Inheritance diagram for aspect::Postprocess::CrystalPreferredOrientation< dim >:

Public Member Functions
	CrystalPreferredOrientation ()

	~CrystalPreferredOrientation ()

void	initialize () override

std::pair< std::string, std::string >	execute (TableHandler &statistics) override

std::list< std::string >	required_other_postprocessors () const override

void	save (std::map< std::string, std::string > &status_strings) const override

void	load (const std::map< std::string, std::string > &status_strings) override

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)

void	parse_parameters (ParameterHandler &prm) override

Public Member Functions inherited from aspect::Plugins::InterfaceBase
virtual	~InterfaceBase ()=default

virtual void	update ()

Public Member Functions inherited from aspect::SimulatorAccess< dim >
	SimulatorAccess ()

	SimulatorAccess (const Simulator< dim > &simulator_object)

virtual	~SimulatorAccess ()=default

virtual void	initialize_simulator (const Simulator< dim > &simulator_object)

const Introspection< dim > &	introspection () const

const Simulator< dim > &	get_simulator () const

const Parameters< dim > &	get_parameters () const

SimulatorSignals< dim > &	get_signals () const

MPI_Comm	get_mpi_communicator () const

TimerOutput &	get_computing_timer () const

const ConditionalOStream &	get_pcout () const

double	get_time () const

double	get_timestep () const

double	get_old_timestep () const

unsigned int	get_timestep_number () const

const TimeStepping::Manager< dim > &	get_timestepping_manager () const

unsigned int	get_nonlinear_iteration () const

const parallel::distributed::Triangulation< dim > &	get_triangulation () const

double	get_volume () const

const Mapping< dim > &	get_mapping () const

std::string	get_output_directory () const

bool	include_adiabatic_heating () const

bool	include_latent_heat () const

bool	include_melt_transport () const

int	get_stokes_velocity_degree () const

double	get_adiabatic_surface_temperature () const

double	get_surface_pressure () const

bool	convert_output_to_years () const

unsigned int	get_pre_refinement_step () const

unsigned int	n_compositional_fields () const

double	get_end_time () const

void	get_refinement_criteria (Vector< float > &estimated_error_per_cell) const

void	get_artificial_viscosity (Vector< float > &viscosity_per_cell, const bool skip_interior_cells=false) const

void	get_artificial_viscosity_composition (Vector< float > &viscosity_per_cell, const unsigned int compositional_variable) const

const LinearAlgebra::BlockVector &	get_current_linearization_point () const

const LinearAlgebra::BlockVector &	get_solution () const

const LinearAlgebra::BlockVector &	get_old_solution () const

const LinearAlgebra::BlockVector &	get_old_old_solution () const

const LinearAlgebra::BlockVector &	get_reaction_vector () const

const LinearAlgebra::BlockVector &	get_mesh_velocity () const

const DoFHandler< dim > &	get_dof_handler () const

const FiniteElement< dim > &	get_fe () const

const LinearAlgebra::BlockSparseMatrix &	get_system_matrix () const

const LinearAlgebra::BlockSparseMatrix &	get_system_preconditioner_matrix () const

const MaterialModel::Interface< dim > &	get_material_model () const

const GravityModel::Interface< dim > &	get_gravity_model () const

const InitialTopographyModel::Interface< dim > &	get_initial_topography_model () const

const std::shared_ptr< const InitialTopographyModel::Interface< dim > >	get_initial_topography_model_pointer () const

const GeometryModel::Interface< dim > &	get_geometry_model () const

const AdiabaticConditions::Interface< dim > &	get_adiabatic_conditions () const

bool	has_boundary_temperature () const

const BoundaryTemperature::Manager< dim > &	get_boundary_temperature_manager () const

const BoundaryConvectiveHeating::Manager< dim > &	get_boundary_convective_heating_manager () const

const BoundaryHeatFlux::Interface< dim > &	get_boundary_heat_flux () const

bool	has_boundary_composition () const

const BoundaryComposition::Manager< dim > &	get_boundary_composition_manager () const

const BoundaryTraction::Manager< dim > &	get_boundary_traction_manager () const

std::shared_ptr< const InitialTemperature::Manager< dim > >	get_initial_temperature_manager_pointer () const

const InitialTemperature::Manager< dim > &	get_initial_temperature_manager () const

