Fix turbulence step 1 (#94)

This PR merges turbulence to canoe but turbulence does not work yet.

cmake/parameters.cmake

@@ -19,6 +19,8 @@ set_if_empty(NCHEMISTRY 0)
 
 set_if_empty(NTRACER 0)
 
+set_if_empty(NTURBULENCE 0)
+
 set_if_empty(NSTATIC 0)
 
 # set_if_empty(TASKLIST ImplicitHydroTasks)

cmake/robert.cmake

@@ -12,3 +12,4 @@ set_if_empty(NUMBER_GHOST_CELLS 3)
 # canoe configure
 set(MPI ON)
 set(PNETCDF ON)
+set(TASKLIST ImplicitHydroTasks)

configure.hpp.in

@@ -6,6 +6,7 @@ enum {
   NCLOUD = @NCLOUD@,
   NCHEMISTRY = @NCHEMISTRY@,
   NTRACER = @NTRACER@,
+  NTURBULENCE = @NTURBULENCE@,
   NSTATIC = @NSTATIC@
 };
 

doc/README-parallel-debug.md

@@ -0,0 +1 @@
+mpirun -n 2 xterm -e gdb robert.debug

src/air_parcel.hpp

@@ -15,7 +15,9 @@
 //  \brief a collection of all physical data in a computational cell
 class AirParcel {
  public:
-  enum { Size = NHYDRO + NCLOUD + NCHEMISTRY + NTRACER + NSTATIC };
+  enum {
+    Size = NHYDRO + NCLOUD + NCHEMISTRY + NTRACER + NTURBULENCE + NSTATIC
+  };
 
   enum class Type { MassFrac = 0, MassConc = 1, MoleFrac = 2, MoleConc = 3 };
 
@@ -24,16 +26,19 @@ class AirParcel {
 
   //! data pointers
   //! hydro data
-  Real *w;
+  Real *const w;
 
   //! cloud data
-  Real *c;
+  Real *const c;
 
   //! chemistry data
-  Real *q;
+  Real *const q;
 
   //! tracer data
-  Real *x;
+  Real *const x;
+
+  //! turbulence data
+  Real *const t;
 
   //! static data
   Real const *s;
@@ -42,26 +47,29 @@ class AirParcel {
   Real const *d;
 
   // constructor
-  explicit AirParcel(Type type = Type::MoleFrac) : mytype_(type) {
-    w = data_.data();
-    c = w + NHYDRO;
-    q = c + NCLOUD;
-    x = q + NCHEMISTRY;
-    s = x + NTRACER;
-    d = s + NSTATIC;
+  explicit AirParcel(Type type = Type::MoleFrac)
+      : mytype_(type),
+        w(data_.data()),
+        c(w + NHYDRO),
+        q(c + NCLOUD),
+        x(q + NCHEMISTRY),
+        t(x + NTRACER),
+        s(t + NTURBULENCE),
+        d(s + NSTATIC) {
     std::fill(data_.begin(), data_.end(), 0.0);
   }
 
   // copy constructor
-  AirParcel(AirParcel const &other) : mytype_(other.mytype_) {
-    data_ = other.data_;
-    w = data_.data();
-    c = w + NHYDRO;
-    q = c + NCLOUD;
-    x = q + NCHEMISTRY;
-    s = x + NTRACER;
-    d = s + NSTATIC;
-  }
+  AirParcel(AirParcel const &other)
+      : mytype_(other.mytype_),
+        data_(other.data_),
+        w(data_.data()),
+        c(w + NHYDRO),
+        q(c + NCLOUD),
+        x(q + NCHEMISTRY),
+        t(x + NTRACER),
+        s(x + NTURBULENCE),
+        d(s + NSTATIC) {}
 
   // Assignment operator
   AirParcel &operator=(const AirParcel &other) {

src/impl.cpp

@@ -24,6 +24,7 @@
 #include "snap/decomposition/decomposition.hpp"
 #include "snap/implicit/implicit_solver.hpp"
 #include "snap/thermodynamics/thermodynamics.hpp"
+#include "snap/turbulence/turbulence_model.hpp"
 
 // microphysics
 #include "microphysics/microphysics.hpp"
@@ -51,16 +52,28 @@ MeshBlock::Impl::Impl(MeshBlock *pmb, ParameterInput *pin) : pmy_block_(pmb) {
   ptracer = std::make_shared<Tracer>(pmb, pin);
 
