boost::tuple<mpl::size_t<MESH_ELEMENTS>,
typename MeshTraits<MeshType>::marker_element_const_iterator,
typename MeshTraits<MeshType>::marker_element_const_iterator>
markedelements( MeshType const& mesh, flag_type flag, rank_type pid, mpl::bool_<true> )
{
return markedelements( *mesh, flag, pid, mpl::bool_<false>() );
}
void updateCinematicViscosity( vf::Expr<ExprT> const& __expr, std::string const& marker = "" )
{
if ( !M_fieldCinematicViscosity ) return;
if ( marker.empty() )
M_fieldCinematicViscosity->on(_range=elements(M_fieldCinematicViscosity->mesh()),_expr=__expr );
else
M_fieldCinematicViscosity->on(_range=markedelements(M_fieldCinematicViscosity->mesh(),marker),_expr=__expr );
}
void updateCinematicViscosity( std::string const& marker = "" )
{
std::string markerUsed = ( marker.empty() )? self_type::defaultMaterialName() : marker;
M_cstCinematicViscosity[markerUsed] = this->cstMu(markerUsed)/this->cstRho(markerUsed);
if ( M_fieldCinematicViscosity )
{
if ( marker.empty() )
M_fieldCinematicViscosity->on(_range=elements(M_fieldCinematicViscosity->mesh()),
_expr=idv(this->fieldMu())/idv(this->fieldRho()) );
else
M_fieldCinematicViscosity->on(_range=markedelements(M_fieldCinematicViscosity->mesh(),marker),
_expr=idv(this->fieldMu())/idv(this->fieldRho()) );
}
}
PreconditionerBlockMS<space_type>::PreconditionerBlockMS(space_ptrtype Xh, // (u)x(p)
ModelProperties model, // model
std::string const& p, // prefix
sparse_matrix_ptrtype AA, value_type relax ) // The matrix
:
M_backend(backend()), // the backend associated to the PC
M_Xh( Xh ),
M_Vh( Xh->template functionSpace<0>() ), // Potential
M_Qh( Xh->template functionSpace<1>() ), // Lagrange
M_Vh_indices( M_Vh->nLocalDofWithGhost() ),
M_Qh_indices( M_Qh->nLocalDofWithGhost() ),
M_uin( M_backend->newVector( M_Vh ) ),
M_uout( M_backend->newVector( M_Vh ) ),
M_pin( M_backend->newVector( M_Qh ) ),
M_pout( M_backend->newVector( M_Qh ) ),
U( M_Xh, "U" ),
M_mass(M_backend->newMatrix(M_Vh,M_Vh)),
M_L(M_backend->newMatrix(M_Qh,M_Qh)),
M_er( 1. ),
M_model( model ),
M_prefix( p ),
M_prefix_11( p+".11" ),
M_prefix_22( p+".22" ),
u(M_Vh, "u"),
ozz(M_Vh, "ozz"),
zoz(M_Vh, "zoz"),
zzo(M_Vh, "zzo"),
M_ozz(M_backend->newVector( M_Vh )),
M_zoz(M_backend->newVector( M_Vh )),
M_zzo(M_backend->newVector( M_Vh )),
X(M_Qh, "X"),
Y(M_Qh, "Y"),
Z(M_Qh, "Z"),
M_X(M_backend->newVector( M_Qh )),
M_Y(M_backend->newVector( M_Qh )),
M_Z(M_backend->newVector( M_Qh )),
phi(M_Qh, "phi"),
M_relax(relax)
{
tic();
LOG(INFO) << "[PreconditionerBlockMS] setup starts";
this->setMatrix( AA );
this->setName(M_prefix);
/* Indices are need to extract sub matrix */
std::iota( M_Vh_indices.begin(), M_Vh_indices.end(), 0 );
std::iota( M_Qh_indices.begin(), M_Qh_indices.end(), M_Vh->nLocalDofWithGhost() );
M_11 = AA->createSubMatrix( M_Vh_indices, M_Vh_indices, true, true);
/* Boundary conditions */
BoundaryConditions M_bc = M_model.boundaryConditions();
