Merge branch 'development'

Exec/DrivenTurbulence/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../..

Exec/DrivenTurbulence/heat_cool_stubs.f90

@@ -53,3 +53,12 @@ subroutine integrate_state(lo, hi, &
                                dx, time, a, half_dt)
 
 end subroutine integrate_state
+
+
+! unused VODE stubs if we are not doing heating/cooling
+module vode_aux_module
+  use amrex_fort_module, only : rt => amrex_real
+  implicit none
+
+  real(rt) :: z_vode
+end module vode_aux_module

Exec/DrivenTurbulence/inputs

@@ -84,7 +84,6 @@ amr.derive_plot_vars = magvort divu MachNumber
 amr.probin_file    = probin
 
 # DIAGNOSTICS & VERBOSITY
-nyx.show_timings   = 0       # show timings
 nyx.sum_interval   = 1       # timesteps between computing mass
 nyx.v              = 2       # verbosity in Castro.cpp
 amr.v              = 2       # verbosity in Amr.cpp

Exec/DrivenTurbulence/inputs.regtest

@@ -81,7 +81,6 @@ amr.derive_plot_vars = forcex forcey forcez magvort MachNumber
 amr.probin_file    = probin
 
 # DIAGNOSTICS & VERBOSITY
-nyx.show_timings   = 0       # show timings
 nyx.sum_interval   = 1       # timesteps between computing mass
 nyx.v              = 2       # verbosity in Castro.cpp
 amr.v              = 2       # verbosity in Amr.cpp

Exec/GravityTests/MacLaurin/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..

Exec/HydroTests/DoubleRarefaction/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..
@@ -11,7 +11,6 @@ USE_MPI = FALSE
 USE_OMP = FALSE
 
 PRECISION = DOUBLE
-DEBUG     = TRUE
 DEBUG     = FALSE
 
 # physics

Exec/HydroTests/Sedov/GNUmakefile

@@ -1,17 +1,16 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..
 
 # compilation options
-COMP    = gcc
+COMP    = intel #gcc
 
 USE_MPI = FALSE
 USE_OMP = FALSE
 
 PRECISION = DOUBLE
-DEBUG     = TRUE
 DEBUG     = FALSE
 
 # physics

Exec/HydroTests/Sod/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..
@@ -11,7 +11,6 @@ USE_MPI = FALSE
 USE_OMP = FALSE
 
 PRECISION = DOUBLE
-DEBUG     = TRUE
 DEBUG     = FALSE
 
 # physics

Exec/HydroTests/StrongShockTube/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..
@@ -11,7 +11,6 @@ USE_MPI = FALSE
 USE_OMP = FALSE
 
 PRECISION = DOUBLE
-DEBUG     = TRUE
 DEBUG     = FALSE
 
 # physics

Exec/HydroTests/TurbForce/GNUmakefile

@@ -1,5 +1,5 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+AMREX_HOME ?= ../../../../amrex
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../../..

Exec/HydroTests/TurbForce/Nyx_setup.cpp

@@ -233,7 +233,7 @@ Nyx::hydro_setup()
          ppm_flatten_before_integrals,
          use_colglaz, use_flattening, corner_coupling, version_2,
          use_const_species, gamma, normalize_species,
-         heat_cool_type, ParallelDescriptor::Communicator());
+         heat_cool_type);
 
     if (use_const_species == 1)
         fort_set_eos_params(h_species, he_species);
@@ -664,7 +664,7 @@ Nyx::no_hydro_setup()
          ppm_flatten_before_integrals,
          use_colglaz, use_flattening, corner_coupling, version_2,
          use_const_species, gamma, normalize_species,
-         heat_cool_type, ParallelDescriptor::Communicator());
+         heat_cool_type);
 
     int coord_type = Geometry::Coord();
     fort_set_problem_params(dm, phys_bc.lo(), phys_bc.hi(), Outflow, Symmetry, coord_type);

Exec/LyA/GNUmakefile

@@ -1,50 +1,35 @@
-# AMREX_HOME defines the directory in which we will find all the BoxLib code
-AMREX_HOME ?= /project/projectdirs/nyx/src/amrex
+# AMREX_HOME defines the directory in which we will find all the AMReX code
+AMREX_HOME ?= ../../../amrex
 
-HPGMG_DIR ?= /global/homes/f/friesen/hpgmg/finite-volume
+HPGMG_DIR ?= ../../Util/hpgmg/finite-volume
+CVODE_LIB_DIR ?= ../../../sundials/sundials-intel/lib
 
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../..
 
