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
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5.064579570 9.240325350 6.252061380 1
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7.673682280 10.460902030 2.083290520 1
7.199201240 8.815331740 4.391008420 1
9.584966700 10.851064730 4.199090290 1
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13.428912480 9.123359090 6.951023210 1
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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
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%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
