--- MITgcm/adjoint/makefile	2001/04/10 22:35:24	1.2
+++ MITgcm/adjoint/makefile	2002/02/11 21:54:05	1.21
@@ -2,60 +2,93 @@
 RM               = rm -f
 LOC              = $(PWD)
 TAMC             = tamc
+###TAMC             = /data43/ralf/tamc/tamc
+TAF              = taf
+###TAF              = ~fastopt/taf-1.3.5/bin/taf
 DEST             = .
 SOURCE_CODE      = ../bin
 ADJOINT_SCRIPT   = ../adjoint
 BASE             = ..
-TAMCFLAGS        = -adjoint -i4 -r4
 PKG		= $(BASE)/pkg
+#
+ADTAMCFLAGS      = -reverse -admark ad -i4 -r4
+ADTAFFLAGS       = -reverse -admark ad -i4 -r4 \
+			-flow taf_flow.log -nonew_arg
+FTLTAMCFLAGS     = -forward -ftlmark g_ -i4 -r4
+FTLTAFFLAGS      = -forward -ftlmark g_ -i4 -r4 \
+			-flow taf_flow.log -nonew_arg
+SVDTAMCFLAGS     = -reverse -forward -pure -i4 -r4
+SVDTAFFLAGS      = -reverse -forward -pure -i4 -r4 \
+			-flow taf_flow.log -nonew_arg
+#
+# -warn_step -flow taf_flow.log
 
-DIFF_FLAGS       = -module the_main_loop		\
+DIFF_FLAGS       = -toplevel the_main_loop		\
 		   -input  '    xx_theta_dummy		\
 				xx_salt_dummy		\
+                                xx_tr1_dummy		\
 				xx_hflux_dummy		\
 				xx_sflux_dummy		\
 				xx_tauu_dummy		\
 				xx_tauv_dummy		\
 				xx_sss_dummy		\
-				xx_sst_dummy'		\
+				xx_sst_dummy		\
+				xx_diffkr_dummy		\
+				xx_kapgm_dummy'		\
                    -output 'fc'
+#
+#                   -output 'objf_vector'
+#                   -output 'fc'
 
-TAMCFLAG         = $(TAMCFLAGS) $(DIFF_FLAGS) -l list_uv -admark ad
+ADTAMCFLAG         = $(ADTAMCFLAGS) $(DIFF_FLAGS)
+ADTAFFLAG          = $(ADTAFFLAGS)  $(DIFF_FLAGS)
 
+FTLTAMCFLAG         = $(FTLTAMCFLAGS) $(DIFF_FLAGS)
+FTLTAFFLAG          = $(FTLTAFFLAGS)  $(DIFF_FLAGS)
+
+SVDTAMCFLAG         = $(SVDTAMCFLAGS) $(DIFF_FLAGS)
+SVDTAFFLAG          = $(SVDTAFFLAGS)  $(DIFF_FLAGS)
 
 # Source files for the MITgcmUV
-SRC_MODEL	= $(PKG)/autodiff/read_write.flow	\
+SRC_MODEL	= \
+		$(PKG)/autodiff/read_write.flow	\
 		$(PKG)/autodiff/read_write_fld.flow	\
 		$(PKG)/autodiff/read_write_rec.flow	\
-		$(PKG)/autodiff/cg2d.flow		\
-		$(PKG)/autodiff/initialisation.flow	\
 		$(PKG)/autodiff/diags.flow		\
+		$(PKG)/autodiff/cg2d.flow		\
+		$(PKG)/autodiff/debug.flow		\
 		$(PKG)/autodiff/dummy_in_stepping.flow	\
