I'm still fighting to find the mismatch, but I got a question now:In the output
file there two coordinate columns one for "Structure of the Left electrode" and
another for "System electrode"
and the coordinates on each column are quite different, what do these columns
represent?
On Thursday, August 20, 2015 12:32 AM, Nick Papior <[email protected]>
wrote:
2015-08-20 8:27 GMT+02:00 Jaret Qi <[email protected]>:
and even though, this system worked well with 3.2 version and now trunk is
complaining about the electrodes! this is completely weird, wrong is wrong
everywhere!
Yes, 3.2 did not check this consistently, hence if you ever did a calculation
with 3.2 with those settings, you would most probably get erroneous results.
The trunk does a bunch of checks for you to ensure you do not do anything
"illegal". This is good!
I do not get what you mean by "wrong is wrong everywhere".
On Thursday, August 20, 2015 12:23 AM, Jaret Qi <[email protected]> wrote:
What siesta is saying does not make sense for me, the input I provided on the
electrode calculations is different from the output file when siesta list what
is called : Structure of the Left electrode | System electrode:
I do not know from where these coordinates came from? so siesta complaining
that the electrode are situated in a different coords.
On Thursday, August 20, 2015 12:08 AM, Nick Papior <[email protected]>
wrote:
What are you asking?It says:
"The electrodes are not situated in the same coordinates. Please correct."Do
that. Please read the output carefully, usually the output really does say what
is wrong.
2015-08-20 8:03 GMT+02:00 Jaret Qi <[email protected]>:
Now I tried another system, and manually made the lattice vectors 0 except the
xx, yy, zz components. In this way I get ride of the previous error which I
still not convinced why it assumes a wrong input file, any ways another wrong
came up :see this output : Left unit cell (Ang): 17.2670 0.0000 0.0000
0.0000 29.6701 0.0000 0.0000 0.0000 8.7000 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
-0.98801 0.14789 0.55424 | -0.96183 0.00570 0.53375 -0.01011
-0.00503 -1.40144 | -0.01110 0.08090 -1.37810 -1.00731 0.14500
-1.94246 | -0.98012 0.15017 -1.89624 1.21362 -0.11359 0.74832 |
1.21463 -0.08877 0.73123 2.45481 -0.17951 0.03416 | 2.45252
-0.08428 0.02266 2.45607 -0.18173 -1.41529 | 2.44706 -0.00238
-1.41106 1.20439 -0.12345 -2.13645 | 1.19729 0.07697 -2.11799
3.69332 -0.21877 0.75385 | 3.67706 -0.15984 0.73257 4.93467
-0.23743 0.03489 | 4.90279 -0.14721 0.02073 4.93482 -0.23957
-1.41489 | 4.91081 -0.07196 -1.41333 3.69486 -0.21754 -2.15170 |
3.67943 0.00279 -2.14295 6.18007 -0.23153 0.74852 | 6.13999
-0.20862 0.72743 7.39923 -0.19692 0.00138 | 7.35650 -0.19598
-0.00579 8.39553 -0.12559 0.55451 | 8.31780 -0.24371 0.52682
7.41070 -0.20245 -1.39979 | 7.37007 -0.12821 -1.38469 8.41783
-0.12898 -1.93709 | 8.34089 -0.11913 -1.90436 6.19090 -0.24262
-2.13528 | 6.16202 -0.06718 -2.12253 -0.02148 -0.18410 4.35996 |
-0.01562 -0.30019 4.28999 -1.02311 -0.27670 4.90463 | -0.98710
-0.30930 4.80788 -0.02300 -0.17766 2.95086 | -0.01630 -0.20081
2.90580 -1.02760 -0.25136 2.41178 | -0.98529 -0.13713 2.38769
1.20117 -0.14577 5.09377 | 1.19596 -0.39046 5.02213 2.45115
-0.15361 4.37341 | 2.43729 -0.36876 4.30821 2.44856 -0.14964
2.91574 | 2.43733 -0.26626 2.86707 1.19159 -0.13852 2.21372 |
