1- How should I define k-points for a system consisted of two semi-infinite
parts (electrodes) and a finite section (fullerene)? Do you have any
sample input file for definition of such a system?
It is extremely important to look carefully on electrode part at first.
The electrodes description in transport properties are saved in a file
named .TSHS that can be generated in electrode calculations. You should do
electrode run with the following tags:
SaveHS T
%block kgrid_Monkhorst_Pack
<N> 0 0 0.0
0 <N> 0 0.0
0 0 <N> 0.0
%endblock kgrid_Monkhorst_Pack
where N is the periodicity along the transport direction.
Is it really necessary to define semi-infinite electrodes?
Yes.
I recommend you to read Electrode description part of SIESTA manual p. 122
and the two following papers:
https://arxiv.org/pdf/cond-mat/0110650.pdf
https://arxiv.org/pdf/1607.04464.pdf
for a better understanding of properties of transport calculations.
On Mon, Jul 3, 2017 at 5:18 PM, Esmaeil Farajpour Bonab <
[email protected]> wrote:
> Dear Siesta users,
>
> I am willing to measure the conductance in a series of functionalized
> [70]fullerene systems via Transiesta.
> To do so, I defined 2 finite gold electrodes and optimized the system with
> the fullerene in between via Siesta 4.0. Now, I realized that to measure
> conductivity, I need to define two semi-infinite electrodes (finite
> electrodes are a wrong choice).
> Yet, something is unclear to me. I would be grateful if you can clarify
> the following questions:
>
> 1- How should I define k-points for a system consisted of two
> semi-infinite parts (electrodes) and a finite section (fullerene)? Do you
> have any sample input file for definition of such a system?
>
> 2- Is it really necessary to define semi-infinite electrodes? If I proceed
> with my setup, will the results be wrong? My input file is as the following:
>
> SystemName goldcalfullerenegold
> SystemLabel aucalc70au
>
> NumberOfAtoms 194
> NumberOfSpecies 2
>
> %block ChemicalSpeciesLabel
> 1 79 Au
> 2 6 C # Species index, atomic number, species label
> %endblock ChemicalSpeciesLabel
>
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> 5.617376860 2.198737970 -14.725625670 1
> 5.694062080 1.978267750 -11.902681970 1
> 6.898836560 3.090692310 -17.170211920 1
> 9.525533810 2.901683060 -15.814082330 1
> 8.220905290 2.075296000 -13.390749270 1
> 9.743503130 2.479917640 -11.012862130 1
> 7.278997720 2.224643950 -9.544635630 1
> 11.078900470 4.087665190 -18.015352530 1
> 12.686500420 2.722984360 -16.011226560 1
> 11.243781440 2.334089260 -13.464597730 1
> 13.239635850 2.378771780 -11.224898320 1
> 11.653515930 3.197937810 -8.918112050 1
> 4.697480680 4.709439530 -15.970198980 1
> 4.627112560 7.074495900 -14.222173150 1
> 4.902780390 4.491247160 -13.036568540 1
> 4.873681660 6.742634130 -11.312605520 1
> 5.045872110 4.155802760 -10.001089360 1
> 8.628208600 5.360013690 -17.399052520 1
> 6.458204720 6.944936920 -16.463281270 1
> 7.259210270 4.564206120 -14.832194520 1
> 9.168925730 6.823226130 -15.052700750 1
> 9.524578050 4.603019550 -13.230307430 1
> 7.243831930 6.684945080 -12.981834710 1
> 7.378181820 4.325743730 -11.440217910 1
> 9.381752050 6.403535190 -11.050631970 1
> 9.023279010 4.400294390 -8.940558410 1
> 6.873468320 6.413208450 -9.229784410 1
> 13.484637050 5.578425370 -17.271898940 1
> 10.963692230 7.035733230 -17.516436590 1
> 11.425871820 5.089611730 -15.356879280 1
> 13.878146960 6.765112870 -14.707251570 1
> 13.557048140 4.073678680 -13.592482210 1
