5026
General Questions and Answers / Re: Error about runtime_parameters
« on: June 29, 2009, 13:09 »Code
if processIsMaster(): file.addToSample(equiv_bulk, 'Au_Z7_Au equivalent bulk system')
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5027
General Questions and Answers / Re: Error about runtime_parameters
« on: June 29, 2009, 11:11 »
Pardon the short answer, I hope it speaks for itself 
http://quantumwise.com/documents/manuals/ATK-2008.10/ref.twoprobeconfiguration.html
Code
equiv_bulk = two_probe_configuration.equivalentBulkSystem()
http://quantumwise.com/documents/manuals/ATK-2008.10/ref.twoprobeconfiguration.html
5028
General Questions and Answers / Re: How to build two probe system based on graphene ribbon of deformation ?
« on: June 26, 2009, 11:09 »
Are the deformations uniform, i.e. corresponding to a stretch of the ribbon in some direction, or local, i.e. different for different sites? If the former is the case, we can probably quite easily figure out how to stretch the unit cell. If the latter, I think you have to do it by hand...
5029
Links to Resources and Publications / Re: Papers from 2009
« on: June 26, 2009, 10:56 »
There are several new publications for 2009 added to the Publication page, on a lot of exciting topics like
Plus of course all the nice work done in 2008, 2007, 2006, ...
- Fermi Level Unpinning and Schottky Barrier Modification by Ti, Sc and V Incorporation at NiSi2/Si Interface
- Strong Conductance Variation in Conformationally Constrained Oligosilane Tunnel Junctions
- Symmetric I-V curves in asymmetric molecular junction of monothiolate alkane
- Rectifying Effect in Polar Conjugated Molecular Junctions
- Designing Nanogadgetry for Nanoelectronic Devices with Nitrogen-Doped Capped Carbon Nanotubes
- Junctions between carbon nanotubes and graphene nanoribbons
- Electron Transport Through Oligoacenes
- Effects of nonmagnetic impurities on the spin transport property of a graphene nanoribbon device
- Graphene nanoribbon as a negative differential resistance device
- Transitions between semiconductor and metal induced by mixed deformation in carbon nanotube devices
- Screening effects in molecular junctions in the Coulomb blockade regime
- Electron Transport Path through the Porphyrin Molecules and Chemisorption of CO
- Manipulating Spin Transport via Vanadium-Iron Cyclopentadienyl Multidecker Sandwich Molecules
- Transport properties of silicon-carbon (Si-C) and alumium-nitrogen (Al-N) nanowires
- Electronic transport properties in doped C60 molecular devices
- Improving gas sensing properties of graphene by introducing dopants and defects
- Electronic transport properties of a diarylethene-based molecular switch with single-walled carbon nanotube electrodes: The effect of chirality
- The size effects of electrodes in molecular devices (transport properties of C60)
Plus of course all the nice work done in 2008, 2007, 2006, ...
5030
General Questions and Answers / Re: Where is the equlibrium fermi level ?
« on: June 25, 2009, 18:50 »
The Fermi level is always computed in the same way, regardless of whether spin is involved or not. The Fermi level is computed such that the total occupation of all level matches the total number of electrons in the system. If the calculation is spin-polarized, some of the levels are spin-up levels and some spin-down, with different energies (they are degenerate if no spin is involved) but there is just one common Fermi level.
5031
Future Releases / Re: Could ATK compute the material's property and transport under magnetic field?
« on: June 25, 2009, 18:43 »
No, sorry, this is currently not possible.
5032
General Questions and Answers / Re: Fermi energy misalignment in graphene-based models
« on: June 22, 2009, 22:15 »
Also note that ATK is parallelized over the transverse k-points, so if you're running on a cluster, and you're in a situation where you are using a lot of k-points, increasing the number of MPI nodes, if possible, can have a substantial influence on the performance.
5033
General Questions and Answers / Re: how to get the table?
« on: June 22, 2009, 16:08 »
You have built a very beautiful and interesting system, but the central region is not a molecule, so it makes no sense to talk about a "molecular" projected Hamiltonian or HOMO/LUMO; these are all concepts related to finite system, not nanowires.
Your nanowire is probably semiconducting, which would explain the small transmission. But at any rate, the relevant concepts are the band structure of the nanowire, and other bulk concepts.
Your nanowire is probably semiconducting, which would explain the small transmission. But at any rate, the relevant concepts are the band structure of the nanowire, and other bulk concepts.
5034
General Questions and Answers / Re: how to get the table?
« on: June 22, 2009, 15:40 »
The MPSH concept as such does not really apply to the kind of system you have, since there is no well-defined "molecule" for which you can compute the spectrum in the absence of the electrodes, to compare to the MPSH spectrum (molecule with electrodes).
