smagorinskyBGK

[H.Yu]

I’m using smagorinsky BGK model

there are some problems

CODE:
// Generates a slowly increasing inflow for the first iTMaxStart timesteps
void setBoundaryValues( SuperLattice<T, DESCRIPTOR>& sLattice,
UnitConverter<T,DESCRIPTOR> const& converter, int iT,
SuperGeometry<T,3>& superGeometry )
{
OstreamManager clout( std::cout,”setBoundaryValues” );

// No of time steps for smooth start-up
int iTmaxStart = converter.getLatticeTime( maxPhysT*0.01 );
int iTupdate = 10;

if ( iT%iTupdate == 0 && iT <= iTmaxStart ) {
// Smooth start curve, sinus
// SinusStartScale<T,int> StartScale(iTmaxStart, T(1));

// Smooth start curve, polynomial
PolynomialStartScale<T,int> StartScale( iTmaxStart, converter.getCharLatticeVelocity() );

// Creates and sets the Poiseuille inflow profile using functors
//int iTvec[1] = {iT};
//T frac[1] = {};
//StartScale( frac,iTvec );
//std::vector<T> maxVelocity( 3,0 );
//maxVelocity[0] = 2.25*frac[0]*converter.getCharLatticeVelocity();
int iTvec[1] = {iT};
T frac[1] = {};
StartScale( frac,iTvec );
std::vector<T> maxVelocity( 3,0 );
maxVelocity[0] = 2.25*frac[0]*converter.getCharLatticeVelocity();

T distance2Wall = converter.getConversionFactorLength()/2.;
RectanglePoiseuille3D<T> poiseuilleU( superGeometry, 3, maxVelocity, distance2Wall, distance2Wall, distance2Wall );
sLattice.defineU( superGeometry, 3, poiseuilleU );

clout << “step=” << iT << “; maxVel=” << maxVelocity[0] << std::endl;

sLattice.setProcessingContext<Array<momenta::FixedVelocityMomentumGeneric::VELOCITY>>(
ProcessingContext::Simulation);
}
}

In the code above, line 9 ‘int iTmaxStart = converter.getLatticeTime( maxPhysT*0.01 );’
Modified MaxPhysT*0.1 to 0.01. The reason was to shorten the time it took to reach the speed i specified. However, when the corresponding place is adjusted, it was confirmed that when the speed gradually increases over time, pressure, aerodynamic performance, density, energy, etc. are displayed as -nan when it is greater than a certain speed.

Why does ‘-nan’ appear?
What are some ways to quickly reach the specified maximum speed?

[FBukreev]

Dear Mr./Mrs. Yu,

in the PolynomialStartScale you give as input the charLatticeVelocity.
After that you take frac[0] and multiply it with the velocity. But the frac[0] in that case is already the velocity, so you don’t need to multiply it with the velocity one more time.

Greetings
Fedor Bukreev

[H.Yu]

thank you

“””
[Timer] step=4000; percent=0.0666667; passedTime=147.41; remTime=220968; MLUPs=12.75
[LatticeStatistics] step=4000; t=0.2; uMax=7.5301; avEnergy=-nan; avRho=-nan
[getResults] pressure1=-nan; pressure2=-nan; pressureDrop=-nan; drag=-nan; lift=-nan
[getResults] yPlusMax=2.22507e-308
“””

However, ‘nan’ still couldn’t solve it.
I tried to calculate the turbulence by referring to the laminar flow cylinder 3D model and the aorta 3D model. Would it be possible for me to help if I upload the full code??

[H.Yu]

CODE :

#include “olb3D.h”
#include “olb3D.hh”

using namespace olb;
using namespace olb::descriptors;
using namespace olb::graphics;
using namespace olb::util;

using T = double;
using DESCRIPTOR = D3Q19<>;
using BulkDynamics = SmagorinskyBGKdynamics<T,DESCRIPTOR>;

#ifndef PLATFORM_GPU_CUDA
#define BOUZIDI
#endif

//simulation parameters
const int N = 100; // resolution of the model
const int M = 20; // time discretization refinement
const int C = 10; // noOfCuboids = 7
const int UT = 10; // iTupdate = 10
const bool bouzidiOn = true; // choice of boundary condition
const T maxPhysT = 300.; // max. simulation time in s, SI unit

// Stores data from stl file in geometry in form of material numbers
void prepareGeometry( UnitConverter<T,DESCRIPTOR> const& converter, IndicatorF3D<T>& indicator,
STLreader<T>& stlReader, SuperGeometry<T,3>& superGeometry )
{

