From 94d3e79a8617f88dc0219cfdeedfa3147833719d Mon Sep 17 00:00:00 2001
From: Adrian Kummerlaender
Date: Mon, 24 Jun 2019 14:43:36 +0200
Subject: Initialize at openlb-1-3
---
examples/turbulence/aorta3d/aorta3d.cpp | 356 ++++++++++++++++++++++++++++++++
1 file changed, 356 insertions(+)
create mode 100644 examples/turbulence/aorta3d/aorta3d.cpp
(limited to 'examples/turbulence/aorta3d/aorta3d.cpp')
diff --git a/examples/turbulence/aorta3d/aorta3d.cpp b/examples/turbulence/aorta3d/aorta3d.cpp
new file mode 100644
index 0000000..356561b
--- /dev/null
+++ b/examples/turbulence/aorta3d/aorta3d.cpp
@@ -0,0 +1,356 @@
+/* Lattice Boltzmann sample, written in C++, using the OpenLB
+ * library
+ *
+ * Copyright (C) 2011-2014 Mathias J. Krause
+ * E-mail contact: info@openlb.net
+ * The most recent release of OpenLB can be downloaded at
+ *
+ *
+ * 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.
+ */
+
+/* aorta3d.cpp:
+ * In this example the fluid flow through a bifurcation is
+ * simulated. The geometry is obtained from a mesh in stl-format.
+ * With Bouzidi boundary conditions the curved boundary is
+ * adequately mapped and initialized fully automatically. As
+ * dynamics a Smagorinsky turbulent BGK model is used to stabilize
+ * the simulation for low resolutions. As output the flux at the
+ * inflow and outflow region is computed. The results has been
+ * validated by comparison with other results obtained with FEM
+ * and FVM.
+ */
+
+
+#include "olb3D.h"
+#ifndef OLB_PRECOMPILED // Unless precompiled version is used,
+#include "olb3D.hh" // include full template code;
+#endif
+#include
+#include
+#include
+#include
+
+using namespace olb;
+using namespace olb::descriptors;
+using namespace olb::graphics;
+using namespace olb::util;
+
+typedef double T;
+#define DESCRIPTOR D3Q19<>
+
+
+//simulation parameters
+const int N = 40; // resolution of the model
+const int M = 20; // time discretization refinement
+const bool bouzidiOn = true; // choice of boundary condition
+const T maxPhysT = 2.; // max. simulation time in s, SI unit
+
+
+// Stores data from stl file in geometry in form of material numbers
+void prepareGeometry( UnitConverter const& converter, IndicatorF3D& indicator,
+ STLreader& stlReader, SuperGeometry3D& superGeometry ) {
+
+ OstreamManager clout( std::cout,"prepareGeometry" );
+ clout << "Prepare Geometry ..." << std::endl;
+
+ superGeometry.rename( 0,2,indicator );
+ superGeometry.rename( 2,1,stlReader );
+
+ superGeometry.clean();
+
+ // Set material number for inflow
+ IndicatorCircle3D inflow( 0.218125 ,0.249987 ,0.0234818, 0., 1.,0., 0.0112342 );
+ IndicatorCylinder3D layerInflow( inflow, 2.*converter.getConversionFactorLength() );
+ superGeometry.rename( 2,3,1,layerInflow );
+
+ // Set material number for outflow0
+ //IndicatorCircle3D outflow0(0.2053696,0.0900099,0.0346537, 2.5522,5.0294,-1.5237, 0.0054686 );
+ IndicatorCircle3D outflow0( 0.2053696,0.0900099,0.0346537, 0.,-1.,0., 0.0054686 );
+ IndicatorCylinder3D layerOutflow0( outflow0, 2.*converter.getConversionFactorLength() );
+ superGeometry.rename( 2,4,1,layerOutflow0 );
+
+ // Set material number for outflow1
+ //IndicatorCircle3D outflow1(0.2388403,0.0900099,0.0343228, -1.5129,5.1039,-2.8431, 0.0058006 );
+ IndicatorCircle3D outflow1( 0.2388403,0.0900099,0.0343228, 0.,-1.,0., 0.0058006 );
