Add input for dodecane_lu 53 spec sk. mech. FlameSheet on GPU. (#207)

* Add input for dodecane_lu 53 spec sk. mech. FlameSheet on GPU.

* Fix change in IAMR.

* Update submodules.

Exec/RegTests/FlameSheet/inputs.3d-regt_GPUdodecaneLu

@@ -0,0 +1,161 @@
+#----------------------DOMAIN DEFINITION------------------------
+geometry.is_periodic = 1 1 0              # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = 0.0 0.0 0.0        # x_lo y_lo (z_lo)
+geometry.prob_hi     = 0.008 0.008 0.016  # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+peleLM.lo_bc = Interior  Interior Inflow
+peleLM.hi_bc = Interior  Interior Outflow
+
+#-------------------------AMR CONTROL----------------------------
+amr.n_cell          = 32 32 64         # Level 0 number of cells in each direction   
+amr.v               = 1                # AMR verbose
+amr.max_level       = 1                # maximum level number allowed
+amr.ref_ratio       = 2 2 2 2          # refinement ratio
+amr.regrid_int      = 2                # 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
+
+#----------------------TIME STEPING CONTROL----------------------
+max_step            = 100               # maximum number of time steps    
+stop_time           = 0.04             # final physical time
+ns.cfl              = 0.5              # cfl number for hyperbolic system
+ns.init_shrink      = 0.0001           # scale back initial timestep
+ns.change_max       = 1.1              # max timestep size increase
+ns.dt_cutoff        = 1.e-10           # level 0 timestep below which we halt
+
+#-------------------------IO CONTROL----------------------------
+amr.checkpoint_files_output = 0
+amr.check_file          = chk          # root name of checkpoint file
+amr.check_int           = 5            # number of timesteps between checkpoints
+amr.plot_file           = plt_         # root name of plot file
+amr.plot_int            = 100          # number of timesteps between plot files
+amr.derive_plot_vars    = rhoRT mag_vort avg_pressure gradpx gradpy sumRhoYdot mass_fractions rhominsumrhoY cpmix mixfrac_only enthalpy
+amr.grid_log            = grdlog       # name of grid logging file
+
+#----------------------- PROBLEM PARAMETERS---------------------
+prob.P_mean = 101325.0
+prob.standoff = -.012
+prob.pertmag = 0.0004
+pmf.datafile = "dodecaneLu_pmf.dat"
+
+#--------------------REFINEMENT CONTROL------------------------
+amr.refinement_indicators = flame_tracer 
+amr.flame_tracer.max_level     = 3
+amr.flame_tracer.value_greater = 2.e-5
+amr.flame_tracer.field_name    = Y(H)
+
+# Refinement according to temperature and gradient of temperature
+#amr.refinement_indicators = lo_temp gradT
+#amr.lo_temp.max_level = 2
+#amr.lo_temp.value_less = 500
+#amr.lo_temp.field_name = temp
+
+#amr.gradT.max_level = 2
+#amr.gradT.adjacent_difference_greater = 300
+#amr.gradT.field_name = temp
+
+# Refinement according to the vorticity, no field_name needed
+#amr.refinement_indicators = magvort
+#amr.magvort.max_level = 3
+#amr.magvort.vorticity_greater = 300
+
+#---------------------PHYSICS CONTROL------------------------
+ns.fuelName          = NC12H26         # Fuel species name
+ns.unity_Le          = 0               # Use unity Le number transport ?
+ns.hack_nochem       = 0               # Bypass chemistry ? 0: no, 1: yes
+ns.gravity           = 0               # body force  (gravity in MKS units)
+peleLM.mixtureFraction.format = Cantera
+peleLM.mixtureFraction.type   = mole
+peleLM.mixtureFraction.oxidTank = O2:0.21 N2:0.79
+peleLM.mixtureFraction.fuelTank = NC12H26:1.0
+peleLM.deltaT_crashOnConvFail = 0
+
+#--------------------NUMERICS CONTROL------------------------
+ns.init_iter         = 3               # Number of initial iterations to def pressure
+ns.num_divu_iters    = 1               # Number of DivU iteration at initialization
+ns.sdc_iterMAX       = 2               # Number of SDC iterations
+ns.num_mac_sync_iter = 1               # Number of mac_sync iterations
+
+
+# --------------- INPUTS TO CHEMISTRY REACTOR ---------------
+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 = GMRES              # CVODE Linear solve type (for Newton direction) 
+cvode.max_order  = 4                  # CVODE max BDF order. 
+
+# ------------------  INPUTS TO ACTIVE CONTROL  ----------------------
+active_control.on = 0                  # Use AC ?