OstreamManager clout( std::cout,”prepareGeometry” );
clout << “Prepare Geometry …” << std::endl;

superGeometry.rename( 0,2,indicator );
superGeometry.rename( 2,1,stlReader );
superGeometry.clean();

Vector<T,3> origin = superGeometry.getStatistics().getMinPhysR( 2 );
origin[1] += converter.getConversionFactorLength()/2.;
origin[2] += converter.getConversionFactorLength()/2.;

Vector<T,3> extend = superGeometry.getStatistics().getMaxPhysR( 2 );
extend[1] = extend[1]-origin[1]-converter.getConversionFactorLength()/2.;
extend[2] = extend[2]-origin[2]-converter.getConversionFactorLength()/2.;

// Set material number for inflow
origin[0] = superGeometry.getStatistics().getMinPhysR( 2 )[0]-converter.getConversionFactorLength();
extend[0] = 2*converter.getConversionFactorLength();
IndicatorCuboid3D<T> inflow( extend,origin );
superGeometry.rename( 2,3,inflow );

// Set material number for outflow
origin[0] = superGeometry.getStatistics().getMaxPhysR( 2 )[0]-converter.getConversionFactorLength();
extend[0] = 2*converter.getConversionFactorLength();
IndicatorCuboid3D<T> outflow( extend,origin );
superGeometry.rename( 2,4,outflow );

// Set material number for cylinder
origin[0] = superGeometry.getStatistics().getMinPhysR( 2 )[0]+converter.getConversionFactorLength();
extend[0] = ( superGeometry.getStatistics().getMaxPhysR( 2 )[0]-superGeometry.getStatistics().getMinPhysR( 2 )[0] )/2.;
std::shared_ptr<IndicatorF3D<T>> naca4412 = std::make_shared<IndicatorCuboid3D<T>>( extend, origin );
superGeometry.rename( 2,5, naca4412 );

// 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( SuperLattice<T,DESCRIPTOR>& sLattice,
UnitConverter<T,DESCRIPTOR> const& converter,
STLreader<T>& stlReader,
SuperGeometry<T,3>& superGeometry )
{
OstreamManager clout( std::cout,”prepareLattice” );
clout << “Prepare Lattice …” << std::endl;

const T omega = converter.getLatticeRelaxationFrequency();

// Material=0 –>do nothing
sLattice.defineDynamics<NoDynamics>(superGeometry, 0);

// Material=1 –>bulk dynamics
sLattice.defineDynamics<BulkDynamics>(superGeometry, 1);

// Material=2 –>bounce back
sLattice.defineDynamics<BounceBack>(superGeometry, 2);

// Setting of the boundary conditions

//if local boundary conditions are chosen
//setLocalVelocityBoundary(sLattice, omega, superGeometry, 3);
//setLocalPressureBoundary(sLattice, omega, superGeometry, 4);

//if interpolated boundary conditions are chosen
//inlet
sLattice.defineDynamics<BulkDynamics>(superGeometry, 3);
setInterpolatedVelocityBoundary<T,DESCRIPTOR>(sLattice, omega, superGeometry, 3);
//outlet
sLattice.defineDynamics<BulkDynamics>(superGeometry.getMaterialIndicator({4}));
setInterpolatedPressureBoundary<T,DESCRIPTOR>(sLattice, omega, superGeometry.getMaterialIndicator({4}));
//setInterpolatedPressureBoundary(sLattice, omega, superGeometry, 4);

// Material=5 –>bouzidi / bounce back
//airfoil
#ifdef BOUZIDI
sLattice.defineDynamics<NoDynamics>(superGeometry, 5);
setBouzidiZeroVelocityBoundary<T,DESCRIPTOR>(sLattice, superGeometry, 5, stlReader);
#else
sLattice.defineDynamics<BounceBack>(superGeometry, 5);
#endif

// Initial conditions
AnalyticalConst3D<T,T> rhoF( 1 );
std::vector<T> velocity( 3,T() );
AnalyticalConst3D<T,T> uF(velocity);

// Initialize all values of distribution functions to their local equilibrium
sLattice.defineRhoU( superGeometry.getMaterialIndicator({1, 2, 3, 4}),rhoF,uF );
sLattice.iniEquilibrium( superGeometry.getMaterialIndicator({1, 2, 3, 4}),rhoF,uF );

sLattice.setParameter<descriptors::OMEGA>(omega);
sLattice.setParameter<collision::LES::Smagorinsky>(0.1);

