support for EB checkpoint files

src/embedded_boundaries/CMakeLists.txt

@@ -12,6 +12,7 @@ target_sources(incflo
    eb_spherecube.cpp
    eb_tuscan.cpp
    eb_twocylinders.cpp
+   eb_chkptfile.cpp
    writeEBsurface.cpp
    eb_if.H
    )

src/embedded_boundaries/Make.package

@@ -5,6 +5,7 @@ CEXE_sources += eb_cylinder.cpp
 CEXE_sources += eb_cyl_tuscan.cpp
 CEXE_sources += eb_regular.cpp
 CEXE_sources += eb_sphere.cpp
+CEXE_sources += eb_chkptfile.cpp
 ifeq ($(DIM), 3)
   CEXE_sources += eb_spherecube.cpp
   CEXE_sources += eb_tuscan.cpp

src/embedded_boundaries/eb_chkptfile.cpp

@@ -0,0 +1,13 @@
+#include <AMReX_EB2.H>
+
+#include <incflo.H>
+
+using namespace amrex;
+
+void incflo::make_eb_chkptfile()
+{
+   // Build index space
+   int max_level_here = 0;
+   int max_coarsening_level = 100;
+   EB2::BuildFromChkptFile("geom_chk", geom.back(), max_level_here, max_level_here + max_coarsening_level);
+}

src/embedded_boundaries/embedded_boundaries.cpp

@@ -1,4 +1,5 @@
 #include <AMReX_ParmParse.H>
+#include <AMReX_EB2.H>
 
 #include <algorithm>
 #include <incflo.H>
@@ -65,11 +66,21 @@ void incflo::MakeEBGeometry()
     amrex::Print() << "\n Building JCAP geometry." << std::endl;
         make_eb_cyl_tuscan();
     }
+    else if(geom_type == "chkptfile")
+    {
+       make_eb_chkptfile();
+    }
     else
     {
     amrex::Print() << "\n No EB geometry declared in inputs => "
                    << " Will build all regular geometry." << std::endl;
         make_eb_regular();
     }
     amrex::Print() << "Done making the geometry ebfactory.\n" << std::endl;
+
+    if (m_write_geom_chk) {
+       const auto& is = amrex::EB2::IndexSpace::top();
+       const auto& eb_level = is.getLevel(geom.back());
+       eb_level.write_to_chkpt_file("geom_chk", amrex::EB2::ExtendDomainFace(), amrex::EB2::max_grid_size);
+    }
 }

src/incflo.H

@@ -439,6 +439,8 @@ private:
        {}
     };
     EBFlow_t m_eb_flow;
+
+    bool m_write_geom_chk = false;
 #else
     // If using Godunov with no EB, default to PPM
     bool m_godunov_ppm         = true;
@@ -816,6 +818,7 @@ private:
     void make_eb_spherecube ();
     void make_eb_cyl_tuscan ();
     void make_eb_tuscan ();
+    void make_eb_chkptfile ();
 #endif
 
     ///////////////////////////////////////////////////////////////////////////

src/setup/init.cpp

@@ -71,6 +71,7 @@ void incflo::ReadParameters ()
             amrex::Abort("redistribution type must be NoRedist, FluxRedist, or StateRedist");
 
         if (m_advection_type == "Godunov" && m_godunov_ppm) amrex::Abort("Cant use PPM with EBGodunov");
+        pp.query("write_geom_chk", m_write_geom_chk);
 #endif
 
         if (m_advection_type == "MOL") m_godunov_include_diff_in_forcing = false;

