Nanosurf Lab

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====== Tutorial H-chain 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 on H-chain ======

===== 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>


**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
**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 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. 

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.


====== 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
}}
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