// 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( SuperLattice<T, DESCRIPTOR>& sLattice,
UnitConverter<T,DESCRIPTOR> const& converter, int iT,
SuperGeometry<T,3>& superGeometry )
{
OstreamManager clout( std::cout,”setBoundaryValues” );

// No of time steps for smooth start-up
int iTmaxStart = converter.getLatticeTime( maxPhysT*0.0001 );
int iTupdate = UT;

if ( iT%iTupdate == 0 && iT <= iTmaxStart ) {
// Smooth start curve, sinus
// SinusStartScale<T,int> StartScale(iTmaxStart, T(1));

// Smooth start curve, polynomial
PolynomialStartScale<T,int> StartScale( iTmaxStart, T( 1 ) );

// Creates and sets the Poiseuille inflow profile using functors
//int iTvec[1] = {iT};
//T frac[1] = {};
//StartScale( frac,iTvec );
//std::vector<T> maxVelocity( 3,0 );
//maxVelocity[0] = 2.25*frac[0]*converter.getCharLatticeVelocity();
int iTvec[1] = {iT};
T frac[1] = {};
StartScale( frac,iTvec );
std::vector<T> maxVelocity( 3,0 );
maxVelocity[0] =frac[0] * 7.5301;

T distance2Wall = converter.getConversionFactorLength()/2.;
RectanglePoiseuille3D<T> poiseuilleU( superGeometry, 3, maxVelocity, distance2Wall, distance2Wall, distance2Wall );
sLattice.defineU( superGeometry, 3, poiseuilleU );

clout << “step=” << iT << “; maxVel=” << maxVelocity[0] << std::endl;

sLattice.setProcessingContext<Array<momenta::FixedVelocityMomentumGeneric::VELOCITY>>(
ProcessingContext::Simulation);

}
}

// Computes the pressure drop between the voxels before and after the cylinder
void getResults( SuperLattice<T, DESCRIPTOR>& sLattice,
UnitConverter<T,DESCRIPTOR> const& converter, int iT,
SuperGeometry<T,3>& superGeometry, util::Timer<T>& timer,
STLreader<T>& stlReader )
{

OstreamManager clout( std::cout,”getResults” );

SuperVTMwriter3D<T> vtmWriter( “ncas4412_turb” );
SuperLatticePhysVelocity3D<T, DESCRIPTOR> velocity( sLattice, converter );
SuperLatticePhysPressure3D<T, DESCRIPTOR> pressure( sLattice, converter );
SuperLatticeYplus3D<T, DESCRIPTOR> yPlus( sLattice, converter, superGeometry, stlReader, 5 );
SuperLatticeRefinementMetricKnudsen3D<T, DESCRIPTOR> quality( sLattice, converter );
SuperRoundingF3D<T, T> roundedQuality ( quality, RoundingMode::NearestInteger );
SuperDiscretizationF3D<T> discretization ( roundedQuality, 0., 2. );

vtmWriter.addFunctor( quality );
vtmWriter.addFunctor( velocity );
vtmWriter.addFunctor( pressure );
vtmWriter.addFunctor( yPlus );

const int vtkIter = converter.getLatticeTime( .3 );
const int statIter = converter.getLatticeTime( .1 );

if ( iT==0 ) {
// Writes the geometry, cuboid no. and rank no. as vti file for visualization
SuperLatticeGeometry3D<T, DESCRIPTOR> geometry( sLattice, superGeometry );
SuperLatticeCuboid3D<T, DESCRIPTOR> cuboid( sLattice );
SuperLatticeRank3D<T, DESCRIPTOR> rank( sLattice );
vtmWriter.write( geometry );
vtmWriter.write( cuboid );
vtmWriter.write( rank );

vtmWriter.createMasterFile();
}

// Writes output on the console
if ( iT%statIter == 0 ) {
sLattice.setProcessingContext(ProcessingContext::Evaluation);

// Timer console output
timer.update( iT );
timer.printStep();

// Lattice statistics console output
sLattice.getStatistics().print( iT,converter.getPhysTime( iT ) );

