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revision 1.1994 by mlosch, Mon May 12 14:15:52 2014 UTC revision 1.2220 by jmc, Wed Jan 6 02:24:41 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/seaice/seaice_do_ridging.F: clean up the insectarium  o coupler pkgs:
8      Finish implementation of optionally-exchanged variable switches (started on
9       Nov 12) with addition of few more exchanged fields, including 2-way exchange
10       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
11       advection in OCN component; this requires sequential coupling.
12      coupler (pkg/atm_ocn_coupler):
13      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
14        routines (useful for debug).
15      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
16         flux, DIC fields) if corresponding switch is ON.
17      - add option to export RunOff to OCN (to use for DIC river input)
18      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
19      components (pkg/atm_ & ocn_compon_interf):
20      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
21        optionally exchanged fields; add a check & stop in cpl_readparms.F.
22        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
23        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
24      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
25        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
26      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
27      - hold in common block coupler optionally-exchanged variable switch
28        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
29      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
30        this is intended to replace the OCN cplFldtave.* output files (not updated
31        to contain new additional exchanged fields).
32    o pkg/dic:
33      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
34    o pkg/thsice:
35      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
36        and writing of thsice pickup files.
37    o pkg/atm_compon_interf:
38      - move all field individual export-call out of cpl_export_import_data.F
39        into new S/R ATM_EXPORT_FIELDS
40    o pkg/atm_compon_interf:
41      - store state variables (for now, only thSIce fields) just before beeing
42        exported (in cpl_export_import_data.F, like on ocean side) instead of from
43        atm_store_my_data.F like all exported fluxes.
44      - new version of pickup_cpl: write field names into meta file and read meta
45        file to find field postion in pickup. Also only write/read fields meeded for
46        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
47    o pkg/dic:
48      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
49    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
50        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
51        value can be from domain [0,1] to average between the two methods
52    o pkg/atm_phys:
53      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
54        hold fixed in time).
55    
56    checkpoint65r (2015/12/21)
57    o pkg/seaice:
58        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
59        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
60    o pkg/seaice:
61      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
62        when SEAICEscaleSurfStress=.TRUE.,
63      - apply areaW and areaS in S/R seaice_calc_lhs
64    o pkg/atm_phys:
65      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
66        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
67        for individual contribution (convection, LSC cond, radiation)
68      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
69        information); activated with: solar_exponent=0. and wv_exponent=-1.
70    o pkg/ggl90:
71      - within IDEMIX add upper limit for horizontal group velocity to
72        avoid instability problems in the explicit horizontal diffusion term for
73        long time steps or high resolution
74    o pkg/diagnostics:
75      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
76        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
77    o testreport:
78      - remove "-v" (verbose option) in default mpirun command.
79    o pkg/seaice/seaice_growth:
80      - catch potential division by zero in ITD code, does not change
81        verification results
82    o pkg/ecco:
83      - retire old codes to the Attic. The calls to retired functions are
84        left in a commented form in case they ever need to be re-activated.
85      - ecco_check.F: issue warning if any old CPP option is
86        defined that corresponds to retired codes -- then stop.
87    o pkg/atm_compon_interf:
88      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
89        coupler: use last time-step value instead of average over cplSendFrq_iter
90        time-step, similar to what is done for seaIceMass.
91        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
92    o eesupp & genmake2:
93      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
94        <= remove until a fix is found for some ifort version on ia32 machine.
95    o pkg/seaice/seaice_evp:
96      - refine residual computation
97    
98    checkpoint65q (2015/11/18)
99    o pkg/seaice/seaice_evp:
100      - fix residual computations so that they no longer affect the actual
101        simulation code
102      - fix seaice_readparams to be able to actually set new parameters
103        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
104    o model/src:
105      - fix wrong truncation (single prec) from "FLOAT" function in expressions
106        like: deltaT*FLOAT(myIter) when myIter is large:
107         a) replaced by DFLOAT (if not seen by TAF);
108         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
109    o pkg/aim_v23:
110      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
111        when pickupSuff is set ; do write rolling pickups + at the end of the run.
112    o pkg/atm_ocn_coupler + ocn_compon_interf:
113      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
114        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
115        add corresponding call in DO_OCEANIC_PHYS.
116    o coupler pkgs:
117      Start a new way to set-up optionally-exchanged variables (previously, only
118       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
119       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
120       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
121       compononent param default can be set accordingly).
122      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
123       but rather applies to a group a fields (going both ways like for DIC)
124       and corresponds to an option of coupling config.
125      coupler (pkg/atm_ocn_coupler):
126      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
127        and read namelist directly (without eessup S/R calls) instead of
128        in the very un-flexible old way, 1 param per line, in fixed order;
129      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
130        cleanly in CPL_CHECK_CPLCONFIG
131      - add new coupling-exchange selectors (some not yet active) including
132        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
133                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
134      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
135        component ; called directly from coupler.F, after comp. registrations;
136      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
137         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
138          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
139      components (pkg/atm_ & ocn_compon_interf):
140      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
141        CPP header file in all pkg source files.
142      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
143        ATM/OCN_CHECK_CPLCONFIG;
144      - add error-counter to track errors (e.g., in "data.cpl") and to stop
145        cleanly in ATM/OCN_CHECK_CPLCONFIG;
146      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
147        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
148        before PACKAGES_READPARMS;
149      verification/cpl_aim+ocn/:
150      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
151        "data.cpl" for coupler (in input_cpl).
152    o eesupp/inc:
153      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
154        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
155        to always cumulate tile local-sum in the same order (still uses
156        MPI_Allreduce like standard code).
157      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
158        that are now identical to standard version (in eesupp/inc).
159    o pkg/shelfice:
160      - add SHELFICETransCoeffTFile for initializing spatially varying
161        heat and salt transfer coefficients
162    o pkg/atm_compon_interf & ocn_compon_interf:
163      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
164        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
165      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
166    o pkg/atm_ocn_coupler:
167      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
168    o pkg/rbcs:
169      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
170        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
171      - add a short report (to STDOUT) about RBCS-mask settings.
