mirror of https://gitlab.com/QEF/q-e.git
473 lines
12 KiB
Bash
Executable File
473 lines
12 KiB
Bash
Executable File
#!/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 shows a calculation of STM maps."
|
|
|
|
# set the needed environment variables
|
|
. ../../../environment_variables
|
|
|
|
# required executables and pseudopotentials
|
|
BIN_LIST="pw.x pp.x plotrho.x projwfc.x sumpdos.x"
|
|
PSEUDO_LIST="Al.pz-vbc.UPF As.pz-bhs.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"
|
|
$ECHO "Aborting"
|
|
exit 1
|
|
fi
|
|
done
|
|
|
|
# check for gnuplot
|
|
GP_COMMAND=`which gnuplot 2>/dev/null`
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
$ECHO
|
|
$ECHO "gnuplot not in PATH"
|
|
$ECHO "Results will not be plotted"
|
|
fi
|
|
|
|
# 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 $PARA_POSTFIX"
|
|
PP_COMMAND="$PARA_PREFIX $BIN_DIR/pp.x $PARA_POSTFIX"
|
|
PLOTRHO_COMMAND="$BIN_DIR/plotrho.x"
|
|
PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
|
|
SUMPDOS_COMMAND="$BIN_DIR/sumpdos.x"
|
|
$ECHO
|
|
$ECHO " running pw.x as: $PW_COMMAND"
|
|
$ECHO " running pp.x as: $PP_COMMAND"
|
|
$ECHO " running plotrho.x as: $PLOTRHO_COMMAND"
|
|
$ECHO " running projwfc.x as: $PROJWFC_COMMAND"
|
|
$ECHO " running sumpdos.x as: $SUMPDOS_COMMAND"
|
|
$ECHO " running gnuplot as: $GP_COMMAND"
|
|
$ECHO
|
|
|
|
# self-consistent calculation
|
|
cat > AlAs110re.scf.in << EOF
|
|
&control
|
|
calculation = 'scf'
|
|
restart_mode='from_scratch',
|
|
title='AlAs 110 surface slab, relaxed (central plane fixed)'
|
|
pseudo_dir = '$PSEUDO_DIR/',
|
|
outdir='$TMP_DIR/',
|
|
prefix='AlAs110'
|
|
/
|
|
&system
|
|
ibrav= 8, celldm(1) =7.424621202, celldm(2)=1.414213576,
|
|
celldm(3)= 6.00000,
|
|
nat= 14, ntyp= 2,
|
|
ecutwfc =14.0,
|
|
/
|
|
&electrons
|
|
mixing_mode = 'plain'
|
|
mixing_beta = 0.7
|
|
conv_thr = 1.0d-6
|
|
/
|
|
ATOMIC_SPECIES
|
|
Al 26.98 Al.pz-vbc.UPF
|
|
As 74.92 As.pz-bhs.UPF
|
|
ATOMIC_POSITIONS alat
|
|
As 0.000000000 -0.044777195 -0.058158722
|
|
Al 0.500000000 0.251460333 0.113525468
|
|
As 0.500000000 0.712279009 0.504183885
|
|
Al 0.000000000 1.067633546 0.480460620
|
|
As 0.000000000 -0.003937059 0.995826731
|
|
Al 0.500000000 0.351400965 1.004220212
|
|
As 0.000000000 -0.003937059 2.004173269
|
|
Al 0.500000000 0.351400965 1.995779788
|
|
As 0.500000000 0.712279009 2.495816115
|
|
Al 0.000000000 1.067633546 2.519539380
|
|
As 0.000000000 -0.044777195 3.058158722
|
|
Al 0.500000000 0.251460333 2.886474532
|
|
As 0.500000000 0.707106800 1.500000000
|
|
Al 0.000000000 1.060660200 1.500000000
|
|
K_POINTS {automatic}
|
|
6 2 1 0 0 0
|
|
EOF
|
|
$ECHO " running the scf calculation...\c"
|
|
$PW_COMMAND < AlAs110re.scf.in > AlAs110re.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
cat > AlAs110re.nonscf.in << EOF
|
|
&control
|
|
calculation = 'nscf'
|
|
restart_mode='from_scratch',
