Public Member Functions | Private Member Functions | Private Attributes | List of all members
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT > Class Template Reference
+ Inheritance diagram for PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >:

Public Member Functions

 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z, const double &domain_height, Mesh *external_mesh_pt)
 Constructor. More...
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void set_initial_condition ()
 Set the initial conditions to a "Poiseuille-style" profile. More...
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
RectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt ()
 Access function for the specific mesh. More...
 
RectangularQuadMesh< BASE_ELEMENT > * base_state_mesh_pt ()
 Access function for the base state mesh. More...
 
void doc_solution (DocInfo &doc_info)
 Doc the solution. More...
 
 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z, const double &domain_height, Mesh *external_mesh_pt)
 Constructor. More...
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void actions_after_adapt ()
 
void set_initial_condition ()
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
RefineableRectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt ()
 Access function for the specific mesh. More...
 
RefineableRectangularQuadMesh< BASE_ELEMENT > * base_state_mesh_pt ()
 Access function for the base state mesh. More...
 
void doc_solution (DocInfo &doc_info)
 Doc the solution. More...
 
 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z, const double &domain_height, Mesh *external_mesh_pt)
 Constructor. More...
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void set_initial_condition ()
 Set initial conditions to a "Poiseuille-style" profile. More...
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
RectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt ()
 Access function for the specific mesh. More...
 
RectangularQuadMesh< BASE_ELEMENT > * base_state_mesh_pt ()
 Access function for the base state mesh. More...
 
SelfStartingBDF2 * time_stepper_pt ()
 Access function for the specific timestepper. More...
 
void doc_solution (DocInfo &doc_info, const bool &output_soln=true)
 Doc the solution. More...
 
void create_trace_file (DocInfo &doc_info)
 Create a trace file. More...
 
void initialise_trace_file ()
 Initialise trace file (print column headings) More...
 
void close_trace_file ()
 Clear and close trace file. More...
 
ofstream & trace_file ()
 Access function for trace file. More...
 
void pass_updated_nondim_parameters_to_elements ()
 
 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z, const double &domain_height, Mesh *external_mesh_pt)
 Constructor. More...
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void actions_after_adapt ()
 
void set_initial_condition ()
 Set initial conditions to a "Poiseuille-style" profile. More...
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
RefineableRectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt ()
 Access function for the specific mesh. More...
 
RefineableRectangularQuadMesh< BASE_ELEMENT > * base_state_mesh_pt ()
 Access function for the base state mesh. More...
 
SelfStartingBDF2 * time_stepper_pt ()
 Access function for the specific timestepper. More...
 
void doc_solution (DocInfo &doc_info, const bool &output_soln=true)
 Doc the solution. More...
 
void create_trace_file (DocInfo &doc_info)
 Create a trace file. More...
 
void initialise_trace_file ()
 Initialise trace file (print column headings) More...
 
void close_trace_file ()
 Clear and close trace file. More...
 
ofstream & trace_file ()
 Access function for trace file. More...
 
void pass_updated_nondim_parameters_to_elements ()
 
 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z, const double &radius_inner_cylinder, const double &radius_outer_cylinder, const double &l_z, Mesh *external_mesh_pt)
 Constructor. More...
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void set_initial_condition ()
 Set initial conditions to a "Poiseuille-style" profile. More...
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
RectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt ()
 Access function for the specific mesh. More...
 
RectangularQuadMesh< BASE_ELEMENT > * base_state_mesh_pt ()
 Access function for the base state mesh. More...
 
SelfStartingBDF2 * time_stepper_pt ()
 Access function for the specific timestepper. More...
 
void doc_solution (DocInfo &doc_info, const bool &output_soln=true)
 Doc the solution. More...
 
void create_trace_file (DocInfo &doc_info)
 Create a trace file. More...
 
void initialise_trace_file ()
 Initialise trace file (print column headings) More...
 
void close_trace_file ()
 Clear and close trace file. More...
 
ofstream & trace_file ()
 Access function for trace file. More...
 
 PerturbedStateProblem (const unsigned &n_r, const unsigned &n_z1, const unsigned &n_z2, const double &h1, const double &h2, SpineMesh *external_bulk_mesh_pt, int azimuthal_mode_number)
 
 ~PerturbedStateProblem ()
 Destructor (empty) More...
 
void set_initial_condition ()
 Set initial conditions (velocities given random values in range [0,1]) More...
 
void set_boundary_conditions ()
 Set up the (homogeneous) boundary conditions. More...
 
TwoLayerSpineMesh< BASE_ELEMENT > * base_state_bulk_mesh_pt ()
 Access function for the base state mesh. More...
 
TIMESTEPPER * time_stepper_pt ()
 Access function for the specific timestepper. More...
 
void doc_solution (DocInfo *&doc_info_pt, const bool &output_soln=true)
 Doc the solution. More...
 
void create_trace_file (DocInfo *&doc_info_pt)
 Create and initialise a trace file. More...
 
void close_trace_file ()
 Clear and close trace file. More...
 
ofstream & trace_file ()
 Access function for trace file. More...
 
void create_interface_elements ()
 Create interface elements at boundary between upper and lower layers. More...
 
TwoLayerPerturbedSpineMesh< PERTURBED_ELEMENT > * bulk_mesh_pt ()
 Access function for bulk mesh. More...
 
Mesh * surface_mesh_pt ()
 Access function for surface mesh. More...
 
- Public Member Functions inherited from oomph::Problem
virtual void debug_hook_fct (const unsigned &i)
 
void set_analytic_dparameter (double *const &parameter_pt)
 
void unset_analytic_dparameter (double *const &parameter_pt)
 
bool is_dparameter_calculated_analytically (double *const &parameter_pt)
 
void set_analytic_hessian_products ()
 
void unset_analytic_hessian_products ()
 
bool are_hessian_products_calculated_analytically ()
 
void set_pinned_values_to_zero ()
 
bool distributed () const
 
virtual void actions_before_adapt ()
 
OomphCommunicator * communicator_pt ()
 access function to the oomph-lib communicator More...
 
const OomphCommunicator * communicator_pt () const
 access function to the oomph-lib communicator, const version More...
 
 Problem ()
 
 Problem (const Problem &dummy)=delete
 Broken copy constructor. More...
 
void operator= (const Problem &)=delete
 Broken assignment operator. More...
 
virtual ~Problem ()
 Virtual destructor to clean up memory. More...
 
Mesh *& mesh_pt ()
 Return a pointer to the global mesh. More...
 
Mesh *const & mesh_pt () const
 Return a pointer to the global mesh (const version) More...
 
Mesh *& mesh_pt (const unsigned &imesh)
 
Mesh *const & mesh_pt (const unsigned &imesh) const
 Return a pointer to the i-th submesh (const version) More...
 
unsigned nsub_mesh () const
 Return number of submeshes. More...
 
unsigned add_sub_mesh (Mesh *const &mesh_pt)
 
void flush_sub_meshes ()
 
void build_global_mesh ()
 
void rebuild_global_mesh ()
 
LinearSolver *& linear_solver_pt ()
 Return a pointer to the linear solver object. More...
 
LinearSolver *const & linear_solver_pt () const
 Return a pointer to the linear solver object (const version) More...
 
LinearSolver *& mass_matrix_solver_for_explicit_timestepper_pt ()
 
LinearSolver * mass_matrix_solver_for_explicit_timestepper_pt () const
 
EigenSolver *& eigen_solver_pt ()
 Return a pointer to the eigen solver object. More...
 
EigenSolver *const & eigen_solver_pt () const
 Return a pointer to the eigen solver object (const version) More...
 
Time *& time_pt ()
 Return a pointer to the global time object. More...
 
Time * time_pt () const
 Return a pointer to the global time object (const version). More...
 
double & time ()
 Return the current value of continuous time. More...
 
double time () const
 Return the current value of continuous time (const version) More...
 
TimeStepper *& time_stepper_pt ()
 
const TimeStepper * time_stepper_pt () const
 
TimeStepper *& time_stepper_pt (const unsigned &i)
 Return a pointer to the i-th timestepper. More...
 
ExplicitTimeStepper *& explicit_time_stepper_pt ()
 Return a pointer to the explicit timestepper. More...
 
unsigned long set_timestepper_for_all_data (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data=false)
 
virtual void shift_time_values ()
 Shift all values along to prepare for next timestep. More...
 
AssemblyHandler *& assembly_handler_pt ()
 Return a pointer to the assembly handler object. More...
 
AssemblyHandler *const & assembly_handler_pt () const
 Return a pointer to the assembly handler object (const version) More...
 
double & minimum_dt ()
 Access function to min timestep in adaptive timestepping. More...
 
double & maximum_dt ()
 Access function to max timestep in adaptive timestepping. More...
 
unsigned & max_newton_iterations ()
 Access function to max Newton iterations before giving up. More...
 
void problem_is_nonlinear (const bool &prob_lin)
 Access function to Problem_is_nonlinear. More...
 
double & max_residuals ()
 
bool & time_adaptive_newton_crash_on_solve_fail ()
 Access function for Time_adaptive_newton_crash_on_solve_fail. More...
 
double & newton_solver_tolerance ()
 
void add_time_stepper_pt (TimeStepper *const &time_stepper_pt)
 
void set_explicit_time_stepper_pt (ExplicitTimeStepper *const &explicit_time_stepper_pt)
 
void initialise_dt (const double &dt)
 
void initialise_dt (const Vector< double > &dt)
 
Data *& global_data_pt (const unsigned &i)
 Return a pointer to the the i-th global data object. More...
 
void add_global_data (Data *const &global_data_pt)
 
void flush_global_data ()
 
LinearAlgebraDistribution *const & dof_distribution_pt () const
 Return the pointer to the dof distribution (read-only) More...
 
unsigned long ndof () const
 Return the number of dofs. More...
 
unsigned ntime_stepper () const
 Return the number of time steppers. More...
 
unsigned nglobal_data () const
 Return the number of global data values. More...
 
unsigned self_test ()
 Self-test: Check meshes and global data. Return 0 for OK. More...
 
void enable_store_local_dof_pt_in_elements ()
 
void disable_store_local_dof_pt_in_elements ()
 
unsigned long assign_eqn_numbers (const bool &assign_local_eqn_numbers=true)
 
void describe_dofs (std::ostream &out= *(oomph_info.stream_pt())) const
 
void enable_discontinuous_formulation ()
 
void disable_discontinuous_formulation ()
 
void get_dofs (DoubleVector &dofs) const
 
void get_dofs (const unsigned &t, DoubleVector &dofs) const
 Return vector of the t'th history value of all dofs. More...
 
void set_dofs (const DoubleVector &dofs)
 Set the values of the dofs. More...
 
void set_dofs (const unsigned &t, DoubleVector &dofs)
 Set the history values of the dofs. More...
 
void set_dofs (const unsigned &t, Vector< double * > &dof_pt)
 
void add_to_dofs (const double &lambda, const DoubleVector &increment_dofs)
 Add lambda x incremenet_dofs[l] to the l-th dof. More...
 
double * global_dof_pt (const unsigned &i)
 
double & dof (const unsigned &i)
 i-th dof in the problem More...
 
double dof (const unsigned &i) const
 i-th dof in the problem (const version) More...
 
double *& dof_pt (const unsigned &i)
 Pointer to i-th dof in the problem. More...
 
double * dof_pt (const unsigned &i) const
 Pointer to i-th dof in the problem (const version) More...
 
virtual void get_inverse_mass_matrix_times_residuals (DoubleVector &Mres)
 
virtual void get_dvaluesdt (DoubleVector &f)
 
virtual void get_residuals (DoubleVector &residuals)
 Get the total residuals Vector for the problem. More...
 
virtual void get_jacobian (DoubleVector &residuals, DenseDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, CRDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, CCDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, SumOfMatrices &jacobian)
 
void get_fd_jacobian (DoubleVector &residuals, DenseMatrix< double > &jacobian)
 Get the full Jacobian by finite differencing. More...
 
void get_derivative_wrt_global_parameter (double *const &parameter_pt, DoubleVector &result)
 
void get_hessian_vector_products (DoubleVectorWithHaloEntries const &Y, Vector< DoubleVectorWithHaloEntries > const &C, Vector< DoubleVectorWithHaloEntries > &product)
 
void solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, Vector< DoubleVector > &eigenvector, const bool &steady=true)
 Solve the eigenproblem. More...
 
void solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, const bool &steady=true)
 
virtual void get_eigenproblem_matrices (CRDoubleMatrix &mass_matrix, CRDoubleMatrix &main_matrix, const double &shift=0.0)
 
void assign_eigenvector_to_dofs (DoubleVector &eigenvector)
 Assign the eigenvector passed to the function to the dofs. More...
 
void add_eigenvector_to_dofs (const double &epsilon, const DoubleVector &eigenvector)
 
void store_current_dof_values ()
 Store the current values of the degrees of freedom. More...
 
void restore_dof_values ()
 Restore the stored values of the degrees of freedom. More...
 
void enable_jacobian_reuse ()
 
void disable_jacobian_reuse ()
 Disable recycling of Jacobian in Newton iteration. More...
 
bool jacobian_reuse_is_enabled ()
 Is recycling of Jacobian in Newton iteration enabled? More...
 
bool & use_predictor_values_as_initial_guess ()
 
void newton_solve ()
 Use Newton method to solve the problem. More...
 
void enable_globally_convergent_newton_method ()
 enable globally convergent Newton method More...
 
void disable_globally_convergent_newton_method ()
 disable globally convergent Newton method More...
 
void newton_solve (unsigned const &max_adapt)
 
void steady_newton_solve (unsigned const &max_adapt=0)
 
void copy (Problem *orig_problem_pt)
 
virtual Problem * make_copy ()
 
virtual void read (std::ifstream &restart_file, bool &unsteady_restart)
 
virtual void read (std::ifstream &restart_file)
 
virtual void dump (std::ofstream &dump_file) const
 
void dump (const std::string &dump_file_name) const
 
void delete_all_external_storage ()
 
virtual void symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ()
 
double * bifurcation_parameter_pt () const
 
void get_bifurcation_eigenfunction (Vector< DoubleVector > &eigenfunction)
 
void activate_fold_tracking (double *const &parameter_pt, const bool &block_solve=true)
 
void activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const bool &block_solve=true)
 
void activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const DoubleVector &normalisation, const bool &block_solve=true)
 
void activate_pitchfork_tracking (double *const &parameter_pt, const DoubleVector &symmetry_vector, const bool &block_solve=true)
 
void activate_hopf_tracking (double *const &parameter_pt, const bool &block_solve=true)
 
void activate_hopf_tracking (double *const &parameter_pt, const double &omega, const DoubleVector &null_real, const DoubleVector &null_imag, const bool &block_solve=true)
 
void deactivate_bifurcation_tracking ()
 
void reset_assembly_handler_to_default ()
 Reset the system to the standard non-augemented state. More...
 
double arc_length_step_solve (double *const &parameter_pt, const double &ds, const unsigned &max_adapt=0)
 
double arc_length_step_solve (Data *const &data_pt, const unsigned &data_index, const double &ds, const unsigned &max_adapt=0)
 
void reset_arc_length_parameters ()
 
int & sign_of_jacobian ()
 
void explicit_timestep (const double &dt, const bool &shift_values=true)
 Take an explicit timestep of size dt. More...
 
void unsteady_newton_solve (const double &dt)
 
void unsteady_newton_solve (const double &dt, const bool &shift_values)
 
void unsteady_newton_solve (const double &dt, const unsigned &max_adapt, const bool &first, const bool &shift=true)
 
double doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const bool &first, const bool &shift=true)
 
double doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const unsigned &suppress_resolve_after_spatial_adapt_flag, const bool &first, const bool &shift=true)
 
double adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon)
 
double adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon, const bool &shift_values)
 
void assign_initial_values_impulsive ()
 
void assign_initial_values_impulsive (const double &dt)
 
void calculate_predictions ()
 Calculate predictions. More...
 
void enable_mass_matrix_reuse ()
 
void disable_mass_matrix_reuse ()
 
bool mass_matrix_reuse_is_enabled ()
 Return whether the mass matrix is being reused. More...
 
void refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)
 
void refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)
 
void refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void refine_uniformly (DocInfo &doc_info)
 
void refine_uniformly_and_prune (DocInfo &doc_info)
 
void refine_uniformly ()
 
void refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform refinement for submesh i_mesh with documentation. More...
 
void refine_uniformly (const unsigned &i_mesh)
 Do uniform refinement for submesh i_mesh without documentation. More...
 
void p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)
 
void p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)
 
void p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void p_refine_uniformly (DocInfo &doc_info)
 
void p_refine_uniformly_and_prune (DocInfo &doc_info)
 
void p_refine_uniformly ()
 
void p_refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform p-refinement for submesh i_mesh with documentation. More...
 
void p_refine_uniformly (const unsigned &i_mesh)
 Do uniform p-refinement for submesh i_mesh without documentation. More...
 
void refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)
 
void refine_selected_elements (const Vector< RefineableElement * > &elements_to_be_refined_pt)
 
void refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)
 
void refine_selected_elements (const unsigned &i_mesh, const Vector< RefineableElement * > &elements_to_be_refined_pt)
 
void refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)
 
void refine_selected_elements (const Vector< Vector< RefineableElement * >> &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)
 
void p_refine_selected_elements (const Vector< PRefineableElement * > &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)
 
void p_refine_selected_elements (const unsigned &i_mesh, const Vector< PRefineableElement * > &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)
 
void p_refine_selected_elements (const Vector< Vector< PRefineableElement * >> &elements_to_be_refined_pt)
 
unsigned unrefine_uniformly ()
 
unsigned unrefine_uniformly (const unsigned &i_mesh)
 
void p_unrefine_uniformly (DocInfo &doc_info)
 
void p_unrefine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform p-unrefinement for submesh i_mesh without documentation. More...
 
void adapt (unsigned &n_refined, unsigned &n_unrefined)
 
void adapt ()
 
void p_adapt (unsigned &n_refined, unsigned &n_unrefined)
 
void p_adapt ()
 
void adapt_based_on_error_estimates (unsigned &n_refined, unsigned &n_unrefined, Vector< Vector< double >> &elemental_error)
 
void adapt_based_on_error_estimates (Vector< Vector< double >> &elemental_error)
 
void get_all_error_estimates (Vector< Vector< double >> &elemental_error)
 
void doc_errors (DocInfo &doc_info)
 Get max and min error for all elements in submeshes. More...
 
void doc_errors ()
 Get max and min error for all elements in submeshes. More...
 
void enable_info_in_newton_solve ()
 
void disable_info_in_newton_solve ()
 Disable the output of information when in the newton solver. More...
 
- Public Member Functions inherited from oomph::ExplicitTimeSteppableObject
 ExplicitTimeSteppableObject ()
 Empty constructor. More...
 
 ExplicitTimeSteppableObject (const ExplicitTimeSteppableObject &)=delete
 Broken copy constructor. More...
 
void operator= (const ExplicitTimeSteppableObject &)=delete
 Broken assignment operator. More...
 
virtual ~ExplicitTimeSteppableObject ()
 Empty destructor. More...
 
virtual void actions_before_explicit_stage ()
 
virtual void actions_after_explicit_stage ()
 

Private Member Functions

void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 
void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 
void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 
void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 
void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 
void actions_before_newton_convergence_check ()
 
void actions_before_newton_solve ()
 Update before solve (empty) More...
 
void actions_after_newton_solve ()
 Update after solve (empty) More...
 
void actions_before_implicit_timestep ()
 Actions before timestep (empty) More...
 
void actions_after_implicit_timestep ()
 Update the problem specs after solve (empty) More...
 
void fix_pressure (const unsigned &e, const unsigned &pdof, const double &pvalue)
 Fix pressure in element e at pressure dof pdof and set to pvalue. More...
 

Private Attributes

Mesh * Base_state_mesh_pt
 Pointer to the base state mesh. More...
 
double Domain_height
 Height of domain. More...
 
ofstream Trace_file
 Trace file. More...
 
double Inner_cylinder_radius
 Inner and outer cylinder radii. More...
 
double Outer_cylinder_radius
 
SpineMesh * Base_state_bulk_mesh_pt
 Pointer to the base state mesh. More...
 
TwoLayerPerturbedSpineMesh< PERTURBED_ELEMENT > * Bulk_mesh_pt
 Pointer to the (specific) "bulk" mesh. More...
 
Mesh * Surface_mesh_pt
 Pointer to the "surface" mesh. More...
 
int Azimuthal_mode_number
 Azimuthal mode number. More...
 
Vector< unsigned > U_nodal_index
 Index at which the i-th velocity component is stored. More...
 
Vector< unsigned > Xhat_nodal_index
 

Additional Inherited Members

- Public Types inherited from oomph::Problem
typedef void(* SpatialErrorEstimatorFctPt) (Mesh *&mesh_pt, Vector< double > &elemental_error)
 Function pointer for spatial error estimator. More...
 
typedef void(* SpatialErrorEstimatorWithDocFctPt) (Mesh *&mesh_pt, Vector< double > &elemental_error, DocInfo &doc_info)
 Function pointer for spatial error estimator with doc. More...
 
- Public Attributes inherited from oomph::Problem
bool Shut_up_in_newton_solve
 
- Static Public Attributes inherited from oomph::Problem
static bool Suppress_warning_about_actions_before_read_unstructured_meshes
 
- Protected Types inherited from oomph::Problem
enum  Assembly_method {
  Perform_assembly_using_vectors_of_pairs , Perform_assembly_using_two_vectors , Perform_assembly_using_maps , Perform_assembly_using_lists ,
  Perform_assembly_using_two_arrays
}
 Enumerated flags to determine which sparse assembly method is used. More...
 
- Protected Member Functions inherited from oomph::Problem
unsigned setup_element_count_per_dof ()
 
virtual void sparse_assemble_row_or_column_compressed (Vector< int * > &column_or_row_index, Vector< int * > &row_or_column_start, Vector< double * > &value, Vector< unsigned > &nnz, Vector< double * > &residual, bool compressed_row_flag)
 
virtual void actions_before_newton_step ()
 
virtual void actions_after_newton_step ()
 
virtual void actions_after_implicit_timestep_and_error_estimation ()
 
virtual void actions_before_explicit_timestep ()
 Actions that should be performed before each explicit time step. More...
 
virtual void actions_after_explicit_timestep ()
 Actions that should be performed after each explicit time step. More...
 
virtual void actions_before_read_unstructured_meshes ()
 
virtual void actions_after_read_unstructured_meshes ()
 
virtual void actions_after_change_in_global_parameter (double *const &parameter_pt)
 
virtual void actions_after_change_in_bifurcation_parameter ()
 
virtual void actions_after_parameter_increase (double *const &parameter_pt)
 
double & dof_derivative (const unsigned &i)
 
double & dof_current (const unsigned &i)
 
virtual double global_temporal_error_norm ()
 
unsigned newton_solve_continuation (double *const &parameter_pt)
 
unsigned newton_solve_continuation (double *const &parameter_pt, DoubleVector &z)
 
void calculate_continuation_derivatives (double *const &parameter_pt)
 
void calculate_continuation_derivatives (const DoubleVector &z)
 
void calculate_continuation_derivatives_fd (double *const &parameter_pt)
 
bool does_pointer_correspond_to_problem_data (double *const &parameter_pt)
 
void set_consistent_pinned_values_for_continuation ()
 
- Protected Attributes inherited from oomph::Problem
Vector< Problem * > Copy_of_problem_pt
 
std::map< double *, bool > Calculate_dparameter_analytic
 
bool Calculate_hessian_products_analytic
 
LinearAlgebraDistribution * Dof_distribution_pt
 
Vector< double * > Dof_pt
 Vector of pointers to dofs. More...
 
