mirror of https://gitlab.com/QEF/q-e.git
158 lines
3.5 KiB
Bash
Executable File
158 lines
3.5 KiB
Bash
Executable File
#!/bin/sh
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# run from directory where this script is
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cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
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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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# function to test the exit status of a job
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. ../check_failure.sh
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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 NH3."
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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="N.blyp-mt.UPF H.blyp-vbc.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 "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 $TMP_DIR/*
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$ECHO " done"
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# molecular dynamics calculation
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cat > nh3.in << EOF
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&control
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title = ' Ammonia Molecule ',
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calculation = 'cp',
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restart_mode = 'from_scratch', ! 'restart',
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ndr = 51,
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ndw = 51,
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nstep = 100,
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iprint = 10,
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isave = 100,
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tstress = .TRUE.,
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tprnfor = .TRUE.,
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dt = 5.0d0,
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etot_conv_thr = 1.d-9,
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ekin_conv_thr = 1.d-4,
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prefix = 'nh3_mol'
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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 = 14,
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celldm(1) = 12.0,
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celldm(2) = 1.0,
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celldm(3) = 1.0,
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celldm(4) = 0.0,
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celldm(5) = 0.0,
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celldm(6) = 0.0,
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nat = 4,
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ntyp = 2,
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nbnd = 4,
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ecutwfc = 80.0,
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! ecfixed = 68.0,
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! qcutz = 68.0,
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! q2sigma = 8.0,
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input_dft = 'BLYP'
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/
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&electrons
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emass = 400.d0,
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emass_cutoff = 2.5d0,
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orthogonalization = 'ortho',
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ortho_eps = 5.d-8,
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ortho_max = 15,
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electron_dynamics = 'sd',
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! electron_damping = 0.3,
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electron_velocities = 'zero',
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electron_temperature = 'not_controlled',
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/
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&ions
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ion_dynamics = 'damp',
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ion_damping = 0.2,
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ion_radius(1) = 0.8d0,
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ion_radius(2) = 0.8d0,
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ion_velocities = 'zero',
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ion_temperature = 'not_controlled',
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ion_nstepe = 10
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/
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&cell
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cell_dynamics = 'none',
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cell_velocities = 'zero',
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press = 0.0d0,
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/
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ATOMIC_SPECIES
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N 16.0d0 N.blyp-mt.UPF
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H 1.0d0 H.blyp-vbc.UPF
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ATOMIC_POSITIONS (bohr)
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N 0.0099 0.0099 0.0000
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H 1.9186 -0.2443 -0.2208
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H -0.2305 1.9214 -0.2144
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H -0.1795 -0.1807 1.9236
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EOF
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$ECHO " running the damped dynamics calculation...\c"
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$FPMD_COMMAND < nh3.in > nh3.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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