Reference documentation for deal.II version Git d435e92be9 2020-09-23 09:04:26 -0400
\(\newcommand{\dealvcentcolon}{\mathrel{\mathop{:}}}\) \(\newcommand{\dealcoloneq}{\dealvcentcolon\mathrel{\mkern-1.2mu}=}\) \(\newcommand{\jump}[1]{\left[\!\left[ #1 \right]\!\right]}\) \(\newcommand{\average}[1]{\left\{\!\left\{ #1 \right\}\!\right\}}\)
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Types | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
DataOutFaces< dim, DoFHandlerType > Class Template Reference

#include <deal.II/numerics/data_out_faces.h>

Inheritance diagram for DataOutFaces< dim, DoFHandlerType >:
[legend]

Public Types

using cell_iterator = typename DataOut_DoFData< DoFHandlerType, dimension - 1, dimension >::cell_iterator
 
using FaceDescriptor = typename std::pair< cell_iterator, unsigned int >
 
enum  DataVectorType
 

Public Member Functions

 DataOutFaces (const bool surface_only=true)
 
virtual void build_patches (const unsigned int n_subdivisions=0)
 
virtual void build_patches (const Mapping< dimension > &mapping, const unsigned int n_subdivisions=0)
 
virtual FaceDescriptor first_face ()
 
virtual FaceDescriptor next_face (const FaceDescriptor &face)
 
void attach_dof_handler (const DoFHandlerType &)
 
void attach_triangulation (const Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension > &)
 
void add_data_vector (const VectorType &data, const std::vector< std::string > &names, const DataVectorType type=type_automatic, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation=std::vector< DataComponentInterpretation::DataComponentInterpretation >())
 
void add_data_vector (const VectorType &data, const std::string &name, const DataVectorType type=type_automatic, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation=std::vector< DataComponentInterpretation::DataComponentInterpretation >())
 
void add_data_vector (const DoFHandlerType &dof_handler, const VectorType &data, const std::vector< std::string > &names, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation=std::vector< DataComponentInterpretation::DataComponentInterpretation >())
 
void add_data_vector (const DoFHandlerType &dof_handler, const VectorType &data, const std::string &name, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation=std::vector< DataComponentInterpretation::DataComponentInterpretation >())
 
void add_data_vector (const VectorType &data, const DataPostprocessor< DoFHandlerType::space_dimension > &data_postprocessor)
 
void add_data_vector (const DoFHandlerType &dof_handler, const VectorType &data, const DataPostprocessor< DoFHandlerType::space_dimension > &data_postprocessor)
 
void add_mg_data_vector (const DoFHandlerType &dof_handler, const MGLevelObject< VectorType > &data, const std::vector< std::string > &names, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation=std::vector< DataComponentInterpretation::DataComponentInterpretation >())
 
void add_mg_data_vector (const DoFHandlerType &dof_handler, const MGLevelObject< VectorType > &data, const std::string &name)
 
void clear_data_vectors ()
 
void clear_input_data_references ()
 
void merge_patches (const DataOut_DoFData< DoFHandlerType2, patch_dim, patch_space_dim > &source, const Point< patch_space_dim > &shift=Point< patch_space_dim >())
 
virtual void clear ()
 
std::size_t memory_consumption () const
 
void write_dx (std::ostream &out) const
 
void write_eps (std::ostream &out) const
 
void write_gmv (std::ostream &out) const
 
void write_gnuplot (std::ostream &out) const
 
void write_povray (std::ostream &out) const
 
void write_tecplot (std::ostream &out) const
 
void write_ucd (std::ostream &out) const
 
void write_vtk (std::ostream &out) const
 
void write_vtu (std::ostream &out) const
 
void write_vtu_in_parallel (const std::string &filename, MPI_Comm comm) const
 
void write_pvtu_record (std::ostream &out, const std::vector< std::string > &piece_names) const
 
std::string write_vtu_with_pvtu_record (const std::string &directory, const std::string &filename_without_extension, const unsigned int counter, const MPI_Comm &mpi_communicator, const unsigned int n_digits_for_counter=numbers::invalid_unsigned_int, const unsigned int n_groups=0) const
 
void write_svg (std::ostream &out) const
 
void write_deal_II_intermediate (std::ostream &out) const
 
XDMFEntry create_xdmf_entry (const DataOutBase::DataOutFilter &data_filter, const std::string &h5_filename, const double cur_time, MPI_Comm comm) const
 
XDMFEntry create_xdmf_entry (const DataOutBase::DataOutFilter &data_filter, const std::string &h5_mesh_filename, const std::string &h5_solution_filename, const double cur_time, MPI_Comm comm) const
 
void write_xdmf_file (const std::vector< XDMFEntry > &entries, const std::string &filename, MPI_Comm comm) const
 
void write_hdf5_parallel (const DataOutBase::DataOutFilter &data_filter, const std::string &filename, MPI_Comm comm) const
 
void write_hdf5_parallel (const DataOutBase::DataOutFilter &data_filter, const bool write_mesh_file, const std::string &mesh_filename, const std::string &solution_filename, MPI_Comm comm) const
 
void write_filtered_data (DataOutBase::DataOutFilter &filtered_data) const
 
void write (std::ostream &out, const DataOutBase::OutputFormat output_format=DataOutBase::default_format) const
 
void set_default_format (const DataOutBase::OutputFormat default_format)
 
void set_flags (const FlagType &flags)
 
std::string default_suffix (const DataOutBase::OutputFormat output_format=DataOutBase::default_format) const
 
void parse_parameters (ParameterHandler &prm)
 

