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revision 1.2005 by jmc, Fri Jun 6 21:17:12 2014 UTC revision 1.2228 by mlosch, Thu Jan 21 16:57:50 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: add two new parameters
8      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
9        parameter is not in any namelist)
10      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
11        a preconditioner for the non-linear Newton iteration of the JFNK
12        solver
13    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
14      affects some experiments at truncation level:
15      - global_ocean.cs32x15.icedyn (11 digits),
16      - global_ocean.cs32x15.seaice (11 digits),
17      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
18      - also update global_ocean.cs32x15 adjoint and tangent-linear results
19    o pkg/salt_plume & pkg/thsice:
20      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
21        connect salt_plume flux to ATM-OCN coupling pkgs interface:
22       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
23         export to coupler interface) even without compiling pkg/salt_plume ;
24       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
25         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
26    o pkg/dic:
27      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
28        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
29        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
30      - move also update with values from ATM-OCN Coupler in the same new S/R
31        (previously done in ocn_apply_import.F).
32    o tools/adjoint_options:
33      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
34        has been changed on Jan 14, 2016.
35    o pkg/ggl90:
36      - add alternative discretisation of vertical shear (off by default), to
37        compute the mean (@ grid-cell center) of vertical shear compon instead of
38        vertical shear of mean flow (@ grid-cell center).
39      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
40        results on adjacent faces of cubed-sphere grids; this fix the restart.
41    o pkg/atm_compon_interf:
42      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
43        pass last value, stored directly before export to CPL ;
44        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
45      - remove atmSLPr from pickup files (no longer needed for restart)
46    
47    checkpoint65s (2016/01/13)
48    o eesupp & genmake2:
49       - first check for Function ETIME and, if it fails, then check for subroutine
50         ETIME and consistent output; use the appropriate version in timers.F
51    o model/src:
52      - to check restart test, add option to apply EXCH to U,V earlier, just before
53        integr_continuity; turned off by default.
54    o pkg/dic:
55      - remove CPP option USE_ATMOSCO2 (not needed)
56    o tools/tst_2+2:
57      - try to ignore difference between +0 and -0 in binary file, causing test
58        to fail for no good reason.
59    o eesupp & genmake2:
60      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
61        but also check (in genmake2) that test runs and returns meaningful results.
62    o coupler pkgs:
63      Finish implementation of optionally-exchanged variable switches (started on
64       Nov 12) with addition of few more exchanged fields, including 2-way exchange
65       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
66       advection in OCN component; this requires sequential coupling.
67      coupler (pkg/atm_ocn_coupler):
68      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
69        routines (useful for debug).
70      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
71         flux, DIC fields) if corresponding switch is ON.
72      - add option to export RunOff to OCN (to use for DIC river input)
73      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
74      components (pkg/atm_ & ocn_compon_interf):
75      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
76        optionally exchanged fields; add a check & stop in cpl_readparms.F.
77        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
78        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
79      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
80        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
81      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
82      - hold in common block coupler optionally-exchanged variable switch
83        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
84      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
85        this is intended to replace the OCN cplFldtave.* output files (not updated
86        to contain new additional exchanged fields).
87    o pkg/dic:
88      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
89    o pkg/thsice:
90      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
91        and writing of thsice pickup files.
92    o pkg/atm_compon_interf:
93      - move all field individual export-call out of cpl_export_import_data.F
94        into new S/R ATM_EXPORT_FIELDS
95    o pkg/atm_compon_interf:
96      - store state variables (for now, only thSIce fields) just before beeing
97        exported (in cpl_export_import_data.F, like on ocean side) instead of from
98        atm_store_my_data.F like all exported fluxes.
99      - new version of pickup_cpl: write field names into meta file and read meta
100        file to find field postion in pickup. Also only write/read fields meeded for
101        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
102    o pkg/dic:
103      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
104    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
105        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
106        value can be from domain [0,1] to average between the two methods
107    o pkg/atm_phys:
108      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
109        hold fixed in time).
110    
111    checkpoint65r (2015/12/21)
112    o pkg/seaice:
113        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
114        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
115    o pkg/seaice:
116      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
117        when SEAICEscaleSurfStress=.TRUE.,
118      - apply areaW and areaS in S/R seaice_calc_lhs
119    o pkg/atm_phys:
120      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
121        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
122        for individual contribution (convection, LSC cond, radiation)
123      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
124        information); activated with: solar_exponent=0. and wv_exponent=-1.
125    o pkg/ggl90:
126      - within IDEMIX add upper limit for horizontal group velocity to
127        avoid instability problems in the explicit horizontal diffusion term for
128        long time steps or high resolution
129    o pkg/diagnostics:
130      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
131        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
132    o testreport:
133      - remove "-v" (verbose option) in default mpirun command.
134    o pkg/seaice/seaice_growth:
135      - catch potential division by zero in ITD code, does not change
136        verification results
137    o pkg/ecco:
138      - retire old codes to the Attic. The calls to retired functions are
139        left in a commented form in case they ever need to be re-activated.
140      - ecco_check.F: issue warning if any old CPP option is
141        defined that corresponds to retired codes -- then stop.
142    o pkg/atm_compon_interf:
143      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
144        coupler: use last time-step value instead of average over cplSendFrq_iter
145        time-step, similar to what is done for seaIceMass.
146        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
147    o eesupp & genmake2:
148      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
149        <= remove until a fix is found for some ifort version on ia32 machine.
150    o pkg/seaice/seaice_evp:
151      - refine residual computation
152    
153    checkpoint65q (2015/11/18)
154    o pkg/seaice/seaice_evp:
155      - fix residual computations so that they no longer affect the actual
156        simulation code
157      - fix seaice_readparams to be able to actually set new parameters
158        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
159    o model/src:
160      - fix wrong truncation (single prec) from "FLOAT" function in expressions
161        like: deltaT*FLOAT(myIter) when myIter is large:
162         a) replaced by DFLOAT (if not seen by TAF);
163         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
164    o pkg/aim_v23:
165      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
166        when pickupSuff is set ; do write rolling pickups + at the end of the run.
167    o pkg/atm_ocn_coupler + ocn_compon_interf:
168      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
169        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
170        add corresponding call in DO_OCEANIC_PHYS.
