mirror of https://gitlab.com/QEF/q-e.git
424 lines
9.8 KiB
Bash
Executable File
424 lines
9.8 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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$ECHO "This example shows how to use PostProc codes to project the DOS on molecular orbitals."
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="pw.x projwfc.x molecularpdos.x"
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PSEUDO_LIST="H_US.van"
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$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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$ECHO "Aborting"
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exit 1
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fi
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done
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# check for gnuplot
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GP_COMMAND=`which gnuplot 2>/dev/null`
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if [ "$GP_COMMAND" = "" ]; then
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$ECHO
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$ECHO "gnuplot not in PATH"
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$ECHO "Results will not be plotted"
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fi
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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 $PARA_POSTFIX"
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PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
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MOLECULARPDOS_COMMAND="$PARA_PREFIX $BIN_DIR/molecularpdos.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running pw.x as: $PW_COMMAND"
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$ECHO " running projwfc.x as: $PROJWFC_COMMAND"
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$ECHO " running molecularpdos.x as: $MOLECULARPDOS_COMMAND"
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$ECHO " running gnuplot as: $GP_COMMAND"
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$ECHO
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# to spin or not to spin?
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nspin=1
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#nspin="2, tot_magnetization=0"
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# how many kpoints to test k-resolved DOS?
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nk=20
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# self-consistent calculation for H chain and H2 molecule
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cat <<EOF > chainH2.scf.in
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&CONTROL
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calculation = "scf",
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prefix = "chainH2",
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tstress = .false.,
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tprnfor = .false.,
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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 = 6,
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celldm(1) = 7.d0
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celldm(3) = 2.0d0
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nat = 12,
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ntyp = 1,
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ecutwfc = 20.0,
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nbnd = 20
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nspin = $nspin
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occupations = 'smearing'
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smearing = 'mv'
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degauss = 0.01d0
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/
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&ELECTRONS
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/
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ATOMIC_SPECIES
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H 1.00 H_US.van
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ATOMIC_POSITIONS crystal
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H 0.0 0.0 0.0
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H 0.0 0.0 0.1
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H 0.0 0.0 0.2
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H 0.0 0.0 0.3
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H 0.0 0.0 0.4
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H 0.0 0.0 0.5
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H 0.0 0.0 0.6
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H 0.0 0.0 0.7
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H 0.0 0.0 0.8
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H 0.0 0.0 0.9
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H 0.35 0.35 0.445
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H 0.35 0.35 0.555
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K_POINTS
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4
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0.0000000 0.0000000 0.0312500 0.2500000
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0.0000000 0.0000000 0.0937500 0.2500000
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0.0000000 0.0000000 0.1562500 0.2500000
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0.0000000 0.0000000 0.2187500 0.2500000
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EOF
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$ECHO " running the scf calculation for H-chain with H2-molecule...\c"
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$PW_COMMAND < chainH2.scf.in > chainH2.scf.out
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check_failure $?
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$ECHO " done"
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# self-consistent calculation for the H2 molecule
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cat <<EOF > H2.scf.in
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&CONTROL
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calculation = "scf",
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prefix = "H2",
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tstress = .false.,
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tprnfor = .false.,
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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 = 6,
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celldm(1) = 7.d0
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celldm(3) = 2.0d0
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nat = 2,
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ntyp = 1,
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ecutwfc = 20.0,
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nspin = $nspin
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occupations = 'smearing'
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smearing = 'mv'
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degauss = 0.01d0
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/
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&ELECTRONS
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/
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ATOMIC_SPECIES
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H 1.00 H_US.van
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ATOMIC_POSITIONS crystal
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H 0.35 0.35 0.445
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H 0.35 0.35 0.555
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K_POINTS
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4
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0.0000000 0.0000000 0.0312500 0.2500000
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0.0000000 0.0000000 0.0937500 0.2500000
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0.0000000 0.0000000 0.1562500 0.2500000
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0.0000000 0.0000000 0.2187500 0.2500000
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EOF
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$ECHO " running the scf calculation for the H2 molecule ${l0}...\c"
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$PW_COMMAND < H2.scf.in > H2.scf.out
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check_failure $?
