AMReX-Combustion · esclapez · Jan 5, 2022 · Jan 5, 2022
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,9 @@
+[submodule "Submodules/amrex"]
+	path = Submodules/amrex
+	url = https://github.com/AMReX-Codes/amrex.git
+[submodule "Submodules/AMReX-Hydro"]
+	path = Submodules/AMReX-Hydro
+	url = https://github.com/AMReX-Codes/AMReX-Hydro.git
+[submodule "Submodules/PelePhysics"]
+	path = Submodules/PelePhysics
+	url = https://github.com/AMReX-Combustion/PelePhysics.git
diff --git a/Exec/Cases/CounterFlow/GNUmakefile b/Exec/Cases/CounterFlow/GNUmakefile
@@ -25,6 +25,6 @@ USE_EFIELD		 = FALSE
 # PelePhysics
 Chemistry_Model = drm19
 Eos_Model	    = Fuego
-Transport_Model = Simple
+Transport_Model = Constant
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX
diff --git a/Exec/Cases/CounterFlow/input.2d-regt b/Exec/Cases/CounterFlow/input.2d-regt
@@ -33,44 +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 = 1
-prob.ignition_SphT = 2200.0
+prob.do_ignition = 0
+prob.ignition_SphT = 1000.0
 
 #-------------------------PeleLM CONTROL----------------------------
-peleLM.v = 1
+peleLM.v = 4
 peleLM.incompressible = 0
 peleLM.rho = 1.17
 peleLM.mu = 0.0
-peleLM.use_wbar = 1
-peleLM.sdc_iterMax = 2
-peleLM.floor_species = 1
+peleLM.use_wbar = 0
+peleLM.sdc_iterMax = 1
+peleLM.floor_species = 0
 peleLM.deltaT_verbose = 0
 
-#amr.restart = chk01500
+#amr.restart = chk00100
 #amr.regrid_on_restart = 1
 amr.check_int = 100
 amr.plot_int = 20
-amr.max_step = 100
-amr.dt_shrink = 0.01
+amr.max_step = 120
+amr.dt_shrink = 0.001
 amr.stop_time = 1.1
 #amr.stop_time = 1.00
-amr.cfl = 0.25
+amr.cfl = 0.4
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
-peleLM.chem_integrator = "ReactorCvode"
+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.max_order  = 2                  # CVODE max BDF order. 
+
+godunov.use_ppm = 1
+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
@@ -96,6 +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
diff --git a/Exec/Cases/PremBunsen2D/input.2d-regt b/Exec/Cases/PremBunsen2D/input.2d-regt
@@ -30,7 +30,7 @@ prob.pertmag = 0.000
 prob.Vin = 2.0
 prob.Vcoflow = 0.4
 prob.slot_width = 0.003
-prob.pmf_datafile = "drm_CH4Air_stoich.dat"
+pmf.datafile = "drm_CH4Air_stoich.dat"
 
 #-------------------------PeleLM CONTROL----------------------------
 peleLM.v = 2
@@ -53,8 +53,12 @@ amr.stop_time = 1.1
 amr.cfl = 0.3
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
-cvode.solve_type = dense               # CVODE Linear solve type (for Newton direction) 
-ode.analytical_jacobian = 0            # Provide analytical jacobian (from Fuego) 
+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 = dense_direct     # CVODE Linear solve type (for Newton direction) 
+cvode.max_order  = 4                  # CVODE max BDF order. 
 
 #--------------------REFINEMENT CONTROL------------------------
 #amr.refinement_indicators = temp

diff --git a/Exec/Cases/PremBunsen3D/GNUmakefile b/Exec/Cases/PremBunsen3D/GNUmakefile
@@ -2,6 +2,7 @@ TOP = ../../../..
 AMREX_HOME         ?= ${TOP}/amrex
 PELELMEX_HOME      ?= ${TOP}/PeleLMeX
 PELE_PHYSICS_HOME  ?= ${TOP}/PelePhysics
+AMREX_HYDRO_HOME   ?= ${TOP}/AMReX-Hydro
 
 
 # AMReX
@@ -19,14 +20,11 @@ USE_CUDA        = FALSE
 USE_HIP         = FALSE
 
 # PeleLMeX
-USE_EFIELD		 = FALSE
+USE_EFIELD		= FALSE
 
 # PelePhysics
-Chemistry_Model = drm19
-Reactions_Model	 = Fuego
-Eos_Model			 = Fuego
-Transport_Model   = Simple
-
-USE_SUNDIALS_PP = TRUE
+Chemistry_Model = CH4Ion_GRI
+Eos_Model       = Fuego
+Transport_Model = Simple
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX
diff --git a/Exec/Cases/PremBunsen3D/input.3d b/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       = 2                # maximum level number allowed
+amr.max_level       = 1                # 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 = 2
+peleLM.v = 4
 peleLM.incompressible = 0
 peleLM.rho = 1.17
 peleLM.mu = 0.0
@@ -41,12 +41,13 @@ peleLM.sdc_iterMax = 1
 peleLM.floor_species = 0
 peleLM.deltaT_verbose = 0
 
