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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2163 by mlosch, Tue Jun 16 16:27:40 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/layers:
8      - remove from common block 3D layers fields (used to diagnose transport
9        in tracer coords) and declare them as local arrays in layers_calc.F
10    o pkg/seaice:
11      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
12        in lab_sea forward experiment (changes results -> updated)
13      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
14    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
15      computations; for SEAICE_VECTORIZE_LSR
16      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
17        sweep to the outside,
18      - remove store directives and add "CADJ loop sequential" directives
19        in analogy to model/src/solve_tridiagonal.F
20      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
21        boundaries to yield more readable code. This has also the charming side
22        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
23        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
24        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
25        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
26        an additional option)
27       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
28       but the adjoint gradients (which are affected by this change) still explode.
29    o coupler (atm & ocn _compon_interf):
30      - avoid using Exch2 IO mapping if not suitable.
31    
32    checkpoint65m (2015/06/15)
33    o pkg/layers:
34      - clean-up old parameters setting (from Sep 2012):
35        + remove old parameters setting from common block (declared locally);
36        + stop if any old parameter is mixed with new parameters;
37        + check for valid or consistent parameter setting (e.g., layers_name)
38      - check that layers_bounds for Pot.Density are in the right range;
39        this is supposed to catch un-updated setting after recently shifting
40        potential density field "prho" by -1000 (now in "sigma" scale).
41    o pkg/layers:
42      - Added missing call to layers_fill for keeping track of tottend in
43        pkg/diagnostics/diagnostics_fill_state.F
44    o pkg/layers:
45      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
46        of diapycnal fluxes
47    o pkg/layers:
48      - reverted changes to interpolation to previous treatment; there
49        was never actually a problem
50    o pkg/layers:
51      - fix interpolation of layers tracers in the presence of partial cells
52      - add lots of new functionality to compute water mass transformation
53        (enabled by CPP flag LAYERS_THERMODYNAMICS)
54      - add new calls from main code (diags_oceanic_surf_flux.F,
55        thermodynamics.F, impldiff.F) and gad to save the necessary fields
56        for layers_thermodynamics calculations
57    o pkg/ptracers:
58      - add capability of stepping a passive tracer forward without advection
59        by setting PTRACERS_advScheme to 0.
60    o pkg/diagnostics:
61      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
62    o pkg/layers:
63      - shift potential density field "prho" by -1000 for density layer averaging so
64        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
65        Note that density bin boundaries (layers_bounds in data.layers) have
66        to be set accordingly (i.e., shifted, in sigma scale).
67    o pkg/layers:
68      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
69      - fix calculation of layer non-weighted velocity and layer probability
70      - add diagnostics for pot.density used for layer averaging
71    o pkg/seaice:
72      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
73        positiveness, modify a few comments and improve variable names,
74      - the changed computation of deltaC affects most seaice-related
75        experiments at the truncation level.
76        seaice_itd.thermo is affected by far the most, with
77        only 7 digits of agreement remaining; update experiments.
78    
79    checkpoint65l (2015/05/04)
80    o pkg/shelfice:
81      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
82        factor drKp1 to zero where it is negative (ie. do not use
83        SHELFICEBoundaryLayer if hFacC>1)
84      - the same for factor drLoc in shelfice_forcing.F
85    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
86        with modules in ptracers, when using testreport option "-small_f"
87    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
88      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
89    o verification/testreport
90      - add new option -small_f
91        with this option testreport first makes the target small_f (*.f files)
92        before running make (all). This is useful for explicit inlining when
93        all sources need to be full available.
94    o pkg/exf/exf_interp.F:
95        remove previous changes related to reverse (decreasing) input grids latitude
96    
97    checkpoint65k (2015/04/01)
98    o pkg/ecco:
99        fix missing cosphi initialization; use eccoiter in place of optimcycle;
100        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
101        instead of active read/write
102    o pkg/ctrl:
103        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
104        instead of active read/write.
105    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
106        return if .NOT.useAUTODIFF
107    o pkg/seaice: add CPP brackets (cost function related).
108    o model/src:
109        add useAUTODIFF run time switch.
110    o pkg/exf/exf_interp.F:
111        add code to allow input grids with latitude starting in the north (i.e. when
112        j=1 corresponds to northern edge of field); modify global_with_exf to test
113        this feature.
114    o verification/testreport:
115      - replace "grep -A3" with POSIX conformal sed command, because there are
116        implementations of grep that cannot do contextual searches
117      - replace "cat -n" by "nl" (two occurrences), because not all implementations
118        of "cat" have the option "-n"
119    o model/src:
120        add new file gsw_teos10.F that contains 3 functions, more or less a copy
121        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
122        convert from conservative to potential temperature. For now they are not
123        called anywhere.