|
|
title='AlAs 110 surface slab, relaxed (central plane fixed)'
|
|
pseudo_dir = '$PSEUDO_DIR/',
|
|
outdir='$TMP_DIR/',
|
|
prefix='AlAs110'
|
|
/
|
|
&system
|
|
ibrav= 8, celldm(1) =7.424621202, celldm(2)=1.414213576,
|
|
celldm(3)= 6.00000,
|
|
nat= 14, ntyp= 2,
|
|
occupations='smearing', smearing='gaussian', degauss=0.01, nbnd=34,
|
|
ecutwfc =14.0,
|
|
/
|
|
&electrons
|
|
mixing_mode = 'plain'
|
|
mixing_beta = 0.7
|
|
conv_thr = 1.0d-6
|
|
/
|
|
ATOMIC_SPECIES
|
|
Al 26.98 Al.pz-vbc.UPF
|
|
As 74.92 As.pz-bhs.UPF
|
|
ATOMIC_POSITIONS alat
|
|
As 0.000000000 -0.044777195 -0.058158722
|
|
Al 0.500000000 0.251460333 0.113525468
|
|
As 0.500000000 0.712279009 0.504183885
|
|
Al 0.000000000 1.067633546 0.480460620
|
|
As 0.000000000 -0.003937059 0.995826731
|
|
Al 0.500000000 0.351400965 1.004220212
|
|
As 0.000000000 -0.003937059 2.004173269
|
|
Al 0.500000000 0.351400965 1.995779788
|
|
As 0.500000000 0.712279009 2.495816115
|
|
Al 0.000000000 1.067633546 2.519539380
|
|
As 0.000000000 -0.044777195 3.058158722
|
|
Al 0.500000000 0.251460333 2.886474532
|
|
As 0.500000000 0.707106800 1.500000000
|
|
Al 0.000000000 1.060660200 1.500000000
|
|
K_POINTS {automatic}
|
|
12 4 1 0 0 0
|
|
EOF
|
|
$ECHO " running the non-scf calculation...\c"
|
|
$PW_COMMAND < AlAs110re.nonscf.in > AlAs110re.nonscf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# post-processing for stm images (sample bias given in Ry!)
|
|
cat > AlAs110.pp_stm-.in << EOF
|
|
&inputpp
|
|
prefix = 'AlAs110'
|
|
outdir='$TMP_DIR/',
|
|
filplot = 'AlAsresm-1.0'
|
|
sample_bias=-0.0735d0,
|
|
plot_num= 5
|
|
/
|
|
&plot
|
|
nfile=1
|
|
filepp(1)='AlAsresm-1.0'
|
|
weight(1)=1.0
|
|
iflag=2
|
|
output_format=2
|
|
e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
|
|
e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
|
|
x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25
|
|
nx=36 ,ny=56
|
|
fileout='AlAs110-1.0'
|
|
/
|
|
EOF
|
|
$ECHO
|
|
$ECHO " running the post-processing phase, negative bias...\c"
|
|
$PP_COMMAND < AlAs110.pp_stm-.in > AlAs110.pp_stm-.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# run plotrho to do the figure
|
|
cat > AlAs110.plotrho-.in << EOF
|
|
AlAs110-1.0
|
|
AlAs110-1.0eV.ps
|
|
n
|
|
0.00005 0.0078 8
|
|
EOF
|
|
$ECHO " running plotrho on negative bias data...\c"
|
|
$PLOTRHO_COMMAND < AlAs110.plotrho-.in > AlAs110.plotrho-.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# post-processing for stm images (negative bias, constant current)
|
|
cat > AlAs110.pp_isostm-.in << EOF
|
|
&inputpp
|
|
/
|
|
&plot
|
|
nfile=1
|
|
filepp(1)='AlAsresm-1.0'
|
|
weight(1)=1.0
|
|
iflag=2
|
|
output_format=7
|
|
fileout='AlAs110.pp_isostm-.dat'
|
|
e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
|
|
e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
|
|
nx=150, ny=150
|
|
isostm_flag=.true.