+active_control.use_temp = 1            # Default in fuel mass, rather use iso-T position ?
+active_control.temperature = 1300.0    # Value of iso-T ?
+active_control.tau = 1.0e-4            # Control tau (should ~ 10 dt)
+active_control.height = 0.0070         # Where is the flame held ? Default assumes coordinate along Y in 2D or Z in 3D.
+active_control.v = 1                   # verbose
+active_control.velMax = 1.5            # Optional: limit inlet velocity
+active_control.changeMax = 0.2         # Optional: limit inlet velocity changes (absolute)
+active_control.flameDir  = 2           # Optional: flame main direction. Default: AMREX_SPACEDIM-1
+
+# ---------------------------------------------------------------
+# ------------------  ADVANCED USER INPUTS ----------------------
+# ---------------------------------------------------------------
+
+#----------------  ADV ALGORITHM CONTROL  -------------------
+ns.sum_interval      = 5               # timesteps between computing mass
+ns.do_reflux         = 1               # 1 => do refluxing
+ns.do_mac_proj       = 1               # 1 => do MAC projection
+ns.do_sync_proj      = 1               # 1 => do Sync Project
+ns.divu_relax_factor = 0.0
+ns.be_cn_theta       = 0.5
+ns.do_temp           = 1
+ns.do_diffuse_sync   = 1
+ns.do_reflux_visc    = 1
+ns.zeroBndryVisc     = 1
+ns.v                 = 1
+
+# 
+ns.divu_ceiling         = 1
+ns.divu_dt_factor       = .4
+ns.min_rho_divu_ceiling = .01
+
+# ------------------  INPUTS TO DIFFUSION CLASS --------------------
+ns.visc_tol              = 1.0e-12     # tolerence for viscous solves
+ns.visc_abs_tol          = 1.0e-12     # tolerence for viscous solves
+diffuse.max_order        = 4
+diffuse.tensor_max_order = 4
+diffuse.v                = 0
+
+# ------------------  INPUTS TO PROJECTION CLASS -------------------
+proj.proj_tol            = 1.0e-11     # tolerence for projections
+proj.proj_abs_tol        = 1.0e-11 
+proj.sync_tol            = 1.0e-11     # tolerence for projections
+proj.rho_wgt_vel_proj    = 0           # 0 => const den proj, 1 => rho weighted
+proj.do_outflow_bcs      = 0
+proj.divu_minus_s_factor = .5
+proj.divu_minus_s_factor = 0.
+proj.proj_2              = 1
+nodal_proj.verbose       = 0
+proj.v                   = 0
+
+# ------------------  INPUTS TO MACPROJ CLASS -------------------
+mac.mac_tol              = 1.0e-11     # tolerence for mac projections
+mac.mac_sync_tol         = 1.0e-11     # tolerence for mac SYNC projection
+mac.mac_abs_tol          = 1.0e-11
+mac.do_outflow_bcs       = 0
+mac.v                    = 0
+
+#--------------------------OMP TILE INPUTS-----------------------------
+#fabarray.mfiter_tile_size = 8 8 8
+
+#--------------------------DEBUG/REGTESTS INPUTS-----------------------------
+amrex.abort_on_out_of_gpu_memory = 1
+#amrex.regtest_reduction=1
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1

Source/PeleLM.cpp

@@ -6688,7 +6688,6 @@ PeleLM::mac_sync ()
                                          advectionType,prev_time,
                                          prev_pres_time,dt,NUM_STATE,
                                          be_cn_theta,
-                                         modify_reflux_normal_vel,
                                          do_mom_diff,
                                          incr_sync,
                                          last_mac_sync_iter);
@@ -6702,7 +6701,7 @@ PeleLM::mac_sync ()
                mac_projector->mac_sync_compute(level,Ucorr,Vsync,comp,
                                                comp,EdgeState, comp,rho_half,
                                                (level > 0 ? &getAdvFluxReg(level):0),
-                                               advectionType,modify_reflux_normal_vel,dt,
+                                               advectionType,dt,
                                                last_mac_sync_iter);
             }
          }
@@ -6733,7 +6732,7 @@ PeleLM::mac_sync ()
             mac_projector->mac_sync_compute(level,Ucorr,Ssync,comp,s_ind,
                                             EdgeState,comp,rho_half,
                                             (level > 0 ? &getAdvFluxReg(level):0),
-                                            advectionType,modify_reflux_normal_vel,dt,
+                                            advectionType,dt,
                                             last_mac_sync_iter);
          }
       }