--- trunk/OOPSE-3.0/ac-tools/configure.in	2005/12/16 21:52:50	2518
+++ trunk/OOPSE-3.0/ac-tools/configure.in	2006/05/16 20:38:23	2753
@@ -1,15 +1,17 @@
 dnl **** Process this file with autoconf to produce a configure script.
-
-AC_INIT(OOPSE, 2.0, gezelter@nd.edu, oopse)
+AC_PREREQ(2.59)
+AC_INIT(OOPSE, 3.0, gezelter@nd.edu, oopse)
 AC_CONFIG_AUX_DIR(ac-tools)
+AC_CONFIG_SRCDIR([src/applications/oopse/oopse.cpp])
+AC_CONFIG_HEADER([src/config.h])
 
-builtin(include, ac-tools/fortran90.m4)
-builtin(include, ac-tools/aclocal.m4)
+builtin(include, ac-tools/OOPSE.m4)
 builtin(include, ac-tools/AC_CXX_HAVE_STL.m4)
 builtin(include, ac-tools/AC_CXX_NAMESPACES.m4)
 builtin(include, ac-tools/AC_CXX_STD.m4)
 
-AC_CONFIG_SRCDIR([src/applications/oopse/oopse.cpp])
+# who am i
+AC_CANONICAL_HOST
 
 AC_PREFIX_DEFAULT("/usr/local")
 
@@ -17,6 +19,23 @@ AC_SUBST(PROGNAME)
 PROGNAME="oopse"
 AC_SUBST(PROGNAME)
 
+AC_EXEEXT
+AC_OBJEXT
+OBJEXT=".$OBJEXT"
+
+OOPSE=oopse
+
+dnl **** define home dir of oopse
+if test "x${prefix}" = "xNONE"
+then
+  OOPSE_HOME=${ac_default_prefix}/oopse
+else
+  OOPSE_HOME=${prefix}/oopse
+fi
+AC_ARG_ENABLE(oopse-home,
+[  --enable-oopse-home=DIR      define oopse home dir [PREFIX/oopse]],
+[OOPSE_HOME="${enableval}"])
+
 # there are two ways to do debugging.  One with the --enable-debug flag
 # and one using the DEBUG environment variable
 
@@ -28,82 +47,70 @@ AC_SUBST(debug)
 fi
 AC_SUBST(debug)
 
