int main(int argc, char* argv[])
{
plbInit(&argc, &argv);
global::directories().setOutputDir("./");
global::IOpolicy().activateParallelIO(false);
plint resolution=0;
plint referenceDirection=0;
string stlFileName, outFileName;
try {
global::argv(1).read(stlFileName);
global::argv(2).read(outFileName);
global::argv(3).read(resolution);
global::argv(4).read(referenceDirection);
}
catch (PlbIOException& exception) {
pcout << "Wrong parameters; the syntax is: "
<< (std::string)global::argv(0) << " inputSTL.stl outputSTL.stl resolution referenceDirection[0,1,2]" << std::endl;
exit(-1);
}
TriangleSet<T>* triangleSet = 0;
try {
triangleSet = new TriangleSet<T>(stlFileName, DBL);
}
catch (PlbIOException& exception) {
pcout << "Error, could not read STL file " << stlFileName
<< ": " << exception.what() << std::endl;
exit(-1);
}
DEFscaledMesh<T> mesh(*triangleSet, resolution, referenceDirection, margin, extraLayer);
TriangleBoundary3D<T> boundary(mesh);
T dx = boundary.getDx();
Array<T,3> location(boundary.getPhysicalLocation());
VoxelizedDomain3D<T> voxelizedDomain (
boundary, typeOfVoxelization, extraLayer, borderWidth, extendedEnvelopeWidth, blockSize );
MultiScalarField3D<T> flagMatrix((MultiBlock3D&)voxelizedDomain.getVoxelMatrix());
setToConstant(flagMatrix, voxelizedDomain.getVoxelMatrix(),
voxelFlag::inside, flagMatrix.getBoundingBox(), 1.0);
setToConstant(flagMatrix, voxelizedDomain.getVoxelMatrix(),
voxelFlag::innerBorder, flagMatrix.getBoundingBox(), 1.0);
pcout << "Number of inside cells: " << computeSum(flagMatrix) << std::endl;
TriangleSet<T> triangles (
vofToTriangles<T,descriptors::D3Q19Descriptor>(
flagMatrix, 0.5, flagMatrix.getBoundingBox().enlarge(-2) ) );
DEFscaledMesh<T> newMesh(triangles);
TriangleBoundary3D<T> newBoundary(newMesh);
newBoundary.getMesh().scale(dx);
newBoundary.getMesh().translate(location);
newBoundary.getMesh().writeBinarySTL(outFileName);
return 0;
}
void iniLattice( MultiBlockLattice3D<T,DESCRIPTOR>& lattice,
VoxelizedDomain3D<T>& voxelizedDomain )
{
// Switch all remaining outer cells to no-dynamics, except the outer
// boundary layer, and keep the rest as BGKdynamics.
defineDynamics(lattice, voxelizedDomain.getVoxelMatrix(), lattice.getBoundingBox(),
new NoDynamics<T,DESCRIPTOR>, voxelFlag::outside);
initializeAtEquilibrium(lattice, lattice.getBoundingBox(), (T) 1., Array<T,3>((T)0.,(T)0.,(T)0.));
lattice.initialize();
}
void runProgram()
{
/*
* Read the obstacle geometry.
*/
pcout << std::endl << "Reading STL data for the obstacle geometry." << std::endl;
Array<T,3> center(param.cx, param.cy, param.cz);
Array<T,3> centerLB(param.cxLB, param.cyLB, param.czLB);
// The triangle-set defines the surface of the geometry.
TriangleSet<T> triangleSet(param.geometry_fname, DBL);
// Place the obstacle in the correct place in the simulation domain.
// Here the "geometric center" of the obstacle is computed manually,
// by computing first its bounding cuboid. In cases that the STL
// file with the geometry of the obstacle contains its center as
// the point, say (0, 0, 0), then the following variable
// "obstacleCenter" must be set to (0, 0, 0) manually.
