Merge branch 'development'

Exec/AMR-density/64sssss_20mpc.nyx

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+../LyA/64sssss_20mpc.nyx

Exec/AMR-density/GNUmakefile

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+# AMREX_HOME defines the directory in which we will find all the AMReX code
+AMREX_HOME ?= ../../../amrex
+
+HPGMG_DIR ?= ../../Util/hpgmg/finite-volume
+CVODE_LIB_DIR ?= $(CVODE_LIB)
+
+# TOP defines the directory in which we will find Source, Exec, etc
+TOP = ../..
+
+# compilation options
+COMP    = intel  # gnu
+USE_MPI = FALSE
+USE_OMP = FALSE
+
+PROFILE       = TRUE
+TRACE_PROFILE = FALSE
+COMM_PROFILE  = FALSE
+TINY_PROFILE  = FALSE
+
+PRECISION = DOUBLE
+USE_SINGLE_PRECISION_PARTICLES = TRUE
+DEBUG     = FALSE
+
+GIMLET = FALSE
+REEBER = FALSE
+
+USE_HPGMG = FALSE
+
+# physics
+DIM      = 3
+USE_GRAV = TRUE
+USE_HEATCOOL = TRUE
+USE_AGN = FALSE
+USE_CVODE = FALSE
+
+Bpack := ./Make.package
+Blocs := .
+
+include $(TOP)/Exec/Make.Nyx
+

Exec/AMR-density/Make.package

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+f90EXE_sources += Prob_${DIM}d.f90
+f90EXE_sources += probdata.f90	

Exec/AMR-density/Nyx_error.cpp

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+
+#include "Nyx.H"
+#include "Nyx_error_F.H"
+
+using namespace amrex;
+
+void
+Nyx::error_setup()
+{
+    err_list.add("total_density",1,ErrorRec::UseAverage,
+                 BL_FORT_PROC_CALL(TAG_OVERDENSITY, tag_overdensity));
+}
+
+void
+Nyx::manual_tags_placement (TagBoxArray&    tags,
+                            const Vector<IntVect>& bf_lev)
+{
+}

Exec/AMR-density/Prob_3d.f90

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+
+      subroutine amrex_probinit (init,name,namlen,problo,probhi) bind(c)
+
+      use amrex_fort_module, only : rt => amrex_real
+      use probdata_module
+      implicit none
+
+      integer init, namlen
+      integer name(namlen)
+      real(rt) problo(3), probhi(3)
+
+      integer untin,i
+
+      namelist /fortin/ max_num_part
+
+!
+!     Build "probin" filename -- the name of file containing fortin namelist.
+!     
+      integer maxlen
+      parameter (maxlen=256)
+      character probin*(maxlen)
+
+      if (namlen .gt. maxlen) then
+         write(6,*) 'probin file name too long'
+         stop
+      end if
+
+      do i = 1, namlen
+         probin(i:i) = char(name(i))
+      end do
+
+!     Read namelists
+      untin = 9
+      open(untin,file=probin(1:namlen),form='formatted',status='old')
+      read(untin,fortin)
+      close(unit=untin)
+
+      end
+
+! ::: -----------------------------------------------------------
+! ::: This routine is called at problem setup time and is used
+! ::: to initialize data on each grid.  
+! ::: 
+! ::: NOTE:  all arrays have one cell of ghost zones surrounding
+! :::        the grid interior.  Values in these cells need not
+! :::        be set here.
+! ::: 
+! ::: INPUTS/OUTPUTS:
+! ::: 
+! ::: level     => amr level of grid
+! ::: time      => time at which to init data             
+! ::: lo,hi     => index limits of grid interior (cell centered)
+! ::: nstate    => number of state components.  You should know
+! :::		   this already!
+! ::: state     <=  Scalar array
+! ::: delta     => cell size
+! ::: xlo,xhi   => physical locations of lower left and upper
+! :::              right hand corner of grid.  (does not include
+! :::		   ghost region).
+! ::: -----------------------------------------------------------
+      subroutine fort_initdata(level,time,lo,hi, &
+                               ns, state   ,s_l1,s_l2,s_l3,s_h1,s_h2,s_h3, &
+                               nd, diag_eos,d_l1,d_l2,d_l3,d_h1,d_h2,d_h3, &
+                               delta,xlo,xhi)  &
+                               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, ZHI_COMP
+
+      implicit none
+
+      integer level, ns, nd
+      integer lo(3), hi(3)
+      integer s_l1,s_l2,s_l3,s_h1,s_h2,s_h3
+      integer d_l1,d_l2,d_l3,d_h1,d_h2,d_h3
+      real(rt) xlo(3), xhi(3), time, delta(3)
+      real(rt)    state(s_l1:s_h1,s_l2:s_h2,s_l3:s_h3,ns)
+      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.
+      if (ns.eq.1 .and. nd.eq.1) then
+
+            state(:,:,:,1)    = 0.0d0
+         diag_eos(:,:,:,1)    = 0.0d0
+
+      ! This is the regular case with NO_HYDRO = FALSE
+      else if (ns.gt.1 .and. nd.ge.2) then
+
+         do k = lo(3), hi(3)
+         do j = lo(2), hi(2)
+         do i = lo(1), hi(1)
+
+            state(i,j,k,URHO)    = 1.5d0 * small_dens
+            state(i,j,k,UMX:UMZ) = 0.0d0
+
+            ! These will both be set later in the call to init_e.
+            state(i,j,k,UEINT) = 0.d0
+            state(i,j,k,UEDEN) = 0.d0
+
+            if (UFS .gt. -1) then
+               state(i,j,k,UFS  ) = XHYDROGEN
+               state(i,j,k,UFS+1) = (1.d0 - XHYDROGEN)
+            end if
+
+            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
+
+      end if
+
+      end subroutine fort_initdata