172    
173    checkpoint65p (2015/10/23)
174    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
175        there is no adjoint test for EVP, we don't know what it does to the adjoint
176        solution, but at least there are no more recomputation warnings left
177    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
178        a chance of giving the same results as a fully converged VP (JFNK) solver
179    o tools/adjoint_options/adjoint_diva:
180      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
181    o pkg/streamice:
182      - spotted bug in streamice_driving_stress using dyG where should have been dxG
183    o pkg/exf:
184      - remove STOP statement that prevented to use wind or (wind-)stress
185        interpolation for constant-in-time forcing fields (wind/stress period = 0).
186    o pkg/seaice:
187      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
188        5 additionals 2D fields and 6 new store directives
189      - change logic in seaice_readparms.F: EVP code can now be turned on in
190        various ways, setting SEAICE_deltaTev is no longer required,
191        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
192        or SEAICEaEVPcoeff
193    o pkg/shelfice/shelfice_thermodynamics.F
194      - redefining uLoc/vLoc to u/v, instead of 2u/v
195    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
196      - this is an intermediate state of a truely converging EVP that has
197        the potential of outperforming implicit VP methods, I do not recommend
198        using it yet.
199      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
200        and all parameters are hardwired
201      - for convergence it still requires very smooth regularisations, that means,
202        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
203        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
204        specific averaging appears to be required, still subject to tuning
205      - still needs cleaning and I need to turn parameter into runtime parameters
206      - add code to compute and print residuals of iteration, compile with
207        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
208    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
209      that entered with r1.54 on Sep04, 2015, -> update results
210    
211    checkpoint65o (2015/09/14)
212    o pkg/mom_vecinv & mom_common:
213      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
214        called from there.
215      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
216        allows to use Vector-Invariant form in deep atmos and anelastic formulation
217    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
218      and Koenig-Beatty+Holland (2012)
219      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
220      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
221      - requires an extra input argument for S/R seaice_calc_viscosities
222      - tensileStrength's depth dependence is different from Itkin et al. (2015)
223        (to be changed and played with, for now exponential)
224    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
225      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
226        by AREA according to Connelly et al. (2004), JPO.
227      - For EVP and the LSR solver, the implicit part of the drag term is
228        the only non-zero term in the denominator when there is no ice (which
229        prevented running the model with zero ice-ocean drag). If
230        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
231        (or zero main diagonals BU/BV) which need to be caught. A practical
232        consequence is that for open water, the momentum equation reduce
233        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
234        they happen to be zero, often leading to a non-zero solution over
235        open water.
236    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
237        efficient EVP method.
238      - introduce area-weighted averages for e12 (analogously to
239        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
240        remain, but also changing the order of terms in the previous average
241        changed the results as much) -> update experiment
242      - add SEAICE_DELTA_SMOOTHREG code
243      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
244        TEM-code
245      - adjust loop bounds so that only required fields are computed
246      - add new averaging code for zetaZ/deltaZ (again similar to
247        seaice_calc_viscosities.F), inactive by default for now (will change
248        results again), but will replace old code eventually
249    o eesupp/src:
250      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
251        to always cumulate tile local-sum in the same order
252        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
253        Still uses MPI_Allreduce (like standard code) but on array of tiles
254        and should be faster than GLOBAL_SUM_SEND_RECV code.
255      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
256        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
257      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
258         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
259         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
260         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
261         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
262    
263    checkpoint65n (2015/07/29)
264    o pkg/thsice:
265      - add a warning when used with pkg/aim but without updating SST
266        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
267    o pkg/offline:
268      - change where Offline-Fields are loaded, from load_fields_driver.F to
269        directly within FORWARD_STEP, just after updating iter number and time;
270      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
271        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
272       These changes allow:
273        a) to recover exactly on-line results using deltaToffline=deltaTClock,
274        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
275        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
276        time-step, both with GM & KPP files and with recomputing these fields;
277        b) no needs to switch on staggerTimeStep anymore;
278        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
279      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
280    o pkg/offline:
281      - change (rarely used) offset-iteration parameter to an offset time (in s):
282        can easily recover previous offset-iter effect by setting offset-time
283        (offlineTimeOffset) to offset-iter x deltaToffline;
284      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
285        in KPP as part of surface buoyancy forcing) in offline run.
286      - fix ptracers KPP non-local term in the case where KPP is re-computed.
287    o OpenAD
288      - Adding preliminary ggl90 test to OpenAD verification.
289        Config. with ggl90 currently diverges after 64 time steps
290        so will need more work to become more stable
291      - Adding preliminary kpp test to OpenAD verification.
292        required small tweakes in kpp_routines.F
293      - Merge and update from Krishna Narayanan's contrib area:
294        * Add one variable for preliminary OpenAD DIVA
295        * Add replacement time-stepping for OpenAD DIVA
296        * genmake2 flag -diva (but only for OpenAD; preliminary)
297        * required modifs for OAD_support
298        successful preliminary test for tutorial_global_oce_biogeo/
299    o pkg/seaice:
300      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
301      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
302        delta with a smooth function in s/r seaice_calc_viscosity
303        (no effect on EVP)
304      - rename local suffix "sqr" into "sq" for more consistent variable names
305    o pkg/seaice:
306        add new parameter SEAICE_deltaMin that is used ***only***
307        for regularizing Delta (and nothing else, like the parameter
308        which is also used for all sorts of things SEAICE_EPS).
309        Defaults to SEAICE_EPS for backward compatibility only.
310    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
311        the wrong key by inialising it before use -> fixes a recomputation
312        problem but does not fix the gradient
313    o pkg/layers:
314      - move resetting of flux arrays to outside the iLa loop
315        (this caused layers_diapycnal to not work with more than one layer coord.)