Cuboid<T> bCuboid = triangleSet.getBoundingCuboid();
Array<T,3> obstacleCenter = 0.5 * (bCuboid.lowerLeftCorner + bCuboid.upperRightCorner);
triangleSet.translate(-obstacleCenter);
triangleSet.scale(1.0/param.dx); // In lattice units from now on...
triangleSet.translate(centerLB);
triangleSet.writeBinarySTL(outputDir+"obstacle_LB.stl");
// The DEFscaledMesh, and the triangle-boundary are more sophisticated data
// structures used internally by Palabos to treat the boundary.
plint xDirection = 0;
plint borderWidth = 1; // Because Guo acts in a one-cell layer.
// Requirement: margin>=borderWidth.
plint margin = 1; // Extra margin of allocated cells around the obstacle, for the case of moving walls.
plint blockSize = 0; // Size of blocks in the sparse/parallel representation.
// Zero means: don't use sparse representation.
DEFscaledMesh<T> defMesh(triangleSet, 0, xDirection, margin, Dot3D(0, 0, 0));
TriangleBoundary3D<T> boundary(defMesh);
//boundary.getMesh().inflate();
pcout << "tau = " << 1.0/param.omega << std::endl;
pcout << "dx = " << param.dx << std::endl;
pcout << "dt = " << param.dt << std::endl;
pcout << "Number of iterations in an integral time scale: " << (plint) (1.0/param.dt) << std::endl;
/*
* Voxelize the domain.
*/
// Voxelize the domain means: decide which lattice nodes are inside the obstacle and which are outside.
pcout << std::endl << "Voxelizing the domain." << std::endl;
plint extendedEnvelopeWidth = 2; // Extrapolated off-lattice BCs.
const int flowType = voxelFlag::outside;
VoxelizedDomain3D<T> voxelizedDomain (
boundary, flowType, param.boundingBox(), borderWidth, extendedEnvelopeWidth, blockSize );
pcout << getMultiBlockInfo(voxelizedDomain.getVoxelMatrix()) << std::endl;
/*
* Generate the lattice, the density and momentum blocks.
*/
pcout << "Generating the lattice, the rhoBar and j fields." << std::endl;
MultiBlockLattice3D<T,DESCRIPTOR> *lattice = new MultiBlockLattice3D<T,DESCRIPTOR>(voxelizedDomain.getVoxelMatrix());
if (param.useSmago) {
defineDynamics(*lattice, lattice->getBoundingBox(),
new SmagorinskyBGKdynamics<T,DESCRIPTOR>(param.omega, param.cSmago));
pcout << "Using Smagorinsky BGK dynamics." << std::endl;
} else {
defineDynamics(*lattice, lattice->getBoundingBox(),
new BGKdynamics<T,DESCRIPTOR>(param.omega));
pcout << "Using BGK dynamics." << std::endl;
}
bool velIsJ = false;
defineDynamics(*lattice, voxelizedDomain.getVoxelMatrix(), lattice->getBoundingBox(),
new NoDynamics<T,DESCRIPTOR>(), voxelFlag::inside);
lattice->toggleInternalStatistics(false);
MultiBlockManagement3D sparseBlockManagement(lattice->getMultiBlockManagement());
// The rhoBar and j fields are used at both the collision and at the implementation of the
// outflow boundary condition.
plint envelopeWidth = 1;
MultiScalarField3D<T> *rhoBar = new MultiScalarField3D<T> (
MultiBlockManagement3D (
sparseBlockManagement.getSparseBlockStructure(),
sparseBlockManagement.getThreadAttribution().clone(),
envelopeWidth ),
defaultMultiBlockPolicy3D().getBlockCommunicator(),
defaultMultiBlockPolicy3D().getCombinedStatistics(),
defaultMultiBlockPolicy3D().getMultiScalarAccess<T>() );
rhoBar->toggleInternalStatistics(false);
MultiTensorField3D<T,3> *j = new MultiTensorField3D<T,3> (
MultiBlockManagement3D (
sparseBlockManagement.getSparseBlockStructure(),
sparseBlockManagement.getThreadAttribution().clone(),
envelopeWidth ),
defaultMultiBlockPolicy3D().getBlockCommunicator(),
defaultMultiBlockPolicy3D().getCombinedStatistics(),
defaultMultiBlockPolicy3D().getMultiTensorAccess<T,3>() );
j->toggleInternalStatistics(false);
std::vector<MultiBlock3D*> lattice_rho_bar_j_arg;
lattice_rho_bar_j_arg.push_back(lattice);
lattice_rho_bar_j_arg.push_back(rhoBar);
lattice_rho_bar_j_arg.push_back(j);
integrateProcessingFunctional(
new ExternalRhoJcollideAndStream3D<T,DESCRIPTOR>(),
lattice->getBoundingBox(), lattice_rho_bar_j_arg, 0);
integrateProcessingFunctional(
new BoxRhoBarJfunctional3D<T,DESCRIPTOR>(),
lattice->getBoundingBox(), lattice_rho_bar_j_arg, 3); // rhoBar and j are computed at level 3 because
// the boundary conditions are on levels 1 and 2.
