Add examples and basic docs

.gitignore

@@ -1,2 +1,9 @@
 *.out
-*.ex
+*.ex
+*.o
+*.d
+*.F90
+Examples/AMReX/plt*
+Examples/AMReX/tmp_build_dir
+Examples/AMReX/Backtrace.*
+

Examples/AMReX/GNUmakefile

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+DEBUG = FALSE
+TEST = TRUE
+USE_ASSERTION = TRUE
+
+USE_EB = TRUE
+
+USE_MPI  = TRUE
+USE_OMP  = FALSE
+
+COMP = gnu
+
+DIM = 3
+
+AMREX_HOME ?= ../../../../amrex
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.defs
+
+include ./Make.package
+
+Pdirs := Base Boundary AmrCore EB
+
+Ppack	+= $(foreach dir, $(Pdirs), $(AMREX_HOME)/Src/$(dir)/Make.package)
+
+include $(Ppack)
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.rules

Examples/AMReX/Make.package

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+CEXE_sources += main.cpp

Examples/AMReX/README.md

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+This example uses the embedded boundary grid generation from AMReX.
+To compile this application, first install AMReX somewhere and point the AMREX_HOME environment variable to it.
+
+Compile and run this application (with MPI) by
+
+    make -s -j8
+    mpirun -np 8 main3d.<something>.ex
+
+To select different geometries, put
+
+* Airfoil geometry:
+
+      mpirun -np 8 main3d.<something>.ex which_geom=0
+
+* Sphere geometry:
+
+      mpirun -np 8 main3d.<something>.ex which_geom=1
+
+* Car geometry:
+
+      mpirun -np 8 main3d.<something>.ex which_geom=2
+

Examples/AMReX/airfoil.ply

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+ply
+format ascii 1.0
+comment VCGLIB generated
+element vertex 34
+property float x
+property float y
+property float z
+element face 64
+property list uchar int vertex_indices
+end_header
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Examples/AMReX/main.cpp

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+/* EBGeometry
+ * Copyright © 2022 Robert Marskar
+ * Please refer to Copyright.txt and LICENSE in the EBGeometry root directory.
+ */
+
+// AMReX includes
+#include <AMReX.H>
+#include <AMReX_EB2.H>
+#include <AMReX_EB2_IF.H>
+#include <AMReX_ParmParse.H>
+#include <AMReX_PlotFileUtil.H>
+
+// Our include
+#include "../../EBGeometry.hpp"
+
+using namespace amrex;
+
+// BVH tree degree
+constexpr int K = 2;
+
+namespace amrex {
+  namespace EB2 {
+
+    class SignedDistanceBVH {
+    public:
+
+      using P    = float;
+      using Vec3 = EBGeometry::Vec3T<P>;
+      using Face = EBGeometry::Dcel::FaceT<P>;      
+      using BV   = EBGeometry::BoundingVolumes::AABBT<P>;
+      using Node = EBGeometry::BVH::NodeT<P, Face, BV, K>;            
+
+      SignedDistanceBVH(const std::string a_filename, const bool a_flipSign) {
+
+	auto mesh = EBGeometry::Dcel::Parser::PLY<P>::readASCII(a_filename);
+
+	m_rootNode = std::make_shared<Node> (mesh->getFaces());
+
+	m_rootNode->topDownSortAndPartitionPrimitives(EBGeometry::Dcel::defaultStopFunction<P, BV, K>,
+						      EBGeometry::Dcel::spatialSplitPartitioner<P, K>,
+						      EBGeometry::Dcel::defaultBVConstructor<P, BV>);
+      }
+
+      SignedDistanceBVH(const SignedDistanceBVH& a_other) {
+	m_rootNode = a_other.m_rootNode;
+	m_flipSign = a_other.m_flipSign;	
+      }
+
+      Real operator() (AMREX_D_DECL(Real x, Real y, Real z)) const noexcept {
+
+	const Real sign = (m_flipSign) ? -1.0 : 1.0;
+
+	return sign * m_rootNode->pruneTree(Vec3(x,y,z));
+      };
+
+    inline Real operator() (const RealArray& p) const noexcept {
+        return this->operator()(AMREX_D_DECL(p[0],p[1],p[2]));
+    }      
+
+    protected:
+
+      std::shared_ptr<Node> m_rootNode;
+
+      bool m_flipSign;
+    };
+  }
+}
+
+int main (int argc, char* argv[])
+{
+    amrex::Initialize(argc, argv);
+
+    {
+        int n_cell = 128;
+        int max_grid_size = 32;
+        int which_geom = 0;
+
+	std::string filename;
+
+        // read parameters
+	ParmParse pp;
+	pp.query("n_cell", n_cell);
+	pp.query("max_grid_size", max_grid_size);
+	pp.query("which_geom", which_geom);
+
+
+        Geometry geom;
+        {
+	  RealBox rb;
+
+	  if(which_geom == 0){// Airfoil case
+	    rb = RealBox({-100,-100,-75}, {400,100,125}); 
+	    filename = "airfoil.ply";
+	  }
+	  else if (which_geom == 1){ // Sphere case
+	    rb = RealBox({-400,-400,-400}, {400,400,400});
+	    filename = "sphere.ply";
+	  }
+	  else if (which_geom == 2){ // Car geometry
+	    rb = RealBox({-20.,-20.,-20.}, {20.,20.,20.});
+	    filename = "porsche.ply";
+	  }
+	  else if (which_geom == 3){ // Orion geometry
+	    rb = RealBox({-10.,-10.,-10.}, {10.,10.,10.});
+	    filename = "orion.ply";
+	  }	  	  
+
+	  Array<int,AMREX_SPACEDIM> is_periodic{false, false, false};
+	  Geometry::Setup(&rb, 0, is_periodic.data());
+	  Box domain(IntVect(0), IntVect(n_cell-1));
+	  geom.define(domain);
+        }
+
+	// Create the signed distance function. 
+	EB2::SignedDistanceBVH sphere(filename, false);
+
+	auto gshop = EB2::makeShop(sphere);
+	EB2::Build(gshop, geom, 0, 0);
+
+	// Put some data
+        MultiFab mf;
+        {
+            BoxArray ba(geom.Domain());
+            ba.maxSize(max_grid_size);
+            DistributionMapping dm{ba};
+
+            std::unique_ptr<EBFArrayBoxFactory> factory
+                = amrex::makeEBFabFactory(geom, ba, dm, {2,2,2}, EBSupport::full);
+
+            mf.define(ba, dm, 1, 0, MFInfo(), *factory);
+            mf.setVal(1.0);
+        }
+
+        EB_WriteSingleLevelPlotfile("plt", mf, {"rho"}, geom, 0.0, 0);
+    }
+
+    amrex::Finalize();
+}