I don't think there is anything strange going on here. What looks like jibberish is really just Esc-sequences to generate syntax highlighting / coloring in the terminal window.
The last "# sc" line indicates that the calculation has converged nicely.
So, the main question is only: what do you mean when you say that it does not generate any result? You should have a file called 'CAP55_1.vnl' in the same directory where you ran ATK, and dropping this file on the Result Browser in VNL you should see the results.
If you do this, and there are no results (as I suspect, based on the output file!), it may because you ran out of memory just at the very end. In that case, restore the calculation and run the analysis (calculation of the DOS and transmission) separately.
To do this, copy the input script to a new file and replace everything (except the first lines of "import" statements) until the line
# Calculate physical properties
by
scf = restoreSelfConsistentCalculation('CAP55_1.nc')
and run the new script.
You should run ATK as
atk CAP55_1.py > CAP55_1.out
otherwise you launch an interactive session, or actually by the looks of it many (you run in parallel?) ...
It is a bit weird that there is no VNL file, there should at least be one with the geometry, but maybe things got messed up with respect to "master process" when you run interactively this way. That could explain why there is no analysis output as well. Either that, or you ran out of memory.
Either way, try the recipe described above to restore and recalculate the analysis part.
The problem is, as usual in these cases, the alignment atoms. It's clear that the system was built with VNL, but whether or not this indicates that the geometry produced by VNL is wrong or not is hard to say at this point... Perhaps you modified it by hand after it came out of the Atomic Manipulator?
Anyway, by changing the equivalent atoms from
equivalent_atoms=([0,0],[2,220])
to
equivalent_atoms=([0,0],[2,195])
I hope you will be able to run the simulation. It will require a lot of memory, and may be difficult to converge, but at least I think the error you obtained should not appear any more.
How did I find this out? It can be useful to know a bit more about how to troubleshoot a system like this...
What I did was to convert the two-probe to its equivalent bulk system. Not by using the functionality in VNL, in the Atomic Manipulator, but by using the NanoLanguage function, which is a method on the two-probe configuration object. Viewing this in VNL clearly showed that the system was misaligned.
After thinking a bit, and trying a lot of different things, what worked was 195 = 220-3*9+2, that is the alignment atom did not, somehow, account for the repetitions. (Here, 3 and 9 are the repetition factors, and 2 is the index for the electrode atoms, seen in the code above.)
Pardon the short answer, I hope it speaks for itself ;)
equiv_bulk = two_probe_configuration.equivalentBulkSystem()
http://quantumwise.com/documents/manuals/ATK-2008.10/ref.twoprobeconfiguration.html
Pardon the short answer, I hope it speaks for itself ;)
equiv_bulk = two_probe_configuration.equivalentBulkSystem()
http://quantumwise.com/documents/manuals/ATK-2008.10/ref.twoprobeconfiguration.html
:( I am sorry . I can modify the equiv_bulk = two_probe_configuration.equivalentBulkSystem()
if processIsMaster(): nlPrint(eqiva-bulk)
if processIsMaster(): file.addToSample(two_probe_configuration, 'Au_Z7_Au')
how could i do that can display the wrong configuration in the Nanocope?
:) :)
if processIsMaster(): file.addToSample(equiv_bulk, 'Au_Z7_Au equivalent bulk system')
equiv_bulk = twoprobe_configuration.equivalentBulkSystem()
if processIsMaster(): nlPrint(equiv_bulk)
if processIsMaster(): file.addToSample(equiv_bulk, 'Au_Z7_Au equivalent bulk system')
if processIsMaster(): file.addToSample(twoprobe_configuration, 'Au_Z7_Au')
Sorry to confuse you (but I didn't have your original script, so it was hard to know the name of the variable). There should be no parameter inside the (), the commands should be exactly as above.
When you have run the script, drop the VNL file on the Result Browser. Then you will see two configuration, and you can drop either one to the Nanoscope to see which is wrong etc.