> 11.432481230 6.751897100 -13.108035460 1
> 11.677662740 4.650705210 -11.359756310 1
> 14.096757370 6.390307290 -11.964536560 1
> 13.923681710 4.890105160 -9.609931550 1
> 11.411262730 6.192594360 -8.898025210 1
> 4.762515740 9.274191720 -16.029933190 1
> 5.568234940 11.519765600 -14.310627860 1
> 4.831602410 9.396581900 -12.516073310 1
> 6.075208170 11.324847820 -10.708605870 1
> 4.907011270 8.917029840 -9.556170300 1
> 8.610636350 8.585228790 -17.187546130 1
> 7.096347410 10.896123390 -16.719233900 1
> 7.094208230 9.075027860 -14.493472390 1
> 9.488878720 10.918919890 -15.135828800 1
> 9.369678840 8.798855350 -12.883525900 1
> 7.984879900 11.338115810 -12.786285450 1
> 7.249826800 8.767706580 -11.057664430 1
> 9.421198240 10.751607910 -10.438235080 1
> 9.195348200 8.280497810 -9.123861030 1
> 7.204444600 10.225724130 -8.313660470 1
> 13.451563410 8.499696380 -16.888919510 1
> 11.031735220 10.015959540 -17.473331280 1
> 11.301969790 8.651436680 -15.035548670 1
> 12.740905150 10.965777250 -15.267622210 1
> 13.410621590 9.075509170 -13.006025980 1
> 11.215409170 10.995681540 -12.739175820 1
> 11.383058460 8.520842750 -10.914639920 1
> 13.202172930 10.573707940 -10.511351040 1
> 13.765696380 7.836916910 -9.545664120 1
> 11.687763620 9.583229290 -8.266953200 1
> 5.496727620 2.020376470 5.237093460 1
> 5.097473530 2.254100650 7.945170390 1
> 7.367757700 2.174285420 3.138966510 1
> 9.837395440 2.382502310 4.757619970 1
> 7.927811670 1.925134590 7.029448350 1
> 9.784747750 2.355657430 9.269853010 1
> 7.006983770 2.431071550 10.017727160 1
> 12.004321920 3.103970700 2.821875780 1
> 13.815099070 2.550302790 5.152982960 1
> 11.626285900 2.133767330 7.025052120 1
> 12.713159510 2.577016470 9.705870040 1
> 10.963549230 3.626692550 11.737613380 1
> 5.212052050 4.248981450 3.410252260 1
> 4.836268830 6.956393470 4.501317400 1
> 4.808804340 4.705673500 6.316253930 1
> 4.839678280 7.017280660 8.026011350 1
> 4.728652150 4.509282390 9.618799600 1
> 9.313615300 4.206718790 2.624568590 1
> 7.283800850 6.234684120 3.107433390 1
> 7.500777970 4.143637140 5.134924880 1
> 9.599613740 6.159790730 4.812551870 1
> 9.647507150 4.275282770 7.014078610 1
> 7.153974900 6.741051280 6.273390370 1
> 7.069281500 4.541263330 8.114707400 1
> 9.004589630 6.671750540 8.567013330 1
> 8.587519500 4.714555340 10.674621110 1
> 6.593824680 6.601797330 10.241741360 1
> 14.181516650 4.950815470 3.607046350 1
> 11.664469840 6.084190210 2.651891860 1
> 11.856214570 4.531258790 5.192559900 1
> 14.105801750 6.584110800 5.949984680 1
> 13.554813290 4.269051870 7.558536180 1
> 11.374538380 6.631889960 6.984876250 1
> 11.247653760 4.969600680 9.229316250 1
> 13.607746410 6.916300230 8.762620770 1
> 13.255090480 5.407019770 11.128268030 1
> 10.611116680 6.542574650 11.552872370 1
> 5.607956970 8.390727390 2.080419960 1
> 5.466788790 10.931160180 3.905011340 1
> 5.064579570 9.240325350 6.252061380 1
> 5.605453690 11.263022690 8.273615930 1
> 5.254494680 9.097970210 10.181374240 1
> 9.526352930 8.262673220 3.028021000 1
> 7.673682280 10.460902030 2.083290520 1
> 7.199201240 8.815331740 4.391008420 1
> 9.584966700 10.851064730 4.199090290 1
> 9.360042340 8.735735510 6.318617310 1
> 7.438293080 11.064024320 6.109441160 1
> 7.246567660 8.929643200 8.231434660 1
> 9.352894160 11.125974370 8.211020890 1
> 8.631481700 8.381931410 10.869752850 1
> 7.543814280 10.963560490 10.382757350 1
> 14.044666720 7.749507170 3.247539580 1
> 11.958964100 9.474291110 1.999131880 1
