Merge branch 'development'

AMReX-Astro · Sep 4, 2018 · 110a5c3 · 110a5c3
2 parents 48f1c02 + 1c7e91e
commit 110a5c3
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diff --git a/Exec/AMR-density/GNUmakefile b/Exec/AMR-density/GNUmakefile
@@ -1,7 +1,6 @@
 # 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
@@ -24,8 +23,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = FALSE
 
-USE_HPGMG = FALSE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/AMR-density/inputs b/Exec/AMR-density/inputs
@@ -155,7 +155,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/AMR-density/inputs.rt b/Exec/AMR-density/inputs.rt
@@ -136,7 +136,6 @@ amr.plot_files_output = 1
 amr.plot_file       = plt
 amr.plot_int        = 10
 amr.plot_nfiles     = 64
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/AMR-zoom/GNUmakefile b/Exec/AMR-zoom/GNUmakefile
@@ -1,7 +1,6 @@
 # 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
@@ -24,8 +23,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = FALSE
 
-USE_HPGMG = FALSE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/AMR-zoom/inputs b/Exec/AMR-zoom/inputs
@@ -155,7 +155,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/GravityTests/MacLaurin/Tagging_3d.f90 b/Exec/GravityTests/MacLaurin/Tagging_3d.f90
@@ -18,10 +18,11 @@
 ! ::: time      => problem evolution time
 ! ::: level     => refinement level of this array
 ! ::: -----------------------------------------------------------
+
       subroutine tag_overdensity(tag,tagl1,tagl2,tagl3,tagh1,tagh2,tagh3, &
                                  set,clear, &
                                  den,denl1,denl2,denl3,denh1,denh2,denh3, &
-                                 lo,hi,nc,delta,level,avg_den)
+                                 lo,hi,nc,domlo,domhi,delta,level,avg_den)
 
       use amrex_fort_module, only : rt => amrex_real
       use probdata_module
@@ -30,7 +31,7 @@ subroutine tag_overdensity(tag,tagl1,tagl2,tagl3,tagh1,tagh2,tagh3, &
       integer set, clear, nc, level
       integer tagl1,tagl2,tagl3,tagh1,tagh2,tagh3
       integer denl1,denl2,denl3,denh1,denh2,denh3
-      integer lo(3), hi(3)
+      integer lo(3), hi(3), domlo(3), domhi(3)
       integer tag(tagl1:tagh1,tagl2:tagh2,tagl3:tagh3)
       real(rt) den(denl1:denh1,denl2:denh2,denl3:denh3,nc)
       real(rt) delta(3), avg_den
@@ -74,21 +75,17 @@ end subroutine tag_overdensity
 ! ::: level     => refinement level of this array
 ! ::: -----------------------------------------------------------
       subroutine tag_region(tag,tagl1,tagl2,tagl3,tagh1,tagh2,tagh3, &
-                            set,clear, &
-                            var,varl1,varl2,varl3,varh1,varh2,varh3, &
-                            lo,hi,nd,domlo,domhi, &
-                            delta,xlo,problo,time,level)
+                            set,lo,hi,domlo,domhi, &
+                            delta,xlo,problo,level)
       use amrex_fort_module, only : rt => amrex_real
       use probdata_module
       implicit none
 
-      integer          :: set, clear, nd, level
+      integer          :: set,level
       integer          :: tagl1,tagl2,tagl3,tagh1,tagh2,tagh3
-      integer          :: varl1,varl2,varl3,varh1,varh2,varh3
       integer          :: lo(3), hi(3), domlo(3), domhi(3)
       integer          :: tag(tagl1:tagh1,tagl2:tagh2,tagl3:tagh3)
-      real(rt) :: var(varl1:varh1,varl2:varh2,varl3:varh3,nd)
-      real(rt) :: delta(3), xlo(3), problo(3), time
+      real(rt) :: delta(3), xlo(3), problo(3)
 
       integer          :: ilo,jlo,klo,ihi,jhi,khi
       integer          :: i,j,k

diff --git a/Exec/HDF5_example/GNUmakefile b/Exec/HDF5_example/GNUmakefile
@@ -1,7 +1,6 @@
 # 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
@@ -24,8 +23,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = FALSE
 
