#! /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