Static Public Member Functions

static void declare_parameters (ParameterHandler &prm)
 

Static Public Attributes

static const unsigned int dimension = DoFHandlerType::dimension
 
static const unsigned int space_dimension = DoFHandlerType::space_dimension
 

Protected Types

using Patch = ::DataOutBase::Patch< patch_dim, patch_space_dim >
 

Protected Member Functions

virtual const std::vector< Patch > & get_patches () const override
 
virtual std::vector< std::string > get_dataset_names () const override
 
std::vector< std::shared_ptr<::hp::FECollection< DoFHandlerType::dimension, DoFHandlerType::space_dimension > > > get_fes () const
 
virtual std::vector< std::tuple< unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation > > get_nonscalar_data_ranges () const override
 
void validate_dataset_names () const
 

Protected Attributes

SmartPointer< const Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension > > triangulation
 
SmartPointer< const DoFHandlerType > dofs
 
std::vector< std::shared_ptr< internal::DataOutImplementation::DataEntryBase< DoFHandlerType > > > dof_data
 
std::vector< std::shared_ptr< internal::DataOutImplementation::DataEntryBase< DoFHandlerType > > > cell_data
 
std::vector< Patchpatches
 
unsigned int default_subdivisions
 

Private Member Functions

void build_one_patch (const FaceDescriptor *cell_and_face, internal::DataOutFacesImplementation::ParallelData< dimension, dimension > &data, DataOutBase::Patch< dimension - 1, space_dimension > &patch)
 

Private Attributes

const bool surface_only
 

Detailed Description

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
class DataOutFaces< dim, DoFHandlerType >

This class generates output from faces of a triangulation. It might be used to generate output only for the surface of the triangulation (this is the default of this class), or for all faces of active cells, as specified in the constructor. The output of this class is a set of patches (as defined by the class DataOutBase::Patch()), one for each face for which output is to be generated. These patches can then be written in several graphical data formats by the functions of the underlying classes.

Interface

The interface of this class is copied from the DataOut class. Furthermore, they share the common parent class DataOut_DoFData. See the reference of these two classes for a discussion of the interface.

Extending this class

The sequence of faces to generate patches from is generated in the same way as in the DataOut class; see there for a description of the respective interface. The functions generating the sequence of faces which shall be used to generate output, are called first_face() and next_face().

Since we need to initialize objects of type FEValues with the faces generated from these functions, it is not sufficient that they only return face iterators. Rather, we need a pair of cell and the number of the face, as the values of finite element fields need not necessarily be unique on a face (think of discontinuous finite elements, where the value of the finite element field depend on the direction from which you approach a face, thus it is necessary to use a pair of cell and face, rather than only a face iterator). Therefore, this class defines an alias which creates a type FaceDescriptor that is an abbreviation for a pair of cell iterator and face number. The functions first_face and next_face operate on objects of this type.

Extending this class might, for example, be useful if you only want output from certain portions of the boundary, e.g. as indicated by the boundary indicator of the respective faces. However, it is also conceivable that one generates patches not from boundary faces, but from interior faces that are selected due to other criteria; one application might be to use only those faces where one component of the solution attains a certain value, in order to display the values of other solution components on these faces. Other applications certainly exist, for which the author is not imaginative enough.

Precondition
This class only makes sense if the first template argument, dim equals the dimension of the DoFHandler type given as the second template argument, i.e., if dim == DoFHandlerType::dimension. This redundancy is a historical relic from the time where the library had only a single DoFHandler class and this class consequently only a single template argument.
Todo:
Reimplement this whole class using actual FEFaceValues and MeshWorker.

Definition at line 116 of file data_out_faces.h.

Member Typedef Documentation

◆ cell_iterator

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
using DataOutFaces< dim, DoFHandlerType >::cell_iterator = typename DataOut_DoFData<DoFHandlerType, dimension - 1, dimension>::cell_iterator

Alias to the iterator type of the dof handler class under consideration.

Definition at line 139 of file data_out_faces.h.

◆ FaceDescriptor

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
using DataOutFaces< dim, DoFHandlerType >::FaceDescriptor = typename std::pair<cell_iterator, unsigned int>

Declare a way to describe a face which we would like to generate output for. The usual way would, of course, be to use an object of type DoFHandler<dim>::face_iterator, but since we have to describe faces to objects of type FEValues, we can only represent faces by pairs of a cell and the number of the face. This pair is here aliased to a name that is better to type.

Definition at line 196 of file data_out_faces.h.

◆ Patch

using DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::Patch = ::DataOutBase::Patch<patch_dim, patch_space_dim>
protectedinherited

Abbreviate the somewhat lengthy name for the Patch class.

Definition at line 980 of file data_out_dof_data.h.

Member Enumeration Documentation

◆ DataVectorType

Type describing what the vector given to add_data_vector() is: a vector that has one entry per degree of freedom in a DoFHandler object (such as solution vectors), or one entry per cell in the triangulation underlying the DoFHandler object (such as error per cell data). The value type_automatic tells add_data_vector() to find out itself (see the documentation of add_data_vector() for the method used).

Definition at line 632 of file data_out_dof_data.h.

