Questions tagged [siesta]
For questions about using the SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) electronic structure program.
199 questions
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How to express velocity with non-orthogonal hamiltonian and overlap matrice?
Suppose H and S are Hamiltonian and overlap matrices for the system with non-orthogonal basis.
I am trying to use Kubo-Greenwood formula, equation (1), to compute the conductance for the 2D materials.
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Siesta PDOS analysis problems
I've been running the PDOS tutorial task
https://docs.siesta-project.org/projects/siesta/en/stable/tutorials/basic/electronic-structure-analysis/pdos/index.html
on siesta-5.0.1.
I've generated the ...
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Errors when installing siesta-5.4.1 with libelpa on Debian GNU/Linux 13 (trixie)
I try to install Siesta-5.4.1 on Debian GNU/Linux 13 (trixie).
I have installed some of the dependencies with dpkg:
...
3
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0
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84
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Persistent large dHmax and dQ in Au(111) device (TranSiesta): why does ts-scf fail to converge(dHmax,dQ are huge)?
Dear Professors and Researchers,
I am seeking your advice regarding an issue in my quantum transport calculations. I am attempting to perform simulations for a gold system, starting with a bulk unit ...
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Why is band structure computed by OpenMX different from that computed by VASP?
I am doing the cross checking for the band structure of one Monolayer Graphene/3 Layers Cobalt.
This is band structure computed with VASP.
This is the parameter settings for the input file with ...
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6
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1
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213
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How to compute the velocity operator with the non-orthogonal basis Hamiltonian?
The Hamiltonian I am dealing with has the non-orthogonal basis. Suppose $v$ is the velocity operator, $c$ is the eigenvector, $\epsilon$ is the eigenvalue, $H$ is the Hamiltonian matrix and $S$ is the ...
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siesta NEB example problem
I want to do NEB calculations so I started with the examples provided with siesta. The first example is running without problems but the second example crashes at second LUA step. Could you help me?
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How to set different temperature for electrodes?
I'm trying to explore thermoelectric effects using transiesta. I'm confused about how to set up electrodes at different temperature to get I-V curve (say, TL=300K, TR=320K). In previous posts Dr.Nick ...
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150
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SIESTA reporting cobalt fcc more stable than hcp
I'm comparing the Murnaghan curves of Co-alpha (fcc) and Co-epsilon (hcp) with SIESTA, but I find that Co-alpha results lower in energy:
Actually Co-epsilon should be more stable than Co-alpha by ...
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Gamma-point calculation with interaction between periodic images Some features might not work optimally: e.g. DM initialization from atomic data
I encountered the following error during the siesta calculation,
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Feasibility of Spin Transport Calculations in 2D Ruddlesden-Popper Perovskites
I am currently working with a two-dimensional Ruddlesden-Popper perovskite and aim to perform spin transport calculations using Au and Ni as the electrodes. In an effort to reduce interfacial strain, ...
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4
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147
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Can TranSIESTA Handle Non-Collinear Antiferromagnetism?
Can the current version of TranSIESTA perform calculations for non-collinear antiferromagnets? Specifically, which SIESTA version is required? I found an article on arXiv stating that TranSIESTA has ...
- 157
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108
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Inconsistent siesta total energy depending on number of cores
I have noticed something strange when testing siesta-5.4.0 . I used a small toy slab system and relaxed atomic positions as shown below and changed the number of cores. Siesta is complied with spack ...
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106
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Employing HSE06 in siesta
I am aware that hybrid functionals like HSE06 are now supported in siesta through libXC. I have successfully installed libxc and compiled siesta with cmake having libxc support ON. Currently on siesta-...
user14817
3
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How to interface Mn₃ZnN electrode with SrTiO₃ scattering region for TranSIESTA device setup?
I need to set up a Mn₃ZnN/SrTiO₃/Mn₃ZnN tunnel junction for TranSIESTA calculating. The central issue is constructing the device geometry by correctly stitching the Mn₃ZnN electrode to the SrTiO₃ ...
- 157
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Transiesta question
My lowest eigenvalue for a transport calculation is ~ -110 eV. Could you guid me a rule of thumb formula for the following keyword values (the values in parentheses are found in the web):
1-TS....
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1
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Error in transiesta - scattering region calculation
I am using transiesta-4.1.5, but with the scattering region job, I am getting this error. What can be the possible reasons for that?
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2
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1
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95
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Why does the magnetic structure change after non-collinear AFM band calculation in SIESTA?
I'm performing a non-collinear antiferromagnetic (AFM) band structure calculation using SIESTA on a Mn-based compound. However, I noticed that after the calculation, the magnetic structure changed: ...
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34
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There are problems when calculating the projected transmission rate using tbtrans
I am calculating a four-electrode single-molecule device based on a graphene-naphthalene molecule-graphene structure, which has a total of 338 atoms. I have already calculated the transmission rate. ...
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I encountered the problem of band crossings when using TBTrans to calculate the projected transmission
I'm calculating a four-electrode single-molecule device based on a graphene-naphthalene molecule-graphene structure, which consists of a total of 338 atoms. I've already calculated the transmission ...
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40
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Problem when performing the calculation of projected transmission using TBTrans
I am calculating a four-electrode single-molecule device based on graphene-naphthalene molecule-graphene, which has a total of 338 atoms. I have already calculated the transmission rate. When using ...
- 21
2
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0
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91
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NEB convegence problem with LUA engine in siesta
I am having problems to converge NEB calculations with LUA engine within SIESTA. The NEB forces remain high after many days of calculations. Many of my NEB calculations so far never converge. I tried ...
