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-revision 1.2085 by gforget,
Tue Oct 21 14:22:26 2014 UTC
+revision 1.2167 by mlosch,
Wed Jul  1 12:27:05 2015 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
- o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
+ o pkg/seaice:
-   AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
+  - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
-   ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
+  - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
-   approach where CPP_OPTIONS.h includes an omnipotent
+    delta with a smooth function in s/r seaice_calc_viscosity
-   ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
+    (no effect on EVP)
- o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
+  - rename local suffix "sqr" into "sq" for more consistent variable names
-   ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
+ o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only***
+   for regularizing Delta (and nothing else, like the parameter
+   which is also used for all sorts of things SEAICE_EPS). Defaults to
+   SEAICE_EPS for backward compatibility only.
+ o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
+   the wrong key by inialising it before use -> fixes a recomputation
+   problem but does not fix the gradient
+ o pkg/layers:
+   - move resetting of flux arrays to outside the iLa loop
+     (this caused layers_diapycnal to not work with more than one layer coord.)
+   - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
+ o pkg/layers:
+   - remove from common block 3D layers fields (used to diagnose transport
+     in tracer coords) and declare them as local arrays in layers_calc.F
+ o pkg/seaice:
+   - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
+     in lab_sea forward experiment (changes results -> updated)
+   - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
+ o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
+   computations; for SEAICE_VECTORIZE_LSR
+   - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
+     sweep to the outside,
+   - remove store directives and add "CADJ loop sequential" directives
+     in analogy to model/src/solve_tridiagonal.F
+   - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
+     boundaries to yield more readable code. This has also the charming side
+     effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
+     SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
+     seaice_lsr_tridiagu/v now requires either of these flags, vectorization
+     still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
+     an additional option)
+    The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
+    but the adjoint gradients (which are affected by this change) still explode.
+ o coupler (atm & ocn _compon_interf):
+   - avoid using Exch2 IO mapping if not suitable.
+ checkpoint65m (2015/06/15)
+ o pkg/layers:
+   - clean-up old parameters setting (from Sep 2012):
+     + remove old parameters setting from common block (declared locally);
+     + stop if any old parameter is mixed with new parameters;
+     + check for valid or consistent parameter setting (e.g., layers_name)
+   - check that layers_bounds for Pot.Density are in the right range;
+     this is supposed to catch un-updated setting after recently shifting
+     potential density field "prho" by -1000 (now in "sigma" scale).
+ o pkg/layers:
+   - Added missing call to layers_fill for keeping track of tottend in
+     pkg/diagnostics/diagnostics_fill_state.F
+ o pkg/layers:
+   - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
+     of diapycnal fluxes
+ o pkg/layers:
+   - reverted changes to interpolation to previous treatment; there
+     was never actually a problem
+ o pkg/layers:
+   - fix interpolation of layers tracers in the presence of partial cells
+   - add lots of new functionality to compute water mass transformation
+     (enabled by CPP flag LAYERS_THERMODYNAMICS)
+   - add new calls from main code (diags_oceanic_surf_flux.F,
+     thermodynamics.F, impldiff.F) and gad to save the necessary fields
+     for layers_thermodynamics calculations
+ o pkg/ptracers:
+   - add capability of stepping a passive tracer forward without advection
+     by setting PTRACERS_advScheme to 0.
+ o pkg/diagnostics:
+   - add few (threads) _BARRIER around any update of "diag_pkgStatus".
+ o pkg/layers:
+   - shift potential density field "prho" by -1000 for density layer averaging so
+     that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
+     Note that density bin boundaries (layers_bounds in data.layers) have
+     to be set accordingly (i.e., shifted, in sigma scale).
+ o pkg/layers:
+   - fix snap-shot output of layer thickness @ V.pt and output of pot.density
+   - fix calculation of layer non-weighted velocity and layer probability
+   - add diagnostics for pot.density used for layer averaging
+ o pkg/seaice:
+   - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
+     positiveness, modify a few comments and improve variable names,
+   - the changed computation of deltaC affects most seaice-related
+     experiments at the truncation level.
