19
votes
Accepted
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:
- 14.9k
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
...
- 9,045
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, ...
- 33.6k
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 ...
- 10.9k
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 ...
- 10.8k
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 ...
- 693
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:
...
- 14.9k
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 ...
- 4,448
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)....
- 2,015
10
votes
Accepted
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. ...
- 7,281
10
votes
Accepted
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)...
- 6,591
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 ...
- 91
9
votes
Accepted
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 ...
- 1,883
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 ...
- 33.6k
9
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 ...
- 33.6k
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 ...
- 1,780
8
votes
Accepted
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 ...
- 3,524
7
votes
Accepted
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 ...
- 33.6k
7
votes
Accepted
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 ...
- 10.8k
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 ...
- 33.6k
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 ...
- 22.3k
7
votes
Accepted
Restart potential energy scan in Gaussian with additional scan points
If I'm understanding correctly, something like this should work.
...
- 15.2k
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 ...
- 9,045
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 ...
- 2,342
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:
...
- 1,491
6
votes
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 ...
- 830
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: ...
- 2,895
6
votes
What is the bond length of O2--?
Starting from the point that it's impossible to obtain a "correct" bond length from a DFT calculation, due to the unknown exchange-correlation functional. By the way, in general terms DFTs ...
Only top scored, non community-wiki answers of a minimum length are eligible