Initialize at openlb-1-3

1 files changed, 557 insertions, 0 deletions

diff --git a/src/geometry/superGeometry3D.hh b/src/geometry/superGeometry3D.hh
new file mode 100644
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+++ b/src/geometry/superGeometry3D.hh
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+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2013, 2014 Mathias J. Krause, Peter Weisbrod
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program 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 General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+ */
+
+/** \file
+ * Representation of the 3D geometry -- generic implementation.
+ */
+
+#ifndef SUPER_GEOMETRY_3D_HH
+#define SUPER_GEOMETRY_3D_HH
+
+#include <cmath>
+#include <math.h>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "geometry/cuboid3D.h"
+#include "geometry/cuboidGeometry3D.h"
+#include "geometry/superGeometry3D.h"
+#include "communication/superStructure3D.h"
+#include "communication/loadBalancer.h"
+#include "functors/analytical/indicator/indicatorF3D.h"
+#include "functors/lattice/indicator/superIndicatorF3D.h"
+#include "functors/analytical/indicator/indicCalc3D.h"
+#include "io/ostreamManager.h"
+
+namespace olb {
+
+template<typename T>
+SuperGeometry3D<T>::SuperGeometry3D(CuboidGeometry3D<T>& cuboidGeometry, LoadBalancer<T>& loadBalancer, int overlap)
+  : SuperStructure3D<T>(cuboidGeometry, loadBalancer, overlap),
+    _statistics(this),
+    clout(std::cout,"SuperGeometry3D")
+{
+  // init communicator
+  this->_communicator.init_nh();
+  this->_communicator.add_cells(this->_overlap);
+  this->_communicator.init();
+  this->_communicationNeeded = true;
+
+  // constructing the block and extended block geometries from the cuboid geometry
+  _blockGeometries.clear();
+
+  for (int iCloc=0; iCloc<this->getLoadBalancer().size(); iCloc++) {
+    int iCglob = this->getLoadBalancer().glob(iCloc);
+    Cuboid3D<T> extendedCuboid(cuboidGeometry.get(iCglob),overlap);
+    _extendedBlockGeometries.emplace_back(extendedCuboid, iCglob);
+  }
+
+  for (int iCloc=0; iCloc<this->getLoadBalancer().size(); iCloc++) {
+    int iCglob = this->getLoadBalancer().glob(iCloc);
+    int nX = cuboidGeometry.get(iCglob).getNx();
+    int nY = cuboidGeometry.get(iCglob).getNy();
+    int nZ = cuboidGeometry.get(iCglob).getNz();
+    _blockGeometries.emplace_back(_extendedBlockGeometries[iCloc],
+                                  overlap, overlap+nX-1,
+                                  overlap, overlap+nY-1,
+                                  overlap, overlap+nZ-1);
+  }
+  _statistics.getStatisticsStatus() = true;
+}
+
+template<typename T>
+SuperGeometry3D<T>::SuperGeometry3D(SuperGeometry3D const& rhs)
+  : SuperStructure3D<T>(rhs._cuboidGeometry, rhs._loadBalancer, rhs._overlap),
+    _statistics(this),
+    clout(std::cout,"SuperGeometry3D")
+{
+  // init communicator
+  this->_communicator.init_nh();
+  this->_communicator.add_cells(this->_overlap);
+  this->_communicator.init();
+  this->_communicationNeeded = true;
+  // copy block and extended block geometries
+  _blockGeometries = rhs._blockGeometries;
+  _extendedBlockGeometries = rhs._extendedBlockGeometries;
+  _statistics.getStatisticsStatus() = true;
+}
+
+template<typename T>
+SuperGeometry3D<T>& SuperGeometry3D<T>::operator=(SuperGeometry3D const& rhs)
+{
+
+  // init communicator
+  this->_communicator.init_nh();
+  this->_communicator.add_cells(this->_overlap);
+  this->_communicator.init();
+  this->_communicationNeeded = true;
+  // copy mother data
+  this->_cuboidGeometry = rhs._cuboidGeometry;
+  this->_loadBalancer = rhs._loadBalancer;
+  this->_overlap = rhs._overlap;
+  // copy block and extended block geometrie
+  _blockGeometries = rhs._blockGeometries;
+  _extendedBlockGeometries = rhs._extendedBlockGeometries;
+  _statistics = SuperGeometryStatistics3D<T>(this);
+  return *this;
+}
+
+template<typename T>
+bool* SuperGeometry3D<T>::operator() (int iCloc, int iX, int iY, int iZ, int iData)
+{
