Change to fit Amanzi Mesh Refactor

amanzi · Jul 19, 2023 · 5904c9b · 5904c9b
1 parent 9130163
commit 5904c9b
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Showing 110 changed files with 1,245 additions and 1,373 deletions.
diff --git a/src/constitutive_relations/column_integrators/EvaluatorColumnIntegrator.hh b/src/constitutive_relations/column_integrators/EvaluatorColumnIntegrator.hh
@@ -83,9 +83,9 @@ EvaluatorColumnIntegrator<Parser, Integrator>::EnsureCompatibility_ToDeps_(State
                                                                      my_keys_.front().second);
   if (fac.Mesh() != Teuchos::null) {
     CompositeVectorSpace dep_fac;
-    dep_fac.SetMesh(fac.Mesh()->parent())
+    dep_fac.SetMesh(fac.Mesh()->getParentMesh())
       ->SetGhosted(true)
-      ->AddComponent("cell", AmanziMesh::CELL, 1);
+      ->AddComponent("cell", AmanziMesh::Entity_kind::CELL, 1);
 
     for (const auto& dep : dependencies_) {
       if (Keys::getDomain(dep.first) == Keys::getDomain(my_keys_.front().first)) {
@@ -122,7 +122,7 @@ EvaluatorColumnIntegrator<Parser, Integrator>::Evaluate_(
     deps.emplace_back(
       S.Get<CompositeVector>(dep.first, dep.second).ViewComponent("cell", false).get());
   }
-  auto mesh = result[0]->Mesh()->parent();
+  auto mesh = result[0]->Mesh()->getParentMesh();
   Integrator integrator(plist_, deps, &*mesh);
 
   Epetra_MultiVector& res = *result[0]->ViewComponent("cell", false);
@@ -131,7 +131,7 @@ EvaluatorColumnIntegrator<Parser, Integrator>::Evaluate_(
     // for each column, loop over cells calling the integrator until stop is
     // requested or the column is complete
     AmanziGeometry::Point val(0., 0.);
-    auto& col_cell = mesh->cells_of_column(col);
+    auto col_cell = mesh->columns.getCells(col);
     for (int i = 0; i != col_cell.size(); ++i) {
       bool completed = integrator.scan(col, col_cell[i], val);
       if (completed) break;

diff --git a/src/constitutive_relations/column_integrators/activelayer_average_temp_evaluator.cc b/src/constitutive_relations/column_integrators/activelayer_average_temp_evaluator.cc
@@ -40,7 +40,7 @@ IntegratorActiveLayerAverageTemp::scan(AmanziMesh::Entity_ID col,
                                        AmanziGeometry::Point& p)
 {
   if ((*temp_)[0][c] >= trans_temp_) {
-    double cv = mesh_->cell_volume(c);
+    double cv = mesh_->getCellVolume(c);
     p[0] += (*temp_)[0][c] * cv;
     p[1] += cv;
     return false;

diff --git a/src/constitutive_relations/generic_evaluators/ExtractionEvaluator.cc b/src/constitutive_relations/generic_evaluators/ExtractionEvaluator.cc
@@ -52,7 +52,7 @@ ExtractionEvaluator::Evaluate_(const State& S, const std::vector<CompositeVector
 
     for (int j = 0; j != result_c.NumVectors(); ++j) {
       for (int i = 0; i != result_c.MyLength(); ++i) {
-        result_c[j][i] = parent_vector_c[j][mesh->entity_get_parent(entity, i)];
+        result_c[j][i] = parent_vector_c[j][mesh->getEntityParent(entity, i)];
       }
     }
   }

diff --git a/src/constitutive_relations/generic_evaluators/SubgridAggregateEvaluator.cc b/src/constitutive_relations/generic_evaluators/SubgridAggregateEvaluator.cc
@@ -46,7 +46,7 @@ SubgridAggregateEvaluator::Evaluate_(const State& S, const std::vector<Composite
       S.Get<CompositeVector>(dep->first, dep->second).ViewComponent("cell", false).get());
     ++dep;
   }
-  ds->DoImport(sources, result_v);
+  ds->doImport(sources, result_v);
 }
 
