--- trunk/OOPSE-4/configure	2004/09/28 22:14:11	1499
+++ trunk/OOPSE-4/configure	2004/10/20 21:16:01	1619
@@ -273,7 +273,7 @@ ac_unique_file="src/applications/oopse.cpp"
 PACKAGE_STRING='OOPSE 2.0'
 PACKAGE_BUGREPORT='gezelter@nd.edu'
 
-ac_unique_file="src/applications/oopse.cpp"
+ac_unique_file="src/applications/oopse/oopse.cpp"
 ac_default_prefix="/usr/local"
 # Factoring default headers for most tests.
 ac_includes_default="\
@@ -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 CPP EGREP LIBOBJS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA LN_S SET_MAKE RANLIB ac_ct_RANLIB YACC LEX LEXLIB LEX_OUTPUT_ROOT AR MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI SPRNG_LIB_DIR SPRNG_INC_DIR SPRNG_LIB USE_SPRNG MKL_LIBDIR MKL_LIB MKL_INC HAVE_MKL 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 MPI_LIB_DIR MPI_INC_DIR MPI_F90_INC MPI_LIB MPI_F90_LIB USE_MPI SPRNG_LIB_DIR SPRNG_INC_DIR SPRNG_LIB USE_SPRNG MKL_LIBDIR MKL_LIB MKL_INC HAVE_MKL 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.
@@ -866,6 +866,10 @@ Optional Features:
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
   --enable-debug          Compile OOPSE in debug mode
+  --enable-doxygen        enable documentation generation with doxygen (auto)
+  --enable-dot            use 'dot' to generate graphs in doxygen (auto)
+  --enable-html-docs      enable HTML generation with doxygen (yes)
+  --enable-latex-docs     enable LaTeX documentation generation with doxygen (no)
   --enable-oopse-home=DIR      define oopse home dir PREFIX/oopse
 
 Optional Packages:
@@ -1813,6 +1817,14 @@ ac_configure="$SHELL $ac_aux_dir/configure" # This sho
 # $SHELLVAR to the Fortran 95 mangled name.  If the SHELLVAR
 # argument is not supplied, it defaults to NAME.
 # AC_F95_FUNC
+
+# AC_F90_MODULE_NAMES
+# -------------------
+#
+# Figure out how the Fortran 90 compiler constructs module file names
+#
+ # AC_F90_MODULE_NAMES
+
 
 
 
@@ -1868,6 +1880,9 @@ ac_configure="$SHELL $ac_aux_dir/configure" # This sho
 
 
 
+
+
+
 # set program name
 PROGNAME="oopse"
 
@@ -1947,6 +1962,8 @@ ac_ext=c
 
 
 
+
+
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -3525,7 +3542,7 @@ F90FLAGS="$F90FLAGS $ac_verb"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_verb"
 
-(eval echo $as_me:3528: \"$ac_link\") >&5
+(eval echo $as_me:3545: \"$ac_link\") >&5
 ac_f90_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f90_v_output" >&5
 F90FLAGS=$ac_save_F90FLAGS
@@ -3602,7 +3619,7 @@ F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 ac_save_F90FLAGS=$F90FLAGS
 F90FLAGS="$F90FLAGS $ac_cv_prog_f90_v"
 
-(eval echo $as_me:3605: \"$ac_link\") >&5
+(eval echo $as_me:3622: \"$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
@@ -4198,7 +4215,234 @@ fi
    rm -f conftest* conf/conftest* conf/CONFTEST* CONFTEST* conf/mpimod*
    if test $madedir = 1 ; then rmdir conf ; fi
 fi
+
+
+echo "$as_me:$LINENO: checking for Fortran 90 module file names" >&5
+echo $ECHO_N "checking for Fortran 90 module file names... $ECHO_C" >&6
+if test "${ac_cv_f90_module_names+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_ext=f90
+ac_compile='$F90 -c $F90FLAGS conftest.$ac_ext >&5'
+ac_link='$F90 -o conftest$ac_exeext $F90FLAGS $LD90FLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f90_compiler_gnu
 
