Ejoin combine sets blocks (#662)

* IOSS: Add a reset_entity_count() function

* EJOIN: Nodeset mesh data now works for combining same-name nodesets

* EJOIN: Transient nodeset data seems to work..

* EJOIN: Clean up patching process

* Committing clang-format changes

* CONJOIN: Fix copyright date range [ci skip]

* IOSS: Fix copyright date range [ci skip]

* EJOIN: Initial impl of element block combining

* Committing clang-format changes

* EJOIN: Initial implementation of sset combine

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

* EJOIN: Minor cleanup of recent changes

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

* EJOIN: Add missing name_in_output property

* EJOIN: Fix output of nodal_nodeset fields

* Committing clang-format changes

* EJOIN: Fix nodal nodeset nodelist node output

* Committing clang-format changes

* EJOIN: Minor tweaks

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

* EJOIN: Refactor build_local_element_map

* EJOIN: Refactor output_input_map access

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

* EJOIN: Add testing of ns merge and combine options

* Committing clang-format changes

* EJOIN: Add input test files

* EJOIN: assert -> SMART_ASSERT

* EJOIN: Handle combined nodesets with conslidated nodes

* EJOIN: handle duplicate nodes in nodesets due to combine and match

* Committing clang-format changes

* EJOIN: Handle multi-component output fields

* Committing clang-format changes

* EJOIN: Update gold files

* EJOIN: Refactor nset dup node handling

* Committing clang-format changes

* EJOIN: Show all diffs in exodiff; minor change in gold files

* EJOIN: Add debug output (to see why tests diffing)

* Committing clang-format changes

* EJOIN: More deterministic sort; update gold

* Committing clang-format changes

* EJOIN: Remove debug output; minor refacrotings

* EJOIN: Tests need exodiff. Make sure it is available

* EJOIN: nset->nodeset, sset->sideset

* EJOIN: Remove beta from version; ready for merge

---------

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: gsjaardema

packages/seacas/applications/conjoin/CJ_Internals.C

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-, 20242024, , , ,  National Technology & Engineering Solutions
+ * Copyright(C) 1999-2025  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.
  *

packages/seacas/applications/ejoin/CMakeLists.txt

@@ -17,3 +17,45 @@ TRIBITS_ADD_EXECUTABLE(
   )
 
 TRIBITS_SUBPACKAGE_POSTPROCESS()
+
+if (${CMAKE_PROJECT_NAME}_ENABLE_SEACASExodiff)
+TRIBITS_ADD_ADVANCED_TEST(ejoin_combine_nes_nodeset_merge
+   TEST_0 EXEC ejoin ARGS --output combine_nes.g --match_nodeset_nodes p1:2,p2:1 --omit_nodeset p1:2,p2:1 --combine_element --combine_sideset --combine_nodeset ${CMAKE_CURRENT_SOURCE_DIR}/test/2block1.g ${CMAKE_CURRENT_SOURCE_DIR}/test/2block2.g
+     NOEXEPREFIX NOEXESUFFIX
+   TEST_1 EXEC exodiff ARGS -show_all_diffs -pedantic ${CMAKE_CURRENT_SOURCE_DIR}/test/2block-nes-gold.g combine_nes.g
+       DIRECTORY ../exodiff
+       NOEXEPREFIX NOEXESUFFIX
+  COMM serial
+  XHOSTTYPE Windows
+  )
+
+TRIBITS_ADD_ADVANCED_TEST(ejoin_nodeset_merge
+   TEST_0 EXEC ejoin ARGS --output ns-merge.g --match_nodeset_nodes p1:2,p2:1 --omit_nodeset p1:2,p2:1 ${CMAKE_CURRENT_SOURCE_DIR}/test/2block1.g ${CMAKE_CURRENT_SOURCE_DIR}/test/2block2.g
+     NOEXEPREFIX NOEXESUFFIX
+   TEST_1 EXEC exodiff ARGS -show_all_diffs -pedantic ${CMAKE_CURRENT_SOURCE_DIR}/test/2block-gold.g ns-merge.g
+       DIRECTORY ../exodiff
+       NOEXEPREFIX NOEXESUFFIX
+  COMM serial
+  XHOSTTYPE Windows
+  )
+
+TRIBITS_ADD_ADVANCED_TEST(ejoin_combine_ne_nodeset_merge
+   TEST_0 EXEC ejoin ARGS --output combine_ne.g --match_nodeset_nodes p1:2,p2:1 --omit_nodeset p1:2,p2:1 --combine_element --combine_nodeset ${CMAKE_CURRENT_SOURCE_DIR}/test/2block1.g ${CMAKE_CURRENT_SOURCE_DIR}/test/2block2.g
+     NOEXEPREFIX NOEXESUFFIX
+   TEST_1 EXEC exodiff ARGS -show_all_diffs -pedantic ${CMAKE_CURRENT_SOURCE_DIR}/test/2block-ne-gold.g combine_ne.g
+       DIRECTORY ../exodiff
+       NOEXEPREFIX NOEXESUFFIX
+  COMM serial
+  XHOSTTYPE Windows
+  )
+
+TRIBITS_ADD_ADVANCED_TEST(ejoin_combine_ns_nodeset_merge
+   TEST_0 EXEC ejoin ARGS -output combine_ns.g --match_nodeset_nodes p1:2,p2:1 --omit_nodeset p1:2,p2:1 --combine_sideset --combine_nodeset ${CMAKE_CURRENT_SOURCE_DIR}/test/2block1.g ${CMAKE_CURRENT_SOURCE_DIR}/test/2block2.g
+     NOEXEPREFIX NOEXESUFFIX
+   TEST_1 EXEC exodiff ARGS -show_all_diffs -pedantic ${CMAKE_CURRENT_SOURCE_DIR}/test/2block-ns-gold.g combine_ns.g
+       DIRECTORY ../exodiff
+       NOEXEPREFIX NOEXESUFFIX
+  COMM serial
+  XHOSTTYPE Windows
+  )
+endif()