Constructor & Destructor Documentation

◆ DataOutFaces()

template<int dim, typename DoFHandlerType >
DataOutFaces< dim, DoFHandlerType >::DataOutFaces ( const bool  surface_only = true)

Constructor determining whether a surface mesh (default) or the whole wire basket is written.

Definition at line 84 of file data_out_faces.cc.

Member Function Documentation

◆ build_patches() [1/2]

template<int dim, typename DoFHandlerType >
void DataOutFaces< dim, DoFHandlerType >::build_patches ( const unsigned int  n_subdivisions = 0)
virtual

This is the central function of this class since it builds the list of patches to be written by the low-level functions of the base class. A patch is, in essence, some intermediate representation of the data on each face of a triangulation and DoFHandler object that can then be used to write files in some format that is readable by visualization programs.

You can find an overview of the use of this function in the general documentation of this class. An example is also provided in the documentation of this class's base class DataOut_DoFData.

Parameters
n_subdivisionsSee DataOut::build_patches() for an extensive description of this parameter.

Definition at line 321 of file data_out_faces.cc.

◆ build_patches() [2/2]

template<int dim, typename DoFHandlerType >
void DataOutFaces< dim, DoFHandlerType >::build_patches ( const Mapping< dimension > &  mapping,
const unsigned int  n_subdivisions = 0 
)
virtual

Same as above, except that the additional first parameter defines a mapping that is to be used in the generation of output. If n_subdivisions>1, the points interior of subdivided patches which originate from cells at the boundary of the domain can be computed using the mapping, i.e. a higher order mapping leads to a representation of a curved boundary by using more subdivisions.

Even for non-curved cells the mapping argument can be used for the Eulerian mappings (see class MappingQ1Eulerian) where a mapping is used not only to determine the position of points interior to a cell, but also of the vertices. It offers an opportunity to watch the solution on a deformed triangulation on which the computation was actually carried out, even if the mesh is internally stored in its undeformed configuration and the deformation is only tracked by an additional vector that holds the deformation of each vertex.

Todo:
The mapping argument should be replaced by a hp::MappingCollection in case of a hp::DoFHandler.

Definition at line 331 of file data_out_faces.cc.

◆ first_face()

template<int dim, typename DoFHandlerType >
DataOutFaces< dim, DoFHandlerType >::FaceDescriptor DataOutFaces< dim, DoFHandlerType >::first_face ( )
virtual

Return the first face which we want output for. The default implementation returns the first face of a (locally owned) active cell or, if the surface_only option was set in the destructor (as is the default), the first such face that is located on the boundary.

If you want to use a different logic to determine which faces should contribute to the creation of graphical output, you can overload this function in a derived class.

Definition at line 420 of file data_out_faces.cc.

◆ next_face()

template<int dim, typename DoFHandlerType >
DataOutFaces< dim, DoFHandlerType >::FaceDescriptor DataOutFaces< dim, DoFHandlerType >::next_face ( const FaceDescriptor face)
virtual

Return the next face after which we want output for. If there are no more faces, dofs->end() is returned as the first component of the return value.

The default implementation returns the next face of a (locally owned) active cell, or the next such on the boundary (depending on whether the surface_only option was provided to the constructor).

This function traverses the mesh active cell by active cell (restricted to locally owned cells), and then through all faces of the cell. As a result, interior faces are output twice, a feature that is useful for discontinuous Galerkin methods or if a DataPostprocessor is used that might produce results that are discontinuous between cells).

This function can be overloaded in a derived class to select a different set of faces. Note that the default implementation assumes that the given face is active, which is guaranteed as long as first_face() is also used from the default implementation. Overloading only one of the two functions should be done with care.

Definition at line 441 of file data_out_faces.cc.

◆ build_one_patch()

template<int dim, typename DoFHandlerType >
void DataOutFaces< dim, DoFHandlerType >::build_one_patch ( const FaceDescriptor cell_and_face,
internal::DataOutFacesImplementation::ParallelData< dimension, dimension > &  data,
DataOutBase::Patch< dimension - 1, space_dimension > &  patch 
)
private

Build one patch. This function is called in a WorkStream context.

Definition at line 94 of file data_out_faces.cc.

◆ attach_dof_handler()

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::attach_dof_handler ( const DoFHandlerType &  )
inherited

Designate a dof handler to be used to extract geometry data and the mapping between nodes and node values. This call is not necessary if all added data vectors are supplemented with a DoFHandler argument.

This call is optional: If you add data vectors with specified DoFHandler object, then that contains all information needed to generate the output.

◆ attach_triangulation()

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::attach_triangulation ( const Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension > &  )
inherited

Designate a triangulation to be used to extract geometry data and the mapping between nodes and node values.

This call is optional: If you add data vectors with specified DoFHandler object, then that contains all information needed to generate the output. This call is useful when you only output cell vectors and no DoFHandler at all, in which case it provides the geometry.

◆ add_data_vector() [1/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const VectorType data,
const std::vector< std::string > &  names,
const DataVectorType  type = type_automatic,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = std::vector< DataComponentInterpretation::DataComponentInterpretation>() 
)
inherited

Add a data vector together with its name.

A pointer to the vector is stored, so you have to make sure the vector exists at that address at least as long as you call the write_* functions.

