strcuture cleaving

[HIMANI]

How to cleave a structure to show its single layer along with a graph for comparison purpose?

[Jess Wellendorff]

This question is not clear to me. You want to cleave a bulk along some direction, e.g. (100), then strip off all atoms not in the top layer, and then do some graphical comparison?

[HIMANI]

No. what I have made is an interface. I just want its single layer (mono layer) to compare with the ELF results. actually I want to map a single layer of my structure over the ELF plot.

[zh]

I know there is a way to draw such plot by the VMD software.
1) export the ELF data into a file with the Gaussian cube format and the atomic structure of monolayer into a file with XYZ format;
2) load them into VMD and adjust the parameters in several options to polish the plot.

Alternatively, you can replace the coordinates of atoms in the Gaussian cube file of ELF data by the coordinates of atoms of monolayer. And then visualize this cube file of ELF data.
For the format of Gaussian cube file, you may see below:
http://paulbourke.net/dataformats/cube/

[Umberto Martinez]

You are able to do that within VNL, of course.
If I understood well, not sure about that, you simply need to open your ELF analysis with the Viewer and choose cut-plane option.
Drag and drop your structure in the same windows afterwards.
Select the atoms that you do not want to visualize and set opacity to zero.

Now possibilities are endless, also considering some new visualization options of VNL 2015 (third beta version available for download from our website).
See screenshots with examples for ELF of graphite.