void
MAST::ComplexAssemblyBase::
residual_and_jacobian_blocked (const libMesh::NumericVector<Real>& X,
libMesh::NumericVector<Real>& R,
libMesh::SparseMatrix<Real>& J,
MAST::Parameter* p) {
libmesh_assert(_system);
libmesh_assert(_discipline);
libmesh_assert(_elem_ops);
START_LOG("residual_and_jacobian()", "ComplexSolve");
MAST::NonlinearSystem& nonlin_sys = _system->system();
R.zero();
J.zero();
// iterate over each element, initialize it and get the relevant
// analysis quantities
RealVectorX
sol;
ComplexVectorX
delta_sol,
vec;
ComplexMatrixX
mat,
dummy;
// get the petsc vector and matrix objects
Mat
jac_bmat = dynamic_cast<libMesh::PetscMatrix<Real>&>(J).mat();
PetscInt ierr;
std::vector<libMesh::dof_id_type> dof_indices;
const libMesh::DofMap& dof_map = nonlin_sys.get_dof_map();
const std::vector<libMesh::dof_id_type>&
send_list = nonlin_sys.get_dof_map().get_send_list();
std::unique_ptr<libMesh::NumericVector<Real> >
localized_base_solution,
localized_complex_sol(libMesh::NumericVector<Real>::build(nonlin_sys.comm()).release());
// prepare a send list for localization of the complex solution
std::vector<libMesh::dof_id_type>
complex_send_list(2*send_list.size());
for (unsigned int i=0; i<send_list.size(); i++) {
complex_send_list[2*i ] = 2*send_list[i];
complex_send_list[2*i+1] = 2*send_list[i]+1;
}
localized_complex_sol->init(2*nonlin_sys.n_dofs(),
2*nonlin_sys.n_local_dofs(),
complex_send_list,
false,
libMesh::GHOSTED);
X.localize(*localized_complex_sol, complex_send_list);
// localize the base solution, if it was provided
if (_base_sol)
localized_base_solution.reset(build_localized_vector(nonlin_sys,
*_base_sol).release());
// if a solution function is attached, initialize it
//if (_sol_function)
// _sol_function->init( X);
libMesh::MeshBase::const_element_iterator el =
nonlin_sys.get_mesh().active_local_elements_begin();
const libMesh::MeshBase::const_element_iterator end_el =
nonlin_sys.get_mesh().active_local_elements_end();
MAST::ComplexAssemblyElemOperations&
ops = dynamic_cast<MAST::ComplexAssemblyElemOperations&>(*_elem_ops);
for ( ; el != end_el; ++el) {
const libMesh::Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
ops.init(*elem);
// get the solution
unsigned int ndofs = (unsigned int)dof_indices.size();
sol.setZero(ndofs);
delta_sol.setZero(ndofs);
vec.setZero(ndofs);
mat.setZero(ndofs, ndofs);
// first set the velocity to be zero
ops.set_elem_velocity(sol);
// next, set the base solution, if provided
if (_base_sol)
for (unsigned int i=0; i<dof_indices.size(); i++)
sol(i) = (*localized_base_solution)(dof_indices[i]);
ops.set_elem_solution(sol);
// set the value of the small-disturbance solution
for (unsigned int i=0; i<dof_indices.size(); i++) {
// get the complex block for this dof
delta_sol(i) = Complex((*localized_complex_sol)(2*dof_indices[i]),
(*localized_complex_sol)(2*dof_indices[i]+1));
}
ops.set_elem_complex_solution(delta_sol);
// if (_sol_function)
// physics_elem->attach_active_solution_function(*_sol_function);
// perform the element level calculations
ops.elem_calculations(true, vec, mat);
// if sensitivity was requested, then ask the element for sensitivity
// of the residual
if (p) {
// set the sensitivity of complex sol to zero
delta_sol.setZero();
ops.set_elem_complex_solution_sensitivity(delta_sol);
vec.setZero();
ops.elem_sensitivity_calculations(*p, vec);
}
ops.clear_elem();
//physics_elem->detach_active_solution_function();
