Questions tagged [periodic-system]

Refers to a model which is treated as infinitely repeating, for example so as to use plane-wave basis functions and capture long-range electrostatic interactions.

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Coupled cluster and periodic systems

I recently found that PySCF supports coupled cluster calculations for periodic systems (link to the documentation: https://pyscf.org/user/pbc/mix_mol.html). That seems pretty unique: of course DFT in ...
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Large energy differences across successive geometry optimization steps in SIESTA

I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5. I have arranged the molecule so that the ring plane is ...
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Computing proton-proton potentials for infinite periodic materials

For electronic structure calculation, when optimizing the wavefunction for an infinite periodic material, the proton-proton energy is needed to monitor the convergence of the SCF loop. How is the ...
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Plane wave expansion of the wavefunction for periodic material modelling

The aim is to do an electronic calculation with static nucleus with Plane wave (PW) basis functions for an infinite periodic material. The number of functions is given by the pairs of reciprocal ...
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Plane-wave basis expansion for periodic material modelling: cutoff energy inequality and number of atoms in the simulation

The calculation of electronic structure of infinite periodic material using Plane-waves is the object of study here. The cutoff energy $E_{cutoff}$ provides information about the accuracy of the ...
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Symmetric issue about the Gaussian basis Hamiltonian

The material system is described by the Hamiltonian and overlap matrice, with the Gaussian basis set. At Gamma point in the reciprocal space, the upper triangle block and the lower triangle block in ...
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How to transform a perturbed surface structure to a reference surface structure?

Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
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Is there any Python library for returning the atoms of a periodic material within a cube?

Is there any Python package that allows to cut defined by the points (0, 0, 0) and (x, y, z)? That is, it should return all the atoms of the unit cell and periodic images inside the shaded region. (...
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How to find the scaling factors for minimum image convention?

Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles). We ...
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Is it possible to find a cubic supercell for a non-cubic crystal structure?

Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
ado sar's user avatar
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What is the difference between a "periodic image" and a "nearest image" in MD simulation?

As far as I understand - In MD, when a particle or coordinate moves beyond one face of the simulation box, it reappears on the opposite face as if the box were replicated infinitely in all directions....
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Screened Coulomb interaction and its direct Fourier transform

I have a question concerning the screened Coulomb interaction in periodic systems. Many first-principle DFT codes provide the possibility to compute linear response functions, such as the irreducible ...
franz's user avatar
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3D band structure plot

I am trying to plot 3D band structure of my system of interest. I have used Quantum Espresso software for calculating the band structure and plotted 2D band diagram. But from here I am unable to ...
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How to calculate the surface area of a stepped surface slab in a unit cell? [closed]

I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
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Unit Cell Parameters for VASP Calculations

For background, I have never used VASP before and have limited knowledge of how the software works. I am working on a program for the automation of structural creation for 2D materials. I am more of a ...
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Guess cell parameters from atomic coordinates

I have a xyz file of a system that doesn't contain any cell information, but which has all its coordinates wrapped inside the same (triclinic) cell. I would like to ...
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Electric quadrupole operator for periodic systems

Considering one component of the electric quadrupole operator $\hat{r}_x \hat{r}_y$, I'm wondering if the following equalities hold: $$ \langle u_{n\mathbf{k}} | \hat{r}_x \hat{r}_y |u_{m\mathbf{k}} \...
Xiaoming Wang's user avatar
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Transition dipole matrix element

When doing DFT calculations of periodic solids, from either $\mathbf{k \cdot p}$ perturbation theory or simply using the trick $\mathbf{r} \rightarrow i\partial_{\mathbf{k}}$, one can obtain $$ \...
Xiaoming Wang's user avatar
11 votes
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Pattern X-Ray Diffraction Fitting

Assuming I have an experimental powder XRD spectra and I have a number of computational structures without any knowledge of which is correct, how can I simulate the powder XRD spectra? Once I have ...
Tristan Maxson's user avatar
12 votes
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Orbital magnetization in periodic solids

The orbital magnetization in periodic solids has been nicely described by the so-called modern theory of magnetization [1,2,3,4]. $$\tag{1} \mathcal{M}_{orb} = -\frac{1}{2} \Im \sum_{n,\mathbf{k}} f_{...
Xiaoming Wang's user avatar
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When do I use the lattice parameters obtained computationally vs experimentally?

I have been trying to simulate the properties of Bi2Se3. But the lattice parameters given in Materials Project (which I believe is obtained computationally) is inconsistent with that of experimental ...
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Moving from VASP to CASTEP for bulk crystal and surface calculations

Can someone that works with CASTEP and VASP explain to me how a workflow might change between the two programs? I am very familiar with VASP but have not used CASTEP before. As an example, assuming ...
Tristan Maxson's user avatar
23 votes
1 answer
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Why is the band structure of a supercell more dense than for simple cell?

In order to do DFT calculations of metallic alloys, the start point is a supercell, whose atoms are changed to match the desired stoichiometry. Gold and Silver, for example, both have FCC structure. ...
Anibal Bezerra's user avatar
19 votes
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What is the status of graphics processing units in plane-wave DFT?

A few years back, I performed a few calculations of metallic slabs using VASP and the Atomic Simulation Environment (ASE). I'm by no means an expert, but I noticed that the calculations were very CPU ...
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28 votes
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How accurate are the most accurate calculations?

Taking into account the fact that the theory of quantum gravity does not exist and the QED calculations are not possible for most realistic chemical systems, what levels of accuracy can we expect from ...
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22 votes
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How are charge transfer processes modeled in materials?

I'm interested in looking at current flow across a nanoscale junction, specifically a pair of electrodes linked by a molecular bridge. How is this sort of problem typically approached? I'm vaguely ...
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What are the positives and negatives of periodic DFT codes that don't use plane-wave basis sets?

Most periodic density functional theory (DFT) codes use plane-wave basis sets in conjunction with three-dimensional periodic boundary conditions. In contrast, for molecular systems of finite size, ...
Andrew Rosen's user avatar
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23 votes
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How to do periodic DFT calculations using Quantum ESPRESSO?

I have only done quantum mechanical computations using non-periodic wavefunctions. I'd like to try to periodic-wavefunction density functional theory. Quantum ESPRESSO seems like a good package ...
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