Merge branch 'development'

Exec/AMR-density/GNUmakefile

@@ -9,8 +9,8 @@ TOP = ../..
 
 # compilation options
 COMP    = intel  # gnu
-USE_MPI = FALSE
-USE_OMP = FALSE
+USE_MPI = TRUE
+USE_OMP = TRUE
 
 PROFILE       = TRUE
 TRACE_PROFILE = FALSE

Exec/HydroTests/TurbForce/Nyx_setup.cpp

@@ -731,7 +731,7 @@ Nyx::no_hydro_setup()
 }
 #endif
 
-#ifdef USE_CVODE
+#ifdef AMREX_USE_CVODE
 void
 Nyx::set_simd_width(const int simd_width)
 {

Exec/LyA/inputs

@@ -1,7 +1,5 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 max_step = 10000000
-max_step = 0
-max_step = 4
 
 amr.mffile_nstreams      = 4
 amr.precreateDirectories = 1
@@ -54,8 +52,8 @@ amr.data_log = runlog
 gravity.gravity_type = PoissonGrav
 gravity.no_sync      = 1
 gravity.no_composite = 1
-gravity.solve_with_cpp = 0
-gravity.solve_with_hpgmg = 1
+gravity.solve_with_mlmg  = 1
+gravity.solve_with_hpgmg = 0
 
 mg.bottom_solver = 4
 

README.md

@@ -89,7 +89,7 @@ be run either "in situ" or "in-transit", or with a combination of both.
 
 
 ## License
-See the [license.txt](license.txt) file for details.
+Nyx is released under the LBL's modified BSD license, see the [license.txt](license.txt) file for details.
 
 
 ## Contact

Source/Constants/constants_cgs.f90

@@ -3,7 +3,6 @@
 module fundamental_constants_module
 
   use amrex_fort_module, only : rt => amrex_real
-  use bl_types
 
   implicit none
 

Source/EOS/eos_stuff.f90

@@ -26,8 +26,6 @@
 
 module eos_module
 
-  use bl_types
-  use bl_space
   use bl_constants_module, only: M_PI, ONE
   use network, only: nspec, aion, zion
   use atomic_rates_module, only: XHYDROGEN

Source/Forcing/forcing_spect.f90

@@ -3,8 +3,6 @@
 module forcing_spect_module
 
   use amrex_fort_module, only : bl_spacedim, rt => amrex_real
-  use bl_types
-  use bl_constants_module, only : ZERO
 
   implicit none
 
@@ -46,9 +44,9 @@ subroutine fort_alloc_spect(length) &
        call bl_abort('number of forcing modes must be positive')
     end if
 
-    modes_even(:,:) = ZERO
-    modes_even(:,:) = ZERO
-    wavevectors(:,:) = ZERO
+    modes_even(:,:) = 0.d0
+    modes_even(:,:) = 0.d0
+    wavevectors(:,:) = 0.d0
 
   end subroutine fort_alloc_spect
 

Source/Gravity/Gravity.cpp

@@ -958,13 +958,11 @@ Gravity::get_old_grav_vector (int       level,
 
     // Fill grow cells in grad_phi, will need to compute grad_phi_cc in 1 grow cell
     const Geometry& geom = parent->Geom(level);
+#if 0
     if (level == 0)
     {
         for (int i = 0; i < BL_SPACEDIM ; i++)
-        {
-            grad_phi_prev[level][i]->setBndry(0);
-            grad_phi_prev[level][i]->FillBoundary(geom.periodicity());
-        }
+           grad_phi_prev[level][i]->setBndry(0.);
     }
     else
     {
@@ -973,11 +971,16 @@ Gravity::get_old_grav_vector (int       level,
         fill_ec_grow(level, amrex::GetVecOfPtrs(grad_phi_prev[level]),
 	                    amrex::GetVecOfPtrs(crse_grad_phi));
     }
+#endif
+
+    // Fill boundary values at the current level
+    for (int i = 0; i < BL_SPACEDIM ; i++)
+       grad_phi_prev[level][i]->FillBoundary(geom.periodicity());
 
     // Average edge-centered gradients to cell centers.
     amrex::average_face_to_cellcenter(grav_vector, 
-				       amrex::GetVecOfConstPtrs(grad_phi_prev[level]),
-				       geom);
+				      amrex::GetVecOfConstPtrs(grad_phi_prev[level]),
+				      geom);
 
