volumetric data for supercell

[mia2Xtran]

I am new to VESTA and will appreciate any help. 

I want to generate a larger cell for LiC6 and visualize the volumetric difference between LiC6 and C6, however, the resulting charge difference can't be modified to corporate with larger cell but rather stay as appearing with one original unit cell. 

How can I do the modification?

Extra question: Later I need to only visualize the charge difference for ONE Li and 12 C's surrounding it, how can this be done?

Thank you so much,

Mia.

file://localhost/Users/ttran/Desktop/CHGCAR_1LiC6_SCF_a.tif

file://localhost/Users/ttran/Desktop/CHGCAR_1LiC6_SCF_aa.tif

[Philip Howie]

Hi Mia,

From your attached images, it looks like you only have one unit cell displayed.  The carbon atoms outside the unit cell only appear because they're bonded to atoms within the cell and you've checked the default 'Search atoms if A1 is included in the boundary' box in the 'Edit | Bonds...' dialogue.  While this draws any extra atoms required to complete the bonds, it doesn't extend the volumetric data in the same way.  Try going to the 'Edit | Bonds...' dialogue and chose 'Do not search atoms beyond the boundary' and you'll see where the actual boundary of your structure is.

If you do wish to extend both the atoms and volumetric data, the correct way is to click on the 'Boundary...' button at the bottom left of the screen and increase the ranges of coordinates.  To reproduce your figure CHGCAR_1LiC6_SCF_a, for example, try plotting over the range -0.5<x<1.5, -0.5<y<1.5, 0<z<1.  If you want a boundary which is not parallel to the (100), (010) and (001) planes of the structure, you can use the bottom half of the 'Boundary...' dialogue to create additional cutoff planes.

The procedure for visualising just one Li atom and its coordinating C atoms is exactly that: adjust your boundary, using the range and cutoff planes as necessary, so that only the required atoms are included within the boundary.  In CHGCAR_1LiC6_SCF_a, I think the appropriate range is -0.5<x<0.5, -0.5<y<0.5, 0<z<1 with no cutoff planes required, but you'll need to check that as I don't have your VESTA files to play with!

I've assumed that all you want to see is those thirteen atoms, isolated from the structure.  It is also possible to show the volumetric data for just one set of atoms, but in context, surrounded by the rest of the crystal structure.  To do this, you'll need to create a second phase with exactly the same unit cell and atomic structure and position it with a displacement of (0,0,0) relative to the first phase.  Now reduce the boundary of the phase with the volumetric data and leave the identical second phase in place to display more atoms.

I hope that helps; do let me know if you need me to explain any of the above steps further.

Philip

[mia2Xtran]

Dear Philip,

Thank you so much for your clear explanation. 

I was able to do everything I questioned and much more.

You are of such great help.

Sincerely,

Mia.

[mia2Xtran]

When trying to subtract two different CHGCAR's generated from VASP as VESTA's Volumetric Data, it is showed "Number of data grids in the 3D data sets do not match each other". 

One CHGCAR is calculated after molecular dynamics and relaxation of an initial POSCAR.

The other one is initial charge density of the previous optimized CONTCAR with one atom short.

Does anyone know why this happened?

Thank you in advance. 

[Al-Mu'minun]

Hey Mia,

even if it has been awhile and no one answered, I´ll tell you the solution to your problem "Number of data grids in the 3D data sets do not match each other". The CHGCAR-files have to be consistent, in other words the number of grid-points in the FFT-mesh along each directions has to be the same. Since I have not seen your  CHGCAR file, look at the first lines. The three integers tell you what your grid points are. You can also look at this in your "OUTCAR-file" (grep NGX=...). See here for more information: http://cms.mpi.univie.ac.at/vasp/vasp/NGX_NGY_NGZ_NGXF_NGYF_NGZF_tags.html
After knowing the number of grid-points, you have to specify the exact grid points manually in your INCAR file and restart the static calculation for the charge density. After that you should be able to subtract the volumetric data from each other. Enjoy your visualization!

Best wishes,
Okan

[Azeema Saeed]

Hi,

I need help with plotting volumetric data in Vesta. My isosurface and atoms are not superimposed on each other. Am thinking it has to do with the boundaries. Can someone please help me rectify this?  Attached is the generated plot at x: 0 1, y:0 1 and z: 0 1.