CreateClustering.hpp

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#pragma once
 
#include <Eigen/Core>
 
#include <algorithm>
 
#include "math/math.hpp"
#include "mesh/Mesh.hpp"
#include "precice/impl/Types.hpp"
#include "query/Index.hpp"
// required for the squared distance computation
#include "mapping/RadialBasisFctSolver.hpp"
 
namespace precice::mapping::impl {
 
using Vertices = std::vector<mesh::Vertex>;
 
// Internal helper functions
namespace {
 
constexpr VertexID zCurve(std::array<unsigned int, 3> ids, std::array<unsigned int, 3> nCells)
{
  return (ids[0] * nCells[1] + ids[1]) * nCells[2] + ids[2];
}
 
// Overload to handle the offsets (via ints) properly
constexpr VertexID zCurve(std::array<int, 3> ids, std::array<unsigned int, 3> nCells)
{
  return (ids[0] * nCells[1] + ids[1]) * nCells[2] + ids[2];
}
 
template <int dim>
std::array<int, math::pow_int<dim>(3) - 1> zCurveNeighborOffsets(std::array<unsigned int, 3> nCells);
 
template <>
std::array<int, 8> zCurveNeighborOffsets<2>(std::array<unsigned int, 3> nCells)
{
  // All  neighbor directions
  const std::array<std::array<int, 3>, 8> neighbors2DIndex = {{{-1, -1, 0}, {-1, 0, 0}, {-1, 1, 0}, {0, -1, 0}, {0, 1, 0}, {1, -1, 0}, {1, 0, 0}, {1, 1, 0}}};
  std::array<int, 8>                      neighbors2D{{}};
  // Uses the int overload of the zCurve
  // @todo: mark the function as constexpr, when moving to C++20 (transform is non-constexpr)
  std::transform(neighbors2DIndex.begin(), neighbors2DIndex.end(), neighbors2D.begin(), [&nCells](auto &v) { return zCurve(v, nCells); });
 
  return neighbors2D;
}
 
template <>
std::array<int, 26> zCurveNeighborOffsets<3>(std::array<unsigned int, 3> nCells)
{
  // All  neighbor directions
  const std::array<std::array<int, 3>, 26> neighbors3DIndex = {{{-1, -1, -1}, {-1, -1, 0}, {-1, -1, 1}, {-1, 0, 0}, {-1, 0, 1}, {-1, 0, -1}, {-1, 1, 0}, {-1, 1, 1}, {-1, 1, -1}, {0, -1, -1}, {0, -1, 0}, {0, -1, 1}, {0, 0, 1}, {0, 0, -1}, {0, 1, 0}, {0, 1, 1}, {0, 1, -1}, {1, -1, -1}, {1, -1, 0}, {1, -1, 1}, {1, 0, 0}, {1, 0, 1}, {1, 0, -1}, {1, 1, 0}, {1, 1, 1}, {1, 1, -1}}};
  std::array<int, 26>                      neighbors3D{{}};
  // Uses the int overload of the zCurve
  std::transform(neighbors3DIndex.begin(), neighbors3DIndex.end(), neighbors3D.begin(), [&nCells](auto &v) { return zCurve(v, nCells); });
 
  return neighbors3D;
}
template <typename ArrayType>
std::vector<VertexID> getNeighborsWithinSphere(const Vertices &vertices, VertexID centerID, double radius, const ArrayType neighborOffsets)
{
  // number of neighbors = (3^dim)-1
  static_assert((neighborOffsets.size() == 26) || (neighborOffsets.size() == 8));
  std::vector<VertexID> result;
  for (auto off : neighborOffsets) {
    // corner case where we have 'dead axis' in the bounding box
    if (off == 0) {
      continue;
    }
    // compute neighbor ID
    // @todo target type should be an unsigned int
    PRECICE_ASSERT(off != 0);
    // Assumption, vertex position in the container == vertex ID
    VertexID neighborID = centerID + off;
    // We might run out of the array bounds along the edges, so we only consider vertices inside
    if (neighborID >= 0 && neighborID < static_cast<int>(vertices.size())) {
      auto &neighborVertex = vertices[neighborID];
      auto &center         = vertices[centerID];
      if (!neighborVertex.isTagged() && (computeSquaredDifference(center.rawCoords(), neighborVertex.rawCoords()) < math::pow_int<2>(radius))) {
        result.emplace_back(neighborID);
      }
    }
  }
  return result;
}
 
