mirror of https://gitlab.com/QEF/q-e.git
188 lines
4.7 KiB
Bash
Executable File
188 lines
4.7 KiB
Bash
Executable File
#!/bin/sh
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# run from directory where this script is
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cd `dirname $0`
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EXAMPLE_DIR=`pwd`
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# check whether echo has the -e option
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if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
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$ECHO
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$ECHO "$EXAMPLE_DIR : starting"
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$ECHO
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$ECHO "This example shows how to use cp.x in combination with external ionic force fields during the molecular dynamics"
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$ECHO "simulation of SiH4."
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="cp.x"
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PSEUDO_LIST="Si.pbe-hgh.UPF H.pbe-hgh.UPF"
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$ECHO
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$ECHO " executables directory: $BIN_DIR"
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$ECHO " pseudo directory: $PSEUDO_DIR"
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$ECHO " temporary directory: $TMP_DIR"
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$ECHO " checking that needed directories and files exist...\c"
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# check for directories
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for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
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if test ! -d $DIR ; then
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$ECHO
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$ECHO "ERROR: $DIR not existent or not a directory"
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$ECHO "Aborting"
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exit 1
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fi
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done
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for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
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if test ! -d $DIR ; then
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mkdir $DIR
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fi
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done
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cd $EXAMPLE_DIR/results
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# check for executables
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for FILE in $BIN_LIST ; do
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if test ! -x $BIN_DIR/$FILE ; then
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$ECHO
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$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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# check for pseudopotentials
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for FILE in $PSEUDO_LIST ; do
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if test ! -r $PSEUDO_DIR/$FILE ; then
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$ECHO
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$ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
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$WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
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fi
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if test $? != 0; then
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$ECHO
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$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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$ECHO " done"
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# how to run executables
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FPMD_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running cp.x as: $FPMD_COMMAND"
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$ECHO
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/cp*
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$ECHO " done"
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# molecular dynamics calculation
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cat > SiH4.inp1 << EOF
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&control
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title = 'SiH4' ,
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calculation = 'cp' ,
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restart_mode = 'from_scratch' ,
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outdir = '$TMP_DIR/',
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pseudo_dir = '$PSEUDO_DIR/',,
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prefix = 'SiH4' ,
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/
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&system
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ibrav = 0 ,
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celldm(1) = 15.0 ,
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nat = 5 ,
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ntyp = 2 ,
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ecutwfc = 20 ,
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ecutrho = 80 ,
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/
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&electrons
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electron_dynamics = 'cg',
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/
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&ions
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ion_dynamics = 'none',
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/
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CELL_PARAMETERS alat
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1.00000000 0.000000000 0.000000000
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0.000000000 1.00000000 0.000000000
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0.000000000 0.000000000 1.00000000
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ATOMIC_SPECIES
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Si 28.08600 Si.pbe-hgh.UPF
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H 1.00000 H.pbe-hgh.UPF
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ATOMIC_POSITIONS bohr
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Si 0.94486306644282E+01 0.94486306644282E+01 0.94486306644282E+01
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H 0.11193736563321E+02 0.11193736698874E+02 0.11073795138710E+02
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H 0.94486306644282E+01 0.94486306644282E+01 0.66094450422239E+01
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H 0.70648871385200E+01 0.10088581790695E+02 0.11073795138710E+02
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H 0.10088581849053E+02 0.70648872790557E+01 0.11073795138710E+02
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EOF
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$ECHO " running the calculation with fixed ions...\c"
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$FPMD_COMMAND < SiH4.inp1 > SiH4.out1
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check_failure $?
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$ECHO " done"
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# molecular dynamics calculation
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cat > SiH4.inp2 << EOF
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&control
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title = 'SiH4' ,
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calculation = 'cp' ,
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restart_mode = 'restart' ,
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iprint = 10,
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isave = 100,
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dt = 3.0d0,
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nstep = 3000,
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prefix = 'SiH4',
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pseudo_dir='$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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/
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&system
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ibrav = 0 ,
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celldm(1) = 15 ,
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nat = 5 ,
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ntyp = 2 ,
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ecutwfc = 20 ,
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ecutrho = 80 ,
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nextffield = 2,
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/
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&electrons
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emass = 10.d0,
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emass_cutoff = 2.5d0,
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electron_dynamics = 'verlet',
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/
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&ions
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ion_dynamics = 'verlet',
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ion_temperature = 'nose',
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fnosep = 5 ,
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/
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CELL_PARAMETERS alat
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1.00000000 0.000000000 0.000000000
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0.000000000 1.00000000 0.000000000
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0.000000000 0.000000000 1.00000000
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ATOMIC_SPECIES
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Si 28.08600 Si.pbe-hgh.UPF
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H 1.00000 H.pbe-hgh.UPF
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ATOMIC_POSITIONS bohr
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Si 0.94486306644282E+01 0.94486306644282E+01 0.94486306644282E+01
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H 0.11193736563321E+02 0.11193736698874E+02 0.11073795138710E+02
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H 0.94486306644282E+01 0.94486306644282E+01 0.66094450422239E+01
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H 0.70648871385200E+01 0.10088581790695E+02 0.11073795138710E+02
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H 0.10088581849053E+02 0.70648872790557E+01 0.11073795138710E+02
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EOF
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cat > extffield.dat << EOF
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1 11
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3 0 6.5 0.0005 300
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1 11
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3 1 11.2 -0.0005 300
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EOF
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$ECHO " running the calculation with ionic dynamics...\c"
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$FPMD_COMMAND < SiH4.inp2 > SiH4.out2
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cp $TMP_DIR/SiH4.extffield .
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check_failure $?
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$ECHO " done"
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$ECHO
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$ECHO "$EXAMPLE_DIR : done"
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