Hi Garam,

      Presently I don't know whats the exact problem with Vesta is ? However, I will tell u how to make a Supercell using a unit cell. Just follow the same procedure that you explained in the point 1 and export it as POSCAR file. But your POSCAR contains more coordinates than your actual super-cell POSCAR should contain. This is because of reprinting of same coordinates in several places. So I suggest you to remove the fake coordinates in the POSCAR file. This can be easily done by checking the fake coordinates using "objects". Check the squares under "L" in objects, if u check these squares one by one the same atoms are shown in the viewer, even though u check the square and the corresponding atom is not shown in viewer indicates the fake coordinate. This is lengthy procedure, how ever can be simplified by practice. Please find the attachment for your perusal.

Thank you very much, Naga!!

That is exactly what I want for my question 1. I should read VESTA manual in detail.

My 2nd question was how I can make the structure with a miller index to make vacuumed super cell structure for surface simulation using VESTA.

The paper I attached explain how to prepare structure file for surface calculation. Following this, transforming coordinates is needed. I have already read the section in VESTA manual but I couldn't understand. Anyway, the fact is that I want to make vacuumed super cell structure file that grown with a specific miller index(hkl).

Dear Naga & Choi, I have also the same question. How to make POSCAR file from VESTA for Surface calculation using VASP ? 

Can anyone please suggest ? 

Thanks

Hi Choi ,

You can also easily make super cell using LMTO.

can you please attach the PtC Cell, I will try to resolve it

Dear Barman,

You can make POSCAR file from VESTA in the 'file - export' menu :) You can also read the paper I attached in the main question of mine.

If you use VASP version under 5.x, you should delete 3rd line indicating your atoms in the POSCAR made.

And I will try LMTO. Thank you.

Dear Naga,

Thank you for your kind:)

I realized I made wrong question. It's my fault.

I have a problem with transform calculation of a cell not making super cell. Following the paper I attached, I should transform the old cell grown with no specific direction to the new cell grown with a specific direction (eg. (1 1 1) direction) 'by hands!'. I don't understand the transform calculation. I will add the content in the paper soon after this answer.

Dear All

A supercell can be easily constructed by VESTA by the following steps:

1) Preparing the unit cell, e.g., in VASP POSCAR format

2) Select the menu "Edit" and then "unit cell"

3) Select the button "Trasform" and them enter you size of the supercell, e. g., 3x3x3 to the the diagonal elements of transformation matrix. Click OK

4) There is an option to export the coordinates in the VASP format.

Regarding the construction of the surface, you can follow the steps in the link below. It is comprehensively written by Emre S. Tasci.

https://www.researchgate.net/publication/256708563_How_to_prepare_an_input_file_for_surface_calculations

Hopefully, these may help you.

Best regards,

Thanayut

Article How to prepare an input file for surface calculations

Dear Thanayut,

Thank you for kind answer.

Actually this question started from the paper you attached (and I also attached at the beginning of this question). Although, I think you could give the answer of my 2nd question.

I want to know how old cell is transformed to new cell with new coordinates in VESTA (Chap. 3.5 in that paper). Where are the eqns (a' = -a+b, c' = a+b+c, etc) from?

I can't get the same result with the result in the paper (the matrix in page 8) calculated by eqn in page 7 (a' = -a+b, b'=-1/2a-1/2b+c, c'=a+b+c) from the origin's coordinate in the table 2.

Could you explain it for me in detail or recommend a source I can learn?

Best regards,

Garam

Hello Garam,

In the paper author selected [111] direction, so c' and nornal to plane are codirectional vectors. Thus c' is vector sum of a, b, c. Next ... c' is vector product of two vectors a' and b', so a' = -a+b   and   b'=-1/2a-1/2b

Best Regards,

Dmitriy

Dear Dmitriy,

I had spent time to solve this transformation and I know how to now.

Sincerely, thank you for kind reply.

Garam Choi

I think you are using .cif file in VESTA. Actually in the .cif, you can find Cd and Co have different occupation for Cd0.52 Co0.48 Cr2 S4 and Cd0.9 Cr2 Cu0.1 S4. And when you export vasp file (POSCAR) using vesta you will always get the same files. This is because in vasp you can not have the option of occupation. You can make this system for vasp by changing the number of atom in the POSCAR.

example: Cd0.50 Co0.50 Cr2 S4 can be done by taking Cd-32, Co-32, Cr-128, S-256

and Cd0.89Cu0.11 Cr2 S4 can be done by taking Cd-57, Co-7, Cr-128, S-256

how i could make super cell for Au gold?

