Merge pull request #4 from pkjha-aero/main

Fix tutorials under Basic and Amr

Author: atmyers

Amr/Advection_AmrCore/Exec/Make.Adv

@@ -1,4 +1,4 @@
-AMREX_HOME = ../../../../amrex
+AMREX_HOME ?= ../../../../amrex
 ADV_DIR    = ../
 
 TOP := $(ADV_DIR)

Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile

@@ -1,4 +1,4 @@
-AMREX_HOME = ../../../../../amrex
+AMREX_HOME ?= ../../../../../amrex
 USE_EB = FALSE
 PRECISION  = DOUBLE
 PROFILE    = FALSE

Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile

@@ -1,4 +1,4 @@
-AMREX_HOME = ../../../../../amrex
+AMREX_HOME ?= ../../../../../amrex
 USE_EB =FALSE
 PRECISION  = DOUBLE
 PROFILE    = FALSE

Basic/HeatEquation_EX1_C/Exec/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the AMReX code.
-AMREX_HOME = ../../../../amrex
+AMREX_HOME ?= ../../../../
 
 DEBUG        = FALSE
 USE_MPI      = FALSE

Basic/HeatEquation_EX1_C/Source/mykernel.H

@@ -15,10 +15,11 @@ void init_phi (int i, int j, int k,
     Real y = prob_lo[1] + (j+Real(0.5)) * dx[1];
 #if (AMREX_SPACEDIM > 2)
     Real z = prob_lo[2] + (k+Real(0.5)) * dx[2];
+    Real r2 = ((x-Real(0.25))*(x-Real(0.25))+(y-Real(0.25))*(y-Real(0.25))+(z-Real(0.25))*(z-Real(0.25)))/Real(0.01);
 #else
     Real z = Real(0.);
+    Real r2 = ((x-Real(0.25))*(x-Real(0.25))+(y-Real(0.25))*(y-Real(0.25)))/Real(0.01);
 #endif
-    Real r2 = ((x-Real(0.25))*(x-Real(0.25))+(y-Real(0.25))*(y-Real(0.25))+(z-Real(0.25))*(z-Real(0.25)))/Real(0.01);
     phi(i,j,k) = Real(1.) + std::exp(-r2);
 }
 

Basic/HeatEquation_EX1_CF/Exec/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the AMReX code.
-AMREX_HOME = ../../../../amrex
+AMREX_HOME ?= ../../../../amrex
 
 DEBUG     = FALSE
 USE_MPI   = FALSE

Basic/HeatEquation_EX1_F/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the AMReX code
-AMREX_HOME = ../../../amrex
+AMREX_HOME ?= ../../../amrex
 
 DEBUG     = TRUE
 

Basic/HeatEquation_EX2_C/Exec/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the AMReX code.
-AMREX_HOME = ../../../../amrex
+AMREX_HOME ?= ../../../../amrex
 
 DEBUG     = FALSE
 USE_MPI   = TRUE 

Basic/HeatEquation_EX2_C/Source/myfunc.cpp

@@ -15,7 +15,7 @@ void advance (MultiFab& phi_old,
     // Fill the ghost cells of each grid from the other grids
     // includes periodic domain boundaries
     phi_old.FillBoundary(geom.periodicity());
-
+    // There are physical boundaries to fill.
     FillDomainBoundary(phi_old, geom, BoundaryCondition);
 
     const BCRec& bc = BoundaryCondition[0];
@@ -27,13 +27,15 @@ void advance (MultiFab& phi_old,
     //
     // =======================================================
 
-    const Real dxinv = geom.InvCellSize(0);
-    const Real dyinv = geom.InvCellSize(1);
-    const Real dzinv = geom.InvCellSize(2);
+    // This example supports both 2D and 3D.  Otherwise,
+    // we would not need to use AMREX_D_TERM.
+    AMREX_D_TERM(const Real dxinv = geom.InvCellSize(0);,
+                 const Real dyinv = geom.InvCellSize(1);,
+                 const Real dzinv = geom.InvCellSize(2););
 
     const Box& domain_bx = geom.Domain();
-    const Dim3 dom_lo = lbound(domain_bx);
-    const Dim3 dom_hi = ubound(domain_bx);
+    const auto dom_lo = lbound(domain_bx);
+    const auto dom_hi = ubound(domain_bx);
 
     // Compute fluxes one grid at a time
     for ( MFIter mfi(phi_old); mfi.isValid(); ++mfi )
@@ -47,8 +49,8 @@ void advance (MultiFab& phi_old,
         auto const& fluxz = flux[2].array(mfi);
 #endif
         const Box& bx = mfi.validbox();
-        const Dim3 lo = lbound(bx);
-        const Dim3 hi = ubound(bx);
+        const auto lo = lbound(bx);
+        const auto hi = ubound(bx);
 
         auto const& phi = phi_old.array(mfi);
 
