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/Makefile | 105 +++++++++ examples/turbulence/aorta3d/aorta3d.cpp | 356 +++++++++++++++++++++++++++++ examples/turbulence/aorta3d/aorta3d.stl | Bin 0 -> 132784 bytes examples/turbulence/aorta3d/definitions.mk | 30 +++ examples/turbulence/aorta3d/module.mk | 29 +++ 5 files changed, 520 insertions(+) create mode 100644 examples/turbulence/aorta3d/Makefile create mode 100644 examples/turbulence/aorta3d/aorta3d.cpp create mode 100644 examples/turbulence/aorta3d/aorta3d.stl create mode 100644 examples/turbulence/aorta3d/definitions.mk create mode 100644 examples/turbulence/aorta3d/module.mk (limited to 'examples/turbulence/aorta3d') diff --git a/examples/turbulence/aorta3d/Makefile b/examples/turbulence/aorta3d/Makefile new file mode 100644 index 0000000..a953954 --- /dev/null +++ b/examples/turbulence/aorta3d/Makefile @@ -0,0 +1,105 @@ +# This file is part of the OpenLB library +# +# Copyright (C) 2007 Mathias 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. + +########################################################################### +## definitions + +include definitions.mk + +include $(ROOT)/global.mk + +OBJECTS := $(foreach file, $(SRC), $(PWD)/$(file:.cpp=.o)) +DEPS := $(foreach file, $(SRC), $(PWD)/$(file:.cpp=.d)) + +########################################################################### +## all + +all : depend compile link + + +########################################################################### +## dependencies + +depend : $(DEPS) + +$(PWD)/%.d : %.cpp + @echo Create dependencies for $< + @$(SHELL) -ec '$(CXX) -M $(CXXFLAGS) $(IDIR) $< \ + | sed -e "s!$*\.o!$(PWD)\/$*\.o!1" > .tmpfile; \ + cp -f .tmpfile $@;' + +########################################################################### +## compile + +compile : $(OBJECTS) + +$(PWD)/%.o: %.cpp + @echo Compile $< + $(CXX) $(CXXFLAGS) $(IDIR) -c $< -o $@ + +########################################################################### +## clean + +clean : cleanrub cleanobj cleandep + +cleanrub: + @echo Clean rubbish files + @rm -f *~ core .tmpfile tmp/*.* $(OUTPUT) + @rm -f tmp/vtkData/*.* tmp/vtkData/data/*.* tmp/imageData/*.* tmp/gnuplotData/*.* tmp/gnuplotData/data/*.* + +cleanobj: + @echo Clean object files + @rm -f $(OBJECTS) + +cleandep: + @echo Clean dependencies files + @rm -f $(DEPS) + +cleanbuild: + @cd $(ROOT); \ + $(MAKE) cleanlib; + +########################################################################### +## update lib + +$(ROOT)/$(LIBDIR)/lib$(LIB).a : + @cd $(ROOT); \ + $(MAKE) all + +########################################################################### +## link + +link: $(OUTPUT) + +$(OUTPUT): $(OBJECTS) $(ROOT)/$(LIBDIR)/lib$(LIB).a + @echo Link $@ + $(CXX) $(foreach file, $(SRC), $(file:.cpp=.o)) $(LDFLAGS) -L$(ROOT)/$(LIBDIR) -l$(LIB) -lz -o $@ + +########################################################################### +## include dependencies + +ifneq "$(strip $(wildcard *.d))" "" + include $(foreach file,$(DEPS),$(file)) +endif + +########################################################################### +########################################################################### 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(); +} diff --git a/examples/turbulence/aorta3d/aorta3d.stl b/examples/turbulence/aorta3d/aorta3d.stl new file mode 100644 index 0000000..340fece Binary files /dev/null and b/examples/turbulence/aorta3d/aorta3d.stl differ diff --git a/examples/turbulence/aorta3d/definitions.mk b/examples/turbulence/aorta3d/definitions.mk new file mode 100644 index 0000000..d15305e --- /dev/null +++ b/examples/turbulence/aorta3d/definitions.mk @@ -0,0 +1,30 @@ +# This file is part of the OpenLB library +# +# Copyright (C) 2007 Mathias 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. + + +########################################################################### +########################################################################### +## DEFINITIONS TO BE CHANGED + +ROOT := ../../.. +SRC := aorta3d.cpp +OUTPUT := aorta3d diff --git a/examples/turbulence/aorta3d/module.mk b/examples/turbulence/aorta3d/module.mk new file mode 100644 index 0000000..1190482 --- /dev/null +++ b/examples/turbulence/aorta3d/module.mk @@ -0,0 +1,29 @@ +# This file is part of the OpenLB library +# +# Copyright (C) 2017 Markus Mohrhard +# 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. + +current_dir := $(dir $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))) + +include global.mk +include rules.mk +include $(addsuffix definitions.mk, $(current_dir)) + +$(eval $(call sample,$(current_dir)$(OUTPUT),$(addprefix $(current_dir), $(SRC)))) -- cgit v1.2.3