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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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4 votes
1 answer
25 views

Electronic transport calculations With Transiesta and Spin-Orbit

What is the version of SIESTA that is capable of performing transport calculations with TranSIESTA, including spin-orbit coupling?
3 votes
0 answers
64 views
+50

Plotting Siesta Band Structure in Origin

I have obtained .bands file for my system using SIESTA. I furthur used the utility gnubands to convert it into ...
2 votes
1 answer
53 views

How to add more electrode layers between the electrode and the scattering region for graphene nanoribbons?

I am repeating results from the paper : 10.1103/PhysRevB.81.205437. my transport device is described in the following image: The following is part of the output. ...
3 votes
1 answer
69 views

Mesh cutoff convergence in SIESTA

By increasing mesh cutoff, the total energy of system is becoming less negativei i.e, increasing. My Siesta File settings for monolayer ZnO are as: ...
2 votes
1 answer
35 views

Transiesta issues: system coordinates of atoms does not coincide with the electrode coordinates found in systemlabel.TSHS

I am repeating results from the paper : 10.1103/PhysRevB.81.205437. my transport device is described in the following image: First, I do a calculation on the electrode. Here is the POSITION file. <...
2 votes
1 answer
71 views

Why does SIESTA 5.0.1 fail to run in parallel but working in serial execution?

I am trying out SIESTA for the first time and while it seems to run without any problem for a serial execution, I am encountering an error everytime I am assigning more than 1 processor. So, the ...
4 votes
1 answer
68 views

Vacuum region in SIESTA

I have been using QuantumEspresso (QE) for quite some time, but I have been thinking about trying SIESTA for some of my structures that are in a slab geometry with vacuum on either side. QE will use ...
4 votes
1 answer
79 views

How may I get reasonable lattice constants of hybrid halide perovskite material ((BA)2PbBr4 here) using SIESTA?

I am relaxing the structures of hybrid halide perovskite material,(BA)2PbBr4 here. I tried to use GGA-PBE or LDA-PW92 exchange functionals, and pseudopotential files come from ...
3 votes
0 answers
23 views

Visualization of phonon modes in siesta

When I try to visualize phonon modes using vib2xsf utility in siesta (DFT code) for a nanowire system, the utility gives an error "Error reading real part of eigenvector 1 iat= ...
3 votes
1 answer
121 views

How should I use SIESTA and Wannier90 for calculation of a system with spin-orbit coupling?

I have tried to calculate for a system with spin-orbit coupling (SOC) using SIESTA and Wannier90, but an error non-collinear spin not implemented yet appears in a SIESTA output file. I would be very ...
5 votes
1 answer
202 views

How may I increase the speed of SCF iterations in SIESTA?

I have experience with VASP and CASTEP, but since I need to use TRANSIESTA to calculate transport properties, I tried to use siesta. I heard that siesta is very fast and can handle large systems, but ...
2 votes
0 answers
26 views

Default ways to compute decomposition and formation enthalpies in Siesta

I was examining the material project database and saw the thermodynamic stability section of crystalline silicon. I noticed that they compute formation and decomposition enthalpies. I wonder if there ...
2 votes
0 answers
30 views

Can Siesta be used to compute XPS spectrum in periodic system?

I am still familiarizing myself with DFT calculations in periodic systems using pseudo potentials. I want to compute the XPS spectrum for our iron oxide surface using SIESTA. I generated my pseudo ...
4 votes
1 answer
44 views

siesta 5.0 compilation issues with spack

I installed spack and a more recent gcc (v13). I followed the steps in the doc. I started with the installation of the serial version using: $ spack install siesta -mpi build_type=Debug However, ...
4 votes
1 answer
101 views

Format of generated .HSX file?

.HSX file in Siesta Where can I find info about the format of the output file .HSX file generated by Siesta
5 votes
1 answer
52 views

Siesta 5.0 compilation fails with "Deferred-length character component 'message' at (1) is not yet supported" message

I am trying to compile the new siesta 5.0 but the compilation fails right from the start with "Deferred-length character component 'message' at (1) is not yet supported" error message. The ...
3 votes
1 answer
132 views

Is there a repository for PSML pseudopotentials files?

I am looking for repositories with tested pseudopotentials in PSML format to be used with SIESTA software. At least in my notebook, the Pseudo-Dojo that claim to support pseudopotentials for different ...
3 votes
1 answer
45 views

Gate voltage on a quantum dot device, including the electrodes

I am trying to simulate the effect of a gate voltage on a quantum dot device, including the electrodes. To do so, I am using the method described in the article "Manipulating the voltage drop in ...
13 votes
2 answers
3k 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 ...
5 votes
0 answers
32 views

What are good test cases for benchmarking and scaling studies of SIESTA on up to a few thousand cores?

