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Messages - Anders Blom

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Questions and Answers / Re: Phonon transmission spectrum
« on: November 19, 2020, 09:10 »
You are using an old version which is no longer supported, but the main problem (although we cannot see you input script) is probably that with your settings a lot of DFT calculations are started at the same time, on that single machine. Each supercell for the dynamical matrix will be 5x5x1 times the original one, which is a very large calculation. Unless you tell the program to only run 1 displacement per node, it will almost certainly run out of memory. In newer versions the default has been updated, but in older version, set the keyword processes_per_displacement in HamiltonianDerivatives/DynamicaMatrix to the number of MPI processes (or number of cores per node, if you run over many nodes) to avoid this.

It's very hard to give a definite answer, but as you noted the Huckel model is actually designed to be non-selfconsistent, and is also originally developed for organic systems, so I think at the very least the results will be "representative" enough to use for real work. You can perhaps search the literature for other work on similar systems using the same model, and see how they treat SCF vs non-SCF.

Actually, if I recall correctly, we mainly added the SCF option for the semi-empirical models to use them in transport simulations, where definitely the effect of charge transfer is crucial, and a non-SCF solution would not be accurate.

Btw, it is not entirely impossible to use DFT for the system size  you mention, at least with a small basis set like SingleZetaPolarized. You might want to give it a try at least :-)

Questions and Answers / Re: Ge Bandstructure pps-PBE
« on: October 8, 2020, 07:36 »

the best approach is to define the PPS explicitly, in the script, like so:

Ge_projector_shift = PseudoPotentialProjectorShift(
basis_set = BasisGGASG15.Germanium_Medium(projector_shift=Ge_projector_shift)


Si_projector_shift = PseudoPotentialProjectorShift(
basis_set = BasisGGASG15.Silicon_Medium(projector_shift=Si_projector_shift)

The reason for this is, that the values for the s,p,d shifts must always be optimized for the material at hand, and also for the pseudopotential used, and perhaps also depending on if you use PBE, revPBE, or LDA, to ensure they provide the best possible values for the band gaps and notably, the lattice parameters (if you also want to use the PPS basis set for geometry optimizations). Just like +U parameters, really.

The built-in basis sets referenced in the tutorial have pre-optimized values that I have quoted above, but these are actually a compromise, to give the best combination of band gaps and lattice parameters. They are only defined for SG15, and only for PBE (notably, the Ge lattice constant comes out a lot better with PBEsol). If you are not going to optimize the structure, you can actually get better band gaps with slightly different parameters.

And of course, the PPS approach is not limited to Si and Ge, so for any new material, the code above shows how to create a PPS basis set for a general case.

2.txt is not a valid CIF file, or at least a "sloppy" one. It declares the start of a section (_symmetry_equiv_pos_as_xyz) which should contain the symmetry operations, but there are none listed. Removing lines 22 and 23 should solve it, or one can add the same lines 24 and 25 from 1.txt.

Well, only in theory, if you assume the 2D layer to infinitesimally thin. You will still see reported measured values given in C/m^2 (such as in To convert to a pure 2D quantity you could multiply by the physical thickness of the 2D layer, but this is hard to estimate.

Questions and Answers / Re: Calculating and plot dI/dV
« on: October 5, 2020, 19:14 »
This method will just return dI/dV for the given transmission spectrum. You will have to collect the values and print them as a function of the bias yourself.

Questions and Answers / Re: Warning on calculating FET
« on: October 2, 2020, 21:07 »
You can ignore this, it's just an information message about the internal workings of the algorithm in QuantumATK

It works just the same way, except you don't need any k-points in the non-periodic direction. QuantumATK, like most codes, treats 2D materials as 3D as well, just with a large vacuum region between each sheet to avoid electrostatic or direct interactions.

Looks like a problem with a particular file in the current project you are in. Does it work ok if you switch to another project?

You can always remove a project from the program (from the Switch project dialog), it doesn't delete any data. Then delete the file project.ini in the actual project itself; again, this doesn't delete any real data, only information about which files are checked etc.

Once you have it back to working condition, you can in principle try to figure out which file that is causing problems by checking them one by one.

Questions and Answers / Re: DOS vs projected DOS
« on: October 2, 2020, 20:53 »
Hard to tell why numbers are different in the two cases without seeing the exact input script. Could be a difference of the energy sampling, like if you are hitting the Fermi level exactly or it's interpolated, same with the Tetrahedron vs Gaussian method, which also depends on k-point sampling. So, please show input and output, else the best anyone can do is guess, and that doesn't typically help resolve an issue like this.

Just add a plot style argument to each plot command. If you want a blue dashed line:

aa.plot(t.energies(), f,t.evaluate(), 'b--', zorder=6,label='1.0 V', )

or more explicitly

aa.plot(t.energies(), f,t.evaluate(), zorder=6, label='1.0 V', color='blue', linestyle='--')

For more  info, see

Questions and Answers / Re: Calculating and plot dI/dV
« on: October 2, 2020, 20:47 »
Use the conductance() query method on the TransmissionSpectrum (

Questions and Answers / Re: IV Characteristic
« on: October 2, 2020, 20:44 »
You can, however, do it manually by just computing the currents without using the IVCharacteristics workflow.

Questions and Answers / Re: superconducting
« on: October 2, 2020, 20:40 »
Maybe :) It is not on our immediate roadmap, but the more users ask for it, the more relevant it might become!

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