packages/seacas/applications/ejoin/EJ_SystemInterface.C

@@ -113,15 +113,29 @@ void SystemInterface::enroll_options()
                   "Combine nodes if they are within tolerance distance of each other.", nullptr);
 
   options_.enroll("match_nodeset_nodes", GetLongOption::MandatoryValue,
-                  "Combine nodes in the specified nodeset(s) if they are within `tolerance` "
-                  "distance of each other.\n"
+                  "Combine nodes in the specified nodeset(s) if they are within\n"
+                  "\t\t`tolerance` distance of each other.\n"
                   "\t\tSpecify nodesets in each part as p#:id1:id2,p#:id2,id4...",
                   nullptr);
 
   options_.enroll("tolerance", GetLongOption::MandatoryValue,
                   "Maximum distance between two nodes to be considered colocated.", nullptr,
                   nullptr, true);
 
+  options_.enroll(
+      "combine_nodesets", GetLongOption::NoValue,
+      "Input nodesets with the same name will be combined into a single nodeset on output.",
+      nullptr);
+  options_.enroll("combine_sidesets", GetLongOption::NoValue,
+                  "Input sidesets with the same name will be combined into a "
+                  "single sideset on output.",
+                  nullptr);
+  options_.enroll("combine_element_blocks", GetLongOption::NoValue,
+                  "Element blocks with the same name and topology will be "
+                  "combined into a\n"
+                  "\t\tsingle element block on output.",
+                  nullptr, nullptr, true);
+
 #if 0
   options_.enroll("match_elem_ids", GetLongOption::NoValue,
                   "Combine elements if their global ids match and they are compatible.\n"
@@ -220,7 +234,8 @@ void SystemInterface::enroll_options()
                   nullptr);
 
   options_.enroll("quantize_nsd", GetLongOption::MandatoryValue,
-                  "Use the lossy quantize compression method.  Value specifies number of digits to "
+                  "Use the lossy quantize compression method.\n"
+                  "\t\tValue specifies number of digits to "
                   "retain (1..15) [exodus only]",
                   nullptr, nullptr, true);
 
