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quantum-espresso/PHonon/examples/example08/run_xml_example

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#!/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 tests ph.x with PAW"
$ECHO "It calculates the phonon modes of C at the gamma and X points"
$ECHO "and the vibrational modes of a molecule (CH4) at Gamma."
$ECHO
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x ph.x"
PSEUDO_LIST="H.pz-kjpaw.UPF C.pz-kjpaw.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 $PARA_POSTFIX"
PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running ph.x as: $PH_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation for C with PAW-PP
cat > c.scf.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>
<input calculation="scf" prefix="C">
<cell type="qecell">
<qecell ibrav="2" alat="6.68">
<real rank="1" n1="5">
0.0 0.0 0.0 0.0 0.0
</real>
</qecell>
</cell>
<atomic_species ntyp="1">
<specie name="C">
<property name="mass">
<real>0.0</real>
</property>
<property name="pseudofile">
<string>C.pz-kjpaw.UPF</string>
</property>
</specie>
</atomic_species>
<atomic_list units="alat" nat="2" >
<atom name="C">
<position>
<real rank="1" n1="3">
0.00 0.00 0.00
</real>
</position>
</atom>
<atom name="C">
<position>
<real rank="1" n1="3">
0.25 0.25 0.25
</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>
27.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
300.0
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-9
</real>
</parameter>
<parameter name="nr1">
<integer>
32
</integer>
</parameter>
<parameter name="nr2">
<integer>
32
</integer>
</parameter>
<parameter name="nr3">
<integer>
32
</integer>
</parameter>
<parameter name="mixing_beta">
<real>
0.7
</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 C...\c"
$PW_COMMAND < c.scf.xml > c.scf.out
check_failure $?
$ECHO " done"
# phonon calculation at G
cat > c.phG.in << EOF
phonons of C at Gamma
&inputph
tr2_ph=1.0d-14,
epsil=.true.,
zue=.true.
prefix='C',
fildyn='Cg.dyn',
outdir='$TMP_DIR/'
/
0.0 0.0 0.0
EOF
$ECHO " running the phonon calculation for C at Gamma...\c"
$PH_COMMAND < c.phG.in > c.phG.out
check_failure $?
$ECHO " done"
# phonon calculation at X
cat > c.phX.in << EOF
phonons of C at X
&inputph
tr2_ph=1.0d-14,
prefix='C',
fildyn='CX.dyn',
outdir='$TMP_DIR/'
/
1.0 0.0 0.0
EOF
$ECHO " running the phonon calculation for C at X...\c"
$PH_COMMAND < c.phX.in > c.phX.out
check_failure $?
$ECHO " done"
# self-consistent calculation for Cu PBE with PAW-PP
cat > Cu.scf_pbe.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>
<input calculation="scf" prefix="Cu">
<cell type="qecell">
<qecell ibrav="2" alat="6.90">
<real rank="1" n1="5">
0.0 0.0 0.0 0.0 0.0
</real>
</qecell>
</cell>
<atomic_species ntyp="1">
<specie name="Cu">
<property name="mass">
<real>0.0</real>
</property>
<property name="pseudofile">
<string>Cu.pbe-kjpaw.UPF</string>
</property>
</specie>
</atomic_species>
<atomic_list units="alat" nat="1" >
<atom name="Cu">
<position>
<real rank="1" n1="3">
0.00 0.00 0.00
</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>
30.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
700.0
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-9
</real>
</parameter>
<parameter name="mixing_beta">
<real>
0.7
</real>
</parameter>
</field>
<field name="Options">
<parameter name="occupations">
<string>
smearing
</string>
</parameter>
<parameter name="smearing">
<string>
mp
</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 Cu with GGA-PBE...\c"
$PW_COMMAND < Cu.scf_pbe.xml > Cu.scf_pbe.out
check_failure $?
$ECHO " done"
# phonon calculation at G
cat > Cu.phG_pbe.in << EOF
phonons of Cu at Gamma
&inputph
tr2_ph=1.0d-14,
prefix='Cu',
fildyn='Cug.dyn',
outdir='$TMP_DIR/'
/
0.0 0.0 0.0
EOF
$ECHO " running the phonon calculation for Cu at Gamma with GGA-PBE...\c"
$PH_COMMAND < Cu.phG_pbe.in > Cu.phG_pbe.out
check_failure $?
$ECHO " done"
# Self consistent calculation for CH4
cat > ch4.scf.xml << EOF
<?xml version="1.0" encoding="UTF-8"?>
<!-- ch4
ch4 molecule in a cubic box -->
<input calculation="scf" prefix="ch4">
<cell type="qecell">
<qecell ibrav="1" alat="15.0">
<real rank="1" n1="5">
0.0 0.0 0.0 0.0 0.0
</real>
</qecell>
</cell>
<atomic_species ntyp="2">
<specie name="H">
<property name="mass">
<real>1.0</real>
</property>
<property name="pseudofile">
<string>H.pz-kjpaw.UPF</string>
</property>
</specie>
<specie name="C">
<property name="mass">
<real>12.0</real>
</property>
<property name="pseudofile">
<string>C.pz-kjpaw.UPF</string>
</property>
</specie>
</atomic_species>
<atomic_list units="alat" nat="5" >
<atom name="H">
<position>
<real rank="1" n1="3">
0.080728893 0.080728893 0.080728893
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
-0.080728893 -0.080728893 0.080728893
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
0.080728893 -0.080728893 -0.080728893
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
-0.080728893 0.080728893 -0.080728893
</real>
</position>
</atom>
<atom name="C">
<position>
<real rank="1" n1="3">
0.000000000 0.000000000 0.0000000000
</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>
<parameter name="tprnfor">
<logical>
true
</logical>
</parameter>
</field>
<field name="Numerics">
<parameter name="ecutwfc">
<real>
25.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
300.0
</real>
</parameter>
<parameter name="mixing_beta">
<real>
0.5
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-10
</real>
</parameter>
</field>
<k_points type="tpiba">
<mesh npoints="1">
<real rank="2" n1="4" n2="1">
0.0 0.0 0.0 1.0
</real>
</mesh>
</k_points>
</input>
EOF
$ECHO " running the scf calculation for CH4...\c"
$PW_COMMAND < ch4.scf.xml > ch4.scf.out
check_failure $?
$ECHO " done"
# normal mode calculation for CH4
cat > ch4.nm.in << EOF
vibrations of ch4
&inputph
tr2_ph=4.0d-17,
prefix='ch4',
outdir='$TMP_DIR',
amass(1)=1.d0,
amass(2)=12.d0,
asr=.true.,
zue=.true.,
epsil=.true.,
trans=.true.,
fildyn='ch4.dyn',
/
0.0 0.0 0.0
EOF
$ECHO " running normal mode calculation for CH4...\c"
$PH_COMMAND < ch4.nm.in > ch4.nm.out
check_failure $?
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
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