316      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
317    o pkg/layers:
318      - remove from common block 3D layers fields (used to diagnose transport
319        in tracer coords) and declare them as local arrays in layers_calc.F
320    o pkg/seaice:
321      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
322        in lab_sea forward experiment (changes results -> updated)
323      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
324    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
325       computations; for SEAICE_VECTORIZE_LSR
326      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
327        sweep to the outside,
328      - remove store directives and add "CADJ loop sequential" directives
329        in analogy to model/src/solve_tridiagonal.F
330      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
331        boundaries to yield more readable code. This has also the charming side
332        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
333        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
334        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
335        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
336        an additional option)
337       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
338       but the adjoint gradients (which are affected by this change) still explode.
339    o coupler (atm & ocn _compon_interf):
340      - avoid using Exch2 IO mapping if not suitable.
341    
342    checkpoint65m (2015/06/15)
343    o pkg/layers:
344      - clean-up old parameters setting (from Sep 2012):
345        + remove old parameters setting from common block (declared locally);
346        + stop if any old parameter is mixed with new parameters;
347        + check for valid or consistent parameter setting (e.g., layers_name)
348      - check that layers_bounds for Pot.Density are in the right range;
349        this is supposed to catch un-updated setting after recently shifting
350        potential density field "prho" by -1000 (now in "sigma" scale).
351    o pkg/layers:
352      - Added missing call to layers_fill for keeping track of tottend in
353        pkg/diagnostics/diagnostics_fill_state.F
354    o pkg/layers:
355      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
356        of diapycnal fluxes
357    o pkg/layers:
358      - reverted changes to interpolation to previous treatment; there
359        was never actually a problem
360    o pkg/layers:
361      - fix interpolation of layers tracers in the presence of partial cells
362      - add lots of new functionality to compute water mass transformation
363        (enabled by CPP flag LAYERS_THERMODYNAMICS)
364      - add new calls from main code (diags_oceanic_surf_flux.F,
365        thermodynamics.F, impldiff.F) and gad to save the necessary fields
366        for layers_thermodynamics calculations
367    o pkg/ptracers:
368      - add capability of stepping a passive tracer forward without advection
369        by setting PTRACERS_advScheme to 0.
370    o pkg/diagnostics:
371      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
372    o pkg/layers:
373      - shift potential density field "prho" by -1000 for density layer averaging so
374        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
375        Note that density bin boundaries (layers_bounds in data.layers) have
376        to be set accordingly (i.e., shifted, in sigma scale).
377    o pkg/layers:
378      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
379      - fix calculation of layer non-weighted velocity and layer probability
380      - add diagnostics for pot.density used for layer averaging
381    o pkg/seaice:
382      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
383        positiveness, modify a few comments and improve variable names,
384      - the changed computation of deltaC affects most seaice-related
385        experiments at the truncation level.
386        seaice_itd.thermo is affected by far the most, with
387        only 7 digits of agreement remaining; update experiments.
388    
389    checkpoint65l (2015/05/04)
390    o pkg/shelfice:
391      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
392        factor drKp1 to zero where it is negative (ie. do not use
393        SHELFICEBoundaryLayer if hFacC>1)
394      - the same for factor drLoc in shelfice_forcing.F
395    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
396        with modules in ptracers, when using testreport option "-small_f"
397    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
398      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
399    o verification/testreport
400      - add new option -small_f
401        with this option testreport first makes the target small_f (*.f files)
402        before running make (all). This is useful for explicit inlining when
403        all sources need to be full available.
404    o pkg/exf/exf_interp.F:
405        remove previous changes related to reverse (decreasing) input grids latitude
406    
407    checkpoint65k (2015/04/01)
408    o pkg/ecco:
409        fix missing cosphi initialization; use eccoiter in place of optimcycle;
410        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
411        instead of active read/write
412    o pkg/ctrl:
413        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
414        instead of active read/write.
415    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
416        return if .NOT.useAUTODIFF
417    o pkg/seaice: add CPP brackets (cost function related).
418    o model/src:
419        add useAUTODIFF run time switch.
420    o pkg/exf/exf_interp.F:
421        add code to allow input grids with latitude starting in the north (i.e. when
422        j=1 corresponds to northern edge of field); modify global_with_exf to test
423        this feature.
424    o verification/testreport:
425      - replace "grep -A3" with POSIX conformal sed command, because there are
426        implementations of grep that cannot do contextual searches
427      - replace "cat -n" by "nl" (two occurrences), because not all implementations
428        of "cat" have the option "-n"
429    o model/src:
430        add new file gsw_teos10.F that contains 3 functions, more or less a copy
431        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
432        convert from conservative to potential temperature. For now they are not
433        called anywhere.
434    o pkg/ggl90: make "useIDEMIX" useful
435      - re-organize code in s/r ggl90_calc a little to move computations that
436        are different for idemix into separate loops (changes verification
437        experiment idemix at truncation level, 12 digits remain -> updated)
438      - requires 2 new 2D fields KappaM, verticalShear
439      - make hFacI and recip_hFacI local 3D variables that are passed to
440        s/r ggl90_idemix
441      - fix and improve some comments
442    
443    checkpoint65j (2015/02/25)
444    o pkg/openad
445      - synchronize seawater.F with version in model/src: replace routine
446        body of sw_temp by calling sw_ptmp and fix/add a few comments.
447    o pkg/mnc:
448      - change default value of pickup_read/write_mnc params to FALSE
449        (since few features are missing in reading MNC pickup files).
450    o model/src:
451      - change default (background) vertical diffusivity for salt to be the
452        temperature (background) vertical diffusivity.
453      - change background vertical diffusivity in vertical mixing pkgs ggl90,
454        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
455        This makes ptracers default diffusivity (that uses salt diffKr) more
456        consistent with vertical mixing schemes.
457    o verification/testreport:
458      - fix typo in "-pcls" option ;
459      - put temp files in /tmp (instead of in local dir)
460      - add option "-ncad" to use genmake2 new option "-nocat4ad"
461      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
462    o pkg/ggl90 (idemix code):
463      - apply few fixes ; add some missing "_d 0" ; update output of exp.
464        global_ocean.90x40x15.idemix
465    o OpenAD
466      - enable active file I/O and begin removal of work-around code
467        for OpenAD for handling control variables (memory vs. active files)
468      - new CPP options file OPENAD_OPTIONS.h
469      - revert to genarr2d gradient check for hs94.1x64x5
470      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
471      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
472    o tools/genmake2:
473      - add option for an alternative Makefile (from Martin) where multiple
474        source files are sent to TAF (instead of all in one file).
