Talk:Mod:Hunt Research Group/Ovito basics

Using Ovito: The Basics

get started

• manual is here http://www.ovito.org/manual/
• this can be a bit unstable, you may have to "open" twice and it may randomly close
• importing data

http://www.ovito.org/manual/usage.import.html

from the top menu select File->load file

ovito only loads the first frame by default

click on the file-name in the right-hand panel, under this click on "File contains time series" to load rest of the trajectory

visualising structures

• the default has odd colours, odd radii and no bonds, and is too bright (ie no depth)

depth perception

• turn on ambient occlusion (modification)

http://www.ovito.org/manual/particles.modifiers.ambient_occlusion.html

• turn on transparency (modification)

http://www.ovito.org/manual/howto.transparent_particles.html

select the compute property modification

under "My property" chose transparency (you will have to scroll down)

paste ReducedPosition.X into the "Expression" box

this only works on the atomic spheres not the bonds so is not actually that useful!

• it can be useful to slice the box to reduce the depth

http://www.ovito.org/manual/particles.modifiers.slice.html

• it might be useful to hide H atoms

reduce the H radius to 0.01 (this leaves bonds)

reduce the C-H bond selection to 0.01

this does leave tiny dots

radii and colours

• two ways to change the radius
• in the display menu, use Particles

choose default radius of 0.5

• in the input menu, use Particle Types

click on "particle types"

click the colour and change the colour

specify a radius of each atom individually in the radius box (0.5) except for H which is 0.3

wrap into the box

wrap at periodic boundaries (modification)

bonds

• create bonds

in the top panel click on "add modification" and select create bonds

http://www.ovito.org/manual/particles.modifiers.create_bonds.html

click on create bonds tab on choose "pair-wise cutoff radii" then add in relevant radii

a note that this does not always work properly, delete the modification and then add it again

set bond width to 3.0

some general parameters

C-H 1.2

C-C 2.0

S-F, N-S, O-S, C-P 2.5

• to measure bonds

to get an idea of good bond distances to choose

click on the little hammer in the upper right, choose "inspect particles"

click on a particle, then cmd-click on another particle and the pair distance will be reported

following particular atoms

• select an atom

select the "Manual selection" (modification)

choose "pick particles"

click on the first atom, then command click on others to select

note that the pick particles is switched off when you rotate or move the frame

you need to re-select pick particles after any movement action

• colour atoms by selection

select the "color coding" (modification)

I found the Blue-white-red useful

select particles, in particle properties: "selection"

tick the keep selection boxes but NOT the color only selected particles

selected atom should be red and all others blue now