void testFieldAdvect(){
tcl::Context context(tcl::DEVICE::GPU, false, false);
cl::Program program = context.loadProgram("../res/simple_fluid.cl");
cl::Kernel advectField(program, "advect_field");
int dim = 4;
//The MAC grid 'values'
float grid[] = {
0, 0, 0, 1,
0, 0, 0, 2,
0, 0, 0, 3,
7, 6, 5, 4,
};
//The velocity fields
float vX[] = {
1, 0, 0, 0, 0,
1, 0, 0, 0, 0,
1, 0, 0, 0, 0,
1, 0, 0, 0, 0
};
float vY[] = {
1, 1, 1, 1,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0
};
float dt = 1.f;
cl::Buffer gridA = context.buffer(tcl::MEM::READ_WRITE, dim * dim * sizeof(float), grid);
cl::Buffer gridB = context.buffer(tcl::MEM::READ_WRITE, dim * dim * sizeof(float), nullptr);
cl::Buffer vXBuf = context.buffer(tcl::MEM::READ_ONLY, dim * (dim + 1) * sizeof(float), vX);
cl::Buffer vYBuf = context.buffer(tcl::MEM::READ_ONLY, dim * (dim + 1) * sizeof(float), vY);
advectField.setArg(0, dt);
advectField.setArg(1, gridA);
advectField.setArg(2, gridB);
advectField.setArg(3, vXBuf);
advectField.setArg(4, vYBuf);
context.runNDKernel(advectField, cl::NDRange(dim, dim), cl::NullRange, cl::NullRange, false);
context.readData(gridB, dim * dim * sizeof(float), grid, 0, true);
for (int i = 0; i < dim * dim; ++i){
if (i != 0 && i % dim == 0){
std::cout << "\n";
}
std::cout << std::setw(6) << std::setprecision(3) << grid[i] << " ";
}
std::cout << std::endl;
}
void testVYFieldAdvect(){
tcl::Context context(tcl::DEVICE::GPU, false, false);
cl::Program program = context.loadProgram("../res/simple_fluid.cl");
cl::Kernel advectField(program, "advect_vy");
int dim = 4;
float vX[] = {
1, 1, 0, 0, 0,
1, 0, 0, 0, 1,
0, 0, 0, 0, 2,
0, 0, 5, 4, 3
};
float vY[] = {
1, 1, 0, 0,
1, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0
};
float dt = 1.f;
cl::Buffer vyA = context.buffer(tcl::MEM::READ_WRITE, dim * (dim + 1) * sizeof(float), vY);
cl::Buffer vyB = context.buffer(tcl::MEM::READ_WRITE, dim * (dim + 1) * sizeof(float), nullptr);
cl::Buffer vxBuf = context.buffer(tcl::MEM::READ_ONLY, dim * (dim + 1) * sizeof(float), vX);
advectField.setArg(0, dt);
advectField.setArg(1, vyA);
advectField.setArg(2, vyB);
advectField.setArg(3, vxBuf);
context.runNDKernel(advectField, cl::NDRange(dim, dim + 1), cl::NullRange, cl::NullRange, false);
context.readData(vyB, dim * (dim + 1) * sizeof(float), vY, 0, false);
for (int i = 0; i < dim * (dim + 1); ++i){
if (i != 0 && i % dim == 0){
std::cout << "\n";
}
std::cout << std::setw(6) << std::setprecision(3) << vY[i] << " ";
}
std::cout << std::endl;
}
//==============================================================================
// MAIN
int main( int argc, char* argv[] )
{
// spatial dimension
const unsigned dim = SPACEDIM;
typedef base::solver::Eigen3 Solver;
// Check input arguments
if ( argc != 2 ) {
std::cerr << "Usage: " << argv[0] << " input.dat\n"
<< "(Compiled for dim=" << dim << ")\n\n";
return -1;
}
// read name of input file
const std::string inputFile = boost::lexical_cast<std::string>( argv[1] );
const InputNucleus<dim> ui( inputFile );
// Simulation attributes
const bool simplex = false;
const bool stokesStabil = false;
typedef mat::hypel::NeoHookeanCompressible Material;
typedef TypesAndAttributes<dim,simplex> TA;
// basic attributes of the computation
base::auxi::BoundingBox<dim> bbox( ui.bbmin, ui.bbmax );
TA::Mesh mesh;
generateMesh( mesh, ui );
// Creates a list of <Element,faceNo> pairs
base::mesh::MeshBoundary meshBoundary;
meshBoundary.create( mesh.elementsBegin(), mesh.elementsEnd() );
TA::BoundaryMesh boundaryMesh;
