--- MITgcm/tools/genmake2	2003/10/10 18:38:57	1.13
+++ MITgcm/tools/genmake2	2003/10/20 04:01:30	1.13.2.1
@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.13 2003/10/10 18:38:57 edhill Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/genmake2,v 1.13.2.1 2003/10/20 04:01:30 edhill Exp $
 #
 # Makefile generator for MITgcm UV codes
 #   created  by cnh 03/98
@@ -332,6 +332,9 @@
     IEEE=$MITGCM_IEEE
 fi
 
+AUTODIFF_PKG_USED=f
+AD_OPTFILE=
+
 #  The following state can be set directly by command-line switches
 gm_s1="OPTFILE PDEPEND PDEFAULT MAKEFILE PLATFORM ROOTDIR MODS DISABLE ENABLE NOOPT"
 gm_s2="FC IEEE MPI JAM DUMPSTATE STANDARDDIRS"
@@ -342,7 +345,12 @@
 gm_s5="TOOLSDIR SOURCEDIRS INCLUDEDIRS PWD MAKE THISHOSTNAME THISDATE MACHINE"
 gm_s6="EXECUTABLE EXEHOOK EXEDIR PACKAGES_CONF"
 
-gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6"
+#  The following are all related to adjoint/tangent-linear stuff
+gm_s7="AUTODIFF_PKG_USED AD_OPTFILE TAMC TAF DIFF_FLAGS AD_TAMC_FLAGS AD_TAF_FLAGS"
+gm_s8="FTL_TAMC_FLAGS FTL_TAF_FLAGS SVD_TAMC_FLAGS SVD_TAF_FLAGS"
+gm_s9=""
+
+gm_state="COMMANDL $gm_s1 $gm_s2 $gm_s3 $gm_s4 $gm_s5 $gm_s6 $gm_s7 $gm_s8"
 
 
 echo
@@ -375,7 +383,6 @@
 #   n=$(( $n + 1 ))
 #done
 #parse_options
-
 ac_prev=
 for ac_option ; do
 
@@ -400,6 +407,11 @@
 	-optfile=* | --optfile=* | -of=* | --of=*)
 	    OPTFILE=$ac_optarg ;;
 	
+	-adoptfile | --adoptfile | -ad | --ad)
+	    ac_prev=AD_OPTFILE ;;
+	-adoptfile=* | --adoptfile=* | -adof=* | --adof=*)
+	    AD_OPTFILE=$ac_optarg ;;
+	
 	-pdepend | --pdepend)
 	    ac_prev=PDEPEND ;;
 	-pdepend=* | --pdepend=*)
@@ -563,6 +575,33 @@
     fi
 fi
 
+echo "  getting AD_OPTFILE information:  "
+if test "x${AD_OPTFILE}" = x ; then
+    if test "x$MITGCM_AD_OF" = x ; then
+	AD_OPTFILE=$ROOTDIR/tools/adjoint_options/adjoint_default
+    else
+	AD_OPTFILE=$MITGCM_AD_OF
+    fi
+fi
+if test "x${AD_OPTFILE}" != xNONE ; then
+    if test -f "$AD_OPTFILE" -a -r "$AD_OPTFILE" ; then
+	echo "    using AD_OPTFILE=\"$AD_OPTFILE\""
+	source "$AD_OPTFILE"
+	RETVAL=$?
+	if test "x$RETVAL" != x0 ; then
+	    echo -n "Error: failed to source AD_OPTFILE \"$AD_OPTFILE\""
+	    echo "--please check that variable syntax is bash-compatible"
+	    exit 1
+	fi
+	if test "x$DUMPSTATE" != xf ; then
+	    cp -f $AD_OPTFILE "genmake_ad_optfile"
+	fi
+    else
+	echo "Error: can't read AD_OPTFILE=\"$AD_OPTFILE\""
+	exit 1
+    fi
+fi
+
 #  Check that FC, LINK, CPP, and S64 are defined.  If not, complain 
 #  and abort!
 if test "x$FC" = x ; then
@@ -838,6 +877,9 @@
     if test -d $adr ; then
 	SOURCEDIRS="$SOURCEDIRS $adr"
 	INCLUDEDIRS="$INCLUDEDIRS $adr"
+	if test "x$i" = xautodiff ; then
+	    AUTODIFF_PKG_USED=t
+	fi
     else
 	echo "Error: the directory \"$adr\" for package $i doesn't exist"
 	exit 1
@@ -1000,6 +1042,33 @@
 done
 
