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--- smeagol_usage [2012/04/27 12:55]
prokop
+++ smeagol_usage [2012/05/02 12:16]
prokop
@@ Line 1: / Line 1: @@
-====== Tutorial in PDF ======
+====== Tutorial H-chain in PDF ======
 There is simple presentation of smeagol usage presented on Smeagol Workshop in Hungary
@@ Line 16: / Line 15: @@
 {{:smeagol:smeagol_h2_tutorial.zip|}}
-====== Wiki Tutorial ======
+====== Wiki Tutorial on H-chain ======
 ===== Intro =====
@@ Line 378: / Line 378: @@
 </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>
+   	NeneT
+-20.0		TEnergI
+.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>

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