deal.II version GIT relicensing-1972-g22a7b89abe 2024-10-11 21:20:00+00:00
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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 } |
using | cell_iterator = typename Triangulation< dim, spacedim >::cell_iterator |
Public Member Functions | |
DataOut_DoFData () | |
virtual | ~DataOut_DoFData () override |
void | attach_dof_handler (const DoFHandler< dim, spacedim > &) |
void | attach_triangulation (const Triangulation< dim, spacedim > &) |
template<typename 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={}) |
template<typename 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={}) |
template<typename VectorType > | |
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={}) |
template<typename VectorType > | |
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={}) |
template<typename VectorType > | |
void | add_data_vector (const VectorType &data, const DataPostprocessor< spacedim > &data_postprocessor) |
template<typename VectorType > | |
void | add_data_vector (const DoFHandler< dim, spacedim > &dof_handler, const VectorType &data, const DataPostprocessor< spacedim > &data_postprocessor) |
template<typename VectorType > | |
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 >()) |
template<typename VectorType > | |
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 () |
template<int dim2, int spacedim2> | |
void | merge_patches (const DataOut_DoFData< dim2, patch_dim, spacedim2, patch_spacedim > &source, const Point< patch_spacedim > &shift=Point< patch_spacedim >()) |
virtual void | clear () |
std::size_t | memory_consumption () const |
virtual const std::vector< Patch > & | get_patches () const override |
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 |
void | write_deal_II_intermediate_in_parallel (const std::string &filename, const MPI_Comm comm, const DataOutBase::CompressionLevel compression) 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) |
template<typename FlagType > | |
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 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 | |
ObserverPointer< const Triangulation< dim, spacedim > > | triangulation |
ObserverPointer< 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< Patch > | patches |
unsigned int | default_subdivisions |
Private Member Functions | |
template<typename VectorType > | |
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) |
Friends | |
template<int , int , int , int > | |
class | DataOut_DoFData |
template<int , class > | |
class | MGDataOut |
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).
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 596 of file data_out_dof_data.h.
using DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::cell_iterator = typename Triangulation<dim, spacedim>::cell_iterator |
Typedef to the iterator type of the dof handler class under consideration.
Definition at line 603 of file data_out_dof_data.h.
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protected |
Abbreviate the somewhat lengthy name for the Patch class.
Definition at line 950 of file data_out_dof_data.h.
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 | |
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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 614 of file data_out_dof_data.h.
DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::DataOut_DoFData | ( | ) |
Constructor
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overridevirtual |
Destructor.
void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::attach_dof_handler | ( | const DoFHandler< dim, spacedim > & | ) |
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< dim, patch_dim, spacedim, patch_spacedim >::attach_triangulation | ( | const Triangulation< dim, spacedim > & | ) |
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< dim, patch_dim, spacedim, patch_spacedim >::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 = {} |
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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 1069 of file data_out_dof_data.h.
void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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 = {} |
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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 1050 of file data_out_dof_data.h.
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 = {} |
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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 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 1108 of file data_out_dof_data.h.
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 = {} |
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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 1087 of file data_out_dof_data.h.
void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::add_data_vector | ( | const VectorType & | data, |
const DataPostprocessor< spacedim > & | 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 1128 of file data_out_dof_data.h.
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 | ||
) |
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< 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 >() |
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) |
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.
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 | ||
) |
Scalar version of the function above.
void DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::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< dim, patch_dim, spacedim, patch_spacedim >::clear_input_data_references | ( | ) |
Release pointers to all input data elements, i.e. pointers 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.
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>() |
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) |
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 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 1142 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 an empty state.
std::size_t DataOut_DoFData< dim, patch_dim, spacedim, patch_spacedim >::memory_consumption | ( | ) | const |
Determine an estimate for the memory consumption (in bytes) of this object.
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overridevirtual |
Function by which the base class's functions get to know what patches they shall write to a file.
Implements DataOutInterface< dim, spacedim >.
Reimplemented in DataOutResample< dim, patch_dim, spacedim >.
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overrideprotectedvirtual |
Virtual function through which the names of data sets are obtained by the output functions of the base class.
Implements DataOutInterface< dim, spacedim >.
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Overload of the respective DataOutInterface::get_nonscalar_data_ranges() function. See there for a more extensive documentation.
Reimplemented from DataOutInterface< dim, spacedim >.
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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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private |
Common function called by the four public add_data_vector methods.
