# Tag Info

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VMD Normal Mode Wizard If you're goal is to create high quality visualizations of vibrations I recommend VMD. It's highly customizable in terms of colors, resolution, and representation. The setup however, is a little bit painful as the normal mode (NMD) input file has to be specially prepared in atomic units and has a special format (see below). The ...

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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 ...

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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 ...

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I believe that these instructions from this YouTube video "How to install Molden on Mac (OS X High Sierra)" work well For some reason the "ftp" button on Molden's website is broken however, the curl command works easily Here is a complete set of instructions from that video: Install Homebrew: /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.... 12 You can use for example pymatgen in python to do this. The tricky part of your question is to find a unit cell in step 2. I outline the steps here: Read your xyz file into a pymatgen structure. Use the SpacegroupAnalyzer class to determine the unit cell. Write the cif file using the class CifWriter. 11 NBO 7.0 The program NBO 7.0 seems to be quite well maintained, with version 7.0.9 released fewer than 30 days ago. Advantages: Has interfaces to ADF, DEMON2K, FIREFLY/PC-GAMESS, GAMESS(US), GAUSSIAN, JAGUAR/SCHROEDINGER, MOLCAS, MOLPRO, NWChem, ORCA, PQS, Psi4, QChem, SPARTAN, TeraChem, TURBOMOLE. At least 2 new releases were issued already in 2020, and at ... 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 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 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 The Jmol software is able to plot different surfaces. In the example below, the system is a Mobius strip and the ESP was calculated using MOPAC but as Jmol is full compatible with Gaussian outputs, I think there will be no problem. Mobius strip structure: Mobius solvent-accessible surface (SAS): Mobius electrostatic potential mapped on solvent-accessible ... 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 NGLVIEW I discovered it very recently when I was using MDAnalysis to play with molecular dynamic trajectories. Therefore, I am not able to write about pros/cons. Site: https://github.com/nglviewer/nglview From the site: An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. ... 9 tldr; they need to be in certain directories to be found. I don't know why the input generators were not part of the install package. Certainly on Mac, and AFAIK on Windows, they are and should be. On the other hand, Linux package maintainers often have rules about how they're supposed to handle such things and perhaps it's a separate package. In Avogadro 2, ... 9 Jmol The Jmol package is able to do what you want. You can produce the animations below just using point & click with your mouse. But you can also use its scripting capabilities to work with batch files, and make the process all automatic. As it is coded in Java, you can used in any operative system. Here are some examples. Below the results for$CH_4$($...

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I found some software that can do this kind of work: Rhino3d 3ds Max

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ADF With the Amsterdam Modeling Suite you can calculate (ADF, DFTB) and plot NBOs in the graphical user interface within the same package. Here's an example applied to NMR analysis. Here's one applied to TDDFT UV/VIS, including NTOs and NBOs. Here's one on NBO and other analysis / visualization (QTAIM) You are welcome to have a Free Trial!

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Q-Chem + Jmol The combination of Q-Chem and Jmol seems to work well (but is not yet well documented). Q-Chem In the Q-Chem input file one has to put $rem ... nbo = 1$end $nbo PLOT$end This calls the NBO program and writes out the information of interest to the files $QCSCRATCH/FILE.[31-39] NBO The content of the files written is FILE.31 Basis set ... 9 I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is unclear for me (please give me some advice), in what form should these scans be visualized: colored map, or 3-d surface which can be rotated, or simply the ... 8 This took some digging, but I can supply at least a partial answer. Assuming you can copy the list of magnetic moments to a list, you could trick whatever software you are using for visualization into outputting it indirectly. A typical POSCAR can look like the following. H 1.00000000000000 25 0 0 0 25 0 0 0 25 H 2 Selective dynamics ... 8 Solution: Install Open Babel The underlying cause is that Open Babel was not installed by default as a dependency of Avogadro 2. I think this is odd, as basic features like geometry optimization depend on it. Anyway, just installing Open Babel separately fixed the problem. To install it, open the terminal and input the following command: sudo apt install ... 8 Magnetic Anisotropy The best way to understand magnetic anisotropy is to visualize it. I think a visualization should be co-produced with every calculation of magnetic anisotropic energy. The following figure shows Magnetocrystalline anisotropy energy calculated for G-type antiferromagnetic LiNbO3-type InFeO3$^1$. Another figure shows MAE of CuO calculated ... 8 VMD I had to dig up the VMD script that I used for this. VMD doesn't detect the file type automatically, so you have to tell it to use VASP_XDATCAR5. In the VMD Tk Console, you can load the XDATCAR file from VASP with the following command: mol new XDATCAR type VASP_XDATCAR5 Or, if GUIs are your thing, you can open File -> New Molecule..., select the ... 8 VASPKIT VASPKIT offers a tool to plot 3D band structure using VASP. The method select K-path on a surface of the Irreducilbe Brillouin zone and calculate the K-dependent band energies on those K-points. An example 3D plot of graphene bandstructure is shown below For more details refer this tutorial A few more plots 8 I'm not sure precisely what you mean, but if you want to convert a Cube file to an ($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(...

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The figure you are showing can be made in Adobe Illustrator or Gimp I've recreated a crude rendition (very quickly) using adobe illustrator The steps to get this far are: create a sphere cut the sphere in half with pathfinder divider tool Revolve the half sphere with the 3d effect in the revolve menu select Wireframe surface in the revolve menu select map ...

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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 ...

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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.

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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.

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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 ...

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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 ...

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