@@ -81,14 +83,19 @@ void advance (MultiFab& phi_old,
         const Box& vbx = mfi.validbox();
         auto const& fluxx = flux[0].array(mfi);
         auto const& fluxy = flux[1].array(mfi);
+#if (AMREX_SPACEDIM > 2)
         auto const& fluxz = flux[2].array(mfi);
+#endif
         auto const& phiOld = phi_old.array(mfi);
         auto const& phiNew = phi_new.array(mfi);
 
         amrex::ParallelFor(vbx,
         [=] AMREX_GPU_DEVICE (int i, int j, int k)
         {
-            update_phi(i,j,k,phiOld,phiNew,fluxx,fluxy,fluxz,dt,dxinv,dyinv,dzinv);
+            update_phi(i,j,k,phiOld,phiNew,
+                       AMREX_D_DECL(fluxx,fluxy,fluxz),
+                       dt,
+                       AMREX_D_DECL(dxinv,dyinv,dzinv));
         });
     }
 }
@@ -104,7 +111,8 @@ void init_phi(amrex::MultiFab& phi_new, amrex::Geometry const& geom){
     {
         const Box& vbx = mfi.validbox();
         auto const& phiNew = phi_new.array(mfi);
-        AMREX_FOR_3D ( vbx, i, j, k,
+        amrex::ParallelFor(vbx,
+        [=] AMREX_GPU_DEVICE(int i, int j, int k)
         {
             init_phi(i,j,k,phiNew,dx,prob_lo);
         });

Basic/HeatEquation_EX2_C/Source/mykernel.H

@@ -9,11 +9,18 @@ void init_phi (int i, int j, int k,
                GpuArray<amrex::Real,AMREX_SPACEDIM> const& dx,
                GpuArray<amrex::Real,AMREX_SPACEDIM> const& prob_lo)
 {
-    amrex::Real x = prob_lo[0] + (i+0.5) * dx[0];
-    amrex::Real y = prob_lo[1] + (j+0.5) * dx[1];
-    amrex::Real z = prob_lo[2] + (k+0.5) * dx[2];
-    amrex::Real r2 = ((x-0.25)*(x-0.25)+(y-0.25)*(y-0.25)+(z-0.25)*(z-0.25))/0.01;
-    phi(i,j,k) = 1. + std::exp(-r2);
+    using amrex::Real;;
+
+    Real x = prob_lo[0] + (i+Real(0.5)) * dx[0];
+    Real y = prob_lo[1] + (j+Real(0.5)) * dx[1];
+#if (AMREX_SPACEDIM > 2)
+    Real z = prob_lo[2] + (k+Real(0.5)) * dx[2];
+    Real r2 = ((x-Real(0.25))*(x-Real(0.25))+(y-Real(0.25))*(y-Real(0.25))+(z-Real(0.25))*(z-Real(0.25)))/Real(0.01);
+#else
+    Real z = Real(0.);
+    Real r2 = ((x-Real(0.25))*(x-Real(0.25))+(y-Real(0.25))*(y-Real(0.25)))/Real(0.01);
+#endif
+    phi(i,j,k) = Real(1.) + std::exp(-r2);
 }
 
 
@@ -93,6 +100,8 @@ void compute_flux_y (int i, int j, int k,
     }
 }
 
+
+#if (AMREX_SPACEDIM > 2)
 AMREX_GPU_DEVICE AMREX_FORCE_INLINE
 void compute_flux_z (int i, int j, int k,
                      amrex::Array4<amrex::Real> const& fluxz,
@@ -130,18 +139,28 @@ void compute_flux_z (int i, int j, int k,
         fluxz(i,j,k) = (phi(i,j,k)-phi(i,j,k-1)) * dzinv;
     }
 }
+#endif
 
 AMREX_GPU_DEVICE AMREX_FORCE_INLINE
 void update_phi (int i, int j, int k,
                  amrex::Array4<amrex::Real const> const& phiold,
                  amrex::Array4<amrex::Real      > const& phinew,
-                 amrex::Array4<amrex::Real const> const& fluxx,
-                 amrex::Array4<amrex::Real const> const& fluxy,
-                 amrex::Array4<amrex::Real const> const& fluxz,
+                 AMREX_D_DECL(amrex::Array4<amrex::Real const> const& fluxx,
+                              amrex::Array4<amrex::Real const> const& fluxy,
+                              amrex::Array4<amrex::Real const> const& fluxz),
                  amrex::Real dt,
-                 amrex::Real dxinv, amrex::Real dyinv, amrex::Real dzinv)
+                 AMREX_D_DECL(amrex::Real dxinv,
+                              amrex::Real dyinv,
+                              amrex::Real dzinv))
 {
-    phinew(i,j,k) = phiold(i,j,k) + dt * dxinv * (fluxx(i+1,j  ,k  ) - fluxx(i,j,k)) + dt * dyinv * (fluxy(i  ,j+1,k  ) - fluxy(i,j,k)) + dt * dzinv * (fluxz(i  ,j  ,k+1) - fluxz(i,j,k));
+    phinew(i,j,k) = phiold(i,j,k)
+        + dt * dxinv * (fluxx(i+1,j  ,k  ) - fluxx(i,j,k))
+        + dt * dyinv * (fluxy(i  ,j+1,k  ) - fluxy(i,j,k))
+#if (AMREX_SPACEDIM > 2)
+        + dt * dzinv * (fluxz(i  ,j  ,k+1) - fluxz(i,j,k));
+#else
+        ;
+#endif
 }
 
 #endif