mirror of https://gitlab.com/QEF/q-e.git
Added script for the SiO2 (alpha-quartz) example using Ultrasoft
pseudopotentials. The example calculate Si K-edge XAS in alpha-quartz using ultrasoft pseudopotentials. Restart is also tested in the script. Christos Gougoussis and Matteo Calandra git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5586 c92efa57-630b-4861-b058-cf58834340f0
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calandra
parent
8ca5b718cb
commit
c494e8a7de
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#!/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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# function to test the exit status of a job
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. ../check_failure.sh
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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="Si_PBE_USPP.UPF O_PBE_USPP.UPF"
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PSEUDO_DIR="$EXAMPLE_DIR/pseudo"
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TMP_DIR="$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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# 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 "# SiO2 #"
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$ECHO "# Calculation of K-edge XAS without #"
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$ECHO "# a core-hole in the final state #"
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$ECHO "# #"
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$ECHO "# The parameters of this run are not #"
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$ECHO "# converged. To obtain converged #"
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$ECHO "# parameters see : #"
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$ECHO "# C. Gougoussis, M.Calandra, #"
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$ECHO "# A. Seitsonen, F. Mauri #"
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$ECHO "# arXiv:0906.0897 #"
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$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/upf2plotcore.sh $PSEUDO_DIR/Si_PBE_USPP.UPF > ./Si.wfc
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$ECHO " done"
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$ECHO "#"
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$ECHO "# self-consistent calculation for SiO2."
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$ECHO "# Ultrasoft pseudopotentials are being used "
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$ECHO "#"
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cat > SiO2.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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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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prefix='SiO2',
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verbosity = 'high',
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wf_collect=.true.,
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&end
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&system
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ibrav = 4 ,
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celldm(1)=9.28630318961333,
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celldm(3)=1.10010,
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nat = 9 ,
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ntyp = 3 ,
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nspin=1,
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ecutwfc = 20.0,
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ecutrho = 150.0,
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nbnd=30,
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smearing='mp',
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occupations='smearing',
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degauss=0.03,
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&end
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&electrons
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diagonalization='david',
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conv_thr = 1.d-9,
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mixing_mode = 'plain',
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mixing_beta = 0.3,
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&end
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ATOMIC_SPECIES
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Sih 28.086 Si_PBE_USPP.UPF
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Si 28.086 Si_PBE_USPP.UPF
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O 15.9994 O_PBE_USPP.UPF
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ATOMIC_POSITIONS crystal
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Sih 0.47000000000000 0.000000000000 0.00000000000000
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Si 0.00000000000000 0.47000000000000 0.6666666666666666
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Si -0.47000000000000 -0.47000000000000 0.333333333333333
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O 0.4131000000000000 0.267700000000000 0.11890000000000
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O 0.267700000000000 0.4131000000000000 .54776666666666666666
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O -0.267700000000000 0.1454000000000000 .78556666666666666666
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O -0.4131000000000000 -0.1454000000000000 .21443333333333333333
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O -0.1454000000000000 -0.4131000000000000 .45223333333333333333
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O 0.1454000000000000 -0.267700000000000 -0.11890000000000
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K_POINTS automatic
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2 2 2 0 0 0
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EOF
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$ECHO " running pw.x for SiO2 ...\c"
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$PW_COMMAND < SiO2.scf.in > SiO2.scf.out
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check_failure $?
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$ECHO " done"
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$ECHO "#"
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$ECHO "# xanes calculations : Si K-edge"
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$ECHO "# ultrasoft pseudopotentials are being used"
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$ECHO "# cutting occupied states "
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$ECHO "#"
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$ECHO "# x-ray absorption spectrum calculation"
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$ECHO "# dipolar part"
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$ECHO "#"
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$ECHO "# epsilon in the plane direction"
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cat > SiO2.xspectra_dip_plane.in << EOF
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&input_xspectra
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calculation='xanes_dipole'
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prefix='SiO2',
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outdir='$TMP_DIR/',
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xonly_plot=.false.,
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xniter=2000,
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xcheck_conv=50,
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xepsilon(1)=1.0,
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xepsilon(2)=1.0,
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xepsilon(3)=0.0,
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xiabs=1,
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x_save_file='SiO2.xspectra_dip_plane.sav',
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xread_wf=.false.,
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ef_r=0.60294618180436781,
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xerror=0.001,
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wf_collect=.true.,
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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=100.0,
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terminator=.true.,
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cut_occ_states=.true.,
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&end
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&pseudos
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filecore='Si.wfc',
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r_paw(1)=2.4,
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&end
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&cut_occ
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cut_desmooth=0.1,
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&end
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3 3 3 0 0 0
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < SiO2.xspectra_dip_plane.in > SiO2.xspectra_dip_plane.out
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check_failure $?
