Fix re-redistribution (#680)

AMReX-Combustion · Aug 23, 2023 · bae27e6 · bae27e6
1 parent b4352fb
commit bae27e6
Show file tree

Hide file tree

Showing 33 changed files with 392 additions and 151 deletions.
diff --git a/Docs/sphinx/geometry/EB.rst b/Docs/sphinx/geometry/EB.rst
@@ -100,9 +100,6 @@ This can be controlled in the code with:
 Re-redistribution
 -----------------
 
-.. note::
-   This used to be supported when PeleC had it's own redistribution procedure. This is no longer the case now that we use the redistribution procedure highlighted above. This section is kept for historical purposes.
-
 .. _eb_re_redist:
 
 .. figure:: EB_re_redist.png
@@ -127,7 +124,7 @@ advanced a single time step, which we refer to as re-redistribution. Specificall
 
 The re-redistribution is implemented as a book-keeping step where the mass distributed are stored during MOL divergence calculation and given to the coarse and fine flux registers to reflux at 
 the end of each time step. The re-redistribution is performed every time the reflux function is called in post_timestep. More details regarding re-redistribution are 
-presented in `Pember et al. <https://www.sciencedirect.com/science/article/pii/S0021999185711655>`_. 
+presented in `Pember et al. <https://www.sciencedirect.com/science/article/pii/S0021999185711655>`_. A forthcoming paper will describe the methodology for this procedure when using state redistribution.
 
 
 Date Structures and utility functions

diff --git a/Exec/RegTests/EB-C1/eb-symmetry.inp b/Exec/RegTests/EB-C1/eb-symmetry.inp
@@ -45,7 +45,7 @@ amr.max_level       = 0       # maximum level number allowed
 #amr.max_level       = 1       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
 

diff --git a/Exec/RegTests/EB-C1/ebmms-1.inp b/Exec/RegTests/EB-C1/ebmms-1.inp
@@ -45,7 +45,7 @@ amr.max_level       = 0       # maximum level number allowed
 #amr.max_level       = 1       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 64
 amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
 

diff --git a/Exec/RegTests/EB-C1/example.inp b/Exec/RegTests/EB-C1/example.inp
@@ -46,7 +46,7 @@ amr.max_level       = 0       # maximum level number allowed
 #amr.max_level       = 1       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 64
 amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
 

diff --git a/Exec/RegTests/EB-C11/eb-c11.inp b/Exec/RegTests/EB-C11/eb-c11.inp
@@ -42,7 +42,7 @@ amr.data_log         = datlog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 64
 amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
 

diff --git a/Exec/RegTests/EB-C11/example.inp b/Exec/RegTests/EB-C11/example.inp
@@ -42,7 +42,7 @@ amr.data_log         = datlog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 64
 amr.n_error_buf     = 2 2 2 2 # number of buffer cells in error est
 