171    o coupler pkgs:
172      Start a new way to set-up optionally-exchanged variables (previously, only
173       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
174       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
175       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
176       compononent param default can be set accordingly).
177      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
178       but rather applies to a group a fields (going both ways like for DIC)
179       and corresponds to an option of coupling config.
180      coupler (pkg/atm_ocn_coupler):
181      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
182        and read namelist directly (without eessup S/R calls) instead of
183        in the very un-flexible old way, 1 param per line, in fixed order;
184      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
185        cleanly in CPL_CHECK_CPLCONFIG
186      - add new coupling-exchange selectors (some not yet active) including
187        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
188                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
189      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
190        component ; called directly from coupler.F, after comp. registrations;
191      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
192         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
193          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
194      components (pkg/atm_ & ocn_compon_interf):
195      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
196        CPP header file in all pkg source files.
197      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
198        ATM/OCN_CHECK_CPLCONFIG;
199      - add error-counter to track errors (e.g., in "data.cpl") and to stop
200        cleanly in ATM/OCN_CHECK_CPLCONFIG;
201      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
202        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
203        before PACKAGES_READPARMS;
204      verification/cpl_aim+ocn/:
205      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
206        "data.cpl" for coupler (in input_cpl).
207    o eesupp/inc:
208      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
209        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
210        to always cumulate tile local-sum in the same order (still uses
211        MPI_Allreduce like standard code).
212      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
213        that are now identical to standard version (in eesupp/inc).
214    o pkg/shelfice:
215      - add SHELFICETransCoeffTFile for initializing spatially varying
216        heat and salt transfer coefficients
217    o pkg/atm_compon_interf & ocn_compon_interf:
218      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
219        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
220      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
221    o pkg/atm_ocn_coupler:
222      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
223    o pkg/rbcs:
224      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
225        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
226      - add a short report (to STDOUT) about RBCS-mask settings.
227    
228    checkpoint65p (2015/10/23)
229    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
230        there is no adjoint test for EVP, we don't know what it does to the adjoint
231        solution, but at least there are no more recomputation warnings left
232    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
233        a chance of giving the same results as a fully converged VP (JFNK) solver
234    o tools/adjoint_options/adjoint_diva:
235      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
236    o pkg/streamice:
237      - spotted bug in streamice_driving_stress using dyG where should have been dxG
238    o pkg/exf:
239      - remove STOP statement that prevented to use wind or (wind-)stress
240        interpolation for constant-in-time forcing fields (wind/stress period = 0).
241    o pkg/seaice:
242      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
243        5 additionals 2D fields and 6 new store directives
244      - change logic in seaice_readparms.F: EVP code can now be turned on in
245        various ways, setting SEAICE_deltaTev is no longer required,
246        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
247        or SEAICEaEVPcoeff
248    o pkg/shelfice/shelfice_thermodynamics.F
249      - redefining uLoc/vLoc to u/v, instead of 2u/v
250    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
251      - this is an intermediate state of a truely converging EVP that has
252        the potential of outperforming implicit VP methods, I do not recommend
253        using it yet.
254      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
255        and all parameters are hardwired
256      - for convergence it still requires very smooth regularisations, that means,
257        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
258        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
259        specific averaging appears to be required, still subject to tuning
260      - still needs cleaning and I need to turn parameter into runtime parameters
261      - add code to compute and print residuals of iteration, compile with
262        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
263    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
264      that entered with r1.54 on Sep04, 2015, -> update results
265    
266    checkpoint65o (2015/09/14)
267    o pkg/mom_vecinv & mom_common:
268      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
269        called from there.
270      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
271        allows to use Vector-Invariant form in deep atmos and anelastic formulation
272    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
273      and Koenig-Beatty+Holland (2012)
274      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
275      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
276      - requires an extra input argument for S/R seaice_calc_viscosities
277      - tensileStrength's depth dependence is different from Itkin et al. (2015)
278        (to be changed and played with, for now exponential)
279    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
280      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
281        by AREA according to Connelly et al. (2004), JPO.
282      - For EVP and the LSR solver, the implicit part of the drag term is
283        the only non-zero term in the denominator when there is no ice (which
284        prevented running the model with zero ice-ocean drag). If
285        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
286        (or zero main diagonals BU/BV) which need to be caught. A practical
287        consequence is that for open water, the momentum equation reduce
288        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
289        they happen to be zero, often leading to a non-zero solution over
290        open water.
291    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
292        efficient EVP method.
293      - introduce area-weighted averages for e12 (analogously to
294        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
295        remain, but also changing the order of terms in the previous average
296        changed the results as much) -> update experiment
297      - add SEAICE_DELTA_SMOOTHREG code
298      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
299        TEM-code
300      - adjust loop bounds so that only required fields are computed
301      - add new averaging code for zetaZ/deltaZ (again similar to
302        seaice_calc_viscosities.F), inactive by default for now (will change
303        results again), but will replace old code eventually
304    o eesupp/src:
305      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
306        to always cumulate tile local-sum in the same order
307        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
308        Still uses MPI_Allreduce (like standard code) but on array of tiles
309        and should be faster than GLOBAL_SUM_SEND_RECV code.
310      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
311        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
312      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
313         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
314         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
315         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
316         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
317    
318    checkpoint65n (2015/07/29)
319    o pkg/thsice:
320      - add a warning when used with pkg/aim but without updating SST
321        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
322    o pkg/offline:
323      - change where Offline-Fields are loaded, from load_fields_driver.F to
324        directly within FORWARD_STEP, just after updating iter number and time;
325      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
326        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
327       These changes allow:
328        a) to recover exactly on-line results using deltaToffline=deltaTClock,
329        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
330        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
331        time-step, both with GM & KPP files and with recomputing these fields;
332        b) no needs to switch on staggerTimeStep anymore;
333        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
334      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
335    o pkg/offline:
336      - change (rarely used) offset-iteration parameter to an offset time (in s):
337        can easily recover previous offset-iter effect by setting offset-time
338        (offlineTimeOffset) to offset-iter x deltaToffline;
339      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
340        in KPP as part of surface buoyancy forcing) in offline run.
341      - fix ptracers KPP non-local term in the case where KPP is re-computed.
