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Questions tagged [vesta]

Questions relating to VESTA (Visualization for Electronic and Structural Analysis). VESTA is a 3D visualization program for structural models, electron/nuclear densities, and crystal morphologies.

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3 votes
0 answers
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Is there any tool/website available by which I can generate VASP input files?

I am familiar with QE input files, but totally new in VASP. I know by using the quantum espresso input generator(https://www.materialscloud.org/work/tools/qeinputgenerator), we can use CIF file to get ...
Md. Jahid Hasan Sagor's user avatar
5 votes
2 answers
145 views

How to make Quantum espresso input file from Vesta?

here is the CIF file of CaCO3 (http://www.crystallography.net/cod/1010962.html). I have opened it using Vesta and get the following data: ...
Md. Jahid Hasan Sagor's user avatar
4 votes
1 answer
49 views

How to get 192 of CeO2 atoms coordinates using Vesta?

Here is the CIF file of CeO2 (http://www.crystallography.net/cod/1562989.html). One of the paper mentioned that they have used 192 CeO2 atoms constructed by 444 primitive cells. To generate the ...
Md. Jahid Hasan Sagor's user avatar
5 votes
0 answers
25 views

How to choose vacuum value for monolayer and heterostructure?

I have read several articles but I am confused how to choose vacuum in case of 2D materials. Should we add vacuum of 20A in one side of monolayer or 10, 10A on both side of monolayer? Kindly suggest ...
Khushi's user avatar
  • 153
2 votes
1 answer
84 views

Can lattice vectors have negative components for DFT calculations?

I am using VASP for DFT calculation where the lattice vectors of POSCAR file for the hexagonal system are as follows. This I generated using VESTA ...
Nilabja Kanti Sarkar's user avatar
3 votes
0 answers
32 views

heterostructure using two monolayers from different crystal systems

How to create a heterostructure using two monolayers from different crystal systems: a hexagonal system (a = b = 3.17 Å, c = 18 Å, α = β = 90°, γ = 120°) and an orthorhombic system (a = 3.77 Å, b = 4....
Zubair Nabi's user avatar
3 votes
0 answers
49 views

Number of atoms is different in xyz file and POSCAR file. Some atom positions of listed in the xyz are missing too in POSCAR. Why?

I am trying to make POSCAR file and xyz file using vasp for NbReSi compound using VESTA. However, I notice that the number of atoms for xyz file is given as 41 whereas for POSCAR is it 36. Further, I ...
Nilabja Kanti Sarkar's user avatar
4 votes
0 answers
37 views

CDD on the surface of a slab and in other types of (finite) systems

What would be the appropriate method of calculating the difference in charges for this type of system? For composite systems it is usually something like: $$ \Delta\rho = \rho_{system}-\sum_{i=1}^{N}\...
Gabriel Elyas's user avatar
3 votes
0 answers
24 views

Assistance Needed in Replicating Charge Density Difference Plot for g-C3N4/Pt System

I'm currently facing a challenge in replicating the charge density difference (CDD) plot showcased in Figure 7(b) of this paper. Specifically, I'm attempting to reproduce the CDD plot for the ...
Nidhi Tiwari's user avatar
5 votes
0 answers
40 views

How to determine the unit cell in heterostructure?

I’ve to create a heterostructure from two monolayers, for example, two graphene sheets or two metal layers. And then I want to rotate the first layer relative to another one by some angle. The ...
Victor's user avatar
  • 49
4 votes
0 answers
73 views

Automatic construction of supercell VESTA

Good afternoon, everyone.Please help me understand my question. When I upload some of my cif structure files, VESTA automatically creates huge supercells. I want to remove this function by standard ...
Agrail616's user avatar
4 votes
0 answers
37 views

Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same

Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
Nilabja Kanti Sarkar's user avatar
6 votes
1 answer
181 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
3 votes
1 answer
99 views

How does VESTA render files with POSCAR format

I have the following POSCAR file of a tubular structure that was created using python ...
Jaafar Mehrez's user avatar
4 votes
1 answer
153 views

How to make Pd(111) supercell (√3×√3)R30 via VESTA

How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
Rubi Agrawal's user avatar
7 votes
1 answer
319 views

For a single unit cell calculation, is it necessary to add a vacuum?