1.19404 -0.18404 2.17223 3.69594 -0.18315 5.10418 | 3.67359
-0.45098 5.02799 4.94180 -0.20956 4.37363 | 4.91105 -0.41793
4.30665 4.94357 -0.20504 2.91541 | 4.91366 -0.31619 2.86563
3.69525 -0.18370 2.19504 | 3.67603 -0.24770 2.14355 6.19292
-0.25537 5.09435 | 6.15145 -0.48949 5.01863 7.41369 -0.32690
4.35984 | 7.36489 -0.43446 4.28640 8.41462 -0.43767 4.89997 |
8.33556 -0.46974 4.80450 7.41469 -0.31848 2.95141 | 7.36807
-0.33679 2.90223 8.41847 -0.40778 2.41518 | 8.33828 -0.30049
2.38415 6.20176 -0.24581 2.21417 | 6.15833 -0.28640
2.16941Coordinates from the electrode repeated out to an FDF file
X (Ang) Y (Ang) Z (Ang) 1.939142323738
-0.202976552456 2.576603284182 0.951129127651 -0.055090126866
3.130847418799 1.929031222723 -0.208004998552
1.175165681613 0.931829436603 -0.057975511949 0.634141817541
3.152764179431 -0.316570360466 3.324919859560
4.393949390636 -0.382486814741 2.610760245902 4.395212335449
-0.384710818873 1.161312571081 3.143529489261
-0.326431184510 0.440149775034 5.632461614258 -0.421743666797
3.330458235135 6.873809761443 -0.440410288775
2.611492828643 6.873958385115 -0.442547868332 1.161713197408
5.634003001907 -0.420515912723 0.424898989294
8.119214740452 -0.434511506786 3.325118664571 9.338375017603
-0.399895000145 2.577985095457 10.334676865028
-0.328563917978 3.131115265507 9.349846274257 -0.405429035801
1.176814134775 10.356975481705 -0.331958650641
0.639513496030 8.130043684278 -0.445591741705 0.441323734628
1.917664923509 -0.387078546598 6.936561309307
0.916032346615 -0.479679493148 7.481235395110 1.916138373518
-0.380641328925 5.527462782049 0.911547297817
-0.454340The electrodes are not situated in the same coordinates. Please
correct.Stopping Program from Node: 0[node15:18157] MPI_ABORT invoked on
rank 0 in communicator MPI_COMM_WORLD with errorcode 1039259
4.988387800959 3.140312082928 -0.348741616443 7.670374513610
4.390294304503 -0.356583843305 6.950011146492
4.387701876374 -0.352613990192 5.492342751461 3.130736245129
-0.341498916784 4.790320923286 5.635081441195
-0.386129063776 7.680786934827 6.880945195904 -0.412535441837
6.950232686290 6.882716001135 -0.408011695428
5.492014083939 5.634394887460 -0.386678512394 4.771645337586
8.132066019763 -0.458343884157 7.670955096133
9.352837137660 -0.529878346426 6.936444165725 10.353764603879
-0.640651358594 7.476573915918 9.353835460203
-0.521458607003 5.528017823710 10.357615863662 -0.610752357764
4.991778712696 8.140904379317 -0.448790345987
4.790777885721The electrodes are not situated in the same coordinates. Please
correct.
On Wednesday, August 19, 2015 5:03 AM, Nick Papior <[email protected]>
wrote:
No it is not, please look at your input file, clearly it isn't.The older
version did not check this specifically, hence it shows up in the trunk version
and not the old.
2015-08-19 12:49 GMT+02:00 Jaret Qi <[email protected]>:
but why do you think the z-axis is skewed, it is indeed orthogonal to the plane
containing x & y. And is the "skewed" a matter for the trunk version, I still
not sure why this issue just appear in the case of trunk version!!
On Wednesday, August 19, 2015 12:52 AM, Nick Papior <[email protected]>
wrote:
there are x and/or y components in your third cell vector.
The third vector needs to be orthogonal to the other two, simultaneously. If
not it is a "skewed" axis.