// extract the real or the imaginary part of the matrix/vector
// The complex system of equations
// (J_R + i J_I) (x_R + i x_I) + (r_R + i r_I) = 0
// is rewritten as
// [ J_R -J_I] {x_R} + {r_R} = {0}
// [ J_I J_R] {x_I} + {r_I} = {0}
//
DenseRealVector v_R, v_I;
DenseRealMatrix m_R, m_I1, m_I2;
std::vector<Real> vals(4);
// copy the real part of the residual and Jacobian
MAST::copy( m_R, mat.real());
MAST::copy(m_I1, mat.imag()); m_I1 *= -1.; // this is the -J_I component
MAST::copy(m_I2, mat.imag()); // this is the J_I component
MAST::copy( v_R, vec.real());
MAST::copy( v_I, vec.imag());
dof_map.constrain_element_matrix(m_R, dof_indices);
dof_map.constrain_element_matrix(m_I1, dof_indices);
dof_map.constrain_element_matrix(m_I2, dof_indices);
dof_map.constrain_element_vector(v_R, dof_indices);
dof_map.constrain_element_vector(v_I, dof_indices);
for (unsigned int i=0; i<dof_indices.size(); i++) {
R.add(2*dof_indices[i], v_R(i));
R.add(2*dof_indices[i]+1, v_I(i));
for (unsigned int j=0; j<dof_indices.size(); j++) {
vals[0] = m_R (i,j);
vals[1] = m_I1(i,j);
vals[2] = m_I2(i,j);
vals[3] = m_R (i,j);
ierr = MatSetValuesBlocked(jac_bmat,
1, (PetscInt*)&dof_indices[i],
1, (PetscInt*)&dof_indices[j],
&vals[0],
ADD_VALUES);
}
}
}
// if a solution function is attached, clear it
//if (_sol_function)
// _sol_function->clear();
R.close();
J.close();
libMesh::out << "R: " << R.l2_norm() << std::endl;
STOP_LOG("residual_and_jacobian()", "ComplexSolve");
}
bool
MAST::NonlinearImplicitAssembly::
sensitivity_assemble (const libMesh::ParameterVector& parameters,
const unsigned int i,
libMesh::NumericVector<Real>& sensitivity_rhs) {
libMesh::NonlinearImplicitSystem& nonlin_sys =
dynamic_cast<libMesh::NonlinearImplicitSystem&>(_system->system());
sensitivity_rhs.zero();
// iterate over each element, initialize it and get the relevant
// analysis quantities
RealVectorX vec, sol;
RealMatrixX mat;
std::vector<libMesh::dof_id_type> dof_indices;
const libMesh::DofMap& dof_map = nonlin_sys.get_dof_map();
std::auto_ptr<MAST::ElementBase> physics_elem;
std::auto_ptr<libMesh::NumericVector<Real> > localized_solution;
localized_solution.reset(_build_localized_vector(nonlin_sys,
*nonlin_sys.solution).release());
// if a solution function is attached, initialize it
if (_sol_function)
_sol_function->init_for_system_and_solution(*_system, *nonlin_sys.solution);
libMesh::MeshBase::const_element_iterator el =
nonlin_sys.get_mesh().active_local_elements_begin();
const libMesh::MeshBase::const_element_iterator end_el =
nonlin_sys.get_mesh().active_local_elements_end();
for ( ; el != end_el; ++el) {
const libMesh::Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
physics_elem.reset(_build_elem(*elem).release());
// get the solution
unsigned int ndofs = (unsigned int)dof_indices.size();
sol.setZero(ndofs);
vec.setZero(ndofs);
mat.setZero(ndofs, ndofs);
for (unsigned int i=0; i<dof_indices.size(); i++)
sol(i) = (*localized_solution)(dof_indices[i]);
physics_elem->sensitivity_param = _discipline->get_parameter(parameters[i]);
physics_elem->set_solution(sol);
if (_sol_function)
physics_elem->attach_active_solution_function(*_sol_function);
// perform the element level calculations
_elem_sensitivity_calculations(*physics_elem, vec);
physics_elem->detach_active_solution_function();
// copy to the libMesh matrix for further processing
DenseRealVector v;
MAST::copy(v, vec);
// constrain the quantities to account for hanging dofs,
// Dirichlet constraints, etc.
