This is an old revision of the document!
There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary
(no much text explanatiobn included)
The input data files for this tutorial could be downloaded here
Smeagol computation is split to 2 parts and 4 independent runs
Currently there are 3 versions of smeagol implementation
As simplest example I will show computation of hydrogen molecule in between hydrogen leads
Let's use this lead geometry
answer.bas
6 1 3.000000 3.000000 1.000000 1 3.000000 3.000000 2.000000 1 3.000000 3.000000 3.000000 1 3.000000 3.000000 4.000000 1 3.000000 3.000000 5.000000 1 3.000000 3.000000 6.000000
cel.lvs
20.000000000 0.000000000 0.000000000 0.000000000 20.000000000 0.000000000 0.000000000 0.000000000 6.000000000
because you have to converge density of lead is infinite system you should use good sampling in z-direction (NOTE: Smeagol always expect current to flow in z-direction !!!)
input.kpts
100 0.0000000000 0.0000000000 -0.5183627873 0.0100000000 0.0000000000 0.0000000000 -0.5078908118 0.0100000000 0.0000000000 0.0000000000 -0.4974188363 0.0100000000 0.0000000000 0.0000000000 -0.4869468608 0.0100000000 0.0000000000 0.0000000000 -0.4764748853 0.0100000000 0.0000000000 0.0000000000 -0.4660029098 0.0100000000 0.0000000000 0.0000000000 -0.4555309343 0.0100000000 0.0000000000 0.0000000000 -0.4450589588 0.0100000000 0.0000000000 0.0000000000 -0.4345869833 0.0100000000 0.0000000000 0.0000000000 -0.4241150078 0.0100000000 0.0000000000 0.0000000000 -0.4136430323 0.0100000000 0.0000000000 0.0000000000 -0.4031710568 0.0100000000 0.0000000000 0.0000000000 -0.3926990813 0.0100000000 0.0000000000 0.0000000000 -0.3822271058 0.0100000000 0.0000000000 0.0000000000 -0.3717551303 0.0100000000 0.0000000000 0.0000000000 -0.3612831548 0.0100000000 0.0000000000 0.0000000000 -0.3508111793 0.0100000000 0.0000000000 0.0000000000 -0.3403392038 0.0100000000 0.0000000000 0.0000000000 -0.3298672283 0.0100000000 0.0000000000 0.0000000000 -0.3193952528 0.0100000000 0.0000000000 0.0000000000 -0.3089232773 0.0100000000 0.0000000000 0.0000000000 -0.2984513018 0.0100000000 0.0000000000 0.0000000000 -0.2879793263 0.0100000000 0.0000000000 0.0000000000 -0.2775073507 0.0100000000 0.0000000000 0.0000000000 -0.2670353753 0.0100000000 0.0000000000 0.0000000000 -0.2565633998 0.0100000000 0.0000000000 0.0000000000 -0.2460914243 0.0100000000 0.0000000000 0.0000000000 -0.2356194488 0.0100000000 0.0000000000 0.0000000000 -0.2251474733 0.0100000000 0.0000000000 0.0000000000 -0.2146754978 0.0100000000 0.0000000000 0.0000000000 -0.2042035223 0.0100000000 0.0000000000 0.0000000000 -0.1937315468 0.0100000000 0.0000000000 0.0000000000 -0.1832595713 0.0100000000 0.0000000000 0.0000000000 -0.1727875958 0.0100000000 0.0000000000 0.0000000000 -0.1623156203 0.0100000000 0.0000000000 0.0000000000 -0.1518436448 0.0100000000 0.0000000000 0.0000000000 -0.1413716693 0.0100000000 0.0000000000 0.0000000000 -0.1308996937 0.0100000000 0.0000000000 0.0000000000 -0.1204277182 0.0100000000 0.0000000000 0.0000000000 -0.1099557427 0.0100000000 0.0000000000 0.0000000000 -0.0994837672 0.0100000000 0.0000000000 0.0000000000 -0.0890117917 0.0100000000 0.0000000000 0.0000000000 -0.0785398163 0.0100000000 0.0000000000 0.0000000000 -0.0680678407 0.0100000000 0.0000000000 0.0000000000 -0.0575958652 0.0100000000 0.0000000000 0.0000000000 -0.0471238897 0.0100000000 0.0000000000 0.0000000000 -0.0366519142 0.0100000000 0.0000000000 0.0000000000 -0.0261799387 0.0100000000 0.0000000000 0.0000000000 -0.0157079633 0.0100000000 0.0000000000 0.0000000000 -0.0052359878 0.0100000000 0.0000000000 0.0000000000 0.0052359878 0.0100000000 