2015-08-19 6:11 GMT+00:00 Jaret Qi <[email protected]>:
What do you mean by "skewed", as I mentioned it works fine for the regular
transits but not with the trunk version, take a look to the input please:
SystemName scat
SystemLabel scat
%block kgrid_Monkhorst_Pack 1 0 0 0.0 0 1 0 0.0 0 0 7
0.0%endblock kgrid_Monkhorst_Pack
xc.functional GGA xc.authors PBE
MeshCutoff 250 Ry SolutionMethod Transiesta
ElectronicTemperature 300 K
SpinPolarized T FixSpin F
MaxSCFIterations 1000 DM.Tolerance 1.d-5
DM.NumberPulay 4 DM.NumberBroyden
0 DM.MixingWeight 0.1000000000
DM.OccupancyTolerance 0.1000000000E-11 DM.NumberKick 0
DM.KickMixingWeight 0.5000000000
UseSaveData T MD.NumCGsteps
0 MD.TypeOfRun CG
MD.VariableCell F MD.MaxCGDispl
0.2000000000 Bohr MD.MaxForceTol 0.05 eV/Ang
Diag.ParallelOverK F
PAO.EnergyShift 0.1 eV PAO.SplitNorm 0.15
PAO.BasisType split PAO.BasisSize
SZP
WriteMullikenPop 0WriteBands FSaveRho
FSaveElectrostaticPotential FSaveTotalPotential
FWriteCoorXmol T
%block ChemicalSpeciesLabel 1
6 C 2 1 H%endblock ChemicalSpeciesLabel
NumberOfAtoms 70NumberOfSpecies 2
LatticeConstant 1.0 Ang
%block LatticeVectors 15.000608 -0.002507 -0.000870 -0.002559
15.202444 0.028047 -0.002026 0.063816 17.367000%endblock
LatticeVectors
AtomicCoordinatesFormat Ang AtomicCoorFormatOut Ang
%block AtomicCoordinatesAndAtomicSpecies -0.01944114 -1.21933112
-0.00853316 2 1 H -0.01011964 -0.11398468 -0.00894973 1
2 C 0.00243181 2.74091618 -0.01351849 1 3 C 0.00211249
4.18689601 -0.01648559 1 4 C -0.00788720 7.04135859
-0.02343916 1 5 C -0.01467966 8.14669117 -0.02402577 2
6 H -0.00559971 0.57653733 1.23077939 1 7 C 0.00101302
2.03148449 1.22870652 1 8 C 0.00060860 4.90074262
1.22284138 1 9 C -0.00460179 6.35563716 1.21875877 1 10
C -0.01958521 -1.21476199 2.47315725 2 11 H -0.01026244
-0.10944990 2.47272129 1 12 C 0.00228797 2.74551492
2.46825433 1 13 C 0.00196759 4.19149927 2.46522564 1 14
C -0.00803067 7.04589818 2.45834591 1 15 C -0.01482229
8.15124496 2.45768323 2 16 H -0.00574923 0.58104895
3.71253079 1 17 C 0.00086792 2.03601112 3.71038387 1 18
C 0.00046350 4.90526927 3.70463772 1 19 C -0.00474439
6.36021178 3.70056966 1 20 C -0.01972850 -1.21019600
4.95487370 2 21 H -0.01040855 -0.10487267 4.95451722 1 22
C 0.00214289 2.75003205 4.94998495 1 23 C 0.00182224
4.19604494 4.94697882 1 24 C -0.00817296 7.05047215
4.94001157 1 25 C -0.01496384 8.15579456 4.93937961 2 26
H -0.00589077 0.58565925 6.19424758 1 27 C 0.00072289
2.04058488 6.19213753 1 28 C 0.00031877 4.90990223
6.18625569 1 29 C -0.00488778 6.36472934 6.18218259 1 30
C -0.01987187 -1.20566787 7.43657183 2 31 H -0.01055880
-0.10030701 7.43619206 1 32 C 0.00200138 2.75458122
7.43163628 1 33 C 0.00167804 4.20060129 7.42857591 1 34
