mirror of https://gitlab.com/QEF/q-e.git
473 lines
12 KiB
Bash
Executable File
473 lines
12 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 a calculation of STM maps."
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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 pp.x plotrho.x projwfc.x sumpdos.x"
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PSEUDO_LIST="Al.pz-vbc.UPF As.pz-bhs.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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$ECHO "Aborting"
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exit 1
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fi
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done
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# check for gnuplot
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GP_COMMAND=`which gnuplot 2>/dev/null`
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if [ "$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 $PARA_POSTFIX"
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PP_COMMAND="$PARA_PREFIX $BIN_DIR/pp.x $PARA_POSTFIX"
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PLOTRHO_COMMAND="$BIN_DIR/plotrho.x"
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PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
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SUMPDOS_COMMAND="$BIN_DIR/sumpdos.x"
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$ECHO
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$ECHO " running pw.x as: $PW_COMMAND"
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$ECHO " running pp.x as: $PP_COMMAND"
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$ECHO " running plotrho.x as: $PLOTRHO_COMMAND"
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$ECHO " running projwfc.x as: $PROJWFC_COMMAND"
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$ECHO " running sumpdos.x as: $SUMPDOS_COMMAND"
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$ECHO " running gnuplot as: $GP_COMMAND"
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$ECHO
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# self-consistent calculation
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cat > AlAs110re.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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title='AlAs 110 surface slab, relaxed (central plane fixed)'
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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prefix='AlAs110'
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/
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&system
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ibrav= 8, celldm(1) =7.424621202, celldm(2)=1.414213576,
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celldm(3)= 6.00000,
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nat= 14, ntyp= 2,
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ecutwfc =14.0,
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/
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&electrons
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mixing_mode = 'plain'
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mixing_beta = 0.7
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conv_thr = 1.0d-6
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/
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ATOMIC_SPECIES
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Al 26.98 Al.pz-vbc.UPF
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As 74.92 As.pz-bhs.UPF
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ATOMIC_POSITIONS alat
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As 0.000000000 -0.044777195 -0.058158722
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Al 0.500000000 0.251460333 0.113525468
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As 0.500000000 0.712279009 0.504183885
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Al 0.000000000 1.067633546 0.480460620
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As 0.000000000 -0.003937059 0.995826731
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Al 0.500000000 0.351400965 1.004220212
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As 0.000000000 -0.003937059 2.004173269
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Al 0.500000000 0.351400965 1.995779788
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As 0.500000000 0.712279009 2.495816115
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Al 0.000000000 1.067633546 2.519539380
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As 0.000000000 -0.044777195 3.058158722
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Al 0.500000000 0.251460333 2.886474532
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As 0.500000000 0.707106800 1.500000000
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Al 0.000000000 1.060660200 1.500000000
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K_POINTS {automatic}
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6 2 1 0 0 0
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EOF
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$ECHO " running the scf calculation...\c"
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$PW_COMMAND < AlAs110re.scf.in > AlAs110re.scf.out
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check_failure $?
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$ECHO " done"
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cat > AlAs110re.nonscf.in << EOF
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&control
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calculation = 'nscf'
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restart_mode='from_scratch',
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title='AlAs 110 surface slab, relaxed (central plane fixed)'
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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prefix='AlAs110'
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/
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&system
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ibrav= 8, celldm(1) =7.424621202, celldm(2)=1.414213576,
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celldm(3)= 6.00000,
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nat= 14, ntyp= 2,
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occupations='smearing', smearing='gaussian', degauss=0.01, nbnd=34,
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ecutwfc =14.0,
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/
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&electrons
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mixing_mode = 'plain'
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mixing_beta = 0.7
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conv_thr = 1.0d-6
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/
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ATOMIC_SPECIES
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Al 26.98 Al.pz-vbc.UPF
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As 74.92 As.pz-bhs.UPF
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ATOMIC_POSITIONS alat
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As 0.000000000 -0.044777195 -0.058158722
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Al 0.500000000 0.251460333 0.113525468
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As 0.500000000 0.712279009 0.504183885
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Al 0.000000000 1.067633546 0.480460620
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As 0.000000000 -0.003937059 0.995826731
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Al 0.500000000 0.351400965 1.004220212
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As 0.000000000 -0.003937059 2.004173269
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Al 0.500000000 0.351400965 1.995779788
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As 0.500000000 0.712279009 2.495816115
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Al 0.000000000 1.067633546 2.519539380
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As 0.000000000 -0.044777195 3.058158722
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Al 0.500000000 0.251460333 2.886474532
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As 0.500000000 0.707106800 1.500000000
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Al 0.000000000 1.060660200 1.500000000
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K_POINTS {automatic}
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12 4 1 0 0 0
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EOF
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$ECHO " running the non-scf calculation...\c"
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$PW_COMMAND < AlAs110re.nonscf.in > AlAs110re.nonscf.out
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check_failure $?