+# carry out the test in a new directory, so that we don't miss anything
+mkdir conftest
+cd conftest
+cat >conftest.$ac_ext <<_ACEOF
+MODULE Bar
+END MODULE Bar
+_ACEOF
+rm -f conftest.$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_f90_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_cv_f90_module_names=
+ac_file_list=*
+for ac_file in $ac_file_list; do
+   case $ac_file in
+      # don't care for original source and object files
+      conftest.$ac_ext | conftest.$ac_objext | conftest.err )
+          :
+          ;;
+      # look for new files derived from the file name
+      *conftest*)
+          ac_pat=`echo $ac_file | sed s/conftest/%FILE%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      # look for new files derived from the module name,
+      # with different case translation schemes
+      *Bar*)
+          ac_pat=`echo $ac_file | sed s/Bar/%Module%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      *bar*)
+          ac_pat=`echo $ac_file | sed s/bar/%module%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+      *BAR*)
+          ac_pat=`echo $ac_file | sed s/BAR/%MODULE%/`
+	    ac_exists=false
+  for ac_i in $ac_cv_f90_module_names; do
+    if test x"$ac_pat" = x"$ac_i"; then
+      ac_exists=true
+      break
+    fi
+  done
+
+  if test x"$ac_exists" = xtrue; then
+  :
+else
+  ac_cv_f90_module_names="$ac_cv_f90_module_names $ac_pat"
+fi
+
+          ;;
+       # Other files - we have no idea how they are generated
+       *)
+          { echo "$as_me:$LINENO: WARNING: Bogus file found: $ac_file" >&5
+echo "$as_me: WARNING: Bogus file found: $ac_file" >&2;}
+          ;;
+   esac
+done
+if test "x$ac_cv_f90_module_names" = "x"; then
+  { echo "$as_me:$LINENO: WARNING: Couldn't determine module file names" >&5
+echo "$as_me: WARNING: Couldn't determine module file names" >&2;}
+fi
+
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_f90_module_names=
+{ echo "$as_me:$LINENO: WARNING: Couldn't determine module file names" >&5
+echo "$as_me: WARNING: Couldn't determine module file names" >&2;}
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+cd ..
+# cleanup
+rm -rf conftest
+ac_ext=f90
+ac_compile='$F90 -c $F90FLAGS conftest.$ac_ext >&5'
+ac_link='$F90 -o conftest$ac_exeext $F90FLAGS $LD90FLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f90_compiler_gnu
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_f90_module_names" >&5
+echo "${ECHO_T}$ac_cv_f90_module_names" >&6 # AC_CACHE_CHECK
+
+# We now generate a shell script that will help us to figure out the correct
+# module file names, using the value of ac_cv_f90_module_names
+
+echo "Generating shell script modnam"
+
+cat > scripts/modnam << EOF
+#! /bin/sh
+# This script is auto-generated by configure
+#
+usage="\\
+Usage: \$0 [FILES]
+
+[FILES] are Fortran 90 source files.
+The output is a list of module file names that the Fortran 90 compiler
+generates when compiling [FILES]."
+
+list=
+empty=
+
+if test \$# -eq 0; then
+   echo "\$usage"; exit 0
+fi
+
+while test \$# != 0; do
+
+  file=\$1
+  shift
+
+# strip suffix
+  base=\`echo \$file | sed 's/[.][^.]*$//'\`
+
+  test ! -f \$file && continue
+
+# Look for module definitions and transform them to upper / lower case
+  mods=\`cat \$file | sed '/^ *[mM][oO][dD][uU][lL][eE]/!d;s/^ *[mM][oO][dD][uU][lL][eE] *\([A-Za-z_][A-Za-z0-9_]*\).*\$/\1/'\`
+  upper=\`echo \$mods | tr a-z A-Z\`
+  lower=\`echo \$mods | tr A-Z a-z\`
+
+# Here, the patterns for generating module file names were inserted by configure
+  for trans in $ac_cv_f90_module_names; do
+
+    pat=\`echo \$trans | sed 's/.*\(%.*%\).*/\1/'\`
+    var=empty
+    case \$pat in
+       %MODULE%)
+          var=upper ;;
+       %Module%)
+          var=mods ;;
+       %module%)
+          var=lower ;;
+       %FILE%)
+          test -n "\$mods" && var=base ;;
+    esac
+    new=\`eval '(for i in \$'\$var '; do echo \$trans | sed s/\$pat/\$i/; done)'\`
+    list="\$list \$new"
+  done
+done
+
+echo \$list
+# end of configure-generated script
+EOF
+chmod 755 scripts/modnam
+
+pat=`echo $ac_cv_f90_module_names | sed 's/.*\(%.*%\).*/\1/'`
+F90_MODULE_NAMES=empty
+case $pat in
+       %MODULE%)
+          F90_MODULE_NAMES=UPPER ;;
+       %Module%)
+          F90_MODULE_NAMES=Mixed ;;
+       %module%)
+          F90_MODULE_NAMES=lower ;;
+       *)
+          F90_MODULE_NAMES=unknown ;;
+esac
 
