ase-gui basics and command line options

General use

Visualizing a system with ASE’s GUI is straight-forward using a regular mouse. The scroll function allows to change the magnification, the left mouse button selects atoms, the right mouse button allows to rotate, and the middle button allows to translate the system on the screen.

Depending on the number of selected atoms, ASE’s GUI automatically measures different quantities:

Selection measurement
single atom xyz position and atomic symbol
two atoms interatomic distance and symbols
three atoms all three internal angles and symbols
four atoms, selected sequentially Measures the dihedral angle, e.g. the angle between bonds 12 and 34
more than four atoms chemical composition of selection.

Files

The ASE’s GUI program can read all the file formats the ASE’s read() function can understand.

$ ase gui N2Fe110-path.traj

Selecting part of a trajectory

A Python-like syntax for selecting a subset of configurations can be used. Instead of the Python syntax list[start:stop:step], you use filaname@start:stop:step:

$ ase gui x.traj@0:10:1  # first 10 images
$ ase gui x.traj@0:10    # first 10 images
$ ase gui x.traj@:10     # first 10 images
$ ase gui x.traj@-10:    # last 10 images
$ ase gui x.traj@0       # first image
$ ase gui x.traj@-1      # last image
$ ase gui x.traj@::2     # every second image

If you want to select the same range from many files, the you can use the -n or --image-number option:

$ ase gui -n -1 *.traj   # last image from all files
$ ase gui -n 0 *.traj    # first image from all files

Tip

Type ase gui -h for a description of all command line options.

Writing files

$ ase gui -n -1 a*.traj -o new.traj

Possible formats are: traj, xyz, cube, pdb, eps, png, and pov. For details, see the io module documentation.

Interactive use

The ASE’s GUI program can also be launched directly from a Python script or interactive session:

>>> from ase import *
>>> atoms = ...
>>> view(atoms)

or

>>> view(atoms, repeat=(3, 3, 2))

or, to keep changes to your atoms:

>>> atoms.edit()

NEB calculations

Use Tools ‣ NEB to plot energy barrier.

$ ase gui --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj

Plotting data from the command line

Plot the energy relative to the energy of the first image as a function of the distance between atom 0 and 5:

$ ase gui -g "d(0,5),e-E[0]" x.traj
$ ase gui -t -g "d(0,5),e-E[0]" x.traj > x.dat  # No GUI, write data to stdout

The symbols are the same as used in the plotting data function.

Defaults

Using a file ~/.ase/gui.py, certain defaults can be set. If it exists, this file is executed after initializing the variables and colours normally used in ASE. One can change the default graphs that are plotted, and the default radii for displaying specific atoms. This example will display the energy evolution and the maximal force in a graph and also display Cu atoms (Z=29) with a radius of 1.6 Angstrom.

gui_default_settings['gui_graphs_string'] = "i, e - min(E), fmax"
gui_default_settings['covalent_radii'] = [[29,1.6]]

High contrast settings

In revision 2600 or later, it is possible to change the foreground and background colors used to draw the atoms, for instance to draw white graphics on a black background. This can be done in ~/.ase/gui.py.

gui_default_settings['gui_foreground_color'] = '#ffffff' #white
gui_default_settings['gui_background_color'] = '#000000' #black

To change the color scheme of graphs it is necessary to change the default behaviour of Matplotlib in a similar way by using a file ~/.matplotlib/matplotlibrc.

patch.edgecolor  : white
text.color       : white
axes.facecolor   : black
axes.edgecolor   : white
axes.labelcolor  : white
axes.color_cycle : b, g, r, c, m, y, w
xtick.color      : white
ytick.color      : white
grid.color       : white
figure.facecolor : 0.1
figure.edgecolor : black

Finally, the color scheme of the windows themselves (i.e. menus, buttons and text etc.) can be changed by choosing a different desktop theme. In Ubuntu it is possible to get white on a dark background by selecting the theme HighContrastInverse under Appearances in the system settings dialog.