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revision 1.2069 by gforget, Mon Sep 22 21:36:02 2014 UTC revision 1.2221 by jmc, Mon Jan 11 22:56:33 2016 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/exf/exf_getffields.F : add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets  o model/src:
8    and activate gentim2d for xx_atemp, xx_aqh, xx_swdown, xx_lwdown, xx_precip    - to check restart test, add option to apply EXCH to U,V earlier, just before
9  o pkg/exf/exf_getsurfacefluxes.F : implement gentim2d for xx_tauu, xx_tauv      integr_continuity; turned off by default.
10    and add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets.  o pkg/dic:
11  o pkg/ecco/cost_forcing.F, cost_hyd.F, cost_internal_params.F :    - remove CPP option USE_ATMOSCO2 (not needed)
12    add .NOT.ctrlUseGen exclusive brackets -- ctrl_cost_driver  o tools/tst_2+2:
13    is used instead when ctrlUseGen is .TRUE.    - try to ignore difference between +0 and -0 in binary file, causing test
14  o pkg/ecco/ecco_cost_final.F : print f_genarr3d to stdout      to fail for no good reason.
15  o pkg/ctrl/ctrl_cost_driver.F : add ctrl_cost_gen3d loop  o eesupp & genmake2:
16      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
17        but also check (in genmake2) that test runs and returns meaningful results.
18    o coupler pkgs:
19      Finish implementation of optionally-exchanged variable switches (started on
20       Nov 12) with addition of few more exchanged fields, including 2-way exchange
21       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
22       advection in OCN component; this requires sequential coupling.
23      coupler (pkg/atm_ocn_coupler):
24      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
25        routines (useful for debug).
26      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
27         flux, DIC fields) if corresponding switch is ON.
28      - add option to export RunOff to OCN (to use for DIC river input)
29      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
30      components (pkg/atm_ & ocn_compon_interf):
31      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
32        optionally exchanged fields; add a check & stop in cpl_readparms.F.
33        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
34        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
35      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
36        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
37      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
38      - hold in common block coupler optionally-exchanged variable switch
39        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
40      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
41        this is intended to replace the OCN cplFldtave.* output files (not updated
42        to contain new additional exchanged fields).
43    o pkg/dic:
44      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
45    o pkg/thsice:
46      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
47        and writing of thsice pickup files.
48    o pkg/atm_compon_interf:
49      - move all field individual export-call out of cpl_export_import_data.F
50        into new S/R ATM_EXPORT_FIELDS
51    o pkg/atm_compon_interf:
52      - store state variables (for now, only thSIce fields) just before beeing
53        exported (in cpl_export_import_data.F, like on ocean side) instead of from
54        atm_store_my_data.F like all exported fluxes.
55      - new version of pickup_cpl: write field names into meta file and read meta
56        file to find field postion in pickup. Also only write/read fields meeded for
57        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
58    o pkg/dic:
59      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
60    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
61        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
62        value can be from domain [0,1] to average between the two methods
63    o pkg/atm_phys:
64      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
65        hold fixed in time).
66    
67    checkpoint65r (2015/12/21)
68    o pkg/seaice:
69        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
70        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
71    o pkg/seaice:
72      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
73        when SEAICEscaleSurfStress=.TRUE.,
74      - apply areaW and areaS in S/R seaice_calc_lhs
75    o pkg/atm_phys:
76      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
77        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
78        for individual contribution (convection, LSC cond, radiation)
79      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
80        information); activated with: solar_exponent=0. and wv_exponent=-1.
81    o pkg/ggl90:
82      - within IDEMIX add upper limit for horizontal group velocity to
83        avoid instability problems in the explicit horizontal diffusion term for
84        long time steps or high resolution
85    o pkg/diagnostics:
86      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
87        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
88    o testreport:
89      - remove "-v" (verbose option) in default mpirun command.
90    o pkg/seaice/seaice_growth:
91      - catch potential division by zero in ITD code, does not change
92        verification results
93    o pkg/ecco:
94      - retire old codes to the Attic. The calls to retired functions are
95        left in a commented form in case they ever need to be re-activated.
96      - ecco_check.F: issue warning if any old CPP option is
97        defined that corresponds to retired codes -- then stop.
98    o pkg/atm_compon_interf:
99      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
100        coupler: use last time-step value instead of average over cplSendFrq_iter
101        time-step, similar to what is done for seaIceMass.
102        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
103    o eesupp & genmake2:
104      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
105        <= remove until a fix is found for some ifort version on ia32 machine.
