cleanup to both SUNDIALS tutorials

AMReX-Codes · Sep 5, 2024 · 1215a42 · 1215a42
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Showing 9 changed files with 25 additions and 32 deletions.
diff --git a/ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/inputs_sundials_mri b/ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/inputs_sundials_mri
@@ -29,7 +29,7 @@ use_MRI = true
 fast_dt_ratio = 0.02
 
 
-# Use adaptive time stepping and set integrator relative and absolute tolerances
+# Use adaptive time stepping (multi-stage integrators only!) and set integrator relative and absolute tolerances
 # adapt_dt = true
 # reltol   = 1.0e-4
 # abstol   = 1.0e-9

diff --git a/ExampleCodes/SUNDIALS/Reaction-Diffusion/Source/main.cpp b/ExampleCodes/SUNDIALS/Reaction-Diffusion/Source/main.cpp
@@ -48,6 +48,10 @@ void main_main ()
     Real reltol = 1.0e-4;
     Real abstol = 1.0e-9;
 
+    // Reaction and Diffusion Coefficients
+    Real reaction_coef = 0.0;
+    Real diffusion_coef = 1.0;
+
     // inputs parameters
     {
         // ParmParse is way of reading inputs from the inputs file
@@ -85,6 +89,8 @@ void main_main ()
         pp.query("reltol",reltol);
         pp.query("abstol",abstol);
 
+        pp.query("reaction_coef",reaction_coef);
+        pp.query("diffusion_coef",diffusion_coef);
     }
 
     // **********************************
@@ -132,7 +138,7 @@ void main_main ()
     // How Boxes are distrubuted among MPI processes
     DistributionMapping dm(ba);
 
-    // we allocate two phi multifabs; one will store the old state, the other the new.
+    // allocate phi MultiFab
     MultiFab phi(ba, dm, Ncomp, Nghost);
 
     // time = starting time in the simulation
@@ -171,8 +177,7 @@ void main_main ()
         WriteSingleLevelPlotfile(pltfile, phi, {"phi"}, geom, time, 0);
     }
 
-    auto rhs_fast_function = [&](MultiFab& S_rhs, MultiFab& S_data,
-                            const Real /* time */) {
+    auto rhs_fast_function = [&](MultiFab& S_rhs, MultiFab& S_data, const Real /* time */) {
 
         // fill periodic ghost cells
         S_data.FillBoundary(geom.periodicity());
@@ -181,12 +186,6 @@ void main_main ()
         auto& phi_data = S_data;
         auto& phi_rhs  = S_rhs;
 
-        //Reaction and Diffusion Coefficients
-        Real reaction_coef = 0.0;
-        Real diffusion_coef = 1.0;
-        ParmParse pp;
-        pp.query("diffusion_coef",diffusion_coef);
-
         for ( MFIter mfi(phi_data); mfi.isValid(); ++mfi )
         {
             const Box& bx = mfi.validbox();
@@ -200,14 +199,14 @@ void main_main ()
                 phi_rhs_array(i,j,k) = diffusion_coef*( (phi_array(i+1,j,k) - 2.*phi_array(i,j,k) + phi_array(i-1,j,k)) / (dx[0]*dx[0])
                                                        +(phi_array(i,j+1,k) - 2.*phi_array(i,j,k) + phi_array(i,j-1,k)) / (dx[1]*dx[1])
 #if (AMREX_SPACEDIM == 3)
-                                                       +(phi_array(i,j,k+1) - 2.*phi_array(i,j,k) + phi_array(i,j,k-1)) / (dx[2]*dx[2]) );
+                                                       +(phi_array(i,j,k+1) - 2.*phi_array(i,j,k) + phi_array(i,j,k-1)) / (dx[2]*dx[2])
 #endif
+                    );
             });
         }
     };
 
-    auto rhs_function = [&](MultiFab& S_rhs, MultiFab& S_data,
-                            const Real /* time */) {
+    auto rhs_function = [&](MultiFab& S_rhs, MultiFab& S_data, const Real /* time */) {
 
         // fill periodic ghost cells
         S_data.FillBoundary(geom.periodicity());
@@ -216,13 +215,6 @@ void main_main ()
         auto& phi_data = S_data;
         auto& phi_rhs  = S_rhs;
 
-        //Reaction and Diffusion Coefficients
-        Real reaction_coef = 0.0;
-        Real diffusion_coef = 1.0;
-        ParmParse pp;
-        pp.query("reaction_coef",reaction_coef);
-        pp.query("diffusion_coef",diffusion_coef);
-
         for ( MFIter mfi(phi_data); mfi.isValid(); ++mfi )
         {
             const Box& bx = mfi.validbox();
@@ -239,15 +231,14 @@ void main_main ()
                     phi_rhs_array(i,j,k) = diffusion_coef*( (phi_array(i+1,j,k) - 2.*phi_array(i,j,k) + phi_array(i-1,j,k)) / (dx[0]*dx[0])
                                                            +(phi_array(i,j+1,k) - 2.*phi_array(i,j,k) + phi_array(i,j-1,k)) / (dx[1]*dx[1])
 #if (AMREX_SPACEDIM == 3)
-                                                           +(phi_array(i,j,k+1) - 2.*phi_array(i,j,k) + phi_array(i,j,k-1)) / (dx[2]*dx[2]) )
+                                                           +(phi_array(i,j,k+1) - 2.*phi_array(i,j,k) + phi_array(i,j,k-1)) / (dx[2]*dx[2])
 #endif
-                                         -1.*reaction_coef*phi_array(i,j,k);
+                        ) - 1.*reaction_coef*phi_array(i,j,k);
                 }
             });
         }
     };
 