0.0000000000 0.0000000000 0.0157079633 0.0100000000 0.0000000000 0.0000000000 0.0261799388 0.0100000000 0.0000000000 0.0000000000 0.0366519143 0.0100000000 0.0000000000 0.0000000000 0.0471238898 0.0100000000 0.0000000000 0.0000000000 0.0575958653 0.0100000000 0.0000000000 0.0000000000 0.0680678408 0.0100000000 0.0000000000 0.0000000000 0.0785398163 0.0100000000 0.0000000000 0.0000000000 0.0890117917 0.0100000000 0.0000000000 0.0000000000 0.0994837672 0.0100000000 0.0000000000 0.0000000000 0.1099557427 0.0100000000 0.0000000000 0.0000000000 0.1204277182 0.0100000000 0.0000000000 0.0000000000 0.1308996937 0.0100000000 0.0000000000 0.0000000000 0.1413716692 0.0100000000 0.0000000000 0.0000000000 0.1518436448 0.0100000000 0.0000000000 0.0000000000 0.1623156203 0.0100000000 0.0000000000 0.0000000000 0.1727875958 0.0100000000 0.0000000000 0.0000000000 0.1832595713 0.0100000000 0.0000000000 0.0000000000 0.1937315468 0.0100000000 0.0000000000 0.0000000000 0.2042035223 0.0100000000 0.0000000000 0.0000000000 0.2146754977 0.0100000000 0.0000000000 0.0000000000 0.2251474732 0.0100000000 0.0000000000 0.0000000000 0.2356194487 0.0100000000 0.0000000000 0.0000000000 0.2460914242 0.0100000000 0.0000000000 0.0000000000 0.2565633997 0.0100000000 0.0000000000 0.0000000000 0.2670353753 0.0100000000 0.0000000000 0.0000000000 0.2775073508 0.0100000000 0.0000000000 0.0000000000 0.2879793263 0.0100000000 0.0000000000 0.0000000000 0.2984513018 0.0100000000 0.0000000000 0.0000000000 0.3089232773 0.0100000000 0.0000000000 0.0000000000 0.3193952528 0.0100000000 0.0000000000 0.0000000000 0.3298672283 0.0100000000 0.0000000000 0.0000000000 0.3403392038 0.0100000000 0.0000000000 0.0000000000 0.3508111793 0.0100000000 0.0000000000 0.0000000000 0.3612831548 0.0100000000 0.0000000000 0.0000000000 0.3717551303 0.0100000000 0.0000000000 0.0000000000 0.3822271058 0.0100000000 0.0000000000 0.0000000000 0.3926990813 0.0100000000 0.0000000000 0.0000000000 0.4031710568 0.0100000000 0.0000000000 0.0000000000 0.4136430323 0.0100000000 0.0000000000 0.0000000000 0.4241150078 0.0100000000 0.0000000000 0.0000000000 0.4345869833 0.0100000000 0.0000000000 0.0000000000 0.4450589588 0.0100000000 0.0000000000 0.0000000000 0.4555309343 0.0100000000 0.0000000000 0.0000000000 0.4660029098 0.0100000000 0.0000000000 0.0000000000 0.4764748853 0.0100000000 0.0000000000 0.0000000000 0.4869468607 0.0100000000 0.0000000000 0.0000000000 0.4974188362 0.0100000000 0.0000000000 0.0000000000 0.5078908117 0.0100000000 0.0000000000 0.0000000000 0.5183627872 0.0100000000
first you have to run SCF calculation to converge charges, use this input file Fireball.in (scf)
&OPTION basisfile = answer.bas lvsfile = cel.lvs icluster = 0 nstepf = 1 sigmatol = 0.0000000001 max_scf_iterations = 100 iqout = 1 ismeagol = 0 ifixcharge = 0 &END &OUTPUT iwrtHSrho = 0 iwrteigen = 1 iwrtdos = 0 &END
then fix charges, activate iwrtHSrho = 1 and run computation again to export LEADs density
&OPTION basisfile = answer.bas lvsfile = cel.lvs icluster = 0 nstepf = 1 sigmatol = 0.0000000001 max_scf_iterations = 100 dt = 0.5 iqout = 1 ismeagol = 0 ifixcharge = 1 &END &OUTPUT iwrtHSrho = 1 iwrteigen = 0 iwrtdos = 0 &END
to do this you have to specify k-point sampling of the SYSTEM you want to use the LEADs in. This kpoints file is called MOLECULE.kpts. In our case it has just gamma point, however in general it could have any sampling in x and y direction. (never in z!!).
MOLECULE.kpts
1 0.0000000000 0.0000000000 0.0000000000 1.0000000000
after the computation you get file called ELECTRODE where k-space representations of Hamiltonian, Density matrix and overplap matrix are stored.
