Mesh.cpp

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#include <Eigen/Core>
#include <Eigen/src/Core/Matrix.h>
#include <algorithm>
#include <array>
#include <boost/container/flat_map.hpp>
#include <functional>
#include <memory>
#include <ostream>
#include <type_traits>
#include <utility>
#include <vector>
 
#include "Edge.hpp"
#include "Mesh.hpp"
#include "Tetrahedron.hpp"
#include "Triangle.hpp"
#include "logging/LogMacros.hpp"
#include "math/geometry.hpp"
#include "mesh/Data.hpp"
#include "mesh/Vertex.hpp"
#include "precice/impl/Types.hpp"
#include "query/Index.hpp"
#include "utils/assertion.hpp"
 
namespace precice::mesh {
 
Mesh::Mesh(
    std::string name,
    int         dimensions,
    MeshID      id,
    bool        isJustInTime)
    : _name(std::move(name)),
      _dimensions(dimensions),
      _id(id),
      _isJustInTime(isJustInTime),
      _boundingBox(dimensions),
      _index(*this)
{
  PRECICE_ASSERT((_dimensions == 2) || (_dimensions == 3), _dimensions);
  PRECICE_ASSERT(_name != std::string(""));
}
Mesh::Mesh( {…}
 
Vertex &Mesh::vertex(VertexID id)
{
  PRECICE_ASSERT(isValidVertexID(id), id, nVertices());
  return _vertices.at(id);
}
Vertex &Mesh::vertex(VertexID id) {…}
 
const Vertex &Mesh::vertex(VertexID id) const
{
  PRECICE_ASSERT(isValidVertexID(id), id, nVertices());
  return _vertices.at(id);
}
const Vertex &Mesh::vertex(VertexID id) const {…}
 
Mesh::VertexContainer &Mesh::vertices()
{
  return _vertices;
}
Mesh::VertexContainer &Mesh::vertices() {…}
 
const Mesh::VertexContainer &Mesh::vertices() const
{
  return _vertices;
}
const Mesh::VertexContainer &Mesh::vertices() const {…}
 
std::size_t Mesh::nVertices() const
{
  return _vertices.size();
}
std::size_t Mesh::nVertices() const {…}
 
Mesh::EdgeContainer &Mesh::edges()
{
  return _edges;
}
Mesh::EdgeContainer &Mesh::edges() {…}
 
const Mesh::EdgeContainer &Mesh::edges() const
{
  return _edges;
}
const Mesh::EdgeContainer &Mesh::edges() const {…}
 
Mesh::TriangleContainer &Mesh::triangles()
{
  return _triangles;
}
Mesh::TriangleContainer &Mesh::triangles() {…}
 
const Mesh::TriangleContainer &Mesh::triangles() const
{
  return _triangles;
}
const Mesh::TriangleContainer &Mesh::triangles() const {…}
 
const Mesh::TetraContainer &Mesh::tetrahedra() const
{
  return _tetrahedra;
}
const Mesh::TetraContainer &Mesh::tetrahedra() const {…}
 
Mesh::TetraContainer &Mesh::tetrahedra()
{
  return _tetrahedra;
}
Mesh::TetraContainer &Mesh::tetrahedra() {…}
 
int Mesh::getDimensions() const
{
  return _dimensions;
}
int Mesh::getDimensions() const {…}
 
Vertex &Mesh::createVertex(const Eigen::Ref<const Eigen::VectorXd> &coords)
{
  PRECICE_ASSERT(coords.size() == _dimensions, coords.size(), _dimensions);
  auto nextID = _vertices.size();
  _vertices.emplace_back(coords, nextID);
  return _vertices.back();
}
Vertex &Mesh::createVertex(const Eigen::Ref<const Eigen::VectorXd> &coords) {…}
 
Edge &Mesh::createEdge(
    Vertex &vertexOne,
    Vertex &vertexTwo)
{
  _edges.emplace_back(vertexOne, vertexTwo);
  return _edges.back();
}
Edge &Mesh::createEdge( {…}
 
