Add vertical mixing tendencies

components/omega/configs/Default.yml

@@ -66,6 +66,8 @@ Omega:
     VelocityVertAdvTendencyEnable: true
     TracerVertAdvTendencyEnable: true
     PressureGradTendencyEnable: true
+    VelVertMixTendencyEnable: true
+    TracerVertMixTendencyEnable: true
   ManufacturedSolution:
     WavelengthX: 5.0e6
     WavelengthY: 4.33013e6

components/omega/src/ocn/OceanInit.cpp

@@ -31,6 +31,7 @@
 #include "Tracers.h"
 #include "VertAdv.h"
 #include "VertCoord.h"
+#include "VertMix.h"
 
 #include "mpi.h"
 
@@ -200,6 +201,7 @@ static int initOmegaModulesImpl(MPI_Comm Comm) {
    AuxiliaryState::init();
    Eos::init();
    PressureGrad::init();
+   VertMix::init();
    Tendencies::init();
 
    // Validate SurfaceTracerRestoring configuration

components/omega/src/ocn/OceanState.h

@@ -48,11 +48,6 @@ class OceanState {
    OceanState(const OceanState &) = delete;
    OceanState(OceanState &&)      = delete;
 
-   // Current time index
-   // this index is circular so that it returns to index 0
-   // if it is over max index
-   I4 CurTimeIndex; ///< Time dimension array index for current level
-
    /// Get the current time level index associated with a time level
    I4 getTimeIndex(const I4 TimeLevel) const;
 
@@ -63,6 +58,11 @@ class OceanState {
 
    std::string Name;
 
+   // Current time index
+   // this index is circular so that it returns to index 0
+   // if it is over max index
+   I4 CurTimeIndex; ///< Time dimension array index for current level
+
    // Sizes and global IDs
    // Note that all sizes are actual counts (1-based) so that loop extents
    // should always use the 0:NCellsXX-1 form.

components/omega/src/ocn/Tendencies.cpp

@@ -20,6 +20,7 @@
 #include "TimeStepper.h"
 #include "Tracers.h"
 #include "VertAdv.h"
+#include "VertMix.h"
 #include <string>
 
 namespace OMEGA {
@@ -39,6 +40,7 @@ void Tendencies::init() {
    TimeStepper *DefTimeStepper = TimeStepper::getDefault();
    Eos *DefEos                 = Eos::getInstance();
    PressureGrad *DefPGrad      = PressureGrad::getDefault();
+   VertMix *DefVertMix         = VertMix::getInstance();
 
    I4 NTracers = Tracers::getNumTracers();
 
@@ -78,9 +80,10 @@ void Tendencies::init() {
    TimeInterval TimeStep = DefTimeStepper->getTimeStep();
 
    // Ceate default tendencies
-   Tendencies::DefaultTendencies = create(
-       "Default", DefHorzMesh, DefVertCoord, DefVertAdv, DefPGrad, DefEos,
-       NTracers, TimeStep, &TendConfig, CustomThickTend, CustomVelTend);
+   Tendencies::DefaultTendencies =
+       create("Default", DefHorzMesh, DefVertCoord, DefVertAdv, DefPGrad,
+              DefEos, DefVertMix, NTracers, TimeStep, &TendConfig,
+              CustomThickTend, CustomVelTend);
 
    DefaultTendencies->readConfig(OmegaConfig);
 
@@ -317,6 +320,30 @@ void Tendencies::readConfig(Config *OmegaConfig ///< [in] Omega config
                HostArray1DI4(TracerIdsToRestoreVec.data(),
                              TracerIdsToRestoreVec.size()));
    }
+
+   // Validate VertMix tendency
+   Err += TendConfig.get("VelVertMixTendencyEnable",
+                         this->VMix->VelVertMixSetup.Enabled);
+   CHECK_ERROR_ABORT(
+       Err, "Tendencies: VelVertMixTendencyEnable not found in TendConfig");
+
+   Err += TendConfig.get("TracerVertMixTendencyEnable",
+                         this->VMix->TracerVertMixSetup.Enabled);
+   CHECK_ERROR_ABORT(
+       Err, "Tendencies: TracerVertMixTendencyEnable not found in TendConfig");
+
+   if (this->VMix->VelVertMixSetup.Enabled ||
+       this->VMix->TracerVertMixSetup.Enabled) {
+
+      if (!this->EqState) {
+         ABORT_ERROR("Tendencies: Eos must be initialized when"
+                     "vertical mixing tendencies are enabled");
+      }
+      if (!this->VMix) {
+         ABORT_ERROR("Tendencies: VertMix must be initialized when"
+                     "vertical mixing tendencies are enabled");
+      }
+   }
 }
 
