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11
I read the manual on polarization, but it only covers calculations for primitive cells, and I don't know if the polarization term can calculate polarization on the interface.
1st question : Is it possible to calculate polarization at the interface of a heterostructure in QuantumATK?
2nd question : How is the area for calculating polarization in QunatumATK polarization? ex) entire bulk configuration
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Hi Cam,

COSMO is QATK is enabled for slab geometries. To set up a slab geometry it is assumed that the surface normal is aligned along the positive C direction. The COSMO surface is then placed on the surface that has the highest C value. Note that if you have a thin film like geometry, only one surface will be placed on the top side of the film. When setting up a slab this can be created using either a SurfaceConfiguration or a BulkConfiguration. In both cases Dirichlet/Neumann boundary conditions should be used along the C direction. Dirichlet can require that the potential is zero at the boundary, anchoring the to total potential to a specific value. Neumann can require that the potential gradient is zero at the boundary. These are both non-periodic boundary conditions and can be used with structures with an overall charge. The A and B directions can use periodic 2D-FFT boundary conditions. In the SurfaceConfiguration the slab is connected to the electrode, which models the extension of the material in the negative C direction. In a BulkConfiguration the bottom side of the surface needs to be terminated in a way so that the top solvated side is relatively unaffected by the termination. It is also recommended that enough vacuum be added on the top and bottom sides to allow the boundary conditions to be easily satisfied at the ends of the cell.

A thin film geometry with solvent on both sides of the surface can be represented as a fragment in a MoleculeConfiguration. Here the transverse directions of the film should be terminated so as not to significantly alter the electron density at the center of the fragment. In a MoleculeConfiguration the entire structure is surrounded by the COSMO surface, which in this case approximates solvent at both sides of the film. If the overall fragment (including any adsorbed molecules) is neutral, then the normal FFT boundary conditions can be used. If the overall fragment carries a charge, then Multipole boundary conditions should be used. The reason is that FFT boundary conditions assume a periodic potential, which is a good approximation for most neutral molecules. Charged molecules have additional long-range electrostatic interactions that are taken into account with the Multipole boundary condition.

I hope that helps you with your simulation.
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General Questions and Answers / Change the temperature of the device.
« Last post by 知昂 on March 23, 2025, 05:51 »
Hello, Quantum ATK Community,
How can the temperature parameter be changed in ATK software to calculate the transport properties at different temperatures when it is set at 0K by default for device transport property calculations?
Thank you!
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Point 2 is probably not a way forward, you'd just end up reimplementing the feature we have.

What did you try so far? The whole point of the effective band structure is that the supercell has a lot more atoms than the original primitive cell, so that is not a fundamental limitation.

Do you have any reference publication for the plot you want to make? I am not sure this is a clearcut application of the effective band structure method. What information will you gain from the effective band structure which is not seen from just doing the corresponding calculation of the supercell (which you need to do anyway)?
Thank you for your reply. In general, I plot effective bandstructure to see the change in curvature of bandstructure, direct/indirect bandgap.

The initial error message I receive when performing the calculation are as below:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 274903 RUNNING AT node05
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions


The above issue was resolved by setting processes_per_kpoint to 2 increasing the threads per process. This leads me to the following questions:
1. Memory Issues? Does this observation suggest that the original error was due to insufficient memory allocation?
2. Optimizing Parallelization: What are the best practices for determining the optimal processes_per_kpoint value and the corresponding number of nodes to use for maximum computational efficiency? Are these parameters related to the k-points of the bulk configuration, the k-points used for the effective band structure calculation, or both?
3. Effective Band Structure Limitations: The effectivebandstructure module has a specific requirement: the 'configuration' must be divisible into an integer number of smaller unit cells, each identical in size and number of basis functions, as defined by the 'primitive_configuration'. This limitation is not present when plotting effective band structures derived from standard Plane-Wave DFT band structure calculations (e.g., VASP). Could you briefly explain the reason for this limitation within the effectivebandstructure module?"
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Can you share the HDF5 files so I don't have to rerun all calculations?
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Point 2 is probably not a way forward, you'd just end up reimplementing the feature we have.

What did you try so far? The whole point of the effective band structure is that the supercell has a lot more atoms than the original primitive cell, so that is not a fundamental limitation.

Do you have any reference publication for the plot you want to make? I am not sure this is a clearcut application of the effective band structure method. What information will you gain from the effective band structure which is not seen from just doing the corresponding calculation of the supercell (which you need to do anyway)?
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Tough question. Since there are many potentials for SiO2 you may want to play around with different ones. Perhaps having partial charges like in COMB will be helpful. Or not. One simple needs to run the simulations to find out.
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Dear Experts,

Good morning, hope you are doing well.  Just to ask: How to modify the surface or immobilize the protein or anti body at the surfaceof CNT? Using Quantum Atk
Ref-
https://www.tandfonline.com/doi/pdf/10.1080/20550324.2018.1478765#:~:text=The%20present%20article%20provides%20an%20overview%20on%20the,applications%20and%20concerns%20in%20the%20field%20are%20addressed.


Regards


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Dear all,

I am trying to study the effect of functionalisation on monolayer MoS2 within a solvent (water). For that, I have added vacuum in the C direction to limit the interactions between layers. I would like to account for the screening effects of water through COSMO solvation model. However, I am struggling to find information about including this model for 2D systems. From my understanding:

1)  If I use 2D-FFT boundary conditions for A and B, and Dirichlet and Neumann for bottom and top, respectively, in the C direction (as suggested for bulk systems), my MoS2 slab will be modelled as the surface layer which continues into the bulk. Additionally, when I functionalise the material, my solvation surface is orientated in the wrong direction, regardless if I set Neumann at the top and Dirichlet at the bottom or vice versa, my solvation layer appears on the side of the slab where no functionalisation.

2) I have also tried to use Multipole boundary conditions with the conjugate gradient Poisson solver (suggested for charged molecules). However, I run into compiling errors.


Would you be able to advise on the correct boundary conditions to use in this case?
Thank you very much,
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I never use the Slater Koster Model, so I can only provide limited suggestion. As the other comment had pointed out, you may need to increase vector_a and vector_b to reduce interaction between neighboring cells. I also don't see any calculation regarding the device hamiltonian, so it is hard to tell whether convergence happens.

Thanks for your kind reply. Highly appreciated.   Ref-
https://sci-hub.st/10.1016/j.aeue.2020.153354. I didn't able to replicate the result from curiosity point of view with the same kind of device structure. ..

Eventually oxide thickness is 1.5nm they have mentioned. Which is showing peculiar at VNL for 7nm technology nodes and 10nm Source /Drain.

Can you please share some suggestions regarding this?
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