Reference documentation for deal.II version Git e038590ef8 2020-10-28 14:38:53 +0100
DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim > Class Template Reference

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

Inheritance diagram for DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >:
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## Public Types

enum  DataVectorType { type_dof_data, type_cell_data, type_automatic }

using cell_iterator = typename Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension >::cell_iterator

## Public Member Functions

DataOut_DoFData ()

virtual ~DataOut_DoFData () override

void attach_dof_handler (const DoFHandlerType &)

void attach_triangulation (const Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension > &)

template<class VectorType >
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 >())

template<class VectorType >
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 >())

template<class VectorType >
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 >())

template<class VectorType >
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 >())

template<class VectorType >
void add_data_vector (const VectorType &data, const DataPostprocessor< DoFHandlerType::space_dimension > &data_postprocessor)

template<class VectorType >
void add_data_vector (const DoFHandlerType &dof_handler, const VectorType &data, const DataPostprocessor< DoFHandlerType::space_dimension > &data_postprocessor)

template<class VectorType >
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 >())

template<class VectorType >
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 ()

template<typename DoFHandlerType2 >
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)

## 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

template<class VectorType >
void add_data_vector_internal (const DoFHandlerType *dof_handler, const VectorType &data, const std::vector< std::string > &names, const DataVectorType type, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation, const bool deduce_output_names)

## Friends

template<class , int , int >
class DataOut_DoFData

template<int , class >
class MGDataOut

## Detailed Description

### template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim> class DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >

This is an abstract class which provides the functionality to generate patches for output by base classes from data vectors on a grid. It allows to attach one or more pointers to a DoFHandler and attached node and cell data denoting functions on the grid which shall later be written in any of the implemented data formats.

### User visible interface

The user visible interface of this class allows the user to specify data in two different ways. One is to make a DoFHandler object known to this class and to add data vectors that all correspond to this DoFHandler or the grid cells which will later be written to a file in some format. The second approach is to pass a DoFHandler object along with the vector. This allows setting data from different DoFHandlers in a neat way (of course, they both need to be based on the same triangulation). Instead of pondering about the different functions, an example for the first kind is probably the best explanation:

...
... // compute solution, which contains nodal values
...
... // compute error_estimator, which contains one value per cell
std::vector<std::string> solution_names;
solution_names.emplace_back ("x-displacement");
solution_names.emplace_back ("y-displacement");
DataOut<dim> data_out;
data_out.attach_dof_handler (dof_handler);
data_out.build_patches ();
ofstream output_file ("output");
data_out.write_xxx (output_file);
data_out.clear();

attach_dof_handler() tells this class that all future operations are to take place with the DoFHandler object and the triangulation it lives on. We then add the solution vector and the error estimator; note that they have different dimensions, because the solution is a nodal vector, here consisting of two components ("x-displacement" and "y-displacement") while the error estimator probably is a vector holding cell data. When attaching a data vector, you have to give a name to each component of the vector, which is done through an object of type vector<string> as second argument; if only one component is in the vector, for example if we are adding cell data as in the second case, or if the finite element used by the DoFHandler has only one component, then you can use the second add_data_vector() function which takes a string instead of the vector<string>.

The add_data_vector() functions have additional arguments (with default values) that can be used to specify certain transformations. In particular, it allows to attach DataPostprocessor arguments to compute derived information from a data vector at each point at which the field will be evaluated so that it can be written to a file (for example, the Mach number in hypersonic flow can be computed from density and velocities; step-29 also shows an example); another piece of information specified through arguments with default values is how certain output components should be interpreted, i.e. whether each component of the data is logically an independent scalar field, or whether some of them together form logically a vector-field (see the DataComponentInterpretation::DataComponentInterpretation enum, and the step-22 tutorial program).

This class does not copy the vector given to it through the add_data_vector() functions, for memory consumption reasons. It only stores a reference to it, so it is in your responsibility to make sure that the data vectors exist long enough.

After adding all data vectors, you need to call a function which generates the patches (i.e., some intermediate data representation) for output from the stored data. Derived classes name this function build_patches(). Finally, you write() the data in one format or other, to a file.

In the example above, an object of type DataOut was used, i.e. an object of a derived class. This is necessary since the current class does not provide means to actually generate the patches, only aids to store and access data. Any real functionality is implemented in derived classes such as DataOut.

Note that the base class of this class, DataOutInterface offers several functions to ease programming with run-time determinable output formats (i.e. you need not use a fixed format by calling DataOutInterface::write_xxx in the above example, but you can select it by a run-time parameter without having to write the if () ... else ... clauses yourself), and also functions and classes offering ways to control the appearance of the output by setting flags for each output format.

### Information for derived classes

What this class lacks is a way to produce the patches for output itself, from the stored data and degree of freedom information. Since this task is often application dependent it is left to derived classes. For example, in many applications, it might be wanted to limit the depth of output to a certain number of refinement levels and write data from finer cells only in a way interpolated to coarser cells, to reduce the amount of output. Also, it might be wanted to use different numbers of subdivisions on different cells when forming a patch, for example to accomplish for different polynomial degrees of the trial space on different cells. Also, the output need not necessarily consist of a patch for each cell, but might be made up of patches for faces, of other things. Take a look at derived classes to what is possible in this respect.

