#!/bin/sh

###############################################################################
##
##  Example of usage for PWcond with LDA+U
##
###############################################################################

# 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="Au.pz-rrkjus_aewfc.UPF C.pz-rrkjus.UPF O.pz-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 Au monatomic wire (LDA)
cat > Auwire.scf.in << EOF
 &control
    calculation = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir = '$TMP_DIR/',
    prefix = 'Auwire'
 /
 &system
    ibrav = 6,
    celldm(1) =15.0,
    celldm(3) =0.316,
    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 = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
ATOMIC_POSITIONS (angstrom)
 Au  0.0  0.0  0.0
K_POINTS (automatic)
 1 1 25 0 0 0
EOF
$ECHO "  running the LDA scf calculation for Au monatomic wire...\c"
$PW_COMMAND < Auwire.scf.in > Auwire.scf.out
check_failure $?
$ECHO " done"

# complex bands of the Au monatomic wire (LDA)
cat > Auwire.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/'
    prefixl='Auwire'
    band_file='bands.Auwire'
    ikind=0
    energy0=1.0d0
    denergy=-0.05d0
    ewind=4.d0
    epsproj=1.d-5
    nz1=3
    cutplot = 1.d0
 /
    1
    0.0 0.0 1.0
    100
EOF
$ECHO "  running pwcond.x to calculate the complex bands of Au wire (LDA)...\c"
$PWCOND_COMMAND < Auwire.cond.in > Auwire.cond.out
check_failure $?
$ECHO " done"


# self-consistent calculation for Au monatomic wire (LDA+U)
cat > AuwireU.scf.in << EOF
 &control
    calculation = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir = '$TMP_DIR/',
    prefix = 'AuwireU'
 /
 &system
    ibrav = 6,
    celldm(1) =15.0,
    celldm(3) =0.316,
    nat= 1,
    ntyp= 1,
    nspin = 1,
    ecutwfc = 25.0,
    ecutrho = 150.0,
    occupations = 'smearing',
    smearing = 'mv',
    degauss = 0.01,
    lda_plus_U = .true.,
    U_projection_type = 'pseudo',
    Hubbard_U = 3.0
 /
 &electrons
    conv_thr = 1.0e-8
    mixing_beta = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
ATOMIC_POSITIONS (angstrom)
 Au  0.0  0.0  0.0
K_POINTS (automatic)
 1 1 25 0 0 0
EOF
$ECHO "  running the LDA+U scf calculation for Au monatomic wire...\c"
$PW_COMMAND < AuwireU.scf.in > AuwireU.scf.out
check_failure $?
$ECHO " done"

# complex bands of the Au monatomic wire (LDA+U)
cat > AuwireU.cond.in << EOF
 &inputcond
    outdir='$TMP_DIR/'
    prefixl='AuwireU'
    band_file='bandsU.Auwire'
    ikind=0
    energy0=1.0d0
    denergy=-0.05d0
    ewind=4.d0
    epsproj=1.d-5
    nz1=3
    cutplot = 1.d0
 /
    1
    0.0 0.0 1.0
    100
EOF
$ECHO "  running pwcond.x to calculate the complex bands of Au wire (LDA+U)...\c"
$PWCOND_COMMAND < AuwireU.cond.in > AuwireU.cond.out
check_failure $?
$ECHO " done"


# self-consistent calculation for Au monatomic wire (LDA)
cat > Auwire1.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='Auwire'
 /
 &system
    ibrav = 6,
    celldm(1) = 15.0,
    celldm(3) = 0.316,
    nat = 1,
    ntyp = 1,
    nspin = 1,
    ecutwfc = 25.0,
    ecutrho = 150.0,
    occupations = 'smearing',
    smearing = 'mv',
    degauss = 0.01
 /
 &electrons
    conv_thr = 1.0d-8,
    mixing_beta = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
ATOMIC_POSITIONS (angstrom)
 Au  0.0  0.0  0.0
K_POINTS (automatic)
 2 2 24 1 1 1
EOF
$ECHO "  running the LDA scf calculation for Au monatomic wire...\c"
$PW_COMMAND < Auwire1.scf.in > Auwire1.scf.out
check_failure $?
$ECHO " done"

