The bash shell script doxygen.sh has been revised.

DOXYGEN=`which doxygen` ;

error=0;

if [[ -d ${LAMMPSSRC} && -d ${LAMMPSDEVELOPERDOC} && -d ${LAMMPSDOC} && -f ${LAMMPSDOCMAKE} && -d ${LAMMPSDOXYGEN} && -f ${LAMMPSDOXYFILE} ]] ;

 then

   cd ${LAMMPSSRC} ;

   make no-all ;

   cd ${LAMMPSBASE} ;

 else

  error=1 ;

  echo "Cannot configure LAMMPS sources - Please run doxygen.sh from the LAMMPS root directory."

   echo "Cannot configure LAMMPS sources - Please run doxygen.sh from the LAMMPS root directory." >&2 ;

   exit 1 ;

 fi ;

if [ ${error} == 0 ] ;

if [ ! -x ${FIG2DEV} ] ;

  then

    if [[ ! -x ${FIG2DEV} ]] ;

      then

        error=1 ;

        echo "${FIG2DEV} not found - Please install ${FIG2DEV} for Your operating system." ;

      fi ;

    echo "${FIG2DEV} not found - Please install ${FIG2DEV} for Your operating system." >&2 ;

    exit 1 ;

  fi ;

if [ ${error} == 0 ] ;

  then

    if [[ -d ${LAMMPSDEVELOPERDOC} ]] ;

if [ -d ${LAMMPSDEVELOPERDOC} ] ;

  then

    ${FIG2DEV} -L png ${LAMMPSDEVELOPERDOC}/classes.fig > tools/doxygen/classes.png ;

    ${FIG2DEV} -L eps ${LAMMPSDEVELOPERDOC}/classes.fig > tools/doxygen/classes.eps ;

  else

        error=1 ;

        echo "LAMMPS developer documentation not found - Please control Your LAMMPS installation." ;

      fi;

    echo "LAMMPS developer documentation not found - Please control Your LAMMPS installation." >&2 ;

    exit 1 ;

  fi ;

if [ ${error} == 0 ] ;

if [ ! -x ${DOXYGEN} ] ;

  then

    if [[ ! -x ${DOXYGEN} ]] ;

      then

        error=1;

        echo "doxygen not found - Please install doxygen for Your operating system." ;

      fi ;

    echo "doxygen not found - Please install doxygen for Your operating system." >&2 ;

    exit 1 ;

  fi ;

if [ ${error} == 0 ] ;

  then

if [[ -d ${LAMMPSSRC} && -f ${LAMMPSDOXYFILE} && -f ${LAMMPSDEVELOPERDOXFILE} ]] ;

  then

    ICS=' ';

    sed -i "s/LAMMPS_VERSION/${version}/g"  ${DEVELOPERDOXFILE} ;

    ${DOXYGEN} ${DOXYFILE} ;

  else

        echo "Doxyfile prototype not found - Please control Your LAMMPS installation." ;

      fi ;

    echo "Doxyfile prototype not found - Please control Your LAMMPS installation." >&2 ;

    exit 1 ;

  fi ;

if [ ${error} == 0 ] ;

  then

if [[ -d ${LAMMPSDOC} && -f ${LAMMPSDOCMAKE} ]] ;

  then

    cd ${LAMMPSDOC} ;

        if [ -d ${LAMMPSDOCTMP} ] ;

         then

          rm -vrf ${LAMMPSDOCTMP} ;

         fi ;

    for d in ${LAMMPSDOCTMP} ;

      do

        rm -vrf $d;

      done ;

    make clean ;

    make html ;

    make pdf ;

    cd ${LAMMPSBASE} ;

    echo "${LAMMPSDOC} exists." ;

  else

      error=1 ;

      echo "Cannot build LAMMPS native documentation - Please run doxygen.sh from the LAMMPS root directory." ;

    fi ;

    echo "Cannot build LAMMPS native documentation - Please run doxygen.sh from the LAMMPS root directory."i >&2 ;

    exit 1 ;

  fi ;

if [ ${error} == 0 ] ;

  then

    if [[ ${error} == 0 && -d ${LAMMPSDOCHTML} ]] ;

if [ -d ${LAMMPSDOCHTML} ] ;

  then

    if [ -d ${LAMMPSDOXYGENDOCMANUAL} ] ;

      then

    cp -av ${LAMMPSDOC}/*.pdf ${LAMMPSDOXYGENDOCMANUAL} ;

    echo "${LAMMPSDOXYGENDOCMANUAL} copied." ;

  else

          error=1 ;

          echo "Cannot include LAMMPS native documentation into the doxygen documentation - Please run doxygen.sh from the LAMMPS root directory." ;

    fi ;

    echo "Cannot include LAMMPS native documentation into the doxygen documentation - Please run doxygen.sh from the LAMMPS root directory." >&2 ;

    exit 1 ;

  fi ;