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AViz FAQs

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    We assume you have read the general instructions, and tried one of our ready examples. These FAQs should help when you start creating your own files.

  1. Q. How do I prepare a datafile? A. Collect your atomic/spin/quadrupole or whatever data in a file with a letter in the first column, x, y and z coordinates in the next three columns, and then other information such as angles and direction. ALL the values must be real numbers!!!!! Then count up how many lines you have, and write this INTEGER number in the first row, and put an identifying comment in the second one, followed by the rows with type (a letter) and real numbers for the coordinates.

  2. Q.How to I prepare a datafile from a Lattice Boltzman simulation? A. All the general instructions apply.
    First row no. lines
    Second Row identifying comment
    All the other rows alphanumeric letter(s) for type, followed by characterization
    Characterization is x,y,z coordinates,then velocities if the object is an arrow, followed by some properties like say scalar speed. All coordinates, velocities etc real numbers. There are sample Lattice Boltzman files made by Eden Segal here , and two screenshots s1.png s2.png of these files, in case you have problems viewing the .xyz files in your browser. After running Eden's data in AViz the resultant images are in the list of .png files and there is also a .gif movie.

  3. Q. Where can I find a set of sample .xyz files and some details on how to run them? A. The file xyzfiles.tar contains a lot of files, and on avizlog you can see a line-by-line description of how to run them.

  4. Q. Are there any examples to help transforming files? A. data can come in all sorts of formats. A good approach to transformation is the read the old file into memory then write the new one. FORTRAN is very good for this since character representation is needed. An example is given here; starting from a file containing only the x, y and z values as integers, like Cluster_3.dat the program vladconv.f that reads this file that contains only integers and outputs an AViz xyz file Cluster_3.xyz. You can view an animation of this cluster , and its further transformation to WebGL by Liran Sharir here. The last link into Liran Sharir's percolation project is interesting to explore independently. (Aside - after all this work we have a slightly improved version of a 3d percolation cluster created by Nir Yefet in 1998! however the new methods are a lot more general and robust.)

  5. Q. HELP!!!! I get nonsense in the viewing window? A. Please double check the numbers are real ones.

  6. Q. HELP!!!! I have a series of files and the filelist freezes A. Please check that there are no blank lines in the filelist list of files, and no extra characters.

  7. Q. HELP!!!! I have a series of files and the filelist runs them out of order A. Please check that they are listed say out.0001.xyz, out.0002.xyz and not out.1.xyz, out.2.xyz....out10.xyz etc.

  8. HELP!!!! The File - Example bar is missing in Ubuntu A. You can choose the location of the current window bar (on window or on top of screen) by going to menubar in settings -> appearance-> behaviour (thanks, Jeremy).

If you would like to contribute to the development of AViz, please send an e-mail to phr76ja@tx.technion.ac.il