1
General Questions and Answers / Re: pdos-mpsh
« on: March 10, 2025, 16:20 »
any one can answer this?
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2
General Questions and Answers / Re: Reliability of optimized junctions
« on: February 21, 2025, 03:00 »
Yes, for zero bias, checking forces and total energy convergence is often enough to ensure the reliability of the optimized junction. NEGF provides transport properties, but it's computationally expensive. Geometry optimization with force and energy checks gives a reliable atomic configuration and is usually sufficient for low-bias or zero-bias cases.
This is what i think. For expert view point, please wait for @Dr Blom reply
This is what i think. For expert view point, please wait for @Dr Blom reply
3
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)
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)
4
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?
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?
5
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.
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.
6
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?
7
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
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
8
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
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
9
General Questions and Answers / Re: Pdos code
« on: December 10, 2024, 00:38 »
Many thanks Dr. Blom, I got the exact dos.
10
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.
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.
11
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()
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()
12
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
13
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.
For more clear concept, wait for response of @Dr Blom.
14
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('Γ','$\Gamma$') for tick in bs._ticksGUI() ]
P.xticks(kticks,ticklabels)
P.grid(kticks)
P.ylim(ymin,ymax)
P.savefig(plotfile)
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('Γ','$\Gamma$') for tick in bs._ticksGUI() ]
P.xticks(kticks,ticklabels)
P.grid(kticks)
P.ylim(ymin,ymax)
P.savefig(plotfile)
15
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.
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.