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inherited |
Obtain data through get_patches() and write it to out
in OpenDX format. See DataOutBase::write_dx.
Definition at line 7595 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in EPS format. See DataOutBase::write_eps.
Definition at line 7647 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in GMV format. See DataOutBase::write_gmv.
Definition at line 7660 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in GNUPLOT format. See DataOutBase::write_gnuplot.
Definition at line 7621 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in POVRAY format. See DataOutBase::write_povray.
Definition at line 7634 of file data_out_base.cc.
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Obtain data through get_patches() and write it to out
in Tecplot format. See DataOutBase::write_tecplot.
Definition at line 7673 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in UCD format for AVS. See DataOutBase::write_ucd.
Definition at line 7608 of file data_out_base.cc.
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inherited |
Obtain data through get_patches() and write it to out
in Vtk format. See DataOutBase::write_vtk.
Definition at line 7686 of file data_out_base.cc.
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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 7697 of file data_out_base.cc.
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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. In order to use this function, you need to be using a file system that supports parallel MPI I/O, and you will get error messages about failed MPI calls if you do not. Also see DataOutInterface::write_vtu().
Definition at line 7720 of file data_out_base.cc.
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Some visualization programs, such as ParaView and VisIt, 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.
pvtu
files that each describe one time step of a time dependent simulation, see the DataOutBase::write_pvd_record() function.pvtu
records. However, it can read visit records as written by the write_visit_record() function. Definition at line 7844 of file data_out_base.cc.
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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
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). For all values other than n_groups==0
, this function calls write_vtu_in_parallel(); for this function to work you need to be using a file system that supports parallel MPI I/O, and you will get error messages about failed MPI calls if you do not.
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.
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.Definition at line 7859 of file data_out_base.cc.
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Obtain data through get_patches() and write it to out
in SVG format. See DataOutBase::write_svg.
Definition at line 7708 of file data_out_base.cc.
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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 7940 of file data_out_base.cc.
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Obtain data through get_patches() and write it using MPI I/O in parallel to the file filename
in the parallel deal.II intermediate format. See DataOutBase::write_deal_II_intermediate_in_parallel().
Definition at line 7954 of file data_out_base.cc.
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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 7973 of file data_out_base.cc.
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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 7987 of file data_out_base.cc.
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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:
Definition at line 8126 of file data_out_base.cc.
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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:
Definition at line 8661 of file data_out_base.cc.
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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 8674 of file data_out_base.cc.
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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 8171 of file data_out_base.cc.
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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 8792 of file data_out_base.cc.
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Set the default format. The value set here is used anytime, output for format default_format
is requested.
Definition at line 8858 of file data_out_base.cc.
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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 8868 of file data_out_base.cc.
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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 8901 of file data_out_base.cc.
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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 8914 of file data_out_base.cc.
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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 8971 of file data_out_base.cc.
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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 9058 of file data_out_base.cc.
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Definition at line 1021 of file data_out_dof_data.h.
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Definition at line 1026 of file data_out_dof_data.h.
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Pointer to the triangulation object.
Definition at line 955 of file data_out_dof_data.h.
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Pointer to the optional handler object.
Definition at line 960 of file data_out_dof_data.h.
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List of data elements with vectors of values for each degree of freedom.
Definition at line 967 of file data_out_dof_data.h.
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List of data elements with vectors of values for each cell.
Definition at line 974 of file data_out_dof_data.h.
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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 981 of file data_out_dof_data.h.
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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 3099 of file data_out_base.h.
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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 3107 of file data_out_base.h.
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Flags to be used upon output of OpenDX data. Can be changed by using the set_flags
function.
Definition at line 3113 of file data_out_base.h.
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Flags to be used upon output of UCD data. Can be changed by using the set_flags
function.
Definition at line 3119 of file data_out_base.h.
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Flags to be used upon output of GNUPLOT data. Can be changed by using the set_flags
function.
Definition at line 3125 of file data_out_base.h.
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Flags to be used upon output of POVRAY data. Can be changed by using the set_flags
function.
Definition at line 3131 of file data_out_base.h.
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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 3137 of file data_out_base.h.
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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 3143 of file data_out_base.h.
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Flags to be used upon output of hdf5 data in one space dimension. Can be changed by using the set_flags
function.
Definition at line 3149 of file data_out_base.h.
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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 3155 of file data_out_base.h.
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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 3161 of file data_out_base.h.
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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 3167 of file data_out_base.h.
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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 3173 of file data_out_base.h.