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