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Messages - Anders Blom

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Might be. Regardless, do I understand correctly that you are able to run the calculation without problems? It looks more like a debug message than a real error.

Questions and Answers / Re: How to set bond length distance
« on: October 5, 2021, 22:29 »
I am not sure why you want to set the C-C distance in a B-N structure, but you can easily create B-N nanoribbons with the desired bond length 1.45 using the NanoRibbon tool in the builder

As for C-B and C-N, it will be impossible to impose those distances just locally, because also the B-N distances will change around the dopant.
Rather, they should be the result of running a geometry optimization on the structure where you have replaced certain atoms by Carbon (I assume you are talking about substitutional doping, based on the distances mentioned).
Fortunately, the forcefield ReaxFF_CHBN_2015 seems to do a decent job so you can use the Quick Optimizer to at least get a good starting structure. But depending on the width of the nanoribbon and the position of the C atom, all bond lengths at least 2-3 neighbors out will be changed (and in fact, even the edge atoms will be moving a bit).

Never seen this issue before an searching for the error message comes up with a wild flora of suggestions, from faulty Windows drivers to problems with anti-virus software...

Can you show a screenshot, to get an idea of how it appears (in a textbox or system message or what)?

(I am having trouble with the formatting of this reply, it smashes all paragraphs together making it very hard to read, but I don't know how to avoid that... So sorry!)

That is just a fun little programming exercise in the Builder!

If you didn't try this already, you can open a Python console within the Builder by clicking the icon in the lower-left corner (it is blue and looks like >_).

To prepare for this, copy/paste the following lines into the terminal:

Code: python
from NL.CommonConcepts.Configurations.Passivate import PassivationParameters
from NL.CommonConcepts.Configurations.PassivationUtilities import DEFAULT_H_LENGTH

This just sets up the imports we need. Second, assuming we just want the simple case of adding O-H to some carbon atoms in a CNT, define two objects which define the hybridization rules we need and the C-O and O-H bond lengths.
It should be somewhat obvious how to modify this for other cases.

Code: python
co_passivation_parameters = PassivationParameters(
    default_h_length={Carbon:1.4},  # C-O bond length
    default_hybridization=4,    # SP3
    tag_map={'C': 'O_C'},
oh_passivation_parameters = PassivationParameters(
    default_h_length=DEFAULT_H_LENGTH,  # For O-H just use the default
    default_hybridization=2,    # SP
    tag_map={'O': 'H_O'},

Now we do the fun part! This part can be repeated and undone (Ctrl+Z x 3) as needed.

First of all, obviously build a CNT, and make sure it has some decent length by repeating it in Z.

Select the atoms you want to "decorate". Click and hold down the "Ctrl" key, or use a quick command:
Code: python
import random
N = len(configuration.elements())
selection = random.sample(list(range(N)), 4)
to randomly select 4 atoms (the 4 could of course also be random!).

The next piece of code will passivate the selected atoms with H, however using a 1.4 Å bond length more suitable for C-O, then change the inserted H atoms to O, then passivate these with H.
Code: python
# How many atoms are we passivating?
n_pass = len(selection)
# Add an oxygen atom to selected atom(s) by pretending they should be SP3 coordinated
configuration = passivate(configuration, selection, co_passivation_parameters)

# Select the n_pass last inserted atom and change them to oxygen
N2 = len(configuration.elements())
selection = list(range(N2-n_pass,N2))
configuration = setElement(configuration, selection, Oxygen)

# Again select the inserted atoms (now O) and "passivate" them with H, using SP
selection = list(range(N2-n_pass,N2))
configuration = passivate(configuration, selection, co_passivation_parameters)

In principle this can of course be placed in a script instead, with the small change that you cannot just assign the magical keywords selection and configuration, you need to use a few more command. But doing this first in the Builder means you see exactly what goes on, and you can play with the commands and see what happens.

After this, you should definitely run some geometry optimization, since they inserted atoms are kind of randomly placed (not really random, but certainly not in the perfect positions). It is probably sufficient with a force-field, using Coordinate Tools>Quick Optimizer.

If you will use this function a lot, just click the red/blue icon to the right of the Console and click New snippet. You can insert all the code from above once and for all, save it, and then just re-run it to make a new selection and passivation each time, for the selected atoms (best to leave that part out, so you have control of the selected atoms, either manually or using a command). See picture attached!

Now you will just have to select the atoms, and click "Run".

Have fun, and do let us know how it works out!

