A fair amount of wrongly commited changed in previous PR, but some we…

…re good. (#42)

Exec/Cases/CounterFlow/GNUmakefile

@@ -25,6 +25,6 @@ USE_EFIELD		 = FALSE
 # PelePhysics
 Chemistry_Model = drm19
 Eos_Model	    = Fuego
-Transport_Model = Constant
+Transport_Model = Simple
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX

Exec/Cases/CounterFlow/input.2d-regt

@@ -33,47 +33,47 @@ prob.inert_radius = 0.0075
 prob.inert_velocity = 0.2
 prob.pertmag = 0.000
 prob.pmf_datafile = "drm_CH4Air_stoich.dat"
-prob.do_ignition = 0
-prob.ignition_SphT = 1000.0
+prob.do_ignition = 1
+prob.ignition_SphT = 2200.0
 
 #-------------------------PeleLM CONTROL----------------------------
-peleLM.v = 4
+peleLM.v = 1
 peleLM.incompressible = 0
 peleLM.rho = 1.17
 peleLM.mu = 0.0
-peleLM.use_wbar = 0
-peleLM.sdc_iterMax = 1
-peleLM.floor_species = 0
+peleLM.use_wbar = 1
+peleLM.sdc_iterMax = 2
+peleLM.floor_species = 1
 peleLM.deltaT_verbose = 0
 
-#amr.restart = chk00100
+#amr.restart = chk01500
 #amr.regrid_on_restart = 1
 amr.check_int = 100
 amr.plot_int = 20
-amr.max_step = 120
-amr.dt_shrink = 0.001
+amr.max_step = 100
+amr.dt_shrink = 0.01
 amr.stop_time = 1.1
 #amr.stop_time = 1.00
-amr.cfl = 0.4
+amr.cfl = 0.25
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
-peleLM.chem_integrator = "ReactorNull"
+peleLM.chem_integrator = "ReactorCvode"
 peleLM.use_typ_vals_chem = 1          # Use species/temp typical values in CVODE
 ode.rtol = 1.0e-6                     # Relative tolerance of the chemical solve
 ode.atol = 1.0e-5                     # Absolute tolerance factor applied on typical values
 cvode.solve_type = denseAJ_direct               # CVODE Linear solve type (for Newton direction) 
-cvode.max_order  = 2                  # CVODE max BDF order. 
+cvode.max_order  = 4                  # CVODE max BDF order. 
 
-godunov.use_ppm = 1
+godunov.use_ppm = 0
 godunov.use_forceInTrans = 0
 
 nodal_proj.verbose = 0
 mac_proj.verbose = 0
 #diffusion.verbose = 2
 
-#peleLM.do_temporals = 1
-#peleLM.temporal_int = 2
-#peleLM.mass_balance = 1
+peleLM.do_temporals = 1
+peleLM.temporal_int = 2
+peleLM.mass_balance = 1
 
 #--------------------REFINEMENT CONTROL------------------------
 amr.refinement_indicators = temp
@@ -99,6 +99,6 @@ amr.temp.field_name    = temp
 #amr.CH2O.value_greater = 1.00e-3
 #amr.CH2O.field_name    = Y(CH2O)
 
-amrex.fpe_trap_invalid = 1
-amrex.fpe_trap_zero = 1
-amrex.fpe_trap_overflow = 1
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1

Exec/Cases/PremBunsen3D/GNUmakefile

@@ -20,10 +20,10 @@ USE_CUDA        = FALSE
 USE_HIP         = FALSE
 
 # PeleLMeX
-USE_EFIELD		= FALSE
+USE_EFIELD      = FALSE
 
 # PelePhysics
-Chemistry_Model = CH4Ion_GRI
+Chemistry_Model = drm19
 Eos_Model       = Fuego
 Transport_Model = Simple
 

Exec/Cases/PremBunsen3D/input.3d

@@ -14,7 +14,7 @@ peleLM.hi_bc = Outflow Outflow Outflow
 #-------------------------AMR CONTROL----------------------------
 amr.n_cell          = 96 96 96      # Level 0 number of cells in each direction   
 amr.v               = 1                # AMR verbose
-amr.max_level       = 1                # maximum level number allowed
+amr.max_level       = 2                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2          # refinement ratio
 amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
@@ -32,7 +32,7 @@ prob.slot_width = 0.003
 pmf.datafile = "drm_CH4Air_stoich.dat"
 
 #-------------------------PeleLM CONTROL----------------------------
-peleLM.v = 4
+peleLM.v = 2
 peleLM.incompressible = 0
 peleLM.rho = 1.17
 peleLM.mu = 0.0
@@ -41,13 +41,12 @@ peleLM.sdc_iterMax = 1
 peleLM.floor_species = 0
 peleLM.deltaT_verbose = 0
 
-amr.restart = chk00010
-#amr.initDataPlt = DRMplt14800
+#amr.restart = chk00000
 #amr.regrid_on_restart = 1
 amr.check_int = 100
 amr.plot_int = 10
-amr.max_step = 10
-amr.dt_shrink = 0.0001
+amr.max_step = 100
+amr.dt_shrink = 0.001
 amr.stop_time = 1.1
 #amr.stop_time = 1.00
 amr.cfl = 0.3