# self-consistent calculation for Au-CO-Au system (LDA)
cat > COatAuwire.scf.in << EOF
 &control
    calculation = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir = '$TMP_DIR/',
    prefix = 'Auwire_CO',
    tprnfor = .true.
 /
 &system
    ibrav = 6,
    celldm(1) = 15.0,
    celldm(3) = 1.896,
    nat = 8,
    ntyp = 3,
    ecutwfc = 25.0,
    ecutrho = 150.0
    occupations = 'smearing',
    smearing = 'mv',
    degauss = 0.01
 /
 &electrons
    conv_thr = 1.0d-8,
    mixing_beta = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
 C    12.0107  C.pz-rrkjus.UPF  
 O    15.9994  O.pz-rrkjus.UPF  
ATOMIC_POSITIONS
C   0.238357456 0.0 0.948
O   0.381346734 0.0 0.948
Au  0.0  0.0  0.000
Au  0.0  0.0  0.316
Au  0.0  0.0  0.632
Au  0.0  0.0  0.948
Au  0.0  0.0  1.264
Au  0.0  0.0  1.580 
K_POINTS (automatic)
 2 2 4 1 1 1
EOF
$ECHO "  running the LDA scf calculation for Au wire with CO impurity...\c"
$PW_COMMAND < COatAuwire.scf.in > COatAuwire.scf.out
check_failure $?
$ECHO " done"

# transmission calculation for the Au-CO-Au system (LDA)
cat > COatAuwire.cond.in << EOF
 &inputcond
    outdir = '$TMP_DIR/',
    prefixl = 'Auwire',
    prefixs = 'Auwire_CO',
    tran_file = 'trans.AuwireCO',
    ikind = 1,
    energy0 = 1.d0,
    denergy=0.d0,
    ewind=4.d0,
    epsproj=1.d-4,
    nz1 = 2,
 /
    1
    0.0  0.0  1.0
16
  1.0
  0.7
  0.5
  0.3
  0.2
  0.15
  0.1
  0.05
  0.0
 -0.2
 -0.3
 -0.5
 -0.7
 -0.8
 -0.9
 -1.0
EOF
$ECHO "  running pwcond.x to calculate the LDA transmission of an Au wire with atop CO...\c"
$PWCOND_COMMAND < COatAuwire.cond.in > COatAuwire.cond.out
check_failure $?
$ECHO " done"


# self-consistent calculation for Au monatomic wire (LDA+U)
cat > Auwire1U.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    prefix='AuwireU'
 /
 &system
    ibrav = 6,
    celldm(1) = 15.0,
    celldm(3) = 0.316,
    nat = 1,
    ntyp = 1,
    nspin = 1,
    ecutwfc = 25.0,
    ecutrho = 150.0,
    occupations = 'smearing',
    smearing = 'mv',
    degauss = 0.01,
    lda_plus_U = .true.,
    U_projection_type = 'pseudo',
    Hubbard_U = 3.0
 /
 &electrons
    conv_thr = 1.0d-8,
    mixing_beta = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
ATOMIC_POSITIONS (angstrom)
 Au  0.0  0.0  0.0
K_POINTS (automatic)
 2 2 24 1 1 1
EOF
$ECHO "  running the LDA+U scf calculation for Au monatomic wire...\c"
$PW_COMMAND < Auwire1U.scf.in > Auwire1U.scf.out
check_failure $?
$ECHO " done"

# self-consistent calculation for Au-CO-Au system (LDA+U)
cat > COatAuwireU.scf.in << EOF
 &control
    calculation = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir = '$TMP_DIR/',
    prefix = 'AuwireU_CO',
    tprnfor = .true.
 /
 &system
    ibrav = 6,
    celldm(1) = 15.0,
    celldm(3) = 1.896,
    nat = 8,
    ntyp = 3,
    ecutwfc = 25.0,
    ecutrho = 150.0
    occupations = 'smearing',
    smearing = 'mv',
    degauss = 0.01,
    lda_plus_U = .true.,
    U_projection_type = 'pseudo',
    Hubbard_U = 3.0
 /
 &electrons
    conv_thr = 1.0d-8,
    mixing_beta = 0.6
 /
ATOMIC_SPECIES
 Au  196.966  Au.pz-rrkjus_aewfc.UPF
 C    12.0107  C.pz-rrkjus.UPF  
 O    15.9994  O.pz-rrkjus.UPF  
ATOMIC_POSITIONS
C   0.238357456 0.0 0.948
O   0.381346734 0.0 0.948
Au  0.0  0.0  0.000
Au  0.0  0.0  0.316
Au  0.0  0.0  0.632
Au  0.0  0.0  0.948
Au  0.0  0.0  1.264
Au  0.0  0.0  1.580 
K_POINTS (automatic)
 2 2 4 1 1 1
EOF
$ECHO "  running the LDA+U scf calculation for Au wire with CO impurity...\c"
$PW_COMMAND < COatAuwireU.scf.in > COatAuwireU.scf.out
check_failure $?
$ECHO " done"