DoubleVectorWithHaloEntries Element_count_per_dof
 
double Relaxation_factor
 
double Newton_solver_tolerance
 
unsigned Max_newton_iterations
 Maximum number of Newton iterations. More...
 
unsigned Nnewton_iter_taken
 
Vector< double > Max_res
 Maximum residuals at start and after each newton iteration. More...
 
double Max_residuals
 
bool Time_adaptive_newton_crash_on_solve_fail
 
bool Jacobian_reuse_is_enabled
 Is re-use of Jacobian in Newton iteration enabled? Default: false. More...
 
bool Jacobian_has_been_computed
 
bool Problem_is_nonlinear
 
bool Pause_at_end_of_sparse_assembly
 
bool Doc_time_in_distribute
 
unsigned Sparse_assembly_method
 
unsigned Sparse_assemble_with_arrays_initial_allocation
 
unsigned Sparse_assemble_with_arrays_allocation_increment
 
Vector< Vector< unsigned > > Sparse_assemble_with_arrays_previous_allocation
 
double Numerical_zero_for_sparse_assembly
 
double FD_step_used_in_get_hessian_vector_products
 
bool Mass_matrix_reuse_is_enabled
 
bool Mass_matrix_has_been_computed
 
bool Discontinuous_element_formulation
 
double Minimum_dt
 Minimum desired dt: if dt falls below this value, exit. More...
 
double Maximum_dt
 Maximum desired dt. More...
 
double DTSF_max_increase
 
double DTSF_min_decrease
 
double Minimum_dt_but_still_proceed
 
bool Scale_arc_length
 Boolean to control whether arc-length should be scaled. More...
 
double Desired_proportion_of_arc_length
 Proportion of the arc-length to taken by the parameter. More...
 
double Theta_squared
 
int Sign_of_jacobian
 Storage for the sign of the global Jacobian. More...
 
double Continuation_direction
 
double Parameter_derivative
 Storage for the derivative of the global parameter wrt arc-length. More...
 
double Parameter_current
 Storage for the present value of the global parameter. More...
 
bool Use_continuation_timestepper
 Boolean to control original or new storage of dof stuff. More...
 
unsigned Dof_derivative_offset
 
unsigned Dof_current_offset
 
Vector< double > Dof_derivative
 Storage for the derivative of the problem variables wrt arc-length. More...
 
Vector< double > Dof_current
 Storage for the present values of the variables. More...
 
double Ds_current
 Storage for the current step value. More...
 
unsigned Desired_newton_iterations_ds
 
double Minimum_ds
 Minimum desired value of arc-length. More...
 
bool Bifurcation_detection
 Boolean to control bifurcation detection via determinant of Jacobian. More...
 
bool Bisect_to_find_bifurcation
 Boolean to control wheter bisection is used to located bifurcation. More...
 
bool First_jacobian_sign_change
 Boolean to indicate whether a sign change has occured in the Jacobian. More...
 
bool Arc_length_step_taken
 Boolean to indicate whether an arc-length step has been taken. More...
 
bool Use_finite_differences_for_continuation_derivatives
 
OomphCommunicator * Communicator_pt
 The communicator for this problem. More...
 
bool Always_take_one_newton_step
 
double Timestep_reduction_factor_after_nonconvergence
 
bool Keep_temporal_error_below_tolerance
 
- Static Protected Attributes inherited from oomph::Problem
static ContinuationStorageScheme Continuation_time_stepper
 Storage for the single static continuation timestorage object. More...
 

Detailed Description

template<class BASE_ELEMENT, class PERTURBED_ELEMENT>
class PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >

////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// Perturbed state problem class for Tuckerman counter-rotating lids problem

////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// Perturbed state problem class for the time-periodic Taylor–Couette problem

Constructor & Destructor Documentation

◆ PerturbedStateProblem() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z,
const double &  domain_height,
Mesh *  external_mesh_pt 
)

Constructor.

Constructor for perturbed state Tuckerman counter-rotating lids problem

452  : Base_state_mesh_pt(external_mesh_pt),
453  Domain_height(domain_height)
454 {
455  // Be less verbose during newton solve
456  this->disable_info_in_newton_solve();
457 
458  // Be less verbose about linear solve timings
459  linear_solver_pt()->disable_doc_time();
460 
461  // Tell problem that it is linear (avoid doing unnecessary checks)
462  Problem::Problem_is_nonlinear = false;
463 
464  // Allocate the timestepper (this constructs the time object as well)
465  add_time_stepper_pt(new BDF<1>);
466 
467  // Build and assign mesh
468  Problem::mesh_pt() =
469  new RectangularQuadMesh<PERTURBED_ELEMENT>(n_r,n_z,0.0,1.0,0.0,domain_height,
470  time_stepper_pt());
471 
472  // --------------------------------------------
473  // Set the boundary conditions for this problem
474  // --------------------------------------------
475 
476  // All nodes are free by default -- just pin the ones that have
477  // Dirichlet conditions here
478 
479  // Determine number of mesh boundaries
480  const unsigned n_boundary = mesh_pt()->nboundary();
481 
482  // Loop over mesh boundaries
483  for(unsigned b=0;b<n_boundary;b++)
484  {
485  // Determine number of nodes on boundary b
486  const unsigned n_node = mesh_pt()->nboundary_node(b);
487 
488  // Loop over nodes on boundary b
489  for(unsigned n=0;n<n_node;n++)
490  {
491  // Set up pointer to node
492  Node* nod_pt = mesh_pt()->boundary_node_pt(b,n);
493 
494  // On all solid boundaries, pin all velocity components
495  if(b!=3)
496  {
497  nod_pt->pin(0); // Radial (real)
498  nod_pt->pin(1); // Radial (imaginary)
499  nod_pt->pin(2); // Axial (real)
500  nod_pt->pin(3); // Axial (imaginary)
501  nod_pt->pin(4); // Azimuthal (real)
502  nod_pt->pin(5); // Azimuthal (imaginary)
503  }
504  // On symmetry boundary, pin only radial and azimuthal velocity
505  // components, unless we are looking at the k=1 azimuthal mode.
506  // In this case, do not pin any velocity components on this boundary
507  else
508  {
509  if(GlobalPhysicalVariables::k!=1)
510  {
511  nod_pt->pin(0); // Radial (real)
512  nod_pt->pin(1); // Radial (imaginary)
513  nod_pt->pin(4); // Azimuthal (real)
514  nod_pt->pin(5); // Azimuthal (imaginary)
515  }
516  }
517  } // End of loop over nodes on boundary b
518  } // End of loop over mesh boundaries
519 
520  // ----------------------------------------------------------------
521  // Complete the problem setup to make the elements fully functional
522  // ----------------------------------------------------------------
523 
524  // Determine number of elements in mesh
525  const unsigned n_element = mesh_pt()->nelement();
526 
527  // Loop over the elements
528  for(unsigned e=0;e<n_element;e++)
529  {
530  // Upcast from GeneralisedElement to the present element
531  PERTURBED_ELEMENT* el_pt
532  = dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e));
533 
534  // Set the Reynolds number
535  el_pt->re_pt() = &GlobalPhysicalVariables::Re;
536 
537  // Set the Womersley number
538  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt;
539 
540  // The mesh remains fixed
541  el_pt->disable_ALE();
542 
543  // Set the azimuthal wavenumber
544  el_pt->azimuthal_mode_number_pt() = &GlobalPhysicalVariables::k;
545 
546  } // End of loop over elements
547 
548  // Fix pressure ONLY when looking for axisymmetric modes
549  if(GlobalPhysicalVariables::k==0) { fix_pressure(0,0,0.0); }
550 
551  // ------------------------------------------------------------
552  // Set up interaction between base and perturbed state problems
553  // ------------------------------------------------------------
554 
555  // First interaction (base state velocities)
556  Multi_domain_functions::
557  setup_multi_domain_interaction<BASE_ELEMENT>
558  (this,mesh_pt(),Base_state_mesh_pt,0);
559 
560  // Second interaction (base state velocity derivatives w.r.t. space)
561  Multi_domain_functions::
562  setup_multi_domain_interaction<BASE_ELEMENT>
563  (this,mesh_pt(),Base_state_mesh_pt,1);
564 
565  // Set up equation numbering scheme
566  std::cout << "Number of equations: " << assign_eqn_numbers() << std::endl;
567 
568 } // End of perturbed state constructor
n
const unsigned n
Definition: CG3DPackingUnitTest.cpp:11
e
Array< double, 1, 3 > e(1./3., 0.5, 2.)
b
Scalar * b
Definition: benchVecAdd.cpp:17
PerturbedStateProblem::mesh_pt
RectangularQuadMesh< PERTURBED_ELEMENT > * mesh_pt()
Access function for the specific mesh.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:405
PerturbedStateProblem::time_stepper_pt
SelfStartingBDF2 * time_stepper_pt()
Access function for the specific timestepper.
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:512
PerturbedStateProblem::fix_pressure
void fix_pressure(const unsigned &e, const unsigned &pdof, const double &pvalue)
Fix pressure in element e at pressure dof pdof and set to pvalue.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:427
PerturbedStateProblem::Base_state_mesh_pt
Mesh * Base_state_mesh_pt
Pointer to the base state mesh.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:424
PerturbedStateProblem::Domain_height
double Domain_height
Height of domain.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:435
oomph::BDF
Definition: timesteppers.h:1165
oomph::Data::pin
void pin(const unsigned &i)
Pin the i-th stored variable.
Definition: nodes.h:385
oomph::LinearSolver::disable_doc_time
void disable_doc_time()
Disable documentation of solve times.
Definition: linear_solver.h:116
oomph::Node
Definition: nodes.h:906
oomph::Problem::add_time_stepper_pt
void add_time_stepper_pt(TimeStepper *const &time_stepper_pt)
Definition: problem.cc:1545
oomph::Problem::linear_solver_pt
LinearSolver *& linear_solver_pt()
Return a pointer to the linear solver object.
Definition: problem.h:1466
oomph::Problem::assign_eqn_numbers
unsigned long assign_eqn_numbers(const bool &assign_local_eqn_numbers=true)
Definition: problem.cc:1989
oomph::Problem::disable_info_in_newton_solve
void disable_info_in_newton_solve()
Disable the output of information when in the newton solver.
Definition: problem.h:2941
oomph::RectangularQuadMesh
Definition: rectangular_quadmesh.template.h:59
GlobalPhysicalVariables::Re
double Re
Reynolds number.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:61
GlobalPhysicalVariables::k
int k
Azimuthal mode number k in e^ik(theta) decomposition.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:73
GlobalPhysicalVariables::ReSt
double ReSt
Product of Reynolds and Strouhal numbers.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:64

References oomph::Problem::add_time_stepper_pt(), oomph::Problem::assign_eqn_numbers(), b, PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Base_state_mesh_pt, oomph::LinearSolver::disable_doc_time(), oomph::Problem::disable_info_in_newton_solve(), e(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure(), GlobalPhysicalVariables::k, oomph::Problem::linear_solver_pt(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt(), n, oomph::Data::pin(), GlobalPhysicalVariables::Re, GlobalPhysicalVariables::ReSt, and PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt().

◆ ~PerturbedStateProblem() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

383 {}

◆ PerturbedStateProblem() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z,
const double &  domain_height,
Mesh *  external_mesh_pt 
)

Constructor.

◆ ~PerturbedStateProblem() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

410 {}

◆ PerturbedStateProblem() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z,
const double &  domain_height,
Mesh *  external_mesh_pt 
)

Constructor.

◆ ~PerturbedStateProblem() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

477 {}

◆ PerturbedStateProblem() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z,
const double &  domain_height,
Mesh *  external_mesh_pt 
)

Constructor.

◆ ~PerturbedStateProblem() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

502 {}

◆ PerturbedStateProblem() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z,
const double &  radius_inner_cylinder,
const double &  radius_outer_cylinder,
const double &  l_z,
Mesh *  external_mesh_pt 
)

Constructor.

Constructor for perturbed state time-periodic Taylor–Couette problem.

