#!/bin/sh

###############################################################################
##
##  HIGH VERBOSITY EXAMPLE
##
###############################################################################

# 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 shows how to use pw.x and pwcond.x to calculate the"
$ECHO "complex bands and the transmission coefficient of an open quantum"
$ECHO "system."

# set the needed environment variables
. ../../../environment_variables

# required executables and pseudopotentials
BIN_LIST="pw.x pwcond.x"
PSEUDO_LIST="H.pz-vbc.UPF Al.pz-vbc.UPF Ni.pz-nd-rrkjus.UPF"

$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$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 $PARA_POSTFIX"
PWCOND_COMMAND="$PARA_PREFIX $BIN_DIR/pwcond.x $PARA_POSTFIX"
$ECHO
$ECHO "  running pw.x as:     $PW_COMMAND"
$ECHO "  running pwcond.x as: $PWCOND_COMMAND"
$ECHO

# clean TMP_DIR
$ECHO "  cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"

# self-consistent calculation for Al bulk along the 001 direction
cat > al.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='al'
 /
 &system
    ibrav = 6,
    celldm(1) =5.3,
    celldm(3) =1.414,
    nat= 2,
    ntyp= 1,
    ecutwfc = 15.0,
    occupations='smearing',
    smearing='mv',
    degauss=0.01
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al 26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Al 0. 0. 0.0
 Al 0.5 0.5 0.707
K_POINTS (automatic)
 4 4 4 1 1 1
EOF
$ECHO "  running the scf calculation for Al...\c"
$PW_COMMAND < al.scf.in > al.scf.out
check_failure $?
$ECHO " done"

# complex bands of Al along the 001 direction K_perp=0
cat > al.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/'
    prefixl='al'
    band_file ='bands.al'
    ikind=0
    energy0=10.d0
    denergy=-0.4d0
    ewind=1.d0
    epsproj=1.d-3
    delgep = 1.d-12
    cutplot = 3.d0
 /
    1
    0.0 0.0 1.0
    60
EOF
$ECHO "  running pwcond.x to calculate the complex bands of Al...\c"
$PWCOND_COMMAND < al.cond.in > al.cond.out
check_failure $?
$ECHO " done"

# self-consistent calculation for Al monatomic wire
cat > alwire.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='alw'
 /
 &system
    ibrav = 6,
    celldm(1) =12.0,
    celldm(3) =0.375,
    nat= 1,
    ntyp= 1,
    nspin = 1,
    ecutwfc = 15.0,
    occupations='smearing',
    smearing='mv',
    degauss=0.01
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al 26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Al 0.0 0.0 0.000
K_POINTS (automatic)
 1 1 15 0 0 0
EOF
$ECHO "  running the scf calculation for Al monatomic wire...\c"
$PW_COMMAND < alwire.scf.in > alwire.scf.out
check_failure $?
$ECHO " done"

# complex bands of the Al monatomic wire
cat > alwire.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/'
    prefixl='alw'
    band_file='bands.alwire'
    ikind=0
    energy0=7.0d0
    denergy=-0.2d0
    ewind=1.d0
    epsproj=1.d-3
    nz1=3
    cutplot = 1.d0
 /
    1
    0. 0. 1.0
    71
EOF
$ECHO "  running pwcond.x to calculate the complex bands of Al wire...\c"
$PWCOND_COMMAND < alwire.cond.in > alwire.cond.out
check_failure $?
$ECHO " done"

# self-consistent calculation for bulk Ni
cat > ni.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='ni'
 /
 &system
    ibrav = 6,
    celldm(1) =4.57,
    celldm(3) =1.414,
    nat= 2,
    ntyp= 1,
    nspin = 2,
    starting_magnetization(1)=0.7,
    ecutwfc = 25.0,
    ecutrho = 250.0
    occupations='smearing',
    smearing='mv',
    degauss=0.01
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Ni 58.69 Ni.pz-nd-rrkjus.UPF
ATOMIC_POSITIONS alat
 Ni 0. 0. 0.
 Ni 0.5 0.5 0.707
K_POINTS (automatic)
 4 4 3 1 1 1
EOF
$ECHO "  running the scf calculation for Ni bulk...\c"
$PW_COMMAND < ni.scf.in > ni.scf.out
check_failure $?
$ECHO " done"

