--- trunk/OOPSE-4/configure	2005/03/04 15:29:03	2081
+++ trunk/OOPSE-4/configure	2005/04/13 22:30:22	2190
@@ -312,7 +312,7 @@ ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKA
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROGNAME debug build build_cpu build_vendor build_os host host_cpu host_vendor host_os CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX OOPSE_TEMPLATE_FLAGS EXTRA_CC_FLAG F90 F90FLAGS ac_ct_F90 PREPFLAG PREPDEFFLAG F90LIBS F90_FUNC F90_FUNC_ MOD F90_WORK_FILES_ARG MODDIRFLAG F90MODINCSPEC F90_MODULE_NAMES CPP EGREP LIBOBJS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA LN_S SET_MAKE RANLIB ac_ct_RANLIB YACC LEX LEXLIB LEX_OUTPUT_ROOT AR PS MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI DOXYGEN DOT DOC enable_dot enable_html_docs enable_latex_docs BATEXT MKINSTALLDIRS OOPSE OOPSE_HOME SUBDIRS FFLAGS LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROGNAME debug build build_cpu build_vendor build_os host host_cpu host_vendor host_os CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX OOPSE_TEMPLATE_FLAGS EXTRA_CC_FLAG F90 F90FLAGS ac_ct_F90 PREPFLAG PREPDEFFLAG F90LIBS F90_FUNC F90_FUNC_ MOD F90_WORK_FILES_ARG MODDIRFLAG F90MODINCSPEC F90_MODULE_NAMES CPP EGREP LIBOBJS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA LN_S SET_MAKE RANLIB ac_ct_RANLIB YACC LEX LEXLIB LEX_OUTPUT_ROOT AR PS MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI CXXCPP USE_CGAL CGAL_INC_DIR CGAL_LIB_DIR CGAL_RLIB_DIR CGAL_DEFINES CGAL_CXXFLAGS CGAL_LIBS DOXYGEN DOT DOC enable_dot enable_html_docs enable_latex_docs BATEXT MKINSTALLDIRS OOPSE OOPSE_HOME SUBDIRS FFLAGS LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
@@ -789,6 +789,10 @@ ac_cv_env_CPP_value=$CPP
 ac_env_CPP_value=$CPP
 ac_cv_env_CPP_set=${CPP+set}
 ac_cv_env_CPP_value=$CPP
+ac_env_CXXCPP_set=${CXXCPP+set}
+ac_env_CXXCPP_value=$CXXCPP
+ac_cv_env_CXXCPP_set=${CXXCPP+set}
+ac_cv_env_CXXCPP_value=$CXXCPP
 
 #
 # Report the --help message.
@@ -876,6 +880,7 @@ Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
   --with-mpi=<prefix>     compile with MPI installed in <prefix> [default=no]
+  --with-cgal-makefile=FILE  CGAL makefile that should be used
 
 Some influential environment variables:
   CC          C compiler command
@@ -889,6 +894,7 @@ Some influential environment variables:
   F90         Fortran 90 compiler command
   F90FLAGS    Fortran 90 compiler flags
   CPP         C preprocessor
+  CXXCPP      C++ preprocessor
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -1880,6 +1886,7 @@ ac_configure="$SHELL $ac_aux_dir/configure" # This sho
 
 
 
+
 # set program name
 PROGNAME="oopse"
 
@@ -3539,7 +3546,7 @@ F90FLAGS="$F90FLAGS $ac_verb"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_verb"
 
