bool EquationSystems::compare (const EquationSystems& other_es,
const Real threshold,
const bool verbose) const
{
// safety check, whether we handle at least the same number
// of systems
std::vector<bool> os_result;
if (this->n_systems() != other_es.n_systems())
{
if (verbose)
{
libMesh::out << " Fatal difference. This system handles "
<< this->n_systems() << " systems," << std::endl
<< " while the other system handles "
<< other_es.n_systems()
<< " systems." << std::endl
<< " Aborting comparison." << std::endl;
}
return false;
}
else
{
// start comparing each system
const_system_iterator pos = _systems.begin();
const const_system_iterator end = _systems.end();
for (; pos != end; ++pos)
{
const std::string& sys_name = pos->first;
const System& system = *(pos->second);
// get the other system
const System& other_system = other_es.get_system (sys_name);
os_result.push_back (system.compare (other_system, threshold, verbose));
}
}
// sum up the results
if (os_result.size()==0)
return true;
else
{
bool os_identical;
unsigned int n = 0;
do
{
os_identical = os_result[n];
n++;
}
while (os_identical && n<os_result.size());
return os_identical;
}
}
/*
* FIXME: This is known to write nonsense on AMR meshes
* and it strips the imaginary parts of complex Numbers
*/
void VTKIO::system_vectors_to_vtk(const EquationSystems& es, vtkUnstructuredGrid*& grid)
{
if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
{
std::map<std::string, std::vector<Number> > vecs;
for (unsigned int i=0; i<es.n_systems(); ++i)
{
const System& sys = es.get_system(i);
System::const_vectors_iterator v_end = sys.vectors_end();
System::const_vectors_iterator it = sys.vectors_begin();
for (; it!= v_end; ++it)
{
// for all vectors on this system
std::vector<Number> values;
// libMesh::out<<"it "<<it->first<<std::endl;
it->second->localize_to_one(values, 0);
// libMesh::out<<"finish localize"<<std::endl;
vecs[it->first] = values;
}
}
std::map<std::string, std::vector<Number> >::iterator it = vecs.begin();
for (; it!=vecs.end(); ++it)
{
vtkDoubleArray *data = vtkDoubleArray::New();
data->SetName(it->first.c_str());
libmesh_assert_equal_to (it->second.size(), es.get_mesh().n_nodes());
data->SetNumberOfValues(it->second.size());
for (unsigned int i=0; i<it->second.size(); ++i)
{
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
libmesh_do_once (libMesh::err << "Only writing the real part for complex numbers!\n"
<< "if you need this support contact " << LIBMESH_PACKAGE_BUGREPORT
<< std::endl);
data->SetValue(i, it->second[i].real());
#else
data->SetValue(i, it->second[i]);
#endif
}
grid->GetPointData()->AddArray(data);
data->Delete();
}
}
}
/**
* FIXME: This is a default implementation - derived classes should
* reimplement it for efficiency.
*/
void ErrorEstimator::estimate_errors(const EquationSystems & equation_systems,
ErrorMap & errors_per_cell,
const std::map<const System *, const NumericVector<Number> *> * solution_vectors,
bool estimate_parent_error)
{
SystemNorm old_error_norm = this->error_norm;
// Find the requested error values from each system
for (unsigned int s = 0; s != equation_systems.n_systems(); ++s)
{
const System & sys = equation_systems.get_system(s);
unsigned int n_vars = sys.n_vars();
for (unsigned int v = 0; v != n_vars; ++v)
{
// Only fill in ErrorVectors the user asks for
if (errors_per_cell.find(std::make_pair(&sys, v)) ==
errors_per_cell.end())
continue;
// Calculate error in only one variable
std::vector<Real> weights(n_vars, 0.0);
weights[v] = 1.0;
this->error_norm =
SystemNorm(std::vector<FEMNormType>(n_vars, old_error_norm.type(v)),
weights);
const NumericVector<Number> * solution_vector = nullptr;
if (solution_vectors &&
solution_vectors->find(&sys) != solution_vectors->end())
solution_vector = solution_vectors->find(&sys)->second;