342    o OpenAD
343      - Adding preliminary ggl90 test to OpenAD verification.
344        Config. with ggl90 currently diverges after 64 time steps
345        so will need more work to become more stable
346      - Adding preliminary kpp test to OpenAD verification.
347        required small tweakes in kpp_routines.F
348      - Merge and update from Krishna Narayanan's contrib area:
349        * Add one variable for preliminary OpenAD DIVA
350        * Add replacement time-stepping for OpenAD DIVA
351        * genmake2 flag -diva (but only for OpenAD; preliminary)
352        * required modifs for OAD_support
353        successful preliminary test for tutorial_global_oce_biogeo/
354    o pkg/seaice:
355      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
356      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
357        delta with a smooth function in s/r seaice_calc_viscosity
358        (no effect on EVP)
359      - rename local suffix "sqr" into "sq" for more consistent variable names
360    o pkg/seaice:
361        add new parameter SEAICE_deltaMin that is used ***only***
362        for regularizing Delta (and nothing else, like the parameter
363        which is also used for all sorts of things SEAICE_EPS).
364        Defaults to SEAICE_EPS for backward compatibility only.
365    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
366        the wrong key by inialising it before use -> fixes a recomputation
367        problem but does not fix the gradient
368    o pkg/layers:
369      - move resetting of flux arrays to outside the iLa loop
370        (this caused layers_diapycnal to not work with more than one layer coord.)
371      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
372    o pkg/layers:
373      - remove from common block 3D layers fields (used to diagnose transport
374        in tracer coords) and declare them as local arrays in layers_calc.F
375    o pkg/seaice:
376      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
377        in lab_sea forward experiment (changes results -> updated)
378      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
379    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
380       computations; for SEAICE_VECTORIZE_LSR
381      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
382        sweep to the outside,
383      - remove store directives and add "CADJ loop sequential" directives
384        in analogy to model/src/solve_tridiagonal.F
385      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
386        boundaries to yield more readable code. This has also the charming side
387        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
388        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
389        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
390        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
391        an additional option)
392       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
393       but the adjoint gradients (which are affected by this change) still explode.
394    o coupler (atm & ocn _compon_interf):
395      - avoid using Exch2 IO mapping if not suitable.
396    
397    checkpoint65m (2015/06/15)
398    o pkg/layers:
399      - clean-up old parameters setting (from Sep 2012):
400        + remove old parameters setting from common block (declared locally);
401        + stop if any old parameter is mixed with new parameters;
402        + check for valid or consistent parameter setting (e.g., layers_name)
403      - check that layers_bounds for Pot.Density are in the right range;
404        this is supposed to catch un-updated setting after recently shifting
405        potential density field "prho" by -1000 (now in "sigma" scale).
406    o pkg/layers:
407      - Added missing call to layers_fill for keeping track of tottend in
408        pkg/diagnostics/diagnostics_fill_state.F
409    o pkg/layers:
410      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
411        of diapycnal fluxes
412    o pkg/layers:
413      - reverted changes to interpolation to previous treatment; there
414        was never actually a problem
415    o pkg/layers:
416      - fix interpolation of layers tracers in the presence of partial cells
417      - add lots of new functionality to compute water mass transformation
418        (enabled by CPP flag LAYERS_THERMODYNAMICS)
419      - add new calls from main code (diags_oceanic_surf_flux.F,
420        thermodynamics.F, impldiff.F) and gad to save the necessary fields
421        for layers_thermodynamics calculations
422    o pkg/ptracers:
423      - add capability of stepping a passive tracer forward without advection
424        by setting PTRACERS_advScheme to 0.
425    o pkg/diagnostics:
426      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
427    o pkg/layers:
428      - shift potential density field "prho" by -1000 for density layer averaging so
429        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
430        Note that density bin boundaries (layers_bounds in data.layers) have
431        to be set accordingly (i.e., shifted, in sigma scale).
432    o pkg/layers:
433      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
434      - fix calculation of layer non-weighted velocity and layer probability
435      - add diagnostics for pot.density used for layer averaging
436    o pkg/seaice:
437      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
438        positiveness, modify a few comments and improve variable names,
439      - the changed computation of deltaC affects most seaice-related
440        experiments at the truncation level.
441        seaice_itd.thermo is affected by far the most, with
442        only 7 digits of agreement remaining; update experiments.
443    
444    checkpoint65l (2015/05/04)
445    o pkg/shelfice:
446      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
447        factor drKp1 to zero where it is negative (ie. do not use
448        SHELFICEBoundaryLayer if hFacC>1)
449      - the same for factor drLoc in shelfice_forcing.F
450    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
451        with modules in ptracers, when using testreport option "-small_f"
452    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
453      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
454    o verification/testreport
455      - add new option -small_f
456        with this option testreport first makes the target small_f (*.f files)
457        before running make (all). This is useful for explicit inlining when
458        all sources need to be full available.
459    o pkg/exf/exf_interp.F:
460        remove previous changes related to reverse (decreasing) input grids latitude
461    
462    checkpoint65k (2015/04/01)
463    o pkg/ecco:
464        fix missing cosphi initialization; use eccoiter in place of optimcycle;
465        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
466        instead of active read/write
467    o pkg/ctrl:
468        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
469        instead of active read/write.
470    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
471        return if .NOT.useAUTODIFF
472    o pkg/seaice: add CPP brackets (cost function related).
473    o model/src:
474        add useAUTODIFF run time switch.
475    o pkg/exf/exf_interp.F:
476        add code to allow input grids with latitude starting in the north (i.e. when
477        j=1 corresponds to northern edge of field); modify global_with_exf to test
478        this feature.
479    o verification/testreport:
480      - replace "grep -A3" with POSIX conformal sed command, because there are
481        implementations of grep that cannot do contextual searches
482      - replace "cat -n" by "nl" (two occurrences), because not all implementations
483        of "cat" have the option "-n"
484    o model/src:
485        add new file gsw_teos10.F that contains 3 functions, more or less a copy
486        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
487        convert from conservative to potential temperature. For now they are not
488        called anywhere.
