Initialize at openlb-1-3

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diff --git a/examples/laminar/cylinder2d/cylinder2d.cpp b/examples/laminar/cylinder2d/cylinder2d.cpp
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+/*  Lattice Boltzmann sample, written in C++, using the OpenLB
+ *  library
+ *
+ *  Copyright (C) 2006-2014 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.
+ */
+
+/* cylinder2d.cpp:
+ * This example examines a steady flow past a cylinder placed in a channel.
+ * The cylinder is offset somewhat from the center of the flow to make the
+ * steady-state symmetrical flow unstable. At the inlet, a Poiseuille profile is
+ * imposed on the velocity, whereas the outlet implements a Dirichlet pressure
+ * condition set by p = 0.
+ * Inspired by "Benchmark Computations of Laminar Flow Around
+ * a Cylinder" by M.Schäfer and S.Turek. For high resolution, low
+ * latticeU, and enough time to converge, the results for pressure drop, drag
+ * and lift lie within the estimated intervals for the exact results.
+ * An unsteady flow with Karman vortex street can be created by changing the
+ * Reynolds number to Re=100.
+ */
+
+
+#include "olb2D.h"
+#ifndef OLB_PRECOMPILED // Unless precompiled version is used,
+#include "olb2D.hh"   // include full template code
+#endif
+#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 D2Q9<>
+
+
+// Parameters for the simulation setup
+const int N = 10;       // resolution of the model
+const T Re = 20.;       // Reynolds number
+const T maxPhysT = 16.; // max. simulation time in s, SI unit
+const T L = 0.1/N;      // latticeL
+const T lengthX = 2.2;
+const T lengthY = .41+L;
+const T centerCylinderX = 0.2;
+const T centerCylinderY = 0.2+L/2.;
+const T radiusCylinder = 0.05;
+
+
+// Stores geometry information in form of material numbers
+void prepareGeometry( UnitConverter<T, DESCRIPTOR> const& converter,
+                      SuperGeometry2D<T>& superGeometry )
+{
+
+  OstreamManager clout( std::cout,"prepareGeometry" );
+  clout << "Prepare Geometry ..." << std::endl;
+
+  Vector<T,2> extend( lengthX,lengthY );
+  Vector<T,2> center( centerCylinderX,centerCylinderY );
+  Vector<T,2> origin;
+  IndicatorCircle2D<T> circle( center, radiusCylinder );
+
+  superGeometry.rename( 0,2 );
+
+  superGeometry.rename( 2,1,1,1 );
+
+  // Set material number for inflow
+  extend[0] = 2.*L;
+  origin[0] = -L;
+  IndicatorCuboid2D<T> inflow( extend, origin );
+  superGeometry.rename( 2,3,1,inflow );
+  // Set material number for outflow
+  origin[0] = lengthX-L;
+  IndicatorCuboid2D<T> outflow( extend, origin );
+  superGeometry.rename( 2,4,1,outflow );
+  // Set material number for cylinder
+  superGeometry.rename( 1,5,circle );
+
+  // Removes all not needed boundary voxels outside the surface
+  superGeometry.clean();
+  superGeometry.checkForErrors();
+
+  superGeometry.print();
+
+  clout << "Prepare Geometry ... OK" << std::endl;
+}
+
+// Set up the geometry of the simulation
+void prepareLattice( SuperLattice2D<T,DESCRIPTOR>& sLattice,
+                     UnitConverter<T, DESCRIPTOR> const& converter,
+                     Dynamics<T, DESCRIPTOR>& bulkDynamics,
+                     sOnLatticeBoundaryCondition2D<T,DESCRIPTOR>& sBoundaryCondition,
+                     sOffLatticeBoundaryCondition2D<T,DESCRIPTOR>& offBc,
+                     SuperGeometry2D<T>& superGeometry )
+{
+
+  OstreamManager clout( std::cout,"prepareLattice" );
+  clout << "Prepare Lattice ..." << std::endl;
+
+  const T omega = converter.getLatticeRelaxationFrequency();
