cleave surface. bottom atoms don't start at 0 0 0. Bottom vacuum exists.

[Luiz Fern]

Hi.

I want to create a surface but can't figure out a way to don't have vacuum at the bottom. Is the default.
Of course, I have set up the bottom vacuum to be 0 layers and 0 angstrom. But still I have ~2.5 A of bottom vacuum.

I know I can translate the surface once it is created. But I really would like to have a default setting for this.

[Jess Wellendorff]

1) The bottom vacuum you get with setting 0 Angstrom simply reflects the periodicity of the lattice.
2) For slab-type surface configurations, it is in general advisable to have some amount of vacuum at the bottom, e.g. 5 Angstrom, and then use non-periodic boundary conditions on the C-faces: Dirichlet at the left face and Neumann in the right face. This avoids spurious interactions between repeated cells along C.

[Anders Blom]

Probably what you need is an option to say, that the specified surface layer (the clicked atom, on the first page of the widget) should be placed at c=0 and not c=1. I agree it can be useful, and we can add that in the future.

[Luiz Fern]

Yes Anders Blom. That's exactly what I need. Until you can add something, do you think there is some way around it?

[Anders Blom]

First of all, why is this important? It's really just a shift of coordinates. Sometimes it IS important, if you want to build further on the model, I realize that, but think about if it really matters for you.

You can always do a wrap or shift as you already wrote. Unless you're doing this 10 times, it's a quite easy operation. Generally we try to avoid making the tools in the Builder full of options, but rather rely on workflows involving a sequence of tools. (For example, no Wrap checkbox in a tool, since the user can always use the Wrap function afterwards.)

[Luiz Fern]

I'm trying to create a slab. It seems that wrap doesn't work here.
Sure, I can shift but just for a matter of organization, I'd like to have the first atom precisely at 0 0 0.
Maybe I need just to accept that that isn't possible with VNL.

Thanks anyway.

[Anders Blom]

It's very possible. Just create the slab, then open the Move tool, select the atom you want at 0,0,0 and enter these coordinates in the dialog. Then wrap as needed.