base::mesh::generateBoundaryMesh( meshBoundary.begin(),
meshBoundary.end(),
mesh, boundaryMesh );
// mesh size (all equal, more or less)
const double h = base::mesh::Size<TA::Mesh::Element>::apply( mesh.elementPtr(0) );
//--------------------------------------------------------------------------
typedef base::cut::LevelSet<dim> LevelSet;
std::vector<LevelSet> levelSetNucleus, levelSetMembrane;
base::cut::analyticLevelSet( mesh,
base::cut::Sphere<dim>( ui.RN, ui.centerN ),
true, levelSetNucleus );
base::cut::analyticLevelSet( mesh,
base::cut::Sphere<dim>( ui.RM, ui.centerM ),
true, levelSetMembrane );
//--------------------------------------------------------------------------
// make cut cell structures
std::vector<TA::Cell> cellsNucleus, cellsMembrane, cellsCS;
base::cut::generateCutCells( mesh, levelSetNucleus, cellsNucleus );
base::cut::generateCutCells( mesh, levelSetMembrane, cellsMembrane );
{
cellsCS = cellsNucleus;
std::for_each( cellsCS.begin(), cellsCS.end(),
boost::bind( &TA::Cell::reverse, _1 ) );
base::cut::generateCutCells( mesh, levelSetMembrane, cellsCS,
base::cut::INTERSECT );
}
// intersection with the box boundary
std::vector<TA::SurfCell> surfaceCells;
base::cut::generateCutCells( boundaryMesh, levelSetMembrane, surfaceCells );
// Elastic material
Material material( mat::Lame::lambda( ui.E, ui.nu),
mat::Lame::mu( ui.E, ui.nu ) );
// Solid and fluid handlers
typedef Solid<TA::Mesh, Material> Solid;
typedef Fluid<TA::Mesh, stokesStabil> Fluid;
typedef SolidFluidInterface<TA::SurfaceMesh,Solid,Fluid> SFI;
typedef FluidFluidInterface<TA::SurfaceMesh,Fluid> FFI;
Solid nucleus( mesh, material );
Fluid gel( mesh, ui.viscosityGel, ui.alpha );
Fluid cytoSkeleton( mesh, ui.viscosityCS, ui.alpha );
// find geometry association for the dofs
std::vector<std::pair<std::size_t,TA::VecDim> > doFLocationD, doFLocationU;
base::dof::associateLocation( nucleus.getDisplacement(), doFLocationD );
base::dof::associateLocation( gel.getVelocity(), doFLocationU );
// Quadrature along a surface
TA::CutQuadrature cutQuadratureNucleus( cellsNucleus, true );
TA::CutQuadrature cutQuadratureGel( cellsMembrane, false );
TA::CutQuadrature cutQuadratureCS( cellsCS, true );
TA::SurfaceQuadrature surfaceQuadrature;
TA::SurfCutQuadrature surfaceCutQuadrature( surfaceCells, true );
//--------------------------------------------------------------------------
// Run a zero-th step in order to write the data before computation
// (store the previously enclosed volume)
double prevVolumeN, initialVolumeCS;
{
std::cout << 0 << " " << 0. << " 0 " << std::flush;
writeVTKFile( "nucleus", 0, mesh,
nucleus.getDisplacement(),
cytoSkeleton.getVelocity(), cytoSkeleton.getPressure(),
gel.getVelocity(), gel.getPressure(),
levelSetNucleus, levelSetMembrane, ui.dt );
// for surface field
TA::SurfaceMesh membrane, envelope;
base::cut::generateSurfaceMesh<TA::Mesh,TA::Cell>( mesh, cellsMembrane, membrane );
base::cut::generateSurfaceMesh<TA::Mesh,TA::Cell>( mesh, cellsNucleus, envelope );
writeSurfaceVTKFile( "membrane", 0, membrane );
writeSurfaceVTKFile( "envelope", 0, envelope );
surfaceFeatures( boundaryMesh, membrane, envelope,
surfaceQuadrature, surfaceCutQuadrature, std::cout );
std::cout << std::endl;
// store the contained volume
prevVolumeN = surf::enclosedVolume( envelope, surfaceQuadrature );
initialVolumeCS =
surf::enclosedVolume( membrane, surfaceQuadrature ) +
surf::enclosedVolume( boundaryMesh, surfaceCutQuadrature );
}
//--------------------------------------------------------------------------
// * Loop over time steps *
