#!/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 K-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="Si_PBE_USPP.UPF O_PBE_USPP.UPF"
PSEUDO_DIR="$EXAMPLE_DIR/pseudo"
BIN_DIR="$EXAMPLE_DIR/../../bin"
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

# 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 "#                  SiO2                   #"
$ECHO "#  Calculation of K-edge XAS  without     #"
$ECHO "#    a core-hole in the final state       #"
$ECHO "#                                         #"
$ECHO "#   The parameters of this run are not    #"
$ECHO "#     converged. To obtain converged      #"
$ECHO "#            parameters see :             #"
$ECHO "#      C. Gougoussis, M.Calandra,         #" 
$ECHO "#       A. Seitsonen, F. Mauri            #"
$ECHO "#   Phys. Rev. B 80, 075102 (2009)        #"
$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/Si_PBE_USPP.UPF > ./Si.wfc
$ECHO " done"

$ECHO "#"
$ECHO "# self-consistent calculation for SiO2."
$ECHO "# Ultrasoft pseudopotentials are being used "
$ECHO "#"

cat > SiO2.scf.in << EOF
 &control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
    prefix='SiO2',
    verbosity = 'high',
 &end
 &system
    ibrav = 4 ,
    celldm(1)=9.28630318961333,
    celldm(3)=1.10010,
    nat = 9 ,
    ntyp = 3 ,
    nspin=1,
    ecutwfc = 20.0,
    ecutrho = 150.0,
    nbnd=30,
    smearing='mp',
    occupations='smearing',
    degauss=0.03,
 &end
 &electrons
    diagonalization='david',
    conv_thr = 1.d-9,
    mixing_mode = 'plain',
    mixing_beta = 0.3,
 &end
ATOMIC_SPECIES
Sih   28.086 Si_PBE_USPP.UPF
Si   28.086 Si_PBE_USPP.UPF
O  15.9994   O_PBE_USPP.UPF
ATOMIC_POSITIONS crystal
Sih 0.47000000000000 0.000000000000 0.00000000000000
Si 0.00000000000000 0.47000000000000 0.6666666666666666
Si -0.47000000000000 -0.47000000000000 0.333333333333333
O 0.4131000000000000 0.267700000000000 0.11890000000000
O 0.267700000000000 0.4131000000000000 .54776666666666666666
O -0.267700000000000 0.1454000000000000 .78556666666666666666
O -0.4131000000000000 -0.1454000000000000 .21443333333333333333
O -0.1454000000000000 -0.4131000000000000 .45223333333333333333
O 0.1454000000000000 -0.267700000000000 -0.11890000000000
K_POINTS automatic
2 2 2 0 0 0
EOF

$ECHO "  running pw.x for SiO2 ...\c"
$PW_COMMAND < SiO2.scf.in > SiO2.scf.out
check_failure $?
$ECHO " done"

$ECHO "#"
$ECHO "# xanes calculations : Si K-edge"
$ECHO "# ultrasoft pseudopotentials are being used"
$ECHO "# cutting occupied states " 
$ECHO "#"
$ECHO "# x-ray absorption spectrum calculation"
$ECHO "# dipolar part"
$ECHO "#"
$ECHO "# epsilon in the plane direction"

cat > SiO2.xspectra_dip_plane.in << EOF
 &input_xspectra
    calculation='xanes_dipole'
    prefix='SiO2',
    outdir='$TMP_DIR/',
    xonly_plot=.false.,
    xniter=2000,
    xcheck_conv=50,
    xepsilon(1)=1.0,
    xepsilon(2)=1.0,
    xepsilon(3)=0.0,
    xiabs=1,
    x_save_file='SiO2.xspectra_dip_plane.sav',
    xerror=0.001,
 / 
 &plot
    xnepoint=1000,
    xgamma=0.8,
    xemin=-10.0,
    xemax=100.0,
    terminator=.true.,
    cut_occ_states=.true.,
 &end
 &pseudos
    filecore='Si.wfc',
    r_paw(1)=2.4,
 &end
 &cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0
EOF
$ECHO "  running xspectra.x ...\c"
$X_COMMAND < SiO2.xspectra_dip_plane.in  > SiO2.xspectra_dip_plane.out
check_failure $?
mv xanes.dat SiO2.xspectra_dip_plane.dat
$ECHO " done"

