#!/bin/sh ############################################################################### ## ## HIGH VERBOSITY EXAMPLE ## ############################################################################### # 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 perform molecular dynamics" $ECHO "in the presence of an electric field described through the" $ECHO "modern theory of the polarization. The example shows how to" $ECHO "calculate high-frequency and static dielectric constants and" $ECHO "Born effective charges." # set the needed environment variables . ../../../environment_variables # required executables and pseudopotentials BIN_LIST="cp.x" PSEUDO_LIST="O.pz-rrkjus.UPF Mg.pz-n-vbc.UPF" $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 $ECHO " done" # how to run executables CP_COMMAND="$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" # molecular dynamics calculation cat > mgo.cp.cg.xml << EOF 0.0 0.0 0.0 0.0 0.0 12.01 O.pz-rrkjus.UPF 0.8d0 24.30 Mg.pz-n-vbc.UPF 0.066300000 0.066300000 0.066300000 4.044300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 4.044300000 0.066300000 0.066300000 8.022300000 4.044300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 12.000300000 0.066300000 8.022300000 0.066300000 4.044300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 4.044300000 0.066300000 8.022300000 8.022300000 4.044300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 12.000300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 4.044300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 12.000300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 4.044300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 12.000300000 0.066300000 0.066300000 4.044300000 4.044300000 4.044300000 4.044300000 4.044300000 0.066300000 8.022300000 0.066300000 4.044300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 4.044300000 12.000300000 4.044300000 0.066300000 15.978300000 0.066300000 4.044300000 15.978300000 0.066300000 8.022300000 4.044300000 4.044300000 12.000300000 4.044300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 12.000300000 12.000300000 4.044300000 8.022300000 15.978300000 0.066300000 12.000300000 15.978300000 8.022300000 0.066300000 4.044300000 12.000300000 4.044300000 4.044300000 12.000300000 0.066300000 8.022300000 8.022300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 4.044300000 12.000300000 12.000300000 0.066300000 15.978300000 8.022300000 4.044300000 15.978300000 8.022300000 8.022300000 4.044300000 12.000300000 12.000300000 4.044300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 12.000300000 12.000300000 12.000300000 8.022300000 15.978300000 8.022300000 12.000300000 15.978300000 $PSEUDO_DIR/ $TMP_DIR/ from_scratch 1 TRUE TRUE random from_input 20.0 160.0 1.d-8 128 1 TRUE 0.0 1 none not_controlled none 1 30 30 30 1000.d0 4.d0 Gram-Schmidt 0.02 TRUE 0.3 250 0.0 1.0 3 EOF $ECHO " running the CG calculation for bulk MgO E_field=0. a.u. ...\c" $CP_COMMAND < mgo.cp.cg.xml > mgo.cp.cg.out check_failure $? $ECHO " done" cat > mgo.cp.cg.efield.xml << EOF 0.0 0.0 0.0 0.0 0.0 12.01 O.pz-rrkjus.UPF 0.8d0 24.30 Mg.pz-n-vbc.UPF 0.066300000 0.066300000 0.066300000 4.044300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 4.044300000 0.066300000 0.066300000 8.022300000 4.044300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 12.000300000 0.066300000 8.022300000 0.066300000 4.044300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 4.044300000 0.066300000 8.022300000 8.022300000 4.044300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 12.000300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 4.044300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 12.000300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 4.044300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 12.000300000 0.066300000 0.066300000 4.044300000 4.044300000 4.044300000 4.044300000 4.044300000 0.066300000 8.022300000 0.066300000 4.044300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 4.044300000 12.000300000 4.044300000 0.066300000 15.978300000 0.066300000 4.044300000 15.978300000 0.066300000 8.022300000 4.044300000 4.044300000 12.000300000 4.044300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 12.000300000 12.000300000 4.044300000 8.022300000 15.978300000 0.066300000 12.000300000 15.978300000 8.022300000 0.066300000 4.044300000 12.000300000 4.044300000 4.044300000 12.000300000 0.066300000 8.022300000 8.022300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 4.044300000 12.000300000 12.000300000 0.066300000 15.978300000 8.022300000 4.044300000 15.978300000 8.022300000 8.022300000 4.044300000 12.000300000 12.000300000 4.044300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 12.000300000 12.000300000 12.000300000 8.022300000 15.978300000 8.022300000 12.000300000 15.978300000 $PSEUDO_DIR/ $TMP_DIR/ restart 1 FALSE TRUE random from_input 20.0 160.0 1.d-8 128 1 TRUE 0.001 1 none not_controlled none 1 30 30 30 1000.d0 4.d0 Gram-Schmidt 0.02 TRUE 0.3 250 0.0 1.0 3 EOF $ECHO " running the CG calculation for bulk MgO E_field=0.001 a.u. ...\c" $CP_COMMAND < mgo.cp.cg.efield.xml > mgo.cp.cg.efield.out check_failure $? $ECHO " done" cat > mgo.cp.damp.efield.xml << EOF 0.0 0.0 0.0 0.0 0.0 1.0 O.pz-rrkjus.UPF 1.0 Mg.pz-n-vbc.UPF 0.066300000 0.066300000 0.066300000 4.044300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 0.066300000 4.044300000 4.044300000 0.066300000 0.066300000 8.022300000 4.044300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 12.000300000 0.066300000 8.022300000 0.066300000 4.044300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 0.066300000 12.000300000 4.044300000 0.066300000 8.022300000 8.022300000 4.044300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 12.000300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 0.066300000 12.000300000 0.066300000 4.044300000 8.022300000 4.044300000 4.044300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 8.022300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 12.000300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 0.066300000 12.000300000 8.022300000 4.044300000 8.022300000 12.000300000 4.044300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 8.022300000 12.000300000 12.000300000 0.066300000 0.066300000 4.044300000 4.044300000 4.044300000 4.044300000 4.044300000 0.066300000 8.022300000 0.066300000 4.044300000 8.022300000 0.066300000 0.066300000 12.000300000 4.044300000 4.044300000 12.000300000 4.044300000 0.066300000 15.978300000 0.066300000 4.044300000 15.978300000 0.066300000 8.022300000 4.044300000 4.044300000 12.000300000 4.044300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 8.022300000 0.066300000 8.022300000 12.000300000 4.044300000 12.000300000 12.000300000 4.044300000 8.022300000 15.978300000 0.066300000 12.000300000 15.978300000 8.022300000 0.066300000 4.044300000 12.000300000 4.044300000 4.044300000 12.000300000 0.066300000 8.022300000 8.022300000 4.044300000 8.022300000 8.022300000 0.066300000 12.000300000 12.000300000 4.044300000 12.000300000 12.000300000 0.066300000 15.978300000 8.022300000 4.044300000 15.978300000 8.022300000 8.022300000 4.044300000 12.000300000 12.000300000 4.044300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 8.022300000 8.022300000 8.022300000 12.000300000 12.000300000 12.000300000 12.000300000 12.000300000 8.022300000 15.978300000 8.022300000 12.000300000 15.978300000 $PSEUDO_DIR/ $TMP_DIR/ restart 100 FALSE TRUE random 20.0 160.0 128 1 TRUE 0.001 20 10.0 verlet none 100 30 30 30 250.d0 3.d0 0.02 0.0 3 damp 30 0.05 EOF $ECHO " running the CP- damped MD calculation for bulk MgO E_field=0.001 a.u. ...\c" $CP_COMMAND < mgo.cp.damp.efield.xml > mgo.cp.damp.efield.out check_failure $? $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR : done"