It is assumed that the vector has the same number of components as there are degrees of freedom in the dof handler, in which case it is assumed to be a vector storing nodal data; or the size may be the number of active cells on the present grid, in which case it is assumed to be a cell data vector. As the number of degrees of freedom and of cells is usually not equal, the function can determine itself which type of vector it is given. However, there are corner cases where this automatic determination does not work. One example is if you compute with piecewise constant elements and have a scalar solution, then there are as many cells as there are degrees of freedom (though they may be numbered differently). Another possibility is if you have a 1d mesh embedded in 2d space and the mesh consists of a closed curve of cells; in this case, there are as many nodes as there are cells, and when using a Q1 element you will have as many degrees of freedom as there are cells. In these cases, you can change the last argument of the function from its default value type_automatic to either type_dof_data or type_cell_data, depending on what the vector represents. Apart from such corner cases, you can leave the argument at its default value and let the function determine the type of the vector itself.

If it is a vector holding DoF data, the names given shall be one for each component of the underlying finite element. If it is a finite element composed of only one subelement, then there is another function following which takes a single name instead of a vector of names.

The data_component_interpretation argument contains information about how the individual components of output files that consist of more than one data set are to be interpreted.

For example, if one has a finite element for the Stokes equations in 2d, representing components (u,v,p), one would like to indicate that the first two, u and v, represent a logical vector so that later on when we generate graphical output we can hand them off to a visualization program that will automatically know to render them as a vector field, rather than as two separate and independent scalar fields.

The default value of this argument (i.e. an empty vector) corresponds is equivalent to a vector of values DataComponentInterpretation::component_is_scalar, indicating that all output components are independent scalar fields. However, if the given data vector represents logical vectors, you may pass a vector that contains values DataComponentInterpretation::component_is_part_of_vector. In the example above, one would pass in a vector with components (DataComponentInterpretation::component_is_part_of_vector, DataComponentInterpretation::component_is_part_of_vector, DataComponentInterpretation::component_is_scalar) for (u,v,p).

The names of a data vector shall only contain characters which are letters, underscore and a few other ones. Refer to the ExcInvalidCharacter exception declared in this class to see which characters are valid and which are not.

Note
The actual type for the vector argument may be any vector type from which FEValues can extract values on a cell using the FEValuesBase::get_function_values() function.
When working in parallel, the vector to be written needs to be ghosted with read access to all degrees of freedom on the locally owned cells, see the step-40 or step-37 tutorial programs for details, i.e., it might be necessary to call data.update_ghost_values().

Definition at line 1100 of file data_out_dof_data.h.

◆ add_data_vector() [2/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const VectorType data,
const std::string &  name,
const DataVectorType  type = type_automatic,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = std::vector< DataComponentInterpretation::DataComponentInterpretation>() 
)
inherited

This function is an abbreviation to the above one (see there for a discussion of the various arguments), intended for use with finite elements that are not composed of subelements. In this case, only one name per data vector needs to be given, which is what this function takes. It simply relays its arguments after a conversion of the name to a vector of strings, to the other add_data_vector() function above.

If data is a vector with multiple components this function will generate distinct names for all components by appending an underscore and the number of each component to name

The actual type for the template argument may be any vector type from which FEValues can extract values on a cell using the FEValuesBase::get_function_values() function.

Definition at line 1081 of file data_out_dof_data.h.

◆ add_data_vector() [3/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const DoFHandlerType &  dof_handler,
const VectorType data,
const std::vector< std::string > &  names,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = std::vector< DataComponentInterpretation::DataComponentInterpretation>() 
)
inherited

This function is an extension of the above one (see there for a discussion of the arguments except the first one) and allows to set a vector with its own DoFHandler object. This DoFHandler needs to be compatible with the other DoFHandler objects assigned with calls to add_data_vector or attach_dof_handler, in the sense that all of the DoFHandler objects need to be based on the same triangulation. This function allows you to export data from multiple DoFHandler objects that describe different solution components. An example of using this function is given in step-61.

Since this function takes a DoFHandler object and hence naturally represents dof data, the data vector type argument present in the other methods above is not necessary.

Definition at line 1139 of file data_out_dof_data.h.

◆ add_data_vector() [4/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const DoFHandlerType &  dof_handler,
const VectorType data,
const std::string &  name,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = std::vector< DataComponentInterpretation::DataComponentInterpretation>() 
)
inherited

This function is an abbreviation of the function above with only a scalar dof_handler given and a single data name.

Definition at line 1118 of file data_out_dof_data.h.

◆ add_data_vector() [5/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const VectorType data,
const DataPostprocessor< DoFHandlerType::space_dimension > &  data_postprocessor 
)
inherited

This function is an alternative to the above ones, allowing the output of derived quantities instead of the given data. This conversion has to be done in a class derived from DataPostprocessor. This function is used in step-29. Other uses are shown in step-32 and step-33.

The names for these derived quantities are provided by the data_postprocessor argument. Likewise, the data_component_interpretation argument of the other add_data_vector() functions is provided by the data_postprocessor argument. As only data of type type_dof_data can be transformed, this type is also known implicitly and does not have to be given.

Note
The actual type for the vector argument may be any vector type from which FEValues can extract values on a cell using the FEValuesBase::get_function_values() function.
The DataPostprocessor object (i.e., in reality the object of your derived class) has to live until the DataOut object is destroyed as the latter keeps a pointer to the former and will complain if the object pointed to is destroyed while the latter still has a pointer to it. If both the data postprocessor and DataOut objects are local variables of a function (as they are, for example, in step-29), then you can avoid this error by declaring the data postprocessor variable before the DataOut variable as objects are destroyed in reverse order of declaration.

