Messages

5086

General Questions and Answers / Re: Speed issue in Two probe configuration

« on: May 25, 2009, 15:26 »

It's kind of hard to troubleshoot such things remotely... Is the difference reproducible each time you run? No other jobs running that might load the nodes with other jobs?

You write threads, but I assume you mean MPI nodes, i.e. on the 8-node cluster you run mpiexec with "-n 8", and "-n 16" on the 16-node cluster?

5087

Scripts, Tutorials and Applications / Re: Script for calculate the bandgap.

« on: May 25, 2009, 09:13 »

The way the picture looks, this system is metallic and hence there is no band gap. The script assumes a band gap exists; if it doesn't you may indeed get weird results. This is a good example of the importance of not just applying a script like this and trust the results blindly, but one must always investigate the results in detail.

5088

General Questions and Answers / Re: question about calculate the local_density_of_states

« on: May 25, 2009, 09:05 »

Sure, it just requires a bit of manual scripting. Use the toArray() function to extract the data as a Numpy array, then you can manipulate the data as you want.

For a similar example, see http://quantumwise.com/forum/index.php?topic=21.0; the script voltagedrop.py in first post there shows how to extract the data and do some simple manipulations. Also see http://quantumwise.com/forum/index.php?topic=39.0.

5089

General Questions and Answers / Re: Choice of basis

« on: May 24, 2009, 22:34 »

A concrete example should make it clear.

Hydrogen
Valence: 1s
SZ: s
DZ: s s'
SZP: s p
DZP: s s' p
DZDP: s s' p p'

Gold
Valence: 6s 5d^10
SZ: s d
DZ: s s' d d'
SZP: s d p
DZP: s s' d d' p
DZP: s s' d d' p p'

By s' we here mean a second s orbital (same major quantum number) to add more radial degrees of freedom; the polarization functions add angular degrees of freedom.

The major quantum number are excluded since the basis orbitals are based on the pseudocore atom. Thus, the 6s valence electrons in the basis set for gold really look like 1s wavefunctions.

For a list of the valence as used by ATK, see http://quantumwise.com/documents/manuals/ATK-2008.10/ref.atomdata.html.

5090

General Questions and Answers / Re: question about calculate the local_density_of_states

« on: May 24, 2009, 19:25 »

My guess is that you used VNL to generate the script, and ticked the box to restore self-consistent calculation from checkpoint. In that case, to proceed with analysis and calculating the LDOS etc, you must also remember to untick the box "Only use initial density" (which is used when you wish to restart a calculation).

5091

General Questions and Answers / Re: two questions on "method" setup in VNL

« on: May 24, 2009, 19:21 »

Confusing as it may be, the "charge" in the basis set parameters has nothing to do with the charge of the atom. It's just a parameter used to generate the basis set. All atoms are assumed to be neutral in ATK, but charge transfer can (and will) occur in a two-probe system.

5092

General Questions and Answers / Re: question about calculate the local_density_of_states

« on: May 24, 2009, 11:10 »

This error does not arise from the lines of code you have quoted, but somewhere earlier (probably) in the script. Most likely you are trying to initialize a new calculation based on an existing checkpoint file (nc file). This only works if they systems are identical in terms of atoms, their order, and the basis set.

The notation for the quantum numbers can be a bit tricky. For the example you show it's a single k-point, at the Fermi energy (given separately) for spin down.

5093

General Questions and Answers / Re: How to set the Quantum numbers when calculating the MPSH?

« on: May 22, 2009, 22:40 »

The VNL checkboxes are really just a quick way to select certain atoms (which, anyway, doesn't work unless the structure conforms to the surface/molecule/surface model). The wavefunctions are always indexed to match the eigenvalues (the spectrum), starting at 0.

5094

General Questions and Answers / Re: Speed issue in Two probe configuration

« on: May 22, 2009, 18:29 »

Do you use the exact same parallelization strategy on the two cluster? I'm particularly referring to the loading of MPI nodes vs. CPUs w.r.t. the number of cores/sockets. You should avoid using more MPI nodes than physical nodes (i.e., if you have for instance 2 dual cores, you may not get very good performance using 4 MPI nodes on this system).

Also, sometimes on Linux the OS will not show the correct number of cores to thread on to the application. You can ensure ATK knows how many threads it can start on each node by setting MKL_NUM_THREADS by hand (see the manual!).

5095

General Questions and Answers / Re: Choice of basis

« on: May 22, 2009, 17:44 »

There is a fundamental difference between TB and the orbitals that are used in e.g. DFT. In TB you focus on the bonds between neighboring atoms, while the orbitals used in ATK are used to expand the electron density in the vicinity of each atom. In this case, the "bonding" comes about from overlap of such orbitals between atoms within a certain range. In ATK we use orbitals with a finite range (hard cutoff), and atoms within this range have a chance to "bond" in this way. The range is independent of the basis set type, but can be controlled by the "energy shift", as described in the manual.

For more information, see also http://quantumwise.com/documents/manuals/ATK-2008.10/ref.atomicorbitals.html.

5096

Scripts, Tutorials and Applications / Re: Script for calculate the bandgap.

« on: May 15, 2009, 13:16 »

The value for (7,0) seems fine, while the negative value for (6,0) probably is due to the fact that it's semi-metallic.

I suggest you look at a plot of band structure and try to relate it to the numbers you get. If you attach those plots (properly zoomed in around the Fermi energy), we can understand the situation better.

5097

General Questions and Answers / Re: question about Li-H2-Li two-probe system

« on: May 14, 2009, 08:38 »

Most likely the calculation has converged to a state with zero charge in the entire system. Au is trickier than Li and requires not only a bit higher temperature but most likely also a longer electrode.

5098

General Questions and Answers / Re: question on two-probe model setting up

« on: May 13, 2009, 13:37 »

It seems your pictures did not get attached to the post.

When it comes to selecting the Li atom, you will not see the actual atom get selected, that's true (and a bit confusing). You just need to have the mouse over it when you right-click to choose translate. Hope this helps.

5099

General Questions and Answers / Re: DOS did not correspond to the T(E)

« on: May 13, 2009, 13:13 »

I don't see any disagreement in the data, I think everything looks fine.

Except for one thing, maybe: the transmission of the pristine CNT should have integer plateaus, as you roughly have. But the "rounding" of the edges indicates that perhaps you have too short electrodes, or maybe even too small unit cell in the XY directions. Unless, that is, you simply have too few points on the black curve (fewer than for the blue and red). But it should really look like a step function, with the slanted parts.

I suggest you use 200 points or so for these plots, and check if the T(E) is really step-like for the pristine tube. But, otherwise in general, I don't see any problems.

5100

General Questions and Answers / Re: What's the physical insight of the variation of HOMO and LUMO with bias voltage?

« on: May 13, 2009, 13:01 »

What complicates matter in this case is that your electrodes are semi-conducting. Thus, I suspect you have no current in the low-bias calculations. However, as the bias exceeds the band gap, you start to get tunneling from the valence band of the left electrode to the conduction band of the right one, via the molecule. I imagine this somehow pins the HOMO to the valence band top of the left electrode, perhaps.