Reference documentation for deal.II version 9.4.0
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Public Types | Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
DataOutResample< dim, patch_dim, spacedim > Class Template Reference

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

Inheritance diagram for DataOutResample< dim, patch_dim, spacedim >:
[legend]

Public Types

enum  DataVectorType
 
using cell_iterator = typename Triangulation< dim, spacedim >::cell_iterator
 

Public Member Functions

 DataOutResample (const Triangulation< patch_dim, spacedim > &patch_tria, const Mapping< patch_dim, spacedim > &patch_mapping)
 
void update_mapping (const Mapping< dim, spacedim > &mapping, const unsigned int n_subdivisions=0)
 
void build_patches (const Mapping< dim, spacedim > &mapping, const unsigned int n_subdivisions=0, const typename DataOut< patch_dim, spacedim >::CurvedCellRegion curved_region=DataOut< patch_dim, spacedim >::CurvedCellRegion::curved_boundary)
 
void build_patches (const typename DataOut< patch_dim, spacedim >::CurvedCellRegion curved_region=DataOut< patch_dim, spacedim >::CurvedCellRegion::curved_boundary)
 
void attach_dof_handler (const DoFHandler< dim, spacedim > &)
 
void attach_triangulation (const Triangulation< dim, spacedim > &)
 
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={})
 
void add_data_vector (const VectorType &data, const std::string &name, const DataVectorType type=type_automatic, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation={})
 
void add_data_vector (const DoFHandler< dim, spacedim > &dof_handler, const VectorType &data, const std::vector< std::string > &names, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation={})
 
void add_data_vector (const DoFHandler< dim, spacedim > &dof_handler, const VectorType &data, const std::string &name, const std::vector< DataComponentInterpretation::DataComponentInterpretation > &data_component_interpretation={})
 
void add_data_vector (const VectorType &data, const DataPostprocessor< spacedim > &data_postprocessor)
 
void add_data_vector (const DoFHandler< dim, spacedim > &dof_handler, const VectorType &data, const DataPostprocessor< spacedim > &data_postprocessor)
 
void add_mg_data_vector (const DoFHandler< dim, spacedim > &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 DoFHandler< dim, spacedim > &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< dim2, patch_dim, spacedim2, patch_spacedim > &source, const Point< patch_spacedim > &shift=Point< patch_spacedim >())
 
void merge_patches (const DataOut_DoFData< DoFHandlerType2::dimension, patch_dim, DoFHandlerType2::space_dimension, patch_spacedim > &source, const Point< patch_spacedim > &shift=Point< patch_spacedim >())
 
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, const 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, const 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, const MPI_Comm &comm) const
 
void write_xdmf_file (const std::vector< XDMFEntry > &entries, const std::string &filename, const MPI_Comm &comm) const
 
void write_hdf5_parallel (const DataOutBase::DataOutFilter &data_filter, const std::string &filename, const 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, const 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_spacedim >
 

Protected Member Functions

virtual const std::vector< typename DataOutBase::Patch< patch_dim, spacedim > > & get_patches () const override
 
virtual std::vector< std::string > get_dataset_names () const override
 
virtual std::vector< std::tuple< unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation > > get_nonscalar_data_ranges () const override
 
std::vector< std::shared_ptr<::hp::FECollection< dim, spacedim > > > get_fes () const
 
void validate_dataset_names () const
 

Protected Attributes

SmartPointer< const Triangulation< dim, spacedim > > triangulation
 
SmartPointer< const DoFHandler< dim, spacedim > > dofs
 
std::vector< std::shared_ptr< internal::DataOutImplementation::DataEntryBase< dim, spacedim > > > dof_data
 
std::vector< std::shared_ptr< internal::DataOutImplementation::DataEntryBase< dim, spacedim > > > cell_data
 
std::vector< Patchpatches
 
unsigned int default_subdivisions
 

Private Member Functions

void add_data_vector_internal (const DoFHandler< dim, spacedim > *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 Attributes

