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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Siesta - Segmentation fault error

I am trying to perform a scattering region calculation but I get this error : (from .err file) ...
Youssef Chlikhy's user avatar
4 votes
1 answer
66 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 ...
Jonghwan Lee's user avatar
7 votes
1 answer
239 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 ...
Camps's user avatar
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2 votes
0 answers
23 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. ...
Mohamed Saleh's user avatar
3 votes
1 answer
68 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 ...
Lenard Carroll's user avatar
2 votes
1 answer
87 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: ...
Youssef Chlikhy's user avatar
2 votes
0 answers
38 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 ...
sushil's user avatar
  • 329
4 votes
1 answer
337 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 ...
sushil's user avatar
  • 329
5 votes
1 answer
79 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 ...
user1420303's user avatar
4 votes
0 answers
28 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 ...
Abhishek Chandel's user avatar
5 votes
1 answer
99 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
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: ...
MANOJ N MATTUR's user avatar
4 votes
1 answer
177 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: ...
abed haidar's user avatar
1 vote
0 answers
51 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 ...
MANOJ N MATTUR's user avatar
3 votes
1 answer
63 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 ...
sushil's user avatar
  • 329
2 votes
1 answer
60 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 ...
Mohamed Amine's user avatar
2 votes
1 answer
41 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-...
Shanmuka Rao's user avatar
2 votes
0 answers
177 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 ...
Elie H's user avatar
  • 1,412
2 votes
1 answer
148 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" ...
Mohamed Amine's user avatar
5 votes
1 answer
76 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
  • 1,227
3 votes
1 answer
86 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: ...
Hananab's user avatar
  • 369
2 votes
0 answers
59 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.
Laura's user avatar
  • 1,227
3 votes
0 answers
21 views

Calculation of Seeback coefficient on Transiesta [closed]

From the paper Improvements on non-equilibrium and transport Green function techniques: The next-generation transiesta, and in particular in figure 10b, an I/V curve is reported. I understand that ...
Laura's user avatar
  • 1,227
5 votes
1 answer
80 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
  • 1,227
3 votes
1 answer
98 views

Applying bias in NEGF calculation on a pristine system -- why is it wrong?

In the tutorial zerothi/ts-tbt-sisl-tutorial/ts_02, it is mentioned that "applying a bias to a bulk system is wrong" and "if you can't immediately figure this out, try and create a ...
Ming's user avatar
  • 45
1 vote
1 answer
43 views

Applicability conditions of NEGF/Transiesta: Is elastic transport necessary?

I am currently studying Siesta (specifically Transiesta) to investigate electronic transport in materials. However, I am confused about the assumptions and applicability of the NEGF method and this ...
Ming's user avatar
  • 45
5 votes
1 answer
176 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
3 votes
1 answer
64 views

Why can graphene nanoribbons be safely used as electrdes, despite having a finite band gap?

I was following the following this tutorial. As far as my understanding goes, one should use bulk-like metallic electrodes to avoid problems with screening and Fermi-level definition. Can someone ...
Laura's user avatar
  • 1,227
4 votes
1 answer
153 views

How to set the different left and right electrodes of transiestaļ¼Ÿ

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
0 answers
71 views

How to locate HOMO-LUMO molecular orbitals in Transmisson and PDOS graphs? [closed]

I have done TBtrans calculations using SIESTA (v4.0.2) and plotted transmission, as well as PDOS Vs Energy graphs. I want to know how to locate HOMO-LUMO MOs in those graphs (or) how can I say which ...
Shanmuka Rao's user avatar
3 votes
1 answer
88 views

Transiesta warning (Error on inverting X6/C7 with error: 1)

I have run into trouble when I try to do transport calculations in TranSIESTA. I got this message in the output file, before reaching convergence: ...
Hananab's user avatar
  • 369
1 vote
0 answers
49 views

how to speed up the scattering region calculation and transmission calculation in Transiesta [closed]

I am currently doing scattering region and transmission calculations using Siesta (4.1.5), the scattering region calculation is taking very long time to complete. I tried using different numbers of ...
Shanmuka Rao's user avatar
1 vote
0 answers
31 views

