Minor updates

Docs/source/LMeXControls.rst

@@ -127,7 +127,13 @@ The following list of derived variables are available in PeleLMeX:
       - Vorticity (2D) or vorticity magnitude (3D)
     * - `kinetic_energy`
       - 1
-      - Kinetic energy
+      - Kinetic energy: 0.5 * rho * (u^2+v^2+w^2)
+    * - `enstrophy`
+      - 1
+      - enstrophy: 0.5 * rho * (\omega_x^2+\omega_y^2+\omega_z^2)
+    * - `HeatRelease`
+      - 1
+      - Heat release rate from chem. reactions
 
 Note that `mixture_fraction` and `progress_variable` requires additional inputs from the users as described below.
 
@@ -203,6 +209,27 @@ Linear solvers are a key component of PeleLMeX algorithm, separate controls are
 Run-time diagnostics
 --------------------
 
+PeleLMeX provides a few diagnostics to check you simulations while it is running as well as adding basic analysis ingredients.
+
+It is often usefull to have an estimate of integrated quantities (kinetic energy, heat release rate, ,..), state extremas
+or other overall balance information to get a sense of the status and sanity of the simulation. To this end, it is possible
+to activate `temporal` diagnostics performing these reductions at given intervals:
+
+::
+
+    #-------------------------TEMPORALS---------------------------
+    peleLM.do_temporals = 1                     # [OPT, DEF=0] Activate temporal diagnostics
+    peleLM.temporal_int = 10                    # [OPT, DEF=5] Temporal freq.
+    peleLM.do_extremas = 1                      # [OPT, DEF=0] Trigger extremas, if temporals activated
+    peleLM.do_mass_balance = 1                  # [OPT, DEF=0] Compute mass balance, if temporals activated
+
+The `do_temporal` flag will trigger the creation of a `temporals` folder in your run directory and the following entries 
+will be appended to an ASCII `temporals/tempState` file: step, time, dt, kin. energy integral, enstrophy integral, mean pressure
+, fuel consumption rate integral, heat release rate integral. Additionnally, if the `do_temporal` flag is activated, one can
+turn on state extremas (stored in `temporals/tempExtremas` as min/max for each state entry) and mass balance (stored in
+`temporals/tempMass`) computing the total mass, dMdt and mass fluxes across the domain boundary as well as the error in
+the balance (dMdt - sum of fluxes).
+
 Combustion diagnostics often involve the use of a mixture fraction and/or a progress variable, both of which can be defined
 at run time and added to the derived variables included in the plotfile. If `mixture_fraction` or `progress_variable` is
 added to the `amr.derive_plot_vars` list, one need to provide input for defining those. The mixture fraction is based on

Exec/Cases/ChallengeProblem/input.3d-regt

@@ -106,8 +106,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 3
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 peleLM.num_init_iter = 1
 peleLM.num_divu_iter = 1
 

Exec/Cases/ChallengeProblem/input.3d-regt_AMR

@@ -106,8 +106,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 3
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 peleLM.num_init_iter = 1
 peleLM.num_divu_iter = 1
 

Exec/Cases/ChallengeProblem/input.3d-regt_Quarter

@@ -65,8 +65,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 3
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 peleLM.num_init_iter = 1
 peleLM.num_divu_iter = 1
 

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

@@ -72,8 +72,7 @@ mac_proj.verbose = 0
 #diffusion.verbose = 2
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #--------------------REFINEMENT CONTROL------------------------
 amr.refinement_indicators = temp

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

@@ -110,8 +110,7 @@ nodal_proj.rtol = 1.0e-10
 #diffusion.verbose = 2
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #--------------------REFINEMENT CONTROL------------------------
 amr.refinement_indicators = temp

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

@@ -41,8 +41,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 0
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #amr.restart = chk00700
 amr.check_int = 20

Exec/RegTests/EB_EnclosedFlame/input.2d-regt_Hypre

@@ -41,8 +41,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 0
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #amr.restart = chk00030
 amr.check_int = 20

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

@@ -41,8 +41,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 1
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #amr.restart = chk00700
 amr.check_int = 20

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

@@ -39,8 +39,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 3
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 amr.check_int = 100
 amr.plot_int = 50

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

@@ -40,8 +40,7 @@ peleLM.num_divu_iter = 1
 peleLM.num_init_iter = 3
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #amr.restart = chk00005
 amr.check_int = 5

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

@@ -40,8 +40,7 @@ peleLM.num_divu_iter = 0
 peleLM.num_init_iter = 1
 
 peleLM.do_temporals = 1
-peleLM.temporal_int = 2
-peleLM.mass_balance = 1
+peleLM.do_mass_balance = 1
 
 #amr.restart = chk01000
 amr.check_int = 100

Exec/RegTests/EB_PipeFlow/input.3d-channel_noEB

@@ -0,0 +1,68 @@
+#----------------------DOMAIN DEFINITION------------------------
+# https://amrex-combustion.github.io/PeleLMeX/LMeXControls.html
+geometry.is_periodic = 1 0 1              # For each dir, 0: non-perio, 1: periodic
+geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
+geometry.prob_lo     = 0.0 -0.005 -0.0075        # x_lo y_lo (z_lo)
+geometry.prob_hi     = 0.03 0.005 0.0075  # x_hi y_hi (z_hi)
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# Interior, Inflow, Outflow, Symmetry,
+# SlipWallAdiab, NoSlipWallAdiab, SlipWallIsotherm, NoSlipWallIsotherm
+# STM: NoSlipWallIsotherm crashes?
+peleLM.lo_bc = Interior NoSlipWallAdiab Interior
+peleLM.hi_bc = Interior NoSlipWallAdiab Interior
+
+
+#-------------------------AMR CONTROL----------------------------
+#amr.n_cell          = 96 32 48         # Level 0 number of cells in each direction   
+#amr.n_cell          = 1152 384 576      # Level 0 number of cells in each direction   
+amr.n_cell           = 384  128 192
+amr.n_cell           = 576  192 256
+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      = 1000             # 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   = 128               # max box size
+
+#--------------------------- Problem -------------------------------
+prob.T_mean = 750.0
+prob.P_mean = 101325.0
+prob.problem_type = 2
+prob.meanFlowMag = 5.0
+
+#-------------------------PeleLM CONTROL----------------------------
+peleLM.v = 1
+peleLM.incompressible = 0
+peleLM.gradP0 = -709.79 0.0 0.0
+
+peleLM.do_temporals = 1
+peleLM.temporal_int = 10
+
+#amr.restart = chk30000
+amr.max_step = 1000
+amr.stop_time = 0.2
+amr.plot_int = 100
+amr.check_int = 100
+amr.cfl = 0.5
+amr.derive_plot_vars = avg_pressure mag_vort
+
+peleLM.chem_integrator   = "ReactorNull"   # Chemistry integrator, from PelePhysics available list
+
+#--------------------REFINEMENT CONTROL------------------------
+#amr.refinement_indicators = temp
+#amr.temp.max_level     = 2
+#amr.temp.value_greater = 305
+#amr.temp.field_name    = temp
+
+amr.refinement_indicators = yLow yHigh
+amr.yLow.in_box_lo = -0.001  -0.0052  -0.0085
+amr.yLow.in_box_hi =  0.031 -0.0045    0.0085
+amr.yHigh.in_box_lo = -0.001  0.0045  -0.0085
+amr.yHigh.in_box_hi =  0.031  0.0052    0.0085
+
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1