Triangle &Mesh::createTriangle(
    Edge &edgeOne,
    Edge &edgeTwo,
    Edge &edgeThree)
{
  PRECICE_ASSERT(
      edgeOne.connectedTo(edgeTwo) &&
      edgeTwo.connectedTo(edgeThree) &&
      edgeThree.connectedTo(edgeOne));
  _triangles.emplace_back(edgeOne, edgeTwo, edgeThree);
  return _triangles.back();
}
Triangle &Mesh::createTriangle( {…}
 
Triangle &Mesh::createTriangle(
    Vertex &vertexOne,
    Vertex &vertexTwo,
    Vertex &vertexThree)
{
  _triangles.emplace_back(vertexOne, vertexTwo, vertexThree);
  return _triangles.back();
}
Triangle &Mesh::createTriangle( {…}
 
Tetrahedron &Mesh::createTetrahedron(
    Vertex &vertexOne,
    Vertex &vertexTwo,
    Vertex &vertexThree,
    Vertex &vertexFour)
{
  _tetrahedra.emplace_back(vertexOne, vertexTwo, vertexThree, vertexFour);
  return _tetrahedra.back();
}
Tetrahedron &Mesh::createTetrahedron( {…}
 
PtrData &Mesh::createData(
    const std::string &name,
    int                dimension,
    DataID             id,
    int                waveformDegree)
{
  PRECICE_TRACE(name, dimension);
  for (const PtrData &data : _data) {
    PRECICE_CHECK(data->getName() != name,
                  "Data \"{}\" cannot be created twice for mesh \"{}\". "
                  "Please rename or remove one of the use-data tags with name \"{}\".",
                  name, _name, name);
  }
  // #rows = dimensions of current mesh #columns = dimensions of corresponding data set
  PtrData data(new Data(name, id, dimension, _dimensions, waveformDegree));
  _data.push_back(data);
  return _data.back();
}
PtrData &Mesh::createData( {…}
 
const Mesh::DataContainer &Mesh::data() const
{
  return _data;
}
const Mesh::DataContainer &Mesh::data() const {…}
 
bool Mesh::hasDataID(DataID dataID) const
{
  auto iter = std::find_if(_data.begin(), _data.end(), [dataID](const auto &dptr) {
    return dptr->getID() == dataID;
  });
  return iter != _data.end(); // if id was not found in mesh, iter == _data.end()
}
bool Mesh::hasDataID(DataID dataID) const {…}
 
const PtrData &Mesh::data(DataID dataID) const
{
  auto iter = std::find_if(_data.begin(), _data.end(), [dataID](const auto &dptr) {
    return dptr->getID() == dataID;
  });
  PRECICE_ASSERT(iter != _data.end(), "Data with id not found in mesh.", dataID, _name);
  return *iter;
}
const PtrData &Mesh::data(DataID dataID) const {…}
 
bool Mesh::hasDataName(std::string_view dataName) const
{
  auto iter = std::find_if(_data.begin(), _data.end(), [&dataName](const auto &dptr) {
    return dptr->getName() == dataName;
  });
  return iter != _data.end(); // if name was not found in mesh, iter == _data.end()
}
bool Mesh::hasDataName(std::string_view dataName) const {…}
 
std::vector<std::string> Mesh::availableData() const
{
  std::vector<std::string> names;
  for (const auto &data : _data) {
    names.push_back(data->getName());
  }
  return names;
}
std::vector<std::string> Mesh::availableData() const {…}
 
const PtrData &Mesh::data(std::string_view dataName) const
{
  auto iter = std::find_if(_data.begin(), _data.end(), [&dataName](const auto &dptr) {
    return dptr->getName() == dataName;
  });
  PRECICE_ASSERT(iter != _data.end(), "Data not found in mesh", dataName, _name);
  return *iter;
}
const PtrData &Mesh::data(std::string_view dataName) const {…}
 
const std::string &Mesh::getName() const
{
  return _name;
}
const std::string &Mesh::getName() const {…}
 
MeshID Mesh::getID() const
{
  return _id;
}
MeshID Mesh::getID() const {…}
 
bool Mesh::isValidVertexID(VertexID vertexID) const
{
  return (0 <= vertexID) && (static_cast<size_t>(vertexID) < nVertices());
}
bool Mesh::isValidVertexID(VertexID vertexID) const {…}
 
void Mesh::allocateDataValues()
{
  PRECICE_TRACE(_vertices.size());
  const auto expectedCount = _vertices.size();
  for (PtrData &data : _data) {
    data->allocateValues(expectedCount);
  }
}
void Mesh::allocateDataValues() {…}
 
void Mesh::computeBoundingBox()
{
  PRECICE_TRACE(_name);
 
  // Keep the bounding box if set via the API function.
  BoundingBox bb = _boundingBox.isDefault() ? BoundingBox(_dimensions) : BoundingBox(_boundingBox);
 
  for (const Vertex &vertex : _vertices) {
    bb.expandBy(vertex);
  }
  _boundingBox = std::move(bb);
  PRECICE_DEBUG("Bounding Box, {}", _boundingBox);
}
void Mesh::computeBoundingBox() {…}
 
void Mesh::clear()
{
  _triangles.clear();
  _edges.clear();
  _vertices.clear();
  _tetrahedra.clear();
  _index.clear();
 
  clearDataStamples();
  for (mesh::PtrData &data : _data) {
    data->values().resize(0);
  }
}
void Mesh::clear() {…}
 
void Mesh::clearPartitioning()
{
  _connectedRanks.clear();
  _communicationMap.clear();
  _vertexDistribution.clear();
  _vertexOffsets.clear();
  _globalNumberOfVertices = 0;
}
void Mesh::clearPartitioning() {…}
 
void Mesh::clearDataStamples()
{
  for (mesh::PtrData &data : _data) {
    data->timeStepsStorage().clear();
  }
}
void Mesh::clearDataStamples() {…}
 
bool Mesh::isPartitionEmpty(Rank rank) const
{
  // Without offset data, we assume non-empty partitions
  if (_vertexOffsets.empty()) {
    return false;
  }
  PRECICE_ASSERT(_vertexOffsets.size() >= static_cast<std::size_t>(rank));
  if (rank == 0) {
    return _vertexOffsets[0] == 0;
  }
  return _vertexOffsets[rank] - _vertexOffsets[rank - 1] == 0;
}
bool Mesh::isPartitionEmpty(Rank rank) const {…}
 
Eigen::VectorXd Mesh::getOwnedVertexData(const Eigen::VectorXd &values)
{
  std::vector<double> ownedDataVector;
  PRECICE_ASSERT(static_cast<std::size_t>(values.size()) >= nVertices());
  if (empty()) {
    return {};
  }
  int valueDim = values.size() / nVertices();
  int index    = 0;
 
  for (const auto &vertex : vertices()) {
    if (vertex.isOwner()) {
      for (int dim = 0; dim < valueDim; ++dim) {
        ownedDataVector.push_back(values[index * valueDim + dim]);
      }
    }
    ++index;
  }
  Eigen::Map<Eigen::VectorXd> ownedData(ownedDataVector.data(), ownedDataVector.size());
 
  return ownedData;
}
Eigen::VectorXd Mesh::getOwnedVertexData(const Eigen::VectorXd &values) {…}
 
void Mesh::tagAll()
{
  for (auto &vertex : _vertices) {
    vertex.tag();
  }
}
void Mesh::tagAll() {…}
 
void Mesh::addMesh(
    Mesh &deltaMesh)
{
  PRECICE_TRACE();
  PRECICE_ASSERT(_dimensions == deltaMesh.getDimensions());
 
  boost::container::flat_map<VertexID, Vertex *> vertexMap;
  vertexMap.reserve(deltaMesh.nVertices());
  Eigen::VectorXd coords(_dimensions);
  for (const Vertex &vertex : deltaMesh.vertices()) {
    coords    = vertex.getCoords();
    Vertex &v = createVertex(coords);
    v.setGlobalIndex(vertex.getGlobalIndex());
    if (vertex.isTagged())
      v.tag();
    v.setOwner(vertex.isOwner());
    PRECICE_ASSERT(vertex.getID() >= 0, vertex.getID());
    vertexMap[vertex.getID()] = &v;
  }
 