475    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
476      - code provided by Carsten Eden as an extension of ggl90
477      - so far the code is turned on within ggl90 by setting a CPP-flag at
478        compile time; a runtime flag implementation is not yet complete
479      - tested in new verification experiment global_ocean.90x40x15.idemix
480    o verification:
481      - reduce length of the AD test run by half for experiments
482        global_ocean.cs32x15 (std + thsice) and isomip
483      - enable active file I/O for OpenAD, adjust verifications accordingly
484      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
485    o verification/testreport:
486      - fix two non-POSIX sed statements so that there are no error messages
487        on Mac OS X
488      - replace hostname -s with hostname | sed 's/\..*$//'
489    o model/src/seawater.F:
490      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
491        (following the matlab code), which would have avoided the bug caught
492        by Matt (see below) in the first place
493    o pkg/shelfice:
494      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
495        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
496      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
497        ice-shelf case (i.e., within surface level).
498      - add config summary in shelfice_check.F
499      - remove global variable recip_SHELFICElatentHeat and replace by a local
500        variable recip_latentHeat
501      - introduce diagnostics for friction velocity uStar (in case of
502        SHELFICEuseGammaFrict)
503      - change verification experiment isomip.htd:
504        + start from pickup (as input_ad at nIter0=8640)
505        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
506        + test SHELFICEuseGammaFrict = .TRUE.
507        + test SHELFICEadvDiffHeatFlux = .TRUE.
508    o model/src:
509      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
510        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
511        update output of experiments global_with_exf.yearly and isomip (all 6).
512    o pkg/shelfice:
513      - change setting of kTopC to also be zero where there is no ice-shelf.
514      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
515        ice-shelf is.
516      - first attempt to get RealFreshWaterFlux effects: for now, only without
517        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
518    o pkg/seaice: add the option to prescribe a fixed thickness PDF
519      for thermodynamic calculations
520      - because of divisions of the type 7/7 not exactly equal to 1, this change
521        affects results of some verification experiments by up to 4 digits:
522        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
523        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
524        adjoint: lab_sea, lab_sea.noseaicedyn
525        -> updated
526    
527    checkpoint65i (2015/01/23)
528    o model/src:
529      - change units of frictionHeating field from W to W/m^2
530      - fix bug in frictional heating from stratospheric drag in
531        S/R ATM_PHYS_TENDENCY_APPLY_V
532      - with synchronous time-stepping: move resetting to zero of frictionHeating
533        field from load_fields_driver.F to thermodynamics.F ;
534      - add diagnostics for frictional heating.
535    o model/src & gmredi K3D:
536      - add frictionHeating field to pickup-files (for synchronous time-stepping)
537      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
538      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
539        and name in pickup file).
540      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
541    o model/src:
542      - move (from ini_forcing.F) initialisation of all arrays in header file
543        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
544        (since Nov 2012) with option selectAddFluid=1.
545    o pkg/shelfice:
546      - change units (+ document) of newly added field "shelfIceMassDynTendency"
547      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
548    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
549    o pkg/seaice: two new runtime parameters:
550      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
551        long overdue
552      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
553        parameterization of tensil stress for fast ice (does not do anything yet)
554    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
555        for LSR: move checking overlaps out of JFNK-if-block
556    o pkg/atm_phys:
557      - move copy of grid and dynamical fields out of atm_phys_driver.F into
558        new S/R ATM_PHYS_DYN2PHYS.
559      - fix level height for Linear Free-Surf case (to be consistent with
560        fixed-in-time pressure levels).
561    o pkg/mom_common (bottomdrag):
562      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
563        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
564        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
565    o pkg/shelfice (u/v_drag):
566      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
567      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
568        (now similar to shelfice_u_drag.F)
569      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
570        from mom_vecinv.F (similar to mom_fluxform calls).
571    o pkg/mom_common (bottomdrag):
572      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
573      - add options for alternative discretisation of velocity norm in quadratic
574        bottom drag: averaging of grid-cell-center KE to U.point and V.point
575        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
576        improves when averaging only the other component (e.g. vVel for U bottom
577        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
578      - add options (bottomVisc_pCell) to account for partial-cell in bottom
579        friction (no-slip BC) thus getting the true distance from the bottom;
580        off by default since this also reduces model stability (explicit bottom
581        friction). Changes produce different machine truncation with linear-drag
582        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
583        front_relax (bvp & mxl, 10 & 11 digits).
584    o model/src & mom pkgs:
585      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
586        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
587      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
588        just copy level Nr value to level Nr+1.
589    o doc:
590      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
591    o pkg/streamice:
592      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
593        SHELFICE.h: move array shelficemass to init_varia, initialise
594        from array shelficemassinit, which is set in init_fixed and
595        has option to be set from file; introduce array
596        shelficeMassDynTend array, set thru file in init_fixed
597      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
598        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
599        pkg/streamice
600      - shelfice_thermodynamics.F: call shelfice_step_icemass if
601        SHELFICEMassStepping = .true.
602      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
603    
604    checkpoint65h (2014/12/17)
605    o verification/global_ocean.90x40x15, global_ocean_ebm:
606      - update to generic controls.
607    o pkg/ctrl:
608      - ctrl_map_ini_genarr.F: test for igen>0
609      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
610      - move gentim2d part of ctrl_map_ini_genarr.F to
611        new separate routine : ctrl_map_ini_gentim2d.F
612      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
613        add time variable weights and cyclic controls (time mean,
614        seasonal cycle, etc) capabilities to gentim2d
615    o pkg/ecco:
616      - move reading of error, conversion to weights from
617        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
618    o global_oce_llc90, cs32:
619      - activte sbo.
620      - CTRL_SIZE.h : add maxCtrlProc.
621      - activate the new genctrl capabilities.
