5011
General Questions and Answers / Re: Error in removing file？
« on: July 13, 2009, 09:59 »
If this becomes a real problem, you may want to instruct your antivirus software to ignore files with the ".nc" extension.
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5012
Scripts, Tutorials and Applications / Re: creation of netCDF files
« on: July 7, 2009, 13:04 »
If you ran this from within VNL (by dropping the script on the Job Manager), the NetCDF file will be created in the system temp directory. This is why the tutorials stress to use an absolute path (like c:/vnl/file.nc).
On Windows the temp directory is C:\Documents and Settings\<username>\Local Settings\Temp, on Linux it's /tmp.
On Windows the temp directory is C:\Documents and Settings\<username>\Local Settings\Temp, on Linux it's /tmp.
5013
General Questions and Answers / Re: DOS for bulk
« on: July 7, 2009, 13:00 »
Tricky bit is you need different algorithms for different dimensionalities, although the most general approach, as used in the 3D bulk case, would work for 1D and 2D (with small modifications).
For spin, Nordland had a suggestion above that certainly would work. However, modifying the script to support spin would perhaps be better; I'll have a look at it!
For spin, Nordland had a suggestion above that certainly would work. However, modifying the script to support spin would perhaps be better; I'll have a look at it!
5014
General Questions and Answers / Re: Do we really have scattering in the "scatering " region ?
« on: July 3, 2009, 23:03 »
All this is absolutely correct.
I just want to add a note, that as ZH already said, the keyword here is coherent transport, which is the regime where the Landauer-Büttiker formalism is valid.
"Scattering" can mean many things, and while ATK does not include any of the inelastic (or elastic, for that matter) listed above, there is still a concept of scattering since the transmission probability of each individual scattering channel may be, and usually is, less than 1.
If you have diffusive transport and remove all scattering centers, phonons, etc, your conductance will go to infinity. This is the "classical zero temperature limit" (which is wrong, as we know). In ballistic transport, conductance is a transmission process, and hence has an upper bound, set by the conductance quantum time the number of modes.
The ballistic regime is obtained when the device size is smaller than the mean free path and the phase decoherence length.
For a more technical presentation, I also recommend another book by Datta, "Electronic Transport in Mesoscopic Systems".
I just want to add a note, that as ZH already said, the keyword here is coherent transport, which is the regime where the Landauer-Büttiker formalism is valid.
"Scattering" can mean many things, and while ATK does not include any of the inelastic (or elastic, for that matter) listed above, there is still a concept of scattering since the transmission probability of each individual scattering channel may be, and usually is, less than 1.
If you have diffusive transport and remove all scattering centers, phonons, etc, your conductance will go to infinity. This is the "classical zero temperature limit" (which is wrong, as we know). In ballistic transport, conductance is a transmission process, and hence has an upper bound, set by the conductance quantum time the number of modes.
The ballistic regime is obtained when the device size is smaller than the mean free path and the phase decoherence length.
For a more technical presentation, I also recommend another book by Datta, "Electronic Transport in Mesoscopic Systems".
5015
General Questions and Answers / Re: DOS for bulk
« on: July 3, 2009, 10:31 »
You are perhaps right, but for the broadening and plotting it doesn't matter where the molecular spectrum comes from 
The ability to compute the full DOS is included as a standard function in ATK (see the manual), while there is a Forum post on how to obtain the PDOS (see http://quantumwise.com/forum/index.php?topic=69.0).
The ability to compute the full DOS is included as a standard function in ATK (see the manual), while there is a Forum post on how to obtain the PDOS (see http://quantumwise.com/forum/index.php?topic=69.0).
5016
Scripts, Tutorials and Applications / Re: ImportError: No module named MonkhorstPack
« on: July 3, 2009, 09:48 »
In the zip file provided along with the tutorial, there is a file called MonkhorstPack.py.
If you are running the scripts from the command line, this file should be placed in the same directory as the main script.
If you are running everything from VNL (by dropping the scripts on the Job Manager), you should place this file in the directory
If you are running the scripts from the command line, this file should be placed in the same directory as the main script.
If you are running everything from VNL (by dropping the scripts on the Job Manager), you should place this file in the directory
- Windows: C:\Program Files\QuantumWise\Virtual NanoLab 2008.10.0\atk\lib\site-packages (modify as needed if you installed the software elsewhere)
- Linux: {vnl}/atk/lib/python2.4/site-packages where {vnl} is the VNL installation directory
5017
General Questions and Answers / Re: ATKError: Species not found
« on: July 1, 2009, 13:50 »
To clarify, this is an unusual error, which doesn't seem related to atom types (like if you just mistyped Phosphorus, which is easy enough to do!), as in that case the file wouldn't run but just return a Python error. This is a C++ error, and might instead indicate a corrupt NetCDF file or something similar.
