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Messages - Jahanzaib

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1
General Questions and Answers / Re: Help in python code
« on: Yesterday at 04:35 »
Sorry Dr. Blom for inconveniences.

Please the find complete code for reference, and I have sent hdf5 file on email (quantumatk-support@synopsys.com) and I cannot share my results. Please have a look.
 1) DOS1
      Herein, I am only interested in p-orbitals of Tin. For "loop", I was trying to say that I have a long stanene nanoribbon (Tin=120 and H=24), is it the way to do to get the DOS for all 120 tin?
Projection(spin=Spin.Up, atoms=[Tin]) + Projection(spin=Spin.Down, atoms=[Tin]) - also i tried this but not worked for me.
then how to do angular_momenta=[1]????

2)DOS2
I think it's clear for you, just interested in Both p - orbitals of Tin, and Fe (atom indices = 144 and d-orbitals).

Thank you

2
General Questions and Answers / Help in python code
« on: December 6, 2023, 05:11 »
Dear Expert
My python code for DOS works perfectly fine but I need to adjust a bit which I already tried but I couldn't succeeded. Can anyone share some tips or tricks so I can get required DOS.

Please find the attached code - there are two part of code
1) # Plot DOS 1 in the first subplot
     Herein, I have stanene nanoribbons consist of Tin 120 and H 24 (total 144 atoms) - my code gives me DOS for complete system but I am interested in
                         - Only p-orbitals of Tin, I know about projection stuff but I don't know how to loop it over complete all Tin.

2) # Plot DOS 2 in the second subplot
    Herein, I adsorbed FeSn10 on stanene nanoribbon and I am interested in
                        - Both p - orbitals of Tin, and Fe (atom indices = 144 and d-orbitals)

Thank you

3
General Questions and Answers / Re: Error
« on: November 29, 2023, 22:29 »
Actually, I was trying to install sea born library there, then I got the error, I am using 2021 version of QATK. I just tap atkpython in interactive window. Could you please suggest any solution for this error?

4
General Questions and Answers / Error
« on: November 28, 2023, 16:36 »
Hello Expert,
I got error, when I used atkpython. Anyone suggest solution.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NL/__init__.py", line 363, in <module>
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NL/ComputerScienceUtilities/Resources.py", line 14, in <module>
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 618, in _load_backward_compatible
  File "<frozen zipimport>", line 281, in load_module
  File "zipdir/NL/ComputerScienceUtilities/Functions.py", line 4, in <module>
  File "build/lib/python3.8/site-packages/scipy-1.2.1-py3.8-linux-x86_64.egg/scipy/sparse/__init__.py", line 230, in <module>
  File "build/lib/python3.8/site-packages/scipy-1.2.1-py3.8-linux-x86_64.egg/scipy/sparse/base.py", line 10, in <module>
  File "build/lib/python3.8/site-packages/scipy-1.2.1-py3.8-linux-x86_64.egg/scipy/sparse/sputils.py", line 16, in <module>
  File "build/lib/python3.8/site-packages/scipy-1.2.1-py3.8-linux-x86_64.egg/scipy/sparse/sputils.py", line 16, in <listcomp>
  File "/u/jem/wolf6252/.quantumwise/lib/python3.8/site-packages/numpy/__init__.py", line 320, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'typeDict'

5
any one please guide me?

6
General Questions and Answers / Regarding band structure and DOS
« on: September 20, 2023, 02:02 »
Dear Expert.

I have a question regarding band structure - I got the band structure for my system which is attached, I am interested to find out which orbital are present at particular band number - For example, If I am interested in band 930 (spin up) to see which orbital are there - is there a way in quantumatk? if yes, can anyone please guide me
Thank you

7
General Questions and Answers / Re: Xc functional
« on: August 29, 2023, 14:56 »
Thank you for answering. Do I only need to compare with transmission with different functional?

8
General Questions and Answers / Xc functional
« on: August 24, 2023, 21:57 »
Dear Expert,
I need your suggestion how to bench mark the exchange correlation functional.

- I have stanene nanoribbon and adsorbed Iron-tin cluster on it (Bulk Studies) using GGA.PBE.
- Geometries are placed between two electrode for Calculated Transport properties.
- I have calculated Transmission spectra, DDOS, IV curve etc.

I am bit confused how to benck mark the Xc functional - do i need to perform all calculation using different Xc functional like LDA - then what to compare with different Xc functional? Need guidance

9
General Questions and Answers / Error
« on: August 22, 2023, 01:56 »
Dear Expert
I am facing the following error:
ValueError: x and y must have same first dimension, but have shapes (8786,) and (600,)

I solved the like this :  # make list of energies
 energies = numpy.linspace(-2,2,8786)*eV

is this correct?

I have checked the output which shows dos and energies and have same values and I tried all the possible path but still couldn't able to solve it . Anyone help me out

10
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.

11
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?


12
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

13
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

14
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

15
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

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