622      - update following reorganization of global_oce_input_fields.tar.gz  
623    o pkg/ctrl/ctrl_ad_diff.list:
624      - add missing ctrl_init_rec.f
625    o tools/OAD_support/keepOriginal:
626      - add ctrl_init_rec.F
627    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
628      - avoid recomputations of xx_gentim2d_dummy.
629    o momentum diagnostics:
630      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
631        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
632    o pkg/seaice/seaice_lsr.F:
633      - fix computation of BU/BV, make sure they are non-zero, only necessary
634        for cubed sphere exchanges and SEAICE_OLx/y>0.
635        This makes calling s/r fill_cs_corner_rl obsolete (removed).
636    o verification/global_ocean.cs32x15/input.seaice
637      - add test for strong implicit coupling and restricted addtive Schwarz
638        methods for LSR
639      - update results/output.seaice.txt
640    o verification/tutorial_global_oce_biogeo:
641      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
642        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
643        update output_adm,_oadm,_tlm.txt
644    o pkg/dic:
645      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
646      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
647        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
648    o verification/tutorial_global_oce_biogeo:
649      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
650        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
651        update output_adm,_oadm,_tlm.txt
652    o eesupp/src:
653      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
654        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
655    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
656      LSR (following Hutchings et al. 2004)
657      - introduce zetaZ as a global variable (requires adjustments in
658        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
659        in seaice_calc_viscosities.F
660      - new flag SEAICEuseStrImpCpl (default off)
661      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
662        momentum equations
663      - JFNK-solver (preconditioner) adjusted to allow using this method
664        (where it does not have any positive effect)
665    o pkg/seaice
666      - add overlap for restrictive additive Schwartz method also to LSR, but
667        turn it off by default (because it only seems to work for non-cubed
668        sphere/llc topologies)
669    o pkg/autodiff
670      - add extra exchanges in addummy_in_steppging also for mnc output
671    o pkg/seaice:
672      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
673        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
674    o pkg/obcs:
675      - add option to specify domain-connected piece Id along OB though files
676        (for now, only used to diagnose PhiVel; default =1 -> global correction)
677      - modify obcs_diag_balance.F to process each connected-part separately;
678        exclude OB where Id = 0 but keep the full divergence there (-> constant
679        Psi along this portion of OB and all inflow derived from grad(Phi))
680      - add example of OB-conect files in verification/so_box_biogeo/input.
681    o pkg/diagnostics:
682      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
683      a) use non zero matrix element across OB and solve for Phi 1 grid point
684         outside OB (i.e, where tracer OBCS are applied).
685      b) global imbalance of inFlow/outFlow across OB: instead of modifying
686         velocity across OB, spread it uniformly along the OB in the RHS.
687    
688    checkpoint65g (2014/11/19)
689    o pkg/diagnostcis:
690      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
691    o pkg/my82,pp81,kl10:
692      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
693        field diffKr as background diffusivity to set minimum diffusivity value.
694    o pkg/seaice:
695      - add new parameter SEAICEuseEVPrev (for revisited EVP by
696        Bouillon et al 2013)
697      - add SEAICE_evpAlpha/Beta to namelist
698      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
699        involve trivial re-ordering of divisions/multiplications that should not
700        have any effects, but ... they do change the results of lab_sea.hb87 so
701        that only 2 digits of agreement remain, in line with the general
702        instability/fragility of the evp-code. For now, I do not care and just
703        update the verification experiment
704    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
705      - remove xx_genarr2d_numsmooth etc
706      - use xx_genarr2d_preproc etc instead
707      - carry out smooth_correl2D at initialization stage rather than during
708        time stepping.
709      - get smoothOpNb from xx_gentim2d_preproc
710    o global_oce_cs32 :
711      - add test of generic ecco capabilities.
712    o pkg/exf/exf_getsurfacefluxes.F :
713      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
714    o pkg/ctrl,ecco :
715      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
716        is defined.
717    o pkg/seaice: add diagnostics for Delta (deformation parameter)
718    o model/src:
719      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
720        diffusivity (background) is specified but ignored.
721    o verification:
722      - in testreport, convert hostname to lower case for default output dir name
723    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
724    o pkg/dic: add modifications from Hajoon:
725      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
726      - light attenuation: add self-shading effect by climatological Chlorophyll
727        (read from file).
728    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
729        compiles when SEAICE_ALLOW_DYNAMICS is undefined
730    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
731        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
732        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
733        approach where CPP_OPTIONS.h includes an omnipotent
734        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
735    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
736        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
737    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
738        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
739        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
740    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
741      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
742      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
743      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
744      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
745    o pkg/ctrl,ecco,exf :
746      - remove variables associated with NON-generic costs,
747        unless ECCO_CTRL_DEPRECATED is defined.
748      - remove NON-generic NON-obcs controls,
749        unless ECCO_CTRL_DEPRECATED is defined.
750    o pkg/ctrl : added ctrl_local_params.h
751    o pkg/ecco : added ecco_local_params.h
752    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
753        experiments, which will progressively be removed once the
754        experiments are revised to use only generic controls/costs.
755    
756    checkpoint65f (2014/10/13)
757    o pkg/ctrl, ecco, seaice : minor changes in headers
758    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
759        cost function and control capabilities added since checkpoint65c.
760    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
761    o pkg/ecco: increase modularity and improve logic
762      - ecco_toolbox.F (new) : basic operations that are often used,
763        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
764        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
765      - cost_gencal.F (new) : determine filnames and records.
766      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
767      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
768        and exploit the above functions leading to more compact code.
769      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
770      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
771        using_ers, using_gfo, using_mdt is now only defined within gencost)
772    o pkg/ecco: extend generic cost capabilities
773      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
774        capabilities via gencost_preproc (+ _c,_i,_r related params),
775        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
776        gencost_outputlevel arguments to cost_generic
777      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
778        and active_read, making room for gencost_preproc to take effect.