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mv xanes.dat SiO2.xspectra_dip_plane.dat
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$ECHO " done"
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$ECHO "#"
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$ECHO "# epsilon in the c axis direction"
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cat > SiO2.xspectra_dip_c.in << EOF
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&input_xspectra
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calculation='xanes_dipole'
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prefix='SiO2',
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outdir='$TMP_DIR/',
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xonly_plot=.false.,
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xniter=2000,
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xcheck_conv=50,
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xepsilon(1)=0.0,
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xepsilon(2)=0.0,
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xepsilon(3)=1.0,
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xiabs=1,
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x_save_file='SiO2.xspectra_dip_c.sav',
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xread_wf=.false.,
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ef_r=0.60294618180436781,
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xerror=0.001,
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wf_collect=.true.,
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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=100.0,
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terminator=.true.,
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cut_occ_states=.true.,
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&end
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&pseudos
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filecore='Si.wfc',
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r_paw(1)=2.4,
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&end
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&cut_occ
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cut_desmooth=0.1,
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&end
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3 3 3 0 0 0
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < SiO2.xspectra_dip_c.in > SiO2.xspectra_dip_c.out
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check_failure $?
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mv xanes.dat SiO2.xspectra_dip_c.dat
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$ECHO " done"
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$ECHO "#"
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$ECHO "# example of the restart mode"
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$ECHO "# a time limit is put is the first calculation"
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$ECHO "# so that it is not finished at the end of the time"
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$ECHO "# then one can restart the calculation of the coefficients"
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$ECHO "# of the continued fraction"
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$ECHO "#"
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$ECHO "# calculation 1 : not finished"
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cat > SiO2.xspectra_dip_restart_1.in << EOF
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&input_xspectra
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calculation='xanes_dipole'
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prefix='SiO2',
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outdir='$TMP_DIR/',
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xonly_plot=.false.,
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xniter=2000,
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xcheck_conv=50,
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xepsilon(1)=0.0,
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xepsilon(2)=0.0,
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xepsilon(3)=1.0,
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xiabs=1,
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x_save_file='SiO2.xspectra_dip_restart_1.sav',
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xread_wf=.false.,
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ef_r=0.60294618180436781,
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xerror=0.001,
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wf_collect=.true.,
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time_limit=10,
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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=100.0,
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terminator=.true.,
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cut_occ_states=.true.,
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&end
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&pseudos
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filecore='Si.wfc',
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r_paw(1)=2.4,
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&end
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&cut_occ
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cut_desmooth=0.1,
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&end
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3 3 3 0 0 0
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < SiO2.xspectra_dip_restart_1.in > SiO2.xspectra_dip_restart_1.out
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check_failure $?
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$ECHO " done"
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$ECHO "#"
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$ECHO "# calculation 2 : finishing the first calculation"
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$ECHO "# the result should be identical to SiO2.xspectra_dip_c.dat"
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$ECHO "# copy SiO2.xspectra_dip_restart_1.sav to SiO2.xspectra_dip_restart_2.sav"
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cp SiO2.xspectra_dip_restart_1.sav SiO2.xspectra_dip_restart_2.sav
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cat > SiO2.xspectra_dip_restart_2.in << EOF
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&input_xspectra
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calculation='xanes_dipole'
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prefix='SiO2',
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outdir='$TMP_DIR/',
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xonly_plot=.false.,
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xniter=2000,
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xcheck_conv=50,
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xepsilon(1)=0.0,
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xepsilon(2)=0.0,
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xepsilon(3)=1.0,
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xiabs=1,
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x_save_file='SiO2.xspectra_dip_restart_2.sav',
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xread_wf=.false.,
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ef_r=0.60294618180436781,
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xerror=0.001,
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wf_collect=.true.,
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restart_mode='restart',
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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=100.0,
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terminator=.true.,
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cut_occ_states=.true.,
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&end
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&pseudos
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filecore='Si.wfc',
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r_paw(1)=2.4,
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&end
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&cut_occ
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cut_desmooth=0.1,
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&end
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3 3 3 0 0 0
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EOF
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$ECHO " running xspectra.x ...\c"
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$X_COMMAND < SiO2.xspectra_dip_restart_2.in > SiO2.xspectra_dip_restart_2.out
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check_failure $?
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mv xanes.dat SiO2.xspectra_dip_restart_2.dat
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$ECHO " done"
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$ECHO "# SiO2.xspectra_dip_restart_1.sav is not complete"
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$ECHO "# SiO2.xspectra_dip_restart_2.sav should be complete"
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