Questions tagged [visualization-software]

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

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15
votes
2answers
511 views

What are good tools for visualizing glide planes and screw axes?

While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including: screw axes glide planes I teach a class on ...
11
votes
4answers
592 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
71 views

How to use gnuplot to draw Bandstructure and DOS from VASP outputs?

I am wondering if you could show me how to use gnuplot to draw bandstructure and DOS plots starting from VASP outputs. If you have any scripts please share them with us. Thanks.
18
votes
1answer
251 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&...
15
votes
1answer
221 views

How to separate the data plot for spin up and spin down band structure into 2 different graphs, in Pymatgen?

I am a beginner user of the Pymatgen package. In order to process the data from VASP DFT calculation software, I use Pymatgen to visualize the output band structure. When I do spin polarised band ...
9
votes
0answers
62 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
12
votes
1answer
295 views

Suggestions for a good crystal structure visualization workflow

Following up on this question about freely available crystal structure visualization codes, I wish to know what procedures people follow from start to finish in preparing images of their materials for ...
11
votes
1answer
115 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
13
votes
1answer
158 views

Visualizing MD generated electron density cubes as trajectories

During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
10
votes
1answer
72 views

Are there any conventions or guidelines to prepare images of molecular/crystal structures?

Preparing good figures is an important part of reporting molecular modeling results. There are many programs that can be used to visualize and generate images from all sorts of programs and approaches....
11
votes
2answers
267 views

3D Visualization of Molecule / Surface by 3D Model (.stl)

I am looking for a software that is capable of converting some generic atomic format such as .xyz or POSCAR into a .stl format. Ideally it would support automatic generation of bonds so that the ...
14
votes
4answers
1k views

How can I visualize the trajectory of a VASP simulation?

Which software package(s) can be used to visualize the trajectory of VASP MD simulation? VMD claims that there is a plugin to read the VASP output, while in the last version for Linux, I did not find ...
9
votes
2answers
96 views

How to visualize MuMax3 shapes?

I'm new to micromagnetics and the finite difference method. The mumax3 software lets you create a variety of geometric shapes. I would like to create a core-shell particle to study magneto-electric ...
9
votes
2answers
132 views

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: ...
9
votes
3answers
523 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, ...
7
votes
2answers
745 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....
7
votes
1answer
442 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 ...
10
votes
1answer
151 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 ...
6
votes
1answer
46 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 ...
10
votes
1answer
134 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 ...
14
votes
1answer
192 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 ...
9
votes
1answer
808 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 ...
14
votes
1answer
156 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?
16
votes
1answer
355 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. ...
14
votes
2answers
760 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. ...
11
votes
5answers
584 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?
13
votes
3answers
523 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)