489    o pkg/ggl90: make "useIDEMIX" useful
490      - re-organize code in s/r ggl90_calc a little to move computations that
491        are different for idemix into separate loops (changes verification
492        experiment idemix at truncation level, 12 digits remain -> updated)
493      - requires 2 new 2D fields KappaM, verticalShear
494      - make hFacI and recip_hFacI local 3D variables that are passed to
495        s/r ggl90_idemix
496      - fix and improve some comments
497    
498    checkpoint65j (2015/02/25)
499    o pkg/openad
500      - synchronize seawater.F with version in model/src: replace routine
501        body of sw_temp by calling sw_ptmp and fix/add a few comments.
502    o pkg/mnc:
503      - change default value of pickup_read/write_mnc params to FALSE
504        (since few features are missing in reading MNC pickup files).
505    o model/src:
506      - change default (background) vertical diffusivity for salt to be the
507        temperature (background) vertical diffusivity.
508      - change background vertical diffusivity in vertical mixing pkgs ggl90,
509        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
510        This makes ptracers default diffusivity (that uses salt diffKr) more
511        consistent with vertical mixing schemes.
512    o verification/testreport:
513      - fix typo in "-pcls" option ;
514      - put temp files in /tmp (instead of in local dir)
515      - add option "-ncad" to use genmake2 new option "-nocat4ad"
516      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
517    o pkg/ggl90 (idemix code):
518      - apply few fixes ; add some missing "_d 0" ; update output of exp.
519        global_ocean.90x40x15.idemix
520    o OpenAD
521      - enable active file I/O and begin removal of work-around code
522        for OpenAD for handling control variables (memory vs. active files)
523      - new CPP options file OPENAD_OPTIONS.h
524      - revert to genarr2d gradient check for hs94.1x64x5
525      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
526      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
527    o tools/genmake2:
528      - add option for an alternative Makefile (from Martin) where multiple
529        source files are sent to TAF (instead of all in one file).
530    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
531      - code provided by Carsten Eden as an extension of ggl90
532      - so far the code is turned on within ggl90 by setting a CPP-flag at
533        compile time; a runtime flag implementation is not yet complete
534      - tested in new verification experiment global_ocean.90x40x15.idemix
535    o verification:
536      - reduce length of the AD test run by half for experiments
537        global_ocean.cs32x15 (std + thsice) and isomip
538      - enable active file I/O for OpenAD, adjust verifications accordingly
539      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
540    o verification/testreport:
541      - fix two non-POSIX sed statements so that there are no error messages
542        on Mac OS X
543      - replace hostname -s with hostname | sed 's/\..*$//'
544    o model/src/seawater.F:
545      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
546        (following the matlab code), which would have avoided the bug caught
547        by Matt (see below) in the first place
548    o pkg/shelfice:
549      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
550        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
551      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
552        ice-shelf case (i.e., within surface level).
553      - add config summary in shelfice_check.F
554      - remove global variable recip_SHELFICElatentHeat and replace by a local
555        variable recip_latentHeat
556      - introduce diagnostics for friction velocity uStar (in case of
557        SHELFICEuseGammaFrict)
558      - change verification experiment isomip.htd:
559        + start from pickup (as input_ad at nIter0=8640)
560        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
561        + test SHELFICEuseGammaFrict = .TRUE.
562        + test SHELFICEadvDiffHeatFlux = .TRUE.
563    o model/src:
564      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
565        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
566        update output of experiments global_with_exf.yearly and isomip (all 6).
567    o pkg/shelfice:
568      - change setting of kTopC to also be zero where there is no ice-shelf.
569      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
570        ice-shelf is.
571      - first attempt to get RealFreshWaterFlux effects: for now, only without
572        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
573    o pkg/seaice: add the option to prescribe a fixed thickness PDF
574      for thermodynamic calculations
575      - because of divisions of the type 7/7 not exactly equal to 1, this change
576        affects results of some verification experiments by up to 4 digits:
577        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
578        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
579        adjoint: lab_sea, lab_sea.noseaicedyn
580        -> updated
581    
582    checkpoint65i (2015/01/23)
583    o model/src:
584      - change units of frictionHeating field from W to W/m^2
585      - fix bug in frictional heating from stratospheric drag in
586        S/R ATM_PHYS_TENDENCY_APPLY_V
587      - with synchronous time-stepping: move resetting to zero of frictionHeating
588        field from load_fields_driver.F to thermodynamics.F ;
589      - add diagnostics for frictional heating.
590    o model/src & gmredi K3D:
591      - add frictionHeating field to pickup-files (for synchronous time-stepping)
592      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
593      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
594        and name in pickup file).
595      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
596    o model/src:
597      - move (from ini_forcing.F) initialisation of all arrays in header file
598        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
599        (since Nov 2012) with option selectAddFluid=1.
600    o pkg/shelfice:
601      - change units (+ document) of newly added field "shelfIceMassDynTendency"
602      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
603    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
604    o pkg/seaice: two new runtime parameters:
605      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
606        long overdue
607      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
608        parameterization of tensil stress for fast ice (does not do anything yet)
609    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
610        for LSR: move checking overlaps out of JFNK-if-block
611    o pkg/atm_phys:
612      - move copy of grid and dynamical fields out of atm_phys_driver.F into
613        new S/R ATM_PHYS_DYN2PHYS.
614      - fix level height for Linear Free-Surf case (to be consistent with
615        fixed-in-time pressure levels).
616    o pkg/mom_common (bottomdrag):
617      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
618        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
619        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
620    o pkg/shelfice (u/v_drag):
621      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
622      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
623        (now similar to shelfice_u_drag.F)
624      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
625        from mom_vecinv.F (similar to mom_fluxform calls).
626    o pkg/mom_common (bottomdrag):
627      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
628      - add options for alternative discretisation of velocity norm in quadratic
629        bottom drag: averaging of grid-cell-center KE to U.point and V.point
630        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
631        improves when averaging only the other component (e.g. vVel for U bottom
632        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
633      - add options (bottomVisc_pCell) to account for partial-cell in bottom
634        friction (no-slip BC) thus getting the true distance from the bottom;
635        off by default since this also reduces model stability (explicit bottom
636        friction). Changes produce different machine truncation with linear-drag
637        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
638        front_relax (bvp & mxl, 10 & 11 digits).
639    o model/src & mom pkgs:
640      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
641        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
642      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
643        just copy level Nr value to level Nr+1.