124    o pkg/ggl90: make "useIDEMIX" useful
125      - re-organize code in s/r ggl90_calc a little to move computations that
126        are different for idemix into separate loops (changes verification
127        experiment idemix at truncation level, 12 digits remain -> updated)
128      - requires 2 new 2D fields KappaM, verticalShear
129      - make hFacI and recip_hFacI local 3D variables that are passed to
130        s/r ggl90_idemix
131      - fix and improve some comments
132    
133    checkpoint65j (2015/02/25)
134    o pkg/openad
135      - synchronize seawater.F with version in model/src: replace routine
136        body of sw_temp by calling sw_ptmp and fix/add a few comments.
137    o pkg/mnc:
138      - change default value of pickup_read/write_mnc params to FALSE
139        (since few features are missing in reading MNC pickup files).
140    o model/src:
141      - change default (background) vertical diffusivity for salt to be the
142        temperature (background) vertical diffusivity.
143      - change background vertical diffusivity in vertical mixing pkgs ggl90,
144        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
145        This makes ptracers default diffusivity (that uses salt diffKr) more
146        consistent with vertical mixing schemes.
147    o verification/testreport:
148      - fix typo in "-pcls" option ;
149      - put temp files in /tmp (instead of in local dir)
150      - add option "-ncad" to use genmake2 new option "-nocat4ad"
151      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
152    o pkg/ggl90 (idemix code):
153      - apply few fixes ; add some missing "_d 0" ; update output of exp.
154        global_ocean.90x40x15.idemix
155    o OpenAD
156      - enable active file I/O and begin removal of work-around code
157        for OpenAD for handling control variables (memory vs. active files)
158      - new CPP options file OPENAD_OPTIONS.h
159      - revert to genarr2d gradient check for hs94.1x64x5
160      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
161      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
162    o tools/genmake2:
163      - add option for an alternative Makefile (from Martin) where multiple
164        source files are sent to TAF (instead of all in one file).
165    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
166      - code provided by Carsten Eden as an extension of ggl90
167      - so far the code is turned on within ggl90 by setting a CPP-flag at
168        compile time; a runtime flag implementation is not yet complete
169      - tested in new verification experiment global_ocean.90x40x15.idemix
170    o verification:
171      - reduce length of the AD test run by half for experiments
172        global_ocean.cs32x15 (std + thsice) and isomip
173      - enable active file I/O for OpenAD, adjust verifications accordingly
174      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
175    o verification/testreport:
176      - fix two non-POSIX sed statements so that there are no error messages
177        on Mac OS X
178      - replace hostname -s with hostname | sed 's/\..*$//'
179    o model/src/seawater.F:
180      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
181        (following the matlab code), which would have avoided the bug caught
182        by Matt (see below) in the first place
183    o pkg/shelfice:
184      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
185        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
186      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
187        ice-shelf case (i.e., within surface level).
188      - add config summary in shelfice_check.F
189      - remove global variable recip_SHELFICElatentHeat and replace by a local
190        variable recip_latentHeat
191      - introduce diagnostics for friction velocity uStar (in case of
192        SHELFICEuseGammaFrict)
193      - change verification experiment isomip.htd:
194        + start from pickup (as input_ad at nIter0=8640)
195        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
196        + test SHELFICEuseGammaFrict = .TRUE.
197        + test SHELFICEadvDiffHeatFlux = .TRUE.
198    o model/src:
199      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
200        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
201        update output of experiments global_with_exf.yearly and isomip (all 6).
202    o pkg/shelfice:
203      - change setting of kTopC to also be zero where there is no ice-shelf.
204      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
205        ice-shelf is.
206      - first attempt to get RealFreshWaterFlux effects: for now, only without
207        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
208    o pkg/seaice: add the option to prescribe a fixed thickness PDF
209      for thermodynamic calculations
210      - because of divisions of the type 7/7 not exactly equal to 1, this change
211        affects results of some verification experiments by up to 4 digits:
212        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
213        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
214        adjoint: lab_sea, lab_sea.noseaicedyn
215        -> updated
216    
217    checkpoint65i (2015/01/23)
218    o model/src:
219      - change units of frictionHeating field from W to W/m^2
220      - fix bug in frictional heating from stratospheric drag in
221        S/R ATM_PHYS_TENDENCY_APPLY_V
222      - with synchronous time-stepping: move resetting to zero of frictionHeating
223        field from load_fields_driver.F to thermodynamics.F ;
224      - add diagnostics for frictional heating.
225    o model/src & gmredi K3D:
226      - add frictionHeating field to pickup-files (for synchronous time-stepping)
227      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
228      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
229        and name in pickup file).
230      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
231    o model/src:
232      - move (from ini_forcing.F) initialisation of all arrays in header file
233        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
234        (since Nov 2012) with option selectAddFluid=1.