void tagEmptyClusters(Vertices &clusterCenters, double clusterRadius, mesh::PtrMesh mesh)
{
  // Alternative implementation: mesh->index().getVerticesInsideBox() == 0
  std::for_each(clusterCenters.begin(), clusterCenters.end(), [&](auto &v) {
    if (!v.isTagged() && !mesh->index().isAnyVertexInsideBox(v, clusterRadius)) {
      v.tag();
    }
  });
}
 
void projectClusterCentersToinputMesh(Vertices &clusterCenters, mesh::PtrMesh mesh)
{
  std::transform(clusterCenters.begin(), clusterCenters.end(), clusterCenters.begin(), [&](auto &v) {
    if (!v.isTagged()) {
      auto closestCenter = mesh->index().getClosestVertex(v.getCoords()).index;
      return mesh::Vertex{mesh->vertex(closestCenter).getCoords(), v.getID()};
    } else {
      return v;
    }
  });
}
 
template <int dim>
void tagDuplicateCenters(Vertices &centers, std::array<unsigned int, 3> nCells, double threshold)
{
  PRECICE_ASSERT(threshold >= 0);
  if (centers.empty())
    return;
 
  // Get the index offsets for the z curve
  auto neighborOffsets = zCurveNeighborOffsets<dim>(nCells);
  static_assert((neighborOffsets.size() == 8 && dim == 2) || (neighborOffsets.size() == 26 && dim == 3));
 
  // For the following to work, the vertexID has to correspond to the position in the centers
  PRECICE_ASSERT(std::all_of(centers.begin(), centers.end(), [idx = 0](auto &v) mutable { return v.getID() == idx++; }));
  // we check all neighbors
  for (auto &v : centers) {
    if (!v.isTagged()) {
      auto ids = getNeighborsWithinSphere(centers, v.getID(), threshold, neighborOffsets);
      // @todo check more selective which one to remove
      if (ids.size() > 0)
        v.tag();
    }
  }
}
 
void removeTaggedVertices(Vertices &container)
{
  container.erase(std::remove_if(container.begin(), container.end(), [](auto &v) { return v.isTagged(); }), container.end());
}
} // namespace
 
inline double estimateClusterRadius(unsigned int verticesPerCluster, mesh::PtrMesh inMesh, const mesh::BoundingBox &bb)
{
  // Step 1: Generate random samples from the input mesh
  std::vector<VertexID> randomSamples;
 
  PRECICE_ASSERT(!bb.isDefault(), "Invalid bounding box.");
  // All samples are 'moved' to the closest vertex from the input mesh in order
  // to avoid empty clusters when we have shell-like meshes (as in surface coupling)
  // The first sample: the vertex closest to the bounding box center
  const auto bbCenter = bb.center();
  randomSamples.emplace_back(inMesh->index().getClosestVertex(bbCenter).index);
  // Now we place samples for each space dimension above and below the bounding box center
  // and look for the closest vertex in the input mesh
  // In 2D the sampling would like this
  // +---------------------+
  // |          x          |
  // |                     |
  // |    x     c      x   |
  // |                     |
  // |          x          |
  // +---------------------+
 
  for (int d = 0; d < inMesh->getDimensions(); ++d) {
    auto sample = bbCenter;
    // Lower as the center
    sample[d] -= bb.getEdgeLength(d) * 0.25;
    randomSamples.emplace_back(inMesh->index().getClosestVertex(sample).index);
    // Higher than the center
    sample[d] += bb.getEdgeLength(d) * 0.5;
    randomSamples.emplace_back(inMesh->index().getClosestVertex(sample).index);
  }
 
  // Step 2: Compute the radius of the randomSamples ('centers'), which would have verticesPerCluster vertices
  std::vector<double> sampledClusterRadii;
  for (auto s : randomSamples) {
    // ask the index tree for the k-nearest neighbors  in order to estimate the point density
    auto kNearestVertexIDs = inMesh->index().getClosestVertices(inMesh->vertex(s).getCoords(), verticesPerCluster);
    // compute the distance of each point to the center
    std::vector<double> squaredRadius(kNearestVertexIDs.size());
    std::transform(kNearestVertexIDs.begin(), kNearestVertexIDs.end(), squaredRadius.begin(), [&inMesh, s](auto i) {
      return computeSquaredDifference(inMesh->vertex(i).rawCoords(), inMesh->vertex(s).rawCoords());
    });
    // Store the maximum distance
    auto maxRadius = std::max_element(squaredRadius.begin(), squaredRadius.end());
    sampledClusterRadii.emplace_back(std::sqrt(*maxRadius));
  }
 