Exec/RegTests/EB_ChallengeProblem/input.3d-regt

@@ -43,13 +43,13 @@ peleLM.temporal_int = 2
 peleLM.mass_balance = 1
 
 #amr.restart = chk00005
-amr.check_int = 20
+amr.check_int = 5
 amr.plot_int = 10
-amr.max_step = 200
+amr.max_step = 5
 amr.dt_shrink = 0.1
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
-amr.cfl = 0.3
+amr.cfl = 0.15
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
 # --------------- INPUTS TO CHEMISTRY REACTOR ---------------
@@ -86,7 +86,7 @@ nodal_proj.verbose = 2
 nodal_proj.mg_max_coarsening_level = 2
 nodal_proj.bottom_solver = "smoother"
 
-#fabarray.mfiter_tile_size = 1024 1024 1024
+fabarray.mfiter_tile_size = 1024 1024 1024
 
 amrex.fpe_trap_invalid = 1
 amrex.fpe_trap_zero = 1

Exec/RegTests/EB_ChallengeProblem/input.3d-regt_Hypre

@@ -13,8 +13,6 @@ peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab NoSlipWallAdiab
 
 #-------------------------AMR CONTROL----------------------------
 amr.n_cell          = 64 64 32      # Level 0 number of cells in each direction   
-amr.n_cell          = 256 256 128      # Level 0 number of cells in each direction   
-amr.n_cell          = 128 128 64      # Level 0 number of cells in each direction   
 amr.v               = 1                # AMR verbose
 amr.max_level       = 0                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
@@ -64,7 +62,7 @@ cvode.max_order  = 4                  # CVODE max BDF order.
 
 #------------------------- EB SETUP -----------------------------
 eb2.geom_type = UserDefined
-eb2.small_volfrac = 1.e-3
+eb2.small_volfrac = 1.e-2
 
 #------------  INPUTS TO CONSTANT TRANSPORT -----------------
 transport.const_viscosity        = 0.0002

Exec/RegTests/EB_EnclosedFlame/GNUmakefile

@@ -6,7 +6,7 @@ AMREX_HYDRO_HOME   ?= ${TOP}/AMReX-Hydro
 
 
 # AMReX
-DIM             = 3
+DIM             = 2
 DEBUG           = FALSE
 PRECISION       = DOUBLE
 VERBOSE         = FALSE
@@ -24,7 +24,7 @@ USE_HIP         = FALSE
 # PeleLMeX
 
 # PelePhysics
-Chemistry_Model = dodecane_lu
+Chemistry_Model = drm19
 Eos_Model		= Fuego
 Transport_Model = Simple
 

Exec/RegTests/EB_EnclosedVortex/GNUmakefile

@@ -12,7 +12,7 @@ PRECISION       = DOUBLE
 VERBOSE         = FALSE
 TINY_PROFILE    = FALSE
 USE_EB			= TRUE
-USE_HYPRE		= TRUE
+USE_HYPRE		= FALSE
 
 # Compilation
 COMP            = gnu

Exec/RegTests/EB_EnclosedVortex/input.2d-regt

@@ -12,9 +12,9 @@ peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 128 128 32      # Level 0 number of cells in each direction   
+amr.n_cell          = 256 256 32      # Level 0 number of cells in each direction   
 amr.v               = 1                # AMR verbose
-amr.max_level       = 1                # maximum level number allowed
+amr.max_level       = 0                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
 amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
@@ -46,7 +46,7 @@ peleLM.mass_balance = 1
 #amr.restart = chk00005
 amr.check_int = 5
 amr.plot_int = 100
-amr.max_step = 5
+amr.max_step = 10
 amr.dt_shrink = 0.1
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
@@ -74,16 +74,16 @@ eb2.small_volfrac = 1.e-4
 #amr.temp.value_greater = 305
 #amr.temp.field_name    = temp
 
-amr.refinement_indicators = magVort
-amr.magVort.max_level     = 1
-amr.magVort.value_greater = 500.0
-amr.magVort.field_name    = mag_vort
+#amr.refinement_indicators = magVort
+#amr.magVort.max_level     = 1
+#amr.magVort.value_greater = 500.0
+#amr.magVort.field_name    = mag_vort
 
 #--------------------LINEAR SOLVER CONTROL------------------------
 nodal_proj.verbose = 1
-#nodal_proj.rtol = 1.0e-10
-#nodal_proj.atol = 1.0e-10
-#nodal_proj.mg_max_coarsening_level = 2
+nodal_proj.rtol = 1.0e-10
+nodal_proj.atol = 1.0e-10
+nodal_proj.mg_max_coarsening_level = 2
 amrex.fpe_trap_invalid = 1
 amrex.fpe_trap_zero = 1
 amrex.fpe_trap_overflow = 1