# transmission calculation for the Au-CO-Au system (LDA+U)
cat > COatAuwireU.cond.in << EOF
 &inputcond
    outdir = '$TMP_DIR/',
    prefixl = 'AuwireU',
    prefixs = 'AuwireU_CO',
    tran_file = 'transU.AuwireCO',
    ikind = 1,
    energy0 = 1.d0,
    denergy=0.d0,
    ewind=4.d0,
    epsproj=1.d-4,
    nz1 = 2,
 /
    1
    0.0  0.0  1.0
16
  1.0
  0.7
  0.5
  0.3
  0.2
  0.15
  0.1
  0.05
  0.0
 -0.2
 -0.3
 -0.5
 -0.7
 -0.8
 -0.9
 -1.0
EOF
$ECHO "  running pwcond.x to calculate the LDA+U transmission of an Au wire with atop CO...\c"
$PWCOND_COMMAND < COatAuwireU.cond.in > COatAuwireU.cond.out
check_failure $?
$ECHO " done"

cat > plot_results.gnu << EOF
##
# Script to visualize the results of the DFT+U PWcond example
##

set style line 11 lt 1 lc rgbcolor 'blue' lw 2 pt 6
set style line 12 lt 2 lc rgbcolor 'cyan' lw 1 pt 6
set style line 21 lt 1 lc rgbcolor 'red' lw 2 pt 2
set style line 22 lt 2 lc rgbcolor 'magenta' lw 1 pt 2
set style arrow 1 nohead lt 3 lc rgbcolor 'dark-green' lw 1.5
set style arrow 2 nohead lt 1 lc rgbcolor 'black' lw 1

#1. compare CBS of Au chain within LDA and LDA+U
set key center right
set xlabel 'Re(k_z)'
set label 'Im(k_z)=0' at 0.02, -2.5 left
set label 'Im(k_z)' at first -0.25, screen 0.03 center
set label 'Re(k_z)=0' at -0.02, -2.5 right
set label 'Re(k_z)+Im(k_z)' at 0.75, screen 0.03 center
set label 'Re(k_z)=0.5' at 0.52, -2.5 left
set ylabel 'E - E_F  (eV)'
set arrow from graph 0,first 0 to graph 1, first 0 as 1
set arrow from 0,graph 0 to 0,graph 1 as 2
set arrow from 0.5,graph 0 to 0.5,graph 1 as 2
set xrange [-0.5:1.0]
plot '< awk "{if(\\\$1>0.0) print}" bands.Auwire.re'  w p ls 11 title 'U=0',\\
     'bands.Auwire.im'  w p ls 11 notitle,\\
     '< awk "{if(\\\$1>0.0) print}" bandsU.Auwire.re' w p ls 21 title 'U=3',\\
     'bandsU.Auwire.im' w p ls 21 notitle

unset arrow
unset label
pause -1  "Hit return to continue"

## extract the number of channels
! echo "# channels" > nch.tmp
! grep Nchannels COatAuwire.cond.out  | cut -d= -f2 >> nch.tmp
! echo "# channels" > nchU.tmp
! grep Nchannels COatAuwireU.cond.out | cut -d= -f2 >> nchU.tmp

#2. compare the ballistic transmission for CO@Au chain
set xlabel 'E - E_F  (eV)'
set ylabel 'Transmittance'
set arrow from 0,graph 0 to 0,graph 1 as 1
set xrange [-1.0:1.0]
plot 'trans.AuwireCO'  u 1:2 w lp ls 11 title 'T(U=0)', \\
     '< paste trans.AuwireCO nch.tmp'  u 1:3 w lp ls 12 title 'N(U=0)', \\
     'transU.AuwireCO' u 1:2 w lp ls 21 title 'T(U=3)',\\
     '< paste transU.AuwireCO nchU.tmp'  u 1:3 w lp ls 22 title 'N(U=3)'


EOF
$ECHO
$ECHO "  (you can visualize the results with Gnuplot using the plot_results.gnu script)"

$ECHO
$ECHO "$EXAMPLE_DIR: done"