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|
#!/bin/sh
###############################################################################
##
## ESM 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 shows how to use ESM to calculate Al(111) and H2O"
$ECHO "using the three available sets of boundary conditions."
$ECHO
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x"
PSEUDO_LIST="Al.pbe-rrkj.UPF H.pbe-rrkjus.UPF O.pbe-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
$ECHO " done"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
# scf calculation for H2O with no ESM
cat > H2O.noesm.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='H2O',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 6, celldm(1) =20.0, celldm(3) = 1.200
nat= 3, ntyp= 2,
ecutwfc = 25.0, ecutrho = 200.0,
occupations='smearing', smearing='gaussian', degauss=0.05,
assume_isolated = 'esm', esm_bc='pbc'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
H 1.00794 H.pbe-rrkjus.UPF
O 55.847 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS
O 0.000000000 0.500000000 0.000000000 0 0 0
H 0.043138813 0.431028632 0.043078297 0 0 0
H 0.036635422 0.576406407 0.035949164
K_POINTS gamma
EOF
$ECHO " running the scf calculation for H2O without ESM...\c"
$PW_COMMAND < H2O.noesm.in > H2O.noesm.out
check_failure $?
$ECHO " done"
# scf calculation for H2O with ESM bc1 (vacuum-slab-vacuum)
cat > H2O.bc1.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='H2O',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 6, celldm(1) =20.0, celldm(3) = 1.200
nat= 3, ntyp= 2,
ecutwfc = 25.0, ecutrho = 200.0,
occupations='smearing', smearing='gaussian', degauss=0.05,
assume_isolated = 'esm', esm_bc='bc1'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
H 1.00794 H.pbe-rrkjus.UPF
O 55.847 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS
O 0.000000000 0.500000000 0.000000000 0 0 0
H 0.043138813 0.431028632 0.043078297 0 0 0
H 0.036635422 0.576406407 0.035949164
K_POINTS gamma
EOF
$ECHO " running the scf calculation for H2O with ESM bc1 (vacuum-slab-vacuum)...\c"
$PW_COMMAND < H2O.bc1.in > H2O.bc1.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/H2O*
$ECHO " done"
# scf calculation for Al(111) with ESM bc2 (metal-slab-metal), no field
cat > Al111.bc2.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al111',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0, celldm(1) = 7.653393855,
nat= 7, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.05
assume_isolated='esm', esm_bc='bc2'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-rrkj.UPF
CELL_PARAMETERS hexagonal
0.707106781 0.000000000 0.000000000
0.353553390 0.612372436 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS angstrom
Al 0.00000 0.00000 -7.01481
Al 0.00000 1.65341 -4.67654
Al 1.43189 0.82670 -2.33827
Al 0.00000 0.00000 0.00000
Al 0.00000 1.65341 2.33827
Al 1.43189 0.82670 4.67654
Al 0.00000 0.00000 7.01481
K_POINTS automatic
8 8 1 0 0 0
EOF
$ECHO " running the scf calculation for Al(111) with ESM bc2 (metal-slab-metal)"
$ECHO " (no applied field)...\c"
$PW_COMMAND < Al111.bc2.in > Al111.bc2.out
check_failure $?
$ECHO " done"
# scf calculation for Al(111) with ESM bc2 (metal-slab-metal), with field
cat > Al111.bc2_efield.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al111',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0, celldm(1) = 7.653393855,
nat= 7, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.05
assume_isolated='esm', esm_bc='bc2', esm_efield=0.00192148511256006
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-rrkj.UPF
CELL_PARAMETERS hexagonal
0.707106781 0.000000000 0.000000000
0.353553390 0.612372436 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS angstrom
Al 0.00000 0.00000 -7.01481
Al 0.00000 1.65341 -4.67654
Al 1.43189 0.82670 -2.33827
Al 0.00000 0.00000 0.00000
Al 0.00000 1.65341 2.33827
Al 1.43189 0.82670 4.67654
Al 0.00000 0.00000 7.01481
K_POINTS automatic
8 8 1 0 0 0
EOF
$ECHO " running the scf calculation for Al(111) with ESM bc2 (metal-slab-metal)"
$ECHO " with applied electric field...\c"
$PW_COMMAND < Al111.bc2_efield.in > Al111.bc2_efield.out
check_failure $?
$ECHO " done"
# scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal), uncharged
cat > Al111.bc3.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al111',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0, celldm(1) = 7.653393855,
nat= 7, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.05
assume_isolated='esm', esm_bc='bc3'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-rrkj.UPF
CELL_PARAMETERS hexagonal
0.707106781 0.000000000 0.000000000
0.353553390 0.612372436 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS angstrom
Al 0.00000 0.00000 -7.01481
Al 0.00000 1.65341 -4.67654
Al 1.43189 0.82670 -2.33827
Al 0.00000 0.00000 0.00000
Al 0.00000 1.65341 2.33827
Al 1.43189 0.82670 4.67654
Al 0.00000 0.00000 7.01481
K_POINTS automatic
8 8 1 0 0 0
EOF
$ECHO " running the scf calculation for Al(111) with ESM bc3 (metal-slab-metal)"
$ECHO " (neutrally charged)...\c"
$PW_COMMAND < Al111.bc3.in > Al111.bc3.out
check_failure $?
$ECHO " done"
# scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal), - charged
cat > Al111.bc3_m005.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al111',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0, celldm(1) = 7.653393855,
tot_charge = -0.005,
nat= 7, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.05
assume_isolated='esm', esm_bc='bc3'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-rrkj.UPF
CELL_PARAMETERS hexagonal
0.707106781 0.000000000 0.000000000
0.353553390 0.612372436 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS angstrom
Al 0.00000 0.00000 -7.01481
Al 0.00000 1.65341 -4.67654
Al 1.43189 0.82670 -2.33827
Al 0.00000 0.00000 0.00000
Al 0.00000 1.65341 2.33827
Al 1.43189 0.82670 4.67654
Al 0.00000 0.00000 7.01481
K_POINTS automatic
8 8 1 0 0 0
EOF
$ECHO " running the scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (-0.005e charged)...\c"
$PW_COMMAND < Al111.bc3_m005.in > Al111.bc3_m005.out
check_failure $?
$ECHO " done"
# scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal), + charged
cat > Al111.bc3_p005.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al111',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0, celldm(1) = 7.653393855,
tot_charge = 0.005,
nat= 7, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.05
assume_isolated='esm', esm_bc='bc3'
/
&electrons
mixing_beta = 0.5
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-rrkj.UPF
CELL_PARAMETERS hexagonal
0.707106781 0.000000000 0.000000000
0.353553390 0.612372436 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS angstrom
Al 0.00000 0.00000 -7.01481
Al 0.00000 1.65341 -4.67654
Al 1.43189 0.82670 -2.33827
Al 0.00000 0.00000 0.00000
Al 0.00000 1.65341 2.33827
Al 1.43189 0.82670 4.67654
Al 0.00000 0.00000 7.01481
K_POINTS automatic
8 8 1 0 0 0
EOF
$ECHO " running the scf calculation for Al(111) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (+0.005e charged)...\c"
$PW_COMMAND < Al111.bc3_p005.in > Al111.bc3_p005.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Al111*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