  // Step 3: Sort (using nth_element) the sampled radii and select the median as cluster radius
  PRECICE_ASSERT(sampledClusterRadii.size() % 2 != 0, "Median calculation is only valid for odd number of elements.");
  PRECICE_ASSERT(sampledClusterRadii.size() > 0);
  unsigned int middle = sampledClusterRadii.size() / 2;
  std::nth_element(sampledClusterRadii.begin(), sampledClusterRadii.begin() + middle, sampledClusterRadii.end());
  double clusterRadius = sampledClusterRadii[middle];
 
  return clusterRadius;
}
inline double estimateClusterRadius(unsigned int verticesPerCluster, mesh::PtrMesh inMesh, const mesh::BoundingBox &bb) {…}
 
inline std::tuple<double, Vertices> createClustering(mesh::PtrMesh inMesh, mesh::PtrMesh outMesh,
                                                     double relativeOverlap, unsigned int verticesPerCluster,
                                                     bool projectClustersToInput)
{
  precice::logging::Logger _log{"impl::createClustering"};
  PRECICE_TRACE();
  PRECICE_ASSERT(relativeOverlap < 1);
  PRECICE_ASSERT(verticesPerCluster > 0);
  PRECICE_ASSERT(inMesh->getDimensions() == outMesh->getDimensions());
 
  // If we have either no input or no output vertices, we return immediately
  if (inMesh->empty() || (outMesh->empty() && !outMesh->isJustInTime())) {
    return {double{}, Vertices{}};
  }
 
  PRECICE_ASSERT(!inMesh->empty());
  PRECICE_ASSERT(!outMesh->empty() || outMesh->isJustInTime());
  // startGridAtEdge boolean switch in order to decide either to start the clustering at the edge of the bounding box in each direction
  // (true) or start the clustering inside the bounding box (edge + 0.5 radius). The latter approach leads to fewer clusters,
  // but might result in a worse clustering
  const bool startGridAtEdge = projectClustersToInput;
 
  PRECICE_DEBUG("Relative overlap: {}", relativeOverlap);
  PRECICE_DEBUG("Vertices per cluster: {}", verticesPerCluster);
 
  // Step 1: Compute the local bounding box of the input mesh manually
  // Note that we don't use the corresponding bounding box functions from
  // precice::mesh (e.g. ::getBoundingBox), as the stored bounding box might
  // have the wrong size (e.g. direct access)
  // @todo: Which mesh should be used in order to determine the cluster centers:
  // pro outMesh: we want perfectly fitting clusters around our output vertices
  // however, this makes the cluster distribution/mapping dependent on the output
  precice::mesh::BoundingBox localBB = inMesh->index().getRtreeBounds();
 
#ifndef NDEBUG
  // Safety check
  precice::mesh::BoundingBox bb_check(inMesh->getDimensions());
  for (const mesh::Vertex &vertex : inMesh->vertices()) {
    bb_check.expandBy(vertex);
  }
  PRECICE_ASSERT(bb_check == localBB);
#endif
 
  // If we have very few vertices in the domain, (in this case twice our cluster
  // size as we decompose most probably at least in 4 clusters) we just use a
  // single cluster. The clustering result of the algorithm further down is in
  // this case not optimal and might lead to too many clusters.
  // The single cluster has in principle a radius of inf. We use here twice the
  // length of the longest bounding box edge length and the center of the bounding
  // box for the center point.
  if (inMesh->nVertices() < verticesPerCluster * 2) {
    double cRadius = localBB.longestEdgeLength();
    if (cRadius == 0) {
      PRECICE_WARN("Determining a cluster radius failed. This is most likely a result of a coupling mesh consisting of just a single vertex. Setting the cluster radius to 1.");
      cRadius = 1;
    }
    return {cRadius * 2, Vertices{mesh::Vertex({localBB.center(), 0})}};
  }
  // We define a convenience alias for the localBB. In case we need to synchronize the clustering across ranks later on, we need
  // to work with the global bounding box of the whole domain.
  auto globalBB = localBB;
 
  // Step 2: Now we pick random samples from the input mesh and ask the index tree for the k-nearest neighbors
  // in order to estimate the point density and determine a proper cluster radius (see also the function documentation)
  double clusterRadius = estimateClusterRadius(verticesPerCluster, inMesh, localBB);
  PRECICE_DEBUG("Vertex cluster radius: {}", clusterRadius);
 
