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quantum-espresso/PHonon/examples/example15/run_example

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#!/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"
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