--- trunk/OOPSE-3.0/ac-tools/configure.in	2004/09/24 04:16:43	1490
+++ trunk/OOPSE-3.0/ac-tools/configure.in	2005/02/14 23:26:25	2023
@@ -1,12 +1,12 @@
 dnl **** Process this file with autoconf to produce a configure script.
 
-AC_INIT(OOPSE, 1.0, gezelter@nd.edu, oopse)
+AC_INIT(OOPSE, 2.0, gezelter@nd.edu, oopse)
 AC_CONFIG_AUX_DIR(ac-tools)
 
 builtin(include, ac-tools/fortran90.m4)
 builtin(include, ac-tools/aclocal.m4)
 
-AC_CONFIG_SRCDIR([src/oopse.cpp])
+AC_CONFIG_SRCDIR([src/applications/oopse/oopse.cpp])
 
 AC_PREFIX_DEFAULT("/usr/local")
 
@@ -28,6 +28,8 @@ dnl Checks for C compiler
 # who am i
 AC_CANONICAL_HOST
 
+
+
 dnl Checks for C compiler
 AC_PROG_CC([icc xlc gcc cc])
 
@@ -97,10 +99,36 @@ AC_LANG_POP
 AC_CHECK_MODSUFFIX
 dnl Fortran 90 module path specifier
 AC_CHECK_MODDIRFLAG
+AC_F90_MODULE_NAMES
+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_SUBST(F90_MODULE_NAMES)
 AC_LANG_POP
 
-dnl check for system getopt
 AC_LANG_PUSH(C)
+AC_CHECK_HEADERS(unistd.h sys/pstat.h sys/sysmp.h sys/sysinfo.h sys/table.h sys/param.h sys/sysctl.h sys/sytemcfg.h machine/hal_sysinfo.h)
+AC_CHECK_FUNCS(pstat_getstatic 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])
+AC_TRY_COMPILE([#include <sys/systemcfg.h>],
+               [double x = _system_configuration.physmem;],
+  [AC_MSG_RESULT([yes])
+  AC_DEFINE(HAVE__SYSTEM_CONFIGURATION, 1,
+            [Define if you have the _system_configuration variable.])],
+  [AC_MSG_RESULT([no])])
+
+dnl check for system getopt
 adl_FUNC_GETOPT_LONG
 
 dnl check for strong optimization options
@@ -126,9 +154,27 @@ fi
   AC_MSG_ERROR(--> Can't find \`ar'!)
   AC_CACHE_SAVE
   exit 1
+fi
+
+AC_PATH_PROG(PS, ps)
+AC_CACHE_CHECK([for POSIX ps], ac_cv_prog_ps_posix, [
+	USER=${USER:-${LOGNAME:-`logname`}}
+	if $PS -U $USER -opid,args >/dev/null 2>&1; then
+		ac_cv_prog_ps_posix=yes
+	else
+		ac_cv_prog_ps_posix=no
+	fi
+])
+if test "$ac_cv_prog_ps_posix" = yes; then
+	PSTYPE=BSD
+else
+	PSTYPE=POSIX
 fi
 
+AC_SUBST(PS)
+AC_SUBST(PSTYPE)
 
+
 AC_ARG_WITH(mpi,
     	[AC_HELP_STRING([--with-mpi=<prefix>],
 		[compile with MPI installed in <prefix> [default=no]])],
@@ -170,6 +216,7 @@ CHECK_MKL
 
 CHECK_MKL
 
+BB_ENABLE_DOXYGEN
 
 AC_EXEEXT
 AC_OBJEXT
@@ -195,9 +242,6 @@ dnl **** Final list of subdirs
 
 MKINSTALLDIRS=`pwd`/ac-tools/"shtool mkdir -p -f"
 
-dnl **** Final list of subdirs
-SUBDIRS="libBASS libmdtools src forceFields samples utils utils/sysbuilder third-party "
-
 dnl **** Define CFLAGS etc empty to prevent configure from setting them
 CFLAGS=${CFLAGS-""}
 CXXFLAGS=${CXXFLAGS-""}
@@ -232,18 +276,8 @@ AC_CONFIG_HEADER([libBASS/config.h libmdtools/config.h
 AC_SUBST(LDFLAGS)
 AC_SUBST(PREPFLAG)
 AC_SUBST(PREPDEFFLAG)
-AC_CONFIG_HEADER([libBASS/config.h libmdtools/config.h])
-AC_CONFIG_FILES([Makefile
-	libBASS/Makefile libmdtools/Makefile src/Makefile utils/Makefile
-	utils/sysbuilder/Makefile  forceFields/Makefile samples/Makefile
-        third-party/Makefile
-	samples/alkane/Makefile samples/argon/Makefile
-	samples/lipid/Makefile samples/minimizer/Makefile
-	samples/metals/Makefile samples/water/Makefile
-        samples/water/dimer/Makefile samples/water/spce/Makefile
-        samples/water/ssd/Makefile samples/water/ssde/Makefile
-        samples/water/tip4p/Makefile samples/water/tip3p_ice/Makefile
-	samples/zcons/Makefile
-])
+AC_SUBST(F90_MODULE_NAMES)
+AC_CONFIG_HEADER([src/config.h])
+AC_CONFIG_FILES([make/Makefile src/utils/Makefile])
 
 AC_OUTPUT