dune-vtk 0.2.0.dev20201218

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Dune-Vtk

File reader and writer for the VTK Format

Summary

Provides structured and unstructured file writers for the VTK XML File Formats that can be opened in the popular ParaView visualization application. Additionally a file reader is provided to import VTK files into Dune grid and data objects.

Installation Instructions

dune-vtk requires the DUNE core modules, version 2.7 or later. Please see the general instructions for building DUNE modules for detailed instructions on how to build the module.

Usage

The VTK writer works similar to the dune-grid VTKWriter. It needs to be bound to a GridView and then data can be added to the points or cells in the grid. Points are not necessarily grid vertices, but any coordinates placed inside the grid cells, so the data must be provided as GridViewFunction to allow the local evaluation in arbitrary local coordinates.

General interface of a VtkWriter

template <class GridView, class DataCollector = DefaultDataCollector<GridView>>
class Vtk[Type]Writer
{
public:
  // Constructor
  Vtk[Type]Writer(GridView, Vtk::FormatTypes = Vtk::FormatTypes::BINARY, Vtk::DataTypes = Vtk::DataTypes::FLOAT32);

  // Bind data to the writer
  Vtk[Type]Writer& addPointData(Function [, std::string name, int numComponents, Vtk::FormatTypes]);
  Vtk[Type]Writer& addCellData(Function [, std::string name, int numComponents, Vtk::FormatTypes]);

  // Write file with filename
  void write(std::string filename);
};

where Function is either a GridViewFunction, i.e. supports bind(), unbind(), and localFunction(Function), or is a legacy VTKFunction from Dune-Grid. The optional parameters name, numComponents and format may be given for a GridViewFunction.

The parameter Vtk::FormatTypes is one of Vtk::FormatTypes::ASCII, Vtk::FormatTypes::BINARY, or Vtk::COMPRESSED and Vtk::DataTypes is one of Vtk::DataTypes::FLOAT32, or Vtk::DataTypes::FLOAT64. The [Type] of a VtkWriter is one of UnstructuredGrid, StructuredGrid, RectilinearGrid, ImageData, or Timeseries, see below for details. A DataCollector may be specified to control how point and cell values are extracted from the GridView and the bound data. See dune/vtk/datacollectors/ of a list of poissible types. The default datacollector extracts a connected grid with continuous data, where points are grid vertices.

See also the src/ directory for more examples.

Comparison with Dune::VTKWriter

In Dune-Grid there is a VTK writer available, that is a bit different from the proposed one. A comparison:

Property	Dune-Grid	Dune-Vtk
VTK version	0.1	0.1/1.0
UnstructuredGrid	x	x
PolyData	(1d)	-
StructuredGrid	-	x
RectilinearGrid	-	x
ImageData	-	x
ASCII	x	x
BASE64	x	-
APPENDED_RAW	x	x
APPENDED_BASE64	x	-
BASE64_COMPRESSED	-	-
APPENDED_COMPRESSED	-	x
Parallel files	x	x
Conforming Data	x	x
NonConforming Data	x	x
Quadratic Data	-	x
Higher-Order Data	-	x
Subdivided Data	x	-
Sequence (PVD)	x	x
Timeseries	-	x

Writers and Readers

Dune-Vtk provides nearly all file formats specified in VTK + 2 time series formats: PVD and VTK-Timeseries.

VtkUnstructuredGridWriter

Implements a VTK file format for unstructured grids with arbitrary element types in 1d, 2d, and 3d. Coordinates are specified explicitly and a connectivity table + element types are specified for all grid elements (of codim 0). Can be used with all Dune grid types.

VtkStructuredGridWriter

Implements a writer for grid composed of cube elements (lines, pixels, voxels) with local numbering similar to Dunes cube(d) numbering. The coordinates of the vertices can be arbitrary but the connectivity is implicitly given and equals that of Dune::YaspGrid or Dune::SPGrid. Might be chosen as writer for a transformed structured grid, using, e.g., a GeometryGrid meta-grid. See src/geometrygrid.cc for an example.