+ IndicatorCylinder3D layerOutflow1( outflow1, 2.*converter.getConversionFactorLength() );
+ superGeometry.rename( 2,5,1,layerOutflow1 );
+
+ // Removes all not needed boundary voxels outside the surface
+ superGeometry.clean();
+ // Removes all not needed boundary voxels inside the surface
+ superGeometry.innerClean( 3 );
+ superGeometry.checkForErrors();
+
+ superGeometry.print();
+ clout << "Prepare Geometry ... OK" << std::endl;
+}
+
+// Set up the geometry of the simulation
+void prepareLattice( SuperLattice3D& lattice,
+ UnitConverter const& converter, Dynamics& bulkDynamics,
+ sOnLatticeBoundaryCondition3D& bc,
+ sOffLatticeBoundaryCondition3D& offBc,
+ STLreader& stlReader, SuperGeometry3D& superGeometry ) {
+
+ OstreamManager clout( std::cout,"prepareLattice" );
+ clout << "Prepare Lattice ..." << std::endl;
+
+ const T omega = converter.getLatticeRelaxationFrequency();
+
+ // material=0 --> do nothing
+ lattice.defineDynamics( superGeometry,0,&instances::getNoDynamics() );
+
+ // material=1 --> bulk dynamics
+ lattice.defineDynamics( superGeometry,1,&bulkDynamics );
+
+ if ( bouzidiOn ) {
+ // material=2 --> no dynamics + bouzidi zero velocity
+ lattice.defineDynamics( superGeometry,2,&instances::getNoDynamics() );
+ offBc.addZeroVelocityBoundary( superGeometry,2,stlReader );
+ // material=3 --> no dynamics + bouzidi velocity (inflow)
+ lattice.defineDynamics( superGeometry,3,&instances::getNoDynamics() );
+ offBc.addVelocityBoundary( superGeometry,3,stlReader );
+ } else {
+ // material=2 --> bounceBack dynamics
+ lattice.defineDynamics( superGeometry, 2, &instances::getBounceBack() );
+ // material=3 --> bulk dynamics + velocity (inflow)
+ lattice.defineDynamics( superGeometry,3,&bulkDynamics );
+ bc.addVelocityBoundary( superGeometry,3,omega );
+ }
+
+ // material=4,5 --> bulk dynamics + pressure (outflow)
+ lattice.defineDynamics( superGeometry.getMaterialIndicator({4, 5}),&bulkDynamics );
+ bc.addPressureBoundary( superGeometry.getMaterialIndicator({4, 5}),omega );
+
+ // Initial conditions
+ AnalyticalConst3D rhoF( 1 );
+ std::vector velocity( 3,T() );
+ AnalyticalConst3D uF( velocity );
+
+ // Initialize all values of distribution functions to their local equilibrium
+ lattice.defineRhoU( superGeometry.getMaterialIndicator({1, 3, 4, 5}),rhoF,uF );
+ lattice.iniEquilibrium( superGeometry.getMaterialIndicator({1, 3, 4, 5}),rhoF,uF );
+
+ // Lattice initialize
+ lattice.initialize();
+
+ clout << "Prepare Lattice ... OK" << std::endl;
+}
+
+// Generates a slowly increasing sinuidal inflow
+void setBoundaryValues( SuperLattice3D& sLattice,
+ sOffLatticeBoundaryCondition3D& offBc,
+ UnitConverter const& converter, int iT,
+ SuperGeometry3D& superGeometry ) {
+
+ // No of time steps for smooth start-up
+ int iTperiod = converter.getLatticeTime( 0.5 );
+ int iTupdate = 50;
+
+ if ( iT%iTupdate == 0 ) {
+ // Smooth start curve, sinus
+ SinusStartScale nSinusStartScale( iTperiod,converter.getCharLatticeVelocity() );
+
+ // Creates and sets the Poiseuille inflow profile using functors
+ int iTvec[1]= {iT};
+ T maxVelocity[1]= {T()};
+ nSinusStartScale( maxVelocity,iTvec );
+ CirclePoiseuille3D velocity( superGeometry,3,maxVelocity[0] );
+
+ if ( bouzidiOn ) {
+ offBc.defineU( superGeometry,3,velocity );
+ } else {
