Questions tagged [visualization-software]

Questions regarding the various types of visualization software for materials modeling.

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7
votes
3answers
210 views

Molecular visualization software in Jupyter (IPython) Notebooks

Jupyter notebooks have always been a great way for me to create high-quality graphs, and write code. The features also continue to improve with packages such as Jupyter Lab, and now Jupyter Books, ...
8
votes
1answer
151 views

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
7
votes
2answers
328 views

Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
6
votes
1answer
87 views

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 ...
6
votes
1answer
34 views

Create an image from scratch with the vectors that represent the Berry phase for parallel transport (classic system)

I want to represent parallel transport as in the following figure, but next to this figure I would like to place a diagram with the two arrows (of the initial state and of the final state that are ...
9
votes
1answer
91 views

How to automatically plot atomic structures with magnetic moments?

I work with magnetic materials and I haven't found a way to automatically plot structures with their corresponding magnetic moments. For this specific project I am using VASP. I am trying to plot ...
11
votes
1answer
62 views

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
11
votes
1answer
138 views

Great computer graphics for matter modelling

I am trying to write some code to automatically generate a judicious set of graphics from DFT/fn-DMC calculations so that users can sanity check their results quickly. My literature review has found ...
16
votes
1answer
227 views

How to map the electrostatic potential from GAUSSIAN, on a solvent accessible surface?

Gaussian cubegen and surface generators in Gaussview seem to only allow to map the ESP on SCF densities. I used G16 for the ESP generation. I would like to plot it on the solvent accessible surface. ...
11
votes
2answers
720 views

What is the most user friendly software for frequency visualization rendering?

I perform my calculations in Q-Chem and would like to make short movies of IR modes. As of now, I render them with IQmol, but I believe graphics properties (colors and resolution) can be much better. ...
13
votes
1answer
121 views

Software to draw 3d micelle configuration

I am looking for a free software able to draw 3d micelle configuration like the figure attached. Any suggestion?
11
votes
5answers
504 views

Plotting of natural bond orbitals (NBOs)

Which quantum chemistry programs can compute natural bond orbitals (NBOs)? Which visualisation tools can I use subsequently to plot pictures of the NBOs?
12
votes
3answers
410 views

9 x 9 x 9 periodic xyz file to cif file format

I have a 9 x 9 x 9 periodic crystal structure in .xyz format and I would like to change it to .cif file format. Does anyone know how to convert the file? (e.g. 9 x 9 x 9 to unit cell then cif)
14
votes
0answers
119 views

How to set up a local server for iQmol on macOS?

I'm trying to set up iQmol as a tool to submit calculations to Q-Chem on our lab machines to make access to it easier for OChem students. Unfortunately, it is not working properly "from the box&...
8
votes
1answer
131 views

Molden installation on macOS?

Today I tried to get an access to Molden to install it and use for processing the results of my calculations. Unfortunately the ftp seems to be down or is it only my personal connection issues? My ...