+  return (bool*)&getExtendedBlockGeometry(iCloc).get(iX+this->_overlap, iY+this->_overlap, iZ+this->_overlap);
+}
+
+template<typename T>
+int SuperGeometry3D<T>::getDataSize() const
+{
+  return 1;
+}
+
+template<typename T>
+int SuperGeometry3D<T>::getDataTypeSize() const
+{
+  return sizeof(int);
+}
+
+
+template<typename T>
+int& SuperGeometry3D<T>::set(int iCglob, int iXloc, int iYloc, int iZloc)
+{
+
+  if ( this->getLoadBalancer().rank(iCglob) == singleton::mpi().getRank() ) {
+    std::cout << "warning: read only access to data which is not available in";
+    this->_communicationNeeded = true;
+    _statistics.getStatisticsStatus() = true;
+    return _extendedBlockGeometries[this->getLoadBalancer().loc(iCglob)].get(iXloc+this->_overlap, iYloc+this->_overlap, iZloc+this->_overlap);
+  }
+  else {
+    std::cout << "error: write access to data which is not available in the any block geometry";
+    exit(-1);
+    //return 0;
+  }
+}
+
+template<typename T>
+int const& SuperGeometry3D<T>::get(int iCglob, int iXloc, int iYloc, int iZloc) const
+{
+  if ( this->getLoadBalancer().rank(iCglob) == singleton::mpi().getRank() ) {
+    return _extendedBlockGeometries[this->getLoadBalancer().loc(iCglob)].get(iXloc+this->_overlap, iYloc+this->_overlap, iZloc+this->_overlap);
+  }
+  else {
+    std::cout << "error: read only access to data which is not available in the any block geometry, returning 0 as default" << std::endl;
+    exit(-1);
+    //return 0;
+  }
+}
+
+template<typename T>
+int SuperGeometry3D<T>::getAndCommunicate(int iCglob, int iXloc, int iYloc, int iZloc) const
+{
+  int material = 0;
+  if ( this->getLoadBalancer().rank(iCglob) == singleton::mpi().getRank() ) {
+    material = _extendedBlockGeometries[this->getLoadBalancer().loc(iCglob)].get(iXloc + this->_overlap,
+               iYloc + this->_overlap,
+               iZloc + this->_overlap);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().bCast(&material, 1, this->_loadBalancer.rank(iCglob));
+#endif
+  return material;
+}
+
+template<typename T>
+int& SuperGeometry3D<T>::set(std::vector<int> latticeR)
+{
+  return set(latticeR[0], latticeR[1], latticeR[2], latticeR[3]);
+}
+
+template<typename T>
+int const& SuperGeometry3D<T>::get(std::vector<int> latticeR) const
+{
+  return get(latticeR[0], latticeR[1], latticeR[2], latticeR[3]);
+}
+
+template<typename T>
+int const& SuperGeometry3D<T>::get(const int latticeR[4]) const
+{
+  return get(latticeR[0], latticeR[1], latticeR[2], latticeR[3]);
+}
+
+template<typename T>
+int SuperGeometry3D<T>::getAndCommunicate(std::vector<int> latticeR) const
+{
+  return getAndCommunicate(latticeR[0], latticeR[1], latticeR[2], latticeR[3]);
+}
+
+template<typename T>
+std::vector<T> SuperGeometry3D<T>::getPhysR(int iCglob, int iX, int iY, int iZ) const
+{
+  T physRv[3];
+  this->_cuboidGeometry.getPhysR(physRv, iCglob, iX, iY, iZ);
+  std::vector<T> physR(physRv,physRv + 3);
+  return physR;
+}
+
+template<typename T>
+std::vector<T> SuperGeometry3D<T>::getPhysR(std::vector<int> latticeR) const
+{
+  T physRv[3];
+  this->_cuboidGeometry.getPhysR(physRv, latticeR[0], latticeR[1], latticeR[2], latticeR[3]);
+  std::vector<T> physR(physRv,physRv + 3);
+  return physR;
+}
+
+template<typename T>
+void  SuperGeometry3D<T>::getPhysR(T physR[3], const int& iCglob,  const int& iX, const int& iY, const int& iZ) const
+{
+  this->_cuboidGeometry.getPhysR(physR, iCglob, iX, iY, iZ);
+}
+
+template<typename T>
+void  SuperGeometry3D<T>::getPhysR(T physR[3], const int latticeR[4]) const
+{
+  this->_cuboidGeometry.getPhysR(physR, latticeR);
+}
+
+
+template<typename T>
+BlockGeometry3D<T>& SuperGeometry3D<T>::getExtendedBlockGeometry(int locIC)
+{
+  _statistics.getStatisticsStatus() = true;
+  return _extendedBlockGeometries[locIC];
+}
+
+template<typename T>
+BlockGeometry3D<T> const& SuperGeometry3D<T>::getExtendedBlockGeometry(int locIC) const
+{
+  return _extendedBlockGeometries[locIC];
+}
+
+template<typename T>
+BlockGeometryView3D<T>& SuperGeometry3D<T>::getBlockGeometry(int locIC)
