Add Chombo3 examples

.github/workflows/docs.yml

@@ -0,0 +1,41 @@
+name: Build and Deploy
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-docs
+  cancel-in-progress: true
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+
+      - name: Install dependencies
+        run: |
+          sudo apt install doxygen
+          sudo apt install graphviz          
+          python3 -m pip install sphinx sphinx_rtd_theme sphinxcontrib-bibtex
+          python3 -m pip install -I docutils==0.16  # Downgrade docutils so that bullet points render properly with Sphinx
+
+      - name: Build doxygen
+        run: |
+          doxygen doxyfile
+
+      - name: Build sphinx
+        run: |
+          cd Sphinx
+          make github
+
+      - name: Deploy
+        if: github.event_name == 'push' && github.repository == 'rmrsk/EBGeometry' && github.ref == 'refs/heads/main'        
+        uses: JamesIves/github-pages-deploy-action@3.7.1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: main
+          folder: docs
+          clean: false

.gitignore

@@ -3,7 +3,18 @@
 *.o
 *.d
 *.F90
-Examples/AMReX/plt*
-Examples/AMReX/tmp_build_dir
-Examples/AMReX/Backtrace.*
+*.hdf5
+pout.*
+*.mod
+docs/**
+Examples/AMReX_DCEL/plt*
+Examples/AMReX_DCEL/tmp_build_dir
+Examples/AMReX_DCEL/Backtrace.*
+Examples/AMReX_Shapes/plt*
+Examples/AMReX_Shapes/tmp_build_dir
+Examples/AMReX_Shapes/Backtrace.*
+Examples/Chombo3_Shapes/d/**
+Examples/Chombo3_Shapes/o/**
+Examples/Chombo3_Shapes/f/**
+Examples/Chombo3_Shapes/d/**
 

Examples/AMReX/main.cpp → Examples/AMReX_DCEL/main.cpp

@@ -158,7 +158,7 @@ int main (int argc, char* argv[]) {
   }
 
   // Create our signed distance function. K is the tree degree while T is the EBGeometry precision. 
-  constexpr int K = 2;
+  constexpr int K = 4;
 
   using T    = float;
   using Vec3 = EBGeometry::Vec3T<T>;

Examples/AMReX_Shapes/GNUmakefile

@@ -0,0 +1,26 @@
+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_Shapes/Make.package

@@ -0,0 +1 @@
+CEXE_sources += main.cpp

Examples/AMReX_Shapes/README.md

@@ -0,0 +1,34 @@
+This example uses the embedded boundary grid generation from AMReX, using analytic SDFs from EBGeometry. 
+To compile this application, first install AMReX somewhere and point the AMREX_HOME environment variable to it.
+
+Compiling
+---------
+
+Compile (with your standard AMReX settings) using
+
+    make -s -j8
+
+Running
+-------
+
+With MPI:
+
+    mpirun -np 8 main3d.<something>.ex eb2.cover_multiple_cuts=1 which_geom=0
+
+Some of the geometries will generate cut-cells which AMReX does not support, so the geometries should be run with eb2.cover_multiple_cuts=1.
+
+Supported geometries
+--------------------
+To select different geometries, set which_geom to one of the below.
+
+* `which_geom = 0` Sphere
+* `which_geom = 1` Plane
+* `which_geom = 2` Infinite cylinder
+* `which_geom = 3` Finite cylinder
+* `which_geom = 4` Capsule
+* `which_geom = 5` Box
+* `which_geom = 6` Rounded box
+* `which_geom = 7` Torus
+* `which_geom = 8` Infinite cone
+* `which_geom = 9` Finite cone
+* `which_geom = 10` Spherical shell

