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General Questions and Answers / Re: Geometry optimization issue
« Last post by AsifShah on July 19, 2023, 02:48 »
I would still recommend increase K points to at least to 3x3. Maybe it will help.

I was trying to test whether the noncolinear SOC along with hybrid functional is implemented in version 2021.06-SP2 using HybridSOGGA.HSE06 in the place of SOLDA.PZ (which ran perfectly). The calculation stopped while calculating the density matrices of the central region showing the error:

atkpython: /slowfs/qatkdev2/bamboo/de02vlbamboo10/bamboo-agent-home/xml-data/build-dir/QL-Q2-BLD/c++/src/physics/blocksparseatompairmatrix.cpp:361: BlockSparseAtomPairMatrix& BlockSparseAtomPairMatrix::operator+=(const BlockSparseAtomPairMatrix&): Assertion `spin_type_ == source.spinType()' failed.

My question would be if it's not implemented why it's only showing problems while doing the calculation of the central region why not the electrodes (attached the log file for your reference)?

P.S: Previously I have asked about the availability of the noncolinear SOC with hybrid functional for device calculation within the NEGF framework is available or not and got the reply from Ulrik that it would be implemented in the newer release. Could you please confirm if the error I'm getting is due to the non-implementation?

Waiting for your quick response!

Thank you,

Dear Ulrik,

Is the hybrid functional with spin-orbit coupling implemented for device calculation in the new release? I'm using quantumatk/2021.06-SP2 where it is not implemented. Did you implement it in the newer version?

Please let me know.


General Questions and Answers / Re: Geometry optimization issue
« Last post by Jahanzaib on July 17, 2023, 12:01 »
Thank you for your response.

My cell is very large in periodic direction having 165 atoms so I don't think I need large k points? I haven't adjust damping factor  - I will adjust them and let's c.
Do you think with very large unit cell, i need larger k points? In principle, if a unit cell is large, then fewer k points are enough.

Thank you
General Questions and Answers / Re: Geometry optimization issue
« Last post by AsifShah on July 16, 2023, 21:35 »
Although I am not sure if this is the right way for magnetic materials but here is the following:
1. Try first optimizing using unpolarized spin GGA.PBE then use optimized geometry to optimize for spin polarized, SGGA.PBE.
2.  Increase your k points. (1x1x1 is very low)
3. Reduce damping_factor to 0.01 and increase max_steps=300
4. Keep max_step_length as default.
Can you check the case where you observe an increase in electrode length when increasing electrode extension length. In that case, is there a distortion/grain boundary kind of thing at the interface between electrode extension and electrode?

Did u try damping 0.01 with history steps 20? Try it, if you haven't yet!
It may work.

Also, what is ur electrode extension length? Is it doped or undoped?
Hi all,

I'm calculating the transmission spectrum of electron transport through a pi-conjugated molecule between 2 Si electrodes (attached structure below).
The transmission spectrum was calculated for bias -2V to 2V with 0.5 increment.

My problem is the transmission spectrum calculation of every bias except -2V converged.
I have already tried changing the "Damping factor" and "History step" in the Pulay Mixer as suggested by the QuantumATK manual. It worked with most of my calculations except for bias -2V.

For bias -2V I have tried changing damping factors: 0.1, 0.05, 0.03, 0.011, 0.01, 0.009, 0.008, 0.007, 0.005; history steps: 5, 10, 15, 20, 25, 30; mixture: damping factor 0.01 + history step 10.

But none of those converged. The energy is stuck at lower energy compared to zero bias energy or converged bias calculation energy.

1. Could you give me any suggestions on what I can do next to make it converge?
2. Can you explain what is the meaning of the phenomenon that energy keeps fluctuating around a value in transport calculation?
3. Can you explain in more detail than the manual on the effect of changing damping factor and history step on the convergence?

Thank you,
General Questions and Answers / Re: Electrode and electrode extension size
« Last post by gozde on July 12, 2023, 11:35 »
Hello again Dr.Blom,

I try to understand how length of the electrodes affects the IV curve of the our device model. Therefore I have made some tests.

I have noticed that, when I increase the electrode extension length, minimal electrode length is also increased to be the same as the electrode extension length. However if I have first increased the size of the central region at the interface of the respective electrode, and secondly I have increased the electrode extension length, minimal electrode length remains same. What is the origin of this difference and which geometry makes sense?

I look forward to hearing from you.
General Questions and Answers / Geometry optimization issue
« Last post by Jahanzaib on July 11, 2023, 03:47 »
Dear Expert
I am facing alot of issues in geometry optimizations -  I just optimized FeSn cluster on my stanene ribbons - I have run my calculation on cluster - but it took more then 4 days still not optimized. I have attached graph so please guide me.
- I have attached the inputfile (output file is too big- not attached) of my system have following geometry optimization parameters   
- In addition, I tried different 3 other options where I changed force, stress and step size
1) max_forces=0.01*eV/Ang, max_stress=0.02*GPa, max_step_length=0.2*Ang,
2) max_forces=0.01*eV/Ang, max_stress=0.02*GPa, max_step_length=0.0005*Ang,
3) max_forces=0.03*eV/Ang, max_stress=0.05*GPa, max_step_length=0.001*Ang,

Can you some one look into my file and guide me what I am doing wrong or why the geometry is not optimized?

Thank you
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