/*
* Generate the off-lattice boundary condition on the obstacle and the outer-domain boundary conditions.
*/
pcout << "Generating boundary conditions." << std::endl;
OffLatticeBoundaryCondition3D<T,DESCRIPTOR,Velocity> *boundaryCondition;
BoundaryProfiles3D<T,Velocity> profiles;
bool useAllDirections=true;
OffLatticeModel3D<T,Velocity>* offLatticeModel=0;
if (param.freeSlipWall) {
profiles.setWallProfile(new FreeSlipProfile3D<T>);
}
else {
profiles.setWallProfile(new NoSlipProfile3D<T>);
}
offLatticeModel =
new GuoOffLatticeModel3D<T,DESCRIPTOR> (
new TriangleFlowShape3D<T,Array<T,3> >(voxelizedDomain.getBoundary(), profiles),
flowType, useAllDirections );
offLatticeModel->setVelIsJ(velIsJ);
boundaryCondition = new OffLatticeBoundaryCondition3D<T,DESCRIPTOR,Velocity>(
offLatticeModel, voxelizedDomain, *lattice);
boundaryCondition->insert();
// The boundary condition algorithm or the outer domain.
OnLatticeBoundaryCondition3D<T,DESCRIPTOR>* outerBoundaryCondition
= createLocalBoundaryCondition3D<T,DESCRIPTOR>();
outerDomainBoundaries(lattice, rhoBar, j, outerBoundaryCondition);
/*
* Implement the outlet sponge zone.
*/
if (param.numOutletSpongeCells > 0) {
T bulkValue;
Array<plint,6> numSpongeCells;
if (param.outletSpongeZoneType == 0) {
pcout << "Generating an outlet viscosity sponge zone." << std::endl;
bulkValue = param.omega;
} else if (param.outletSpongeZoneType == 1) {
pcout << "Generating an outlet Smagorinsky sponge zone." << std::endl;
bulkValue = param.cSmago;
} else {
pcout << "Error: unknown type of sponge zone." << std::endl;
exit(-1);
}
// Number of sponge zone lattice nodes at all the outer domain boundaries.
// So: 0 means the boundary at x = 0
// 1 means the boundary at x = nx-1
// 2 means the boundary at y = 0
// and so on...
numSpongeCells[0] = 0;
numSpongeCells[1] = param.numOutletSpongeCells;
numSpongeCells[2] = 0;
numSpongeCells[3] = 0;
numSpongeCells[4] = 0;
numSpongeCells[5] = 0;
std::vector<MultiBlock3D*> args;
args.push_back(lattice);
if (param.outletSpongeZoneType == 0) {
applyProcessingFunctional(new ViscositySpongeZone<T,DESCRIPTOR>(
param.nx, param.ny, param.nz, bulkValue, numSpongeCells),
lattice->getBoundingBox(), args);
} else {
applyProcessingFunctional(new SmagorinskySpongeZone<T,DESCRIPTOR>(
param.nx, param.ny, param.nz, bulkValue, param.targetSpongeCSmago, numSpongeCells),
lattice->getBoundingBox(), args);
}
}
/*
* Setting the initial conditions.
*/
// Initial condition: Constant pressure and velocity-at-infinity everywhere.