616  : Base_state_mesh_pt(external_mesh_pt),
617  Inner_cylinder_radius(radius_inner_cylinder),
618  Outer_cylinder_radius(radius_outer_cylinder),
619  Domain_height(l_z)
620 {
621  // Be less verbose during newton solve
622  Problem::disable_info_in_newton_solve();
623 
624  // Be less verbose about linear solve timings
625  linear_solver_pt()->disable_doc_time();
626 
627  // Allocate the timestepper (this constructs the time object as well)
628  add_time_stepper_pt(new SelfStartingBDF2);
629 
630  // Build and assign mesh
631  Problem::mesh_pt() =
632  new RectangularQuadMesh<PERTURBED_ELEMENT>(n_r,n_z,radius_inner_cylinder,
633  radius_outer_cylinder,0.0,l_z,
634  time_stepper_pt());
635 
636  // --------------------------------------------
637  // Set the boundary conditions for this problem
638  // --------------------------------------------
639 
640  // All nodes are free by default -- just pin the ones that have
641  // Dirichlet conditions here
642 
643  // Determine number of mesh boundaries
644  const unsigned n_boundary = mesh_pt()->nboundary();
645 
646  // Loop over mesh boundaries
647  for(unsigned b=0;b<n_boundary;b++)
648  {
649  // Determine number of nodes on boundary b
650  const unsigned n_node = mesh_pt()->nboundary_node(b);
651 
652  // Loop over nodes on boundary b
653  for(unsigned n=0;n<n_node;n++)
654  {
655  // Pin values for axial velocity components on all boundaries
656  mesh_pt()->boundary_node_pt(b,n)->pin(2); // Axial (real)
657  mesh_pt()->boundary_node_pt(b,n)->pin(3); // Axial (imaginary)
658 
659  // Pin values for radial and azimuthal velocity components on
660  // all solid boundaries
661  if(b==1 || b==3)
662  {
663  mesh_pt()->boundary_node_pt(b,n)->pin(0); // Radial (real)
664  mesh_pt()->boundary_node_pt(b,n)->pin(1); // Radial (imaginary)
665  mesh_pt()->boundary_node_pt(b,n)->pin(4); // Azimuthal (real)
666  mesh_pt()->boundary_node_pt(b,n)->pin(5); // Azimuthal (imaginary)
667  }
668  } // End of loop over nodes on boundary b
669  } // End of loop over mesh boundaries
670 
671  // ----------------------------------------------------------------
672  // Complete the problem setup to make the elements fully functional
673  // ----------------------------------------------------------------
674 
675  // Determine number of elements in mesh
676  const unsigned n_element = mesh_pt()->nelement();
677 
678  // Loop over the elements
679  for(unsigned e=0;e<n_element;e++)
680  {
681  // Upcast from GeneralisedElement to the present element
682  PERTURBED_ELEMENT* el_pt
683  = dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e));
684 
685  // Set the Reynolds number
686  el_pt->re_pt() = &GlobalPhysicalVariables::Re;
687 
688  // Set the Womersley number
689  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt;
690 
691  // The mesh remains fixed
692  el_pt->disable_ALE();
693 
694  // Set the azimuthal wavenumber
695  el_pt->azimuthal_mode_number_pt() = &GlobalPhysicalVariables::k;
696 
697  } // End of loop over elements
698 
699  // Set the pressure in first element at 'node' 0 to 0.0
700  fix_pressure(0,0,0.0);
701 
702  // ------------------------------------------------------------
703  // Set up interaction between base and perturbed state problems
704  // ------------------------------------------------------------
705 
706  // First interaction (base state velocities)
707  Multi_domain_functions::
708  setup_multi_domain_interaction<BASE_ELEMENT>
709  (this,mesh_pt(),Base_state_mesh_pt,0);
710 
711  // Second interaction (base state velocity derivatives w.r.t. space)
712  Multi_domain_functions::
713  setup_multi_domain_interaction<BASE_ELEMENT>
714  (this,mesh_pt(),Base_state_mesh_pt,1);
715 
716  // Set up equation numbering scheme
717  std::cout << "Number of equations: " << assign_eqn_numbers() << std::endl;
718 
719 } // End of perturbed state constructor
PerturbedStateProblem::Outer_cylinder_radius
double Outer_cylinder_radius
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:582
PerturbedStateProblem::Inner_cylinder_radius
double Inner_cylinder_radius
Inner and outer cylinder radii.
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:581
oomph::SelfStartingBDF2
Self-starting BDF2 timestepper class.
Definition: self_starting_BDF2_timestepper.h:37

References oomph::Problem::add_time_stepper_pt(), oomph::Problem::assign_eqn_numbers(), b, PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Base_state_mesh_pt, oomph::LinearSolver::disable_doc_time(), e(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure(), GlobalPhysicalVariables::k, oomph::Problem::linear_solver_pt(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt(), n, GlobalPhysicalVariables::Re, GlobalPhysicalVariables::ReSt, and PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt().

◆ ~PerturbedStateProblem() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

507 {}

◆ PerturbedStateProblem() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT , class TIMESTEPPER >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT, TIMESTEPPER >::PerturbedStateProblem ( const unsigned &  n_r,
const unsigned &  n_z1,
const unsigned &  n_z2,
const double &  h1,
const double &  h2,
SpineMesh *  external_bulk_mesh_pt,
int  azimuthal_mode_number 
)

Constructor: Pass the width of the domain in the r direction, and the heights of both bottom (fluid 1) and top (fluid 2) layers. Also pass the number of elements in both horizontal regions in the r direction and the number of elements in all three vertical regions in the z direction, along with the fractions which determine the spacings of those regions. Also pass a pointer to the base state mesh.

Constructor for perturbed state Tuckerman counter-rotating lids problem

673  : Base_state_bulk_mesh_pt(external_bulk_mesh_pt),
674  Azimuthal_mode_number(azimuthal_mode_number)
675 {
676  // Always take one newton step even if the initial residuals are
677  // below the required tolerance
678  Problem::Always_take_one_newton_step = true;
679 
680  // Allocate the timestepper (this constructs the time object as well)
681  add_time_stepper_pt(new TIMESTEPPER);
682 
683  // Build and assign mesh
684  Bulk_mesh_pt = new TwoLayerPerturbedSpineMesh<PERTURBED_ELEMENT>
685  (n_r,n_z1,n_z2,1.0,h1,h2,Base_state_bulk_mesh_pt,time_stepper_pt());
686 
687  // Create "surface mesh" that will contain only the interface elements.
688  // The constructor just creates the mesh without giving it any elements,
689  // nodes, etc.
690  Surface_mesh_pt = new Mesh;
691 
692  // Add the two sub meshes to the problem
693  add_sub_mesh(Bulk_mesh_pt);
694  add_sub_mesh(Surface_mesh_pt);
695 
696  // Combine all submeshes into a single Mesh
697  build_global_mesh();
698 
699  // -------------------------------------------------------------------
700  // Get information from elements about the order of nodal data storage
701  // -------------------------------------------------------------------
702 
703  // Get a pointer to the first element in the mesh -- note that we
704  // are assuming that the indices will be the same in each element
705  PERTURBED_ELEMENT* el_pt = dynamic_cast<PERTURBED_ELEMENT*>
706  (Bulk_mesh_pt->element_pt(0));
707 
708  // Determine indices at which the perturbations to the nodal positions
709  // are stored
710  this->Xhat_nodal_index.resize(4);
711  for(unsigned i=0;i<4;i++)
712  {
713  Xhat_nodal_index[i] = el_pt->xhat_index_lin_axi_nst(i);
714  }
715 
716  // Determine indices at which velocities are stored
717  this->U_nodal_index.resize(6);
718  for(unsigned i=0;i<6;i++)
719  {
720  U_nodal_index[i] = el_pt->u_index_lin_axi_nst(i);
721  }
722 
723  // Pass nodal indices of cosine (i=2) and sine (i=3) components of the
724  // perturbation to the nodal z-position to the bulk mesh. This
725  // information is used in the node_update function
726  Bulk_mesh_pt->set_perturbation_to_nodal_positions_indices
727  (Xhat_nodal_index[2],Xhat_nodal_index[3]);
728 
729  // --------------------------------------------
730  // Set the boundary conditions for this problem
731  // --------------------------------------------
732 
733  // All nodes are free by default -- just pin the ones that have
734  // Dirichlet conditions here
735 
736  // Determine number of mesh boundaries
737  const unsigned n_boundary = mesh_pt()->nboundary();
738 
739  // Loop over mesh boundaries
740  for(unsigned b=0;b<n_boundary;b++)
741  {
742  // Determine number of nodes on boundary b
743  const unsigned n_node = mesh_pt()->nboundary_node(b);
744 
745  // Loop over nodes on boundary b
746  for(unsigned n=0;n<n_node;n++)
747  {
748  // On top and bottom solid boundaries, pin all velocity components
749  if(b==0 || b==2)
750  {
751  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[0]);
752  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[1]);
753  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[2]);
754  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[3]);
755  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[4]);
756  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[5]);
757  }
758  // On outer wall, pin only radial and azimuthal velocities
759  // (slippery outer wall)
760  else if(b==1)
761  {
762  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[0]);
763  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[1]);
764  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[4]);
765  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[5]);
766  }
767  // On symmetry boundary, boundary conditions differ depending on
768  // the azimuthal mode number
769  else if(b==3)
770  {
771  // If k=0, pin only radial and azimuthal velocity components
772  if(Azimuthal_mode_number==0)
773  {
774  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[0]);
775  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[1]);
776  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[4]);
777  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[5]);
778  }
779  // If k is ODD, pin axial velocity only
780  else if(Azimuthal_mode_number%2)
781  {
782  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[2]);
783  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[3]);
784  }
785  // If k is EVEN (and non-zero), pin all velocity components
786  else
787  {
788  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[0]);
789  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[1]);
790  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[2]);
791  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[3]);
792  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[4]);
793  mesh_pt()->boundary_node_pt(b,n)->pin(U_nodal_index[5]);
794  }
795  }
796  } // End of loop over nodes on boundary b
797  } // End of loop over mesh boundaries
798 
799  // Pin all perturbations to the nodal positions (since these are
800  // dependent variables and therefore not dofs)
801  const unsigned n_node = Bulk_mesh_pt->nnode();
802  for(unsigned n=0;n<n_node;n++)
803  {
804  for(unsigned i=0;i<4;i++)
805  {
806  Bulk_mesh_pt->node_pt(n)->pin(Xhat_nodal_index[i]);
807  }
808  }
809 
810  // ---------------------------------------------------
811  // If k==0, pin all dofs corresponding to "sine parts"
812  // ---------------------------------------------------
813  if(Azimuthal_mode_number==0)
814  {
815  // Pin all the sine components of the velocity values
816  for(unsigned n=0;n<n_node;n++)
817  {
818  Bulk_mesh_pt->node_pt(n)->pin(U_nodal_index[1]);
819  Bulk_mesh_pt->node_pt(n)->pin(U_nodal_index[3]);
820  Bulk_mesh_pt->node_pt(n)->pin(U_nodal_index[5]);
821  }
822 
823  // Pin all the sine components of the pressure dofs
824  const unsigned n_element = Bulk_mesh_pt->nelement();
825  for(unsigned e=0;e<n_element;e++)
826  {
827  // Loop over the three pressure dofs (sine parts)
828  for(unsigned i=0;i<3;i++)
829  {
830  // Pin the values and set them equal to zero
831  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))->
832  fix_sine_component_of_pressure(i,0.0);
833  }
834  }
835 
836  // Pin all the sine components of the perturbed spine heights and set
837  // them to zero
838  const unsigned n_perturbed_spine = Bulk_mesh_pt->nspine();
839  for(unsigned i=0;i<n_perturbed_spine;i++)
840  {
841  Bulk_mesh_pt->perturbed_spine_pt(i)->height_pt()->pin(1);
842  Bulk_mesh_pt->perturbed_spine_pt(i)->height(1) = 0.0;
843  }
844  } // End of if k==0
845 
846  // -------------------------------------------------------------------
847  // If k>0, pin interface height on the symmetry axis (both components)
848  // -------------------------------------------------------------------
849  if(Azimuthal_mode_number>0)
850  {
851  Bulk_mesh_pt->perturbed_spine_pt(0)->height_pt()->pin(0);
852  Bulk_mesh_pt->perturbed_spine_pt(0)->height_pt()->pin(1);
853  Bulk_mesh_pt->perturbed_spine_pt(0)->height(0) = 0.0;
854  Bulk_mesh_pt->perturbed_spine_pt(0)->height(1) = 0.0;
855  }
856 
857  // ----------------------------------------------------------------
858  // Complete the problem setup to make the elements fully functional
859  // ----------------------------------------------------------------
860 
861  // Determine number of bulk elements in lower and upper fluid
862  const unsigned n_lower = Bulk_mesh_pt->nlower();
863  const unsigned n_upper = Bulk_mesh_pt->nupper();
864 
865  // Loop over bulk elements in lower fluid
866  for(unsigned e=0;e<n_lower;e++)
867  {
868  // Upcast from GeneralisedElement to the present element
869  PERTURBED_ELEMENT* el_pt = dynamic_cast<PERTURBED_ELEMENT*>
870  (Bulk_mesh_pt->lower_layer_element_pt(e));
871 
872  // Set the Reynolds number
873  el_pt->re_pt() = &GlobalPhysicalVariables::Re;
874 
875  // Set the Womersley number
876  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt;
877 
878  // Set the product of the Reynolds number and inverse Froude number
879  el_pt->re_invfr_pt() = &GlobalPhysicalVariables::ReInvFr;
880 
881  // Set the direction of gravity
882  el_pt->g_pt() = &GlobalPhysicalVariables::G;
883 
884  // Set the azimuthal mode number
885  el_pt->azimuthal_mode_number_pt() = &Azimuthal_mode_number;
886 
887  // These terms in the Jacobian matrix are provided analytically, so
888  // by filling them in from geometric data we would be "double counting"
889  el_pt->enable_bypass_fill_in_jacobian_from_geometric_data();
890 
891  } // End of loop over bulk elements in lower fluid
892 
893  // Loop over bulk elements in upper fluid
894  for(unsigned e=0;e<n_upper;e++)
895  {
896  // Upcast from GeneralisedElement to the present element
897  PERTURBED_ELEMENT* el_pt = dynamic_cast<PERTURBED_ELEMENT*>
898  (Bulk_mesh_pt->upper_layer_element_pt(e));
899 
900  // Set the Reynolds number
901  el_pt->re_pt() = &GlobalPhysicalVariables::Re;
902 
903  // Set the Womersley number
904  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt;
905 
906  // Set the product of the Reynolds number and inverse Froude number
907  el_pt->re_invfr_pt() = &GlobalPhysicalVariables::ReInvFr;
908 
909  // Set the direction of gravity
910  el_pt->g_pt() = &GlobalPhysicalVariables::G;
911 
912  // Set the viscosity ratio
913  el_pt->viscosity_ratio_pt() = &GlobalPhysicalVariables::Viscosity_Ratio;
914 
915  // Set the density ratio
916  el_pt->density_ratio_pt() = &GlobalPhysicalVariables::Density_Ratio;
917 
918  // Set the azimuthal mode number
919  el_pt->azimuthal_mode_number_pt() = &Azimuthal_mode_number;
920 
921  // These terms in the Jacobian matrix are provided analytically, so
922  // by filling them in from geometric data we would be "double counting"
923  el_pt->enable_bypass_fill_in_jacobian_from_geometric_data();
924 
925  } // End of loop over bulk elements in upper fluid
926 
927  // Fix pressure ONLY when looking for axisymmetric modes
928  if(Azimuthal_mode_number==0) { fix_pressure(0,0,0.0); }
929 
930  // ------------------------------------------------------------
931  // Set up interaction between base and perturbed state problems
932  // ------------------------------------------------------------
933 
934  // First interaction (base state velocities)
935  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
936  (this,mesh_pt(),external_bulk_mesh_pt,0);
937 
938  // Second interaction (base state velocity derivatives w.r.t.
939  // global spatial coordinates)
940  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
941  (this,mesh_pt(),external_bulk_mesh_pt,1);
942 
943  // Third interaction (base state pressure)
944  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
945  (this,mesh_pt(),external_bulk_mesh_pt,2);
946 
947  // Fourth interaction (base state velocity derivatives w.r.t. time)
948  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
949  (this,mesh_pt(),external_bulk_mesh_pt,3);
950 
951  // Fourth interaction (base state velocity derivatives w.r.t. time)
952  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
953  (this,mesh_pt(),external_bulk_mesh_pt,3);
954 
955  // Fifth interaction (base state velocity derivatives w.r.t.
956  // local spatial coordinates)
957  Multi_domain_functions::setup_multi_domain_interaction<BASE_ELEMENT>
958  (this,mesh_pt(),external_bulk_mesh_pt,4);
959 
960  // Set up equation numbering scheme
961  std::cout << "Number of equations: " << assign_eqn_numbers() << std::endl;
962 
963 } // End of perturbed state constructor
i
int i
Definition: BiCGSTAB_step_by_step.cpp:9
PerturbedStateProblem::Surface_mesh_pt
Mesh * Surface_mesh_pt
Pointer to the "surface" mesh.
Definition: two_layer_interface_nonaxisym_perturbations.cc:643
PerturbedStateProblem::Azimuthal_mode_number
int Azimuthal_mode_number
Azimuthal mode number.
Definition: two_layer_interface_nonaxisym_perturbations.cc:649
PerturbedStateProblem::Bulk_mesh_pt
TwoLayerPerturbedSpineMesh< PERTURBED_ELEMENT > * Bulk_mesh_pt
Pointer to the (specific) "bulk" mesh.
Definition: two_layer_interface_nonaxisym_perturbations.cc:640
PerturbedStateProblem::Xhat_nodal_index
Vector< unsigned > Xhat_nodal_index
Definition: two_layer_interface_nonaxisym_perturbations.cc:656
PerturbedStateProblem::Base_state_bulk_mesh_pt
SpineMesh * Base_state_bulk_mesh_pt
Pointer to the base state mesh.
Definition: two_layer_interface_nonaxisym_perturbations.cc:637
PerturbedStateProblem::U_nodal_index
Vector< unsigned > U_nodal_index
Index at which the i-th velocity component is stored.
Definition: two_layer_interface_nonaxisym_perturbations.cc:652
oomph::Mesh
Definition: mesh.h:67
oomph::Mesh::element_pt
GeneralisedElement *& element_pt(const unsigned long &e)
Return pointer to element e.
Definition: mesh.h:448
oomph::Mesh::nnode
unsigned long nnode() const
Return number of nodes in the mesh.
Definition: mesh.h:596
oomph::Mesh::nelement
unsigned long nelement() const
Return number of elements in the mesh.
Definition: mesh.h:590
oomph::PerturbedSpineMesh::nspine
unsigned long nspine() const
Return the number of perturbed spines in the mesh.
Definition: perturbed_spines.h:581
oomph::PerturbedSpineMesh::node_pt
PerturbedSpineNode * node_pt(const unsigned long &n)
Return a pointer to the n-th global PerturbedSpineNode.
Definition: perturbed_spines.h:590
oomph::PerturbedSpineMesh::perturbed_spine_pt
PerturbedSpine *const & perturbed_spine_pt(const unsigned long &i) const
Return the i-th perturbed spine in the mesh.
Definition: perturbed_spines.h:575
oomph::PerturbedSpine::height_pt
Data *& height_pt()
Access function to Data object that stores the spine "heights".
Definition: perturbed_spines.h:114
oomph::PerturbedSpine::height
double & height(const unsigned &i)
Access function to i-th component of spine "height".
Definition: perturbed_spines.h:101
oomph::Problem::add_sub_mesh
unsigned add_sub_mesh(Mesh *const &mesh_pt)
Definition: problem.h:1330
oomph::Problem::build_global_mesh
void build_global_mesh()
Definition: problem.cc:1493
oomph::TwoLayerPerturbedSpineMesh::nlower
unsigned long nlower() const
Number of elements in top layer.
Definition: two_layer_perturbed_spine_mesh.template.h:134
oomph::TwoLayerPerturbedSpineMesh::set_perturbation_to_nodal_positions_indices
const void set_perturbation_to_nodal_positions_indices(const unsigned &cosine_index, const unsigned &sine_index)
Definition: two_layer_perturbed_spine_mesh.template.h:176
oomph::TwoLayerPerturbedSpineMesh::upper_layer_element_pt
FiniteElement *& upper_layer_element_pt(const unsigned long &i)
Access functions for pointers to elements in upper layer.
Definition: two_layer_perturbed_spine_mesh.template.h:123
oomph::TwoLayerPerturbedSpineMesh::lower_layer_element_pt
FiniteElement *& lower_layer_element_pt(const unsigned long &i)
Access functions for pointers to elements in lower layer.
Definition: two_layer_perturbed_spine_mesh.template.h:127
oomph::TwoLayerPerturbedSpineMesh::nupper
unsigned long nupper() const
Number of elements in upper layer.
Definition: two_layer_perturbed_spine_mesh.template.h:131
GlobalPhysicalVariables::ReInvFr
double ReInvFr
Product of Rynolds number and inverse of Froude number.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:67
GlobalPhysicalVariables::Viscosity_Ratio
double Viscosity_Ratio
Definition: two_layer_interface_nonaxisym_perturbations.cc:85
GlobalPhysicalVariables::G
Vector< double > G(3)
Direction of gravity.
GlobalPhysicalVariables::Density_Ratio
double Density_Ratio
Definition: two_layer_interface_nonaxisym_perturbations.cc:89