//--------------------------------------------------------------------------
const double supportThreshold = std::numeric_limits<double>::min();
for ( unsigned step = 0; step < ui.numLoadSteps; step++ ) {
// for surface field
TA::SurfaceMesh membrane, envelope;
base::cut::generateSurfaceMesh<TA::Mesh,TA::Cell>( mesh, cellsMembrane, membrane );
base::cut::generateSurfaceMesh<TA::Mesh,TA::Cell>( mesh, cellsNucleus, envelope );
// Interface handler
SFI envelopeHandler( envelope,
nucleus.getDisplacement(),
cytoSkeleton.getVelocity(), cytoSkeleton.getPressure(),
ui.viscosityCS );
FFI membraneHandler( membrane,
cytoSkeleton.getVelocity(), cytoSkeleton.getPressure(),
gel.getVelocity(), gel.getPressure(),
cellsMembrane,
ui.viscosityCS, ui.viscosityGel, ui.sigma );
std::cout << step+1 << " " << (step+1) * ui.dt << " " << std::flush;
//----------------------------------------------------------------------
// 0) Solve Lagrangian problem
// compute supports
std::vector<double> supportsD, supportsUCS, supportsPCS, supportsUGel, supportsPGel;
base::cut::supportComputation( mesh, nucleus.getDisplacement(),
cutQuadratureNucleus, supportsD );
base::cut::supportComputation( mesh, cytoSkeleton.getVelocity(),
cutQuadratureCS, supportsUCS );
base::cut::supportComputation( mesh, cytoSkeleton.getPressure(),
cutQuadratureCS, supportsPCS );
base::cut::supportComputation( mesh, gel.getVelocity(),
cutQuadratureGel, supportsUGel );
base::cut::supportComputation( mesh, gel.getPressure(),
cutQuadratureGel, supportsPGel );
// Hard-wired Dirichlet constraints (fluid BC)
{
// apply to outer material = gel
base::dof::constrainBoundary<Fluid::FEBasisU>(
meshBoundary.begin(),
meshBoundary.end(),
mesh, gel.getVelocity(),
boost::bind( &dirichletBC<dim,Fluid::DoFU>,
_1, _2, ui.ubar, bbox, ui.bc ) );
// in case of boundary intersections, apply to cytoskeleton
base::dof::constrainBoundary<Fluid::FEBasisU>(
meshBoundary.begin(),
meshBoundary.end(),
mesh, cytoSkeleton.getVelocity(),
boost::bind( &dirichletBC<dim,Fluid::DoFU>,
_1, _2, ui.ubar, bbox, ui.bc ) );
// Fix first pressure dof in case of closed cavity flow
if ( ui.bc == CAVITY ) {
Fluid::Pressure::DoFPtrIter pIter = gel.getPressure().doFsBegin();
(*pIter) -> constrainValue( 0, 0.0 );
}
}
// Basis stabilisation
base::cut::stabiliseBasis( mesh, nucleus.getDisplacement(), supportsD, doFLocationD );
base::cut::stabiliseBasis( mesh, cytoSkeleton.getVelocity(), supportsUCS, doFLocationU );
base::cut::stabiliseBasis( mesh, cytoSkeleton.getPressure(), supportsPCS, doFLocationD );
base::cut::stabiliseBasis( mesh, gel.getVelocity(), supportsUGel, doFLocationU );
base::cut::stabiliseBasis( mesh, gel.getPressure(), supportsPGel, doFLocationD );
// number DoFs
const std::size_t activeDoFsD =
base::dof::numberDoFsConsecutively( nucleus.getDisplacement().doFsBegin(),
nucleus.getDisplacement().doFsEnd() );
const std::size_t activeDoFsUCS =
base::dof::numberDoFsConsecutively( cytoSkeleton.getVelocity().doFsBegin(),
cytoSkeleton.getVelocity().doFsEnd(),
activeDoFsD );
const std::size_t activeDoFsPCS =
base::dof::numberDoFsConsecutively( cytoSkeleton.getPressure().doFsBegin(),
cytoSkeleton.getPressure().doFsEnd(),
activeDoFsD + activeDoFsUCS );
const std::size_t activeDoFsUGel =
base::dof::numberDoFsConsecutively( gel.getVelocity().doFsBegin(),
gel.getVelocity().doFsEnd(),
activeDoFsD + activeDoFsUCS + activeDoFsPCS );
const std::size_t activeDoFsPGel =
base::dof::numberDoFsConsecutively( gel.getPressure().doFsBegin(),
gel.getPressure().doFsEnd(),
