void CleverNodeInjection<TYPE>::coarsen(
SAMRAI::hier::Patch& coarse,
const SAMRAI::hier::Patch& fine,
const int dst_component,
const int src_component,
const SAMRAI::hier::Box& coarse_box,
const SAMRAI::hier::IntVector& ratio) const
{
boost::shared_ptr<CleverNodeData<TYPE> > fine_data(
SHARED_PTR_CAST(CleverNodeData<TYPE> ,
fine.getPatchData(src_component)));
boost::shared_ptr<CleverNodeData<TYPE> > coarse_data(
SHARED_PTR_CAST(CleverNodeData<TYPE> ,
coarse.getPatchData(dst_component)));
const SAMRAI::hier::Box coarse_ghost_box =
SAMRAI::pdat::NodeGeometry::toNodeBox(coarse_data->getGhostBox());
const SAMRAI::hier::Box fine_ghost_box =
SAMRAI::pdat::NodeGeometry::toNodeBox(fine_data->getGhostBox());
const hier::Index filo = fine_data->getGhostBox().lower();
const hier::Index fihi = fine_data->getGhostBox().upper();
const hier::Index cilo = coarse_data->getGhostBox().lower();
const hier::Index cihi = coarse_data->getGhostBox().upper();
const hier::Index ifirstc = coarse_box.lower();
const hier::Index ilastc = coarse_box.upper();
for(int depth = 0; depth < coarse_data->getDepth(); depth++) {
if (fine.getDim() == SAMRAI::tbox::Dimension(2)) {
F90_FUNC(conavgclevernodedoub2d, CONAVGCLEVERNODEDOUB2D)
(ifirstc(0), ifirstc(1), ilastc(0), ilastc(1),
filo(0), filo(1), fihi(0), fihi(1),
cilo(0), cilo(1), cihi(0), cihi(1),
&ratio[0],
fine_data->getPointer(depth),
coarse_data->getPointer(depth));
} else {
TBOX_ERROR("CleverNodeInjection error...\n"
<< "dim != 2 not supported." << std::endl);
}
}
}
void Stokes::FACOps::residual_3D
(SAMRAI::pdat::CellData<double> &p,
SAMRAI::pdat::SideData<double> &v,
SAMRAI::pdat::CellData<double> &cell_viscosity,
SAMRAI::pdat::CellData<double> &p_rhs,
SAMRAI::pdat::SideData<double> &v_rhs,
SAMRAI::pdat::CellData<double> &p_resid,
SAMRAI::pdat::SideData<double> &v_resid,
SAMRAI::hier::Patch &patch,
const SAMRAI::hier::Box &pbox,
const SAMRAI::geom::CartesianPatchGeometry &geom)
{
boost::shared_ptr<SAMRAI::pdat::EdgeData<double> > edge_viscosity_ptr =
boost::dynamic_pointer_cast<SAMRAI::pdat::EdgeData<double> >
(patch.getPatchData(edge_viscosity_id));
SAMRAI::pdat::EdgeData<double> &edge_viscosity(*edge_viscosity_ptr);
const double *Dx = geom.getDx();
const SAMRAI::hier::Index ip(1,0,0), jp(0,1,0), kp(0,0,1);
const SAMRAI::hier::Index pp[]={ip,jp,kp};
SAMRAI::pdat::CellIterator cend(SAMRAI::pdat::CellGeometry::end(pbox));
for(SAMRAI::pdat::CellIterator ci(SAMRAI::pdat::CellGeometry::begin(pbox));
ci!=cend; ++ci)
{
const SAMRAI::pdat::CellIndex ¢er(*ci);
SAMRAI::pdat::CellIndex up(center), down(center), right(center),
left(center), front(center), back(center);