-(eval echo $as_me:3542: \"$ac_link\") >&5
+(eval echo $as_me:3549: \"$ac_link\") >&5
 ac_f90_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f90_v_output" >&5
 F90FLAGS=$ac_save_F90FLAGS
@@ -3616,7 +3623,7 @@ F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 
-(eval echo $as_me:3619: \"$ac_link\") >&5
+(eval echo $as_me:3626: \"$ac_link\") >&5
 ac_f90_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f90_v_output" >&5
 F90FLAGS=$ac_save_F90FLAGS
@@ -7812,14 +7819,683 @@ echo "${ECHO_T}found $MPI_F90_LIB" >&6
 fi
 echo "$as_me:$LINENO: result: found $MPI_F90_LIB" >&5
 echo "${ECHO_T}found $MPI_F90_LIB" >&6
+
+
+fi
+
+
+
+
+USE_CGAL=no
+cgal_makefile=auto
+
+# Check whether --with-cgal-makefile or --without-cgal-makefile was given.
+if test "${with_cgal_makefile+set}" = set; then
+  withval="$with_cgal_makefile"
+  cgal_makefile="$withval"
+fi;
+
+if test "x$cgal_makefile" != xno; then
+
+  if test "x$cgal_makefile" = xauto -a "x$CGAL_MAKEFILE" != x; then
+    cgal_makefile="$CGAL_MAKEFILE"
+  fi
+
+  echo "cgal_makefile      $cgal_makefile"
+
+  if test -f "$cgal_makefile"; then
+
+    cat >config.tmp.Makefile <<EOF
+include $cgal_makefile
+default:
+	@echo CGAL_OS_COMPILER=\"\${CGAL_OS_COMPILER}\" >config.tmp.cgalvariables
+	@echo CGAL_INCLDIR=\"\${CGAL_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo CGAL_INCLCONFDIR=\"\${CGAL_INCL_CONF_DIR}\" >>config.tmp.cgalvariables
+	@echo CGAL_LIBDIR=\"\${CGAL_LIB_DIR}/\${CGAL_OS_COMPILER}\" >>config.tmp.cgalvariables
+	@echo CGAL_RLIBDIR=\"\${CGAL_LIB_DIR}/\${CGAL_OS_COMPILER}\" >>config.tmp.cgalvariables
+	@echo CGAL_CXXFLAGS=\"\${CGAL_CXXFLAGS}\" >>config.tmp.cgalvariables
+	@echo GMP_INCLDIR=\"\${GMP_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo GMP_LIBDIR=\"\${GMP_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo GMP_RLIBDIR=\"\${GMP_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_INCLDIR=\"\${LEDA_INCL_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_LIBDIR=\"\${LEDA_LIB_DIR}\" >>config.tmp.cgalvariables
+	@echo LEDA_RLIBDIR=\"\${LEDA_LIB_DIR}\" >>config.tmp.cgalvariables
+EOF
+
+    make -s -f config.tmp.Makefile
+    . config.tmp.cgalvariables
+
+    rm -f config.tmp.Makefile config.tmp.cgalvariables
+
+    if test "x$CGAL_INCLDIR" = "x"; then
+      CGAL_INCLDIR=""
+    fi
+
+    if test "x$CGAL_LIBDIR" = "x"; then
+      CGAL_LIBDIR=""
+    fi
+
+    if test "x$CGAL_RLIBDIR" = "x"; then
+      CGAL_RLIBDIR=""
+    fi
+
+    if test "x$LEDA_INCLDIR" = "x"; then
+      LEDA_INCLDIR=""
+    fi
+
+    if test "x$LEDA_LIBDIR" = "x"; then
+      LEDA_LIBDIR=""
+    fi
+
+    if test "x$LEDA_RLIBDIR" = "x"; then
+      LEDA_RLIBDIR=""
+    fi
+
+    if test "x$GMP_INCLDIR" = "x"; then
+      GMP_INCLDIR=""
+    fi
+
+    if test "x$GMP_LIBDIR" = "x"; then
+      GMP_LIBDIR=""
+    fi
+
+    if test "x$GMP_RLIBDIR" = "x"; then
+      GMP_RLIBDIR=""
+    fi
+
+    echo "CGAL_OS_COMPILER   $CGAL_OS_COMPILER"
+    echo "CGAL_INCLDIR       $CGAL_INCLDIR"
+    echo "CGAL_INCLCONFDIR   $CGAL_INCLCONFDIR"
+    echo "CGAL_LIBDIR        $CGAL_LIBDIR"
+    echo "CGAL_CXXFLAGS      $CGAL_CXXFLAGS"
+    echo "LEDA_INCLDIR       $LEDA_INCLDIR"
+    echo "LEDA_LIBDIR        $LEDA_LIBDIR"
+    echo "GMP_INCLDIR        $GMP_INCLDIR"
+    echo "GMP_LIBDIR         $GMP_LIBDIR"
+
+    ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+    save_CXXFLAGS="$CXXFLAGS"
+    CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6
+if test -z "$CXXCPP"; then
+  if test "${ac_cv_prog_CXXCPP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+      # Double quotes because CXXCPP needs to be expanded
+    for CXXCPP in "$CXX -E" "/lib/cpp"
+    do
+      ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
+  # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.$ac_ext
 
