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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 tests L2 and L23-edge X-ray absorption spectra calculation"
$ECHO
# set the needed environment variables
. ../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x xspectra.x "
PSEUDO_LIST="Cu_halfh_US_PBE_3pj.UPF Cu_US_PBE_3pj_lowE.UPF"
PSEUDO_DIR="$EXAMPLE_DIR/pseudo"
BIN_DIR="$EXAMPLE_DIR/../../bin/"
TMP_DIR="$EXAMPLE_DIR/results/tmp"
# TMP_DIR="$EXAMPLE_DIR/results/tmp"
$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"
$ECHO "Aborting"
exit 1
fi
done
# clean directory results
rm -rf ./results/*
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
cd $EXAMPLE_DIR/results
# clean directory results
rm -rf ./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 "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 $PARA_POSTFIX"
X_COMMAND="$PARA_PREFIX $BIN_DIR/xspectra.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running xspectra.x as: $X_COMMAND"
$ECHO
$ECHO
$ECHO "WARNING : All these calculations are underconverged"
$ECHO " (These are simple quick tests) "
$ECHO
$ECHO
$ECHO
$ECHO " #################################################"
$ECHO " # Cu with no core-hole in the final state #"
$ECHO " #################################################"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# extracting core wavefunction
$ECHO " extracting core wavefunction from pseudo...\c"
../../../XSpectra/tools/upf2plotcore.sh $PSEUDO_DIR/Cu_US_PBE_3pj_lowE.UPF > ./Cu.wfc
$ECHO " done"
$ECHO "#"
$ECHO "# self-consistent calculation without hole. "
$ECHO "# "
cat > Cu.scf.in << EOF
&control
calculation='scf',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='Cu',
/
&system
ibrav= 2,
celldm(1) = 6.8048679,
ecutwfc = 20.,
ecutrho = 200.,
nat= 1,
ntyp= 1,
nbnd=20,
occupations="smearing",
smearing='mp',
degauss=0.03,
/
&electrons
diagonalization='david',
mixing_mode = 'plain',
conv_thr = 1.0d-6,
/&end
ATOMIC_SPECIES
Cu 1.0 Cu_US_PBE_3pj_lowE.UPF
K_POINTS automatic
3 3 3 0 0 0
ATOMIC_POSITIONS crystal
Cu 0.0 0.0 0.0
EOF
$ECHO " running pw.x for Cu...\c"
$PW_COMMAND < Cu.scf.in > Cu.scf.out
check_failure $?
$ECHO " done"
$ECHO "#"
$ECHO "# self-consistent calculation with half hole"
$ECHO "# in a 3 x 3 x 3 supercell "
$ECHO "# "
cat > Cu_halfh.scf.in << EOF
&control
calculation='scf',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='Cu_halfh',
/
&system
ibrav= 2,
celldm(1) = 20.4146037
ecutwfc = 20.,
ecutrho = 200.,
nat= 27,
ntyp= 2,
tot_charge = 0.5
occupations="smearing",
smearing='mp',
degauss=0.03,
/&end
&electrons
diagonalization='david',
mixing_mode = 'plain',
mixing_beta = 0.3,
conv_thr = 1.0d-6,
/&end
ATOMIC_SPECIES
Cuh 1.0 Cu_halfh_US_PBE_3pj.UPF
Cu 1.0 Cu_US_PBE_3pj_lowE.UPF
K_POINTS automatic
1 1 1 0 0 0
ATOMIC_POSITIONS crystal
Cu 0. 0. 0.
Cuh 0.3333333333 0. 0.
Cu 0. 0. 0.3333333333
Cu 0. 0.3333333333 0.
Cu 0.3333333333 0. 0.3333333333
Cu 0. 0.3333333333 0.3333333333
Cu 0.3333333333 0.3333333333 0.
Cu 0.6666666666 0. 0.
Cu 0. 0.6666666666 0.
Cu 0. 0. 0.6666666666
Cu 0.6666666666 0.6666666666 0.6666666666
Cu 0.6666666666 0.6666666666 0.3333333333
Cu 0.6666666666 0.3333333333 0.6666666666
Cu 0.3333333333 0.6666666666 0.6666666666
Cu 0. 0.6666666666 0.6666666666
Cu 0.3333333333 0.6666666666 0.3333333333
Cu 0.6666666666 0.6666666666 0.
Cu 0.6666666666 0.3333333333 0.3333333333
Cu 0.6666666666 0. 0.6666666666
Cu 0.3333333333 0.3333333333 0.6666666666
Cu 0.3333333333 0.6666666666 0.
Cu 0.6666666666 0.3333333333 0.