779        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
780      - pkg/ecco/cost_generic.F :
781        compute and store misfit maks*(model-data) in localdif that is
782        then used in cost and for output, output misfit if outlev.GT.0
783      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
784        rather gencost_barfile for deciding whether to write barfile
785      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
786      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
787        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
788      - pkg/ecco/ecco_summary.F : report gencost variables
789      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
790    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
791    o pkg/ecco: internal re-organization
792      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
793        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
794        mv relevant variables definition from ecco_cost.h to ecco.h,
795        make sure gencost routines only include ecco.h)
796      - throughout : add missing CCP switches, rm unused variables,
797        and rm un-necessary CPP switches
798      - throughout gencost routines : replace modelstartdate with
799        gencost_startdate when needed
800      - cost_bp_read.F : use arguments, instead of common blocs
801        so that it can be used also by (new) cost_gencost_bpv4.F
802      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
803      - ecco_phys.F : compute etanFull
804      - ecco_readparms.F : rename using_topex as using_tpj, add
805        bpv4-grace to gencost list, initialize added parameters
806      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
807    
808    checkpoint65e (2014/09/28)
809    o pkg/obcs:
810      - replaced the just-added CPP options with run-time variables
811        (see pkg/obcs/OBCS_PARAMS.h for details)
812    o pkg/obcs:
813      - add additional CPP options for sponge boundary layers
814        (see pkg/obcs/OBCS_OPTIONS.h for details)
815    o pkg/atm_phys:
816      - implement simple (obliquity only, assuming circular planet orbit)
817        seasonal cycle for incoming insolation ; used when run-time parameter
818        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
819    o pkg/exf, pkg/ecco, pkg/ctrl:
820      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
821      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
822      - implement gentim2d for xx_tauu, xx_tauv
823    o pkg/ctrl, pkg/ecco :
824      - fix and complement the generic controls implementation
825    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
826        pkg/shelfice/shelfice_thermodynamics.F,
827        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
828        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
829      - add weight in CTRL_GET_GEN calls
830    o pkg/ctrl :
831      - ctrl_get_gen.F : add weight as input parameter, and apply
832        it directly rather than using smooth_correl2Dw (to be retired).
833      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
834    o pkg/ctrl :
835      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
836        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
837      - re-activate ctrl_summary (call in ctrl_init.F)
838    o pkg/ctrl/ctrl_cost_gen.F :
839      - fix CCP brackets, remove un-necessary myiter, mytime
840    o pkg/ecco, pkg/ctrl :
841      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
842      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
843      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
844      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
845    
846    checkpoint65d (2014/09/15)
847    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
848      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
849        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
850    o pkg/ctrl/ctrl_map_ini_genarr.F :
851      - remove compilation failure
852      - replace hard coded example
853      - use ctrl_map_ini_gen2D, 3D
854    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
855      - on/off switch based upon xx_genarr2d_weight,3d
856    o src/packages_init_variables.F :
857      - regroup pkg/estimation calls
858      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
859        (moved to ctrl_init_variables)
860    o cost/cost_init_varia.F :
861      - remove ecco_cost_init_varia
862        (moved to ecco_init_varia)
863    o ctrl/ctrl_init_variables.F :
864      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
865      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
866    o ctrl/ctrl_map_ini.F :
867      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
868        (moved to ctrl_init_variables)
869    o ctrl/ctrl_map_ini_ecco.F :
870      - remove ECCO_PHYS (mv to ecco_init_varia)
871      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
872    o ecco/ecco_ad_diff.list :
873      - add ecco_init_varia.f
874    o ecco/ecco_init_varia.F
875      - new routine
876    o pkg/streamice:
877      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
878        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
879      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
880    o pkg/generic_advdiff:
881      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
882    o pkg/exf:
883      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
884         xxg_precip capability
885      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
886    o pkg/ctrl:
887      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
888    o model/src/load_fields_driver.F :
889      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
890        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
891    o OpenAD verification experiments:
892      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
893        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
894        for now, only in pkgs used in OpenAD verification experiments.
895      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
896        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
897        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
898        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
899    o OpenAD verification tests:
900      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
901      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
902        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
903      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
904        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
905    o model/src & generic_advdiff:
906      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
907        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
908        dynamics requires valid tracer forcing only over tile interior but, for
909        some diagnostics, may need to extend it over 1 point in tile halo region.
910      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
911        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
912        setting in temp/salt/ptracer_integrate.F
913    o pkg/dic:
914      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
915        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
916        in gchem_forcing_sep.F
917    o pkg/autodiff & obcs:
918      - add storage of current OB values for U & V (was already done for T & S).
919    
920    checkpoint65c (2014/08/30)
921    o pkg/dic:
922      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
923        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
924        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
925    o verification:
926      - new experiment testing OBCS and DIC pkgs, using params & output from
927        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
928        passage: take OBCS from the last year of a 2 yrs simulation and initial
929        conditions from t=1.yr while keeping the same forcing.
930    o model/src:
931      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
932        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
933    o pkg/diagnostics (Stats-Diags):
934      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
935        a) refine region where stats are computed, excluding where arrhFac=0 ;
936        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
937        c) extend regional stats over the region edges (for U or V pt location).
938    o pkg/gchem:
939      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
940        pkg/dic is currently changing/updating ptracers values beyond the OB).
941    o verification (hs94):
942      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
943        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
944        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
945        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
946    o pkg/ptracers:
947      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
948        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
949      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
950        with AB-2 code (so that it get tested).
951    o model/src:
952      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
953        with AB-2 code (previously only available with AB-3 code).
954        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
955        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
956        there, by calling CYCLE_AB_TRACER).
957    o pkg/generic_advdiff:
958      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
959        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
960        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
961        S/R temp/salt/ptracers_integrate.F
962    o model/src & pkg/ptracers:
963      - remove common block variables gT,gS (in DYNVARS.h), except when
964         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
965      - remove common block variable gPtr.
966    o model/src & pkgs:
967      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
968         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
969         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
970         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
971      + change accordingly all calling S/R.
