mirror of https://gitlab.com/QEF/q-e.git
244 lines
6.3 KiB
Bash
Executable File
244 lines
6.3 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 neb.x to calculate the"
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$ECHO "minimum energy path (MEP) of the H atom on Al(001) surface"
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$ECHO "with ESM method."
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$ECHO
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="neb.x"
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PSEUDO_LIST="Al.pbe-n-van.UPF H.pbe-van_ak.UPF"
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$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 $PARA_POSTFIX"
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NEB_COMMAND="$PARA_PREFIX $BIN_DIR/neb.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running Born-Oppenheimer NEB as: $NEB_COMMAND"
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$ECHO
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# NEB calculation for Al001+H with bc3 (vacuum-slab-metal),
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cat > Al001+H_bc3.in << EOF
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BEGIN
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BEGIN_PATH_INPUT
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&PATH
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restart_mode = 'from_scratch',
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string_method = 'neb',
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nstep_path = 50,
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opt_scheme = 'broyden',
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num_of_images = 5,
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/
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END_PATH_INPUT
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BEGIN_ENGINE_INPUT
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&CONTROL
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prefix = 'Al001+H_bc3'
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outdir = '$TMP_DIR/',
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pseudo_dir = '$PSEUDO_DIR/',
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/
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&SYSTEM
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ibrav = 0,
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nat = 5,
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ntyp = 2,
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ecutwfc = 20.0,
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occupations = 'smearing',
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nosym = .TRUE.
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smearing = 'mv',
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degauss = 0.02,
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assume_isolated='esm',
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esm_bc='bc3',
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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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Al 26.981538 Al.pbe-n-van.UPF
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H 1.00794 H.pbe-van_ak.UPF
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BEGIN_POSITIONS
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FIRST_IMAGE
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ATOMIC_POSITIONS bohr
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Al 0.00000000 0.00000000 0.00000000 0 0 0
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Al 5.41113843 0.00000000 0.00000000 0 0 0
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Al 0.00000000 5.41113843 0.00000000 0 0 0
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Al 5.41113843 5.41113843 0.00000000 0 0 0
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H 0.00000000 0.00000000 3.11055367 0 0 1
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LAST_IMAGE
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ATOMIC_POSITIONS bohr
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Al 0.00000000 0.00000000 0.00000000 0 0 0
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Al 5.41113843 0.00000000 0.00000000 0 0 0
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Al 0.00000000 5.41113843 0.00000000 0 0 0
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Al 5.41113843 5.41113843 0.00000000 0 0 0
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H 5.41113843 5.41113843 3.11055367 0 0 1
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END_POSITIONS
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K_POINTS automatic
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6 6 1 1 1 0
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CELL_PARAMETERS bohr
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10.82227686 0.00000000 0.00000000
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0.00000000 10.82227686 0.00000000
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0.00000000 0.00000000 22.67672253
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running NEB calculation for Al001+H with ESM (constant-N)"
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$NEB_COMMAND -inp Al001+H_bc3.in > Al001+H_bc3.out
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check_failure $?
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$ECHO " done"
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# clean current dir & $TMP_DIR
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$ECHO " cleaning ./ & $TMP_DIR...\c"
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rm -rf neb.dat pw_1.in pw_2.in out.1_0 out.2_0
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rm -rf $TMP_DIR/Al001+H_bc3.*
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rm -rf $TMP_DIR/Al001+H_bc3_*/Al001+H_bc3.save
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rm -rf $TMP_DIR/Al001+H_bc3_*/Al001+H_bc3.update
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rm -rf $TMP_DIR/Al001+H_bc3_*/Al001+H_bc3.wfc*
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rm -rf $TMP_DIR/Al001+H_bc3_*/PW.out
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mv $TMP_DIR/Al001+H_bc3_* .
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# NEB calculation for Al001+H with bc3 (vacuum-slab-metal).
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# Constant-N calculation with tot_charge = 0.0215
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cat > Al001+H_bc3_n215.in << EOF
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BEGIN
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BEGIN_PATH_INPUT
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&PATH
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restart_mode = 'from_scratch',
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string_method = 'neb',
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nstep_path = 50,
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opt_scheme = 'broyden',
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num_of_images = 5,
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/
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END_PATH_INPUT
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BEGIN_ENGINE_INPUT
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&CONTROL
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prefix = 'Al001+H_bc3_n215'
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outdir = '$TMP_DIR/',
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pseudo_dir = '$PSEUDO_DIR/',
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/
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&SYSTEM
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ibrav = 0,
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nat = 5,
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ntyp = 2,
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ecutwfc = 20.0,
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occupations = 'smearing',
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nosym = .TRUE.
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smearing = 'mv',
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degauss = 0.02,
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assume_isolated='esm',
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esm_bc='bc3',
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tot_charge = 0.0215,
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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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Al 26.981538 Al.pbe-n-van.UPF
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H 1.00794 H.pbe-van_ak.UPF
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BEGIN_POSITIONS
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FIRST_IMAGE
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ATOMIC_POSITIONS bohr
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Al 0.00000000 0.00000000 0.00000000 0 0 0
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Al 5.41113843 0.00000000 0.00000000 0 0 0
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Al 0.00000000 5.41113843 0.00000000 0 0 0
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Al 5.41113843 5.41113843 0.00000000 0 0 0
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H 0.00000000 0.00000000 3.11055367 0 0 1
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LAST_IMAGE
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ATOMIC_POSITIONS bohr
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Al 0.00000000 0.00000000 0.00000000 0 0 0
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Al 5.41113843 0.00000000 0.00000000 0 0 0
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Al 0.00000000 5.41113843 0.00000000 0 0 0
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Al 5.41113843 5.41113843 0.00000000 0 0 0
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H 5.41113843 5.41113843 3.11055367 0 0 1
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END_POSITIONS
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K_POINTS automatic
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6 6 1 1 1 0
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CELL_PARAMETERS bohr
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10.82227686 0.00000000 0.00000000
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0.00000000 10.82227686 0.00000000
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0.00000000 0.00000000 22.67672253
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running NEB calculation for Al001+H with ESM (constant-N)"
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$NEB_COMMAND -inp Al001+H_bc3_n215.in > Al001+H_bc3_n215.out
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check_failure $?
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$ECHO " done"
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# clean current dir & $TMP_DIR
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$ECHO " cleaning ./ & $TMP_DIR...\c"
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rm -rf neb.dat pw_1.in pw_2.in out.1_0 out.2_0
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rm -rf $TMP_DIR/Al001+H_bc3_n215.*
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rm -rf $TMP_DIR/Al001+H_bc3_n215_*/Al001+H_bc3_n215.save
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rm -rf $TMP_DIR/Al001+H_bc3_n215_*/Al001+H_bc3_n215.update
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rm -rf $TMP_DIR/Al001+H_bc3_n215_*/Al001+H_bc3_n215.wfc*
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rm -rf $TMP_DIR/Al001+H_bc3_n215_*/PW.out
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mv $TMP_DIR/Al001+H_bc3_n215_* .
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/
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$ECHO " done"
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$ECHO
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$ECHO "run_example_ESM: done"
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