235    o pkg/shelfice:
236      - change units (+ document) of newly added field "shelfIceMassDynTendency"
237      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
238    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
239    o pkg/seaice: two new runtime parameters:
240      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
241        long overdue
242      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
243        parameterization of tensil stress for fast ice (does not do anything yet)
244    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
245        for LSR: move checking overlaps out of JFNK-if-block
246    o pkg/atm_phys:
247      - move copy of grid and dynamical fields out of atm_phys_driver.F into
248        new S/R ATM_PHYS_DYN2PHYS.
249      - fix level height for Linear Free-Surf case (to be consistent with
250        fixed-in-time pressure levels).
251    o pkg/mom_common (bottomdrag):
252      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
253        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
254        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
255    o pkg/shelfice (u/v_drag):
256      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
257      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
258        (now similar to shelfice_u_drag.F)
259      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
260        from mom_vecinv.F (similar to mom_fluxform calls).
261    o pkg/mom_common (bottomdrag):
262      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
263      - add options for alternative discretisation of velocity norm in quadratic
264        bottom drag: averaging of grid-cell-center KE to U.point and V.point
265        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
266        improves when averaging only the other component (e.g. vVel for U bottom
267        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
268      - add options (bottomVisc_pCell) to account for partial-cell in bottom
269        friction (no-slip BC) thus getting the true distance from the bottom;
270        off by default since this also reduces model stability (explicit bottom
271        friction). Changes produce different machine truncation with linear-drag
272        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
273        front_relax (bvp & mxl, 10 & 11 digits).
274    o model/src & mom pkgs:
275      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
276        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
277      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
278        just copy level Nr value to level Nr+1.
279    o doc:
280      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
281    o pkg/streamice:
282      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
283        SHELFICE.h: move array shelficemass to init_varia, initialise
284        from array shelficemassinit, which is set in init_fixed and
285        has option to be set from file; introduce array
286        shelficeMassDynTend array, set thru file in init_fixed
287      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
288        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
289        pkg/streamice
290      - shelfice_thermodynamics.F: call shelfice_step_icemass if
291        SHELFICEMassStepping = .true.
292      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
293    
294    checkpoint65h (2014/12/17)
295    o verification/global_ocean.90x40x15, global_ocean_ebm:
296      - update to generic controls.
297    o pkg/ctrl:
298      - ctrl_map_ini_genarr.F: test for igen>0
299      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
300      - move gentim2d part of ctrl_map_ini_genarr.F to
301        new separate routine : ctrl_map_ini_gentim2d.F
302      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
303        add time variable weights and cyclic controls (time mean,
304        seasonal cycle, etc) capabilities to gentim2d
305    o pkg/ecco:
306      - move reading of error, conversion to weights from
307        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
308    o global_oce_llc90, cs32:
309      - activte sbo.
310      - CTRL_SIZE.h : add maxCtrlProc.
311      - activate the new genctrl capabilities.
312      - update following reorganization of global_oce_input_fields.tar.gz  
313    o pkg/ctrl/ctrl_ad_diff.list:
314      - add missing ctrl_init_rec.f
315    o tools/OAD_support/keepOriginal:
316      - add ctrl_init_rec.F
317    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
318      - avoid recomputations of xx_gentim2d_dummy.
319    o momentum diagnostics:
320      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
321        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
322    o pkg/seaice/seaice_lsr.F:
323      - fix computation of BU/BV, make sure they are non-zero, only necessary
324        for cubed sphere exchanges and SEAICE_OLx/y>0.
325        This makes calling s/r fill_cs_corner_rl obsolete (removed).
326    o verification/global_ocean.cs32x15/input.seaice
327      - add test for strong implicit coupling and restricted addtive Schwarz
328        methods for LSR
329      - update results/output.seaice.txt
330    o verification/tutorial_global_oce_biogeo:
331      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
332        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
333        update output_adm,_oadm,_tlm.txt
334    o pkg/dic:
335      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
336      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
337        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
338    o verification/tutorial_global_oce_biogeo:
339      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
340        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
341        update output_adm,_oadm,_tlm.txt
342    o eesupp/src:
343      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
344        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
345    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
346      LSR (following Hutchings et al. 2004)
347      - introduce zetaZ as a global variable (requires adjustments in
348        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
349        in seaice_calc_viscosities.F
350      - new flag SEAICEuseStrImpCpl (default off)
351      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
352        momentum equations
353      - JFNK-solver (preconditioner) adjusted to allow using this method
354        (where it does not have any positive effect)
355    o pkg/seaice
356      - add overlap for restrictive additive Schwartz method also to LSR, but
357        turn it off by default (because it only seems to work for non-cubed
358        sphere/llc topologies)
359    o pkg/autodiff
360      - add extra exchanges in addummy_in_steppging also for mnc output
361    o pkg/seaice:
362      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
363        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
364    o pkg/obcs:
365      - add option to specify domain-connected piece Id along OB though files
366        (for now, only used to diagnose PhiVel; default =1 -> global correction)
367      - modify obcs_diag_balance.F to process each connected-part separately;
368        exclude OB where Id = 0 but keep the full divergence there (-> constant
369        Psi along this portion of OB and all inflow derived from grad(Phi))
370      - add example of OB-conect files in verification/so_box_biogeo/input.