  // maximum distance between cluster centers lying diagonal to each other. The maximum distance takes the overlap condition into
  // account: example for 2D: if the distance between the centers is sqrt( 4 / 2 ) * radius, we violate the overlap condition between
  // diagonal clusters
  const int    inDim                 = inMesh->getDimensions();
  const double maximumCenterDistance = std::sqrt(4. / inDim) * clusterRadius * (1 - relativeOverlap);
 
  // Step 3: using the maximum distance and the bounding box, compute the number of clusters in each direction
  // we ceil the number of clusters in order to guarantee the desired overlap
  std::array<unsigned int, 3> nClustersGlobal{1, 1, 1};
  for (int d = 0; d < globalBB.getDimension(); ++d)
    nClustersGlobal[d] = std::ceil(std::max(1., globalBB.getEdgeLength(d) / maximumCenterDistance));
 
  // Step 4: Determine the centers of the clusters
  Vertices centers;
  // Vector used to temporarily store each center coordinates
  std::vector<double> centerCoords(inDim);
  // Vector storing the distances between the cluster in each direction
  std::vector<double> distances(inDim);
  // Vector storing the starting coordinates in each direction
  std::vector<double> start(inDim);
  // Fill the constant vectos, i.e., the distances and the start
  for (unsigned int d = 0; d < distances.size(); ++d) {
    // this distance calculation guarantees that we have at least the minimal specified overlap, as we ceil the division for the number of clusters
    // as an alternative, once could use distance = const = maximumCenterDistance, which might lead to better results when projecting and removing duplicates (?)
    distances[d] = globalBB.getEdgeLength(d) / (nClustersGlobal[d]);
    start[d]     = globalBB.minCorner()(d);
  }
  PRECICE_DEBUG("Distances: {}", distances);
 
  // Step 5: Take care of the starting layer: if we start the grid at the globalBB edge we have an additional layer in each direction
  if (startGridAtEdge) {
    for (int d = 0; d < inDim; ++d) {
      if (globalBB.getEdgeLength(d) > math::NUMERICAL_ZERO_DIFFERENCE) {
        nClustersGlobal[d] += 1;
      }
    }
  } // If we don't start at the edge, we shift the starting layer into the middle by 0.5 * distance
  else {
    std::transform(start.begin(), start.end(), distances.begin(), start.begin(), [](auto s, auto d) { return s + 0.5 * d; });
  }
 
  // Print some information
  PRECICE_DEBUG("Global cluster distribution: {}", nClustersGlobal);
  unsigned int nTotalClustersGlobal = std::accumulate(nClustersGlobal.begin(), nClustersGlobal.end(), 1U, std::multiplies<unsigned int>());
  PRECICE_DEBUG("Global number of total clusters (tentative): {}", nTotalClustersGlobal);
 
  // Step 6: transform the global metrics (number of clusters and starting layer) into local ones
  // Since the local and global bounding boxes are the same in the current implementation, the
  // global metrics and the local metrics will be the same.
  // First, we need to update the starting points of our clustering scheme
  std::array<unsigned int, 3> nClustersLocal{1, 1, 1};
  for (unsigned int d = 0; d < start.size(); ++d) {
    // Exclude the case where we have no distances (nClustersGlobal[d] == 1 )
    if (distances[d] > 0) {
      start[d] += std::ceil(((localBB.minCorner()(d) - start[d]) / distances[d]) - math::NUMERICAL_ZERO_DIFFERENCE) * distances[d];
      // One cluster for the starting point and a further one for each distance we can fit into the BB
      nClustersLocal[d] = 1 + std::floor(((localBB.maxCorner()(d) - start[d]) / distances[d]) + math::NUMERICAL_ZERO_DIFFERENCE);
    }
  }
 
  unsigned int nTotalClustersLocal = std::accumulate(nClustersLocal.begin(), nClustersLocal.end(), 1U, std::multiplies<unsigned int>());
  centers.resize(nTotalClustersLocal, mesh::Vertex({centerCoords, -1}));
 
  // Print some information
  PRECICE_DEBUG("Local cluster distribution: {}", nClustersLocal);
  PRECICE_DEBUG("Local number of total clusters (tentative): {}", nTotalClustersLocal);
 