nonlin_sys.get_dof_map().constrain_element_vector(v, dof_indices);
// add to the global matrices
sensitivity_rhs.add_vector(v, dof_indices);
}
// if a solution function is attached, initialize it
if (_sol_function)
_sol_function->clear();
sensitivity_rhs.close();
return true;
}
void
MAST::ComplexAssemblyBase::
residual_and_jacobian_field_split (const libMesh::NumericVector<Real>& X_R,
const libMesh::NumericVector<Real>& X_I,
libMesh::NumericVector<Real>& R_R,
libMesh::NumericVector<Real>& R_I,
libMesh::SparseMatrix<Real>& J_R,
libMesh::SparseMatrix<Real>& J_I) {
libmesh_assert(_system);
libmesh_assert(_discipline);
libmesh_assert(_elem_ops);
MAST::NonlinearSystem& nonlin_sys = _system->system();
R_R.zero();
R_I.zero();
J_R.zero();
J_I.zero();
// iterate over each element, initialize it and get the relevant
// analysis quantities
RealVectorX sol, vec_re;
RealMatrixX mat_re;
ComplexVectorX delta_sol, vec;
ComplexMatrixX mat;
std::vector<libMesh::dof_id_type> dof_indices;
const libMesh::DofMap& dof_map = _system->system().get_dof_map();
std::unique_ptr<libMesh::NumericVector<Real> >
localized_base_solution,
localized_real_solution,
localized_imag_solution;
// localize the base solution, if it was provided
if (_base_sol)
localized_base_solution.reset(build_localized_vector(nonlin_sys,
*_base_sol).release());
// localize sol to real vector
localized_real_solution.reset(build_localized_vector(nonlin_sys,
X_R).release());
// localize sol to imag vector
localized_imag_solution.reset(build_localized_vector(nonlin_sys,
X_I).release());
// if a solution function is attached, initialize it
//if (_sol_function)
// _sol_function->init( X);
libMesh::MeshBase::const_element_iterator el =
nonlin_sys.get_mesh().active_local_elements_begin();
const libMesh::MeshBase::const_element_iterator end_el =
nonlin_sys.get_mesh().active_local_elements_end();
MAST::ComplexAssemblyElemOperations&
ops = dynamic_cast<MAST::ComplexAssemblyElemOperations&>(*_elem_ops);
for ( ; el != end_el; ++el) {
const libMesh::Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
ops.init(*elem);
// get the solution
unsigned int ndofs = (unsigned int)dof_indices.size();
sol.setZero(ndofs);
delta_sol.setZero(ndofs);
vec.setZero(ndofs);
mat.setZero(ndofs, ndofs);
// first set the velocity to be zero
ops.set_elem_velocity(sol);
// next, set the base solution, if provided
if (_base_sol)
for (unsigned int i=0; i<dof_indices.size(); i++)
sol(i) = (*localized_base_solution)(dof_indices[i]);
ops.set_elem_solution(sol);
// set the value of the small-disturbance solution
for (unsigned int i=0; i<dof_indices.size(); i++)
delta_sol(i) = Complex((*localized_real_solution)(dof_indices[i]),
(*localized_imag_solution)(dof_indices[i]));
ops.set_elem_complex_solution(delta_sol);
// if (_sol_function)
// physics_elem->attach_active_solution_function(*_sol_function);
// perform the element level calculations
ops.elem_calculations(true,
vec,
mat);
ops.clear_elem();
vec *= -1.;
//physics_elem->detach_active_solution_function();
// extract the real or the imaginary part of the matrix/vector
// The complex system of equations
// (J_R + i J_I) (x_R + i x_I) + (r_R + i r_I) = 0
// is rewritten as
// [ J_R -J_I] {x_R} + {r_R} = {0}
// [ J_I J_R] {x_I} + {r_I} = {0}
//
DenseRealVector v;
DenseRealMatrix m;
// copy the real part of the residual and Jacobian
MAST::copy(v, vec.real());
MAST::copy(m, mat.real());
dof_map.constrain_element_matrix_and_vector(m, v, dof_indices);
R_R.add_vector(v, dof_indices);
J_R.add_matrix(m, dof_indices);
// copy the imag part of the residual and Jacobian
v.zero();
m.zero();
MAST::copy(v, vec.imag());
MAST::copy(m, mat.imag());
dof_map.constrain_element_matrix_and_vector(m, v, dof_indices);
R_I.add_vector(v, dof_indices);
J_I.add_matrix(m, dof_indices);
}
// if a solution function is attached, clear it
//if (_sol_function)
// _sol_function->clear();
R_R.close();
R_I.close();
J_R.close();
J_I.close();
libMesh::out << "R_R: " << R_R.l2_norm() << " R_I: " << R_I.l2_norm() << std::endl;
}