References oomph::Problem::add_sub_mesh(), oomph::Problem::add_time_stepper_pt(), oomph::Problem::assign_eqn_numbers(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Azimuthal_mode_number, b, PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Base_state_bulk_mesh_pt, oomph::Problem::build_global_mesh(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Bulk_mesh_pt, GlobalPhysicalVariables::Density_Ratio, e(), oomph::Mesh::element_pt(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure(), GlobalPhysicalVariables::G, oomph::PerturbedSpine::height(), oomph::PerturbedSpine::height_pt(), i, oomph::TwoLayerPerturbedSpineMesh< ELEMENT >::lower_layer_element_pt(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt(), n, oomph::Mesh::nelement(), oomph::TwoLayerPerturbedSpineMesh< ELEMENT >::nlower(), oomph::Mesh::nnode(), oomph::PerturbedSpineMesh::node_pt(), oomph::PerturbedSpineMesh::nspine(), oomph::TwoLayerPerturbedSpineMesh< ELEMENT >::nupper(), oomph::PerturbedSpineMesh::perturbed_spine_pt(), oomph::Data::pin(), GlobalPhysicalVariables::Re, GlobalPhysicalVariables::ReInvFr, GlobalPhysicalVariables::ReSt, oomph::TwoLayerPerturbedSpineMesh< ELEMENT >::set_perturbation_to_nodal_positions_indices(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Surface_mesh_pt, PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt(), PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::U_nodal_index, oomph::TwoLayerPerturbedSpineMesh< ELEMENT >::upper_layer_element_pt(), GlobalPhysicalVariables::Viscosity_Ratio, and PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Xhat_nodal_index.

◆ ~PerturbedStateProblem() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::~PerturbedStateProblem ( )
inline

Destructor (empty)

536 {}

Member Function Documentation

◆ actions_after_adapt() [1/2]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_adapt ( )
inlinevirtual

After adaptation: Pin pressure again (the previously pinned value might have disappeared) and pin redudant pressure dofs

Reimplemented from oomph::Problem.

427  {
428  // Unpin all pressure dofs
429  RefineableLinearisedAxisymmetricNavierStokesEquations::
430  unpin_all_pressure_dofs(mesh_pt()->element_pt());
431 
432  // Pin redudant pressure dofs
433  RefineableLinearisedAxisymmetricNavierStokesEquations::
434  pin_redundant_nodal_pressures(mesh_pt()->element_pt());
435 
436  // Fix pressure ONLY when looking for axisymmetric modes
437  if(GlobalPhysicalVariables::k==0) { fix_pressure(0,0,0.0); }
438 
439  // Set external elements for the multi-domain solution
440 
441  // First interaction (base state velocities)
442  Multi_domain_functions::
443  setup_multi_domain_interaction<BASE_ELEMENT>
444  (this,mesh_pt(),Base_state_mesh_pt,0);
445 
446  // Second interaction (base state velocity derivatives w.r.t. space)
447  Multi_domain_functions::
448  setup_multi_domain_interaction<BASE_ELEMENT>
449  (this,mesh_pt(),Base_state_mesh_pt,1);
450 
451  } // End of actions_after_adapt

References GlobalPhysicalVariables::k.

◆ actions_after_adapt() [2/2]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_adapt ( )
inlinevirtual

After adaptation: Pin pressure again (the previously pinned value might have disappeared) and pin redudant pressure dofs

Reimplemented from oomph::Problem.

519  {
520  // Unpin all pressure dofs
521  RefineableLinearisedAxisymmetricNavierStokesEquations::
522  unpin_all_pressure_dofs(mesh_pt()->element_pt());
523 
524  // Pin redudant pressure dofs
525  RefineableLinearisedAxisymmetricNavierStokesEquations::
526  pin_redundant_nodal_pressures(mesh_pt()->element_pt());
527 
528  // Fix pressure ONLY when looking for axisymmetric modes
529  if(GlobalPhysicalVariables::k==0) { fix_pressure(0,0,0.0); }
530 
531  // Set external elements for the multi-domain solution
532 
533  // First interaction (base state velocities)
534  Multi_domain_functions::
535  setup_multi_domain_interaction<BASE_ELEMENT>
536  (this,mesh_pt(),Base_state_mesh_pt,0);
537 
538  // Second interaction (base state velocity derivatives w.r.t. space)
539  Multi_domain_functions::
540  setup_multi_domain_interaction<BASE_ELEMENT>
541  (this,mesh_pt(),Base_state_mesh_pt,1);
542 
543  } // End of actions_after_adapt

References GlobalPhysicalVariables::k.

