MD's xmas present: EB Godunov (#731)

Co-authored-by: Jon Rood <[email protected]> Co-authored-by: Bruce Perry <[email protected]> Co-authored-by: Bruce Perry <[email protected]>
AMReX-Combustion · Jan 5, 2024 · a0d0d32 · a0d0d32
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diff --git a/Docs/sphinx/Algorithms.rst b/Docs/sphinx/Algorithms.rst
@@ -502,6 +502,11 @@ than PPM simulations.
    Three dimensional energy spectrum at :math:`t = 5\tau`. Solid red: PPM at :math:`N=128^3`; dashed green: MOL at :math:`N=128^3`; dot-dashed  blue: PPM at :math:`N=512^3`; dotted orange: MOL at :math:`N=512^3`; dashed black: spectral code.
 
 
+Advection schemes and EB
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The two main advection schemes (PLM and MOL) described above support the use of complex geometry in the domain (as implemented using the :ref:`Embedded Boundary (EB) formulation <EB>`). While the PLM advection scheme is preferred numerically (less dissipative scheme), the PLM implementation with EB is a recent addition and has not had the same extensive testing as the MOL scheme with EB. Both PLM and MOL may also have issues when the EB intersects the boundary at an angle (this remains to be solved).
+
 
 Diffusion
 ---------

diff --git a/Exec/RegTests/EB-C1/eb-symmetry.inp → Exec/RegTests/EB-C1/eb-symmetry-mol.inp b/Exec/RegTests/EB-C1/eb-symmetry.inp → Exec/RegTests/EB-C1/eb-symmetry-mol.inp
diff --git a/Exec/RegTests/EB-C1/eb-symmetry-plm.inp b/Exec/RegTests/EB-C1/eb-symmetry-plm.inp
@@ -0,0 +1,71 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 100
+stop_time = 0.000005
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0 0 0
+geometry.coord_sys   = 0  # 0 => cart, 1 => RZ  2=>spherical
+geometry.prob_lo     =  -1.0 -1.0 -1.0
+geometry.prob_hi     =   1.0  1.0  1.0
+# use with single level
+amr.n_cell           =  16    16    16
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# 0 = Interior           3 = Symmetry
+# 1 = Inflow             4 = SlipWall
+# 2 = Outflow            5 = NoSlipWall
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+pelec.lo_bc       = "Hard" "Hard" "Hard"
+pelec.hi_bc       = "Hard" "Hard" "Hard"
+
+# WHICH PHYSICS
+pelec.do_hydro = 1
+pelec.diffuse_vel = 1
+pelec.diffuse_temp = 1
+pelec.do_mol = 0
+pelec.do_react = 0
+pelec.do_mms = 1
+pelec.masa_solution_name = ad_cns_3d_les_sph
+
+# TIME STEP CONTROL
+pelec.cfl            = 0.1     # cfl number for hyperbolic system
+pelec.init_shrink    = 0.3     # scale back initial timestep
+pelec.change_max     = 1.1     # max time step growth
+pelec.dt_cutoff      = 5.e-20  # level 0 timestep below which we halt
+
+# 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 mmslog
+#amr.grid_log        = grdlog  # name of grid logging file
+
+# REFINEMENT / REGRIDDING
+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 = 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
+
+# CHECKPOINT FILES
+amr.check_file      = chk        # root name of checkpoint file
+amr.check_int       = 1000        # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_file       = plt        # root name of plotfile
+amr.plot_int        = 1000        # number of timesteps between plotfiles
+amr.plot_vars  =  density Temp
+amr.derive_plot_vars = x_velocity y_velocity z_velocity magvel magvort pressure rhommserror ummserror vmmserror wmmserror pmmserror
+
+# PROBLEM PARAMETERS
+prob.rho_x_fact = 0.0
+
+# EB
+eb2.geom_type = sphere
+eb2.sphere_radius = 0.25
+eb2.sphere_center = 0.0 0.0  0.0
+eb2.sphere_has_fluid_inside = 0
+pelec.eb_isothermal = 0
+ebd.boundary_grad_stencil_type=0
diff --git a/Exec/RegTests/EB-C1/ebmms-2.inp b/Exec/RegTests/EB-C1/ebmms-2.inp
@@ -0,0 +1,71 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 100
+stop_time = 0.000005
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0 0 0
+geometry.coord_sys   = 0  # 0 => cart, 1 => RZ  2=>spherical
+geometry.prob_lo     =  -1.0 -1.0 -1.0
+geometry.prob_hi     =   1.0  1.0  1.0
+# use with single level
+amr.n_cell           =  16    16    16
+
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+# 0 = Interior           3 = Symmetry
+# 1 = Inflow             4 = SlipWall
+# 2 = Outflow            5 = NoSlipWall
+# >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
+pelec.lo_bc       = "Hard" "Hard" "Hard"
+pelec.hi_bc       = "Hard" "Hard" "Hard"