-# who am i
-AC_CANONICAL_HOST
-
-
-
-dnl Checks for C compiler
-AC_PROG_CC([pathcc icc xlc gcc cc])
-
-dnl Checks for C++ compiler
-AC_PROG_CXX([pathCC icpc icc xlc++ xlC CC g++ c++])
-
-dnl Checks for C preprocessor
+# Checks for programs.
+AC_PROG_CXX([icpc icc pgCC pathCC c++ xlc++ xlC g++ CC])
+AC_PROG_CC([icc pgcc pathcc cc xlc gcc])
+AC_PROG_FC([ifort ifc pgf95 pathf95 xlf95 lf95 epcf90 pathf90 xlf90 f95 f90 gfortran g95 fort], 95)
 AC_PROG_CPP
-
-dnl Checks for grep and egrep
 AC_PROG_EGREP
-
-dnl If we are not running g++ then we might need some other flags
-dnl to get the templates compiled correctly
-OOPSE_TEMPLATE_FLAGS=""
-if test $ac_cv_prog_gxx = no; then
-  AC_MSG_CHECKING([checking whether ${CXX} accepts -ptused -no_prelink])
-  echo 'void f(){}' > conftest.cc
-  if test -z "`${CXX} -ptused -no_prelink -c conftest.cc 2>&1`"; then
-    AC_MSG_RESULT(yes)
-    OOPSE_TEMPLATE_FLAGS="-ptused -no_prelink"
-  else
-    AC_MSG_RESULT(no)
-  fi
-  rm -f conftest*
-  AC_MSG_CHECKING([checking whether ${CXX} accepts -instances=static])
-  echo 'void f(){}' > conftest.cc
-  if test -z "`${CXX} -instances=static -c conftest.cc 2>&1`"; then
-    AC_MSG_RESULT(yes)
-    OOPSE_TEMPLATE_FLAGS="-instances=static"
-  else
-    AC_MSG_RESULT(no)
-  fi
-  rm -f conftest*
-  AC_MSG_CHECKING([checking whether ${CXX} accepts -pto])
-  echo 'void f(){}' > conftest.cc
-  if test -z "`${CXX} -pto -c conftest.cc 2>&1`"; then
-    AC_MSG_RESULT(yes)
-    OOPSE_TEMPLATE_FLAGS="-pto"
-  else
-    AC_MSG_RESULT(no)
-  fi
-  rm -f conftest*
-  AC_MSG_CHECKING([checking whether ${CXX} accepts -LANG:std])
-  echo 'void f(){}' > conftest.cc
-  if test -z "`${CXX} -LANG:std -c conftest.cc 2>&1`"; then
-    AC_MSG_RESULT(yes)
-    
-
-    EXTRA_CC_FLAG=${EXTRA_CC_FLAG}" -LANG:std"
-  else
-    AC_MSG_RESULT(no)
-  fi
+AC_PROG_LN_S
+AC_PROG_MAKE_SET
+AC_PROG_RANLIB
+AX_SYS_PERLSHARPBANG
+AC_PROG_INSTALL
+case "x$INSTALL" in
+   x/*) ;;
+   *) INSTALL=`pwd`/ac-tools/"shtool install -c" ;
+esac
+MKINSTALLDIRS=`pwd`/ac-tools/"shtool mkdir -p -f"
+AC_CHECK_PROG(AR, ar, ar, NONE)
+if test "$AR" = "NONE"; then
+  AC_CACHE_SAVE
+  exit 1
 fi
-AC_SUBST(OOPSE_TEMPLATE_FLAGS)
-AC_SUBST(EXTRA_CC_FLAG)
+AC_PATH_PROG(PS, ps)
+AC_CACHE_CHECK([for POSIX or BSD ps syntax], ac_cv_prog_ps_syntax, [
+	if $PS ax -o rss > /dev/null 2>&1; then
+		ac_cv_prog_ps_ax=yes
+	else
+		ac_cv_prog_ps_ax=no
+	fi
+	if $PS -ef -o rss > /dev/null 2>&1; then
+		ac_cv_prog_ps_ef=yes
+	else
+		ac_cv_prog_ps_ef=no
+	fi
+	if test "$ac_cv_prog_ps_ax" = yes; then
+		ac_cv_prog_ps_syntax=BSD
+        else
+		if test "$ac_cv_prog_ps_ef" = yes; then
+			ac_cv_prog_ps_syntax=POSIX
+		else
+			AC_MSG_ERROR(Could not determine ps syntax)
+		fi
+	fi
+])
+AC_DEFINE_UNQUOTED(PSCOMMAND, $PS, [Path to ps program])
+if test "$ac_cv_prog_ps_syntax" = BSD; then
+  AC_DEFINE(PSTYPE_IS_BSD, 1, [ps uses BSD-style arguments])
+else
+   if test "$ac_cv_prog_ps_syntax" = POSIX; then
+       AC_DEFINE(PSTYPE_IS_POSIX, 1, [ps uses POSIX-style arguments])
+   else
+       AC_MSG_ERROR(Unknown ps syntax type!)
+   fi
+fi
 
-dnl Fortran 90 compilation checks are next
-
-AC_PROG_F90([pathf95 ifort ifc f90 xlf90 pgf90 epcf90 f95 xlf95 lf95 fort g95])
+AC_LANG_PUSH(Fortran)
+AC_FC_SRCEXT(F90)
 dnl Check the flag for Fortran90 preprocessing
 ACX_PROG_F90_PREPFLAG
 dnl Check to see if a flag is required for preprocessing defines
 ACX_PROG_F90_PREPDEFFLAG
-AC_LANG_PUSH(Fortran 90)
-AC_LANG_PREPROC(Fortran 90)
-AC_F90_LIBRARY_LDFLAGS
-dnl How does Fortran mangle function names
-AC_F90_WRAPPERS
-AC_SUBST(F90_FUNC)
-AC_SUBST(F90_FUNC_)
+AC_FC_WRAPPERS
+AC_SUBST(FC_FUNC)
+AC_SUBST(FC_FUNC_)
+AC_FC_LIBRARY_LDFLAGS
 dnl Fortran 90 module suffix
 AC_CHECK_MODSUFFIX
 dnl Fortran 90 module path specifier
@@ -124,21 +131,38 @@ AC_LANG_CPLUSPLUS
 AC_SUBST(F90_MODULE_NAMES)
 AC_LANG_POP
 