DoFHandler< patch_dim, spacedim > patch_dof_handler
 
const SmartPointer< const Mapping< patch_dim, spacedim > > patch_mapping
 
DataOut< patch_dim, spacedim > patch_data_out
 
Utilities::MPI::RemotePointEvaluation< dim, spacedim > rpe
 
std::shared_ptr< Utilities::MPI::Partitionerpartitioner
 
std::vector< types::global_dof_indexpoint_to_local_vector_indices
 
SmartPointer< const Mapping< dim, spacedim > > mapping
 
DataOutBase::OutputFormat default_fmt
 
DataOutBase::DXFlags dx_flags
 
DataOutBase::UcdFlags ucd_flags
 
DataOutBase::GnuplotFlags gnuplot_flags
 
DataOutBase::PovrayFlags povray_flags
 
DataOutBase::EpsFlags eps_flags
 
DataOutBase::GmvFlags gmv_flags
 
DataOutBase::TecplotFlags tecplot_flags
 
DataOutBase::VtkFlags vtk_flags
 
DataOutBase::SvgFlags svg_flags
 
DataOutBase::Deal_II_IntermediateFlags deal_II_intermediate_flags
 

Detailed Description

template<int dim, int patch_dim, int spacedim>
class DataOutResample< dim, patch_dim, spacedim >

A DataOut-like class that does not output a numerical solution on the cells of the original triangulation but interpolates the result onto a second triangulation (that can be completely unrelated). By using this class, one can output the result obtained on an unstructured mesh onto a structured one or one can create a slice in 3D.

The following code snippet shows the steps how to use the class when the solution is given for a three dimensional triangulation and the result should be outputted on a (2D) slice:

// setup and first usage
data_out.add_data_vector(dof_handler, vector, "solution");
data_out.build_patches(mapping);
// ... no changes in triangulation and mapping -> reuse internal data
structures data_out.build_patches();
// ... changes in triangulation or mapping -> reinitialize internal data
structures data_out.build_patches(mapping);
SmartPointer< const Mapping< dim, spacedim > > mapping
const SmartPointer< const Mapping< patch_dim, spacedim > > patch_mapping
Note
While the dimension of the two triangulations might differ, their space dimension need to coincide.

Definition at line 59 of file data_out_resample.h.

Member Typedef Documentation

◆ cell_iterator

using DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::cell_iterator = typename Triangulation<dim, spacedim>::cell_iterator
inherited

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

Definition at line 604 of file data_out_dof_data.h.

◆ Patch

using DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::Patch = ::DataOutBase::Patch<patch_dim, patch_spacedim>
protectedinherited

Abbreviate the somewhat lengthy name for the Patch class.

Definition at line 963 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 615 of file data_out_dof_data.h.

Constructor & Destructor Documentation

◆ DataOutResample()

template<int dim, int patch_dim, int spacedim>
DataOutResample< dim, patch_dim, spacedim >::DataOutResample ( const Triangulation< patch_dim, spacedim > &  patch_tria,
const Mapping< patch_dim, spacedim > &  patch_mapping 
)

Constructor taking the triangulation and mapping for which the patches should be generated.

Definition at line 34 of file data_out_resample.cc.

Member Function Documentation

◆ update_mapping()

template<int dim, int patch_dim, int spacedim>
void DataOutResample< dim, patch_dim, spacedim >::update_mapping ( const Mapping< dim, spacedim > &  mapping,
const unsigned int  n_subdivisions = 0 
)

Update the mapping of original triangulation. One needs to call this function if the mapping has changed. Just like in the DataOut context, n_subdivisions determines how many "patches" this function will build out of every cell.

This function involves an expensive setup: evaluation points are generated and their owners are determined, which is used to set up the communication pattern.

Note
If you use the version of build_patches() that does not take a mapping, this function has to be called before its first usage.

Definition at line 45 of file data_out_resample.cc.