+  # OK, works on sane cases.  Now check whether non-existent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
 fi
+if test -z "$ac_cpp_err"; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.$ac_ext
 
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  break
+fi
 
+    done
+    ac_cv_prog_CXXCPP=$CXXCPP
 
+fi
+  CXXCPP=$ac_cv_prog_CXXCPP
+else
+  ac_cv_prog_CXXCPP=$CXXCPP
+fi
+echo "$as_me:$LINENO: result: $CXXCPP" >&5
+echo "${ECHO_T}$CXXCPP" >&6
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
+  # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.$ac_ext
+
+  # OK, works on sane cases.  Now check whether non-existent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  :
+else
+  { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&5
+echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+ac_ext=cc
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
+  echo "$as_me:$LINENO: checking for CGAL/Cartesian.h" >&5
+echo $ECHO_N "checking for CGAL/Cartesian.h... $ECHO_C" >&6
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+echo "$as_me:$LINENO: result: $ac_cv_header_CGAL_Cartesian_h" >&5
+echo "${ECHO_T}$ac_cv_header_CGAL_Cartesian_h" >&6
+else
+  # Is the header compilable?
+echo "$as_me:$LINENO: checking CGAL/Cartesian.h usability" >&5
+echo $ECHO_N "checking CGAL/Cartesian.h usability... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <CGAL/Cartesian.h>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_cxx_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest.$ac_objext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_header_compiler=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6
+
+# Is the header present?
+echo "$as_me:$LINENO: checking CGAL/Cartesian.h presence" >&5
+echo $ECHO_N "checking CGAL/Cartesian.h presence... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <CGAL/Cartesian.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+  (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null; then
+  if test -s conftest.err; then
+    ac_cpp_err=$ac_cxx_preproc_warn_flag
+    ac_cpp_err=$ac_cpp_err$ac_cxx_werror_flag
+  else
+    ac_cpp_err=
+  fi
+else
+  ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+rm -f conftest.err conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: present but cannot be compiled" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: CGAL/Cartesian.h: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: CGAL/Cartesian.h: in the future, the compiler will take precedence" >&2;}
+    (
+      cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to gezelter@nd.edu ##
+## ------------------------------ ##
+_ASBOX
+    ) |
+      sed "s/^/$as_me: WARNING:     /" >&2
+    ;;
+esac
+echo "$as_me:$LINENO: checking for CGAL/Cartesian.h" >&5
+echo $ECHO_N "checking for CGAL/Cartesian.h... $ECHO_C" >&6
+if test "${ac_cv_header_CGAL_Cartesian_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_header_CGAL_Cartesian_h=$ac_header_preproc
+fi
+echo "$as_me:$LINENO: result: $ac_cv_header_CGAL_Cartesian_h" >&5
+echo "${ECHO_T}$ac_cv_header_CGAL_Cartesian_h" >&6
+
+fi
+if test $ac_cv_header_CGAL_Cartesian_h = yes; then
+  cgal=yes
+else
+  cgal=no
+fi
+
+
+    CXXFLAGS="$save_CXXFLAGS"
+
+    if test "x$cgal" = xyes; then
+      echo "$as_me:$LINENO: checking for CGAL version" >&5
+echo $ECHO_N "checking for CGAL version... $ECHO_C" >&6
+      LOCATION=${CGAL_INCLDIR}
+      LOCATION=${LOCATION:-/usr/include}
+      if test -f $LOCATION/CGAL/version.h; then
+        CGAL_VERSION=`grep '#define.*\<CGAL_VERSION\>.*' $LOCATION/CGAL/version.h | sed 's/[^0-9\.]*//g'`
+      else
+        CGAL_VERSION=`grep '#define.*\<CGAL_VERSION\>.*' $LOCATION/CGAL/config.h | sed 's/[^0-9\.]*//g'`
+      fi
+      if echo $CGAL_VERSION | grep -q "^[3456789]"; then
+        echo "$as_me:$LINENO: result: ($CGAL_VERSION) yes" >&5
+echo "${ECHO_T}($CGAL_VERSION) yes" >&6
+      else
+        echo "$as_me:$LINENO: result: ($CGAL_VERSION) no" >&5
+echo "${ECHO_T}($CGAL_VERSION) no" >&6
+        cgal=no
+      fi
+    fi
+
+    if test "x$cgal" = xyes; then
+      CGAL_LIBS="-lCGAL"
+      echo "$as_me:$LINENO: checking whether CGAL uses LEDA" >&5
+echo $ECHO_N "checking whether CGAL uses LEDA... $ECHO_C" >&6
+      if echo $CGAL_CXXFLAGS | grep -q -- -DCGAL_USE_LEDA; then
+        CGAL_USES_LEDA=yes
+        echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+        CGAL_DEFINES="-DCGAL_USE_LEDA -DLEDA_PREFIX"
+      else
+        echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+        CGAL_USES_LEDA=no
+      fi
+
+      echo "$as_me:$LINENO: checking whether CGAL uses GMP" >&5
