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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 compute the equilibrium geometry"
$ECHO "of a simple molecule, CO, and of an Al (001) slab."
$ECHO "In the latter case the relaxation is performed in two ways:"
$ECHO "1) using the quasi-Newton BFGS algorithm"
$ECHO "2) using a damped dynamics algorithm."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST=" O.pz-rrkjus.UPF C.pz-rrkjus.UPF Al.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"
$ECHO
# self-consistent calculation
cat > co.rx.in << EOF
&CONTROL
calculation = "relax",
prefix = "CO",
pseudo_dir = "$PSEUDO_DIR",
outdir = "$TMP_DIR",
/
&SYSTEM
ibrav = 0,
nat = 2,
ntyp = 2,
ecutwfc = 24.D0,
ecutrho = 144.D0,
/
&ELECTRONS
conv_thr = 1.D-7,
mixing_beta = 0.7D0,
/
&IONS
/
CELL_PARAMETERS bohr
12.0 0.0 0.0
0.0 12.0 0.0
0.0 0.0 12.0
ATOMIC_SPECIES
O 1.00 O.pz-rrkjus.UPF
C 1.00 C.pz-rrkjus.UPF
ATOMIC_POSITIONS {bohr}
C 2.256 0.0 0.0
O 0.000 0.0 0.0 0 0 0
K_POINTS {Gamma}
EOF
$ECHO " running the geometry relaxation for CO...\c"
$PW_COMMAND < co.rx.in > co.rx.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/CO*
$ECHO " done"
# self-consistent calculation
cat > al001.rx.in << EOF
&CONTROL
calculation = "relax",
pseudo_dir = "$PSEUDO_DIR",
prefix = "Al"
outdir = "$TMP_DIR",
/
&SYSTEM
ibrav = 6,
celldm(1) = 5.3033D0,
celldm(3) = 8.D0,
nat = 7,
ntyp = 1,
ecutwfc = 12.D0,
occupations = "smearing",
smearing = "marzari-vanderbilt",
degauss = 0.05D0,
/
&ELECTRONS
conv_thr = 1.D-6,
mixing_beta = 0.3D0,
/
&IONS
bfgs_ndim = 3,
/
ATOMIC_SPECIES
Al 1.0 Al.pz-vbc.UPF
ATOMIC_POSITIONS alat
Al 0.5000000 0.5000000 -2.121320
Al 0.0000000 0.0000000 -1.414213
Al 0.5000000 0.5000000 -0.707107
Al 0.0000000 0.0000000 0.000000
Al 0.5000000 0.5000000 0.707107
Al 0.0000000 0.0000000 1.414213
Al 0.5000000 0.5000000 2.121320
K_POINTS
3
0.125 0.125 0.0 1.0
0.125 0.375 0.0 2.0
0.375 0.375 0.0 1.0
EOF
$ECHO " running the geometry relaxation for Al (001) using BFGS...\c"
$PW_COMMAND < al001.rx.in > al001.rx.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Al*
$ECHO " done"
# self-consistent calculation
rm -f e eal ave p avec tv
cat > al001.mm.in << EOF
&CONTROL
calculation = "relax",
dt = 30.D0,
pseudo_dir = "$PSEUDO_DIR",
outdir = "$TMP_DIR",
prefix = "Al"
/
&SYSTEM
ibrav = 6,
celldm(1) = 5.3033D0,
celldm(3) = 8.D0,
nat = 7,
ntyp = 1,
ecutwfc = 12.D0,
occupations = "smearing",
smearing = "marzari-vanderbilt",
degauss = 0.05D0,
/
&ELECTRONS
conv_thr = 1.D-7,
mixing_beta = 0.3D0,
/
&IONS
ion_dynamics = "damp",
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
Al 1.D0 Al.pz-vbc.UPF
ATOMIC_POSITIONS alat
Al 0.5000000 0.5000000 -2.121320
Al 0.0000000 0.0000000 -1.414213
Al 0.5000000 0.5000000 -0.707107
Al 0.0000000 0.0000000 0.000000
Al 0.5000000 0.5000000 0.707107
Al 0.0000000 0.0000000 1.414213
Al 0.5000000 0.5000000 2.121320
K_POINTS
3
0.125 0.125 0.0 1.0
0.125 0.375 0.0 2.0
0.375 0.375 0.0 1.0
EOF
$ECHO " running the geometry relaxation for Al (001) using damped MD...\c"
$PW_COMMAND < al001.mm.in > al001.mm.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Al*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
