# Tag Info

## Hot answers tagged visualization-software

13

Jmol is completely capable to do what you want. It reads cube file format and works with scripts. Take a look at this link related to making movies. The idea is: Your filenames must consist of a combination of text and a sequence of ordered numbers (e.g. myfiles_0001.cube, myfiles_0002.cube, etc.), Make a loop, and inside it: Load each file, Plot the ...

13

Here I provide an example with my own python scripts to realize your purpose rather than using Pymatgen (You can save data firstly with Pymatgen and plot with python). I assume that you can perform correctly the band and dos calculations with the VASP code. The example I pick up is the monolayer FM NiBr$_2$ and the final result is the following: Example ...

11

OpenBabel This masterpiece of software can convert between a huge amount of different file formats. The mains site can be accessed here. In my Linux box running OpenBabel 3.0.0, the commands for reading and writing return the following: Exporting/writing formats (obabel -L formats write): (stl -- STL 3D-printing format is in the list) acesin -- ACES input ...

11

ASE You can use ASE environment to visualize, it has different options as well. e.g., you can use this command: ase gui vasprun.xml

11

Jmol/JSmol Did you consider Jmol/JSmol? It is freely available for Windows / Mac / Linux, scriptable, may export what is being displayed in formats relevant to chemistry (e.g., .pdb, .sdf), as image (e.g., .png, .pngj, [animated] .gif) and already is in use to teach symmetry in molecules and crystals. As an example, the interactive compilations by Symmetry@...

10

Consider a graphene Hamiltonian, whose dispersion looks a lot like the one in your figure. Per these notes, its k-space Hamiltonian may be written as: $$H(k)=-t \sum_{\delta} [\cos(k\cdot\delta)\sigma_x-\sin(k\cdot\delta)\sigma_y],$$ where $k=(k_x,k_y)$, $\delta$ are nearest-neighbor vectors, $\sigma_i$ are Pauli matrices and $t$ is a hopping parameter. ...

9

I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is unclear for me (please give me some advice), in what form should these scans be visualized: colored map, or 3-d surface which can be rotated, or simply the ...

8

VMD I had to dig up the VMD script that I used for this. VMD doesn't detect the file type automatically, so you have to tell it to use VASP_XDATCAR5. In the VMD Tk Console, you can load the XDATCAR file from VASP with the following command: mol new XDATCAR type VASP_XDATCAR5 Or, if GUIs are your thing, you can open File -> New Molecule..., select the ...

8

VASPKIT VASPKIT offers a tool to plot 3D band structure using VASP. The method select K-path on a surface of the Irreducilbe Brillouin zone and calculate the K-dependent band energies on those K-points. An example 3D plot of graphene bandstructure is shown below For more details refer this tutorial A few more plots

8

I'm not sure precisely what you mean, but if you want to convert a Cube file to an ($N\times4$) matrix where $N$ is the number of points and the 4 columns are (x,y,z,value), you can try the following code snippet taken from my GitHub repository here, which I reproduce below: cube_filepath = '/path/to/mycube.cube' # Path to Cube File def cube_to_xyzval(...

8

You can install xcrysden using Xming and Cygwin without resorting to WSL and it worked well for me. Install XMing and RUN Install CYGWIN with the following packages: tcl-tk, tcl-togl, fftw3, libGL1, xorg-server, bash, bc,coreutils, grep, gzip less, util-linux, ImageMagick, tcl-tk8.6, tcl-togl, ImageMagick, xinit, mesa libfftw3_3, ...

6

ORBKIT This uses the ORBKIT package. Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. Comput. Chem. 2016, 37, 1511-1520. import orbkit as ok ok.options.filename = '/path/to/86....

6

Let start with p4vasp p4vasp is postprocessing tool for VASP output written in python and some C++. It is very easy to install and you can check in its official website http://www.p4vasp.at/#/home For ploting band structure or DOS , this package need vasprun.xml as input which is output of VASP. Once we load input, it will automatically show DOS or you can ...

6

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...

6

I second nglview for any kind of molecular visualization, it's fast and works well with large simulations. For atomistic visualization of crystal structures (e.g. small-cell inorganic crystals), Crystal Toolkit has a nice Jupyter integration that is closely integrated into pymatgen. This option is intended for people doing materials science and who want ...

6

I have found a site with a web-app interface called MuMax-view. But inorder to view the geometries, the initial shape should be created, set as the geometry and saved. Running that file results in a geom*.ovf file which could be opened in the web-app. Hope this is useful.

