Tools#
Graphs#
For graphing different quantities for a given trajectory. ASE uses matplotlib as a backend, allowing some manipulation of the generated plot and for the plot to be saved to a file.
The Graphs window requires an instruction string that controls what is plotted. The following expressions can be used to create the instructions:
Symbol |
Interpretation |
|---|---|
e |
total energy |
epot |
potential energy |
ekin |
kinetic energy |
fmax |
maximum force |
fave |
average force |
d(n1,n2) |
distance between two atoms |
R[n,0-2] |
position of atom number n |
i |
current image number |
E[i] |
energy of image number i |
F[n,0-2] |
force on atom number n |
M[n] |
magnetic moment of atom number n |
A[0-2,0-2] |
unit-cell basis vectors |
s |
path length |
a(n1,n2,n3) |
angle between atoms n1, n2 and n3, centered on n2 |
dih(n1,n2,n3,n4) |
dihedral angle between n1, n2, n3, and n4 |
T |
temperature (requires velocity) |
Variables should be separated by commas. The window presents two
Plot buttons. The first (x, y1, y2, ...) places the first
variable in the list as the x-axis. The other (y1, y2, ...) plots all
variables on the y-axis and uses the current image number as the x-axis.
This example plots the energy and the maximal force for each image i (e.g. to help in investigating the convergence properties for geometry relaxations):
i, e-min(E), fmax
Movie#
For navigating between images when several of them are open at the same time or for animating said navigation. Allows one to play the current trajectory as a movie using a number of different settings such as the frame rate. By default, the frame rate and number of structures skipped is adjusted to cycle through all images in ca. 5 s.
Constraints#
For setting (or removing) the ase.constraints.FixAtoms to/from the
currently selected atoms. These constraints will be then be saved to a file
with the structure if the chosen file type allows it.
Render scene#
Graphical interface to the ASE povray interface. Ideally it requires that povray is installed on your computer to function, but it also can be used just to export the complete set of povray files.
The texture of each atom is adjustable: The default texture is applied
to all atoms, but then additional textures can be defined based on
selections (Create new texture from current selection). These can
be obtained either from selecting atoms by hand or by defining a
selection with a boolean expression, for example Z==6 and x>5 and
y<0 will select all carbons with coordinates x>5 and y<0. The
available commands are listed in the Help on textures window.
A movie-making mode (render all N frames) is also available. After
rendering, the frames can be stitched together using the convert
unix program e.g.
localhost:doc hanke$ convert -delay 4.17 temp.*.png temp.gif
For this particular application it might be a good idea to use a white background instead of the default transparent option.
Move / Rotate selected atoms#
ctrl+M (Move) / ctrl+R (Rotate)
Allows selected atoms to be manipulated using the arrow keys. The default direction of movement is parallel to the plane of the screen. Holding down ctrl will enable movement/rotation along the view axis instead. Furthermore, shift + arrow keys will slow down the speed of the movement/roration by a factor of 10. It is also possible to move/rotate the selection using the mouse by holding down both shift and the right mouse button.
NEB plot#
Assuming you have opened a series of images corresponding to a NEB trajectory, use to plot the energy barrier.
Bulk modulus#
Interface to ase.eos.plot()
Reciprocal space#
For visualizing the irreducible Brillouin zone and band path in an interactive graph window.
Wrap atoms#
ctrl+W
Brings atoms that are outside of the cell area into the cell, if possible within the periodic boundary conditions set.