map_vector_field<FEELPP_DIM,1,2> m_dirichlet_u { M_bc.getVectorFields<FEELPP_DIM> ( "u", "Dirichlet" ) };
map_scalar_field<2> m_dirichlet_p { M_bc.getScalarFields<2> ( "phi", "Dirichlet" ) };
/* Compute the mass matrix (needed in first block, constant) */
auto f2A = form2(_test=M_Vh, _trial=M_Vh, _matrix=M_mass);
auto f1A = form1(_test=M_Vh);
f2A = integrate(_range=elements(M_Vh->mesh()), _expr=inner(idt(u),id(u))); // M
for(auto const & it : m_dirichlet_u )
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_11<<"\n";
f2A += on(_range=markedfaces(M_Vh->mesh(),it.first), _expr=it.second,_rhs=f1A, _element=u, _type="elimination_symmetric");
}
/* Compute the L (= er * grad grad) matrix (the second block) */
auto f2L = form2(_test=M_Qh,_trial=M_Qh, _matrix=M_L);
#if 0
//If you want to manage the relative permittivity materials per material,
//here is the entry to deal with.
for(auto it : M_model.materials() )
{
f2L += integrate(_range=markedelements(M_Qh->mesh(),marker(it)), _expr=M_er*inner(gradt(phi), grad(phi)));
}
#else
f2L += integrate(_range=elements(M_Qh->mesh()), _expr=M_er*inner(gradt(phi), grad(phi)));
#endif
auto f1LQ = form1(_test=M_Qh);
for(auto const & it : m_dirichlet_p)
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_22<<"\n";
f2L += on(_range=markedfaces(M_Qh->mesh(),it.first),_element=phi, _expr=it.second, _rhs=f1LQ, _type="elimination_symmetric");
}
toc( "[PreconditionerBlockMS] setup done ", FLAGS_v > 0 );
}
void
TestInterpolationHCurl3D::testInterpolation( std::string one_element_mesh )
{
//auto myexpr = unitX() + unitY() + unitZ() ; //(1,1,1)
auto myexpr = vec( cst(1.), cst(1.), cst(1.));
// one element mesh
auto mesh_name = one_element_mesh + ".msh"; //create the mesh and load it
fs::path mesh_path( mesh_name );
mesh_ptrtype oneelement_mesh = loadMesh( _mesh=new mesh_type,
_filename=mesh_name);
// refined mesh (export)
auto refine_level = std::floor(1 - math::log( 0.1 )); //Deduce refine level from meshSize (option)
mesh_ptrtype mesh = loadMesh( _mesh=new mesh_type,
_filename=mesh_name,
_refine=( int )refine_level);
space_ptrtype Xh = space_type::New( oneelement_mesh );
std::vector<std::string> faces = {"yzFace","xyzFace","xyFace"};
std::vector<std::string> edges = {"zAxis","yAxis","yzAxis","xyAxis","xzAxis","xAxis"};
element_type U_h_int = Xh->element();
element_type U_h_on = Xh->element();
element_type U_h_on_boundary = Xh->element();
submesh1d_ptrtype edgeMesh( new submesh1d_type );
edgeMesh = createSubmesh(oneelement_mesh, boundaryedges(oneelement_mesh) ); //submesh of edges
// Tangents on ref element
auto t0 = vec(cst(0.),cst(0.),cst(-2.));
auto t1 = vec(cst(0.),cst(2.),cst(0.));
auto t2 = vec(cst(0.),cst(-2.),cst(2.));
auto t3 = vec(cst(2.),cst(-2.),cst(0.));
auto t4 = vec(cst(2.),cst(0.),cst(-2.));
auto t5 = vec(cst(2.),cst(0.),cst(0.));
// Jacobian of geometrical transforms
std::string jac;
if(mesh_path.stem().string() == "one-elt-ref-3d" || mesh_path.stem().string() == "one-elt-real-h**o-3d" )