Definition at line 1159 of file data_out_dof_data.h.

◆ add_data_vector() [6/6]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector ( const DoFHandlerType &  dof_handler,
const VectorType data,
const DataPostprocessor< DoFHandlerType::space_dimension > &  data_postprocessor 
)
inherited

Same function as above, but with a DoFHandler object that does not need to coincide with the DoFHandler initially set. Note that the postprocessor can only read data from the given DoFHandler and solution vector, not other solution vectors or DoFHandlers.

◆ add_mg_data_vector() [1/2]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_mg_data_vector ( const DoFHandlerType &  dof_handler,
const MGLevelObject< VectorType > &  data,
const std::vector< std::string > &  names,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = std::vector< DataComponentInterpretation::DataComponentInterpretation>() 
)
inherited

Add a multilevel data vector.

This function adds the vector-valued multilevel vector data in the form of a vector on each level that belongs to the DoFHandler dof_handler to the graphical output. This function is typically used in conjunction with a call to set_cell_selection() that selects cells on a specific level and not the active cells (the default).

A vector data can be obtained in several ways, for example by using Multigrid::solution or Multigrid::defect during or after a multigrid cycle or by interpolating a solution via MGTransferMatrixFree::interpolate_to_mg().

The handling of names and data_component_interpretation is identical to the add_data_vector() function.

◆ add_mg_data_vector() [2/2]

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_mg_data_vector ( const DoFHandlerType &  dof_handler,
const MGLevelObject< VectorType > &  data,
const std::string &  name 
)
inherited

Scalar version of the function above.

◆ clear_data_vectors()

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear_data_vectors ( )
inherited

Release the pointers to the data vectors. This allows output of a new set of vectors without supplying the DoF handler again. Therefore, the DataOut object can be used in an algebraic context. Note that besides the data vectors also the patches already computed are deleted.

◆ clear_input_data_references()

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear_input_data_references ( )
inherited

Release pointers to all input data elements, i.e. pointers to data vectors and to the DoF handler object. This function may be useful when you have called the build_patches function of derived class, since then the patches are built and the input data is no more needed, nor is there a need to reference it. You can then output the patches detached from the main thread and need not make sure anymore that the DoF handler object and vectors must not be deleted before the output thread is finished.

◆ merge_patches()

void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::merge_patches ( const DataOut_DoFData< DoFHandlerType2, patch_dim, patch_space_dim > &  source,
const Point< patch_space_dim > &  shift = Point<patch_space_dim>() 
)
inherited

This function can be used to merge the patches that were created using the build_patches function of the object given as argument into the list of patches created by this object. This is sometimes handy if one has, for example, a domain decomposition algorithm where each block is represented by a DoFHandler of its own, but one wants to output the solution on all the blocks at the same time.

For this to work, the given argument and this object need to have the same number of output vectors, and they need to use the same number of subdivisions per patch. The output will probably look rather funny if patches in both objects overlap in space.

If you call build_patches() for this object after merging in patches, the previous state is overwritten, and the merged-in patches are lost.

The second parameter allows to shift each node of the patches in the object passed in in the first parameter by a certain amount. This is sometimes useful to generate "exploded" views of a collection of blocks.

This function will fail if either this or the other object did not yet set up any patches.

Definition at line 1173 of file data_out_dof_data.h.

◆ clear()

virtual void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear ( )
virtualinherited

Release the pointers to the data vectors and the DoF handler. You have to set all data entries again using the add_data_vector() function. The pointer to the dof handler is cleared as well, along with all other data. In effect, this function resets everything to a virgin state.

◆ memory_consumption()

std::size_t DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::memory_consumption ( ) const
inherited

Determine an estimate for the memory consumption (in bytes) of this object.

◆ get_patches()

virtual const std::vector<Patch>& DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_patches ( ) const
overrideprotectedvirtualinherited

Function by which the base class's functions get to know what patches they shall write to a file.

Implements DataOutInterface< patch_dim, patch_space_dim >.

◆ get_dataset_names()

virtual std::vector<std::string> DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_dataset_names ( ) const
overrideprotectedvirtualinherited

Virtual function through which the names of data sets are obtained by the output functions of the base class.

Implements DataOutInterface< patch_dim, patch_space_dim >.

◆ get_fes()

std::vector< std::shared_ptr<::hp::FECollection<DoFHandlerType::dimension, DoFHandlerType::space_dimension> > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_fes ( ) const
protectedinherited

Extracts the finite elements stored in the dof_data object, including a dummy object of FE_DGQ<dim>(0) in case only the triangulation is used.

◆ get_nonscalar_data_ranges()

virtual std::vector< std::tuple<unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation> > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_nonscalar_data_ranges ( ) const
overrideprotectedvirtualinherited

Overload of the respective DataOutInterface::get_nonscalar_data_ranges() function. See there for a more extensive documentation.

Reimplemented from DataOutInterface< patch_dim, patch_space_dim >.

◆ write_dx()

void DataOutInterface< dim, spacedim >::write_dx ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in OpenDX format. See DataOutBase::write_dx.

Definition at line 6917 of file data_out_base.cc.

◆ write_eps()

void DataOutInterface< dim, spacedim >::write_eps ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in EPS format. See DataOutBase::write_eps.

Definition at line 6969 of file data_out_base.cc.

◆ write_gmv()

void DataOutInterface< dim, spacedim >::write_gmv ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in GMV format. See DataOutBase::write_gmv.