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$ECHO " done"
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# post-processing for stm images (sample bias given in Ry!)
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cat > AlAs110.pp_stm-.in << EOF
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&inputpp
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prefix = 'AlAs110'
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outdir='$TMP_DIR/',
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filplot = 'AlAsresm-1.0'
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sample_bias=-0.0735d0,
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plot_num= 5
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/
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&plot
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nfile=1
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filepp(1)='AlAsresm-1.0'
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weight(1)=1.0
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iflag=2
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output_format=2
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e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
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e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
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x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25
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nx=36 ,ny=56
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fileout='AlAs110-1.0'
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/
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EOF
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$ECHO
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$ECHO " running the post-processing phase, negative bias...\c"
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$PP_COMMAND < AlAs110.pp_stm-.in > AlAs110.pp_stm-.out
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check_failure $?
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$ECHO " done"
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# run plotrho to do the figure
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cat > AlAs110.plotrho-.in << EOF
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AlAs110-1.0
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AlAs110-1.0eV.ps
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n
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0.00005 0.0078 8
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EOF
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$ECHO " running plotrho on negative bias data...\c"
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$PLOTRHO_COMMAND < AlAs110.plotrho-.in > AlAs110.plotrho-.out
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check_failure $?
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$ECHO " done"
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# post-processing for stm images (negative bias, constant current)
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cat > AlAs110.pp_isostm-.in << EOF
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&inputpp
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/
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&plot
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nfile=1
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filepp(1)='AlAsresm-1.0'
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weight(1)=1.0
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iflag=2
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output_format=7
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fileout='AlAs110.pp_isostm-.dat'
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e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
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e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
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nx=150, ny=150
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isostm_flag=.true.
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isovalue=0.00005
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heightmin=0.4
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heightmax=0.75
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direction=1
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/
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EOF
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$ECHO
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$ECHO " STM image, negative bias and constant current...\c"
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$PP_COMMAND < AlAs110.pp_isostm-.in > AlAs110.pp_isostm-.out
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check_failure $?
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$ECHO " done"
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# run gnuplot to do the figure
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if [ "$GP_COMMAND" = "" ]; then
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break
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else
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cat > gnuplot.tmp <<EOF
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set term postscript enhanced color solid lw 3 24
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set output 'AlAs110-1.0eV.isoplot.ps'
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set xlabel "x (bohr)"
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set ylabel "y (bohr)"
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set pm3d map
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set size ratio -1
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set palette rgb 21,22,23
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set tics out
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unset key
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splot [0:51.972][0:52.500] 'AlAs110.pp_isostm-.dat'
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EOF
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$ECHO
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$ECHO " plotting results ...\c"
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$GP_COMMAND < gnuplot.tmp
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$ECHO " done"
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rm gnuplot.tmp
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fi
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# post-processing for stm images (as before, but positive bias)
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cat > AlAs110.pp_stm+.in << EOF
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&inputpp
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prefix = 'AlAs110'
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outdir='$TMP_DIR/',
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filplot = 'AlAsresm+1.0'
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sample_bias=0.0735d0,
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plot_num= 5
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/
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&plot
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nfile=1
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filepp(1)='AlAsresm+1.0'
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weight(1)=1.0
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iflag=2
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output_format=2
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e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
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e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
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x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25
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nx=36 ,ny=56
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fileout='AlAs110+1.0'
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/
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EOF
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$ECHO " running the post-processing phase, positive bias...\c"
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$PP_COMMAND < AlAs110.pp_stm+.in > AlAs110.pp_stm+.out
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check_failure $?
