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Messages - Anders Blom

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1
General Questions and Answers / Re: Random Swap of Elements
« on: Yesterday at 00:17 »
Python coding...
You can easily access the elements in a structure with configuration.elements(), that gives a list of the elements, you can then use the random.random() function to pick indices in a relevant way, replace an element and then put it back into the configuration with the secret method configuration._changeAtoms(elements=new_elements).

Or you can just remake the configuration from it's old parts:
new_configuration = BulkConfiguration(old_configuration.bravaisLattice(), new_elements, old_configuration.cartesianCoordinates())

2
General Questions and Answers / Re: Orbital coefficients
« on: May 9, 2024, 21:42 »
Lucky for you I actually wrote a script to do this about 10 years ago, but nobody seemed to need the functionality so we never made it a feature in the software.

The usage is pretty obvious; the return is a list (one entry per eigenstate) of arrays, which contain the "contributions" (projections) onto the angular momenta s, p, d, and f.

I tested with NH3 from the example in the manual (https://docs.quantumatk.com/manual/Types/ElectronDensity/ElectronDensity.html) and the run this slightly clumsy code

Code: python
from PartialNorm import getPartialNorms
molecule = nlread("nh3.hdf5", MoleculeConfiguration)[0]
# HOMO state is 3
ix = 3
partial_norms = getPartialNorms(molecule, projection_atoms=[0])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[1])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[2])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[3])
print(partial_norms[ix])

We can then see that the HOMO level derives almost 90% from Nitrogen (mostly p-states), but if we change to ix=4 we note that LUMO has a lot more H contributions (and the LUMO state is, as expected, dominated by s-states). Hopefully this is helpful for the analysis of your molecule too.

This function can be used for a lot of other cool things, like mapping out where s and p states dominate in the band structure of GaAs (RGB color scale mapped from spd contributions) as in the attached picture!

3
General Questions and Answers / Re: Can't find builder(bulk, selection, device etc.) tools on the right
« on: May 9, 2024, 20:32 »
Yes the same trick should work

4
General Questions and Answers / Re: Building type 1, 2, 3 quaternary heusler alloy
« on: May 9, 2024, 20:32 »
Yeah that should be enough. Are these DOS lines at very low energy or around the Fermi level? Really hard to provide any help without the actual input and output...

5
General Questions and Answers / Re: Unit trouble dipole moments
« on: May 9, 2024, 20:30 »
I don't think there should be any confusion about units? It prints
X Y Z of dipole: [ 7.50489746e-07 -5.50684384e-05  6.86097535e-01] Bohr**4*e
to the file, and if you had printed the magnitude as you perhaps intended (you write m1 to the file) it would have shown
0.686097536725 Bohr**4*e

(The numbers are not your numbers as I don't have your molecule, I just use NH3 as an example)

Oh, I see you still use the old wrong script from the manual. You need to remove * length_unit**3 from the line defining dV

6
General Questions and Answers / Re: Building type 1, 2, 3 quaternary heusler alloy
« on: May 7, 2024, 18:48 »
Maybe too few k-points?

7
General Questions and Answers / Re: Unit trouble dipole moments
« on: May 7, 2024, 18:46 »
QuantumATK does not print anything you don't tell it to (apart from the self-consistent log) so this really depends on what your script looks like, which I don't know. Also, all quantities are kept internally with a unit attached, so there should never be a doubt about the unit, unless some special instructions are used to remove it. But you would have to share the script for us to help.

8
General Questions and Answers / Re: Unit trouble dipole moments
« on: May 6, 2024, 23:12 »
If you mean ferroelectric polarization this can be evaluated (in-plane at least) the same way as for 3D bulk: https://docs.quantumatk.com/tutorials/polarization/polarization.html

9
General Questions and Answers / Re: Interfering and non-interfering contributions of the transmission function
« on: May 6, 2024, 21:29 »
Did you check https://docs.quantumatk.com/tutorials/low_level_entities/low_level_entities.html? In principle all components are there, I think.

10
General Questions and Answers / Re: Orbital coefficients
« on: May 6, 2024, 21:22 »
As you say, we might call it something else, but therefore we need to know how *you* define these coefficients :-)
And, it might help to know what you need them for, i.e. what analysis you can perform with them.

On the surface it sounds like you can just extract the Mulliken populations to know how much s, p, d contribution there is to a state, although it's a bit of a rough analysis.

11
General Questions and Answers / Re: Regarding one existed .py file from software tutorial itself. Opening at builder
« on: May 3, 2024, 20:47 »
Well, that is what the tutorial describes, and also you can study 100s of papers with QuantumATK on similar devices. As mentioned, we can answer specific questions, but we don't offer individual tutoring on using the software.

12
General Questions and Answers / Re: Regarding one existed .py file from software tutorial itself. Opening at builder
« on: May 2, 2024, 19:14 »
Not to be impolite but I honestly do not understand what you are asking, you need to be be clearer.

If you are following the tutorial and something doesn't work or you have a question on a particular step, you can ask about that. But don't expect other people to do your work for you...

13
General Questions and Answers / Re: Unit trouble dipole moments
« on: May 1, 2024, 20:10 »
I think the way we evaluate the dipole from the electron density is basically limited to molecules. For monolayers with voltages applied etc, it's more relevant to consider the dielectric response, i.e. the field gradient in the material vs. the external electric field.

14
General Questions and Answers / Re: Unit trouble dipole moments
« on: April 30, 2024, 20:28 »
Yes, it's a mistake. At some point in the ancient past numpy.dot would strip off the unit so we had to reapply now, but now it gets multiplied in with the unit already applied.

Just skip the length_unit**3 and it works better! However, also see https://forum.quantumatk.com/index.php?topic=10790 about why you should use the ElectronDifferenceDensity, rather.

15
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« on: April 30, 2024, 20:19 »
Aha, interesting... I'll make sure to forward this to our developers, however at least now you have a workable way to run the calculations fast, and correctly!

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