644    o doc:
645      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
646    o pkg/streamice:
647      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
648        SHELFICE.h: move array shelficemass to init_varia, initialise
649        from array shelficemassinit, which is set in init_fixed and
650        has option to be set from file; introduce array
651        shelficeMassDynTend array, set thru file in init_fixed
652      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
653        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
654        pkg/streamice
655      - shelfice_thermodynamics.F: call shelfice_step_icemass if
656        SHELFICEMassStepping = .true.
657      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
658    
659    checkpoint65h (2014/12/17)
660    o verification/global_ocean.90x40x15, global_ocean_ebm:
661      - update to generic controls.
662    o pkg/ctrl:
663      - ctrl_map_ini_genarr.F: test for igen>0
664      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
665      - move gentim2d part of ctrl_map_ini_genarr.F to
666        new separate routine : ctrl_map_ini_gentim2d.F
667      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
668        add time variable weights and cyclic controls (time mean,
669        seasonal cycle, etc) capabilities to gentim2d
670    o pkg/ecco:
671      - move reading of error, conversion to weights from
672        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
673    o global_oce_llc90, cs32:
674      - activte sbo.
675      - CTRL_SIZE.h : add maxCtrlProc.
676      - activate the new genctrl capabilities.
677      - update following reorganization of global_oce_input_fields.tar.gz  
678    o pkg/ctrl/ctrl_ad_diff.list:
679      - add missing ctrl_init_rec.f
680    o tools/OAD_support/keepOriginal:
681      - add ctrl_init_rec.F
682    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
683      - avoid recomputations of xx_gentim2d_dummy.
684    o momentum diagnostics:
685      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
686        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
687    o pkg/seaice/seaice_lsr.F:
688      - fix computation of BU/BV, make sure they are non-zero, only necessary
689        for cubed sphere exchanges and SEAICE_OLx/y>0.
690        This makes calling s/r fill_cs_corner_rl obsolete (removed).
691    o verification/global_ocean.cs32x15/input.seaice
692      - add test for strong implicit coupling and restricted addtive Schwarz
693        methods for LSR
694      - update results/output.seaice.txt
695    o verification/tutorial_global_oce_biogeo:
696      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
697        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
698        update output_adm,_oadm,_tlm.txt
699    o pkg/dic:
700      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
701      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
702        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
703    o verification/tutorial_global_oce_biogeo:
704      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
705        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
706        update output_adm,_oadm,_tlm.txt
707    o eesupp/src:
708      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
709        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
710    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
711      LSR (following Hutchings et al. 2004)
712      - introduce zetaZ as a global variable (requires adjustments in
713        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
714        in seaice_calc_viscosities.F
715      - new flag SEAICEuseStrImpCpl (default off)
716      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
717        momentum equations
718      - JFNK-solver (preconditioner) adjusted to allow using this method
719        (where it does not have any positive effect)
720    o pkg/seaice
721      - add overlap for restrictive additive Schwartz method also to LSR, but
722        turn it off by default (because it only seems to work for non-cubed
723        sphere/llc topologies)
724    o pkg/autodiff
725      - add extra exchanges in addummy_in_steppging also for mnc output
726    o pkg/seaice:
727      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
728        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
729    o pkg/obcs:
730      - add option to specify domain-connected piece Id along OB though files
731        (for now, only used to diagnose PhiVel; default =1 -> global correction)
732      - modify obcs_diag_balance.F to process each connected-part separately;
733        exclude OB where Id = 0 but keep the full divergence there (-> constant
734        Psi along this portion of OB and all inflow derived from grad(Phi))
735      - add example of OB-conect files in verification/so_box_biogeo/input.
736    o pkg/diagnostics:
737      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
738      a) use non zero matrix element across OB and solve for Phi 1 grid point
739         outside OB (i.e, where tracer OBCS are applied).
740      b) global imbalance of inFlow/outFlow across OB: instead of modifying
741         velocity across OB, spread it uniformly along the OB in the RHS.
742    
743    checkpoint65g (2014/11/19)
744    o pkg/diagnostcis:
745      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
746    o pkg/my82,pp81,kl10:
747      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
748        field diffKr as background diffusivity to set minimum diffusivity value.
749    o pkg/seaice:
750      - add new parameter SEAICEuseEVPrev (for revisited EVP by
751        Bouillon et al 2013)
752      - add SEAICE_evpAlpha/Beta to namelist
753      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
754        involve trivial re-ordering of divisions/multiplications that should not
755        have any effects, but ... they do change the results of lab_sea.hb87 so
756        that only 2 digits of agreement remain, in line with the general
757        instability/fragility of the evp-code. For now, I do not care and just
758        update the verification experiment
759    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
760      - remove xx_genarr2d_numsmooth etc
761      - use xx_genarr2d_preproc etc instead
762      - carry out smooth_correl2D at initialization stage rather than during
763        time stepping.
764      - get smoothOpNb from xx_gentim2d_preproc
765    o global_oce_cs32 :
766      - add test of generic ecco capabilities.
767    o pkg/exf/exf_getsurfacefluxes.F :
768      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
769    o pkg/ctrl,ecco :
770      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
771        is defined.
772    o pkg/seaice: add diagnostics for Delta (deformation parameter)
773    o model/src:
774      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
775        diffusivity (background) is specified but ignored.
776    o verification:
777      - in testreport, convert hostname to lower case for default output dir name
778    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
779    o pkg/dic: add modifications from Hajoon:
780      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
781      - light attenuation: add self-shading effect by climatological Chlorophyll
782        (read from file).
783    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
784        compiles when SEAICE_ALLOW_DYNAMICS is undefined
785    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
786        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
787        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
788        approach where CPP_OPTIONS.h includes an omnipotent
789        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
790    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
791        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
792    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
793        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
794        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
795    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
796      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
797      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
798      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
799      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
800    o pkg/ctrl,ecco,exf :
801      - remove variables associated with NON-generic costs,
802        unless ECCO_CTRL_DEPRECATED is defined.
803      - remove NON-generic NON-obcs controls,
804        unless ECCO_CTRL_DEPRECATED is defined.
805    o pkg/ctrl : added ctrl_local_params.h
806    o pkg/ecco : added ecco_local_params.h
807    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
808        experiments, which will progressively be removed once the
809        experiments are revised to use only generic controls/costs.
