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3

The computational chemistry software ORCA (requires the registration of an account, although both registration and the software itself is free for academic users; for a tutorial that is viewable without registration, see https://www.orcasoftware.de/tutorials_orca/index.html). In ORCA one can compute XAS/XES/RIXS at the TDDFT, DFT/ROCIS (a spin-adapted, ...


5

Atomsk Creating surface based on Miller indices is tough work if it is not cubic lattice. for example $\langle011\rangle$ direction and $(011)$ plane normal in case of $c>a$ is not same. So, in case you are trying to create orthogonal simulation box, you may end up in a situation where orthogonal box is quite large or periodicity is not found. Dependency ...


4

For most organic molecules, you can use xtb as a low level of theory to generate an optimized structure with a full frequency analysis. While xtb is semi-emperical, you might find that for a qualitative or even semi-quantitative analysis it can be quite good. You will also find calculations can be performed in at most a couple minutes for even fairly large ...


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The Atomic Simulation Environment can generate surfaces and run LAMMPS.


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Not a fully GUI solution but if we can assume you get a primitive cell to work with, Atomic Simulation Environment can generate your surface. For some extra spice, its common to want to make root surfaces such as $\sqrt{2}$x$\sqrt{2}$, so I included a final step which will do this assuming there is a valid $\sqrt{2}$x$\sqrt{2}$ to make. There is also a ...


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1. Interactive Phonon visualizer by Materials Cloud https://interactivephonon.materialscloud.io/ This tool allows to visualize the phonon dispersion calculated with an external software and display graphically the eigenstates, i.e., the normal modes of the lattice vibrations. With this tool, you can i) visualize the phonon dispersion along a path in the ...


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I also manage to do the bond lengths in a slightly different way. I also used RDKit and my code is based on this discussion. I wanted to upload my answer earlier but the holidays are busy days. First of all, as I was working with .mol files instead of the smiles I noticed that GetBondLength was giving me the wrong values. Then, I calculated the distances ...


11

Only a half answer (bond lengths), but maybe interesting for people working with the RDKit. The code was written in a Jupyter Noteboook. Calculate the 3D shape of a molecule for the bond lengths and the 2D shape for the depiction. Get the bond lengths and add them to the 2D structure. from rdkit.Chem import AllChem as Chem from rdkit.Chem import ...


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Using Jmol you can label all the bonds, angle, etc. but in 3D using the command measure: Renders a measurement between the specified atoms. See also set (measure). Two general syntaxes are available. In the older syntax, a series of two to four atom numbers are given, and the appropriate measure (distance, angle, or dihedral angle) is then displayed. The ...


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