-#amr.restart = chk00000
+amr.restart = chk00010
+#amr.initDataPlt = DRMplt14800
 #amr.regrid_on_restart = 1
 amr.check_int = 100
 amr.plot_int = 10
-amr.max_step = 100
-amr.dt_shrink = 0.001
+amr.max_step = 10
+amr.dt_shrink = 0.0001
 amr.stop_time = 1.1
 #amr.stop_time = 1.00
 amr.cfl = 0.3

diff --git a/Exec/Cases/PremBunsen3D/pelelm_prob.H b/Exec/Cases/PremBunsen3D/pelelm_prob.H
@@ -143,7 +143,7 @@ bcnormal(
       if ( zone == 3 ) {
          s_ext[VELZ] = prob_parm.Vin * ( 1.0 - (rad_xy/prob_parm.slot_width) * (rad_xy/prob_parm.slot_width) );
       } else if ( zone == 1 ) {
-         s_ext[VELZ] = prob_parm.Vcoflow * ( 1.0 + (rad_xy)/0.025);
+         s_ext[VELZ] = prob_parm.Vcoflow * ( 1.0 + 1.5*(rad_xy)/0.025);
          if ( rad_xy <= prob_parm.slot_width*1.4 ) s_ext[VELZ] = 0.0;
       }
 

diff --git a/Exec/Efield/FlameSheetIons/GNUmakefile b/Exec/Efield/FlameSheetIons/GNUmakefile
@@ -23,7 +23,7 @@ USE_HIP         = FALSE
 USE_EFIELD      = TRUE
 
 # PelePhysics
-Chemistry_Model = CH4Ion_LuSk
+Chemistry_Model = CH4Ion_GRI
 Eos_Model	    = Fuego
 Transport_Model = Simple
 

diff --git a/Exec/Efield/FlameSheetIons/input.2d-regt b/Exec/Efield/FlameSheetIons/input.2d-regt
@@ -27,7 +27,7 @@ amr.max_grid_size   = 128               # max box size
 prob.P_mean = 101325.0
 prob.standoff = -.01
 prob.pertmag = 0.0000
-prob.pmf_datafile = "pmf_CH4Air_1p0.dat"
+pmf.datafile = "pmf_CH4Air_1p0.dat"
 prob.PhiV_y_hi = 1000.0
 
 #-------------------------PeleLM CONTROL----------------------------
@@ -36,14 +36,14 @@ peleLM.incompressible = 0
 peleLM.rho = 1.17
 peleLM.mu = 0.0
 peleLM.use_wbar = 1
-peleLM.sdc_iterMax = 1
-peleLM.floor_species = 1
+peleLM.sdc_iterMax = 2
+peleLM.floor_species = 0
 peleLM.num_init_iter = 2
 
 #amr.restart = chk00005
 #amr.check_int = 2000
 amr.plot_int = 10
-amr.max_step = 50
+amr.max_step = 100
 amr.dt_shrink = 0.01
 amr.stop_time = 0.001
 #amr.stop_time = 1.00
@@ -52,12 +52,14 @@ amr.cfl = 0.5
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions chargedistrib efieldy
 
 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
+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. 
 
+godunov.use_ppm = 0
+
 #--------------------REFINEMENT CONTROL------------------------
 ef.phiV_lo_bc = Interior Dirichlet
 ef.phiV_hi_bc = Interior Dirichlet

diff --git a/Exec/RegTests/EB_ChallengeProblem/input.3d-regt b/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 = 5
+amr.check_int = 20
 amr.plot_int = 10
-amr.max_step = 5
+amr.max_step = 200
 amr.dt_shrink = 0.1
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
-amr.cfl = 0.15
+amr.cfl = 0.3
 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

diff --git a/Exec/RegTests/EB_ChallengeProblem/input.3d-regt_Hypre b/Exec/RegTests/EB_ChallengeProblem/input.3d-regt_Hypre
@@ -13,6 +13,8 @@ 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
@@ -62,7 +64,7 @@ cvode.max_order  = 4                  # CVODE max BDF order.
 
