#!/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 \
                http://www.quantum-espresso.org/pseudo/1.3/UPF/$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/*
$ECHO " done"

# self-consistent calculation for Al bulk along the 001 direction
cat > al.scf.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>


<input calculation="scf" prefix="al">

	<cell type="qecell">
		<qecell ibrav="6" alat="5.3">
			<real rank="1" n1="5">
				0.0 1.414 0.0 0.0 0.0
			</real>
		</qecell>
	</cell>

	<atomic_species ntyp="1">
		<specie name="Al">
			<property name="mass">
				<real>26.98</real>
			</property>
			<property name="pseudofile">
				<string>Al.pz-vbc.UPF</string>
			</property>
		</specie>
	</atomic_species>

	<atomic_list units="alat" nat="2" >
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.0 0.0 0.0
				</real>
			</position>
		</atom>
		
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.5 0.5 0.707
				</real>
			</position>
		</atom>						
	</atomic_list>	
	
	
	<field name="InputOutput">

		<parameter name="restart_mode">
			<string>
				from_scratch
			</string>
		</parameter>

		<parameter name="pseudo_dir">
			<string>
				$PSEUDO_DIR/
			</string>
		</parameter>
		
		<parameter name="outdir">
			<string>
				$TMP_DIR/
			</string>
		</parameter>
					
	</field>
	
	<field name="Numerics">

		<parameter name="ecutwfc">
			<real>
				15.0
			</real>
		</parameter>
		
		<parameter name="mixing_beta">
			<real>
				0.7
			</real>
		</parameter>
		
		<parameter name="conv_thr">
			<real>
				1.0e-8
			</real>
		</parameter>
	
	</field>
	
	<field name="Options">

		<parameter name="occupations">
			<string>
				smearing
			</string>
		</parameter>
		
		<parameter name="smearing">
			<string>
				methfessel-paxton
			</string>
		</parameter>
		
		<parameter name="degauss">
			<real>
				0.01
			</real>
		</parameter>		
	
	</field>	
	
	<k_points type="automatic">
		<mesh>
			<integer rank="1" n1="6">
				4 4 4 1 1 1
			</integer>
		</mesh> 
	</k_points>
	
</input>
EOF
$ECHO "  running the scf calculation for Al...\c"
$PW_COMMAND < al.scf.xml > 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.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>


<input calculation="scf" prefix="alw">

	<cell type="qecell">
		<qecell ibrav="6" alat="12.0">
			<real rank="1" n1="5">
				0.0 0.375 0.0 0.0 0.0
			</real>
		</qecell>
	</cell>

	<atomic_species ntyp="1">
		<specie name="Al">
			<property name="mass">
				<real>26.98</real>
			</property>
			<property name="pseudofile">
				<string>Al.pz-vbc.UPF</string>
			</property>
		</specie>
	</atomic_species>

	<atomic_list units="alat" nat="1" >
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.0 0.0 0.000
				</real>
			</position>
		</atom>				
	</atomic_list>		
	
	
	<field name="InputOutput">

		<parameter name="restart_mode">
			<string>
				from_scratch
			</string>
		</parameter>

		<parameter name="pseudo_dir">
			<string>
				$PSEUDO_DIR/
			</string>
		</parameter>
		
		<parameter name="outdir">
			<string>
				$TMP_DIR/
			</string>
		</parameter>
					
	</field>
	
	<field name="Numerics">

		<parameter name="ecutwfc">
			<real>
				15.0
			</real>
		</parameter>
		
		<parameter name="mixing_beta">
			<real>
				0.7
			</real>
		</parameter>
		
		<parameter name="conv_thr">
			<real>
				1.0e-8
			</real>
		</parameter>
	
	</field>
	
	<field name="Options">

		<parameter name="occupations">
			<string>
				smearing
			</string>
		</parameter>
		
		<parameter name="smearing">
			<string>
				methfessel-paxton
			</string>
		</parameter>
		
		<parameter name="degauss">
			<real>
				0.01
			</real>
		</parameter>		
	
	</field>
	
	<field name="Fields">

		<parameter name="nspin">
			<integer>
				1
			</integer>
		</parameter>
	
	</field>	
	
	<k_points type="automatic">
		<mesh>
			<integer rank="1" n1="6">
				1 1 15 0 0 0
			</integer>
		</mesh> 
	</k_points>
	
