Topics

1

General Questions and Answers / DOS vs TS

« on: October 5, 2024, 04:01 »

Dear Expert
I have attached photo for my system where I have shown you DOS and TS. In DOS, there are some peak on the fermi level but in TS its not? I dont understand this? Is a way to make TS
peaks smooter like DOS attached in pics.

Thank you

2

General Questions and Answers / Help with Choosing Quantum Numbers for MPSH Eigenstates

« on: September 12, 2024, 02:56 »

Hello Experts,
I followed the tutorial on molecular devices (https://docs.quantumatk.com/tutorials/molecular_device/molecular_device.html), but I am unclear about a few steps. Specifically:

When MPSH with atom indices (37, 38, 39, 40, 41, 42, 43, 44, 45, 46) is computed, I don't understand how or why quantum numbers 13, 14, 15, and 16 are chosen in the next step.

I have my own system, as shown in the attached pictures, and I am interested in observing the overlap between tin atoms 40, 92, and 95. I've calculated MPSH, but I am unsure how to choose the correct quantum numbers for eigenstate analysis?

3

General Questions and Answers / Current at each bias

« on: September 2, 2024, 15:44 »

Dear Expert,
I hope you are doing well.

I am interested in calculating the current at each bias given in code below. This code work well, but I don't have an idea how to calculate current at each bias, any suggestion?

pos_bias_list = [0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70]*Volt

# Read DeviceConfiguration
zero_bias_file = '/home/hartree/jem/wolf6252/N-P/Device/Fe-H-D/Fe-H-D-3-3/Fe-H-D-3-3.hdf5'
device_configuration = nlread(zero_bias_file, DeviceConfiguration)[0]

for bias in pos_bias_list:
    if processIsMaster():
        print("Bias is now: ", bias)
    # Get the calculator
    calculator = device_configuration.calculator()

    # Set the bias voltage
    calculator=calculator(electrode_voltages=(bias/2, -bias/2))

    # Attach the calculator and use the old initial state
    device_configuration.setCalculator(
      calculator(),
      initial_state=device_configuration)
    device_configuration.update()
    nlsave('device_bias_%.2f.hdf5' % bias.inUnitsOf(Volt), device_configuration)
    nlprint(device_configuration)

4

General Questions and Answers / Transmission Spectra

« on: August 12, 2024, 02:13 »

Hello Expert
I have attached transmission spectra for my system. I found that peak look weird I don't know why? Can anyone suggest/guide me what is wrong here?
Peaks does not look proper, I guess. I am using 1*1*100 kpoint in C-direction

Many thanks

5

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

6

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'

7

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

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 / 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?

11

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

12

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

13

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?

14

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

15

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