Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
215 questions
2 votes
0 answers
38 views
how to make square root supercell in vesta? [closed]
How to make (√7 × √7) supercell of CdS (001) in VESTA?
4 votes
0 answers
42 views
Exporting images (PDF) using the Python CSD API
I would like to export a visual representation (e.g. ORTEP) of a crystal structure from a .cif file to an image (preferably PDF) using the Python CSD API through Mercury, since I want to use that ...
- 41
3 votes
0 answers
78 views
Pymatgen: make molecules whole?
Is there any way in Pymatgen (or some similar python library such as ASE or whatever) to make all molecules read from a .cif whole (i.e. not broken due to PBC)? This is useful for organic molecules ...
- 211
4 votes
1 answer
88 views
How does one make a slab for molecular crystals for a particular Miller index in VESTA, without some molecules getting bisected in the middle?
I want to make a slab for a particular Miller index of a molecular crystal using VESTA. The issue is that some molecules are getting bisected from the middle which may create issues. How does one ...
- 43
2 votes
0 answers
75 views
Graphical utilities for analyzing cell edges in crystals
My Chemcraft program supports the visualization of crystallographic files, in particular .cif files. I want to add some more features to the program, which can make working with crystal files more ...
- 596
2 votes
0 answers
38 views
Correct dislocation insertion in OVITO using python script
When writing a Python script for ovito, to insert screw and edge dislocations, how to make sure that when changing the Burgers vector and dislocation line, the overall picture does not change, that is,...
- 21
5 votes
1 answer
300 views
How to dive between different input geometries in Quantum ESPRESSO?
At first, I'd like to apologize for my straightforward question that may sound trivial. I would like to ask for help in clarifying the difference between three methods of expressing crystal structure ...
- 569
2 votes
0 answers
192 views
How to export vector image of crystal structure in VESTA correctly?
I have a .cif file with crystal structure of Ca3Mn2O7. I tried to export it as vector image in Vesta but when I open the resulting .eps file in Adobe Illustrator I see only halfs of atoms and bonds. I ...
- 21
3 votes
0 answers
35 views
How does CRYSTAL14 properties use fort.98 to generate 3D charge density from ECH3?
I’m using the properties program from CRYSTAL14, and I want to understand how the ECH3 function processes the fort.98 file to compute the 3D charge density grid (i.e., the values written in DENS_CUBE....
1 vote
0 answers
41 views
Combining AI Methods with PXRD structure detemination : Seeking Software for Direct Method-Generated Electron Density Maps or Phase Retrieval
I am currently working on integrating AI approaches with PXRD (Powder X-ray Diffraction) to analyze crystal structures. I am looking for recommendations on software that can export electron density ...
- 51
5 votes
0 answers
93 views
POSCAR file for heterostructures [closed]
I'm working on SrNbO3 and BaSnO3 and struggling with generating the POSCAR file for the heterostructure. I modelled one using VESTA, but running the simulation resulted in an error. I need a guide on ...
- 81
3 votes
0 answers
73 views
Is carbon diamond with a vacancy every 10Å a conductor?
I'm doing some DFT simulations and not feeling very confident. The material is bulk diamond carbon and was made with the Tersoff potential at 300K. The xc functional is LDA. The basis is atomic ...
- 487
3 votes
2 answers
139 views
I wanted XCrySDen on ubuntu 20.04 but failed at intallation of "libtogol2"
I wanted XCrySDen on Ubuntu 20.04 but failed at line 2: sudo apt-get install tk sudo apt-get install libtogl2 and sudo apt-get install xcrysden with error message: ...
- 51
2 votes
0 answers
83 views
Creating a Surface to run DFT calculations
I am creating a surface to do some DFT calculations and had some things I was uncertain on. So I have created a 111 surface by rotating the matrix using Rodrigues rotation formula so that the 111 face ...
4 votes
0 answers
56 views
Replicating thermal conductivty measurments from MD paper
I'd like to replicate the results from this paper: https://doi.org/10.1103/PhysRevB.80.165203 But I've had some issues as of now. The paper describes their set up as: 'A fully relaxed structure has ...