 //------------------------------------------------------------------------------
@@ -380,6 +407,7 @@ Tendencies::Tendencies(const std::string &Name_, ///< [in] Name for tendencies
                        VertAdv *VAdv,            ///< [in] Vertical advection
                        PressureGrad *PGrad,      ///< [in] Pressure gradient
                        Eos *EqState,             ///< [in] Equation of state
+                       VertMix *VMix,            ///< [in] Vertical mixing
                        int NTracersIn,           ///< [in] Number of tracers
                        TimeInterval TimeStepIn,  ///< [in] Time step
                        Config *Options,          ///< [in] Configuration options
@@ -393,7 +421,8 @@ Tendencies::Tendencies(const std::string &Name_, ///< [in] Name for tendencies
       TracerDiffusion(Mesh, VCoord), TracerHyperDiff(Mesh, VCoord),
       TracerHorzAdv(Mesh, VCoord), SurfaceTracerRestoring(Mesh),
       CustomThicknessTend(InCustomThicknessTend),
-      CustomVelocityTend(InCustomVelocityTend), EqState(EqState), PGrad(PGrad) {
+      CustomVelocityTend(InCustomVelocityTend), EqState(EqState), PGrad(PGrad),
+      VMix(VMix) {
 
    // Tendency arrays
    PseudoThicknessTend = Array2DReal("PseudoThicknessTend", Mesh->NCellsSize,
@@ -418,10 +447,11 @@ Tendencies::Tendencies(const std::string &Name_, ///< [in] Name for tendencies
                        VertAdv *VAdv,            ///< [in] Vertical advection
                        PressureGrad *PGrad,      ///< [in] Pressure gradient
                        Eos *EqState,             ///< [in] Equation of state
+                       VertMix *VMix,            ///< [in] Vertical mixing
                        int NTracersIn,           ///< [in] Number of tracers
                        TimeInterval TimeStepIn,  ///< [in] Time step
                        Config *Options)          ///< [in] Configuration options
-    : Tendencies(Name_, Mesh, VCoord, VAdv, PGrad, EqState, NTracersIn,
+    : Tendencies(Name_, Mesh, VCoord, VAdv, PGrad, EqState, VMix, NTracersIn,
                  TimeStepIn, Options, CustomTendencyType{},
                  CustomTendencyType{}) {}
 

components/omega/src/ocn/Tendencies.h

@@ -41,6 +41,7 @@
 #include "TimeMgr.h"
 #include "VertAdv.h"
 #include "VertCoord.h"
+#include "VertMix.h"
 
 #include <functional>
 #include <memory>
@@ -169,6 +170,7 @@ class Tendencies {
               VertAdv *VAdv,           ///< [in] Vertical advection
               PressureGrad *PGrad,     ///< [in] Pressure gradient
               Eos *EqState,            ///< [in] Equation of state
+              VertMix *VMix,           ///< [in] Vertical mixing
               int NTracersIn,          ///< [in] Number of tracers
               TimeInterval TimeStep,   ///< [in] Time step
               Config *Options,         ///< [in] Configuration options
@@ -181,6 +183,7 @@ class Tendencies {
               VertAdv *VAdv,           ///< [in] Vertical advection
               PressureGrad *PGrad,     ///< [in] Pressure gradient
               Eos *EqState,            ///< [in] Equation of state
+              VertMix *VMix,           ///< [in] Vertical mixing
               int NTracersIn,          ///< [in] Number of tracers
               TimeInterval TimeStep,   ///< [in] Time step
               Config *Options          ///< [in] Configuration options
@@ -199,6 +202,7 @@ class Tendencies {
    CustomTendencyType CustomVelocityTend;
    Eos *EqState;          ///< Pointer to equation of state
    PressureGrad *PGrad;   ///< Pointer to pressure gradient
+   VertMix *VMix;         ///< Pointer to vertical mixing
    I4 NTracers;           ///< Number of tracers
    TimeInterval TimeStep; ///< Time step