@@ -276,10 +291,10 @@ bool SystemInterface::parse_options(int argc, char **argv)
   size_t part_count = inputFiles_.size();
   blockOmissions_.resize(part_count);
   blockInclusions_.resize(part_count);
-  nsetOmissions_.resize(part_count);
-  ssetOmissions_.resize(part_count);
+  nodesetOmissions_.resize(part_count);
+  sidesetOmissions_.resize(part_count);
   assemblyOmissions_.resize(part_count);
-  nsetMatch_.resize(part_count);
+  nodesetMatch_.resize(part_count);
 
   // Get options from environment variable also...
   char *options = getenv("EJOIN_OPTIONS");
@@ -349,10 +364,6 @@ bool SystemInterface::parse_options(int argc, char **argv)
     }
   }
 
-  if (options_.retrieve("omit_part_assemblies") != nullptr) {
-    createAssemblies_ = false;
-  }
-
   {
     const char *temp = options_.retrieve("extract_blocks");
     if (temp != nullptr) {
@@ -363,7 +374,7 @@ bool SystemInterface::parse_options(int argc, char **argv)
   {
     const char *temp = options_.retrieve("match_nodeset_nodes");
     if (temp != nullptr) {
-      parse_omissions(temp, &nsetMatch_, "nodelist", true);
+      parse_omissions(temp, &nodesetMatch_, "nodelist", true);
     }
   }
 
@@ -374,7 +385,7 @@ bool SystemInterface::parse_options(int argc, char **argv)
         omitNodesets_ = true;
       }
       else {
-        parse_omissions(temp, &nsetOmissions_, "nodelist", false);
+        parse_omissions(temp, &nodesetOmissions_, "nodelist", false);
       }
     }
     else {
@@ -389,7 +400,7 @@ bool SystemInterface::parse_options(int argc, char **argv)
         omitSidesets_ = true;
       }
       else {
-        parse_omissions(temp, &ssetOmissions_, "surface", false);
+        parse_omissions(temp, &sidesetOmissions_, "surface", false);
       }
     }
     else {
@@ -421,24 +432,25 @@ bool SystemInterface::parse_options(int argc, char **argv)
   {
     const char *temp = options_.retrieve("nsetvar");
     if (temp != nullptr) {
-      parse_variable_names(temp, &nsetVarNames_);
+      parse_variable_names(temp, &nodesetVarNames_);
     }
   }
 
   {
     const char *temp = options_.retrieve("ssetvar");
     if (temp != nullptr) {
-      parse_variable_names(temp, &ssetVarNames_);
+      parse_variable_names(temp, &sidesetVarNames_);
     }
   }
 
+  createAssemblies_        = options_.retrieve("omit_part_assemblies") != nullptr;
   disableFieldRecognition_ = options_.retrieve("disable_field_recognition") != nullptr;
   useNetcdf4_              = options_.retrieve("netcdf4") != nullptr;
   ignoreElementIds_        = options_.retrieve("ignore_element_ids") != nullptr;
-
-  if (options_.retrieve("64-bit") != nullptr) {
-    ints64bit_ = true;
-  }
+  combineNodesets_         = options_.retrieve("combine_nodesets") != nullptr;
+  combineSidesets_         = options_.retrieve("combine_sidesets") != nullptr;
+  combineElementBlocks_    = options_.retrieve("combine_element_blocks") != nullptr;
+  ints64bit_               = options_.retrieve("64-bit") != nullptr;
 
   zlib_ = (options_.retrieve("zlib") != nullptr);
   szip_ = (options_.retrieve("szip") != nullptr);

packages/seacas/applications/ejoin/EJ_SystemInterface.h

@@ -24,7 +24,7 @@ class SystemInterface
   double tolerance() const { return tolerance_; }
   bool   match_node_ids() const { return matchNodeIds_; }
   bool   match_node_xyz() const { return matchNodeXYZ_; }
-  bool   match_nodeset_nodes() const { return !nsetMatch_.empty(); }
+  bool   match_nodeset_nodes() const { return !nodesetMatch_.empty(); }
   bool   match_elem_ids() const { return matchElemIds_; }
   bool   omit_nodesets() const { return omitNodesets_; }
   bool   omit_sidesets() const { return omitSidesets_; }
@@ -49,20 +49,23 @@ class SystemInterface
   int step_max() const { return stepMax_; }
   int step_interval() const { return stepInterval_; }
 
