Topics

1

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

2

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'

3

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

4

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

5

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

6

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?

7

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

8

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

9

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?

10

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

11

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

12

General Questions and Answers / Broadening in TS

« on: May 30, 2023, 22:50 »

Hello Expert,
I have attached .py file for my Transmission spectra code - I am afraid I don't have an idea "how to broaden the transmission curve".
Is there a way I can add gaussian or tetrahedron broadening?


Thank you

13

General Questions and Answers / I-V curve

« on: May 17, 2023, 14:24 »

Hello Expert,
Could anyone please provide guidance on the recommended procedure for obtaining the current-voltage (I-V) curve in the context of quantum transport calculations? Specifically, I would like to understand if it is necessary to calculate the transmission spectra (at zero or finite bias) beforehand and subsequently utilize the .hdf5 file containing the transmission data for the construction of the I-V curve or we directly calculate I-V curve.

Your expertise in this matter would be greatly appreciated.

Thank you

14

General Questions and Answers / Error

« on: May 12, 2023, 14:31 »

I am calculating IV curve and got error.
How to get rid of this error
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 14172 RUNNING AT comp0208
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 14172 RUNNING AT comp0208
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
   Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================
~                                                                                     

15

General Questions and Answers / Code for Transmission spectra

« on: May 8, 2023, 16:19 »

I have calculated the transmission spectra for device configuration, wants to gets the graph using atkpython. I modify the code for transmission up and down but got error - I modify like
T(up) = df["T(up)"].values
T(down) = df["T(down)"].values

for DOS, It was this way but i dont have an idea how to adjust the below for transmission spectra
# calculate the DOS spectrum with spin up
dos_Up = dos.gaussianSpectrum(energies, broadening = 0.01*eV, spin=Spin.Up)
# calculate the DOS spectrum with spin up
dos_Down = dos.gaussianSpectrum(energies, broadening = 0.01*eV, spin=Spin.Down)


 I have attached .pyfile for complete code. Anyone guide me how I modify this and get my spectra in atkpython.

Thank you so much