   // turbulence
-  // pturb = std::make_shared<KEpsilonTurbulence>(pmb, pin);
+  if (pin->DoesParameterExist("hydro", "turbulence")) {
+    std::string turbulence_model = pin->GetString("hydro", "turbulence");
+    if (turbulence_model == "none") {
+      pturb = std::make_shared<TurbulenceModel>(pmb, pin);
+    } else if (turbulence_model == "kepsilon") {
+      pturb = std::make_shared<KEpsilonTurbulence>(pmb, pin);
+      if (NTURBULENCE < 2)
+        throw NotImplementedError(
+            "NTURBULENCE must be at least 2 for k-epsilon model");
+    } else {
+      throw NotImplementedError(turbulence_model);
+    }
+  }
 
   // radiation
   prad = std::make_shared<Radiation>(pmb, pin);
 
   // inversion queue
   fitq = Inversion::NewInversionQueue(pmb, pin);
 
-  // reference pressure
 #ifdef HYDROSTATIC
+  // reference pressure
   reference_pressure_ = pin->GetReal("mesh", "ReferencePressure");
 
   // pressure scale height

src/snap/turbulence/k_epsilon_turbulence.cpp

@@ -6,11 +6,9 @@
 
 // Athena++ headers
 #include <athena/athena.hpp>
-#include <athena/athena_arrays.hpp>
 #include <athena/coordinates/coordinates.hpp>
-#include <athena/eos/eos.hpp>  // reapply floors to face-centered reconstructed states
 #include <athena/hydro/hydro.hpp>
-#include <athena/reconstruct/reconstruction.hpp>
+#include <athena/mesh/mesh.hpp>
 
 // snap
 #include "turbulence_model.hpp"
@@ -22,6 +20,7 @@ KEpsilonTurbulence::KEpsilonTurbulence(MeshBlock *pmb, ParameterInput *pin)
   c2_ = pin->GetOrAddReal("turbulence", "kepsilon.c2", 1.92);
   sigk_ = pin->GetOrAddReal("turbulence", "kepsilon.sigk", 1.0);
   sige_ = pin->GetOrAddReal("turbulence", "kepsilon.sige", 1.3);
+
   // velocity scale, v ~ 1 m/s, tke ~ v^2 ~ 1 m^2/s^2
   Real tke0 = pin->GetOrAddReal("turbulence", "kepsilon.tke0", 1.);
 
@@ -43,23 +42,26 @@ KEpsilonTurbulence::KEpsilonTurbulence(MeshBlock *pmb, ParameterInput *pin)
   for (int k = kl; k <= ku; ++k)
     for (int j = jl; j <= ju; ++j)
       for (int i = il; i <= iu; ++i) {
-        r(1, k, j, i) = tke0;
+        w(1, k, j, i) = tke0;
         // eps ~ tke/T ~ v^2/(dx/v) ~ v^3/dx
         Real volume = pmb->pcoord->GetCellVolume(k, j, i);
         Real eps0 = pow(tke0, 1.5) / pow(volume, 1. / 3.);
-        r(0, k, j, i) = eps0;
+        w(0, k, j, i) = eps0;
       }
 }
 
-void KEpsilonTurbulence::Initialize(AthenaArray<Real> const &w) {
-  MeshBlock *pmb = pmy_block;
+void KEpsilonTurbulence::Initialize() {
+  auto pmb = pmy_block;
+  auto phydro = pmb->phydro;
+
   for (int k = pmb->ks; k <= pmb->ke; ++k)
     for (int j = pmb->js; j <= pmb->je; ++j)
       for (int i = pmb->is; i <= pmb->ie; ++i) {
-        s(0, k, j, i) = r(0, k, j, i) * w(IDN, k, j, i);
-        s(1, k, j, i) = r(1, k, j, i) * w(IDN, k, j, i);
-        mut(k, j, i) = cmu_ * w(IDN, k, j, i) * r(1, k, j, i) * r(1, k, j, i) /
-                       r(0, k, j, i);
+        Real rhod = phydro->w(IDN, k, j, i);
+        u(0, k, j, i) = w(0, k, j, i) * rhod;
+        u(1, k, j, i) = w(1, k, j, i) * rhod;
+        mut(k, j, i) =
+            cmu_ * rhod * w(1, k, j, i) * w(1, k, j, i) / w(0, k, j, i);
       }
 }
 
