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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 initial state contribution for a Rh011 slab"
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x initial_state.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 $PARA_POSTFIX"
IS_COMMAND="$PARA_PREFIX $BIN_DIR/initial_state.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running initial_state.x as: $IS_COMMAND"
$ECHO
#
# self-consistent calculation. Note the definitions in ATOMIC_SPECIES and ntyp in &system
#
cat > rh011slab.scf.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Rh011',
pseudo_dir = '$PSEUDO_DIR',
outdir='$TMP_DIR'
/
&system
nat=5, ntyp=2,
ibrav=0, celldm(1)=10.31510000,
ecutwfc = 25, occupations='smearing', degauss = 0.02, smearing='mv',
/
&electrons
mixing_beta = 0.3
conv_thr = 1.0d-6
/
CELL_PARAMETERS
0.50000000 0.00000000 0.00000000
0.00000000 0.70710678 0.00000000
0.00000000 0.00000000 3.00000000
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
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 slab...\c"
$PW_COMMAND < rh011slab.scf.in > rh011slab.scf.out
check_failure $?
$ECHO " done"
# Initial state calculation as a post-processing tool
#
cat > rh011slab.istate.in << EOF
&inputpp
prefix='Rh011',
outdir='$TMP_DIR'
excite(1) = 2,
/
EOF
$ECHO
$ECHO " running initial_state.x for RhUS->RhsUS ...\c"
$IS_COMMAND < rh011slab.istate.in > rh011slab.istate.out
check_failure $?
$ECHO " done"
#
# Extract data and write results
#
enbulk=$(grep "atom 3 type 1" rh011slab.istate.out | head -n1 | cut -d" " -f 19)
enlay1=$(grep "atom 2 type 1" rh011slab.istate.out | head -n1 | cut -d" " -f 19)
ensurf=$(grep "atom 1 type 1" rh011slab.istate.out | head -n1 | cut -d" " -f 19)
clssurfry=$(echo "scale=5; ($enbulk)-($ensurf)" | bc)
clssurfev=$(echo "scale=5; (($enbulk)-($ensurf))*13.6" | bc)
clslay1ry=$(echo "scale=5; ($enbulk)-($enlay1)" | bc)
clslay1ev=$(echo "scale=5; (($enbulk)-($enlay1))*13.6" | bc)
$ECHO "" > initial-state.txt
$ECHO "IS contribution for the bulk atom: $enbulk (Ry)" >> initial-state.txt
$ECHO "IS contribution for the surface atom: $ensurf (Ry)" >> initial-state.txt
$ECHO "IS contribution for the layer(-1) atom: $enlay1 (Ry)" >> initial-state.txt
$ECHO "" >> initial-state.txt
$ECHO "------------------------------------------" >> initial-state.txt
$ECHO "" >> initial-state.txt
$ECHO "IS shift surface: $clssurfev (eV)" >> initial-state.txt
$ECHO "IS shift layer(-1): $clslay1ev (eV)" >> initial-state.txt
$ECHO
$ECHO " Results written in results/initial-state.txt !"
$ECHO
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Rh011.*
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
