Messages

16

General Questions and Answers / Re: Convergence test for electrodes

« on: August 9, 2023, 14:08 »

I solve the problem, added the lattice in it - but I am using LCAO calculator and I copied the basis set from DFTB Directory (usr/local/QuantumATK-S-2021.06-SP2/share/basissets/LCAO/) but still got the error
> 55 basis_set = DFTBDirectory('/home/hartree/jem/wolf6252/usr/local/QuantumATK-S-2021.06-SP2/share/basissets/LCAO/')
     56
     57 #----------------------------------------

/usr/local/QuantumATK-S-2021.06-SP2/lib/python38.zip/NL/Calculators/SemiEmpirical/SlaterKosterCalculator/Parameters/SlaterKosterDirectory.pyc in __init__(self, path)

/usr/local/QuantumATK-S-2021.06-SP2/lib/python38.zip/NL/Calculators/SemiEmpirical/SlaterKosterCalculator/Parameters/SlaterKosterDirectory.pyc in __init__(self, path)

/usr/local/QuantumATK-S-2021.06-SP2/lib/python38.zip/NL/ComputerScienceUtilities/FileUtilities.pyc in checkDirectory(directory, parameter_name, base_path, length_limit)

NLValueError: The parameter '' must be a string to an existing directory.
The directory /home/hartree/jem/wolf6252/usr/local/QuantumATK-S-2021.06-SP2/share/basissets/LCAO/ was not found.


I have tin nanoribbons. I think it might be the issue of pathway.

17

General Questions and Answers / Convergence test for electrodes

« on: August 8, 2023, 02:15 »

Dear Administration,
I am interested in doing convergences test and followed the following link: https://docs.quantumatk.com/tutorials/atk_transport_calculations/atk_transport_calculations.html.

I got error:
NameError: name 'lattice' is not defined

I am not sure about the role of pair potential? Can any one look into my script and suggest me changing?

18

General Questions and Answers / Re: Geometry optimization issue

« 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

19

General Questions and Answers / Geometry optimization issue

« 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   
    max_forces=0.1*eV/Ang,
    max_stress=0.2*GPa,
    max_step_length=0.005*Ang,
- 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

20

General Questions and Answers / Re: Optimization Issue

« on: July 4, 2023, 11:31 »

any one guide me?
why with different Force, stress values etc - my geometry is not converging?

Thanks

21

General Questions and Answers / Optimization Issue

« on: July 4, 2023, 02:47 »

Dear Experts
- 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 the inputfile (output file is too big- not attached) of my system have following geometry optimization parameters   
    max_forces=0.1*eV/Ang,
    max_stress=0.2*GPa,
    max_step_length=0.2*Ang,
- 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

22

General Questions and Answers / Re: Kpoints vs DOS

« on: June 28, 2023, 02:59 »

I think my structure is symmetrical that may play a role in obtaining the same energy for different k-points. 
- I already optimized the geometry, is there a way I can put symmetrical=False in DOS.

or some one guide me from my previous post.

Thank you

23

General Questions and Answers / Kpoints vs DOS

« on: June 26, 2023, 17:23 »

Dear Expert
I am really confused about the issue I am facing that I calculated DOS for my system with different K points (1,3,5,7 in C direction and A=B=1) and got the exactly same energy in every case.

- the way I do - I optimized my geometry in first step
- I given the path of optimized geometry, then calculated the DOS to perform convergences test.

I studied online and nothing found something more relavent to my problem - just got "The energy *will* be the same if your system only has localised states, for example a molecule in a large simulation cell".

For the reference, I have attached optimized file and then DOS with 1 kpoints. Can some one suggest me what's the issue and why I am getting the same energy?

24

General Questions and Answers / Re: Charge of central region

« on: June 23, 2023, 02:00 »

Thank you, Dr. Blom, for your valuable guidance and assistance. I appreciate your efforts in helping me understand this concept better.

25

General Questions and Answers / Re: Charge of central region

« on: June 22, 2023, 23:58 »

- I am sorry I am not getting your point.

- As cluster is already bonded to the surface - should I add -3 charge in the central region, if yes how to do so in device input?

- or Should I do calculation both with and without charge to see the impact?


Thank you

26

General Questions and Answers / Re: Charge of central region

« on: June 22, 2023, 00:22 »

Experimentally, it is proved the cluster I'm using have 3- charge so keeping in mind, I am thinking to add for my bulk and for device - I am not sure what is the physical significance? but I think adding charge will alter the electronic properties due to charge distribution.

I also haven't find anything in literature.

27

General Questions and Answers / Re: Charge of central region

« on: June 21, 2023, 23:26 »

Thank you Dr. Blom for your guidance.

The tutorial you mentioned I already studied this - I have three Fe in my cluster, if i add charge to each Fe - Is it effecting the transmission for my device system and even for bulk do I need to add the charge for each Fe?

28

General Questions and Answers / Charge of central region

« on: June 21, 2023, 16:59 »

Dear Expert
I have optimized Fe-Sn cluster on stanene nanoribbons, and cluster placed well on stanene nanoribbon. For device, I placed the optimized geometry between electrode, Now the issue I don't have an idea how to put charges on central region as cluster already formed bond with nanoribbon.

I have attached .py file for my system. Can anyone guide me please how to solve the issue?

Thank you

29

General Questions and Answers / Re: Code for Transmission spectra

« on: June 14, 2023, 02:21 »

Yes, Dr Blom -  you are right.

I got the similar graph - just adjusted my python code a bit. but

I don't understand why it's -0.15 to 0.15, when I applied -0.3V. I couldn't figure out the concept behind it. Explain it please.

30

General Questions and Answers / LBFGS

« on: June 6, 2023, 00:25 »

Dear Expert
I have studied the LBFGS algorithms and found that during optimization it follow the following steps
•   Minimizing Forces
•   Compute the gradient
•   Update the search directions
•   Line search
•   Update the variables and memory history   
•   Check convergences

I am still confused about LBFGS the how this step could be explain mathematically, Expert please guide me a bit