Rename `LayerThickness` --> `PseudoThickness` #327

xylar · 2025-12-19T13:08:00Z

Do we also need to rename FluxLayerThickEdge and MeanLayerThickEdge?

xylar · 2025-12-19T12:52:17Z

Here and in the user's guide, there's a reference to LayerThicknessPStar, now PseudoThicknessPStar, but I didn't see this in the code itself.

xylar · 2025-12-19T12:51:29Z

This whole document needs some updating but I don't want to distract from the purpose of this PR to do it.

xylar · 2025-12-19T13:05:19Z

Suggested change

The `OceanState` class provides a container for the non-tracer prognostic variables in Omega, namely `normalVelocity` and `PseudoThickness`.

The `OceanState` class provides a container for the non-tracer prognostic variables in Omega, namely `NormalVelocity` and `PseudoThickness`.

xylar · 2025-12-19T12:53:07Z

Here and in the developer's guide, there's a reference to LayerThicknessPStar, now PseudoThicknessPStar, but I didn't see this in the code itself.

-Original file line number
+Diff line change
@@ Expand Up @@
     | ----- | ------------------- | ------- |
     | KineticAuxVars | KineticEnergyCell ||
     || VelocityDiv ||
-    | LayerThicknessAuxVars | FluxLayerThickEdge | Center or Upwind|
+    | PseudoThicknessAuxVars | FluxLayerThickEdge | Center or Upwind|
     || MeanLayerThickEdge ||
     | VorticityAuxVars |  RelVortVertex ||
     ||  NormRelVortVertex ||
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
                        const int NTimeLevels_   ///< [in] Number of time levels
     );
     ```
-    allocates the `NormalVelocity` and `LayerThickness` arrays for a given number of time levels.
+    allocates the `NormalVelocity` and `PseudoThickness` arrays for a given number of time levels.
     The current time level is then registered with the IO infrastructure.
     After initialization, the default state object can be retrieved via:
@@ Expand Down Expand Up / @@ -60,14 +60,14 @@ to the current time level. @@
     The arrays associated with a given time level can be accessed with the functions:
     ```c++
     Array2DReal LayerThick;
-    Err = State->getLayerThickness(LayerThick, TimeLevel);
+    Err = State->getPseudoThickness(LayerThick, TimeLevel);
     Array2DReal NormVel;
     Err = State->getNormalVelocity(NormVel, TimeLevel);
     ```
     for the device arrays and
     ```c++
     HostArray2DReal LayerThickH;
-    Err = State->getLayerThicknessH(LayerThickH, TimeLevel);
+    Err = State->getPseudoThicknessH(LayerThickH, TimeLevel);
     HostArray2DReal NormVelH;
     Err = State->getNormalVelocityH(NormVelH, TimeLevel);
     ```
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
     meshes. At the moment, mesh files need to be copied or linked to specifically
     named files under the `test` directory. Appropriate mesh files can be
     downloaded from:
-    - [Ocean Mesh](https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/mpas-o/oQU240/ocean.QU.240km.151209.nc)
-    - [Global Mesh](https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/polaris_cache/global_convergence/icos/cosine_bell/Icos480/init/initial_state.230220.nc)
-    - [Planar Mesh](https://gist.github.com/mwarusz/f8caf260398dbe140d2102ec46a41268/raw/e3c29afbadc835797604369114321d93fd69886d/PlanarPeriodic48x48.nc)
+    - [Ocean Mesh](https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/ocean.QU.240km.omega_vars.251219.nc)
+    - [Global Mesh](https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/cosine_bell_icos480.omega_vars.250219.nc)
+    - [Planar Mesh](https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/PlanarPeriodic48x48.omega_vars.251219.nc)
     ```sh
-    wget -O ocean_test_mesh.nc https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/mpas-o/oQU240/ocean.QU.240km.151209.nc
-    wget -O global_test_mesh.nc https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/polaris_cache/global_convergence/icos/cosine_bell/Icos480/init/initial_state.230220.nc
-    wget -O planar_test_mesh.nc https://gist.github.com/mwarusz/f8caf260398dbe140d2102ec46a41268/raw/e3c29afbadc835797604369114321d93fd69886d/PlanarPeriodic48x48.nc
     cd test
-    ln -sf  ../ocean_test_mesh.nc OmegaMesh.nc
-    ln -sf  ../global_test_mesh.nc OmegaSphereMesh.nc
-    ln -sf  ../planar_test_mesh.nc OmegaPlanarMesh.nc
+    wget -O OmegaMesh.nc https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/ocean.QU.240km.omega_vars.251219.nc
+    wget -O OmegaSphereMesh.nc https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/cosine_bell_icos480.omega_vars.250219.nc
+    wget -O OmegaPlanarMesh.nc https://web.lcrc.anl.gov/public/e3sm/polaris/ocean/omega_ctest/PlanarPeriodic48x48.omega_vars.251219.nc
     cd ..
     ```
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -321,7 +321,7 @@ Omega: @@
           Filename: init.nc
           Contents:
           - NormalVelocity
-          - LayerThickness
+          - PseudoThickness
         RestartRead: {}
         History:
           Filename: output.nc
@@ Expand All / @@ -333,7 +333,7 @@ Omega: @@
           FileFreqUnits: years
           Contents:
           - NormalVelocity
-          - LayerThickness
+          - PseudoThickness
           - SshCell
     ```
     For more details on updating either the map or the YAML files for individual
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
     | ZInterface | Real | NCellsSize, NVertLayersP1|
     | ZMid | Real | NCellsSize, NVertLayers |
     | GeopotentialMid | Real | NCellsSize, NVertLayers |
-    | LayerThicknessPStar | Real | NCellsSize, NVertLayers|
+    | PseudoThicknessPStar | Real | NCellsSize, NVertLayers|
     | MinLayerCell | Integer | NCellsSize |
     | MaxLayerCell | Integer | NCellsSize |
     | MinLayerEdgeTop | Integer| NEdgesSize |
@@ Expand All @@
     | MinLayerVertexBot | Integer | NVerticesSize |
     | MaxLayerVertexBot | Integer | NVerticesSize |
     | VertCoordMovementWeights | Real | NCellsSize, NVertLayers |
-    | RefLayerThickness | Real | NCellsSize, NVertLayers |
+    | RefPseudoThickness | Real | NCellsSize, NVertLayers |
     | BottomDepth | Real | NCellsSize |
     ### Removal
@@ Expand Down Expand Up / @@ -113,7 +113,7 @@ Kokkos::parallel_reduce( @@
         Kokkos::TeamThreadRange(Member, KMin, KMax + 1),
         [=](const int K, Real &LocalWh) {
            LocalWh += VertCoordMovementWeights(ICell, K) *
-                      RefLayerThickness(ICell, K);
+                      RefPseudoThickness(ICell, K);
         },
         SumWh);
     ```
@@ Expand Down @@