++right[0];
--left[0];
++up[1];
--down[1];
++front[2];
--back[2];
/* p */
if(center[0]!=pbox.upper(0) && center[1]!=pbox.upper(1)
&& center[2]!=pbox.upper(2))
{
const SAMRAI::pdat::SideIndex
x(center,0,SAMRAI::pdat::SideIndex::Lower),
y(center,1,SAMRAI::pdat::SideIndex::Lower),
z(center,2,SAMRAI::pdat::SideIndex::Lower);
double dvx_dx=(v(x+ip) - v(x))/Dx[0];
double dvy_dy=(v(y+jp) - v(y))/Dx[1];
double dvz_dz=(v(z+kp) - v(z))/Dx[2];
p_resid(center)=p_rhs(center) - dvx_dx - dvy_dy - dvz_dz;
}
for(Gamra::Dir ix=0;ix<3;++ix)
{
const Gamra::Dir iy(ix.next(3));
const Gamra::Dir iz(iy.next(3));
const SAMRAI::pdat::SideIndex
x(center,ix,SAMRAI::pdat::SideIndex::Lower),
y(center,iy,SAMRAI::pdat::SideIndex::Lower),
z(center,iz,SAMRAI::pdat::SideIndex::Lower);
const SAMRAI::pdat::EdgeIndex
edge_y(center,iy,SAMRAI::pdat::EdgeIndex::LowerLeft),
edge_z(center,iz,SAMRAI::pdat::EdgeIndex::LowerLeft);
if(center[iy]!=pbox.upper(iy) && center[iz]!=pbox.upper(iz))
{
if((center[ix]==pbox.lower(ix) && v(x-pp[ix])==boundary_value)
|| (center[ix]==pbox.upper(ix) && v(x+pp[ix])==boundary_value))
{
v_resid(x)=0;
}
else
{
v_resid(x)=v_rhs(x)
- v_operator_3D(v,p,cell_viscosity,edge_viscosity,
center,edge_y,edge_z,x,y,z,
pp[ix],pp[iy],pp[iz],Dx[ix],Dx[iy],Dx[iz]);
}
}
}
}
}
void Elastic::Boundary_Conditions::set_dirichlet
(SAMRAI::pdat::SideData<double> &v,
const boost::shared_ptr<SAMRAI::pdat::SideData<double> > &dv_mixed_ptr,
const SAMRAI::hier::Index unit[],
const Gamra::Dir &dim,
const SAMRAI::hier::Box &pbox,
const SAMRAI::hier::Box &gbox,
const boost::shared_ptr<SAMRAI::geom::CartesianPatchGeometry> geom,
const double *dx,
const bool &homogeneous) const
{
for(Gamra::Dir ix=0; ix<dim; ++ix)
{
double offset[]={0.5,0.5,0.5};
offset[ix]=0;
for(Gamra::Dir iy=ix.next(dim); iy!=ix; iy=iy.next(dim))
{
const Gamra::Dir ix_iy(index_map(ix,iy,dim));
SAMRAI::hier::Box x_box(gbox);
x_box.setLower(ix,(geom->getTouchesRegularBoundary(ix,0)
&& is_dirichlet[ix][ix][0]) ?
pbox.lower(ix)+1 : pbox.lower(ix));
x_box.setUpper(ix,(geom->getTouchesRegularBoundary(ix,1)
&& is_dirichlet[ix][ix][1]) ?
pbox.upper(ix)-1 : pbox.upper(ix));
if(geom->getTouchesRegularBoundary(iy,0) && is_dirichlet[ix][iy][0])
{
SAMRAI::hier::Box y_box(x_box);
y_box.setUpper(iy,y_box.lower(iy));
SAMRAI::pdat::SideIterator
end(SAMRAI::pdat::SideGeometry::end(y_box,ix));
for(SAMRAI::pdat::SideIterator
si(SAMRAI::pdat::SideGeometry::begin(y_box,ix));
si!=end; ++si)
{
const SAMRAI::pdat::SideIndex &x(*si);
v(x)=-v(x+unit[iy]);
if(!homogeneous)
{
std::vector<double> coord(dim);
coord[iy]=geom->getXLower()[iy];
for(int d=(iy+1)%dim;d!=iy;d=(d+1)%dim)
