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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 cp.x to perform molecular dynamics"
$ECHO "simulation of SiO2."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="cp.x"
PSEUDO_LIST="Si.pz-vbc.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
$ECHO " done"
# how to run executables
CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO " running cp.x as: $CP_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/cp*
$ECHO " done"
# molecular dynamics calculation
cat > sio2.cp.start.in << EOF
&control
calculation='cp',
restart_mode='from_scratch',
nstep=20, iprint=20, isave=20,
dt=5.0,
ndr=90, ndw=91,
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
nat=18, ntyp=2, nbnd=48, nspin=1,
ecutwfc=20.0, ecutrho=150.0,
nr1b=16, nr2b=16, nr3b=16,
qcutz=150., q2sigma=2.0, ecfixed=16.0,
/
&electrons
electron_dynamics='damp', electron_damping=0.2,
startingwfc='random', ampre=0.01,
emass=700., emass_cutoff=3.,
/
&ions
ion_dynamics='none',
ion_radius(1)=1.0, ion_radius(2)=1.0,
/
ATOMIC_SPECIES
O 16.00 O.pz-rrkjus.UPF
Si 28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
O 3.18829368 14.83237039 1.22882961
O 7.83231469 6.78704039 1.22882961
O 2.07443467 5.99537992 4.73758250
O 6.72031366 14.04231898 4.73758250
O 3.96307134 11.26989826 7.87860582
O 8.60802134 3.22295920 7.87860582
O 3.96307134 4.81915267 9.14625133
O 8.60802134 12.86448267 9.14625133
O 3.18736469 1.25668055 5.58029607
O 7.83324368 9.30201055 5.58029607
O 2.07536366 10.09206195 2.07358613
O 6.71938467 2.04673195 2.07358613
Si 0.28891589 8.04533000 3.40456284
Si 4.93386589 0.00000000 3.40456284
Si 2.13389003 12.27717358 -0.04188031
Si 6.77884003 4.23184358 -0.04188031
Si 2.13389003 3.81348642 6.85202747
Si 6.77884003 11.85881642 6.85202747
EOF
$ECHO " running the calculation with fixed ions...\c"
$CP_COMMAND < sio2.cp.start.in > sio2.cp.start.out
check_failure $?
$ECHO " done"
# molecular dynamics calculation
cat > sio2.cp.restart.in << EOF
&control
calculation='cp',
restart_mode='reset_counters',
nstep=50, iprint=50, isave=50,
dt=15.0,
ndr=91, ndw=92,
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
nat=18, ntyp=2, nbnd=48, nspin=1,
ecutwfc=20.0, ecutrho=150.0,
nr1b=16, nr2b=16, nr3b=16,
qcutz=150., q2sigma=2.0, ecfixed=16.0,
/
&electrons
electron_dynamics='damp', electron_damping=0.2,
emass=700., emass_cutoff=3.,
/
&ions
ion_dynamics='none',
ion_radius(1)=1.0, ion_radius(2)=1.0,
/
ATOMIC_SPECIES
O 16.00 O.pz-rrkjus.UPF
Si 28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
O 3.18829368 14.83237039 1.22882961
O 7.83231469 6.78704039 1.22882961
O 2.07443467 5.99537992 4.73758250
O 6.72031366 14.04231898 4.73758250
O 3.96307134 11.26989826 7.87860582
O 8.60802134 3.22295920 7.87860582
O 3.96307134 4.81915267 9.14625133
O 8.60802134 12.86448267 9.14625133
O 3.18736469 1.25668055 5.58029607
O 7.83324368 9.30201055 5.58029607
O 2.07536366 10.09206195 2.07358613
O 6.71938467 2.04673195 2.07358613
Si 0.28891589 8.04533000 3.40456284
Si 4.93386589 0.00000000 3.40456284
Si 2.13389003 12.27717358 -0.04188031
Si 6.77884003 4.23184358 -0.04188031
Si 2.13389003 3.81348642 6.85202747
Si 6.77884003 11.85881642 6.85202747
EOF
$ECHO " running the calculation with fixed ions, restart...\c"
$CP_COMMAND < sio2.cp.restart.in > sio2.cp.restart.out
check_failure $?