@@ -143,59 +145,59 @@ inline Real ShearProduction_(AthenaArray<Real> const &w, int k, int j, int i,
   return result;
 }
 
-void KEpsilonTurbulence::driveTurbulence(AthenaArray<Real> &s,
-                                         AthenaArray<Real> const &r,
-                                         AthenaArray<Real> const &w, Real dt) {
+void KEpsilonTurbulence::DriveTurbulence(Real dt) {
   // std::cout << "driving turbulence" << std::endl;
-  MeshBlock *pmb = pmy_block;
+  auto pmb = pmy_block;
+  auto phydro = pmb->phydro;
+
   int ks = pmb->ks, js = pmb->js, is = pmb->is;
   int ke = pmb->ke, je = pmb->je, ie = pmb->ie;
 
   AthenaArray<Real> eps, tke;
-  eps.InitWithShallowSlice(const_cast<AthenaArray<Real> &>(r), 4, 0, 1);
-  tke.InitWithShallowSlice(const_cast<AthenaArray<Real> &>(r), 4, 1, 1);
+  eps.InitWithShallowSlice(w, 4, 0, 1);
+  tke.InitWithShallowSlice(w, 4, 1, 1);
 
   Real s1, s2, s3;
   for (int k = ks; k <= ke; ++k)
     for (int j = js; j <= je; ++j)
       for (int i = is; i <= ie; ++i) {
+        Real rhod = phydro->w(IDN, k, j, i);
         // shear production
         Real shear = ShearProduction_(w, k, j, i, pmb->pcoord);
         // std::cout << "shear = " << shear << std::endl;
 
         // turbulent dissipation, de/dt, eq2.2-1
         s1 = c1_ * mut(k, j, i) * eps(k, j, i) / tke(k, j, i) * shear;
         s2 = Laplace_(mut, eps, k, j, i, pmb->pcoord) / sige_;
-        s3 =
-            -c2_ * eps(k, j, i) * eps(k, j, i) / tke(k, j, i) * w(IDN, k, j, i);
-        s(0, k, j, i) += (s1 + s2) * dt;
-        if (s(0, k, j, i) + s3 * dt > 0)
-          s(0, k, j, i) += s3 * dt;
+        s3 = -c2_ * eps(k, j, i) * eps(k, j, i) / tke(k, j, i) * rhod;
+        u(0, k, j, i) += (s1 + s2) * dt;
+        if (u(0, k, j, i) + s3 * dt > 0)
+          u(0, k, j, i) += s3 * dt;
         else
-          s(0, k, j, i) /= 2.;
-        // std::cout << "s = " << s(0,k,j,i) << std::endl;
+          u(0, k, j, i) /= 2.;
+        // std::cout << "u = " << u(0,k,j,i) << std::endl;
 
         // turbulent kinetic energy, dk/dt, eq 2.2-2
         s1 = mut(k, j, i) * shear;
         s2 = Laplace_(mut, tke, k, j, i, pmb->pcoord) / sigk_;
-        s3 = -eps(k, j, i) * w(IDN, k, j, i);
-        s(1, k, j, i) += (s1 + s2) * dt;
-        if (s(1, k, j, i) + s3 * dt > 0.)
-          s(1, k, j, i) += s3 * dt;
+        s3 = -eps(k, j, i) * rhod;
+        u(1, k, j, i) += (s1 + s2) * dt;
+        if (u(1, k, j, i) + s3 * dt > 0.)
+          u(1, k, j, i) += s3 * dt;
         else
-          s(1, k, j, i) /= 2.;
+          u(1, k, j, i) /= 2.;
       }
 }
 
-void KEpsilonTurbulence::setDiffusivity(AthenaArray<Real> &nu,
+void KEpsilonTurbulence::SetDiffusivity(AthenaArray<Real> &nu,
                                         AthenaArray<Real> &kappa,
                                         const AthenaArray<Real> &prim,
                                         const AthenaArray<Real> &bcc, int il,
                                         int iu, int jl, int ju, int kl,
                                         int ku) {
   AthenaArray<Real> eps, tke;
-  eps.InitWithShallowSlice(r, 4, 0, 1);
-  tke.InitWithShallowSlice(r, 4, 1, 1);
+  eps.InitWithShallowSlice(w, 4, 0, 1);
+  tke.InitWithShallowSlice(w, 4, 1, 1);
 
   for (int k = kl; k <= ku; ++k) {
     for (int j = jl; j <= ju; ++j) {