</input>
EOF
$ECHO "  running the scf calculation for Al monatomic wire...\c"
$PW_COMMAND < alwire.scf.xml > 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.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>

<input calculation="scf" prefix="ni">

	<cell type="qecell">
		<qecell ibrav="6" alat="4.57">
			<real rank="1" n1="5">
				0.0 1.414 0.0 0.0 0.0
			</real>
		</qecell>
	</cell>

	<atomic_species ntyp="1">
		<specie name="Ni">
			<property name="mass">
				<real>58.69</real>
			</property>
			<property name="pseudofile">
				<string>Ni.pz-nd-rrkjus.UPF</string>
			</property>
			<property name="starting_magnetization">
				<real>
					0.7
				</real>
			</property>
		</specie>
	</atomic_species>

	<atomic_list units="alat" nat="2" >
		<atom name="Ni">
			<position>
				<real rank="1" n1="3">
					0.0 0.0 0.0
				</real>
			</position>
		</atom>	
		<atom name="Ni">
			<position>
				<real rank="1" n1="3">
					0.5 0.5 0.707
				</real>
			</position>
		</atom>							
	</atomic_list>	
	
	
	<field name="InputOutput">

		<parameter name="restart_mode">
			<string>
				from_scratch
			</string>
		</parameter>

		<parameter name="pseudo_dir">
			<string>
				$PSEUDO_DIR/
			</string>
		</parameter>
		
		<parameter name="outdir">
			<string>
				$TMP_DIR/
			</string>
		</parameter>
		
	</field>
	
	<field name="Numerics">

		<parameter name="ecutwfc">
			<real>
				25.0
			</real>
		</parameter>
		
		<parameter name="ecutrho">
			<real>
				250.0
			</real>
		</parameter>
		
		<parameter name="mixing_beta">
			<real>
				0.7
			</real>
		</parameter>
		
		<parameter name="conv_thr">
			<real>
				1.0e-8
			</real>
		</parameter>
		
	</field>
	
	<field name="Options">

		<parameter name="occupations">
			<string>
				smearing
			</string>
		</parameter>
		
		<parameter name="smearing">
			<string>
				methfessel-paxton
			</string>
		</parameter>
		
		<parameter name="degauss">
			<real>
				0.01
			</real>
		</parameter>
		
	</field>	
	
	<field name="Fields">

		<parameter name="nspin">
			<integer>
				2
			</integer>
		</parameter>
	
	</field>
	
	<k_points type="automatic">
		<mesh>
			<integer rank="1" n1="6">
				4 4 3 1 1 1
			</integer>
		</mesh> 
	</k_points>
</input>
EOF
$ECHO "  running the scf calculation for Ni bulk...\c"
$PW_COMMAND < ni.scf.xml > 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.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>


<input calculation="scf" prefix="alw">

	<cell type="qecell">
		<qecell ibrav="6" alat="12.0">
			<real rank="1" n1="5">
				0.0 0.375 0.0 0.0 0.0
			</real>
		</qecell>
	</cell>

	<atomic_species ntyp="1">
		<specie name="Al">
			<property name="mass">
				<real>26.98</real>
			</property>
			<property name="pseudofile">
				<string>Al.pz-vbc.UPF</string>
			</property>
		</specie>
	</atomic_species>

	<atomic_list units="alat" nat="1" >
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.0 0.0 0.000
				</real>
			</position>
		</atom>				
	</atomic_list>			
	
	
	<field name="InputOutput">

		<parameter name="restart_mode">
			<string>
				from_scratch
			</string>
		</parameter>

		<parameter name="pseudo_dir">
			<string>
				$PSEUDO_DIR/
			</string>
		</parameter>
		
		<parameter name="outdir">
			<string>
				$TMP_DIR/
			</string>
		</parameter>
					
	</field>
	
	<field name="Numerics">

		<parameter name="ecutwfc">
			<real>
				25.0
			</real>
		</parameter>
		
		<parameter name="ecutrho">
			<real>
				150.0
			</real>
		</parameter>
		
		<parameter name="mixing_beta">
			<real>
				0.7
			</real>
		</parameter>
		
		<parameter name="conv_thr">
			<real>
				1.0e-8
			</real>
		</parameter>
	
	</field>
	
	<field name="Options">

		<parameter name="occupations">
			<string>
				smearing
			</string>
		</parameter>
		