coord[d]=geom->getXLower()[d]
+ dx[d]*(x[d]-pbox.lower()[d]+offset[d]);
if(have_faults())
v(x)+= -(*dv_mixed_ptr)(x+unit[iy],ix_iy+1);
v(x)+=2*expression[ix][iy][0].eval(coord.data());
}
}
}
if(geom->getTouchesRegularBoundary(iy,1) && is_dirichlet[ix][iy][1])
{
SAMRAI::hier::Box y_box(x_box);
y_box.setLower(iy,y_box.upper(iy));
SAMRAI::pdat::SideIterator
end(SAMRAI::pdat::SideGeometry::end(y_box,ix));
for(SAMRAI::pdat::SideIterator
si(SAMRAI::pdat::SideGeometry::begin(y_box,ix));
si!=end; ++si)
{
const SAMRAI::pdat::SideIndex &x(*si);
v(x)=-v(x-unit[iy]);
if(!homogeneous)
{
std::vector<double> coord(dim);
coord[iy]=geom->getXUpper()[iy];
for(int d=(iy+1)%dim;d!=iy;d=(d+1)%dim)
coord[d]=geom->getXLower()[d]
+ dx[d]*(x[d]-pbox.lower()[d]+offset[d]);
if(have_faults())
v(x)+= -(*dv_mixed_ptr)(x-unit[iy],ix_iy);
v(x)+=2*expression[ix][iy][1].eval(coord.data());
}
}
}
}
SAMRAI::hier::Box box(gbox);
if(geom->getTouchesRegularBoundary(ix,0) && is_dirichlet[ix][ix][0])
{
SAMRAI::hier::Box x_box(box);
x_box.setUpper(ix,x_box.lower(ix));
SAMRAI::pdat::SideIterator
end(SAMRAI::pdat::SideGeometry::end(x_box,ix));
for(SAMRAI::pdat::SideIterator
si(SAMRAI::pdat::SideGeometry::begin(x_box,ix)); si!=end; ++si)
{
const SAMRAI::pdat::SideIndex &x(*si);
if(x[ix]<pbox.lower(ix))
v(x)=boundary_value;
else
{
if(homogeneous)
{
v(x)=0;
}
else
{
std::vector<double> coord(dim);
for(int d=0;d<dim;++d)
coord[d]=geom->getXLower()[d]
+ dx[d]*(x[d]-pbox.lower()[d]+offset[d]);
v(x)=expression[ix][ix][0].eval(coord.data());
}
}
}
}
if(geom->getTouchesRegularBoundary(ix,1) && is_dirichlet[ix][ix][1])
{
SAMRAI::hier::Box x_box(box);
x_box.setLower(ix,x_box.upper(ix));
SAMRAI::pdat::SideIterator
end(SAMRAI::pdat::SideGeometry::end(x_box,ix));
for(SAMRAI::pdat::SideIterator
si(SAMRAI::pdat::SideGeometry::begin(x_box,ix)); si!=end; ++si)
{
const SAMRAI::pdat::SideIndex &x(*si);
if(x[ix]>pbox.upper(ix)+1)
v(x)=boundary_value;
else
{
if(homogeneous)
{
v(x)=0;
}
else
{
std::vector<double> coord(dim);
for(int d=0;d<dim;++d)
coord[d]=geom->getXLower()[d]
+ dx[d]*(x[d]-pbox.lower()[d]+offset[d]);
v(x)=expression[ix][ix][1].eval(coord.data());
}
}
}
}
}
}
/*
*************************************************************************
* Set up the initial guess and problem parameters *
* and solve the Stokes problem. We explicitly initialize and *
* deallocate the solver state in this example. *
*************************************************************************
*/
bool Stokes::FAC::solve()
{
if (!d_hierarchy) {
TBOX_ERROR(d_object_name
<< "Cannot solve using an uninitialized object.\n");
}
int ln;
/*
* Fill in the initial guess.