106    o pkg/seaice/seaice_evp:
107      - refine residual computation
108    
109    checkpoint65q (2015/11/18)
110    o pkg/seaice/seaice_evp:
111      - fix residual computations so that they no longer affect the actual
112        simulation code
113      - fix seaice_readparams to be able to actually set new parameters
114        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
115    o model/src:
116      - fix wrong truncation (single prec) from "FLOAT" function in expressions
117        like: deltaT*FLOAT(myIter) when myIter is large:
118         a) replaced by DFLOAT (if not seen by TAF);
119         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
120    o pkg/aim_v23:
121      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
122        when pickupSuff is set ; do write rolling pickups + at the end of the run.
123    o pkg/atm_ocn_coupler + ocn_compon_interf:
124      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
125        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
126        add corresponding call in DO_OCEANIC_PHYS.
127    o coupler pkgs:
128      Start a new way to set-up optionally-exchanged variables (previously, only
129       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
130       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
131       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
132       compononent param default can be set accordingly).
133      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
134       but rather applies to a group a fields (going both ways like for DIC)
135       and corresponds to an option of coupling config.
136      coupler (pkg/atm_ocn_coupler):
137      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
138        and read namelist directly (without eessup S/R calls) instead of
139        in the very un-flexible old way, 1 param per line, in fixed order;
140      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
141        cleanly in CPL_CHECK_CPLCONFIG
142      - add new coupling-exchange selectors (some not yet active) including
143        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
144                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
145      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
146        component ; called directly from coupler.F, after comp. registrations;
147      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
148         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
149          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
150      components (pkg/atm_ & ocn_compon_interf):
151      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
152        CPP header file in all pkg source files.
153      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
154        ATM/OCN_CHECK_CPLCONFIG;
155      - add error-counter to track errors (e.g., in "data.cpl") and to stop
156        cleanly in ATM/OCN_CHECK_CPLCONFIG;
157      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
158        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
159        before PACKAGES_READPARMS;
160      verification/cpl_aim+ocn/:
161      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
162        "data.cpl" for coupler (in input_cpl).
163    o eesupp/inc:
164      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
165        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
166        to always cumulate tile local-sum in the same order (still uses
167        MPI_Allreduce like standard code).
168      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
169        that are now identical to standard version (in eesupp/inc).
170    o pkg/shelfice:
171      - add SHELFICETransCoeffTFile for initializing spatially varying
172        heat and salt transfer coefficients
173    o pkg/atm_compon_interf & ocn_compon_interf:
174      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
175        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
176      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
177    o pkg/atm_ocn_coupler:
178      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
179    o pkg/rbcs:
180      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
181        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
182      - add a short report (to STDOUT) about RBCS-mask settings.
183    
184    checkpoint65p (2015/10/23)
185    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
186        there is no adjoint test for EVP, we don't know what it does to the adjoint
187        solution, but at least there are no more recomputation warnings left
188    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
189        a chance of giving the same results as a fully converged VP (JFNK) solver
190    o tools/adjoint_options/adjoint_diva:
191      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
192    o pkg/streamice:
193      - spotted bug in streamice_driving_stress using dyG where should have been dxG
194    o pkg/exf:
195      - remove STOP statement that prevented to use wind or (wind-)stress
196        interpolation for constant-in-time forcing fields (wind/stress period = 0).
197    o pkg/seaice:
198      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
199        5 additionals 2D fields and 6 new store directives
200      - change logic in seaice_readparms.F: EVP code can now be turned on in
201        various ways, setting SEAICE_deltaTev is no longer required,
202        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
203        or SEAICEaEVPcoeff
204    o pkg/shelfice/shelfice_thermodynamics.F
205      - redefining uLoc/vLoc to u/v, instead of 2u/v
206    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
207      - this is an intermediate state of a truely converging EVP that has
208        the potential of outperforming implicit VP methods, I do not recommend
209        using it yet.
210      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
211        and all parameters are hardwired
212      - for convergence it still requires very smooth regularisations, that means,
213        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
214        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
215        specific averaging appears to be required, still subject to tuning
216      - still needs cleaning and I need to turn parameter into runtime parameters
217      - add code to compute and print residuals of iteration, compile with
218        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
219    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
220      that entered with r1.54 on Sep04, 2015, -> update results
221    
222    checkpoint65o (2015/09/14)
223    o pkg/mom_vecinv & mom_common:
224      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
225        called from there.
226      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
227        allows to use Vector-Invariant form in deep atmos and anelastic formulation
228    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
229      and Koenig-Beatty+Holland (2012)
230      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
231      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
232      - requires an extra input argument for S/R seaice_calc_viscosities
233      - tensileStrength's depth dependence is different from Itkin et al. (2015)
234        (to be changed and played with, for now exponential)
235    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
236      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
237        by AREA according to Connelly et al. (2004), JPO.