810    
811    checkpoint65f (2014/10/13)
812    o pkg/ctrl, ecco, seaice : minor changes in headers
813    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
814        cost function and control capabilities added since checkpoint65c.
815    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
816    o pkg/ecco: increase modularity and improve logic
817      - ecco_toolbox.F (new) : basic operations that are often used,
818        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
819        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
820      - cost_gencal.F (new) : determine filnames and records.
821      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
822      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
823        and exploit the above functions leading to more compact code.
824      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
825      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
826        using_ers, using_gfo, using_mdt is now only defined within gencost)
827    o pkg/ecco: extend generic cost capabilities
828      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
829        capabilities via gencost_preproc (+ _c,_i,_r related params),
830        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
831        gencost_outputlevel arguments to cost_generic
832      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
833        and active_read, making room for gencost_preproc to take effect.
834        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
835      - pkg/ecco/cost_generic.F :
836        compute and store misfit maks*(model-data) in localdif that is
837        then used in cost and for output, output misfit if outlev.GT.0
838      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
839        rather gencost_barfile for deciding whether to write barfile
840      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
841      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
842        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
843      - pkg/ecco/ecco_summary.F : report gencost variables
844      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
845    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
846    o pkg/ecco: internal re-organization
847      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
848        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
849        mv relevant variables definition from ecco_cost.h to ecco.h,
850        make sure gencost routines only include ecco.h)
851      - throughout : add missing CCP switches, rm unused variables,
852        and rm un-necessary CPP switches
853      - throughout gencost routines : replace modelstartdate with
854        gencost_startdate when needed
855      - cost_bp_read.F : use arguments, instead of common blocs
856        so that it can be used also by (new) cost_gencost_bpv4.F
857      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
858      - ecco_phys.F : compute etanFull
859      - ecco_readparms.F : rename using_topex as using_tpj, add
860        bpv4-grace to gencost list, initialize added parameters
861      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
862    
863    checkpoint65e (2014/09/28)
864    o pkg/obcs:
865      - replaced the just-added CPP options with run-time variables
866        (see pkg/obcs/OBCS_PARAMS.h for details)
867    o pkg/obcs:
868      - add additional CPP options for sponge boundary layers
869        (see pkg/obcs/OBCS_OPTIONS.h for details)
870    o pkg/atm_phys:
871      - implement simple (obliquity only, assuming circular planet orbit)
872        seasonal cycle for incoming insolation ; used when run-time parameter
873        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
874    o pkg/exf, pkg/ecco, pkg/ctrl:
875      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
876      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
877      - implement gentim2d for xx_tauu, xx_tauv
878    o pkg/ctrl, pkg/ecco :
879      - fix and complement the generic controls implementation
880    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
881        pkg/shelfice/shelfice_thermodynamics.F,
882        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
883        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
884      - add weight in CTRL_GET_GEN calls
885    o pkg/ctrl :
886      - ctrl_get_gen.F : add weight as input parameter, and apply
887        it directly rather than using smooth_correl2Dw (to be retired).
888      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
889    o pkg/ctrl :
890      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
891        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
892      - re-activate ctrl_summary (call in ctrl_init.F)
893    o pkg/ctrl/ctrl_cost_gen.F :
894      - fix CCP brackets, remove un-necessary myiter, mytime
895    o pkg/ecco, pkg/ctrl :
896      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
897      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
898      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
899      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
900    
901    checkpoint65d (2014/09/15)
902    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
903      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
904        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
905    o pkg/ctrl/ctrl_map_ini_genarr.F :
906      - remove compilation failure
907      - replace hard coded example
908      - use ctrl_map_ini_gen2D, 3D
909    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
910      - on/off switch based upon xx_genarr2d_weight,3d
911    o src/packages_init_variables.F :
912      - regroup pkg/estimation calls
913      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
914        (moved to ctrl_init_variables)
915    o cost/cost_init_varia.F :
916      - remove ecco_cost_init_varia
917        (moved to ecco_init_varia)
918    o ctrl/ctrl_init_variables.F :
919      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
920      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
921    o ctrl/ctrl_map_ini.F :
922      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
923        (moved to ctrl_init_variables)
924    o ctrl/ctrl_map_ini_ecco.F :
925      - remove ECCO_PHYS (mv to ecco_init_varia)
926      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
927    o ecco/ecco_ad_diff.list :
928      - add ecco_init_varia.f
929    o ecco/ecco_init_varia.F
930      - new routine
931    o pkg/streamice:
932      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
933        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
934      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
935    o pkg/generic_advdiff:
936      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
937    o pkg/exf:
938      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
939         xxg_precip capability
940      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
941    o pkg/ctrl:
942      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
943    o model/src/load_fields_driver.F :
944      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
945        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
946    o OpenAD verification experiments:
947      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
948        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
949        for now, only in pkgs used in OpenAD verification experiments.
950      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
951        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
952        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
953        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
954    o OpenAD verification tests:
955      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
956      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
957        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
958      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
959        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
960    o model/src & generic_advdiff:
961      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
962        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
963        dynamics requires valid tracer forcing only over tile interior but, for
964        some diagnostics, may need to extend it over 1 point in tile halo region.
965      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
966        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
967        setting in temp/salt/ptracer_integrate.F
968    o pkg/dic:
969      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
970        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
971        in gchem_forcing_sep.F
972    o pkg/autodiff & obcs:
973      - add storage of current OB values for U & V (was already done for T & S).
974    
975    checkpoint65c (2014/08/30)
976    o pkg/dic:
977      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
978        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
979        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
980    o verification:
981      - new experiment testing OBCS and DIC pkgs, using params & output from
982        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
983        passage: take OBCS from the last year of a 2 yrs simulation and initial
984        conditions from t=1.yr while keeping the same forcing.
985    o model/src:
986      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
987        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
988    o pkg/diagnostics (Stats-Diags):
989      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
990        a) refine region where stats are computed, excluding where arrhFac=0 ;
991        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
992        c) extend regional stats over the region edges (for U or V pt location).
993    o pkg/gchem:
994      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
995        pkg/dic is currently changing/updating ptracers values beyond the OB).