Maybe the error is more related to the directories into which the files are copied? There is no direct error message in what you showed indicating the sftp-server is not working, but maybe the default directory where the copy operation goes to is not the "home" directory that the machine manager references...? I'm mostly guessing though, I am not able to install a full Linux subsystem for testing.

Are there further messages in the log file that could help or is that the end of it?

Are you able to copy any files from the machine to itself, using "scp" from the Powershell bash command line?

Questions and Answers / Re: xsf or axsf format file
« on: September 16, 2021, 20:22 »
A few specific data types might be possible to import, like charge density, but we are not putting much priority on interfacing other packages these days, to be honest, especially after we implemented our own plane-wave basis set, and have a much more efficient HSE model in LCAO than you can even find in plane-wave.

So it's much easier to calculate these with QuantumATK, then you can visualize anything you want :-)

Questions and Answers / Re: xsf or axsf format file
« on: September 15, 2021, 21:18 »
Are you thinking of full output files to analyze e.g. the electron density, or you just want to get the atomic structures?
QuantumATK can already read the native QE output files, see

Questions and Answers / Re: OSError: Unable to open file
« on: September 15, 2021, 21:13 »
Looks like the Job Manager settings file(s) have been corrupted somehow. Unfortunately this happens now and then, and can usually be resolved by removing the "job" files in $HOME/.vnl/job_manager_<version>, and if that doesn't work try to also remove the "state.hdf5" file.

Questions and Answers / Re: The setting of Interatomic
« on: September 15, 2021, 21:09 »
Chemical bonding is a surprisingly loosely defined concept! On the input side, in DFT we don't even need bonds for the calculation, only the atom positions.

On the output side, to analyze chemical bonding there are multiple models and theories in the literature, each one having advantages and disadvantages, and yielding slightly different results.

The closest built-in function we have is the Mulliken bond populations (see which at least can give a hint about the degree of bonding between different atoms; also you could quite easily implement Löwdin overlap populations in a script. But more advanced analysis of the type where you break up the electron density into atomistic contributions and use that to ascribe bond strengths etc is not implemented.

What exactly were you looking to compute for your cases, ainunK?

Questions and Answers / Re: MPIDU_Complete_posted_with_error(1710)
« on: September 15, 2021, 20:55 »
I suspect it simply runs out of memory, primarily because the automatic setting for repetitions for the DynamicalMatrix returns 5x5x3, and you end up with each calculation for the displacements having 5*5*3*12=900 atoms.

For a 2D material you only need 1 repetition in the C direction, but your system has a slightly too small vacuum spacing in the Z axis. So you can either increase this vacuum to 20 Å or so (and check in the Scripter or log file that it now correctly detects 5x5x1 repetitions), or just set the repetitions explicitly to 5x5x1 instead (300 atoms, big difference!).

Never seen this, if you can attach the script we can try it in the new version, but 2016 is an ancient version that is no longer supported

I have never tried this on Windows. I think you have the right idea to use the OpenSSH client/server in Windows 10, and the yes, we require bash as the shell (perhaps not mentioned in the manual).

I would have thought OpenSSH handles file copy requests via "scp" protocol but maybe it needs sftp-server started as a service for that to work? I have some trouble installing OpenSSH on my machine, but once I do I can test a few things.

Questions and Answers / Re: hdf5 file is not be saved
« on: August 30, 2021, 19:57 »
I can only guess some file got corrupted, maybe a crash during an exit operation or similar. It is not common so hopefully you should never see this error again :)

The point of the device model is to run transport calculations, not stability. What this means is, unless you suspect that the stability is somehow changed by applying a bias to the device, you should just carry out the stability analysis on the material itself, in a usual bulk or molecule configuration. The same typically goes for optimizing the geometry that goes into building the device. Unless the bias would change the atom positions significantly, we always just create the structure under no bias (in which case we don't need a device configuration or NEGF, which is much slower).

If you run a Spacegroup analysis on this crystal structure, it comes out as Monoclinic. It just so happens that your initial structure has the angle 90 degrees but that can be seen as a special case of a monoclinic lattice. So since the space group is constrained (number 15), it is free to relax this angle. If you want the lattice to remain hexagonal, you need to make sure the symmetries of the atoms actually correspond to a hexagonal space group.

I am not sure what Nb2S4 crystal this is supposed to be... The Nb-S bond length is very large (3 Å) compared to the more common compounds with Nb and S, where the bond is about 2.5 Å only. Are you sure the structure is correct? You can search for and download several Nb+S structure from the Materials Project database within NanoLab, maybe check these out.

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