+     seaice_itd.thermo is affected by far the most, with
+     only 7 digits of agreement remaining; update experiments.
+ checkpoint65l (2015/05/04)
+ o pkg/shelfice:
+   - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
+     factor drKp1 to zero where it is negative (ie. do not use
+     SHELFICEBoundaryLayer if hFacC>1)
+   - the same for factor drLoc in shelfice_forcing.F
+ o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
+     with modules in ptracers, when using testreport option "-small_f"
+ o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
+   - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
+ o verification/testreport
+   - add new option -small_f
+     with this option testreport first makes the target small_f (*.f files)
+     before running make (all). This is useful for explicit inlining when
+     all sources need to be full available.
+ o pkg/exf/exf_interp.F:
+     remove previous changes related to reverse (decreasing) input grids latitude
+ checkpoint65k (2015/04/01)
+ o pkg/ecco:
+     fix missing cosphi initialization; use eccoiter in place of optimcycle;
+     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+     instead of active read/write
+ o pkg/ctrl:
+     if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
+     instead of active read/write.
+ o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
+     return if .NOT.useAUTODIFF
+ o pkg/seaice: add CPP brackets (cost function related).
+ o model/src:
+     add useAUTODIFF run time switch.
+ o pkg/exf/exf_interp.F:
+     add code to allow input grids with latitude starting in the north (i.e. when
+     j=1 corresponds to northern edge of field); modify global_with_exf to test
+     this feature.
+ o verification/testreport:
+   - replace "grep -A3" with POSIX conformal sed command, because there are
+     implementations of grep that cannot do contextual searches
+   - replace "cat -n" by "nl" (two occurrences), because not all implementations
+     of "cat" have the option "-n"
+ o model/src:
+     add new file gsw_teos10.F that contains 3 functions, more or less a copy
+     of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
+     convert from conservative to potential temperature. For now they are not
+     called anywhere.
+ o pkg/ggl90: make "useIDEMIX" useful
+   - re-organize code in s/r ggl90_calc a little to move computations that
+     are different for idemix into separate loops (changes verification
+     experiment idemix at truncation level, 12 digits remain -> updated)
+   - requires 2 new 2D fields KappaM, verticalShear
+   - make hFacI and recip_hFacI local 3D variables that are passed to
+     s/r ggl90_idemix
+   - fix and improve some comments
+ checkpoint65j (2015/02/25)
+ o pkg/openad
+   - synchronize seawater.F with version in model/src: replace routine
+     body of sw_temp by calling sw_ptmp and fix/add a few comments.
+ o pkg/mnc:
+   - change default value of pickup_read/write_mnc params to FALSE
+     (since few features are missing in reading MNC pickup files).
+ o model/src:
+   - change default (background) vertical diffusivity for salt to be the
+     temperature (background) vertical diffusivity.
+   - change background vertical diffusivity in vertical mixing pkgs ggl90,
+     kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
+     This makes ptracers default diffusivity (that uses salt diffKr) more
+     consistent with vertical mixing schemes.
+ o verification/testreport:
+   - fix typo in "-pcls" option ;
+   - put temp files in /tmp (instead of in local dir)
+   - add option "-ncad" to use genmake2 new option "-nocat4ad"
+   - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
+ o pkg/ggl90 (idemix code):
+   - apply few fixes ; add some missing "_d 0" ; update output of exp.
+     global_ocean.90x40x15.idemix
+ o OpenAD
+   - enable active file I/O and begin removal of work-around code
+     for OpenAD for handling control variables (memory vs. active files)
+   - new CPP options file OPENAD_OPTIONS.h
+   - revert to genarr2d gradient check for hs94.1x64x5
+   - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
+   - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
+ o tools/genmake2:
+   - add option for an alternative Makefile (from Martin) where multiple
+     source files are sent to TAF (instead of all in one file).
