mirror of https://gitlab.com/QEF/q-e.git
346 lines
7.9 KiB
Bash
Executable File
346 lines
7.9 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 how to use pw.x and ph.x to compute IR and Raman spectra"
|
|
$ECHO "for a CO2 molecule and for ZnO in the Wurtzite structure."
|
|
$ECHO "After the calculation, a gnuplot window posp up with both spectra."
|
|
$ECHO "NOTE: Raman calculation currently disabled (not implemented for GGA)."
|
|
$ECHO " "
|
|
|
|
# set the needed environment variables
|
|
. ../../../environment_variables
|
|
|
|
# Uncomment the following line if you want to calculate in parallel and the PARA_PREFIX was not set
|
|
#PARA_PREFIX="mpirun -np 8 "
|
|
|
|
|
|
# required executables and pseudopotentials
|
|
BIN_LIST="pw.x ph.x dynmat.x"
|
|
PSEUDO_LIST=" C.pbe-hgh.UPF O.pbe-hgh.UPF Zn.pbe-d-hgh.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"
|
|
|
|
|
|
$ECHO
|
|
# how to run executables
|
|
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
|
|
$ECHO " running pw.x as: $PW_COMMAND"
|
|
PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX"
|
|
$ECHO " running ph.x as: $PH_COMMAND"
|
|
DM_COMMAND=" $BIN_DIR/dynmat.x"
|
|
$ECHO " running dynmat.x as: $DM_COMMAND"
|
|
$ECHO
|
|
|
|
# check for gnuplot
|
|
GP_COMMAND=`which gnuplot 2>/dev/null`
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
$ECHO
|
|
$ECHO "gnuplot not in PATH"
|
|
$ECHO "Results will not be plotted"
|
|
fi
|
|
|
|
|
|
# clean TMP_DIR
|
|
$ECHO " cleaning $TMP_DIR...\c"
|
|
rm -rf $TMP_DIR/CO2*
|
|
rm -rf $TMP_DIR/_ph0/CO2*
|
|
$ECHO " done"
|
|
|
|
|
|
# self-consistent calculation for CO2
|
|
cat > co2.scf.in << EOF
|
|
&CONTROL
|
|
calculation = "scf",
|
|
prefix = "CO2",
|
|
pseudo_dir = "$PSEUDO_DIR",
|
|
outdir = "$TMP_DIR",
|
|
/
|
|
&SYSTEM
|
|
ibrav = 1,
|
|
celldm(1) =14.0,
|
|
nat = 3,
|
|
ntyp = 2,
|
|
ecutwfc = 80.D0, !better 120
|
|
/
|
|
&ELECTRONS
|
|
conv_thr = 1.D-8,
|
|
mixing_beta = 0.7,
|
|
/
|
|
&IONS
|
|
/
|
|
ATOMIC_SPECIES
|
|
C 12.010 C.pbe-hgh.UPF
|
|
O 15.999 O.pbe-hgh.UPF
|
|
ATOMIC_POSITIONS (angstrom)
|
|
C 3.000042068 3.000042068 3.544613556
|
|
O 3.835408973 3.835408973 3.543705292
|
|
O 2.164548959 2.164548959 3.543681153
|
|
K_POINTS (automatic)
|
|
1 1 1 0 0 0
|
|
EOF
|
|
|
|
$ECHO " running the SCF for CO2...\c"
|
|
$PW_COMMAND < co2.scf.in > co2.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# self-consistent phonon calculation with ph.x for CO2
|
|
cat > co2.ph.in << EOF
|
|
Normal modes for CO2
|
|
&inputph
|
|
tr2_ph=1.0d-14,
|
|
prefix='CO2',
|
|
amass(1)=12.010,
|
|
amass(2)=15.999,
|
|
outdir='$TMP_DIR'
|
|
epsil=.true.,
|
|
trans=.true.,
|
|
asr=.true.
|
|
! lraman=.true.
|
|
fildyn='dmat.co2'
|
|
/
|
|
0.0 0.0 0.0
|
|
EOF
|
|
$ECHO " running phonon calculation of CO2...\c"
|
|
$PH_COMMAND < co2.ph.in > co2.ph.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# extract phonon data with dynmat.x
|
|
cat > co2.dm.in << EOF
|
|
&input fildyn='dmat.co2', asr='zero-dim' /
|
|
EOF
|
|
$ECHO " Extracting phonon data with dynmat...\c"
|
|
$DM_COMMAND < co2.dm.in > co2.dm.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
|
|
$ECHO "The data for spectrum is after '# mode [cm-1] [THz] IR' on co2.dm.out"
|
|
awk 'NR==1,/mode/{next}/DYNMAT/,NR==0{next}{print}' co2.dm.out > plotdata_co2.dat
|
|
|
|
$ECHO "Trying to plot it with gnuplot..."
