mirror of https://gitlab.com/QEF/q-e.git
246 lines
6.5 KiB
Bash
Executable File
246 lines
6.5 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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$ECHO
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$ECHO "$EXAMPLE_DIR : starting"
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$ECHO
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$ECHO "This example will calculate the final state contribution for a Rh011 slab"
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="pw.x"
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PSEUDO_LIST="Rh.pbe-rrkjus_lb.UPF Rhs.pbe-rrkjus_lb.UPF"
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$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
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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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PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running pw.x as: $PW_COMMAND"
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$ECHO
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#
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# In this run the atom with the core-excited PP is the bulk atom (bulk is
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# intended as the atom in the middle of the slab). This calculation will
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# define the energy_GS of the reference atom
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#
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cat > rh011bulk.scf.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Rh011bulk',
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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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nat=5, ntyp=2,
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ibrav=0, celldm(1)=10.31510000,
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ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
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/
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&electrons
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mixing_beta = 0.3
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conv_thr = 1.0d-6
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/
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CELL_PARAMETERS alat
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1.00000000 0.00000000 0.00000000
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0.00000000 1.41421400 0.00000000
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0.00000000 0.00000000 2.50000000
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ATOMIC_SPECIES
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Rh 1.0 Rh.pbe-rrkjus_lb.UPF
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Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
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ATOMIC_POSITIONS (alat)
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Rh 0.25000000 0.35000000 0.50000000
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Rh 0.00000000 0.00000000 0.25000000
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Rhs 0.25000000 0.35000000 0.00000000 ! Bulk atom core-excited
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Rh 0.00000000 0.00000000 -0.25000000
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Rh 0.25000000 0.35000000 -0.50000000
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K_POINTS {gamma}
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EOF
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$ECHO
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$ECHO " running pw.x for Rh011_[bulk-excited] slab...\c"
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$PW_COMMAND < rh011bulk.scf.in > rh011bulk.scf.out
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check_failure $?
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$ECHO " done"
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#
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# Now we run a calculation exciting everytime one single atom we want to study.
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# The first calculation is for the surface atom.
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#
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cat > rh011surf.scf.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Rh011surf',
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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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nat=5, ntyp=2,
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ibrav=0, celldm(1)=10.31510000,
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ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
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/
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&electrons
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mixing_beta = 0.3
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conv_thr = 1.0d-6
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/
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CELL_PARAMETERS alat
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1.00000000 0.00000000 0.00000000
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0.00000000 1.41421400 0.00000000
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0.00000000 0.00000000 2.50000000
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ATOMIC_SPECIES
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Rh 1.0 Rh.pbe-rrkjus_lb.UPF
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Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
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ATOMIC_POSITIONS (alat)
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Rhs 0.25000000 0.35000000 0.50000000 ! Surface atom core-excited
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Rh 0.00000000 0.00000000 0.25000000
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Rh 0.25000000 0.35000000 0.00000000
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Rh 0.00000000 0.00000000 -0.25000000
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Rh 0.25000000 0.35000000 -0.50000000
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K_POINTS {gamma}
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EOF
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$ECHO
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$ECHO " running pw.x for Rh011_[surface-excited] slab...\c"
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$PW_COMMAND < rh011surf.scf.in > rh011surf.scf.out
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check_failure $?
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$ECHO " done"
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#
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# Now another simulation for the atom in the first layer under the surface.
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#
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cat > rh011layer1.scf.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Rh011lay1',
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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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nat=5, ntyp=2,
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ibrav=0, celldm(1)=10.31510000,
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ecutwfc = 25, occupations='smearing', degauss = 0.03, smearing='mv',
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/
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&electrons
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mixing_beta = 0.3
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conv_thr = 1.0d-6
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/
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CELL_PARAMETERS alat
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1.00000000 0.00000000 0.00000000
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0.00000000 1.41421400 0.00000000
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0.00000000 0.00000000 2.50000000
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ATOMIC_SPECIES
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Rh 1.0 Rh.pbe-rrkjus_lb.UPF
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Rhs 1.0 Rhs.pbe-rrkjus_lb.UPF
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ATOMIC_POSITIONS (alat)
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Rh 0.25000000 0.35000000 0.50000000
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Rhs 0.00000000 0.00000000 0.25000000 ! Layer1 atom core-excited
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Rh 0.25000000 0.35000000 0.00000000
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Rh 0.00000000 0.00000000 -0.25000000
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Rh 0.25000000 0.35000000 -0.50000000
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K_POINTS {gamma}
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EOF
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$ECHO
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$ECHO " running pw.x for Rh011_[layer(-1)-excited] slab...\c"
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$PW_COMMAND < rh011layer1.scf.in > rh011layer1.scf.out
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check_failure $?
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$ECHO " done"
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#
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# Extract data and write results
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#
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enbulk=`cat rh011bulk.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
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ensurf=`cat rh011surf.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
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enlayer1=`cat rh011layer1.scf.out | grep -e ! | egrep -o "([+-])?[0-9]+(\.[0-9]+)?"`
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clssurfry=$(echo "scale=5; ($enbulk)-($ensurf)" | bc)
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clssurfev=$(echo "scale=5; (($enbulk)-($ensurf))*13.6" | bc)
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clslay1ry=$(echo "scale=5; ($enbulk)-($enlayer1)" | bc)
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clslay1ev=$(echo "scale=5; (($enbulk)-($enlayer1))*13.6" | bc)
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$ECHO "" > final-state.txt
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$ECHO "GS energy in the bulk configuration: $enbulk (Ry)" >> final-state.txt
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$ECHO "GS energy in the surface configuration: $ensurf (Ry)" >> final-state.txt
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$ECHO "GS energy in the layer(-1) configuration: $enlayer1 (Ry)" >> final-state.txt
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$ECHO "" >> final-state.txt
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$ECHO "------------------------------------------" >> final-state.txt
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$ECHO "FS shift for the surface atom: $clssurfev (eV)" >> final-state.txt
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$ECHO "FS shift for the layer(-1) atom: $clslay1ev (eV)" >> final-state.txt
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$ECHO
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$ECHO " Results written in results/final-state.txt !"
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$ECHO
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/Rh011????.*
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$ECHO
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$ECHO "$EXAMPLE_DIR: done"
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