this->estimate_error
(sys, *errors_per_cell[std::make_pair(&sys, v)],
solution_vector, estimate_parent_error);
}
}
// Restore our old state before returning
this->error_norm = old_error_norm;
}
void ErrorEstimator::estimate_errors(const EquationSystems & equation_systems,
ErrorVector & error_per_cell,
const std::map<const System *, SystemNorm> & error_norms,
const std::map<const System *, const NumericVector<Number> *> * solution_vectors,
bool estimate_parent_error)
{
SystemNorm old_error_norm = this->error_norm;
// Sum the error values from each system
for (unsigned int s = 0; s != equation_systems.n_systems(); ++s)
{
ErrorVector system_error_per_cell;
const System & sys = equation_systems.get_system(s);
if (error_norms.find(&sys) == error_norms.end())
this->error_norm = old_error_norm;
else
this->error_norm = error_norms.find(&sys)->second;
const NumericVector<Number> * solution_vector = nullptr;
if (solution_vectors &&
solution_vectors->find(&sys) != solution_vectors->end())
solution_vector = solution_vectors->find(&sys)->second;
this->estimate_error(sys, system_error_per_cell,
solution_vector, estimate_parent_error);
if (s)
{
libmesh_assert_equal_to (error_per_cell.size(), system_error_per_cell.size());
for (std::size_t i=0; i != error_per_cell.size(); ++i)
error_per_cell[i] += system_error_per_cell[i];
}
else
error_per_cell = system_error_per_cell;
}
// Restore our old state before returning
this->error_norm = old_error_norm;
}
// The matrix assembly function to be called at each time step to
// prepare for the linear solve.
void assemble_solid (EquationSystems& es,
const std::string& system_name)
{
//es.print_info();
#if LOG_ASSEMBLE_PERFORMANCE
PerfLog perf_log("Assemble");
perf_log.push("assemble stiffness");
#endif
// Get a reference to the auxiliary system
//TransientExplicitSystem& aux_system = es.get_system<TransientExplicitSystem>("Newton-update");
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert (system_name == "Newton-update");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the Stokes system object.
TransientLinearImplicitSystem & newton_update =
es.get_system<TransientLinearImplicitSystem> ("Newton-update");
// New
TransientLinearImplicitSystem & last_non_linear_soln =
es.get_system<TransientLinearImplicitSystem> ("Last-non-linear-soln");
TransientLinearImplicitSystem & fluid_system_vel =
es.get_system<TransientLinearImplicitSystem> ("fluid-system-vel");
#if VELOCITY
TransientLinearImplicitSystem& velocity = es.get_system<TransientLinearImplicitSystem>("velocity-system");
#endif
#if UN_MINUS_ONE
TransientLinearImplicitSystem & unm1 =
es.get_system<TransientLinearImplicitSystem> ("unm1-system");
#endif
test(62);
const System & ref_sys = es.get_system("Reference-Configuration");
test(63);
// Numeric ids corresponding to each variable in the system
const unsigned int u_var = last_non_linear_soln .variable_number ("u");
const unsigned int v_var = last_non_linear_soln .variable_number ("v");
const unsigned int w_var = last_non_linear_soln .variable_number ("w");
#if INCOMPRESSIBLE
const unsigned int p_var = last_non_linear_soln .variable_number ("p");
#endif
#if FLUID_P_CONST
const unsigned int m_var = fluid_system_vel.variable_number ("fluid_M");
std::vector<unsigned int> dof_indices_m;
#endif
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v".
FEType fe_vel_type = last_non_linear_soln.variable_type(u_var);
test(64);
#if INCOMPRESSIBLE
// Get the Finite Element type for "p".
FEType fe_pres_type = last_non_linear_soln .variable_type(p_var);
#endif
// Build a Finite Element object of the specified type for
// the velocity variables.
AutoPtr<FEBase> fe_vel (FEBase::build(dim, fe_vel_type));
#if INCOMPRESSIBLE
// Build a Finite Element object of the specified type for
// the pressure variables.
