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smeagol_usage [2011/12/02 14:58] prokop |
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- | ====== Tutorial in PDF ====== | ||
- | |||
- | |||
- | |||
- | There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary | ||
- | |||
- | {{:smeagol:smeagol_tutorial.pdf|}} | ||
- | |||
- | (no much text explanatiobn included) | ||
- | |||
- | |||
- | The input data files for this tutorial could be downloaded here | ||
- | |||
- | {{: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 | ||
- | |||
- | As simplest example I will show computation of hydrogen molecule in between hydrogen leads | ||
- | |||
- | ===== LEADS computation ===== | ||
- | |||
- | Let's use this lead geometry | ||
- | |||
- | 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> | ||
- | |||
- | first you have to run SCF calculation to converge charges, use this input file | ||
- | Fireball.in (scf) | ||
- | <code> | ||
- | &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 | ||
- | </code> | ||
- | |||
- | then fix charges, activate iwrtHSrho = 1 and run computation again to export LEADs density | ||
- | <code> | ||
- | &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 | ||
- | </code> | ||
- | |||
- | 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 | ||
- | <code> | ||
- | 1 | ||
- | 0.0000000000 0.0000000000 0.0000000000 1.0000000000 | ||
- | </code> | ||
- | |||
- | after the computation you get file called ELECTRODE where k-space representations of Hamiltonian, Density matrix and overplap matrix are stored. | ||
- | |||
- | ===== SYSTEM computation ===== | ||
- | |||
- | 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 | ||
- | <code> | ||
- | 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 | ||
- | </code> | ||
- | |||
- | cel.lvs | ||
- | <code> | ||
- | 20.000000000 0.000000000 0.000000000 | ||
- | 0.000000000 20.000000000 0.000000000 | ||
- | 0.000000000 0.000000000 26.000000000 | ||
- | </code> | ||
- | |||
- | Your kpoint sampling MUST be the same as MOLECULE.kpts in LEADs calculation. Otherweis ELECTRODE files are incompatible. | ||
- | input.kpts | ||
- | <code> | ||
- | 1 | ||
- | 0.0000000000 0.0000000000 0.0000000000 1.0000000000 | ||
- | </code> | ||
- | |||
- | 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) | ||
- | <code> | ||
- | &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 | ||
- | </code> | ||
- | |||
- | 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 | ||
- | <code> | ||
- | &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 | ||
- | </code> | ||
- | |||
- | |||
- | You should also specify smeagol parameters in smeagol.optional | ||
- | <code> | ||
- | 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 | ||
- | </code> | ||
- | |||
- | 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 | ||
- | - V = -VBias/2 for -infinity< r <r_left | ||
- | - V = -VBias/2 + (r - r_left)/(r_right - r_left) for r_right < r <r_left | ||
- | - V = +VBias/2 for r_right < r < +infinity | ||
- | |||
- | 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 | ||
- | <code> | ||
- | # 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 | ||
- | </code> | ||
- | 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) | ||
- | <code> | ||
- | 0.70561919D-02 0.19849858D-06 | ||
- | </code> | ||
- | 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. | ||
- | |||
- | | ||
- | |||