Messages

5131

General Questions and Answers / Re: calculateEnergyBands() and hexagonal lattice

« on: May 7, 2009, 02:55 »

Yes, you are correct General W

A point (k1,k2,k3) is located at k1*b1+k2*b2+k3*b3 in reciprocal Cartesian space, where bi (i=1,2,3) are the reciprocal unit vectors.

As Quantamania suggests, you'll want to run your calculation via the symmetry points, and VNL automatically suggests such a route for you, except it doesn't tell you the labels of those points.

We're working on a much improved way to compute band structures; there is a prototype tutorial (note: this link may stop working when the tutorial is published; if so, look for it at the general Tutorial page). To run those calculations, you also need the scripts attached to this post.

5132

General Questions and Answers / Re: Is the negative current meaningful?

« on: May 6, 2009, 05:02 »

None of these calculations have converged to a meaningful state, so the current is also wrong. Well, it's zero (1e-21 Ampere is zero) as expected since there are no electrons in the system any more (q is also zero, almost).

This is one of the most usual problems in calculations, and there are many discussions on the Forum how to cure the problem (search for "zero charge"). Most important is to have a wide enough electrode, after that to have enough k-point sampling and perhaps increase the temperature.

If you post the geometry and parameters, we can perhaps give more direct tips on where to improve it. Also see the Tutorial on how to converge FeMgO for specific hints on avoiding charge run-away.

5133

Scripts, Tutorials and Applications / Re: Script for creating nanotubes

« on: May 5, 2009, 14:37 »

I guess you meant R, not P.

Just to be clear: padding is NOT the same thing as screening. The screening layers are part of C.

Again, from the perspective of how you set up the geometry, you specify to the program a "left electrode", a "right electrode", and a "central region" geometry. These are L, R, and C, and they are stitched together as L-C-R. The voltage drop etc occurs over this region. The whole padding idea is really just related to how the code handles things internally.

5134

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 5, 2009, 05:12 »

Thanks for the invitation! I have been to Beijing once, a few years ago. I enjoyed it very much, although it was very cold (November)

5135

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 5, 2009, 04:52 »

I must really apologize, it was a typing mistake on my part (which is obvious from the error message ). It should be isProcessMaster(), not isProcessMaster. Small details, simple to find when you know. And yes, I should have tested the script in parallel, but as I wrote before I forgot to do it, and right now I don't have any parallel computer at hand (I'm travelling).

I have updated the script in the original post; really hope this version finally works properly! (Fortunately, not too much time is wasted before the error occurs.)

Is the Forum working really slow for you too? It's strange, normally it responds fast, but right now it's really sluggish... I've tried optimizing the tables and checking for errors, but it seems ok... Can only hope it solves itself.

5136

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 5, 2009, 04:32 »

What is a bit confusing for me is that now we edited scripts left and right, plus you run both on Windows and Linux. As far as I understand, you can run properly in serial on Windows (via the VNL Job Manager, perhaps), but it fails in parallel on Linux, is that correct? And it complains about the VNL file not existing?

Please make a habit of posting the error message when there is one. Even if it seems the same as before, there could be a small crucial difference that helps in finding out what's wrong. For instance, if you are indeed using the new script, it should fail on line 80, not line 79. Also, the error should contain the full path of the "lih.vnl" file.

5137

Scripts, Tutorials and Applications / Re: k-point labeling problem in ATK and Virtual NanoLab results

« on: May 5, 2009, 04:30 »

A tutorial/add-on module for band structure calculations based on symmetry labels for the common lattices (not monoclinic...) is being developed. I've sent you a preview by email, enjoy!

5138

Scripts, Tutorials and Applications / Re: Script for creating nanotubes

« on: May 5, 2009, 03:42 »

Although, from the user's perspective of how the geometry is defined, it is the electrode

For definiteness, the system which ATK actually performs the calculation on, looks like

L-LP-C-RP-R           (p for padding)

where C=central region and L/LP and R/RP are the left and right electrode geometries. During the self-consistent two-probe calculation, the real space quantities in L and R are fixed to their bulk values, while those in LP and RP are allowed to vary.

So, again, from the perspective of how the system is defined (names of variables etc), the system is L-C-R, and the real space density and effective potential vary freely across this region.

5139

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 4, 2009, 15:39 »

Hang on, I think the error might be different. You were running in parallel, and the script doesn't actually check that only the master node writes to the VNL file. Shame on me, that's really bad.

I have fixed the script in the original post; download it and replace your existing file, and try again.

5140

Scripts, Tutorials and Applications / Re: Script for calculating the effective mass in semi-conductors.

« on: May 4, 2009, 15:29 »

The M-L path is called U.

I don't think the concept of effective mass applies in this case. It's a quantity used in simpler models, where the band structure is close to parabolic, such that you don't need the detailed band structure, but it suffices to use a simplified picture of it, i.e. a perfect parabola. If the band structure doesn't look like that, there is no point in trying to compute an effective mass, since it cannot be used for anything meaningful...

5141

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 4, 2009, 12:49 »

In the call to runIVCurve you must give the name of the VNL file with full path, like you did when it was defined

Code

if processIsMaster(): file = VNLFile('C:/Users/617/Desktop/lih.vnl')

So change to

Code

ivcurve.runIVcurve (
    twoprobe_configuration,
    two_probe_method,
    runtime_parameters,
    voltages,
    vnl_filename='C:/Users/617/Desktop/lih.vnl', sample_name='lih',
    current_k_point_sampling = (1,1),
    current_number_of_points = 100
  )

and it should work better!

5142

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 4, 2009, 12:33 »

Well, please post the script You can remove the whole definition of the geometry, it's not needed and maybe you want to keep it secret, that's fine. Just remove those lines from the script, and attach the remains. Then it will be immediately obvious for us what's wrong, it's just a small detail in the Python code somewhere.

5143

Scripts, Tutorials and Applications / Re: Voltage sweep (I-V curve)

« on: May 4, 2009, 12:26 »

Impossible to say without seeing the script. Somehow the file, which it tries to add the current to, is not opened. Perhaps there is a missing ifProcessIsMaster(), so a node is trying to write to the VNL file, but only the master node has opened it. Or there is some other typo in the script.

5144

Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software

« on: April 30, 2009, 09:19 »

The sort order is actually just controlled by permuting the order of the lines

Code

for ii in range(shape[0]):
    for jj in range(shape[1]):
        for kk in range(shape[2]):

To sort as you wish, the only change needed is to instead write

Code

for kk in range(shape[2]):
    for jj in range(shape[1]):
        for ii in range(shape[0]):

Don't forget to change in two places, for spin-polarized and not!

The rule is simple: the coordinate to sort primarily by, comes first (Z is kk in shape[2]), then the next-level sorting (Y, in your case, jj in shape[1]), and finally the third-level (the coordinate which changes immediately, in your case X, ii in shape[0]).

However, I also note that the print order is a bit different in your example; the script prints Z, Y, X, so if you really want the order Z, X, Y, you also must modify the print statement.

5145

Gallery / Periodic table of VNL colors

« on: April 29, 2009, 21:23 »

VNL uses the JMol color map to assign a unique color to each element. There is a reference in the manual too, but I find the attached pictures to be quite useful.

In addition to the color, they also indicate the van der Waals and covalent radii in a nice way.

I have also attached the input file I created to generate the figures. It's a simple XYZ file of the periodic table; just import it in VNL and drop it on the Nanoscope!