If you have possibility, I strongly recommend you to upgrade to VNL and ATK 2008.10. You don't specify which ATK version you use, but I assume it's an older version.
If you have possibility, I strongly recommend you to upgrade to VNL and ATK 2008.10. You don't specify which ATK version you use, but I assume it's an older version.
5018
General Questions and Answers / Re: ATKError: Species not found
« on: July 1, 2009, 13:47 »
Can you share the script with us, it makes it a lot easier to troubleshoot.
5019
Scripts, Tutorials and Applications / Re: NLValueError: The self-consistent calculation must contain a two-probe system
« on: July 1, 2009, 12:48 »
This calculation has not finished. Either it's still running, or it was terminated (perhaps due to out of memory, it's quite a big system).
5020
Scripts, Tutorials and Applications / Re: NLValueError: The self-consistent calculation must contain a two-probe system
« on: July 1, 2009, 12:37 »
Any chance you have the log for the 2probe scf calculation? That's where we could see if it converged or not.
PS: If possible, please keep the extension of the files, like .py for scripts and .vnl for VNL files. Makes it easier to download them
PS: If possible, please keep the extension of the files, like .py for scripts and .vnl for VNL files. Makes it easier to download them
5021
Scripts, Tutorials and Applications / Re: NLValueError: The self-consistent calculation must contain a two-probe system
« on: July 1, 2009, 11:39 »
This error can only mean one thing, that the checkpoint (NC) file you are referring to is not a two-probe calculation (or, that the two-probe calculation did not converge).
Perhaps you have mixed up two different file? If possible, please attach the log and input script of the two-probe calculation, perhaps there is some minor typo or so...
Perhaps you have mixed up two different file? If possible, please attach the log and input script of the two-probe calculation, perhaps there is some minor typo or so...
5022
General Questions and Answers / Re: DOS for bulk
« on: June 30, 2009, 10:54 »
As I said, it's really just matter of which atoms you select to project on. You can include or exclude the H atoms, and a certain number of C atoms (you probably don't want them all anyway), it's entirely up to you, and you just need to modify the "projection_atoms" parameter.
5023
General Questions and Answers / Re: DOS for bulk
« on: June 30, 2009, 10:43 »
I think the only difference is which atoms you choose to project on.
The script will work also for a pure molecule, with minor adjustments.
The script will work also for a pure molecule, with minor adjustments.
5024
General Questions and Answers / MPSH DOS
« on: June 30, 2009, 10:10 »
Some people have asked how to plot the DOS like in APL 94, 173110 (2009).
Although it's not explained in detail how the DOS in Fig. 2a is calculated, a reasonable guess is that they have just taken the MPSH spectrum and applied some broadening to the peaks. Attached is a script that shows how to do this!
The only thing you need to do, to use this script to calculate the "MPSH DOS" is to specify, at the top of the script,
Then run the script, either from the command line or by dropping it on the Job Manager in VNL, and pipe the output to a file (or copy the contents of the Log Window in VNL) into the plotting program of your choice.
The output will be two columns, with energy (in eV) and DOS (in a.u.).
Attached is a picture showing the result (plotted in GNUPlot) for Li-H2-Li (projected on the two H atoms, parameters as in the script).
Although it's not explained in detail how the DOS in Fig. 2a is calculated, a reasonable guess is that they have just taken the MPSH spectrum and applied some broadening to the peaks. Attached is a script that shows how to do this!
The only thing you need to do, to use this script to calculate the "MPSH DOS" is to specify, at the top of the script,
- Name of the two-probe checkpoint file (with full path, esp. important if you run the script from VNL)
- MPSH projection atoms
- Broadening (values in the range 0.025-0.1 eV seem reasonable)
- Energy resolution (something like 0.1 eV)
Then run the script, either from the command line or by dropping it on the Job Manager in VNL, and pipe the output to a file (or copy the contents of the Log Window in VNL) into the plotting program of your choice.
The output will be two columns, with energy (in eV) and DOS (in a.u.).
Attached is a picture showing the result (plotted in GNUPlot) for Li-H2-Li (projected on the two H atoms, parameters as in the script).
5025
General Questions and Answers / Re: How to build two probe system based on graphene ribbon of deformation ?
« on: June 29, 2009, 18:37 »
One way to do this would be to build perfect "building blocks" (without strain) and then bring them into the Bulk Builder. If you keep the fractional coordinates fixed, but change the unit cell, then you obtains a stretched structure! Then just just put the pieces back together again (electrode + central region).
This is quite easy to do as long as the deformation is parallel or perpendicular to the transport directions. Well, anyway, you can always decompose a general deformation in two components, as long as it's a simple strain (or even some version of hydrostatic pressure) and not a "shear" stress.
This is quite easy to do as long as the deformation is parallel or perpendicular to the transport directions. Well, anyway, you can always decompose a general deformation in two components, as long as it's a simple strain (or even some version of hydrostatic pressure) and not a "shear" stress.