std::shared_ptr< const InitialComposition::Manager< dim > >	get_initial_composition_manager_pointer () const

const InitialComposition::Manager< dim > &	get_initial_composition_manager () const

const std::set< types::boundary_id > &	get_fixed_temperature_boundary_indicators () const

const std::set< types::boundary_id > &	get_fixed_heat_flux_boundary_indicators () const

const std::set< types::boundary_id > &	get_fixed_convective_heating_boundary_indicators () const

const std::set< types::boundary_id > &	get_fixed_composition_boundary_indicators () const

const std::set< types::boundary_id > &	get_mesh_deformation_boundary_indicators () const

const BoundaryVelocity::Manager< dim > &	get_boundary_velocity_manager () const

const HeatingModel::Manager< dim > &	get_heating_model_manager () const

const MeshRefinement::Manager< dim > &	get_mesh_refinement_manager () const

const MeltHandler< dim > &	get_melt_handler () const

const VolumeOfFluidHandler< dim > &	get_volume_of_fluid_handler () const

const NewtonHandler< dim > &	get_newton_handler () const

const MeshDeformation::MeshDeformationHandler< dim > &	get_mesh_deformation_handler () const

const LateralAveraging< dim > &	get_lateral_averaging () const

const AffineConstraints< double > &	get_current_constraints () const

bool	simulator_is_past_initialization () const

double	get_pressure_scaling () const

bool	pressure_rhs_needs_compatibility_modification () const

bool	model_has_prescribed_stokes_solution () const

TableHandler &	get_statistics_object () const

const Postprocess::Manager< dim > &	get_postprocess_manager () const

unsigned int	n_particle_managers () const

const Particle::Manager< dim > &	get_particle_manager (const unsigned int particle_manager_index) const

Particle::Manager< dim > &	get_particle_manager (const unsigned int particle_manager_index)

bool	is_stokes_matrix_free ()

const StokesMatrixFreeHandler< dim > &	get_stokes_matrix_free () const

RotationProperties< dim >	compute_net_angular_momentum (const bool use_constant_density, const LinearAlgebra::BlockVector &solution, const bool limit_to_top_faces=false) const

void	remove_nullspace (LinearAlgebra::BlockVector &solution, LinearAlgebra::BlockVector &distributed_stokes_solution) const

double	normalize_pressure (LinearAlgebra::BlockVector &vector) const

void	denormalize_pressure (const double pressure_adjustment, LinearAlgebra::BlockVector &vector) const

Static Public Member Functions
static void	declare_parameters (ParameterHandler &prm)

Static Public Member Functions inherited from aspect::Plugins::InterfaceBase
static void	declare_parameters (ParameterHandler &prm)

Static Public Member Functions inherited from aspect::SimulatorAccess< dim >
static void	get_composition_values_at_q_point (const std::vector< std::vector< double >> &composition_values, const unsigned int q, std::vector< double > &composition_values_at_q_point)

Private Types
enum	Output { Output::VolumeFraction, Output::RotationMatrix, Output::EulerAngles, Output::not_found }

Private Member Functions
Output	string_to_output_enum (const std::string &string)

void	set_last_output_time (const double current_time)

Static Private Member Functions
static void	writer (const std::string &filename, const std::string &temporary_filename, const std::string &file_contents, const bool compress_contents)

Private Attributes
std::mt19937	random_number_generator

unsigned int	random_number_seed

double	output_interval

double	last_output_time

unsigned int	output_file_number

std::vector< std::string >	output_formats

std::vector< std::pair< double, std::string > >	times_and_pvtu_file_names

std::vector< std::pair< double, std::vector< std::string > > >	times_and_vtu_file_names

std::vector< std::vector< std::string > >	output_file_names_by_timestep

std::vector< XDMFEntry >	xdmf_entries

unsigned int	group_files

std::string	temporary_output_location

bool	write_in_background_thread

std::thread	background_thread_main

std::vector< std::pair< unsigned int, Output > >	write_raw_cpo

bool	compute_raw_euler_angles

std::thread	background_thread_content_raw

std::vector< std::pair< unsigned int, Output > >	write_draw_volume_weighted_cpo

bool	compute_weighted_rotation_matrix

std::thread	background_thread_content_draw_volume_weighting

bool	compress_cpo_data_files

Detailed Description

template<int dim>
class aspect::Postprocess::CrystalPreferredOrientation< dim >

A Postprocessor that writes out CPO specific particle data. It can write out the CPO data as it is stored (raw) and/or as a random draw volume weighted representation. The latter one is recommended for plotting against real data. For both representations the specific output fields and their order can be set.