-USE_HPGMG = TRUE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/HDF5_example/inputs b/Exec/HDF5_example/inputs
@@ -155,7 +155,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/LyA/GNUmakefile b/Exec/LyA/GNUmakefile
@@ -1,7 +1,6 @@
 # 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
@@ -26,8 +25,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = FALSE
 
-USE_HPGMG = TRUE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/LyA/inputs b/Exec/LyA/inputs
@@ -155,7 +155,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/LyA/inputs_gimlet_in_transit.dsc b/Exec/LyA/inputs_gimlet_in_transit.dsc
@@ -127,7 +127,6 @@ amr.plot_file       = plt
 amr.plot_int        = 20
 amr.plot_nfiles     = 86
 #nyx.plot_z_values   = 4.0 3.5 3.0 2.5 2.25 2.0
-#particles.write_in_plotfile = 1
 
 amr.plot_vars        = density
 #amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/LyA_AGN/GNUmakefile b/Exec/LyA_AGN/GNUmakefile
@@ -1,7 +1,6 @@
 # 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
@@ -10,7 +9,7 @@ TOP = ../..
 # compilation options
 COMP    = intel  # gnu
 USE_MPI = TRUE
-USE_OMP = TRUE
+USE_OMP = FALSE
 
 PROFILE       = TRUE
 TRACE_PROFILE = FALSE
@@ -24,8 +23,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = TRUE
 
-USE_HPGMG = TRUE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/LyA_AGN/inputs b/Exec/LyA_AGN/inputs
@@ -144,7 +144,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density

diff --git a/Exec/MiniSB/GNUmakefile b/Exec/MiniSB/GNUmakefile
@@ -1,8 +1,6 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
 AMREX_HOME ?= ../../../amrex
 
-HPGMG_DIR ?= ../../Util/hpgmg/finite-volume
-
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../..
 
@@ -15,8 +13,6 @@ USE_OMP = FALSE
 # Analysis
 REEBER = FALSE
 
-USE_HPGMG = FALSE
-
 PRECISION = DOUBLE
 DEBUG     = FALSE
 

diff --git a/Exec/RegressionTest/GNUmakefile b/Exec/RegressionTest/GNUmakefile
@@ -12,6 +12,7 @@ USE_OMP = FALSE
 
 PRECISION = DOUBLE
 DEBUG     = FALSE
+DEBUG     = TRUE
 
 # physics
 DIM      = 3

diff --git a/Exec/RegressionTest/Prob_3d.f90 b/Exec/RegressionTest/Prob_3d.f90
@@ -81,24 +81,33 @@ subroutine fort_initdata(level,time,lo,hi, &
 
       integer i,j,k
 
-      do k = lo(3), hi(3)
-      do j = lo(2), hi(2)
-      do i = lo(1), hi(1)
-         state(i,j,k,URHO)    = 1.d0
-         state(i,j,k,UMX:UMZ) = 0.0d0
-
-         state(i,j,k,UEINT) = 10.d0
-         state(i,j,k,UEDEN) = state(i,j,k,UEINT) + 0.5d0 / state(i,j,k,URHO) *  &
-            (state(i,j,k,UMX)**2 + state(i,j,k,UMY)**2 + state(i,j,k,UMZ)**2) 
-
-         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) = 1000.d0
-      enddo
-      enddo
-      enddo
+      if (ns.gt.1) 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.d0
+            state(i,j,k,UMX:UMZ) = 0.0d0
+
+            state(i,j,k,UEINT) = 10.d0
+            state(i,j,k,UEDEN) = state(i,j,k,UEINT) + 0.5d0 / state(i,j,k,URHO) *  &
+               (state(i,j,k,UMX)**2 + state(i,j,k,UMY)**2 + state(i,j,k,UMZ)**2) 
+
+            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) = 1000.d0
+         enddo
+         enddo
+         enddo
+
+      else
+
+         state(lo(1):hi(1),lo(2):hi(2),lo(3):hi(3),URHO)    = 1.d0
+
+      endif
+
 
       end subroutine fort_initdata
diff --git a/Exec/RegressionTest/inputs.mass.nosub b/Exec/RegressionTest/inputs.mass.nosub
@@ -69,8 +69,6 @@ nyx.particle_init_type = AsciiFile
 nyx.ascii_particle_file = particle_file.mass
 particles.particle_output_file = final_particles
 