371    o pkg/diagnostics:
372      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
373      a) use non zero matrix element across OB and solve for Phi 1 grid point
374         outside OB (i.e, where tracer OBCS are applied).
375      b) global imbalance of inFlow/outFlow across OB: instead of modifying
376         velocity across OB, spread it uniformly along the OB in the RHS.
377    
378    checkpoint65g (2014/11/19)
379    o pkg/diagnostcis:
380      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
381    o pkg/my82,pp81,kl10:
382      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
383        field diffKr as background diffusivity to set minimum diffusivity value.
384    o pkg/seaice:
385      - add new parameter SEAICEuseEVPrev (for revisited EVP by
386        Bouillon et al 2013)
387      - add SEAICE_evpAlpha/Beta to namelist
388      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
389        involve trivial re-ordering of divisions/multiplications that should not
390        have any effects, but ... they do change the results of lab_sea.hb87 so
391        that only 2 digits of agreement remain, in line with the general
392        instability/fragility of the evp-code. For now, I do not care and just
393        update the verification experiment
394    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
395      - remove xx_genarr2d_numsmooth etc
396      - use xx_genarr2d_preproc etc instead
397      - carry out smooth_correl2D at initialization stage rather than during
398        time stepping.
399      - get smoothOpNb from xx_gentim2d_preproc
400    o global_oce_cs32 :
401      - add test of generic ecco capabilities.
402    o pkg/exf/exf_getsurfacefluxes.F :
403      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
404    o pkg/ctrl,ecco :
405      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
406        is defined.
407    o pkg/seaice: add diagnostics for Delta (deformation parameter)
408    o model/src:
409      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
410        diffusivity (background) is specified but ignored.
411    o verification:
412      - in testreport, convert hostname to lower case for default output dir name
413    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
414    o pkg/dic: add modifications from Hajoon:
415      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
416      - light attenuation: add self-shading effect by climatological Chlorophyll
417        (read from file).
418    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
419        compiles when SEAICE_ALLOW_DYNAMICS is undefined
420    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
421        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
422        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
423        approach where CPP_OPTIONS.h includes an omnipotent
424        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
425    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
426        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
427    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
428        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
429        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
430    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
431      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
432      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
433      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
434      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
435    o pkg/ctrl,ecco,exf :
436      - remove variables associated with NON-generic costs,
437        unless ECCO_CTRL_DEPRECATED is defined.
438      - remove NON-generic NON-obcs controls,
439        unless ECCO_CTRL_DEPRECATED is defined.
440    o pkg/ctrl : added ctrl_local_params.h
441    o pkg/ecco : added ecco_local_params.h
442    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
443        experiments, which will progressively be removed once the
444        experiments are revised to use only generic controls/costs.
445    
446    checkpoint65f (2014/10/13)
447    o pkg/ctrl, ecco, seaice : minor changes in headers
448    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
449        cost function and control capabilities added since checkpoint65c.
450    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
451    o pkg/ecco: increase modularity and improve logic
452      - ecco_toolbox.F (new) : basic operations that are often used,
453        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
454        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
455      - cost_gencal.F (new) : determine filnames and records.
456      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
457      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
458        and exploit the above functions leading to more compact code.
459      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
460      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
461        using_ers, using_gfo, using_mdt is now only defined within gencost)
462    o pkg/ecco: extend generic cost capabilities
463      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
464        capabilities via gencost_preproc (+ _c,_i,_r related params),
465        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
466        gencost_outputlevel arguments to cost_generic
467      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
468        and active_read, making room for gencost_preproc to take effect.