 		$(PKG)/autodiff/external_fields_load.flow	\
 		$(PKG)/autodiff/eesupp.flow		\
 		$(PKG)/autodiff/active_file.flow	\
 		$(PKG)/autodiff/write_state.flow	\
-		$(PKG)/autodiff/write_time_averages.flow\
+		$(PKG)/autodiff/ecco_check_exp.flow	\
 		$(PKG)/autodiff/exch_ad.flow		\
+		$(PKG)/autodiff/exch_z_ad.flow		\
+		$(PKG)/autodiff/exch_uv_ad.flow		\
 		$(PKG)/autodiff/global_sum_ad.flow	\
 		$(PKG)/autodiff/global_max_ad.flow	\
+		$(PKG)/autodiff/initialisation.flow	\
 		$(PKG)/autodiff/mdsio.flow		\
+		$(PKG)/autodiff/monitor.flow		\
 		$(PKG)/autodiff/checkpoint.flow		\
 		$(PKG)/autodiff/print_message.flow	\
 		$(PKG)/autodiff/open_copy_data_file.flow\
 		$(PKG)/autodiff/timeave.flow		\
 		  		  				\
-		$(SOURCE_CODE)/grad_sigma.f			\
+		$(SOURCE_CODE)/adams_bashforth2.f		\
 		$(SOURCE_CODE)/calc_buoyancy.f			\
 		$(SOURCE_CODE)/calc_common_factors.f		\
 		$(SOURCE_CODE)/calc_diffusivity.f		\
 		$(SOURCE_CODE)/calc_div_ghat.f			\
+		$(SOURCE_CODE)/calc_exact_eta.f			\
 		$(SOURCE_CODE)/calc_grad_phi_surf.f		\
 		$(SOURCE_CODE)/calc_gs.f			\
 		$(SOURCE_CODE)/calc_gt.f			\
+		$(SOURCE_CODE)/calc_gtr1.f			\
 		$(SOURCE_CODE)/calc_ivdc.f			\
-		$(SOURCE_CODE)/calc_mom_rhs.f			\
 		$(SOURCE_CODE)/calc_phi_hyd.f			\
+		$(SOURCE_CODE)/calc_viscosity.f			\
 		$(SOURCE_CODE)/comm_stats.f			\
 		$(SOURCE_CODE)/convect.f			\
 		$(SOURCE_CODE)/convective_adjustment.f		\
@@ -70,31 +103,113 @@
 		$(SOURCE_CODE)/external_forcing_surf.f		\
 		$(SOURCE_CODE)/find_alpha.f			\
 		$(SOURCE_CODE)/find_rho.f			\
+		$(SOURCE_CODE)/forward_step.f			\
 		$(SOURCE_CODE)/freeze.f				\
-		$(SOURCE_CODE)/get_offline_fields.f		\
+								\
+		$(SOURCE_CODE)/gad_advection.f			\
+		$(SOURCE_CODE)/gad_biharm_x.f			\
+		$(SOURCE_CODE)/gad_biharm_y.f			\
+		$(SOURCE_CODE)/gad_c2_adv_r.f			\
+		$(SOURCE_CODE)/gad_c2_adv_x.f			\
+		$(SOURCE_CODE)/gad_c2_adv_y.f			\
+		$(SOURCE_CODE)/gad_c4_adv_r.f			\
+		$(SOURCE_CODE)/gad_c4_adv_x.f			\
+		$(SOURCE_CODE)/gad_c4_adv_y.f			\
+		$(SOURCE_CODE)/gad_calc_rhs.f			\
+		$(SOURCE_CODE)/gad_del2.f			\
+		$(SOURCE_CODE)/gad_diff_r.f			\
+		$(SOURCE_CODE)/gad_diff_x.f			\
+		$(SOURCE_CODE)/gad_diff_y.f			\
+		$(SOURCE_CODE)/gad_dst3_adv_x.f                 \
+		$(SOURCE_CODE)/gad_dst3_adv_y.f                 \