diff --git a/Exec/RegTests/EB-C12/eb-c12.inp b/Exec/RegTests/EB-C12/eb-c12.inp
@@ -47,7 +47,7 @@ amr.data_log         = datlog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C12/example.inp b/Exec/RegTests/EB-C12/example.inp
@@ -46,7 +46,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C13/example.inp b/Exec/RegTests/EB-C13/example.inp
@@ -53,7 +53,7 @@ amr.data_log         = datlog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C3/eb-c3.inp b/Exec/RegTests/EB-C3/eb-c3.inp
@@ -49,7 +49,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C3/example.inp b/Exec/RegTests/EB-C3/example.inp
@@ -49,7 +49,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C4-5/eb-c4.inp b/Exec/RegTests/EB-C4-5/eb-c4.inp
@@ -53,7 +53,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C4-5/eb-c5.inp b/Exec/RegTests/EB-C4-5/eb-c5.inp
@@ -52,7 +52,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C4-5/example.inp b/Exec/RegTests/EB-C4-5/example.inp
@@ -53,7 +53,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C8/eb-c8-rere.inp b/Exec/RegTests/EB-C8/eb-c8-rere.inp
@@ -0,0 +1,90 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 10000
+stop_time =  1.959e-6 #final time is 0.2*L*sqrt(rhoL/pL)
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0  0  1
+geometry.coord_sys   = 0  # 0 => cart, 1 => RZ  2=>spherical
+geometry.prob_lo     = 0.0  -0.13  0.0
+geometry.prob_hi     = 0.87 0.653 0.0435
+amr.n_cell           =  160 144 8
+
+# >>>>>>>>>>>>>  BC KEYWORDS <<<<<<<<<<<<<<<<<<<<<<
+# Interior, UserBC, Symmetry, SlipWall, NoSlipWall
+# >>>>>>>>>>>>>  BC KEYWORDS <<<<<<<<<<<<<<<<<<<<<<
+pelec.lo_bc       =  "FOExtrap"  "NoSlipWall"  "Interior"
+pelec.hi_bc       =  "FOExtrap"  "NoSlipWall"  "Interior"
+
+# WHICH PHYSICS
+pelec.do_hydro = 1
+pelec.do_mol = 1
+pelec.diffuse_vel = 0
+pelec.diffuse_temp = 0
+pelec.diffuse_spec = 0
+pelec.do_react = 0
+pelec.diffuse_enth = 0
+
+# TIME STEP CONTROL
+pelec.dt_cutoff      = 5.e-20  # level 0 timestep below which we halt
+pelec.cfl            = 0.2     # cfl number for hyperbolic system
+pelec.init_shrink    = 0.8     # scale back initial timestep
+pelec.change_max     = 1.05    # scale back initial timestep
+
+# DIAGNOSTICS & VERBOSITY
+pelec.sum_interval   = 1       # timesteps between computing mass
+pelec.v              = 1       # verbosity in PeleC.cpp
+amr.v                = 1       # verbosity in Amr.cpp
+amr.data_log         = datlog
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 1       # maximum level number allowed
+amr.ref_ratio       = 2 2 2 2 # refinement ratio
+amr.regrid_int      = 2 2 2 2 # how often to regrid
+amr.n_error_buf     = 0 0 0 0 # number of buffer cells in error est
+amr.blocking_factor = 8       # block factor in grid generation
+amr.max_grid_size   = 64
+amr.grid_eff        = 0.99
+
+# CHECKPOINT FILES
+amr.checkpoint_files_output = 0
+amr.check_file      = chk        # root name of checkpoint file
+amr.check_int       = -1        # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_files_output = 1
+amr.plot_file       = plt        # root name of plotfile
+amr.plot_int        = 100        # number of timesteps between plotfiles
+amr.derive_plot_vars = ALL
+
+# PROBLEM PARAMETERS
+prob.p_l = 1e7
+prob.rho_l = 9.6e-4
+prob.p_r = 1e6
+prob.rho_r = 1.2e-4
+prob.angle = 30.0
+prob.left_gas = N2
+prob.right_gas = HE
+
+# Problem setup
+pelec.eb_boundary_T = 300.
+pelec.eb_isothermal = 0
+
+# TAGGING
+tagging.denerr = 1e20
+tagging.dengrad = 4e-5
+tagging.max_denerr_lev = 3
+tagging.max_dengrad_lev = 3
+tagging.tempgrad = 50.0
+tagging.max_tempgrad_lev = 3
+tagging.max_vfracerr_lev = 0
+tagging.eb_refine_type = "adaptive"
+tagging.max_eb_refine_lev = 0
+tagging.min_eb_refine_lev = 0
+
+eb2.geom_type = "rotated_box"
+eb2.box_lo = -10.0 -0.172 -10.0
+eb2.box_hi = 10.0 0.172 10.0
+eb2.box_rotation = 30.0
+eb2.box_rotation_axe = 2
+eb2.box_has_fluid_inside = 1
+ebd.boundary_grad_stencil_type = 0
diff --git a/Exec/RegTests/EB-C8/eb-c8.inp b/Exec/RegTests/EB-C8/eb-c8.inp
@@ -40,8 +40,10 @@ amr.data_log         = datlog
 amr.max_level       = 1       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
+amr.n_error_buf     = 0 0 0 0 # number of buffer cells in error est
 amr.blocking_factor = 8       # block factor in grid generation
-amr.max_grid_size   = 32
+amr.max_grid_size   = 64
+amr.grid_eff        = 0.99
 
 # CHECKPOINT FILES
 amr.checkpoint_files_output = 0
@@ -75,13 +77,10 @@ tagging.max_dengrad_lev = 3
 tagging.tempgrad = 50.0
 tagging.max_tempgrad_lev = 3
 
