mirror of https://gitlab.com/QEF/q-e.git
469 lines
13 KiB
Bash
Executable File
469 lines
13 KiB
Bash
Executable File
#!/bin/sh
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###############################################################################
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##
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## ESM EXAMPLE
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##
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###############################################################################
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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 "run_example_ESM : starting"
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$ECHO
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$ECHO "This example shows how to use ESM to calculate H2O and Al(001)"
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$ECHO "using the three available sets of boundary conditions."
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$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"
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PSEUDO_LIST="Al.pbe-n-van.UPF H.pbe-van_ak.UPF O.pbe-van_ak.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 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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echo $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE
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$WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
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fi
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if test $? != 0; then
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$ECHO
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$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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$ECHO " done"
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# how to run executables
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PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running pw.x as: $PW_COMMAND"
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$ECHO
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# scf calculation for H2O with no ESM
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cat > H2O_pbc.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='H2O_pbc',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 3, ntyp= 2,
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ecutwfc = 25.0, ecutrho = 200.0,
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occupations='smearing', smearing='mp', degauss=0.03,
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assume_isolated = 'esm', esm_bc='pbc'
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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H 1.00794 H.pbe-van_ak.UPF
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O 55.847 O.pbe-van_ak.UPF
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CELL_PARAMETERS angstrom
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10.5835400000 0.0000000000 0.0000000000
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0.0000000000 10.5835400000 0.0000000000
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0.0000000000 0.0000000000 12.7002480000
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ATOMIC_POSITIONS angstrom
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O 0.0000000000 5.2917700000 0.0000000000
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H 0.4565612154 4.5618084292 0.4559209112
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H 0.3877322213 6.1004201907 0.3804697962
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K_POINTS gamma
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EOF
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$ECHO " running the calculation for H2O without ESM...\c"
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$PW_COMMAND < H2O_pbc.in > H2O_pbc.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/H2O_pbc.esm1 $TMP_DIR/H2O_pbc.xml .
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# scf calculation for H2O with ESM bc1 (vacuum-slab-vacuum)
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cat > H2O_bc1.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='H2O_bc1',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 3, ntyp= 2,
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ecutwfc = 25.0, ecutrho = 200.0,
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occupations='smearing', smearing='mp', degauss=0.03,
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assume_isolated = 'esm', esm_bc='bc1'
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/
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&electrons
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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H 1.00794 H.pbe-van_ak.UPF
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O 55.847 O.pbe-van_ak.UPF
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CELL_PARAMETERS angstrom
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10.5835400000 0.0000000000 0.0000000000
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0.0000000000 10.5835400000 0.0000000000
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0.0000000000 0.0000000000 12.7002480000
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ATOMIC_POSITIONS angstrom
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O 0.0000000000 5.2917700000 0.0000000000
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H 0.4565612154 4.5618084292 0.4559209112
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H 0.3877322213 6.1004201907 0.3804697962
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K_POINTS gamma
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EOF
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$ECHO " running the calculation for H2O with ESM bc1 (vacuum-slab-vacuum)...\c"
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$PW_COMMAND < H2O_bc1.in > H2O_bc1.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/H2O_bc1.esm1 $TMP_DIR/H2O_bc1.xml .
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/H2O*
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$ECHO " done"
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# calculation for Al(001) without ESM
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cat > Al001_pbc.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_pbc',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='pbc'
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) without ESM\c"
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$PW_COMMAND < Al001_pbc.in > Al001_pbc.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_pbc.esm1 $TMP_DIR/Al001_pbc.xml .
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# calculation for Al(001) with ESM bc1 (vacuum-slab-vacuum)
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cat > Al001_bc1.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc1',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc1'
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc1 (vacuum-slab-vacuuml)"
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$PW_COMMAND < Al001_bc1.in > Al001_bc1.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_bc1.esm1 $TMP_DIR/Al001_bc1.xml .
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# calculation for Al(001) with ESM bc2 (metal-slab-metal), no field
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cat > Al001_bc2.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc2',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc2'
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc2 (metal-slab-metal)"
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$ECHO " (no applied field)...\c"
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$PW_COMMAND < Al001_bc2.in > Al001_bc2.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_bc2.esm1 $TMP_DIR/Al001_bc2.xml .
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# calculation for Al(001) with ESM bc2 (metal-slab-metal), with field
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cat > Al001_bc2_efield.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc2_efield',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc2', esm_efield=0.00192148511256006
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc2 (metal-slab-metal)"
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$ECHO " with applied electric field...\c"
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$PW_COMMAND < Al001_bc2_efield.in > Al001_bc2_efield.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_bc2_efield.esm1 $TMP_DIR/Al001_bc2_efield.xml .
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# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), uncharged
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cat > Al001_bc3.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc3',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc3'
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
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$ECHO " (neutrally charged)...\c"
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$PW_COMMAND < Al001_bc3.in > Al001_bc3.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_bc3.esm1 $TMP_DIR/Al001_bc3.xml .
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# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), - charged
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cat > Al001_bc3_m002.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc3_m002',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc3'
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tot_charge = -0.02,
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
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$ECHO " (-0.02e charged)...\c"
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$PW_COMMAND < Al001_bc3_m002.in > Al001_bc3_m002.out
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check_failure $?
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$ECHO " done"
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mv $TMP_DIR/Al001_bc3_m002.esm1 $TMP_DIR/Al001_bc3_m002.xml .
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# calculation for Al(001) with ESM bc3 (vacuum-slab-metal), + charged
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cat > Al001_bc3_p002.in << EOF
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&control
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calculation='scf',
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restart_mode='from_scratch',
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prefix='Al001_bc3_p002',
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pseudo_dir = '$PSEUDO_DIR/',
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outdir='$TMP_DIR/',
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tprnfor = .TRUE.
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/
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&system
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ibrav = 0,
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nat= 4, ntyp= 1,
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ecutwfc = 20.0,
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occupations='smearing', smearing='mp', degauss=0.03
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assume_isolated='esm', esm_bc='bc3'
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tot_charge = 0.02,
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/
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&electrons
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diagonalization = 'rmm-davidson'
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mixing_beta = 0.3
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/
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ATOMIC_SPECIES
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Al 26.981538 Al.pbe-n-van.UPF
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CELL_PARAMETERS angstrom
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5.7269000760 0.0000000000 0.0000000000
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0.0000000000 5.7269000760 0.0000000000
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0.0000000000 0.0000000000 11.9999975199
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ATOMIC_POSITIONS angstrom
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Al 0.0000000000 0.0000000000 0.0000000000
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Al 2.8634500380 0.0000000000 0.0000000000
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Al 0.0000000000 2.8634500380 0.0000000000
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Al 2.8634500380 2.8634500380 0.0000000000
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K_POINTS automatic
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6 6 1 1 1 0
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EOF
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$ECHO " running the calculation for Al(001) with ESM bc3 (vacuum-slab-metal)"
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$ECHO " (+0.02e charged)...\c"
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$PW_COMMAND < Al001_bc3_p002.in > Al001_bc3_p002.out
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|
check_failure $?
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|
$ECHO " done"
|
|
mv $TMP_DIR/Al001_bc3_p002.esm1 $TMP_DIR/Al001_bc3_p002.xml .
|
|
|
|
# clean TMP_DIR
|
|
$ECHO " cleaning $TMP_DIR...\c"
|
|
rm -rf $TMP_DIR/
|
|
$ECHO " done"
|
|
|
|
$ECHO
|
|
$ECHO "run_example_ESM: done"
|