40 votes

Is there a database where we can find previously determined geometries of materials?

I agree with the other answer but there are many other resources: Open Crystallographic Database which includes a large set of experimental crystal structures. There's a related Theoretical ...
Geoff Hutchison's user avatar
39 votes

Is there a database where we can find previously determined geometries of materials?

There is the Materials Project: https://materialsproject.org/ From the site: Harnessing the power of supercomputing and state of the art electronic structure methods, the Materials Project provides ...
Camps's user avatar
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31 votes
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Is there a database where we can find previously determined geometries of materials?

2DMatPedia An open computational database of two-dimensional materials. A large dataset of 2D materials, with more than 6,000 monolayer structures, obtained from both top-down and bottom-up ...
Thomas's user avatar
  • 9,072
26 votes

Is there a database where we can find previously determined geometries of materials?

Depending on what kind of materials looking for the following crystallographic databases can be relevant, too (unfortunately, for a cost): Inorganic Crystal Structure Database (ICSD) by Karlsruhe ...
Greg's user avatar
  • 1,807
24 votes

Is there a database where we can find previously determined geometries of materials?

In addition to above recommendations, I also use American Mineralogist Crystal Structure Database. http://rruff.geo.arizona.edu/AMS/amcsd.php The good thing about this place is that you can check ...
exsonic01's user avatar
  • 873
18 votes
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When should geometry relaxation not be performed?

Geometry optimization corresponds to a system in equilibrium. It is the "average" position of a molecule vibrating in a well. However, there are many cases where the system is "non-equilibrium" ...
Cody Aldaz's user avatar
  • 8,017
18 votes

Is there a database where we can find previously determined geometries of materials?

Awesome Materials Informatics The community-edited awesome materials informatics list has a section on "machine-readable datasets", many of which contain atomic structures of materials.
leopold.talirz's user avatar
17 votes
Accepted

What are the parameters that need to be calculated to design the structure of a molecule?

Ah, yes, the fun of force-field building. For the answer to a simple geometry optimization, see I. Camps response below. Skip to the end if you want what is a more general answer to building an entire ...
B. Kelly's user avatar
  • 4,366
13 votes
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Where to obtain MOF structures suitable for carrying out DFT simulations?

In the examples below, you can generate a POSCAR by using a variety of tools, such as the Atomic Simulation Environment, to convert between ...
Andrew Rosen's user avatar
  • 7,361
10 votes

What are the parameters that need to be calculated to design the structure of a molecule?

All Gaussian jobs when completed without any error, will have, at the end of the output file, a phrase/thought/quote from someone famous. It is kind off an easteregg. My latest Gaussian successful job ...
Camps's user avatar
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10 votes
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Do the U values affect structure optimization with the DFT+U simulation to optimize crystal structure?

This isn't possible to answer with any certainty without trying it. Strictly speaking, if you need a Hubbard U to correct for the spurious self-interaction, then you need it to model the material ...
Phil Hasnip's user avatar
  • 7,262
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
9 votes

Tools for structural analysis on LAMMPS trajectories

There are three main Python tools that I am aware of that can do what you want and much more (and in all fairness, since you have access to all coordinates, you can code up literally whatever you want ...
Godzilla's user avatar
  • 1,918
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 ...
Nike Dattani - No Free Time's user avatar
8 votes

Is there a database where we can find previously determined geometries of materials?

As an additional comment, the OPTIMADE consortium is developing a standard REST API to query many different databases with the same API. Version 1.0 of the specs is out (on GitHub, and a version with ...
Giovanni Pizzi's user avatar
7 votes

Tools for structural analysis on LAMMPS trajectories

You can use OVITO as well which allows you to post-process your dump file https://www.ovito.org/
Lazarus's user avatar
  • 71
7 votes

How to calculate a structure factor from a radial distribution function?

Without data to test exactly what you are doing it's difficult to say for absolute certain, but it looks to me that your main problem is that your first equation, the equation you are using for your ...
Ian Bush's user avatar
  • 775
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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6 votes
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Where to find organic molecules atomic coordinates

There are a few sites where you can find geometries, for example PubChem https://pubchem.ncbi.nlm.nih.gov/ CCCBDB: Computational Chemistry Comparison and Benchmark Database https://cccbdb.nist.gov/...
Susi Lehtola's user avatar
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6 votes

Can I do a "constrained" geometry optimization in Quantum ESPRESSO, such that certain dopants appear in certain positions even after relaxation?

Yes, you can! In the Quantum ESPRESSO input file, in the "ATOMIC_POSITIONS" card, you have to present the atom name and its coordinates, something like: ATOMIC_POSITIONS {crystal} ...
Anibal Bezerra's user avatar
6 votes
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How do you calculate a radial distribution function on a lattice?

As others have commented, discretization does not matter. Below you can see a picture that tries to explain this point. The $\mathrm{d}r$, or more correctly for the approximation we are making the $\...
Erik Kjellgren's user avatar
6 votes

How to characterize surface features in proteins?

Normally, if various proteins have the "same" cavities/clefts, this means that they are part of the same family and the amino acids that form the cavity are conserved. I really don't think ...
Camps's user avatar
  • 23.3k
6 votes

Noob Question: How can I write bulk, monolayer and bilayer structure in input file for visualizing it

Indeed, this input represents a bulk structure The trick here is that the input is using fractional coordinates: ...
Camps's user avatar
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5 votes
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How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?

1) Using CALYPSO with Quantum ESPRESSO I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster ...
Anoop A Nair's user avatar
  • 4,476
5 votes

Are all molecules under the same peak in g(r) always found in the same solvation shell?

Yes, it is possible for configurations which contribute to a particular peak in $g(r)$ to be outside of that solvation shell. As pointed out in the comments, this is only possible if you have a ...
jheindel's user avatar
  • 3,534
5 votes

Linear interpolation between two molecular structures in internal coordinates

I am not exactly sure what type of interpolation you want, but I believe you want an interpolation to generate an intial path that can be later relaxed via nudged elastic band (NEB) or a similar ...
S R Maiti's user avatar
  • 6,851
4 votes
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Order of diffraction pattern confusion in XRD experiment

In Bragg's law, $n\lambda=2d\sin(\theta)$. Here, $n$ is the order of the reflection, and corresponds to the path length difference between X-rays diffracted from two different layers of atoms, in ...
Kevin J. May's user avatar
  • 3,161
4 votes
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How to convert a hexagonal unit cell to rhombohedral unit cell?

The VESTA package should be able to do it. But I'm not sure if it had rhombohedral or not. I recommend that you download and try Edit data -> Unit cell option. ...
PBH's user avatar
  • 2,653
4 votes
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Is there a software that has implemented forces of TDDFT calculations for solids?

The SIESTA code has a branch (rel-Max-2) developed by researchers from Max Plank institute that include the calculations of forces and real-time TDDFT. The TDDFT is merged into the main development ...
Camps's user avatar
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