Section 14 Exercise: Project 2, Part 3

Today's exercise is the third and final part of Project 2. In the previous two exercises you have created the data, seen two tools to analyze the data and obtained skills needed to make the final Twiki report. This exercise adds to the previous exercises, by showing how to make simple movies of the computational data. Finally there is a description of the desired content of the final report. Today, there is only one place to get the final credits, namely by finishing the report and let us evaluate the outcome.

Note: convert and ffmpeg do not exist on the DCSC-KU nodes (gifsicle does). We may (or may not) be able to convince the sysadmin to install them, but in any case these tools are available on the host astro03. You may not have a home directory there, but logging in is possible from fend03, and directories (for scp in and out) can be made under /tmp, if needed. You may also have these tools on your own laptop -- they can easily be installed under Linux, Mac and CygWin.

Movies from Paraview

Producing animation files from images

• An animated GIF is an old standard format used on web pages. It has the advantage that it is easy to construct and runs in all web browsers. The disadvantage is the lack of control when the animation is running. You just follow it as it runs - - you can't stop or restart it from a given frame...
  • To use convert to turn a series of jpg images into an animated GIF file one can use the command

      convert *.jpg anim.gif

    or, if the movie is too fast it can be slowed down with for example

      convert *.jpg -delay 20 anim.gif

    which sets the speed to roughly 5 frames per second.

    Convert is a part of the ImageMagic package - - you can find help on convert here - -

  • To use gifsicle to make an animated GIF file you first have to convert the images to GIF format:

      convert -write im%02d.gif *.jpg

    That converts all *.jpg images into .gif images with the same numbers, without removing the original image files, and the gif files can now be combined into a single gif animation with the command:

      gifsicle - -loopcount im*.gif > final_animation.gif

    If the movie is too fast it can be slowed down, as with "convert" above:

      gifsicle - -delay 20 - -loopcount im*.gif > final_animation.gif

    Gifsicle is a small program that can do lots of editing of gif animations.... check the webpage or the man pages to see some of these possibilities.

• MPEG movies is another standard. Here, again, there are a number of different options, especially if one includes Windows and MAC.
  • As part of the last exercise we showed how the xinteranimate IDL procedure could be used for making mpeg movies. One could still use this, reading in the relevant images and look at the animation in IDL, before saving it to a mpeg movie.
  • Another possibility to use convert. To convert a series of images into a movie do

      convert *.jpg movie.mpg

  • Applications available under Windows and MAC are generally more easy to control, for example with respect to the balance between compression and movie quality, and with respect to the viewing speed of the MPEG file. VideoMach is a good example (find it with Google).

    To "slow down" a movie with VideoMach, right click on the source (left hand side panel) and choose for example 5 frames per second input rate (under "speed and direction"). Then choose "keep original duration" under output options ("video" panel under "save as").

    VideoMach can also make .avi files, which have the advantage of supporting 15 frames per second frame rate (MPEG generally assumes 30 or 25 frames per second), and that they work very smoothly in PowerPoint presentation. Most web-browsers also support AVI files.

  • You can view the mpg movie using:

           mplayer -loop 0 -fps 5 density.mpg
    

    This loops the movie and plays it with 5 frames per second instead of the default 25 that convert creates it with. You can pause it using the space bar, toggle it to full screen using f - - or use -fs as option. Check the man pages for more info!

  • ffmpeg is another a package that can be used to make different video formats mpeg, avi, flash...

          ffmpeg -pass 1 -r 10 -y -b 8500 -i movie%03d.png -vcodec msmpeg4 -vtag MP43 -acodec mp3 movie.avi
          ffmpeg -pass 2 -r 10 -y -b 8500 -i movie%03d.png -vcodec msmpeg4 -vtag MP43 -acodec mp3 movie.avi
          rm ffmpeg2pass-0.log
    

    Check their web page for more information.

To access the TWiki page and register as a user you need to follow the instruction on this page

The report should be a description of the experiment you have been running, with emphasis on showing the time evolution in some genius detail such that visitors of the web page can understand what is taking place. To do this you need to include the following main items:

• Front page.
  • A representative illustration of the experiment.
  • Name of the author.
  • Table of content / links to the sections below (not mandatory)
• A brief description of the experiment.
  • Discussion of the initial setup.
  • Solution method.
• A description of the structure and time evolution of the magnetic relaxation experiment.
  • Include the 3D images you made of a combination of the five visualization "instances"
  • Time evolution and other relevant data including animations (see below).
  • Simple 2D plots of the time evolution of the peak and average values of relevant quantities. Mark where the other images are located in time.
• Discussions and conclusions
  • Some remarks regarding the experiment.
  • Other remarks related to the use of the different visualization tools and their aid in providing you with the answers you were trying to reach.
• Appendix containing links to paraview saved session, paraview_saved.pvsm, idl scripts, and what else you have used producing the above visualization (use the upload feature on the Twiki page).

There is a template page, also available via a link on the main report page.

It is preferable to keep everything on one TWiki page. If you prefer to make several independent TWiki pages, then use the same first part of the name and add something at the end (this is to avoid page names conflicting with your fellow students' pages), and remember to include the magic line that makes the page readable only by you and us for now (we will remove this restriction after everyone has finished!)

The main emphasis of your effort should be on the description section of the report. Here are some ideas - not all of which need to be used! - (see also the page discussing the basic physical principles):

There are, in principle, two phases of the:

• The initial phase, where the initial lorentz forces accelerates the magnetic field in different regions. This converts magnetic energy into kinetic energy.
• Pinching by the velocity field, where the accelerated plasma distorts the magnetic field structure. This allows the null points to move towards each other and eventually collapse to a region much smaller than the initial one.
• Magnetic reconnection is important for letting the magnetic flux contained in the null point region around the central null escape out of this region, allowing the region to collapse (tracking this in detail is difficult).
• The final state is very much simpler than the initial one and resembels the initial field where only one wave vector is used. Something close to a constant alpha magnetic field has been obtained. Due to the field approaching a constant alpha field the diffuseion time becomes very long, which is why the later part of the experiment only changes very slowly.

Once you are satisfied with the report, submit it by confirming here:

OK, I have submitted my project and I'm happy with the final result! Credits: 100/0 OK

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