Array<T,3> uBoundary(param.getInletVelocity(0), 0.0, 0.0);
initializeAtEquilibrium(*lattice, lattice->getBoundingBox(), 1.0, uBoundary);
applyProcessingFunctional(
new BoxRhoBarJfunctional3D<T,DESCRIPTOR>(),
lattice->getBoundingBox(), lattice_rho_bar_j_arg); // Compute rhoBar and j before VirtualOutlet is executed.
lattice->executeInternalProcessors(1); // Execute all processors except the ones at level 0.
lattice->executeInternalProcessors(2);
lattice->executeInternalProcessors(3);
/*
* Particles (streamlines).
*/
// This part of the code that relates to particles, is purely for visualization
// purposes. Particles are used to compute streamlines essentially.
// Definition of a particle field.
MultiParticleField3D<ParticleFieldT>* particles = 0;
if (param.useParticles) {
particles = new MultiParticleField3D<ParticleFieldT> (
lattice->getMultiBlockManagement(),
defaultMultiBlockPolicy3D().getCombinedStatistics() );
std::vector<MultiBlock3D*> particleArg;
particleArg.push_back(particles);
std::vector<MultiBlock3D*> particleFluidArg;
particleFluidArg.push_back(particles);
particleFluidArg.push_back(lattice);
// Functional that advances the particles to their new position at each predefined time step.
integrateProcessingFunctional (
new AdvanceParticlesEveryWhereFunctional3D<T,DESCRIPTOR>(param.cutOffSpeedSqr),
lattice->getBoundingBox(), particleArg, 0);
// Functional that assigns the particle velocity according to the particle's position in the fluid.
integrateProcessingFunctional (
new FluidToParticleCoupling3D<T,DESCRIPTOR>((T) param.particleTimeFactor),
lattice->getBoundingBox(), particleFluidArg, 1 );
// Definition of a domain from which particles will be injected in the flow field.
Box3D injectionDomain(0, 0, centerLB[1]-0.25*param.ny, centerLB[1]+0.25*param.ny,
centerLB[2]-0.25*param.nz, centerLB[2]+0.25*param.nz);
// Definition of simple mass-less particles.
Particle3D<T,DESCRIPTOR>* particleTemplate=0;
particleTemplate = new PointParticle3D<T,DESCRIPTOR>(0, Array<T,3>(0.,0.,0.), Array<T,3>(0.,0.,0.));
// Functional which injects particles with predefined probability from the specified injection domain.
std::vector<MultiBlock3D*> particleInjectionArg;
particleInjectionArg.push_back(particles);
integrateProcessingFunctional (
new InjectRandomParticlesFunctional3D<T,DESCRIPTOR>(particleTemplate, param.particleProbabilityPerCell),
injectionDomain, particleInjectionArg, 0 );
// Definition of an absorbtion domain for the particles.
Box3D absorbtionDomain(param.outlet);
// Functional which absorbs the particles which reach the specified absorbtion domain.
integrateProcessingFunctional (
new AbsorbParticlesFunctional3D<T,DESCRIPTOR>, absorbtionDomain, particleArg, 0 );
particles->executeInternalProcessors();
}
/*
* Starting the simulation.
*/
plb_ofstream energyFile((outputDir+"average_energy.dat").c_str());
pcout << std::endl;
pcout << "Starting simulation." << std::endl;
for (plint i = 0; i < param.maxIter; ++i) {
if (i <= param.initialIter) {
Array<T,3> uBoundary(param.getInletVelocity(i), 0.0, 0.0);
setBoundaryVelocity(*lattice, param.inlet, uBoundary);
}
if (i % param.statIter == 0) {
pcout << "At iteration " << i << ", t = " << i*param.dt << std::endl;
Array<T,3> force(boundaryCondition->getForceOnObject());
T factor = util::sqr(util::sqr(param.dx)) / util::sqr(param.dt);
pcout << "Force on object over fluid density: F[x] = " << force[0]*factor << ", F[y] = "
<< force[1]*factor << ", F[z] = " << force[2]*factor << std::endl;
T avEnergy = boundaryCondition->computeAverageEnergy() * util::sqr(param.dx) / util::sqr(param.dt);
pcout << "Average kinetic energy over fluid density: E = " << avEnergy << std::endl;
energyFile << i*param.dt << " " << avEnergy << std::endl;
pcout << std::endl;
}
if (i % param.vtkIter == 0) {
pcout << "Writing VTK at time t = " << i*param.dt << endl;
writeVTK(*boundaryCondition, i);
if (param.useParticles) {
writeParticleVtk<T,DESCRIPTOR> (
*particles, createFileName(outputDir+"particles_", i, PADDING) + ".vtk",
param.maxNumParticlesToWrite );
}
}
if (i % param.imageIter == 0) {
pcout << "Writing PPM image at time t = " << i*param.dt << endl;
writePPM(*boundaryCondition, i);
}
lattice->executeInternalProcessors();
lattice->incrementTime();
if (param.useParticles && i % param.particleTimeFactor == 0) {
particles->executeInternalProcessors();
}
}
energyFile.close();
delete outerBoundaryCondition;
delete boundaryCondition;
if (param.useParticles) {
delete particles;
}
delete j;
delete rhoBar;
delete lattice;
}
int main(int argc, char* argv[])
{
plbInit(&argc, &argv);
global::directories().setOutputDir("./");
// Create the cylinder surface as a set of triangles.
