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19 votes
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How to explain Miller indices to someone outside nanomaterials?

You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal. [001] plane of NaCl: [101] plane of NaCl: [111] plane of NaCl:
Jack's user avatar
  • 15.2k
17 votes

Convert XYZ coordinates to Z-matrix

ASE The ASE library has an atom object with built-in get_angle, get_dihedral and ...
16 votes

Convert XYZ coordinates to Z-matrix

Open Babel First, the command-line version: obabel c60.xyz -oreport Yields: All interatomic distances All bond angles All connected torsions Also, partial charges ...
Geoff Hutchison's user avatar
16 votes

Convert XYZ coordinates to Z-matrix

Easiest free tool to do this (no download necessary): What you are describing, is the conversion from XYZ format to ZMAT format. How to do this, has been asked here on the Chemistry Stack Exchange, ...
Nike Dattani - No Free Time's user avatar
14 votes

Logic of published geometry optimization results without checking phonons

In general it is not justified to published the geometry of a system without performing a phonon calculation. This is where you may end up in the potential energy surface depending on which type of ...
ProfM's user avatar
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14 votes

Logic of published geometry optimization results without checking phonons

Phonon calculations tend to be very expensive to run. That being said, for gas phase molecules it is very common and expected that frequency calculations are run to ensure the molecule is not on a ...
Tristan Maxson's user avatar
13 votes

How to explain Miller indices to someone outside nanomaterials?

Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type ...
Jason M Gray's user avatar
13 votes
Accepted

Geometry optimization for n-layers in VASP

What is the best way to optimize monolayer geometry in VASP? For the geometric optimization of the monolayer in VASP, you should use the following key tags: ...
Jack's user avatar
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12 votes

Extracting molecular structure from CIF file using VESTA or Mercury

VESTA I'm an avid user of VESTA and haven't quite used Mercury. So I'll the steps to do it in VESTA (it's quite easy though) Step 1: Open your file in VESTA Step 2: Choose the selection tool in the ...
Anoop A Nair's user avatar
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12 votes

Geometry optimization for n-layers in VASP

I highly recommend reading: Efficient creation and convergence of surface slabs The following answer will assume a reasonable level of VASP knowledge (where keywords can be looked up at the VASP wiki)....
Wychh's user avatar
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10 votes
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What are the methods that can be used to ensure that an optimized geometry is a local minimum?

This depends on what you are studying. For molecular systems without periodicity, the simplest approach is to carry out a vibrational frequency analysis and confirm that there are no imaginary modes. ...
Andrew Rosen's user avatar
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10 votes
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Functional group detection from geometry

You can probably do it with only OpenBabel or RDKit using SMARTS search strings, but you can get a much easier solution if you combine OpenBabel with checkmol (which you have mentioned in the question)...
S R Maiti's user avatar
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10 votes

Inconsistencies in a famous point group table

After hours of conversation with three participants including me, I can make the following conclusions. Answer to the question It's likely an unintentional "error" in the publication. In ...
Nike Dattani - No Free Time's user avatar
9 votes

Convert XYZ coordinates to Z-matrix

Maybe this comes a bit late. There are some tools which can do this. But I was also interested in doing such a calculation using python. I first started with an iterative process which was terribly ...
rsdel's user avatar
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9 votes
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What is the "formula unit surface area"?

In the paper you linked, the relevant phrase is "$A_{\mathrm{fu}}$ is the per formula unit total surface area of $\mathrm{TiS_2}$." The "per formula unit surface area" part is ...
wcw's user avatar
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9 votes
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How to eliminate imaginary frequencies during a Gaussian geometry optimization?

Use tighter convergence criteria. If the geometry is already converged with default convergence criteria, then just using tighter convergence thresholds should work. Look at the tight option in the ...
jheindel's user avatar
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9 votes

Geometry optimization with Moller-Plesset MP4

Gaussian can do all the way up to MP5 for single-point energies, but analytic gradients are only available for MP2, MP3, MP4(DQ) and MP4(SDQ), the latter including only single, double and quadruple ...
Nike Dattani - No Free Time's user avatar
8 votes

Rotation of crystal structure to match another structure of the same compound/polymorph

If you know which atoms correspond to each other in the two structures, you can use a structural superposition method. Least-squares superposition methods find the rotation matrix and translation that ...
marcin's user avatar
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7 votes
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How do I create geometry files for carbon nanoribbons and molecular junctions for DFTB+?

Since you know how to use Avogadro to create XYZ files, a very simple solution to your problem is to simply create the XYZ file then use an xyz2gen script to ...
Nike Dattani - No Free Time's user avatar
7 votes
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Converting input file into XYZ format using ASE

Here is a more concise way of doing the same thing. from ase.io import read bec = read("bec_replaced.vasp").write("bec_replaced.xyz") It is not ...
Tristan Maxson's user avatar
7 votes

How would one find a material's equilibrium structure at any specific temperature?

You mentioned DFT, which is typically used to calculate the electronic energy at zero temperature. You can adjust the geometry until this electronic energy is lowest, but then you might ask why for a ...
Nike Dattani - No Free Time's user avatar
7 votes

Geometry optimization with Moller-Plesset MP4

Complementing the @Nike answer: Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? Yes. If yes what keyword do we have to add? You need to add the ...
Camps's user avatar
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7 votes
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Restart potential energy scan in Gaussian with additional scan points

If I'm understanding correctly, something like this should work. ...
Tyberius's user avatar
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7 votes

Print chemical formula from list of atoms in Python?

The tricky part comes if you have multiple fragments and want disconnected formulas. But in general, the Hill system for chemical formulas is used, and available in Open Babel, RDKit, etc. As ...
Geoff Hutchison's user avatar
6 votes

Is there a difference in performance when the symmetry is specified via ibrav in Quantum ESPRESSO?

There is no guaranteed increase in performance if you specify a non-zero value for ibrav. There is an additional layer to this - Whether the atomic positions are specified in cartesian or crystal ...
Xivi76's user avatar
  • 2,392
6 votes

Geometry optimization for n-layers in VASP

There is a patch of vasp used to fix any axis. For a monolayer materials, to fix c-axis is a good choice. https://github.com/Chengcheng-Xiao/VASP_OPT_AXIS When you want to optimize n-layer materials (...
LeiWang's user avatar
  • 391
6 votes

Rotation of crystal structure to match another structure of the same compound/polymorph

If you're familiar with Python, this can be done using pymatgen fairly easily. To illustrate, let's first define our problem: ...
Matt Horton's user avatar
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6 votes

Convert XYZ coordinates to Z-matrix

...
Jose Pinto's user avatar
6 votes

Convert XYZ coordinates to Z-matrix

This is not a xyz file. If you have xyz file then you can use numpy.genfromtxt() module to read from the data. create an numpy array having each component as an element of the array. Using eular's ...
Pro's user avatar
  • 1,024
6 votes

Convert XYZ coordinates to Z-matrix

RDKIT Getting the distance between atoms, angle and dihedral between atoms can be achieved with a python library called rdkit. For the sake of brevity, I will demonstrate using a simple compound: ...
Vandan Revanur's user avatar

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