Your system should contain the geometry of leads in it's geometry description, it should also contain some region where charge redistribution is screened in order to smoothly align with LEADs, because LEADs itselfs represent infinite bulk and their chrage distribution is fixed during the computation. Order of atoms MUST be exactly the same as in LEADs calculation and left lead must be at the begining, and right lead must be at the end of file. For example:
answer.bas
24 1 3.000000000 3.000000000 1.000000000 #start LEAD.left 1 3.000000000 3.000000000 2.000000000 1 3.000000000 3.000000000 3.000000000 1 3.000000000 3.000000000 4.000000000 1 3.000000000 3.000000000 5.000000000 1 3.000000000 3.000000000 6.000000000 # end LEAD.left 1 3.000000000 3.000000000 7.000000000 # screening region (left) 1 3.000000000 3.000000000 8.000000000 1 3.000000000 3.000000000 9.000000000 1 3.000000000 3.000000000 10.000000000 1 3.000000000 3.000000000 11.000000000 1 3.000000000 3.000000000 13.000000000 # molecule itselfs 1 3.000000000 3.000000000 14.000000000 1 3.000000000 3.000000000 16.000000000 # screening region (right) 1 3.000000000 3.000000000 17.000000000 1 3.000000000 3.000000000 18.000000000 1 3.000000000 3.000000000 19.000000000 1 3.000000000 3.000000000 20.000000000 1 3.000000000 3.000000000 21.000000000 #start LEAD.right 1 3.000000000 3.000000000 22.000000000 1 3.000000000 3.000000000 23.000000000 1 3.000000000 3.000000000 24.000000000 1 3.000000000 3.000000000 25.000000000 1 3.000000000 3.000000000 26.000000000 # end LEAD.left
cel.lvs
20.000000000 0.000000000 0.000000000 0.000000000 20.000000000 0.000000000 0.000000000 0.000000000 26.000000000
Your kpoint sampling MUST be the same as MOLECULE.kpts in LEADs calculation. Otherweis ELECTRODE files are incompatible. input.kpts
1 0.0000000000 0.0000000000 0.0000000000 1.0000000000
first you should run SCF run with fireball (with smeagol off), it's much faster than doing smeagol directly from neutral atom charges. Also, currently smeagol SCF implementation in fireball is not perfect.
fireball.in (scf)
&OPTION basisfile = answer.bas lvsfile = cel.lvs icluster = 0 nstepf = 1 sigmatol = 0.0000000001 max_scf_iterations = 100 iqout = 1 ismeagol=0 &END &OUTPUT iwrtHSrho = 0 &END
After convergence of charges, you need to copy ELECTRODE files from LEADs calculation. Rename it ELECTRODE.left, and ELECTRODE.right. You can use different leads on left and right. Both left and right lead should have the same order (top to down in z-direction) it means right lead SHOULD NOT be in reverse order (mirror).
Then you can run the smeagol calculation. To do this set ismeagol = 1 in fireball.in.
fireball.in
&OPTION basisfile = answer.bas lvsfile = cel.lvs icluster = 0 nstepf = 1 sigmatol = 0.000001 max_scf_iterations = 199 dt = 0.5 iqout = 1 ismeagol=1 tempfe=300 &END &OUTPUT iwrtHSrho = 0 &END
You should also specify smeagol parameters in smeagol.optional
500 NEnergR 90 NEnergIC 20 NEnergIL 10 NPoles 0.001 Delta -45.0 EnergLB 1 NSlices T TrCoeff 1000 NeneT -20.0 TEnergI 30.0 TEnergF -4.3217 Fermi_level 0.1 V_Bias 12.0 r_left 12.5 r_right 1 useLeads? 4.50 r_start_fithop 0.25 r_scale_fithop
most of the parameters should be used default.Only what you should care about EnergLB - should be set reasonably lower than lowest energy in molecular spectrum. Be ware that in case of non-equlibrium selfconsistency computation the levels energy could change considerably. If some level become lower than EnergLB the selfconsistency would not conserve charges makes it imposible to converge. TrCoeff (T for true, F for False) specify if Transmission spectrum should be ploted (set T most of the time) NeneT is number of points in transmisison spectrum and TEnergI and TEnergF minimum an maximum of energy interval.
In case of non-selfconsistent computation (which we discribe here) you should set also Fermi_level to fermilevel of LEADs (from your LEADs calculation). If you are interested in current at nonzero voltage, set VBias and r_left, r_right to specify potential ramp which is addet to hamiltonian. Potential ramp is
At Last, there is possibylity to fit extended basis-functions at apex region in order to mimic realistic decay in vacuum for non-contact tuneling current computation in bigger distance. To do this set useLeads = 1, r_start_fithop define distace where the hopping integral start to change from standard to extended. r_scale_fithop define width of the intermediate region. r_scale_fithop=0.0 means stepwise change.
After do computation otuptfiles smeagol.CUR and smeagol.TRC are generated. .CUR for current and .TRC for transmission coefficient.
Format of output files is as flows
# V = 0.0071 k-points: 1 -0.1567831D+02 0.2257147D-30 0.2257147D-30 0 -0.1562826D+02 0.2227090D-30 0.2227090D-30 0 -0.1557821D+02 0.2197281D-30 0.2197281D-30 0 -0.1552816D+02 0.2167719D-30 0.2167719D-30 0 -0.1547811D+02 0.2138402D-30 0.2138402D-30 0 -0.1542806D+02 0.2109329D-30 0.2109329D-30 0 -0.1537801D+02 0.2080497D-30 0.2080497D-30 0
first column is Energy in [eV], second and third are Transmission coefficient for spin Up and Down. Currently computation is not spin resolved, and both colums are identical.
in .CUR is current (second column) and for given voltage (first column)
0.70561919D-02 0.19849858D-06
at the moment curent is computed always for one voltage. In future there should be increasing voltage from zero (equlibrium) gradually to maximum voltage. This would be effective for convergence of nonequlibrium density.