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Rename `LayerThickness` --> `PseudoThickness` #327

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xylar Dec 19, 2025

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xylar Dec 19, 2025 •

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-Original file line number
+Diff line change
@@ Expand Up @@
     | ZInterface | z height of layer interfaces | m |
     | ZMid | z height of layer midpoint | m |
     | GeopotentialMid | geopotential at layer mid points | m$^2$/s$^2$|
-    | LayerThicknessPStar | desired layer thickness based on total perturbation from the reference thickness | - |
+    | PseudoThicknessPStar | desired layer thickness based on total perturbation from the reference thickness | - |
     | MinLayerCell | first active layer for cell | - |
     | MaxLayerCell | last active layer for cell | - |
     | MinLayerEdgeTop | min of the first active layers for cells on edge | - |
@@ Expand All @@
     | MinLayerVertexBot | max of the first active layer for cells on vertex | - |
     | MaxLayerVertexBot | max of the last active layer for cells on vertex | - |
     | VertCoordMovementWeights | weights to specify how total column thickness changes are distributed across layers | - |
-    | RefLayerThickness | reference layer thickness used to distribute total column thickness changes | m |
+    | RefPseudoThickness | reference layer thickness used to distribute total column thickness changes | m |
     | BottomDepth | positive down distance from the reference geoid to the bottom | m |
     ### Configuration options
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
                                    int NVertLayers, int NTracers)
         : Mesh(Mesh), VCoord(VCoord), MeshHalo(MeshHalo), Name(stripDefault(Name)),
           KineticAux(stripDefault(Name), Mesh, NVertLayers),
-          LayerThicknessAux(stripDefault(Name), Mesh, NVertLayers),
+          PseudoThicknessAux(stripDefault(Name), Mesh, NVertLayers),
           VorticityAux(stripDefault(Name), Mesh, NVertLayers),
           VelocityDel2Aux(stripDefault(Name), Mesh, VCoord, NVertLayers),
           WindForcingAux(stripDefault(Name), Mesh),
@@ Expand All @@
        auto AuxGroup = FieldGroup::create(GroupName);
        KineticAux.registerFields(GroupName, AuxMeshName);
-       LayerThicknessAux.registerFields(GroupName, AuxMeshName);
+       PseudoThicknessAux.registerFields(GroupName, AuxMeshName);
        VorticityAux.registerFields(GroupName, AuxMeshName);
        VelocityDel2Aux.registerFields(GroupName, AuxMeshName);
        WindForcingAux.registerFields(GroupName, AuxMeshName);
@@ Expand All @@
     // state field group.
     AuxiliaryState::~AuxiliaryState() {
        KineticAux.unregisterFields();
-       LayerThicknessAux.unregisterFields();
+       PseudoThicknessAux.unregisterFields();
        VorticityAux.unregisterFields();
        VelocityDel2Aux.unregisterFields();
        WindForcingAux.unregisterFields();
@@ Expand All @@
                                        int VelTimeLevel) const {
        Array2DReal LayerThickCell;
        Array2DReal NormalVelEdge;
-       State->getLayerThickness(LayerThickCell, ThickTimeLevel);
+       State->getPseudoThickness(LayerThickCell, ThickTimeLevel);
        State->getNormalVelocity(NormalVelEdge, VelTimeLevel);
        const int NVertLayers = LayerThickCell.extent_int(1);
        const int NChunks     = NVertLayers / VecLength;
        OMEGA_SCOPE(LocKineticAux, KineticAux);
-       OMEGA_SCOPE(LocLayerThicknessAux, LayerThicknessAux);
+       OMEGA_SCOPE(LocPseudoThicknessAux, PseudoThicknessAux);
        OMEGA_SCOPE(LocVorticityAux, VorticityAux);
        OMEGA_SCOPE(LocVelocityDel2Aux, VelocityDel2Aux);
        OMEGA_SCOPE(LocWindForcingAux, WindForcingAux);