TriangleSet<T> triangleSet;
triangleSet = constructCylinder<T>(originalCenter, radius, radius, length, nAxial, nCirc);
// The next few lines of code are typical. They transform the surface geometry of the
// tube to more efficient data structures that are internally used by palabos.
// The TriangleBoundary3D structure will be later used to assign proper boundary conditions.
DEFscaledMesh<T> defMesh(triangleSet, ny, yDirection, margin, extraLayer);
defMesh.getMesh().inflate();
TriangleBoundary3D<T> boundary(defMesh);
pcout << "Number of inlets/outlets which were closed: "
<< boundary.getInletOutlet(xDirection).size() << std::endl;
inletCenter = computeBaryCenter(boundary.getMesh(),boundary.getInletOutlet(xDirection)[0]);
outletCenter = computeBaryCenter(boundary.getMesh(),boundary.getInletOutlet(xDirection)[1]);
radius = computeInnerRadius(boundary.getMesh(),boundary.getInletOutlet(xDirection)[0]);
pcout << "Inlet center: " << inletCenter[0] << "," << inletCenter[1] << "," << inletCenter[2] << std::endl;
pcout << "Outlet center: " << outletCenter[0] << "," << outletCenter[1] << "," << outletCenter[2] << std::endl;
T nu = uAverage * 2.*radius / Reynolds;
T omega = 1./(3.*nu+0.5);
pcout << "omega=" << omega << std::endl;
boundary.getMesh().writeAsciiSTL("cylinder.stl");
pcout << "Number of triangles: " << boundary.getMesh().getNumTriangles() << std::endl;
// The tube simulation is an interior (as opposed to exterior) flow problem. For
// this reason, the lattice nodes that lie inside the computational domain must
// be identified and distinguished from the ones that lie outside of it. This is
// handled by the following voxelization process.
pcout << std::endl << "Voxelizing the domain." << std::endl;
const int flowType = voxelFlag::inside;
VoxelizedDomain3D<T> voxelizedDomain (
boundary, flowType, extraLayer, borderWidth, extendedEnvelopeWidth, blockSize);
pcout << getMultiBlockInfo(voxelizedDomain.getVoxelMatrix()) << std::endl;
std::auto_ptr<MultiBlockLattice3D<T,DESCRIPTOR> > lattice
= generateMultiBlockLattice<T,DESCRIPTOR> (
voxelizedDomain.getVoxelMatrix(), extendedEnvelopeWidth, new BGKdynamics<T,DESCRIPTOR>(omega) );
// The Guo off lattice boundary condition is set up.
pcout << "Creating boundary condition." << std::endl;
BoundaryProfiles3D<T,Velocity> profiles;
profiles.defineInletOutletTags(boundary, xDirection);
profiles.setInletOutlet (
new PoiseuilleProfile3D<T>(uAverage),
new PoiseuilleProfile3D<T>(-uAverage) );
GuoOffLatticeModel3D<T,DESCRIPTOR>* model =
new GuoOffLatticeModel3D<T,DESCRIPTOR> (
new TriangleFlowShape3D<T,Array<T,3> > (
voxelizedDomain.getBoundary(), profiles),
flowType, useAllDirections );
model->selectUseRegularizedModel(useRegularized);
OffLatticeBoundaryCondition3D<T,DESCRIPTOR,Velocity> boundaryCondition (
model, voxelizedDomain, *lattice);
boundaryCondition.insert();
pcout << std::endl << "Initializing lattice." << std::endl;
iniLattice(*lattice, voxelizedDomain);
// Particles
// Definition of a particle field.
