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