-AC_LANG_CPLUSPLUS
-AC_HEADER_STDC
-AC_CXX_NAMESPACES
-AC_CXX_STD
+AC_LANG_C
 
 dnl Checks for libraries.
 AC_CHECK_LIB(m, asin, , exit)
-
 ACX_CHECK_ZLIB
-dnl Checks for header files.
-AC_CHECK_HEADERS([stdlib.h string.h sys/param.h unistd.h sys/time.h stdio.h conio.h strstream.h iostream.h fstream.h math.h time.h sys/pstat.h sys/sysmp.h sys/sysinfo.h sys/table.h sys/sysctl.h sys/sytemcfg.h machine/hal_sysinfo.h])
-AC_LANG_CPLUSPLUS
-AC_CHECK_HEADERS([ctype.h iostream fstream sstream strstream])
-AC_LANG_C
-AC_CHECK_FUNCS([rint snprintf sranddev strcasecmp strncasecmp stricmp strnicmp pstat_getstatic sysmp getsysinfo sysctl table])
+ACX_CHECK_FFTW
+
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([conio.h dlfcn.h fstream.h iostream.h libintl.h limits.h machine/hal_sysinfo.h math.h stddef.h stdio.h stdlib.h string.h strings.h strstream.h sys/param.h sys/pstat.h sys/sysmp.h sys/sysctl.h sys/sysinfo.h sys/systemcfg.h sys/table.h sys/time.h time.h unistd.h zlib.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_CONST
+AC_C_INLINE
+AC_C_RESTRICT
+AC_TYPE_SIZE_T
+AC_HEADER_TIME
+AC_CHECK_TYPES(clock_t)
+AC_C_CONST
+AC_C_INLINE
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_MEMCMP
+AC_FUNC_REALLOC
+AC_FUNC_SELECT_ARGTYPES
+AC_FUNC_STRFTIME
+AC_FUNC_STRTOD
+AC_CHECK_FUNCS([floor getpagesize gettimeofday memchr memmove memset pow pstat_getdynamic pstat_getstatic rint select snprintf sranddev sqrt strcasecmp strchr strdup stricmp strncasecmp strnicmp strrchr strstr strtol sysmp getsysinfo sysctl table])
+
 # special check for _system_configuration because AIX <4.3.2 do not
 # contain the `physmem' member.
 AC_MSG_CHECKING([for external symbol _system_configuration])
@@ -148,30 +172,14 @@ AC_HEADER_TIME
   AC_DEFINE(HAVE__SYSTEM_CONFIGURATION, 1,
             [Define if you have the _system_configuration variable.])],
   [AC_MSG_RESULT([no])])
-AC_HEADER_TIME
 
-dnl Checks for typedefs, structures, and compiler characteristics.
-AC_CHECK_TYPES(clock_t)
-AC_C_CONST
-AC_C_INLINE
-
-
 dnl check for system getopt
 adl_FUNC_GETOPT_LONG
 
-dnl check for strong optimization options
-
-case $debug in
-  1) 
-     ;;
-  *) 
-   ACX_PROG_CC_MAXOPT
-   ACX_PROG_CXX_MAXOPT
-   ACX_PROG_F90_MAXOPT
-     ;;
-esac
-
 AC_LANG_CPLUSPLUS
+AC_CXX_NAMESPACES
+AC_CXX_STD
+AC_CHECK_HEADERS([ctype.h iostream fstream sstream strstream])
 # AC_CPP_FUNC
 # ------------------ #
 # Checks to see if ANSI C99 CPP variable __func__ works.
@@ -200,58 +208,23 @@ AC_LANG_C
 
 AC_CPP_FUNC
 AC_SUBST(__func__)
-AC_LANG_C
 
-AC_PROG_INSTALL
-AC_PROG_LN_S
-AC_PROG_MAKE_SET
-AC_PROG_RANLIB
-AC_PROG_YACC
-AC_PROG_LEX
-AX_SYS_PERLSHARPBANG
-AC_CHECK_PROG(AR, ar, ar, NONE)
-if test "$AR" = "NONE"; then
-  AC_MSG_ERROR(--> Can't find \`ar'!)
-  AC_CACHE_SAVE
-  exit 1
-fi
 
-AC_PATH_PROG(PS, ps)
-AC_CACHE_CHECK([for POSIX or BSD ps syntax], ac_cv_prog_ps_syntax, [
-	if $PS ax -o rss > /dev/null 2>&1; then
-		ac_cv_prog_ps_ax=yes
-	else
-		ac_cv_prog_ps_ax=no
-	fi
-	if $PS -ef -o rss > /dev/null 2>&1; then
-		ac_cv_prog_ps_ef=yes
-	else
-		ac_cv_prog_ps_ef=no
-	fi
-	if test "$ac_cv_prog_ps_ax" = yes; then
-		ac_cv_prog_ps_syntax=BSD
-        else
-		if test "$ac_cv_prog_ps_ef" = yes; then
-			ac_cv_prog_ps_syntax=POSIX
-		else
-			AC_MSG_ERROR(Could not determine ps syntax)
-		fi
-	fi
-])
+dnl check for strong optimization options
 
-AC_DEFINE_UNQUOTED(PSCOMMAND, $PS, [Path to ps program])
-AC_DEFINE([OBAPI], [], [Used to export symbols for DLL / shared library builds])
+case $debug in
+  1) 
+     ;;
+  *) 
+   ACX_PROG_FC_MAXOPT
+   ACX_PROG_CC_MAXOPT
+   ACX_PROG_CXX_MAXOPT
+     ;;
+esac
 
