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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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 ...
Camps's user avatar
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13 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 ...
Camps's user avatar
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12 votes
1 answer
1k 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 ...
Paul Logan's user avatar
11 votes
1 answer
2k 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 ...
Brentdb's user avatar
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10 votes
4 answers
1k 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 ...
Shad0w7's user avatar
  • 373
10 votes
1 answer
955 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 ...
epsilon02fft's user avatar
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10 votes
1 answer
1k 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, ...
Paul Logan's user avatar
10 votes
2 answers
250 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 ...
Camps's user avatar
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10 votes
1 answer
105 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 ...
Camps's user avatar
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9 votes
1 answer
355 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 ...
astha's user avatar
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9 votes
1 answer
470 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 ...
Ashique Lal's user avatar
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9 votes
1 answer
316 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, (...
sushil's user avatar
  • 167
9 votes
1 answer
258 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 ...
PBH's user avatar
  • 2,603
9 votes
1 answer
1k 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 ...
Thomas's user avatar
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9 votes
1 answer
243 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 ...
PBH's user avatar
  • 2,603
9 votes
1 answer
216 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 ...
PBH's user avatar
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9 votes
1 answer
269 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 ...
PBH's user avatar
  • 2,603
8 votes
1 answer
196 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 ...
PBH's user avatar
  • 2,603
8 votes
1 answer
481 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 ...
Milan Kumar Jena's user avatar
8 votes
1 answer
539 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 (...
PBH's user avatar
  • 2,603
8 votes
1 answer
250 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 ...
PBH's user avatar
  • 2,603
8 votes
1 answer
250 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 ...
Maheshuni Sankush Krishna's user avatar
7 votes
1 answer
823 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 ...
Camps's user avatar
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7 votes
1 answer
2k 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 ...
Camps's user avatar
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7 votes
2 answers
443 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, ...
Shad0w7's user avatar
  • 373
7 votes
1 answer
105 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 ...
Elie H's user avatar
  • 1,402
7 votes
1 answer
70 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 ...
PBH's user avatar
  • 2,603
6 votes
3 answers
381 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 ...
Camps's user avatar
  • 22.3k
6 votes
1 answer
185 views

Transport calculations using Transiesta

I have recently started calculating transport properties using Transiesta and TBTrans. However, I have noticed that: the TS.Contours.Eq.Pole value recommended is the default. In the last version of ...
Laura's user avatar
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6 votes
1 answer
471 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,...
Jack's user avatar
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6 votes
1 answer
226 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 ...
PBH's user avatar
  • 2,603
6 votes
1 answer
140 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.
Aggelos Avramopoulos's user avatar
6 votes
0 answers
223 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 ...
masoud's user avatar
  • 61
5 votes
1 answer
77 views

Why am I getting a wrong lattice constant from these SIESTA calculations?

I am currently learning to perform calculations on solids and am attempting to manually optimize the size of a face-centered cubic (FCC) cell of Nickel (Ni) using SIESTA (v. 4.1.5) with the Perdew-...
user1420303's user avatar
5 votes
1 answer
62 views

I/V curve on Transiesta paper

In the paper 'Improvements on non-equilibrium and transport Green function techniques: The next-generation transiesta and in particular in figure 10b, the I/V curve of a specific model is reported. ...
Laura's user avatar
  • 967
5 votes
1 answer
145 views

Regarding SISL package of siesta

I want to visualise MPSH (molecular projected self-consistent Hamiltonian) orbitals using SISL package of siesta, is there any manual or guide for it. I have searched in internet but didn't get any ...
Shanmuka Rao's user avatar
5 votes
1 answer
326 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 , ...
A H's user avatar
  • 359
5 votes
1 answer
166 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 ...
Jack's user avatar
  • 1,977
5 votes
1 answer
149 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 ...
PBH's user avatar
  • 2,603
5 votes
1 answer
70 views

Post-processing in TBTrans

I would like to write a simple code calculating Conductance and Seebeck coefficients in function of the chemical potential. To do this, I would like to use the equation: $$L_n(\mu, T)=\frac{2}{h}\int ...
Laura's user avatar
  • 967
5 votes
1 answer
84 views

Empty orbitals in Transiesta

I have noticed some difficulties in converging Transiesta calculations when including empty orbitals in the basis set, particularly when a non-zero bias is applied. In particular, I have tried to ...
Laura's user avatar
  • 967
5 votes
0 answers
63 views

simulate dynamic response to laser impulse with TDDFT in SIESTA [closed]

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 ...
Jack's user avatar
  • 1,977
5 votes
0 answers
95 views

How does the VIBRA module of SIESTA compute IR intensities? [closed]

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 ...
Elie H's user avatar
  • 1,402
4 votes
1 answer
318 views

How can I justify that in DFT entalphy is Gibbs free energy?

I am working in my final undergraduate Project about predicting belite (Ca2Si04) polymorphs using DFT calculations and I need to justify why my SIESTA run is looking for minimum enthalpy and not free ...
leire's user avatar
  • 183
4 votes
1 answer
397 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 ...
Elie H's user avatar
  • 1,402
4 votes
1 answer
80 views

Transiesta geometry optimization

Reading the transiesta manual, I understand that it would be sufficient to optimize the structure within siesta and then use the result for a transiesta run. However, I have also read that it would be ...
Laura's user avatar
  • 967
4 votes
1 answer
132 views

Query related to GGA+U calculation in SIESTA

I want to calculate the electronic band structure for CuWO4 using the GGA+U method. Is it necessary to optimize the structure using the same GGA+U method or only we can incorporate GGA+U parameter in ...
Jyotirmoy Deb's user avatar
4 votes
1 answer
174 views

The relation between applied voltage and band gap in Transport calculation (DFT+NEGF)

Hello Dear StackExchange Comunity, Based on some interesting papers related to quantum transport calculation (Transiesta published paper...), the voltage applied in the device shifts the Fermi level ...
A H's user avatar
  • 359
4 votes
1 answer
102 views

How to set the different left and right electrodes of transiesta?

I am using transiesta, which works when the left and right electrode structures are consistent. Now I want to know how to set up the different left and right electrodes, how I should prepare the ...
peng's user avatar
  • 41
4 votes
1 answer
138 views

regarding electrode setup in scattering region

I am having a doubt regarding electrode setup in scattering region calculation (transiesta) firstly, I have done molecular junction relaxation using using 3 layers of electrodes attached to both the ...
Shanmuka Rao's user avatar