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
@@ -4702,7 +4946,7 @@ done
 
 
   # clean out junk possibly left behind by a previous configuration
-  rm -f utils/getopt.h
+  rm -f src/utils/getopt.h
   # Check for getopt_long support
 
 for ac_header in getopt.h
@@ -5042,7 +5286,7 @@ esac
   *) LIBOBJS="$LIBOBJS getopt1.$ac_objext" ;;
 esac
 
-                ac_config_links="$ac_config_links utils/getopt.h:utils/gnugetopt.h"
+                ac_config_links="$ac_config_links src/utils/getopt.h:src/utils/gnugetopt.h"
 
 fi
 
@@ -5136,7 +5380,7 @@ if test "$ac_test_CFLAGS" != "set"; then
         fi;;
    *darwin*)
 	if test "$CC" = xlc -o "$CC" = cc; then
-        	CFLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
+        	CFLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
         fi;;
   esac
 
@@ -5588,7 +5832,7 @@ if test "$ac_test_CXXFLAGS" != "set"; then
         fi;;
    *darwin*)
 	if test "$CXX" = xlc++; then
-        	CXXFLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
+        	CXXFLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto -qaltivec"
         fi;;
   esac
 
@@ -6000,7 +6244,7 @@ if test x"$F90FLAGS" = x ; then
         fi;;
    *darwin*)
 	if test "$F90" = f90 -o "$F90" = xlf90 -o "$F90" = xlf95; then
-        	F90FLAGS="-qthreaded -O5 -qtune=auto -qarch=auto -qunroll=auto"
+        	F90FLAGS="-qthreaded -O -qtune=auto -qarch=auto -qunroll=auto"
         fi;;
   esac
 
@@ -6991,7 +7235,78 @@ fi
 fi
 
 fi
+$as_unset ac_cv_lib_mpich_MPI_Init
+if test x = x"$MPI_LIB"; then
+        echo "$as_me:$LINENO: checking for MPI_Init in -lmpich" >&5
+echo $ECHO_N "checking for MPI_Init in -lmpich... $ECHO_C" >&6
+if test "${ac_cv_lib_mpich_MPI_Init+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lmpich "-lpmpich" $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
 
+/* Override any gcc2 internal prototype to avoid an error.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+/* We use char because int might match the return type of a gcc2
+   builtin and then its argument prototype would still apply.  */
+char MPI_Init ();
+int
+main ()
+{
+MPI_Init ();
+  ;
+  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_c_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 $ac_status); }; }; then
+  ac_cv_lib_mpich_MPI_Init=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_lib_mpich_MPI_Init=no
+fi
+rm -f conftest.err conftest.$ac_objext \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+echo "$as_me:$LINENO: result: $ac_cv_lib_mpich_MPI_Init" >&5
+echo "${ECHO_T}$ac_cv_lib_mpich_MPI_Init" >&6
+if test $ac_cv_lib_mpich_MPI_Init = yes; then
+  MPI_LIB="-lmpich -lpmpich"
+fi
+
+fi
+
 $as_unset ac_cv_lib_mpi_MPI_Init
 if test x = x"$MPI_LIB"; then
 echo "$as_me:$LINENO: checking for MPI_Init in -lmpi" >&5
@@ -7507,13 +7822,152 @@ echo "${ECHO_T}no" >&6
 