Definition at line 48 of file crystal_preferred_orientation.h.

Member Enumeration Documentation

§ Output

template<int dim>

enum aspect::Postprocess::CrystalPreferredOrientation::Output

strongprivate

Enums specifying what information to write:

VolumeFraction: Write the volume fraction RotationMatrix: Write the whole rotation matrix of a grain (in deal.ii order) EulerAngles: Write out the Z-X-Z Euler angle of a grain not_found: Error enum, the requested output was not found

Enumerator
VolumeFraction
RotationMatrix
EulerAngles
not_found

Definition at line 122 of file crystal_preferred_orientation.h.

Constructor & Destructor Documentation

§ CrystalPreferredOrientation()

template<int dim>

aspect::Postprocess::CrystalPreferredOrientation< dim >::CrystalPreferredOrientation ( )

Constructor.

§ ~CrystalPreferredOrientation()

template<int dim>

aspect::Postprocess::CrystalPreferredOrientation< dim >::~CrystalPreferredOrientation ( )

Destructor.

Member Function Documentation

§ initialize()

template<int dim>

void aspect::Postprocess::CrystalPreferredOrientation< dim >::initialize ( )

overridevirtual

Initialize function.

Reimplemented from aspect::Plugins::InterfaceBase.

§ execute()

template<int dim>

std::pair<std::string,std::string> aspect::Postprocess::CrystalPreferredOrientation< dim >::execute ( TableHandler & statistics )

overridevirtual

A Postprocessor that writes out CPO specific particle data. It can write out the CPO data as it is stored (raw) and/or as a random draw volume weighted representation. The latter one is recommended for plotting against real data. For both representations the specific output fields and their order can be set.

Implements aspect::Postprocess::Interface< dim >.

§ required_other_postprocessors()

template<int dim>

std::list<std::string> aspect::Postprocess::CrystalPreferredOrientation< dim >::required_other_postprocessors ( ) const

overridevirtual

This function ensures that the particle postprocessor is run before this postprocessor.

Reimplemented from aspect::Postprocess::Interface< dim >.

§ save()

template<int dim>

void aspect::Postprocess::CrystalPreferredOrientation< dim >::save ( std::map< std::string, std::string > & status_strings ) const

overridevirtual

Save the state of this object.

Reimplemented from aspect::Postprocess::Interface< dim >.

§ load()

template<int dim>

void aspect::Postprocess::CrystalPreferredOrientation< dim >::load ( const std::map< std::string, std::string > & status_strings )

overridevirtual

Restore the state of the object.

Reimplemented from aspect::Postprocess::Interface< dim >.

§ serialize()

template<int dim>

template<class Archive >

void aspect::Postprocess::CrystalPreferredOrientation< dim >::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize the contents of this class as far as they are not read from input parameter files.

§ declare_parameters()

template<int dim>

static void aspect::Postprocess::CrystalPreferredOrientation< dim >::declare_parameters ( ParameterHandler & prm )

static

Declare the parameters this class takes through input files.

§ parse_parameters()

template<int dim>

void aspect::Postprocess::CrystalPreferredOrientation< dim >::parse_parameters ( ParameterHandler & prm )

overridevirtual

Read the parameters this class declares from the parameter file.

Reimplemented from aspect::Plugins::InterfaceBase.

§ string_to_output_enum()

template<int dim>

Output aspect::Postprocess::CrystalPreferredOrientation< dim >::string_to_output_enum ( const std::string & string )

private

Converts a string to an Output enum.

§ set_last_output_time()

template<int dim>

void aspect::Postprocess::CrystalPreferredOrientation< dim >::set_last_output_time ( const double current_time )

private

Set the time output was supposed to be written. In the simplest case, this is the previous last output time plus the interval, but in general we'd like to ensure that it is the largest supposed output time, which is smaller than the current time, to avoid falling behind with last_output_time and having to catch up once the time step becomes larger. This is done after every output.