# complex bands of Ni
cat > ni.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/'
    prefixl='ni'
    band_file = 'bands.ni_down'
    ikind=0
    iofspin = 2
    energy0=1.d0
    denergy=-0.2d0
    ewind=3.d0
    epsproj=1.d-4
    nz1=3
 /
    1
    0.0 0.0 1.0
    30
EOF
$ECHO "  running pwcond.x to calculate the complex bands of Ni...\c"
$PWCOND_COMMAND < ni.cond.in > ni.cond.out
check_failure $?
$ECHO " done"

# self-consistent calculation for Al monatomic wire
cat > alwire1.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='alw'
 /
 &system
    ibrav = 6,
    celldm(1) =12.0,
    celldm(3) =0.375,
    nat= 1,
    ntyp= 1,
    nspin = 1,
    ecutwfc = 25.0,
    ecutrho = 150.0
    occupations='smearing',
    smearing='mv',
    degauss=0.01
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al 26.98 Al.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Al 0.0 0.0 0.000
K_POINTS (automatic)
 2 2 24 1 1 1
EOF
$ECHO "  running the scf calculation for Al monatomic wire...\c"
$PW_COMMAND < alwire1.scf.in > alwire1.scf.out
check_failure $?
$ECHO " done"

# self-consistent calculation for  Al-H-Al system
cat > AlwireH.scf.in << EOF
 &control
    calculation='scf',
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
    prefix='alh'
 /
 &system
    ibrav = 6,
    celldm(1) =12.0,
    celldm(3) =1.875,
    nat= 6,
    ntyp= 2,
    ecutwfc = 25.0,
    ecutrho = 150.0
    occupations='smearing',
    smearing='mv',
    degauss=0.01
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Al 26.98 Al.pz-vbc.UPF
 H  1.0   H.pz-vbc.UPF
ATOMIC_POSITIONS alat
Al     0.00000000     0.00000000     0.0000
Al     0.00000000     0.00000000     0.375
Al    -0.02779870     0.00000000     .75537515
H      0.19269012     0.00000000     .93750000
Al    -0.02779870     0.00000000     1.11962485
Al     0.00000000     0.00000000     1.5
K_POINTS (automatic)
 2 2 2 1 1 1
EOF
$ECHO "  running the scf calculation for Al wire with H impurity...\c"
$PW_COMMAND < AlwireH.scf.in > AlwireH.scf.out
check_failure $?
$ECHO " done"

# transmission calculation for the perfect Al wire
cat > AlwireAl.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/',
    prefixl='alw',
    prefixs='alw',
    tran_file='trans.alwire',
    ikind=1,
    energy0=2.95d0,
    denergy=-0.1d0,
    ewind=1.d0,
    epsproj=1.d-3,
    nz1 = 1
 /
    1
    0.0  0.0  1.0
    100
EOF
$ECHO "  running pwcond.x to calculate transmission of a perfect Al wire ...\c"
$PWCOND_COMMAND < AlwireAl.cond.in > AlwireAl.cond.out
check_failure $?
$ECHO " done"

# transmission calculation for the Al-C-Al
cat > AlwireH.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/',
    prefixl='alw',
    prefixs='alh',
    tran_file='trans.alwireh',
    ikind = 1,
    energy0=3.d0,
    denergy=0.d0,
    ewind=1.d0,
    epsproj=1.d-3,
    nz1 = 1,
 /
    1
    0.0  0.0  1.0
18
  3.0
  2.7
  2.5
  1.6
  1.0
  0.9
  0.1
 -0.1
 -0.25
 -1.15
 -1.45
 -1.9
 -3.0
 -4.0
 -5.0
 -6.0
 -6.2
 -6.45
EOF
$ECHO "  running pwcond.x to calculate transmission of an Al wire with H...\c"
$PWCOND_COMMAND < AlwireH.cond.in > AlwireH.cond.out
check_failure $?
$ECHO " done"

$ECHO
$ECHO "$EXAMPLE_DIR: done"