     echo "$as_me:$LINENO: result: no" >&5
 echo "${ECHO_T}no" >&6
+
+fi;
+
 
+
+# Check whether --enable-doxygen or --disable-doxygen was given.
+if test "${enable_doxygen+set}" = set; then
+  enableval="$enable_doxygen"
+
 fi;
+# Check whether --enable-dot or --disable-dot was given.
+if test "${enable_dot+set}" = set; then
+  enableval="$enable_dot"
+
+fi;
+# Check whether --enable-html-docs or --disable-html-docs was given.
+if test "${enable_html_docs+set}" = set; then
+  enableval="$enable_html_docs"
+
+else
+   enable_html_docs=yes
+fi;
+# Check whether --enable-latex-docs or --disable-latex-docs was given.
+if test "${enable_latex_docs+set}" = set; then
+  enableval="$enable_latex_docs"
+
+else
+   enable_latex_docs=no
+fi;
+if test "x$enable_doxygen" = xno; then
+        enable_doc=no
+else
+        # Extract the first word of "doxygen", so it can be a program name with args.
+set dummy doxygen; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_DOXYGEN+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $DOXYGEN in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_DOXYGEN="$DOXYGEN" # Let the user override the test with a path.
+  ;;
+  *)
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_DOXYGEN="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+
+  ;;
+esac
+fi
+DOXYGEN=$ac_cv_path_DOXYGEN
+
+if test -n "$DOXYGEN"; then
+  echo "$as_me:$LINENO: result: $DOXYGEN" >&5
+echo "${ECHO_T}$DOXYGEN" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+        if test "x$DOXYGEN" = x; then
+                if test "x$enable_doxygen" = xyes; then
+                        { { echo "$as_me:$LINENO: error: could not find doxygen" >&5
+echo "$as_me: error: could not find doxygen" >&2;}
+   { (exit 1); exit 1; }; }
+                fi
+                enable_doc=no
+        else
+                enable_doc=yes
+                # Extract the first word of "dot", so it can be a program name with args.
+set dummy dot; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_path_DOT+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $DOT in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_DOT="$DOT" # Let the user override the test with a path.
+  ;;
+  *)
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_path_DOT="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
 
+  ;;
+esac
+fi
+DOT=$ac_cv_path_DOT
 
+if test -n "$DOT"; then
+  echo "$as_me:$LINENO: result: $DOT" >&5
+echo "${ECHO_T}$DOT" >&6
+else
+  echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
 
+        fi
+fi
 
+if test "x$enable_doc" = xyes; then
+  DOC=1
+else
+  DOC=0
+fi
 
+
+if test x$DOT = x; then
+        if test "x$enable_dot" = xyes; then
+                { { echo "$as_me:$LINENO: error: could not find dot" >&5
+echo "$as_me: error: could not find dot" >&2;}
+   { (exit 1); exit 1; }; }
+        fi
+        enable_dot=no
+else
+        enable_dot=yes
+fi
+
+
+
+
+
+
+
 OBJEXT=".$OBJEXT"
 
 OOPSE=oopse
@@ -7570,9 +8024,10 @@ esac
 
 
 
+
           ac_config_headers="$ac_config_headers src/config.h"
 
-          ac_config_files="$ac_config_files make/Make.conf"
+          ac_config_files="$ac_config_files make/Makefile"
 
 
 cat >confcache <<\_ACEOF
@@ -8103,8 +8558,8 @@ do
 do
   case "$ac_config_target" in
   # Handling of arguments.
-  "make/Make.conf" ) CONFIG_FILES="$CONFIG_FILES make/Make.conf" ;;
-  "utils/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS utils/getopt.h:utils/gnugetopt.h" ;;
+  "make/Makefile" ) CONFIG_FILES="$CONFIG_FILES make/Makefile" ;;
+  "src/utils/getopt.h" ) CONFIG_LINKS="$CONFIG_LINKS src/utils/getopt.h:src/utils/gnugetopt.h" ;;
   "src/config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
 echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
@@ -8225,6 +8680,7 @@ s,@CPP@,$CPP,;t t
 s,@F90_WORK_FILES_ARG@,$F90_WORK_FILES_ARG,;t t
 s,@MODDIRFLAG@,$MODDIRFLAG,;t t
 s,@F90MODINCSPEC@,$F90MODINCSPEC,;t t
+s,@F90_MODULE_NAMES@,$F90_MODULE_NAMES,;t t
 s,@CPP@,$CPP,;t t
 s,@EGREP@,$EGREP,;t t
 s,@LIBOBJS@,$LIBOBJS,;t t
@@ -8254,6 +8710,12 @@ s,@BATEXT@,$BATEXT,;t t
 s,@MKL_LIB@,$MKL_LIB,;t t
 s,@MKL_INC@,$MKL_INC,;t t
 s,@HAVE_MKL@,$HAVE_MKL,;t t
+s,@DOXYGEN@,$DOXYGEN,;t t
+s,@DOT@,$DOT,;t t
+s,@DOC@,$DOC,;t t
+s,@enable_dot@,$enable_dot,;t t
+s,@enable_html_docs@,$enable_html_docs,;t t
+s,@enable_latex_docs@,$enable_latex_docs,;t t
 s,@BATEXT@,$BATEXT,;t t
 s,@MKINSTALLDIRS@,$MKINSTALLDIRS,;t t
 s,@OOPSE@,$OOPSE,;t t