jac = "{1,0,0,0,1,0,0,0,1}:x:y:z";
else if(mesh_path.stem().string() == "one-elt-real-rotx" )
jac = "{1,0,0,0,0,-1,0,1,0}:x:y:z";
else if(mesh_path.stem().string() == "one-elt-real-roty" )
jac = "{0,0,1,0,1,0,-1,0,0}:x:y:z";
else if(mesh_path.stem().string() == "one-elt-real-rotz" )
jac = "{0,-1,0,1,0,0,0,0,1}:x:y:z";
U_h_int(0) = integrate( markedelements(edgeMesh, edges[0]), trans(expr<3,3>(jac)*t0)*myexpr ).evaluate()(0,0);
U_h_int(1) = integrate( markedelements(edgeMesh, edges[1]), trans(expr<3,3>(jac)*t1)*myexpr ).evaluate()(0,0);
U_h_int(2) = integrate( markedelements(edgeMesh, edges[2]), trans(expr<3,3>(jac)*t2)*myexpr ).evaluate()(0,0);
U_h_int(3) = integrate( markedelements(edgeMesh, edges[3]), trans(expr<3,3>(jac)*t3)*myexpr ).evaluate()(0,0);
U_h_int(4) = integrate( markedelements(edgeMesh, edges[4]), trans(expr<3,3>(jac)*t4)*myexpr ).evaluate()(0,0);
U_h_int(5) = integrate( markedelements(edgeMesh, edges[5]), trans(expr<3,3>(jac)*t5)*myexpr ).evaluate()(0,0);
for(int i=0; i<edges.size(); i++)
{
double edgeLength = integrate( markedelements(edgeMesh, edges[i]), cst(1.) ).evaluate()(0,0);
U_h_int(i) /= edgeLength;
}
#if 0 //Doesn't work for now
for(int i=0; i<Xh->nLocalDof(); i++)
{
CHECK( edgeMesh->hasMarkers( {edges[i]} ) );
U_h_int(i) = integrate( markedelements(edgeMesh, edges[i]), trans( print(T(),"T=") )*myexpr ).evaluate()(0,0);
std::cout << "U_h_int(" << i << ")= " << U_h_int(i) << std::endl;
}
#endif
// nedelec interpolant using on keyword
// interpolate on element
U_h_on.zero();
U_h_on.on(_range=elements(oneelement_mesh), _expr=myexpr);
U_h_on_boundary.on(_range=boundaryfaces(oneelement_mesh), _expr=myexpr);
auto exporter_proj = exporter( _mesh=mesh, _name=( boost::format( "%1%" ) % this->about().appName() ).str() );
exporter_proj->step( 0 )->add( "U_interpolation_handly_"+mesh_path.stem().string(), U_h_int );
exporter_proj->step( 0 )->add( "U_interpolation_on_"+mesh_path.stem().string(), U_h_on );
exporter_proj->save();
// print coefficient only for reference element
U_h_int.printMatlab( "U_h_int_" + mesh_path.stem().string() + ".m" );
U_h_on.printMatlab( "U_h_on_" + mesh_path.stem().string() + ".m" );
U_h_on_boundary.printMatlab( "U_h_on_boundary_" + mesh_path.stem().string() + ".m" );
//L2 norm of error
auto error = vf::project(_space=Xh, _range=elements(oneelement_mesh), _expr=idv(U_h_int) - idv(U_h_on) );
double L2error = error.l2Norm();
std::cout << "L2 error (elements) = " << L2error << std::endl;
auto error_boundary = vf::project(_space=Xh, _range=elements(oneelement_mesh), _expr=idv(U_h_int) - idv(U_h_on_boundary) );
double L2error_boundary = error_boundary.l2Norm();
std::cout << "L2 error (boundary) = " << L2error_boundary << std::endl;
BOOST_CHECK_SMALL( L2error_boundary - L2error, 1e-13 );
}
void
ThermalBlockMinimalVersion::initModel()
{
gamma_dir=option(_name="gamma_dir").template as<double>();