◆ actions_after_implicit_timestep() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

395 {}

◆ actions_after_implicit_timestep() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

422 {}

◆ actions_after_implicit_timestep() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

489 {}

◆ actions_after_implicit_timestep() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

514 {}

◆ actions_after_implicit_timestep() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

519 {}

◆ actions_after_implicit_timestep() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_implicit_timestep ( )
inlineprivatevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

626 {}

◆ actions_after_newton_solve() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

389 {}

◆ actions_after_newton_solve() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

416 {}

◆ actions_after_newton_solve() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

483 {}

◆ actions_after_newton_solve() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

508 {}

◆ actions_after_newton_solve() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

513 {}

◆ actions_after_newton_solve() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_after_newton_solve ( )
inlineprivatevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

609 {}

◆ actions_before_implicit_timestep() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlinevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

392 {}

◆ actions_before_implicit_timestep() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlinevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

419 {}

◆ actions_before_implicit_timestep() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlinevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

486 {}

◆ actions_before_implicit_timestep() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlinevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

511 {}

◆ actions_before_implicit_timestep() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlinevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

516 {}

◆ actions_before_implicit_timestep() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_implicit_timestep ( )
inlineprivatevirtual

Actions before timestep (empty)

Reimplemented from oomph::Problem.

613  {
614  // Shift perturbed spine height history values
615  // -------------------------------------------
616 
617  const unsigned n_perturbed_spine = Bulk_mesh_pt->nspine();
618  for(unsigned i=0;i<n_perturbed_spine;i++)
619  {
620  Bulk_mesh_pt->perturbed_spine_pt(i)->height_pt()->time_stepper_pt()->
621  shift_time_values(Bulk_mesh_pt->perturbed_spine_pt(i)->height_pt());
622  }
623  }
oomph::Data::time_stepper_pt
TimeStepper *& time_stepper_pt()
Return the pointer to the timestepper.
Definition: nodes.h:238
oomph::Problem::shift_time_values
virtual void shift_time_values()
Shift all values along to prepare for next timestep.
Definition: problem.cc:11634

References i.

◆ actions_before_newton_convergence_check()

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_convergence_check ( )
inlineprivatevirtual

Update mesh to have nodal positions equal to that of the base state mesh

Reimplemented from oomph::Problem.

601  {
602  Bulk_mesh_pt->node_update();
603  }
oomph::PerturbedSpineMesh::node_update
void node_update(const bool &update_all_solid_nodes=false)
Definition: perturbed_spines.cc:147

◆ actions_before_newton_solve() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

386 {}

◆ actions_before_newton_solve() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

413 {}

◆ actions_before_newton_solve() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

480 {}

◆ actions_before_newton_solve() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

505 {}

◆ actions_before_newton_solve() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

510 {}

◆ actions_before_newton_solve() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::actions_before_newton_solve ( )
inlineprivatevirtual

Update before solve (empty)

Reimplemented from oomph::Problem.

606 {}

◆ base_state_bulk_mesh_pt()

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
TwoLayerSpineMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_bulk_mesh_pt ( )
inline

Access function for the base state mesh.

546  {
547  return dynamic_cast<TwoLayerSpineMesh<BASE_ELEMENT>*>
548  (Base_state_bulk_mesh_pt);
549  }

◆ base_state_mesh_pt() [1/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_mesh_pt ( )
inline

Access function for the base state mesh.

413  {
414  return dynamic_cast<RectangularQuadMesh<BASE_ELEMENT>*>
415  (Base_state_mesh_pt);
416  }

◆ base_state_mesh_pt() [2/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RefineableRectangularQuadMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_mesh_pt ( )
inline

Access function for the base state mesh.

469  {
470  return dynamic_cast<RefineableRectangularQuadMesh<BASE_ELEMENT>*>
471  (Base_state_mesh_pt);
472  }
oomph::RefineableRectangularQuadMesh
Definition: rectangular_quadmesh.template.h:326

◆ base_state_mesh_pt() [3/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_mesh_pt ( )
inline

Access function for the base state mesh.

506  {
507  return dynamic_cast<RectangularQuadMesh<BASE_ELEMENT>*>
508  (Base_state_mesh_pt);
509  }

◆ base_state_mesh_pt() [4/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RefineableRectangularQuadMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_mesh_pt ( )
inline

Access function for the base state mesh.

560  {
561  return dynamic_cast<RefineableRectangularQuadMesh<BASE_ELEMENT>*>
562  (Base_state_mesh_pt);
563  }

◆ base_state_mesh_pt() [5/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<BASE_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::base_state_mesh_pt ( )
inline

Access function for the base state mesh.

536  {
537  return dynamic_cast<RectangularQuadMesh<BASE_ELEMENT>*>
538  (Base_state_mesh_pt);
539  }

◆ bulk_mesh_pt()

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
TwoLayerPerturbedSpineMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::bulk_mesh_pt ( )
inline

Access function for bulk mesh.

586  {
587  return Bulk_mesh_pt;
588  }

◆ close_trace_file() [1/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::close_trace_file ( )
inline

Clear and close trace file.

539 { Trace_file.clear(); Trace_file.close(); }
PerturbedStateProblem::Trace_file
ofstream Trace_file
Trace file.
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:578

References oomph::Problem_Parameter::Trace_file.

◆ close_trace_file() [2/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::close_trace_file ( )
inline

Clear and close trace file.

593 { Trace_file.clear(); Trace_file.close(); }

References oomph::Problem_Parameter::Trace_file.

◆ close_trace_file() [3/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::close_trace_file ( )
inline

Clear and close trace file.

570  {
571  Trace_file.clear();
572  Trace_file.close();
573  }

References oomph::Problem_Parameter::Trace_file.

◆ close_trace_file() [4/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::close_trace_file ( )
inline

Clear and close trace file.

576 { Trace_file.clear(); Trace_file.close(); }

References oomph::Problem_Parameter::Trace_file.

◆ create_interface_elements()

template<class BASE_ELEMENT , class PERTURBED_ELEMENT , class TIMESTEPPER >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT, TIMESTEPPER >::create_interface_elements

Create interface elements at boundary between upper and lower layers.

Create Interface Elements at the free surface between the two fluids in the mesh pointed to by bulk_mesh_pt and add the elements to the Mesh object pointeed to by surface_mesh_pt.

1056 {
1057  // Determine the number of horizontal elements
1058  const unsigned n_r = this->Bulk_mesh_pt->nx();
1059 
1060  // Determine number of bulk elements in the lower layer
1061  const unsigned n_z1 = this->Bulk_mesh_pt->ny1();
1062 
1063  // Loop over the horizontal elements
1064  for(unsigned e=0;e<n_r;e++)
1065  {
1066  // Construct a new 1D line element on the face on which the local
1067  // coordinate 1 is fixed at its max. value (1) -- Face 2
1068  FiniteElement* interface_element_element_pt =
1069  new PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1070  <PERTURBED_ELEMENT>
1071  (this->Bulk_mesh_pt->finite_element_pt(n_r*(n_z1-1)+e),2);
1072 
1073  // Add the interface element to the surface mesh
1074  this->Surface_mesh_pt->add_element_pt(interface_element_element_pt);
1075  }
1076 
1077  // ----------------------------------------------------------------
1078  // Complete the problem setup to make the elements fully functional
1079  // ----------------------------------------------------------------
1080 
1081  // Determine number of 1D interface elements in mesh
1082  const unsigned n_interface_element = this->Surface_mesh_pt->nelement();
1083 
1084  // Loop over interface elements
1085  for(unsigned e=0;e<n_interface_element;e++)
1086  {
1087  // Upcast from GeneralisedElement to the present element
1088  PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1089  <PERTURBED_ELEMENT>* el_pt =
1090  dynamic_cast<PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1091  <PERTURBED_ELEMENT>*>(this->Surface_mesh_pt->element_pt(e));
1092 
1093  // Set the Strouhal number
1094  el_pt->st_pt() = &GlobalPhysicalVariables::St;
1095 
1096  // Set the Capillary number
1097  el_pt->ca_pt() = &GlobalPhysicalVariables::Ca;
1098 
1099  // Set the azimuthal mode number
1100  el_pt->azimuthal_mode_number_pt() = &Azimuthal_mode_number;
1101 
1102  // These terms in the Jacobian matrix are provided analytically, so
1103  // by filling them in from geometric data we would be "double counting"
1104  el_pt->enable_bypass_fill_in_jacobian_from_geometric_data();
1105  }
1106 
1107 } // End of create_interface_elements
oomph::FiniteElement
Definition: elements.h:1313
oomph::LinearisedAxisymmetricFluidInterfaceElement::st_pt
double *& st_pt()
Return a pointer to the Strouhal number.
Definition: linearised_axisymmetric_fluid_interface_elements.h:185
oomph::Mesh::finite_element_pt
FiniteElement * finite_element_pt(const unsigned &e) const
Definition: mesh.h:473
oomph::Mesh::add_element_pt
void add_element_pt(GeneralisedElement *const &element_pt)
Add a (pointer to) an element to the mesh.
Definition: mesh.h:617
oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
Definition: linearised_axisymmetric_fluid_interface_elements.h:260
oomph::RectangularQuadMesh::nx
const unsigned & nx() const
Return number of elements in x direction.
Definition: rectangular_quadmesh.template.h:224
oomph::TwoLayerPerturbedSpineMesh::ny1
const unsigned & ny1() const
Access function for number of elements in lower layer.
Definition: two_layer_perturbed_spine_mesh.template.h:168
GlobalPhysicalVariables::St
double St
Strouhal number.
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:62
GlobalPhysicalVariables::Ca
double Ca
Capillary number.
Definition: two_layer_interface_nonaxisym_perturbations.cc:92

References GlobalPhysicalVariables::Ca, e(), GlobalPhysicalVariables::St, and oomph::LinearisedAxisymmetricFluidInterfaceElement::st_pt().

◆ create_trace_file() [1/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::create_trace_file ( DocInfo &  doc_info)
inline

Create a trace file.

522  {
523  // Open trace file
524  char filename[256];
525  sprintf(filename,"%s/perturbed_trace_k%i_Re%4.2f.dat",
526  doc_info.directory().c_str(),
527  GlobalPhysicalVariables::k,
528  GlobalPhysicalVariables::Re_current);
529  Trace_file.open(filename);
530  }
oomph::DocInfo::directory
std::string directory() const
Output directory.
Definition: oomph_utilities.h:524
GlobalPhysicalVariables::Re_current
double Re_current
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:70
MergeRestartFiles.filename
string filename
Definition: MergeRestartFiles.py:39

References oomph::DocInfo::directory(), MergeRestartFiles::filename, GlobalPhysicalVariables::k, GlobalPhysicalVariables::Re_current, and oomph::Problem_Parameter::Trace_file.

◆ create_trace_file() [2/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::create_trace_file ( DocInfo &  doc_info)
inline

Create a trace file.

576  {
577  // Open trace file
578  char filename[256];
579  sprintf(filename,"%s/perturbed_trace_k%i_Re%4.2f.dat",
580  doc_info.directory().c_str(),
581  GlobalPhysicalVariables::k,
582  GlobalPhysicalVariables::Re_current);
583  Trace_file.open(filename);
584  }

References oomph::DocInfo::directory(), MergeRestartFiles::filename, GlobalPhysicalVariables::k, GlobalPhysicalVariables::Re_current, and oomph::Problem_Parameter::Trace_file.

◆ create_trace_file() [3/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::create_trace_file ( DocInfo &  doc_info)
inline

Create a trace file.

552  {
553  // Open trace file
554  char filename[256];
555  sprintf(filename,"%s/perturbed_trace_epsilon%2.1f_Re%4.2f.dat",
556  doc_info.directory().c_str(),
557  GlobalPhysicalVariables::Epsilon,
558  GlobalPhysicalVariables::MMC_Re_current);
559  Trace_file.open(filename);
560  }
GlobalPhysicalVariables::Epsilon
double Epsilon
Dimensionless modulation amplitude (epsilon)
Definition: time_periodic_taylor_couette.cc:84
GlobalPhysicalVariables::MMC_Re_current
double MMC_Re_current
Definition: time_periodic_taylor_couette.cc:73

References oomph::DocInfo::directory(), GlobalPhysicalVariables::Epsilon, MergeRestartFiles::filename, GlobalPhysicalVariables::MMC_Re_current, and oomph::Problem_Parameter::Trace_file.

◆ create_trace_file() [4/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::create_trace_file ( DocInfo *&  doc_info_pt)
inline

Create and initialise a trace file.