+		$(SOURCE_CODE)/gad_dst3_adv_r.f			\
+		$(SOURCE_CODE)/gad_dst3fl_adv_x.f               \
+		$(SOURCE_CODE)/gad_dst3fl_adv_y.f               \
+		$(SOURCE_CODE)/gad_dst3fl_adv_r.f		\
+		$(SOURCE_CODE)/gad_fluxlimit_adv_r.f		\
+		$(SOURCE_CODE)/gad_fluxlimit_adv_x.f		\
+		$(SOURCE_CODE)/gad_fluxlimit_adv_y.f		\
+		$(SOURCE_CODE)/gad_grad_x.f			\
+		$(SOURCE_CODE)/gad_grad_y.f			\
+		$(SOURCE_CODE)/gad_u3_adv_r.f			\
+		$(SOURCE_CODE)/gad_u3_adv_x.f			\
+		$(SOURCE_CODE)/gad_u3_adv_y.f			\
+								\
+		$(SOURCE_CODE)/grad_sigma.f			\
 		$(SOURCE_CODE)/impldiff.f			\
+		$(SOURCE_CODE)/ini_autodiff.f			\
 		$(SOURCE_CODE)/ini_cartesian_grid.f		\
 		$(SOURCE_CODE)/ini_cg2d.f			\
 		$(SOURCE_CODE)/ini_communication_patterns.f	\
 		$(SOURCE_CODE)/ini_cori.f			\
+		$(SOURCE_CODE)/ini_curvilinear_grid.f		\
 		$(SOURCE_CODE)/ini_depths.f			\
 		$(SOURCE_CODE)/ini_fields.f			\
 		$(SOURCE_CODE)/ini_forcing.f			\
 		$(SOURCE_CODE)/ini_grid.f			\
+		$(SOURCE_CODE)/ini_linear_phisurf.f		\
 		$(SOURCE_CODE)/ini_masks_etc.f			\
-		$(SOURCE_CODE)/ini_procs.f			\
+		$(SOURCE_CODE)/ini_mixing.f			\
+		$(SOURCE_CODE)/ini_p_ground.f			\
+		$(SOURCE_CODE)/ini_pnh.f			\
 		$(SOURCE_CODE)/ini_psurf.f			\
 		$(SOURCE_CODE)/ini_salt.f			\
 		$(SOURCE_CODE)/ini_spherical_polar_grid.f	\
 		$(SOURCE_CODE)/ini_theta.f			\
-		$(SOURCE_CODE)/ini_uvel.f			\
+		$(SOURCE_CODE)/ini_tr1.f			\
+		$(SOURCE_CODE)/ini_dynvars.f			\
+		$(SOURCE_CODE)/ini_vel.f			\
 		$(SOURCE_CODE)/ini_vertical_grid.f		\
-		$(SOURCE_CODE)/ini_vvel.f			\
-		$(SOURCE_CODE)/ini_wvel.f			\
 		$(SOURCE_CODE)/initialise_varia.f		\
 		$(SOURCE_CODE)/integrate_for_w.f		\
 		$(SOURCE_CODE)/modeldata_example.f		\
-		$(SOURCE_CODE)/nml_filter.f			\
+								\
+		$(SOURCE_CODE)/mom_fluxform.f			\
+		$(SOURCE_CODE)/mom_hdissip.f			\
+		$(SOURCE_CODE)/mom_vecinv.f			\
+		$(SOURCE_CODE)/mom_calc_hfacz.f			\
+		$(SOURCE_CODE)/mom_calc_ke.f			\
+		$(SOURCE_CODE)/mom_calc_strain.f		\
+		$(SOURCE_CODE)/mom_calc_tension.f		\
+		$(SOURCE_CODE)/mom_cdscheme.f			\
+		$(SOURCE_CODE)/mom_u_adv_uu.f			\
+		$(SOURCE_CODE)/mom_u_adv_vu.f			\
+		$(SOURCE_CODE)/mom_u_adv_wu.f			\
+		$(SOURCE_CODE)/mom_u_bottomdrag.f		\
+		$(SOURCE_CODE)/mom_u_coriolis.f			\
+		$(SOURCE_CODE)/mom_u_del2u.f			\
