Questions tagged [siesta]

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

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How to identify/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 ...
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0answers
34 views

Geometry relaxation/optimization in SIESTA

I am currently trying to get some IR / RAMAN spectra on a periodic graphene based material in SIESTA (if you have any advice on this I would love it). As I understand it, there are multiple ways to go ...
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2answers
63 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 ...
6
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1answer
91 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 (...
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0answers
40 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 ...
9
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1answer
56 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 ...
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0answers
47 views

Spin-orbit coupling in Siesta

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 ...
5
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1answer
44 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 ...
8
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1answer
113 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 ...
6
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1answer
98 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 ...
8
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1answer
102 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 ...
9
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3answers
133 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 ...
8
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1answer
218 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 ...
5
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0answers
48 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 ...
6
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1answer
68 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 ...
9
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1answer
209 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 ...
9
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1answer
294 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
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1answer
348 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 ...
10
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1answer
312 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 ...
10
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1answer
229 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 ...
9
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1answer
95 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 ...
9
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2answers
129 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 ...
9
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1answer
394 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 ...
5
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1answer
103 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.
6
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1answer
551 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 ...
11
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2answers
995 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 ...
14
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3answers
289 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 ...