AutoPtr<FEBase> fe_pres (FEBase::build(dim, fe_pres_type));
#endif
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_vel_type.default_quadrature_order());
// Tell the finite element objects to use our quadrature rule.
fe_vel->attach_quadrature_rule (&qrule);
test(65);
// AutoPtr<QBase> qrule2(fe_vel_type.default_quadrature_rule(dim));
// fe_vel->attach_quadrature_rule (qrule2.get());
#if INCOMPRESSIBLE
fe_pres->attach_quadrature_rule (&qrule);
#endif
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe_vel->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe_vel->get_phi();
// The element shape function gradients for the velocity
// variables evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> >& dphi = fe_vel->get_dphi();
test(66);
#if INCOMPRESSIBLE
// The element shape functions for the pressure variable
// evaluated at the quadrature points.
const std::vector<std::vector<Real> >& psi = fe_pres->get_phi();
#endif
const std::vector<Point>& coords = fe_vel->get_xyz();
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
// in future examples.
const DofMap & dof_map = last_non_linear_soln .get_dof_map();
#if FLUID_P_CONST
const DofMap & dof_map_fluid = fluid_system_vel .get_dof_map();
#endif
// K will be the jacobian
// F will be the Residual
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke), Kuw(Ke),
Kvu(Ke), Kvv(Ke), Kvw(Ke),
Kwu(Ke), Kwv(Ke), Kww(Ke);
#if INCOMPRESSIBLE
DenseSubMatrix<Number> Kup(Ke),Kvp(Ke),Kwp(Ke), Kpu(Ke), Kpv(Ke), Kpw(Ke), Kpp(Ke);
#endif;
DenseSubVector<Number>
Fu(Fe), Fv(Fe), Fw(Fe);
#if INCOMPRESSIBLE
DenseSubVector<Number> Fp(Fe);
#endif
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<unsigned int> dof_indices;
std::vector<unsigned int> dof_indices_u;
std::vector<unsigned int> dof_indices_v;
std::vector<unsigned int> dof_indices_w;
#if INCOMPRESSIBLE
std::vector<unsigned int> dof_indices_p;
#endif
#if INERTIA
test(67);
const unsigned int a_var = last_non_linear_soln.variable_number ("a");
const unsigned int b_var = last_non_linear_soln.variable_number ("b");
const unsigned int c_var = last_non_linear_soln.variable_number ("c");
//B block
DenseSubMatrix<Number>
Kua(Ke), Kub(Ke), Kuc(Ke),
Kva(Ke), Kvb(Ke), Kvc(Ke),
Kwa(Ke), Kwb(Ke), Kwc(Ke);
//C block
DenseSubMatrix<Number>
Kau(Ke), Kav(Ke), Kaw(Ke),
Kbu(Ke), Kbv(Ke), Kbw(Ke),
Kcu(Ke), Kcv(Ke), Kcw(Ke);
//D block
DenseSubMatrix<Number>
Kaa(Ke), Kab(Ke), Kac(Ke),
Kba(Ke), Kbb(Ke), Kbc(Ke),
Kca(Ke), Kcb(Ke), Kcc(Ke);
DenseSubVector<Number>
Fa(Fe), Fb(Fe), Fc(Fe);
std::vector<unsigned int> dof_indices_a;
std::vector<unsigned int> dof_indices_b;
std::vector<unsigned int> dof_indices_c;
test(68);
#endif
DenseMatrix<Real> stiff;
DenseVector<Real> res;
VectorValue<Gradient> grad_u_mat;
VectorValue<Gradient> grad_u_mat_old;
const Real dt = es.parameters.get<Real>("dt");
const Real progress = es.parameters.get<Real>("progress");
#if PORO
DenseVector<Real> p_stiff;
DenseVector<Real> p_res;
PoroelasticConfig material(dphi,psi);
#endif
// Just calculate jacobian contribution when we need to
material.calculate_linearized_stiffness = true;
MeshBase::const_element_iterator el = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el = mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
test(69);
const Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_w, w_var);
#if INCOMPRESSIBLE
dof_map.dof_indices (elem, dof_indices_p, p_var);
#endif
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
const unsigned int n_w_dofs = dof_indices_w.size();
#if INCOMPRESSIBLE
const unsigned int n_p_dofs = dof_indices_p.size();
#endif
#if FLUID_P_CONST
dof_map_fluid.dof_indices (elem, dof_indices_m, m_var);
#endif
//elem->print_info();
fe_vel->reinit (elem);
#if INCOMPRESSIBLE
fe_pres->reinit (elem);
#endif
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kuw.reposition (u_var*n_u_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kup.reposition (u_var*n_u_dofs, p_var*n_u_dofs, n_u_dofs, n_p_dofs);
#endif
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvw.reposition (v_var*n_v_dofs, w_var*n_v_dofs, n_v_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kvp.reposition (v_var*n_v_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
