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smeagol_usage [2012/04/27 12:31]
prokop
smeagol_usage [2012/11/30 15:21]
prokop
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-====== Tutorial in PDF ======+====== Tutorial ​H-chain ​in PDF ======
    
- 
  
 There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary
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 {{:​smeagol:​smeagol_h2_tutorial.zip|}} {{:​smeagol:​smeagol_h2_tutorial.zip|}}
  
-====== Wiki Tutorial ======+ 
 +====== Wiki Tutorial ​on H-chain ​======
  
 ===== Intro ===== ===== Intro =====
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-**useLeads**shoudl be always set to 1 otherweise the Transition spectrum can not be computed ( 0 is just for debug purpose)+**useLeads** shoudl be always set to 1 otherweise the Transition spectrum can not be computed ( 0 is just for debug purpose)
  
 most of the parameters should be used default. Only what you should care about most of the parameters should be used default. Only what you should care about
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 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. ​ 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 copy appropriate ​files of fitted hoppings to the directory,  ​**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.+To do this you have to provide ''​interaction.optional''​ and files contanting overlap ''​interaction_S_X_Y.optional''​ and interaction hamiltonian ''​interaction_H_X_Y.optional''​ for pairs of elements X,Y. for Example you should provide ''​interaction_S_79_79.optional''​ nad ''​interaction_H_79_79.optional''​ for interaction of two gold electrodes. 
 + 
 +The method of is automatically switched on if ''​interaction.optional''​ is provided, and of if it is not avaible in the directory
 + 
 +Than you should set up transition betwen original basisfunctions and the new one in ''​smeagol.optional''​. ​**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. ​ After do computation otuptfiles ​  ​smeagol.CUR and smeagol.TRC are generated. .CUR for current and .TRC for transmission coefficient. ​
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 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. 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.
  
-  ​ 
  
 +====== Scripted tutorial on BiThioBenzene on gold 100 ======
 +
 +After finishing H-chain tutorial (wich computational time ~20 second is short enought for learning purpose ), you can approach to much more computationaly demanding task of computation of transmission coefficient for molecule between gold electrodes. The computationl time of this example would be arround 1 day, but can by shotened by setting shorter and less densly sampled energy region in smeagol optional by
 +
 +<​code>​
 + ​1000 ​  ​ NeneT
 +-20.0 TEnergI
 + ​30.0 ​          ​TEnergF
 +</​code>​
 +
 +All the input files and a script to successively execute all the neccesary steps is provided in this .zip package.
 +
 +{{:​smeagol:​au_dtb_input.zip|}}
 +
 +In order to run this tutorial it is necessary to make a link of Fdata in both '''​Au100-LEADS-1k'''​ and '''​AuBTB-1k'''​ directory.
 +than you have just tu run the script **run_all**. The script is suposed to be submitted to the PBS front system, form the directory and use variable $PBS_O_WORKDIR for correct function.
 +If you are going to run it interactively outside the PBS front system, remove the line 
 +
 +<​code>​
 +cd $PBS_O_WORKDIR
 +</​code>​
 +
 +form the script
 +
 +We can comment successive compuatational steps in script now.
 +
 +<​code>​
 +#! /bin/bash
 +
 +LEADSdir="​Au100-LEADS-1k"​
 +SYSTEMdir="​AuBTB-1k"​
 +cd $PBS_O_WORKDIR
 +
 +
 +# ================= 1 ====================== #
 +
 +# Start LEADS computation
 +
 +cd $LEADSdir
 +
 +# remove old files
 +rm NEIGHBORS
 +rm NEIGHBORS_PP
 +rm ELECTRODE*
 +rm fort.*
 +rm core.*
 +rm ERR*
 +rm OUT*
 +rm CHARGES*
 +
 +
 +# Compute self consistent equlibirum CHARGE distribution in LEADS
 +cp fireball.in-scf fireball.in
 +../fireball >OUTscf 2>ERRscf
 +
 +# Export ELECTRODE files
 +cp fireball.in-leads fireball.in
 +../fireball >​OUTleads 2>​ERRleads
 +
 +# end LEADS computation
 +cd ..
 +
 +# ================= 2 ====================== #
 +
 +# Copy files from LEADS to SYSTEM
 +
 +cp -f $LEADSdir/​ELECTRODE ​    ​$SYSTEMdir/​ELECTRODE.left ​
 +cp -f $LEADSdir/​ELECTRODE ​    ​$SYSTEMdir/​ELECTRODE.right
 +cp -f $LEADSdir/​CHARGES ​      ​$SYSTEMdir/​CHARGES.left
 +cp -f $LEADSdir/​CHARGES ​      ​$SYSTEMdir/​CHARGES.right
 +cp -f $LEADSdir/​MOLECULE.kpts $SYSTEMdir/​input.kpts
 +
 +# set LEADS fermilevel for smeagl
 +fermi=`grep Fermi $LEADSdir/​OUTscf | tail -1 |  cut -b 17-`
 +sed "​s/​AAA/​$fermi/​g"​ $SYSTEMdir/​smeagol.optional-0 > $SYSTEMdir/​smeagol.optional
 +
 +# ================= 3 ====================== #
 +
 +# Start SYSTEM computation
 +
 +cd $SYSTEMdir
 +
 +# remove old files
 +rm NEIGHBORS
 +rm NEIGHBORS_PP
 +rm fort.*
 +rm core.*
 +rm ERR*
 +rm OUT*
 +rm CHARGES
 +rm smeagol.TRC
 +
 +# Compute self consistent equlibirum CHARGE distribution of SYSTEM
 +cp fireball.in-scf fireball.in
 +../fireball >OUTscf 2>ERRscf
 +
 +# Smeagol computation
 +cp fireball.in-smeagol fireball.in
 +../fireball >​OUTsmeagol 2>​ERRsmeagol
 +</​code>​
 +
 +We recommand you to follow the script order line by line, watching on the description of manual succesive executing of each steps which is described in H-chain tutorial section above.
 +We also recommand you to examine imput files like 
 +
 +<​code>​
 +Au100-LEADS-1k/​fireball.in-scf
 +Au100-LEADS-1k/​fireball.in-leads ​
 +Au100-LEADS-1k/​answer.bas
 +AuBTB-1k/​fireball.in-scf
 +AuBTB-1k/​fireball.in-smeagol
 +AuBTB-1k/​smeagol.optional
 +AuBTB-1k/​answer.bas ​
 +</​code>​
 +
 +which determine the computation.
 +
 +We provide this script as a template for furter modification for specific computations you are going to do.
 +
 +finally, after the computation is successfully finished, you should plot the outputfile with transmission coefficient ​
 +
 +AuBTB-1k/​**smeagol.TRC**
 +
 +the plot for our basis set looks like this, but it can differ slightly with basiset
 +
 + ​Transmussion coefficient for Dithiobenzene between gold 100 electrodes with 1 k-point. Basis used was  ​
 +H_s3.8 ​ C_s4.0_p4.5_d5.40 S_s4.2_p4.7_d5.5 Au_s5.0_p5.6_d4.7
 +
 +{{:​smeagol:​au-dtb-trcoef.png| Transmussion coefficient for Dithiobenzene between gold 100 electrodes with 1 k-point. Basis used was  ​
 +H_s3.8 ​ C_s4.0_p4.5_d5.40 S_s4.2_p4.7_d5.5 Au_s5.0_p5.6_d4.7
 +}}
smeagol_usage.txt · Last modified: 2012/11/30 15:21 (external edit)