Subject says it all. I'm looking for SIESTA test cases suitable for benchmarking and scaling studies on clusters having up to a few thousand cores.
5 votes
1 answer
62 views

Generating a plot of the Hartree potential in a certain direction

Good morning everyone, it's my first question here, so please forgive me all the possible errors. For training purposes, I've done a Siesta+Transiesta calculation (using Siesta 4.1-b4 version) for a ...
2 votes
0 answers
20 views

Siesta-grid generation time

Dear Siesta Users/Developers I use siesta with ASE to do a NEB job. In a NEB calculation, many image files are generated and each one should be converged. The most of time for my calculation is ...
4 votes
1 answer
179 views

Transiesta, not converging with semi-conductor electrodes

Hello transiesta users. I am trying to calculate the I-V curves of 2D blue phosphorene(electrodes are made of the same material the semiconductor 2D blue phosphorene ) by using transiesta code. First ...
4 votes
1 answer
65 views

Siesta - Segmentation fault error

I am trying to perform a scattering region calculation but I get this error : (from .err file) ...
6 votes
1 answer
452 views

TBtrans/Transiesta, error: "connectivity is not perfect"

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
85 views

How can I solve the error in TRANSIESTA calculations? [duplicate]

Recently, I've been trying to calculate the transmission coefficients for the molecular junction (Au lattice - molecule - Au lattice) using SIESTA, TRANSIESTA, and TBtrans. As you know, the procedure ...
7 votes
1 answer
273 views

Better SIESTA workflows system?

Normally, I run all my SIESTA calculations manually and then go to post-processing the results, also manually. I would like to know which of the tools below is "better" (more complete?) in ...
2 votes
0 answers
49 views

SIESTA basis set optimization (Enthalpy vs total energy)

Using SIESTA for bulk Si (not optimized, downloaded from materialsproject.org), I am trying to optimize the DZP basis set using the PAO.EnergyShift parameter. ...
3 votes
1 answer
74 views

How to write .TBTGF files using sisl for TranSIESTA

Good day, I trust you are doing well. I am trying to calculate transport properties for a 3D structure stacked between two gold electrodes along the c-axis. The 3D structure and the electrodes should ...
2 votes
1 answer
132 views

Transiesta scattering calculation not converging

I am trying to perform electron transport calculations. At the level of the scattering region calculations, I have noticed that the values of energies are no longer changing: ...
2 votes
0 answers
44 views

Treatment of f-electrons in SIESTA

Please suggest me, how to treat pseudopotential and basis for f block elements like Sm in simulating Sm2O3. I used the psml pseudopotential from pseudo-dojo database, which gives quite accurate ...
2 votes
1 answer
75 views

Transiesta convergence [duplicate]

I'm trying to find the I-Vg curve of a specefic system using transiesta implementation of gate. The problem that I encountered is the non-convergence of calculation even though they get below the ...
3 votes
1 answer
99 views

Error in TranSIESTA: "The electrode down-folding region is 0 in the device region"

When I run a tranSIESTA calculation, the SCF converges, and the TBtrans output shows the following error: ...
2 votes
1 answer
177 views

Gate potential wiith siesta/transiesta

I want to study the effect of adding a gate to quantum transport device, the problem that i encounter is that in siesta manual there are two methods to do so, the first is "Geometry.Charge" ...
1 vote
0 answers
57 views

Transiesta convergence issue [duplicate]

I have a graphene system (94 atoms - defective graphene) I was able to converge both right and left electrode runs in just 8 iterations. But the scattering run (transiesta) is not converging even ...
4 votes
1 answer
371 views

Charged defects in siesta

I want to calculate defect formation energy for a substitutionally doped system (bulk) in a charged state. Is it possible to do such calculation using SIESTA code? If yes, what changes do I make in my ...
9 votes
1 answer
709 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 ...
5 votes
1 answer
94 views

Large energy differences across successive geometry optimization steps in SIESTA

I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5. I have arranged the molecule so that the ring plane is ...
4 votes
0 answers
38 views

Why am I observing spin-orbit coupling in only one direction (spin up or spin down) in SIESTA (DFT)? [closed]

Can someone provide guidance on how to include Spin-orbit Coupling (SoC) for the band structure calcualtion using SIESTA? I have used the #Flag #Spin spin-orbit, but I only obtained spin dependence in ...
5 votes
1 answer
111 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-...
4 votes
1 answer
256 views

Transiesta with siesta version 4.1.5 not converging

Good evening everyone, With previous Transiesta versions, we would not have issues with finding the transport involving graphene. However, this was not the case with the latest version. We tried: ...
2 votes
0 answers
47 views

transiesta convergence for defective graphene [duplicate]

I have a defective graphene system - 94 atoms (32 in both electrodes and 30 in scattering). The transiesta run is just not converging. I get this message: ...
3 votes
1 answer
83 views

Implemetation of NEGF in TranSIESTA

I have a general query regarding NEGF approach: In TranSIESTA code, when self-energy of the electrodes is calculated, does it require the coupling elements of the electrode with the central scattering ...
2 votes
1 answer
54 views

How to attach new layers of electrodes to the optimized molecular junction (molecule with few layers of electrode) scattering region

initially, after optimization of the pristine molecule, I attached a few layers of electrodes to either side of the molecule to make a scattering region after optimization the electrodes will be re-...
2 votes
0 answers
226 views

Graphene Band Structure with SIESTA [closed]

I am struggling with getting a correct band structure for even pristine graphene using SIESTA. The issue is almost certainly the K point path. My graphene sheet (128C atoms) isn't the traditional ...
4 votes
1 answer
195 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 ...
5 votes
1 answer
81 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 ...
5 votes
1 answer
95 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. ...
2 votes
0 answers
62 views

Figure-of-merit with Transiesta/TBtrans [closed]

Would it be possible to calculate the figure-of-merit: $$ZT =\frac{S^2\sigma}{\kappa}T,\tag{1}$$ with Transiesta and TBTrans? If not, which other programs can be used? I've only read about Gollum.