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$ECHO " done"
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# projwfc calculation for the H2 molecule with H-chain and alone
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for prefix in chainH2 H2; do
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cat <<EOF > $prefix.projwfc.in
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&PROJWFC
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outdir='$TMP_DIR/'
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prefix = '$prefix'
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ngauss = 0
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degauss = 0.01470
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deltae = 0.05
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/
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EOF
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$ECHO " running the projwfc calculation for $prefix...\c"
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$PROJWFC_COMMAND < $prefix.projwfc.in > $prefix.projwfc.out
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check_failure $?
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$ECHO " done"
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$ECHO " copying atomic_proj.xml file to $prefix.atomic_proj.xml"
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cp -p $TMP_DIR/$prefix.save/atomic_proj.xml $prefix.atomic_proj.xml
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done
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# project the DOS on the molecular orbitals of the H2 molecule
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cat <<EOF > chainH2_onto_H2.in
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&INPUTMOPDOS
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xmlfile_full='chainH2.atomic_proj.xml'
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i_atmwfc_beg_full=11,
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i_atmwfc_end_full=12,
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i_bnd_beg_full=1,
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i_bnd_end_full=20,
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xmlfile_part='H2.atomic_proj.xml'
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i_atmwfc_beg_part=1,
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i_atmwfc_end_part=2,
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i_bnd_beg_part=1,
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i_bnd_end_part=2,
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fileout ='chainH2_onto_H2'
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ngauss=0,
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degauss=0.01470,
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DeltaE=0.05,
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kresolveddos=.false.
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/
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EOF
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$ECHO " running the molecular orbital projection of the DOS...\c"
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$MOLECULARPDOS_COMMAND < chainH2_onto_H2.in > chainH2_onto_H2.out
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check_failure $?
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$ECHO " done"
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# now with DOS k-resolved with nk+1 k-points
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# bands calculation for H chain and H2 molecule
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cat <<EOF > chainH2.bands.in
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&CONTROL
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calculation = "bands",
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prefix = "chainH2",
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tstress = .false.,
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tprnfor = .false.,
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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 = 6,
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celldm(1) = 7.d0
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celldm(3) = 2.0d0
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nat = 12,
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ntyp = 1,
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ecutwfc = 20.0,
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nbnd = 20
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nspin = $nspin
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occupations = 'smearing'
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smearing = 'mv'
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degauss = 0.01d0
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/
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&ELECTRONS
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conv_thr_init = 1.d-6
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/
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ATOMIC_SPECIES
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H 1.00 H_US.van
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ATOMIC_POSITIONS crystal
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H 0.0 0.0 0.0
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H 0.0 0.0 0.1
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H 0.0 0.0 0.2
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H 0.0 0.0 0.3
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H 0.0 0.0 0.4
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H 0.0 0.0 0.5
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H 0.0 0.0 0.6
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H 0.0 0.0 0.7
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H 0.0 0.0 0.8
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H 0.0 0.0 0.9
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H 0.35 0.35 0.445
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H 0.35 0.35 0.555
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K_POINTS crystal_b
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2
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0.0 0.0 0.0 $nk
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0.0 0.0 0.5 0
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EOF
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$ECHO " running the bands calculation for H-chain with H2-molecule...\c"
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$PW_COMMAND < chainH2.bands.in > chainH2.bands.out
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check_failure $?
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$ECHO " done"
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# bands calculation for the H2 molecule
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cat <<EOF > H2.bands.in
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&CONTROL
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calculation = "bands",
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prefix = "H2",
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tstress = .false.,
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tprnfor = .false.,
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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 = 6,
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celldm(1) = 7.d0
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celldm(3) = 2.0d0
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nat = 2,
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ntyp = 1,
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ecutwfc = 20.0,
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nspin = $nspin
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occupations = 'smearing'
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smearing = 'mv'
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degauss = 0.01d0
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/
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&ELECTRONS
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conv_thr_init = 1.d-6
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/
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ATOMIC_SPECIES
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H 1.00 H_US.van
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ATOMIC_POSITIONS crystal
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H 0.35 0.35 0.445
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H 0.35 0.35 0.555
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K_POINTS crystal_b
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2
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0.0 0.0 0.0 $nk
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0.0 0.0 0.5 0
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EOF
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$ECHO " running the bands calculation for the H2 molecule ${l0}...\c"
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$PW_COMMAND < H2.bands.in > H2.bands.out
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check_failure $?