Much of the information I find is about super-cells. What about for a single unit cell? Is it necessary to add a vacuum space?
Gabriel Elyas's user avatar
2 votes
0 answers
146 views

VESTA object selection not working reliably

I am now working with VESTA and need to hide certain polyhedra for plotting purposes. I am having trouble selecting single and groups of polyhedra though, as the program selects a random other object ...
Pietrocarmine's user avatar
4 votes
1 answer
89 views

Having difficulty creating the β-tellurene structure in VESTA

I've recently started with VESTA and am having some trouble building the β-Tellurene structure (monoclinic, space group nº 12). I know that the lattice vectors are: $$\vec {a} = a\hat x \\ \vec {b} = ...
Gabriel Elyas's user avatar
5 votes
0 answers
124 views

Color of isosurface in charge density visualization

I am trying to visualize the charge density of a crystal through VESTA. However the intersection surface of the isosurface and the boundary turns into blue, which is certainly not included in my ...
蕭力諶's user avatar
  • 441
2 votes
0 answers
182 views

Clarifying local magnetic moment axes in VASP: cartesian vs crystal (for MAGMOM/M_CONSTR)

In VASP, one can set the local magnetic moments of each ion in a non-collinear SOC calculation along a certain direction using the MAGMOM/M_CONSTR tags. The manual linked to states that these local ...
TribalChief's user avatar
  • 2,361
5 votes
1 answer
134 views

VESTA using command line

Can anyone please show me how to make a supercell with VESTA using a single command line without opening a GUI.
hakou elhaj's user avatar
3 votes
1 answer
90 views

Hetrobilayer charge density by using quantume espresso

When I want to visualize charge density in VESTA I got this error "**Number of data grids in the 3D data sets do not match each other" How can I fix this problem
ahmed hassan's user avatar
3 votes
0 answers
22 views

Is there a way to configure some parameters in a system before opening a structure in VESTA?

I have several structures to visualize and print out. I previously opened them using terminal commands in Linux: ~/VESTA-gtk3/VESTA POSCAR But I need to set up ...
Gabriel Reynald's user avatar
5 votes
0 answers
245 views

How can I properly plot this .cube file in Python?

Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-...
D_C's user avatar
  • 133
3 votes
0 answers
33 views

How can I add the extra elements in the available CIF file for refinement?

I have prepared Lithium ferrite samples doped with Zinc, Titanium, and Manganese. After taking the XRD data I wanted to perform Rietveld refinement. But the problem is that I have cif data available ...
Raj Roshan's user avatar
2 votes
0 answers
204 views

How to integrate CHGCAR data of VASP, in z-direction and have xy-plane charge density at each grid point on xy-plane?

i asked this query in another forum, waiting for answer. However, also posting it here. i got a CHGCAR file written for both optimised and non-optimised (single point run) runs of a lattice model. So, ...
skm's user avatar
  • 196
4 votes
0 answers
310 views

Why VESTA displays much more atoms beyond the cell boundaries?

I was trying to follow this recipe, NanoCrystal / Graphene Heterostructure in VESTA step by step but instead of an Au nanocrystal, I put a small graphene nanoflake approximately 3.35 Å on top of ...
Vladislav Gladkikh's user avatar
3 votes
1 answer
129 views

How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?

For example, I intend to generate the remaining sites of the Cr cubic lattice but the POSCAR file provides limited info on the number of atoms present as shown below. Is there a way to implement this ...
Pranoy Ray's user avatar
  • 1,635
4 votes
1 answer
604 views

How can visualize a rectangular super cell of Graphene by VESTA

How can I build (visualize) a rectangular supercell of graphene as shown in the figure? Can I use VESTA to do that and how?
ahmed hassan's user avatar
3 votes
1 answer
229 views

Why I got more atoms than expected when generating POSCAR from VESTA

I tried to generate a perovskite structure with VESTA, and the following are my settings: The generated structure seems to be correct. However, when I tried to export it as POSCAR I got the following:...
蕭力諶's user avatar
  • 441
6 votes
2 answers
467 views

Change cif file into vesta format

I have 100 .cif files. I want to convert them all to .vesta files through vesta software (https://jp-minerals.org/vesta/en/download.html). I know I can choose them one by one and convert them. Is ...
Sanu's user avatar
  • 61
3 votes
1 answer
74 views

Do I have to use Rwp, RI, Rf and atomic displacement parameter B to create a CIF file?

I want to create the CIF file of CuI using VESTA software.I used the following parameters to create my CIF : space group, lattice parameter, the angles (alpha, beta and gamma), atomic positions of Cu ...
Camilla's user avatar
  • 2,169
2 votes
1 answer
264 views

How do I know which is the asymmetric unit of a unit cell?

