Messages

1

General Questions and Answers / Different colors for different transmission eigenchannels

« on: September 13, 2026, 22:01 »

I'm using QuantumATK to plot transmission eigenchannels as isosurfaces.

Problem 1: When I look at the same system but at different energies, the orbital colors are different every time. Why does this happen? I want them to all show the same color. I checked the manual but couldn't find an answer.

Problem 2: Every time, I have to manually adjust the isosurface value to see what the orbital looks like. Is there a way to do this automatically — so it shows the "real" shape of the orbital — instead of me setting the value by hand each time?

2

General Questions and Answers / Re: Different phase colors for different transmission eigenchannels

« on: August 29, 2026, 21:45 »

Many thanks for your reply.

Is there any tip or recommended approach for adjusting the transmission eigenstate isovalue to clearly identify which orbitals contribute to the transmission spectrum? Or do we need to adjust the isovalue manually until we obtain a clear representation of the orbital contributions?

3

General Questions and Answers / Different phase colors for different transmission eigenchannels

« on: August 24, 2026, 14:01 »

I'm plotting transmission eigenchannels in QuantumATK using isosurfaces with the BlueRed colormap, where color shows Phase (radians). When I plot two different eigenchannels at the same energy, they show different color/phase patterns even though they're in the same spot on the molecule. Is this normal, or does it mean something is wrong with my setup? Also, if I just want to compare how "big" or "spread out" the two channels are (not their phase), should I be plotting something else instead, like the magnitude/amplitude?

4

General Questions and Answers / HOMO LUMO

« on: July 18, 2026, 03:29 »

I have optimized the geometry of an isolated molecular system using DFT-LCAO in QuantumATK. For device calculations, I understand that the Molecular Projected Self-Consistent Hamiltonian (MPSH) is used to obtain the molecular energy levels in the presence of electrodes.

However, for a simple isolated molecule (MoleculeConfiguration) without any electrodes, what is the recommended way to calculate and visualize the HOMO and LUMO in QuantumATK?

5

General Questions and Answers / Fat Band Structure

« on: March 27, 2026, 23:07 »

Dear Experts,
I am currently working on calculating the fat-band structure of my system and would like to analyze the electronic states around the Fermi level. In particular, I am interested in identifying which Ni (d) orbitals overlap with Sn (p) orbitals for both spin-up and spin-down channels.

I would also like to know whether it is possible to estimate the percentage contribution of each orbital character from the fat-band analysis.

For reference, I am using the following code:

# -------------------------------------------------------------

# Fat-band structure

# -------------------------------------------------------------

fat_bandstructure = FatBandstructure(
configuration=configuration,
route=['G', 'Z'],
points_per_segment=20,
bands_above_fermi_level=All,
projections=ProjectionGenerator(
atoms=ElementsProjection,
l_quantum_numbers=True,
spin=UpDownProjection,
),
)

nlsave('fat-bs.hdf5', fat_bandstructure)

I would appreciate any guidance or suggestions on how to extract and interpret this information.

6

General Questions and Answers / Mulliken population

« on: March 10, 2026, 00:16 »

Dear Expert,
I have a system in which a CrSn cluster is embedded on a stanene sheet. I have calculated the Mulliken spin density for the whole system. I was wondering whether it is possible to obtain the Mulliken population for only the Cr atom, or if I need to follow same approach, such as calculating the Mulliken population by adding a separate transition metal (TM) atom and then evaluating it.

Currently, I calculate the Mulliken population for the entire system using the following script:
# -------------------------------------------------------------
# Mulliken Population
# -------------------------------------------------------------
mulliken_population = MullikenPopulation(configuration)
nlsave('MP.hdf5', mulliken_population)
nlprint(mulliken_population)

7

General Questions and Answers / Re: pdos-mpsh

« on: March 10, 2025, 16:20 »

any one can answer this?

8

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

9

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)

10

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?

11

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.

12

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?

13

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

14

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

15

General Questions and Answers / Re: Pdos code

« on: December 10, 2024, 00:38 »

Many thanks Dr. Blom, I got the exact dos.