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smeagol_usage [2011/12/02 11:01] prokop |
smeagol_usage [2012/11/30 15:21] |
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- | ====== Tutorial in PDF ====== | ||
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- | There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary | ||
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- | {{:smeagol:smeagol_tutorial.pdf|}} | ||
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- | (no much text explanatiobn included) | ||
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- | The input data files for this tutorial could be downloaded here | ||
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- | {{:smeagol:smeagol_h2_tutorial.zip|}} | ||
- | |||
- | ====== Wiki Tutorial ====== | ||
- | |||
- | ===== Intro ===== | ||
- | |||
- | Smeagol computation is split to 2 parts and 4 independent runs | ||
- | |||
- | - LEADs computation | ||
- | - Fireball SCF (converge equlibrium density of LEADs) | ||
- | - Export LEADs files | ||
- | - SYSTEM computation | ||
- | - Fireball SCF (converge equlibrium density of molecule with leads) | ||
- | - Smeagol computation (Get current, conductivity, transmission spectra) | ||
- | |||
- | Currently there are 3 versions of smeagol implementation | ||
- | - non-SCF smeagol - there you use equlibrium density from Fireball. It's much faster than nonequlibrium SCF-loop in smeagol. Currently this is the only version which looks to work fine. | ||
- | - SCF with Kohn-Sham grid - This should be almost identical to siesta implementation of smeagol. Currently it looks working in principle but there are problems with discontinuity on bonundary of leads. | ||
- | - McWeda smeagol - There is a problem with tranformation of overlap matrix, so consider it as non-working | ||
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- | As simplest example I will show computation of hydrogen molecule in between hydrogen leads | ||
- | |||
- | ===== LEADS computation ===== | ||
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- | Let's use this lead geometry | ||
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- | answer.bas | ||
- | <code> | ||
- | 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 | ||
- | </code> | ||
- | |||
- | cel.lvs | ||
- | <code> | ||
- | 20.000000000 0.000000000 0.000000000 | ||
- | 0.000000000 20.000000000 0.000000000 | ||
- | 0.000000000 0.000000000 6.000000000 | ||
- | </code> | ||
- | |||
- | 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 | ||
- | <code> | ||
- | 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 | ||
- | </code> | ||
- | |||
- | |||
- | |||