this->setFunctionSpaces( Pch<1>( loadMesh( _mesh=new Mesh<Simplex<2>> ) ) );
auto mesh = Xh->mesh();
if( Environment::worldComm().isMasterRank() )
{
std::cout << "Number of local dof " << Xh->nLocalDof() << "\n";
std::cout << "Number of dof " << Xh->nDof() << "\n";
}
auto mu_min = Dmu->element();
auto mu_max = Dmu->element();
mu_min << 0.1 , 0.1 , 0.1 , 0.1 , 0.1 , 0.1 , 0.1 , 0.1 ;
mu_max << 10 , 10 , 10 , 10 , 10 , 10 , 10 , 10 ;
Dmu->setMin( mu_min );
Dmu->setMax( mu_max );
auto u = Xh->element();
auto v = Xh->element();
auto M = backend()->newMatrix( Xh , Xh );
double mu_min_coeff=0.1;
// on boundary north we have u=0 so term from weak dirichlet condition
// vanish in the right hand side
//rhs
auto f0 = form1( _test=Xh );
f0 = integrate( _range=markedfaces( mesh,"south_domain-1" ), _expr= id( v ) )
+ integrate( _range=markedfaces( mesh,"south_domain-2" ), _expr= id( v ) )
+ integrate( _range=markedfaces( mesh,"south_domain-3" ), _expr= id( v ) );
this->addRhs( { f0, "1" } );
//lhs
auto a0 = form2( _trial=Xh, _test=Xh);
a0 = integrate( markedelements( mesh, "domain-1" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a0 , "1" } );
auto a1 = form2( _trial=Xh, _test=Xh);
a1 = integrate( markedelements( mesh, "domain-2" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a1 , "mu0" } );
auto a2 = form2( _trial=Xh, _test=Xh);
a2 = integrate( markedelements( mesh, "domain-3" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a2 , "mu1" } );
auto a3 = form2( _trial=Xh, _test=Xh);
a3 = integrate( markedelements( mesh, "domain-4" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a3 , "mu2" } );
auto a4 = form2( _trial=Xh, _test=Xh);
a4 = integrate( markedelements( mesh, "domain-5" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a4 , "mu3" } );
auto a5 = form2( _trial=Xh, _test=Xh);
a5 = integrate( markedelements( mesh, "domain-6" ), gradt( u )*trans( grad( v ) ) );
this->addLhs( { a5 , "mu4" } );
auto a6 = form2( _trial=Xh, _test=Xh);
a6 = integrate( markedelements( mesh, "domain-7" ), gradt( u )*trans( grad( v ) ) )
+integrate( markedfaces( mesh, "north_domain-7" ),
-gradt( u )*vf::N()*id( v )
-grad( u )*vf::N()*idt( v )
);
this->addLhs( { a6 , "mu5" } );
auto a7 = form2( _trial=Xh, _test=Xh);
a7 = integrate( markedelements( mesh, "domain-8" ), gradt( u )*trans( grad( v ) ) )
+integrate( markedfaces( mesh, "north_domain-8" ),
-gradt( u )*vf::N()*id( v )
-grad( u )*vf::N()*idt( v )
);
this->addLhs( { a7 , "mu6" } );
auto a8 = form2( _trial=Xh, _test=Xh);
a8 = integrate( markedelements( mesh, "domain-9" ), gradt( u )*trans( grad( v ) ) )
+integrate( markedfaces( mesh, "north_domain-9" ),
-gradt( u )*vf::N()*id( v )
-grad( u )*vf::N()*idt( v )
);
this->addLhs( { a8 , "mu7" } );
auto a9 = form2( _trial=Xh, _test=Xh);
a9 = integrate( markedfaces( mesh, "north_domain-7" ),gamma_dir*idt( u )*id( v )/h() )
+integrate( markedfaces( mesh, "north_domain-8" ),gamma_dir*idt( u )*id( v )/h() )
