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Reference documentation for deal.II version 9.0.0
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Reference documentation for deal.II version 9.0.0
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#include <deal.II/numerics/data_out_dof_data.h>
Public Types | |
| enum | DataVectorType { type_dof_data, type_cell_data, type_automatic } |
| typedef Triangulation< DoFHandlerType::dimension, DoFHandlerType::space_dimension >::cell_iterator | cell_iterator |
Public Member Functions | |
| DataOut_DoFData () | |
| virtual | ~DataOut_DoFData () |
| 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) |
| 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 |
 Public Member Functions inherited from DataOutInterface< patch_dim, patch_space_dim > | |
| DataOutInterface () | |
| virtual | ~DataOutInterface ()=default |
| 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_tecplot_binary (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 char *filename, MPI_Comm comm) const |
| void | write_pvtu_record (std::ostream &out, const std::vector< std::string > &piece_names) 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) |
| std::size_t | memory_consumption () const |
Protected Types | |
| typedef ::DataOutBase::Patch< patch_dim, patch_space_dim > | Patch |
Protected Member Functions | |
| virtual const std::vector< Patch > & | get_patches () const |
| virtual std::vector< std::string > | get_dataset_names () const |
| 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 > > | get_vector_data_ranges () const |
| Protected Member Functions inherited from DataOutInterface< patch_dim, patch_space_dim > | |
| 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< Patch > | patches |
| Protected Attributes inherited from DataOutInterface< patch_dim, patch_space_dim > | |
| 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 |
Additional Inherited Members | |
| Static Public Member Functions inherited from DataOutInterface< patch_dim, patch_space_dim > | |
| static void | declare_parameters (ParameterHandler &prm) |
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.
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:
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.
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 546 of file data_out_dof_data.h.
| typedef Triangulation<DoFHandlerType::dimension,DoFHandlerType::space_dimension>::cell_iterator DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::cell_iterator |
Typedef to the iterator type of the dof handler class under consideration.
Definition at line 554 of file data_out_dof_data.h.
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protected |
Abbreviate the somewhat lengthy name for the Patch class.
Definition at line 853 of file data_out_dof_data.h.
| enum DataOut_DoFData::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).
| 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 567 of file data_out_dof_data.h.
| DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::DataOut_DoFData | ( | ) |
Constructor
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virtual |
Destructor.
| 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.
| 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.
| 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, |
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| const std::vector< DataComponentInterpretation::DataComponentInterpretation > & | data_component_interpretation = std::vector<DataComponentInterpretation::DataComponentInterpretation>() |
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| ) |
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.
Definition at line 957 of file data_out_dof_data.h.
| void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::add_data_vector | ( | const VectorType & | data, |
| const std::string & | name, | ||
| const DataVectorType | type = type_automatic, |
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| const std::vector< DataComponentInterpretation::DataComponentInterpretation > & | data_component_interpretation = std::vector<DataComponentInterpretation::DataComponentInterpretation>() |
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| ) |
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 940 of file data_out_dof_data.h.
| 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>() |
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| ) |
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 the DoFHandler objects need to be based on the same triangulation. This function allows you to export data from multiple DoFHandlers that describe different solution components.
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 skipped.
Definition at line 989 of file data_out_dof_data.h.
| 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>() |
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| ) |
This function is an abbreviation of the function above with only a scalar dof_handler given and a single data name.
Definition at line 973 of file data_out_dof_data.h.
| 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.
Definition at line 1003 of file data_out_dof_data.h.
| 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.
| 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.
| 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.
| void DataOut_DoFData< DoFHandlerType, patch_dim, patch_space_dim >::merge_patches | ( | const DataOut_DoFData< DoFHandlerType2, patch_dim, patch_space_dim > & | source, |
| const Point< patch_space_dim > & | shift = Point<patch_space_dim>() |
||
| ) |
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 1016 of file data_out_dof_data.h.
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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.
| 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.
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protectedvirtual |
Function by which the base class's functions get to know what patches they shall write to a file.
Implements DataOutInterface< patch_dim, patch_space_dim >.
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Virtual function through which the names of data sets are obtained by the output functions of the base class.
Implements DataOutInterface< patch_dim, patch_space_dim >.
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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.
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protectedvirtual |
Overload of the respective DataOutInterface::get_vector_data_ranges() function. See there for a more extensive documentation.
Reimplemented from DataOutInterface< patch_dim, patch_space_dim >.
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private |
Common function called by the four public add_data_vector methods.
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friend |
Make all template siblings friends. Needed for the merge_patches() function.
Definition at line 916 of file data_out_dof_data.h.
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Pointer to the triangulation object.
Definition at line 858 of file data_out_dof_data.h.
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protected |
Pointer to the optional handler object.
Definition at line 863 of file data_out_dof_data.h.
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protected |
List of data elements with vectors of values for each degree of freedom.
Definition at line 868 of file data_out_dof_data.h.
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protected |
List of data elements with vectors of values for each cell.
Definition at line 873 of file data_out_dof_data.h.
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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 880 of file data_out_dof_data.h.
1.8.14