+dnl OpenBabel needs this:
+AC_DEFINE([OBAPI], [], [Used to export symbols for DLL / shared library builds])
 
-if test "$ac_cv_prog_ps_syntax" = BSD; then
-  AC_DEFINE(PSTYPE_IS_BSD, 1, [ps uses BSD-style arguments])
-else
-   if test "$ac_cv_prog_ps_syntax" = POSIX; then
-       AC_DEFINE(PSTYPE_IS_POSIX, 1, [ps uses POSIX-style arguments])
-   else
-       AC_MSG_ERROR(Unknown ps syntax type!)
-   fi
-fi
 
 AC_ARG_WITH(mpi,
     	[AC_HELP_STRING([--with-mpi=<prefix>],
@@ -272,25 +245,6 @@ dnl AC_ARG_WITH(sprng,
 fi
 AC_SUBST(USE_MPI)
 
-dnl AC_ARG_WITH(sprng,
-dnl    	[AC_HELP_STRING([--with-sprng=<prefix>],
-dnl		[compile with SPRNG installed in <prefix> [default=/usr/local]])],
-dnl	with_sprng=$withval,
-dnl	with_sprng="/usr/local")
-dnl
-dnl case "x$with_sprng" in
-dnl        xyes | "x")  USE_SPRNG=yes;;
-dnl        xno) USE_SPRNG=no ;;
-dnl        *) SPRNG="$with_sprng"; USE_SPRNG=yes ;;
-dnl esac
-dnl if test "$USE_SPRNG" = "yes" -a -z "$with_sprng"; then
-dnl        SPRNG="/usr/local"
-dnl fi
-dnl if test "$USE_SPRNG" = "yes"; then
-dnl         ACX_SPRNG
-dnl fi
-dnl AC_SUBST(USE_SPRNG)
-
 dnl ########################################
 dnl # Check for CGAL headers and libraries #
 dnl ########################################
@@ -490,53 +444,8 @@ dnl CHECK_MKL
 AC_SUBST(CGAL_CXXFLAGS)
 AC_SUBST(CGAL_LIBS)
 
-dnl CHECK_MKL
-
 BB_ENABLE_DOXYGEN
 
-AC_EXEEXT
-AC_OBJEXT
-OBJEXT=".$OBJEXT"
-
-OOPSE=oopse
-
-dnl **** define home dir of oopse
-if test "x${prefix}" = "xNONE"
-then
-  OOPSE_HOME=${ac_default_prefix}/oopse
-else
-  OOPSE_HOME=${prefix}/oopse
-fi
-AC_ARG_ENABLE(oopse-home,
-[  --enable-oopse-home=DIR      define oopse home dir [PREFIX/oopse]],
-[OOPSE_HOME="${enableval}"])
-
-case "x$INSTALL" in
-   x/*) ;;
-   *) INSTALL=`pwd`/ac-tools/"shtool install -c" ;
-esac
-
-MKINSTALLDIRS=`pwd`/ac-tools/"shtool mkdir -p -f"
-
-dnl **** Define CFLAGS etc empty to prevent configure from setting them
-CFLAGS=${CFLAGS-""}
-CXXFLAGS=${CXXFLAGS-""}
-CPPFLAGS=${CPPFLAGS-""}
-FFLAGS=${FFLAGS-""}
-F90FLAGS=${F90FLAGS-""}
-LDFLAGS=${LDFLAGS-""}
-DEBUG=${DEBUG-"-g"}
-
-case $debug in
-  1) 
-     FFLAGS="$DEBUG $FFLAGS"
-     F90FLAGS="$DEBUG $F90FLAGS"
-     ;;
-  *) 
-     ;;
-esac
-
-
 AC_SUBST(EXEEXT)
 AC_SUBST(OBJEXT)
 AC_SUBST(BATEXT)
@@ -547,13 +456,10 @@ AC_SUBST(FFLAGS)
 AC_SUBST(CFLAGS)
 AC_SUBST(CXXFLAGS)
 AC_SUBST(CPPFLAGS)
-AC_SUBST(FFLAGS)
-AC_SUBST(F90FLAGS)
+AC_SUBST(FCFLAGS)
 AC_SUBST(LDFLAGS)
-AC_SUBST(PREPFLAG)
 AC_SUBST(PREPDEFFLAG)
 AC_SUBST(F90_MODULE_NAMES)
-AC_CONFIG_HEADER([src/config.h])
 AC_CONFIG_FILES([make/Makefile src/utils/Makefile src/applications/nanoRodBuilder/Makefile scripts/filepp], [chmod 0755 scripts/*])
 
 AC_OUTPUT