mirror of https://gitlab.com/QEF/q-e.git
312 lines
8.7 KiB
Bash
Executable File
312 lines
8.7 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 to perform molecular dynamics"
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$ECHO "simulation of SiO2."
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="cp.x"
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PSEUDO_LIST="Si.pz-vbc.UPF O.pz-rrkjus.UPF"
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$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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CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running cp.x as: $CP_COMMAND"
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$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 > sio2.cp.start.in << EOF
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&control
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calculation='cp',
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restart_mode='from_scratch',
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nstep=20, iprint=20, isave=20,
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dt=5.0,
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ndr=90, ndw=91,
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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=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
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nat=18, ntyp=2, nbnd=48, nspin=1,
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ecutwfc=20.0, ecutrho=150.0,
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nr1b=16, nr2b=16, nr3b=16,
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qcutz=150., q2sigma=2.0, ecfixed=16.0,
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/
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&electrons
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electron_dynamics='damp', electron_damping=0.2,
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startingwfc='random', ampre=0.01,
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emass=700., emass_cutoff=3.,
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/
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&ions
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ion_dynamics='none',
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ion_radius(1)=1.0, ion_radius(2)=1.0,
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/
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ATOMIC_SPECIES
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O 16.00 O.pz-rrkjus.UPF
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Si 28.00 Si.pz-vbc.UPF
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ATOMIC_POSITIONS bohr
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O 3.18829368 14.83237039 1.22882961
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O 7.83231469 6.78704039 1.22882961
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O 2.07443467 5.99537992 4.73758250
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O 6.72031366 14.04231898 4.73758250
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O 3.96307134 11.26989826 7.87860582
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O 8.60802134 3.22295920 7.87860582
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O 3.96307134 4.81915267 9.14625133
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O 8.60802134 12.86448267 9.14625133
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O 3.18736469 1.25668055 5.58029607
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O 7.83324368 9.30201055 5.58029607
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O 2.07536366 10.09206195 2.07358613
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O 6.71938467 2.04673195 2.07358613
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Si 0.28891589 8.04533000 3.40456284
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Si 4.93386589 0.00000000 3.40456284
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Si 2.13389003 12.27717358 -0.04188031
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Si 6.77884003 4.23184358 -0.04188031
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Si 2.13389003 3.81348642 6.85202747
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Si 6.77884003 11.85881642 6.85202747
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EOF
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$ECHO " running the calculation with fixed ions...\c"
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$CP_COMMAND < sio2.cp.start.in > sio2.cp.start.out
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check_failure $?
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$ECHO " done"
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# molecular dynamics calculation
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cat > sio2.cp.restart.in << EOF
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&control
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calculation='cp',
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restart_mode='reset_counters',
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nstep=50, iprint=50, isave=50,
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dt=15.0,
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ndr=91, ndw=92,
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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=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
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nat=18, ntyp=2, nbnd=48, nspin=1,
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ecutwfc=20.0, ecutrho=150.0,
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nr1b=16, nr2b=16, nr3b=16,
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qcutz=150., q2sigma=2.0, ecfixed=16.0,
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/
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&electrons
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electron_dynamics='damp', electron_damping=0.2,
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emass=700., emass_cutoff=3.,
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/
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&ions
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ion_dynamics='none',
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ion_radius(1)=1.0, ion_radius(2)=1.0,
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/
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ATOMIC_SPECIES
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O 16.00 O.pz-rrkjus.UPF
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Si 28.00 Si.pz-vbc.UPF
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ATOMIC_POSITIONS bohr
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O 3.18829368 14.83237039 1.22882961
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O 7.83231469 6.78704039 1.22882961
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O 2.07443467 5.99537992 4.73758250
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O 6.72031366 14.04231898 4.73758250
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O 3.96307134 11.26989826 7.87860582
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O 8.60802134 3.22295920 7.87860582
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O 3.96307134 4.81915267 9.14625133
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O 8.60802134 12.86448267 9.14625133
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O 3.18736469 1.25668055 5.58029607
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O 7.83324368 9.30201055 5.58029607
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O 2.07536366 10.09206195 2.07358613
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O 6.71938467 2.04673195 2.07358613
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Si 0.28891589 8.04533000 3.40456284
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Si 4.93386589 0.00000000 3.40456284
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Si 2.13389003 12.27717358 -0.04188031
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Si 6.77884003 4.23184358 -0.04188031
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Si 2.13389003 3.81348642 6.85202747
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Si 6.77884003 11.85881642 6.85202747
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EOF
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$ECHO " running the calculation with fixed ions, restart...\c"
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$CP_COMMAND < sio2.cp.restart.in > sio2.cp.restart.out
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check_failure $?
