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Messages - Jahanzaib

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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 / Re: Eigenvalues and eigenstates
« on: January 10, 2025, 12:55 »
Many thanks, Dr. Blom, for such a detailed answer. A lot of concepts have been clarified.

What am I looking for? I have transmission spectra, and I am particularly interested in identifying the orbitals associated with a specific energy level, for example, E = -0.14 eV. Specifically, I want to determine which orbitals contribute to the current flow at that energy.

As mentioned earlier, when I adjust the iso value close to zero, everything disappears, and when I increase it, the details are obscured. I have not been able to find a way to resolve this issue for my system.

4
General Questions and Answers / Re: Eigenvalues and eigenstates
« on: January 10, 2025, 01:32 »
Thanks Dr. Blom, the code works fine, but I got confused how to set isovalue in quantuatk, at particular energy I change - some time it separate out to whole nanoribbon and sometime not, is there a way in quantumatk that automatically set isovalue?

5
General Questions and Answers / Re: Eigenvalues and eigenstates
« on: December 13, 2024, 23:59 »
Many thanks Dr Blom. I tired to use this script and it shows the following error:

TypeError                                 Traceback (most recent call last)
<ipython-input-13-2772cb4c8c17> in <module>
      4 energy_zero_parameter=AverageFermiLevel,
      5 spin = Spin.Up
----> 6 eigenvalues = TransmissionEigenvalues(device_configuration, energy, k_point, spin)
      7 nlprint(eigenvalues)
      8 # Check the printout to see which states you need, then use the line below to set it to 0, 1, 2, etc

TypeError: 'module' object is not callable

6
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

7
General Questions and Answers / Re: Pdos code
« on: December 10, 2024, 00:38 »
Many thanks Dr. Blom, I got the exact dos.

8
General Questions and Answers / Re: Pdos code
« on: December 10, 2024, 00:20 »
Dr. Blom, Thank you for the reply.

I have already mentioned my question in previous request. The code I shared, provides the separate DOS for Tin and Hydrogen, but I am interested in obtaining the combined DOS for both Tin and Hydrogen, as shown in the pictures. If you look at the pictures, I have selected only the edge Tin and Hydrogen atoms.

9
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()

10
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

11
General Questions and Answers / Re: Current or current density
« on: November 12, 2024, 19:57 »
The formula deals with the total current through a quantum device, where electrons are treated as wave-like entities confined to specific channels. Unlike classical transport where current density is a meaningful quantity distributed over a cross-sectional area, the concept is less useful in a quantum regime where the focus is on transmission through discrete energy levels.

For more clear concept, wait for response of @Dr Blom.

12
General Questions and Answers / Re: Band Structure
« on: November 11, 2024, 23:47 »
I am using this code to extract BS, but I got error i tried to fix but its not done. The error is (ValueError: x and y must have same first dimension, but have shapes (21,) and (2, 21, 3395))

from NanoLanguage import *
import pylab as P

# Parameters
ncfile = '/u/jem/wolf6252/N-P/With-hyd/Fe/BS/BS.hdf5'
plotfile = 'plot.png'
ymin = -0.5
ymax = 0.5
# Colors for each band structure (add more if you have more than 4 band structures in the file)
colors = ['r','b','g','m']

bandstructures = nlread(ncfile, Bandstructure)

for i,bs in enumerate(bandstructures):
     P.plot(bs._axisGUI(), bs.evaluate(), colors)

# Set x-ticks = the symmetry points
kticks = [ tick[0] for tick in bs._ticksGUI() ]
ticklabels = [ tick[1].replace('&Gamma;','$\Gamma$') for tick in bs._ticksGUI() ]
P.xticks(kticks,ticklabels)

P.grid(kticks)
P.ylim(ymin,ymax)

P.savefig(plotfile)

13
General Questions and Answers / Re: Band Structure
« on: November 11, 2024, 15:58 »
Many thanks Habib, I am able to change the color.
I have my code to extract DOS, PDOS but I am also interested to refine my code for BS, So I can make my plot more better.

14
General Questions and Answers / Re: Band Structure
« on: November 10, 2024, 01:41 »
Hello Expert
Is there a way to change the colors for spin up and down bands in the given figure below? I have checked and tried and I haven't find anything to change color. Please see the attached pictures.

Im previous discussion, I was interested to extract BS using python code?

15
General Questions and Answers / Re: Band Structure
« on: November 1, 2024, 04:12 »
Actually I saw your code in the previous discussion where you mentioned to extract BS using python code. The code is given below:
So, I am interested for my sytem, but it doesnot given what I saw in GUI. I already knew how to combine both BS and DOS in GUI, but i think using python code, both looks more better for publication ;D ;D

from NanoLanguage import *

# -----------------------------------------------
# Parameters
# -----------------------------------------------
max_band = 100
min_band = 0
min_energy = -20
max_energy = 10
show_grid = True
title = 'Gold FCC'

# Read the bandstructure from a file.
bs = nlread('bandstructure.nc', Bandstructure)[0]

# Read the data in.
data = bs.evaluate()

# Setup the axises.
axixes = bs._axisGUI()
ticks = bs._ticksGUI()
loc = [ t[0] for t in ticks]
label = [ t[1] for t in ticks]
for i in range(len(label)):
    if len(label) != 1:
        label = r'$\Gamma$'

# Slice the data.
sliced_data = data[:,min_band:max_band]

import pylab
pylab.figure()
pylab.plot(axixes, sliced_data, 'k-')
pylab.plot(axixes, numpy.array(axixes)*0.0, 'k--')
pylab.xlabel('K')
pylab.ylabel(r'$\epsilon_i$ / eV')
pylab.xticks( loc, label)
pylab.ylim(min_energy, max_energy)
pylab.grid(show_grid)
pylab.title(title)
pylab.show()


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