◆ build_patches() [1/2]

template<int dim, int patch_dim, int spacedim>
void DataOutResample< dim, patch_dim, spacedim >::build_patches ( const Mapping< dim, spacedim > &  mapping,
const unsigned int  n_subdivisions = 0,
const typename DataOut< patch_dim, spacedim >::CurvedCellRegion  curved_region = DataOut<patch_dim, spacedim>::CurvedCellRegion::curved_boundary 
)

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 cell of a triangulation and DoFHandler object that can then be used to write files in some format that is readable by visualization programs.

Since this function calls internally at the beginning update_mapping(), this function also involves an expensive setup.

Just like in the DataOut::build_patches() context, n_subdivisions determines how many "patches" this function will build out of every cell.

Definition at line 109 of file data_out_resample.cc.

◆ build_patches() [2/2]

template<int dim, int patch_dim, int spacedim>
void DataOutResample< dim, patch_dim, spacedim >::build_patches ( const typename DataOut< patch_dim, spacedim >::CurvedCellRegion  curved_region = DataOut<patch_dim, spacedim>::CurvedCellRegion::curved_boundary)

Just like the above function, this function builds a list of patches to be written by the low-level functions of the base class. However it skips the update of the mapping and reuses the one registered via update_mapping(). This allows to skip the expensive setup of the internal communication routines.

Note
This function can be only used if a mapping has been registered via update_mapping() or the other build_patches() function. The same n_subdivisions previously passed to these functions is used.

Definition at line 122 of file data_out_resample.cc.

◆ get_patches()

template<int dim, int patch_dim, int spacedim>
const std::vector< typename DataOutBase::Patch< patch_dim, spacedim > > & DataOutResample< dim, patch_dim, spacedim >::get_patches
overrideprotectedvirtual

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

Reimplemented from DataOut_DoFData< dim, patch_dim, spacedim, spacedim >.

Definition at line 191 of file data_out_resample.cc.

◆ attach_dof_handler()

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::attach_dof_handler ( const DoFHandler< dim, spacedim > &  )
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< dim, patch_dim, spacedim, patch_spacedim >::attach_triangulation ( const Triangulation< dim, spacedim > &  )
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< dim, patch_dim, spacedim, patch_spacedim >::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 = {} 
)
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.

Definition at line 731 of file data_out_dof_data.h.

◆ add_data_vector() [2/6]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector ( const VectorType &  data,
const std::string &  name,
const DataVectorType  type = type_automatic,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = {} 
)
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 756 of file data_out_dof_data.h.

◆ add_data_vector() [3/6]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector ( const DoFHandler< dim, spacedim > &  dof_handler,
const VectorType &  data,
const std::vector< std::string > &  names,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = {} 
)
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 780 of file data_out_dof_data.h.

◆ add_data_vector() [4/6]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector ( const DoFHandler< dim, spacedim > &  dof_handler,
const VectorType &  data,
const std::string &  name,
const std::vector< DataComponentInterpretation::DataComponentInterpretation > &  data_component_interpretation = {} 
)
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 794 of file data_out_dof_data.h.

◆ add_data_vector() [5/6]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector ( const VectorType &  data,
const DataPostprocessor< spacedim > &  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 829 of file data_out_dof_data.h.

◆ add_data_vector() [6/6]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector ( const DoFHandler< dim, spacedim > &  dof_handler,
const VectorType &  data,
const DataPostprocessor< spacedim > &  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< dim, patch_dim, spacedim, patch_spacedim >::add_mg_data_vector ( const DoFHandler< dim, spacedim > &  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< dim, patch_dim, spacedim, patch_spacedim >::add_mg_data_vector ( const DoFHandler< dim, spacedim > &  dof_handler,
const MGLevelObject< VectorType > &  data,
const std::string &  name 
)
inherited

Scalar version of the function above.

◆ clear_data_vectors()

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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< dim, patch_dim, spacedim, patch_spacedim >::clear_input_data_references ( )
inherited

Release pointers to all input data elements, i.e. pointers to 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 must not be deleted before the output thread is finished.