  // you cannot just take the vertices from the edge and add them,
  // since you need the vertices from the new mesh
  // (which may differ in IDs)
  for (const Edge &edge : deltaMesh.edges()) {
    VertexID vertexIndex1 = edge.vertex(0).getID();
    VertexID vertexIndex2 = edge.vertex(1).getID();
    PRECICE_ASSERT((vertexMap.count(vertexIndex1) == 1) &&
                   (vertexMap.count(vertexIndex2) == 1));
    createEdge(*vertexMap[vertexIndex1], *vertexMap[vertexIndex2]);
  }
 
  for (const Triangle &triangle : deltaMesh.triangles()) {
    VertexID vertexIndex1 = triangle.vertex(0).getID();
    VertexID vertexIndex2 = triangle.vertex(1).getID();
    VertexID vertexIndex3 = triangle.vertex(2).getID();
    PRECICE_ASSERT((vertexMap.count(vertexIndex1) == 1) &&
                   (vertexMap.count(vertexIndex2) == 1) &&
                   (vertexMap.count(vertexIndex3) == 1));
    createTriangle(*vertexMap[vertexIndex1], *vertexMap[vertexIndex2], *vertexMap[vertexIndex3]);
  }
 
  for (const Tetrahedron &tetra : deltaMesh.tetrahedra()) {
    VertexID vertexIndex1 = tetra.vertex(0).getID();
    VertexID vertexIndex2 = tetra.vertex(1).getID();
    VertexID vertexIndex3 = tetra.vertex(2).getID();
    VertexID vertexIndex4 = tetra.vertex(3).getID();
 
    PRECICE_ASSERT((vertexMap.count(vertexIndex1) == 1) &&
                   (vertexMap.count(vertexIndex2) == 1) &&
                   (vertexMap.count(vertexIndex3) == 1) &&
                   (vertexMap.count(vertexIndex4) == 1));
    createTetrahedron(*vertexMap[vertexIndex1], *vertexMap[vertexIndex2], *vertexMap[vertexIndex3], *vertexMap[vertexIndex4]);
  }
  _index.clear();
}
void Mesh::addMesh( {…}
 
const BoundingBox &Mesh::getBoundingBox() const
{
  return _boundingBox;
}
const BoundingBox &Mesh::getBoundingBox() const {…}
 
void Mesh::expandBoundingBox(const BoundingBox &boundingBox)
{
  _boundingBox.expandBy(boundingBox);
}
void Mesh::expandBoundingBox(const BoundingBox &boundingBox) {…}
 
void Mesh::preprocess()
{
  removeDuplicates();
  generateImplictPrimitives();
}
void Mesh::preprocess() {…}
 
void Mesh::removeDuplicates()
{
  // Remove duplicate tetrahedra
  auto tetrahedraCnt = _tetrahedra.size();
  std::sort(_tetrahedra.begin(), _tetrahedra.end());
  auto lastTetrahedron = std::unique(_tetrahedra.begin(), _tetrahedra.end());
  _tetrahedra          = TetraContainer{_tetrahedra.begin(), lastTetrahedron};
 
  // Remove duplicate triangles
  auto triangleCnt = _triangles.size();
  std::sort(_triangles.begin(), _triangles.end());
  auto lastTriangle = std::unique(_triangles.begin(), _triangles.end());
  _triangles        = TriangleContainer{_triangles.begin(), lastTriangle};
 
  // Remove duplicate edges
  auto edgeCnt = _edges.size();
  std::sort(_edges.begin(), _edges.end());
  auto lastEdge = std::unique(_edges.begin(), _edges.end());
  _edges        = EdgeContainer{_edges.begin(), lastEdge};
 
  PRECICE_DEBUG("Compression removed {} tetrahedra ({} to {}), {} triangles ({} to {}), and {} edges ({} to {})",
                tetrahedraCnt - _tetrahedra.size(), tetrahedraCnt, _tetrahedra.size(),
                triangleCnt - _triangles.size(), triangleCnt, _triangles.size(),
                edgeCnt - _edges.size(), edgeCnt, _edges.size());
}
void Mesh::removeDuplicates() {…}
 
namespace {
 
template <class Primitive, int... Indices>
auto sortedVertexPtrsForImpl(Primitive &p, std::integer_sequence<int, Indices...>)
{
  std::array<Vertex *, Primitive::vertexCount> vs{&p.vertex(Indices)...};
  std::sort(vs.begin(), vs.end());
  return std::tuple_cat(vs);
}
 
template <class Primitive>
auto sortedVertexPtrsFor(Primitive &p)
{
  return sortedVertexPtrsForImpl(p, std::make_integer_sequence<int, Primitive::vertexCount>{});
}
} // namespace
 
void Mesh::generateImplictPrimitives()
{
  if (_triangles.empty() && _tetrahedra.empty()) {
    PRECICE_DEBUG("No implicit primitives required");
    return; // no implicit primitives
  }
 
