mirror of https://gitlab.com/QEF/q-e.git
528 lines
12 KiB
Bash
Executable File
528 lines
12 KiB
Bash
Executable File
#!/bin/sh
|
|
|
|
###############################################################################
|
|
##
|
|
## Example of usage for PWcond with DFT+U
|
|
##
|
|
###############################################################################
|
|
|
|
# run from directory where this script is
|
|
cd `dirname $0`
|
|
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*
|
|
$ECHO " done"
|
|
|
|
|
|
# self-consistent calculation for Au monatomic wire (DFT)
|
|
cat > Auwire.scf.in << EOF
|
|
&control
|
|
calculation = 'scf',
|
|
restart_mode = 'from_scratch',
|
|
pseudo_dir = '$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 DFT scf calculation for Au monatomic wire...\c"
|
|
$PW_COMMAND < Auwire.scf.in > Auwire.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# complex bands of the Au monatomic wire (DFT)
|
|
cat > Auwire.cond.in << EOF
|
|
&inputcond
|
|
outdir='$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 (DFT)...\c"
|
|
$PWCOND_COMMAND < Auwire.cond.in > Auwire.cond.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
|
|
# self-consistent calculation for Au monatomic wire (DFT+U)
|
|
cat > AuwireU.scf.in << EOF
|
|
&control
|
|
calculation = 'scf',
|
|
restart_mode = 'from_scratch',
|
|
pseudo_dir = '$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,
|
|
/
|
|
&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
|
|
HUBBARD {pseudo}
|
|
U Au-5d 3.0
|
|
EOF
|
|
$ECHO " running the DFT+U scf calculation for Au monatomic wire...\c"
|
|
$PW_COMMAND < AuwireU.scf.in > AuwireU.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# complex bands of the Au monatomic wire (DFT+U)
|
|
cat > AuwireU.cond.in << EOF
|
|
&inputcond
|
|
outdir='$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 (DFT+U)...\c"
|
|
$PWCOND_COMMAND < AuwireU.cond.in > AuwireU.cond.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
|
|
# self-consistent calculation for Au monatomic wire (DFT)
|
|
cat > Auwire1.scf.in << EOF
|
|
&control
|
|
calculation='scf'
|
|
restart_mode='from_scratch',
|
|
pseudo_dir = '$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 DFT scf calculation for Au monatomic wire...\c"
|
|
$PW_COMMAND < Auwire1.scf.in > Auwire1.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# self-consistent calculation for Au-CO-Au system (DFT)
|
|
cat > COatAuwire.scf.in << EOF
|
|
&control
|
|
calculation = 'scf',
|
|
restart_mode = 'from_scratch',
|
|
pseudo_dir = '$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 alat
|
|
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 DFT scf calculation for Au wire with CO impurity...\c"
|
|
$PW_COMMAND < COatAuwire.scf.in > COatAuwire.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# transmission calculation for the Au-CO-Au system (DFT)
|
|
cat > COatAuwire.cond.in << EOF
|
|
&inputcond
|
|
outdir = '$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 DFT transmission of an Au wire with atop CO...\c"
|
|
$PWCOND_COMMAND < COatAuwire.cond.in > COatAuwire.cond.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
|
|
# self-consistent calculation for Au monatomic wire (DFT+U)
|
|
cat > Auwire1U.scf.in << EOF
|
|
&control
|
|
calculation='scf'
|
|
restart_mode='from_scratch',
|
|
pseudo_dir = '$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,
|
|
/
|
|
&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
|
|
HUBBARD {pseudo}
|
|
U Au-5d 3.0
|
|
EOF
|
|
$ECHO " running the DFT+U scf calculation for Au monatomic wire...\c"
|
|
$PW_COMMAND < Auwire1U.scf.in > Auwire1U.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# self-consistent calculation for Au-CO-Au system (DFT+U)
|
|
cat > COatAuwireU.scf.in << EOF
|
|
&control
|
|
calculation = 'scf',
|
|
restart_mode = 'from_scratch',
|
|
pseudo_dir = '$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,
|
|
/
|
|
&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 alat
|
|
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
|
|
HUBBARD {pseudo}
|
|
U Au-5d 3.0
|
|
EOF
|
|
$ECHO " running the DFT+U scf calculation for Au wire with CO impurity...\c"
|
|
$PW_COMMAND < COatAuwireU.scf.in > COatAuwireU.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# transmission calculation for the Au-CO-Au system (DFT+U)
|
|
cat > COatAuwireU.cond.in << EOF
|
|
&inputcond
|
|
outdir = '$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 DFT+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 DFT and DFT+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"
|