+ sLattice.defineU( superGeometry,3,velocity );
+ }
+ }
+}
+
+// Computes flux at inflow and outflow
+void getResults( SuperLattice3D& sLattice,
+ UnitConverter& converter, int iT,
+ Dynamics& bulkDynamics,
+ SuperGeometry3D& superGeometry, Timer& timer, STLreader& stlReader ) {
+
+ OstreamManager clout( std::cout,"getResults" );
+
+ SuperVTMwriter3D vtmWriter( "aorta3d" );
+ SuperLatticePhysVelocity3D velocity( sLattice, converter );
+ SuperLatticePhysPressure3D pressure( sLattice, converter );
+ vtmWriter.addFunctor( velocity );
+ vtmWriter.addFunctor( pressure );
+
+ const int vtkIter = converter.getLatticeTime( .1 );
+ const int statIter = converter.getLatticeTime( .1 );
+
+ if ( iT==0 ) {
+ // Writes the geometry, cuboid no. and rank no. as vti file for visualization
+ SuperLatticeGeometry3D geometry( sLattice, superGeometry );
+ SuperLatticeCuboid3D cuboid( sLattice );
+ SuperLatticeRank3D rank( sLattice );
+ vtmWriter.write( geometry );
+ vtmWriter.write( cuboid );
+ vtmWriter.write( rank );
+
+ vtmWriter.createMasterFile();
+ }
+
+ // Writes the vtk files
+ if ( iT%vtkIter==0 ) {
+ vtmWriter.write( iT );
+
+ SuperEuklidNorm3D normVel( velocity );
+ BlockReduction3D2D planeReduction( normVel, {0,0,1}, 600, BlockDataSyncMode::ReduceOnly );
+ // write output as JPEG
+ heatmap::write(planeReduction, iT);
+ }
+
+ // Writes output on the console
+ if ( iT%statIter==0 ) {
+ // Timer console output
+ timer.update( iT );
+ timer.printStep();
+
+ // Lattice statistics console output
+ sLattice.getStatistics().print( iT,converter.getPhysTime( iT ) );
+
+ // Flux at the inflow and outflow region
+ std::vector materials = { 1, 3, 4, 5 };
+
+ IndicatorCircle3D inflow( 0.218125 ,0.249987-2.*converter.getConversionFactorLength() ,0.0234818, 0., -1.,0., 0.0112342+2*converter.getConversionFactorLength() );
+ SuperPlaneIntegralFluxVelocity3D vFluxInflow( sLattice, converter, superGeometry, inflow, materials, BlockDataReductionMode::Discrete );
+ vFluxInflow.print( "inflow","ml/s" );
+ SuperPlaneIntegralFluxPressure3D pFluxInflow( sLattice, converter, superGeometry, inflow, materials, BlockDataReductionMode::Discrete );
+ pFluxInflow.print( "inflow","N","mmHg" );
+
+ IndicatorCircle3D outflow0( 0.2053696,0.0900099+2.*converter.getConversionFactorLength(),0.0346537, 0.,1.,0., 0.0054686+2*converter.getConversionFactorLength() );
+ SuperPlaneIntegralFluxVelocity3D vFluxOutflow0( sLattice, converter, superGeometry, outflow0, materials, BlockDataReductionMode::Discrete );
+ vFluxOutflow0.print( "outflow0","ml/s" );
+ SuperPlaneIntegralFluxPressure3D pFluxOutflow0( sLattice, converter, superGeometry, outflow0, materials, BlockDataReductionMode::Discrete );
+ pFluxOutflow0.print( "outflow0","N","mmHg" );
+
+ IndicatorCircle3D outflow1( 0.2388403,0.0900099+2.*converter.getConversionFactorLength(),0.0343228, 0.,1.,0., 0.0058006+2*converter.getConversionFactorLength() );
+ SuperPlaneIntegralFluxVelocity3D vFluxOutflow1( sLattice, converter, superGeometry, outflow1, materials, BlockDataReductionMode::Discrete );
+ vFluxOutflow1.print( "outflow1","ml/s" );
+ SuperPlaneIntegralFluxPressure3D pFluxOutflow1( sLattice, converter, superGeometry, outflow1, materials, BlockDataReductionMode::Discrete );
+ pFluxOutflow1.print( "outflow1","N","mmHg" );
+
+ if ( bouzidiOn ) {