  // Step 7: fill the center container using the zCurve for indexing. For the further processing, it is also important to ensure
  // that the ID within the center Vertex class coincides with the position of the center vertex in the container.
  // We start with the (bottom left) corner and iterate over all dimension
  PRECICE_ASSERT(inDim >= 2);
  if (inDim == 2) {
    centerCoords[0] = start[0];
    for (unsigned int x = 0; x < nClustersLocal[0]; ++x, centerCoords[0] += distances[0]) {
      centerCoords[1] = start[1];
      for (unsigned int y = 0; y < nClustersLocal[1]; ++y, centerCoords[1] += distances[1]) {
        auto id = zCurve(std::array<unsigned int, 3>{{x, y, 0}}, nClustersLocal);
        PRECICE_ASSERT(id < static_cast<int>(centers.size()) && id >= 0);
        centers[id] = mesh::Vertex({centerCoords, id});
      }
    }
  } else {
    centerCoords[0] = start[0];
    for (unsigned int x = 0; x < nClustersLocal[0]; ++x, centerCoords[0] += distances[0]) {
      centerCoords[1] = start[1];
      for (unsigned int y = 0; y < nClustersLocal[1]; ++y, centerCoords[1] += distances[1]) {
        centerCoords[2] = start[2];
        for (unsigned int z = 0; z < nClustersLocal[2]; ++z, centerCoords[2] += distances[2]) {
          auto id = zCurve(std::array<unsigned int, 3>{{x, y, z}}, nClustersLocal);
          PRECICE_ASSERT(id < static_cast<int>(centers.size()) && id >= 0);
          centers[id] = mesh::Vertex({centerCoords, id});
        }
      }
    }
  }
 
  // Step 8: tag vertices, which should be removed later on
 
  // Step 8a: tag empty clusters
  tagEmptyClusters(centers, clusterRadius, inMesh);
  if (!outMesh->isJustInTime()) {
    tagEmptyClusters(centers, clusterRadius, outMesh);
  }
  PRECICE_DEBUG("Number of non-tagged centers after empty clusters were filtered: {}", std::count_if(centers.begin(), centers.end(), [](auto &v) { return !v.isTagged(); }));
 
  // Step 9: Move the cluster centers if desired
  if (projectClustersToInput) {
    projectClusterCentersToinputMesh(centers, inMesh);
    // @todo: The duplication should probably be defined in terms of the target distance, not the actual distance. Find good default values
    const auto duplicateThreshold = 0.4 * (*std::min_element(distances.begin(), distances.end()));
    PRECICE_DEBUG("Tagging duplicates using the threshold value {} for the regular distances {}", duplicateThreshold, distances);
    // usually inMesh->getDimensions() == 2
    // to also cover the case where we have only a single layer in a 3D computation we use the number of clusters in z direction
    // Step 8b or 9a: Moving cluster centers might lead to duplicate centers or centers being too close to each other. Therefore,
    // we tag duplicate centers (see also the documentation of \ref tagDuplicateCenters ).
    if (nClustersLocal[2] == 1) {
      tagDuplicateCenters<2>(centers, nClustersLocal, duplicateThreshold);
    } else {
      tagDuplicateCenters<3>(centers, nClustersLocal, duplicateThreshold);
    }
    // the tagging here won't filter out a lot of clusters, but finding them anyway allows us to allocate the right amount of
    // memory for the cluster vector in the mapping, which would otherwise be expensive
    // we cannot hit any empty vertices in the inputmesh
    if (!outMesh->isJustInTime()) {
      tagEmptyClusters(centers, clusterRadius, outMesh);
    }
    PRECICE_DEBUG("Number of non-tagged centers after duplicate tagging : {}", std::count_if(centers.begin(), centers.end(), [](auto &v) { return !v.isTagged(); }));
  }
  PRECICE_ASSERT(std::all_of(centers.begin(), centers.end(), [idx = 0](auto &v) mutable { return v.getID() == idx++; }));
 
  // Step 10: finally, remove the vertices from the center container
  removeTaggedVertices(centers);
  PRECICE_ASSERT(std::none_of(centers.begin(), centers.end(), [](auto &v) { return v.isTagged(); }));
  PRECICE_CHECK(centers.size() > 0, "Too many vertices have been filtered out.");
 
  return {clusterRadius, centers};
}
inline std::tuple<double, Vertices> createClustering(mesh::PtrMesh inMesh, mesh::PtrMesh outMesh, {…}
} // namespace precice::mapping::impl
namespace precice::mapping::impl {…}