ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

1.All atoms are visible.
ASE Manual, Release 3.6.1.2828
2.If PrimiPlotter.set_invisible() has be used to specify invisible atoms, any atoms for which the value is
non-zero becomes invisible.
3.If an invisiblility function has been set with PrimiPlotter.set_invisibility_function(), it is called with
the atoms as argument. It is expected to return an integer per atom, any non-zero value makes that
atom invisible.
4.If a cut has been specified using set_cut, any atom outside the cut is made invisible.
Note that invisible atoms are still included in the algorithm for positioning and scaling the plot.
The following output devices are implemented.
PostScriptFile(prefix): Create PS files names prefix0000.ps etc.
PnmFile(prefix): Similar, but makes PNM files.
GifFile(prefix): Similar, but makes GIF files.
JpegFile(prefix): Similar, but makes JPEG files.
X11Window(): Show the plot in an X11 window using ghostscript.
Output devices writing to files take an extra optional argument to the constructor, compress, specifying if
the output file should be gzipped. This is not allowed for some (already compressed) file formats.
Instead of a filename prefix, a filename containing a % can be used. In that case the filename is expected to
expand to a real filename when used with the Python string formatting operator (%) with the frame number
as argument. Avoid generating spaces in the file names: use e.g. %03d instead of %3d.
Parameters to the constructor:
atoms: The atoms to be plottet.
verbose = 0: Write progress information to stderr.
timing = 0: Collect timing information.
interval = 1: If specified, a plot is only made every interval’th time update() is called. Deprecated, normally
you should use the interval argument when attaching the plotter to e.g. the dynamics.
initframe = 0: Initial frame number, i.e. the number of the first plot.
log(message)
logs a message to the file set by set_log.
plot()
Create a plot now. Does not respect the interval timer.
This method makes a plot unconditionally. It does not look at the interval variable, nor is this plot
taken into account in the counting done by the update() method if an interval variable was specified.
set_color_function(colors)
Set a color function, to be used to color the atoms.
set_colors(colors)
Explicitly set the colors of the atoms.
set_dimensions(dims)
Set the size of the canvas (a 2-tuple).
set_invisibility_function(invfunc)
Set an invisibility function.
set_invisible(inv)
Choose invisible atoms.
set_log(log)
Sets a file for logging.
7.12. Visualization 105