+		$(SOURCE_CODE)/mom_u_metric_nh.f		\
+		$(SOURCE_CODE)/mom_u_metric_sphere.f		\
+		$(SOURCE_CODE)/mom_u_rviscflux.f		\
+		$(SOURCE_CODE)/mom_u_sidedrag.f			\
+		$(SOURCE_CODE)/mom_u_xviscflux.f		\
+		$(SOURCE_CODE)/mom_u_yviscflux.f		\
+		$(SOURCE_CODE)/mom_v_adv_uv.f			\
+		$(SOURCE_CODE)/mom_v_adv_vv.f			\
+		$(SOURCE_CODE)/mom_v_adv_wv.f			\
+		$(SOURCE_CODE)/mom_v_bottomdrag.f		\
+		$(SOURCE_CODE)/mom_v_coriolis.f			\
+		$(SOURCE_CODE)/mom_v_del2v.f			\
+		$(SOURCE_CODE)/mom_v_metric_nh.f		\
+		$(SOURCE_CODE)/mom_v_metric_sphere.f		\
+		$(SOURCE_CODE)/mom_v_rviscflux.f		\
+		$(SOURCE_CODE)/mom_v_sidedrag.f			\
+		$(SOURCE_CODE)/mom_v_xviscflux.f		\
+		$(SOURCE_CODE)/mom_v_yviscflux.f		\
+		$(SOURCE_CODE)/mom_vi_calc_absvort3.f		\
+		$(SOURCE_CODE)/mom_vi_calc_hdiv.f		\
+		$(SOURCE_CODE)/mom_vi_calc_ke.f			\
+		$(SOURCE_CODE)/mom_vi_calc_relvort3.f		\
+		$(SOURCE_CODE)/mom_vi_coriolis.f		\
+		$(SOURCE_CODE)/mom_vi_del2uv.f			\
+		$(SOURCE_CODE)/mom_vi_hdissip.f			\
+		$(SOURCE_CODE)/mom_vi_u_coriolis.f		\
+		$(SOURCE_CODE)/mom_vi_u_grad_ke.f		\
+		$(SOURCE_CODE)/mom_vi_u_vertshear.f		\
+		$(SOURCE_CODE)/mom_vi_v_coriolis.f		\
+		$(SOURCE_CODE)/mom_vi_v_grad_ke.f		\
+		$(SOURCE_CODE)/mom_vi_v_vertshear.f		\
+		  						\
 		$(SOURCE_CODE)/packages_init_variables.f	\
 		$(SOURCE_CODE)/plot_field.f			\
 		$(SOURCE_CODE)/solve_for_pressure.f		\
@@ -102,11 +217,13 @@
 		$(SOURCE_CODE)/timestep.f			\
 		$(SOURCE_CODE)/the_correction_step.f		\
 		$(SOURCE_CODE)/the_main_loop.f			\
+		$(SOURCE_CODE)/thermodynamics.f			\
 		$(SOURCE_CODE)/timestep_tracer.f		\
 		$(SOURCE_CODE)/swfrac.f				\
 		  						\
 		$(SOURCE_CODE)/kpp_calc.f			\
 		$(SOURCE_CODE)/kpp_calc_diff.f			\
+		$(SOURCE_CODE)/kpp_calc_visc.f			\
 		$(SOURCE_CODE)/kpp_do_diags.f			\
 		$(SOURCE_CODE)/kpp_init.f			\
 		$(SOURCE_CODE)/kpp_open_diags.f			\
@@ -128,7 +245,27 @@
 		  						\
 		$(SOURCE_CODE)/cost_final.f			\
 		$(SOURCE_CODE)/cost_init.f			\
+		$(SOURCE_CODE)/cost_tile.f			\
 		$(SOURCE_CODE)/cost_test.f			\
+		$(SOURCE_CODE)/cost_tracer.f			\
+		$(SOURCE_CODE)/cost_atlantic_heat.f		\
+		$(SOURCE_CODE)/cost_vector.f			\
+		  						\
+		$(SOURCE_CODE)/shap_filt_apply_ts.f		\
+		$(SOURCE_CODE)/shap_filt_apply_uv.f		\
+		$(SOURCE_CODE)/shap_filt_tracer_s1.f		\
