Merge pull request #1195 from sandialabs/bartgol/fo-thickness-omegah

Add omegah version of Humboldt thickness-coupled test

Author: bartgol

src/disc/extruded/Albany_ExtrudedDiscretization.cpp

@@ -150,6 +150,12 @@ checkForAdaptation (const Teuchos::RCP<const Thyra_Vector>& /* solution */,
                     const Teuchos::RCP<const Thyra_Vector>& /* solution_dotdot */,
                     const Teuchos::RCP<const Thyra_MultiVector>& /* dxdp */)
 {
+  auto& adapt_params = m_disc_params->sublist("Mesh Adaptivity");
+  auto adapt_type = adapt_params.get<std::string>("Type","None");
+  auto adapt_data = Teuchos::rcp(new AdaptationData());
+  if (adapt_type=="None") {
+    return adapt_data;
+  }
   // We can't just do
   //  return m_basal_disc->checkForAdaptation(solution,solution_dot,solution_dotdot);
   // We need to decide WHAT to bass to basal disc: the whole solution or the projection?
@@ -698,6 +704,11 @@ ExtrudedDiscretization::computeSideSets()
             " - elem nodes gids: " + util::join(elem_nodes,",") + "\n");
         return pos;
       };
+      // Track added side GIDs to avoid duplicates. This matters for "lateralside",
+      // which is built from all basal side sets. If those side sets overlap (e.g.,
+      // boundary_side_set contains boundary_side_set_1 and boundary_side_set_2),
+      // iterating all of them would add the same 3D face multiple times.
+      std::set<GO> added_side_GIDs;
       for (int ws=0; ws<m_basal_disc->getNumWorksets(); ++ws) {
         for (const auto& basal_ssn : basal_ss_names) {
           auto basal_ss = m_basal_disc->getSideSets(ws).at(basal_ssn);
@@ -709,6 +720,9 @@ ExtrudedDiscretization::computeSideSets()
               sStruct.elem_GID = layers_data.cell.gid->getId(basal_elem_gid,ilev);
               sStruct.side_GID = 2*num_glb_basal_elems + side_layers_gid.getId(basal_side.side_GID,ilev);
 
+              // Skip if this side was already added (can happen when basal side sets overlap)
+              if (!added_side_GIDs.insert(sStruct.side_GID).second) continue;
+
               auto elem_LID = cell_indexer->getLocalElement(sStruct.elem_GID);
               sStruct.ws_elem_idx = m_elem_ws_idx[elem_LID].idx;
               side_GIDs.push_back(sStruct.side_GID);

src/disc/omegah/Albany_OmegahDiscretization.cpp

@@ -177,6 +177,7 @@ updateMesh ()
     switch (st->dim.size()) {
       case 2: numComps = 1; break;
       case 3: numComps = st->dim[2]; break;
+      case 4: numComps = st->dim[2]*st->dim[3]; break;
       default:
         throw std::runtime_error(
             "[OmegahDiscretization::updateMesh] Error! Unsupported nodal state rank.\n"

src/disc/omegah/Albany_OmegahGenericMesh.cpp

@@ -281,10 +281,12 @@ loadOmegahMesh ()
 
     this->declare_part(pn, topo, is_in_part, mark_downward);
 
-    if (ent_dim==0) {
-      nsNames.push_back(pn);
-    } else if (ent_dim==m_mesh->dim()-1) {
+    if (ent_dim>=m_mesh->dim()-1) {
       ssNames.push_back(pn);
+      if (mark_downward)
+        nsNames.push_back(pn);
+    } else if (ent_dim==0) {
+      nsNames.push_back(pn);
     }
   }
 

tests/landIce/AsciiMeshes/Humboldt/CMakeLists.txt

@@ -50,3 +50,5 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/A_notLumped_humboldt.mm
                ${CMAKE_CURRENT_BINARY_DIR}/A_notLumped_humboldt.mm COPYONLY)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/D_notLumped_humboldt.mm
                ${CMAKE_CURRENT_BINARY_DIR}/D_notLumped_humboldt.mm COPYONLY)
+
+add_subdirectory(humboldt_contiguous_2d.osh)

