vis3d

synopsis

vis3d

examples

You can use vis3d to visualize individual datasets or movies from the command line or from a simulation code. Here, we cover the command line example.

Visualizing Data From a File

Assume we have data in vis format in a file called vis_data.txt.

$ cat vis_data.txt
S 0 0 0 - ;
S 1 2 3 - ;
...

$ vis3d < vis_data.txt    #shows data on screen

Often, data is not in vis format. Therefore, we must use format converters. Consider a data file in .xyz (Rasmol) format.

$ cat xyz_data.txt
1000

O 1 1 1
N 2 3 4
S 4 5 6
....

$ cat xyz_data.txt | xyz2vis
S 1 1 1 - ;
c 0.5 0.5 0.5
...

$ cat xyz_data.txt | xyz2vis | vis3d      #shows data on screen

We can also easily show a movie from a directory of .xyz data in separate files.

$ ls xyz_directory | sort -n
1.xyz
2.xyz
3.xyz
...

$ ls xyz_directory | sort -n | catp | xyz2vis | vis3d

Here the first command "$ ls xyz_directory | sort -n" sorts all of the files in the directory in numerical order. The catp function "cats" the filenames passed from the pipe. The files are converted to vis format using xyz2vis.

It is straightforward to show how the same type of method can be applied to visualize a real-time movie of a simulation.

$ ./md_simulation
S 0 0 0 - ;
S 1 1 1 - ;
...
^C

$ ./md_simulation | vis3d