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Messages - krabidix

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Thanks a lot for your nice input. I will keep these things for further calculations.
I encountered numerical artifacts during optimization, for example:

Consider 2D square lattice with two atoms (A&B) basis (side of square lattice = a*sqrt(2)) where 'a' is the bond length, the atomic position in fractional coordinates A(0,0,0.5) & B(0.5,0.5,0.5). Now upon geometry optimization, the fractional coordinates remain the same but the cartesian coordinates show some non-zero values in of x and y plane for atom A, of the order of 10^-10 or even smaller time. Like atom A being at ( -10^-12, -10^9, 0.5).

Is this numerical noise could be the cause of imaginary modes?

Thanks for working on the script.
Indeed the results are reproduced.
By tuning the max_interaction_range we need to set 'use_wigner_seitz_scheme=False'. QATK allows setting use_wigner_seitz_scheme=True only when we consider the max_interaction_range (Default) which includes all atoms. And with this (True) setting when one checks repetitions = checkNumberOfRepetitions(bulk_configuration) the automatic algorithm of ATK suggest a larger supercell.
So, one can limit the max_intr_range and use a smaller supercell as ATK suggests with
repetitions = checkNumberOfRepetitions(bulk_configuration,    max_interaction_range=4.0*Angstrom).
The parameters used in the dynamical matrix calculations affect too much on phonon calculations.
One thing I also noticed is that during optimization the symmetry gets broken for some 2D structures, which leads to the imaginary phonon frequencies also.
At the same time when we enforce the symmetry using constraints, the next issue came up with force and stress convergence. Which also affects the phonon energy relations.

Is the tuning of parameters the only way to check or there is a robust rule of thumb on which one can rely and move on to study the next structure if imaginary frequencies showed up?


Hi Tue,
Thanks for the comment!
I used the DFT-PW method, and I have also shared the .py file already.
First I optimized the structure and then use repetitions=(7, 7, 1).
You may consider a look at the script.

Best Regards,

Here is the screenshot, of how the atk is showing up.

General Questions and Answers / Data preview is not visible!
« on: January 3, 2023, 12:24 »

In QuantumATK 2022.12 version how can we enable data preview? The data preview is not visible.


Is there anyone who can comment?

Dear QuantumATK experts,

I tried to replicate the phonon band structure of a simple system (hexagonal monolayer of Cu) as done in (see Fig 3 or attached image Phonon_bs_ref.PNG)
The results from QuantumATK have imaginary frequencies and even after tuning parameters (e.g: max_interaction_range, atomic_displacement) that control the force constants, I am not able to vanish the imaginary frequencies (see attached Phonon_bs_qatk.PNG).

Please, comment on how can I rid of these imaginary frequencies.

The input file is also attached.


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