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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 H2O and Al(001)"
$ECHO "using the three available sets of boundary conditions."
$ECHO "This example also shows how to use ESM to calculate stress of"
$ECHO "graphene 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-n-van.UPF H.pbe-van_ak.UPF O.pbe-van_ak.UPF C.pz-van_ak.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"
echo $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE
$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"
$ECHO
# scf calculation for H2O with no ESM
cat > H2O_pbc.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='H2O_pbc',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 3, ntyp= 2,
ecutwfc = 25.0, ecutrho = 200.0,
occupations='smearing', smearing='mp', degauss=0.03,
assume_isolated = 'esm', esm_bc='pbc'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
H 1.00794 H.pbe-van_ak.UPF
O 55.847 O.pbe-van_ak.UPF
CELL_PARAMETERS angstrom
10.5835400000 0.0000000000 0.0000000000
0.0000000000 10.5835400000 0.0000000000
0.0000000000 0.0000000000 12.7002480000
ATOMIC_POSITIONS angstrom
O 0.0000000000 5.2917700000 0.0000000000
H 0.4565612154 4.5618084292 0.4559209112
H 0.3877322213 6.1004201907 0.3804697962
K_POINTS gamma
EOF
$ECHO " running the calculation for H2O without ESM...\c"
$PW_COMMAND < H2O_pbc.in > H2O_pbc.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/H2O_pbc.esm1 .
# scf calculation for H2O with ESM bc1 (vacuum-slab-vacuum)
cat > H2O_bc1.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='H2O_bc1',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 3, ntyp= 2,
ecutwfc = 25.0, ecutrho = 200.0,
occupations='smearing', smearing='mp', degauss=0.03,
assume_isolated = 'esm', esm_bc='bc1'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
H 1.00794 H.pbe-van_ak.UPF
O 55.847 O.pbe-van_ak.UPF
CELL_PARAMETERS angstrom
10.5835400000 0.0000000000 0.0000000000
0.0000000000 10.5835400000 0.0000000000
0.0000000000 0.0000000000 12.7002480000
ATOMIC_POSITIONS angstrom
O 0.0000000000 5.2917700000 0.0000000000
H 0.4565612154 4.5618084292 0.4559209112
H 0.3877322213 6.1004201907 0.3804697962
K_POINTS gamma
EOF
$ECHO " running the calculation for H2O with ESM bc1 (vacuum-slab-vacuum)...\c"
$PW_COMMAND < H2O_bc1.in > H2O_bc1.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/H2O_bc1.esm1 .
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/H2O*
$ECHO " done"
# calculation for Al(001) without ESM
cat > Al001_pbc.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_pbc',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='pbc'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) without ESM\c"
$PW_COMMAND < Al001_pbc.in > Al001_pbc.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_pbc.esm1 .
# calculation for Al(001) with ESM bc1 (vacuum-slab-vacuum)
cat > Al001_bc1.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc1',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc1'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc1 (vacuum-slab-vacuuml)"
$PW_COMMAND < Al001_bc1.in > Al001_bc1.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc1.esm1 .
# calculation for Al(001) with ESM bc2 (metal-slab-metal), no field
cat > Al001_bc2.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc2',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc2'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc2 (metal-slab-metal)"
$ECHO " (no applied field)...\c"
$PW_COMMAND < Al001_bc2.in > Al001_bc2.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc2.esm1 .
# calculation for Al(001) with ESM bc2 (metal-slab-metal), with field
cat > Al001_bc2_efield.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc2_efield',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc2', esm_efield=0.00192148511256006
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc2 (metal-slab-metal)"
$ECHO " with applied electric field...\c"
$PW_COMMAND < Al001_bc2_efield.in > Al001_bc2_efield.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc2_efield.esm1 .
# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), uncharged
cat > Al001_bc3.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc3',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (neutrally charged)...\c"
$PW_COMMAND < Al001_bc3.in > Al001_bc3.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3.esm1 .
# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), - charged
cat > Al001_bc3_m002.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc3_m002',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
tot_charge = -0.02,
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (-0.02e charged)...\c"
$PW_COMMAND < Al001_bc3_m002.in > Al001_bc3_m002.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3_m002.esm1 .
# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), + charged
cat > Al001_bc3_p002.in << EOF
&control
calculation='scf',
restart_mode='from_scratch',
prefix='Al001_bc3_p002',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
tot_charge = 0.02,
/
&electrons
mixing_beta = 0.3
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (+0.02e charged)...\c"
$PW_COMMAND < Al001_bc3_p002.in > Al001_bc3_p002.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3_p002.esm1 .
# constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal),
# target mu = potential of zero charge (neutral surface)
cat > Al001_bc3_v00.in << EOF
&control
calculation='relax',
restart_mode='from_scratch',
prefix='Al001_bc3_v00',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
lfcpopt = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
fcp_mu = -0.312573,
/
&electrons
mixing_beta = 0.3
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (target mu = 0V vs pzc)...\c"
$PW_COMMAND < Al001_bc3_v00.in > Al001_bc3_v00.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3_v00.esm1 .
# constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal),
# target mu = +0.5V vs pzc
cat > Al001_bc3_vp05.in << EOF
&control
calculation='relax',
restart_mode='from_scratch',
prefix='Al001_bc3_vp05',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
lfcpopt = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
fcp_mu = -0.275809,
/
&electrons
mixing_beta = 0.3
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (target mu = +0.5V vs pzc)...\c"
$PW_COMMAND < Al001_bc3_vp05.in > Al001_bc3_vp05.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3_vp05.esm1 .
# constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal),
# target mu = -0.5V vs pzc
cat > Al001_bc3_vm05.in << EOF
&control
calculation='relax',
restart_mode='from_scratch',
prefix='Al001_bc3_vm05',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .TRUE.
lfcpopt = .TRUE.
/
&system
ibrav = 0,
nat= 4, ntyp= 1,
ecutwfc = 20.0,
nosym=.TRUE.
occupations='smearing', smearing='mp', degauss=0.03
assume_isolated='esm', esm_bc='bc3'
fcp_mu = -0.349338,
/
&electrons
mixing_beta = 0.3
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
Al 26.981538 Al.pbe-n-van.UPF
CELL_PARAMETERS angstrom
5.7269000760 0.0000000000 0.0000000000
0.0000000000 5.7269000760 0.0000000000
0.0000000000 0.0000000000 11.9999975199
ATOMIC_POSITIONS angstrom
Al 0.0000000000 0.0000000000 0.0000000000
Al 2.8634500380 0.0000000000 0.0000000000
Al 0.0000000000 2.8634500380 0.0000000000
Al 2.8634500380 2.8634500380 0.0000000000
K_POINTS automatic
6 6 1 1 1 0
EOF
$ECHO " running the constant-mu calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
$ECHO " (target mu = -0.5V vs pzc)...\c"
$PW_COMMAND < Al001_bc3_vm05.in > Al001_bc3_vm05.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/Al001_bc3_vm05.esm1 .
# stress calculation for graphene with PBC (slab-slab-slab)
cat > graphene_pbc.in << EOF
&control
calculation = 'scf',
restart_mode='from_scratch',
prefix='graphene_pbc',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'none', esm_bc = 'pbc'
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.3229425000 2.2914025571 0.0000000000
0.0000000000 0.0000000000 5.2917700000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the stress calculation for graphene with PBC (slab-slab-slab)"
$PW_COMMAND < graphene_pbc.in > graphene_pbc.out
check_failure $?
$ECHO " done"
# stress calculation for graphene with ESM bc1 (vacuum-slab-vacuum)
cat > graphene_bc1.in << EOF
&control
calculation = 'scf',
restart_mode='from_scratch',
prefix='graphene_bc1',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'esm', esm_bc = 'bc1'
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.3229425000 2.2914025571 0.0000000000
0.0000000000 0.0000000000 16.0000000000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the stress calculation for graphene with BC1 (vacuum-slab-vacuum)"
$PW_COMMAND < graphene_bc1.in > graphene_bc1.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/graphene_bc1.esm1 .
