mirror of https://gitlab.com/QEF/q-e.git
311 lines
7.8 KiB
Bash
Executable File
311 lines
7.8 KiB
Bash
Executable File
#!/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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$ECHO
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$ECHO "$EXAMPLE_DIR : starting"
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$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 collinear proton transfer reaction:"
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$ECHO " H2+H <==> H+H2, within the Born-Oppenheimer approximation."
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$ECHO
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$ECHO "!!! Beware: neb.x DOES NOT READ FROM STANDARD INPUT"
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$ECHO "!!! run as 'neb.x -inp input_file_name > output_file_name'"
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$ECHO
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="neb.x"
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PSEUDO_LIST="HUSPBE.RRKJ3"
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$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 $PSEUDO_DIR...\c"
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$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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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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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/pwscf*
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$ECHO " done"
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# NEB calculation. Automatic choice of the climbing image.
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cat > H2+H.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 = 20,
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ds = 2.D0,
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opt_scheme = "broyden",
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num_of_images = 7,
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k_max = 0.3D0,
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k_min = 0.2D0,
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CI_scheme = "auto",
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path_thr = 0.1D0,
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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 = "H2+H"
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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 = 3,
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ntyp = 1,
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ecutwfc = 20.0D0,
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ecutrho = 100.0D0,
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nspin = 2,
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starting_magnetization = 0.5D0,
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occupations = "smearing",
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degauss = 0.03D0,
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/
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&ELECTRONS
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conv_thr = 1.D-8,
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mixing_beta = 0.3D0,
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/
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&IONS
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/
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ATOMIC_SPECIES
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H 1.00794 HUSPBE.RRKJ3
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BEGIN_POSITIONS
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FIRST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -4.56670009 0.00000000 0.00000000 1 0 0
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H 0.00000000 0.00000000 0.00000000 0 0 0
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H 1.55776676 0.00000000 0.00000000 1 0 0
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LAST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -1.55776676 0.00000000 0.00000000
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H 0.00000000 0.00000000 0.00000000
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H 4.56670009 0.00000000 0.00000000
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END_POSITIONS
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K_POINTS { gamma }
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CELL_PARAMETERS { bohr }
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12.00000 0.00000 0.00000
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0.00000 5.00000 0.00000
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0.00000 0.00000 5.00000
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running Born-Oppenheimer NEB calculation for H2+H => H+H2...\c"
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$NEB_COMMAND -inp H2+H.in > H2+H.out
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check_failure $?
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$ECHO " done"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/pwscf*
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$ECHO " done"
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# NEB calculation. Climbing image is not used
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cat > symmetric_H2+H.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 = 20,
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ds = 2.D0,
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opt_scheme = "broyden",
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num_of_images = 8,
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k_max = 0.3D0,
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k_min = 0.2D0,
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path_thr = 0.2D0,
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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 = "symmetric_H2+H"
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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 = 3,
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ntyp = 1,
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ecutwfc = 20.0D0,
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ecutrho = 100.0D0,
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nspin = 2,
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starting_magnetization = 0.5D0,
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occupations = "smearing",
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degauss = 0.03D0,
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/
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&ELECTRONS
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conv_thr = 1.D-8,
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mixing_beta = 0.3D0,
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/
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&IONS
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/
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ATOMIC_SPECIES
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H 1.00794 HUSPBE.RRKJ3
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K_POINTS { gamma }
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CELL_PARAMETERS { bohr }
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12.00000 0.00000 0.00000
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0.00000 5.00000 0.00000
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0.00000 0.00000 5.00000
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BEGIN_POSITIONS
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FIRST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -4.56670009 0.00000000 0.00000000 1 0 0
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H 0.00000000 0.00000000 0.00000000 0 0 0
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H 1.55776676 0.00000000 0.00000000 1 0 0
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LAST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -1.55776676 0.00000000 0.00000000
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H 0.00000000 0.00000000 0.00000000
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H 4.56670009 0.00000000 0.00000000
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END_POSITIONS
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running Born-Oppenheimer NEB calculation for symmetric H2+H => H+H2...\c"
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$NEB_COMMAND -inp symmetric_H2+H.in > symmetric_H2+H.out
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check_failure $?
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$ECHO " done"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/pwscf*
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$ECHO " done"
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# the name of the restart file is changed in order to conform to the
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# prefix of the new run
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# the restart file asymmetric_H2+H.neb is modified (second row)
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# since a new simulation (from the old path) is started
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cat symmetric_H2+H.path | \
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awk '{if(NR==2){printf" 0\n"}; if(NR!=2){print}}' > asymmetric_H2+H.path
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# NEB calculation. The image that has to climb is manually chosen
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cat > asymmetric_H2+H.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 = 'restart'
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string_method = 'neb',
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nstep_path = 20,
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ds = 2.D0,
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opt_scheme = "broyden",
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num_of_images = 8,
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k_max = 0.3D0,
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k_min = 0.2D0,
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path_thr = 0.05D0,
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CI_scheme = "manual"
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/
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CLIMBING_IMAGES
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5
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END_PATH_INPUT
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BEGIN_ENGINE_INPUT
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&CONTROL
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prefix = "asymmetric_H2+H"
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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 = 3,
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ntyp = 1,
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ecutwfc = 20.0D0,
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ecutrho = 100.0D0,
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nspin = 2,
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starting_magnetization = 0.5D0,
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occupations = "smearing",
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degauss = 0.03D0,
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/
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&ELECTRONS
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conv_thr = 1.D-8,
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mixing_beta = 0.3D0,
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/
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&IONS
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/
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ATOMIC_SPECIES
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H 1.00794 HUSPBE.RRKJ3
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K_POINTS { gamma }
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CELL_PARAMETERS { bohr }
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12.00000 0.00000 0.00000
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0.00000 5.00000 0.00000
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0.00000 0.00000 5.00000
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BEGIN_POSITIONS
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FIRST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -4.56670009 0.00000000 0.00000000 1 0 0
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H 0.00000000 0.00000000 0.00000000 0 0 0
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H 1.55776676 0.00000000 0.00000000 1 0 0
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LAST_IMAGE
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ATOMIC_POSITIONS { bohr }
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H -1.55776676 0.00000000 0.00000000
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H 0.00000000 0.00000000 0.00000000
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H 4.56670009 0.00000000 0.00000000
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END_POSITIONS
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running Born-Oppenheimer NEB calculation for asymmetric H2+H => H+H2...\c"
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$NEB_COMMAND -inp asymmetric_H2+H.in > asymmetric_H2+H.out
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check_failure $?
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$ECHO " done"
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/pwscf*
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$ECHO " done"
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$ECHO
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$ECHO "$EXAMPLE_DIR: done"
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