*/
for (ln = 0; ln <= d_hierarchy->getFinestLevelNumber(); ++ln) {
boost::shared_ptr<SAMRAI::hier::PatchLevel> level = d_hierarchy->getPatchLevel(ln);
SAMRAI::hier::PatchLevel::Iterator ip(level->begin());
SAMRAI::hier::PatchLevel::Iterator iend(level->end());
for ( ; ip!=iend; ++ip) {
boost::shared_ptr<SAMRAI::hier::Patch> patch = *ip;
boost::shared_ptr<SAMRAI::pdat::CellData<double> > p =
boost::dynamic_pointer_cast<SAMRAI::pdat::CellData<double> >
(patch->getPatchData(p_id));
boost::shared_ptr<SAMRAI::geom::CartesianPatchGeometry> geom =
boost::dynamic_pointer_cast<SAMRAI::geom::CartesianPatchGeometry>
(patch->getPatchGeometry());
if(p_initial.empty())
{
p->fill(0.0);
}
else
{
const int dim=d_dim.getValue();
const double *dx=geom->getDx();
std::vector<double> xyz(dim);
std::vector<double> dx_p(dim);
for(int d=0;d<dim;++d)
dx_p[d]=(p_initial_xyz_max[d]
- p_initial_xyz_min[d])/(p_initial_ijk[d]-1);
std::vector<int> di(dim);
di[0]=1;
for(int d=1;d<dim;++d)
di[d]=di[d-1]*p_initial_ijk[d-1];
SAMRAI::hier::Box pbox = p->getBox();
SAMRAI::pdat::CellIterator
cend(SAMRAI::pdat::CellGeometry::end(p->getGhostBox()));
for(SAMRAI::pdat::CellIterator
ci(SAMRAI::pdat::CellGeometry::begin(p->getGhostBox()));
ci!=cend; ++ci)
{
const SAMRAI::pdat::CellIndex &c(*ci);
std::vector<double> xyz(dim);
/* VLA's not allowed by clang */
double weight[3][2];
for(int d=0;d<dim;++d)
xyz[d]=geom->getXLower()[d]
+ dx[d]*(c[d]-pbox.lower()[d] + 0.5);
int ijk(0);
std::vector<int> ddi(dim);
for(int d=0;d<dim;++d)
{
int i=static_cast<int>(xyz[d]*(p_initial_ijk[d]-1)
/(p_initial_xyz_max[d]
- p_initial_xyz_min[d]));
i=std::max(0,std::min(p_initial_ijk[d]-1,i));
ijk+=i*di[d];
if(i==p_initial_ijk[d]-1)
{
weight[d][0]=1;
weight[d][1]=0;
ddi[d]=0;
}
else
{
weight[d][1]=
(xyz[d]-(i*dx_p[d] + p_initial_xyz_min[d]))/dx_p[d];
weight[d][0]=1-weight[d][1];
ddi[d]=di[d];
}
}
if(dim==2)
{
(*p)(c)=p_initial[ijk]*weight[0][0]*weight[1][0]
+ p_initial[ijk+ddi[0]]*weight[0][1]*weight[1][0]
+ p_initial[ijk+ddi[1]]*weight[0][0]*weight[1][1]
+ p_initial[ijk+ddi[0]+ddi[1]]*weight[0][1]*weight[1][1];
}
else
{
(*p)(c)=p_initial[ijk]*weight[0][0]*weight[1][0]*weight[2][0]
+ p_initial[ijk+ddi[0]]*weight[0][1]*weight[1][0]*weight[2][0]
+ p_initial[ijk+ddi[1]]*weight[0][0]*weight[1][1]*weight[2][0]
+ p_initial[ijk+ddi[0]+ddi[1]]*weight[0][1]*weight[1][1]*weight[2][0]
+ p_initial[ijk+ddi[2]]*weight[0][0]*weight[1][0]*weight[2][1]
+ p_initial[ijk+ddi[0]+ddi[2]]*weight[0][1]*weight[1][0]*weight[2][1]
+ p_initial[ijk+ddi[1]+ddi[2]]*weight[0][0]*weight[1][1]*weight[2][1]
+ p_initial[ijk+ddi[0]+ddi[1]+ddi[2]]*weight[0][1]*weight[1][1]*weight[2][1];
}
}
}
boost::shared_ptr<SAMRAI::pdat::SideData<double> > v =
boost::dynamic_pointer_cast<SAMRAI::pdat::SideData<double> >
(patch->getPatchData(v_id));
v->fill(0.0);
}
d_stokes_fac_solver.set_boundaries(p_id,v_id,level,false);
}
fix_viscosity();
d_stokes_fac_solver.initializeSolverState
(p_id,cell_viscosity_id,edge_viscosity_id,dp_id,p_rhs_id,v_id,v_rhs_id,
d_hierarchy,0,d_hierarchy->getFinestLevelNumber());
SAMRAI::tbox::plog << "solving..." << std::endl;
