Messages

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

General Questions and Answers / Re: Regarding band structure and DOS

« on: September 28, 2023, 00:33 »

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

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.

11

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?

12

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

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