|
|
isovalue=0.00005
|
|
heightmin=0.4
|
|
heightmax=0.75
|
|
direction=1
|
|
/
|
|
EOF
|
|
$ECHO
|
|
$ECHO " STM image, negative bias and constant current...\c"
|
|
$PP_COMMAND < AlAs110.pp_isostm-.in > AlAs110.pp_isostm-.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# run gnuplot to do the figure
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
break
|
|
else
|
|
cat > gnuplot.tmp <<EOF
|
|
set term postscript enhanced color solid lw 3 24
|
|
set output 'AlAs110-1.0eV.isoplot.ps'
|
|
set xlabel "x (bohr)"
|
|
set ylabel "y (bohr)"
|
|
set pm3d map
|
|
set size ratio -1
|
|
set palette rgb 21,22,23
|
|
set tics out
|
|
unset key
|
|
splot [0:51.972][0:52.500] 'AlAs110.pp_isostm-.dat'
|
|
EOF
|
|
$ECHO
|
|
$ECHO " plotting results ...\c"
|
|
$GP_COMMAND < gnuplot.tmp
|
|
$ECHO " done"
|
|
rm gnuplot.tmp
|
|
fi
|
|
|
|
# post-processing for stm images (as before, but positive bias)
|
|
cat > AlAs110.pp_stm+.in << EOF
|
|
&inputpp
|
|
prefix = 'AlAs110'
|
|
outdir='$TMP_DIR/',
|
|
filplot = 'AlAsresm+1.0'
|
|
sample_bias=0.0735d0,
|
|
plot_num= 5
|
|
/
|
|
&plot
|
|
nfile=1
|
|
filepp(1)='AlAsresm+1.0'
|
|
weight(1)=1.0
|
|
iflag=2
|
|
output_format=2
|
|
e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
|
|
e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
|
|
x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25
|
|
nx=36 ,ny=56
|
|
fileout='AlAs110+1.0'
|
|
/
|
|
EOF
|
|
$ECHO " running the post-processing phase, positive bias...\c"
|
|
$PP_COMMAND < AlAs110.pp_stm+.in > AlAs110.pp_stm+.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# plotrho
|
|
cat > AlAs110.plotrho+.in << EOF
|
|
AlAs110+1.0
|
|
AlAs110+1.0eV.ps
|
|
n
|
|
0.00002 0.0021 8
|
|
EOF
|
|
$ECHO " running plotrho on positive bias data...\c"
|
|
$PLOTRHO_COMMAND < AlAs110.plotrho+.in > AlAs110.plotrho+.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# post-processing for stm images (positive bias, constant current)
|
|
cat > AlAs110.pp_isostm+.in << EOF
|
|
&inputpp
|
|
/
|
|
&plot
|
|
nfile=1
|
|
filepp(1)='AlAsresm+1.0'
|
|
weight(1)=1.0
|
|
iflag=2
|
|
output_format=7
|
|
fileout='AlAs110.pp_isostm+.dat'
|
|
e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
|
|
e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
|
|
nx=150, ny=150
|
|
isostm_flag=.true.
|
|
isovalue=0.00005
|
|
heightmin=0.4
|
|
heightmax=0.75
|
|
direction=1
|
|
/
|
|
EOF
|
|
$ECHO
|
|
$ECHO " STM image, positive bias and constant current...\c"
|
|
$PP_COMMAND < AlAs110.pp_isostm+.in > AlAs110.pp_isostm+.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# run gnuplot to do the figure
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
break
|
|
else
|
|
cat > gnuplot.tmp <<EOF
|
|
set term postscript enhanced color solid lw 3 24
|
|
set output 'AlAs110+1.0eV.isoplot.ps'
|
|
set xlabel "x (bohr)"
|
|
set ylabel "y (bohr)"
|
|
set pm3d map
|
|
set size ratio -1
|
|
set palette rgb 21,22,23
|
|
set tics out
|
|
unset key
|
|
splot [0:51.972][0:52.500] 'AlAs110.pp_isostm+.dat'
|
|
EOF
|
|
$ECHO
|
|
$ECHO " plotting results ...\c"
|
|
$GP_COMMAND < gnuplot.tmp
|
|
$ECHO " done"
|
|
rm gnuplot.tmp
|
|
fi
|
|
|
|
# Projection of the DOS on volumes (boxes)
|
|
cat > AlAs110.box.projwfc.in << EOF
|
|
&projwfc
|
|
prefix = 'AlAs110'
|
|
outdir='$TMP_DIR/',
|
|
ngauss=0
|
|
degauss=0.01
|
|
DeltaE=0.02
|
|
tdosinboxes=.true.
|
|
plotboxes=.true.
