--- MITgcm/tools/adjoint_options/adjoint_tamc_compatibility	2013/08/07 16:20:03	1.7
+++ MITgcm/tools/adjoint_options/adjoint_tamc_compatibility	2013/08/09 18:28:36	1.8
@@ -1,11 +1,10 @@
 #!/bin/bash
 #
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/adjoint_options/adjoint_tamc_compatibility,v 1.7 2013/08/07 16:20:03 heimbach Exp $
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/adjoint_options/adjoint_tamc_compatibility,v 1.8 2013/08/09 18:28:36 jmc Exp $
 #  $Name:  $
-#
 
-#  This file contains the default settings for the adjoint and 
-#  tangent-linear compilers.  If you need to change these settings,
+#  This file contains the TAMC-like settings for the adjoint
+#  and tangent-linear compilers.  If you need to change these settings,
 #  please make a separate (local) copy of this file.
 
 # TAMC=/data43/ralf/tamc/tamc
@@ -15,13 +14,20 @@
 TAF=staf
 TAMC=tamc
 
-AD_TAMC_FLAGS='-reverse -admark ad -i4 -r4 -l tamc_ad.log'
-#AD_TAF_FLAGS='  -reverse -i4 -r4 -intrinsic system,flush -l taf_ad.log'
-AD_TAF_FLAGS="-v1 -nonew_arg  -reverse -i4 -r4 -intrinsic system,flush -l taf_ad.log $AD_TAF_FLAGS"
-FTL_TAMC_FLAGS='-forward -ftlmark g_ -i4 -r4 -l tamc_ftl.log'
-FTL_TAF_FLAGS='-v1 -nonew_arg  -forward -i4 -r4 -intrinsic system,flush -l taf_ftl.log'
-SVD_TAMC_FLAGS='-reverse -forward -pure -i4 -r4 -l tamc_svd.log'
-SVD_TAF_FLAGS='-v1 -nonew_arg  -reverse -forward -pure -i4 -r4 -intrinsic system,flush -l taf_svd.log'
+AD_TAMC_FLAGS="-reverse -admark ad -i4 -r4 -l tamc_ad.log $AD_TAMC_FLAGS"
+FTL_TAMC_FLAGS="-forward -ftlmark g_ -i4 -r4 -l tamc_ftl.log $FTL_TAMC_FLAGS"
+SVD_TAMC_FLAGS="-reverse -forward -pure -i4 -r4 -l tamc_svd.log $SVD_TAMC_FLAGS"
+
+AD_TAF_FLAGS="-v1 -nonew_arg -reverse -i4 -r4 -intrinsic system,flush -l taf_ad.log $AD_TAF_FLAGS"
+FTL_TAF_FLAGS="-v1 -nonew_arg -forward -i4 -r4 -intrinsic system,flush -l taf_ftl.log $FTL_TAF_FLAGS"
+SVD_TAF_FLAGS="-v1 -nonew_arg -reverse -forward -pure -i4 -r4 -intrinsic system,flush -l taf_svd.log $SVD_TAF_FLAGS"
+
+#- in case we need to show some MPI code to TAF:
+#if test "x$MPI" != x ; then
+#  AD_TAF_FLAGS="$AD_TAF_FLAGS"' -mpi -include $(LOCAL_MPI_HEADERS) -I./mpi_headers/'
+#  FLT_TAF_FLAGS="$FLT_TAF_FLAGS"' -mpi -include $(LOCAL_MPI_HEADERS) -I./mpi_headers/'
+#  SVD_TAF_FLAGS="$SVD_TAF_FLAGS"' -mpi -include $(LOCAL_MPI_HEADERS) -I./mpi_headers/'
+#fi
 
 DIFF_FLAGS="-toplevel 'the_main_loop'    \
             -input 'xx_theta_dummy       \
@@ -53,7 +59,7 @@
                     xx_depth_dummy       \
                     xx_diffkr_dummy      \
                     xx_kapgm_dummy       \
-                    xx_kapredi_dummy       \
+                    xx_kapredi_dummy     \
                     xx_bottomdrag_dummy  \
                     xx_efluxy_dummy      \
                     xx_efluxp_dummy      \
@@ -62,11 +68,15 @@
                     xx_uvel_dummy        \
                     xx_vvel_dummy        \
                     xx_etan_dummy        \
+                    xx_gen2d_dummy       \
+                    xx_gen3d_dummy       \
                     xx_genarr2d_dummy    \
                     xx_genarr3d_dummy    \
-                    xx_siarea_dummy        \
-                    xx_siheff_dummy        \
-                    xx_sihsnow_dummy        \
+                    xx_gentim2d_dummy    \
+                    xx_siarea_dummy      \
+                    xx_siheff_dummy      \
+                    xx_sihsnow_dummy     \
+                    xx_shifwflx_dummy    \
                     xx_relaxsst_dummy    \
                     xx_relaxsss_dummy    \
                     xx_atemp_mean_dummy  \
@@ -74,7 +84,7 @@
                     xx_precip_mean_dummy \
                     xx_swdown_mean_dummy \
                     xx_uwind_mean_dummy  \
-                    xx_vwind_mean_dummy'   \
+                    xx_vwind_mean_dummy' \
             -output 'fc'"
 
 AD_TAMC_FLAGS="$AD_TAMC_FLAGS $DIFF_FLAGS"