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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transiesta convergence for defective graphene

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
2 votes
1 answer
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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
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Transiesta convergence issue

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
2 votes
1 answer
42 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
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Transiesta convergence

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
31 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
63 views

Graphene Band Structure with SIESTA

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
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1 vote
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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
2 votes
0 answers
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Request for Transiesta - Tbtrans error: "The electrode down-folding region is 0 in the device region"

When I run transiesta calculation, the scf converges, and the tbtrans output shows the following error, ...
A H's user avatar
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4 votes
1 answer
67 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
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3 votes
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61 views

The electrode down-folding region is 0 in the device region

When I run transiesta calculation, the scf converges, and the tbtrans output shows the following error, ...
A H's user avatar
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1 vote
0 answers
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Figure-of-merit with Transiesta/TBtrans

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
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2 votes
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Calculation of Seeback coefficient on Transiesta

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
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4 votes
1 answer
53 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
  • 907
3 votes
1 answer
91 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
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1 vote
1 answer
34 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
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5 votes
1 answer
133 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
55 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
  • 907
4 votes
1 answer
75 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
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4 votes
0 answers
43 views

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

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
84 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: ...
A H's user avatar
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1 vote
0 answers
36 views

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

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
28 views

Regarding scattering region calculation

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
126 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
46 views

Current value changes with contour values in SIESTA

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
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1 vote
0 answers
23 views

Transiesta electrodes with GNR structures

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
  • 907
2 votes
0 answers
39 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
54 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
  • 907
3 votes
1 answer
100 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
  • 907
1 vote
0 answers
24 views

Conductance and Seeback coefficient calculations with tbtrans

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
  • 907
3 votes
1 answer
207 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
56 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
  • 907
2 votes
0 answers
83 views

Transiesta SCF not converged

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 ...
A H's user avatar
  • 359
4 votes
1 answer
67 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
  • 907
3 votes
0 answers
47 views

Transiesta and Hartree potential

When performing TranSiesta calculations, I wanted to check if the Hartree potential is flat at the edges of the device cell in order to be sure that the device that I am considering is large enough. ...
Laura's user avatar
  • 907
4 votes
1 answer
233 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
81 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
46 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
103 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
  • 907
4 votes
1 answer
101 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
316 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
  • 907
5 votes
1 answer
81 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
  • 907
5 votes
1 answer
152 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
  • 907
1 vote
0 answers
60 views

Inelastica Pakage [closed]

I'm use the Inelastica package to compute MPSH states and analyze the (HOMO/LUMO). For that, I run the Eigenchannels command with : ...
A H's user avatar
  • 359
4 votes
1 answer
149 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
72 views

Siesta surface passivation

I am trying to passivate the surface of $\ce{ZnO}$ quantum dot using siesta. I generated pseudo-hydrogens with fractional charges of 1.5e (to passivate Zn) and .5e (to passivate O) using the siesta ...
Nitta's user avatar
  • 41
2 votes
0 answers
48 views

Current curve (Transiesta code)

What is the difference between this figure: and this figure:
A H's user avatar
  • 359
3 votes
1 answer
132 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 ...
A H's user avatar
  • 359
5 votes
1 answer
286 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
4 votes
1 answer
159 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 ...
sushil's user avatar
  • 157