# stress calculation for graphene with ESM bc2 (metal-slab-metal)
cat > graphene_bc2.in << EOF
&control
calculation = 'scf',
restart_mode='from_scratch',
prefix='graphene_bc2',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'esm', esm_bc = 'bc2'
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.3229425000 2.2914025571 0.0000000000
0.0000000000 0.0000000000 16.0000000000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the stress calculation for graphene with BC2 (metal-slab-metal)"
$PW_COMMAND < graphene_bc2.in > graphene_bc2.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/graphene_bc2.esm1 .
# stress calculation for graphene with ESM bc3 (vacuum-slab-metal)
cat > graphene_bc3.in << EOF
&control
calculation = 'scf',
restart_mode='from_scratch',
prefix='graphene_bc3',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'esm', esm_bc = 'bc3'
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.3229425000 2.2914025571 0.0000000000
0.0000000000 0.0000000000 16.0000000000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the stress calculation for graphene with BC3 (vacuum-slab-metal)"
$PW_COMMAND < graphene_bc3.in > graphene_bc3.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/graphene_bc3.esm1 .
# vc-relax calculation for graphene with ESM bc1 (vacuum-slab-vacuum)
# Angle of lattice vector starts from 117 degree, and it will be optimized to
# 120 degree.
cat > graphene_bc1_vc-relax.in << EOF
&control
calculation = 'vc-relax',
restart_mode='from_scratch',
prefix='graphene_bc1_vc-relax',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'esm', esm_bc = 'bc1',
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
&ions
ion_dynamics = 'bfgs'
/
&cell
cell_dofree="2Dxy"
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.1906482500 2.3628520357 0.0000000000
0.0000000000 0.0000000000 16.0000000000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the vc-relax calculation for graphene with BC1 (vacuum-slab-vacuum)"
$PW_COMMAND < graphene_bc1_vc-relax.in > graphene_bc1_vc-relax.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/graphene_bc1_vc-relax.esm1 .
# vc-relax calculation for graphene with ESM bc3 (vacuum-slab-metal) + charged
# Angle of lattice vector starts from 117 degree, and it will be optimized to
# 120 degree.
cat > graphene_bc3_vc-relax_p002.in << EOF
&control
calculation = 'vc-relax',
restart_mode='from_scratch',
prefix='graphene_bc3_vc-relax_p002',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav = 0,
nat = 2, ntyp = 1,
ecutwfc = 36.0, ecutrho = 144.0,
occupations = 'smearing', smearing = 'mp', degauss = 0.03,
assume_isolated = 'esm', esm_bc = 'bc3',
tot_charge = 0.02,
/
&electrons
mixing_beta = 0.7, conv_thr = 1.0d-8
/
&ions
ion_dynamics = 'bfgs'
/
&cell
cell_dofree="2Dxy"
/
ATOMIC_SPECIES
C 12.0107 C.pz-van_ak.UPF
CELL_PARAMETERS angstrom
2.6458850000 0.0000000000 0.0000000000
-1.1906482500 2.3628520357 0.0000000000
0.0000000000 0.0000000000 16.0000000000
ATOMIC_POSITIONS angstrom
C 0.0000000000 0.0000000000 0.0000000000
C 0.0000000000 1.5276024985 0.0000000000
K_POINTS {automatic}
12 12 1 0 0 0
EOF
$ECHO " running the vc-relax calculation for graphene with BC3 (vacuum-slab-metal) + charged"
$PW_COMMAND < graphene_bc3_vc-relax_p002.in > graphene_bc3_vc-relax_p002.out
check_failure $?
$ECHO " done"
mv $TMP_DIR/graphene_bc3_vc-relax_p002.esm1 .
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