I highly recommend using Virtual NanoLab to do the task. It is a very easy-to-use tool. Start by the Builder and add a new structure from Database. Chose the desired option and press (+) symbol. At Builder window, use Bulk Tools menu to create a supercell, keeping the symmetries. For Gold, the unit cell is a Face Centered Cubic (FCC) cell.

I've worked the band sructur for GaAs but it was not perfect I used spin=2. Is there a way to get an ideal band using a program vasp. thank you

ISPIN 2 is for spin polarized calculations and that should be the case for GaAs . Did you select correct Kpoints . Check for your brillouin zone and select correct Kmesh Only then results would be perfect. GaAs is a cubic crystal . Was your optimization correct ?

Thanks,

Aakanksha

hallo,

i ned your help, I have an article titled (Ab initio density functional theory study on the atomic and

electronic structure of GaP/Si(001) heterointerfaces )and I want to implement it through the program Vasح but do not know how to start please can you help me?

Dear Marsel,

First thing to be answered is if you have access to an active licence of Vasp. There are also free options as Quantum Espresso.

Dear Anibal,

I work with vasp But I have little experience about it .

Hi, Is there any formula to convert one coordinate to another by using different volume of unit cell. For example, In CO2, each atom has different coordinate value (0.5 0.5 0.5) in 10x10x10 unit cell. if i want to convert these individual atom coordinate into 9x9x20 unit cell then how can i convert??

Hallo ,

can you please help me

when i have Gap/Si and treminated by H.

in POSCAR when i have some si (F F F) and some H2(F F F) kept fixed

after relaxation

in CONTCAR the Fixed hydrogen atoms change .

i dont understand why?

Hi, Can anyone help me to add vaccum in a unit cell in VESTA? Thanks

Mirwaiz Rahaman

Materials Square(http://matsq.com) provides several atomic manipulation tools such as vacuum, strain, add/delete atom(s) and crystal builder.

I attached materials square manual to add vacuum in your structure

The best way to convert a 10x10x10 supercell into any other size would be to reduce it to 1x1x1 and then do periodic replication. This will be easy and reduce any chance of possible mistakes.

Mirwaiz Rahaman@

This video can help you to add vacuum in a unit cell in VESTA

How can we apply sqrt(3) X sqrt(3) X 1 transformation to my unit cell

In VESTA, go to Edit-->Edit Data-->Unit cell-->Transform,

then change the Rotation matrix accordingly.

Dear Mr.Pulkit,

could you send your email, please ? I know from on online survay that you worked on (Oxygen effects on crystal plasticity of Titanium: A multiscalecalibration and validation framework)

Thanks a lot

how would you create sqrt 2 sqrt 2 1 supercell? Can someone explain the rotation matrix method or share some source to understand it?

Kajal Madaan

As far as the 3rd index is 1, it's enough to speak on what goes in x-y plane.

Imagine a square grid, for example, NaCl, with Na atoms in grid knots, and Cl atoms on the center of the square formed by Na atoms. Each cell contains 1 Na and 1 Cl atom. The shortest Na-Na distance is unit cell vector, we can name it "a". If you look at the second nearest neighbor, it will be on the opposite corner of the square, and the distance to it would be diagonal of primitive cell, a*sqrt(2). Thus the new cell is turned 45degrees to the initial, it has Na atoms in knots+1 atom in the center of the square, while chlorines are on centers of edges. Supercell contains 2 atoms of each kind and its volume is sqrt(2)*sqrt(2)=twice bigger than of primitive cell.

The same operation can be performed once again, the result will be exactly equivalent to 2x2x1 cell.

If we are speaking on cubic or tetragonal cell

New "a" vector directed as 110 (of old vectors),

New "b" vector directed as -110

New "c" vector 001

What is 211 supercell is unclear for me. 211 surface has nothing to do with the question. If you mean a cell that is defined with 200, 010, 001 (of old vectors) - it has the same volume and number of atoms to "110, -110, 001" cell, but might be less useful for slabs or study of anisotropy.