$ECHO "#"
$ECHO "# epsilon in the c axis direction"

cat > SiO2.xspectra_dip_c.in << EOF
 &input_xspectra
    calculation='xanes_dipole'
    prefix='SiO2',
    outdir='$TMP_DIR/',
    xonly_plot=.false.,
    xniter=2000,
    xcheck_conv=50,
    xepsilon(1)=0.0,
    xepsilon(2)=0.0,
    xepsilon(3)=1.0,
    xiabs=1,
    x_save_file='SiO2.xspectra_dip_c.sav',
    xerror=0.001,
 /
 &plot
    xnepoint=1000,
    xgamma=0.8,
    xemin=-10.0,
    xemax=100.0,
    terminator=.true.,
    cut_occ_states=.true.,
 &end
 &pseudos
    filecore='Si.wfc',
    r_paw(1)=2.4,
 &end
 &cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0
EOF
$ECHO "  running xspectra.x ...\c"
$X_COMMAND < SiO2.xspectra_dip_c.in  > SiO2.xspectra_dip_c.out
check_failure $?
mv xanes.dat SiO2.xspectra_dip_c.dat
$ECHO " done"

$ECHO "#"
$ECHO "# example of the restart mode"
$ECHO "# a time limit is put is the first calculation"
$ECHO "# so that it is not finished at the end of the time"
$ECHO "# then one can restart the calculation of the coefficients"
$ECHO "# of the continued fraction"
$ECHO "#"
$ECHO "# calculation 1 : not finished"

cat > SiO2.xspectra_dip_restart_1.in << EOF
 &input_xspectra
    calculation='xanes_dipole'
    prefix='SiO2',
    outdir='$TMP_DIR/',
    xonly_plot=.false.,
    xniter=2000,
    xcheck_conv=50,
    xepsilon(1)=0.0,
    xepsilon(2)=0.0,
    xepsilon(3)=1.0,
    xiabs=1,
    x_save_file='SiO2.xspectra_dip_restart_1.sav',
    xerror=0.001,
    time_limit=10,
 /
 &plot
    xnepoint=1000,
    xgamma=0.8,
    xemin=-10.0,
    xemax=100.0,
    terminator=.true.,
    cut_occ_states=.true.,
 &end
 &pseudos
    filecore='Si.wfc',
    r_paw(1)=2.4,
 &end
 &cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0
EOF
$ECHO "  running xspectra.x ...\c"
$X_COMMAND < SiO2.xspectra_dip_restart_1.in  > SiO2.xspectra_dip_restart_1.out
check_failure $?
$ECHO " done"
$ECHO "#"
$ECHO "# calculation 2 : finishing the first calculation"
$ECHO "# the result should be identical to SiO2.xspectra_dip_c.dat"
$ECHO "# copy SiO2.xspectra_dip_restart_1.sav to SiO2.xspectra_dip_restart_2.sav"
cp SiO2.xspectra_dip_restart_1.sav SiO2.xspectra_dip_restart_2.sav

cat > SiO2.xspectra_dip_restart_2.in << EOF
 &input_xspectra
    calculation='xanes_dipole'
    prefix='SiO2',
    outdir='$TMP_DIR/',
    xonly_plot=.false.,
    xniter=2000,
    xcheck_conv=50,
    xepsilon(1)=0.0,
    xepsilon(2)=0.0,
    xepsilon(3)=1.0,
    xiabs=1,
    x_save_file='SiO2.xspectra_dip_restart_2.sav',
    xerror=0.001,
    restart_mode='restart',
 /
 &plot
    xnepoint=1000,
    xgamma=0.8,
    xemin=-10.0,
    xemax=100.0,
    terminator=.true.,
    cut_occ_states=.true.,
 &end
 &pseudos
    filecore='Si.wfc',
    r_paw(1)=2.4,
 &end
 &cut_occ
    cut_desmooth=0.1,
 &end
3 3 3 0 0 0
EOF
$ECHO "  running xspectra.x ...\c"
$X_COMMAND < SiO2.xspectra_dip_restart_2.in  > SiO2.xspectra_dip_restart_2.out
check_failure $?
mv xanes.dat SiO2.xspectra_dip_restart_2.dat
$ECHO " done"
$ECHO "# SiO2.xspectra_dip_restart_1.sav is not complete"
$ECHO "# SiO2.xspectra_dip_restart_2.sav should be complete"
