--- trunk/OOPSE-3.0/ac-tools/configure.in	2004/09/24 04:16:43	1490
+++ trunk/OOPSE-3.0/ac-tools/configure.in	2005/01/14 20:09:26	1946
@@ -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])
 
@@ -97,6 +99,20 @@ 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
@@ -170,6 +186,7 @@ CHECK_MKL
 
 CHECK_MKL
 
+BB_ENABLE_DOXYGEN
 
 AC_EXEEXT
 AC_OBJEXT
@@ -195,9 +212,6 @@ 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 +246,8 @@ 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