469        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
470      - pkg/ecco/cost_generic.F :
471        compute and store misfit maks*(model-data) in localdif that is
472        then used in cost and for output, output misfit if outlev.GT.0
473      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
474        rather gencost_barfile for deciding whether to write barfile
475      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
476      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
477        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
478      - pkg/ecco/ecco_summary.F : report gencost variables
479      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
480    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
481    o pkg/ecco: internal re-organization
482      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
483        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
484        mv relevant variables definition from ecco_cost.h to ecco.h,
485        make sure gencost routines only include ecco.h)
486      - throughout : add missing CCP switches, rm unused variables,
487        and rm un-necessary CPP switches
488      - throughout gencost routines : replace modelstartdate with
489        gencost_startdate when needed
490      - cost_bp_read.F : use arguments, instead of common blocs
491        so that it can be used also by (new) cost_gencost_bpv4.F
492      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
493      - ecco_phys.F : compute etanFull
494      - ecco_readparms.F : rename using_topex as using_tpj, add
495        bpv4-grace to gencost list, initialize added parameters
496      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
497    
498    checkpoint65e (2014/09/28)
499    o pkg/obcs:
500      - replaced the just-added CPP options with run-time variables
501        (see pkg/obcs/OBCS_PARAMS.h for details)
502    o pkg/obcs:
503      - add additional CPP options for sponge boundary layers
504        (see pkg/obcs/OBCS_OPTIONS.h for details)
505    o pkg/atm_phys:
506      - implement simple (obliquity only, assuming circular planet orbit)
507        seasonal cycle for incoming insolation ; used when run-time parameter
508        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
509    o pkg/exf, pkg/ecco, pkg/ctrl:
510      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
511      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
512      - implement gentim2d for xx_tauu, xx_tauv
513    o pkg/ctrl, pkg/ecco :
514      - fix and complement the generic controls implementation
515    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
516        pkg/shelfice/shelfice_thermodynamics.F,
517        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
518        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
519      - add weight in CTRL_GET_GEN calls
520    o pkg/ctrl :
521      - ctrl_get_gen.F : add weight as input parameter, and apply
522        it directly rather than using smooth_correl2Dw (to be retired).
523      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
524    o pkg/ctrl :
525      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
526        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
527      - re-activate ctrl_summary (call in ctrl_init.F)
528    o pkg/ctrl/ctrl_cost_gen.F :
529      - fix CCP brackets, remove un-necessary myiter, mytime
530    o pkg/ecco, pkg/ctrl :
531      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
532      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
533      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
534      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
535    
536    checkpoint65d (2014/09/15)
537    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
538      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
539        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
540    o pkg/ctrl/ctrl_map_ini_genarr.F :
541      - remove compilation failure
542      - replace hard coded example
543      - use ctrl_map_ini_gen2D, 3D
544    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
545      - on/off switch based upon xx_genarr2d_weight,3d
546    o src/packages_init_variables.F :
547      - regroup pkg/estimation calls
548      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
549        (moved to ctrl_init_variables)
550    o cost/cost_init_varia.F :
551      - remove ecco_cost_init_varia
552        (moved to ecco_init_varia)
553    o ctrl/ctrl_init_variables.F :
554      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
555      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
556    o ctrl/ctrl_map_ini.F :
557      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
558        (moved to ctrl_init_variables)
559    o ctrl/ctrl_map_ini_ecco.F :
560      - remove ECCO_PHYS (mv to ecco_init_varia)
561      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
562    o ecco/ecco_ad_diff.list :
563      - add ecco_init_varia.f
564    o ecco/ecco_init_varia.F
565      - new routine
566    o pkg/streamice:
567      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
568        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
569      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
570    o pkg/generic_advdiff:
571      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
572    o pkg/exf:
573      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
574         xxg_precip capability
575      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
576    o pkg/ctrl:
577      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
578    o model/src/load_fields_driver.F :
579      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
580        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
581    o OpenAD verification experiments:
582      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
583        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
584        for now, only in pkgs used in OpenAD verification experiments.
585      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
586        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
587        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
588        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
589    o OpenAD verification tests:
590      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
591      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
592        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
593      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
594        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
595    o model/src & generic_advdiff:
596      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
597        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
598        dynamics requires valid tracer forcing only over tile interior but, for
599        some diagnostics, may need to extend it over 1 point in tile halo region.
600      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
601        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
602        setting in temp/salt/ptracer_integrate.F
603    o pkg/dic:
604      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
605        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
606        in gchem_forcing_sep.F
607    o pkg/autodiff & obcs:
608      - add storage of current OB values for U & V (was already done for T & S).
609    
610    checkpoint65c (2014/08/30)
611    o pkg/dic:
612      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
613        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
614        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
615    o verification:
616      - new experiment testing OBCS and DIC pkgs, using params & output from
617        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
618        passage: take OBCS from the last year of a 2 yrs simulation and initial
619        conditions from t=1.yr while keeping the same forcing.
620    o model/src:
621      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
622        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
623    o pkg/diagnostics (Stats-Diags):
624      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
625        a) refine region where stats are computed, excluding where arrhFac=0 ;
626        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
627        c) extend regional stats over the region edges (for U or V pt location).
628    o pkg/gchem:
629      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
630        pkg/dic is currently changing/updating ptracers values beyond the OB).
631    o verification (hs94):
632      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
633        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
634        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
635        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
636    o pkg/ptracers:
637      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
638        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
639      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
640        with AB-2 code (so that it get tested).
641    o model/src:
642      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
643        with AB-2 code (previously only available with AB-3 code).
644        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
645        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
646        there, by calling CYCLE_AB_TRACER).
647    o pkg/generic_advdiff:
648      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
649        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
650        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
651        S/R temp/salt/ptracers_integrate.F
652    o model/src & pkg/ptracers:
653      - remove common block variables gT,gS (in DYNVARS.h), except when
654         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
655      - remove common block variable gPtr.