|
|
n_proj_boxes=8
|
|
|
|
!! Boxes centered on the first vacuum layer:
|
|
!! 1) above the surface Al
|
|
irmin(1,1)= 0, irmax(1,1)= 2, irmin(2,1)= 0, irmax(2,1)= 2, irmin(3,1)=63, irmax(3,1)=65,
|
|
!! 2) above the surface As
|
|
irmin(1,2)= 9, irmax(1,2)=11, irmin(2,2)= 5, irmax(2,2)= 7, irmin(3,2)=63, irmax(3,2)=65,
|
|
!! 3) above the 2nd layer Al
|
|
irmin(1,3)= 9, irmax(1,3)=11, irmin(2,3)=14, irmax(2,3)=16, irmin(3,3)=63, irmax(3,3)=65,
|
|
!! 4) as large as the surface unit cell
|
|
irmin(1,4)= 1, irmax(1,4)=18, irmin(2,4)= 1, irmax(2,4)=27, irmin(3,4)=63, irmax(3,4)=65,
|
|
|
|
!! Same as above, centered on the second vacuum layer:
|
|
irmin(1,5)= 0, irmax(1,5)= 2, irmin(2,5)= 0, irmax(2,5)= 2, irmin(3,5)=72, irmax(3,5)=74,
|
|
irmin(1,6)= 9, irmax(1,6)=11, irmin(2,6)= 5, irmax(2,6)= 7, irmin(3,6)=72, irmax(3,6)=74,
|
|
irmin(1,7)= 9, irmax(1,7)=11, irmin(2,7)=14, irmax(2,7)=16, irmin(3,7)=72, irmax(3,7)=74,
|
|
irmin(1,8)= 1, irmax(1,8)=18, irmin(2,8)= 1, irmax(2,8)=27, irmin(3,8)=72, irmax(3,8)=74,
|
|
/
|
|
EOF
|
|
$ECHO
|
|
$ECHO " running local DOS calculation...\c"
|
|
$PROJWFC_COMMAND < AlAs110.box.projwfc.in > AlAs110.box.projwfc.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# Projection of the DOS on atomic wavefunctions
|
|
cat > AlAs110.projwfc.in << EOF
|
|
&projwfc
|
|
prefix = 'AlAs110'
|
|
outdir='$TMP_DIR/',
|
|
ngauss=0
|
|
degauss=0.01
|
|
DeltaE=0.02
|
|
tdosinboxes=.false.
|
|
/
|
|
EOF
|
|
$ECHO
|
|
$ECHO " running projected DOS calculation...\c"
|
|
$PROJWFC_COMMAND < AlAs110.projwfc.in > AlAs110.projwfc.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
$ECHO
|
|
$ECHO " summing the atomic PDOS...\c"
|
|
$SUMPDOS_COMMAND AlAs110.pdos_atm\#10\(Al\)_wfc* > "AlAs110.pdos_atm#10(Al)" 2> /dev/null
|
|
$SUMPDOS_COMMAND AlAs110.pdos_atm\#11\(As\)_wfc* > "AlAs110.pdos_atm#11(As)" 2> /dev/null
|
|
$ECHO " done"
|
|
|
|
#
|
|
# if gnuplot was found, the results are plotted
|
|
#
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
break
|
|
else
|
|
eFermi=`grep "Fermi" AlAs110re.nonscf.out | cut -d \ -f 14`
|
|
cat > gnuplot.tmp <<EOF
|
|
set term postscript enhanced color solid lw 3 24
|
|
set output 'AlAs110.box.projwfc.ps'
|
|
ef=$eFermi
|
|
set xlabel "Energy - E_F (eV)"
|
|
set ylabel "Local DOS (states/eV)"
|
|
set style data lines
|
|
set key top left Left reverse
|
|
set border 31 lw 0.2
|
|
set title "Projected DOS"
|
|
plot \\
|
|
'./AlAs110.pdos_atm#10(Al)' u (\$1-ef):2 t "Surface Al" ,\\
|
|
'./AlAs110.pdos_atm#11(As)' u (\$1-ef):2 t "Surface As"
|
|
set title "Local DOS centered in the first vacuum layer"
|
|
plot \\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):4 t "Above Al" ,\\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):5 t "Above As" ,\\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):(\$7/54) t "Surface average"
|
|
set title "Local DOS centered in the second vacuum layer"
|
|
plot \\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):8 t "Above Al" ,\\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):9 t "Above As" ,\\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):(\$11/54) t "Surface average"
|
|
EOF
|
|
$ECHO
|
|
$ECHO " plotting DOS results ...\c"
|
|
$GP_COMMAND < gnuplot.tmp
|
|
$ECHO " done"
|
|
rm gnuplot.tmp
|
|
fi
|
|
|
|
$ECHO
|
|
$ECHO " To visualize a volume in which the DOS is integrated, execute:"
|
|
$ECHO " xcrysden --xsf results/AlAs110.box#1.xsf"
|
|
$ECHO " and plot the isosurface corresponding to isovalue 0.5"
|
|
|
|
$ECHO
|
|
# clean TMP_DIR
|
|
$ECHO " cleaning $TMP_DIR...\c"
|
|
rm -rf $TMP_DIR/AlAs110.*
|
|
$ECHO
|
|
$ECHO " $EXAMPLE_DIR: done"
|