Dear All,
Here I quote part of a terminated transiesta output (under
siesta_trunk_462 environment). In this specific calculation, the left
electrode contains 6 layers (4x4 atoms per gold layer) and 1 tip layer
(3 gold atoms). When I compare "structure of the Left electrode" with
"system electrode", the "system electrode" reflects the first 2 layers
of 4x4 atoms, while the "structure of the Left electrode" only
recognizes the first 13 atoms out of 16 atoms in the first layer. Is
this the problem that the error message "The electrodes are not situated
in the same coordinates" refers to?
You will be appreciated for your any comments on how to fix this issue?
Cheers!
Jin
*********************************************************************
Creating Green's function file for: left
Left unit cell (Ang):
11.5372 0.0000 0.0000
-5.7686 9.9915 0.0000
0.0000 0.0000 15.5430
Structure of the Left electrode | System electrode:
X (Ang) Y (Ang) Z (Ang) | X (Ang) Y (Ang) Z (Ang)
0.00000 0.00000 0.00000 | 0.00000 0.00000 0.00000
-10.09502 2.49786 0.00000 | 2.88428 0.00000 0.00000
-7.21073 2.49786 0.00000 | 5.76857 0.00002 0.00000
-4.32644 2.49786 0.00000 | 8.65286 0.00002 0.00000
-1.44215 2.49786 0.00000 | -1.44215 2.49787 0.00000
-11.53716 4.99572 0.00000 | 1.44214 2.49787 0.00000
-8.65288 4.99572 0.00000 | 4.32643 2.49788 0.00000
-5.76858 4.99573 0.00000 | 7.21071 2.49788 0.00000
-2.88430 4.99573 0.00000 | -2.88430 4.99574 0.00000
-12.97932 7.49359 0.00000 | -0.00001 4.99574 0.00000
-10.09502 7.49359 0.00000 | 2.88428 4.99575 0.00000
-7.21074 7.49359 0.00000 | 5.76857 4.99575 0.00000
-4.32644 7.49360 0.00000 | -4.32644 7.49360 0.00000
-10.09501 -0.83264 2.35501 | -1.44215 7.49361 0.00000
-7.21073 -0.83264 2.35501 | 1.44213 7.49362 0.00000
-4.32644 -0.83262 2.35501 | 4.32642 7.49362 0.00000
-1.44215 -0.83262 2.35501 | 1.44214 -0.83261 2.35501
-11.53716 1.66523 2.35501 | 4.32643 -0.83261 2.35501
-8.65287 1.66523 2.35501 | 7.21072 -0.83261 2.35501
-5.76858 1.66524 2.35501 | 10.09500 -0.83261 2.35501
-2.88430 1.66524 2.35501 | 0.00000 1.66526 2.35501
-12.97931 4.16310 2.35501 | 2.88428 1.66526 2.35501
-10.09502 4.16310 2.35501 | 5.76857 1.66526 2.35501
-7.21073 4.16311 2.35501 | 8.65286 1.66526 2.35501
-4.32644 4.16311 2.35501 | -1.44215 4.16312 2.35501
-14.42145 6.66096 2.35501 | 1.44214 4.16312 2.35501
-11.53716 6.66097 2.35501 | 4.32642 4.16312 2.35501
-8.65288 6.66098 2.35501 | 7.21072 4.16313 2.35501
-5.76859 6.66098 2.35501 | -2.88430 6.66098 2.35501
-8.65287 3.33048 4.71002 | -0.00001 6.66098 2.35501
-10.09502 5.82834 4.71002 | 2.88428 6.66098 2.35501
-7.21073 5.82834 4.71002 | 5.76857 6.66099 2.35501
Coordinates from the electrode repeated out to an FDF file
X (Ang) Y (Ang) Z (Ang)
8.652870000000 -3.330480000000 9.420060000000
-1.442150000000 -0.832620000000 9.420060000000
1.442140000000 -0.832620000000 9.420060000000
4.326430000000 -0.832620000000 9.420060000000
7.210720000000 -0.832620000000 9.420060000000
-2.884290000000 1.665240000000 9.420060000000
-0.000010000000 1.665240000000 9.420060000000
2.884290000000 1.665250000000 9.420060000000
5.768570000000 1.665250000000 9.420060000000
-4.326450000000 4.163110000000 9.420060000000
-1.442150000000 4.163110000000 9.420060000000
1.442130000000 4.163110000000 9.420060000000
4.326430000000 4.163120000000 9.420060000000
-1.442140000000 -4.163120000000 11.775070000000
1.442140000000 -4.163120000000 11.775070000000
4.326430000000 -4.163100000000 11.775070000000
7.210720000000 -4.163100000000 11.775070000000
-2.884290000000 -1.665250000000 11.775070000000
0.000000000000 -1.665250000000 11.775070000000
2.884290000000 -1.665240000000 11.775070000000
5.768570000000 -1.665240000000 11.775070000000
-4.326440000000 0.832620000000 11.775070000000
-1.442150000000 0.832620000000 11.775070000000
1.442140000000 0.832630000000 11.775070000000
4.326430000000 0.832630000000 11.775070000000
-5.76858000The electrodes are not situated in the same
coordinates. Please correct.
0000 3.330480000000 11.775070000000
-2.884290000000 3.330490000000 11.775070000000
-0.000010000000 3.330500000000 11.775070000000
2.884280000000 3.330500000000 11.775070000000
0.000000000000 0.000000000000 14.130080000000
-1.442150000000 2.497860000000 14.130080000000
1.442140000000 2.497860000000 14.130080000000
The electrodes are not situated in the same coordinates. Please correct.
Stopping Program from Node: 0
Stopping Program from Node: 0
***************************************************************************
On 18/12/2014 6:17 PM, Nick Papior Andersen wrote:
I can't really see any ambiguity in the error message?
It really does mean:
'The electrodes are not situated in the same coordinates.'
The electrode atomic coordinates (from the separate electrode
calculation) does not match the electrode atomic coordinates in the
system calculation.
Transiesta (the trunk version) is so kind to actually print out the
electrode coordinates... So you could just copy-paste those...
I can't remember how it worked in 3.2... But try a wrong electrode
coordinate to see if it checks the coordinates at all. :)
2014-12-18 6:25 GMT+01:00 Jingxian Yu <[email protected]
<mailto:[email protected]>>:
Dear All,
I did my transiesta calculations with Siesta 3.2. All ran well! At
least, I didn't see any error messages. However when I test these
same jobs with Siesta-trunk-462, I get the error message 'The
electrodes are not situated in the same coordinates. Please correct.'
Can anyone explain what it means? Any hints on how I should check
my electrode coordinates? I feel a bit lost since I quoted this
set of electrode coordinates from a previous article published by
other group.
Cheers!
JIn
--
Kind regards Nick
