Beta release!
Please note that the library has not been "officially" released. While we continue to work on the documentation, these web pages are likely to contain broken links and documents in draft form. Please send an email to

oomph-lib AT maths DOT man DOT ac DOT uk
if you wish to be informed of the library's "official" release.

Visualising oomph-lib's output files with Paraview

All of oomph-lib's existing elements implement the GeneralisedElement::output(...) functions, allowing the computed solution to be documented via a simple call to the Mesh::output(...) function, e.g.

// Open output file
ofstream output_file("output.dat")

// Call the mesh's output function which loops over the 
// element and calls theirs...
Problem::mesh_pt()->output(output_file);

By default, the output is written in a format that is suitable for displaying the data with tecplot, a powerful and easy-to-use commercial plotting package -- possibly a somewhat odd choice for a an open-source library.

The FAQ contain an entry that discusses how to display oomph-lib's output with gnuplot and how to adjust oomph-lib's output functions to different formats.

Angelo Simone has written a python script that converts oomph-lib's output to the vtu format that can be read by paraview, an open-source 3D plotting package. The conversion script can currently deal with output from meshes that are composed of 2D quad elements -- the extension to 3D is work in progress.

The oomph-lib distribution contains three scripts:

bin/oomph-convert.py : The python conversion script itself.
bin/oomph-convert : A shell script wrapper that allows the processing of multiple files.
bin/makePvd: A shell script the creates the * .pvd files required by paraview to produce animations.

The oomph-convert.py script for single files

An example session

Add oomph-lib's bin directory to your path (in the example shown here, oomph-lib is installed in the directory /home/mheil/version185/oomph):
```
   biowulf: 10:31:50$ PATH=$PATH:/home/mheil/version185/oomph/bin
```
Here is what's in the current directory at the moment: soln0.dat is the oomph-lib output produced by the adaptive solution of a Poisson equation in a fish-shaped domain.
```
   biowulf: 11:05:10$ ll
   total 824
   -rw-r--r--    1 mheil    users        2292 May 21 09:19 soln0.dat
```

Run oomph-convert.py

    biowulf: 11:16:18$  oomph-convert soln0.dat

    -- Processing soln0.dat
 oomph-convert.py, ver. 20080514
    Convert from oomph-lib Tecplot format to VTK XML format.
    Dimension of the problem: 2
    Plot cells defined
    Field variables =  1
    Conversion started
    Coordinate defined
    Connectivities defined
    Offset defined
    Element types defined
    Field data defined
    Conversion done
 Output file name: soln0.vtu

We now have the corresponding * .vtu file

   biowulf: 11:32:08$ ll
   total 1024
   -rw-r--r--    1 mheil    users      329874 May 21 09:19 soln0.dat
   -rw-r--r--    1 mheil    users      705294 May 21 11:16 soln0.vtu

...which we can visualise with paraview:

   biowulf: 11:34:08$ paraview --data=soln0.vtu

Screenshots from the paraview session

Here are a few screenshots from a paraview session, to get you started. When paraview starts up you see the following screen:

Select the "Display" tab...

...and make the data visible:

Now choose to colour the plot by the first (and, in the present example, only) variable to obtain a contour plot of the solution.

Switching to a wireframe representation shows the underlying mesh (each element is represented as a 5x5 sub-grid).

The oomph-convert and makePvd scripts for multiple files and animations

An example session

Here is a quick demonstration of oomph-convert and makePvd scripts in action

Add oomph-lib's bin directory to your path (in the example shown here, oomph-lib is installed in the directory /home/mheil/version185/oomph):
```
   biowulf: 10:31:50$ PATH=$PATH:/home/mheil/version185/oomph/bin
```

Here is what's in the current directory at the moment: soln?. dat are the oomph-lib output files that illustrate the progress of the mesh adaptation during the adaptive solution of a Poisson equation in a fish-shaped domain.

   biowulf: 11:05:10$ ll
   total 824
   -rw-r--r--    1 mheil    users        2292 May 21 09:19 soln0.dat
   -rw-r--r--    1 mheil    users      176776 May 21 09:19 soln1.dat
   -rw-r--r--    1 mheil    users      278117 May 21 09:19 soln2.dat
   -rw-r--r--    1 mheil    users      367408 May 21 09:19 soln3.dat

Run oomph-convert on all files (the -z option adds zeroes to the numbers -- this is only required if the files are to combined into an animation by paraview)

   biowulf: 11:16:13$ oomph-convert -z soln*.dat


   -- Processing soln0.dat
 oomph-convert.py, ver. 20080514
   Convert from oomph-lib Tecplot format to VTK XML format.
   Dimension of the problem: 2
   Plot cells defined
   Field variables =  1
   Conversion started
   Coordinate defined
   Connectivities defined
   Offset defined
   Element types defined
   Field data defined
   Conversion done
 Output file name: soln00000.vtu

   -- Processing soln1.dat
 oomph-convert.py, ver. 20080514
   Convert from oomph-lib Tecplot format to VTK XML format.
   Dimension of the problem: 2
   Plot cells defined
   Field variables =  1
   Conversion started
   Coordinate defined
   Connectivities defined
   Offset defined
   Element types defined
   Field data defined
   Conversion done
 Output file name: soln00001.vtu



   [further output suppressed]

We now have the corresponding * .vtu files

   biowulf: 12:37:05$ ll
   total 2568
   -rw-r--r--    1 mheil    users        5979 May 21 12:37 soln00000.vtu
   -rw-r--r--    1 mheil    users      377490 May 21 12:37 soln00001.vtu
   -rw-r--r--    1 mheil    users      592990 May 21 12:37 soln00002.vtu
   -rw-r--r--    1 mheil    users      789325 May 21 12:37 soln00003.vtu
   -rw-r--r--    1 mheil    users        2292 May 21 09:19 soln0.dat
   -rw-r--r--    1 mheil    users      176776 May 21 09:19 soln1.dat
   -rw-r--r--    1 mheil    users      278117 May 21 09:19 soln2.dat
   -rw-r--r--    1 mheil    users      367408 May 21 09:19 soln3.dat

These * .vtu files can be displayed individually as discussed above.

To produce an animation of the results with paraview, create a * .pvd file using makePvd
```
   biowulf: 12:40:56$ makePvd soln mysoln.pvd
   --> File mysoln.pvd created
```

...and visualise it:

   biowulf: 12:42:08$ paraview --data=mysoln.pvd

Screenshots from the paraview session

Here's a screenshot from the paraview session: Once the * .pvd file is loaded you can customise the plot style as discussed in the previous example, and then use the "play/stop/..." buttons to animate the progress of the mesh adaptation.

Paraview allows you to save the animation in an avi file. However, note that the file cannot be displayed with xanim. mplayer seems to do the trick, though. Try it by downloading this animation.

PDF file

A pdf version of this document is available.

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