Cu 0.6666666666 0. 0.3333333333
Cu 0.3333333333 0. 0.6666666666
Cu 0. 0.3333333333 0.6666666666
Cu 0. 0.6666666666 0.3333333333
Cu 0.3333333333 0.3333333333 0.3333333333
EOF
$ECHO " running pw.x for half hole Cu in a supercell...\c"
$PW_COMMAND < Cu_halfh.scf.in > Cu_halfh.scf.out
check_failure $?
$ECHO " done"
$ECHO " #"
$ECHO "# x-ray absorption spectrum calculation"
cat > Cu_xspectra.in << EOF
&input_xspectra
calculation='xanes_dipole',
edge='L2',
verbosity='high',
prefix='Cu',
outdir='$TMP_DIR/',
xniter=5000,
xcheck_conv=500,
xepsilon(1)=1.0,
xepsilon(2)=1.0,
xepsilon(3)=1.0,
xe0=11.5335,
xerror=0.01,
/
&plot
xnepoint=1000,
xgamma=0.5,
xemin=-10.,
xemax=80.0,
terminator=.true.,
cut_occ_states=.true.,
/
&pseudos
filecore='Cu.wfc',
r_paw(0) = 2.
r_paw(2) = 2.
/
&cut_occ
/
3 3 3 0 0 0
EOF
$ECHO " running xspectra.x on the simple cell ...\c"
$X_COMMAND < Cu_xspectra.in > Cu_xspectra.out
check_failure $?
$ECHO " done"
exit
mv xanes.dat Cu_xanes_L2.dat
mv xanes.sav Cu_xanes_L2.sav
cat > Cu_xspectra_lplus.in << EOF
&input_xspectra
calculation='xanes_dipole',
edge='L2',
lplus = .true.,
verbosity='high',
prefix='Cu',
outdir='$TMP_DIR/',
xniter=5000,
xcheck_conv=500,
xepsilon(1)=1.0,
xepsilon(2)=1.0,
xepsilon(3)=1.0,
xe0=11.5335,
xerror=0.01,
/
&plot
xnepoint=1000,
xgamma=0.5,
xemin=-10.,
xemax=80.0,
terminator=.true.,
cut_occ_states=.true.,
/
&pseudos
filecore='Cu.wfc',
r_paw(0) = 2.
r_paw(2) = 2.
/
&cut_occ
/
3 3 3 0 0 0
EOF
$ECHO " running xspectra.x with \delta_l = 1 rule ...\c"
$X_COMMAND < Cu_xspectra_lplus.in > Cu_xspectra_lplus.out
check_failure $?
$ECHO " done"
mv xanes.dat Cu_xanes_L2_lplus.dat
mv xanes.sav Cu_xanes_L2_lplus.sav
cat > Cu_halfh_xspectra.in << EOF
&input_xspectra
calculation='xanes_dipole',
edge='L2',
verbosity='low',
prefix='Cu_halfh',
outdir='$TMP_DIR/',
xniter=5000,
xcheck_conv=500,
xepsilon(1)=1.0,
xepsilon(2)=1.0,
xepsilon(3)=1.0,
ef_r=0.98,
xerror=0.01,
/
&plot
xnepoint=1000,
xgamma=0.5,
xemin=-10.,
xemax=80.0,
terminator=.true.,
cut_occ_states=.true.,
/
&pseudos
filecore='Cu.wfc',
r_paw(0) = 2.
r_paw(2) = 2.
/
&cut_occ
/
1 1 1 0 0 0
EOF
$ECHO " running xspectra.x on the supercell ...\c"
$X_COMMAND < Cu_halfh_xspectra.in > Cu_halfh_xspectra.out
check_failure $?
$ECHO " done"
mv xanes.dat Cuhalfh_xanes_L2.dat
mv xanes.sav Cuhalfh_xanes_L2.sav
cat > Cu_halfh_xspectra_xonlyplot.in << EOF
&input_xspectra
calculation='xanes_dipole',
edge='L2',
verbosity='low',
prefix='Cu_halfh',
outdir='$TMP_DIR/',
xniter=5000,
xcheck_conv=500,
xepsilon(1)=1.0,
xepsilon(2)=1.0,
xepsilon(3)=1.0,
ef_r=0.98,
xerror=0.01,
x_save_file='Cuhalfh_xanes_L2.sav',
xonly_plot=.true.,
/
&plot
xnepoint=1000,
xgamma=0.5,
xemin=-10.,
xemax=80.0,
terminator=.true.,
cut_occ_states=.true.,
/
&pseudos
filecore='Cu.wfc',
r_paw(0) = 2.
r_paw(2) = 2.
/
&cut_occ
/
1 1 1 0 0 0
EOF
$ECHO " running xspectra.x on the supercell ...\c"
$X_COMMAND < Cu_halfh_xspectra_xonlyplot.in > Cu_halfh_xspectra_xonlyplot.out
check_failure $?
$ECHO " done"
mv xanes.dat Cuhalfh_xanes_L2_xonlyplot.dat
|