 # compilation options
-COMP    = gcc
+COMP    = intel  # gnu
 USE_MPI = TRUE
 USE_OMP = TRUE
 
-PROFILE       = FALSE
+PROFILE       = TRUE
 TRACE_PROFILE = FALSE
 COMM_PROFILE  = FALSE
 
 PRECISION = DOUBLE
+USE_SINGLE_PRECISION_PARTICLES = TRUE
 DEBUG     = FALSE
 
 GIMLET = FALSE
 REEBER = FALSE
 
-GIMLET_DIR ?= /home/vince/Development/gimlet
-# Gimlet needs FFTW MPI.
-FFTW_INC ?= /usr/include
-FFTW_DIR ?= /usr/lib/x86_64-linux-gnu
-
-REEBER_HOME ?= /project/projectdirs/nyx/ghweber/reeber2
-# Reeber needs Boost (both headers and libraries) and diy2.
-BOOST_INCLUDE_DIR ?= /project/projectdirs/nyx/ghweber/boost-1.61.0-noarch/include
-DIY_INCLUDE_DIR ?= /project/projectdirs/nyx/ghweber/diy/include
-
-USE_HPGMG = FALSE
-HPGMG_FCYCLES = FALSE
-HPGMG_POST_F_CYCLE_TYPE = V
-HPGMG_HELMHOLTZ = FALSE
-HPGMG_STENCIL_VARIABLE_COEFFICIENT = FALSE
-HPGMG_USE_SUBCOMM = TRUE
-HPGMG_BOTTOM_SOLVER= BICGSTAB
-HPGMG_SMOOTHER = GSRB
+USE_HPGMG = TRUE
 
 # physics
 DIM      = 3
 USE_GRAV = TRUE
 USE_HEATCOOL = TRUE
-
+USE_AGN = FALSE
 USE_CVODE = FALSE
 
 Bpack := ./Make.package

Exec/LyA/Make.package

@@ -1,5 +1,2 @@
 f90EXE_sources += Prob_${DIM}d.f90
 f90EXE_sources += probdata.f90	
-ifeq ($(USE_CVODE), TRUE)
-  f90EXE_sources += fcvode_extras.f90
-endif

Exec/LyA/Prob_3d.f90

@@ -65,10 +65,11 @@ subroutine fort_initdata(level,time,lo,hi, &
                                bind(C, name="fort_initdata")
 
       use amrex_fort_module, only : rt => amrex_real
+      use amrex_parmparse_module
       use probdata_module
       use atomic_rates_module, only : XHYDROGEN
       use meth_params_module, only : URHO, UMX, UMZ, UEDEN, UEINT, UFS, &
-                                     small_dens, TEMP_COMP, NE_COMP
+                                     small_dens, TEMP_COMP, NE_COMP, ZHI_COMP
 
       implicit none
 
@@ -81,6 +82,13 @@ subroutine fort_initdata(level,time,lo,hi, &
       real(rt) diag_eos(d_l1:d_h1,d_l2:d_h2,d_l3:d_h3,nd)
 
       integer i,j,k
+      real(rt) z_in
+
+      type(amrex_parmparse) :: pp
+
+      call amrex_parmparse_build(pp, "nyx")
+      call pp%query("initial_z", z_in)
+      call amrex_parmparse_destroy(pp)
 
       ! This is the case where we have compiled with states defined 
       !  but they have only one component each so we fill them this way.
@@ -90,7 +98,7 @@ subroutine fort_initdata(level,time,lo,hi, &
          diag_eos(:,:,:,1)    = 0.0d0
 
       ! This is the regular case with NO_HYDRO = FALSE
-      else if (ns.gt.1 .and. nd.eq.2) then
+      else if (ns.gt.1 .and. nd.ge.2) then
 
          do k = lo(3), hi(3)
          do j = lo(2), hi(2)
@@ -108,8 +116,13 @@ subroutine fort_initdata(level,time,lo,hi, &
                state(i,j,k,UFS+1) = (1.d0 - XHYDROGEN)
             end if
 
-            diag_eos(i,j,k,TEMP_COMP) = 1000.d0
-            diag_eos(i,j,k,  NE_COMP) =    0.d0
+            diag_eos(i,j,k,TEMP_COMP) = 0.021d0*(1.0d0 + z_in)**2
+            diag_eos(i,j,k,  NE_COMP) = 0.d0
+
+            if (ZHI_COMP .gt. -1) then
+               diag_eos(i,j,k, ZHI_COMP) = 7.5d0
+            endif
+
          enddo
          enddo
          enddo