+echo $ECHO_N "checking whether CGAL uses GMP... $ECHO_C" >&6
+      if echo $CGAL_CXXFLAGS | grep -q -- -DCGAL_USE_GMP; then
+        CGAL_USES_GMP=yes
+        echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+        CGAL_DEFINES="-DCGAL_USE_GMP $CGAL_DEFINES"
+      else
+        echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+        CGAL_USES_GMP=no
+      fi
+
+      CGAL_LIBS="$CGAL_LIBS -lm"
+
+      CGAL_CXXFLAGS="-ftemplate-depth-50"
+
+      echo "CGAL_USES_LEDA     $CGAL_USES_LEDA"
+      echo "CGAL_USES_GMP      $CGAL_USES_GMP"
+      echo "CGAL_INCLDIR       $CGAL_INCLDIR"
+      echo "CGAL_LIBDIR        $CGAL_LIBDIR"
+      echo "CGAL_DEFINES       $CGAL_DEFINES"
+      echo "CGAL_CXXFLAGS      $CGAL_CXXFLAGS"
+      echo "CGAL_LIBS          $CGAL_LIBS"
+    fi
+
+    if test "x$cgal" = xyes; then
+      save_LIBS="$LIBS"
+      LIBS="$LIBS -L$CGAL_LIBDIR"
+      if test "x$CGAL_USES_LEDA" = xyes; then
+        LIBS="-lL $LIBS -L$LEDA_LIBDIR"
+      fi
+      # if test "x$CGAL_USES_GMP" = xyes; then
+      #   LIBS="-lgmp $LIBS $GMP_LIBDIR"
+      # fi
+      echo "$as_me:$LINENO: checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL" >&5
+echo $ECHO_N "checking for ::CGAL::Cartesian<int>::Point_2 in -lCGAL... $ECHO_C" >&6
+save_CXXFLAGS_CHECK_CXX_LIB="$CXXFLAGS"
+CXXFLAGS="$CXXFLAGS -I$CGAL_INCLDIR -I$CGAL_INCLCONFDIR"
+save_LIBS_CHECK_CXX_LIB="$LIBS"
+LIBS="-lCGAL  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <CGAL/Cartesian.h>
+int
+main ()
+{
+::CGAL::Cartesian<int>::Point_2 P
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } &&
+	 { ac_try='test -z "$ac_cxx_werror_flag"
+			 || test ! -s conftest.err'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; } &&
+	 { ac_try='test -s conftest$ac_exeext'
+  { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+  (eval $ac_try) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+cgal=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+cgal=no
+fi
+rm -f conftest.err conftest.$ac_objext \
+      conftest$ac_exeext conftest.$ac_ext
+CXXFLAGS="$save_CXXFLAGS_CHECK_CXX_LIB"
+LIBS="$save_LIBS_CHECK_CXX_LIB"
+      LIBS="$save_LIBS"
+    fi
+
+  fi
+  ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+fi
+
+if test "x$cgal" = xyes; then
+  USE_CGAL=yes
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_CGAL 1
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define CGAL_VERSION $CGAL_VERSION
+_ACEOF
+
+  if ! echo $CGAL_VERSION | grep -q "^3.0"; then
+    { echo "$as_me:$LINENO: WARNING: *****************************************************" >&5
+echo "$as_me: WARNING: *****************************************************" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Warning: Your CGAL version is newer than the  ***" >&5
+echo "$as_me: WARNING: *** Warning: Your CGAL version is newer than the  ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** supported versions. It may still work though. ***" >&5
+echo "$as_me: WARNING: *** supported versions. It may still work though. ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *****************************************************" >&5
+echo "$as_me: WARNING: *****************************************************" >&2;}
+  fi
+else
+   if test "x$cgal_makefile" != xno; then
+    { echo "$as_me:$LINENO: WARNING: *********************************************************" >&5
+echo "$as_me: WARNING: *********************************************************" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Warning: CGAL was not found.                      ***" >&5
+echo "$as_me: WARNING: *** Warning: CGAL was not found.                      ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** Run \"configure\" with the appropriate options.     ***" >&5
+echo "$as_me: WARNING: *** Run \"configure\" with the appropriate options.     ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *** CGAL support will be disabled.                    ***" >&5
+echo "$as_me: WARNING: *** CGAL support will be disabled.                    ***" >&2;}
+    { echo "$as_me:$LINENO: WARNING: *********************************************************" >&5
+echo "$as_me: WARNING: *********************************************************" >&2;}
+  fi
+  CGAL_INCLDIR=
+  CGAL_LIBDIR=
+  CGAL_RLIBDIR=
+  CGAL_DEFINES=
+  CGAL_CXXFLAGS=
+  CGAL_LIBS=
+fi
+
+
+CGAL_INC_DIR="${CGAL_INCLDIR} ${CGAL_INCLCONFDIR}"
+
+CGAL_LIB_DIR=${CGAL_LIBDIR}
+
+CGAL_RLIB_DIR=${CGAL_RLIBDIR}
+
+
+
+
+
+
+
 # Check whether --enable-doxygen or --disable-doxygen was given.
 if test "${enable_doxygen+set}" = set; then
   enableval="$enable_doxygen"
@@ -8020,7 +8696,7 @@ esac
 