#endif
Kwu.reposition (w_var*n_w_dofs, u_var*n_w_dofs, n_w_dofs, n_u_dofs);
Kwv.reposition (w_var*n_w_dofs, v_var*n_w_dofs, n_w_dofs, n_v_dofs);
Kww.reposition (w_var*n_w_dofs, w_var*n_w_dofs, n_w_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kwp.reposition (w_var*n_w_dofs, p_var*n_w_dofs, n_w_dofs, n_p_dofs);
Kpu.reposition (p_var*n_u_dofs, u_var*n_u_dofs, n_p_dofs, n_u_dofs);
Kpv.reposition (p_var*n_u_dofs, v_var*n_u_dofs, n_p_dofs, n_v_dofs);
Kpw.reposition (p_var*n_u_dofs, w_var*n_u_dofs, n_p_dofs, n_w_dofs);
Kpp.reposition (p_var*n_u_dofs, p_var*n_u_dofs, n_p_dofs, n_p_dofs);
#endif
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fw.reposition (w_var*n_u_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Fp.reposition (p_var*n_u_dofs, n_p_dofs);
#endif
#if INERTIA
//B block
Kua.reposition (u_var*n_u_dofs, 3*n_u_dofs + n_p_dofs, n_u_dofs, n_u_dofs);
Kub.reposition (u_var*n_u_dofs, 4*n_u_dofs + n_p_dofs, n_u_dofs, n_v_dofs);
Kuc.reposition (u_var*n_u_dofs, 5*n_u_dofs + n_p_dofs, n_u_dofs, n_w_dofs);
Kva.reposition (v_var*n_v_dofs, 3*n_u_dofs + n_p_dofs, n_v_dofs, n_u_dofs);
Kvb.reposition (v_var*n_v_dofs, 4*n_u_dofs + n_p_dofs, n_v_dofs, n_v_dofs);
Kvc.reposition (v_var*n_v_dofs, 5*n_u_dofs + n_p_dofs, n_v_dofs, n_w_dofs);
Kwa.reposition (w_var*n_w_dofs, 3*n_u_dofs + n_p_dofs, n_w_dofs, n_u_dofs);
Kwb.reposition (w_var*n_w_dofs, 4*n_u_dofs + n_p_dofs, n_w_dofs, n_v_dofs);
Kwc.reposition (w_var*n_w_dofs, 5*n_u_dofs + n_p_dofs, n_w_dofs, n_w_dofs);
test(701);
//C block
Kau.reposition (3*n_u_dofs + n_p_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kav.reposition (3*n_u_dofs + n_p_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kaw.reposition (3*n_u_dofs + n_p_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
Kbu.reposition (4*n_u_dofs + n_p_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kbv.reposition (4*n_u_dofs + n_p_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kbw.reposition (4*n_u_dofs + n_p_dofs, w_var*n_v_dofs, n_v_dofs, n_w_dofs);
Kcu.reposition (5*n_u_dofs + n_p_dofs, u_var*n_w_dofs, n_w_dofs, n_u_dofs);
Kcv.reposition (5*n_u_dofs + n_p_dofs, v_var*n_w_dofs, n_w_dofs, n_v_dofs);
Kcw.reposition (5*n_u_dofs + n_p_dofs, w_var*n_w_dofs, n_w_dofs, n_w_dofs);
//D block
Kaa.reposition (3*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_u_dofs, n_u_dofs);
Kab.reposition (3*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_u_dofs, n_v_dofs);
Kac.reposition (3*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_u_dofs, n_w_dofs);
Kba.reposition (4*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_v_dofs, n_u_dofs);
Kbb.reposition (4*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_v_dofs, n_v_dofs);
Kbc.reposition (4*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_v_dofs, n_w_dofs);
Kca.reposition (5*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_w_dofs, n_u_dofs);
Kcb.reposition (5*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_w_dofs, n_v_dofs);
Kcc.reposition (5*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_w_dofs, n_w_dofs);
Fa.reposition (3*n_u_dofs + n_p_dofs, n_u_dofs);
Fb.reposition (4*n_u_dofs + n_p_dofs, n_v_dofs);
Fc.reposition (5*n_u_dofs + n_p_dofs, n_w_dofs);
dof_map.dof_indices (elem, dof_indices_a, a_var);
dof_map.dof_indices (elem, dof_indices_b, b_var);
dof_map.dof_indices (elem, dof_indices_c, c_var);
test(71);
#endif
System& aux_system = es.get_system<System>("Reference-Configuration");
std::vector<unsigned int> undefo_index;
std::vector<unsigned int> vel_index;
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
Point rX;
for (unsigned int l=0; l<n_u_dofs; l++)
{
rX(0) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_u[l]);
rX(1) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_v[l]);
rX(2) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_w[l]);
}
#if INERTIA || DT
test(72);
Real rho_s=15;
Point current_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
current_x(0) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_u[l]);
current_x(1) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_v[l]);