 void
@@ -65,7 +65,7 @@ SubgridAggregateEvaluator::EnsureEvaluators(State& S)
   if (dependencies_.size() == 0) {
     auto ds = S.GetDomainSet(source_domain_);
     Tag dep_tag = Keys::readTag(plist_, my_keys_.front().second);
-    if (ds->get_referencing_parent() == Teuchos::null) {
+    if (ds->getReferencingParent() == Teuchos::null) {
       Errors::Message msg;
       msg << "SubgridAggregateEvaluator: DomainSet \"" << source_domain_
           << "\" does not have a referencing parent but must have one to aggregate.";
@@ -92,8 +92,8 @@ SubgridAggregateEvaluator::EnsureCompatibility_Structure_(State& S)
   if (dep_fac.HasComponent("cell")) {
     S.Require<CompositeVector, CompositeVectorSpace>(my_keys_.front().first,
                                                      my_keys_.front().second)
-      .SetMesh(ds->get_referencing_parent())
-      ->AddComponent("cell", AmanziMesh::CELL, dep_fac.NumVectors("cell"));
+      .SetMesh(ds->getReferencingParent())
+      ->AddComponent("cell", AmanziMesh::Entity_kind::CELL, dep_fac.NumVectors("cell"));
   }
 
   if (S.GetRecordSet(dependencies_.front().first).subfieldnames()) {
@@ -116,7 +116,7 @@ SubgridAggregateEvaluator::EnsureCompatibility_ToDeps_(State& S)
                                                                 "cell",
                                                               },
                                                               {
-                                                                AmanziMesh::CELL,
+                                                                AmanziMesh::Entity_kind::CELL,
                                                               },
                                                               {
                                                                 num_vectors,

diff --git a/src/constitutive_relations/generic_evaluators/SubgridDisaggregateEvaluator.cc b/src/constitutive_relations/generic_evaluators/SubgridDisaggregateEvaluator.cc
@@ -39,7 +39,7 @@ SubgridDisaggregateEvaluator::Evaluate_(const State& S, const std::vector<Compos
 {
   auto tag = my_keys_.front().second;
   auto ds = S.GetDomainSet(domain_set_);
-  ds->DoExport(domain_index_,
+  ds->doExport(domain_index_,
                *S.Get<CompositeVector>(source_key_, tag).ViewComponent("cell", false),
                *result[0]->ViewComponent("cell", false));
 }
@@ -64,7 +64,7 @@ SubgridDisaggregateEvaluator::EnsureCompatibility_ToDeps_(State& S)
   if (my_fac.HasComponent("cell")) {
     int num_vectors = my_fac.NumVectors("cell");
     CompositeVectorSpace fac;
-    fac.SetMesh(S.GetMesh(source_domain_))->AddComponent("cell", AmanziMesh::CELL, num_vectors);
+    fac.SetMesh(S.GetMesh(source_domain_))->AddComponent("cell", AmanziMesh::Entity_kind::CELL, num_vectors);
     EvaluatorSecondaryMonotypeCV::EnsureCompatibility_ToDeps_(S, fac);
   }
 }

diff --git a/...ive_relations/surface_subsurface_fluxes/overland_source_from_subsurface_flux_evaluator.cc b/...ive_relations/surface_subsurface_fluxes/overland_source_from_subsurface_flux_evaluator.cc
@@ -77,24 +77,21 @@ OverlandSourceFromSubsurfaceFluxEvaluator::IdentifyFaceAndDirection_(const State
   Teuchos::RCP<const AmanziMesh::Mesh> surface = S.GetMesh(domain_surf_);
 
   // allocate space for face IDs and directions
-  int ncells = surface->num_entities(AmanziMesh::CELL, AmanziMesh::Parallel_type::OWNED);
+  int ncells = surface->getNumEntities(AmanziMesh::Entity_kind::CELL, AmanziMesh::Parallel_kind::OWNED);
   face_and_dirs_ = Teuchos::rcp(new std::vector<FaceDir>(ncells));
 
   for (int c = 0; c != ncells; ++c) {
     // Get the face on the subsurface mesh corresponding to the cell
     // of the surface mesh.
-    AmanziMesh::Entity_ID domain_face = surface->entity_get_parent(AmanziMesh::CELL, c);
+    AmanziMesh::Entity_ID domain_face = surface->getEntityParent(AmanziMesh::Entity_kind::CELL, c);
 