-eb2.geom_type = "extruded_triangles"
-extruded_triangles.num_tri = 2
-extruded_triangles.tri_0_point_0 = -20.0 -11.662475437630437 0.0
-extruded_triangles.tri_0_point_1 = 22.0 -20.0 0.0
-extruded_triangles.tri_0_point_2 = 22.0 12.586235868333839 0.0
-
-extruded_triangles.tri_1_point_0 = -20.0 -11.431535329954588 0.0
-extruded_triangles.tri_1_point_1 = 22.0 12.817175976009688 0.0
-extruded_triangles.tri_1_point_2 = -20.0 20.0 0.0
-ebd.boundary_grad_stencil_type = 0
+eb2.geom_type = "rotated_box"
+eb2.box_lo = -10.0 -0.172 -10.0
+eb2.box_hi = 10.0 0.172 10.0
+eb2.box_rotation = 30.0
+eb2.box_rotation_axe = 2
+eb2.box_has_fluid_inside = 1
+ebd.boundary_grad_stencil_type = 0
diff --git a/Exec/RegTests/EB-C8/example.inp b/Exec/RegTests/EB-C8/example.inp
@@ -73,13 +73,10 @@ tagging.dengrad = 4e-5
 tagging.max_denerr_lev = 3
 tagging.max_dengrad_lev = 3
 
-eb2.geom_type = "extruded_triangles"
-extruded_triangles.num_tri = 2
-extruded_triangles.tri_0_point_0 = -20.0 -11.662475437630437 0.0
-extruded_triangles.tri_0_point_1 = 22.0 -20.0 0.0
-extruded_triangles.tri_0_point_2 = 22.0 12.586235868333839 0.0
-
-extruded_triangles.tri_1_point_0 = -20.0 -11.431535329954588 0.0
-extruded_triangles.tri_1_point_1 = 22.0 12.817175976009688 0.0
-extruded_triangles.tri_1_point_2 = -20.0 20.0 0.0
-ebd.boundary_grad_stencil_type = 0
+eb2.geom_type = "rotated_box"
+eb2.box_lo = -10.0 -0.172 -10.0
+eb2.box_hi = 10.0 0.172 10.0
+eb2.box_rotation = 30.0
+eb2.box_rotation_axe = 2
+eb2.box_has_fluid_inside = 1
+ebd.boundary_grad_stencil_type = 0
diff --git a/Exec/RegTests/EB-C8/simple-advection.inp b/Exec/RegTests/EB-C8/simple-advection.inp
@@ -41,7 +41,7 @@ amr.data_log         = datlog extremalog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2 2 2 2 # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES
@@ -78,13 +78,5 @@ tagging.dengrad = 4e-5
 tagging.max_denerr_lev = 3
 tagging.max_dengrad_lev = 3
 
-# eb2.geom_type = "extruded_triangles"
-# extruded_triangles.num_tri = 2
-# extruded_triangles.tri_0_point_0 = -20.0 -11.662475437630437 0.0
-# extruded_triangles.tri_0_point_1 = 22.0 -20.0 0.0
-# extruded_triangles.tri_0_point_2 = 22.0 12.586235868333839 0.0
-# extruded_triangles.tri_1_point_0 = -20.0 -11.431535329954588 0.0
-# extruded_triangles.tri_1_point_1 = 22.0 12.817175976009688 0.0
-# extruded_triangles.tri_1_point_2 = -20.0 20.0 0.0
 ebd.boundary_grad_stencil_type = 0
 eb2.geom_type = "all_regular"
diff --git a/Exec/RegTests/EB-C9/eb-c9.inp b/Exec/RegTests/EB-C9/eb-c9.inp
@@ -47,7 +47,7 @@ amr.data_log         = datlog
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/EB-C9/example.inp b/Exec/RegTests/EB-C9/example.inp
@@ -46,7 +46,7 @@ amr.v                = 1       # verbosity in Amr.cpp
 amr.max_level       = 0       # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 # refinement ratio
 amr.regrid_int      = 2       # how often to regrid
-amr.blocking_factor = 4       # block factor in grid generation
+amr.blocking_factor = 8       # block factor in grid generation
 amr.max_grid_size   = 32
 
 # CHECKPOINT FILES

diff --git a/Exec/RegTests/Sod/sod-3.inp b/Exec/RegTests/Sod/sod-3.inp
@@ -81,8 +81,6 @@ tagging.min_eb_refine_lev = 0
 
 tagging.refinement_indicators = box
 tagging.box.in_box_lo =  0.6  0.125  0.125
-#tagging.box.in_box_lo =  0.6  0.0  0.125
-#tagging.box.in_box_hi =  0.8  0.25  0.25
 tagging.box.in_box_hi =  0.8  0.22  0.25
 
 # EB