 #ifdef CGRAV
     if (gravity_type == "CompositeGrav")
@@ -999,6 +1002,8 @@ Gravity::get_old_grav_vector (int       level,
 
     // This is a hack-y way to fill the ghost cell values of grav_vector
     //   before returning it
+    // Note that this fills ghost cells over the coarse grid from interpolation, 
+    //  not from the ghost cell values previously filled after the fill_ec_grow stuff.
     AmrLevel* amrlev = &parent->getLevel(level);
     int ng = grav_vector.nGrow();
     AmrLevel::FillPatch(*amrlev,grav_vector,ng,time,Gravity_Type,0,BL_SPACEDIM);
@@ -1022,6 +1027,7 @@ Gravity::get_new_grav_vector (int       level,
         // Fill grow cells in `grad_phi`, will need to compute `grad_phi_cc` in
         // 1 grow cell
         const Geometry& geom = parent->Geom(level);
+#if 0
         if (level == 0)
         {
             for (int i = 0; i < BL_SPACEDIM ; i++)
@@ -1037,6 +1043,10 @@ Gravity::get_new_grav_vector (int       level,
             fill_ec_grow(level, amrex::GetVecOfPtrs(grad_phi_curr[level]),
                                 amrex::GetVecOfPtrs(crse_grad_phi));
         }
+#endif
+
+        for (int i = 0; i < BL_SPACEDIM ; i++)
+            grad_phi_curr[level][i]->FillBoundary(geom.periodicity());
 
         // Average edge-centered gradients to cell centers, excluding grow cells
         amrex::average_face_to_cellcenter(grav_vector,
@@ -1068,6 +1078,8 @@ Gravity::get_new_grav_vector (int       level,
 
     // This is a hack-y way to fill the ghost cell values of grav_vector
     //   before returning it
+    // Note that this fills ghost cells over the coarse grid from interpolation, 
+    //  not from the ghost cell values previously filled after the fill_ec_grow stuff.
     AmrLevel* amrlev = &parent->getLevel(level) ;
     int ng = grav_vector.nGrow();
     AmrLevel::FillPatch(*amrlev,grav_vector,ng,time,Gravity_Type,0,BL_SPACEDIM);

Source/HeatCool/integrate_state_3d.f90

@@ -1,7 +1,7 @@
 subroutine integrate_state(lo, hi, &
                            state   , s_l1, s_l2, s_l3, s_h1, s_h2, s_h3, &
                            diag_eos, d_l1, d_l2, d_l3, d_h1, d_h2, d_h3, &
-                           dx, time, a, half_dt, min_iter, max_iter) &
+                           a, half_dt, min_iter, max_iter) &
                            bind(C, name="integrate_state")
 
 !
@@ -17,10 +17,6 @@ subroutine integrate_state(lo, hi, &
 !       The state vars
 !   diag_eos* : double arrays
 !       Temp and Ne
-!   src_* : double arrays
-!       The source terms to be added to state (iterative approx.)
-!   double array (3)
-!       The low corner of the entire domain
 !   a : double
 !       The current a
 !   half_dt : double
@@ -43,7 +39,7 @@ subroutine integrate_state(lo, hi, &
     integer         , intent(in   ) :: d_l1, d_l2, d_l3, d_h1, d_h2, d_h3
     real(rt), intent(inout) ::    state(s_l1:s_h1, s_l2:s_h2,s_l3:s_h3, NVAR)
     real(rt), intent(inout) :: diag_eos(d_l1:d_h1, d_l2:d_h2,d_l3:d_h3, NDIAG)
-    real(rt), intent(in   ) :: dx(3), time, a, half_dt
+    real(rt), intent(in   ) :: a, half_dt
     integer         , intent(inout) :: min_iter, max_iter
 
     if (heat_cool_type .eq. 1) then

Source/HydroFortran/Make.package

@@ -2,6 +2,7 @@ f90EXE_sources += add_grav_source_3d.f90
 f90EXE_sources += analriem.f90
 f90EXE_sources += enforce_minimum_density_3d.f90
 f90EXE_sources += flatten_3d.f90
+f90EXE_sources += make_hydro_sources_3d.f90
 f90EXE_sources += normalize_species_3d.f90
 f90EXE_sources += Nyx_advection_3d.f90
 f90EXE_sources += ppm_3d.f90