996    o verification (hs94):
997      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
998        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
999        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1000        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1001    o pkg/ptracers:
1002      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1003        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1004      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1005        with AB-2 code (so that it get tested).
1006    o model/src:
1007      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1008        with AB-2 code (previously only available with AB-3 code).
1009        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1010        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1011        there, by calling CYCLE_AB_TRACER).
1012    o pkg/generic_advdiff:
1013      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1014        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1015        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1016        S/R temp/salt/ptracers_integrate.F
1017    o model/src & pkg/ptracers:
1018      - remove common block variables gT,gS (in DYNVARS.h), except when
1019         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1020      - remove common block variable gPtr.
1021    o model/src & pkgs:
1022      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1023         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1024         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1025         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1026      + change accordingly all calling S/R.
1027      - use local temperature/salinity/ptracer tendency array (without bi,bj)
1028        in S/R temp/salt/ptracers_integrate.F
1029    o pkg/seaice:
1030      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1031        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1032      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1033        in seaice_lsr
1034      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1035        in s/r seaice_lsr_calc_coeffs
1036    o pkg/mdsio:
1037      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1038        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1039        too long (e.g., > MAX_LEN_FNAM/2 )
1040    
1041    checkpoint65b (2014/08/12)
1042    o pkg/matrix:
1043      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1044    o model/src:
1045      - fix initialisation of geothermalFile; compile geothermal-flux code in
1046        natl_box verification experiment.
1047    o model/src & pkg/down_slope:
1048      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1049      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1050        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1051        results at machine truncation level: update output of experiments
1052        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1053    o pkg/diagnostics (Stats-Diags):
1054      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1055        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1056        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1057        times (but Min,Max and StD are still wrong).
1058    o model/src:
1059      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1060        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1061    o model/src:
1062      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1063        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1064        arrays are already updated while adjustments (filters, conv.adjustment) are
1065        still applied later, in S/R TRACERS_CORRECTION_STEP.
1066    o model/src:
1067      - store in common bloc array "rhoInSitu" the virtual potential temperature
1068        anomaly that is used to compute geopotential: this make the atmos code
1069        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1070    o pkg/seaice/seaice_lsr.F
1071      - rename integer variable ilcall to ipass (that's what it is called
1072        in the residual diagnostics
1073      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1074        default) for improved non-linear convergence of the first few steps
1075      - adjust a few comments and add new ones to explain some of the store
1076        directives
1077    o pkg/generic_advdiff (& ptracers):
1078      - re-work the code to check for valid advection scheme and for minimum
1079        size of overlap (now stored in local common bloc in gad_advscheme.F)
1080    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1081      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1082      - add an auxilliary variable "bet" and fix store directives and keys in
1083        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1084        less exact gradients in my tests); but there are still
1085        recomputation warning (although gradients are sort of OK), when
1086        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1087        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1088      - update verification experiments lab_sea.
1089      - change some comments in S/R seaice_calc_viscosities
1090    o model/src:
1091      - if staggerTimeStep=T, always apply exchange to velocity field in
1092        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1093        (independent of using multi-dim advection or not); no effect on FWD run
1094        but affects AD results (at machine truncation level): update output of
1095        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1096        and isomip (oad: 12.d).
1097    o pkg/generic_advdiff:
1098      - stop if doAB_onGtGs is set to FALSE but ignored
1099      - refine warning related to stability of tracer time-stepping
1100        regarding internal wave dynamics.
1101      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1102        on staggerTimeStep & implicitIntGravWave (will now get a warning
1103        if potentially unstable).
1104    o pkg/kl10:
1105      - add new pkg "kl10" for mixing due to internal wave breaking, from
1106        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1107        (contribution from Jody Klymak), tested in verification experiment
1108        verification/internal_wave/input.kl10/
1109    o isomip experiment:
1110      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1111        (input.htd) and update the output.
1112    o cd_code experiments:
1113      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1114        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1115        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1116        update the corresponding output.
1117    o pkg/seaice:
1118      - reduce the number of include files and store directives in
1119        S/R seaice_lsr_tridiagu/v
1120      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1121        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1122        get rid off one store directive (a TAF bug?)
1123      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1124        S/R seaice_lsr_tridiagv to change the loop range for consistency
1125      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1126      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1127        S/R seaice_lsr_tridiagu/v (requires update of
1128        offline_exf_seaice/input.dyn_jfnk)
1129    
1130    checkpoint65a (2014/07/27)
1131    o model/src:
1132      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1133        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1134        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1135        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1136    o model/src:
1137      - collect momentum forcing tendency into local 2-D array (passed as argument
1138        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1139        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1140        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1141      - collect T & S forcing tendency into local 2-D array (passed as argument to
1142        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1143        affects results at machine truncation level (e.g., ocean: if using
1144        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1145        correction due to vertical advection).
1146      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1147        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1148        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1149        obcs_ctrl (ad & fwd grd @ 12 & 7).
1150    o pkg/ptracers & diagnostics:
1151      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1152        title (to avoid some unexpected truncation); sort out ptracers diags units.
1153      - collect ptracer forcing tendency into local 2-D array (passed as argument
1154        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1155    
1156    checkpoint65 (2014/07/18)
1157    o pkg/fizhi:
1158      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1159        affects results at machine truncation level. Update output of experiments
1160        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1161    o pkg/seaice: more clean up
1162      - rename TAF common block tapes to be more consistent and remove
1163        unnecessary duplicates
1164      - add store directives to remove more recomputations, but use smaller
1165        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1166        The idea behind this flag is to reduce the memory footprint when the
1167        adjoint of the LSR is not required. As of now, defining the flag
1168        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1169        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1170        For experiment offline_exf_seaice, this means on a linux box with gfortran
1171        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1172        this experiment):
1173        > size mitgcmuv_ad
1174        text    data        bss     dec        hex
1175        5100659 1216  220458952  225560827  d71c8fb
1176        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1177        but only a moderate increase of 36% for global_ocean.cs32x15:
1178        text    data        bss     dec        hex
1179        6695027 1648 1014578664 1021275339 3cdf6ccb
1180        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1181      - note: there are still recomputations in global_ocean.cs32x15 and
1182        offline_exf_seaice and the gradient agreement changes (gets a
1183        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1184      - in general, the AD gradients still are wrong
1185    o OpenAD
1186      - clean up code_oad/ directories somewhat by moving files
1187        dontCompile, dontTransform, keepOriginal to OAD_support/
1188    o model/src:
1189      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1190        (not currently tested): add dissipation terms before NLFS rescaling of
1191        tendencies (previously done after).
