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+/*  Lattice Boltzmann sample, written in C++, using the OpenLB
+ *  library
+ *
+ *  Copyright (C) 2006-2015 Fabian Klemens, Jonas Latt, Mathias J. Krause
+ *  Vojtech Cvrcek, 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.
+ */
+
+/* settlingCube3d.cpp:
+ * The case examines the settling of a cubical silica particle
+ * under the influence of gravity.
+ * The object is surrounded by water in a rectangular domain
+ * limited by no-slip boundary conditions.
+ * For the calculation of forces an DNS approach is chosen
+ * which also leads to a back-coupling of the particle on the fluid,
+ * inducing a flow.
+ *
+ * The simulation is based on the homogenised lattice Boltzmann approach
+ * (HLBM) introduced in "Particle flow simulations with homogenised
+ * lattice Boltzmann methods" by Krause et al.
+ * and extended in "Towards the simulation of arbitrarily shaped 3D particles
+ * using a homogenised lattice Boltzmann method" by Trunk et al.
+ * for the simulation of 3D particles.
+ *
+ * This example demonstrates the usage of HLBM in the OpenLB framework.
+ */
+
+#include "olb3D.h"
+#include "olb3D.hh"     // use generic version only!
+
+#include <vector>
+#include <cmath>
+#include <iostream>
+#include <fstream>
+
+using namespace olb;
+using namespace olb::descriptors;
+using namespace olb::graphics;
+using namespace olb::util;
+using namespace std;
+
+typedef double T;
+#define DESCRIPTOR D3Q19<POROSITY,VELOCITY_NUMERATOR,VELOCITY_DENOMINATOR>
+
+#define WriteVTK
+
+// Discretization Settings
+int res = 30;
+T const charLatticeVelocity = 0.01;
+
+// Time Settings
+T const maxPhysT = 0.5;       // max. simulation time in s
+T const iTwrite = 0.02;       // write out intervall in s
+
+// Domain Settings
+T const lengthX = 0.01;     
+T const lengthY = 0.01;     
+T const lengthZ = 0.05;
+
+// Fluid Settings 
+T const physDensity = 1000;
+T const physViscosity = 1E-5;
+
+//Particle Settings
+T centerX = lengthX*.5;
+T centerY = lengthY*.5;
+T centerZ = lengthZ*.9;
+T const cubeDensity = 2500;              
+T const cubeEdgeLength = 0.0025; 
+Vector<T,3> cubeCenter = {centerX,centerY,centerZ};
+Vector<T,3> cubeOrientation = {0.,15.,0.}; 
+Vector<T,3> cubeVelocity = {0.,0.,0.};
+Vector<T,3> externalAcceleration = {.0, .0, -9.81 * (1. - physDensity / cubeDensity)};
+
+// Characteristic Quantities
+T const charPhysLength = lengthX;
+T const charPhysVelocity = 0.15;    // Assumed maximal velocity
+
+
+// Prepare geometry
+void prepareGeometry(UnitConverter<T,DESCRIPTOR> const& converter,
+                     SuperGeometry3D<T>& superGeometry)
+{
+  OstreamManager clout(std::cout, "prepareGeometry");
+  clout << "Prepare Geometry ..." << std::endl;
+
+  superGeometry.rename(0, 2);
+  superGeometry.rename(2, 1, 1, 1, 1);
+
+  superGeometry.clean();
+  superGeometry.innerClean();
+
+  superGeometry.checkForErrors();
+  superGeometry.getStatistics().print();
+  clout << "Prepare Geometry ... OK" << std::endl;
+  return;
+}
+
+
+// Set up the geometry of the simulation
+void prepareLattice(
+  SuperLattice3D<T, DESCRIPTOR>& sLattice, UnitConverter<T,DESCRIPTOR> const& converter,
+  Dynamics<T, DESCRIPTOR>& designDynamics,
+  sOnLatticeBoundaryCondition3D<T, DESCRIPTOR>& sBoundaryCondition,
+  SuperGeometry3D<T>& superGeometry)
+{
+  OstreamManager clout(std::cout, "prepareLattice");
+  clout << "Prepare Lattice ..." << std::endl;