Definition at line 6982 of file data_out_base.cc.

◆ write_gnuplot()

void DataOutInterface< dim, spacedim >::write_gnuplot ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in GNUPLOT format. See DataOutBase::write_gnuplot.

Definition at line 6943 of file data_out_base.cc.

◆ write_povray()

void DataOutInterface< dim, spacedim >::write_povray ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in POVRAY format. See DataOutBase::write_povray.

Definition at line 6956 of file data_out_base.cc.

◆ write_tecplot()

void DataOutInterface< dim, spacedim >::write_tecplot ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in Tecplot format. See DataOutBase::write_tecplot.

Definition at line 6995 of file data_out_base.cc.

◆ write_ucd()

void DataOutInterface< dim, spacedim >::write_ucd ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in UCD format for AVS. See DataOutBase::write_ucd.

Definition at line 6930 of file data_out_base.cc.

◆ write_vtk()

void DataOutInterface< dim, spacedim >::write_vtk ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in Vtk format. See DataOutBase::write_vtk.

Note
VTK is a legacy format and has largely been supplanted by the VTU format (an XML-structured version of VTK). In particular, VTU allows for the compression of data and consequently leads to much smaller file sizes that equivalent VTK files for large files. Since all visualization programs that support VTK also support VTU, you should consider using the latter file format instead, by using the write_vtu() function.

Definition at line 7008 of file data_out_base.cc.

◆ write_vtu()

void DataOutInterface< dim, spacedim >::write_vtu ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in Vtu (VTK's XML) format. See DataOutBase::write_vtu.

Some visualization programs, such as ParaView, can read several separate VTU files to parallelize visualization. In that case, you need a .pvtu file that describes which VTU files form a group. The DataOutInterface::write_pvtu_record() function can generate such a centralized record. Likewise, DataOutInterface::write_visit_record() does the same for older versions of VisIt (although VisIt can also read pvtu records since version 2.5.1). Finally, DataOutInterface::write_pvd_record() can be used to group together the files that jointly make up a time dependent simulation.

Definition at line 7019 of file data_out_base.cc.

◆ write_vtu_in_parallel()

void DataOutInterface< dim, spacedim >::write_vtu_in_parallel ( const std::string &  filename,
MPI_Comm  comm 
) const
inherited

Collective MPI call to write the solution from all participating nodes (those in the given communicator) to a single compressed .vtu file on a shared file system. The communicator can be a sub communicator of the one used by the computation. This routine uses MPI I/O to achieve high performance on parallel filesystems. Also see DataOutInterface::write_vtu().

Definition at line 7041 of file data_out_base.cc.

◆ write_pvtu_record()

void DataOutInterface< dim, spacedim >::write_pvtu_record ( std::ostream &  out,
const std::vector< std::string > &  piece_names 
) const
inherited

Some visualization programs, such as ParaView, can read several separate VTU files that all form part of the same simulation, in order to parallelize visualization. In that case, you need a .pvtu file that describes which VTU files (written, for example, through the DataOutInterface::write_vtu() function) form a group. The current function can generate such a centralized record.

The central record file generated by this function contains a list of (scalar or vector) fields that describes which fields can actually be found in the individual files that comprise the set of parallel VTU files along with the names of these files. This function gets the names and types of fields through the get_dataset_names() and get_nonscalar_data_ranges() functions of this class. The second argument to this function specifies the names of the files that form the parallel set.

Note
Use DataOutBase::write_vtu() and DataOutInterface::write_vtu() for writing each piece. Also note that only one parallel process needs to call the current function, listing the names of the files written by all parallel processes.
The use of this function is explained in step-40.
In order to tell Paraview to group together multiple pvtu files that each describe one time step of a time dependent simulation, see the DataOutBase::write_pvd_record() function.
Older versions of VisIt (before 2.5.1), can not read pvtu records. However, it can read visit records as written by the write_visit_record() function.

Definition at line 7144 of file data_out_base.cc.

◆ write_vtu_with_pvtu_record()

std::string DataOutInterface< dim, spacedim >::write_vtu_with_pvtu_record ( const std::string &  directory,
const std::string &  filename_without_extension,
const unsigned int  counter,
const MPI_Comm &  mpi_communicator,
const unsigned int  n_digits_for_counter = numbers::invalid_unsigned_int,
const unsigned int  n_groups = 0 
) const
inherited

This function writes several .vtu files and a .pvtu record in parallel and constructs the filenames automatically. It is a combination of DataOutInterface::write_vtu() or DataOutInterface::write_vtu_in_parallel(), and DataOutInterface::write_pvtu_record().

For example, running write_vtu_with_pvtu_record("output/", "solution", 3, comm, 4, 2) on 10 processes generates the files

output/solution_0003.0.vtu
output/solution_0003.1.vtu
output/solution_0003.pvtu

where the .0.vtu file contains the output of the first half of the processes grouped together, and the .1.vtu the data from the remaining half.

A specified directory and a filename_without_extension form the first part of the filename. The filename is then extended with a counter labeling the current timestep/iteration/etc., the processor ID, and finally the .vtu/.pvtu ending. Since the number of timesteps to be written depends on the application, the number of digits to be reserved in the filename can be specified as parameter n_digits_for_counter, and the number is not padded with leading zeros if this parameter is left at its default value numbers::invalid_unsigned_int. If more than one file identifier is needed (e.g. time step number and iteration counter of solver), the last identifier is used as counter, while all other identifiers have to be added to filename_without_extension when calling this function.