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$ECHO " done"
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# molecular dynamics calculation
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cat > sio2.vc-cp.in << EOF
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&control
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calculation='vc-cp',
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restart_mode='reset_counters',
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nstep=10, iprint=10, isave=10,
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dt=12.0,
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ndr=92, ndw=93,
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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=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
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nat=18, ntyp=2, nbnd=48, nspin=1,
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ecutwfc=20.0, ecutrho=150.0,
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nr1b=16, nr2b=16, nr3b=16,
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qcutz=150., q2sigma=2.0, ecfixed=16.0,
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/
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&electrons
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electron_dynamics='verlet', ortho_max=30,
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emass=700., emass_cutoff=3.,
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/
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&ions
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ion_dynamics='verlet', ion_temperature='nose',
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tempw=300, fnosep=6.6666,
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ion_radius(1)=1.0, ion_radius(2)=1.0,
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/
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&cell
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cell_dynamics='pr', cell_temperature='nose',
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temph=300., fnoseh=8.6071, press=1.0,
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/
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ATOMIC_SPECIES
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O 16.00 O.pz-rrkjus.UPF
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Si 28.00 Si.pz-vbc.UPF
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ATOMIC_POSITIONS bohr
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O 3.18829368 14.83237039 1.22882961
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O 7.83231469 6.78704039 1.22882961
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O 2.07443467 5.99537992 4.73758250
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O 6.72031366 14.04231898 4.73758250
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O 3.96307134 11.26989826 7.87860582
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O 8.60802134 3.22295920 7.87860582
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O 3.96307134 4.81915267 9.14625133
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O 8.60802134 12.86448267 9.14625133
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O 3.18736469 1.25668055 5.58029607
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O 7.83324368 9.30201055 5.58029607
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O 2.07536366 10.09206195 2.07358613
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O 6.71938467 2.04673195 2.07358613
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Si 0.28891589 8.04533000 3.40456284
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Si 4.93386589 0.00000000 3.40456284
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Si 2.13389003 12.27717358 -0.04188031
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Si 6.77884003 4.23184358 -0.04188031
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Si 2.13389003 3.81348642 6.85202747
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Si 6.77884003 11.85881642 6.85202747
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EOF
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$ECHO " running the variable-cell calculation...\c"
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$CP_COMMAND < sio2.vc-cp.in > sio2.vc-cp.out
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check_failure $?
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$ECHO " done"
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# molecular dynamics calculation
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cat > sio2.vc-cp.restart.in << EOF
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&control
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calculation='vc-cp',
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restart_mode='reset_counters',
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nstep=10, iprint=10, isave=10,
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dt=12.0,
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ndr=93, ndw=94,
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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=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
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nat=18, ntyp=2, nbnd=48, nspin=1,
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ecutwfc=20.0, ecutrho=150.0,
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nr1b=16, nr2b=16, nr3b=16,
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qcutz=150., q2sigma=2.0, ecfixed=16.0,
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/
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&electrons
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electron_dynamics='verlet', ortho_max=30,
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emass=700., emass_cutoff=3.,
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/
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&ions
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ion_dynamics='verlet', ion_temperature='nose',
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tempw=300, fnosep=6.6666,
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ion_radius(1)=1.0, ion_radius(2)=1.0,
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/
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&cell
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cell_dynamics='pr', cell_temperature='nose',
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temph=300., fnoseh=8.6071, press=1.0,
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/
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ATOMIC_SPECIES
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O 16.00 O.pz-rrkjus.UPF
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Si 28.00 Si.pz-vbc.UPF
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ATOMIC_POSITIONS bohr
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O 3.18829368 14.83237039 1.22882961
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O 7.83231469 6.78704039 1.22882961
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O 2.07443467 5.99537992 4.73758250
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O 6.72031366 14.04231898 4.73758250
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O 3.96307134 11.26989826 7.87860582
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O 8.60802134 3.22295920 7.87860582
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O 3.96307134 4.81915267 9.14625133
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O 8.60802134 12.86448267 9.14625133
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O 3.18736469 1.25668055 5.58029607
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O 7.83324368 9.30201055 5.58029607
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O 2.07536366 10.09206195 2.07358613
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O 6.71938467 2.04673195 2.07358613
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Si 0.28891589 8.04533000 3.40456284
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Si 4.93386589 0.00000000 3.40456284
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Si 2.13389003 12.27717358 -0.04188031
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Si 6.77884003 4.23184358 -0.04188031
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Si 2.13389003 3.81348642 6.85202747
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Si 6.77884003 11.85881642 6.85202747
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EOF
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$ECHO " running the variable-cell calculation, restart...\c"
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$CP_COMMAND < sio2.vc-cp.restart.in > sio2.vc-cp.restart.out
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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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