current_x(2) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_w[l]);
}
Point old_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
old_x(0) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_u[l]);
old_x(1) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_v[l]);
old_x(2) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_w[l]);
}
#if INERTIA
Point old_vel;
for (unsigned int l=0; l<n_u_dofs; l++)
{
old_vel(0) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_a[l]);
old_vel(1) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_b[l]);
old_vel(2) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_c[l]);
}
Point current_vel;
for (unsigned int l=0; l<n_u_dofs; l++)
{
current_vel(0) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_a[l]);
current_vel(1) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_b[l]);
current_vel(2) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_c[l]);
}
#endif
#if UN_MINUS_ONE
Point unm1_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
unm1_x(0) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_u[l]);
unm1_x(1) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_v[l]);
unm1_x(2) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_w[l]);
}
#endif
Point value_acc;
Point value_acc_alt;
#if DT
for (unsigned int d = 0; d < dim; ++d) {
value_acc_alt(d) = (rho_s)*( ((current_x(d)-rX(d))-(old_x(d)-rX(d)))-((old_x(d)-rX(d))- (unm1_x(d)-rX(d))) );
value_acc(d) = (rho_s)*((current_x(d))-2*(old_x(d))+ (unm1_x(d)));
value_acc(d) = (rho_s)*((current_x(d))-(old_x(d)));
}
#endif
Point res_1;
Point res_2;
#if INERTIA
for (unsigned int d = 0; d < dim; ++d) {
res_1(d) = (rho_s)*((current_vel(d))-(old_vel(d)));
res_2(d) = current_x(d)-dt*current_vel(d)-old_x(d);
}
/*
std::cout<<" current_vel "<<current_vel<<std::endl;
std::cout<<" res_1 "<<res_1<<std::endl;
std::cout<<" res_2 "<<res_2<<std::endl;
*/
#endif
test(73);
#endif
Number p_solid = 0.;
#if MOVING_MESH
grad_u_mat(0) = grad_u_mat(1) = grad_u_mat(2) = 0;
for (unsigned int d = 0; d < dim; ++d) {
std::vector<Number> u_undefo;
//Fills the vector di with the global degree of freedom indices for the element. :dof_indicies
aux_system.get_dof_map().dof_indices(elem, undefo_index,d);
aux_system.current_local_solution->get(undefo_index, u_undefo);
for (unsigned int l = 0; l != n_u_dofs; l++)
grad_u_mat(d).add_scaled(dphi[l][qp], u_undefo[l]);
}
#endif
//#include "fixed_mesh_in_solid_assemble_code.txt"
#if INCOMPRESSIBLE
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_solid += psi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_p[l]);
}
#endif
#if INCOMPRESSIBLE
Real m=0;
Real p_fluid=0;
#if FLUID_VEL
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_fluid += psi[l][qp]*fluid_system_vel.current_local_solution->el(dof_indices_p[l]);
}
//As outlined in Chappel p=(p_curr-p_old)/2
Real p_fluid_old=0;
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_fluid_old += psi[l][qp]*fluid_system_vel.old_local_solution->el(dof_indices_p[l]);
}
p_fluid=0.5*p_fluid+0.5*p_fluid_old;
Real m_old=0;
#if FLUID_P_CONST
for (unsigned int l=0; l<n_p_dofs; l++)
{
m += psi[l][qp]*fluid_system_vel.current_local_solution->el(dof_indices_m[l]);
}
for (unsigned int l=0; l<n_p_dofs; l++)
{
m_old += psi[l][qp]*fluid_system_vel.old_local_solution->el(dof_indices_m[l]);
}
#endif
material.init_for_qp(grad_u_mat, p_solid, qp, 1.0*m+0.0*m_old, p_fluid);
#endif
#endif //#if INCOMPRESSIBLE
#if INCOMPRESSIBLE && ! PORO
material.init_for_qp(grad_u_mat, p_solid, qp);
#endif
for (unsigned int i=0; i<n_u_dofs; i++)
{
res.resize(dim);
material.get_residual(res, i);
res.scale(JxW[qp]);
#if INERTIA
res.scale(dt);
#endif
#if DT
res.scale(dt);
#endif
//std::cout<< "res "<<res<<std::endl;
Fu(i) += res(0);
Fv(i) += res(1) ;
Fw(i) += res(2);
#if GRAVITY
Real grav=0.0;
Fu(i) += progress*grav*JxW[qp]*phi[i][qp];
#endif
#if INERTIA
Fu(i) += JxW[qp]*phi[i][qp]*res_1(0);
Fv(i) += JxW[qp]*phi[i][qp]*res_1(1);
Fw(i) += JxW[qp]*phi[i][qp]*res_1(2);
Fa(i) += JxW[qp]*phi[i][qp]*res_2(0);
Fb(i) += JxW[qp]*phi[i][qp]*res_2(1);
Fc(i) += JxW[qp]*phi[i][qp]*res_2(2);
#endif
// Matrix contributions for the uu and vv couplings.
