ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
7.12.2 PrimiPlotter
The PrimiPlotter is intended to do on-the-fly plotting of the positions of the atoms during long molecular dynamics
simulations. The module ase.visualize.primiplotter contains the PrimiPlotter and the various output
modules, see below.
class ase.visualize.primiplotter.PrimiPlotter(atoms, verbose=0, timing=0, interval=1,
initframe=0)
Primitive PostScript-based plots during a simulation.
The PrimiPlotter plots atoms during simulations, extracting the relevant information from the list of atoms.
It is created using the list of atoms as an argument to the constructor. Then one or more output devices must
be attached using set_output(device). The list of supported output devices is at the end.
The atoms are plotted as circles. The system is first rotated using the angles specified by set_rotation([vx,
vy, vz]). The rotation is vx degrees around the x axis (positive from the y toward the z axis), then vy degrees
around the y axis (from x toward z), then vz degrees around the z axis (from x toward y). The rotation
matrix is the same as the one used by RasMol.
Per default, the system is scaled so it fits within the canvas (autoscale mode). Autoscale mode is enabled and
disables using autoscale(“on”) or autoscale(“off”). A manual scale factor can be set with set_scale(scale),
this implies autoscale(“off”). The scale factor (from the last autoscale event or from set_scale) can be
obtained with get_scale(). Finally, an explicit autoscaling can be triggered with autoscale(“now”), this is
mainly useful before calling get_scale or before disabling further autoscaling. Finally, a relative scaling
factor can be set with SetRelativeScaling(), it is multiplied to the usual scale factor (from autoscale or from
set_scale). This is probably only useful in connection with autoscaling.
The radii of the atoms are obtained from the first of the following methods which work:
1.If the radii are specified using PrimiPlotter.set_radii(r), they are used. Must be an array, or a single
number.
2.If the atoms has a get_atomic_radii() method, it is used. This is unlikely.
3.If the atoms has a get_atomic_numbers() method, the corresponding covalent radii are extracted from
the ASE.ChemicalElements module.
4.If all else fails, the radius is set to 1.0 Angstrom.
The atoms are colored using the first of the following methods which work.
1.If colors are explicitly set using PrimiPlotter.set_colors(), they are used.
2.If these colors are specified as a dictionary, the tags (from atoms.get_tags()) are used as an index into
the dictionary to get the actual colors of the atoms.
3.If a color function has been set using PrimiPlotter.set_color_function(), it is called with the atoms as
an argument, and is expected to return an array of colors.
4.If the atoms have a get_colors() method, it is used to get the colors.
5.If these colors are specified as a dictionary, the tags (from atoms.get_tags()) are used as an index into
the dictionary to get the actual colors of the atoms.
6.If all else fails, the atoms will be white.
The colors are specified as an array of colors, one color per atom. Each color is either a real number from
0.0 to 1.0, specifying a grayscale (0.0 = black, 1.0 = white), or an array of three numbers from 0.0 to 1.0,
specifying RGB values. The colors of all atoms are thus a Numerical Python N-vector or a 3xN matrix.
In cases 1a and 3a above, the keys of the dictionary are integers, and the values are either numbers
(grayscales) or 3-vectors (RGB values), or strings with X11 color names, which are then translated to RGB
values. Only in case 1a and 3a are strings recognized as colors.
Some atoms may be invisible, and thus left out of the plot. Invisible atoms are determined from the following
algorithm. Unlike the radius or the coloring, all points below are tried and if an atom is invisible by any
criterion, it is left out of the plot.
104 Chapter 7. Documentation for modules in ASE