+		$(SOURCE_CODE)/shap_filt_tracer_s2.f		\
+		$(SOURCE_CODE)/shap_filt_tracer_s2g.f		\
+		$(SOURCE_CODE)/shap_filt_tracer_s4.f		\
+		$(SOURCE_CODE)/shap_filt_uv_s1.f		\
+		$(SOURCE_CODE)/shap_filt_uv_s2.f		\
+		$(SOURCE_CODE)/shap_filt_uv_s2g.f		\
+		$(SOURCE_CODE)/shap_filt_uv_s4.f		\
+		  						\
+
+#		$(SOURCE_CODE)/calc_ep_forcing.f		\
+#		$(SOURCE_CODE)/cost_entropy.f			\
+#		$(SOURCE_CODE)/ini_ep.f				\
 		  						\
 
 
@@ -136,19 +273,53 @@
 # rules
 #--------------------------------------------------------
 
-adcode:
-	cd $(DEST) ; cat $(SRC_MODEL) >! tamc_code_ecco.f
-admodel:
-	cd $(DEST) ; $(TAMC) $(TAMCFLAG) tamc_code_ecco.f	\
-           >! tamc_code_ecco.prot
+allcode:
+	cd $(DEST) ; cat $(SRC_MODEL) >! tamc_code.f
+
+admodeltamc:
+	cd $(DEST) ; $(TAMC) $(ADTAMCFLAG) tamc_code.f	\
+           >! tamc_code_ad.prot
+
+admodeltaf:
+	cd $(DEST) ; $(TAF) $(ADTAFFLAG) tamc_code.f
+
+ftlmodeltamc:
+	cd $(DEST) ; $(TAMC) $(FTLTAMCFLAG) tamc_code.f	\
+           >! tamc_code_ftl.prot
+
+ftlmodeltaf:
+	cd $(DEST) ; $(TAF) $(FTLTAFFLAG) tamc_code.f
+
+svdmodeltaf:
+	cd $(DEST) ; $(TAF) $(SVDTAFFLAG) tamc_code.f
 
 adchange:
-	${ADJOINT_SCRIPT}/adjoint_ecco_sed.com \
-           >! tamc_code_ecco_sed_ad.f ;  \
+	${ADJOINT_SCRIPT}/adjoint_sed.com \
+           >! tamc_code_sed_ad.f ;  \
         cp $(PKG)/autodiff/adjoint_model.F		\
            $(PKG)/autodiff/adjoint_model.F_old ;	\
-        cat tamc_code_ecco_sed_ad.f >> $(PKG)/autodiff/adjoint_model.F
+        cat tamc_code_sed_ad.f >> $(PKG)/autodiff/adjoint_model.F
+
+ftlchange:
+	cp $(PKG)/autodiff/tangentlinear_model.F		\
+           $(PKG)/autodiff/tangentlinear_model.F_old ;	\
+        cat tamc_code_ftl.f >> $(PKG)/autodiff/tangentlinear_model.F
+
 adrestore:
 	cp $(PKG)/autodiff/adjoint_model.F_template	\
            $(PKG)/autodiff/adjoint_model.F
-adall:  adcode admodel
+
+ftlrestore:
+	cp $(PKG)/autodiff/tangentlinear_model.F_template	\
+           $(PKG)/autodiff/tangentlinear_model.F
+
+adtamc:  adrestore ftlrestore allcode admodeltamc
+
+adtaf:  adrestore ftlrestore allcode admodeltaf
+
+ftltamc:  adrestore ftlrestore allcode ftlmodeltamc
+
+ftltaf:  adrestore ftlrestore allcode ftlmodeltaf
+
+svdtaf:  adrestore ftlrestore allcode svdmodeltaf
+