I need the number of independent atoms in the asymmetric unit I have to introduce them in this form: ...
leire's user avatar
  • 183
4 votes
1 answer
830 views

Maximum bond length in Vesta

I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond lengths between two atomic species. ...
rik's user avatar
  • 91
6 votes
1 answer
511 views

How are the simulated powder diffraction patterns calculated in CCDC Mercury?

From my understanding, programs like CCDC Mercury and VESTA are able to extract some information from imported .CIF files of molecules but then complete calculations to output a simulated X-ray ...
John's user avatar
  • 63
1 vote
0 answers
62 views

How Can I Create a 2D Silicon Carbide Structure using VESTA [closed]

I'm just getting started with VESTA. SO I'm fairly new to it. Can anyone suggest me how to build a 2D structure of Silicon Carbide (SiC)? Or any documentation would also help. Thanks .
Ikram's user avatar
  • 19
7 votes
2 answers
154 views

Modelling Pd(111) and Pd(100) Surface Oxides Through VESTA

I want to build unit cells for Pd surface oxide models, but I am not sure how to begin as I am new to using VESTA. On Pd(100), the most stable surface oxide structure is √5x√5 R27o. On Pd(111), the ...
Manasi Vyas's user avatar
2 votes
0 answers
321 views

How to rotate layer of heterostructure and save it to fractional coordinate using VESTA? [closed]

I'm building multilayer structure. I build the heterostructure importing the the to phase of structure in VESTA File -> New structure -> Phase -> Import ...
gvd's user avatar
  • 121
3 votes
1 answer
640 views

How to export .xyz files from VESTA of crystal viewed along different crystallographic axes

I've only been able to export atomic coordinates for a crystal when looking down the c axis, but I need to do so along the a and b axis as well. I've tried changing the Projection Vector in the ...
user5060's user avatar
4 votes
0 answers
552 views

Changing global cartesian coordinate system with VESTA [closed]

I began with an imported a .cif file from materials project and have updated the structure to my specifications. I would like to change the global cartesian coordinate system so that I can project the ...
aRockStr's user avatar
  • 141
4 votes
0 answers
352 views

Space group issue with XYZ, VASP formats in VESTA [closed]

I am facing an issue while converting .cif/.vesta files into .xyz and ...
user14295847's user avatar
7 votes
2 answers
4k views

How to transform lattice in VESTA

Can anyone please help me transform $\ce{LiCoO2}$ hexagonal cell ($a \times a \times c$) to orthorhombic cell ($a \times a \sqrt{3} \times 1$) and hexagonal cell ($a \sqrt{3} \times a \sqrt{3}\times 1$...
Binh Thien's user avatar
  • 2,095
8 votes
1 answer
1k views

Unit Cell Parameters for VASP Calculations

For background, I have never used VASP before and have limited knowledge of how the software works. I am working on a program for the automation of structural creation for 2D materials. I am more of a ...
user avatar
8 votes
1 answer
1k views

How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis

In this paper, they have rotated the unit cell using a rotation matrix, so the axes are aligned with the atomic bonds. I would like to know how they calculated that rotation matrix, and which software ...
Chi Kou's user avatar
  • 5,833
7 votes
1 answer
274 views

Changing orientation of SQS structure generated from ATAT

I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format) ...
Aman's user avatar
  • 71
6 votes
0 answers
499 views

How to create a CIF using VESTA? [closed]

I am looking into double perovskite materials. One of the possible materials is $\ce{Cs4CuSb2Cl12}$. Now, although there are a few papers which have done ab intio calculations but none of the common ...
Parmeet Singh EP 066's user avatar
4 votes
1 answer
283 views

wurtzite unit cell of ZnO

am looking to draw wurtzite unit cell of ZnO, and i find two of them and the second one how can I draw the first one in software like vesta?
jasoon's user avatar
  • 43
6 votes
1 answer
1k views

How to work with unit cells in Vesta

I am really confused about why whenever I add one molecule into vesta, around 6 show up randomly not at that position? What's the correct procedure for working unit cells? Thank you!
Shad0w7's user avatar
  • 373
10 votes
2 answers
2k views

Help understanding square root notation of supercell

I often see supercells and slabs explained like this: $2\sqrt{2} \times 6$ slab of $\ce{MoS2}$ (001) $\sqrt{2} \times \sqrt{2} \times 2$ supercell of $\ce{Y Ba(1−x)Sr(x)CuFeO5}$ (see here). Take $\...
user1029384756's user avatar
9 votes
1 answer
461 views

Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software

I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic ...
Collodial_machine 's user avatar