           ac_config_headers="$ac_config_headers src/config.h"
 
-                    ac_config_files="$ac_config_files make/Makefile src/utils/Makefile"
+                              ac_config_files="$ac_config_files make/Makefile src/utils/Makefile src/applications/nanoRodBuilder/Makefile"
 
 
 cat >confcache <<\_ACEOF
@@ -8553,6 +9229,7 @@ do
   # Handling of arguments.
   "make/Makefile" ) CONFIG_FILES="$CONFIG_FILES make/Makefile" ;;
   "src/utils/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/utils/Makefile" ;;
+  "src/applications/nanoRodBuilder/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/applications/nanoRodBuilder/Makefile" ;;
   "src/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS src/getopt.h:src/utils/gnugetopt.h" ;;
   "src/config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
@@ -8697,6 +9374,14 @@ s,@DOXYGEN@,$DOXYGEN,;t t
 s,@MPI_LIB@,$MPI_LIB,;t t
 s,@MPI_F90_LIB@,$MPI_F90_LIB,;t t
 s,@USE_MPI@,$USE_MPI,;t t
+s,@CXXCPP@,$CXXCPP,;t t
+s,@USE_CGAL@,$USE_CGAL,;t t
+s,@CGAL_INC_DIR@,$CGAL_INC_DIR,;t t
+s,@CGAL_LIB_DIR@,$CGAL_LIB_DIR,;t t
+s,@CGAL_RLIB_DIR@,$CGAL_RLIB_DIR,;t t
+s,@CGAL_DEFINES@,$CGAL_DEFINES,;t t
+s,@CGAL_CXXFLAGS@,$CGAL_CXXFLAGS,;t t
+s,@CGAL_LIBS@,$CGAL_LIBS,;t t
 s,@DOXYGEN@,$DOXYGEN,;t t
 s,@DOT@,$DOT,;t t
 s,@DOC@,$DOC,;t t