PABLO: add node and edge periodic neighbours

examples/CMakeLists.txt

@@ -63,6 +63,7 @@ if(BUILD_EXAMPLES)
 	list(APPEND EXAMPLE_LIST "PABLO_example_00008")
 	list(APPEND EXAMPLE_LIST "PABLO_example_00009")
 	list(APPEND EXAMPLE_LIST "PABLO_example_00010")
+	list(APPEND EXAMPLE_LIST "PABLO_example_00011")
 	list(APPEND EXAMPLE_LIST "patchkernel_example_00001")
 	list(APPEND EXAMPLE_LIST "volcartesian_example_00001")
 	list(APPEND EXAMPLE_LIST "POD_example_00001")

examples/PABLO_example_00011.cpp

@@ -0,0 +1,162 @@
+/*---------------------------------------------------------------------------*\
+ *
+ *  bitpit
+ *
+ *  Copyright (C) 2015-2020 OPTIMAD engineering Srl
+ *
+ *  -------------------------------------------------------------------------
+ *  License
+ *  This file is part of bitpit.
+ *
+ *  bitpit is free software: you can redistribute it and/or modify it
+ *  under the terms of the GNU Lesser General Public License v3 (LGPL)
+ *  as published by the Free Software Foundation.
+ *
+ *  bitpit is distributed in the hope that it will be useful, but WITHOUT
+ *  ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ *  FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+ *  License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with bitpit. If not, see <http://www.gnu.org/licenses/>.
+ *
+\*---------------------------------------------------------------------------*/
+
+#if BITPIT_ENABLE_MPI==1
+#include <mpi.h>
+#endif
+
+#include "bitpit_PABLO.hpp"
+
+using namespace bitpit;
+
+// =================================================================================== //
+/*!
+    \example PABLO_example_00011.cpp
+
+    \brief 3D adaptive mesh refinement (AMR) using PABLO
+
+    This example creates a 3D Octree mesh on the cube domain [0,1]x[0,1]x[0,1].
+
+    The domain is refined globally one time and periodic conditions are imposed
+    on the boundaries of the domain.
+    Then, the face, vertex and edge neighbors of the cells are found and print.
+
+    <b>To run</b>: ./PABLO_example_00011 \n
+
+    Thanks to <a href="https://www.surrey.ac.uk/people/maxime-delorme">Maxime Delorme</a> for this example.
+*/
+// =================================================================================== //
+
+/**
+ * Run the example.
+ */
+void run()
+{
+    /**<Instantation of a 3D pablo uniform object.*/
+    PabloUniform pablo11(3);
+
+    /** Set Periodic boundary conditions */
+    pablo11.setPeriodic(0);
+    pablo11.setPeriodic(2);
+    pablo11.setPeriodic(4);
+
+    /**<Compute the connectivity and write the octree.*/
+    pablo11.computeConnectivity();
+    pablo11.write("pablo000011.0");
+
+    /**<Refine globally one level and write the octree.*/
+    pablo11.adaptGlobalRefine();
+    pablo11.updateConnectivity();
+    pablo11.write("pablo000011.1");
+
+    /**<Extract and print face neighbors.*/
+    uint32_t nOct = pablo11.getNumOctants();
+    log::cout() << "Number of Octants : " << nOct << std::endl;
+    log::cout() << "Extracting the four face neighbours of each Octant " << std::endl;
+    for (uint32_t iOct = 0; iOct < nOct; ++iOct) {
+        std::vector<uint32_t> neigh;
+        std::vector<bool> isGhost;
+        log::cout() << ". Octant index : " << iOct << std::endl;
+        for (uint8_t iFace=0; iFace<pablo11.getNfaces(); ++iFace) {
+            pablo11.findNeighbours(iOct, iFace, 1, neigh, isGhost);
+            log::cout() << " - For face " << (int)iFace << "; " << neigh.size() << " neighbours: [ ";
+            for (auto iNeigh : neigh) {
+                log::cout() << iNeigh << " ";
+            }
+            log::cout() << "]" << std::endl;
+        }
+    }
+
+    /**<Extract and print vertex neighbors .*/
+    log::cout() << "Extracting the four vertex neighbours of each Octant " << std::endl;
+    for (uint32_t iOct = 0; iOct < nOct; ++iOct) {
+        std::vector<uint32_t> neigh;
+        std::vector<bool> isGhost;
+        log::cout() << ". Octant index : " << iOct << std::endl;
+        for (uint8_t iVertex=0; iVertex<pablo11.getNnodes(); ++iVertex) {
+            pablo11.findNeighbours(iOct, iVertex, 3, neigh, isGhost);
+            log::cout() << " - For vertex " << (int)iVertex << "; " << neigh.size() << " neighbours: [ ";
+            for (auto iNeigh: neigh) {
+                log::cout() << iNeigh << " ";
+            }
+            log::cout() << "]" << std::endl;
+        }
+    }
+
+    /**<Extract and print edge neighbors .*/
+    log::cout() << "Extracting the four edge neighbours of each Octant " << std::endl;
+    for (uint32_t iOct=0; iOct < nOct; ++iOct) {
+        std::vector<uint32_t> neigh;
+        std::vector<bool> isGhost;
+        log::cout() << ". Octant index : " << iOct << std::endl;
+        for (uint8_t iEdge = 0; iEdge<pablo11.getNedges(); ++iEdge) {
+            pablo11.findNeighbours(iOct, iEdge, 2, neigh, isGhost);
+            log::cout() << " - For edge " << (int)iEdge << "; " << neigh.size() << " neighbours: [ ";
+            for (auto iNeigh: neigh) {
+                log::cout() << iNeigh << " ";
+            }
+            log::cout() << "]" << std::endl;
+        }
+    }
+}
+
+/*!
+* Main program.
+*/
+int main(int argc, char *argv[])
+{
+#if BITPIT_ENABLE_MPI==1
+    MPI_Init(&argc,&argv);
+#else
+    BITPIT_UNUSED(argc);
+    BITPIT_UNUSED(argv);
+#endif
+
+    int nProcs;
+    int rank;
+#if BITPIT_ENABLE_MPI==1
+    MPI_Comm_size(MPI_COMM_WORLD, &nProcs);
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+#else
+    nProcs = 1;
+    rank   = 0;
+#endif
+
+    // Initialize the logger
+    log::manager().initialize(log::SEPARATE, false, nProcs, rank);
+    log::cout() << fileVerbosity(log::NORMAL);
+    log::cout() << consoleVerbosity(log::QUIET);
+
+    // Run the example
+    try {
+        run();
+    } catch (const std::exception &exception) {
+        log::cout() << exception.what();
+        exit(1);
+    }
+
+#if BITPIT_ENABLE_MPI==1
+    MPI_Finalize();
+#endif
+}