tests/landIce/AsciiMeshes/Humboldt/humboldt_contiguous_2d.osh/0.osh

@@ -0,0 +1,6 @@
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/0.osh
+               ${CMAKE_CURRENT_BINARY_DIR}/0.osh COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nparts
+               ${CMAKE_CURRENT_BINARY_DIR}/nparts COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/version
+               ${CMAKE_CURRENT_BINARY_DIR}/version COPYONLY)

tests/landIce/AsciiMeshes/Humboldt/humboldt_contiguous_2d.osh/CMakeLists.txt

@@ -0,0 +1 @@
+1

tests/landIce/AsciiMeshes/Humboldt/humboldt_contiguous_2d.osh/nparts

@@ -0,0 +1 @@
+11

tests/landIce/AsciiMeshes/Humboldt/humboldt_contiguous_2d.osh/version

@@ -347,7 +347,7 @@ IF(NOT Kokkos_ENABLE_CUDA)
   #see issue #420. 
   set (testName ${testNameRoot}_CoupledThickness)
   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/input_fo_gis_coupled.yaml
-                  ${CMAKE_CURRENT_BINARY_DIR}/input_fo_gis_coupled.yaml)
+                 ${CMAKE_CURRENT_BINARY_DIR}/input_fo_gis_coupled.yaml)
 
   add_test(${testName} ${Albany.exe} input_fo_gis_coupled.yaml)
   set_tests_properties(${testName}  PROPERTIES LABELS "LandIce;Forward")
@@ -361,13 +361,37 @@ IF(NOT Kokkos_ENABLE_CUDA)
     set_tests_properties(${testName}  PROPERTIES LABELS "LandIce;Forward" FIXTURES_REQUIRED humboldtMeshSetup)
 
   else()
-    set (testName ${testNameRoot}_Humboldt_Transient)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/input_fo_humboldt_transient.yaml
-                  ${CMAKE_CURRENT_BINARY_DIR}/input_fo_humboldt_transient.yaml)
-    add_test(${testName} ${Albany.exe} input_fo_humboldt_transient.yaml)
+    set (testName ${testNameRoot}_Humboldt_Transient_STK3D)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/input_fo_humboldt_transient_stk3d.yaml
+                   ${CMAKE_CURRENT_BINARY_DIR}/input_fo_humboldt_transient_stk3d.yaml)
+    add_test(${testName} ${Albany.exe} input_fo_humboldt_transient_stk3d.yaml)
+    set_tests_properties(${testName}  PROPERTIES LABELS "LandIce;Forward" FIXTURES_REQUIRED humboldtMeshSetup)
+
+    set (testName ${testNameRoot}_Humboldt_Transient_STK)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/input_fo_humboldt_transient_stk.yaml
+                   ${CMAKE_CURRENT_BINARY_DIR}/input_fo_humboldt_transient_stk.yaml)
+    add_test(${testName} ${Albany.exe} input_fo_humboldt_transient_stk.yaml)
     set_tests_properties(${testName}  PROPERTIES LABELS "LandIce;Forward" FIXTURES_REQUIRED humboldtMeshSetup)
-  endif()
 
+    if (ALBANY_OMEGAH)
+      # TODO: when exo2osh treats nodesets correctly, we can uncomment this (and remove code in AsciiMeshes/Humboldt)
+      # set (testName ${testNameRoot}_Humboldt_Transient_Omega_h)
+      # add_test (NAME ${testName}_CreateHumboldtOsh
+      #       COMMAND ${OMEGAH_EXO2OSH} humboldt_contiguous_2d.exo humboldt_contiguous_2d.osh
+      #       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../AsciiMeshes/Humboldt)
+      # set_tests_properties (${testName}_CreateHumboldtOsh PROPERTIES
+      #     LABELS "LandIce;Forward;Omega_h"
+      #     FIXTURES_SETUP CreateHumboldtOshMesh)
+
+      configure_file(${CMAKE_CURRENT_SOURCE_DIR}/input_fo_humboldt_transient_omegah.yaml
+                     ${CMAKE_CURRENT_BINARY_DIR}/input_fo_humboldt_transient_omegah.yaml)
+      add_test(${testName} ${Albany.exe} input_fo_humboldt_transient_omegah.yaml)
+      set_tests_properties(${testName}  PROPERTIES
+        LABELS "LandIce;Forward;Omega_h")
+      # set_tests_properties(${testName}  PROPERTIES
+      #   FIXTURES_REQUIRED CreateHumboldtOshMesh)
+    endif()
+  endif()
 endif()
 
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