test_2d/benchmark.eb_chkptfile.read

@@ -0,0 +1,89 @@
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            SIMULATION STOP            #
+#.......................................#
+stop_time               =   0.025       # Max (simulated) time to evolve
+max_step                =   -1          # Max number of time steps
+steady_state            =   0           # Steady-state solver? 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#         TIME STEP COMPUTATION         #
+#.......................................#
+incflo.fixed_dt         =   -1.0        # Use this constant dt if > 0
+incflo.cfl              =   0.45        # CFL factor
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            INPUT AND OUTPUT           #
+#.......................................#
+amr.plot_per_exact      =   0.01        # Steps between plot files
+amr.check_int           =   1000        # Steps between checkpoint files
+amr.restart             =   ""          # Checkpoint to restart from 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#               PHYSICS                 #
+#.......................................#
+incflo.gravity          =   0.  0.      # Gravitational force (3D)
+incflo.ro_0             =   1.          # Reference density 
+
+incflo.fluid_model      =   "newtonian" # Fluid model (rheology)
+incflo.mu               =   0.001       # Dynamic viscosity coefficient
+
+incflo.constant_density =   true        #
+
+incflo.ntrac            =   1           # Number of tracers
+incflo.advect_tracer    =   true        # Should we update them?
+incflo.mu_s             =   0.001       # Scalar diffusion coefficient
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#        ADAPTIVE MESH REFINEMENT       #
+#.......................................#
+amr.n_cell              =   96 32       # Grid cells at coarsest AMRlevel
+amr.max_level           =   1           # Max AMR level in hierarchy 
+amr.grid_eff            =   0.7 
+amr.n_error_buf         =   8
+amr.max_grid_size_x     =   1024
+amr.max_grid_size_y     =   1024
+amr.max_grid_size_z     =   1024
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              GEOMETRY                 #
+#.......................................#
+geometry.prob_lo        =   0.  0.      # Lo corner coordinates
+geometry.prob_hi        =   1.2 0.4     # Hi corner coordinates
+geometry.is_periodic    =   0   0       # Periodicity x y z (0/1)
+
+# Boundary conditions
+ylo.type                =   "nsw"
+ylo.velocity            =   0.  0.  0.
+yhi.type                =   "nsw"
+yhi.velocity            =   0.  0.  0.
+
+xlo.type                =   "mi"
+xlo.velocity            =   1.  0.  0.
+xlo.tracer              =   1.
+xhi.type                =   "po"
+xhi.pressure            =   0.0
+
+# Add cylinder
+incflo.geometry         = "chkptfile"
+#sphere.internal_flow    = false
+#sphere.radius           = 0.05000001
+#sphere.center           = 0.15  0.2 0.0
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#           INITIAL CONDITIONS          #
+#.......................................#
+incflo.probtype         =   31
+incflo.ic_u             =   1.0         #
+incflo.ic_v             =   0.0         #
+incflo.ic_p             =   0.0         #
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              VERBOSITY                #
+#.......................................#
+incflo.verbose            =   1         # incflo itself
+mac_proj.verbose          =   1         # MAC Projector
+nodal_proj.verbose        =   1         # Nodal Projector
+scalar_diffusion.verbose  =   1         # Scalar Diffusion 
+tensor_diffusion.verbose  =   1         # Tensor Diffusion
+
+amr.plt_ccse_regtest    =   1

test_2d/benchmark.eb_chkptfile.write

@@ -0,0 +1,91 @@
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            SIMULATION STOP            #
+#.......................................#
+stop_time               =   0.025       # Max (simulated) time to evolve
+max_step                =   -1          # Max number of time steps
+steady_state            =   0           # Steady-state solver? 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#         TIME STEP COMPUTATION         #
+#.......................................#
+incflo.fixed_dt         =   -1.0        # Use this constant dt if > 0
+incflo.cfl              =   0.45        # CFL factor
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            INPUT AND OUTPUT           #
+#.......................................#
+amr.plot_per_exact      =   0.01        # Steps between plot files
+amr.check_int           =   1000        # Steps between checkpoint files
+amr.restart             =   ""          # Checkpoint to restart from 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#               PHYSICS                 #
+#.......................................#
+incflo.gravity          =   0.  0.      # Gravitational force (3D)
+incflo.ro_0             =   1.          # Reference density 
+
+incflo.fluid_model      =   "newtonian" # Fluid model (rheology)
+incflo.mu               =   0.001       # Dynamic viscosity coefficient
+
+incflo.constant_density =   true        #
+
+incflo.ntrac            =   1           # Number of tracers
+incflo.advect_tracer    =   true        # Should we update them?
+incflo.mu_s             =   0.001       # Scalar diffusion coefficient
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#        ADAPTIVE MESH REFINEMENT       #
+#.......................................#
+amr.n_cell              =   96 32       # Grid cells at coarsest AMRlevel
+amr.max_level           =   1           # Max AMR level in hierarchy 
+amr.grid_eff            =   0.7 
+amr.n_error_buf         =   8
+amr.max_grid_size_x     =   1024
+amr.max_grid_size_y     =   1024
+amr.max_grid_size_z     =   1024
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              GEOMETRY                 #
+#.......................................#
+geometry.prob_lo        =   0.  0.      # Lo corner coordinates
+geometry.prob_hi        =   1.2 0.4     # Hi corner coordinates
+geometry.is_periodic    =   0   0       # Periodicity x y z (0/1)
+
+# Boundary conditions
+ylo.type                =   "nsw"
+ylo.velocity            =   0.  0.  0.
+yhi.type                =   "nsw"
+yhi.velocity            =   0.  0.  0.
+
+xlo.type                =   "mi"
+xlo.velocity            =   1.  0.  0.
+xlo.tracer              =   1.
+xhi.type                =   "po"
+xhi.pressure            =   0.0
+
+# Add cylinder
+incflo.geometry         = "sphere"
+sphere.internal_flow    = false
+sphere.radius           = 0.05000001
+sphere.center           = 0.15  0.2 0.0
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#           INITIAL CONDITIONS          #
+#.......................................#
+incflo.probtype         =   31
+incflo.ic_u             =   1.0         #
+incflo.ic_v             =   0.0         #
+incflo.ic_p             =   0.0         #
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              VERBOSITY                #
+#.......................................#
+incflo.verbose            =   1         # incflo itself
+mac_proj.verbose          =   1         # MAC Projector
+nodal_proj.verbose        =   1         # Nodal Projector
+scalar_diffusion.verbose  =   1         # Scalar Diffusion 
+tensor_diffusion.verbose  =   1         # Tensor Diffusion
+
+amr.plt_ccse_regtest    =   1
+
+incflo.write_geom_chk   =   1

