--- Makefile.orig	2009-09-22 14:45:57.000000000 -0500
+++ Makefile	2012-03-31 21:58:24.000000000 -0500
@@ -17,7 +17,7 @@
 #                           UNCOMMENT TO SELECT DOUBLE PRECISION
 #--------------------------------------------------------------------------
 
-#            FLAG_1 =  -DDOUBLE_PRECISION 
+             FLAG_1 =  -DDOUBLE_PRECISION 
 
 #--------------------------------------------------------------------------
 #        SPHERICAL          SELECT SPHERICAL COORDINATES FOR INTEGRATION
@@ -35,7 +35,7 @@
 #                           UNCOMMENT TO INCLUDE FLOODYING/DRYING
 #--------------------------------------------------------------------------
 
-#             FLAG_3 = -DWET_DRY
+             FLAG_3 = -DWET_DRY
 
 #--------------------------------------------------------------------------
 #        MULTI_PROCESSOR    INCLUDES PARALLELIZATION WITH MPI
@@ -45,13 +45,14 @@
 #                           UNCOMMENT TO INCLUDE MPI PARALLEL CAPABILITY
 #--------------------------------------------------------------------------
 
-              FLAG_4 = -DMULTIPROCESSOR
+#              FLAG_4 = -DMULTIPROCESSOR
 
 # For em64t computers at SMAST (guppy)
 #              PARLIB = -L/hosts/salmon01/data00/medm/em64t/lib64 -lmetis 
 
 # For i386 computers at SMAST (salmon and minke)
 #              PARLIB = -L/hosts/salmon01/data00/medm/lib -lmetis 
+#              PARLIB = -L${LOCALBASE}/lib -lmetis 
               PARLIB = -L../METIS_source -lmetis 
 
 # For Typhoeus and Hydra
@@ -67,7 +68,7 @@
 #                           UNCOMMENT TO INCLUDE WATER QUALITY MODEL
 #--------------------------------------------------------------------------
 
-#             FLAG_5 = -DWATER_QUALITY
+             FLAG_5 = -DWATER_QUALITY
 
 #--------------------------------------------------------------------------
 #        NETCDF OUTPUT      DUMP OUTPUT INTO NETCDF FILES (yes/no)
@@ -79,8 +80,10 @@
 #                           UNCOMMENT TO INCLUDE NETCDF OUTPUT CAPABILITY
 #--------------------------------------------------------------------------
            FLAG_6       =  -DNETCDF_IO
-             IOLIBS       =  -L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib  -lnetcdf
-             IOINCS       =  -I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
+# FreeBSD ports netcdf fortran support is separate from the standard
+# netcdf library. Must have both -lnetcdff and -lnetcdf
+             IOLIBS       =  -L${LOCALBASE}/lib -lnetcdff -lnetcdf
+             IOINCS       =  -I${LOCALBASE}/include
 
 # For em64t computers at SMAST (guppy)
 #             IOLIBS       =  -L/hosts/salmon01/data00/medm/em64t/lib64  -lnetcdf
@@ -107,7 +110,7 @@
 #                           UNCOMMENT TO INCLUDE DATA ASSIMILATION 
 #--------------------------------------------------------------------------
 
-#             FLAG_7 = -DNG_OI_ASSIM
+             FLAG_7 = -DNG_OI_ASSIM
 
 # For Build on em64t computer (Guppy) 
 #             OILIB  = -L/usr/X11R6/lib64 -L/usr/local/lib64 -lmkl_lapack -lmkl_em64t -lguide -lpthread
@@ -381,15 +384,15 @@
 #--------------------------------------------------------------------------
 #  Intel/MPI Compiler Definitions (SMAST)      
 #--------------------------------------------------------------------------
-          CPP      = /usr/bin/cpp
-          CPPFLAGS = $(DEF_FLAGS) -DINTEL   
-          FC       = mpif90 
-         DEBFLGS  = #-check all
+#          CPP      = /usr/bin/cpp
+#          CPPFLAGS = $(DEF_FLAGS) -DINTEL   
+#          FC       = mpif90 
+#         DEBFLGS  = #-check all
 # Use 'OPT = -O0 -g'  for fast compile to test the make 
 # Use 'OPT = -xP'      for fast run on em64t (Hydra, Typhoeus and Guppy)
 # Use 'OPT = -xN'      for fast run on em64t (Salmon and Minke)
 #         OPT      = -O0 -g 
-          OPT      = -xP
+#          OPT      = -xP
 #          OPT      = -xN
 
 # Do not set static for use with visit!
@@ -398,12 +401,11 @@
 #--------------------------------------------------------------------------
 #  gfortran defs 
 #--------------------------------------------------------------------------
-#         CPP      = /usr/bin/cpp 
-#         CPPFLAGS = $(DEF_FLAGS)  -DGFORTRAN
-#         FC       = gfortran  -O3 
-#         DEBFLGS  = 
-#         OPT      = 
-#         CLIB     = 
+         CPP      = cpp 
+         CPPFLAGS = $(DEF_FLAGS)  -DGFORTRAN
+         DEBFLGS  = -g
+         OPT      = -O
+         CLIB     = 
 #--------------------------------------------------------------------------
 #  absoft / mac os x defs
 #--------------------------------------------------------------------------
@@ -448,7 +450,8 @@
 #--------------------------------------------------------------------------
 #  CAT Preprocessing Flags
 #--------------------------------------------------------------------------
-           CPPARGS =  $(CPPFLAGS) $(DEF_FLAGS) $(FLAG_1) $(FLAG_2) \
+           CPPARGS =  $(CPPFLAGS) $(DEF_FLAGS) $(PORT_CPP_FLAGS) \
+   $(FLAG_1) $(FLAG_2) \
    $(FLAG_3) $(FLAG_4) $(FLAG_5) $(FLAG_6)  \
    $(FLAG_7) $(FLAG_8) $(FLAG_9) $(FLAG_10) \
    $(FLAG_11) $(FLAG_12) $(FLAG_13) $(FLAG_14) \
@@ -463,7 +466,7 @@
 
             LIBS  =	$(PV3LIB) $(CLIB)  $(PARLIB) $(IOLIBS)	\
 			$(MPILIB) $(GOTMLIB) $(KFLIB) $(BIOLIB)	\
-			$(OILIB) $(VISITLIB) $(PETSC_LIB)
+			$(OILIB) $(VISITLIB) $(PETSC_LIB) -llapack -lblas
 
             INCS  = 	$(IOINCS) $(GOTMINCS) $(BIOINCS) $(VISITINC) $(PETSC_FC_INCLUDES)
 
@@ -539,6 +542,8 @@
 #  Linking Directives
 #--------------------------------------------------------------------------
 
+all:		$(EXEC)
+
 $(EXEC):	$(OBJS)
 		$(FC) $(FFLAGS) $(VISOPT) $(LDFLAGS) $(OBJS) $(LIBS) -o $(EXEC)