+
+  // Material=0 -->do nothing
+  sLattice.defineDynamics( superGeometry, 0, &instances::getNoDynamics<T, DESCRIPTOR>() );
+
+  // Material=1 -->bulk dynamics
+  // Material=3 -->bulk dynamics (inflow)
+  // Material=4 -->bulk dynamics (outflow)
+  auto bulkIndicator = superGeometry.getMaterialIndicator({1, 3, 4});
+  sLattice.defineDynamics( bulkIndicator, &bulkDynamics );
+
+  // Material=2 -->bounce back
+  sLattice.defineDynamics( superGeometry, 2, &instances::getBounceBack<T, DESCRIPTOR>() );
+
+  // Setting of the boundary conditions
+  sBoundaryCondition.addVelocityBoundary( superGeometry, 3, omega );
+  sBoundaryCondition.addPressureBoundary( superGeometry, 4, omega );
+
+  // Material=5 -->bounce back
+  //sLattice.defineDynamics(superGeometry, 5, &instances::getBounceBack<T, DESCRIPTOR>());
+
+  // Material=5 -->bouzidi
+
+  Vector<T,2> center( centerCylinderX,centerCylinderY );
+  IndicatorCircle2D<T> circle( center, radiusCylinder );
+
+  sLattice.defineDynamics( superGeometry, 5, &instances::getNoDynamics<T,DESCRIPTOR>() );
+  offBc.addZeroVelocityBoundary( superGeometry, 5, circle );
+
+  // Initial conditions
+  AnalyticalConst2D<T,T> rhoF( 1 );
+  std::vector<T> velocity( 2,T( 0 ) );
+  AnalyticalConst2D<T,T> uF( velocity );
+
+  // Initialize all values of distribution functions to their local equilibrium
+  sLattice.defineRhoU( bulkIndicator, rhoF, uF );
+  sLattice.iniEquilibrium( bulkIndicator, rhoF, uF );
+
+  // Make the lattice ready for simulation
+  sLattice.initialize();
+
+  clout << "Prepare Lattice ... OK" << std::endl;
+}
+
+// Generates a slowly increasing inflow for the first iTMaxStart timesteps
+void setBoundaryValues( SuperLattice2D<T, DESCRIPTOR>& sLattice,
+                        UnitConverter<T, DESCRIPTOR> const& converter, int iT,
+                        SuperGeometry2D<T>& superGeometry )
+{
+
+  OstreamManager clout( std::cout,"setBoundaryValues" );
+
+  // No of time steps for smooth start-up
+  int iTmaxStart = converter.getLatticeTime( maxPhysT*0.4 );
+  int iTupdate = 5;
+
+  if ( iT%iTupdate==0 && iT<= iTmaxStart ) {
+    // Smooth start curve, sinus
+    // SinusStartScale<T,int> StartScale(iTmaxStart, T(1));
+
+    // Smooth start curve, polynomial
+    PolynomialStartScale<T,T> StartScale( iTmaxStart, T( 1 ) );
+
+    // Creates and sets the Poiseuille inflow profile using functors
+    T iTvec[1] = {T( iT )};
+    T frac[1] = {};
+    StartScale( frac,iTvec );
+    T maxVelocity = converter.getCharLatticeVelocity()*3./2.*frac[0];
+    T distance2Wall = L/2.;
+    Poiseuille2D<T> poiseuilleU( superGeometry, 3, maxVelocity, distance2Wall );
+
+    sLattice.defineU( superGeometry, 3, poiseuilleU );
+  }
+
+}
+
+// Computes the pressure drop between the voxels before and after the cylinder
+void getResults( SuperLattice2D<T, DESCRIPTOR>& sLattice,
+                 UnitConverter<T, DESCRIPTOR> const& converter, int iT,
+                 SuperGeometry2D<T>& superGeometry, Timer<T>& timer,
+                 CircularBuffer<T>& buffer )
+{
+
+  OstreamManager clout( std::cout,"getResults" );
+
+  SuperVTMwriter2D<T> vtmWriter( "cylinder2d" );
+  SuperLatticePhysVelocity2D<T, DESCRIPTOR> velocity( sLattice, converter );
+  SuperLatticePhysPressure2D<T, DESCRIPTOR> pressure( sLattice, converter );
+  vtmWriter.addFunctor( velocity );
+  vtmWriter.addFunctor( pressure );
+
+  const int vtkIter  = converter.getLatticeTime( .3 );
+  const int statIter = converter.getLatticeTime( .1 );
+
+  T point[2] = {};
+  point[0] = centerCylinderX + 3*radiusCylinder;