In a parallel setting, several files are typically written per time step. The number of files written in parallel depends on the number of MPI processes (see parameter mpi_communicator), and a specified number of n_groups with default value 0. The background is that VTU file output supports grouping files from several CPUs into a given number of files using MPI I/O when writing on a parallel filesystem. The default value of n_groups is 0, meaning that every MPI rank will write one file. A value of 1 will generate one big file containing the solution over the whole domain, while a larger value will create n_groups files (but not more than there are MPI ranks).

Note that only one processor needs to generate the .pvtu file, where processor zero is chosen to take over this job.

The return value is the filename of the centralized file for the pvtu record.

Note
The code simply combines the strings directory and filename_without_extension, i.e., the user has to make sure that directory contains a trailing character, e.g. "/", that separates the directory from the filename.
Use an empty string "" for the first argument if output is to be written in the current working directory.

Definition at line 7157 of file data_out_base.cc.

◆ write_svg()

void DataOutInterface< dim, spacedim >::write_svg ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in SVG format. See DataOutBase::write_svg.

Definition at line 7030 of file data_out_base.cc.

◆ write_deal_II_intermediate()

void DataOutInterface< dim, spacedim >::write_deal_II_intermediate ( std::ostream &  out) const
inherited

Obtain data through get_patches() and write it to out in deal.II intermediate format. See DataOutBase::write_deal_II_intermediate.

Note that the intermediate format is what its name suggests: a direct representation of internal data. It isn't standardized and will change whenever we change our internal representation. You can only expect to process files written in this format using the same version of deal.II that was used for writing.

Definition at line 7239 of file data_out_base.cc.

◆ create_xdmf_entry() [1/2]

XDMFEntry DataOutInterface< dim, spacedim >::create_xdmf_entry ( const DataOutBase::DataOutFilter data_filter,
const std::string &  h5_filename,
const double  cur_time,
MPI_Comm  comm 
) const
inherited

Create an XDMFEntry based on the data in the data_filter. This assumes the mesh and solution data were written to a single file. See write_xdmf_file() for an example of usage.

Definition at line 7252 of file data_out_base.cc.

◆ create_xdmf_entry() [2/2]

XDMFEntry DataOutInterface< dim, spacedim >::create_xdmf_entry ( const DataOutBase::DataOutFilter data_filter,
const std::string &  h5_mesh_filename,
const std::string &  h5_solution_filename,
const double  cur_time,
MPI_Comm  comm 
) const
inherited

Create an XDMFEntry based on the data in the data_filter. This assumes the mesh and solution data were written to separate files. See write_xdmf_file() for an example of usage.

Definition at line 7266 of file data_out_base.cc.

◆ write_xdmf_file()

void DataOutInterface< dim, spacedim >::write_xdmf_file ( const std::vector< XDMFEntry > &  entries,
const std::string &  filename,
MPI_Comm  comm 
) const
inherited

Write an XDMF file based on the provided vector of XDMFEntry objects. Below is an example of how to use this function with HDF5 and the DataOutFilter:

DataOutBase::DataOutFilter data_filter(flags);
std::vector<XDMFEntry> xdmf_entries;
// Filter the data and store it in data_filter
data_out.write_filtered_data(data_filter);
// Write the filtered data to HDF5
data_out.write_hdf5_parallel(data_filter, "solution.h5", MPI_COMM_WORLD);
// Create an XDMF entry detailing the HDF5 file
auto new_xdmf_entry = data_out.create_xdmf_entry(data_filter,
"solution.h5",
simulation_time,
MPI_COMM_WORLD);
// Add the XDMF entry to the list
xdmf_entries.push_back(new_xdmf_entry);
// Create an XDMF file from all stored entries
data_out.write_xdmf_file(xdmf_entries, "solution.xdmf", MPI_COMM_WORLD);

Definition at line 7339 of file data_out_base.cc.

◆ write_hdf5_parallel() [1/2]

void DataOutInterface< dim, spacedim >::write_hdf5_parallel ( const DataOutBase::DataOutFilter data_filter,
const std::string &  filename,
MPI_Comm  comm 
) const
inherited

Write the data in data_filter to a single HDF5 file containing both the mesh and solution values. Below is an example of how to use this function with the DataOutFilter:

DataOutBase::DataOutFilter data_filter(flags);
// Filter the data and store it in data_filter
data_out.write_filtered_data(data_filter);
// Write the filtered data to HDF5
data_out.write_hdf5_parallel(data_filter, "solution.h5", MPI_COMM_WORLD);

Definition at line 7517 of file data_out_base.cc.

◆ write_hdf5_parallel() [2/2]

void DataOutInterface< dim, spacedim >::write_hdf5_parallel ( const DataOutBase::DataOutFilter data_filter,
const bool  write_mesh_file,
const std::string &  mesh_filename,
const std::string &  solution_filename,
MPI_Comm  comm 
) const
inherited

Write the data in data_filter to HDF5 file(s). If write_mesh_file is false, the mesh data will not be written and the solution file will contain only the solution values. If write_mesh_file is true and the filenames are the same, the resulting file will contain both mesh data and solution values.

Definition at line 7529 of file data_out_base.cc.

