mirror of https://gitlab.com/QEF/q-e.git
339 lines
7.0 KiB
Bash
Executable File
339 lines
7.0 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 tests K-edge X-ray absorption spectra calculation"
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$ECHO
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# set the needed environment variables
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. ../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="pw.x xspectra.x "
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PSEUDO_LIST="Ch_PBE_TM_2pj.UPF C_PBE_TM_2pj.UPF "
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PSEUDO_DIR="$EXAMPLE_DIR/pseudo"
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BIN_DIR="$EXAMPLE_DIR/../../bin/"
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TMP_DIR="$EXAMPLE_DIR/results/tmp"
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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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# clean directory results
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rm -rf ./results/*
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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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# clean directory results
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rm -rf ./results/*
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# check for executables
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for FILE in $BIN_LIST ; do
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if test ! -x $BIN_DIR/$FILE ; then
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$ECHO
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$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
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$ECHO "Aborting"
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!exit 1
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fi
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done
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# check for pseudopotentials
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for FILE in $PSEUDO_LIST ; do
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if test ! -r $PSEUDO_DIR/$FILE ; then
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$ECHO
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$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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$ECHO " done"
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# how to run executables
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PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
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X_COMMAND="$PARA_PREFIX $BIN_DIR/xspectra.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 xspectra.x as: $X_COMMAND"
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$ECHO
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$ECHO
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$ECHO "WARNING : All these calculations are underconverged"
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$ECHO " (These are simple quick tests) "
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$ECHO
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$ECHO
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$ECHO
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$ECHO " #################################################"
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$ECHO " # diamond with no core-hole in the final state #"
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$ECHO " #################################################"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/*
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$ECHO " done"
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# extracting core wavefunction
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$ECHO " extracting core wavefunction from pseudo...\c"
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../../../XSpectra/tools/upf2plotcore.sh $PSEUDO_DIR/C_PBE_TM_2pj.UPF > ./C.wfc
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$ECHO " done"
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$ECHO "#"
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$ECHO "# self-consistent calculation . "
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$ECHO "# "
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cat > diamond.scf.in << EOF
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&control
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calculation='scf',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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prefix='diamond',
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/
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&system
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ibrav = 1,
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celldm(1) = 6.740256,
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nat=8,
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ntyp=2,
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nbnd=16,
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ecutwfc=40.0,
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/
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&electrons
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mixing_beta = 0.3,
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/
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ATOMIC_SPECIES
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C_h 12.0 C_PBE_TM_2pj.UPF
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C 12.0 C_PBE_TM_2pj.UPF
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ATOMIC_POSITIONS crystal
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C_h 0.0 0.0 0.0
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C 0.0 0.5 0.5
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C 0.5 0.0 0.5
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C 0.5 0.5 0.0
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C 0.75 0.75 0.25
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C 0.75 0.25 0.75
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C 0.25 0.75 0.75
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C 0.25 0.25 0.25
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K_POINTS automatic
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4 4 4 0 0 0
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EOF
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$ECHO " running pw.x for diamond...\c"
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$PW_COMMAND < diamond.scf.in > diamond.scf.out
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check_failure $?
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$ECHO " done"
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$ECHO " # "
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$ECHO " # x-ray absorption spectrum calculation "
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$ECHO " # including occupied states "
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$ECHO " # "
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cat > diamond.xspectra.in << EOF
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&input_xspectra
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calculation='xanes_dipole',
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prefix='diamond',
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outdir='$TMP_DIR/',
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xniter=1000,
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xcheck_conv=50,
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xepsilon(1)=1.0,
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xepsilon(2)=0.0,
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xepsilon(3)=0.0,
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xiabs=1,
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x_save_file='diamond.xspectra.sav',
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xerror=0.001,
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/
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&plot
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xnepoint=300,
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xgamma=0.8,
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xemin=-10.0,
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xemax=30.0,
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terminator=.true.,
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cut_occ_states=.false.,
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/
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&pseudos
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filecore='C.wfc',
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r_paw(1)=3.2,
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/
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&cut_occ
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/
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4 4 4 1 1 1
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < diamond.xspectra.in > diamond.xspectra.out
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check_failure $?
