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,...
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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 ...
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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 ...
- 21.5k
11
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 ...
- 1,146
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/...
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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.
...
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10
votes
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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 ...
- 17k
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....
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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 ...
- 2,959
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 ...
- 2,959
7
votes
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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. ...
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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 ...
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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 ...
- 3,188
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 $\...
- 3,188
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 ...
- 2,959
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 ...
- 2,593
6
votes
Generating SIESTA FDF File from xyz or vasp?
You can use OpenBabel to convert between several formats:
...
- 21.5k
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 ...
- 8,712
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 ...
- 2,959
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 ...
- 31.6k
5
votes
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 ...
- 2,959
5
votes
Accepted
Generating a Gamma centered uniform k mesh in SIESTA DFT
The siesta kgrid specification looks like this:
...
- 2,959
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 ...
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 ...
- 1,317
5
votes
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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 ...
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5
votes
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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 ...
- 2,959
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 (...
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5
votes
Accepted
RAMAN calculation with SIESTA and ASE-SIESTA
I've been using Pynao and Siesta recently. I made it work just a couple of days ago.
Regarding your questions:
I am not sure, but I think ASE has a database for elements. You said about graphene, and ...
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5
votes
How to resolve "Error in Cholesky factorisation in cdiag" in SIESTA?
Generally a failure in the Cholesky factorization happens when two orbitals are extremely similar and thus the overlap matrix $\mathbf S$ becomes singular. If you get this error first check the ...
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