test_3d/benchmark.eb_chkptfile.read

@@ -0,0 +1,88 @@
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            SIMULATION STOP            #
+#.......................................#
+stop_time               =   0.025       # Max (simulated) time to evolve
+max_step                =  -1           # Max number of time steps
+steady_state            =   0           # Steady-state solver? 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#         TIME STEP COMPUTATION         #
+#.......................................#
+incflo.fixed_dt         =   -1.0        # Use this constant dt if > 0
+incflo.cfl              =   0.45        # CFL factor
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#            INPUT AND OUTPUT           #
+#.......................................#
+amr.plot_per_exact      =   0.01        # Steps between plot files
+amr.check_int           =   1000        # Steps between checkpoint files
+amr.restart             =   ""          # Checkpoint to restart from 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#               PHYSICS                 #
+#.......................................#
+incflo.gravity          =   0.  0.  0.  # Gravitational force (3D)
+incflo.ro_0             =   1.          # Reference density 
+
+incflo.fluid_model      =   "newtonian" # Fluid model (rheology)
+incflo.mu               =   0.001       # Dynamic viscosity coefficient
+
+incflo.ntrac            =   1           # Number of tracers
+incflo.advect_tracer    =   true        # Should we update them?
+incflo.mu_s             =   0.001       # Scalar diffusion coefficient
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#        ADAPTIVE MESH REFINEMENT       #
+#.......................................#
+amr.n_cell              =   96 32  8    # Grid cells at coarsest AMRlevel
+amr.max_level           =   1           # Max AMR level in hierarchy 
+amr.grid_eff            =   0.7 
+amr.n_error_buf         =   8
+amr.max_grid_size_x     =   1024
+amr.max_grid_size_y     =   1024
+amr.max_grid_size_z     =   1024
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              GEOMETRY                 #
+#.......................................#
+geometry.prob_lo        =   0.  0.  0.  # Lo corner coordinates
+geometry.prob_hi        =   1.2 0.4 0.1 # Hi corner coordinates
+geometry.is_periodic    =   0   0   1   # Periodicity x y z (0/1)
+
+# Boundary conditions
+ylo.type                =   "nsw"
+ylo.velocity            =   0.  0.  0.
+yhi.type                =   "nsw"
+yhi.velocity            =   0.  0.  0.
+xlo.type                =   "mi"
+xlo.velocity            =   1.  0.  0.
+xlo.tracer              =   1.
+xhi.type                =   "po"
+xhi.pressure            =   0.0
+
+# Add cylinder 
+incflo.geometry         = "chkptfile"
+#cylinder.internal_flow  = false
+#cylinder.radius         = 0.05000001
+#cylinder.direction      = 2
+#cylinder.center         = 0.151  0.2  0.0 
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#           INITIAL CONDITIONS          #
+#.......................................#
+incflo.probtype         =   31
+incflo.ic_u             =   1.0         #
+incflo.ic_v             =   0.0         #
+incflo.ic_w             =   0.0         #
+incflo.ic_p             =   0.0         #
+
+#¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
+#              VERBOSITY                #
+#.......................................#
+incflo.verbose            =   1         # incflo itself
+mac_proj.verbose          =   1         # MAC Projector
+nodal_proj.verbose        =   1         # Nodal Projector
+scalar_diffusion.verbose  =   1         # Scalar Diffusion 
+tensor_diffusion.verbose  =   1         # Tensor Diffusion
+
+amr.plt_ccse_regtest    =   1