How to remove unwanted charge isosurfaces?

[jghe]

Hi Philip,

To make the figure clearer, sometimes we just want to show partial of isosurface and keep the whole atom position. So we need to delete the other part of isosurfaces. I found i can not do that. I only can delete atom. Is there some way to do that? Where is the information of isosurface? I tried to modify .vesta file. But it does not work.

Thank you!

Best,

Jiangang

[Philip Howie]

Hi Jiangang,

I'm very flattered to have been addressed directly!  I've never been part of the VESTA team - you can thank Koichi Momma for such a useful program - but I will happily try and help you.

If you'd like to remove the isosurface(s) from the whole cell, Isosurface settings can be accessed from the 'Properties...' button at the bottom left and then the 'Isosurfaces' tab.  You can select isosurfaces from the list, create and delete them as required.  For each isosurface you can choose a level, as well as whether you'd like it to appear at only positive, only negative or both positive and negative values.  You can adjust the colour and transparency to get a good figure.

If, on the other hand, you'd like to create a 'cutaway' diagram in which the isosurface is stripped away from a certain part of the cell but the atoms remain, the procedure is a little more complicated:  First, create a new phase with the same atom positions and with the same origin and orientation.  Hide the atoms from one phase and use boundary planes (from the 'Boundary...' button, bottom left) to strip back the isosurface display.  Use the atoms from the other phase, without boundary planes.

I hope that helps; do let me know!

Best,

Philip

[jghe]

Hi Philip,

Thanks for your reply!

I do not understand "Hide the atoms from one phase and use boundary planes ...". Could you explain it a little bit more detail?

Thank you very much!

Best,

Jiangang

[Philip Howie]

Hi Jiangang,

I'm sorry not to have been online over the weekend to reply.  If you want to create a figure with atoms in the whole of the unit cell but the isosurfaces stripped back, the procedure is as follows:

Go to Edit | Edit Data | Phase... and click on 'Copy' to create a copy of the phase, including both structural (atomic) and volumetric data.  Go to the 'Volumetric data' tab and delete the volumetric data from, say, phase 2.  Click 'Ok' to get back to the main VESTA window.

Now click on 'Boundary...', at the bottom of the left hand column, and select phase 1 (i.e. the one which still has volumetric data).  Create one or more cutoff planes by inputting Miller indices and distances from the origin.  Any volumetric data beyond the planes you define will be hidden.  (I recommend unticking the 'Apply symmetry operations' box, to keep things a little more predictable!)

I've attached a quick example showing a cutaway view of the electronic density in an NbCr2 Laves phase, so that you can see how I've done it.  I hope I've understood your question correctly, and that my answer has been helpful!

Best,

Philip

On Friday, 26 July 2013 20:49:07 UTC+1, jghe wrote:

Hi Philip,

[jghe]

Hi Philip,

Thank you very much!

Now i understand what you said and i do can hide part of isosurface using plane in boundary section. However, this method is still inconvenient for me. For example, i want to hide the area between two parallel planes. This method looks failed.

I think the best way is to delete the isosurface as we do for atom (select and delete). May be this is impossible in VESTA.

Best,

Jiangang

[Philip Howie]

Hi Jiangang,

I'm glad I could be of use.

You could hide the region between two parallel plates by using a THIRD phase, perhaps: one for the volumetric data one side of the cutout, one for the volumetric data the other side of the cutout and one for the atoms.  To do this, you'll need to set one of the cutoff planes to the negative of the other and give it a negative distance from the origin.  As an example, I've just tried it with a (111) plane 1d from the origin on one phase and a (-1-1-1) plane -2d from the origin on the other.

I'm afraid after that, I'm out of ideas!

Best,

Philip

On Tuesday, 30 July 2013 19:19:52 UTC+1, jghe wrote:

Hi Philip,

[Rayan Chakraborty]

Hi all, 

I am not sure if this is still useful, but here is a way to achieve the same effect (since VESTA has not implemented this in the last ten years!!):

Export the file as a vector graphic (pdf or eps) and open it in graphic design software (e.g., illustrator); then, you can delete all unnecessary surfaces and objects. One drawback is that the process requires a considerable amount of memory and is inherently slow. 

Best, Rayan

[buxiang rangnizhidao]

Hi all:

 I have a question about the atomic radii in the VESTA software package. Is the default atomic radius in the software based on its ionic radius or covalent radius? Or, which paper does the software refer to for default atomic radii?

thanks a lot