int solver_ret;
solver_ret = d_stokes_fac_solver.solveSystem(p_id,p_rhs_id,v_id,v_rhs_id);
double avg_factor, final_factor;
d_stokes_fac_solver.getConvergenceFactors(avg_factor, final_factor);
SAMRAI::tbox::plog << "\t" << (solver_ret ? "" : "NOT ") << "converged " << "\n"
<< " iterations: "
<< d_stokes_fac_solver.getNumberOfIterations() << "\n"
<< " residual: "<< d_stokes_fac_solver.getResidualNorm()
<< "\n"
<< " average convergence: "<< avg_factor << "\n"
<< " final convergence: "<< final_factor << "\n"
<< std::flush;
d_stokes_fac_solver.deallocateSolverState();
return solver_ret;
}
void Elastic::Boundary_Conditions::set_embedded_boundary
(const SAMRAI::hier::Patch& patch, const int &level_set_id,
const int &dv_mixed_id)
{
boost::shared_ptr<SAMRAI::pdat::SideData<double> > level_set_ptr=
boost::dynamic_pointer_cast<SAMRAI::pdat::SideData<double> >
(patch.getPatchData(level_set_id));
SAMRAI::pdat::SideData<double> &level_set(*level_set_ptr);
boost::shared_ptr<SAMRAI::pdat::SideData<double> > dv_mixed_ptr;
if(dv_mixed_id!=invalid_id)
dv_mixed_ptr=boost::dynamic_pointer_cast
<SAMRAI::pdat::SideData<double> >(patch.getPatchData(dv_mixed_id));
const SAMRAI::tbox::Dimension dimension(patch.getDim());
const Gamra::Dir dim(dimension.getValue());
const SAMRAI::hier::Box gbox=level_set.getGhostBox();
const SAMRAI::hier::Box box=level_set.getBox();
boost::shared_ptr<SAMRAI::geom::CartesianPatchGeometry> geom =
boost::dynamic_pointer_cast<SAMRAI::geom::CartesianPatchGeometry>
(patch.getPatchGeometry());
/* Corners are not synced, so we set the level set to a generic
* negative value and dv_mixed to zero. Setting dv_mixed to zero
* implies that we do not care about faults that intersect that
* corner (nor should we). */
for(Gamra::Dir ix=0; ix<dim; ++ix)
{
const Gamra::Dir iy(ix.next(dim));
const Gamra::Dir iz(iy.next(dim));
std::vector<std::vector<int> > corners(dim);
corners[ix].push_back(box.lower(ix));
corners[ix].push_back(box.upper(ix)+1);
if(geom->getTouchesRegularBoundary(iy,0))
corners[iy].push_back(gbox.lower(iy));
if(geom->getTouchesRegularBoundary(iy,1))
corners[iy].push_back(gbox.upper(iy));
if(dim==3)
{
if(geom->getTouchesRegularBoundary(iz,0))
corners[iz].push_back(gbox.lower(iz));
if(geom->getTouchesRegularBoundary(iz,1))
corners[iz].push_back(gbox.upper(iz));
}
SAMRAI::pdat::SideIndex x(SAMRAI::hier::Index(dimension),ix,
SAMRAI::pdat::SideIndex::Lower);
for(std::vector<int>::iterator i=corners[ix].begin();
i!=corners[ix].end(); ++i)
{
x[ix]=*i;
if(dim==2)
{
for(std::vector<int>::iterator j=corners[iy].begin();
j!=corners[iy].end();++j)
{
x[iy]=*j;
set_embedded_values(x,dim,level_set,dv_mixed_ptr);
}
}
else
{
for(std::vector<int>::iterator j=corners[iy].begin();
j!=corners[iy].end();++j)
for(int kk=gbox.lower(iz); kk<=gbox.upper(iz); ++kk)
{
x[iy]=*j;
x[iz]=kk;
set_embedded_values(x,dim,level_set,dv_mixed_ptr);
}
for(std::vector<int>::iterator k=corners[iz].begin();
k!=corners[iz].end();++k)
{
for(int jj=gbox.lower(iy); jj<=gbox.upper(iy); ++jj)
{
x[iy]=jj;
x[iz]=*k;
set_embedded_values(x,dim,level_set,dv_mixed_ptr);
}
}
}
}
}
}