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mv xanes.dat diamond.xspectra.dat # this is the xanes cross section
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$ECHO " done"
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$ECHO " # "
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$ECHO " # x-ray absorption spectrum calculation "
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$ECHO " # cutting occupied states and reading "
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$ECHO " # save file already calculated in previous"
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$ECHO " # run"
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$ECHO " # "
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cat > diamond.xspectra_replot.in << EOF
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&input_xspectra
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calculation='xanes_dipole',
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prefix='diamond',
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outdir='$TMP_DIR/',
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xonly_plot=.true.,
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xniter=1000,
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xcheck_conv=50,
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xepsilon(1)=1.0,
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xepsilon(2)=0.0,
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xepsilon(3)=0.0,
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xiabs=1,
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x_save_file='diamond.xspectra.sav',
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xerror=0.001,
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/
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&plot
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xnepoint=1000,
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xgamma=0.8,
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xemin=-10.0,
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xemax=30.0,
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terminator=.true.,
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cut_occ_states=.true.,
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/
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&pseudos
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filecore='C.wfc',
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r_paw(1)=3.2,
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/
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&cut_occ
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cut_desmooth=0.1,
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cut_stepl=0.01,
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/
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4 4 4 1 1 1
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < diamond.xspectra_replot.in > diamond.xspectra_replot.out
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check_failure $?
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mv xanes.dat diamond.xspectra_replot.dat # this is the xanes cross section
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$ECHO "done"
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$ECHO " ###########################################"
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$ECHO " #diamond with core hole in the final state#"
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$ECHO " ###########################################"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/*
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$ECHO " done"
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# extracting core wavefunction
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$ECHO " extracting core wavefunction from pseudo...\c"
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../../../XSpectra/tools/upf2plotcore.sh $PSEUDO_DIR/C_PBE_TM_2pj.UPF > ./C.wfc
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$ECHO " done"
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#
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# self-consistent calculation for diamond with core hole.
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#
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cat > diamondh.scf.in << EOF
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&control
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calculation='scf',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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prefix='diamondh',
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/
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&system
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ibrav = 1,
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celldm(1) = 6.740256,
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nat=8,
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ntyp=2,
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nbnd=16,
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tot_charge=+1.0,
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ecutwfc=40.0,
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/
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&electrons
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mixing_beta = 0.3,
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/
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ATOMIC_SPECIES
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C_h 12.0 Ch_PBE_TM_2pj.UPF
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C 12.0 C_PBE_TM_2pj.UPF
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ATOMIC_POSITIONS crystal
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C_h 0.0 0.0 0.0
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C 0.0 0.5 0.5
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C 0.5 0.0 0.5
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C 0.5 0.5 0.0
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C 0.75 0.75 0.25
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C 0.75 0.25 0.75
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C 0.25 0.75 0.75
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C 0.25 0.25 0.25
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K_POINTS automatic
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4 4 4 0 0 0
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EOF
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$ECHO " running pw.x for diamond with core hole...\c"
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$PW_COMMAND < diamondh.scf.in > diamondh.scf.out
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check_failure $?
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$ECHO " done"
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$ECHO "# "
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$ECHO "# x-ray absorption spectrum calculation"
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$ECHO "# cutting occupied states"
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$ECHO "# "
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cat > diamondh.xspectra.in << EOF
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&input_xspectra
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calculation='xanes_dipole',
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prefix='diamondh',
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outdir='$TMP_DIR/',
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xonly_plot=.false.,
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xniter=1000,
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xcheck_conv=10,
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xepsilon(1)=1.0,
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xepsilon(2)=0.0,
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xepsilon(3)=0.0,
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xiabs=1,
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x_save_file='diamondh.xspectra.sav',
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xerror=0.001,
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/
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&plot
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xnepoint=1000,
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xgamma=0.8,
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xemin=-10.0,
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xemax=30.0,
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terminator=.true.,
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cut_occ_states=.true.,
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/
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&pseudos
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filecore='C.wfc',
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r_paw(1)=3.2,
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/
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&cut_occ
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cut_desmooth=0.1,
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cut_stepl=0.01,
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/
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4 4 4 1 1 1
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < diamondh.xspectra.in > diamondh.xspectra.out
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check_failure $?
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mv xanes.dat diamondh.xspectra.dat
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$ECHO " done"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/*
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$ECHO " done"
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