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