+integrate( markedfaces( mesh, "north_domain-9" ),gamma_dir*idt( u )*id( v )/h() );
this->addLhs( { a9 , "1" } );
form2( Xh, Xh, M ) = integrate( markedelements( mesh, "domain-1" ), gradt( u )*trans( grad( v ) ) );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-2" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-3" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-4" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-5" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-6" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-7" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-8" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedelements( mesh, "domain-9" ), gradt( u )*trans( grad( v ) ) * mu_min_coeff );
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-7" ),
-gradt( u )*vf::N()*id( v ) * mu_min_coeff
-grad( u )*vf::N()*idt( v ) * mu_min_coeff
);
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-8" ),
-gradt( u )*vf::N()*id( v ) * mu_min_coeff
-grad( u )*vf::N()*idt( v ) * mu_min_coeff
);
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-9" ),
-gradt( u )*vf::N()*id( v ) * mu_min_coeff
-grad( u )*vf::N()*idt( v ) * mu_min_coeff
);
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-7" ),gamma_dir*idt( u )*id( v )/h() );
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-8" ),gamma_dir*idt( u )*id( v )/h() );
form2( Xh, Xh, M ) += integrate( markedfaces( mesh, "north_domain-9" ),gamma_dir*idt( u )*id( v )/h() );
this->addEnergyMatrix( M );
}//initModel()
PreconditionerBlockMS<space_type>::PreconditionerBlockMS(space_ptrtype Xh, // (u)x(p)
ModelProperties model, // model
std::string const& p, // prefix
sparse_matrix_ptrtype AA ) // The matrix
:
M_backend(backend()), // the backend associated to the PC
M_Xh( Xh ),
M_Vh( Xh->template functionSpace<0>() ), // Potential
M_Qh( Xh->template functionSpace<1>() ), // Lagrange
M_Vh_indices( M_Vh->nLocalDofWithGhost() ),
M_Qh_indices( M_Qh->nLocalDofWithGhost() ),
M_uin( M_backend->newVector( M_Vh ) ),
M_uout( M_backend->newVector( M_Vh ) ),
M_pin( M_backend->newVector( M_Qh ) ),
M_pout( M_backend->newVector( M_Qh ) ),
U( M_Xh, "U" ),
M_mass(M_backend->newMatrix(M_Vh,M_Vh)),
M_L(M_backend->newMatrix(M_Qh,M_Qh)),
M_er( 1. ),
M_model( model ),
M_prefix( p ),
M_prefix_11( p+".11" ),
M_prefix_22( p+".22" ),
u(M_Vh, "u"),
ozz(M_Vh, "ozz"),
zoz(M_Vh, "zoz"),
zzo(M_Vh, "zzo"),
M_ozz(M_backend->newVector( M_Vh )),
M_zoz(M_backend->newVector( M_Vh )),
M_zzo(M_backend->newVector( M_Vh )),
X(M_Qh, "X"),
Y(M_Qh, "Y"),
Z(M_Qh, "Z"),
M_X(M_backend->newVector( M_Qh )),
M_Y(M_backend->newVector( M_Qh )),
M_Z(M_backend->newVector( M_Qh )),
phi(M_Qh, "phi")
{
tic();
LOG(INFO) << "[PreconditionerBlockMS] setup starts";
this->setMatrix( AA );
this->setName(M_prefix);
/* Indices are need to extract sub matrix */
std::iota( M_Vh_indices.begin(), M_Vh_indices.end(), 0 );
std::iota( M_Qh_indices.begin(), M_Qh_indices.end(), M_Vh->nLocalDofWithGhost() );