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$ECHO " done"
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# plotrho
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cat > AlAs110.plotrho+.in << EOF
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AlAs110+1.0
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AlAs110+1.0eV.ps
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n
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0.00002 0.0021 8
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EOF
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$ECHO " running plotrho on positive bias data...\c"
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$PLOTRHO_COMMAND < AlAs110.plotrho+.in > AlAs110.plotrho+.out
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check_failure $?
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$ECHO " done"
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# post-processing for stm images (positive bias, constant current)
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cat > AlAs110.pp_isostm+.in << EOF
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&inputpp
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/
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&plot
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nfile=1
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filepp(1)='AlAsresm+1.0'
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weight(1)=1.0
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iflag=2
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output_format=7
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fileout='AlAs110.pp_isostm+.dat'
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e1(1)=7.0, e1(2)=0.0, e1(3)=0.0
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e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0
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nx=150, ny=150
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isostm_flag=.true.
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isovalue=0.00005
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heightmin=0.4
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heightmax=0.75
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direction=1
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/
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EOF
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$ECHO
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$ECHO " STM image, positive bias and constant current...\c"
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$PP_COMMAND < AlAs110.pp_isostm+.in > AlAs110.pp_isostm+.out
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check_failure $?
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$ECHO " done"
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# run gnuplot to do the figure
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if [ "$GP_COMMAND" = "" ]; then
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break
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else
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cat > gnuplot.tmp <<EOF
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set term postscript enhanced color solid lw 3 24
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set output 'AlAs110+1.0eV.isoplot.ps'
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set xlabel "x (bohr)"
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set ylabel "y (bohr)"
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set pm3d map
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set size ratio -1
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set palette rgb 21,22,23
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set tics out
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unset key
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splot [0:51.972][0:52.500] 'AlAs110.pp_isostm+.dat'
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EOF
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$ECHO
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$ECHO " plotting results ...\c"
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$GP_COMMAND < gnuplot.tmp
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$ECHO " done"
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rm gnuplot.tmp
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fi
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# Projection of the DOS on volumes (boxes)
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cat > AlAs110.box.projwfc.in << EOF
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&projwfc
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prefix = 'AlAs110'
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outdir='$TMP_DIR/',
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ngauss=0
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degauss=0.01
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DeltaE=0.02
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tdosinboxes=.true.
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plotboxes=.true.
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n_proj_boxes=8
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!! Boxes centered on the first vacuum layer:
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!! 1) above the surface Al
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irmin(1,1)= 0, irmax(1,1)= 2, irmin(2,1)= 0, irmax(2,1)= 2, irmin(3,1)=63, irmax(3,1)=65,
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!! 2) above the surface As
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irmin(1,2)= 9, irmax(1,2)=11, irmin(2,2)= 5, irmax(2,2)= 7, irmin(3,2)=63, irmax(3,2)=65,
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!! 3) above the 2nd layer Al
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irmin(1,3)= 9, irmax(1,3)=11, irmin(2,3)=14, irmax(2,3)=16, irmin(3,3)=63, irmax(3,3)=65,
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!! 4) as large as the surface unit cell
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irmin(1,4)= 1, irmax(1,4)=18, irmin(2,4)= 1, irmax(2,4)=27, irmin(3,4)=63, irmax(3,4)=65,
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!! Same as above, centered on the second vacuum layer:
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irmin(1,5)= 0, irmax(1,5)= 2, irmin(2,5)= 0, irmax(2,5)= 2, irmin(3,5)=72, irmax(3,5)=74,
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irmin(1,6)= 9, irmax(1,6)=11, irmin(2,6)= 5, irmax(2,6)= 7, irmin(3,6)=72, irmax(3,6)=74,
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irmin(1,7)= 9, irmax(1,7)=11, irmin(2,7)=14, irmax(2,7)=16, irmin(3,7)=72, irmax(3,7)=74,
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irmin(1,8)= 1, irmax(1,8)=18, irmin(2,8)= 1, irmax(2,8)=27, irmin(3,8)=72, irmax(3,8)=74,
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/
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EOF
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$ECHO
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$ECHO " running local DOS calculation...\c"
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$PROJWFC_COMMAND < AlAs110.box.projwfc.in > AlAs110.box.projwfc.out
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check_failure $?