activeDoFsD + activeDoFsUCS + activeDoFsPCS +
activeDoFsUGel );
// start from 0 for the increments, set rest to zero too
base::dof::clearDoFs( nucleus.getDisplacement() );
base::dof::clearDoFs( cytoSkeleton.getPressure() );
base::dof::clearDoFs( cytoSkeleton.getVelocity() );
base::dof::clearDoFs( gel.getPressure() );
base::dof::clearDoFs( gel.getVelocity() );
//----------------------------------------------------------------------
// Nonlinear iterations
unsigned iter = 0;
for ( ; iter < ui.maxIter; iter++ ) {
// Create a solver object
Solver solver( activeDoFsD + activeDoFsUCS + activeDoFsPCS +
activeDoFsUGel + activeDoFsPGel );
// register to solver
nucleus.registerInSolver( solver );
cytoSkeleton.registerInSolver( solver );
gel.registerInSolver( solver );
membraneHandler.registerInSolver( solver );
envelopeHandler.registerInSolver( solver );
// Compute as(d,dd) and Da(d,dd)[Delta d]
nucleus.assembleBulk( cutQuadratureNucleus, solver, iter );
// Body force
nucleus.bodyForce( cutQuadratureNucleus, solver,
boost::bind( unitForce<0,dim>, _1, ui.forceValue ) );
// Computate af(u,p; du,dp)
cytoSkeleton.assembleBulk( cutQuadratureCS, solver );
gel.assembleBulk( cutQuadratureGel, solver );
// Penalty terms for int_Gamma (dot(d) - u) (E delta d - mu delta u) ds
envelopeHandler.assemblePenaltyTerms( surfaceQuadrature, solver, ui.penaltyFac, ui.dt );
membraneHandler.assemblePenaltyTerms( surfaceQuadrature, solver, ui.penaltyFac );
// Boundary energy terms (beta = 0) [ -int_Gamma (...) ds ]
envelopeHandler.assembleEnergyTerms( surfaceQuadrature, solver, ui.dt );
membraneHandler.assembleEnergyTerms( surfaceQuadrature, solver );
// surface tension
membraneHandler.surfaceTension( surfaceQuadrature, solver );
// Finalise assembly
solver.finishAssembly();
// norm of residual
const double conv1 = solver.norm(0, activeDoFsD) / ui.E;
if ( isnan( conv1 ) ) return 1;
if ( ( iter > 0 ) and ( conv1 < ui.tolerance ) ) {
std::cout << "schon" << std::endl;
break;
}
// Solve
#ifdef LOAD_PARDISO
solver.pardisoLUSolve();
#else
#ifdef LOAD_UMFPACK
solver.umfPackLUSolve();
#else
solver.superLUSolve();
//solver.biCGStabSolve();
#endif
#endif
// distribute results back to dofs
base::dof::addToDoFsFromSolver( solver, nucleus.getDisplacement() ); //<>
base::dof::setDoFsFromSolver( solver, cytoSkeleton.getVelocity() );
base::dof::setDoFsFromSolver( solver, cytoSkeleton.getPressure() );
base::dof::setDoFsFromSolver( solver, gel.getVelocity() );
base::dof::setDoFsFromSolver( solver, gel.getPressure() );
const double conv2 = solver.norm(0, activeDoFsD);
if ( conv2 < ui.tolerance ) break;
} // finish non-linear iteration
std::cout << iter << " " << std::flush;
// write a vtk file
writeVTKFile( "nucleus", step+1, mesh,
nucleus.getDisplacement(),
cytoSkeleton.getVelocity(), cytoSkeleton.getPressure(),
gel.getVelocity(), gel.getPressure(),
levelSetNucleus, levelSetMembrane, ui.dt );
writeSurfaceVTKFile( "membrane", step+1, membrane );
writeSurfaceVTKFile( "envelope", step+1, envelope );
//----------------------------------------------------------------------
// 1) Pass Data to complementary domain of solid
{
const double extL = h; // extrapolation length
// pass extrapolated solution to inactive DoFs
extrapolateToFictitious( mesh, nucleus.getDisplacement(),
extL, doFLocationD, levelSetNucleus, bbox );
}
//----------------------------------------------------------------------
// 2) Geometry update
// a) Nucleus
{
// get shape features
const double volumeN = surf::enclosedVolume( envelope, surfaceQuadrature );
const TA::VecDim momentN =
