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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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?
- 105
6
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1
answer
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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?
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0
answers
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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 ...
4
votes
1
answer
73
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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} = ...
- 145
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1
answer
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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 ...
- 391
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0
answers
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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 ...
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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.
- 161
3
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1
answer
57
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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
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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 ...
5
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0
answers
95
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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-...
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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 ...
- 31
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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, ...
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answers
143
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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 ...
3
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1
answer
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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 ...
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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?
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answer
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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:...
- 391
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votes
2
answers
359
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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 ...
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votes
1
answer
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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 ...
- 1,957
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0
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58
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Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta? [closed]
I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software.
Could you please recommend a free software to build ...
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votes
1
answer
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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:
...
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4
votes
1
answer
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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. ...
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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 ...
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0
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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 .
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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 ...
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0
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265
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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
...
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3
votes
1
answer
508
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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 ...
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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 ...
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0
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293
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Space group issue with XYZ, VASP formats in VESTA [closed]
I am facing an issue while converting .cif/.vesta files into .xyz and ...
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2
answers
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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 ($a \sqrt{3} \times a \sqrt{3}\times 1$...
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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 ...
user1441
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1
answer
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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 ...
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Changing orientation of SQS structure generated from ATAT
I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format)
...
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0
answers
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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 ...
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1
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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?
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answer
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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!
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2
answers
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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 $\...
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1
answer
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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 ...
13
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1
answer
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Extracting molecular structure from CIF file using VESTA or Mercury
I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following ...
8
votes
1
answer
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When import volumetric data (spin density of CHGCAR) to VESTA which option should we pick here?
I am trying to plot SPIN DENSITY isosurfaces using VESTA. I have used vaspkit option 312 to create ...
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2
answers
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Extracting the coordinates of a super cell in Vesta or Avogadro
I am trying to use a program such as Vesta or Avogadro to build a super cell from a .cif file for a molecular crystal. In neither program can I seem to figure out how to order the output of the ...
user2026
5
votes
1
answer
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SiC surface reconstruction
I know how to cleave surfaces with integer Miller indices, however I wonder how I could cleave a $(\sqrt{3} \times \sqrt{3}) R30$ reconstruction of $(001)\,\, 4H-SiC$.
I have found a nice link to O-...
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Generating glass nanocomposite structure in VESTA
I want to draw Pd(75)Au(5)Si(20) metallic glass nanocomposite. How to draw exact this metallic glass nanocomposite.
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Build VESTA supercell with two domains
I would like to build a supercell with vesta.
As a starting point I have a unit cell with polarization, I used it as my first structure in Vesta.
File -> New Structure -> Import
The supercell ...
- 261
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votes
2
answers
440
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Lattice representation: change of unit cell
(I use VESTA to visualize supercells with the VASP POSCAR format.)
Consider the following cell which has haunted me:
...
- 5,125
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answer
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How to predict new Half Metallic materials with higher degree of spin polarization?
Using DFT calculations, how one can predict the new half metallic materials with higher degree of spin polarization. I want to know the steps which have to be followed in prediction of new materials. ...
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How to build matter modeling models with appropriate tools?
When we perform matter simulation with first-principles calculation, building a reasonable model always be the very first and important step. However, people utilize different tools to build their ...
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acceptable range of stretching of a lattice unit cell when we do the heterostructure
Currently, I have to put two different materials together to form a heterostructure. I've already transformed the unit cell of material A from trigonal to cubic. Now the unit cell has a rectangular ...
- 2,793
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2
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Creating a heterostructure in VESTA
I have two different crystal structure and I want to create a heterostructure but the problem is that the shape of their unit cell is different. I know how to combine them if their unit cell are same. ...
- 2,793
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Atom legend in VESTA
Is it possible to to display the atom legend in VESTA and export the structure including the legend as a vector/raster image?
I found this discussion from 2013 requesting this feature. Has it been ...
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