Messages

1

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.

2

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)

3

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.

4

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?

5

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

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()

6

General Questions and Answers / Re: Band Structure

« on: October 31, 2024, 00:53 »

Thank you so much. Is there a way to extract BS using python code?

7

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!

8

General Questions and Answers / Re: Information from transmission spectrum

« on: October 15, 2024, 03:48 »

You can extract alot of information
1) Spin-Dependent Conductance
2) Spin Polarization of the Current
3) Transmission Pathways
4) Magnetoresistance etc

Detail for transmission spectrum is (https://docs.quantumatk.com/manual/Types/TransmissionSpectrum/TransmissionSpectrum.html). There are alot of tutorial in quantumatk website, use keyword "transmission" to see the relavant tutorials.

9

General Questions and Answers / Re: DOS vs TS

« on: October 8, 2024, 21:49 »

Thank you Dr Blom.

The reason for using only a few k-points for the TS calculation in my case is that I have a very long stanene nanoribbon, which generally requires only a few k-points. In some cases, I observed a bigger peak in the DOS, but when I examined the transmission spectrum (TS) at zero bias for the same system, that peak was not present. To my understanding, the transmission function T(E), which can be considered a density of states (DOS) weighted by the probability of electron transfer from the device region to the left or right electrodes.

I think if I increase the number of k-points in the B direction only in stanene nanoribbon, I might observe similar peaks. For a 1D system like this, I assume that increasing k-points in the B direction should be fine??

10

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

11

General Questions and Answers / Re: Brodening in LCAO calculator

« on: September 24, 2024, 14:39 »

A follow up question on that:
I have a long stanene nanoribbon, and I am optimizing iron-tin cluster on it. My system is large in C direction so I need only few k-points, may be 1 k-point in C direction. So, I needs large broadening value?

This is what I understand from the discussion

12

General Questions and Answers / Re: Brodening in LCAO calculator

« on: September 23, 2024, 13:15 »

The default broadening value of 1000 K typically refers to the temperature used to define the width of the electronic states in energy calculations.

13

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

« on: September 13, 2024, 23:12 »

Many thanks - I got the your point.

14

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?

15

General Questions and Answers / Re: Geometry Optimization of the two Probe System(organic molecule between 2 electro

« on: September 11, 2024, 00:25 »

The way I approach the two-probe system optimization is by dividing it into smaller parts.  Instead of optimizing the entire device at once, which is a massive task, I find it faster and more efficient to build the device from optimized components.

I first separately optimize the central region, which in this case includes the organic molecules and similarly, optimize the gold electrodes. Then, place the optimized organic molecules between the optimized gold electrodes.

Each part is already optimized, then no need to optimize complete device again.

If you want expert comments, you should wait for a response from @Anders Blom.