|
|
|
|
|
|
cat > plot_command_co2.cmd << EOF
|
|
set lmargin 8
|
|
set rmargin 3
|
|
|
|
set multiplot
|
|
set key left top
|
|
set origin 0.0,0.5
|
|
set size 1,0.5
|
|
set yrange [0:]
|
|
set format x ""
|
|
set tmargin 1
|
|
plot 'plotdata_co2.dat' u (\$2):(\$3) title ' CO2-RAMAN' w i lw 2
|
|
|
|
set key left bottom
|
|
set origin 0.0,0.0
|
|
set size 1,0.587
|
|
set yrange [0:] reverse
|
|
set format x
|
|
set xlabel "Wavenumber [cm-1]"
|
|
set bmargin 3
|
|
set ylabel "Intensity" offset 0,5
|
|
plot 'plotdata_co2.dat' u (\$2):(\$4) title 'CO2-IR' w i lw 2 lc 2
|
|
set nomultiplot
|
|
EOF
|
|
|
|
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
$ECHO "No plot will be produced, because gnuplot was not found in the \$PATH "
|
|
break
|
|
else
|
|
$GP_COMMAND -persist plot_command_co2.cmd &
|
|
|
|
fi
|
|
|
|
# clean TMP_DIR
|
|
$ECHO " cleaning $TMP_DIR...\c"
|
|
rm -rf $TMP_DIR/ZNO*
|
|
rm -rf $TMP_DIR/_ph0/ZNO*
|
|
$ECHO " done"
|
|
|
|
|
|
|
|
# self-consistent calculation for Wurtzite (ZnO)
|
|
cat > zno.scf.in << EOF
|
|
&CONTROL
|
|
calculation = "scf",
|
|
prefix = "ZNO",
|
|
pseudo_dir = "$PSEUDO_DIR",
|
|
outdir = "$TMP_DIR",
|
|
/
|
|
&SYSTEM
|
|
ibrav=0, celldm(1) =6.330582528, nat=4, ntyp= 2,
|
|
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
|
|
ecutwfc =80.0, !better 140
|
|
/
|
|
&ELECTRONS
|
|
mixing_mode='plain'
|
|
mixing_beta = 0.5,
|
|
startingwfc='random',
|
|
conv_thr = 1.0d-8
|
|
/
|
|
CELL_PARAMETERS alat
|
|
1.55820896 0.00000000 0.00000000
|
|
0.00000000 0.86602540 -0.50000000
|
|
0.00000000 0.00000000 1.00000000
|
|
ATOMIC_SPECIES
|
|
Zn 65.409 Zn.pbe-d-hgh.UPF
|
|
O 15.999 O.pbe-hgh.UPF
|
|
ATOMIC_POSITIONS (alat)
|
|
Zn 2.010975287 0.487933254 -0.051360548
|
|
Zn 1.234717421 0.199473387 0.448322227
|
|
O 1.051679030 0.488287222 -0.051814333
|
|
O 1.830251369 0.199830262 0.448810714
|
|
K_POINTS (automatic)
|
|
2 2 2 0 0 0
|
|
|
|
EOF
|
|
|
|
$ECHO " running the SCF for Wurtzite...\c"
|
|
$PW_COMMAND < zno.scf.in > zno.scf.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# self-consistent phonon calculation with ph.x for Wurtzite
|
|
cat > zno.ph.in << EOF
|
|
Normal modes for Wurtzite
|
|
&inputph
|
|
tr2_ph=1.0d-14,
|
|
prefix='ZNO',
|
|
amass(1)=65.409,
|
|
amass(2)=15.999,
|
|
outdir='$TMP_DIR'
|
|
epsil=.false.,
|
|
! lraman=.true.
|
|
trans=.true.,
|
|
asr=.true.
|
|
fildyn='dmat.zno'
|
|
/
|
|
0.0 0.0 0.0
|
|
EOF
|
|
$ECHO " running phonon calculation of ZnO...\c"
|
|
$PH_COMMAND < zno.ph.in > zno.ph.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
# extract phonon data with dynmat.x
|
|
cat > zno.dm.in << EOF
|
|
&input fildyn='dmat.zno', asr='zero-dim' /
|
|
EOF
|
|
$ECHO " Extracting phonon data with dynmat...\c"
|
|
$DM_COMMAND < zno.dm.in > zno.dm.out
|
|
check_failure $?
|
|
$ECHO " done"
|
|
|
|
|
|
$ECHO "The data for spectrum is after '# mode [cm-1] [THz] IR' on zno.dm.out"
|
|
awk 'NR==1,/mode/{next}/DYNMAT/,NR==0{next}{print}' zno.dm.out > plotdata_zno.dat
|
|
|
|
$ECHO "Trying to plot it with gnuplot..."
|
|
|
|
|
|
cat > plot_command_zno.cmd << EOF
|
|
set lmargin 8
|
|
set rmargin 3
|
|
|
|
set multiplot
|
|
set key left top
|
|
set origin 0.0,0.5
|
|
set size 1,0.5
|
|
set yrange [0:]
|
|
set format x ""
|
|
set tmargin 1
|
|
plot 'plotdata_zno.dat' u (\$2):(\$3) title ' ZnO-RAMAN' w i lw 2
|
|
|
|
set key left bottom
|
|
set origin 0.0,0.0
|
|
set size 1,0.587
|
|
set yrange [0:] reverse
|
|
set format x
|
|
set xlabel "Frequency [cm-1]"
|
|
set bmargin 3
|
|
set ylabel "Intensity" offset 0,5
|
|
plot 'plotdata_zno.dat' u (\$2):(\$4) title 'ZnO-IR' w i lw 2 lc 2
|
|
set nomultiplot
|
|
EOF
|
|
|
|
|
|
if [ "$GP_COMMAND" = "" ]; then
|
|
$ECHO "No plot will be produced, because gnuplot was not found in the \$PATH "
|
|
break
|
|
else
|
|
$GP_COMMAND -persist plot_command_zno.cmd &
|
|
|
|
fi
|
|
|
|
|
|
$ECHO "The results on the ZnO spectrum can be compared with"
|
|
$ECHO "http://www.nature.com/srep/2013/131021/srep02999/pdf/srep02999.pdf"
|
|
$ECHO " providing acceptable values for such a cheap calculation."
|
|
|
|
|
|
|
|
|
|
$ECHO
|
|
$ECHO "$EXAMPLE_DIR: done"
|