C -0.00832165 7.05503820 7.42170619 1 35 C -0.01510878
8.16035611 7.42108387 2 36 H -0.00603494 0.59025395
8.67588804 1 37 C 0.00057837 2.04511036 8.67376688 1 38
C 0.00017467 4.91443789 8.66791869 1 39 C -0.00502951
6.36932258 8.66382875 1 40 C -0.02001788 -1.20108357
9.91826736 2 41 H -0.01069938 -0.09575472 9.91783804 1 42
C 0.00185222 2.75916864 9.91337237 1 43 C 0.00153455
4.20516447 9.91034659 1 44 C -0.00846675 7.05956566
9.90339873 1 45 C -0.01525715 8.16490829 9.90277938 2 46
H -0.00617850 0.59472536 11.15762975 1 47 C 0.00043313
2.04969465 11.15554780 1 48 C 0.00002965 4.91895973
11.14969254 1 49 C -0.00517683 6.37387077 11.14566636 1
50 C -0.02016405 -1.19652219 12.39998540 2 51 H -0.01084339
-0.09121981 12.39960604 1 52 C 0.00170979 2.76375868
12.39507944 1 53 C 0.00138811 4.20973724 12.39205797 1
54 C -0.00861037 7.06415795 12.38514175 1 55 C -0.01539851
8.16949035 12.38447673 2 56 H -0.00632537 0.59933422
13.63934342 1 57 C 0.00028979 2.05424723 13.63722182 1
58 C -0.00011498 4.92352841 13.63142647 1 59 C -0.00532098
6.37843442 13.62733663 1 60 C -0.02031063 -1.19197861
14.88167485 2 61 H -0.01098945 -0.08663448 14.88133008 1
62 C 0.00156658 2.76827996 14.87681092 1 63 C 0.00124607
4.21426076 14.87379290 1 64 C -0.00875280 7.06871706
14.86677245 1 65 C -0.01554355 8.17402286 14.86618051 2
66 H -0.00647139 0.60389354 16.12106024 1 67 C 0.00014533
2.05880086 16.11889627 1 68 C -0.00025895 4.92813406
16.11301066 1 69 C -0.00546700 6.38300938 16.10891490 1
70 C%endblock AtomicCoordinatesAndAtomicSpecies
SolutionMethod Transiesta # GENGF
OPTIONSTS.ComplexContour.Emin -30 eV TS.ComplexContour.NPoles
16TS.ComplexContour.NCircle 30TS.ComplexContour.NLine 10 # BIAS
OPTIONSTS.biasContour.NumPoints 40
# TS OPTIONSTS.Voltage $i eV
# TBT OPTIONSTS.TBT.Emin -3 eVTS.TBT.Emax +3 eVTS.TBT.NPoints 500TS.TBT.NEigen
3TS.TBT.Eta 0.000001 Ry
# Write electrode hamiltonianTS.SaveHS .true.TS.SaveLead .true.
# LEFT ELECTRODETS.HSFileLeft ./LE.TSHS TS.NumUsedAtomsLeft 10
# RIGHT ELECTRODETS.HSFileRight ./RE.TSHS TS.NumUsedAtomsRight 10
On Wednesday, August 19, 2015 12:06 AM, Nick Papior <[email protected]>
wrote:
You have a skewed z-direction, that is not allowed.
2015-08-19 5:51 GMT+00:00 Jaret Qi <[email protected]>:
Dear transiesta users,I'm working on 4ZGNR to get the IV characteristic, but I
have this error when I use the trunk version:
>>ERROR: Unitcell has the electrode extend into the transport direction
>>Electrodes extend into the transport direction. Please change the geometry.
The same structure works well using the regular transiesta, this error only
occurs when I switch to the trunk version of transiesta.
Any help?
--
Kind regards Nick
--
Kind regards Nick
--
Kind regards Nick
--
Kind regards Nick
--
Kind regards Nick