◆ write_filtered_data()

void DataOutInterface< dim, spacedim >::write_filtered_data ( DataOutBase::DataOutFilter filtered_data) const
inherited

DataOutFilter is an intermediate data format that reduces the amount of data that will be written to files. The object filled by this function can then later be used again to write data in a concrete file format; see, for example, DataOutBase::write_hdf5_parallel().

Definition at line 7389 of file data_out_base.cc.

◆ write()

void DataOutInterface< dim, spacedim >::write ( std::ostream &  out,
const DataOutBase::OutputFormat  output_format = DataOutBase::default_format 
) const
inherited

Write data and grid to out according to the given data format. This function simply calls the appropriate write_* function. If no output format is requested, the default_format is written.

An error occurs if no format is provided and the default format is default_format.

Definition at line 7924 of file data_out_base.cc.

◆ set_default_format()

void DataOutInterface< dim, spacedim >::set_default_format ( const DataOutBase::OutputFormat  default_format)
inherited

Set the default format. The value set here is used anytime, output for format default_format is requested.

Definition at line 7990 of file data_out_base.cc.

◆ set_flags()

void DataOutInterface< dim, spacedim >::set_flags ( const FlagType &  flags)
inherited

Set the flags to be used for output. This method expects flags to be a member of one of the child classes of OutputFlagsBase.

Definition at line 8000 of file data_out_base.cc.

◆ default_suffix()

std::string DataOutInterface< dim, spacedim >::default_suffix ( const DataOutBase::OutputFormat  output_format = DataOutBase::default_format) const
inherited

A function that returns the same string as the respective function in the base class does; the only exception being that if the parameter is omitted, then the value for the present default format is returned, i.e. the correct suffix for the format that was set through set_default_format() or parse_parameters() before calling this function.

Definition at line 8035 of file data_out_base.cc.

◆ declare_parameters()

void DataOutInterface< dim, spacedim >::declare_parameters ( ParameterHandler prm)
staticinherited

Declare parameters for all output formats by declaring subsections within the parameter file for each output format and call the respective declare_parameters functions of the flag classes for each output format.

Some of the declared subsections may not contain entries, if the respective format does not export any flags.

Note that the top-level parameters denoting the number of subdivisions per patch and the output format are not declared, since they are only passed to virtual functions and are not stored inside objects of this type. You have to declare them yourself.

Definition at line 8048 of file data_out_base.cc.

◆ parse_parameters()

void DataOutInterface< dim, spacedim >::parse_parameters ( ParameterHandler prm)
inherited

Read the parameters declared in declare_parameters() and set the flags for the output formats accordingly.

The flags thus obtained overwrite all previous contents of the flag objects as default-constructed or set by the set_flags() function.

Definition at line 8101 of file data_out_base.cc.

◆ validate_dataset_names()

void DataOutInterface< dim, spacedim >::validate_dataset_names ( ) const
protectedinherited

Validate that the names of the datasets returned by get_dataset_names() and get_nonscalar_data_ranges() are valid. This currently consists of checking that names are not used more than once. If an invalid state is encountered, an Assert() will be triggered in debug mode.

Definition at line 8183 of file data_out_base.cc.

Member Data Documentation

◆ dimension

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
const unsigned int DataOutFaces< dim, DoFHandlerType >::dimension = DoFHandlerType::dimension
static

An abbreviation for the dimension of the DoFHandler object we work with. Faces are then dimension-1 dimensional objects.

Definition at line 125 of file data_out_faces.h.

◆ space_dimension

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
const unsigned int DataOutFaces< dim, DoFHandlerType >::space_dimension = DoFHandlerType::space_dimension
static

An abbreviation for the spatial dimension within which the triangulation and DoFHandler are embedded in.

Definition at line 131 of file data_out_faces.h.

◆ surface_only

template<int dim, typename DoFHandlerType = DoFHandler<dim>>
const bool DataOutFaces< dim, DoFHandlerType >::surface_only
private

Parameter deciding between surface meshes and full wire basket.

Definition at line 240 of file data_out_faces.h.

◆ triangulation

SmartPointer<const Triangulation<DoFHandlerType::dimension, DoFHandlerType::space_dimension> > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::triangulation
protectedinherited

Pointer to the triangulation object.

Definition at line 987 of file data_out_dof_data.h.

◆ dofs

SmartPointer<const DoFHandlerType> DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::dofs
protectedinherited

Pointer to the optional handler object.

Definition at line 992 of file data_out_dof_data.h.

◆ dof_data

std::vector<std::shared_ptr< internal::DataOutImplementation::DataEntryBase<DoFHandlerType> > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::dof_data
protectedinherited

List of data elements with vectors of values for each degree of freedom.

Definition at line 999 of file data_out_dof_data.h.

◆ cell_data

std::vector<std::shared_ptr< internal::DataOutImplementation::DataEntryBase<DoFHandlerType> > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::cell_data
protectedinherited

List of data elements with vectors of values for each cell.

Definition at line 1006 of file data_out_dof_data.h.

◆ patches

std::vector<Patch> DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::patches
protectedinherited

This is a list of patches that is created each time build_patches() is called. These patches are used in the output routines of the base classes.

Definition at line 1013 of file data_out_dof_data.h.

◆ default_subdivisions

unsigned int DataOutInterface< dim, spacedim >::default_subdivisions
protectedinherited

The default number of subdivisions for patches. This is filled by parse_parameters() and should be obeyed by build_patches() in derived classes.

Definition at line 3016 of file data_out_base.h.


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