     // Get the direction corresponding to that face wrt its only cell.
     // -- get the cell
-    AmanziMesh::Entity_ID_List cells;
-    subsurface->face_get_cells(domain_face, AmanziMesh::Parallel_type::OWNED, &cells);
+    auto cells = subsurface->getFaceCells(domain_face, AmanziMesh::Parallel_kind::OWNED);
     AMANZI_ASSERT(cells.size() == 1);
 
     // -- Get directions
-    AmanziMesh::Entity_ID_List faces;
-    std::vector<int> fdirs;
-    subsurface->cell_get_faces_and_dirs(cells[0], &faces, &fdirs);
+    const auto& [faces, fdirs] = subsurface->getCellFacesAndDirections(cells[0]);
     int index = std::find(faces.begin(), faces.end(), domain_face) - faces.begin();
 
     // Put (face,dir) into cached data.
@@ -121,9 +118,8 @@ OverlandSourceFromSubsurfaceFluxEvaluator::Evaluate_(const State& S,
 
     int ncells = result[0]->size("cell", false);
     for (int c = 0; c != ncells; ++c) {
-      AmanziMesh::Entity_ID_List cells;
-      subsurface->face_get_cells(
-        (*face_and_dirs_)[c].first, AmanziMesh::Parallel_type::OWNED, &cells);
+      auto cells = subsurface->getFaceCells(
+        (*face_and_dirs_)[c].first, AmanziMesh::Parallel_kind::OWNED);
       AMANZI_ASSERT(cells.size() == 1);
 
       res_v[0][c] =
@@ -132,9 +128,8 @@ OverlandSourceFromSubsurfaceFluxEvaluator::Evaluate_(const State& S,
   } else {
     int ncells = result[0]->size("cell", false);
     for (int c = 0; c != ncells; ++c) {
-      AmanziMesh::Entity_ID_List cells;
-      subsurface->face_get_cells(
-        (*face_and_dirs_)[c].first, AmanziMesh::Parallel_type::OWNED, &cells);
+      auto cells = subsurface->getFaceCells(
+        (*face_and_dirs_)[c].first, AmanziMesh::Parallel_kind::OWNED);
       AMANZI_ASSERT(cells.size() == 1);
 
       res_v[0][c] = flux[0][(*face_and_dirs_)[c].first] * (*face_and_dirs_)[c].second;

diff --git a/src/constitutive_relations/surface_subsurface_fluxes/surface_top_cells_evaluator.cc b/src/constitutive_relations/surface_subsurface_fluxes/surface_top_cells_evaluator.cc
@@ -49,14 +49,13 @@ SurfaceTopCellsEvaluator::Evaluate_(const State& S, const std::vector<CompositeV
 
 
   int ncells_surf =
-    result[0]->Mesh()->num_entities(AmanziMesh::CELL, AmanziMesh::Parallel_type::OWNED);
+    result[0]->Mesh()->getNumEntities(AmanziMesh::Entity_kind::CELL, AmanziMesh::Parallel_kind::OWNED);
   for (unsigned int c = 0; c != ncells_surf; ++c) {
     // get the face on the subsurface mesh
-    AmanziMesh::Entity_ID f = result[0]->Mesh()->entity_get_parent(AmanziMesh::CELL, c);
+    AmanziMesh::Entity_ID f = result[0]->Mesh()->getEntityParent(AmanziMesh::Entity_kind::CELL, c);
 
     // get the cell interior to the face
-    AmanziMesh::Entity_ID_List cells;
-    sub_vector->Mesh()->face_get_cells(f, AmanziMesh::Parallel_type::ALL, &cells);
+    auto cells = sub_vector->Mesh()->getFaceCells(f, AmanziMesh::Parallel_kind::ALL);
     AMANZI_ASSERT(cells.size() == 1);
 
     result_cells[0][c] = sub_vector_cells[0][cells[0]];
@@ -70,7 +69,7 @@ SurfaceTopCellsEvaluator::EnsureCompatibility_ToDeps_(State& S)
   auto domain_name = Keys::getDomain(my_keys_.front().first);
 
