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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 neb.x to calculate the"
$ECHO "minimum energy path (MEP) of the collinear proton transfer reaction:"
$ECHO " H2+H <==> H+H2, within the Born-Oppenheimer approximation."
$ECHO
$ECHO "!!! Beware: neb.x DOES NOT READ FROM STANDARD INPUT"
$ECHO "!!! run as 'neb.x -inp input_file_name > output_file_name'"
$ECHO
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="neb.x"
PSEUDO_LIST="HUSPBE.RRKJ3"
$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
$ECHO " done"
# how to run executables
NEB_COMMAND="$PARA_PREFIX $BIN_DIR/neb.x $PARA_POSTFIX"
$ECHO
$ECHO " running Born-Oppenheimer NEB as: $NEB_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# NEB calculation. Automatic choice of the climbing image.
cat > H2+H.in << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 20,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 7,
k_max = 0.3D0,
k_min = 0.2D0,
CI_scheme = "auto",
path_thr = 0.1D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "H2+H"
outdir = "$TMP_DIR",
pseudo_dir = "$PSEUDO_DIR",
/
&SYSTEM
ibrav = 0,
nat = 3,
ntyp = 1,
ecutwfc = 20.0D0,
ecutrho = 100.0D0,
nspin = 2,
starting_magnetization = 0.5D0,
occupations = "smearing",
degauss = 0.03D0,
/
&ELECTRONS
conv_thr = 1.D-8,
mixing_beta = 0.3D0,
/
&IONS
/
ATOMIC_SPECIES
H 1.00794 HUSPBE.RRKJ3
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { bohr }
H -4.56670009 0.00000000 0.00000000 1 0 0
H 0.00000000 0.00000000 0.00000000 0 0 0
H 1.55776676 0.00000000 0.00000000 1 0 0
LAST_IMAGE
ATOMIC_POSITIONS { bohr }
H -1.55776676 0.00000000 0.00000000
H 0.00000000 0.00000000 0.00000000
H 4.56670009 0.00000000 0.00000000
END_POSITIONS
K_POINTS { gamma }
CELL_PARAMETERS { bohr }
12.00000 0.00000 0.00000
0.00000 5.00000 0.00000
0.00000 0.00000 5.00000
END_ENGINE_INPUT
END
EOF
$ECHO " running Born-Oppenheimer NEB calculation for H2+H => H+H2...\c"
$NEB_COMMAND -inp H2+H.in > H2+H.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# NEB calculation. Climbing image is not used
cat > symmetric_H2+H.in << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 20,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 8,
k_max = 0.3D0,
k_min = 0.2D0,
path_thr = 0.2D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "symmetric_H2+H"
outdir = "$TMP_DIR",
pseudo_dir = "$PSEUDO_DIR",
/
&SYSTEM
ibrav = 0,
nat = 3,
ntyp = 1,
ecutwfc = 20.0D0,
ecutrho = 100.0D0,
nspin = 2,
starting_magnetization = 0.5D0,
occupations = "smearing",
degauss = 0.03D0,
/
&ELECTRONS
conv_thr = 1.D-8,
mixing_beta = 0.3D0,
/
&IONS
/
ATOMIC_SPECIES
H 1.00794 HUSPBE.RRKJ3
K_POINTS { gamma }
CELL_PARAMETERS { bohr }
12.00000 0.00000 0.00000
0.00000 5.00000 0.00000
0.00000 0.00000 5.00000
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { bohr }
H -4.56670009 0.00000000 0.00000000 1 0 0
H 0.00000000 0.00000000 0.00000000 0 0 0
H 1.55776676 0.00000000 0.00000000 1 0 0
LAST_IMAGE
ATOMIC_POSITIONS { bohr }
H -1.55776676 0.00000000 0.00000000
H 0.00000000 0.00000000 0.00000000
H 4.56670009 0.00000000 0.00000000
END_POSITIONS
END_ENGINE_INPUT
END
EOF
$ECHO " running Born-Oppenheimer NEB calculation for symmetric H2+H => H+H2...\c"
$NEB_COMMAND -inp symmetric_H2+H.in > symmetric_H2+H.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# the name of the restart file is changed in order to conform to the
# prefix of the new run
# the restart file asymmetric_H2+H.neb is modified (second row)
# since a new simulation (from the old path) is started
cat symmetric_H2+H.path | \
awk '{if(NR==2){printf" 0\n"}; if(NR!=2){print}}' > asymmetric_H2+H.path
# NEB calculation. The image that has to climb is manually chosen
cat > asymmetric_H2+H.in << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'restart'
string_method = 'neb',
nstep_path = 20,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 8,
k_max = 0.3D0,
k_min = 0.2D0,
path_thr = 0.05D0,
CI_scheme = "manual"
/
CLIMBING_IMAGES
5
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "asymmetric_H2+H"
outdir = "$TMP_DIR",
pseudo_dir = "$PSEUDO_DIR",
/
&SYSTEM
ibrav = 0,
nat = 3,
ntyp = 1,
ecutwfc = 20.0D0,
ecutrho = 100.0D0,
nspin = 2,
starting_magnetization = 0.5D0,
occupations = "smearing",
degauss = 0.03D0,
/
&ELECTRONS
conv_thr = 1.D-8,
mixing_beta = 0.3D0,
/
&IONS
/
ATOMIC_SPECIES
H 1.00794 HUSPBE.RRKJ3
K_POINTS { gamma }
CELL_PARAMETERS { bohr }
12.00000 0.00000 0.00000
0.00000 5.00000 0.00000
0.00000 0.00000 5.00000
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { bohr }
H -4.56670009 0.00000000 0.00000000 1 0 0
H 0.00000000 0.00000000 0.00000000 0 0 0
H 1.55776676 0.00000000 0.00000000 1 0 0
LAST_IMAGE
ATOMIC_POSITIONS { bohr }
H -1.55776676 0.00000000 0.00000000
H 0.00000000 0.00000000 0.00000000
H 4.56670009 0.00000000 0.00000000
END_POSITIONS
END_ENGINE_INPUT
END
EOF
$ECHO " running Born-Oppenheimer NEB calculation for asymmetric H2+H => H+H2...\c"
$NEB_COMMAND -inp asymmetric_H2+H.in > asymmetric_H2+H.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