656    o model/src & pkgs:
657      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
658         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
659         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
660         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
661      + change accordingly all calling S/R.
662      - use local temperature/salinity/ptracer tendency array (without bi,bj)
663        in S/R temp/salt/ptracers_integrate.F
664    o pkg/seaice:
665      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
666        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
667      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
668        in seaice_lsr
669      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
670        in s/r seaice_lsr_calc_coeffs
671    o pkg/mdsio:
672      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
673        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
674        too long (e.g., > MAX_LEN_FNAM/2 )
675    
676    checkpoint65b (2014/08/12)
677    o pkg/matrix:
678      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
679    o model/src:
680      - fix initialisation of geothermalFile; compile geothermal-flux code in
681        natl_box verification experiment.
682    o model/src & pkg/down_slope:
683      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
684      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
685        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
686        results at machine truncation level: update output of experiments
687        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
688    o pkg/diagnostics (Stats-Diags):
689      - do not cumulate the full volume when DIAGNOSTICS_FILL is
690        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
691        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
692        times (but Min,Max and StD are still wrong).
693    o model/src:
694      - add geothermal flux forcing: read in ini_forcing.F as time-constant
695        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
696    o model/src:
697      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
698        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
699        arrays are already updated while adjustments (filters, conv.adjustment) are
700        still applied later, in S/R TRACERS_CORRECTION_STEP.
701    o model/src:
702      - store in common bloc array "rhoInSitu" the virtual potential temperature
703        anomaly that is used to compute geopotential: this make the atmos code
704        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
705    o pkg/seaice/seaice_lsr.F
706      - rename integer variable ilcall to ipass (that's what it is called
707        in the residual diagnostics
708      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
709        default) for improved non-linear convergence of the first few steps
710      - adjust a few comments and add new ones to explain some of the store
711        directives
712    o pkg/generic_advdiff (& ptracers):
713      - re-work the code to check for valid advection scheme and for minimum
714        size of overlap (now stored in local common bloc in gad_advscheme.F)
715    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
716      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
717      - add an auxilliary variable "bet" and fix store directives and keys in
718        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
719        less exact gradients in my tests); but there are still
720        recomputation warning (although gradients are sort of OK), when
721        SEAICE_LSR_VECTORIZE is not defined, so this flag and
722        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
723      - update verification experiments lab_sea.
724      - change some comments in S/R seaice_calc_viscosities
725    o model/src:
726      - if staggerTimeStep=T, always apply exchange to velocity field in
727        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
728        (independent of using multi-dim advection or not); no effect on FWD run
729        but affects AD results (at machine truncation level): update output of
730        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
731        and isomip (oad: 12.d).
732    o pkg/generic_advdiff:
733      - stop if doAB_onGtGs is set to FALSE but ignored
734      - refine warning related to stability of tracer time-stepping
735        regarding internal wave dynamics.
736      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
737        on staggerTimeStep & implicitIntGravWave (will now get a warning
738        if potentially unstable).
739    o pkg/kl10:
740      - add new pkg "kl10" for mixing due to internal wave breaking, from
741        http://www.sciencedirect.com/science/article/pii/S1463500310000144
742        (contribution from Jody Klymak), tested in verification experiment
743        verification/internal_wave/input.kl10/
744    o isomip experiment:
745      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
746        (input.htd) and update the output.
747    o cd_code experiments:
748      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
749        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
750        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
751        update the corresponding output.
752    o pkg/seaice:
753      - reduce the number of include files and store directives in
754        S/R seaice_lsr_tridiagu/v
755      - change the order of loops in one case in S/R seaice_lsr_tridiagv
756        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
757        get rid off one store directive (a TAF bug?)
758      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
759        S/R seaice_lsr_tridiagv to change the loop range for consistency
760      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
761      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
762        S/R seaice_lsr_tridiagu/v (requires update of
763        offline_exf_seaice/input.dyn_jfnk)
764    
765    checkpoint65a (2014/07/27)
766    o model/src:
767      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
768        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
769        (topo in p-coords, ice-shelf in z-coords); update output of experiments
770        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
771    o model/src:
772      - collect momentum forcing tendency into local 2-D array (passed as argument
773        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
774        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
775        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
776      - collect T & S forcing tendency into local 2-D array (passed as argument to
777        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
778        affects results at machine truncation level (e.g., ocean: if using
779        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
780        correction due to vertical advection).
781      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
782        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
783        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
784        obcs_ctrl (ad & fwd grd @ 12 & 7).
785    o pkg/ptracers & diagnostics:
786      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
787        title (to avoid some unexpected truncation); sort out ptracers diags units.
788      - collect ptracer forcing tendency into local 2-D array (passed as argument
789        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
790    
791    checkpoint65 (2014/07/18)
792    o pkg/fizhi:
793      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
794        affects results at machine truncation level. Update output of experiments
795        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
796    o pkg/seaice: more clean up
797      - rename TAF common block tapes to be more consistent and remove
798        unnecessary duplicates
799      - add store directives to remove more recomputations, but use smaller
800        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
801        The idea behind this flag is to reduce the memory footprint when the
802        adjoint of the LSR is not required. As of now, defining the flag
803        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
804        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
805        For experiment offline_exf_seaice, this means on a linux box with gfortran
806        nearly a factor of 10 (but keep in mind there is mostly seaice code in
807        this experiment):
808        > size mitgcmuv_ad
809        text    data        bss     dec        hex
810        5100659 1216  220458952  225560827  d71c8fb
811        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
812        but only a moderate increase of 36% for global_ocean.cs32x15:
813        text    data        bss     dec        hex
814        6695027 1648 1014578664 1021275339 3cdf6ccb
815        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
816      - note: there are still recomputations in global_ocean.cs32x15 and
817        offline_exf_seaice and the gradient agreement changes (gets a
818        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
819      - in general, the AD gradients still are wrong
820    o OpenAD
821      - clean up code_oad/ directories somewhat by moving files
822        dontCompile, dontTransform, keepOriginal to OAD_support/
823    o model/src:
824      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
825        (not currently tested): add dissipation terms before NLFS rescaling of
826        tendencies (previously done after).
827    o pkg/diagnostics:
828      - write stats-diags in ascii file with more digits (same as in monitor).
829    o pkg/down_slope:
830      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
831        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
832    o model/src:
833      - new file "apply_forcing.F" containing all the code previously in
834        external_forcing.F, but with new argument list: pass, as new argument,
835        the current level tendency array to update (instead of a direct update
836        of the common bloc array). Change the corresponding calls.
837      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
838        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
839    o pkg/seaice/seaice_lsr, a little bit of clean up
840      - rearrange some code blocks, so that now all calculations for
841        setting up the right-hand-sides done within one single block
842        (I find that easier to read and understand)
843      - rearrange freedrift-code to reduce the number of ifdefs
844      - adjust some indentations and comments
845    
846    checkpoint64z (2014/07/10)
847    o model/src and several pkgs:
848      - change argument list of all S/R called from external_forcing.F and
849        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
850        to pass, as argument, the current level tendency array to update
851        (instead of a direct update of the common bloc array).
852      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
853      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
854    o pkg/seaice/seaice_lsr.F
855      - always initialize local arrays in seaice_lsr_tridiagu/v
856      - add more local tapes to seaice_lsr_tridiagu/v
857      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
858        keep it in bi/bj loop; this seems to be essential
859      - gradients are still wrong but only by 4-7 orders of magnitude
860        instead of 15 orders of magnitude, lab_sea improves a little
861    o pkg/seaice
862      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
863        generates unnecessary code in seaice_lsr_ad
864      - add more store directives in seaice_lsr to avoid unnecessary code
865        in seaice_lsr_ad
866      - exclude some residual computations in seaice_lsr when
867        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
868        in seaice_lsr_ad
869      - add more storing, a new tape (model/src/the_main_loop.F) and
870        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
871        and klockey should be checked by a specialist)
872      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
873        and update lab_sea after previous changes in pkg/seaice below
874    o pkg/autodiff:
875      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
876        viscFacInAd : run time parameters allowing for adjoint switches
877        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
878    o pkg/ecco:
879      - introduce cost_gencost_boxmean.F that computes a box mean
880        temperature (for use in adjoint sensitivity studies).
881    o model/src/set_defaults.F : initialize viscFacAdj to 1.
882    o pkg/mom_common/mom_calc_visc.F:
883      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
884    o pkg/seaice/seaice_summary.F:
885      - statement for SEAICEadjMODE now in autodiff_readparms.F
886    o pkg/seaice:
887      - remove some store directives and add new ones in an effort to get
888        finally rid off the recomputation warnings. This is successful
889        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
890        defined (i.e. no extensive recomputation warnings left), but there
891        are still too many recomputations on the solver iteration level
892      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
893      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
894        SEAICE_SIZE.h
895      - add a store directive in S/R seaice_calc_viscosities
896    o pkg/seaice (ITD code):
897      - fix definition of Hlimit for multi-threaded case
898      - use double precision arithmetic to compute Hlimit: this affects results;
899        update output of experiment seaice_itd.
900    o replace content of verification/seaice_itd
901      - instead of a 1D column use the configuration of offline_exf_seaice
902        to test the ice thickness distribution code with ridging
903      - this is a first shot at this experiment
904      - change of some defaults of ridging parameters SEAICEhStar (from
905        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
906        and lot of new comments.
907    
908    checkpoint64y (2014/06/20)
909    o pkg/seaice/seaice_reg_ridge.F:
910      - modify the regularization of very small volumes of ice; only check
911        total volume HEFF, and do not apply correction to individual ice
912        classes because that leads to funny patterns in the heat and fw-fluxes
913        into the ocean. Adjust seaice_itd/results/output.txt
914      - replace nITD by SEAICE_multDim in loop-ranges
915    o pkg/exf:
916      - add code to process the case field period = -12. with UV interpolation.
917      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
918        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
919    o verification/global_with_exf:
920      - switch all fields period to -12. (was previously untested) in input/data.exf
921        (but keep secondary test ".yearly" unchanged); update the reference output.
922    o pkg/cal:
923      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
924    o pkg/exf:
925      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
926        to replace logical switch "exf_verbose"
927      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
928    o pkg/sbo:
929      - update from Katherine Quinn: evaluate mass directly from density and SSH
930        (budget using Finite Volume method) instead of from bottom pressure.
931      - allow testreport to collect few selected SBO output ; tested in exp.
932        global_ocean.90x40x15 (after updating the results, to include SBO output).
933      - fix some multi-threading issues (in output part).
934    o model/src & most packages:
935      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
936      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
937        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
938        "data.{pkg}" exist ; and leave the S/R (return) just after.
939      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
940        + call LAND_READPARMS from packages_readparms.F
941    o pkg/seaice:
942      - remove code that resets useThSice in S/R seaice_readparms and
943        replace it by a warning in S/R seaice_check
944      - remove parameter MULTDIM, replace with nITD and runtime
945        parameter SEAICE_multDim (still hard-wired to nITD if
946        SEAICE_ITD is defined)
947    
948    checkpoint64x (2014/05/24)
949    o verification/lab_sea:
950      - update adjoint and TLM output following changes to pkg/salt_plume
951      - un-do the update after putting back local recip_Cp in few places.
952    o pkg/salt_plume: modifications by An Nguyen:
953      - add capability to do brine rejection (salt-plume) as function of
954        volume+tracers (instead of only salinity tracer).
955      - conserve volume by exchanging volume from each kLev to above to
956        accommodate in-coming brine volume
957      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
958      - switch KPP surf buoyancy due to brine forcing to 3-d
959        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
960      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
961      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
962        in East/West Arctic.
963    o pkg/sbo:
964      - incorporate modifications from Katherine Quinn to enable the use of sbo
965        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
966        output for future testreport verification (unfinished).
967    o pkg/atm_phys:
968      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
969        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
970        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
971    o pkg/seaice
972      seaice_calc_ice_strength.F: modify expression to avoid divisions
973        (affects truncation)
974      seaice_do_ridging.F: clean up the insectarium
975      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
976      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
977      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
978      - add some debugging information and error messages (warnings)
979    o model/src: modifications relatd to atmosphere p*:
980      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
981      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
982        of vertical profile tRef in geopotential background and anomaly.
983      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
984        and pkg/atm_phys.
985      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
986        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
987    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
988    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
989        not used right now, but can be used in BGC packages to fix conservation.
990    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
991        other packages too.
992    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
993        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
994    o model/src:
995      - since we have several heat capacity (even in model/src), define "recip_Cp"
996        as local variable (no longer in common block) to avoid any confusion.
997      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
998    o pkg/exf:
999      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1000        air density as function of air Temp, Humidity and atm pressure.
1001    
1002    checkpoint64w (2014/05/02)
1003    o verification:
1004      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1005        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1006        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1007        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1008        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1009    o model/src: for atmosphere in p* coords:
1010      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1011      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1012        but not yet activated.
1013    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1014      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1015      - this changes the results (but not for any verification experiment, because
1016        none tests this), but avoids having an extra field in the restart files
1017    o pkg/seaice: remove global variable TICE (not needed)
1018      - replace by TICES or local variable where necessary (cost_seaice_test,
1019        seaice_diagnostics_state)
1020      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1021      - use specific read/write routines for reading and writing individual leves
1022        of a multilevel field
1023    o pkg/ctrl & model/inc:
1024      - move additional anomaly fields of control vars (related to options:
1025         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1026        from DYNVARS.h into new header file: CTRL_FIELDS.h
1027    o pkg/seaice: some small modifications to the ridging code
1028      - make fw2ObyRidge a global variable and add the freshwater flux to
1029        seaice_growth
1030      - pass actual thickness from seaice_prepare_ridging, so that it is
1031        computed only in one place and compute it in the same way as in
1032        seaice_growth
1033      - initialise more fields in seaice_do_ridging that where cause floating
1034        point exceptions over land
1035  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1036    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
1037      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
1038      advection call the actual ridging routine;      advection call the actual ridging routine;
1039    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1040      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1041    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1042    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
1043      more readable (this is probably subjective)      more readable (this is probably subjective)
1044    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
1045      conditions in the correct category      conditions in the correct category
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