  // count explicit primitives for debug
  const auto explTriangles = _triangles.size();
  const auto explEdges     = _triangles.size();
 
  // First handle all explicit tetrahedra
 
  // Build a set of all explicit triangles
  using ExisitingTriangle = std::tuple<Vertex *, Vertex *, Vertex *>;
  std::set<ExisitingTriangle> triangles;
  for (auto &t : _triangles) {
    triangles.insert(sortedVertexPtrsFor(t));
  }
 
  // Generate all missing implicit triangles of explicit tetrahedra
  // Update the triangles set used by the implicit edge generation
  auto createTriangleIfMissing = [&](Vertex *a, Vertex *b, Vertex *c) {
    if (triangles.count({a, b, c}) == 0) {
      triangles.emplace(a, b, c);
      createTriangle(*a, *b, *c);
    };
  };
  for (auto &t : _tetrahedra) {
    auto [a, b, c, d] = sortedVertexPtrsFor(t);
    // Make sure these are in the same order as above
    createTriangleIfMissing(a, b, c);
    createTriangleIfMissing(a, b, d);
    createTriangleIfMissing(a, c, d);
    createTriangleIfMissing(b, c, d);
  }
 
  // Second handle all triangles, both explicit and implicit from the tetrahedron phase
  // Build an set of all explicit triangles
  using ExisitingEdge = std::tuple<Vertex *, Vertex *>;
  std::set<ExisitingEdge> edges;
  for (auto &e : _edges) {
    edges.emplace(sortedVertexPtrsFor(e));
  }
 
  // generate all missing implicit edges of implicit and explicit triangles
  auto createEdgeIfMissing = [&](Vertex *a, Vertex *b) {
    if (edges.count({a, b}) == 0) {
      edges.emplace(a, b);
      createEdge(*a, *b);
    };
  };
  for (auto &t : _triangles) {
    auto [a, b, c] = sortedVertexPtrsFor(t);
    // Make sure these are in the same order as above
    createEdgeIfMissing(a, b);
    createEdgeIfMissing(a, c);
    createEdgeIfMissing(b, c);
  }
 
  PRECICE_DEBUG("Generated {} implicit triangles and {} implicit edges",
                _triangles.size() - explTriangles,
                _edges.size() - explEdges);
}
void Mesh::generateImplictPrimitives() {…}
 
bool Mesh::operator==(const Mesh &other) const
{
  bool equal = true;
  equal &= _vertices.size() == other._vertices.size() &&
           std::is_permutation(_vertices.begin(), _vertices.end(), other._vertices.begin());
  equal &= _edges.size() == other._edges.size() &&
           std::is_permutation(_edges.begin(), _edges.end(), other._edges.begin());
  equal &= _triangles.size() == other._triangles.size() &&
           std::is_permutation(_triangles.begin(), _triangles.end(), other._triangles.begin());
  return equal;
}
bool Mesh::operator==(const Mesh &other) const {…}
 
bool Mesh::operator!=(const Mesh &other) const
{
  return !(*this == other);
}
bool Mesh::operator!=(const Mesh &other) const {…}
 
std::ostream &operator<<(std::ostream &os, const Mesh &m)
{
  os << "Mesh \"" << m.getName() << "\", dimensionality = " << m.getDimensions() << ":\n";
  os << "GEOMETRYCOLLECTION(\n";
  const auto  token = ", ";
  const auto *sep   = "";
  for (auto &vertex : m.vertices()) {
    os << sep << vertex;
    sep = token;
  }
  sep = ",\n";
  for (auto &edge : m.edges()) {
    os << sep << edge;
    sep = token;
  }
  sep = ",\n";
  for (auto &triangle : m.triangles()) {
    os << sep << triangle;
    sep = token;
  }
  os << "\n)";
  return os;
}
std::ostream &operator<<(std::ostream &os, const Mesh &m) {…}
 
} // namespace precice::mesh