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run_scf_Mg2Si24
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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
# function to test the exit status of a job
. ../check_failure.sh
$ECHO
$ECHO "$EXAMPLE_DIR : starting SCF"
$ECHO
# set the needed environment variables
. ../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x dos.x projwfc.x kvecs_FS.x bands_FS.x"
$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 "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 $PARA_POSTFIX"
KUBO_COMMAND="$PARA_PREFIX $BIN_DIR/kubo.x $PARA_POSTFIX"
DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
KVECS_COMMAND="$BIN_DIR/kvecs_FS.x "
BANDS_COMMAND="$BIN_DIR/bands_FS.x "
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running dos.x as: $DOS_COMMAND"
$ECHO " running projwfc.x as: $PROJWFC_COMMAND"
$ECHO " running kvecs_FS.x as: $KVECS_COMMAND"
$ECHO " running bands_FS.x as: $BANDS_COMMAND"
$ECHO
# time step for molecular dynamics is in Rydberg atomic units 1 a.u.=4.8378 * 10^-17 s
# phys rev b 38 2 methfessel states fundamental freq of Si is ~42.25 Thz
# 1/10 of fundamental is about 50.0 a.u. then
#the thermal expansion of Mg2Si at 800K is ~42 10^-6 K^-1
# reference anastassakis and hawranek say 6.338 A at 300K
# reference baranek and schamps say 6.351 A at 300K
# by Y. S. Raptis et al. the expansion from 300K to 800K is 2.379%
# so lets take the average of the data and expand by that
# lattice spacing at 800K : 6.4954 (proably more significant digits than valid).
# degauss should be kT in eV
# k = 8.6173324(78)×10-5 eV/K
# at 100K : 0.0086173324
# at 500K : 0.043086662
# at 800K : 0.0689386592
cat > scf_Mg2Si_24.in << EOF
&control
calculation = 'scf'
restart_mode='restart',
pseudo_dir = '$PSEUDO_DIR',
outdir='./',
prefix='Mg2Si24',
disk_io ='low'
wf_collect=.true.,
/
&SYSTEM
ibrav = 0,
celldm(1) = 1.889725989,
ntyp = 2,
nat = 24,
ecutwfc =50.0,
occupations = 'smearing',
degauss = 0.004,
smearing = 'fd'
nosym = .true.
/
&electrons
electron_maxstep = 999 ,
conv_thr = 1.0e-6 ,
mixing_beta = 0.3 ,
startingwfc = 'atomic+random' ,
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
Mg 12.0000 Mg.pz-n-vbc.UPF
ATOMIC_POSITIONS (crystal)
Si 0.00000000 0.00000000 0.00000000
Mg 0.12500000 0.12500000 0.12500000
Mg 0.37500000 0.37500000 0.37500000
Si 0.50000000 0.00000000 0.00000000
Mg 0.62500000 0.12500000 0.12500000
Mg 0.87500000 0.37500000 0.37500000
Si 0.00000000 0.50000000 0.00000000
Mg 0.12500000 0.62500000 0.12500000
Mg 0.37500000 0.87500000 0.37500000
Si 0.50000000 0.50000000 0.00000000
Mg 0.62500000 0.62500000 0.12500000
Mg 0.87500000 0.87500000 0.37500000
Si 0.00000000 0.00000000 0.50000000
Mg 0.12500000 0.12500000 0.62500000
Mg 0.37500000 0.37500000 0.87500000
Si 0.50000000 0.00000000 0.50000000
Mg 0.62500000 0.12500000 0.62500000
Mg 0.87500000 0.37500000 0.87500000
Si 0.00000000 0.50000000 0.50000000
Mg 0.12500000 0.62500000 0.62500000
Mg 0.37500000 0.87500000 0.87500000
Si 0.50000000 0.50000000 0.50000000
Mg 0.62500000 0.62500000 0.62500000
Mg 0.87500000 0.87500000 0.87500000
CELL_PARAMETERS (cubic)
10.60694378 3.75012094 6.49540000
0.00000000 11.25036282 6.49540000
0.00000000 0.00000000 12.99080000
K_POINTS (automatic)
8 8 8 0 0 0
EOF
$ECHO " running the SCF calculation for Mg2Si...\c"
mpiexec -n 8 $PW_COMMAND < scf_Mg2Si_24.in > scf_Mg2Si24.out
check_failure $?
$ECHO " done"