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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 to perform molecular dynamics for"
$ECHO "2- and 8-atom cells of Si starting with compressed bonds along (111)."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST="Si.pz-vbc.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
$ECHO " done"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
# MD in a 2-atom cell
cat > si.md2.in << EOF
&control
calculation='md'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
dt=20,
nstep=100,
disk_io='high'
/
&system
ibrav= 2, celldm(1)=10.18, nat= 2, ntyp= 1,
ecutwfc = 8.0, nosym=.true.
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
&ions
pot_extrapolation='second-order'
wfc_extrapolation='second-order'
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
Si -0.123 -0.123 -0.123
Si 0.123 0.123 0.123
K_POINTS {automatic}
1 1 1 0 0 0
EOF
$ECHO " running the MD calculation for Si in a 2 atom cell. G-point...\c"
$PW_COMMAND < si.md2.in > si.md2.out
check_failure $?
$ECHO " done"
awk '/Ekin/{ek=$3;et=$11; print it,time,ek,u,et}/Dynamics/{it=$5;time=$8}/^\!/{u=$5}' si.md2.out > MD2
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# MD in a 8-atom cell
cat > si.md8.in << EOF
&control
calculation='md'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
dt=20,
nstep=100,
disk_io='high'
/
&system
ibrav= 1, celldm(1)=10.18, nat= 8, ntyp= 1,
ecutwfc = 8.0, nosym=.true.
/
&electrons
conv_thr = 1.0d-8,
mixing_beta = 0.7
/
&ions
pot_extrapolation='second-order'
wfc_extrapolation='second-order'
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
Si -0.123 -0.123 -0.123
Si 0.377 0.377 -0.123
Si 0.377 -0.123 0.377
Si -0.123 0.377 0.377
Si 0.123 0.123 0.123
Si 0.623 0.623 0.123
Si 0.623 0.123 0.623
Si 0.123 0.623 0.623
K_POINTS {automatic}
1 1 1 0 0 0
EOF
$ECHO " running the MD calculation for Si in a 8 atom cell. G-point...\c"
$PW_COMMAND < si.md8.in > si.md8.out
check_failure $?
$ECHO " done"
awk '/Ekin/{ek=$3;et=$11; print it,time,ek,u,et}/Dynamics/{it=$5;time=$8}/^\!/{u=$5}' si.md8.out > MD8
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# MD in a 2-atom cell. Gamma+3X
cat > si.md2_G3X.in << EOF
&control
calculation='md'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
dt=20,
nstep=100,
disk_io='high'
/
&system
ibrav= 2, celldm(1)=10.18, nat= 2, ntyp= 1,
ecutwfc = 8.0, nosym=.true.
/
&electrons
conv_thr = 1.0d-8,
mixing_beta = 0.7
/
&ions
pot_extrapolation='second-order'
wfc_extrapolation='second-order'
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
Si -0.123 -0.123 -0.123
Si 0.123 0.123 0.123
K_POINTS
4
0.0 0.0 0.0 1.0
1.0 0.0 0.0 1.0
0.0 1.0 0.0 1.0
0.0 0.0 1.0 1.0
EOF
$ECHO " running the MD calculation for Si in a 2 atom cell. G3X-points...\c"
$PW_COMMAND < si.md2_G3X.in > si.md2_G3X.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
awk '/Ekin/{ek=$3;et=$11; print it,time,ek,u,et} \
/Dynamics/{it=$5;time=$8}/^\!/{u=$5}' si.md2_G3X.out > MD2_G3X
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