+  point[1] = centerCylinderY;
+  AnalyticalFfromSuperF2D<T> intpolateP( pressure, true );
+  T p;
+  intpolateP( &p,point );
+  buffer.insert(p);
+
+  if ( iT == 0 ) {
+    // Writes the geometry, cuboid no. and rank no. as vti file for visualization
+    SuperLatticeGeometry2D<T, DESCRIPTOR> geometry( sLattice, superGeometry );
+    SuperLatticeCuboid2D<T, DESCRIPTOR> cuboid( sLattice );
+    SuperLatticeRank2D<T, DESCRIPTOR> rank( sLattice );
+    vtmWriter.write( geometry );
+    vtmWriter.write( cuboid );
+    vtmWriter.write( rank );
+
+    vtmWriter.createMasterFile();
+  }
+
+  // Writes the vtk files
+  if ( iT%vtkIter == 0 && iT > 0 ) {
+    vtmWriter.write( iT );
+
+    SuperEuklidNorm2D<T, DESCRIPTOR> normVel( velocity );
+    BlockReduction2D2D<T> planeReduction( normVel, 600, BlockDataSyncMode::ReduceOnly );
+    // write output as JPEG
+    heatmap::write(planeReduction, iT);
+  }
+
+  // Gnuplot constructor (must be static!)
+  // for real-time plotting: gplot("name", true) // experimental!
+  static Gnuplot<T> gplot( "drag" );
+
+  // write pdf at last time step
+  if ( iT == converter.getLatticeTime( maxPhysT )-1 ) {
+    // writes pdf
+    gplot.writePDF();
+  }
+
+  // Writes output on the console
+  if ( iT%statIter == 0 ) {
+    // Timer console output
+    timer.update( iT );
+    timer.printStep();
+    clout << "Circular buffer test: moving average pointwise value=" << buffer.average() << std::endl;
+
+    // Lattice statistics console output
+    sLattice.getStatistics().print( iT,converter.getPhysTime( iT ) );
+
+    // Drag, lift, pressure drop
+    AnalyticalFfromSuperF2D<T> intpolatePressure( pressure, true );
+    SuperLatticePhysDrag2D<T,DESCRIPTOR> drag( sLattice, superGeometry, 5, converter );
+
+
+    T point1[2] = {};
+    T point2[2] = {};
+
+    point1[0] = centerCylinderX - radiusCylinder;
+    point1[1] = centerCylinderY;
+
+    point2[0] = centerCylinderX + radiusCylinder;
+    point2[1] = centerCylinderY;
+
+    T p1, p2;
+    intpolatePressure( &p1,point1 );
+    intpolatePressure( &p2,point2 );
+
+    clout << "pressure1=" << p1;
+    clout << "; pressure2=" << p2;
+
+    T pressureDrop = p1-p2;
+    clout << "; pressureDrop=" << pressureDrop;
+
+    int input[3] = {};
+    T _drag[drag.getTargetDim()];
+    drag( _drag,input );
+    clout << "; drag=" << _drag[0] << "; lift=" << _drag[1] << endl;
+
+    // set data for gnuplot: input={xValue, yValue(s), names (optional), position of key (optional)}
+    gplot.setData( converter.getPhysTime( iT ), {_drag[0], 5.58}, {"drag(openLB)", "drag(schaeferTurek)"}, "bottom right", {'l','l'} );
+    // writes a png in one file for every timestep, if the file is open it can be used as a "liveplot"
+    gplot.writePNG();
+
+    // every (iT%vtkIter) write an png of the plot
+    if ( iT%( vtkIter ) == 0 ) {
+      // writes pngs: input={name of the files (optional), x range for the plot (optional)}
+      gplot.writePNG( iT, maxPhysT );
+    }
+  }
+}
+
+int main( int argc, char* argv[] )
+{
+
+  // === 1st Step: Initialization ===
+  olbInit( &argc, &argv );
+  singleton::directories().setOutputDir( "./tmp/" );
+  OstreamManager clout( std::cout,"main" );
+  // display messages from every single mpi process
+  //clout.setMultiOutput(true);
+
+  UnitConverterFromResolutionAndRelaxationTime<T, DESCRIPTOR> const converter(
+    int {N},                        // resolution: number of voxels per charPhysL
+    (T)   0.56,                     // latticeRelaxationTime: relaxation time, have to be greater than 0.5!
