Questions tagged [structure]

Question relating to structure in materials modeling. Can be on any scale.

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5
votes
1answer
51 views

How to convert a hexagonal unit cell to rhombohedral unit cell?

Hexagonal unit cells can be converted to rhombohedral unit cells, and the latter unit cells have fewer atoms. But how can I convert them? Is there any software or codes that are able to do this ...
6
votes
2answers
267 views

Geometry optimization with Moller-Plesset MP4

Can we optimize a molecular structure using Moller-Plesset MP4 method on GAUSSIAN software? If yes what keyword do we have to add?
7
votes
1answer
48 views

How to determine the more stable configuration between a flat and a buckled monolayer with DFT?

Using first principles methods (quantum espresso code) I would like to find if a monolayer of a material is flat or buckled. Using the van der Waals interaction in the calculation I found that the ...
10
votes
1answer
98 views

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

I am studying the magnetic properties of bulk ZnO, so I am doping it with transition metal elements in order to observe the magnetic spectrum. I replace a Zn atom with a transition metal element at ...
5
votes
1answer
78 views

Order of diffraction pattern confusion in XRD experiment

Somewhere I came across this phrase: "expected diffraction angle for first order reflection." With respect to XRD do I take this as a rule of thumb that the diffraction will always be a ...
9
votes
1answer
308 views

Where to obtain MOF structures suitable for carrying out DFT simulations?

For bulk and two-dimensional materials, we can download the structures from many databases, such as Materials Project and CMR. Are there also similar databases for MOF (metal-organic framework) ...
6
votes
0answers
103 views

Is this statement correct: "All structural variations are energy driven"? [closed]

In modelling using molecular mechanics can one state that "all structural variations are energy driven?". The statement is related to protein-ligand binding in modelling. Sometimes one can ...
14
votes
1answer
178 views

Is there a software that has implemented forces of TDDFT calculations for solids?

I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
8
votes
2answers
244 views

Tools for structural analysis on LAMMPS trajectories

I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
10
votes
1answer
237 views

How do I predict the structure of a nanoparticle with Calypso and 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 structure is Calypso which is PSO-based. I'm ...
4
votes
1answer
83 views

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

Is there a threshold? Could I say that my final geometries are the same with 'energy difference = 0.05 meV/atom' ?
15
votes
1answer
91 views

How to characterize surface features in proteins?

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...
14
votes
2answers
289 views

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

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
16
votes
1answer
94 views

When should geometry relaxation not be performed?

My understanding is that geometry relaxation (i.e. letting the nuclei follow the force gradients of the PES until they reach local minima) should usually be performed in order to get the correct ...
16
votes
1answer
44 views

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

This is a particular aspect I'm interested in, from the more generic question "Does the thermal evolution of chemical structures critically affect the validity of the calculated physical properties?". ...
53
votes
7answers
862 views

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

For small molecules, NIST has a database of experimentally determined geometries here, and ab initio geometries here. I wonder if there is something similar for materials?