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13

Band structure is a concept for periodic system only. As proteins are not periodic structures, they don't have electronic bands. The fact that you can download a PDB file (or a CIF file) with information about the crystal, it is just due to one of the ways we found to determine the protein structure that is crystalizing the protein and then using single ...


13

They do not have an easy interface, however, there are some tutorials and examples that can be used, you can use as an input parameter: github.com/siesta-project/tutorials. The input file is in .fdf, you can try to generate only the structure through nanolab> 2015 with commercial or academic version. But the calculator will always be set manually, with ...


11

This is not the exact response to your question, but I would like to present a very good youtube channel QuantumNerd. Its content is vast and interesting, concerning materials simulation. Recently, he posted a video about a project of making multi-platform GUI for Quantum ESPRESSO, he mentioned though the possibility of growing the project to other DFT ...


10

This depends a lot on how the DOS is calculated. I don't know the options one has for this when using VASP or SIESTA, but I am aware of different approaches. The central problem is that you don't know which state at a certain k point is "connected" to some other state at another k point. When calculating a DOS you have to integrate over the ...


9

If VASP is a possibility, then check out this very nice python package by Lucy Whalley: https://github.com/lucydot/effmass Associated paper is Phys. Rev. B 99, 085207 or via https://arxiv.org/pdf/1811.02281.pdf


9

Comparing what each software is capable off, is relative easy: open both webpages and look for feature pages. From SIESTA project page: Total and partial energies. Atomic forces. Stress tensor. Electric dipole moment. Atomic, orbital and bond populations (Mulliken). Electron density. Geometry relaxation, fixed or variable cell. Constant-temperature ...


9

There is no energy cut off test for calculations that employ atomic basis sets, in general: the calculation is well-defined with just the atomic basis set. For comparison, the Gaussian-basis PySCF program implements four ways to compute the Coulomb interactions in crystalline systems: Gaussian-basis density fitting mixed Gaussian-plane wave density fitting ...


6

The k-point discretization has the same meaning in plane wave codes as LCAO based codes. In fact, it has the same meaning in all DFT related codes. It defines the integration of the Brillouin zone. You want the integration to be good enough to capture the relevant physics (e.g. graphene with k-point sampling touching the Dirac point vs Gamma-only) but also ...


6

GUI4dft - A SIESTA oriented GUI GUI4dft is a new Graphical User Interface for Density Functional Theory for users of SIESTA. GUI4dft is written in Python language, falls under an MIT license and is a free cross-platform software. GUI4dft allows the user to work with standard SIESTA files and prepare manuscript-quality figures of the atomic structure and ...


6

Nice question! My answer will be based on the optical response that can be obtained with the Quantum ESPRESSO package, not the Photoluminescence specifically, but the responses can be correlated. The absorption spectrum can be correlated to the photoluminescence one since it preserves the selection rules from inter and intra-band transitions. Quantum ...


5

Effective mass is related to the electronic band curvature along a specific direction across the momentum space. For semiconductors, in general, it is worth knowing the effective mass around the $\Gamma$ high-symmetry point ($\Gamma \equiv \vec k=(0,0,0)$), for both the highest occupied band (the valence band) and the lowest unoccupied band (the conduction ...


5

Boltzmann Transport Transport of electrons in the presence of electric field and magnetic field can be described uisng Boltzmann transport equation. There are Classical and semi-classical formalisms and a detailed analysis can be found here. Codes like BoltzTrap2, BoltzWann, LanTrap etc. have implemented BTE and can be used to study thermoelectric and ...


5

Siesta relies on the LCAO method which is different from the plane wave (PW) formalism encountered in the VASP and QE codes. A noteworthy difference between the two types of methods is the convergence of precision. In PW there is basically a single value (the plane-wave cutoff) that you simply increase to improve precision. In LCAO the basis set is more ...


5

Yes, see e.g. the hydrogen molecule cation.


5

Each electron has an associated transmission probability, put in another common nomenclature is that for every channel you'll have a transmission probability between 0 and 1. So if you have 2 channels you can get between 0 and 2 and so forth. So your simulations seems perfectly fine. For bulk systems you can see the number of channels in the bandstructure. ...


4

A mixing weight of 0.25 is pretty high, if not excessively high in this case. Did you try, say 0.02, or something like that? Also, kicks are only necessary when you have problems with stalls in convergence. If you stall after 50 SCF, you should have a kick at that point, but definitely not at every 3rd SCF, that may worsen your convergence. Generally one ...


3

I believe the plane-wave codes can utilise a form of the wave-function matching technique to calculate device modes coupled to scattering states in the bulk parts, see e.g. http://dx.doi.org/10.1103/PhysRevB.74.245404.


2

I strongly suggest that you start from simple calculations instead going directly for transport calculations. Transport calculation in SIESTA are tricky: you have to define the electrodes, the main region, run optimization calculations for each one, match all of them and finally, do the transport calculation. In the SIESTA page, you can find links for ...


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