@@ Expand Down Expand Up @@
            "edgeAuxState2", {Mesh->NEdgesAll, NChunks},
            KOKKOS_LAMBDA(int IEdge, int KChunk) {
               LocVorticityAux.computeVarsOnEdge(IEdge, KChunk);
-              LocLayerThicknessAux.computeVarsOnEdge(IEdge, KChunk, LayerThickCell,
-                                                     NormalVelEdge);
+              LocPseudoThicknessAux.computeVarsOnEdge(IEdge, KChunk, LayerThickCell,
+                                                      NormalVelEdge);
               LocVelocityDel2Aux.computeVarsOnEdge(IEdge, KChunk, VelocityDivCell,
                                                    RelVortVertex);
            });
@@ Expand All @@
        parallelFor(
            "cellAuxState3", {Mesh->NCellsAll, NChunks},
            KOKKOS_LAMBDA(int ICell, int KChunk) {
-              LocLayerThicknessAux.computeVarsOnCells(ICell, KChunk,
-                                                      LayerThickCell);
+              LocPseudoThicknessAux.computeVarsOnCells(ICell, KChunk,
+                                                       LayerThickCell);
            });
        Pacer::stop("AuxState:cellAuxState3", 2);
@@ Expand All / @@ -149,7 +149,7 @@ void AuxiliaryState::computeAll(const OceanState *State, @@
                                     int ThickTimeLevel, int VelTimeLevel) const {
        Array2DReal LayerThickCell;
        Array2DReal NormalVelEdge;
-       State->getLayerThickness(LayerThickCell, ThickTimeLevel);
+       State->getPseudoThickness(LayerThickCell, ThickTimeLevel);
        State->getNormalVelocity(NormalVelEdge, VelTimeLevel);
        const int NVertLayers = LayerThickCell.extent_int(1);
@@ Expand All / @@ -171,7 +171,7 @@ void AuxiliaryState::computeAll(const OceanState *State, @@
            });
        Pacer::stop("AuxState:edgeAuxState4", 2);
-       const auto &MeanLayerThickEdge = LayerThicknessAux.MeanLayerThickEdge;
+       const auto &MeanLayerThickEdge = PseudoThicknessAux.MeanLayerThickEdge;
        Pacer::start("AuxState:cellAuxState4", 2);
        parallelFor(
@@ Expand Down Expand Up @@
            Err, "AuxiliaryState: FluxThicknessType not found in AdvectConfig");
        if (FluxThickTypeStr == "Center") {
-          this->LayerThicknessAux.FluxThickEdgeChoice = FluxThickEdgeOption::Center;
+          this->PseudoThicknessAux.FluxThickEdgeChoice =
+              FluxThickEdgeOption::Center;
        } else if (FluxThickTypeStr == "Upwind") {
-          this->LayerThicknessAux.FluxThickEdgeChoice = FluxThickEdgeOption::Upwind;
+          this->PseudoThicknessAux.FluxThickEdgeChoice =
+              FluxThickEdgeOption::Upwind;
        } else {
           ABORT_ERROR("AuxiliaryState: Unknown FluxThicknessType requested");
        }
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ @@
     #include "Tracers.h"
     #include "VertCoord.h"
     #include "auxiliaryVars/KineticAuxVars.h"
-    #include "auxiliaryVars/LayerThicknessAuxVars.h"
+    #include "auxiliaryVars/PseudoThicknessAuxVars.h"
     #include "auxiliaryVars/TracerAuxVars.h"
     #include "auxiliaryVars/VelocityDel2AuxVars.h"
     #include "auxiliaryVars/VorticityAuxVars.h"
@@ Expand All / @@ -35,7 +35,7 @@ class AuxiliaryState { @@
        // Auxiliary variables
        KineticAuxVars KineticAux;
-       LayerThicknessAuxVars LayerThicknessAux;
+       PseudoThicknessAuxVars PseudoThicknessAux;
        TracerAuxVars TracerAux;
        VorticityAuxVars VorticityAux;
        VelocityDel2AuxVars VelocityDel2Aux;
@@ Expand Down @@

Rename LayerThickness --> PseudoThickness #327

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Rename `LayerThickness` --> `PseudoThickness` #327

Rename `LayerThickness` --> `PseudoThickness` #327

xylar Dec 19, 2025 •

edited

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