Visualizing a system with ase-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-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. |
ase-gui can save the following file formats:
File format | Comment |
---|---|
xyz | XYZ file |
traj | ASE trajectory |
pdb | PDB file |
cube | Gaussian cube file |
py | Python script |
vnl | VNL file |
png | Portable Network Graphics |
pov | Persistance of Vision |
eps | Encapsulated PostScript |
in | FHI-aims geometry input |
POSCAR | VASP geometry input |
bundle | ASE bundle trajectory |
cif | Crystallographic Information File |
The ase-gui program can read all the file formats the ASE’s read() function can understand.
$ ase-gui N2Fe110-path.traj
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.
$ 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.
The ase-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()
Use Tools ‣ NEB to plot energy barrier.
$ ase-gui --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj
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.
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-gui. 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]]
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.