// Drag, lift, pressure drop
AnalyticalFfromSuperF3D<T> intpolatePressure( pressure, true );
SuperLatticePhysDrag3D<T,DESCRIPTOR> drag( sLattice, superGeometry, 5, converter );

olb::Vector<T, 3> point1V = superGeometry.getStatistics().getCenterPhysR( 5 );
olb::Vector<T, 3> point2V = superGeometry.getStatistics().getCenterPhysR( 5 );
T point1[3] = {};
T point2[3] = {};
for ( int i = 0; i<3; i++ ) {
point1[i] = point1V[i];
point2[i] = point2V[i];
}
point1[0] = superGeometry.getStatistics().getMinPhysR( 5 )[0] – converter.getConversionFactorLength();
point2[0] = superGeometry.getStatistics().getMaxPhysR( 5 )[0] + converter.getConversionFactorLength();

T p1, p2;
intpolatePressure( &p1,point1 );
intpolatePressure( &p2,point2 );

clout << “pressure1=” << p1;
clout << “; pressure2=” << p2;

T pressureDrop = p1-p2;
clout << “; pressureDrop=” << pressureDrop;

T dragA[3];
int input1[0];
drag( dragA, input1 );
clout << “; drag=” << dragA[0] << “; lift=” << dragA[1] << std::endl;

int input[4] = {};
SuperMax3D<T> yPlusMaxF( yPlus, superGeometry, 1 );
T yPlusMax[1];
yPlusMaxF( yPlusMax,input );
clout << “yPlusMax=” << yPlusMax[0] << std::endl;
}

// Writes the vtk files
if ( iT%vtkIter == 0 ) {
vtmWriter.write( iT );

{
SuperEuklidNorm3D<T, DESCRIPTOR> normVel( velocity );
BlockReduction3D2D<T> planeReduction( normVel, Vector<T,3>({0, 0, 1}) );
// write output as JPEG
heatmap::write(planeReduction, iT);
}

{
BlockReduction3D2D<T> planeReduction( discretization, Vector<T,3>({0, 0, 1}) );
heatmap::plotParam<T> jpeg_scale;
jpeg_scale.colour = “blackbody”;
jpeg_scale.name = “quality”;
heatmap::write( planeReduction, iT, jpeg_scale );
}
}
}

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<T, DESCRIPTOR> converter(
(T) 1/N, // physDeltaX: spacing between two lattice cells in __m__
(T) 0.1/(M*N), // physDeltaT: time step in __s__
(T) 0.1, // charPhysLength: reference length of simulation geometry
(T) 7.5301, // charPhysVelocity: maximal/highest expected velocity during simulation in __m / s__
(T) 0.00001506, // physViscosity: physical kinematic viscosity in __m^2 / s__
(T) 1.2 // 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(“naca4412_turb”);

// === 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<T> stlReader( “naca4412_0deg.stl”, converter.getConversionFactorLength(), 0.001 );
IndicatorLayer3D<T> extendedDomain( stlReader, converter.getConversionFactorLength() );

// Instantiation of a cuboidGeometry with weights
#ifdef PARALLEL_MODE_MPI
const int noOfCuboids = singleton::mpi().getSize();
#else
const int noOfCuboids = C;
#endif
CuboidGeometry3D<T> cuboidGeometry( extendedDomain, converter.getConversionFactorLength(), noOfCuboids );

// Instantiation of a loadBalancer
HeuristicLoadBalancer<T> loadBalancer( cuboidGeometry );

// Instantiation of a superGeometry
SuperGeometry<T,3> superGeometry( cuboidGeometry, loadBalancer );

prepareGeometry( converter, extendedDomain, stlReader, superGeometry );

// === 3rd Step: Prepare Lattice ===
SuperLattice<T, DESCRIPTOR> sLattice( superGeometry );

//prepareLattice and set boundaryCondition
prepareLattice( sLattice, converter, stlReader, superGeometry );

util::Timer<T> timer1( converter.getLatticeTime( maxPhysT ), superGeometry.getStatistics().getNvoxel() );
timer1.start();

prepareLattice( sLattice, converter, stlReader, superGeometry );

timer1.stop();
timer1.printSummary();

// === 4th Step: Main Loop with Timer ===
clout << “starting simulation…” << std::endl;
util::Timer<T> timer( converter.getLatticeTime( maxPhysT ), superGeometry.getStatistics().getNvoxel() );
timer.start();

for (std::size_t 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, stlReader );
}

timer.stop();
timer.printSummary();
}

[FBukreev]

Sorry, we don’t check full codes here. If you want more precise help, please visit our spring school.

[H.Yu]

Sorry for the rude question

[qiong]

Hi Yu,

I have the same problem of ‘nan’. It seems there is something with the parameters. May I ask if you have figured it out?

[Author]

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