972      - use local temperature/salinity/ptracer tendency array (without bi,bj)
973        in S/R temp/salt/ptracers_integrate.F
974    o pkg/seaice:
975      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
976        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
977      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
978        in seaice_lsr
979      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
980        in s/r seaice_lsr_calc_coeffs
981    o pkg/mdsio:
982      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
983        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
984        too long (e.g., > MAX_LEN_FNAM/2 )
985    
986    checkpoint65b (2014/08/12)
987    o pkg/matrix:
988      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
989    o model/src:
990      - fix initialisation of geothermalFile; compile geothermal-flux code in
991        natl_box verification experiment.
992    o model/src & pkg/down_slope:
993      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
994      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
995        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
996        results at machine truncation level: update output of experiments
997        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
998    o pkg/diagnostics (Stats-Diags):
999      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1000        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1001        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1002        times (but Min,Max and StD are still wrong).
1003    o model/src:
1004      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1005        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1006    o model/src:
1007      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1008        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1009        arrays are already updated while adjustments (filters, conv.adjustment) are
1010        still applied later, in S/R TRACERS_CORRECTION_STEP.
1011    o model/src:
1012      - store in common bloc array "rhoInSitu" the virtual potential temperature
1013        anomaly that is used to compute geopotential: this make the atmos code
1014        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1015    o pkg/seaice/seaice_lsr.F
1016      - rename integer variable ilcall to ipass (that's what it is called
1017        in the residual diagnostics
1018      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1019        default) for improved non-linear convergence of the first few steps
1020      - adjust a few comments and add new ones to explain some of the store
1021        directives
1022    o pkg/generic_advdiff (& ptracers):
1023      - re-work the code to check for valid advection scheme and for minimum
1024        size of overlap (now stored in local common bloc in gad_advscheme.F)
1025    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1026      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1027      - add an auxilliary variable "bet" and fix store directives and keys in
1028        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1029        less exact gradients in my tests); but there are still
1030        recomputation warning (although gradients are sort of OK), when
1031        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1032        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1033      - update verification experiments lab_sea.
1034      - change some comments in S/R seaice_calc_viscosities
1035    o model/src:
1036      - if staggerTimeStep=T, always apply exchange to velocity field in
1037        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1038        (independent of using multi-dim advection or not); no effect on FWD run
1039        but affects AD results (at machine truncation level): update output of
1040        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1041        and isomip (oad: 12.d).
1042    o pkg/generic_advdiff:
1043      - stop if doAB_onGtGs is set to FALSE but ignored
1044      - refine warning related to stability of tracer time-stepping
1045        regarding internal wave dynamics.
1046      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1047        on staggerTimeStep & implicitIntGravWave (will now get a warning
1048        if potentially unstable).
1049    o pkg/kl10:
1050      - add new pkg "kl10" for mixing due to internal wave breaking, from
1051        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1052        (contribution from Jody Klymak), tested in verification experiment
1053        verification/internal_wave/input.kl10/
1054    o isomip experiment:
1055      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1056        (input.htd) and update the output.
1057    o cd_code experiments:
1058      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1059        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1060        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1061        update the corresponding output.
1062    o pkg/seaice:
1063      - reduce the number of include files and store directives in
1064        S/R seaice_lsr_tridiagu/v
1065      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1066        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1067        get rid off one store directive (a TAF bug?)
1068      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1069        S/R seaice_lsr_tridiagv to change the loop range for consistency
1070      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1071      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1072        S/R seaice_lsr_tridiagu/v (requires update of
1073        offline_exf_seaice/input.dyn_jfnk)
1074    
1075    checkpoint65a (2014/07/27)
1076    o model/src:
1077      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1078        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1079        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1080        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1081    o model/src:
1082      - collect momentum forcing tendency into local 2-D array (passed as argument
1083        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1084        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1085        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1086      - collect T & S forcing tendency into local 2-D array (passed as argument to
1087        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1088        affects results at machine truncation level (e.g., ocean: if using
1089        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1090        correction due to vertical advection).
1091      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1092        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1093        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1094        obcs_ctrl (ad & fwd grd @ 12 & 7).
1095    o pkg/ptracers & diagnostics:
1096      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1097        title (to avoid some unexpected truncation); sort out ptracers diags units.
1098      - collect ptracer forcing tendency into local 2-D array (passed as argument
1099        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1100    
1101    checkpoint65 (2014/07/18)
1102    o pkg/fizhi:
1103      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1104        affects results at machine truncation level. Update output of experiments
1105        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1106    o pkg/seaice: more clean up
1107      - rename TAF common block tapes to be more consistent and remove
1108        unnecessary duplicates
1109      - add store directives to remove more recomputations, but use smaller
1110        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1111        The idea behind this flag is to reduce the memory footprint when the
1112        adjoint of the LSR is not required. As of now, defining the flag
1113        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1114        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1115        For experiment offline_exf_seaice, this means on a linux box with gfortran
1116        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1117        this experiment):
1118        > size mitgcmuv_ad
1119        text    data        bss     dec        hex
1120        5100659 1216  220458952  225560827  d71c8fb
1121        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1122        but only a moderate increase of 36% for global_ocean.cs32x15:
1123        text    data        bss     dec        hex
1124        6695027 1648 1014578664 1021275339 3cdf6ccb
1125        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1126      - note: there are still recomputations in global_ocean.cs32x15 and
1127        offline_exf_seaice and the gradient agreement changes (gets a
1128        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1129      - in general, the AD gradients still are wrong
1130    o OpenAD
1131      - clean up code_oad/ directories somewhat by moving files
1132        dontCompile, dontTransform, keepOriginal to OAD_support/
1133    o model/src:
1134      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1135        (not currently tested): add dissipation terms before NLFS rescaling of
1136        tendencies (previously done after).
1137    o pkg/diagnostics:
1138      - write stats-diags in ascii file with more digits (same as in monitor).
1139    o pkg/down_slope:
1140      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1141        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1142    o model/src:
1143      - new file "apply_forcing.F" containing all the code previously in
1144        external_forcing.F, but with new argument list: pass, as new argument,
1145        the current level tendency array to update (instead of a direct update
1146        of the common bloc array). Change the corresponding calls.