+  bool                    combine_nodesets() const { return combineNodesets_; }
+  bool                    combine_sidesets() const { return combineSidesets_; }
+  bool                    combine_element_blocks() const { return combineElementBlocks_; }
   vector3d                offset() const { return offset_; }
   const std::vector<int> &information_record_parts() const { return infoRecordParts_; }
   const StringIdVector   &global_var_names() const { return globalVarNames_; }
   const StringIdVector   &node_var_names() const { return nodeVarNames_; }
   const StringIdVector   &elem_var_names() const { return elemVarNames_; }
-  const StringIdVector   &nset_var_names() const { return nsetVarNames_; }
-  const StringIdVector   &sset_var_names() const { return ssetVarNames_; }
+  const StringIdVector   &nodeset_var_names() const { return nodesetVarNames_; }
+  const StringIdVector   &sideset_var_names() const { return sidesetVarNames_; }
 
   const Omissions &block_inclusions() const { return blockInclusions_; }
   const Omissions &block_omissions() const { return blockOmissions_; }
-  const Omissions &nset_omissions() const { return nsetOmissions_; }
-  const Omissions &sset_omissions() const { return ssetOmissions_; }
+  const Omissions &nodeset_omissions() const { return nodesetOmissions_; }
+  const Omissions &sideset_omissions() const { return sidesetOmissions_; }
   const Omissions &assembly_omissions() const { return assemblyOmissions_; }
-  const Omissions &nset_match() const { return nsetMatch_; }
+  const Omissions &nodeset_match() const { return nodesetMatch_; }
 
   const std::string &block_prefix() const { return blockPrefix_; }
 
@@ -112,6 +115,10 @@ class SystemInterface
   bool useNetcdf4_{false};
   bool ignoreElementIds_{false};
 
+  bool combineElementBlocks_{false};
+  bool combineNodesets_{false};
+  bool combineSidesets_{false};
+
   bool createAssemblies_{true};
 
   std::string blockPrefix_{"p"};
@@ -122,17 +129,17 @@ class SystemInterface
   Omissions blockInclusions_;
   Omissions blockOmissions_;
   Omissions assemblyOmissions_;
-  Omissions nsetOmissions_;
-  Omissions ssetOmissions_;
+  Omissions nodesetOmissions_;
+  Omissions sidesetOmissions_;
 
-  Omissions nsetMatch_;
+  Omissions nodesetMatch_;
 
   std::vector<int> nodesetConvertParts_;
   std::vector<int> infoRecordParts_;
 
   StringIdVector globalVarNames_;
   StringIdVector nodeVarNames_;
   StringIdVector elemVarNames_;
-  StringIdVector nsetVarNames_;
-  StringIdVector ssetVarNames_;
+  StringIdVector nodesetVarNames_;
+  StringIdVector sidesetVarNames_;
 };

packages/seacas/applications/ejoin/EJ_Version.h

@@ -9,6 +9,6 @@
 
 static const std::array<std::string, 3> qainfo{
     "ejoin",
-    "2025/05/14",
-    "1.7.0",
+    "2025/06/04",
+    "1.8.1",
 };

packages/seacas/applications/ejoin/EJ_mapping.C

@@ -256,37 +256,52 @@ template void build_reverse_node_map(Ioss::Region &global, RegionVector &part_me
                                      std::vector<int64_t> &local_node_map);
 
 template <typename INT>
-void build_local_element_map(RegionVector &part_mesh, std::vector<INT> &local_element_map)
+std::vector<INT> build_local_element_map(RegionVector &part_mesh, Ioss::Region &output_region,
+                                         const IO_map &output_input_map)
 {
-  size_t global = 0;
-  size_t offset = 0;
-  for (auto &p : part_mesh) {
+  INT element_offset = 0;
+  for (auto &pm : part_mesh) {
+    pm->property_add(Ioss::Property("element_offset", element_offset));
+    INT local_elem_count = pm->get_property("element_count").get_int();
+    element_offset += local_elem_count;
+  }
 