Regarding scattering region calculation [closed]

I am doing scattering region calculation when I checked the output file of scattering region calculation i got warning like this Begin: TS Checks and Warnings Electrode Left will not update cross-...
Shanmuka Rao's user avatar
4 votes
1 answer
154 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
2 votes
0 answers
64 views

Current value changes with contour values in SIESTA [duplicate]

My question is related to the topic solved here: DOS calculation with TBTrans Here, in the answer, the imaginary contour manipulation is proposed to smooth the DOS. I noticed, however, that doing this ...
Laura's user avatar
  • 1,227
1 vote
0 answers
31 views

Transiesta electrodes with GNR structures [closed]

As far as I understand, it would be better to use metallic electrodes in a Transiesta calculation and avoid the usage of semiconducting electrodes. It should be related to the bad screening of the ...
Laura's user avatar
  • 1,227
2 votes
0 answers
40 views

Getting Error while doing a scattering region calculation using transiesta in SIESTA version 4.1.5 [duplicate]

I am using SIESTA version 4.1.5, when doing scattering region calculation using transiesta iam getting error as: ...
Shanmuka Rao's user avatar
2 votes
1 answer
76 views

Transmittive states plotting in TBTrans

I have been using transiesta and TBTrans to calculate the transmission curves of some materials. Could I theoretically compare the Transmission states with the states in the Density of States and the ...
Laura's user avatar
  • 1,227
3 votes
1 answer
148 views

DOS calculation with TBTrans

I calculated the Transmission curves and the Density of States using TBTrans. In particular, if I have pristine graphene (just for the sake of the example), I obtain as Transmission curve and DOS ...
Laura's user avatar
  • 1,227
1 vote
0 answers
31 views

Conductance and Seeback coefficient calculations with tbtrans [closed]

Like the title says, in TranSiesta I can easily calculate the transmission curves. I know that it is related to the conductance. However, how can I calculate the conductance with tbtrans? Moreover, to ...
Laura's user avatar
  • 1,227
3 votes
1 answer
286 views

Gamma-only error for electrode in a device calculation

I am using SIESTA 4.1.5 version, I have done electrode Calculation using K-grid values 3X3X100 for both the electrodes, and currently i am doing transmission calculation, I tried different K-grid ...
Shanmuka Rao's user avatar
3 votes
1 answer
99 views

Transiesta calculation at non-zero bias

I have followed the transiesta tutorials regarding calculations with different bias. I am now using a similar input for my calculations. However, I found these input parameters ...
Laura's user avatar
  • 1,227
3 votes
0 answers
125 views

Transiesta SCF not converged [duplicate]

I have encountered a convergence problem in my structure device in Transiesta calculation, the calculation doesn't converge. Recently I try to decrease the mixing weight parameter to 0.00001. For some ...
Hananab's user avatar
  • 369
4 votes
1 answer
96 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
  • 1,227
4 votes
1 answer
465 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
0 answers
103 views

An issue of running Phonopy for graphene using Siesta [closed]

I have used Siesta in the example attached with phonopy to run phonon for graphene, and when I typed the command to create force ...
Omar Alrawi's user avatar
3 votes
0 answers
55 views

Error during siesta calculation [closed]

I am optimizing $\ce{NiCuWO4}$/$\textrm{g}\ce{C3N4}$ system but the calculation terminated showing the error SCF did not converge after the maximum number of steps. As per the suggestion given by Prof....
Jyotirmoy Deb's user avatar
2 votes
1 answer
159 views

Transiesta procedure when relaxing the structure

As the title says, I'm interested in performing Transiesta calculations with a device region that needs to be optimized. I read the slides reported here: https://departments.icmab.es/leem/...
Laura's user avatar
  • 1,227
4 votes
1 answer
152 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
483 views

What is the transiesta+tbtrans procedure?

I have tried to run some calculations on transiesta/tbtrans with a non-zero voltage. I started with a zero voltage calculation and copied the .TSDE file to run a calculation with V=0.25. However, I ...
Laura's user avatar
  • 1,227