Questions tagged [visualization-software]
Questions regarding the various types of visualization software for materials modeling.
106 questions
5 votes
1 answer
209 views
Is there any tool/software that can directly visualize Z-matrix format?
If we want to visualize Z-matrix style molecule in tools like PyMol, we have to convert it into 'xyz' format first. is there any tool/software that can directly visualize Z-matrix format? Anything ...
- 323
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
59 views
How can i plot the Charge-Density with only the VASP "OUTPUT" file
My cluster is down for maintenance and I can't see any of my files at the moment. I have the pure system of my material as well as the relaxed structures for it with various defects. Once my external ...
- 163
6 votes
1 answer
195 views
What is the method to examine atomic bonds and hydrogen interactions after an optimization calculation?
I am currently working on a project to construct an energy profile for a reaction, which involves many optimization calculations. As a result, I need to verify numerous structures and ensure the ...
- 141
7 votes
3 answers
768 views
Programs for file transfer/visualization between remote cluster and laptop
I understand there have been many questions asked about what software to use to view your output data. I am more interested in programs that allow simpler transportation of files from my remote ...
- 163
4 votes
2 answers
270 views
How do I visualise VASP output using VESTA or ASE?
I work with VASP, and wanted to visualize the output (Final coordinates) that I obtain from it using either VESTA or ASE. What is the procedure to do so?
- 41
4 votes
0 answers
81 views
Periodic crystal editors and visualizer
I'm trying to find a visualizer and editor for my periodic crystals (in .cif format) for my tasks. I have used VESTA before and now to view the periodic structure, but I need an editing functionality (...
- 81
2 votes
0 answers
59 views
Problem in Xcrysden GUI
When I open Xcrysden in WSL the GUI shows some weird noisy lines, making it difficult to use. Does anyone knows how to fix this?
- 143
3 votes
1 answer
154 views
How to visualize SIESTA relaxation output?
After a structural relaxation calculation using SIESTA, I want to visualize (like a GIF animation or a video) the ionic coordinate and/or cell structure relaxation. I can visualize a single structure ...
- 4,941
3 votes
0 answers
179 views
Error in VMD when trying to visualize MD trajectory
I am trying to load a trajectory, in the form of a .trj file into VMD. VMD loads my inital .xyz molecule fine. But when I try to load into the molecule my .trj file (with Gromacs TRJ trajectory file ...
- 131
2 votes
0 answers
287 views
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 ...
- 4,941
2 votes
1 answer
88 views
How to draw the double perovskite Sr2FeMoO6 by software/hand?
https://tgc.ac.in/pdf/study-material/chemistry/Ionic_Bonding_Sem_II_G.E._and_D.S.C..pdf "In the structure of the double perovskite Sr2FeMoO6, MO6 (M = Fe2+, Mo6+) octahedra share all their ...
- 131
5 votes
0 answers
81 views
Rich editing of ASE images
I want to produce some images related to graphene-like materials. I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
- 51
2 votes
2 answers
390 views
Tool for plotting spin texture
Is there a tool that can plot a spin texture graph like these two examples below: Or does anyone know an example using matplotlib?
- 521
6 votes
2 answers
444 views
Exploring Band Structure and Density of States Visualization Tools for VASP Calculations
I'm currently working with VASP and need recommendations for the best tools to effectively plot band structures and density of states obtained from VASP calculations. Could you please share your ...
- 781