as != nullptr) {
+              as->property_add(Ioss::Property(std::string("omitted"), 1));
+            }
+          }
+        }
+      }
+    }
+  }
 } // namespace
diff --git a/packages/seacas/libraries/exodus/include/exodusII.h b/packages/seacas/libraries/exodus/include/exodusII.h
@@ -52,12 +52,12 @@
 #endif
 
 /* EXODUS version number */
-#define EXODUS_VERSION       "8.20"
+#define EXODUS_VERSION       "8.21"
 #define EXODUS_VERSION_MAJOR 8
-#define EXODUS_VERSION_MINOR 20
+#define EXODUS_VERSION_MINOR 21
 #define EXODUS_RELEASE_DATE  "May 1, 2023"
 
-#define EX_API_VERS       8.20f
+#define EX_API_VERS       8.21f
 #define EX_API_VERS_NODOT (100 * EXODUS_VERSION_MAJOR + EXODUS_VERSION_MINOR)
 #define EX_VERS           EX_API_VERS
 
diff --git a/packages/seacas/libraries/exodus/src/ex_put_name.c b/packages/seacas/libraries/exodus/src/ex_put_name.c
diff --git a/packages/seacas/libraries/ioss/src/Ioss_Region.C b/packages/seacas/libraries/ioss/src/Ioss_Region.C