238      - For EVP and the LSR solver, the implicit part of the drag term is
239        the only non-zero term in the denominator when there is no ice (which
240        prevented running the model with zero ice-ocean drag). If
241        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
242        (or zero main diagonals BU/BV) which need to be caught. A practical
243        consequence is that for open water, the momentum equation reduce
244        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
245        they happen to be zero, often leading to a non-zero solution over
246        open water.
247    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
248        efficient EVP method.
249      - introduce area-weighted averages for e12 (analogously to
250        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
251        remain, but also changing the order of terms in the previous average
252        changed the results as much) -> update experiment
253      - add SEAICE_DELTA_SMOOTHREG code
254      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
255        TEM-code
256      - adjust loop bounds so that only required fields are computed
257      - add new averaging code for zetaZ/deltaZ (again similar to
258        seaice_calc_viscosities.F), inactive by default for now (will change
259        results again), but will replace old code eventually
260    o eesupp/src:
261      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
262        to always cumulate tile local-sum in the same order
263        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
264        Still uses MPI_Allreduce (like standard code) but on array of tiles
265        and should be faster than GLOBAL_SUM_SEND_RECV code.
266      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
267        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
268      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
269         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
270         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
271         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
272         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
273    
274    checkpoint65n (2015/07/29)
275    o pkg/thsice:
276      - add a warning when used with pkg/aim but without updating SST
277        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
278    o pkg/offline:
279      - change where Offline-Fields are loaded, from load_fields_driver.F to
280        directly within FORWARD_STEP, just after updating iter number and time;
281      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
282        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
283       These changes allow:
284        a) to recover exactly on-line results using deltaToffline=deltaTClock,
285        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
286        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
287        time-step, both with GM & KPP files and with recomputing these fields;
288        b) no needs to switch on staggerTimeStep anymore;
289        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
290      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
291    o pkg/offline:
292      - change (rarely used) offset-iteration parameter to an offset time (in s):
293        can easily recover previous offset-iter effect by setting offset-time
294        (offlineTimeOffset) to offset-iter x deltaToffline;
295      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
296        in KPP as part of surface buoyancy forcing) in offline run.
297      - fix ptracers KPP non-local term in the case where KPP is re-computed.
298    o OpenAD
299      - Adding preliminary ggl90 test to OpenAD verification.
300        Config. with ggl90 currently diverges after 64 time steps
301        so will need more work to become more stable
302      - Adding preliminary kpp test to OpenAD verification.
303        required small tweakes in kpp_routines.F
304      - Merge and update from Krishna Narayanan's contrib area:
305        * Add one variable for preliminary OpenAD DIVA
306        * Add replacement time-stepping for OpenAD DIVA
307        * genmake2 flag -diva (but only for OpenAD; preliminary)
308        * required modifs for OAD_support
309        successful preliminary test for tutorial_global_oce_biogeo/
310    o pkg/seaice:
311      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
312      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
313        delta with a smooth function in s/r seaice_calc_viscosity
314        (no effect on EVP)
315      - rename local suffix "sqr" into "sq" for more consistent variable names
316    o pkg/seaice:
317        add new parameter SEAICE_deltaMin that is used ***only***
318        for regularizing Delta (and nothing else, like the parameter
319        which is also used for all sorts of things SEAICE_EPS).
320        Defaults to SEAICE_EPS for backward compatibility only.
321    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
322        the wrong key by inialising it before use -> fixes a recomputation
323        problem but does not fix the gradient
324    o pkg/layers:
325      - move resetting of flux arrays to outside the iLa loop
326        (this caused layers_diapycnal to not work with more than one layer coord.)
327      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
328    o pkg/layers:
329      - remove from common block 3D layers fields (used to diagnose transport
330        in tracer coords) and declare them as local arrays in layers_calc.F
331    o pkg/seaice:
332      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
333        in lab_sea forward experiment (changes results -> updated)
334      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
335    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
336       computations; for SEAICE_VECTORIZE_LSR
337      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
338        sweep to the outside,
339      - remove store directives and add "CADJ loop sequential" directives
340        in analogy to model/src/solve_tridiagonal.F
341      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
342        boundaries to yield more readable code. This has also the charming side
343        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
344        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
345        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
346        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
347        an additional option)
348       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
349       but the adjoint gradients (which are affected by this change) still explode.
350    o coupler (atm & ocn _compon_interf):
351      - avoid using Exch2 IO mapping if not suitable.
352    
353    checkpoint65m (2015/06/15)
354    o pkg/layers:
355      - clean-up old parameters setting (from Sep 2012):
356        + remove old parameters setting from common block (declared locally);
357        + stop if any old parameter is mixed with new parameters;
358        + check for valid or consistent parameter setting (e.g., layers_name)
359      - check that layers_bounds for Pot.Density are in the right range;
360        this is supposed to catch un-updated setting after recently shifting
361        potential density field "prho" by -1000 (now in "sigma" scale).
362    o pkg/layers:
363      - Added missing call to layers_fill for keeping track of tottend in
364        pkg/diagnostics/diagnostics_fill_state.F
365    o pkg/layers:
366      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
367        of diapycnal fluxes
368    o pkg/layers:
369      - reverted changes to interpolation to previous treatment; there
370        was never actually a problem
371    o pkg/layers:
372      - fix interpolation of layers tracers in the presence of partial cells
373      - add lots of new functionality to compute water mass transformation
374        (enabled by CPP flag LAYERS_THERMODYNAMICS)
375      - add new calls from main code (diags_oceanic_surf_flux.F,
376        thermodynamics.F, impldiff.F) and gad to save the necessary fields
377        for layers_thermodynamics calculations
378    o pkg/ptracers:
379      - add capability of stepping a passive tracer forward without advection
380        by setting PTRACERS_advScheme to 0.
381    o pkg/diagnostics:
382      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
383    o pkg/layers:
384      - shift potential density field "prho" by -1000 for density layer averaging so
385        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
386        Note that density bin boundaries (layers_bounds in data.layers) have
387        to be set accordingly (i.e., shifted, in sigma scale).
388    o pkg/layers:
389      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
390      - fix calculation of layer non-weighted velocity and layer probability
391      - add diagnostics for pot.density used for layer averaging
392    o pkg/seaice:
393      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
394        positiveness, modify a few comments and improve variable names,
395      - the changed computation of deltaC affects most seaice-related
396        experiments at the truncation level.
397        seaice_itd.thermo is affected by far the most, with
398        only 7 digits of agreement remaining; update experiments.
399    
400    checkpoint65l (2015/05/04)
401    o pkg/shelfice:
402      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
403        factor drKp1 to zero where it is negative (ie. do not use
404        SHELFICEBoundaryLayer if hFacC>1)
405      - the same for factor drLoc in shelfice_forcing.F
406    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
407        with modules in ptracers, when using testreport option "-small_f"
408    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
409      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
410    o verification/testreport
411      - add new option -small_f
412        with this option testreport first makes the target small_f (*.f files)
413        before running make (all). This is useful for explicit inlining when
414        all sources need to be full available.
415    o pkg/exf/exf_interp.F:
416        remove previous changes related to reverse (decreasing) input grids latitude
417    
418    checkpoint65k (2015/04/01)
419    o pkg/ecco:
420        fix missing cosphi initialization; use eccoiter in place of optimcycle;
421        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
422        instead of active read/write
423    o pkg/ctrl:
424        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
425        instead of active read/write.
426    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
427        return if .NOT.useAUTODIFF
428    o pkg/seaice: add CPP brackets (cost function related).
429    o model/src:
430        add useAUTODIFF run time switch.
431    o pkg/exf/exf_interp.F:
432        add code to allow input grids with latitude starting in the north (i.e. when
433        j=1 corresponds to northern edge of field); modify global_with_exf to test
434        this feature.
435    o verification/testreport:
436      - replace "grep -A3" with POSIX conformal sed command, because there are
437        implementations of grep that cannot do contextual searches
438      - replace "cat -n" by "nl" (two occurrences), because not all implementations
439        of "cat" have the option "-n"
440    o model/src:
441        add new file gsw_teos10.F that contains 3 functions, more or less a copy
442        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
443        convert from conservative to potential temperature. For now they are not
444        called anywhere.
445    o pkg/ggl90: make "useIDEMIX" useful
446      - re-organize code in s/r ggl90_calc a little to move computations that
447        are different for idemix into separate loops (changes verification
448        experiment idemix at truncation level, 12 digits remain -> updated)
449      - requires 2 new 2D fields KappaM, verticalShear
450      - make hFacI and recip_hFacI local 3D variables that are passed to
451        s/r ggl90_idemix
452      - fix and improve some comments
453    
454    checkpoint65j (2015/02/25)
455    o pkg/openad
456      - synchronize seawater.F with version in model/src: replace routine
457        body of sw_temp by calling sw_ptmp and fix/add a few comments.
458    o pkg/mnc:
459      - change default value of pickup_read/write_mnc params to FALSE
460        (since few features are missing in reading MNC pickup files).
461    o model/src:
462      - change default (background) vertical diffusivity for salt to be the
463        temperature (background) vertical diffusivity.
464      - change background vertical diffusivity in vertical mixing pkgs ggl90,
465        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
466        This makes ptracers default diffusivity (that uses salt diffKr) more
467        consistent with vertical mixing schemes.
468    o verification/testreport:
469      - fix typo in "-pcls" option ;
470      - put temp files in /tmp (instead of in local dir)
471      - add option "-ncad" to use genmake2 new option "-nocat4ad"
472      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
473    o pkg/ggl90 (idemix code):
474      - apply few fixes ; add some missing "_d 0" ; update output of exp.
475        global_ocean.90x40x15.idemix
476    o OpenAD
477      - enable active file I/O and begin removal of work-around code
478        for OpenAD for handling control variables (memory vs. active files)
479      - new CPP options file OPENAD_OPTIONS.h
480      - revert to genarr2d gradient check for hs94.1x64x5
481      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
482      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
483    o tools/genmake2:
484      - add option for an alternative Makefile (from Martin) where multiple
485        source files are sent to TAF (instead of all in one file).
486    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
487      - code provided by Carsten Eden as an extension of ggl90
488      - so far the code is turned on within ggl90 by setting a CPP-flag at
489        compile time; a runtime flag implementation is not yet complete
490      - tested in new verification experiment global_ocean.90x40x15.idemix
491    o verification:
492      - reduce length of the AD test run by half for experiments
493        global_ocean.cs32x15 (std + thsice) and isomip
494      - enable active file I/O for OpenAD, adjust verifications accordingly
495      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
496    o verification/testreport:
497      - fix two non-POSIX sed statements so that there are no error messages
498        on Mac OS X
499      - replace hostname -s with hostname | sed 's/\..*$//'
500    o model/src/seawater.F:
501      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
502        (following the matlab code), which would have avoided the bug caught
503        by Matt (see below) in the first place
504    o pkg/shelfice:
505      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
506        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
507      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
508        ice-shelf case (i.e., within surface level).
509      - add config summary in shelfice_check.F
510      - remove global variable recip_SHELFICElatentHeat and replace by a local
511        variable recip_latentHeat
512      - introduce diagnostics for friction velocity uStar (in case of
513        SHELFICEuseGammaFrict)
514      - change verification experiment isomip.htd:
515        + start from pickup (as input_ad at nIter0=8640)
516        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
517        + test SHELFICEuseGammaFrict = .TRUE.
518        + test SHELFICEadvDiffHeatFlux = .TRUE.
519    o model/src:
520      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
521        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
522        update output of experiments global_with_exf.yearly and isomip (all 6).
523    o pkg/shelfice:
524      - change setting of kTopC to also be zero where there is no ice-shelf.
525      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
526        ice-shelf is.
527      - first attempt to get RealFreshWaterFlux effects: for now, only without
528        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
529    o pkg/seaice: add the option to prescribe a fixed thickness PDF
530      for thermodynamic calculations
531      - because of divisions of the type 7/7 not exactly equal to 1, this change
532        affects results of some verification experiments by up to 4 digits:
533        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
534        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
535        adjoint: lab_sea, lab_sea.noseaicedyn
536        -> updated
537    
538    checkpoint65i (2015/01/23)
539    o model/src:
540      - change units of frictionHeating field from W to W/m^2
541      - fix bug in frictional heating from stratospheric drag in
542        S/R ATM_PHYS_TENDENCY_APPLY_V
543      - with synchronous time-stepping: move resetting to zero of frictionHeating
544        field from load_fields_driver.F to thermodynamics.F ;
545      - add diagnostics for frictional heating.
546    o model/src & gmredi K3D:
547      - add frictionHeating field to pickup-files (for synchronous time-stepping)
548      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
549      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
550        and name in pickup file).
551      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
552    o model/src:
553      - move (from ini_forcing.F) initialisation of all arrays in header file
554        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
555        (since Nov 2012) with option selectAddFluid=1.
556    o pkg/shelfice:
557      - change units (+ document) of newly added field "shelfIceMassDynTendency"
558      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
559    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
560    o pkg/seaice: two new runtime parameters:
561      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
562        long overdue
563      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
564        parameterization of tensil stress for fast ice (does not do anything yet)
565    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
566        for LSR: move checking overlaps out of JFNK-if-block
567    o pkg/atm_phys:
568      - move copy of grid and dynamical fields out of atm_phys_driver.F into
569        new S/R ATM_PHYS_DYN2PHYS.
570      - fix level height for Linear Free-Surf case (to be consistent with
571        fixed-in-time pressure levels).
572    o pkg/mom_common (bottomdrag):
573      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
574        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
575        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
576    o pkg/shelfice (u/v_drag):
577      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
578      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
579        (now similar to shelfice_u_drag.F)
580      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
581        from mom_vecinv.F (similar to mom_fluxform calls).
582    o pkg/mom_common (bottomdrag):
583      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
584      - add options for alternative discretisation of velocity norm in quadratic
585        bottom drag: averaging of grid-cell-center KE to U.point and V.point
586        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
587        improves when averaging only the other component (e.g. vVel for U bottom
588        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
589      - add options (bottomVisc_pCell) to account for partial-cell in bottom
590        friction (no-slip BC) thus getting the true distance from the bottom;
591        off by default since this also reduces model stability (explicit bottom
592        friction). Changes produce different machine truncation with linear-drag
593        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
594        front_relax (bvp & mxl, 10 & 11 digits).
595    o model/src & mom pkgs:
596      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
597        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
598      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
599        just copy level Nr value to level Nr+1.
600    o doc:
601      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
602    o pkg/streamice:
603      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
604        SHELFICE.h: move array shelficemass to init_varia, initialise
605        from array shelficemassinit, which is set in init_fixed and
606        has option to be set from file; introduce array
607        shelficeMassDynTend array, set thru file in init_fixed
608      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
609        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
610        pkg/streamice
611      - shelfice_thermodynamics.F: call shelfice_step_icemass if
612        SHELFICEMassStepping = .true.
613      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
614    
615    checkpoint65h (2014/12/17)
616    o verification/global_ocean.90x40x15, global_ocean_ebm:
617      - update to generic controls.
618    o pkg/ctrl:
619      - ctrl_map_ini_genarr.F: test for igen>0
620      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
621      - move gentim2d part of ctrl_map_ini_genarr.F to
622        new separate routine : ctrl_map_ini_gentim2d.F
623      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
624        add time variable weights and cyclic controls (time mean,
625        seasonal cycle, etc) capabilities to gentim2d
626    o pkg/ecco:
627      - move reading of error, conversion to weights from
628        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
629    o global_oce_llc90, cs32:
630      - activte sbo.
631      - CTRL_SIZE.h : add maxCtrlProc.
632      - activate the new genctrl capabilities.
633      - update following reorganization of global_oce_input_fields.tar.gz  
634    o pkg/ctrl/ctrl_ad_diff.list:
635      - add missing ctrl_init_rec.f
636    o tools/OAD_support/keepOriginal:
637      - add ctrl_init_rec.F
638    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
639      - avoid recomputations of xx_gentim2d_dummy.
640    o momentum diagnostics:
641      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
642        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
643    o pkg/seaice/seaice_lsr.F:
644      - fix computation of BU/BV, make sure they are non-zero, only necessary
645        for cubed sphere exchanges and SEAICE_OLx/y>0.
646        This makes calling s/r fill_cs_corner_rl obsolete (removed).
647    o verification/global_ocean.cs32x15/input.seaice
648      - add test for strong implicit coupling and restricted addtive Schwarz
649        methods for LSR
650      - update results/output.seaice.txt
651    o verification/tutorial_global_oce_biogeo:
652      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
653        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
654        update output_adm,_oadm,_tlm.txt
655    o pkg/dic:
656      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
657      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
658        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
659    o verification/tutorial_global_oce_biogeo:
660      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
661        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
662        update output_adm,_oadm,_tlm.txt
663    o eesupp/src:
664      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
665        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
666    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
667      LSR (following Hutchings et al. 2004)
668      - introduce zetaZ as a global variable (requires adjustments in
669        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
670        in seaice_calc_viscosities.F
671      - new flag SEAICEuseStrImpCpl (default off)
672      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
673        momentum equations
674      - JFNK-solver (preconditioner) adjusted to allow using this method
675        (where it does not have any positive effect)
676    o pkg/seaice
677      - add overlap for restrictive additive Schwartz method also to LSR, but
678        turn it off by default (because it only seems to work for non-cubed
679        sphere/llc topologies)
680    o pkg/autodiff
681      - add extra exchanges in addummy_in_steppging also for mnc output
682    o pkg/seaice:
683      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
684        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
685    o pkg/obcs:
686      - add option to specify domain-connected piece Id along OB though files
687        (for now, only used to diagnose PhiVel; default =1 -> global correction)
688      - modify obcs_diag_balance.F to process each connected-part separately;
689        exclude OB where Id = 0 but keep the full divergence there (-> constant
690        Psi along this portion of OB and all inflow derived from grad(Phi))
691      - add example of OB-conect files in verification/so_box_biogeo/input.
692    o pkg/diagnostics:
693      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
694      a) use non zero matrix element across OB and solve for Phi 1 grid point
695         outside OB (i.e, where tracer OBCS are applied).
696      b) global imbalance of inFlow/outFlow across OB: instead of modifying
697         velocity across OB, spread it uniformly along the OB in the RHS.
698    
699    checkpoint65g (2014/11/19)
700    o pkg/diagnostcis:
701      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
702    o pkg/my82,pp81,kl10:
703      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
704        field diffKr as background diffusivity to set minimum diffusivity value.
705    o pkg/seaice:
706      - add new parameter SEAICEuseEVPrev (for revisited EVP by
707        Bouillon et al 2013)
708      - add SEAICE_evpAlpha/Beta to namelist
709      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
710        involve trivial re-ordering of divisions/multiplications that should not
711        have any effects, but ... they do change the results of lab_sea.hb87 so
712        that only 2 digits of agreement remain, in line with the general
713        instability/fragility of the evp-code. For now, I do not care and just
714        update the verification experiment
715    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
716      - remove xx_genarr2d_numsmooth etc
717      - use xx_genarr2d_preproc etc instead
718      - carry out smooth_correl2D at initialization stage rather than during
719        time stepping.
720      - get smoothOpNb from xx_gentim2d_preproc
721    o global_oce_cs32 :
722      - add test of generic ecco capabilities.
723    o pkg/exf/exf_getsurfacefluxes.F :
724      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
725    o pkg/ctrl,ecco :
726      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
727        is defined.
728    o pkg/seaice: add diagnostics for Delta (deformation parameter)
729    o model/src:
730      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
731        diffusivity (background) is specified but ignored.
732    o verification:
733      - in testreport, convert hostname to lower case for default output dir name
734    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
735    o pkg/dic: add modifications from Hajoon:
736      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
737      - light attenuation: add self-shading effect by climatological Chlorophyll
738        (read from file).
739    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
740        compiles when SEAICE_ALLOW_DYNAMICS is undefined
741    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
742        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
743        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
744        approach where CPP_OPTIONS.h includes an omnipotent
745        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
746    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
747        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
748    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
749        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
750        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
751    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
752      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
753      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
754      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
755      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
756    o pkg/ctrl,ecco,exf :
757      - remove variables associated with NON-generic costs,
758        unless ECCO_CTRL_DEPRECATED is defined.
759      - remove NON-generic NON-obcs controls,
760        unless ECCO_CTRL_DEPRECATED is defined.
761    o pkg/ctrl : added ctrl_local_params.h
762    o pkg/ecco : added ecco_local_params.h
763    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
764        experiments, which will progressively be removed once the
765        experiments are revised to use only generic controls/costs.
766    
767    checkpoint65f (2014/10/13)
768    o pkg/ctrl, ecco, seaice : minor changes in headers
769    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
770        cost function and control capabilities added since checkpoint65c.
771    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
772    o pkg/ecco: increase modularity and improve logic
773      - ecco_toolbox.F (new) : basic operations that are often used,
774        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
775        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
776      - cost_gencal.F (new) : determine filnames and records.
777      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
778      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
779        and exploit the above functions leading to more compact code.
780      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
781      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
782        using_ers, using_gfo, using_mdt is now only defined within gencost)
783    o pkg/ecco: extend generic cost capabilities
784      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
785        capabilities via gencost_preproc (+ _c,_i,_r related params),
786        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
787        gencost_outputlevel arguments to cost_generic
788      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
789        and active_read, making room for gencost_preproc to take effect.
790        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
791      - pkg/ecco/cost_generic.F :
792        compute and store misfit maks*(model-data) in localdif that is
793        then used in cost and for output, output misfit if outlev.GT.0
794      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
795        rather gencost_barfile for deciding whether to write barfile
796      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
797      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
798        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
799      - pkg/ecco/ecco_summary.F : report gencost variables
800      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
801    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
802    o pkg/ecco: internal re-organization
803      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
804        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
805        mv relevant variables definition from ecco_cost.h to ecco.h,
806        make sure gencost routines only include ecco.h)
807      - throughout : add missing CCP switches, rm unused variables,
808        and rm un-necessary CPP switches
809      - throughout gencost routines : replace modelstartdate with
810        gencost_startdate when needed
811      - cost_bp_read.F : use arguments, instead of common blocs
812        so that it can be used also by (new) cost_gencost_bpv4.F
813      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
814      - ecco_phys.F : compute etanFull
815      - ecco_readparms.F : rename using_topex as using_tpj, add
816        bpv4-grace to gencost list, initialize added parameters
817      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
818    
819    checkpoint65e (2014/09/28)
820    o pkg/obcs:
821      - replaced the just-added CPP options with run-time variables
822        (see pkg/obcs/OBCS_PARAMS.h for details)
823    o pkg/obcs:
824      - add additional CPP options for sponge boundary layers
825        (see pkg/obcs/OBCS_OPTIONS.h for details)
826    o pkg/atm_phys:
827      - implement simple (obliquity only, assuming circular planet orbit)
828        seasonal cycle for incoming insolation ; used when run-time parameter
829        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
830    o pkg/exf, pkg/ecco, pkg/ctrl:
831      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
832      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
833      - implement gentim2d for xx_tauu, xx_tauv
834    o pkg/ctrl, pkg/ecco :
835      - fix and complement the generic controls implementation
836  o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,  o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
837    pkg/shelfice/shelfice_thermodynamics.F,      pkg/shelfice/shelfice_thermodynamics.F,
838    verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,      verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
839    verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :      verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
840   -  add weight in CTRL_GET_GEN calls    - add weight in CTRL_GET_GEN calls
 o pkg/ctrl :  
  - ctrl_get_gen.F : add weight as input parameter, and apply  
    it directly rather than using smooth_correl2Dw (to be retired).  
  - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call  
841  o pkg/ctrl :  o pkg/ctrl :
842   - CTRL_GENARR.h : add xx_gentim2d_numsmooth    - ctrl_get_gen.F : add weight as input parameter, and apply
843   - ctrl_cost_driver.F : bug fix (iarr, not 1)      it directly rather than using smooth_correl2Dw (to be retired).
844   - ctrl_init.F : bug fix (missing iarr)    - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
  - ctrl_readparms.F : add xx_gentim2d_numsmooth, improve numsmooth defaults  
  - ctrl_summary.F : improved report of controls settings  
 o pkg/ecco/ecco_cost_final.F : add genarr2d, genarr3d cost contributions  
845  o pkg/ctrl :  o pkg/ctrl :
846   - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,    - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
847     ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)      ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
848   - re-activate ctrl_summary (call in ctrl_init.F)    - re-activate ctrl_summary (call in ctrl_init.F)
849  o pkg/ctrl/ctrl_cost_gen.F :  o pkg/ctrl/ctrl_cost_gen.F :
850   - rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask}    - fix CCP brackets, remove un-necessary myiter, mytime
851     as {xx_gen_wmean,xx_gen_weight,xx_gen_mask}  o pkg/ecco, pkg/ctrl :
852   - add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D)    - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
853  o pkg/ctrl/CTRL_GENARR.h :    - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
854   - add objf_genarr2d,  num_genarr2d, mult_genarr2d    - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
855   - add objf_genarr3d,  num_genarr3d, mult_genarr3d    - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
  - add wgenarr2d, wgenarr3d  
 o pkg/ctrl/ctrl_readparms.F :  
  - add mult_genarr2d,mult_genarr3d in namelist  
 o pkg/ctrl_map_ini_genarr.F :  
  - bug fixes  
 o pkg/ctrl/ctrl_cost_driver.F :  
  - remove un-necessary cal.h, fix CCP brackets, remove un-necessary  
    myiter, mytime, add return  
 o pkg/ctrl/ctrl_cost_gen.F :  
  - fix CCP brackets, remove un-necessary myiter, mytime  
 o pkg/ecco :  
    - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)  
    - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)  
    - update cost_forcing_gen calls in cost_forcing.F  
    - update cost_genctrl call in ecco_cost_driver.F  
    - update ecco_ad_diff.list accordingly  
 o pkg/ctrl :  
    - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)  
    - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)  
    - update ctrl_ad_diff.list accordingly  
856    
857  checkpoint65d (2014/09/15)  checkpoint65d (2014/09/15)
858  o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :  o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
# Line 334  o pkg/seaice: more clean up Line 1127  o pkg/seaice: more clean up
1127      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
1128      this experiment):      this experiment):
1129      > size mitgcmuv_ad      > size mitgcmuv_ad
1130      text    data        bss     dec        hex        text    data        bss     dec        hex
1131      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1132      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1133      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1134      text    data        bss     dec        hex      text    data        bss     dec        hex
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