Topics

1

General Questions and Answers / pdos-mpsh

« on: February 11, 2025, 02:41 »

Dear Expert,

This is my code for MPSH, where I am analyzing atom 112 (Ni) to determine which d-orbitals contribute to the valence and conduction bands. I have also obtained the PDOS and attempted to map the energy levels with the PDOS. I have explored multiple approaches, including this one and some other options. I have attached both the PDOS and MPSH results for reference. my question is - in MPSH, is there a way to adjust the code where we can d-orbital splitting (like which one is dxy etc)
# -------------------------------------------------------------
# Molecular Energy Spectrum
# -------------------------------------------------------------
molecular_energy_spectrum = MolecularEnergySpectrum(
    configuration=configuration,
    energy_zero_parameter=FermiLevel,
    projection_list=ProjectionList(atoms=[112], angular_momenta=[2])
    )
nlsave('MPSH.hdf5', molecular_energy_spectrum)
nlprint(molecular_energy_spectrum)

2

General Questions and Answers / IV stop

« on: January 11, 2025, 00:19 »

Hello Expert,
I want to re run my IV job as it stops, I have gone throught this (https://docs.quantumatk.com/tutorials/restarting_calculations/restarting_calculations.html) but in my case, I calculated the TS, then give path to TS and then calculated IV curve? Is there a other way to rerun from the last step?

3

General Questions and Answers / Eigenvalues and eigenstates

« on: December 10, 2024, 18:51 »

Dear Expert,
I am using QuantumATK V-2023.09. I have attached the pics for my Transmission spectra, I am interested to explore the eigenvalue and eigenstate at energy = -0.14 with spin up only. In previous version, if you click on the peak at certain energy, you can eigenvalue and eigenstates.

Any suggestion

4

General Questions and Answers / Pdos code

« on: December 9, 2024, 03:04 »

Dear Expert,
I am working with a code that generates the PDOS for Hydrogen and Tin separately. However, I am interested in obtaining a combined PDOS, as shown in the attached picture . I have attached pics - Any suggestion please

The code is:
 #plot the spectra using pylab
 import pylab
 import matplotlib.pyplot as plt

 # read DOS object from file
 dos = nlread('/home/dos.hdf5', DensityOfStates)[0]

 # Get the actual energy values from the DOS object
 energies = dos.energies()

 # Calculate the DOS spectrum with spin up
 dos_Up = dos.evaluate(projection_list=ProjectionList(atoms=[96,97,98,99,100,101,126,127,128,129,130,131], elements=[Tin], angular_momenta=[1]), spin=Spin.Up)
 dos_Up1 = dos.evaluate(projection_list=ProjectionList(atoms=[60,61,62,63,64,65,138,139,140,141,142,143], elements=[Hydrogen], angular_momenta=[0]), spin=Spin.Up)

 # Calculate the DOS spectrum with spin down
 dos_Down = dos.evaluate(projection_list=ProjectionList(atoms=[96,97,98,99,100,101,126,127,128,129,130,131], elements=[Tin], angular_momenta=[1]), spin=Spin.Down)
 dos_Down1 = dos.evaluate(projection_list=ProjectionList(atoms=[60,61,62,63,64,65,138,139,140,141,142,143], elements=[Hydrogen], angular_momenta=[0]), spin=Spin.Down)
 # Plot the spectra using pylab
 import pylab
 pylab.figure(figsize=(5, 10))
 pylab.plot(dos_Up.inUnitsOf(eV**-1), energies.inUnitsOf(eV), color='darkblue', label='Spin Up')
 pylab.plot(dos_Down.inUnitsOf(eV**-1), energies.inUnitsOf(eV), color='darkblue', linestyle='--', label='Spin Down')
 pylab.plot(dos_Up1.inUnitsOf(eV**-1), energies.inUnitsOf(eV), color='darkblue', label='Spin Up')
 pylab.plot(dos_Down1.inUnitsOf(eV**-1), energies.inUnitsOf(eV), color='darkblue', linestyle='--', label='Spin Down')

 # Add a dotted line at E-EF=0
 pylab.axhline(y=0, linestyle='dotted', color='gray')

 pylab.xlim(0,15)
 pylab.ylim(-2,2)

 # Save the figure as a high-resolution PNG image
 #plt.savefig('Fe-PDOS.png', dpi=300, bbox_inches='tight')

 # Add the legend in the upper right corner
 pylab.legend(loc='upper right')

 pylab.xlabel("PDOS (1/eV)")
 pylab.ylabel("E-E$_{f}$/eV")
 pylab.legend()
 pylab.show()

5

General Questions and Answers / Query Regarding Transmission Spectra Analysis Features in QuantumATK

« on: November 25, 2024, 15:11 »

The FatBandstructure is used to visualize the contribution of different orbitals to the band structure of a bulk system. For Transmission Spectra analysis, what features or tools does QuantumATK support to facilitate comparison with Transmission Spectra results? Need suggestion please

6

General Questions and Answers / Band Structure

« on: October 30, 2024, 15:41 »

Dear Expert,

I have attached my band structure plot, and I would like to recreate this plot using "atkpython." Is there a way to extract the necessary information using a script?

Additionally, I already have a script for the density of states of the same system, and I was wondering if it would be possible to plot both BS and DOS side by side.

Thank you!

7

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 or is there a way to add broadening in TS? I want TS peak a bit smoother.

Thank you

8

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?

9

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)

10

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

11

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

12

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'

13

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

14

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

15

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