# Tools¶

## Graphs¶

Allows to graph different quantities for a given trajectory. A ‘save’ button also gives the opportunity to save the data to file.

This example plots the maximal force for each image i and could help in investigating the convergence properties for relaxations:

i, e-min(E), fmax


These are the symbols that can be used:

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)

tangle 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)

## Movie¶

Allows to play the current trajectory as a movie using a number of different settings. Default duration is 5 s.

## Constraints¶

Allows to set (or remove) constraints based on the currently selected atoms.

## Render scene¶

(Currently disabled)

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 atoms¶

Allows selected atoms to be moved using the arrow keys. The direction is always parallel to the plane of the screen. Two possible movements are available: Just pressing the arrow keys will move by 0.1 Angstrom, shift + arrow keys will move by 0.01 Angstrom.