Questions tagged [siesta]
For questions about using the SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) electronic structure program.
92
questions
2
votes
1
answer
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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 ...
- 22.3k
3
votes
1
answer
70
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:
...
- 33.6k
1
vote
1
answer
112
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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" ...
- 33.6k
4
votes
0
answers
23
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Why am I observing spin-orbit coupling in only one direction (spin up or spin down) in SIESTA (DFT)?
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 ...
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5
votes
1
answer
77
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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-...
- 1,402
4
votes
1
answer
122
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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:
...
- 323
2
votes
0
answers
30
views
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:
...
- 15.2k
1
vote
0
answers
31
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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 ...
- 3,084
3
votes
1
answer
49
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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 ...
- 3,084
1
vote
0
answers
34
views
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 ...
- 2,895
2
votes
1
answer
34
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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-...
- 3,084
2
votes
0
answers
120
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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 ...
- 2,895
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 ...
- 476
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:
$$L_n(\mu, T)=\frac{2}{h}\int ...
- 3,084
2
votes
0
answers
34
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Request for Transiesta - Tbtrans error: "The electrode down-folding region is 0 in the device region"
When I run transiesta calculation, the scf converges, and the tbtrans output shows the following error,
...
- 359
5
votes
1
answer
62
views
I/V curve on Transiesta paper
In the paper 'Improvements on non-equilibrium and transport Green function techniques: The next-generation transiesta and in particular in figure 10b, the I/V curve of a specific model is reported.
...
- 3,084
2
votes
0
answers
55
views
Figure-of-merit with Transiesta/TBtrans [closed]
Would it be possible to calculate the figure-of-merit:
$$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.
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3
votes
0
answers
20
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 ...
- 967
3
votes
1
answer
93
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 ...
- 3,084
1
vote
1
answer
37
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 ...
- 3,084
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 ...
- 2,895
3
votes
1
answer
59
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 ...
- 3,084
4
votes
0
answers
54
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 ...
- 15.2k
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:
...
- 33.6k
1
vote
0
answers
38
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 ...
- 329
1
vote
0
answers
30
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-...
- 33.6k
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 ...
- 967
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 ...
- 3,084
2
votes
0
answers
63
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 ...
- 967
1
vote
0
answers
28
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 ...
- 967
3
votes
1
answer
238
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 ...
- 3,084
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:
...
- 33.6k
2
votes
1
answer
64
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 ...
- 3,084
3
votes
1
answer
118
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 ...
- 3,084
1
vote
0
answers
28
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 ...
- 967
3
votes
1
answer
70
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
...
- 3,084
2
votes
0
answers
94
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 ...
- 33.6k
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 ...
- 3,084
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 ...
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votes
0
answers
54
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.
...
- 967
4
votes
0
answers
87
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 ...
- 22.3k
3
votes
0
answers
47
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....
- 33.6k
2
votes
1
answer
126
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/...
- 3,084
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 ...
- 3,084
4
votes
1
answer
388
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 ...
- 3,084
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 ...
- 6,637
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 ...
- 3,084
1
vote
0
answers
63
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 :
...
- 3,084
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 ...
- 15.2k
4
votes
1
answer
78
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 ...
- 51