◆ merge_patches() [1/2]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::merge_patches ( const DataOut_DoFData< dim2, patch_dim, spacedim2, patch_spacedim > &  source,
const Point< patch_spacedim > &  shift = Point<patch_spacedim>() 
)
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 927 of file data_out_dof_data.h.

◆ merge_patches() [2/2]

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::merge_patches ( const DataOut_DoFData< DoFHandlerType2::dimension, patch_dim, DoFHandlerType2::space_dimension, patch_spacedim > &  source,
const Point< patch_spacedim > &  shift = Point<patch_spacedim>() 
)
inherited
Deprecated:
Use merge_patches() without the DoFHandlerType2 template instead.

Definition at line 937 of file data_out_dof_data.h.

◆ clear()

virtual void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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< dim, patch_dim, spacedim, patch_spacedim >::memory_consumption ( ) const
inherited

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

◆ get_dataset_names()

virtual std::vector< std::string > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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_spacedim >.

◆ get_nonscalar_data_ranges()

virtual std::vector< std::tuple< unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation > > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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_spacedim >.

◆ get_fes()

std::vector< std::shared_ptr<::hp::FECollection< dim, spacedim > > > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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.

◆ add_data_vector_internal()

void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector_internal ( const DoFHandler< dim, spacedim > *  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 
)
privateinherited

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 2618 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 2625 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 2632 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 2639 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 2646 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 2653 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 2660 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 2674 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 2691 of file data_out_base.cc.

◆ write_vtu_in_parallel()

void DataOutInterface< dim, spacedim >::write_vtu_in_parallel ( const std::string &  filename,
const 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 2702 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 2739 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 2801 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 2814 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 2827 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,
const 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 2835 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,
const 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 2846 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,
const 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 2877 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,
const 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 2896 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,
const 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 2908 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 2921 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 2933 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 2942 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 2951 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 2962 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 2980 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 2990 of file data_out_base.cc.

◆ validate_dataset_names()

void DataOutInterface< dim, spacedim >::validate_dataset_names
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 3050 of file data_out_base.cc.

Member Data Documentation

◆ patch_dof_handler

template<int dim, int patch_dim, int spacedim>
DoFHandler<patch_dim, spacedim> DataOutResample< dim, patch_dim, spacedim >::patch_dof_handler
private

Intermediate DoFHandler

Definition at line 133 of file data_out_resample.h.

◆ patch_mapping

template<int dim, int patch_dim, int spacedim>
const SmartPointer<const Mapping<patch_dim, spacedim> > DataOutResample< dim, patch_dim, spacedim >::patch_mapping
private

Mapping used in connection with patch_tria.

Definition at line 138 of file data_out_resample.h.

◆ patch_data_out

template<int dim, int patch_dim, int spacedim>
DataOut<patch_dim, spacedim> DataOutResample< dim, patch_dim, spacedim >::patch_data_out
private

DataOut object that does the actual building of the patches.

Definition at line 143 of file data_out_resample.h.

◆ rpe

template<int dim, int patch_dim, int spacedim>
Utilities::MPI::RemotePointEvaluation<dim, spacedim> DataOutResample< dim, patch_dim, spacedim >::rpe
private

Object to evaluate

Definition at line 148 of file data_out_resample.h.

◆ partitioner

template<int dim, int patch_dim, int spacedim>
std::shared_ptr<Utilities::MPI::Partitioner> DataOutResample< dim, patch_dim, spacedim >::partitioner
private

Partitioner to create internally distributed vectors.

Definition at line 153 of file data_out_resample.h.

◆ point_to_local_vector_indices

template<int dim, int patch_dim, int spacedim>
std::vector<types::global_dof_index> DataOutResample< dim, patch_dim, spacedim >::point_to_local_vector_indices
private

Process local indices to access efficiently internal distributed vectors.

Definition at line 158 of file data_out_resample.h.