§ writer()

template<int dim>

static void aspect::Postprocess::CrystalPreferredOrientation< dim >::writer	(	const std::string &	filename,
		const std::string &	temporary_filename,
		const std::string &	file_contents,
		const bool	compress_contents
	)

staticprivate

A function that writes the text in the second argument to a file with the name given in the first argument. The function is run on a separate thread to allow computations to continue even though writing data is still continuing. The function takes over ownership of these arguments and deletes them at the end of its work.

Member Data Documentation

§ random_number_generator

template<int dim>

std::mt19937 aspect::Postprocess::CrystalPreferredOrientation< dim >::random_number_generator

mutableprivate

Random number generator used for random draw volume weighting.

Definition at line 135 of file crystal_preferred_orientation.h.

§ random_number_seed

template<int dim>

unsigned int aspect::Postprocess::CrystalPreferredOrientation< dim >::random_number_seed

private

Random number generator seed used to initialize the random number generator.

Definition at line 140 of file crystal_preferred_orientation.h.

§ output_interval

template<int dim>

double aspect::Postprocess::CrystalPreferredOrientation< dim >::output_interval

private

Interval between output (in years if appropriate simulation parameter is set, otherwise seconds)

Definition at line 146 of file crystal_preferred_orientation.h.

§ last_output_time

template<int dim>

double aspect::Postprocess::CrystalPreferredOrientation< dim >::last_output_time

private

Records time for next output to occur

Definition at line 151 of file crystal_preferred_orientation.h.

§ output_file_number

template<int dim>

unsigned int aspect::Postprocess::CrystalPreferredOrientation< dim >::output_file_number

private

Consecutively counted number indicating the how-manyth time we will create output the next time we get to it.

Definition at line 167 of file crystal_preferred_orientation.h.

§ output_formats

template<int dim>

std::vector<std::string> aspect::Postprocess::CrystalPreferredOrientation< dim >::output_formats

private

Graphical output format.

Definition at line 172 of file crystal_preferred_orientation.h.

§ times_and_pvtu_file_names

template<int dim>

std::vector<std::pair<double,std::string> > aspect::Postprocess::CrystalPreferredOrientation< dim >::times_and_pvtu_file_names

private

A list of pairs (time, pvtu_filename) that have so far been written and that we will pass to DataOutInterface::write_pvd_record to create a main file that can make the association between simulation time and corresponding file name (this is done because there is no way to store the simulation time inside the .pvtu or .vtu files).

Definition at line 182 of file crystal_preferred_orientation.h.

§ times_and_vtu_file_names

template<int dim>

std::vector<std::pair<double,std::vector<std::string> > > aspect::Postprocess::CrystalPreferredOrientation< dim >::times_and_vtu_file_names

private

A corresponding variable that we use for the .visit files created by DataOutInterface::write_visit_record. The second part of a pair contains all files that together form a time step.

Definition at line 189 of file crystal_preferred_orientation.h.

§ output_file_names_by_timestep

template<int dim>

std::vector<std::vector<std::string> > aspect::Postprocess::CrystalPreferredOrientation< dim >::output_file_names_by_timestep

private

A list of list of filenames, sorted by timestep, that correspond to what has been created as output. This is used to create a main .visit file for the entire simulation.

Definition at line 196 of file crystal_preferred_orientation.h.

§ xdmf_entries

template<int dim>

std::vector<XDMFEntry> aspect::Postprocess::CrystalPreferredOrientation< dim >::xdmf_entries

private

A set of data related to XDMF file sections describing the HDF5 heavy data files created. These contain things such as the dimensions and names of data written at all steps during the simulation.

Definition at line 204 of file crystal_preferred_orientation.h.

§ group_files

template<int dim>

unsigned int aspect::Postprocess::CrystalPreferredOrientation< dim >::group_files

private

VTU file output supports grouping files from several CPUs into one file using MPI I/O when writing on a parallel filesystem. 0 means no grouping (and no parallel I/O). 1 will generate one big file containing the whole solution.

Definition at line 212 of file crystal_preferred_orientation.h.

§ temporary_output_location

template<int dim>

std::string aspect::Postprocess::CrystalPreferredOrientation< dim >::temporary_output_location

private

On large clusters it can be advantageous to first write the output to a temporary file on a local file system and later move this file to a network file system. If this variable is set to a non-empty string it will be interpreted as a temporary storage location.

Definition at line 221 of file crystal_preferred_orientation.h.

§ write_in_background_thread

template<int dim>

bool aspect::Postprocess::CrystalPreferredOrientation< dim >::write_in_background_thread

private

File operations can potentially take a long time, blocking the progress of the rest of the model run. Setting this variable to 'true' moves this process into a background thread, while the rest of the model continues.

Definition at line 229 of file crystal_preferred_orientation.h.

§ background_thread_main

template<int dim>

std::thread aspect::Postprocess::CrystalPreferredOrientation< dim >::background_thread_main

private

Handle to a thread that is used to write main file data in the background. The writer() function runs on this background thread.

Definition at line 235 of file crystal_preferred_orientation.h.

§ write_raw_cpo

template<int dim>

std::vector<std::pair<unsigned int,Output> > aspect::Postprocess::CrystalPreferredOrientation< dim >::write_raw_cpo

private

What "raw" CPO data to write out.

Definition at line 240 of file crystal_preferred_orientation.h.

§ compute_raw_euler_angles

template<int dim>

bool aspect::Postprocess::CrystalPreferredOrientation< dim >::compute_raw_euler_angles

private

Whether computing raw Euler angles is needed.

Definition at line 245 of file crystal_preferred_orientation.h.

§ background_thread_content_raw

template<int dim>

std::thread aspect::Postprocess::CrystalPreferredOrientation< dim >::background_thread_content_raw

private

Handle to a thread that is used to write content file data in the background. The writer() function runs on this background thread.

Definition at line 251 of file crystal_preferred_orientation.h.

§ write_draw_volume_weighted_cpo

template<int dim>

std::vector<std::pair<unsigned int,Output> > aspect::Postprocess::CrystalPreferredOrientation< dim >::write_draw_volume_weighted_cpo

private

What "draw volume weighted" CPO data to write out. Draw volume weighted means the grain properties (size and rotation) are put in a list sorted based by volume and picked randomly, with large volumes having a higher chance of being picked.

Definition at line 258 of file crystal_preferred_orientation.h.

§ compute_weighted_rotation_matrix

template<int dim>

bool aspect::Postprocess::CrystalPreferredOrientation< dim >::compute_weighted_rotation_matrix

private

Whether computing weighted A matrix is needed.

Definition at line 263 of file crystal_preferred_orientation.h.

§ background_thread_content_draw_volume_weighting

template<int dim>

std::thread aspect::Postprocess::CrystalPreferredOrientation< dim >::background_thread_content_draw_volume_weighting

private

Handle to a thread that is used to write content file data in the background. The writer() function runs on this background thread.

Definition at line 269 of file crystal_preferred_orientation.h.

§ compress_cpo_data_files

template<int dim>

bool aspect::Postprocess::CrystalPreferredOrientation< dim >::compress_cpo_data_files

private

Whether to compress the raw and weighed cpo data output files with zlib.

Definition at line 274 of file crystal_preferred_orientation.h.

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

/home/bob/source/include/aspect/postprocess/crystal_preferred_orientation.h

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

template<int dim> class aspect::Postprocess::CrystalPreferredOrientation< dim >

Member Enumeration Documentation

§ Output

Constructor & Destructor Documentation

§ CrystalPreferredOrientation()

§ ~CrystalPreferredOrientation()

Member Function Documentation

§ initialize()

§ execute()

§ required_other_postprocessors()

§ save()

§ load()

§ serialize()

§ declare_parameters()

§ parse_parameters()

§ string_to_output_enum()

§ set_last_output_time()

§ writer()

Member Data Documentation

§ random_number_generator

§ random_number_seed

§ output_interval

§ last_output_time

§ output_file_number

§ output_formats

§ times_and_pvtu_file_names

§ times_and_vtu_file_names

§ output_file_names_by_timestep

§ xdmf_entries

§ group_files

§ temporary_output_location

§ write_in_background_thread

§ background_thread_main

§ write_raw_cpo

§ compute_raw_euler_angles

§ background_thread_content_raw

§ write_draw_volume_weighted_cpo

§ compute_weighted_rotation_matrix

§ background_thread_content_draw_volume_weighting

§ compress_cpo_data_files

template<int dim>
class aspect::Postprocess::CrystalPreferredOrientation< dim >