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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Why can't the VESTA recognise the charge information of CHGCAR? And why there are negative values in my CHGCAR?
I carried out static calculation on a semiconductor surface structure containing defects and wanted to analyze its CHGCAR and ELFCAR, but I found that there were negative values in CHGCAR, and when I ...
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1
answer
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How to convert packmol output to VASP format?
I want to model some cells with liquid water using VASP. I use the Packmol package to generate the initial configuration, but when I try to convert the pdb output file into the POSCAR format, the ...
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Interpretation of Spin Density for FeCl₂ Monolayer Visualized in VESTA
I have performed spin density calculations for an FeCl₂ monolayer using VASP and visualized the results in VESTA. While I can see the spin density distribution, I am seeking guidance on how to ...
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45
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How to visualize geometry optimization using VESTA?
Using XCrySDen, I can generate animation in GIF/MP4 format from the Quantum ESPRESSO relaxation calculation output (as shown below). I know it is also possible through ASE to visualize the BFGS ...
3
votes
1
answer
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What are the specific differences between these two notations of supercell denoted by (√3×√3)R30∘ and (√3×√3)?
I am studying the super-cell structures in crystallography and came across two different notations:
(√3×√3)R30∘ and (√3×√3). I would like to understand whether these two notations represent the same ...
- 587
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36
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Supercell Symmetry with VESTA
I have recently generated a Supercell of TiO2 rutile with VESTA. I have started from the CIF file and then I selected the option "search atoms in the new unit cell and add them as new sites" ...
- 407
3
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41
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How to make a heterostructure
I have two hexagonal structures with lattice parameters 3.425 and 3.14. I try supercell or sqrt3 method but lattice mismatch does not reduced. Is there in way to make a heterostructure from these ...
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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 ...
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2
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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:
...
- 835
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answer
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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 ...
- 835
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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 ...
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97
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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
...
3
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answers
52
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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....
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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 ...
4
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answers
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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}\...
- 481
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answers
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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 ...
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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 ...
- 49
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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 ...
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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 ...
6
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1
answer
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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
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1
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199
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How does VESTA render files with POSCAR format
I have the following POSCAR file of a tubular structure that was created using python
...
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1
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177
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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?
- 587
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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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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
98
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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} = ...
- 481
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answers
174
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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 ...
- 451
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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
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votes
1
answer
106
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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
- 344
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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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answers
357
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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 ...
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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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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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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:...
- 451
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votes
2
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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 ...
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333
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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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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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648
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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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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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367
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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
728
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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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409
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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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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