◆ mapping

template<int dim, int patch_dim, int spacedim>
SmartPointer<const Mapping<dim, spacedim> > DataOutResample< dim, patch_dim, spacedim >::mapping
private

Mapping of the original triangulation provided in update_mapping().

Definition at line 163 of file data_out_resample.h.

◆ triangulation

SmartPointer<const Triangulation<dim, spacedim> > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::triangulation
protectedinherited

Pointer to the triangulation object.

Definition at line 968 of file data_out_dof_data.h.

◆ dofs

SmartPointer<const DoFHandler<dim, spacedim> > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::dofs
protectedinherited

Pointer to the optional handler object.

Definition at line 973 of file data_out_dof_data.h.

◆ dof_data

std::vector<std::shared_ptr< internal::DataOutImplementation::DataEntryBase<dim, spacedim> > > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::dof_data
protectedinherited

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

Definition at line 980 of file data_out_dof_data.h.

◆ cell_data

std::vector<std::shared_ptr< internal::DataOutImplementation::DataEntryBase<dim, spacedim> > > DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::cell_data
protectedinherited

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

Definition at line 987 of file data_out_dof_data.h.

◆ patches

std::vector<Patch> DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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 994 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 3058 of file data_out_base.h.

◆ default_fmt

DataOutBase::OutputFormat DataOutInterface< dim, spacedim >::default_fmt
privateinherited

Standard output format. Use this format, if output format default_format is requested. It can be changed by the set_format function or in a parameter file.

Definition at line 3066 of file data_out_base.h.

◆ dx_flags

DataOutBase::DXFlags DataOutInterface< dim, spacedim >::dx_flags
privateinherited

Flags to be used upon output of OpenDX data. Can be changed by using the set_flags function.

Definition at line 3072 of file data_out_base.h.

◆ ucd_flags

DataOutBase::UcdFlags DataOutInterface< dim, spacedim >::ucd_flags
privateinherited

Flags to be used upon output of UCD data. Can be changed by using the set_flags function.

Definition at line 3078 of file data_out_base.h.

◆ gnuplot_flags

DataOutBase::GnuplotFlags DataOutInterface< dim, spacedim >::gnuplot_flags
privateinherited

Flags to be used upon output of GNUPLOT data. Can be changed by using the set_flags function.

Definition at line 3084 of file data_out_base.h.

◆ povray_flags

DataOutBase::PovrayFlags DataOutInterface< dim, spacedim >::povray_flags
privateinherited

Flags to be used upon output of POVRAY data. Can be changed by using the set_flags function.

Definition at line 3090 of file data_out_base.h.

◆ eps_flags

DataOutBase::EpsFlags DataOutInterface< dim, spacedim >::eps_flags
privateinherited

Flags to be used upon output of EPS data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3096 of file data_out_base.h.

◆ gmv_flags

DataOutBase::GmvFlags DataOutInterface< dim, spacedim >::gmv_flags
privateinherited

Flags to be used upon output of gmv data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3102 of file data_out_base.h.

◆ tecplot_flags

DataOutBase::TecplotFlags DataOutInterface< dim, spacedim >::tecplot_flags
privateinherited

Flags to be used upon output of Tecplot data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3108 of file data_out_base.h.

◆ vtk_flags

DataOutBase::VtkFlags DataOutInterface< dim, spacedim >::vtk_flags
privateinherited

Flags to be used upon output of vtk data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3114 of file data_out_base.h.

◆ svg_flags

DataOutBase::SvgFlags DataOutInterface< dim, spacedim >::svg_flags
privateinherited

Flags to be used upon output of svg data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3120 of file data_out_base.h.

◆ deal_II_intermediate_flags

DataOutBase::Deal_II_IntermediateFlags DataOutInterface< dim, spacedim >::deal_II_intermediate_flags
privateinherited

Flags to be used upon output of deal.II intermediate data in one space dimension. Can be changed by using the set_flags function.

Definition at line 3126 of file data_out_base.h.


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