+
+# WHICH PHYSICS
+pelec.do_hydro = 1
+pelec.diffuse_vel = 1
+pelec.diffuse_temp = 1
+pelec.do_mol = 0
+pelec.do_react = 0
+pelec.do_mms = 1
+pelec.masa_solution_name = ad_cns_3d_les_sph
+
+# TIME STEP CONTROL
+pelec.cfl            = 0.1     # cfl number for hyperbolic system
+pelec.init_shrink    = 0.3     # scale back initial timestep
+pelec.change_max     = 1.1     # max time step growth
+pelec.dt_cutoff      = 5.e-20  # level 0 timestep below which we halt
+
+# 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 mmslog
+#amr.grid_log        = grdlog  # name of grid logging file
+
+# REFINEMENT / REGRIDDING
+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 = 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
+
+# CHECKPOINT FILES
+amr.check_file      = chk        # root name of checkpoint file
+amr.check_int       = 1000        # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_file       = plt        # root name of plotfile
+amr.plot_int        = 1000        # number of timesteps between plotfiles
+amr.plot_vars  =  density Temp
+amr.derive_plot_vars = x_velocity y_velocity z_velocity magvel magvort pressure rhommserror ummserror vmmserror wmmserror pmmserror
+
+# PROBLEM PARAMETERS
+
+# EB
+eb2.geom_type = sphere
+eb2.sphere_radius = 0.25
+eb2.sphere_center = 0.0 0.0  0.0
+eb2.sphere_has_fluid_inside = 0
+pelec.eb_boundary_T = 300.
+pelec.eb_isothermal = 1
+ebd.boundary_grad_stencil_type=0
diff --git a/Exec/RegTests/EB-C8/eb-c8-rere.inp → Exec/RegTests/EB-C8/eb-c8-rere-mol.inp b/Exec/RegTests/EB-C8/eb-c8-rere.inp → Exec/RegTests/EB-C8/eb-c8-rere-mol.inp
diff --git a/Exec/RegTests/EB-C8/eb-c8-rere-plm.inp b/Exec/RegTests/EB-C8/eb-c8-rere-plm.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 = 0
+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            = 0.8     # 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/MassCons/masscons-mol-eb.inp b/Exec/RegTests/MassCons/masscons-mol-eb.inp
@@ -0,0 +1,84 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 30
+stop_time =  0.2
+
+# PROBLEM SIZE & GEOMETRY
+geometry.is_periodic = 0 0 0
+geometry.coord_sys   = 0  # 0 => cart, 1 => RZ  2=>spherical
+geometry.prob_lo     = -0.5 -0.5 -0.5
+geometry.prob_hi     =  0.5  0.5  0.5
+amr.n_cell           = 8 8 8
+
+# >>>>>>>>>>>>>  BC KEYWORDS <<<<<<<<<<<<<<<<<<<<<<
+# Interior, UserBC, Symmetry, SlipWall, NoSlipWall
+# >>>>>>>>>>>>>  BC KEYWORDS <<<<<<<<<<<<<<<<<<<<<<
+
+pelec.lo_bc       = "SlipWall"   "NoSlipWall" "Symmetry"
+pelec.hi_bc       = "Hard"       "Hard"       "Hard"
+prob.wall_type    = 1            0            1
+
+# WHICH PHYSICS
+pelec.mol_iorder = 2
+pelec.do_hydro = 1
+pelec.do_mol = 1
+pelec.diffuse_vel = 1
+pelec.diffuse_temp = 1
+pelec.diffuse_spec = 1
+pelec.do_react = 0
+pelec.diffuse_enth = 1
+pelec.add_ext_src = 0
+pelec.external_forcing = 0.0 0.0 0.0
+
+transport.const_viscosity = 1
+transport.const_conductivity = 2.7271624e+04
+
+# TIME STEP CONTROL
+pelec.cfl            = 0.1     # cfl number for hyperbolic system
+pelec.init_shrink    = 1.0     # scale back initial timestep
+pelec.change_max     = 1.05    # scale back initial timestep
+pelec.dt_cutoff      = 5.e-20  # level 0 timestep below which we halt
+
+# 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       = 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 = 8       # block factor in grid generation
+amr.max_grid_size   = 64
+amr.n_error_buf     = 12 8 2 2 # number of buffer cells in error est
+
+# CHECKPOINT FILES
+amr.checkpoint_files_output = 0
+amr.check_file      = chk        # root name of checkpoint file
+amr.check_int       = 500        # number of timesteps between checkpoints
+
+# PLOTFILES
+amr.plot_files_output = 0
+amr.plot_file       = plt        # root name of plotfile
+amr.plot_int        = -1       # number of timesteps between plotfiles
+amr.plot_vars  =  density Temp
+amr.derive_plot_vars = x_velocity y_velocity z_velocity magvel magvort pressure
+pelec.plot_rhoy = 0
+pelec.plot_massfrac = 1
+
+# PROBLEM PARAMETERS
+prob.T_mean = 750.0
+prob.u0 = 10000.0
+prob.v0 =  8000.0
+prob.w0 =  5000.0
+
+# Problem setup
+eb2.geom_type = sphere
+eb2.sphere_center = 0.0 0.0 0.0
+eb2.sphere_radius = 0.2
+eb2.sphere_has_fluid_inside = 0
+pelec.eb_isothermal = 0
+
+#amrex.fpe_trap_invalid = 1
+#amrex.fpe_trap_zero = 1
+#amrex.fpe_trap_overflow = 1