1192    o pkg/diagnostics:
1193      - write stats-diags in ascii file with more digits (same as in monitor).
1194    o pkg/down_slope:
1195      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1196        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1197    o model/src:
1198      - new file "apply_forcing.F" containing all the code previously in
1199        external_forcing.F, but with new argument list: pass, as new argument,
1200        the current level tendency array to update (instead of a direct update
1201        of the common bloc array). Change the corresponding calls.
1202      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1203        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1204    o pkg/seaice/seaice_lsr, a little bit of clean up
1205      - rearrange some code blocks, so that now all calculations for
1206        setting up the right-hand-sides done within one single block
1207        (I find that easier to read and understand)
1208      - rearrange freedrift-code to reduce the number of ifdefs
1209      - adjust some indentations and comments
1210    
1211    checkpoint64z (2014/07/10)
1212    o model/src and several pkgs:
1213      - change argument list of all S/R called from external_forcing.F and
1214        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1215        to pass, as argument, the current level tendency array to update
1216        (instead of a direct update of the common bloc array).
1217      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1218      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1219    o pkg/seaice/seaice_lsr.F
1220      - always initialize local arrays in seaice_lsr_tridiagu/v
1221      - add more local tapes to seaice_lsr_tridiagu/v
1222      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1223        keep it in bi/bj loop; this seems to be essential
1224      - gradients are still wrong but only by 4-7 orders of magnitude
1225        instead of 15 orders of magnitude, lab_sea improves a little
1226    o pkg/seaice
1227      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1228        generates unnecessary code in seaice_lsr_ad
1229      - add more store directives in seaice_lsr to avoid unnecessary code
1230        in seaice_lsr_ad
1231      - exclude some residual computations in seaice_lsr when
1232        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1233        in seaice_lsr_ad
1234      - add more storing, a new tape (model/src/the_main_loop.F) and
1235        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1236        and klockey should be checked by a specialist)
1237      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1238        and update lab_sea after previous changes in pkg/seaice below
1239    o pkg/autodiff:
1240      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1241        viscFacInAd : run time parameters allowing for adjoint switches
1242        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1243    o pkg/ecco:
1244      - introduce cost_gencost_boxmean.F that computes a box mean
1245        temperature (for use in adjoint sensitivity studies).
1246    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1247    o pkg/mom_common/mom_calc_visc.F:
1248      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1249    o pkg/seaice/seaice_summary.F:
1250      - statement for SEAICEadjMODE now in autodiff_readparms.F
1251    o pkg/seaice:
1252      - remove some store directives and add new ones in an effort to get
1253        finally rid off the recomputation warnings. This is successful
1254        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1255        defined (i.e. no extensive recomputation warnings left), but there
1256        are still too many recomputations on the solver iteration level
1257      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1258      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1259        SEAICE_SIZE.h
1260      - add a store directive in S/R seaice_calc_viscosities
1261    o pkg/seaice (ITD code):
1262      - fix definition of Hlimit for multi-threaded case
1263      - use double precision arithmetic to compute Hlimit: this affects results;
1264        update output of experiment seaice_itd.
1265    o replace content of verification/seaice_itd
1266      - instead of a 1D column use the configuration of offline_exf_seaice
1267        to test the ice thickness distribution code with ridging
1268      - this is a first shot at this experiment
1269      - change of some defaults of ridging parameters SEAICEhStar (from
1270        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1271        and lot of new comments.
1272    
1273    checkpoint64y (2014/06/20)
1274    o pkg/seaice/seaice_reg_ridge.F:
1275      - modify the regularization of very small volumes of ice; only check
1276        total volume HEFF, and do not apply correction to individual ice
1277        classes because that leads to funny patterns in the heat and fw-fluxes
1278        into the ocean. Adjust seaice_itd/results/output.txt
1279      - replace nITD by SEAICE_multDim in loop-ranges
1280    o pkg/exf:
1281      - add code to process the case field period = -12. with UV interpolation.
1282      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1283        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1284  o verification/global_with_exf:  o verification/global_with_exf:
1285    - swith all fields period to -12. (was previously untested) in input/data.exf    - switch all fields period to -12. (was previously untested) in input/data.exf
1286      (but keep secondary test ".yearly" unchanged); update the reference output.      (but keep secondary test ".yearly" unchanged); update the reference output.
1287  o pkg/cal:  o pkg/cal:
1288    - new calendar type "noLeapYear" for 365 days calendar without any leap year.    - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1289  o pkg/exf:  o pkg/exf:
1290    - new integer parameter "exf_debugLev" (default set to main model debugLevel)    - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1291      to replace logical switch "exf_verbose"      to replace logical switch "exf_verbose"
1292    - report in STDOUT when loading a new reccord (if exf_debugLev >= 3)    - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1293  o pkg/sbo:  o pkg/sbo:
1294    - update from Katherine Quinn: evaluate mass directly from density and SSH    - update from Katherine Quinn: evaluate mass directly from density and SSH
1295      (budget using Finite Volume method) instead of from bottom pressure.      (budget using Finite Volume method) instead of from bottom pressure.
# Line 28  o model/src & most packages: Line 1305  o model/src & most packages:
1305      + call LAND_READPARMS from packages_readparms.F      + call LAND_READPARMS from packages_readparms.F
1306  o pkg/seaice:  o pkg/seaice:
1307    - remove code that resets useThSice in S/R seaice_readparms and    - remove code that resets useThSice in S/R seaice_readparms and
1308      replace by a warning in S/R seaice_check      replace it by a warning in S/R seaice_check
1309    - remove parameter MULTDIM, replace with nITD and runtime    - remove parameter MULTDIM, replace with nITD and runtime
1310      parameter SEAICE_multDim (still hard-wired to nITD if      parameter SEAICE_multDim (still hard-wired to nITD if
1311      SEAICE_ITD is defined)      SEAICE_ITD is defined)
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