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$ECHO " done"
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# Projection of the DOS on atomic wavefunctions
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cat > AlAs110.projwfc.in << EOF
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&projwfc
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prefix = 'AlAs110'
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outdir='$TMP_DIR/',
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ngauss=0
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degauss=0.01
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DeltaE=0.02
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tdosinboxes=.false.
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/
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EOF
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$ECHO
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$ECHO " running projected DOS calculation...\c"
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$PROJWFC_COMMAND < AlAs110.projwfc.in > AlAs110.projwfc.out
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check_failure $?
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$ECHO " done"
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$ECHO
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$ECHO " summing the atomic PDOS...\c"
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$SUMPDOS_COMMAND AlAs110.pdos_atm\#10\(Al\)_wfc* > "AlAs110.pdos_atm#10(Al)" 2> /dev/null
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$SUMPDOS_COMMAND AlAs110.pdos_atm\#11\(As\)_wfc* > "AlAs110.pdos_atm#11(As)" 2> /dev/null
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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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eFermi=`grep "Fermi" AlAs110re.nonscf.out | cut -d \ -f 14`
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cat > gnuplot.tmp <<EOF
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set term postscript enhanced color solid lw 3 24
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set output 'AlAs110.box.projwfc.ps'
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ef=$eFermi
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set xlabel "Energy - E_F (eV)"
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set ylabel "Local DOS (states/eV)"
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set style data lines
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set key top left Left reverse
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set border 31 lw 0.2
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set title "Projected DOS"
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plot \\
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'./AlAs110.pdos_atm#10(Al)' u (\$1-ef):2 t "Surface Al" ,\\
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'./AlAs110.pdos_atm#11(As)' u (\$1-ef):2 t "Surface As"
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set title "Local DOS centered in the first vacuum layer"
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plot \\
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'./AlAs110.ldos_boxes' u (\$1-ef):4 t "Above Al" ,\\
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'./AlAs110.ldos_boxes' u (\$1-ef):5 t "Above As" ,\\
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'./AlAs110.ldos_boxes' u (\$1-ef):(\$7/54) t "Surface average"
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|
set title "Local DOS centered in the second vacuum layer"
|
|
plot \\
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|
'./AlAs110.ldos_boxes' u (\$1-ef):8 t "Above Al" ,\\
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|
'./AlAs110.ldos_boxes' u (\$1-ef):9 t "Above As" ,\\
|
|
'./AlAs110.ldos_boxes' u (\$1-ef):(\$11/54) t "Surface average"
|
|
EOF
|
|
$ECHO
|
|
$ECHO " plotting DOS results ...\c"
|
|
$GP_COMMAND < gnuplot.tmp
|
|
$ECHO " done"
|
|
rm gnuplot.tmp
|
|
fi
|
|
|
|
$ECHO
|
|
$ECHO " To visualize a volume in which the DOS is integrated, execute:"
|
|
$ECHO " xcrysden --xsf results/AlAs110.box#1.xsf"
|
|
$ECHO " and plot the isosurface corresponding to isovalue 0.5"
|
|
|
|
$ECHO
|
|
# clean TMP_DIR
|
|
$ECHO " cleaning $TMP_DIR...\c"
|
|
rm -rf $TMP_DIR/AlAs110.*
|
|
$ECHO
|
|
$ECHO " $EXAMPLE_DIR: done"
|