6

JMol To give you another option you can try Jmol which runs on Java and should be fairly straight forward to compile on a Linux machine. Although to be honest I personally do not use it, just figured I would add to the list here.

5

If you have access to CrystalMaker, you can output .stl (and other 3D formats) with bonds retained. You can then pop it into Blender or PowerPoint or any other program to view the 3D structure. Mercury also has some 3D file output formats. For some examples, you can see my post here. SAMSON now has an option to output 3D .obj files.

5

VESTA I'll list the features I played with in making the above cell, I'll update the answer whenever I find other features: The properties window allows most of the aesthetic editing options. Atoms have better sizes relative to each other when represented with van der Waals radii. Width of bonds matters on the overall appearance of the cell. Each colour (...

5

I will start by re-stating your question to make sure I understand what you mean. You have a cell with lattice vectors written in Cartesian coordinates as follows:  \begin{pmatrix} \mathbf{a}=\hat{\mathbf{x}}-\hat{\mathbf{y}}-\hat{\mathbf{z}} \\ \mathbf{b}=\hat{\mathbf{x}}+\hat{\mathbf{y}}-\hat{\mathbf{z}} \\ \mathbf{c}=1.5\hat{\mathbf{x}}+2.5\hat{\mathbf{...

5

I used the structure manipulation scripts provided by AIRSS to generate the conventional cell associated with your primitive cell. I think AIRSS uses Spglib under the hood for this task, so you could probably use Spglib directly if you wanted. Original cell New cell POSCAR file POSCAR 1.0000000000000000 10.0886200000 0.0000000000 0.0000000000 0....

5

In terms of the colours, the main elements in organic chemistry are usually represented via the following colours: H - white C - black N - blue O - red S - yellow Cl - green In terms of sphere radius, it makes sense to use a value that is specific to the atom, for example the van-der-Waals radius (e.g. 25% of the van-der-Walls radius). If you use that, ...

5

CCDC Mercury The Cambridge Crystallographic Data Centre (CCDC) provides a free-to-use visualization program Mercury that offers a wide variety of features for crystal structures including, perhaps not surprisingly crystallographic symmetry. The trick, of course, is to have appropriate crystal structures to illustrate points. CCDC does provide a free teaching ...

4

Finally got the solution to visualize pores of a membrane. The first thing you need to do is to check your lattice parameters. I had a membrane of 110*110*70 angstroms, but the pdb file contains the dimensions as 120*120*100. This is the main issue for me. Step 1 Change the lattice parameters here, build -> build crystal -> options -> lattice ...

4

For a general case, create you input inside a loop: Define the starting k point. Generate the k-points path. Export your input. Call and execute your DFT (using the input file generated in previous step). Read the output in the corresponding band structure file. Add the band data (1D array) to a column in a matrix. Change the starting k-point. Back to step ...

4

I will share here the script I use to plot bands/DOS/PDOS from SIESTA output. After working with thee raw output from SIESTA, if a spin polarized calculation was done, we have two files (one for each spin) for the bands in the form: (the file consist in three columns with k energy spin) # GNUBANDS: Utility for SIESTA to transform bands output into Gnuplot ...

4

I do not think the server setup is the problem per se. By default, IQmol is setup to submit jobs to a server that is owned by Q-Chem and those jobs are time-limited at 5-10 min. (The precise limit has varied over time.) The job failed to finish error reflects this limit. That said, I am a bit surprised that $\ce{H2}$ frequencies failed to finish. Is it ...

4

I solved the problem via a simple change in a directory name: When I installed Avogadro2 (1.93.0-3) in Linux Mint 20.1 Xfce (based on Ubuntu 20.04), it installed the auxiliary files (including the input generators) in the following directory: /home/user/.local/share/OpenChemistry/Avogadro/other However, the Avogadro2 application looks in the following ...

3

OVITO Another option is the Open VIsualistion TOol (OVITO) which has a user friendly interface, usable on multiple platform, and has some post processing and analysis tools readily available (plus a python interface to implement your own). According to the documentation it supports the following file formats : POSCAR / XDATCAR / CHGCAR

3

The web-app interface (Mumax-View) mentioned in the previous answer is fine. However, you could try to use "Muview" locally on your computer. You could find the software here. This is a very useful software to visualize the spin configuration of the geometry.

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