 #------------------------- EB SETUP -----------------------------
 eb2.geom_type = UserDefined
-eb2.small_volfrac = 1.e-2
+eb2.small_volfrac = 1.e-3
 
 #------------  INPUTS TO CONSTANT TRANSPORT -----------------
 transport.const_viscosity        = 0.0002

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

diff --git a/Exec/RegTests/EB_EnclosedFlame/input.3d-regt b/Exec/RegTests/EB_EnclosedFlame/input.3d-regt
@@ -38,7 +38,7 @@ peleLM.use_wbar = 1
 peleLM.sdc_iterMax = 2
 peleLM.floor_species = 0
 peleLM.num_divu_iter = 1
-peleLM.num_init_iter = 0
+peleLM.num_init_iter = 1
 
 peleLM.do_temporals = 1
 peleLM.temporal_int = 2

diff --git a/Exec/RegTests/EB_EnclosedFlame/pelelm_prob.H b/Exec/RegTests/EB_EnclosedFlame/pelelm_prob.H
@@ -49,9 +49,8 @@ void pelelm_initdata(int i, int j, int k,
     amrex::Real massfrac[NUM_SPECIES] = {0.0};
     amrex::Real pert = 0.0;
 
-    amrex::Real radius = std::sqrt(AMREX_D_TERM(  (x-xc)*(x-xc),
-                                                + (y-yc)*(y-yc),
-                                                + (z-zc)*(z-zc)));
+    amrex::Real radius = std::sqrt(   (x-xc)*(x-xc)
+                                    + (y-yc)*(y-yc));
 
     if (prob_parm.pertmag > 0.0) 
     {
@@ -60,8 +59,6 @@ void pelelm_initdata(int i, int j, int k,
        amrex::Real angle = std::atan2((y-yc),(x-xc));
        pert = prob_parm.pertmag * 
              (0.7 * std::sin(2*angle) +
-              //1.023 * std::sin(2 * (angle - 0.004598) / radius2) +
-              //0.945 * std::sin(3 * (angle - 0.00712435) / radius2) +
               0.9 * std::sin(8 * angle ) +
               1.4 * std::sin(4 * angle  ));
     }
@@ -70,16 +67,16 @@ void pelelm_initdata(int i, int j, int k,
     amrex::Real y2 = 3.6 - (radius - prob_parm.standoff + 1.42*dx[1] + pert)*100;
 
 #elif ( AMREX_SPACEDIM == 3 )
-
+       amrex::Real pertLz = (prob_parm.pertLz > 0.0) ? prob_parm.pertLz 
+                                                     : Lz;
        amrex::Real angle = std::atan2((y-yc),(x-xc));
-       amrex::Real angle2 = std::atan2((z-zc),(y-yc));
        pert = prob_parm.pertmag * 
-             (0.7 * std::sin(2*angle) +
-              0.9 * std::sin(8 * angle ) +
-              1.4 * std::sin(4 * angle  )) *
-             (1.2 * std::sin(2*angle2) +
-              0.5 * std::sin(8 * angle2 ) +
-              0.9 * std::sin(16 * angle2  ));
+             (0.974 * std::sin(3 * angle ) *
+              0.995 * std::sin(2 * Pi * (z - 0.00712435) / pertLz) +
+              0.983 * std::sin(11 * (angle-0.63578) ) *
+              0.982 /* std::sin(2 * Pi * 3 * (z - 0.0014234)  / pertLz)*/ +
+              1.022 * std::sin(7 * angle ) *
+              0.945 * std::sin(2 * Pi * 2 * (z - 0.0039765) / pertLz));
     }
 
     amrex::Real y1 = 3.6 - (radius - prob_parm.standoff - 1.42*dx[1] + pert)*100;
@@ -96,12 +93,12 @@ void pelelm_initdata(int i, int j, int k,
     }
     eos.X2Y(molefrac, massfrac);
 
-    vel(i,j,k,0) = 0.0;
+    vel(i,j,k,0) = 0.1;
 #if ( AMREX_SPACEDIM == 2 )
-    vel(i,j,k,1) = pmf_vals[1]*1e-2;
+    vel(i,j,k,1) = 0.1;
 #elif ( AMREX_SPACEDIM == 3 )
-    vel(i,j,k,1) = 0.0;
-    vel(i,j,k,2) = pmf_vals[1]*1e-2;
+    vel(i,j,k,1) = 0.1;
+    vel(i,j,k,2) = 0.0;
 #endif
 
     amrex::Real P_cgs = prob_parm.P_mean * 10.0;

diff --git a/Exec/RegTests/EB_EnclosedFlame/pelelm_prob.cpp b/Exec/RegTests/EB_EnclosedFlame/pelelm_prob.cpp
@@ -9,14 +9,9 @@ void PeleLM::readProbParm()
    pp.query("P_mean",   PeleLM::prob_parm->P_mean);
    pp.query("standoff", PeleLM::prob_parm->standoff);
    pp.query("pertmag",  PeleLM::prob_parm->pertmag);
+#if (AMREX_SPACEDIM == 3)
+   pp.query("pertLz",  PeleLM::prob_parm->pertLz);
+#endif
 
    PeleLM::pmf_data.initialize();
-
-   auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
-   amrex::ParmParse pptr("transport");
-   pp.query("const_viscosity", trans_parm.const_viscosity);
-   pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);
-   pp.query("const_conductivity", trans_parm.const_conductivity);
-   pp.query("const_diffusivity", trans_parm.const_diffusivity);
-   PeleLM::trans_parms.sync_to_device();
 }