562  {
563  // Open trace file
564  char filename[256];
565  sprintf(filename,"%s/perturbed_trace_k%i.dat",
566  doc_info_pt->directory().c_str(),
567  Azimuthal_mode_number);
568  Trace_file.open(filename);
569 
570  // Initialise
571  Trace_file << "time, height (cosine), height (sine), growth_rate, d_kinetic_energy_dt, kinetic_energy"
572  << std::endl;
573  }

References oomph::DocInfo::directory(), MergeRestartFiles::filename, and oomph::Problem_Parameter::Trace_file.

◆ doc_solution() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::doc_solution ( DocInfo &  doc_info)

Doc the solution.

Document the perturbed state solution.

667 {
668  ofstream some_file;
669  char filename[256];
670 
671  // Set number of plot points (in each coordinate direction)
672  const unsigned npts = 5;
673 
674  // Open solution output file
675  sprintf(filename,"%s/perturbed_soln%i.dat",
676  doc_info.directory().c_str(),
677  doc_info.number());
678  some_file.open(filename);
679 
680  // Output solution to file
681  mesh_pt()->output(some_file,npts);
682 
683  // Close solution output file
684  some_file.close();
685 
686 } // End of doc_solution for perturbed state
oomph::DocInfo::number
unsigned & number()
Number used (e.g.) for labeling output files.
Definition: oomph_utilities.h:554

References oomph::DocInfo::directory(), MergeRestartFiles::filename, and oomph::DocInfo::number().

◆ doc_solution() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::doc_solution ( DocInfo &  doc_info)

Doc the solution.

◆ doc_solution() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::doc_solution ( DocInfo &  doc_info,
const bool &  output_soln = true 
)

Doc the solution.

Document the perturbed state solution.

808 {
809  // Create vector of dofs
810  DoubleVector dofs;
811 
812  // Get dofs
813  this->get_dofs(dofs);
814 
815  // Get L2 norm of dof vector
816  const double dof_norm = dofs.norm();
817 
818  // Document in trace file
819  Trace_file << time_pt()->time() << " " << dof_norm << std::endl;
820 
821  // If desired, output solution to file
822  if(output_soln)
823  {
824  ofstream some_file;
825  char filename[256];
826 
827  // Set number of plot points (in each coordinate direction)
828  const unsigned npts = 5;
829 
830  // Open solution output file
831  sprintf(filename,"%s/perturbed_soln_k%i_Re%4.2f_soln%i.dat",
832  doc_info.directory().c_str(),
833  GlobalPhysicalVariables::k,
834  GlobalPhysicalVariables::Re_current,
835  doc_info.number());
836  some_file.open(filename);
837 
838  // Output solution to file
839  mesh_pt()->output(some_file,npts);
840 
841  // Close solution output file
842  some_file.close();
843  }
844 } // End of doc_solution for perturbed state
oomph::DoubleVector
Definition: double_vector.h:58
oomph::DoubleVector::norm
double norm() const
compute the 2 norm of this vector
Definition: double_vector.cc:867
oomph::Problem::get_dofs
void get_dofs(DoubleVector &dofs) const
Definition: problem.cc:2479
oomph::Problem::time_pt
Time *& time_pt()
Return a pointer to the global time object.
Definition: problem.h:1504
oomph::Time::time
double & time()
Return the current value of the continuous time.
Definition: timesteppers.h:123

References oomph::DocInfo::directory(), MergeRestartFiles::filename, GlobalPhysicalVariables::k, oomph::DoubleVector::norm(), oomph::DocInfo::number(), GlobalPhysicalVariables::Re_current, and oomph::Problem_Parameter::Trace_file.

◆ doc_solution() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::doc_solution ( DocInfo &  doc_info,
const bool &  output_soln = true 
)

Doc the solution.

◆ doc_solution() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::doc_solution ( DocInfo &  doc_info,
const bool &  output_soln = true 
)

Doc the solution.

◆ doc_solution() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT , class TIMESTEPPER >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT, TIMESTEPPER >::doc_solution ( DocInfo *&  doc_info_pt,
const bool &  output_soln = true 
)

Doc the solution.

Document the perturbed state solution.

1189 {
1190  // Decide which spine to use for documenting heights in trace file
1191  // ---------------------------------------------------------------
1192 
1193  // Initialise "trace spine"
1194  unsigned trace_spine = 0;
1195 
1196  // Determine the number of spines in the mesh
1197  const unsigned n_spine = Bulk_mesh_pt->nspine();
1198 
1199  // Make decision based on azimuthal mode number
1200  if(Azimuthal_mode_number==0) { trace_spine = 0; }
1201  else { trace_spine = (n_spine-1)/2; }
1202 
1203  // Compute kinetic energy of perturbation
1204  // --------------------------------------
1205 
1206  // Initialise kinetic energy and its derivative w.r.t. time
1207  double kinetic_energy = 0.0;
1208  double d_kinetic_energy_dt = 0.0;
1209 
1210  // Loop over bulk elements in lower layer
1211  const unsigned n_lower = Bulk_mesh_pt->nlower();
1212  for(unsigned e=0;e<n_lower;e++)
1213  {
1214  // Upcast from GeneralisedElement to the present element
1215  PERTURBED_ELEMENT *el_pt = dynamic_cast<PERTURBED_ELEMENT*>
1216  (Bulk_mesh_pt->lower_layer_element_pt(e));
1217 
1218  // Initialise element's contributions to kinetic energy and its deriv
1219  double el_kinetic_energy = 0.0;
1220  double el_d_kinetic_energy_dt = 0.0;
1221 
1222  // Compute element's contributions to kinetic energy and its deriv
1223  el_pt->dkin_energy_dt(d_kinetic_energy_dt,el_kinetic_energy);
1224 
1225  // Add contribution to "global" kinetic energy and its deriv
1226  // (Don't forget to multiply through by the element's density ratio
1227  // in both cases)
1228  kinetic_energy += (el_pt->density_ratio())*el_kinetic_energy;
1229  d_kinetic_energy_dt += (el_pt->density_ratio())*el_d_kinetic_energy_dt;
1230  }
1231 
1232  // Loop over bulk elements in upper layer
1233  const unsigned n_upper = Bulk_mesh_pt->nupper();
1234  for(unsigned e=0;e<n_upper;e++)
1235  {
1236  // Upcast from GeneralisedElement to the present element
1237  PERTURBED_ELEMENT *el_pt = dynamic_cast<PERTURBED_ELEMENT*>
1238  (Bulk_mesh_pt->upper_layer_element_pt(e));
1239 
1240  // Initialise element's contributions to kinetic energy and its deriv
1241  double el_kinetic_energy = 0.0;
1242  double el_d_kinetic_energy_dt = 0.0;
1243 
1244  // Compute element's contributions to kinetic energy and its deriv
1245  el_pt->dkin_energy_dt(d_kinetic_energy_dt,el_kinetic_energy);
1246 
1247  // Add contribution to "global" kinetic energy and its deriv
1248  // (Don't forget to multiply through by the element's density ratio
1249  // in both cases)
1250  kinetic_energy += (el_pt->density_ratio())*el_kinetic_energy;
1251  d_kinetic_energy_dt += (el_pt->density_ratio())*el_d_kinetic_energy_dt;
1252  }
1253 
1254  // Compute growth rate by considering relative growth
1255  // (see A. Hazel and R. Hewitt's torus linear stab paper 2011, page 21)
1256  double growth_rate = 0.0;
1257  if(kinetic_energy!=0.0)
1258  {
1259  growth_rate = (0.5*d_kinetic_energy_dt)/kinetic_energy;
1260  }
1261 
1262  // Document in trace file
1263  Trace_file << time_pt()->time() << " "
1264  << Bulk_mesh_pt->perturbed_spine_pt(trace_spine)->height(0)
1265  << " "
1266  << Bulk_mesh_pt->perturbed_spine_pt(trace_spine)->height(1)
1267  << " "
1268  << growth_rate << " "
1269  << d_kinetic_energy_dt << " "
1270  << kinetic_energy << std::endl;
1271 
1272  // If desired, output solution to file
1273  if(output_soln)
1274  {
1275  ofstream some_file;
1276  char filename[256];
1277 
1278  // Set number of plot points (in each coordinate direction)
1279  const unsigned npts_bulk = 5;
1280  const unsigned npts_surface = 5;
1281 
1282  // Open solution output file
1283  sprintf(filename,"%s/perturbed_k%i_soln%i.dat",
1284  doc_info_pt->directory().c_str(),
1285  Azimuthal_mode_number,
1286  doc_info_pt->number());
1287  some_file.open(filename);
1288 
1289  // Output solution to file
1290  Bulk_mesh_pt->output(some_file,npts_bulk);
1291 
1292  // Close solution output file
1293  some_file.close();
1294 
1295  // Open interface solution output file
1296  sprintf(filename,
1297  "%s/perturbation_to_interface_k%i_soln%i.dat",
1298  doc_info_pt->directory().c_str(),
1299  Azimuthal_mode_number,
1300  doc_info_pt->number());
1301  some_file.open(filename);
1302 
1303  // Output solution to file
1304  const unsigned n_interface_element = Surface_mesh_pt->nelement();
1305  for(unsigned e=0;e<n_interface_element;e++)
1306  {
1307  // Upcast from GeneralisedElement to the present element
1308  PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1309  <PERTURBED_ELEMENT>* el_pt =
1310  dynamic_cast<PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1311  <PERTURBED_ELEMENT>*>(Surface_mesh_pt->element_pt(e));
1312 
1313  // Output solution to file
1314  el_pt->output_perturbation_to_interface(some_file,npts_surface);
1315  }
1316 
1317  // Close solution output file
1318  some_file.close();
1319 
1320  // Open interface solution output file
1321  sprintf(filename,
1322  "%s/combined_interface_position_k%i_soln%i.dat",
1323  doc_info_pt->directory().c_str(),
1324  Azimuthal_mode_number,
1325  doc_info_pt->number());
1326  some_file.open(filename);
1327 
1328  // Output solution to file
1329  for(unsigned e=0;e<n_interface_element;e++)
1330  {
1331  // Upcast from GeneralisedElement to the present element
1332  PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1333  <PERTURBED_ELEMENT>* el_pt =
1334  dynamic_cast<PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement
1335  <PERTURBED_ELEMENT>*>(Surface_mesh_pt->element_pt(e));
1336 
1337  // Output solution to file
1338  el_pt->output_interface_position(some_file,npts_surface);
1339  }
1340 
1341  // Close solution output file
1342  some_file.close();
1343 
1344  }
1345 
1346 } // End of doc_solution for perturbed state
oomph::Mesh::output
void output(std::ostream &outfile)
Output for all elements.
Definition: mesh.cc:2027
oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement::output_perturbation_to_interface
void output_perturbation_to_interface(std::ostream &outfile, const unsigned &nplot)
Output the perturbation to the interface position.
Definition: linearised_axisymmetric_fluid_interface_elements.cc:129
oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement::output_interface_position
void output_interface_position(std::ostream &outfile, const unsigned &nplot)
Output just the interface position (base + perturbation)
Definition: linearised_axisymmetric_fluid_interface_elements.cc:171

References oomph::DocInfo::directory(), e(), MergeRestartFiles::filename, oomph::DocInfo::number(), oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement< ELEMENT >::output_interface_position(), oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement< ELEMENT >::output_perturbation_to_interface(), and oomph::Problem_Parameter::Trace_file.

◆ fix_pressure() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

429  {
430  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
431  ->fix_pressure(pdof,pvalue);
432  }

References e().

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ fix_pressure() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

485  {
486  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
487  ->fix_pressure(pdof,pvalue);
488  }

References e().

◆ fix_pressure() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

572  {
573  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
574  ->fix_pressure(pdof,pvalue);
575  }

References e().

◆ fix_pressure() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

626  {
627  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
628  ->fix_pressure(pdof,pvalue);
629  }

References e().

◆ fix_pressure() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

586  {
587  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
588  ->fix_pressure(pdof,pvalue);
589  }

References e().

◆ fix_pressure() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::fix_pressure ( const unsigned &  e,
const unsigned &  pdof,
const double &  pvalue 
)
inlineprivate

Fix pressure in element e at pressure dof pdof and set to pvalue.

631  {
632  dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e))
633  ->fix_pressure(pdof,pvalue);
634  }

References e().

◆ initialise_trace_file() [1/3]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::initialise_trace_file ( )
inline

Initialise trace file (print column headings)

534  {
535  Trace_file << "time, norm_of_dof_vector" << std::endl;
536  }

References oomph::Problem_Parameter::Trace_file.