+  clout << "setting Velocity Boundaries ..." << std::endl;
+
+  /// Material=0 -->do nothing
+  sLattice.defineDynamics(superGeometry, 0, &instances::getNoDynamics<T, DESCRIPTOR>());
+  sLattice.defineDynamics(superGeometry, 1, &designDynamics);
+  sLattice.defineDynamics(superGeometry, 2, &instances::getBounceBack<T, DESCRIPTOR>());
+
+  clout << "Prepare Lattice ... OK" << std::endl;
+}
+
+
+//Set Boundary Values
+void setBoundaryValues(SuperLattice3D<T, DESCRIPTOR>& sLattice,
+                       UnitConverter<T,DESCRIPTOR> const& converter, int iT,
+                       SuperGeometry3D<T>& superGeometry)
+{
+  OstreamManager clout(std::cout, "setBoundaryValues");
+
+  if (iT == 0) {
+    AnalyticalConst3D<T, T> zero(0.);
+    AnalyticalConst3D<T, T> one(1.);
+    sLattice.defineField<descriptors::POROSITY>(superGeometry.getMaterialIndicator({0,1,2}), one);    
+    // Set initial condition
+    AnalyticalConst3D<T, T> ux(0.);
+    AnalyticalConst3D<T, T> uy(0.);
+    AnalyticalConst3D<T, T> uz(0.);
+    AnalyticalConst3D<T, T> rho(1.);
+    AnalyticalComposed3D<T, T> u(ux, uy, uz);
+
+    //Initialize all values of distribution functions to their local equilibrium
+    sLattice.defineRhoU(superGeometry, 1, rho, u);
+    sLattice.iniEquilibrium(superGeometry, 1, rho, u);
+
+    // Make the lattice ready for simulation
+    sLattice.initialize();
+  }
+}
+
+
+/// Computes the pressure drop between the voxels before and after the cylinder
+void getResults(SuperLattice3D<T, DESCRIPTOR>& sLattice,
+                UnitConverter<T,DESCRIPTOR> const& converter, int iT,
+                SuperGeometry3D<T>& superGeometry, Timer<double>& timer,
+                ParticleDynamics3D<T, DESCRIPTOR> particleDynamics)
+{
+  OstreamManager clout(std::cout, "getResults");
+
+#ifdef WriteVTK
+  SuperVTMwriter3D<T> vtkWriter("sedimentation");
+  SuperLatticePhysVelocity3D<T, DESCRIPTOR> velocity(sLattice, converter);
+  SuperLatticePhysPressure3D<T, DESCRIPTOR> pressure(sLattice, converter);
+  SuperLatticePhysExternalPorosity3D<T, DESCRIPTOR> externalPor(sLattice, converter);
+  vtkWriter.addFunctor(velocity);
+  vtkWriter.addFunctor(pressure);
+  vtkWriter.addFunctor(externalPor);
+
+  if (iT == 0) {
+    /// Writes the converter log file
+    SuperLatticeGeometry3D<T, DESCRIPTOR> geometry(sLattice, superGeometry);
+    SuperLatticeCuboid3D<T, DESCRIPTOR> cuboid(sLattice);
+    SuperLatticeRank3D<T, DESCRIPTOR> rank(sLattice);
+    vtkWriter.write(geometry);
+    vtkWriter.write(cuboid);
+    vtkWriter.write(rank);
+    vtkWriter.createMasterFile();
+  }
+
+  if (iT % converter.getLatticeTime(iTwrite) == 0) {
+    vtkWriter.write(iT);
+  }
+#endif
+
+  /// Writes output on the console
+  if (iT % converter.getLatticeTime(iTwrite) == 0) {
+    timer.update(iT);
+    timer.printStep();
+    sLattice.getStatistics().print(iT, converter.getPhysTime(iT));
+    particleDynamics.print(); 
+  }
+}
+
+int main(int argc, char* argv[])
+{
+  /// === 1st Step: Initialization ===
+  olbInit(&argc, &argv);
+  singleton::directories().setOutputDir("./tmp/");
+  OstreamManager clout(std::cout, "main");
+
+  UnitConverterFromResolutionAndLatticeVelocity<T,DESCRIPTOR> converter(
+    (int)   res,                  //resolution
+    ( T )   charLatticeVelocity,  //charLatticeVelocity
+    ( T )   charPhysLength,       //charPhysLength
+    ( T )   charPhysVelocity,     //charPhysVelocity
+    ( T )   physViscosity,        //physViscosity
+    ( T )   physDensity           //physDensity
+  );
+  converter.print();
+
+  /// === 2rd Step: Prepare Geometry ===
+  /// Instantiation of a cuboidGeometry with weights
+  std::vector<T> extend(3, T());
+  extend[0] = lengthX;
+  extend[1] = lengthY;
+  extend[2] = lengthZ;
+  std::vector<T> origin(3, T());
+  IndicatorCuboid3D<T> cuboid(extend, origin);
+
+#ifdef PARALLEL_MODE_MPI
+  CuboidGeometry3D<T> cuboidGeometry(cuboid, converter.getConversionFactorLength(), singleton::mpi().getSize());
+#else
+  CuboidGeometry3D<T> cuboidGeometry(cuboid, converter.getConversionFactorLength(), 7);
+#endif
+  cuboidGeometry.print();
+
+  HeuristicLoadBalancer<T> loadBalancer(cuboidGeometry);
+  SuperGeometry3D<T> superGeometry(cuboidGeometry, loadBalancer, 2);
+  prepareGeometry(converter, superGeometry);
+
+  /// === 3rd Step: Prepare Lattice ===
+  SuperLattice3D<T, DESCRIPTOR> sLattice(superGeometry);
+
+  PorousParticleBGKdynamics<T, DESCRIPTOR, false> designDynamics(converter.getLatticeRelaxationFrequency(), instances::getBulkMomenta<T, DESCRIPTOR>());
+
+  sOnLatticeBoundaryCondition3D<T, DESCRIPTOR> sBoundaryCondition(sLattice);
+  createLocalBoundaryCondition3D<T, DESCRIPTOR>(sBoundaryCondition);
+
+  prepareLattice(sLattice, converter, designDynamics, sBoundaryCondition, superGeometry);
+
+  /// === 4th Step: Main Loop with Timer ===
+  Timer<double> timer(converter.getLatticeTime(maxPhysT), superGeometry.getStatistics().getNvoxel());
+  timer.start();
+
+  // Create Particle Dynamics
+  ParticleDynamics3D<T, DESCRIPTOR> particleDynamics(sLattice, converter, superGeometry, lengthX, lengthY, lengthZ, externalAcceleration);
+  
+  // Create Cube Indicator
+  T epsilon = 0.5*converter.getConversionFactorLength();
+  
+  //Cube indicator
+  SmoothIndicatorCuboid3D<T, T, true> particleIndicator(cubeCenter, cubeEdgeLength, cubeEdgeLength, cubeEdgeLength, epsilon, cubeOrientation, cubeDensity, cubeVelocity);
+  
+  //Sphere indicator
+  //SmoothIndicatorSphere3D<T, T, true> particleIndicator(cubeCenter, 0.5*cubeEdgeLength, epsilon, cubeDensity, cubeVelocity);
+  
+  //Cylinder indicator
+  //SmoothIndicatorCylinder3D<T, T, true> particleIndicator(cubeCenter, { 1, 0, 0 }, 0.5*cubeEdgeLength, cubeEdgeLength, epsilon, cubeOrientation, cubeDensity, cubeVelocity);
+
+  SuperExternal3D<T,DESCRIPTOR,POROSITY> superExtPorosity(superGeometry, sLattice, sLattice.getOverlap());
+  SuperExternal3D<T,DESCRIPTOR,VELOCITY_NUMERATOR> superExtNumerator(superGeometry, sLattice, sLattice.getOverlap());
+  SuperExternal3D<T,DESCRIPTOR,VELOCITY_DENOMINATOR> superExtDenominator(superGeometry, sLattice, sLattice.getOverlap());
+  particleDynamics.addParticle( particleIndicator );
+  particleDynamics.print();
+
+  /// === 5th Step: Definition of Initial and Boundary Conditions ===
+  setBoundaryValues(sLattice, converter, 0, superGeometry);
+
+  clout << "MaxIT: " << converter.getLatticeTime(maxPhysT) << std::endl;
+  for (int iT = 0; iT < converter.getLatticeTime(maxPhysT)+10; ++iT) {
+    particleDynamics.simulateTimestep("verlet");
+    getResults(sLattice, converter, iT, superGeometry, timer, particleDynamics);
+    sLattice.collideAndStream();
+    superExtPorosity.communicate();
+    superExtNumerator.communicate();
+    superExtDenominator.communicate();
+  }
+
+  timer.stop();
+  timer.printSummary();
+}