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|
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example will calculate the final state contribution for a Rh011 slab"
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST="Rh.pbe-rrkjus_lb.UPF Rhs.pbe-rrkjus_lb.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO
$ECHO " checking that needed directories and files exist...\c"
# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
if test ! -d $DIR ; then
$ECHO
$ECHO "ERROR: $DIR not existent or not a directory"
$ECHO "Aborting"
exit 1
fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
cd $EXAMPLE_DIR/results
# check for executables
for FILE in $BIN_LIST ; do
if test ! -x $BIN_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
$ECHO "Aborting"
exit 1
fi
done
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
if test ! -r $PSEUDO_DIR/$FILE ; then
$ECHO
$ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
$WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
fi
if test $? != 0; then
$ECHO
$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
$ECHO "Aborting"
exit 1
fi
done
$ECHO " done"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
#
# In this run the atom with the core-excited PP is the bulk atom (bulk is
# intended as the atom in the middle of the slab). This calculation will
# define the energy_GS of the reference atom
#
cat > rh011bulk.scf.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Rh011bulk',
pseudo_dir = '$PSEUDO_DIR',
outdir='$TMP_DIR'
/
&system
nat=5, ntyp=2,
ibrav=0, celldm(1)=10.31510000,
ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
/
&electrons
mixing_beta = 0.3
conv_thr = 1.0d-6
/
CELL_PARAMETERS alat
1.00000000 0.00000000 0.00000000
0.00000000 1.41421400 0.00000000
0.00000000 0.00000000 2.50000000
ATOMIC_SPECIES
Rh 1.0 Rh.pbe-rrkjus_lb.UPF
Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
ATOMIC_POSITIONS (alat)
Rh 0.25000000 0.35000000 0.50000000
Rh 0.00000000 0.00000000 0.25000000
Rhs 0.25000000 0.35000000 0.00000000 ! Bulk atom core-excited
Rh 0.00000000 0.00000000 -0.25000000
Rh 0.25000000 0.35000000 -0.50000000
K_POINTS {gamma}
EOF
$ECHO
$ECHO " running pw.x for Rh011_[bulk-excited] slab...\c"
$PW_COMMAND < rh011bulk.scf.in > rh011bulk.scf.out
check_failure $?
$ECHO " done"
#
# Now we run a calculation exciting everytime one single atom we want to study.
# The first calculation is for the surface atom.
#
cat > rh011surf.scf.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Rh011surf',
pseudo_dir = '$PSEUDO_DIR',
outdir='$TMP_DIR'
/
&system
nat=5, ntyp=2,
ibrav=0, celldm(1)=10.31510000,
ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
/
&electrons
mixing_beta = 0.3
conv_thr = 1.0d-6
/
CELL_PARAMETERS alat
1.00000000 0.00000000 0.00000000
0.00000000 1.41421400 0.00000000
0.00000000 0.00000000 2.50000000
ATOMIC_SPECIES
Rh 1.0 Rh.pbe-rrkjus_lb.UPF
Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
ATOMIC_POSITIONS (alat)
Rhs 0.25000000 0.35000000 0.50000000 ! Surface atom core-excited
Rh 0.00000000 0.00000000 0.25000000
Rh 0.25000000 0.35000000 0.00000000
Rh 0.00000000 0.00000000 -0.25000000
Rh 0.25000000 0.35000000 -0.50000000
K_POINTS {gamma}
EOF
$ECHO
$ECHO " running pw.x for Rh011_[surface-excited] slab...\c"
$PW_COMMAND < rh011surf.scf.in > rh011surf.scf.out
check_failure $?
$ECHO " done"
#
# Now another simulation for the atom in the first layer under the surface.
#
cat > rh011layer1.scf.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Rh011lay1',
pseudo_dir = '$PSEUDO_DIR',
outdir='$TMP_DIR'
/
&system
nat=5, ntyp=2,
ibrav=0, celldm(1)=10.31510000,
ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
/
&electrons
mixing_beta = 0.3
conv_thr = 1.0d-6
/
CELL_PARAMETERS alat
1.00000000 0.00000000 0.00000000
0.00000000 1.41421400 0.00000000
0.00000000 0.00000000 2.50000000
ATOMIC_SPECIES
Rh 1.0 Rh.pbe-rrkjus_lb.UPF
Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
ATOMIC_POSITIONS (alat)
Rh 0.25000000 0.35000000 0.50000000
Rhs 0.00000000 0.00000000 0.25000000 ! Layer1 atom core-excited
Rh 0.25000000 0.35000000 0.00000000
Rh 0.00000000 0.00000000 -0.25000000
Rh 0.25000000 0.35000000 -0.50000000
K_POINTS {gamma}
EOF
$ECHO
$ECHO " running pw.x for Rh011_[layer(-1)-excited] slab...\c"
$PW_COMMAND < rh011layer1.scf.in > rh011layer1.scf.out
check_failure $?
$ECHO " done"
#
# Extract data and write results
#
enbulk=`cat rh011bulk.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
ensurf=`cat rh011surf.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
enlayer1=`cat rh011layer1.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
clssurfry=$(echo "scale=5; ($enbulk)-($ensurf)" | bc)
clssurfev=$(echo "scale=5; (($enbulk)-($ensurf))*13.6" | bc)
clslay1ry=$(echo "scale=5; ($enbulk)-($enlayer1)" | bc)
clslay1ev=$(echo "scale=5; (($enbulk)-($enlayer1))*13.6" | bc)
$ECHO "" > final-state.txt
$ECHO "GS energy in the bulk configuration: $enbulk (Ry)" >> final-state.txt
$ECHO "GS energy in the surface configuration: $ensurf (Ry)" >> final-state.txt
$ECHO "GS energy in the layer(-1) configuration: $enlayer1 (Ry)" >> final-state.txt
$ECHO "" >> final-state.txt
$ECHO "------------------------------------------" >> final-state.txt
$ECHO "FS shift for the surface atom: $clssurfev (eV)" >> final-state.txt
$ECHO "FS shift for the layer(-1) atom: $clslay1ev (eV)" >> final-state.txt
$ECHO
$ECHO " Results written in results/final-state.txt !"
$ECHO
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Rh011????.*
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