Exec/RegTests/EB_EnclosedVortex/input.3d-regt

@@ -12,15 +12,15 @@ peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab Symmetry
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 128 128 32      # Level 0 number of cells in each direction   
+amr.n_cell          = 64 64 32      # Level 0 number of cells in each direction   
 amr.v               = 1                # AMR verbose
-amr.max_level       = 3                # maximum level number allowed
+amr.max_level       = 2                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
 amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
 amr.grid_eff        = 0.7              # what constitutes an efficient grid
 amr.blocking_factor = 16               # block factor in grid generation (min box size)
-amr.max_grid_size   = 64               # max box size
+amr.max_grid_size   = 128               # max box size
 
 
 #--------------------------- Problem -------------------------------
@@ -43,23 +43,23 @@ peleLM.do_temporals = 1
 peleLM.temporal_int = 2
 peleLM.mass_balance = 1
 
-amr.restart = chk01000
+#amr.restart = chk01000
 amr.check_int = 100
-amr.plot_int = 50
-amr.max_step = 2000
+amr.plot_int = 100
+amr.max_step = 10
 amr.dt_shrink = 0.1
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
-amr.cfl = 0.5
+amr.cfl = 0.15
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
 # --------------- INPUTS TO CHEMISTRY REACTOR ---------------
 peleLM.chem_integrator = "ReactorNull"
 #peleLM.use_typ_vals_chem = 1          # Use species/temp typical values in CVODE
 #ode.rtol = 1.0e-6                     # Relative tolerance of the chemical solve
 #ode.atol = 1.0e-5                     # Absolute tolerance factor applied on typical values
-#cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction) 
-#cvode.max_order  = 4                  # CVODE max BDF order. 
+cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction) 
+cvode.max_order  = 4                  # CVODE max BDF order. 
 
 #------------------------- EB SETUP -----------------------------
 eb2.geom_type = sphere
@@ -85,9 +85,9 @@ amr.magVort.field_name    = mag_vort
 nodal_proj.verbose = 1
 nodal_proj.rtol = 1.0e-10
 nodal_proj.atol = 1.0e-10
-#nodal_proj.mg_max_coarsening_level = 2
+nodal_proj.mg_max_coarsening_level = 2
 
-fabarray.mfiter_tile_size = 1024 1024 1024
+#fabarray.mfiter_tile_size = 1024 1024 1024
 
 amrex.fpe_trap_invalid = 1
 amrex.fpe_trap_zero = 1

Exec/RegTests/EB_FlowPastCylinder/input.2d-regt

@@ -42,7 +42,7 @@ peleLM.rho = 1.17
 peleLM.mu = 0.0003
 
 amr.plot_int = 20
-amr.max_step = 5
+amr.max_step = 20
 amr.dt_shrink = 0.1
 amr.stop_time = 0.02
 amr.cfl = 0.7

Exec/RegTests/EnclosedFlame/input.2d-regt

@@ -7,12 +7,12 @@ geometry.prob_hi     =  0.02  0.02 0.016        # x_hi y_hi (z_hi)
 # >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
 # Interior, Inflow, Outflow, Symmetry,
 # SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
-peleLM.lo_bc = Outflow Outflow
-peleLM.hi_bc = Outflow Outflow
+peleLM.lo_bc = NoSlipWallAdiab NoSlipWallAdiab
+peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 256 256 32      # Level 0 number of cells in each direction   
+amr.n_cell          = 128 128 32      # Level 0 number of cells in each direction   
 amr.v               = 1                # AMR verbose
 amr.max_level       = 2                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
@@ -26,7 +26,7 @@ amr.max_grid_size   = 128               # max box size
 #--------------------------- Problem -------------------------------
 prob.P_mean = 101325.0
 prob.standoff = -0.002
-prob.pertmag = 0.000
+prob.pertmag = 0.0002
 pmf.datafile = "drm19_pmf.dat"
 pmf.do_cellAverage = 0
 
@@ -48,8 +48,8 @@ peleLM.mass_balance = 1
 #amr.restart = chk00005
 amr.check_int = 100
 amr.plot_int = 100
-amr.max_step = 100
-amr.dt_shrink = 0.001
+amr.max_step = 10
+amr.dt_shrink = 0.0001
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
 amr.cfl = 0.15

Exec/RegTests/FlameSheet/GNUmakefile

@@ -10,7 +10,7 @@ DIM             = 2
 DEBUG           = FALSE
 PRECISION       = DOUBLE
 VERBOSE         = FALSE
-TINY_PROFILE    = TRUE
+TINY_PROFILE    = FALSE
 
 # Compilation
 COMP            = gnu

Exec/RegTests/FlameSheet/input.2d-regt

@@ -45,7 +45,7 @@ peleLM.mass_balance = 1
 #amr.restart = chk00005
 #amr.check_int = 2000
 amr.plot_int = 100
-amr.max_step = 2
+amr.max_step = 20
 amr.dt_shrink = 0.0001
 amr.stop_time = 0.001
 #amr.stop_time = 1.00