Questions tagged [visualization-software]

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

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7
votes
1answer
70 views

How to visualize pores using material studio?

I am a newbie to material studio. I have a membrane, coordinates are in pdb format. I am trying to visualize the pores of this membrane. I tried Atoms and Volume surfaces, but the result was that the ...
2
votes
0answers
45 views

How to plot a charge density from a CHGCAR file in Python?

I can convert a CHGCAR file on the NxNxN grid into a 3D array of shape (N,N,N) for better handling, if that helps. At the end of the day, I want plot/visualize the ...
6
votes
1answer
295 views

Can a file in the Gaussian CUBE format be voxelized?

My aim is to voxelize a CHGCAR file. I am trying to build up a workflow to do the same. With the aid of the Matter Modeling community members, I have figured out a way to convert a CHGCAR file into ...
13
votes
1answer
134 views

Generating numpy-compatible electron density from Molden / QC calculation

I'd like to use a variety of Python tools (e.g., matplotlib and Mayavi) to analyze orbitals plot electron density contours, etc. ...
12
votes
3answers
376 views

How to create a 3D band structure from DFT band structure calculation?

How can I create such a 3D plot using matplotlib? Like the one in Figure (a) below: I want to create it using DFT bandstructure calculation result
17
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2answers
533 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 ...
7
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2answers
120 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.
10
votes
1answer
116 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. ...
13
votes
1answer
163 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 ...
11
votes
1answer
176 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 ...
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....
16
votes
1answer
289 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 ...
11
votes
2answers
313 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 ...
15
votes
4answers
2k 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
115 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 ...
12
votes
1answer
311 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 ...
9
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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
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3answers
695 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, ...
11
votes
4answers
779 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
973 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
597 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
52 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
194 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 ...
10
votes
1answer
193 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
213 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
390 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
769 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. ...
14
votes
1answer
171 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
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5answers
636 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
618 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)
18
votes
1answer
267 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&...
9
votes
1answer
1k 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 ...