bool
MAST::HeatConductionElementBase::
surface_convection_residual(bool request_jacobian,
                            RealVectorX& f,
                            RealMatrixX& jac,
                            const unsigned int s,
                            MAST::BoundaryConditionBase& p) {
    
    // prepare the side finite element
    std::auto_ptr<libMesh::FEBase> fe;
    std::auto_ptr<libMesh::QBase> qrule;
    _get_side_fe_and_qrule(get_elem_for_quadrature(), s, fe, qrule);

    // get the function from this boundary condition
    const MAST::FieldFunction<Real>
    &coeff = p.get<MAST::FieldFunction<Real> >("convection_coeff"),
    &T_amb = p.get<MAST::FieldFunction<Real> >("ambient_temperature");
    
    const std::vector<Real> &JxW               = fe->get_JxW();
    const std::vector<libMesh::Point>& qpoint  = fe->get_xyz();
    const std::vector<std::vector<Real> >& phi = fe->get_phi();
    const unsigned int n_phi                   = (unsigned int)phi.size();
    
    
    RealVectorX  phi_vec  = RealVectorX::Zero(n_phi);
    RealMatrixX  mat      = RealMatrixX::Zero(n_phi, n_phi);
    Real temp, amb_temp, h_coeff;
    libMesh::Point pt;
    MAST::FEMOperatorMatrix Bmat;
    
    
    for (unsigned int qp=0; qp<qpoint.size(); qp++) {
        
        _local_elem->global_coordinates_location (qpoint[qp], pt);
        
        // now set the shape function values
        for ( unsigned int i_nd=0; i_nd<n_phi; i_nd++ )
            phi_vec(i_nd) = phi[i_nd][qp];
        
        // value of flux
        coeff(pt, _time, h_coeff);
        T_amb(pt, _time, amb_temp);
        temp  = phi_vec.dot(_sol);
        
        // normal flux is given as:
        // qi_ni = h_coeff * (T - T_amb)
        //
        f   += JxW[qp] * phi_vec * h_coeff * (temp - amb_temp);
        
        if (request_jacobian) {
            
            Bmat.reinit(1, phi_vec);
            Bmat.right_multiply_transpose(mat, Bmat);
            jac += JxW[qp] * mat * h_coeff;
        }
    }
    
    return request_jacobian;
}
bool
MAST::HeatConductionElementBase::
surface_radiation_residual(bool request_jacobian,
                           RealVectorX& f,
                           RealMatrixX& jac,
                           MAST::BoundaryConditionBase& p) {
    
    // get the function from this boundary condition
    const MAST::FieldFunction<Real>
    &emissivity = p.get<MAST::FieldFunction<Real> >("emissivity");
    
    const MAST::Parameter
    &T_amb      = p.get<MAST::Parameter>("ambient_temperature"),
    &T_ref_zero = p.get<MAST::Parameter>("reference_zero_temperature"),
    &sb_const   = p.get<MAST::Parameter>("stefan_bolzmann_constant");
    
    
    const std::vector<Real> &JxW               = _fe->get_JxW();
    const std::vector<libMesh::Point>& qpoint  = _fe->get_xyz();
    const std::vector<std::vector<Real> >& phi = _fe->get_phi();
    const unsigned int n_phi                   = (unsigned int)phi.size();
    
    RealVectorX phi_vec  = RealVectorX::Zero(n_phi);
    RealMatrixX mat      = RealMatrixX::Zero(n_phi, n_phi);
    const Real
    sbc      = sb_const(),
    amb_temp = T_amb(),
    zero_ref = T_ref_zero();
    Real temp, emiss;
    libMesh::Point pt;
    MAST::FEMOperatorMatrix Bmat;
    
    for (unsigned int qp=0; qp<qpoint.size(); qp++) {
        
        _local_elem->global_coordinates_location (qpoint[qp], pt);
        
        // now set the shape function values
        for ( unsigned int i_nd=0; i_nd<n_phi; i_nd++ )
            phi_vec(i_nd) = phi[i_nd][qp];
        
        // value of flux
        emissivity(pt, _time, emiss);
        temp  = phi_vec.dot(_sol);
        
        f   += JxW[qp] * phi_vec * sbc * emiss *
        (pow(temp-zero_ref, 4.) - pow(amb_temp-zero_ref, 4.));
        
        if (request_jacobian) {
            
            Bmat.reinit(1, phi_vec);
            Bmat.right_multiply_transpose(mat, Bmat);
            jac +=  JxW[qp] * mat * sbc * emiss * 4. * pow(temp-zero_ref, 3.);
        }
    }
    
    
    return request_jacobian;
}
bool
MAST::HeatConductionElementBase::velocity_residual (bool request_jacobian,
                                                    RealVectorX& f,
                                                    RealMatrixX& jac_xdot,
                                                    RealMatrixX& jac) {
    MAST::FEMOperatorMatrix Bmat;
    
    const std::vector<Real>& JxW                 = _fe->get_JxW();
    const std::vector<libMesh::Point>& xyz       = _fe->get_xyz();
    
    const unsigned int
    n_phi      = _fe->n_shape_functions(),
    dim        = _elem.dim();
    
    RealMatrixX
    material_mat    = RealMatrixX::Zero(dim, dim),
    mat_n2n2        = RealMatrixX::Zero(n_phi, n_phi);
    RealVectorX
    vec1    = RealVectorX::Zero(1),
    vec2_n2 = RealVectorX::Zero(n_phi);
    
    std::auto_ptr<MAST::FieldFunction<RealMatrixX> > capacitance =
    _property.thermal_capacitance_matrix(*this);
    
    libMesh::Point p;
    
    for (unsigned int qp=0; qp<JxW.size(); qp++) {
        
        _initialize_mass_fem_operator(qp, Bmat);
        Bmat.right_multiply(vec1, _sol);               //  B * T
        
        if (_active_sol_function)
            dynamic_cast<MAST::MeshFieldFunction<RealVectorX>*>
            (_active_sol_function)->set_element_quadrature_point_solution(vec1);

        _local_elem->global_coordinates_location(xyz[qp], p);
        
        (*capacitance)(p, _time, material_mat);
        
        Bmat.right_multiply(vec1, _vel);               //  B * T_dot
        Bmat.vector_mult_transpose(vec2_n2, vec1);     //  B^T * B * T_dot
        
        f      += JxW[qp] * material_mat(0,0) * vec2_n2; // (rho*cp)*JxW B^T B T_dot
        
        if (request_jacobian) {
            
            Bmat.right_multiply_transpose(mat_n2n2, Bmat);  // B^T B
            jac_xdot += JxW[qp] * material_mat(0,0) * mat_n2n2;  // B^T B * JxW (rho*cp)
            
            // Jacobian contribution from int_omega B T d(rho*cp)/dT B
            if (_active_sol_function) {
                // get derivative of the conductance matrix wrt temperature
                capacitance->derivative(MAST::PARTIAL_DERIVATIVE,
                                        *_active_sol_function,
                                        p,
                                        _time, material_mat);
                
                if (material_mat(0,0) != 0.) { // no need to process for zero terms
                    
                    // B^T (T d(rho cp)/dT) B
                    jac += JxW[qp] * vec1(0) * material_mat(0,0) * mat_n2n2;
                }
            }
        }
    }
    
    
    if (_active_sol_function)
        dynamic_cast<MAST::MeshFieldFunction<RealVectorX>*>
        (_active_sol_function)->clear_element_quadrature_point_solution();

    return request_jacobian;
}