Updates for terrain / grid stretching

Docs/sphinx_doc/Inputs.rst

@@ -172,7 +172,8 @@ This automatically activates **erf.use_terrain**. By default, the
 problem-specific terrain is initialized to be flat at an elevation of z=0.
 These inputs are used to automatically generate the staggered z levels used to
 calculate the grid metric transformation. Alternatively, arbitrary z levels may
-be specified with the **erf.terrain_z_levels** parameter.
+be specified with the **erf.terrain_z_levels** parameter, which should vary
+from 0 (at the surface) to the domain height.
 
 .. _list-of-parameters-3:
 

Exec/ABL/prob.H

@@ -68,11 +68,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "ABL"; }
 

Exec/ABL/prob.cpp

@@ -164,28 +164,3 @@ Problem::init_custom_pert(
  }
  });
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,0) = 0.;
- });
- }
-}

Exec/ABL_input_sounding/prob.H

@@ -67,11 +67,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "ABL with input sounding"; }
 

Exec/ABL_input_sounding/prob.cpp

@@ -157,28 +157,3 @@ Problem::init_custom_pert(
  }
  });
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,0) = 0.;
- });
- }
-}

Exec/DevTests/MiguelDev/prob.H

@@ -57,11 +57,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "ABL test"; }
 

Exec/DevTests/MiguelDev/prob.cpp

@@ -140,31 +140,3 @@ Problem::init_custom_pert(
  });
 
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- // Bottom of domain
- int k0 = 0;
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> const& z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,k0) = 0.0;
- });
- }
-}

Exec/DevTests/MultiBlock/prob.H

@@ -46,11 +46,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "MultiBlock"; }
 

Exec/DevTests/MultiBlock/prob.cpp

@@ -111,31 +111,3 @@ Problem::init_custom_pert(
 
  amrex::Gpu::streamSynchronize();
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- // Bottom of domain
- int k0 = 0;
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> const& z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,k0) = 0.0;
- });
- }
-}

Exec/LLJ/prob.H

@@ -39,11 +39,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "Low-Level Jet"; }
 

Exec/LLJ/prob.cpp

@@ -42,28 +42,3 @@ Problem::init_custom_pert(
 {
  amrex::Print() << "Dummy function..Needed for linking" << std::endl;
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,0) = 0.;
- });
- }
-}

Exec/Radiation/prob.H

@@ -46,11 +46,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
  void erf_init_rayleigh (
  amrex::Vector<amrex::Real>& tau,
  amrex::Vector<amrex::Real>& ubar,

Exec/Radiation/prob.cpp

@@ -212,34 +212,6 @@ Problem::init_custom_pert(
  amrex::Gpu::streamSynchronize();
 }
 
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- // Bottom of domain
- int k0 = 0;
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> const& z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,k0) = 0.0;
- });
- }
-}
-
 void
 Problem::erf_init_rayleigh(
  amrex::Vector<amrex::Real>& tau,

Exec/RegTests/Bubble/prob.H

@@ -72,11 +72,6 @@ public:
  std::unique_ptr<amrex::MultiFab>& z_phys_nd,
  amrex::Geometry const& geom) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
  AMREX_FORCE_INLINE
  AMREX_GPU_HOST_DEVICE
  amrex::Real compute_theta (const amrex::Real T_b, const amrex::Real p_b);

Exec/RegTests/Bubble/prob.cpp

@@ -457,31 +457,3 @@ Problem::init_custom_pert(
 
  amrex::Gpu::streamSynchronize();
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- // Bottom of domain
- int k0 = 0;
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> const& z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,k0) = 0.0;
- });
- }
-}

Exec/RegTests/CouetteFlow/prob.H

@@ -41,11 +41,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "Couette Flow"; }
 

Exec/RegTests/CouetteFlow/prob.cpp

@@ -75,28 +75,3 @@ Problem::init_custom_pert(
  z_vel(i, j, k) = parms.w_0;
  });
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,0) = 0.;
- });
- }
-}

Exec/RegTests/DensityCurrent/prob.H

@@ -44,11 +44,6 @@ public:
  amrex::Array4<amrex::Real const> const& mf_v,
  const SolverChoice& sc) override;
 
- void init_custom_terrain (
- const amrex::Geometry& geom,
- amrex::MultiFab& z_phys_nd,
- const amrex::Real& time) override;
-
 protected:
  std::string name() override { return "Density Current"; }
 

Exec/RegTests/DensityCurrent/prob.cpp

@@ -148,32 +148,3 @@ Problem::init_custom_pert(
 
  amrex::Gpu::streamSynchronize();
 }
-
-void
-Problem::init_custom_terrain(
- const Geometry& /*geom*/,
- MultiFab& z_phys_nd,
- const Real& /*time*/)
-{
- // Number of ghost cells
- int ngrow = z_phys_nd.nGrow();
-
- // Bottom of domain
- int k0 = 0;
-
- for ( MFIter mfi(z_phys_nd, TilingIfNotGPU()); mfi.isValid(); ++mfi )
- {
- // Grown box with no z range
- amrex::Box xybx = mfi.growntilebox(ngrow);
- xybx.setRange(2,0);
-
- Array4<Real> const& z_arr = z_phys_nd.array(mfi);
-
- ParallelFor(xybx, [=] AMREX_GPU_DEVICE (int i, int j, int) {
-
- // Flat terrain with z = 0 at k = 0
- z_arr(i,j,k0) = 0.0;
- });
- }
-}
-