Questions tagged [structure]
Question relating to structure in materials modeling. Can be on any scale.
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How to define the space group of a new material?
I am preparing the following strcture of CdAlCRO4 using Material Studio to further study its properties. However, I am facing difficulty in deciding the space group it belongs to.
How to find the ...
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Inconsistencies in a famous point group table
The original resource
"Tables for Group Theory" By Peter Atkins, Mark Child and Courtenay Phillips (1970). I have been using this 2008 version, in which Pg. 37 has the following table:
Some ...
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Noob Question: How can I write bulk, monolayer and bilayer structure in input file for visualizing it
I'm getting my bachelor degree in physics and in my structure of matter course we never talked about bulk, monolayer and so on. I can understand Bravais lattice , reciprocal lattice and so on but I'm ...
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How to draw multiple Lewis structures from the same molecular formula?
I am learning about Lewis octet theory and the following formulae were shown as guidelines to draw Lewis structures:
$$
\begin{align}
V &= \text{total valence electrons}\\
R &= \text{required ...
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Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?
I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
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Is there a program to compare different structures?
I am looking for a program that can compare different structures and determine if they are equal or not. After performing DFT calculations, the obtained structures may be identical but for reasons ...
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Do I have to use the same functional for dielectric function calculations, as the one used for relaxing the structure?
This is a general question regarding the practices of doing optical calculations and the role of the ionic contribution to the dielectric function (with heavy reference to VASP).
Based on VASP's ...
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Are all molecules under the same peak in g(r) always found in the same solvation shell?
For a liquid, the peaks in $g(r)$ are typically associated with the solvation shells: nearest neighbors, next-nearest neighbors, and so on. However, the $g(r)$ is averaging over many configurations, ...
user2026
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How to generate a polymer in different conformations?
I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this?
Let'...
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How are bulk cut structures obtained? [closed]
I am studying nanoclusters in which I have searched the DFT energy landscape and data mining was performed. As the next step, I am trying to prepare a few bulk cut structures but I have no experience ...
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How to calculate a structure factor from a radial distribution function?
I have been trying to take an FFT of the radial distribution function to calculate a structure factor. My understanding is this is the same as the regular FFT from the time to frequency domain. The ...
user2026
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How do you calculate a radial distribution function on a lattice?
For the radial distribution function
$$g(r)=\frac{N(r)}{4\pi r^{2}dr \rho}$$
how do you do the calculation of the volume of the spherical shell in the denominator, $4\pi r^{2} dr$, when the simulation ...
user2026
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How to cut a Nano material from a cif file properly [closed]
I am not asking which software to use to or how to remove atoms from a supercell. But rather how to decide which part should be removed. Like do I give preference to some surfaces or some particular ...
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Do the U values affect structure optimization with the DFT+U simulation to optimize crystal structure?
I am trying to do structure optimization of TiO2, since titanium is a transition metal, I need to use DFT+U to simulate the right band structure, but the electronic band structure would also affect ...
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Where to find organic molecules atomic coordinates
I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules ...
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What ways are there to sort drug molecules into structurally similar groups?
I would like to use a program to automate sorting drug molecules into structurally similar groups. What protocols, or better yet, software, is available to aid this endeavour?
For instance, I know one ...
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A structural transformation package? [duplicate]
What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
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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 ...
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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?
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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 ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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' ?
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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 ...
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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(...
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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 ...
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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?". ...
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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?
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