MultiParticleField3D<DenseParticleField3D<T,DESCRIPTOR> >* particles=0;
particles = new MultiParticleField3D<DenseParticleField3D<T,DESCRIPTOR> > (
lattice->getMultiBlockManagement(),
defaultMultiBlockPolicy3D().getCombinedStatistics() );
std::vector<MultiBlock3D*> particleArg;
particleArg.push_back(particles);
std::vector<MultiBlock3D*> particleFluidArg;
particleFluidArg.push_back(particles);
particleFluidArg.push_back(lattice.get());
// Functional that advances the particles to their new position at each
// predefined time step.
integrateProcessingFunctional (
new AdvanceParticlesFunctional3D<T,DESCRIPTOR>(cutOffSpeedSqr),
lattice->getBoundingBox(), particleArg, 0);
// Functional that assigns the particle velocity according to the particle's
// position in the fluid.
integrateProcessingFunctional (
new FluidToParticleCoupling3D<T,DESCRIPTOR>((T)particleTimeFactor),
lattice->getBoundingBox(), particleFluidArg, 1 );
// Definition of a domain from which particles will be injected in the flow field.
// The specific domain is close to the inlet of the tube.
Box3D injectionDomain(lattice->getBoundingBox());
injectionDomain.x0 = inletCenter[0] +2;
injectionDomain.x1 = inletCenter[0] +4;
// Definition of simple mass-less particles.
Particle3D<T,DESCRIPTOR>* particleTemplate=0;
particleTemplate = new PointParticle3D<T,DESCRIPTOR>(0, Array<T,3>(0.,0.,0.), Array<T,3>(0.,0.,0.));
// For the sake of illustration, particles are being injected in an area close to the
// center of the tube.
T injectionRadius = radius/4.;
// Functional which injects particles with predefined probability from the specified injection domain.
integrateProcessingFunctional (
new AnalyticalInjectRandomParticlesFunctional3D<T,DESCRIPTOR,CircularInjection> (
particleTemplate, particleProbabilityPerCell, CircularInjection(injectionRadius, inletCenter) ),
injectionDomain, particleArg, 0 );
// Definition of an absorbtion domain for the particles. The specific domain is very close to the
// exit of the tube.
Box3D absorbtionDomain(lattice->getBoundingBox());
absorbtionDomain.x0 = outletCenter[0] -2;
absorbtionDomain.x1 = outletCenter[0] -2;
// Functional which absorbs the particles which reach the specified absorbtion domain.
integrateProcessingFunctional (
new AbsorbParticlesFunctional3D<T,DESCRIPTOR>,
absorbtionDomain, particleArg, 0 );
particles->executeInternalProcessors();
pcout << std::endl << "Starting simulation." << std::endl;
for (plint i=0; i<maxIter; ++i) {
if (i%outIter==0) {
pcout << "Iteration= " << i << "; "
<< "Average energy: "
<< boundaryCondition.computeAverageEnergy() << std::endl;
pcout << "Number of particles in the tube: "
<< countParticles(*particles, particles->getBoundingBox()) << std::endl;
}
if (i%saveIter==0 && i>0) {
pcout << "Write visualization files." << std::endl;
VtkImageOutput3D<T> vtkOut("volume", 1.);
vtkOut.writeData<float>(*boundaryCondition.computePressure(), "p", 1.);
vtkOut.writeData<float>(*boundaryCondition.computeVelocityNorm(), "u", 1.);
pcout << "Write particle output file." << std::endl;
writeAsciiParticlePos(*particles, "particle_positions.dat");
writeParticleVtk(*particles, "particles.vtk");
}
lattice->collideAndStream();
if (i%particleTimeFactor==0) {
particles->executeInternalProcessors();
}
}
delete particles;
delete particleTemplate;
return 0;
}