5035
General Questions and Answers / Re: how to get the table?
« on: June 22, 2009, 10:16 »
Yes, the marks in Figs. 3 and 5 are the MPSH eigenvalues. However, to get the correct spectrum you must project the Hamiltonian onto the molecule atoms only; from the number of eigenvalues, I believe in your case you have not selected any projection atoms.
Also, I wouldn't expect to get the same results as in that paper, since your electrodes are Li, while the paper used Au.
Also, I wouldn't expect to get the same results as in that paper, since your electrodes are Li, while the paper used Au.
5036
Future Releases / Re: Voltage sweep command would be useful
« on: June 22, 2009, 09:23 »
There isn't really anything magical about sweeping the voltage. The script showed in the post you refer to can by tweaked extremely easily to support a different kind of sweeping. All you need to do, basically, is modify the "voltages" list. For instance, to run from 0 V to -3 V in steps of 0.5 V, use
or for more flexibility, use NumPy:
and so on. You can just as well sweep backwards,
but note that it can be hard to converge the high-bias calculation without initializing it from a lower-bias self-consistent density.
The updated version of the ivcurve script in this post should also be of relevance, esp. for the case of starting from a high bias, which perhaps is converged by climbing up from zero bias.
Code
voltages = [0.,-0.5,-1.,-1.5,-2.,-2.5,-3.]*Voltor for more flexibility, use NumPy:
Code
import numpy
voltages = numpy.linspace(0.,-3.,7)*Voltand so on. You can just as well sweep backwards,
Code
voltages = [3,2,1,0]*Voltbut note that it can be hard to converge the high-bias calculation without initializing it from a lower-bias self-consistent density.
The updated version of the ivcurve script in this post should also be of relevance, esp. for the case of starting from a high bias, which perhaps is converged by climbing up from zero bias.
5037
General Questions and Answers / Re: how to get the table?
« on: June 22, 2009, 09:11 »
You have mixed up completely different concepts here, I'm afraid
THE MPSH eigenvalues, as used in the reference you mention, show how the molecular levels are affected by the coupling to the electrodes. MPSH = molecular projected self-consistent Hamiltonian. By diagonalizing this projected Hamiltonian, and comparing the eigenvalues to the isolated molecule, you can see how the levels are shifted due to the influence of the electrodes. Often, it's the change of the HOMO-LUMO gap which is of interest.
The transmission eigenvalues show how the transmission spectrum is broken down into components. For a particular energy E, there may be several channels contributing to the transmission, and by computing the transmission eigenvalues you see how many. Each transmission eigenvalue must be <=1 but the total transmission T(E) can be > 1 if you add up the channels.
In your case, the transmission eigenvalues are all zero, meaning the transmission itself at this energy is also zero.
THE MPSH eigenvalues, as used in the reference you mention, show how the molecular levels are affected by the coupling to the electrodes. MPSH = molecular projected self-consistent Hamiltonian. By diagonalizing this projected Hamiltonian, and comparing the eigenvalues to the isolated molecule, you can see how the levels are shifted due to the influence of the electrodes. Often, it's the change of the HOMO-LUMO gap which is of interest.
The transmission eigenvalues show how the transmission spectrum is broken down into components. For a particular energy E, there may be several channels contributing to the transmission, and by computing the transmission eigenvalues you see how many. Each transmission eigenvalue must be <=1 but the total transmission T(E) can be > 1 if you add up the channels.
In your case, the transmission eigenvalues are all zero, meaning the transmission itself at this energy is also zero.
5038
Scripts, Tutorials and Applications / Re: Script for calculating the effective mass in semi-conductors.
« on: June 17, 2009, 10:20 »
Please note that the symmetry points for tIn (body-centered tetragonal) and the orthorhombic ones are under evaluation. I just found some mistakes in them. I will post an update as soon as possible.
5039
Installation and License Questions / Re: No Display found. Running in console mode not supported.
« on: June 17, 2009, 09:55 »
The best thing is always to install and run VNL on your local computer, not on the server. It's only the license that must reside on the license server, since it's locked to that host.
5040
Scripts, Tutorials and Applications / Re: Script for calculating the effective mass in semi-conductors.
« on: June 16, 2009, 21:49 »
Some caution is required. The 111 direction is not necessarily the same as (1,1,1) in units of the primitive reciprocal lattice vectors. The "111" direction refers to the corresponding conventional system, thus in each case one needs to consider which combination of the primitive vectors that make up this "Cartesian" direction. For fcc, it is towards the X-point at (1,1,1)/2, i.e. the relevant point to use in this script would rather be (1e-6,0,1e-6).