Add vertical advection

components/omega/configs/Default.yml

@@ -23,8 +23,11 @@ Omega:
   State:
     NTimeLevels: 2
   Advection:
+    Coef3rdOrder: 0.25
     FluxThicknessType: Center
     FluxTracerType: Center
+    VerticalTracerFluxLimiterEnabled: true
+    VerticalTracerFluxOrder: 3
   WindStress:
     InterpType: Isotropic
   VertCoord:
@@ -50,6 +53,9 @@ Omega:
     EddyDiff4: 0.0
     UseCustomTendency: false
     ManufacturedSolutionTendency: false
+    ThicknessVertAdvTendencyEnable: true
+    VelocityVertAdvTendencyEnable: true
+    TracerVertAdvTendencyEnable: true
   Tracers:
     Base: [Temperature, Salinity]
     Debug: [Debug1, Debug2, Debug3]

components/omega/src/infra/OmegaKokkos.h

@@ -78,6 +78,8 @@ using ScratchMemSpace = ExecSpace::scratch_memory_space;
 using Kokkos::MemoryUnmanaged;
 using Kokkos::PerTeam;
 using Kokkos::TeamThreadRange;
+using RealScratchArray =
+    Kokkos::View<Real *, ScratchMemSpace, Kokkos::MemoryUnmanaged>;
 
 /// team_size for hierarchical parallelism
 #ifdef OMEGA_TARGET_DEVICE
@@ -321,7 +323,8 @@ KOKKOS_INLINE_FUNCTION void teamBarrier(const TeamMember &Team) {
 // parallelForOuter: with label
 template <int N, class F>
 inline void parallelForOuter(const std::string &Label,
-                             const int (&UpperBounds)[N], F &&Functor) {
+                             const int (&UpperBounds)[N], F &&Functor,
+                             int ScratchValsPerTeam = 0) {
 
    auto LinFunctor = LinearIdxWrapper{std::forward<F>(Functor), UpperBounds};
    int LinBound    = 1;
@@ -330,6 +333,12 @@ inline void parallelForOuter(const std::string &Label,
    }
 
    auto Policy = TeamPolicy(LinBound, OMEGA_TEAMSIZE);
+
+   if (ScratchValsPerTeam > 0) {
+      Policy.set_scratch_size(
+          0, Kokkos::PerTeam(ScratchValsPerTeam * sizeof(Real)));
+   }
+
    Kokkos::parallel_for(
        Label, Policy, KOKKOS_LAMBDA(const TeamMember &Team) {
           const int TeamId = Team.league_rank();
@@ -339,8 +348,10 @@ inline void parallelForOuter(const std::string &Label,
 
 // parallelForOuter: without label
 template <int N, class F>
-inline void parallelForOuter(const int (&UpperBounds)[N], F &&Functor) {
-   parallelForOuter("", UpperBounds, std::forward<F>(Functor));
+inline void parallelForOuter(const int (&UpperBounds)[N], F &&Functor,
+                             int ScratchValsPerTeam = 0) {
+   parallelForOuter("", UpperBounds, std::forward<F>(Functor),
+                    ScratchValsPerTeam);
 }
 
 // parallelForInner

components/omega/src/ocn/AuxiliaryState.cpp

@@ -196,8 +196,9 @@ void AuxiliaryState::computeMomAux(const OceanState *State, int ThickTimeLevel,
 
           parallelForInner(
               Team, KRange, INNER_LAMBDA(int KChunk) {
-                 LocLayerThicknessAux.computeVarsOnCells(ICell, KChunk,
-                                                         LayerThickCell);
+                 LocLayerThicknessAux.computeVarsOnCells(
+                     ICell, KChunk, LayerThickCell, NormalVelEdge, 0._Real);
+                 // TODO: make timestep available to this call
               });
        });
    Pacer::stop("AuxState:cellAuxState3", 2);

components/omega/src/ocn/CustomTendencyTerms.cpp

@@ -10,6 +10,7 @@
 #include "Config.h"
 #include "GlobalConstants.h"
 #include "TimeStepper.h"
+#include "VertCoord.h"
 
 namespace OMEGA {
 
@@ -76,8 +77,8 @@ void ManufacturedSolution::init() {
    /// This test case assumes that the restingThickness is horizontally uniform
    /// and that only one vertical level is used so only one set of indices is
    /// used here.
-   HorzMesh *DefHorzMesh = HorzMesh::getDefault();
-   R8 H0                 = DefHorzMesh->BottomDepthH(0);
+   VertCoord *DefVCoord = VertCoord::getDefault();
+   R8 H0                = DefVCoord->BottomDepthH(0);
 
    // Define and compute common constants
    R8 Kx      = TwoPi / WavelengthX;                      // Wave in X-dir

components/omega/src/ocn/HorzMesh.cpp

@@ -111,9 +111,6 @@ HorzMesh::HorzMesh(const std::string &Name, //< [in] Name for new mesh
    // Read x/y/z and lon/lat coordinates for cells, edges, and vertices
    readCoordinates();
 
-   // Read the cell-centered bottom depth
-   readBottomDepth();
-
    // Read the mesh areas, lengths, and angles
    readMeasurements();
 
@@ -439,12 +436,6 @@ void HorzMesh::readCoordinates() {
 
 } // end readCoordinates
 
-//------------------------------------------------------------------------------
-// Read the cell-centered bottom depth
-void HorzMesh::readBottomDepth() {
-   readCellArray(BottomDepthH, "bottomDepth");
-} // end readDepth
-
 //------------------------------------------------------------------------------
 // Read the mesh areas (cell, triangle, and kite),
 // lengths (between centers and vertices), and edge angles
@@ -600,7 +591,6 @@ void HorzMesh::copyToDevice() {
    AngleEdge         = createDeviceMirrorCopy(AngleEdgeH);
    WeightsOnEdge     = createDeviceMirrorCopy(WeightsOnEdgeH);
    FVertex           = createDeviceMirrorCopy(FVertexH);
-   BottomDepth       = createDeviceMirrorCopy(BottomDepthH);
    FEdge             = createDeviceMirrorCopy(FEdgeH);
    XCell             = createDeviceMirrorCopy(XCellH);
    YCell             = createDeviceMirrorCopy(YCellH);

components/omega/src/ocn/HorzMesh.h

@@ -42,16 +42,12 @@ class HorzMesh {
 
    void readCoordinates();
 
-   void readBottomDepth();
-
    void readMeasurements();
 
    void readWeights();
 
    void readCoriolis();
 
-   // void computeEdgeSign();
-
    void copyToDevice();
 
    // int computeMesh();
@@ -232,11 +228,6 @@ class HorzMesh {
    Array1DReal FVertex;      ///< Coriolis parameter at vertices (radians s^-1)
    HostArray1DReal FVertexH; ///< Coriolis parameter at vertices (radians s^-1)
 
-   // Depth
-
-   Array1DReal BottomDepth;      ///< Depth of the bottom of the ocean (m)
-   HostArray1DReal BottomDepthH; ///< Depth of the bottom of the ocean (m)
-
    // Edge sign
 
    Array2DReal EdgeSignOnCell;      ///< Sign of vector connecting cells