$ECHO " done"
# molecular dynamics calculation
cat > sio2.vc-cp.in << EOF
&control
calculation='vc-cp',
restart_mode='reset_counters',
nstep=10, iprint=10, isave=10,
dt=12.0,
ndr=92, ndw=93,
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
nat=18, ntyp=2, nbnd=48, nspin=1,
ecutwfc=20.0, ecutrho=150.0,
nr1b=16, nr2b=16, nr3b=16,
qcutz=150., q2sigma=2.0, ecfixed=16.0,
/
&electrons
electron_dynamics='verlet', ortho_max=30,
emass=700., emass_cutoff=3.,
/
&ions
ion_dynamics='verlet', ion_temperature='nose',
tempw=300, fnosep=6.6666,
ion_radius(1)=1.0, ion_radius(2)=1.0,
/
&cell
cell_dynamics='pr', cell_temperature='nose',
temph=300., fnoseh=8.6071, press=1.0,
/
ATOMIC_SPECIES
O 16.00 O.pz-rrkjus.UPF
Si 28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
O 3.18829368 14.83237039 1.22882961
O 7.83231469 6.78704039 1.22882961
O 2.07443467 5.99537992 4.73758250
O 6.72031366 14.04231898 4.73758250
O 3.96307134 11.26989826 7.87860582
O 8.60802134 3.22295920 7.87860582
O 3.96307134 4.81915267 9.14625133
O 8.60802134 12.86448267 9.14625133
O 3.18736469 1.25668055 5.58029607
O 7.83324368 9.30201055 5.58029607
O 2.07536366 10.09206195 2.07358613
O 6.71938467 2.04673195 2.07358613
Si 0.28891589 8.04533000 3.40456284
Si 4.93386589 0.00000000 3.40456284
Si 2.13389003 12.27717358 -0.04188031
Si 6.77884003 4.23184358 -0.04188031
Si 2.13389003 3.81348642 6.85202747
Si 6.77884003 11.85881642 6.85202747
EOF
$ECHO " running the variable-cell calculation...\c"
$CP_COMMAND < sio2.vc-cp.in > sio2.vc-cp.out
check_failure $?
$ECHO " done"
# molecular dynamics calculation
cat > sio2.vc-cp.restart.in << EOF
&control
calculation='vc-cp',
restart_mode='reset_counters',
nstep=10, iprint=10, isave=10,
dt=12.0,
ndr=93, ndw=94,
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
nat=18, ntyp=2, nbnd=48, nspin=1,
ecutwfc=20.0, ecutrho=150.0,
nr1b=16, nr2b=16, nr3b=16,
qcutz=150., q2sigma=2.0, ecfixed=16.0,
/
&electrons
electron_dynamics='verlet', ortho_max=30,
emass=700., emass_cutoff=3.,
/
&ions
ion_dynamics='verlet', ion_temperature='nose',
tempw=300, fnosep=6.6666,
ion_radius(1)=1.0, ion_radius(2)=1.0,
/
&cell
cell_dynamics='pr', cell_temperature='nose',
temph=300., fnoseh=8.6071, press=1.0,
/
ATOMIC_SPECIES
O 16.00 O.pz-rrkjus.UPF
Si 28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
O 3.18829368 14.83237039 1.22882961
O 7.83231469 6.78704039 1.22882961
O 2.07443467 5.99537992 4.73758250
O 6.72031366 14.04231898 4.73758250
O 3.96307134 11.26989826 7.87860582
O 8.60802134 3.22295920 7.87860582
O 3.96307134 4.81915267 9.14625133
O 8.60802134 12.86448267 9.14625133
O 3.18736469 1.25668055 5.58029607
O 7.83324368 9.30201055 5.58029607
O 2.07536366 10.09206195 2.07358613
O 6.71938467 2.04673195 2.07358613
Si 0.28891589 8.04533000 3.40456284
Si 4.93386589 0.00000000 3.40456284
Si 2.13389003 12.27717358 -0.04188031
Si 6.77884003 4.23184358 -0.04188031
Si 2.13389003 3.81348642 6.85202747
Si 6.77884003 11.85881642 6.85202747
EOF
$ECHO " running the variable-cell calculation, restart...\c"
$CP_COMMAND < sio2.vc-cp.restart.in > sio2.vc-cp.restart.out
check_failure $?
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR : done"
|