-
     TimeIntegrator<MultiFab> integrator(phi, time);
     integrator.set_rhs(rhs_function);
     if (use_MRI) {

diff --git a/ExampleCodes/SUNDIALS/CMakeLists.txt → ...Codes/SUNDIALS/Single-Rate/CMakeLists.txt b/ExampleCodes/SUNDIALS/CMakeLists.txt → ...Codes/SUNDIALS/Single-Rate/CMakeLists.txt
diff --git a/ExampleCodes/SUNDIALS/Exec/GNUmakefile → ...des/SUNDIALS/Single-Rate/Exec/GNUmakefile b/ExampleCodes/SUNDIALS/Exec/GNUmakefile → ...des/SUNDIALS/Single-Rate/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
@@ -17,9 +17,9 @@ INCLUDE_LOCATIONS += ../Source
 
 ifeq ($(USE_SUNDIALS),TRUE)
   ifeq ($(USE_CUDA),TRUE)
-    SUNDIALS_ROOT ?= $(TOP)../../../../sundials/instdir_cuda
+    SUNDIALS_ROOT ?= $(TOP)../../../../../sundials/instdir_cuda
   else
-    SUNDIALS_ROOT ?= $(TOP)../../../../sundials/instdir
+    SUNDIALS_ROOT ?= $(TOP)../../../../../sundials/instdir
   endif
   ifeq ($(NERSC_HOST),perlmutter)
     SUNDIALS_LIB_DIR ?= $(SUNDIALS_ROOT)/lib64

diff --git a/ExampleCodes/SUNDIALS/Exec/README_sundials → ...SUNDIALS/Single-Rate/Exec/README_sundials b/ExampleCodes/SUNDIALS/Exec/README_sundials → ...SUNDIALS/Single-Rate/Exec/README_sundials
diff --git a/ExampleCodes/SUNDIALS/Exec/inputs → ...pleCodes/SUNDIALS/Single-Rate/Exec/inputs b/ExampleCodes/SUNDIALS/Exec/inputs → ...pleCodes/SUNDIALS/Single-Rate/Exec/inputs
@@ -13,6 +13,11 @@ dt = 1.e-4
 #plot_int = 20
 #dt = 2.5e-5
 
+# Use adaptive time stepping (multi-stage integrators only!) and set integrator relative and absolute tolerances
+# adapt_dt = true
+# reltol   = 1.0e-4
+# abstol   = 1.0e-9
+
 # INTEGRATION
 ## integration.type can take on the following values:
 ## 0 or "ForwardEuler" => Native AMReX Forward Euler integrator

diff --git a/ExampleCodes/SUNDIALS/Source/Make.package → .../SUNDIALS/Single-Rate/Source/Make.package b/ExampleCodes/SUNDIALS/Source/Make.package → .../SUNDIALS/Single-Rate/Source/Make.package
diff --git a/ExampleCodes/SUNDIALS/Source/main.cpp → ...odes/SUNDIALS/Single-Rate/Source/main.cpp b/ExampleCodes/SUNDIALS/Source/main.cpp → ...odes/SUNDIALS/Single-Rate/Source/main.cpp
@@ -38,7 +38,7 @@ void main_main ()
     Real dt;
 
     // use adaptive time step (dt used to set output times)
-    int adapt_dt = 0;
+    bool adapt_dt = false;
 
     // adaptive time step relative and absolute tolerances
     Real reltol = 1.0e-4;
@@ -129,9 +129,6 @@ void main_main ()
     // time = starting time in the simulation
     Real time = 0.0;
 
-    Print() << "dt = " << dt << std::endl;
-    Print() << "Diffusive CFL time step = " << dx[0]*dx[0]/(2.*AMREX_SPACEDIM) << std::endl;
-
     // **********************************
     // INITIALIZE DATA
 
@@ -165,15 +162,15 @@ void main_main ()
         WriteSingleLevelPlotfile(pltfile, phi, {"phi"}, geom, time, 0);
     }
 
-    auto rhs_function = [&](MultiFab& S_rhs, MultiFab& S_data,
-                            const Real /* time */) {
+    auto rhs_function = [&](MultiFab& S_rhs, MultiFab& S_data, const Real /* time */) {
 
         // fill periodic ghost cells
         S_data.FillBoundary(geom.periodicity());
 
         // loop over boxes
         auto& phi_data = S_data;
         auto& phi_rhs  = S_rhs;
+
         for ( MFIter mfi(phi_data); mfi.isValid(); ++mfi )
         {
             const Box& bx = mfi.validbox();

diff --git a/ExampleCodes/SUNDIALS/Source/myfunc.H → ...odes/SUNDIALS/Single-Rate/Source/myfunc.H b/ExampleCodes/SUNDIALS/Source/myfunc.H → ...odes/SUNDIALS/Single-Rate/Source/myfunc.H