-    const auto &ebs = p->get_element_blocks();
-    auto        i   = ebs.begin();
-
-    while (i != ebs.end()) {
-      const auto *eb       = *i++;
-      size_t      num_elem = eb->entity_count();
-      if (entity_is_omitted(eb)) {
-        // Fill local_element_map with -1 for the omitted elements.
-        for (size_t j = 0; j < num_elem; j++) {
-          local_element_map[offset + j] = -1;
-        }
-      }
-      else {
-        for (size_t j = 0; j < num_elem; j++) {
-          local_element_map[offset + j] = global++;
+  std::vector<INT>                   local_element_map(element_offset, -1);
+  const Ioss::ElementBlockContainer &ebs = output_region.get_element_blocks();
+
+  size_t global = 0;
+  for (const auto &oeb : ebs) {
+    const auto &itr = output_input_map.find(oeb);
+    assert(itr != output_input_map.end());
+    const auto &[key, oeb_inputs] = *itr;
+    for (const auto &[ieb, offset] : oeb_inputs) {
+      if (ieb != nullptr) {
+        int64_t ieb_count = ieb->entity_count();
+
+        auto  *input_region = dynamic_cast<const Ioss::Region *>(ieb->contained_in());
+        size_t ireg_offset  = input_region->get_property("element_offset").get_int();
+        size_t ieb_offset   = dynamic_cast<Ioss::EntityBlock *>(ieb)->get_offset();
+
+        // Element block `ieb` has `ieb_count` elements that run
+        // from `ieb_offset` to `ieb_offset + ieb_count` in
+        // `input_region` In `local_element_map, they run from
+        // `ireg_offset + ieb_offset` to `ireg_offset +
+        // ieb_offset + ieb_count`.
+        for (int64_t i = 0; i < ieb_count; i++) {
+          local_element_map[ireg_offset + ieb_offset + i] = global++;
         }
       }
-      offset += num_elem;
     }
   }
+  return local_element_map;
 }
 
-template void build_local_element_map(RegionVector &part_mesh, std::vector<int> &local_element_map);
-template void build_local_element_map(RegionVector         &part_mesh,
-                                      std::vector<int64_t> &local_element_map);
+template std::vector<int>     build_local_element_map(RegionVector &part_mesh,
+                                                      Ioss::Region &output_region,
+                                                      const IO_map &output_input_map);
+template std::vector<int64_t> build_local_element_map(RegionVector &part_mesh,
+                                                      Ioss::Region &output_region,
+                                                      const IO_map &output_input_map);
 
 template <typename INT>
 void generate_element_ids(RegionVector &part_mesh, const std::vector<INT> &local_element_map,

packages/seacas/applications/ejoin/EJ_mapping.h

@@ -7,6 +7,9 @@
 
 #include "EJ_CodeTypes.h"
 
+using IO_map =
+    std::map<Ioss::GroupingEntity *, std::vector<std::pair<Ioss::GroupingEntity *, size_t>>>;
+
 template <typename INT>
 void eliminate_omitted_nodes(RegionVector &part_mesh, std::vector<INT> &global_node_map,
                              std::vector<INT> &local_node_map, bool fill_global);
@@ -16,7 +19,8 @@ void build_reverse_node_map(Ioss::Region &output_region, RegionVector &part_mesh
                             std::vector<INT> &global_node_map, std::vector<INT> &local_node_map);
 
 template <typename INT>
-void build_local_element_map(RegionVector &part_mesh, std::vector<INT> &local_element_map);
+std::vector<INT> build_local_element_map(RegionVector &part_mesh, Ioss::Region &output_region,
+                                         const IO_map &output_input_map);
 
 template <typename INT>
 void generate_element_ids(RegionVector &part_mesh, const std::vector<INT> &local_element_map,

packages/seacas/applications/ejoin/EJ_match.C

@@ -223,7 +223,7 @@ void match_nodeset_nodes(RegionVector &part_mesh, double tolerance,
   // Select all nodes that are in the listed nodeset(s)...
   // On return, `local_node_map` will have >=0 entries for all nodeset nodes.
   // entries = -1 for active, but non-nodeset, and -2 for omitted nodes.
-  select_nodeset_nodes(part_mesh, local_node_map, interFace.nset_match());
+  select_nodeset_nodes(part_mesh, local_node_map, interFace.nodeset_match());
 
   match_nodes(part_mesh, tolerance, global_node_map, local_node_map);
 }