Questions tagged [visualization-software]

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

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How to create the vector image of crystal structure?

I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
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3 votes
0 answers
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Atomic Simulation Environment (ASE) is unable to read a big trajectory file

The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
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8 votes
2 answers
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Limits of periodic box from pdb

I have a pdb file of some solvent molecules in a box of 20 Angstroms I have built using Tinker. I have opened the file with Chimera, Molden, Pymol and Avogadro... but I would like to see, and maybe ...
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6 votes
3 answers
346 views

Unable to install P4Vasp

I am currently learning how to use VASP and was looking at how to get the DOS plots. I have been recommended to use P4VASP but due to some reason I am not able to install it on my Ubuntu 20.04. When I ...
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10 votes
1 answer
398 views

Best software to plot Charge densities

I have obtained cube files of charge density difference using Quantum Espresso. I am trying to plot these as a contour plot in an aesthetically pleasing manner with good quality. I'm aware that ...
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4 votes
0 answers
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xcrysden on a macOS Monterey

It seems that Xcrysden is the best software to visualize quantum espresso files. I've followed the directions from Xcrysden and was able to install it on macOS Monterey using MacPorts. However, I ...
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  • 201
10 votes
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155 views

How to visualize natural atomic orbitals from PySCF

I'm trying to visualize the different methods of getting localized orbital (LO) given in the User Guide. I went through the example, saved the orbitals as cube files, then opened the files in ...
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  • 193
5 votes
1 answer
148 views

How to add a bond between two atoms in VMD?

I want to add a bond between specific atoms. I found on VMD page that one can use topotools (e.g. topo addbond 1 2 ), but I have a lot of residues so this method ...
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7 votes
1 answer
80 views

How to move atom coordinates along a normal mode given the eigenvector?

I need to displace atoms along a complicated normal mode involving many atoms. I have the normal mode eigenvector, I just don't know how to turn the eigenvector into an algorithm to translate the ...
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3 votes
0 answers
55 views

Why extra lines in PDOS plot using xmgrace

Input file for 221 MoS2 &projwfc prefix = 'MoS2', outdir = './out', deltae = 0.1, filproj = 'MoS2-pdos.dat', Another file run ...
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10 votes
1 answer
191 views

Tools to Visualize Phonons

Software such as ChemCraft or GaussView is easy to find for vibrational calculations in gas phase, but I am finding it much more difficult to find good visualization software for phonons. I have ...
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6 votes
1 answer
212 views

How to visualize protein-ligand complex MD run using VMD

GROMACS version: gmx, version 2021.4 GROMACS modification: No I'm following the Protein-Ligand Complex tutorial. I'd like to visualize the binding using VMD. I use the output from these commands: <...
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9 votes
5 answers
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Recommended software to open NetCDF files?

I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
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16 votes
3 answers
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How can I use a GUI on a supercomputer?

I am trying to make plots based to VASP simulation results, but I am struggling with how to download so much data from the server. A lot of examples on the internet are taught using the local desktop ...
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13 votes
1 answer
391 views

How to plot a Gaussian cube file with python/matplotlib?

I know there are programs that can automatically visualize .cube files (like VMD), but I'm trying to do it myself in python/matplotlib (or equivalent) to better understand what the numbers mean. I ...
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5 votes
2 answers
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How to determine the right size of gnuplot terminal output?

When using gnuplot scripts to generate graphs in PDF format, there is the size option. I would like to know how one can estimate the right size of the output graph ...
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8 votes
0 answers
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Visualizing wavefunctions in real space [closed]

I would like to generate wavefunctions as functions of spatial coordinates (X, Y, Z) using Gaussian G09 and then visualize them. How might I go about doing this? I am using Linux and my preferred ...
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8 votes
1 answer
229 views

Structure visualization software for Windows

I have been using Quantum ESPRESSO for my calculations and I do most of my processing in Linux. Recently I bought a new laptop and it came with Windows and I need to keep it like that for several ...
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7 votes
1 answer
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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 ...
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  • 974
2 votes
0 answers
70 views

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

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 ...
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  • 1,154
6 votes
1 answer
363 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 ...
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  • 1,154
13 votes
1 answer
198 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. ...
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12 votes
3 answers
1k 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
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17 votes
2 answers
607 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 ...
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7 votes
2 answers
770 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.
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10 votes
1 answer
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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. ...
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  • 589
14 votes
1 answer
230 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 ...
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  • 1,940
11 votes
1 answer
443 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 ...
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10 votes
1 answer
76 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....
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16 votes
1 answer
485 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 ...
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  • 2,673
11 votes
2 answers
432 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 ...
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16 votes
4 answers
3k 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 ...
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  • 1,029
9 votes
2 answers
174 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 ...
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  • 4,268
13 votes
1 answer
395 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 ...
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10 votes
2 answers
197 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: ...
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9 votes
3 answers
1k 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, ...
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  • 7,744
11 votes
4 answers
2k 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....
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  • 3,696
7 votes
2 answers
2k 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....
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7 votes
1 answer
1k 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 ...
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6 votes
1 answer
54 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 ...
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10 votes
1 answer
307 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 ...
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10 votes
1 answer
364 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 ...
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15 votes
1 answer
268 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 ...
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  • 359
16 votes
1 answer
452 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. ...
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  • 363
14 votes
2 answers
800 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. ...
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14 votes
1 answer
249 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?
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11 votes
5 answers
887 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?
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  • 1,411
13 votes
3 answers
951 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)
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  • 758
18 votes
1 answer
315 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&...
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10 votes
1 answer
2k 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 ...
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