1147      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1148        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1149    o pkg/seaice/seaice_lsr, a little bit of clean up
1150      - rearrange some code blocks, so that now all calculations for
1151        setting up the right-hand-sides done within one single block
1152        (I find that easier to read and understand)
1153      - rearrange freedrift-code to reduce the number of ifdefs
1154      - adjust some indentations and comments
1155    
1156    checkpoint64z (2014/07/10)
1157    o model/src and several pkgs:
1158      - change argument list of all S/R called from external_forcing.F and
1159        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1160        to pass, as argument, the current level tendency array to update
1161        (instead of a direct update of the common bloc array).
1162      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1163      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1164    o pkg/seaice/seaice_lsr.F
1165      - always initialize local arrays in seaice_lsr_tridiagu/v
1166      - add more local tapes to seaice_lsr_tridiagu/v
1167      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1168        keep it in bi/bj loop; this seems to be essential
1169      - gradients are still wrong but only by 4-7 orders of magnitude
1170        instead of 15 orders of magnitude, lab_sea improves a little
1171    o pkg/seaice
1172      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1173        generates unnecessary code in seaice_lsr_ad
1174      - add more store directives in seaice_lsr to avoid unnecessary code
1175        in seaice_lsr_ad
1176      - exclude some residual computations in seaice_lsr when
1177        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1178        in seaice_lsr_ad
1179      - add more storing, a new tape (model/src/the_main_loop.F) and
1180        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1181        and klockey should be checked by a specialist)
1182      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1183        and update lab_sea after previous changes in pkg/seaice below
1184    o pkg/autodiff:
1185      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1186        viscFacInAd : run time parameters allowing for adjoint switches
1187        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1188    o pkg/ecco:
1189      - introduce cost_gencost_boxmean.F that computes a box mean
1190        temperature (for use in adjoint sensitivity studies).
1191    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1192    o pkg/mom_common/mom_calc_visc.F:
1193      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1194    o pkg/seaice/seaice_summary.F:
1195      - statement for SEAICEadjMODE now in autodiff_readparms.F
1196    o pkg/seaice:
1197      - remove some store directives and add new ones in an effort to get
1198        finally rid off the recomputation warnings. This is successful
1199        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1200        defined (i.e. no extensive recomputation warnings left), but there
1201        are still too many recomputations on the solver iteration level
1202      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1203      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1204        SEAICE_SIZE.h
1205      - add a store directive in S/R seaice_calc_viscosities
1206    o pkg/seaice (ITD code):
1207      - fix definition of Hlimit for multi-threaded case
1208      - use double precision arithmetic to compute Hlimit: this affects results;
1209        update output of experiment seaice_itd.
1210    o replace content of verification/seaice_itd
1211      - instead of a 1D column use the configuration of offline_exf_seaice
1212        to test the ice thickness distribution code with ridging
1213      - this is a first shot at this experiment
1214      - change of some defaults of ridging parameters SEAICEhStar (from
1215        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1216        and lot of new comments.
1217    
1218    checkpoint64y (2014/06/20)
1219    o pkg/seaice/seaice_reg_ridge.F:
1220      - modify the regularization of very small volumes of ice; only check
1221        total volume HEFF, and do not apply correction to individual ice
1222        classes because that leads to funny patterns in the heat and fw-fluxes
1223        into the ocean. Adjust seaice_itd/results/output.txt
1224      - replace nITD by SEAICE_multDim in loop-ranges
1225    o pkg/exf:
1226      - add code to process the case field period = -12. with UV interpolation.
1227      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1228        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1229    o verification/global_with_exf:
1230      - switch all fields period to -12. (was previously untested) in input/data.exf
1231        (but keep secondary test ".yearly" unchanged); update the reference output.
1232    o pkg/cal:
1233      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1234    o pkg/exf:
1235      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1236        to replace logical switch "exf_verbose"
1237      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1238    o pkg/sbo:
1239      - update from Katherine Quinn: evaluate mass directly from density and SSH
1240        (budget using Finite Volume method) instead of from bottom pressure.
1241      - allow testreport to collect few selected SBO output ; tested in exp.
1242        global_ocean.90x40x15 (after updating the results, to include SBO output).
1243      - fix some multi-threading issues (in output part).
1244    o model/src & most packages:
1245      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1246      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1247        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1248        "data.{pkg}" exist ; and leave the S/R (return) just after.
1249      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1250        + call LAND_READPARMS from packages_readparms.F
1251    o pkg/seaice:
1252      - remove code that resets useThSice in S/R seaice_readparms and
1253        replace it by a warning in S/R seaice_check
1254      - remove parameter MULTDIM, replace with nITD and runtime
1255        parameter SEAICE_multDim (still hard-wired to nITD if
1256        SEAICE_ITD is defined)
1257    
1258    checkpoint64x (2014/05/24)
1259    o verification/lab_sea:
1260      - update adjoint and TLM output following changes to pkg/salt_plume
1261      - un-do the update after putting back local recip_Cp in few places.
1262    o pkg/salt_plume: modifications by An Nguyen:
1263      - add capability to do brine rejection (salt-plume) as function of
1264        volume+tracers (instead of only salinity tracer).
1265      - conserve volume by exchanging volume from each kLev to above to
1266        accommodate in-coming brine volume
1267      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1268      - switch KPP surf buoyancy due to brine forcing to 3-d
1269        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1270      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1271      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1272        in East/West Arctic.
1273    o pkg/sbo:
1274      - incorporate modifications from Katherine Quinn to enable the use of sbo
1275        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1276        output for future testreport verification (unfinished).
1277    o pkg/atm_phys:
1278      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1279        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1280        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1281    o pkg/seaice
1282      seaice_calc_ice_strength.F: modify expression to avoid divisions
1283        (affects truncation)
1284      seaice_do_ridging.F: clean up the insectarium
1285    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1286    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1287    - set closing/openingRate to zero where no extra iteration is need (3rd bug)    - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1288    - add some debugging information and error messages (warnings)    - add some debugging information and error messages (warnings)
1289  o model/src: modifications relatd to atmosphere p*:  o model/src: modifications relatd to atmosphere p*:
1290    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1291    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
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