38 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 ...
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38 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 ...
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  • 19k
28 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 ...
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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 ...
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  • 1,648
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 ...
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  • 783
17 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" ...
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  • 7,784
16 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.
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16 votes
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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 ...
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  • 4,066
12 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 ...
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  • 6,942
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 ...
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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 ...
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  • 1,788
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 ...
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8 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 ...
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  • 3,947
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 ...
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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/
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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 ...
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  • 609
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 ...
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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/...
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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} ...
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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 ...
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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 ...
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  • 4,268
4 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 $\...
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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 ...
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  • 2,891
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. ...
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  • 2,516
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 ...
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  • 19k
2 votes

How much energy difference could be used to distinguish optimized results from different initial geometries for the same structure?

The question makes no sense, since a solid state system might have different phases, or a molecule might have different conformers. They may all be proper local minima of the energy functional, and ...
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2 votes

Does the thermal evolution of molecular structures critically affect the validity of the calculated magnetic anisotropy?

Not always the research pipeline is from experimental to theory. The group of Professor Artem Oganov had very interesting results where they started predicting theoretical structures (at extreme ...
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  • 19k
1 vote

What ways are there to sort drug molecules into structurally similar groups?

According to the highly cited Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? The Tanimoto index, Dice index, Cosine coefficient and Soergel distance were ...
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