		<parameter name="smearing">
			<string>
				methfessel-paxton
			</string>
		</parameter>
		
		<parameter name="degauss">
			<real>
				0.01
			</real>
		</parameter>		
	
	</field>
	
	<field name="Fields">

		<parameter name="nspin">
			<integer>
				1
			</integer>
		</parameter>
	
	</field>	
	
	<k_points type="automatic">
		<mesh>
			<integer rank="1" n1="6">
				2 2 24 1 1 1
			</integer>
		</mesh> 
	</k_points>
	
</input>
EOF
$ECHO "  running the scf calculation for Al monatomic wire...\c"
$PW_COMMAND < alwire1.scf.xml > alwire1.scf.out
check_failure $?
$ECHO " done"

# self-consistent calculation for  Al-H-Al system
cat > AlwireH.scf.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>


<input calculation="scf" prefix="alh">

	<cell type="qecell">
		<qecell ibrav="6" alat="12.0">
			<real rank="1" n1="5">
				0.0 1.875 0.0 0.0 0.0
			</real>
		</qecell>
	</cell>

	<atomic_species ntyp="2">
		<specie name="Al">
			<property name="mass">
				<real>26.98</real>
			</property>
			<property name="pseudofile">
				<string>Al.pz-vbc.UPF</string>
			</property>
		</specie>
		<specie name="H">
			<property name="mass">
				<real>1.0</real>
			</property>
			<property name="pseudofile">
				<string>H.pz-vbc.UPF</string>
			</property>
		</specie>
	</atomic_species>

	<atomic_list units="alat" nat="6" >
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.00000000     0.00000000     0.0000
				</real>
			</position>
		</atom>	
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.00000000     0.00000000     0.375
				</real>
			</position>
		</atom>
		<atom name="Al">
			<position>
				<real rank="1" n1="3">
					-0.02779870     0.00000000     .75537515
				</real>
			</position>
		</atom><atom name="H">
			<position>
				<real rank="1" n1="3">
					0.19269012     0.00000000     .93750000
				</real>
			</position>
		</atom><atom name="Al">
			<position>
				<real rank="1" n1="3">
					-0.02779870     0.00000000     1.11962485
				</real>
			</position>
		</atom><atom name="Al">
			<position>
				<real rank="1" n1="3">
					0.00000000     0.00000000     1.5
				</real>
			</position>
		</atom>			
	</atomic_list>
	
	
	<field name="InputOutput">

		<parameter name="restart_mode">
			<string>
				from_scratch
			</string>
		</parameter>

		<parameter name="pseudo_dir">
			<string>
				$PSEUDO_DIR/
			</string>
		</parameter>
		
		<parameter name="outdir">
			<string>
				$TMP_DIR/
			</string>
		</parameter>
					
	</field>
	
	<field name="Numerics">

		<parameter name="ecutwfc">
			<real>
				25.0
			</real>
		</parameter>
		
		<parameter name="ecutrho">
			<real>
				150.0
			</real>
		</parameter>
		
		<parameter name="mixing_beta">
			<real>
				0.7
			</real>
		</parameter>
		
		<parameter name="conv_thr">
			<real>
				1.0e-8
			</real>
		</parameter>
	
	</field>
	
	<field name="Options">

		<parameter name="occupations">
			<string>
				smearing
			</string>
		</parameter>
		
		<parameter name="smearing">
			<string>
				methfessel-paxton
			</string>
		</parameter>
		
		<parameter name="degauss">
			<real>
				0.01
			</real>
		</parameter>		
	
	</field>
	
	<k_points type="automatic">
		<mesh>
			<integer rank="1" n1="6">
				2 2 2 1 1 1
			</integer>
		</mesh> 
	</k_points>
	
</input>
EOF
$ECHO "  running the scf calculation for Al wire with H impurity...\c"
$PW_COMMAND < AlwireH.scf.xml > 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"