surf::enclosedVolumeMoment( envelope, surfaceQuadrature );
const TA::VecDim centroidN = momentN / volumeN;
const double factorN = std::pow( prevVolumeN / volumeN,
1./static_cast<double>( dim ) );
// Move with velocity solution
moveSurface( mesh, cytoSkeleton.getVelocity(),
envelope, ui.dt, factorN, centroidN );
// compute new level set for envelope of nucleus
base::cut::bruteForce( mesh, envelope, true, levelSetNucleus );
// update the cut cell structure
base::cut::generateCutCells( mesh, levelSetNucleus, cellsNucleus );
// store the contained volume
prevVolumeN = surf::enclosedVolume( envelope, surfaceQuadrature );
}
// b) CS
{
// get shape features
const double volumeCS =
surf::enclosedVolume( membrane, surfaceQuadrature ) +
surf::enclosedVolume( boundaryMesh, surfaceCutQuadrature );
const TA::VecDim momentCS =
surf::enclosedVolumeMoment( membrane, surfaceQuadrature ) +
surf::enclosedVolumeMoment( boundaryMesh, surfaceCutQuadrature );
const TA::VecDim centroidCS = momentCS / volumeCS;
// Move with velocity solution
moveSurface( mesh, gel.getVelocity(), membrane, ui.dt, 1.0, centroidCS );
// rescale in order to preserve initial volume
rescaleSurface( membrane, initialVolumeCS, volumeCS, centroidCS );
// compute new level set for membrane
base::cut::bruteForce( mesh, membrane, true, levelSetMembrane );
// update the cut cell structure
base::cut::generateCutCells( mesh, levelSetMembrane, cellsMembrane );
base::cut::generateCutCells( boundaryMesh, levelSetMembrane, surfaceCells );
}
// new structure for cytoskeleton
{
cellsCS = cellsNucleus;
std::for_each( cellsCS.begin(), cellsCS.end(),
boost::bind( &TA::Cell::reverse, _1 ) );
base::cut::generateCutCells( mesh, levelSetMembrane, cellsCS,
base::cut::INTERSECT );
}
//----------------------------------------------------------------------
// 3) advect data
{
base::cut::supportComputation( mesh, nucleus.getDisplacement(),
cutQuadratureNucleus, supportsD );
// Find the location of the DoFs in the previous configuration
std::vector<std::pair<std::size_t,TA::VecDim> > previousDoFLocation;
findPreviousDoFLocations( mesh, nucleus.getDisplacement(), supportsD,
doFLocationD, previousDoFLocation, bbox,
supportThreshold, ui.findTolerance, 10 );
// add previous solution to current solution: u_{n+1} = \Delta u + u_n
{
Solid::Displacement::DoFPtrIter dIter = nucleus.getDisplacement().doFsBegin();
Solid::Displacement::DoFPtrIter dEnd = nucleus.getDisplacement().doFsEnd();
for ( ; dIter != dEnd; ++dIter ) {
for ( unsigned d = 0; d < dim; d++ ) {
const double prevU = (*dIter) -> getHistoryValue<1>( d );
const double deltaU = (*dIter) -> getHistoryValue<0>( d );
const double currU = prevU + deltaU;
(*dIter) -> setValue( d, currU );
}
}
}
// advect displacement field from previous to new location
advectField( mesh, nucleus.getDisplacement(), previousDoFLocation, supportsD,
supportThreshold );
}
//----------------------------------------------------------------------
// push history
base::dof::pushHistory( nucleus.getDisplacement() );
// remove the linear constraints used in the stabilisation process
base::dof::clearConstraints( nucleus.getDisplacement() );
base::dof::clearConstraints( cytoSkeleton.getVelocity() );
base::dof::clearConstraints( cytoSkeleton.getPressure() );
base::dof::clearConstraints( gel.getVelocity() );
base::dof::clearConstraints( gel.getPressure() );
surfaceFeatures( boundaryMesh, membrane, envelope,
surfaceQuadrature, surfaceCutQuadrature, std::cout );
std::cout << std::endl;
} // end load-steps
return 0;
}