+ o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
+   - code provided by Carsten Eden as an extension of ggl90
+   - so far the code is turned on within ggl90 by setting a CPP-flag at
+     compile time; a runtime flag implementation is not yet complete
+   - tested in new verification experiment global_ocean.90x40x15.idemix
+ o verification:
+   - reduce length of the AD test run by half for experiments
+     global_ocean.cs32x15 (std + thsice) and isomip
+   - enable active file I/O for OpenAD, adjust verifications accordingly
+   - halfpipe_streamice: change gradient check from genarr2d to gentim2d
+ o verification/testreport:
+   - fix two non-POSIX sed statements so that there are no error messages
+     on Mac OS X
+   - replace hostname -s with hostname | sed 's/\..*$//'
+ o model/src/seawater.F:
+   - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
+     (following the matlab code), which would have avoided the bug caught
+     by Matt (see below) in the first place
+ o pkg/shelfice:
+   - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
+     and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
+   - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
+     ice-shelf case (i.e., within surface level).
+   - add config summary in shelfice_check.F
+   - remove global variable recip_SHELFICElatentHeat and replace by a local
+     variable recip_latentHeat
+   - introduce diagnostics for friction velocity uStar (in case of
+     SHELFICEuseGammaFrict)
+   - change verification experiment isomip.htd:
+     + start from pickup (as input_ad at nIter0=8640)
+     + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
+     + test SHELFICEuseGammaFrict = .TRUE.
+     + test SHELFICEadvDiffHeatFlux = .TRUE.
+ o model/src:
+   - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
+     in-situ Temp) and in routine SW_TEMP (in pkg/openad);
+     update output of experiments global_with_exf.yearly and isomip (all 6).
+ o pkg/shelfice:
+   - change setting of kTopC to also be zero where there is no ice-shelf.
+   - zero out surface forcing arrays (for now, for T & S + EmPmR) where
+     ice-shelf is.
+   - first attempt to get RealFreshWaterFlux effects: for now, only without
+     SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
+ o pkg/seaice: add the option to prescribe a fixed thickness PDF
+   for thermodynamic calculations
+   - because of divisions of the type 7/7 not exactly equal to 1, this change
+     affects results of some verification experiments by up to 4 digits:
+     global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
+     seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
+     adjoint: lab_sea, lab_sea.noseaicedyn
+     -> updated
+ checkpoint65i (2015/01/23)
+ o model/src:
+   - change units of frictionHeating field from W to W/m^2
+   - fix bug in frictional heating from stratospheric drag in
+     S/R ATM_PHYS_TENDENCY_APPLY_V
+   - with synchronous time-stepping: move resetting to zero of frictionHeating
+     field from load_fields_driver.F to thermodynamics.F ;
+   - add diagnostics for frictional heating.
+ o model/src & gmredi K3D:
+   - add frictionHeating field to pickup-files (for synchronous time-stepping)
+   - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
+   - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
+     and name in pickup file).
+   - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
+ o model/src:
+   - move (from ini_forcing.F) initialisation of all arrays in header file
+     FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
+     (since Nov 2012) with option selectAddFluid=1.
+ o pkg/shelfice:
+   - change units (+ document) of newly added field "shelfIceMassDynTendency"
+   - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
+ o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
+ o pkg/seaice: two new runtime parameters:
+   - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
+     long overdue
+   - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
+     parameterization of tensil stress for fast ice (does not do anything yet)
+ o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
+     for LSR: move checking overlaps out of JFNK-if-block
+ o pkg/atm_phys:
+   - move copy of grid and dynamical fields out of atm_phys_driver.F into
+     new S/R ATM_PHYS_DYN2PHYS.
+   - fix level height for Linear Free-Surf case (to be consistent with
+     fixed-in-time pressure levels).
+ o pkg/mom_common (bottomdrag):
+   - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
+     to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
+     update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
+ o pkg/shelfice (u/v_drag):
+   - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
+   - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
+     (now similar to shelfice_u_drag.F)
+   - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
+     from mom_vecinv.F (similar to mom_fluxform calls).
+ o pkg/mom_common (bottomdrag):
+   - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
+   - add options for alternative discretisation of velocity norm in quadratic
+     bottom drag: averaging of grid-cell-center KE to U.point and V.point
+     (selectBotDragQuadr=0, original code) can produce noisy patterns; this
+     improves when averaging only the other component (e.g. vVel for U bottom
+     drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
+   - add options (bottomVisc_pCell) to account for partial-cell in bottom
+     friction (no-slip BC) thus getting the true distance from the bottom;
+     off by default since this also reduces model stability (explicit bottom
+     friction). Changes produce different machine truncation with linear-drag
+     + no-slip BC: update output of experiments exp4.stevens (10 digits) and
+     front_relax (bvp & mxl, 10 & 11 digits).