   CompositeVectorSpace fac;
-  fac.SetMesh(S.GetMesh(domain_name)->parent())->AddComponent("cell", AmanziMesh::CELL, 1);
+  fac.SetMesh(S.GetMesh(domain_name)->getParentMesh())->AddComponent("cell", AmanziMesh::Entity_kind::CELL, 1);
   EvaluatorSecondaryMonotypeCV::EnsureCompatibility_ToDeps_(S, fac);
 }
 

diff --git a/src/constitutive_relations/surface_subsurface_fluxes/top_cells_surface_evaluator.cc b/src/constitutive_relations/surface_subsurface_fluxes/top_cells_surface_evaluator.cc
@@ -48,14 +48,13 @@ TopCellsSurfaceEvaluator::Evaluate_(const State& S, const std::vector<CompositeV
   Epetra_MultiVector& result_cells = *result[0]->ViewComponent("cell", false);
 
   int ncells_surf =
-    surf_vector->Mesh()->num_entities(AmanziMesh::CELL, AmanziMesh::Parallel_type::OWNED);
+    surf_vector->Mesh()->getNumEntities(AmanziMesh::Entity_kind::CELL, AmanziMesh::Parallel_kind::OWNED);
   for (unsigned int c = 0; c != ncells_surf; ++c) {
     // get the face on the subsurface mesh
-    AmanziMesh::Entity_ID f = surf_vector->Mesh()->entity_get_parent(AmanziMesh::CELL, c);
+    AmanziMesh::Entity_ID f = surf_vector->Mesh()->getEntityParent(AmanziMesh::Entity_kind::CELL, c);
 
     // get the cell interior to the face
-    AmanziMesh::Entity_ID_List cells;
-    result[0]->Mesh()->face_get_cells(f, AmanziMesh::Parallel_type::ALL, &cells);
+    auto cells = result[0]->Mesh()->getFaceCells(f, AmanziMesh::Parallel_kind::ALL);
     AMANZI_ASSERT(cells.size() == 1);
 
     result_cells[0][cells[0]] = surf_vector_cells[0][c];
@@ -68,7 +67,7 @@ void
 TopCellsSurfaceEvaluator::EnsureCompatibility_ToDeps_(State& S)
 {
   CompositeVectorSpace fac;
-  fac.SetMesh(S.GetMesh(domain_surf_))->AddComponent("cell", AmanziMesh::CELL, 1);
+  fac.SetMesh(S.GetMesh(domain_surf_))->AddComponent("cell", AmanziMesh::Entity_kind::CELL, 1);
   EvaluatorSecondaryMonotypeCV::EnsureCompatibility_ToDeps_(S, fac);
 }
 

diff --git a/src/constitutive_relations/surface_subsurface_fluxes/volumetric_darcy_flux_evaluator.cc b/src/constitutive_relations/surface_subsurface_fluxes/volumetric_darcy_flux_evaluator.cc
@@ -64,10 +64,9 @@ Volumetric_FluxEvaluator::Evaluate_(const State& S, const std::vector<CompositeV
   Epetra_MultiVector& res_v = *result[0]->ViewComponent("face", false);
 
   const auto& mesh = *result[0]->Mesh();
-  int nfaces_owned = mesh.num_entities(AmanziMesh::FACE, AmanziMesh::Parallel_type::OWNED);
-  AmanziMesh::Entity_ID_List cells;
+  int nfaces_owned = mesh.getNumEntities(AmanziMesh::Entity_kind::FACE, AmanziMesh::Parallel_kind::OWNED);
   for (int f = 0; f < nfaces_owned; f++) {
-    mesh.face_get_cells(f, AmanziMesh::Parallel_type::ALL, &cells);
+    auto cells = mesh.getFaceCells(f, AmanziMesh::Parallel_kind::ALL);
     double n_liq = 0.;
     for (int c = 0; c < cells.size(); c++) n_liq += molar_density[0][c];
     n_liq /= cells.size();

diff --git a/src/executables/CMakeLists.txt b/src/executables/CMakeLists.txt
@@ -88,7 +88,6 @@ set(amanzi_link_libs
   dbg       
   data_structures
   mesh
-  mesh_audit
   mesh_functions
   functions
   geometry