14 votes

Is there a (free) GUI to setup transport calculations using SIESTA?

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,...
Denner Ferreira's user avatar
13 votes

Is there a (free) GUI to setup transport calculations using SIESTA?

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 ...
Anibal Bezerra's user avatar
12 votes
Accepted

Increasing k-point grid to take DOS calculation

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 ...
Gregor Michalicek's user avatar
12 votes

How to calculate the band structure of a protein molecule

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 ...
Camps's user avatar
  • 23.3k
10 votes

How to calculate the effective mass from DFT band calculations?

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/...
linjiang's user avatar
  • 101
10 votes

Quantum espresso vs SIESTA

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. ...
Camps's user avatar
  • 23.3k
10 votes
Accepted

Energy cut-off test meaning in atomic-like basis functions' DFT

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 ...
Susi Lehtola's user avatar
  • 19.1k
9 votes

Spin polarized calculation gives different solution in SIESTA and Quantum ESPRESSO

When running spin polarized calculations with SIESTA, the logical keyword DM.InitSpin.AF will define the initial magnetization. From the SIESTA manual (v4.1.5): DM....
Camps's user avatar
  • 23.3k
8 votes
Accepted

Better SIESTA workflows system?

This answer is based on the current state of things (and will likely change rather quickly). In the following I differentiate between a workflow and post-processing. workflow: A workflow is, IMHO, ...
nickpapior's user avatar
  • 3,286
7 votes
Accepted

Why is Energy Cut-off and K-Point Convergence necessary in LCAO-based codes like SIESTA?

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. ...
nickpapior's user avatar
  • 3,286
7 votes

Generating SIESTA FDF File from xyz or vasp?

You can use the sisl code to convert and manage fdf files. Say reading the xyz file and converting this to the appropriate fdf ...
nickpapior's user avatar
  • 3,286
7 votes

Is there a (free) GUI to setup transport calculations using SIESTA?

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 ...
Thomas's user avatar
  • 9,072
7 votes

How to calculate the photoluminescence spectrum from DFT band calculations?

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 ...
Anibal Bezerra's user avatar
7 votes

How to calculate the effective mass from DFT band calculations?

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 $\...
Anibal Bezerra's user avatar
7 votes

How to make SCF converge in SIESTA?

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 ...
nickpapior's user avatar
  • 3,286
7 votes
Accepted

Transiesta output through a single gold atom

With a single atom there might be leakage current. Probably, if you had more Au atoms the transmission would be fully suppressed. The 4 eV peak is likely close to a van-Hove singularity of the ...
nickpapior's user avatar
  • 3,286
6 votes

Generating SIESTA FDF File from xyz or vasp?

You can use OpenBabel to convert between several formats: ...
Camps's user avatar
  • 23.3k
6 votes

Evaluating Seebeck coefficient using DFT

I'm posting this here as an answer so that if anyone else runs into the same problem, they can get it clarified. After searching endlessly (because the SIESTA to BoltzTraP2 interface provided by the ...
PBH's user avatar
  • 2,653
6 votes

Theories for electronic transport calculations

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 ...
Thomas's user avatar
  • 9,072
6 votes
Accepted

How is SIESTA and TranSIESTA different from plane wave DFT codes?

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 ...
nickpapior's user avatar
  • 3,286
6 votes
Accepted

Citing a pseudopotential

Other answers are most welcome, but here I will outline the process through which I went to find a reference that you can cite for a hydrogen pseudopotential. Hopefully this will help you find ...
I have no free time anymore's user avatar
6 votes
Accepted

Transport calculations using Transiesta

On testing a few systems it showed to not depend too much on these two values. The reason is that typical systems use 300 K as the electronic temperature, and the number of poles for a fixed pole ...
nickpapior's user avatar
  • 3,286
5 votes

Can I have a bond formed for only one spin?

Yes, see e.g. the hydrogen molecule cation.
Susi Lehtola's user avatar
  • 19.1k
5 votes
Accepted

Can transmission spectrum value exceed 1 within bias window?

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 ...
nickpapior's user avatar
  • 3,286
5 votes

SIESTA output wavefunctions: all vs selected?

I believe both can technically be used. Let me first point out that your calculation must have been long and heavy ! Good luck with those. Your fullBZ.WFSX files are used for the COOP bonding analysis ...
Elie H's user avatar
  • 1,412
5 votes
Accepted

How to evaluate the electron relaxation time of nanostructures computationally

The electronic relaxation time cannot be predicted from the band-structure alone, because it depends on additional physics. The dominant mechanism for electron relaxation in materials is usually the ...
Phil Hasnip's user avatar
  • 7,262
5 votes
Accepted

Generating a Gamma centered uniform k mesh in SIESTA DFT

The siesta kgrid specification looks like this: ...
nickpapior's user avatar
  • 3,286
5 votes

Generating SIESTA FDF File from xyz or vasp?

Another option is c2x which supports both Siesta and Vasp, amongst others, and has Mac binaries for download. [Declaration of interest: I wrote c2x.] c2x --fdf POSCAR out.fdf etc. Converting from xyz ...
Michael Rutter's user avatar
5 votes
Accepted

SIESTA output wavefunctions: all vs selected?

The two different files contain different things: *.fullBZ.WFSX contains all wavefunctions for the SCF sampled Brillouin zone, i.e. for all k-points defined in the ...
nickpapior's user avatar
  • 3,286
5 votes
Accepted

How to treat delocalized pi bonds in DFT

The most common form of the self-consistent field (SCF) calculations, which are used in DFT and Hartree-Fock, assumes that each molecular orbital is a linear combination of all the atomic orbitals (...
S R Maiti's user avatar
  • 6,841

Only top scored, non community-wiki answers of a minimum length are eligible