+    (T)   2.0*radiusCylinder,       // charPhysLength: reference length of simulation geometry
+    (T)   0.2,                      // charPhysVelocity: maximal/highest expected velocity during simulation in __m / s__
+    (T)   0.2*2.*radiusCylinder/Re, // physViscosity: physical kinematic viscosity in __m^2 / s__
+    (T)   1.0                       // physDensity: physical density in __kg / m^3__
+  );
+  // Prints the converter log as console output
+  converter.print();
+  // Writes the converter log in a file
+  converter.write("cylinder2d");
+
+  // === 2rd Step: Prepare Geometry ===
+  Vector<T,2> extend( lengthX,lengthY );
+  Vector<T,2> origin;
+  IndicatorCuboid2D<T> cuboid( extend, origin );
+
+  // Instantiation of a cuboidGeometry with weights
+#ifdef PARALLEL_MODE_MPI
+  const int noOfCuboids = singleton::mpi().getSize();
+#else
+  const int noOfCuboids = 7;
+#endif
+  CuboidGeometry2D<T> cuboidGeometry( cuboid, L, noOfCuboids );
+
+  // Instantiation of a loadBalancer
+  HeuristicLoadBalancer<T> loadBalancer( cuboidGeometry );
+
+  // Instantiation of a superGeometry
+  SuperGeometry2D<T> superGeometry( cuboidGeometry, loadBalancer, 2 );
+
+  prepareGeometry( converter, superGeometry );
+
+  // === 3rd Step: Prepare Lattice ===
+  SuperLattice2D<T, DESCRIPTOR> sLattice( superGeometry );
+
+  BGKdynamics<T, DESCRIPTOR> bulkDynamics( converter.getLatticeRelaxationFrequency(), instances::getBulkMomenta<T, DESCRIPTOR>() );
+
+  // choose between local and non-local boundary condition
+  sOnLatticeBoundaryCondition2D<T,DESCRIPTOR> sBoundaryCondition( sLattice );
+  // createInterpBoundaryCondition2D<T,DESCRIPTOR>(sBoundaryCondition);
+  createLocalBoundaryCondition2D<T,DESCRIPTOR>( sBoundaryCondition );
+
+  sOffLatticeBoundaryCondition2D<T, DESCRIPTOR> sOffBoundaryCondition( sLattice );
+  createBouzidiBoundaryCondition2D<T, DESCRIPTOR> ( sOffBoundaryCondition );
+
+  prepareLattice( sLattice, converter, bulkDynamics, sBoundaryCondition, sOffBoundaryCondition, superGeometry );
+
+  // === 4th Step: Main Loop with Timer ===
+  CircularBuffer<T> buffer(converter.getLatticeTime(.2));
+  clout << "starting simulation..." << endl;
+  Timer<T> timer( converter.getLatticeTime( maxPhysT ), superGeometry.getStatistics().getNvoxel() );
+  timer.start();
+
+  for ( int iT = 0; iT < converter.getLatticeTime( maxPhysT ); ++iT ) {
+    // === 5th Step: Definition of Initial and Boundary Conditions ===
+    setBoundaryValues( sLattice, converter, iT, superGeometry );
+
+    // === 6th Step: Collide and Stream Execution ===
+    sLattice.collideAndStream();
+
+    // === 7th Step: Computation and Output of the Results ===
+    getResults( sLattice, converter, iT, superGeometry, timer, buffer );
+  }
+
+  timer.stop();
+  timer.printSummary();
+}