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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 (a water molecule) shows how to use cp.x to perform"
$ECHO "molecular dynamics with variable parameters using AUTOPILOT."
$ECHO "The variables are changed without stopping and starting cp.x."
$ECHO "For example the dt value can be changed from 3 to 5 to 10 to 15"
$ECHO "at predefined time steps. For other advanced options like STRING"
$ECHO "(send a signal to a running cp.x process to change some parameter"
$ECHO "on the fly) or Pause please consult the AUTOPILOT documentation."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="cp.x"
PSEUDO_LIST="H_US.van O_US.van"
$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
$ECHO " done"
# how to run executables
CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO " running cp.x as: $CP_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# molecular dynamics calculation
cat > water.autopilot.in << EOF
&CONTROL
calculation='cp',
title="WATER",
restart_mode='from_scratch',
nstep=10000, iprint=30, isave=30,
tstress=.FALSE.,
tprnfor=.FALSE.,
dt = 3.,
ndr=90,
ndw=91,
ekin_conv_thr=1e-09
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&SYSTEM
ibrav = 1,
celldm(1) = 10.,
nat =3,
ntyp =2,
nbnd =4,
ecutwfc =25.0,
ecutrho =200.0,
nr1b=20, nr2b=20, nr3b=20,
occupations = 'fixed',
nspin=1,
ecfixed =25.0
/
&ELECTRONS
emass = 700.,
emass_cutoff = 3.,
orthogonalization = 'ortho',
electron_maxstep = 200,
ortho_eps = 1.e-10,
ortho_max = 250,
electron_dynamics= 'damp',
electron_damping =0.15,
startingwfc='random'
ampre=0.02
/
&IONS
ion_dynamics = 'none',
ion_radius = 1.0,
ion_damping = 0.0,
ion_positions = 'default',
ion_temperature = 'not_controlled',
tempw=800,
fnosep=37.22179
/
AUTOPILOT
on_step = 31 : dt=5
on_step = 61 : dt=10
on_step = 91 : dt=15
on_step = 91 : iprint=100
on_step = 91 : isave=100
on_step = 191 : ion_dynamics = 'damp'
on_step = 191 : electron_damping =0.00
on_step = 191 : isave=500
on_step = 191 : isave=500
on_step = 691 : ion_temperature = 'nose'
on_step = 691 : tempw=150
on_step = 1191 : tempw=300
on_step = 1691 : tempw=500
on_step = 2191 : iprint=50
on_step = 2191 : isave=50
on_step = 2191 : electron_damping = 0.10
on_step = 2191 : ion_dynamics = 'none'
on_step = 2191 : ion_temperature ='not_controlled'
on_step = 2241 : iprint=200
on_step = 2241 : isave=200
on_step = 2241 : electron_damping =0.00
on_step = 2241 : ion_dynamics = 'damp'
on_step = 2441 : iprint=900
on_step = 2441 : isave=500
on_step = 2441 : electron_damping =0.15
on_step = 2441 : ion_temperature = 'nose'
on_step = 2441 : tempw=800
on_step = 3341 : iprint=200
on_step = 3341 : isave=200
on_step = 3341 : electron_damping =0.00
on_step = 3541 : iprint=50
on_step = 3541 : isave=50
on_step = 3541 : ion_dynamics = 'none'
on_step = 3541 : ion_temperature = 'not_controlled'
on_step = 3591 : iprint=2000
on_step = 3591 : isave=2000
on_step = 3591 : ion_dynamics = 'damp'
on_step = 3591 : ion_temperature = 'nose'
on_step = 6591 : iprint=10000
on_step = 6591 : isave=500
on_step = 6591 : electron_damping =0.00
on_step = 6591 : ion_temperature = 'nose'
ENDRULES
ATOMIC_SPECIES
H 1.00794000 H_US.van
O 15.99940000 O_US.van
ATOMIC_POSITIONS {bohr}
H 0.57164238 0.94335166 0.96565043
H -0.24339682 -0.43501513 -1.37874473
O -0.32824556 -0.50852550 0.41309430
EOF
$ECHO " running CP calculation with AUTOPILOT option...\c"
$CP_COMMAND < water.autopilot.in > water.autopilot.out
$ECHO " done"
exit 0
|