+ SuperLatticeYplus3D yPlus( sLattice, converter, superGeometry, stlReader, 3 );
+ SuperMax3D yPlusMaxF( yPlus, superGeometry, 1 );
+ int input[4]= {};
+ T yPlusMax[1];
+ yPlusMaxF( yPlusMax,input );
+ clout << "yPlusMax=" << yPlusMax[0] << std::endl;
+ }
+ }
+
+ if ( sLattice.getStatistics().getMaxU() > 0.3 ) {
+ clout << "PROBLEM uMax=" << sLattice.getStatistics().getMaxU() << std::endl;
+ vtmWriter.write( iT );
+ std::exit( 0 );
+ }
+}
+
+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);
+
+ UnitConverter converter(
+ (T) 0.02246/N, // physDeltaX: spacing between two lattice cells in __m__
+ (T) 0.02246/(M*N), // physDeltaT: time step in __s__
+ (T) 0.02246, // charPhysLength: reference length of simulation geometry
+ (T) 0.45, // charPhysVelocity: maximal/highest expected velocity during simulation in __m / s__
+ (T) 0.003/1055., // physViscosity: physical kinematic viscosity in __m^2 / s__
+ (T) 1055 // 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("aorta3d");
+
+ // === 2nd Step: Prepare Geometry ===
+
+ // Instantiation of the STLreader class
+ // file name, voxel size in meter, stl unit in meter, outer voxel no., inner voxel no.
+ STLreader stlReader( "aorta3d.stl", converter.getConversionFactorLength(), 0.001, 0, true );
+ IndicatorLayer3D extendedDomain( stlReader, converter.getConversionFactorLength() );
+
+ // Instantiation of a cuboidGeometry with weights
+#ifdef PARALLEL_MODE_MPI
+ const int noOfCuboids = std::min( 16*N,2*singleton::mpi().getSize() );
+#else
+ const int noOfCuboids = 2;
+#endif
+ CuboidGeometry3D cuboidGeometry( extendedDomain, converter.getConversionFactorLength(), noOfCuboids );
+
+ // Instantiation of a loadBalancer
+ HeuristicLoadBalancer loadBalancer( cuboidGeometry );
+
+ // Instantiation of a superGeometry
+ SuperGeometry3D superGeometry( cuboidGeometry, loadBalancer, 2 );
+
+ prepareGeometry( converter, extendedDomain, stlReader, superGeometry );
+
+ // === 3rd Step: Prepare Lattice ===
+ SuperLattice3D sLattice( superGeometry );
+
+ SmagorinskyBGKdynamics bulkDynamics( converter.getLatticeRelaxationFrequency(),
+ instances::getBulkMomenta(), 0.1 );
+
+ // choose between local and non-local boundary condition
+ sOnLatticeBoundaryCondition3D sBoundaryCondition( sLattice );
+ createInterpBoundaryCondition3D( sBoundaryCondition );
+ // createLocalBoundaryCondition3D(sBoundaryCondition);
+
+ sOffLatticeBoundaryCondition3D sOffBoundaryCondition( sLattice );
+ createBouzidiBoundaryCondition3D ( sOffBoundaryCondition );
+
+ Timer timer1( converter.getLatticeTime( maxPhysT ), superGeometry.getStatistics().getNvoxel() );
+ timer1.start();
+
+ prepareLattice( sLattice, converter, bulkDynamics,
+ sBoundaryCondition, sOffBoundaryCondition,
+ stlReader, superGeometry );
+
+ timer1.stop();
+ timer1.printSummary();
+
+ // === 4th Step: Main Loop with Timer ===
+ clout << "starting simulation..." << std::endl;
+ Timer 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, sOffBoundaryCondition, converter, iT, superGeometry );
+
+ // === 6th Step: Collide and Stream Execution ===
+ sLattice.collideAndStream();
+
+ // === 7th Step: Computation and Output of the Results ===
+ getResults( sLattice, converter, iT, bulkDynamics, superGeometry, timer, stlReader );
+ }
+
+ timer.stop();
+ timer.printSummary();
+}
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