+ o model/src & mom pkgs:
+   - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
+     since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
+   - for now and until vertical mixing scheme are updated to fill up level Nr+1,
+     just copy level Nr value to level Nr+1.
+ o doc:
+   - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
+ o pkg/streamice:
+   - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
+     SHELFICE.h: move array shelficemass to init_varia, initialise
+     from array shelficemassinit, which is set in init_fixed and
+     has option to be set from file; introduce array
+     shelficeMassDynTend array, set thru file in init_fixed
+   - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
+     shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
+     pkg/streamice
+   - shelfice_thermodynamics.F: call shelfice_step_icemass if
+     SHELFICEMassStepping = .true.
+   - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
+ checkpoint65h (2014/12/17)
+ o verification/global_ocean.90x40x15, global_ocean_ebm:
+   - update to generic controls.
+ o pkg/ctrl:
+   - ctrl_map_ini_genarr.F: test for igen>0
+   - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
+   - move gentim2d part of ctrl_map_ini_genarr.F to
+     new separate routine : ctrl_map_ini_gentim2d.F
+   - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
+     add time variable weights and cyclic controls (time mean,
+     seasonal cycle, etc) capabilities to gentim2d
+ o pkg/ecco:
+   - move reading of error, conversion to weights from
+     ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
+ o global_oce_llc90, cs32:
+   - activte sbo.
+   - CTRL_SIZE.h : add maxCtrlProc.
+   - activate the new genctrl capabilities.
+   - update following reorganization of global_oce_input_fields.tar.gz
+ o pkg/ctrl/ctrl_ad_diff.list:
+   - add missing ctrl_init_rec.f
+ o tools/OAD_support/keepOriginal:
+   - add ctrl_init_rec.F
+ o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
+   - avoid recomputations of xx_gentim2d_dummy.
+ o momentum diagnostics:
+   - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
+     mom_vecinv.F to timestep.F (to include Smag-3D contribution).
+ o pkg/seaice/seaice_lsr.F:
+   - fix computation of BU/BV, make sure they are non-zero, only necessary
+     for cubed sphere exchanges and SEAICE_OLx/y>0.
+     This makes calling s/r fill_cs_corner_rl obsolete (removed).
+ o verification/global_ocean.cs32x15/input.seaice
+   - add test for strong implicit coupling and restricted addtive Schwarz
+     methods for LSR
+   - update results/output.seaice.txt
+ o verification/tutorial_global_oce_biogeo:
+   - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
+     and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
+     update output_adm,_oadm,_tlm.txt
+ o pkg/dic:
+   - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
+   - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
+     for tracer 1 & 2 is set (to avoid double counting of dilution effect).
+ o verification/tutorial_global_oce_biogeo:
+   - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
+     dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
+     update output_adm,_oadm,_tlm.txt
+ o eesupp/src:
+   - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
+     and call it in seaice_lsr when using nonzero SEAICE_OLx/y
+ o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
+   LSR (following Hutchings et al. 2004)
+   - introduce zetaZ as a global variable (requires adjustments in
+     seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
+     in seaice_calc_viscosities.F
+   - new flag SEAICEuseStrImpCpl (default off)
+   - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
+     momentum equations
+   - JFNK-solver (preconditioner) adjusted to allow using this method
+     (where it does not have any positive effect)
+ o pkg/seaice
+   - add overlap for restrictive additive Schwartz method also to LSR, but
+     turn it off by default (because it only seems to work for non-cubed
+     sphere/llc topologies)
+ o pkg/autodiff
+   - add extra exchanges in addummy_in_steppging also for mnc output
+ o pkg/seaice:
+   - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
+     to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
+ o pkg/obcs:
+   - add option to specify domain-connected piece Id along OB though files
+     (for now, only used to diagnose PhiVel; default =1 -> global correction)
+   - modify obcs_diag_balance.F to process each connected-part separately;
+     exclude OB where Id = 0 but keep the full divergence there (-> constant
+     Psi along this portion of OB and all inflow derived from grad(Phi))
+   - add example of OB-conect files in verification/so_box_biogeo/input.