For this reason, it is left to a derived class to provide a function, named usually build_patches() or the like, which fills the patches array of this class.

Regarding the templates of this class, it needs three values: first the space dimension in which the triangulation and the DoF handler operate, second the dimension of the objects which the patches represent. Although in most cases they are equal, there are also classes for which this does not hold, for example if one outputs the result of a computation exploiting rotational symmetry in the original domain (in which the space dimension of the output would be one higher than that of the DoF handler, see the DataOut_Rotation() class), or one might conceive that one could write a class that only outputs the solution on a cut through the domain, in which case the space dimension of the output is less than that of the DoF handler. The last template argument denotes the dimension of the space into which the patches are embedded; usually, this dimension is the same as the dimensio of the patches themselves (which is also the default value of the template parameter), but there might be cases where this is not so. For example, in the DataOut_Faces() class, patches are generated from faces of the triangulation. Thus, the dimension of the patch is one less than the dimension of the embedding space, which is, in this case, equal to the dimension of the triangulation and DoF handler. However, for the cut through the domain mentioned above, if the cut is a straight one, then the cut can be embedded into a space of one dimension lower than the dimension of the triangulation, so that the last template parameter has the same value as the second one.

Definition at line 612 of file data_out_dof_data.h.

## ◆ cell_iterator

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 using DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::cell_iterator = typename Triangulation::cell_iterator

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

Definition at line 621 of file data_out_dof_data.h.

## ◆ Patch

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 using DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::Patch = ::DataOutBase::Patch
protected

Abbreviate the somewhat lengthy name for the Patch class.

Definition at line 980 of file data_out_dof_data.h.

## ◆ DataVectorType

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>

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).

Enumerator
type_dof_data

Data vector entries are associated to degrees of freedom

type_cell_data

Data vector entries are one per grid cell

type_automatic

Find out automatically

Definition at line 632 of file data_out_dof_data.h.

## ◆ DataOut_DoFData()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::DataOut_DoFData ( )

Constructor

## ◆ ~DataOut_DoFData()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 virtual DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::~DataOut_DoFData ( )
overridevirtual

Destructor.

## ◆ attach_dof_handler()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::attach_dof_handler ( const DoFHandlerType & )

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()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::attach_triangulation ( const Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension > & )

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.

template<typename DoFHandlerType , int patch_dim, int patch_space_dim>
template<typename VectorType >
 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>() )

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.

template<typename DoFHandlerType , int patch_dim, int patch_space_dim>
template<typename VectorType >
 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>() )

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.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim>
template<typename VectorType >
 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>() )

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.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim>
template<typename VectorType >
 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>() )

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.

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

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.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<class VectorType >
 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 )

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.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<class VectorType >
 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 >() )

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.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<class VectorType >
 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 )

Scalar version of the function above.

## ◆ clear_data_vectors()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear_data_vectors ( )

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()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear_input_data_references ( )

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()

template<typename DoFHandlerType , int patch_dim, int patch_space_dim>
template<typename DoFHandlerType2 >
 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() )

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()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 virtual void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::clear ( )
virtual

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()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 std::size_t DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::memory_consumption ( ) const

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

## ◆ get_patches()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 virtual const std::vector& DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_patches ( ) const
overrideprotectedvirtual

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

## ◆ get_dataset_names()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 virtual std::vector DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_dataset_names ( ) const
overrideprotectedvirtual

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

## ◆ get_fes()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 std::vector< std::shared_ptr<::hp::FECollection > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_fes ( ) const
protected

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()

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 virtual std::vector< std::tuple > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::get_nonscalar_data_ranges ( ) const
overrideprotectedvirtual

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 >.

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<class VectorType >
 void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector_internal ( const DoFHandlerType * dof_handler, const VectorType & data, const std::vector< std::string > & names, const DataVectorType type, const std::vector< DataComponentInterpretation::DataComponentInterpretation > & data_component_interpretation, const bool deduce_output_names )
private

Common function called by the four public add_data_vector methods.

## ◆ 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 6997 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 7049 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 7062 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 7023 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 7036 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 7075 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 7010 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 7088 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 7099 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 7121 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 7224 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 7237 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 7110 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 7319 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 7332 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 7346 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 7419 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 7597 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 7609 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 7469 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 8004 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 8070 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 8080 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 8115 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 8128 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 8181 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 8263 of file data_out_base.cc.

## ◆ DataOut_DoFData

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<class , int , int >
 friend class DataOut_DoFData
friend

Definition at line 1052 of file data_out_dof_data.h.

## ◆ MGDataOut

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
template<int , class >
 friend class MGDataOut
friend

Definition at line 1057 of file data_out_dof_data.h.

## ◆ triangulation

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 SmartPointer > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::triangulation
protected

Pointer to the triangulation object.

Definition at line 987 of file data_out_dof_data.h.

## ◆ dofs

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 SmartPointer DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::dofs
protected

Pointer to the optional handler object.

Definition at line 992 of file data_out_dof_data.h.

## ◆ dof_data

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 std::vector > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::dof_data
protected

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

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 std::vector > > DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::cell_data
protected

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

Definition at line 1006 of file data_out_dof_data.h.

## ◆ patches

template<typename DoFHandlerType, int patch_dim, int patch_space_dim = patch_dim>
 std::vector DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::patches
protected

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 file: