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