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$ECHO " done"
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# projwfc calculation for the H2 molecule with H-chain and alone
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for prefix in chainH2 H2; do
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cat <<EOF > $prefix.k.projwfc.in
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&PROJWFC
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outdir='$TMP_DIR/'
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prefix = '$prefix'
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ngauss = 0
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degauss = 0.01470
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deltae = 0.05
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kresolveddos = .true.
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filpdos = '$prefix.k'
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/
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EOF
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$ECHO " running the k-resolved projwfc calculation for $prefix...\c"
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$PROJWFC_COMMAND < $prefix.k.projwfc.in > $prefix.k.projwfc.out
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check_failure $?
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$ECHO " done"
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$ECHO " copying atomic_proj.xml file to $prefix.k.atomic_proj.xml"
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cp -p $TMP_DIR/$prefix.save/atomic_proj.xml $prefix.k.atomic_proj.xml
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done
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# project the DOS on the molecular orbitals of the H2 molecule
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cat <<EOF > chainH2_onto_H2.k.in
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&INPUTMOPDOS
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xmlfile_full='chainH2.k.atomic_proj.xml'
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i_atmwfc_beg_full=11,
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i_atmwfc_end_full=12,
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i_bnd_beg_full=1,
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i_bnd_end_full=20,
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xmlfile_part='H2.k.atomic_proj.xml'
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i_atmwfc_beg_part=1,
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i_atmwfc_end_part=2,
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i_bnd_beg_part=1,
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i_bnd_end_part=2,
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fileout ='chainH2_onto_H2.k'
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ngauss=0,
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degauss=0.01470,
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DeltaE=0.05,
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kresolveddos=.true.
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/
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EOF
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$ECHO " running the molecular orbital projection of the DOS...\c"
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$MOLECULARPDOS_COMMAND < chainH2_onto_H2.k.in > chainH2_onto_H2.k.out
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check_failure $?
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$ECHO " done"
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#
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# if gnuplot was found, the results are plotted
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#
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if [ "$GP_COMMAND" = "" ]; then
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break
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else
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cat > gnuplot.tmp <<EOF
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#!$GP_COMMAND
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#
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set term post color solid enh
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set out 'project_chainH2_onto_H2.ps'
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set xlabel "Energy (eV)"
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set ylabel "DOS (states/eV)"
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ef=`awk '/Fermi/{printf $(NF-1)}' chainH2.scf.out`
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set xra [-15:5]
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set yzeroaxis
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set style data lines
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set origin 0,0
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set size 1,1
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set multiplot
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set origin 0,1./2
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set size 0.5,1./2
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plot 'chainH2_onto_H2.mopdos_tot' u (\$1-ef):2 lc 3 t "total H_2-projected DOS"
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set origin 0,0./2
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set size 0.5,1./2
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plot "<awk '(\$1==1)' chainH2_onto_H2.mopdos" u (\$2-ef):3 t "bonding H_2 orbital", "<awk '(\$1==2)' chainH2_onto_H2.mopdos" u (\$2-ef):3 t "anti-bonding H_2 orbital"
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set origin 0.5,0
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set size 0.5,1
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#set ytics 0.5
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set ylabel "k_z (crystal)"
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scaledos=20
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set key title "K-resolved"
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plot "<awk '(\$2==1)' chainH2_onto_H2.k.mopdos" u (\$3-ef):((\$1-1)/$nk*0.5+\$4/scaledos) t "bonding H_2 orbital", "<awk '(\$2==2)' chainH2_onto_H2.k.mopdos" u (\$3-ef):((\$1-1)/$nk*0.5+\$4/scaledos) t "anti-bonding H_2 orbital"
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unset multiplot
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EOF
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$ECHO
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$ECHO " plotting molecular orbital projected DOS ...\c"
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$GP_COMMAND < gnuplot.tmp
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$ECHO " done"
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#rm gnuplot.tmp
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fi
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/*H2.*
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$ECHO
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$ECHO "$EXAMPLE_DIR: done"
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