> 11.711710470 8.231482660 4.735752340 1
> 13.355513930 10.407539790 4.259456160 1
> 13.428912480 9.123359090 6.951023210 1
> 11.421366270 10.962313630 6.339355810 1
> 10.914350460 8.730093350 8.756813160 1
> 12.610308690 10.877631760 9.099746880 1
> 12.630741120 8.484403830 10.976106120 1
> 10.411595100 10.554382100 10.909736840 1
> 7.796142480 9.052445090 0.261149600 2
> 8.569319560 9.942938110 -0.586019090 2
> 8.523470170 7.979844540 0.864719620 2
> 9.945608480 9.886531820 -0.642581440 2
> 10.601727590 10.079065560 -1.887804250 2
> 9.902917450 10.440740070 -3.060023420 2
> 10.517281770 10.109023930 -4.283745170 2
> 6.847268950 6.317272330 0.216241160 2
> 6.161274690 7.359989460 -0.514399170 2
> 8.008991680 6.630752250 0.931251010 2
> 6.634220450 8.666408810 -0.517991270 2
> 6.641767930 9.399545470 -1.751303430 2
> 6.068524950 8.891013660 -2.932427870 2
> 6.552141450 9.426006770 -4.150377230 2
> 8.471684610 10.485731730 -3.006435390 2
> 7.830447290 10.181828270 -1.787533010 2
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> 9.075377070 4.548014550 0.102788600 2
> 7.881616490 4.271033550 -0.630630850 2
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> 6.797723380 5.135648560 -0.573077230 2
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> 5.675395200 6.790161380 -1.738756600 2
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> 11.453135380 6.138775720 0.044770860 2
> 11.345091500 4.950006000 -0.748755050 2
> 10.339717050 6.540339590 0.798792320 2
> 10.185722270 4.187726830 -0.721453970 2
> 9.678310700 3.624622450 -1.932662050 2
> 10.369743380 3.744187790 -3.150468240 2
> 9.594054850 3.640291590 -4.326437040 2
> 7.484977170 3.856250570 -3.043278150 2
> 8.246372120 3.674481200 -1.880358960 2
> 8.160105210 3.695071670 -4.273581100 2
> 10.712511360 8.940192290 0.158268620 2
> 11.775586180 8.461739750 -0.719138630 2
> 9.924747480 7.910607430 0.745856490 2
> 12.139898000 7.125968350 -0.755303600 2
> 12.492254410 6.526029030 -1.998216130 2
> 12.569978190 7.270549910 -3.191433490 2
> 12.397918450 6.550897590 -4.387221460 2
> 11.568424250 4.558728430 -3.179012170 2
> 11.997353650 5.180943160 -2.000780260 2
> 11.910118730 5.203604650 -4.390222630 2
> 12.177869800 8.658615660 -3.156741260 2
> 11.729852200 9.203636960 -1.942120290 2
> 11.647507530 9.230566950 -4.337892190 2
> 11.247498560 6.188133560 -6.387285340 2
> 11.961345040 7.172448400 -5.595956710 2
> 11.605368230 8.524304250 -5.573525480 2
> 10.048908080 6.620697470 -7.045337750 2
> 8.835718170 4.590699020 -6.318183430 2
> 10.011899200 4.209860390 -5.577077410 2
> 11.184437660 4.987190660 -5.607324870 2
> 8.850056060 5.794242860 -7.114550110 2
> 6.602400940 6.384927150 -6.191394460 2
> 6.608438910 5.186135110 -5.436449080 2
> 7.698394840 4.299715300 -5.488021580 2
> 7.694797540 6.712531910 -7.042158170 2
> 7.527865360 9.155041820 -6.278439320 2
> 6.450810860 8.723220260 -5.393698760 2
> 5.996525570 7.409949880 -5.378722390 2
> 8.226692740 8.057062740 -6.906867010 2
> 10.498294790 9.034033110 -6.380768540 2
> 9.775079700 9.953018410 -5.494856100 2
> 8.383164750 10.003619150 -5.446023660 2
> 9.642128500 7.983991340 -6.877378370 2
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> MeshCutoff 300.0 Ry
>
> PAO.BasisSize DZ
> PAO.BasisType split
> PAO.EnergyShift 400.0 meV
> PAO.SplitNorm 0.40
>
> MD.TypeOfRun CG
> MD.NumCGSteps 1000
> MD.MaxForTol 0.05 eV/Ang
>
> DM.UseSaveDM Y
> DM.NumberPulay 6
> DM.MixingWeight 0.10
>
> I am looking forward to hearing from you.
>
> Respectfully,
> Esi
>