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6
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How to Keep Spin Vectors Fixed in Non-Collinear Antiferromagnetic SIESTA Calculations？
When using SIESTA to perform structural relaxation on non-collinear antiferromagnetic systems, I would like to incorporate magnetic effects while ensuring that the spin directions of certain atoms ...
- 157
1
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1
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95
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Elec: transfer matrix has 0 elements. The self-energy cannot be calculated. Please check your electrode electronic structure
Here I added my electrode and scattering zone files. I would like to ask if there is any problem with the settings here. Z is the transport direction, xy is the periodic direction, and here I set the ...
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115
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Question about Band Structure Oscillations in Siesta Results
I have a question regarding the band structure results calculated using Siesta. I am currently comparing the band structure of a doped monolayer Bi system (48 Bi atoms + 2 Sb atoms in a 50-atom ...
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Installing SIESTA using SPACK
I am following the instruction from here to install SIESTA using SPACK.
The command spack repo list, return, as expected:
...
anon
3
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1
answer
58
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Are PAO.Basis and PAO.BasisSizes able to be used with the same or different tag in the SIESTA input file?
The system we are working on contains a variety of atom types; for some, PAO.Basis is available on the website, but for others, it is not. As a result, we must use <...
2
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127
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Installation of siesta on apple silicon
I am trying to install siesta 5.2.2 on macbook air with apple silicon chip. But, I am getting errors while installing using cmake.
First I executed ...
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When (if ever) siesta-bdg will be deployed? [closed]
When (if ever) siesta-bdg will be deployed?
Krzysztof, WUT Warsaw
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IR intensity calculation extremely slow in siesta
I want to calculate the infrared spectrum of a material containing ~800 atoms in the primitive unit cell. I performed a geometry optimization with symmetry constraints using ase and siesta. When ...
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0
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131
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Is the following self-consistent energy calculation of a GaAs supercell correct?
I have a GaAs supercell in which the atoms are perturbed. I would like to calculate the self-consistent energy with Siesta. Will the following input do the job? I understand that convergence tests ...
3
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133
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Building Siesta with cmake: BLAS doesn't work
I've been trying to build siesta 5.2.1 with cmake on a linux cluster. I installed all dependencies (or I loaded the available ones as modules). In the installation guide it says to use the command <...
4
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1
answer
127
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Does the PAW type potential match the pseudo-atomic-orbital (PAO) basis?
I reviewed some DFT codes with the atomic-orbital basis; such as SIESTA, OpenMX. I found that the pseudopotential in these codes is the norm-conserving type one. I did not see any DFT code with the ...
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Problem building SIESTA - linking with scalapack [closed]
I am trying to build SIESTA (siesta-5.2.1) with the gnu compiler suite (gnu9.4.0) and openmpi (openmpi4.1.1). The scalapack library directory is ...
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Why Does SIESTA Automatically Modify the Unit Cell in My Calculation? [duplicate]
I am running a calculation for a 2D material in SIESTA and have explicitly defined my unit cell in the input file. However, during the calculation, SIESTA seems to modify or use an automatic unit cell ...
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Why Does the Unit Cell Change During My SIESTA Calculation
I am performing calculations using SIESTA, and I noticed that the unit cell dimensions are changing during the simulation. Could someone please help me understand why this is happening and how to ...
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3
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1
answer
154
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How to visualize SIESTA relaxation output?
After a structural relaxation calculation using SIESTA, I want to visualize (like a GIF animation or a video) the ionic coordinate and/or cell structure relaxation. I can visualize a single structure ...
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When performing the transiesta calculation, the device does not converge
I am attempting to perform an electronic transport calculation, where the electrode calculations are converging normally, but the device as a whole is not converging.
...
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1
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Band structure using NEGF method in Transiesta
I have used transiesta to calculate electronic transmission functions using NEGF approach. Is there any way to calculate the band structure of the central scattering region in transiesta supercell? So,...
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1
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Number of orbitals per atom in the electrode does not match the system electrode
I had the following question during transiesta calculation.
...
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Defining the k-path in a tbtrans calculation
The TBtrans manual mentions the possibility of defining a k-path for calculating transport properties:
path: Defines a Brillouin zone path with equi-spaced k-points. For example:
path 10
from 0.0 0.0 ...
3
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How to correctly set the high-symmetry point path block when there are breakpoints in the recommended path?
I watched Dr. Mohan's tutorial video, and the settings he provided are as follows:
...
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pseudohydrogen (Z = 1.25) surface passivation in SIESTA
i am dealing with the passivation of a GaAs surface with pseudohydrogens (i.e. hydrogens with nuclear charge Z = 1.25). However, in ATOM, i can only generate PP with Z=1.2 or 1.3, and a bigger problem ...
2
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96
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Molecular orbital *.cube file using denchar from Siesta output
I am trying to visualize specific molecular orbitals from Siesta. As I am very used to Gaussian cube files (*.cube) I want to use denchar to generate a .cube file from the .WFSX files.
The whole thing ...
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how to model gate oxide in transiesta?
The gate oxide is located between the gate electrode and the channel of semiconductor material, acting as an insulating layer to prevent current from flowing directly from the gate into the ...
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2
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What would happen if I did not set up %block TBT.HS.Files correctly?
I have calculated the SCF solution of a certain system at 21 different applied bias from 0.0 to 2.0 at steps of 0.1 eV.
However, when I set up block TBT.HS.Files, I ...
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47
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Difference in DOS and Transmission in the ballistic regime
Regarding the calculation of the transmission function, I understand that this is related to the number of modes * the transmission probability, and in the case of ballistic calculations the ...
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What can we learn from the local device density of states?
Many papers on quantum transport show results on local device density of states.
What can we learn by inspecting local device density of states?
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