+{
+  _statistics.getStatisticsStatus() = true;
+  return _blockGeometries[locIC];
+}
+
+template<typename T>
+BlockGeometryView3D<T> const& SuperGeometry3D<T>::getBlockGeometry(int locIC) const
+{
+  return _blockGeometries[locIC];
+}
+
+
+template<typename T>
+SuperGeometryStatistics3D<T>& SuperGeometry3D<T>::getStatistics()
+{
+  if (this->_communicationNeeded) {
+    this->communicate();
+    getStatisticsStatus()=true;
+  }
+  return _statistics;
+}
+
+template<typename T>
+bool& SuperGeometry3D<T>::getStatisticsStatus()
+{
+  return _statistics.getStatisticsStatus();
+}
+
+template<typename T>
+bool const& SuperGeometry3D<T>::getStatisticsStatus() const
+{
+  return _statistics.getStatisticsStatus();
+}
+
+template<typename T>
+void SuperGeometry3D<T>::updateStatistics(bool verbose)
+{
+  if (this->_communicationNeeded) {
+    this->communicate(verbose);
+    getStatisticsStatus()=true;
+  }
+  _statistics.update(verbose);
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    _extendedBlockGeometries[iC].getStatistics().update(verbose);
+  }
+}
+
+template<typename T>
+int SuperGeometry3D<T>::clean(bool verbose)
+{
+  this->communicate();
+  int counter=0;
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    counter+=_extendedBlockGeometries[iC].clean(false);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().reduceAndBcast(counter, MPI_SUM);
+#endif
+
+  if (verbose) {
+    clout << "cleaned "<< counter << " outer boundary voxel(s)" << std::endl;
+  }
+  if (counter>0) {
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  return counter;
+}
+
+template<typename T>
+int SuperGeometry3D<T>::clean(int material, bool verbose)
+{
+  this->communicate();
+  int counter=0;
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    counter+=_extendedBlockGeometries[iC].clean(material, false);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().reduceAndBcast(counter, MPI_SUM);
+#endif
+
+  if (verbose) {
+    clout << "cleaned "<< counter << " outer boundary voxel(s)" << std::endl;
+  }
+  if (counter>0) {
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  return counter;
+}
+
+template<typename T>
+int SuperGeometry3D<T>::outerClean(bool verbose)
+{
+  this->communicate();
+  int counter=0;
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    counter+=_extendedBlockGeometries[iC].outerClean(false);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().reduceAndBcast(counter, MPI_SUM);
+#endif
+
+  if (verbose) {
+    clout << "cleaned "<< counter << " outer fluid voxel(s)" << std::endl;
+  }
+  if (counter>0) {
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  return counter;
+}
+
+template<typename T>
+int SuperGeometry3D<T>::innerClean(bool verbose)
+{
+  this->communicate();
+  int counter=0;
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    counter+=_extendedBlockGeometries[iC].innerClean(false);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().barrier();
+  singleton::mpi().reduceAndBcast(counter, MPI_SUM);
+#endif
+
+  if (verbose) {
+    clout << "cleaned "<< counter << " inner boundary voxel(s)" << std::endl;
+  }
+  if (counter>0) {
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  return counter;
+}
+
+template<typename T>
+int SuperGeometry3D<T>::innerClean(int bcType, bool verbose)
+{
+  this->communicate();
+  int counter=0;
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    counter+=_extendedBlockGeometries[iC].innerClean(bcType,false);
+  }
+#ifdef PARALLEL_MODE_MPI
+  singleton::mpi().reduceAndBcast(counter, MPI_SUM);
+#endif
+
+  if (verbose) {
+    clout << "cleaned "<< counter << " inner boundary voxel(s) of Type " << bcType << std::endl;
+  }
+  if (counter>0) {
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  return counter;
+}
+
+template<typename T>
+bool SuperGeometry3D<T>::checkForErrors(bool verbose)
+{
+  this->communicate();
+  bool error = false;
+  for (unsigned iC=0; iC<_blockGeometries.size(); iC++) {
+    if (_blockGeometries[iC].checkForErrors(false)) {
+      error = true;
+    }
+  }
+  if (verbose) {
+    if (error) {
+      this->clout << "error!" << std::endl;
+    }
+    else {
+      this->clout << "the model is correct!" << std::endl;
+    }
+  }
+  return error;
+}
+
+
+template<typename T>
+void SuperGeometry3D<T>::rename(int fromM, int toM)
+{
+
+  this->communicate();
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    _blockGeometries[iC].rename(fromM,toM);
+  }
+  _statistics.getStatisticsStatus() = true;
+  this->_communicationNeeded = true;
+}
+
+template<typename T>
+void SuperGeometry3D<T>::rename(int fromM, int toM, FunctorPtr<IndicatorF3D<T>>&& condition)
+{
+
+  this->communicate();
+
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    _extendedBlockGeometries[iC].rename(fromM,toM,*condition);
+  }
+  _statistics.getStatisticsStatus() = true;
+}
+
+template<typename T>
+void SuperGeometry3D<T>::rename(int fromM, int toM, unsigned offsetX, unsigned offsetY, unsigned offsetZ)
+{
+
+  if ( offsetX<=unsigned(this->_overlap)
+       && offsetY<=unsigned(this->_overlap)
+       && offsetZ<=unsigned(this->_overlap) ) {
+    this->communicate();
+    for (unsigned iC=0; iC<_blockGeometries.size(); iC++) {
+      _blockGeometries[iC].rename(fromM,toM,offsetX, offsetY, offsetZ);
+    }
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  else {
+    clout << "error rename only implemented for offset<=overlap" << std::endl;
+  }
+}
+
+template<typename T>
+void SuperGeometry3D<T>::rename(int fromM, int toM, int testM, std::vector<int> testDirection)
+{
+
+  if ( testDirection[0]*testDirection[0]<=(this->_overlap)*(this->_overlap)
+       && testDirection[1]*testDirection[1]<=(this->_overlap)*(this->_overlap)
+       && testDirection[2]*testDirection[2]<=(this->_overlap)*(this->_overlap) ) {
+    this->communicate();
+    for (unsigned iC=0; iC<_blockGeometries.size(); iC++) {
+      _blockGeometries[iC].rename(fromM,toM,testM,testDirection);
+    }
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  else {
+    clout << "error rename only implemented for |testDirection[i]|<=overlap" << std::endl;
+  }
+}
+
+template<typename T>
+void SuperGeometry3D<T>::rename(int fromBcMat, int toBcMat, int fluidMat,
+                                FunctorPtr<IndicatorF3D<T>>&& condition)
+{
+  if (this->_overlap>1) {
+    this->communicate();
+    rename(fromBcMat, toBcMat, *condition);
+    std::vector<int> testDirection = this->getStatistics().computeDiscreteNormal(toBcMat);
+
+    //std::cout << testDirection[0]<<testDirection[1]<<testDirection[2]<<std::endl;
+    this->communicate();
+    for (unsigned iC=0; iC<_blockGeometries.size(); iC++) {
+      _blockGeometries[iC].rename(fromBcMat,toBcMat,fluidMat,*condition,testDirection);
+    }
+    _statistics.getStatisticsStatus() = true;
+    this->_communicationNeeded = true;
+  }
+  else {
+    clout << "error rename only implemented for overlap>=2" << std::endl;
+  }
+}
+
+template<typename T>
+void SuperGeometry3D<T>::copyMaterialLayer(IndicatorF3D<T>& condition, int discreteNormal[3], int numberOfLayers)
+{
+
+  this->communicate();
+
+  for (unsigned iC=0; iC<_extendedBlockGeometries.size(); iC++) {
+    _extendedBlockGeometries[iC].copyMaterialLayer(condition, discreteNormal, numberOfLayers);
+  }
+  _statistics.getStatisticsStatus() = true;
+
+}
+
+
+template<typename T>
+void SuperGeometry3D<T>::print()
+{
+  this->_cuboidGeometry.print();
+  getStatistics().print();
+}
+
+template<typename T>
+std::unique_ptr<SuperIndicatorF3D<T>> SuperGeometry3D<T>::getMaterialIndicator(
+                                     std::vector<int>&& materials)
+{
+  return this->getIndicator<SuperIndicatorMaterial3D>(
+           std::forward<std::vector<int>>(materials));
+}
+
+template<typename T>
+std::unique_ptr<SuperIndicatorF3D<T>> SuperGeometry3D<T>::getMaterialIndicator(
+                                     int material)
+{
+  return this->getMaterialIndicator(std::vector<int> { material });
+}
+
+
+} // namespace olb
+
+#endif