Reference documentation for deal.II version Git 78a8940608 2021-04-17 09:24:19 -0400
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Classes | Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Private Types | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
MatrixOut Class Reference

#include <deal.II/lac/matrix_out.h>

Inheritance diagram for MatrixOut:
[legend]

Classes

struct  Options
 

Public Types

using size_type = types::global_dof_index
 

Public Member Functions

virtual ~MatrixOut () override=default
 
template<class Matrix >
void build_patches (const Matrix &matrix, const std::string &name, const Options options=Options(false, 1, false))
 
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)
 
std::size_t memory_consumption () const
 

Static Public Member Functions

static void declare_parameters (ParameterHandler &prm)
 

Protected Member Functions

virtual std::vector< std::tuple< unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation > > get_nonscalar_data_ranges () const
 
void validate_dataset_names () const
 

Protected Attributes

unsigned int default_subdivisions
 

Private Types

using Patch = DataOutBase::Patch< 2, 2 >
 

Private Member Functions

virtual const std::vector< Patch > & get_patches () const override
 
virtual std::vector< std::string > get_dataset_names () const override
 

Static Private Member Functions

template<class Matrix >
static double get_gridpoint_value (const Matrix &matrix, const size_type i, const size_type j, const Options &options)
 

Private Attributes

std::vector< Patchpatches
 
std::string name
 

Detailed Description

Output a matrix in graphical form using the generic format independent output routines of the base class. The matrix is converted into a list of patches on a 2d domain where the height is given by the elements of the matrix. The functions of the base class can then write this "mountain representation" of the matrix in a variety of graphical output formats. The coordinates of the matrix output are that the columns run with increasing x-axis, as usual, starting from zero, while the rows run into the negative y-axis, also starting from zero. Note that due to some internal restrictions, this class can only output one matrix at a time, i.e. it can not take advantage of the multiple dataset capabilities of the base class.

A typical usage of this class would be as follows:

// fill matrix M with some values
...
// now write out M:
MatrixOut matrix_out;
std::ofstream out ("M.gnuplot");
matrix_out.build_patches (M, "M");
matrix_out.write_gnuplot (out);

Of course, you can as well choose a different graphical output format. Also, this class supports any matrix, not only of type FullMatrix, as long as it satisfies a number of requirements, stated with the member functions of this class.

The generation of patches through the build_patches() function can be modified by giving it an object holding certain flags. See the documentation of the members of the Options class for a description of these flags.

Definition at line 71 of file matrix_out.h.

Member Typedef Documentation

◆ size_type

Declare type for container size.

Definition at line 77 of file matrix_out.h.

◆ Patch

using MatrixOut::Patch = DataOutBase::Patch<2, 2>
private

Abbreviate the somewhat lengthy name for the DataOutBase::Patch class.

Definition at line 149 of file matrix_out.h.

Constructor & Destructor Documentation

◆ ~MatrixOut()

virtual MatrixOut::~MatrixOut ( )
overridevirtualdefault

Destructor. Declared in order to make it virtual.

Member Function Documentation

◆ build_patches()

template<class Matrix >
void MatrixOut::build_patches ( const Matrix &  matrix,
const std::string &  name,
const Options  options = Options(false, 1, false) 
)

Generate a list of patches from the given matrix and use the given string as the name of the data set upon writing to a file. Once patches have been built, you can use the functions of the base class to write the data into a files, using one of the supported output formats.

You may give a structure holding various options. See the description of the fields of this structure for more information.

Note that this function requires that we can extract elements of the matrix, which is done using the get_element() function declared in an internal namespace. By adding specializations, you can extend this class to other matrix classes which are not presently supported. Furthermore, we need to be able to extract the size of the matrix, for which we assume that the matrix type offers member functions m() and n(), which return the number of rows and columns, respectively.

Definition at line 325 of file matrix_out.h.

◆ get_patches()

const std::vector< MatrixOut::Patch > & MatrixOut::get_patches ( ) const
overrideprivatevirtual

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

Implements DataOutInterface< 2, 2 >.

Definition at line 32 of file matrix_out.cc.

◆ get_dataset_names()

std::vector< std::string > MatrixOut::get_dataset_names ( ) const
overrideprivatevirtual

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

Implements DataOutInterface< 2, 2 >.

Definition at line 40 of file matrix_out.cc.

◆ get_gridpoint_value()

template<class Matrix >
double MatrixOut::get_gridpoint_value ( const Matrix &  matrix,
const size_type  i,
const size_type  j,
const Options options 
)
inlinestaticprivate

Get the value of the matrix at gridpoint (i,j). Depending on the given flags, this can mean different things, for example if only absolute values shall be shown then the absolute value of the matrix entry is taken. If the block size is larger than one, then an average of several matrix entries is taken.

Definition at line 282 of file matrix_out.h.

◆ 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 7086 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 7138 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 7151 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 7112 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 7125 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 7164 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 7099 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 7177 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 7188 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 7210 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 7313 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 7326 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 7199 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 7408 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 7421 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 7435 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 7508 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 7686 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 7698 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 7558 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 8090 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 8156 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 8166 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 8201 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 8214 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 8267 of file data_out_base.cc.

◆ memory_consumption()

std::size_t DataOutInterface< dim, spacedim >::memory_consumption ( ) const
inherited

Return an estimate for the memory consumption, in bytes, of this object. This is not exact (but will usually be close) because calculating the memory usage of trees (e.g., std::map) is difficult.

Definition at line 8314 of file data_out_base.cc.

◆ get_nonscalar_data_ranges()

std::vector< std::tuple< unsigned int, unsigned int, std::string, DataComponentInterpretation::DataComponentInterpretation > > DataOutInterface< dim, spacedim >::get_nonscalar_data_ranges ( ) const
protectedvirtualinherited

This functions returns information about how the individual components of output files that consist of more than one data set are to be interpreted.

It returns a list of index pairs and corresponding name and type indicating which components of the output are to be considered vector- or tensor-valued rather than just a collection of scalar data. The index pairs are inclusive; for example, if we have a Stokes problem in 2d with components (u,v,p), then the corresponding vector data range should be (0,1), and the returned list would consist of only a single element with a tuple such as (0,1,"velocity",component_is_part_of_vector).

Since some of the derived classes do not know about non-scalar data, this function has a default implementation that simply returns an empty string, meaning that all data is to be considered a collection of scalar fields.

Definition at line 8337 of file data_out_base.cc.

◆ validate_dataset_names()

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

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

Definition at line 8349 of file data_out_base.cc.

Member Data Documentation

◆ patches

std::vector<Patch> MatrixOut::patches
private

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 156 of file matrix_out.h.

◆ name

std::string MatrixOut::name
private

Name of the matrix to be written.

Definition at line 161 of file matrix_out.h.

◆ default_subdivisions

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

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

Definition at line 3016 of file data_out_base.h.


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