 
+#  Here, we build the list of files to be "run through" the adjoint
+#  compiler.
+if test -f ./ad_files ; then
+    rm -f ./ad_files
+fi
+echo "  Creating the list of files for the adjoint compiler."
+for i in $SOURCEDIRS . ; do
+    list_files=`( cd $i && ls -1 *.list 2>/dev/null )`
+    for j in $list_files ; do
+	cat $i/$j >> ad_files
+    done
+done
+cat <<EOF > adjoint_sed
+
+ sed 's/call adopen(/call adopen ( mythid,\
+     \&           /g
+     s/call adclose(/call adclose( mythid,\
+     \&           /g
+     s/call adread(/call adread ( mythid,\
+     \&           /g
+     s/call adwrite(/call adwrite( mythid,\
+     \&           /g' < ad_code_ad.f
+
+EOF
+chmod +x adjoint_sed
+
+
 echo
 echo "===  Creating the Makefile  ==="
 echo "  setting INCLUDES"
@@ -1105,6 +1174,9 @@
 EXECUTABLE  = \$(EXEDIR)/${EXECUTABLE}
 TOOLSDIR    = ${TOOLSDIR}
 
+#eh3  new defines for the adjoint work
+AUTODIFF    = ${ROOTDIR}/pkg/autodiff
+
 EOF
 
 #  Note: figure out some way to add Hyades JAM libraries here
@@ -1154,6 +1226,7 @@
 cat csrclist.inc   >> $MAKEFILE
 cat f90srclist.inc >> $MAKEFILE
 cat hlist.inc      >> $MAKEFILE
+echo               >> $MAKEFILE
 echo 'F77FILES =  $(SRCFILES:.F=.f)'                                           >> $MAKEFILE
 echo 'F90FILES =  $(F90SRCFILES:.F90=.f90)'                                    >> $MAKEFILE
 echo 'OBJFILES =  $(SRCFILES:.F=.o) $(CSRCFILES:.c=.o) $(F90SRCFILES:.F90=.o)' >> $MAKEFILE
@@ -1217,6 +1290,58 @@
 .p.f:
 	\$(KPP) \$(KFLAGS1)\$@ \$(KFLAGS2) \$<
 
+#=========================================
+#===  Automatic Differentiation Rules  ===
+
+TAMC           = ${TAMC}
+TAF            = ${TAF}
+
+EOF
+
+ad_vars="AD_TAMC_FLAGS AD_TAF_FLAGS"
+ad_vars="$ad_vars FTL_TAMC_FLAGS FTL_TAF_FLAGS"
+ad_vars="$ad_vars SVD_TAMC_FLAGS SVD_TAF_FLAGS"
+for i in $ad_vars ; do
+    name=$i
+    t1="t2=\$"`echo $i`
+    eval $t1
+    printf "%-20s = " $name >> $MAKEFILE
+    echo $t2 >> $MAKEFILE
+done
+
+echo "  Add the source list for AD code generation"
+echo >> $MAKEFILE
+echo -n "AD_FILES = " >> $MAKEFILE
+AD_FILES=`cat ad_files`
+for i in $AD_FILES ; do
+    echo    " \\" >> $MAKEFILE
+    echo -n " $i" >> $MAKEFILE
+done
+echo >> $MAKEFILE
+
+cat >>$MAKEFILE <<EOF
+
+# AD_FILES_SMALLF = \$(AD_FILES:.F=.f)
+
+EXE_AD_TAMC    = ${EXECUTABLE}_ad_tamc
+\$(EXE_AD_TAMC): \$(OBJFILES)
+
+EXE_AD_TAF     = ${EXECUTABLE}_ad_taf
+\$(EXE_AD_TAF): \$(OBJFILES)
+	cat \$(AD_FILES) >! ad_input_code.f
+	\$(TAF) \$(AD_TAF_FLAGS) ad_input_code.f
+	./adjoint_sed >! ad_output_code.f
+	@make ad_output_code.o
+	\$(LINK) -o \$@ \$(FFLAGS) \$(FOPTIM) \$(OBJFILES) ad_output_code.o \$(LIBS) 
+
+EXE_FTL_TAMC   = ${EXECUTABLE}_ftl_tamc
+EXE_FTL_TAF    = ${EXECUTABLE}_ftl_taf
+
+EXE_SVD_TAF    = ${EXECUTABLE}_ftl_taf
+EXE_BOTH_TAF   = ${EXECUTABLE}_ftl_taf
+
+#=========================================
+
 EOF
 
 if test "x$EXEHOOK" != x ; then