+ o pkg/diagnostics:
+   - improve treatment of Open-Boundaries in Velocity-Potential calculation:
+   a) use non zero matrix element across OB and solve for Phi 1 grid point
+      outside OB (i.e, where tracer OBCS are applied).
+   b) global imbalance of inFlow/outFlow across OB: instead of modifying
+      velocity across OB, spread it uniformly along the OB in the RHS.
+ checkpoint65g (2014/11/19)
+ o pkg/diagnostcis:
+   - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
+ o pkg/my82,pp81,kl10:
+   - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
+     field diffKr as background diffusivity to set minimum diffusivity value.
+ o pkg/seaice:
+   - add new parameter SEAICEuseEVPrev (for revisited EVP by
+     Bouillon et al 2013)
+   - add SEAICE_evpAlpha/Beta to namelist
+   - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
+     involve trivial re-ordering of divisions/multiplications that should not
+     have any effects, but ... they do change the results of lab_sea.hb87 so
+     that only 2 digits of agreement remain, in line with the general
+     instability/fragility of the evp-code. For now, I do not care and just
+     update the verification experiment
+ o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
+   - remove xx_genarr2d_numsmooth etc
+   - use xx_genarr2d_preproc etc instead
+   - carry out smooth_correl2D at initialization stage rather than during
+     time stepping.
+   - get smoothOpNb from xx_gentim2d_preproc
+ o global_oce_cs32 :
+   - add test of generic ecco capabilities.
+ o pkg/exf/exf_getsurfacefluxes.F :
+   - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
+ o pkg/ctrl,ecco :
+   - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
+     is defined.
+ o pkg/seaice: add diagnostics for Delta (deformation parameter)
+ o model/src:
+   - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
+     diffusivity (background) is specified but ignored.
+ o verification:
+   - in testreport, convert hostname to lower case for default output dir name
+ o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
+ o pkg/dic: add modifications from Hajoon:
+   - add iron sedimentation flux function of the flux of PO4 out of bottom layer
+   - light attenuation: add self-shading effect by climatological Chlorophyll
+     (read from file).
+ o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
+     compiles when SEAICE_ALLOW_DYNAMICS is undefined
+ o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
+     AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
+     ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
+     approach where CPP_OPTIONS.h includes an omnipotent
+     ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
+ o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
+     ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
-   to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
+     to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
-   (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
+     (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
  o pkg/ctrl,ecco,exf :
    - remove variables associated with NON-generic costs,
      unless ECCO_CTRL_DEPRECATED is defined.
    - remove NON-generic NON-obcs controls,
      unless ECCO_CTRL_DEPRECATED is defined.
  o pkg/ctrl : added ctrl_local_params.h
  o pkg/ecco : added ecco_local_params.h
  o verification : added ECCO_CTRL_DEPRECATED to most as and oad
-   experiments, which will progressively be removed once the
+     experiments, which will progressively be removed once the
-   experiments are revised to use only generic controls/costs.
+     experiments are revised to use only generic controls/costs.
  checkpoint65f (2014/10/13)
  o pkg/ctrl, ecco, seaice : minor changes in headers
  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
-   cost function and control capabilities added since checkpoint65c.
+     cost function and control capabilities added since checkpoint65c.
  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
  o pkg/ecco: increase modularity and improve logic
    - ecco_toolbox.F (new) : basic operations that are often used,
-Line 393 
 o pkg/seaice: more clean up
+Line 823 
 o pkg/seaice: more clean up
      nearly a factor of 10 (but keep in mind there is mostly seaice code in
      this experiment):
      > size mitgcmuv_ad
      text    data        bss     dec        hex
      5100659 1216  220458952  225560827  d71c8fb
      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
      but only a moderate increase of 36% for global_ocean.cs32x15:
      text    data        bss     dec        hex

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