VtkRectilinearGridWriter

Rectilinear grids are tensor-product grids with given coordinates along the x, y, and z axes. Therefore, the grid must allow to extract these 1d coordinates and a specialization for a StructuredDataCollector must be provided, that implements the ordinates() function. By default, it assumes constant grid spacing starting from a lower left corner. For YaspGrid a specialization is implemented if the coordinates type is TensorProductCoordinates. See src/structuredgridwriter.cc for an example.

VtkImageDataWriter

The most structured grid is composed of axis-parallel cube elements with constant size along each axis. The is implemented in the VtkImageDataWriter. A specialization of the StructuredDataCollector must implement origin() for the lower left corner, wholeExtent() for the range of cell numbers along each axis in the global grid, extent() for the range in the local grid, and spacing() for the constant grid spacing in each direction.

PvdWriter

A sequence writer, i.e. a collection of timestep files, in the ParaView Data (PVD) format. Supports all VtkWriters for the timestep output. In each timestep a collection (.pvd) file is created.

VtkTimseriesWriter

A timeseries is a collection of timesteps stored in one file, instead of separate files for each timestep value. Since in the Vtk::FormatTypes::APPENDED mode, the data is written as binary blocks in the appended section of the file and references by an offset in the XML DataArray attributes, it allows to reuse written data. An example of usage is when the grid points and cells do not change over time, but just the point-/cell-data. Then, the grid is written only once and the data is just appended.

Timeseries file are create a bit differently from other Vtk file. There, in the first write the grid points and cells are stored in a separate file, and in each timestep just the data is written also to temporary files. When you need the timeseries file, these stored temporaries are collected and combined to one VTK file. Thus, only the minimum amount of data is written in each timestep. The intermediate files are stored, by default, in a /tmp folder, with (hopefully) fast write access.

VtkReader

Reading unstructured grid files (.vtu files) and creating a new grid, using a GridFactory, can be performed using the VtkReader class. The reader allows to create the grid in multiple ways, by providing a GridCreator template parameter. The ContinuousGridCreator reads the connectivity of the grid as it is and assumes that the elements are already connected correctly. On the other hand, a DiscontinuousGridCreator reconnects separated elements, by identifying matching coordinates of the cell vertices. See more possible grid-creators in the directory dune/vtk/gridcreators.

General interface of a VtkReader

template <class Grid, class GridCreator = ContinuousGridCreator<Grid>, class FieldType = double>
class VtkReader
{
public:
  // Constructors
  VtkReader();                    // Construct a GridCreator with internal stored GridFactory
  VtkReader(GridFactory<Grid>&);  // Construct a GridCreator referencing the passed GridFactory
  VtkReader(GridCreator&);        // Reference the passed GridCreator

  // Read the data from a file with filename
  void read(std::string filename);

  // Construct the Grid from the data read before.
  std::unique_ptr<Grid> createGrid() const;

  // Static method to construct the Grid directly
  static std::unique_ptr<Grid> createGridFromFile(std::string file);

  // Extract data from the reader
  _PointDataGridFunction_ getPointData(std::string name) const;
  _CellDataGridFunction_  getCellData(std::string name) const;
};

where Grid is a dune grid type providing a GridFactory specialization, GridCreator is the policy type implementing how the raw data from the file is transformed in data that can be passed to the GridFactory and FieldType` is the data for for internal storage of value data from the file, i.e. point-data or cell-data.

The grid can either be created using the static method createGridFromFile() or by first constructing the VtkReader with its GridCreator, calling read() and finally createGrid(). The latter allows to access data stored in the reader, like point-data or cell-data.

Value from point-data or cell-data cannot be accessed directly, but through the interface of a grid-function. These grid-functions are provided by the getPointData() or getCellData() member functions of the reader. The interface of a dune-functions grid-function concept is implemented by these two types. The reason why the reader does not provide the data directly is, that it is quiet complicated to associate the specific value to a DOF in the grid, since the GridFactory is allows to change the global indexing and even to change to local indexing in the elements such that even the local element coordinates might need a transformation compared to that of the element stored in the file. All these renumbering and coordinate transformations are performed by the grid-functions internally.

The VtkReader supports grid creation in parallel. If a partition file .pvtu is provided, all partitions can be read by either one processor and distributed later on (SerialGridCreator) or read directly in parallel (ParallelGridCreator). The later is currently only available in dune-alugrid 2.6.