◆ initialise_trace_file() [2/3]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::initialise_trace_file ( )
inline

Initialise trace file (print column headings)

588  {
589  Trace_file << "time, norm_of_dof_vector" << std::endl;
590  }

References oomph::Problem_Parameter::Trace_file.

◆ initialise_trace_file() [3/3]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::initialise_trace_file ( )
inline

Initialise trace file (print column headings)

564  {
565  Trace_file << "time, norm_of_dof_vector" << std::endl;
566  }

References oomph::Problem_Parameter::Trace_file.

◆ mesh_pt() [1/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt ( )
inline

Access function for the specific mesh.

406  {
407  return dynamic_cast<RectangularQuadMesh<PERTURBED_ELEMENT>*>
408  (Problem::mesh_pt());
409  }

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ mesh_pt() [2/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RefineableRectangularQuadMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt ( )
inline

Access function for the specific mesh.

462  {
463  return dynamic_cast<RefineableRectangularQuadMesh<PERTURBED_ELEMENT>*>
464  (Problem::mesh_pt());
465  }

◆ mesh_pt() [3/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt ( )
inline

Access function for the specific mesh.

499  {
500  return dynamic_cast<RectangularQuadMesh<PERTURBED_ELEMENT>*>
501  (Problem::mesh_pt());
502  }

◆ mesh_pt() [4/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RefineableRectangularQuadMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt ( )
inline

Access function for the specific mesh.

553  {
554  return dynamic_cast<RefineableRectangularQuadMesh<PERTURBED_ELEMENT>*>
555  (Problem::mesh_pt());
556  }

◆ mesh_pt() [5/5]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
RectangularQuadMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::mesh_pt ( )
inline

Access function for the specific mesh.

529  {
530  return dynamic_cast<RectangularQuadMesh<PERTURBED_ELEMENT>*>
531  (Problem::mesh_pt());
532  }

◆ pass_updated_nondim_parameters_to_elements() [1/2]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::pass_updated_nondim_parameters_to_elements ( )
inline
545  {
546  // Determine number of elements in mesh
547  const unsigned n_element = this->mesh_pt()->nelement();
548 
549  // Loop over the elements
550  for(unsigned e=0;e<n_element;e++)
551  {
552  // Upcast from GeneralisedElement to the present element
553  PERTURBED_ELEMENT* el_pt
554  = dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e));
555 
556  // Set the Reynolds number
557  el_pt->re_pt() = &GlobalPhysicalVariables::Re_current;
558 
559  // Set the Womersley number
560  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt_current;
561  }
562  }
GlobalPhysicalVariables::ReSt_current
double ReSt_current
Definition: linearised_axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:71

References e(), GlobalPhysicalVariables::Re_current, and GlobalPhysicalVariables::ReSt_current.

◆ pass_updated_nondim_parameters_to_elements() [2/2]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::pass_updated_nondim_parameters_to_elements ( )
inline
599  {
600  // Determine number of elements in mesh
601  const unsigned n_element = this->mesh_pt()->nelement();
602 
603  // Loop over the elements
604  for(unsigned e=0;e<n_element;e++)
605  {
606  // Upcast from GeneralisedElement to the present element
607  PERTURBED_ELEMENT* el_pt
608  = dynamic_cast<PERTURBED_ELEMENT*>(mesh_pt()->element_pt(e));
609 
610  // Set the Reynolds number
611  el_pt->re_pt() = &GlobalPhysicalVariables::Re_current;
612 
613  // Set the Womersley number
614  el_pt->re_st_pt() = &GlobalPhysicalVariables::ReSt_current;
615  }
616  }

References e(), GlobalPhysicalVariables::Re_current, and GlobalPhysicalVariables::ReSt_current.

◆ set_boundary_conditions() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT , class TIMESTEPPER >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT, TIMESTEPPER >::set_boundary_conditions

Set up the (homogeneous) boundary conditions.

Set the (homogeneous) boundary conditions for the perturbed state.

616 {
617  // Determine number of mesh boundaries
618  const unsigned n_boundary = mesh_pt()->nboundary();
619 
620  // Loop over mesh boundaries
621  for(unsigned b=0;b<n_boundary;b++)
622  {
623  // Determine number of nodes on boundary b
624  const unsigned n_node = mesh_pt()->nboundary_node(b);
625 
626  // Loop over nodes on boundary b
627  for(unsigned n=0;n<n_node;n++)
628  {
629  // Set up pointer to node
630  Node* nod_pt = mesh_pt()->boundary_node_pt(b,n);
631 
632  // For the solid boundaries set all components to zero
633  if(b!=3)
634  {
635  nod_pt->set_value(0,0,0.0); // Radial
636  nod_pt->set_value(0,1,0.0); // Radial
637  nod_pt->set_value(0,2,0.0); // Axial
638  nod_pt->set_value(0,3,0.0); // Axial
639  nod_pt->set_value(0,4,0.0); // Azimuthal
640  nod_pt->set_value(0,5,0.0); // Azimuthal
641  }
642  // On symmetry boundary, set only radial and azimuthal components to
643  // zero, unless we are looking at the k=1 azimuthal mode. In this
644  // case, do not set the value of any of the velocity components
645  else
646  {
647  if(GlobalPhysicalVariables::k!=1)
648  {
649  nod_pt->set_value(0,0,0.0); // Radial
650  nod_pt->set_value(0,1,0.0); // Radial
651  nod_pt->set_value(0,4,0.0); // Azimuthal
652  nod_pt->set_value(0,5,0.0); // Azimuthal
653  }
654  }
655  } // End of loop over nodes on boundary b
656  } // End of loop over mesh boundaries
657 } // End of set_boundary_conditions for perturbed state
oomph::Data::set_value
void set_value(const unsigned &i, const double &value_)
Definition: nodes.h:271

References b, GlobalPhysicalVariables::k, n, and oomph::Data::set_value().

◆ set_boundary_conditions() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_boundary_conditions ( )

Set up the (homogeneous) boundary conditions.

◆ set_boundary_conditions() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_boundary_conditions ( )

Set up the (homogeneous) boundary conditions.

◆ set_boundary_conditions() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_boundary_conditions ( )

Set up the (homogeneous) boundary conditions.

◆ set_boundary_conditions() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_boundary_conditions ( )

Set up the (homogeneous) boundary conditions.

◆ set_boundary_conditions() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_boundary_conditions ( )

Set up the (homogeneous) boundary conditions.

◆ set_initial_condition() [1/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT , class TIMESTEPPER >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT, TIMESTEPPER >::set_initial_condition
virtual

Set the initial conditions to a "Poiseuille-style" profile.

Perturb the interface.

Set the three velocity components to a smoothly varying, non-zero profile

Set the three velocity components to a smoothly-varying, non-zero profile

Reimplemented from oomph::Problem.

579 {
580  // Determine number of nodes in mesh
581  const unsigned n_node = mesh_pt()->nnode();
582 
583  // Loop over all nodes in mesh
584  for(unsigned n=0;n<n_node;n++)
585  {
586  // Loop over the six velocity components
587  for(unsigned i=0;i<6;i++)
588  {
589  // Get x and y position of node
590  const double x = mesh_pt()->node_pt(n)->x(0);
591  const double y = mesh_pt()->node_pt(n)->x(1);
592 
593  // Assign "Poiseuille-style" initial conditions
594  const double value = 4.0*x*(x-1.0)*y*(y-Domain_height);
595 
596  mesh_pt()->node_pt(n)->set_value(i,value);
597  }
598  } // End of loop over nodes in mesh
599 
600  // Note that we do not need to set any history values as we are
601  // using a self-starting timestepper (BDF<1>)
602 
603  // Set the boundary conditions
604  set_boundary_conditions();
605 
606 } // End of set_initial_condition for perturbed state
PerturbedStateProblem::set_boundary_conditions
void set_boundary_conditions()
Set up the (homogeneous) boundary conditions.
Definition: axisym_navier_stokes/counter_rotating_disks/counter_rotating_disks.cc:615
y
Scalar * y
Definition: level1_cplx_impl.h:128
Eigen::value
squared absolute value
Definition: GlobalFunctions.h:87
plotDoE.x
list x
Definition: plotDoE.py:28

References i, n, Eigen::value, plotDoE::x, and y.

◆ set_initial_condition() [2/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_initial_condition ( )
virtual

Set the three velocity components to a smoothly varying, non-zero profile

Reimplemented from oomph::Problem.

◆ set_initial_condition() [3/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_initial_condition ( )
virtual

Set initial conditions to a "Poiseuille-style" profile.

Reimplemented from oomph::Problem.

◆ set_initial_condition() [4/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_initial_condition ( )
virtual

Set initial conditions to a "Poiseuille-style" profile.

Reimplemented from oomph::Problem.

◆ set_initial_condition() [5/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_initial_condition ( )
virtual

Set initial conditions to a "Poiseuille-style" profile.

Reimplemented from oomph::Problem.

◆ set_initial_condition() [6/6]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
void PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::set_initial_condition ( )
virtual

Set initial conditions (velocities given random values in range [0,1])

Reimplemented from oomph::Problem.

◆ surface_mesh_pt()

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
Mesh* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::surface_mesh_pt ( )
inline

Access function for surface mesh.

592  {
593  return Surface_mesh_pt;
594  }

◆ time_stepper_pt() [1/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
SelfStartingBDF2* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt ( )
inline

Access function for the specific timestepper.

513  {
514  return dynamic_cast<SelfStartingBDF2*>(Problem::time_stepper_pt());
515  }

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ time_stepper_pt() [2/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
SelfStartingBDF2* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt ( )
inline

Access function for the specific timestepper.

567  {
568  return dynamic_cast<SelfStartingBDF2*>(Problem::time_stepper_pt());
569  }

◆ time_stepper_pt() [3/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
SelfStartingBDF2* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt ( )
inline

Access function for the specific timestepper.

543  {
544  return dynamic_cast<SelfStartingBDF2*>(Problem::time_stepper_pt());
545  }

◆ time_stepper_pt() [4/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
TIMESTEPPER* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::time_stepper_pt ( )
inline

Access function for the specific timestepper.

553  {
554  return dynamic_cast<TIMESTEPPER*>(Problem::time_stepper_pt());
555  }

◆ trace_file() [1/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
ofstream& PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::trace_file ( )
inline

Access function for trace file.

542 { return Trace_file; }

References oomph::Problem_Parameter::Trace_file.

◆ trace_file() [2/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
ofstream& PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::trace_file ( )
inline

Access function for trace file.

596 { return Trace_file; }

References oomph::Problem_Parameter::Trace_file.

◆ trace_file() [3/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
ofstream& PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::trace_file ( )
inline

Access function for trace file.

576 { return Trace_file; }

References oomph::Problem_Parameter::Trace_file.

◆ trace_file() [4/4]

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
ofstream& PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::trace_file ( )
inline

Access function for trace file.

579 { return Trace_file; }

References oomph::Problem_Parameter::Trace_file.

Member Data Documentation

◆ Azimuthal_mode_number

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
int PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Azimuthal_mode_number
private

Azimuthal mode number.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Base_state_bulk_mesh_pt

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
SpineMesh* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Base_state_bulk_mesh_pt
private

Pointer to the base state mesh.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Base_state_mesh_pt

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
Mesh * PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Base_state_mesh_pt
private

Pointer to the base state mesh.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Bulk_mesh_pt

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
TwoLayerPerturbedSpineMesh<PERTURBED_ELEMENT>* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Bulk_mesh_pt
private

Pointer to the (specific) "bulk" mesh.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Domain_height

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
double PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Domain_height
private

Height of domain.

◆ Inner_cylinder_radius

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
double PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Inner_cylinder_radius
private

Inner and outer cylinder radii.

◆ Outer_cylinder_radius

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
double PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Outer_cylinder_radius
private

◆ Surface_mesh_pt

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
Mesh* PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Surface_mesh_pt
private

Pointer to the "surface" mesh.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Trace_file

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
ofstream PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Trace_file
private

Trace file.

◆ U_nodal_index

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
Vector<unsigned> PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::U_nodal_index
private

Index at which the i-th velocity component is stored.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

◆ Xhat_nodal_index

template<class BASE_ELEMENT , class PERTURBED_ELEMENT >
Vector<unsigned> PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::Xhat_nodal_index
private

Index at which the i-th component of the perturbation to the nodal coordinate is stored.

Referenced by PerturbedStateProblem< BASE_ELEMENT, PERTURBED_ELEMENT >::PerturbedStateProblem().

The documentation for this class was generated from the following files: