mirror of https://gitlab.com/QEF/q-e.git
513 lines
8.8 KiB
Bash
Executable File
513 lines
8.8 KiB
Bash
Executable File
#!/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 cp.x to calculate Wannier functions and"
|
|
$ECHO "to perform dynamics with an external electric field."
|
|
|
|
# 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
|
|
$ECHO " checking that needed directories and files exist...\c"
|
|
|
|
# check for directories
|
|
for DIR in "$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
|
|
$ECHO " done"
|
|
|
|
# how to run executables
|
|
CP_COMMAND="$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"
|
|
|
|
cat > h2o.wannier.xml << EOF
|
|
<?xml version="1.0" encoding="UTF-8"?>
|
|
|
|
|
|
<input calculation="cp-wf" prefix="h2o_mol">
|
|
|
|
<cell type="qecell">
|
|
<qecell ibrav="1" alat="20.0">
|
|
<real rank="1" n1="5">
|
|
0.0 0.0 0.0 0.0 0.0
|
|
</real>
|
|
</qecell>
|
|
</cell>
|
|
|
|
<atomic_species ntyp="2">
|
|
<specie name="O">
|
|
<property name="mass">
|
|
<real>16.D0</real>
|
|
</property>
|
|
<property name="pseudofile">
|
|
<string>O_US.van</string>
|
|
</property>
|
|
</specie>
|
|
<specie name="H">
|
|
<property name="mass">
|
|
<real>2.D0</real>
|
|
</property>
|
|
<property name="pseudofile">
|
|
<string>H_US.van</string>
|
|
</property>
|
|
</specie>
|
|
</atomic_species>
|
|
|
|
<atomic_list units="bohr" nat="3" >
|
|
<atom name="O">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
10.0000 10.0000 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
<atom name="H">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
11.7325 9.6757 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
<atom name="H">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
9.6757 11.7325 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
</atomic_list>
|
|
|
|
|
|
<field name="InputOutput">
|
|
|
|
<parameter name="pseudo_dir">
|
|
<string>
|
|
$PSEUDO_DIR/
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="outdir">
|
|
<string>
|
|
$TMP_DIR/
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="restart_mode">
|
|
<string>
|
|
from_scratch
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="iprint">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
<field name="Numerics">
|
|
|
|
<parameter name="ecutwfc">
|
|
<real>
|
|
25.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="etot_conv_thr">
|
|
<real>
|
|
1.D-16
|
|
</real>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
<field name="CP">
|
|
|
|
<!--nstep, dt e ion_dynamics esistono anche nel PW ma nn sapevo in che field metterli -->
|
|
<parameter name="nstep">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="dt">
|
|
<real>
|
|
4.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="ion_dynamics">
|
|
<string>
|
|
none
|
|
</string>
|
|
</parameter>
|
|
<!-- Da qui in poi esistono solo in CP-->
|
|
<parameter name="isave">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr1b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr2b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr3b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="electron_dynamics">
|
|
<string>
|
|
damp
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="electron_damping">
|
|
<real>
|
|
0.15
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="emass">
|
|
<real>
|
|
350.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="emass_cutoff">
|
|
<real>
|
|
3.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="ortho_eps">
|
|
<real>
|
|
5.D-8
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="ortho_max">
|
|
<integer>
|
|
250
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="ekin_conv_thr">
|
|
<real>
|
|
1.D-16
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="adapt">
|
|
<logical>
|
|
TRUE
|
|
</logical>
|
|
</parameter>
|
|
|
|
<parameter name="nsteps">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
</input>
|
|
EOF
|
|
$ECHO " running the Wannier functions calculation...\c"
|
|
$CP_COMMAND < h2o.wannier.xml > h2o.wannier.out
|
|
check_failure $?
|
|
$ECHO " Wannier functions spreads...\c">> h2o.wannier.out
|
|
$ECHO "">> h2o.wannier.out
|
|
tail -4 $TMP_DIR/h2o_mol.spr >> h2o.wannier.out
|
|
$ECHO " Wannier functions centers...\c">> h2o.wannier.out
|
|
$ECHO "">> h2o.wannier.out
|
|
tail -4 $TMP_DIR/h2o_mol.wfc >> h2o.wannier.out
|
|
$ECHO " done"
|
|
|
|
# calculation with an electric field
|
|
cat > h2o.efield.xml << EOF
|
|
<?xml version="1.0" encoding="UTF-8"?>
|
|
|
|
|
|
<input calculation="cp-wf" prefix="h2o_mol">
|
|
|
|
<cell type="qecell">
|
|
<qecell ibrav="1" alat="20.0">
|
|
<real rank="1" n1="5">
|
|
0.0 0.0 0.0 0.0 0.0
|
|
</real>
|
|
</qecell>
|
|
</cell>
|
|
|
|
<atomic_species ntyp="2">
|
|
<specie name="O">
|
|
<property name="mass">
|
|
<real>16.D0</real>
|
|
</property>
|
|
<property name="pseudofile">
|
|
<string>O_US.van</string>
|
|
</property>
|
|
</specie>
|
|
<specie name="H">
|
|
<property name="mass">
|
|
<real>2.D0</real>
|
|
</property>
|
|
<property name="pseudofile">
|
|
<string>H_US.van</string>
|
|
</property>
|
|
</specie>
|
|
</atomic_species>
|
|
|
|
<atomic_list units="bohr" nat="3" >
|
|
<atom name="O">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
10.0000 10.0000 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
<atom name="H">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
11.7325 9.6757 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
<atom name="H">
|
|
<position>
|
|
<real rank="1" n1="3">
|
|
9.6757 11.7325 10.000
|
|
</real>
|
|
</position>
|
|
</atom>
|
|
</atomic_list>
|
|
|
|
|
|
<field name="InputOutput">
|
|
|
|
<parameter name="pseudo_dir">
|
|
<string>
|
|
$PSEUDO_DIR/
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="outdir">
|
|
<string>
|
|
$TMP_DIR/
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="restart_mode">
|
|
<string>
|
|
reset_counters
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="iprint">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
<field name="Numerics">
|
|
|
|
<parameter name="ecutwfc">
|
|
<real>
|
|
25.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
<field name="CP">
|
|
|
|
<!--nstep, dt e ion_dynamics esistono anche nel PW ma nn sapevo in che field metterli -->
|
|
<parameter name="nstep">
|
|
<integer>
|
|
200
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="dt">
|
|
<real>
|
|
6.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="ion_dynamics">
|
|
<string>
|
|
verlet
|
|
</string>
|
|
</parameter>
|
|
<!-- Da qui in poi esistono solo in CP-->
|
|
<parameter name="isave">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr1b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr2b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="nr3b">
|
|
<integer>
|
|
10
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="electron_dynamics">
|
|
<string>
|
|
verlet
|
|
</string>
|
|
</parameter>
|
|
|
|
<parameter name="emass">
|
|
<real>
|
|
350.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="emass_cutoff">
|
|
<real>
|
|
3.D0
|
|
</real>
|
|
</parameter>
|
|
|
|
|
|
<parameter name="ndw">
|
|
<integer>
|
|
51
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="ortho_eps">
|
|
<real>
|
|
5.D-8
|
|
</real>
|
|
</parameter>
|
|
|
|
<parameter name="ortho_max">
|
|
<integer>
|
|
250
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="wf_efield">
|
|
<logical>
|
|
TRUE
|
|
</logical>
|
|
</parameter>
|
|
|
|
<parameter name="wf_switch">
|
|
<logical>
|
|
TRUE
|
|
</logical>
|
|
</parameter>
|
|
|
|
<parameter name="sw_len">
|
|
<integer>
|
|
100
|
|
</integer>
|
|
</parameter>
|
|
|
|
<parameter name="efz1">
|
|
<real>
|
|
0.5D-2
|
|
</real>
|
|
</parameter>
|
|
|
|
</field>
|
|
|
|
</input>
|
|
EOF
|
|
$ECHO " running the calculation with electric field...\c"
|
|
$CP_COMMAND < h2o.efield.xml > h2o.efield.out
|
|
check_failure $?
|
|
|
|
$ECHO
|
|
$ECHO "$EXAMPLE_DIR: done"
|