Questions tagged [siesta]

For questions about using the SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) electronic structure program.

Filter by
Sorted by
Tagged with
2 votes
0 answers
20 views

Current curve (Transiesta code)

What is the difference between this figure: and this figure:
2 votes
0 answers
20 views

Quantum transport in device (Transiesta code)

I want to understand how the current (or electron) is normally transported in a device like a graphene, under the Transiesta code. It is based on which principle: a gate is applied, or there is a ...
5 votes
1 answer
84 views

TBT Transiesta Calculation error

I have a problem with a Transiesta calculation, I could not get the transmission (TBT calculation) as well DOS and current. I perform the I-V for graphene nanoribbons (electrode containing 20 atom , ...
4 votes
1 answer
68 views

SIESTA Compilation

I have recently installed SIESTA v.4.1.5 in ubuntu 22.04 LTS without any error. But, it's taking a very large time for the same SCF calculations done in past. Does this issue occur due to versions of ...
  • 135
5 votes
0 answers
27 views

simulate dynamic response to laser impulse with TDDFT in SIESTA

I am trying to simulate the dynamic response of semiconductors to laser impulse, but I am not sure how to do it with TDDFT in siesta, I checked the siesta-doc, and it seems I need to construct an ...
  • 1,843
6 votes
1 answer
175 views

How to transform the k coordinate into the k path used in the band structure?

When drawing the band structure, I need to transform the coordinate of k-points into a k-path, but I am not sure what the formula is. I checked the result of siesta,...
  • 1,843
4 votes
1 answer
38 views

How to maximise the parallel efficiency of siesta?

Are there any options I should optimize in the input file to maximize the parallel efficiency? Like in the VASP, there are two options NCORE and ...
  • 1,843
2 votes
1 answer
53 views

Any software for creating the atom configuration used in the siesta input file?

Is there any software that could generate the atom configurations used in the .fdf files? I am currently using wxDragon to convert the .cif file, but it would automatically reduce the atom number by ...
  • 1,843
2 votes
0 answers
39 views

Any software that could convert the format of pseudopotential files?

I am using SIESTA 3.2, which seems to only support the .psf pseudopotential format, is there any tools that allow me to convert the pseudopotential files into another format? Or when generating the ...
  • 1,843
9 votes
1 answer
272 views

Transiesta output through a single gold atom

I am looking for the electron transport study in a single gold atom, like the system of single carbon atom shown in transiesta paper by Nick Papior et al. Computer Physics Communications, 212, 8-24, (...
  • 135
5 votes
0 answers
41 views

How does the VIBRA module of SIESTA compute IR intensities?

I am working with Fluoro-Graphene (let's assume a fully relaxed monolayer on the XY plane with 16C-1F cell where the F is "covalently" bound to the graphene on top of it with respect to the ...
  • 1,266
8 votes
1 answer
162 views

How to resolve "Error in Cholesky factorisation in cdiag" in SIESTA?

I have worked with the SIESTA code last 2 years. Recently, I faced some errors Error in Cholesky factorisation in cdiag during graphene-BC3 heterostructure ...
9 votes
1 answer
225 views

Spin polarized calculation gives different solution in SIESTA and Quantum ESPRESSO

I was trying to optimize Vanadium doped 4x4 MoS2 using SIESTA. Plotting the band structure I was able to see the symmetry breaking at K and K'. But when I tried to do the same calculation in Quantum ...
  • 1,521
8 votes
1 answer
141 views

Citing a pseudopotential

I conduct my DFT calculations using the SIESTA DFT package. For this, I obtained the pseudopotentials from this site which says that they have obtained the data from the Abinit database. However I do ...
  • 2,528
7 votes
2 answers
174 views

SIESTA error: must be in PAO.Basis, (it has semicore states)

I keep getting this error with Siesta every time I do a calculation, ...
  • 373
4 votes
1 answer
177 views

RAMAN calculation with SIESTA and ASE-SIESTA

I have been using the ASE-SIESTA-PyNAO module to attempt some RAMAN/IR mode calculations on graphene (if anyone has any experience with this please send me a message maybe we can chat about it). At no ...
  • 1,266
7 votes
1 answer
55 views

Defining an Anion/Cation in SIESTA

I have a very simple technical question with regards to the SIESTA software. When defining an anion/cation for a given species, is it sufficient to add an electron when defining a given species? For ...
  • 1,266
9 votes
1 answer
169 views

How to treat delocalized pi bonds in DFT

For a structure such benzene, the pi bonds between the carbon atoms are said to be de-localized. Therefore the electrons are expected to be exchanged in between individual C-C bonds. When dealing with ...
  • 2,528
6 votes
2 answers
166 views

SIESTA output wavefunctions: all vs selected?