for (unsigned int j=0; j<n_u_dofs; j++)
{
material.get_linearized_stiffness(stiff, i, j);
stiff.scale(JxW[qp]);
#if DT
res.scale(dt);
#endif
#if INERTIA
stiff.scale(dt);
Kua(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kvb(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kwc(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kau(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kbv(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kcw(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kaa(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
Kbb(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
Kcc(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
#endif
Kuu(i,j)+= stiff(u_var, u_var);
Kuv(i,j)+= stiff(u_var, v_var);
Kuw(i,j)+= stiff(u_var, w_var);
Kvu(i,j)+= stiff(v_var, u_var);
Kvv(i,j)+= stiff(v_var, v_var);
Kvw(i,j)+= stiff(v_var, w_var);
Kwu(i,j)+= stiff(w_var, u_var);
Kwv(i,j)+= stiff(w_var, v_var);
Kww(i,j)+= stiff(w_var, w_var);
#if GRAVITY
Kuu(i,j)+= 1*JxW[qp]*phi[i][qp]*phi[j][qp];
#endif
}
}
#if INCOMPRESSIBLE && FLUID_P_CONST
for (unsigned int i = 0; i < n_p_dofs; i++) {
material.get_p_residual(p_res, i);
p_res.scale(JxW[qp]);
Fp(i) += p_res(0);
}
for (unsigned int i = 0; i < n_u_dofs; i++) {
for (unsigned int j = 0; j < n_p_dofs; j++) {
material.get_linearized_uvw_p_stiffness(p_stiff, i, j);
p_stiff.scale(JxW[qp]);
Kup(i, j) += p_stiff(0);
Kvp(i, j) += p_stiff(1);
Kwp(i, j) += p_stiff(2);
}
}
for (unsigned int i = 0; i < n_p_dofs; i++) {
for (unsigned int j = 0; j < n_u_dofs; j++) {
material.get_linearized_p_uvw_stiffness(p_stiff, i, j);
p_stiff.scale(JxW[qp]);
Kpu(i, j) += p_stiff(0);
Kpv(i, j) += p_stiff(1);
Kpw(i, j) += p_stiff(2);
}
}
#endif
#if CHAP && ! FLUID_P_CONST
for (unsigned int i = 0; i < n_p_dofs; i++) {
Fp(i) += 0*JxW[qp]*psi[i][qp];
}
for (unsigned int i = 0; i < n_p_dofs; i++) {
for (unsigned int j = 0; j < n_p_dofs; j++) {
Kpp(i, j) += 1*JxW[qp]*psi[i][qp]*psi[j][qp];
}
}
#endif
}//end of qp loop
newton_update.matrix->add_matrix (Ke, dof_indices);
newton_update.rhs->add_vector (Fe, dof_indices);
} // end of element loop
// dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
newton_update.rhs->close();
newton_update.matrix->close();
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.pop("assemble stiffness");
#endif
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.push("assemble bcs");
#endif
//Assemble the boundary conditions.
assemble_bcs(es);
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.pop("assemble bcs");
#endif
std::ofstream lhs_out("lhsoutS3.dat");
Ke.print(lhs_out);
lhs_out.close();
return;
}