-particles.write_in_plotfile = 1
-
 # >>>>>>>>>>>>>  PARTICLE AGGREGATION OPTIONS <<<<<<<<<<<<<<<<
 #  "None"    "Cell"     "Flow"
 # >>>>>>>>>>>>>  PARTICLE AGGREGATION OPTIONS <<<<<<<<<<<<<<<<

diff --git a/Exec/RegressionTest/inputs.mass.sub b/Exec/RegressionTest/inputs.mass.sub
@@ -71,8 +71,6 @@ nyx.particle_init_type = AsciiFile
 nyx.ascii_particle_file = particle_file.mass
 particles.particle_output_file = final_particles
 
-particles.write_in_plotfile = 1
-
 # >>>>>>>>>>>>>  PARTICLE AGGREGATION OPTIONS <<<<<<<<<<<<<<<<
 #  "None"    "Cell"     "Flow"
 # >>>>>>>>>>>>>  PARTICLE AGGREGATION OPTIONS <<<<<<<<<<<<<<<<

diff --git a/Exec/SanityCheck/GNUmakefile b/Exec/SanityCheck/GNUmakefile
@@ -0,0 +1,39 @@
+# AMREX_HOME defines the directory in which we will find all the AMReX code
+AMREX_HOME ?= ../../../amrex
+
+CVODE_LIB_DIR ?= $(CVODE_LIB)
+
+# TOP defines the directory in which we will find Source, Exec, etc
+TOP = ../..
+
+# compilation options
+COMP    = gnu
+USE_MPI = TRUE
+USE_OMP = FALSE
+
+PROFILE       = FALSE
+TRACE_PROFILE = FALSE
+COMM_PROFILE  = FALSE
+TINY_PROFILE  = FALSE
+
+PRECISION = DOUBLE
+USE_SINGLE_PRECISION_PARTICLES = TRUE
+DEBUG     = FALSE
+
+GIMLET = FALSE
+REEBER = FALSE
+
+USE_SDC   = TRUE
+
+# physics
+DIM      = 3
+USE_GRAV = TRUE
+USE_HEATCOOL = TRUE
+USE_AGN = FALSE
+USE_CVODE = FALSE
+
+Bpack := ./Make.package
+Blocs := .
+
+include $(TOP)/Exec/Make.Nyx
+
diff --git a/Exec/SantaBarbara/GNUmakefile b/Exec/SantaBarbara/GNUmakefile
@@ -1,8 +1,6 @@
 # AMREX_HOME defines the directory in which we will find all the BoxLib code
 AMREX_HOME ?= ../../../amrex
 
-HPGMG_DIR ?= ../../Util/hpgmg/finite-volume
-
 # TOP defines the directory in which we will find Source, Exec, etc
 TOP = ../..
 
@@ -15,8 +13,6 @@ PRECISION = DOUBLE
 USE_SINGLE_PRECISION_PARTICLES = FALSE
 DEBUG     = FALSE
 
-USE_HPGMG = FALSE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/Scaling/GNUmakefile b/Exec/Scaling/GNUmakefile
@@ -1,16 +1,15 @@
 # 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 = TRUE
-USE_OMP = TRUE
+COMP    = gnu
+USE_MPI = FALSE
+USE_OMP = FALSE
 
 PROFILE       = TRUE
 TRACE_PROFILE = FALSE
@@ -24,8 +23,6 @@ DEBUG     = FALSE
 GIMLET = FALSE
 REEBER = FALSE
 
-USE_HPGMG = TRUE
-
 # physics
 DIM      = 3
 USE_GRAV = TRUE

diff --git a/Exec/Scaling/inputs b/Exec/Scaling/inputs
@@ -139,7 +139,6 @@ amr.plot_file       = plt
 amr.plot_int        = -1
 amr.plot_nfiles     = 64
 nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
-particles.write_in_plotfile = 1
 
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density