Examples/AMReX_Shapes/main.cpp

@@ -0,0 +1,176 @@
+/* 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;
+
+using T    = float;
+using SDF  = EBGeometry::SignedDistanceFunction<T>;
+using Vec3 = EBGeometry::Vec3T<T>;    
+
+namespace amrex {
+  namespace EB2 {
+
+    /*!
+      @brief This is just an EBGeometry-exposed signed distance field usable with AMReX.
+    */
+    class AMReXSDF {
+    public:
+
+      /*!
+	@brief Full constructor.
+	@param[in] a_filename File name. Must be a PLY file and will be parser by the PLY parser.
+	@param[in] a_flipSign Hook for swapping inside/outside. 
+      */
+      AMReXSDF(std::shared_ptr<SDF>& a_sdf){
+	m_sdf = a_sdf;
+      }
+
+      /*!
+	@brief Copy constructor. 
+	@param[in] a_other Other SDF. 
+      */
+      AMReXSDF(const AMReXSDF& a_other) {
+	this->m_sdf = a_other.m_sdf;
+      }
+
+      /*!
+	@brief AMReX's implicit function definition. 
+      */
+      Real operator() (AMREX_D_DECL(Real x, Real y, Real z)) const noexcept {
+	return m_sdf->signedDistance(Vec3(x,y,z));
+      };
+
+      /*!
+	@brief Also an AMReX implicit function implementation
+      */
+      inline Real operator() (const RealArray& p) const noexcept {
+        return this->operator()(AMREX_D_DECL(p[0],p[1],p[2]));
+      }
+
+    protected:
+
+      /*!
+	@brief EBGeometry signed distance function. 
+      */
+      std::shared_ptr<SDF> m_sdf;
+    };
+  }
+}
+
+int main (int argc, char* argv[]) {
+  amrex::Initialize(argc, argv);
+
+  int n_cell = 128;
+  int max_grid_size = 32;
+  int whichGeom = 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", whichGeom);
+
+
+  Geometry geom;
+  RealBox rb;
+
+  std::shared_ptr<SDF> func;
+  if(whichGeom == 0){ // Sphere.
+    rb = RealBox({-1,-1,-1}, {1,1,1});
+    func = std::make_shared<EBGeometry::SphereSDF<T>> (Vec3::zero(), T(0.5), false);      
+  }
+  else if(whichGeom == 1){ // Plane.
+    rb = RealBox({-1,-1,-1}, {1,1,1});
+
+    func = std::make_shared<EBGeometry::PlaneSDF<T> > (Vec3::zero(), Vec3::one(), false);
+  }
+  else if(whichGeom == 2){ // Infinite cylinder. 
+    rb = RealBox({-1,-1,-1}, {1,1,1});
+
+    func = std::make_shared<EBGeometry::InfiniteCylinderSDF<T> > (Vec3::zero(), T(0.1), 2, false);
+  }  
+  else if(whichGeom == 3){ // Finite cylinder.
+    rb = RealBox({-2,-2,-2}, {2,2,2});
+
+    func = std::make_shared<EBGeometry::CylinderSDF<T> > (-Vec3::one(), Vec3::one(), 0.25, false);
+  }
+  else if(whichGeom == 4){ // Capsule.
+    rb = RealBox({-2,-2,-2}, {2,2,2});
+
+    func = std::make_shared<EBGeometry::CapsuleSDF<T> > (-Vec3::one(), Vec3::one(), 0.25, false);
+  }
+  else if(whichGeom == 5){ // Box.
+    rb = RealBox({-2,-2,-2}, {2,2,2});    
+
+    func = std::make_shared<EBGeometry::BoxSDF<T> > (-Vec3::one(), Vec3::one(), false);
+  }
+  else if(whichGeom == 6){ // Rounded box.
+    rb = RealBox({-2,-2,-2}, {2,2,2});        
+
+    auto box = std::make_shared<EBGeometry::BoxSDF<T> > (-Vec3::one(), Vec3::one(), false);
+    func = std::make_shared<EBGeometry::RoundedSDF<T> >(box, 0.25);
+  }
+  else if(whichGeom == 7){ // Torus.
+    rb = RealBox({-2,-2,-2}, {2,2,2});            
+
+    func = std::make_shared<EBGeometry::TorusSDF<T> >(Vec3::zero(), 1.0, 0.25, false);
+  }
+  else if(whichGeom == 8){ // Infinite cone.
+    rb = RealBox({-2,-2,-2}, {2,2,2});                
+
+    func = std::make_shared<EBGeometry::InfiniteConeSDF<T> >(Vec3(0.0, 0.0, 1.0), 30.0, false);
+  }
+  else if(whichGeom == 9){ // Finite cone.
+    rb = RealBox({-2,-2,-2}, {2,2,2});                    
+
+    func = std::make_shared<EBGeometry::ConeSDF<T> >(Vec3(0.0, 0.0, 1.0), 2.0, 30, false);
+  }
+  if(whichGeom == 10){ // Spherical shell.
+    rb = RealBox({-1,-1,-1}, {1,1,1});                        
+
+    auto sphere = std::make_shared<EBGeometry::SphereSDF<T>> (Vec3::zero(), T(0.5), false);
+    func = std::make_shared<EBGeometry::AnnularSDF<T>> (sphere, 0.1);
+  }      
+
+  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);
+
+  EB2::AMReXSDF sdf(func);
+
+  auto gshop = EB2::makeShop(sdf);
+  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();
+}

Examples/Chombo3_DCEL/GNUmakefile

@@ -0,0 +1,12 @@
+
+# Things for the Chombo makefile system. 
+ebase    = main
+
+#CHOMBO_HOME = /home/robertm/Projects/Chombo_3.2/lib
+
+LibNames = EBAMRElliptic EBAMRTools Workshop EBTools AMRElliptic  AMRTools BoxTools
+
+base_dir = .
+src_dirs = ../../
+
+include $(CHOMBO_HOME)/mk/Make.example

Examples/Chombo3_DCEL/README.md

@@ -0,0 +1,28 @@
+This example uses the embedded boundary grid generation from Chombo3, and shows how to use DCEL functionality from EBGeometry. 
+To compile this application, first install Chombo somewhere and point the CHOMBO_HOME environment variable to it.
+
+Compiling
+---------
+
+Compile (with your standard Chombo settings) using
+
+    make -s -j8 DIM=3 OPT=HIGH main
+
+Running
+-------
+
+With MPI:
+
+    mpirun -np 8 main3d.<something>.ex examples.inputs
+
+Supported geometries
+--------------------
+To select different geometries, set which_geom to one of the below.
+
+* `which_geom = 0` Airfoil
+* `which_geom = 1` Sphere
+* `which_geom = 2` Dodecahedron
+* `which_geom = 3` Horse
+* `which_geom = 4` Porsche
+* `which_geom = 5` Orion capsule
+* `which_geom = 6` Armadillo

Examples/Chombo3_DCEL/examples.inputs

@@ -0,0 +1,3 @@
+ncells     = 128
+grid_size  = 16
+which_geom = 0