Messages

61

General Questions and Answers / Re: Using MTP forcefield that has more than required elements

« on: February 9, 2024, 20:30 »

Yes, that should be safe with any MTP. The question on transferability of forcefields is more about which kinds of systems they are fitted for, rather than the exact amount of elements. You could for example have a forcefield for carbon, but it's only created for diamond, so it would not work for graphene. In the MTP case for GeTe, it's fitted and tested for both crystalline and amorphous materials (mainly 3D), so for your purposes it should work fine.

62

General Questions and Answers / Re: Phonon spectrum error

« on: February 5, 2024, 19:52 »

Just now noticed that the error appears in an older version (2022.03). We strongly suggest running with the new 2023.12, containing many new features and at least in this case also possibly a fix for this problem (by accident or some bug we solved).

63

General Questions and Answers / Re: Error on Cluster

« on: February 2, 2024, 20:15 »

In almost all cases it means the calculation ran out of memory. There are many techniques to reduce memory, incl. different parallelization strategies, see https://docs.quantumatk.com/manual/technicalnotes/advanced_performance/advanced_performance.html

64

General Questions and Answers / Re: ComplexMatrix error in fatbandstructure calculation

« on: January 31, 2024, 23:08 »

We have tried to run the system and didn't have any problem. It does use a lot of memory, so a suggestion is to reduce the number of bands above the Fermi level (50 should be enough), and maybe also the number of points on the segments. It's also possible the DOS takes up a lot of memory, so you can rerun without including that. Note that you don't need to rerun the whole calculation, just the FatBS part, replacing the "update" and "nlsave" lines with a corresponding

mos2_wte2_60degree_ortho_pointcheck = nlread("MoS2_WTe2_60degree_ortho_pointcheck_results.hdf5", BulkConfiguration)[-1]

65

General Questions and Answers / Re: Phonon spectrum error

« on: January 29, 2024, 19:37 »

We are investigating

66

General Questions and Answers / Re: Transmission with Different electrodes

« on: January 26, 2024, 20:53 »

Zero bias really just means no external bias. If the two electrodes are different, they will have different Fermi level and thus an internal bias still exists. So there is no special treatment of this case, the calculations proceed as for any device, except that the crucial in which the two Fermi levels are brought into alignment (no bias!) results in a shift of the bands in one electrode, and a current will flow from occupied to unoccupied bands (but backwards, since current is opposite electron flow). That is why left-right and right-left currents might differ in this case.

67

General Questions and Answers / Re: Output file of IV is not printing

« on: January 26, 2024, 20:47 »

I suppose it will print it when it's finished. Note that the IVCharacteristics study object is designed to run a lot of different calculations distributed across many (very many!) nodes and cores, so it will wait to collect all results until the end, as some tasks might finish before others.

68

General Questions and Answers / Re: Length of left and right electrode

« on: January 26, 2024, 20:42 »

If they not made of the same material, they should not be equal... Each electrode should have the length needed to make it periodic.

69

General Questions and Answers / Re: Device design

« on: January 26, 2024, 20:42 »

It's really not possible to answer better than the general info unless you share what the system looks like, in detail. You can email the Python file to me if you don't want to share it publicly.

70

General Questions and Answers / Re: Papers related to DFT-PPS method

« on: January 24, 2024, 21:06 »

Correct, but HSE with LCAO is still reasonable for NEGF, we have tested it with 1000+ atoms. Needs a lot of memory though, that might be an even larger benefit of ADMM which, for now, we cannot obtain in NEGF,

71

General Questions and Answers / Re: Device design

« on: January 22, 2024, 22:17 »

It's kind of hard to do by yourself, it's really best to let the Builder do it. In theory the method is simple though, you need to identify a part of the left and right sides that are periodic, and then extend these in both directions. You can practice or test with a much simpler configuration, or see https://docs.quantumatk.com/tutorials/atk_transport_calculations/atk_transport_calculations.html for some guidance. But getting the exact script right by hand requires a bit of experience, for sure.

72

General Questions and Answers / Re: Phonon spectrum error

« on: January 22, 2024, 21:58 »

Looking at the structure, I would recommend centering the atoms in the Z direction, so that the 2D sheet is in the middle of the cell, instead of straddling the periodic boundary, since the structure is actually not supposed to be periodic in the Z direction (although it always will be in practice, but with a large vacuum gap). Perhaps the algorithm doesn't know what to do when there are bonds and symmetries extended across a direction in which you have 1 repetitions for the dynamical matrix, as you correctly should have for this calculation.

So, in the Builder, just shift all atoms by say fractional 0.3 in the z direction, then wrap and center, and try that geometry instead.

Also, remember to check if the structure is optimized first. It seems somewhat unlikely that the lattice constant will be EXACTLY 4 Angstrom...

73

General Questions and Answers / Re: IV-curve question

« on: January 19, 2024, 02:01 »

It will do it inside if needed, but if you leave the update line it will not do it twice.

74

General Questions and Answers / Re: Can't find builder(bulk, selection, device etc.) tools on the right

« on: January 19, 2024, 01:53 »

The toolbar can be detached and made floating. Probably it's on a second screen or hiding behind another window on your desktop, but you can always restore it via the menu View>Restore Builder layout.

Edit: Oh, you say that doesn't work, that is indeed puzzling...

Try to open $HOME/.quantumatk/main.ini and remove the line DockState in the Builder section (make a backup of this file first).

75

General Questions and Answers / Re: problems with Hgga_hse06 and MGGA calculation to transmission spectrum

« on: January 19, 2024, 01:46 »

A few things to check and comment on here.

First, do you see the same thing with LDA or GGA, i.e. is it specifically a problem of MGGA? If it is, it makes it a bit more interesting to investigate.

However, apart from perhaps a somewhat instructive tutorial example, the calculation doesn't really have any value. The transmission spectrum of any bulk material should really just be counting the states at each energy; in 1D this is trivial and gives you an integer staircase, while in 2D and 3D it's a bit more complex due to k-point sampling, but conceptually still the same. To make an interesting calculation, one should create an extended device with some scattering centers. If also in this case the transmission is non-zero in the band gap, I agree there is a big problem, but we have never seen that.

Now, I am not trying to minimize the potential issue, we should probably look into it, but it's also not a serious problem if this is isolated to the bulk transmission, as that is generally not something you need to compute; we support it mainly for legacy reasons. Or, to some extent for educational purposes, so again, it should of course calculate it correctly. Thus, if you can check it with LDA also, it will help us a bit.