Using SIESTA, I want to plot the wavefunctions around the Fermi level (similar to HOMO/LUMO). Also, I want to do COOP analysis. From the SIESTA manual, I can setup to write the wavefunctions ...
  • 19.3k
8 votes
1 answer
257 views

How to evaluate the electron relaxation time of nanostructures computationally

I am working with Si nanowires using the SIESTA ab initio code and the BoltzTraP2 Boltzmann transport equation solver. However, the output of the BoltzTraP2 code comes per relaxation time (...
  • 2,528
7 votes
1 answer
63 views

Comments on the electronic relaxation time variation between nanowire configurations

I am studying Si nanowires with different cross sections. In my work, I plan to evaluate the thermoelectric performance variation between different configurations. To achieve this, my current approach ...
  • 2,528
9 votes
1 answer
109 views

How to identify localized surface states in the band structure

After calculating the band diagram of a structure, is there a way to identify localized surface states? I am working with Si nanowires with different cross sections. I want to determine the band gap ...
  • 2,528
6 votes
0 answers
117 views

Spin-orbit coupling in Siesta [closed]

I am going to simulate the electronic structure of the Au 111 surface including Fe-centered porphyrin on top. Since the molecule includes Fe, I first did spin-polarized calculations. Using converged ...
  • 61
5 votes
1 answer
71 views

Tool to saturate the dangling bonds at the surface of nanostructures

When it comes to studying 2D, 1D or 0D nanomaterials, saturating the dangling bonds in the surface helps remove unwanted localized surface states from the band structure 1. However, so far I have not ...
  • 2,528
9 votes
1 answer
180 views

Geometry optimization using DFT

I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows. Once it is optimized, the structure would change to ...
  • 2,528
8 votes
1 answer
148 views

Generating a Gamma centered uniform k mesh in SIESTA DFT

The SIESTA DFT software provides to incorporate a Monkhorst-Pack k grid in DFT calculations. However to use the results with the BoltzTraP2 software, a Gamma centered k-grid with uniform distribution ...
  • 2,528
9 votes
1 answer
166 views

Evaluating Seebeck coefficient using DFT

I am working with semiconductor materials using the SIESTA DFT package. I have tried the BoltzTraP2 software interface with SIESTA, however the results (Seebeck coefficient of MgO and Si) did not ...
  • 2,528
10 votes
4 answers
532 views

Generating SIESTA FDF File from xyz or vasp?

I was using SIESTA, and just learning the program in general, however, was having trouble finding a suitable way to automatically generate FDF files, I understand this can be done manually, and have ...
  • 373
8 votes
1 answer
235 views

Can transmission spectrum value exceed 1 within bias window?

I'm trying to simulate a ZnO nanoribbon structure using TranSIESTA in the siesta package. When I performed the transport calculations, for a few bias points within the bias window, the transmission ...
6 votes
1 answer
123 views

Nanowire Band Structure using Siesta DFT

I'm working with the Siesta DFT software, and managed to reproduce the band structure of bulk Si without any issues. However, when trying the same with a Si nanowire, the band structure looks nowhere ...
  • 2,528
7 votes
1 answer
311 views

How to make SCF converge in SIESTA?

I am trying to optimize some 4 atom Ni clusters. There are 4 types: one linear, one zigzag, one 2D and one 3D. Using the setup below, I don't get the calculations to converge even after 1000 SCF steps ...
  • 19.3k
10 votes
1 answer
528 views

Quantum espresso vs SIESTA

I want to know which particular calculations are suitable for each of them. Is SIESTA free, as in can you work on it without license. (question is based on the fact for now that all these will be done ...
10 votes
1 answer
415 views

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

I have been using SIESTA code to perform some practicals in my college and I have run energy cut-off tests before calculating properties of semi-conductors or insulator. As far as I am concerned, ...
11 votes
1 answer
752 views

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

I am new to DFT-simulation and I wish to understand how it works behind the scene. As the title suggests I don't understand why LCAO-based codes have to define K-points and cut-off energies. I ...
  • 113
11 votes
1 answer
600 views

Increasing k-point grid to take DOS calculation

I was trying to compute some electronic properties for Pd using SIESTA and VASP for some computer practicals in my university, specially focused on band structure and density of states (DOS) using LDA ...
9 votes
1 answer
264 views

How to calculate the band structure of a protein molecule

I want to calculate the band structure of a protein molecule. How can I do it using Siesta of Gaussian? I am thinking about QE/VASP as the number of atoms are 600 and computationally it is not ...
  • 1,643
9 votes
1 answer
98 views

Can I have a bond formed for only one spin?

I'm making a topological analysis of a nanotube interacting with some metals. The steps for the calculations were: Optimizing the geometry (I am using SIESTA code). Obtain the electronic density for ...
  • 19.3k
10 votes
2 answers
164 views

Theories for electronic transport calculations

Both software I know that do electronic transport calculations (TranSIESTA and QuantumATK) , use Non-equilibrium Green's function (NEGF) method. Are there other theoretical methods that can be used to ...
  • 19.3k
9 votes
1 answer
667 views

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

This question is complementary to a previous question. I have experience with the plane-wave DFT codes VASP and Quantum ESPRESSO. I would like to try SIESTA for the main purpose of using TranSIESTA ...
  • 8,432
6 votes
1 answer
118 views

Conductivity Computations of Molecular Wires [closed]

I am interested to compute the conductivity properties of some molecular organic wires in SIESTA. Since I am new in SIESTA, I would appreciate a guide for beginners to this field.
7 votes
1 answer
919 views

How to calculate the photoluminescence spectrum from DFT band calculations?

Photoluminescence (PL) spectrum is one of the experimental observable used, among other things, to have an accurate idea about the material band structure. It can be calculated using the band ...
  • 19.3k
12 votes
2 answers
2k views

How to calculate the effective mass from DFT band calculations?

One of the properties used in Solid State Physics, and specially in semiconductor physics, is the effective mass. It can be calculated from the energy dispersion relationship. The simple form, for ...
  • 19.3k
14 votes
3 answers
423 views

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

I am very interested in doing transport calculation with SIESTA. My problem is that it is a little hard for me to understand and setup the input files to be used with TranSIESTA (the module that do ...
  • 19.3k