M_11 = AA->createSubMatrix( M_Vh_indices, M_Vh_indices, true, true);
/* Boundary conditions */
BoundaryConditions M_bc = M_model.boundaryConditions();
map_vector_field<FEELPP_DIM,1,2> m_dirichlet_u { M_bc.getVectorFields<FEELPP_DIM> ( "u", "Dirichlet" ) };
map_scalar_field<2> m_dirichlet_p { M_bc.getScalarFields<2> ( "phi", "Dirichlet" ) };
/* Compute the mass matrix (needed in first block, constant) */
auto f2A = form2(_test=M_Vh, _trial=M_Vh, _matrix=M_mass);
auto f1A = form1(_test=M_Vh);
f2A = integrate(_range=elements(M_Vh->mesh()), _expr=inner(idt(u),id(u))); // M
for(auto const & it : m_dirichlet_u )
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_11<<"\n";
f2A += on(_range=markedfaces(M_Vh->mesh(),it.first), _expr=it.second,_rhs=f1A, _element=u, _type="elimination_symmetric");
}
/* Compute the L (= er * grad grad) matrix (the second block) */
auto f2L = form2(_test=M_Qh,_trial=M_Qh, _matrix=M_L);
for(auto it : M_model.materials() )
{
f2L += integrate(_range=markedelements(M_Qh->mesh(),marker(it)), _expr=M_er*inner(gradt(phi), grad(phi)));
}
auto f1LQ = form1(_test=M_Qh);
for(auto const & it : m_dirichlet_p)
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_22<<"\n";
f2L += on(_range=markedfaces(M_Qh->mesh(),it.first),_element=phi, _expr=it.second, _rhs=f1LQ, _type="elimination_symmetric");
}
if(soption(_name="pc-type", _prefix=M_prefix_11) == "ams")
#if FEELPP_DIM == 3
{
M_grad = Grad( _domainSpace=M_Qh, _imageSpace=M_Vh);
// This preconditioner is linked to that backend : the backend will
// automatically use the preconditioner.
auto prec = preconditioner(_pc=pcTypeConvertStrToEnum(soption(M_prefix_11+".pc-type")),
_backend=backend(_name=M_prefix_11),
_prefix=M_prefix_11,
_matrix=M_11
);
prec->setMatrix(M_11);
prec->attachAuxiliarySparseMatrix("G",M_grad.matPtr());
if(boption(M_prefix_11+".useEdge"))
{
LOG(INFO) << "[ AMS ] : using SetConstantEdgeVector \n";
ozz.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(1),cst(0),cst(0)));
zoz.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(0),cst(1),cst(0)));
zzo.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(0),cst(0),cst(1)));
*M_ozz = ozz; M_ozz->close();
*M_zoz = zoz; M_zoz->close();
*M_zzo = zzo; M_zzo->close();
prec->attachAuxiliaryVector("Px",M_ozz);
prec->attachAuxiliaryVector("Py",M_zoz);
prec->attachAuxiliaryVector("Pz",M_zzo);
}
else
{
LOG(INFO) << "[ AMS ] : using SetCoordinates \n";
X.on(_range=elements(M_Vh->mesh()),_expr=Px());
Y.on(_range=elements(M_Vh->mesh()),_expr=Py());
Z.on(_range=elements(M_Vh->mesh()),_expr=Pz());
*M_X = X; M_X->close();
*M_Y = Y; M_Y->close();
*M_Z = Z; M_Z->close();
prec->attachAuxiliaryVector("X",M_X);
prec->attachAuxiliaryVector("Y",M_Y);
prec->attachAuxiliaryVector("Z",M_Z);
}
}
#else
std::cerr << "ams preconditioner is not interfaced in two dimensions\n";
#endif
toc( "[PreconditionerBlockMS] setup done ", FLAGS_v > 0 );
}
