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quantum-espresso/NEB/examples/example01/run_xml_example

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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 with neb.x -inp input_file_name > output_file_name."
$ECHO
$ECHO "xml format is automatically detected."
# 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 \
http://www.quantum-espresso.org/pseudo/1.3/UPF/$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 $PARA_POSTFIX"
CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO " running Born-Oppenheimer NEB as: $PW_COMMAND"
$ECHO " running cp.x as: $CP_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$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
<?xml version="1.0" encoding="UTF-8"?>
<input calculation="scf" prefix="H2+H">
<cell type="matrix">
<matrix units="bohr">
<real rank="2" n1="3" n2="3">
12.0 0.0 0.0
0.0 5.0 0.0
0.0 0.0 5.0
</real>
</matrix>
</cell>
<atomic_species ntyp="1">
<specie name="H">
<property name="mass">
<real>1.00794 </real>
</property>
<property name="pseudofile">
<string>HUSPBE.RRKJ3</string>
</property>
<property name="starting_magnetization">
<real>0.5</real>
</property>
</specie>
</atomic_species>
BEGIN_POSITIONS
FIRST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
-4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="0" ify="0" ifz="0">
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
LAST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position>
<real rank="1" n1="3">
-1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
END_POSITIONS
<field name="InputOutput">
<parameter name="restart_mode">
<string>
from_scratch
</string>
</parameter>
<parameter name="pseudo_dir">
<string>
$PSEUDO_DIR
</string>
</parameter>
<parameter name="outdir">
<string>
$TMP_DIR/
</string>
</parameter>
</field>
<field name="Numerics">
<parameter name="ecutwfc">
<real>
20.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
100.0
</real>
</parameter>
<parameter name="mixing_beta">
<real>
0.3
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-8
</real>
</parameter>
</field>
<field name="Options">
<parameter name="occupations">
<string>
smearing
</string>
</parameter>
<parameter name="degauss">
<real>
0.01
</real>
</parameter>
</field>
<field name="Fields">
<parameter name="nspin">
<integer>
2
</integer>
</parameter>
</field>
<k_points type="gamma">
</k_points>
</input>
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/*
$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
<?xml version="1.0" encoding="UTF-8"?>
<input calculation="scf" prefix="symmetric_H2+H">
<cell type="matrix">
<matrix units="bohr">
<real rank="2" n1="3" n2="3">
12.0 0.0 0.0
0.0 5.0 0.0
0.0 0.0 5.0
</real>
</matrix>
</cell>
<atomic_species ntyp="1">
<specie name="H">
<property name="mass">
<real>1.00794 </real>
</property>
<property name="pseudofile">
<string>HUSPBE.RRKJ3</string>
</property>
<property name="starting_magnetization">
<real>0.5</real>
</property>
</specie>
</atomic_species>
BEGIN_POSITIONS
FIRST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
-4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="0" ify="0" ifz="0">
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
LAST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position>
<real rank="1" n1="3">
-1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
END_POSITIONS
<field name="InputOutput">
<parameter name="restart_mode">
<string>
from_scratch
</string>
</parameter>
<parameter name="pseudo_dir">
<string>
$PSEUDO_DIR
</string>
</parameter>
<parameter name="outdir">
<string>
$TMP_DIR/
</string>
</parameter>
</field>
<field name="Numerics">
<parameter name="ecutwfc">
<real>
20.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
100.0
</real>
</parameter>
<parameter name="mixing_beta">
<real>
0.3
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-8
</real>
</parameter>
</field>
<field name="Options">
<parameter name="occupations">
<string>
smearing
</string>
</parameter>
<parameter name="degauss">
<real>
0.01
</real>
</parameter>
</field>
<field name="Fields">
<parameter name="nspin">
<integer>
2
</integer>
</parameter>
</field>
<k_points type="gamma">
</k_points>
</input>
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/*
$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
<?xml version="1.0" encoding="UTF-8"?>
<input calculation="scf" prefix="asymmetric_H2+H">
<cell type="matrix">
<matrix units="bohr">
<real rank="2" n1="3" n2="3">
12.0 0.0 0.0
0.0 5.0 0.0
0.0 0.0 5.0
</real>
</matrix>
</cell>
<atomic_species ntyp="1">
<specie name="H">
<property name="mass">
<real>1.00794 </real>
</property>
<property name="pseudofile">
<string>HUSPBE.RRKJ3</string>
</property>
<property name="starting_magnetization">
<real>0.5</real>
</property>
</specie>
</atomic_species>
BEGIN_POSITIONS
FIRST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
-4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="0" ify="0" ifz="0">
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position ifx="1" ify="0" ifz="0">
<real rank="1" n1="3">
1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
LAST_IMAGE
<atomic_list units="bohr" nat="3" >
<atom name="H">
<position>
<real rank="1" n1="3">
-1.55776676 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
0.00000000 0.00000000 0.00000000
</real>
</position>
</atom>
<atom name="H">
<position>
<real rank="1" n1="3">
4.56670009 0.00000000 0.00000000
</real>
</position>
</atom>
</atomic_list>
END_POSITIONS
<field name="InputOutput">
<parameter name="restart_mode">
<string>
from_scratch
</string>
</parameter>
<parameter name="pseudo_dir">
<string>
$PSEUDO_DIR
</string>
</parameter>
<parameter name="outdir">
<string>
$TMP_DIR/
</string>
</parameter>
</field>
<field name="Numerics">
<parameter name="ecutwfc">
<real>
20.0
</real>
</parameter>
<parameter name="ecutrho">
<real>
100.0
</real>
</parameter>
<parameter name="mixing_beta">
<real>
0.3
</real>
</parameter>
<parameter name="conv_thr">
<real>
1.0d-8
</real>
</parameter>
</field>
<field name="Options">
<parameter name="occupations">
<string>
smearing
</string>
</parameter>
<parameter name="degauss">
<real>
0.01
</real>
</parameter>
</field>
<field name="Fields">
<parameter name="nspin">
<integer>
2
</integer>
</parameter>
</field>
<k_points type="gamma">
</k_points>
</input>
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/*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
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