5071
General Questions and Answers / Re: About MPSH
« on: May 31, 2009, 22:28 »
I suppose the system is metallic in the central region.
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5072
General Questions and Answers / Re: How to calculate the density of states (DOS) of isolated region in graphene?
« on: May 29, 2009, 15:29 »
Yes and no 
You approach will give the molecular energy levels of the isolated segment corresponding to the central region. This does not take into account the possible shifts of these levels induced by the coupling to the electrodes. Moreover, if you just take out a piece of graphene ribbon like that without considering the edge termination etc, you may get the wrong results. Also, the alignment of the level w.r.t. the Fermi level of the transmission spectrum will not be correct.
A more proper approach is to use the functionality in ATK called MPSH spectrum. Some details can be found in the manual, and you can also search the Forum for "MPSH". This way you get is the molecular spectrum taking into account the electrode coupling, normalized to a common Fermi level.
I have not made the bilayer structures, because as I said there it depends on how the edges should look like. If you have an idea about how you would like them, then I can look into the Python code to make it.
You approach will give the molecular energy levels of the isolated segment corresponding to the central region. This does not take into account the possible shifts of these levels induced by the coupling to the electrodes. Moreover, if you just take out a piece of graphene ribbon like that without considering the edge termination etc, you may get the wrong results. Also, the alignment of the level w.r.t. the Fermi level of the transmission spectrum will not be correct.
A more proper approach is to use the functionality in ATK called MPSH spectrum. Some details can be found in the manual, and you can also search the Forum for "MPSH". This way you get is the molecular spectrum taking into account the electrode coupling, normalized to a common Fermi level.
I have not made the bilayer structures, because as I said there it depends on how the edges should look like. If you have an idea about how you would like them, then I can look into the Python code to make it.
5073
General Questions and Answers / Re: How to calculate the density of states (DOS) of isolated region in graphene?
« on: May 29, 2009, 08:49 »
They don't explicitly write how they compute the "scattering region DOS" shown in the APL paper you mention (which is a very recent and nice application of ATK to graphene), but my guess is they perform a molecular calculation for the central region (more specifically, I think they use the MPSH functionality in ATK for this), and then plot the energy levels broadened by some Gaussian distribution. It doesn't really matter, they could just as well just have plotted the DOS as sharp molecular level, since the peaks are so narrow anyway.
5074
General Questions and Answers / Re: How to set up bilayer graphene model?
« on: May 29, 2009, 08:37 »
Yes, we sure do use ATK for the simulations
I guess some care has to be taken when setting up a bilayer structure, when it comes to the edge termination. It's probably a good idea to see how others have tackled this (e.g. APL 92, 223106 (2008)).
I guess some care has to be taken when setting up a bilayer structure, when it comes to the edge termination. It's probably a good idea to see how others have tackled this (e.g. APL 92, 223106 (2008)).
5075
General Questions and Answers / Re: How to set up bilayer graphene model?
« on: May 28, 2009, 10:28 »
You can use graphite for this, by just changing the c lattice constant while keeping the layer separation fixed. Are you considering ribbons or infinite graphene? Or rather, where do you take the graphene model from, from the Crystal Cupboard or the graphene tutorial scripts?
5076
General Questions and Answers / Re: How to calculate the density of states (DOS) of isolated region in graphene?
« on: May 28, 2009, 10:26 »
The question is a bit ambiguous. The concept of density of states applies to a system which is infinite and periodic in at least some directions. Therefore, there is no DOS for an isolated region... Or, well, you can of course say that a molecule has a spectrum of delta function-like spikes, which is like a DOS.
But perhaps you mean more something like the DOS for an infinite 2D sheet of graphene, or something like that?
But perhaps you mean more something like the DOS for an infinite 2D sheet of graphene, or something like that?
5077
General Questions and Answers / Re: Speed issue in Two probe configuration
« on: May 26, 2009, 10:43 »
The 8 and 16 CPUs, how are the distributed w.r.t. RAM? That is, for 8 CPUs, for instance, are they located in 8 separate boxes, or in 4 machines with two sockets, or 2 machines with 4 sockets, for instance? Same for the 16.
Competition for RAM, cache and communication bandwidth will depend critically on these factors.
Competition for RAM, cache and communication bandwidth will depend critically on these factors.
5078
General Questions and Answers / Re: Speed issue in Two probe configuration
« on: May 26, 2009, 09:20 »
I was just about the suggest running without MPI...
Cache size can certainly play a role when you are shuffling huge amounts of data around.
Another thing, do you have the same OS on both machines?
When you measure the time per SCF cycle, is that done by taking the total compute time divided by number of steps, or timing of each cycle (using verbosity=20)? If you use the total time, note that the calculation may take different number of steps on the two machines in the MPI case, so take care to normalize by each respective number of steps...
Cache size can certainly play a role when you are shuffling huge amounts of data around.
Another thing, do you have the same OS on both machines?
When you measure the time per SCF cycle, is that done by taking the total compute time divided by number of steps, or timing of each cycle (using verbosity=20)? If you use the total time, note that the calculation may take different number of steps on the two machines in the MPI case, so take care to normalize by each respective number of steps...
5079
General Questions and Answers / Re: question about calculate the local_density_of_states
« on: May 26, 2009, 09:11 »
Did you figure it out? I got a notification of a reply to this topic, but it seems you deleted you post? Hope it means all is working
5080
General Questions and Answers / Re: Cannot run script in parallel
« on: May 25, 2009, 21:03 »
My primary suggestion would be to generate the structures first, in serial, on your local machine. Then you read in the geometries when you perform the calculations in parallel. That way you have no randomness in parallel. Generating the geometries anyway will not parallelize, so there is no performance difference.
Otherwise it seems you already have a "parallel" random function, the one you posted. I'm not how it can be improved because you need a seed which is common on all nodes, but you have no way of communicating it between the nodes, so it must be taken externally. In principle you can use any combination of day of week, year, minute, hour, etc..., all of which are common on all nodes.
Otherwise it seems you already have a "parallel" random function, the one you posted. I'm not how it can be improved because you need a seed which is common on all nodes, but you have no way of communicating it between the nodes, so it must be taken externally. In principle you can use any combination of day of week, year, minute, hour, etc..., all of which are common on all nodes.
5081
General Questions and Answers / Re: How to set up the parameters to "Geometric Constraints" in VNL?
« on: May 25, 2009, 16:09 »
The electrode atoms cannot be moved during a relaxation, so if all atoms in the central region will be allowed to move, you do not need to set up any constraints. However, it is often a very good idea to keep at least the first layer or two of the surface region (the part of the central region which is like the electrodes) fixed to have a better match to the electrodes, and to reduce the computation time.
5082
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?
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?
5083
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.
5084
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.
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.
5085
General Questions and Answers / Re: Choice of basis
« on: May 24, 2009, 22:34 »
A concrete example should make it clear.
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.
Quote
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.