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revision 1.1942 by jmc, Tue Nov 19 22:16:45 2013 UTC revision 1.2081 by gforget, Sat Oct 11 19:42:33 2014 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/ctrl, ecco, seaice : minor changes in headers
8    o global_oce_llc90 :
9      - ecco_v4 verification experiments now test generic cost
10        function and control capabilities added since checkpoint65c.
11    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
12    o pkg/ecco: increase modularity and improve logic
13      - ecco_toolbox.F (new) : basic operations that are often used,
14        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
15        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
16      - cost_gencal.F (new) : determine filnames and records.
17      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
18      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
19        and exploit the above functions leading to more compact code.
20      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
21      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
22        using_ers, using_gfo, using_mdt is now only defined within gencost)
23    o pkg/ecco: extend generic cost capabilities
24      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
25        capabilities via gencost_preproc (+ _c,_i,_r related params),
26        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
27        gencost_outputlevel arguments to cost_generic
28      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
29        and active_read, making room for gencost_preproc to take effect.
30        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
31      - pkg/ecco/cost_generic.F :
32        compute and store misfit maks*(model-data) in localdif that is
33        then used in cost and for output, output misfit if outlev.GT.0
34      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
35        rather gencost_barfile for deciding whether to write barfile
36      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
37      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
38        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
39      - pkg/ecco/ecco_summary.F : report gencost variables
40      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
41    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
42    o pkg/ecco: internal re-organization
43      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
44        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
45        mv relevant variables definition from ecco_cost.h to ecco.h,
46        make sure gencost routines only include ecco.h)
47      - throughout : add missing CCP switches, rm unused variables,
48        and rm un-necessary CPP switches
49      - throughout gencost routines : replace modelstartdate with
50        gencost_startdate when needed
51      - cost_bp_read.F : use arguments, instead of common blocs
52        so that it can be used also by (new) cost_gencost_bpv4.F
53      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
54      - ecco_phys.F : compute etanFull
55      - ecco_readparms.F : rename using_topex as using_tpj, add
56        bpv4-grace to gencost list, initialize added parameters
57      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
58    
59    checkpoint65e (2014/09/28)
60    o pkg/obcs:
61      - replaced the just-added CPP options with run-time variables
62        (see pkg/obcs/OBCS_PARAMS.h for details)
63    o pkg/obcs:
64      - add additional CPP options for sponge boundary layers
65        (see pkg/obcs/OBCS_OPTIONS.h for details)
66    o pkg/atm_phys:
67      - implement simple (obliquity only, assuming circular planet orbit)
68        seasonal cycle for incoming insolation ; used when run-time parameter
69        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
70    o pkg/exf, pkg/ecco, pkg/ctrl:
71      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
72      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
73      - implement gentim2d for xx_tauu, xx_tauv
74    o pkg/ctrl, pkg/ecco :
75      - fix and complement the generic controls implementation
76    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
77        pkg/shelfice/shelfice_thermodynamics.F,
78        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
79        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
80      - add weight in CTRL_GET_GEN calls
81    o pkg/ctrl :
82      - ctrl_get_gen.F : add weight as input parameter, and apply
83        it directly rather than using smooth_correl2Dw (to be retired).
84      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
85    o pkg/ctrl :
86      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
87        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
88      - re-activate ctrl_summary (call in ctrl_init.F)
89    o pkg/ctrl/ctrl_cost_gen.F :
90      - fix CCP brackets, remove un-necessary myiter, mytime
91    o pkg/ecco, pkg/ctrl :
92      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
93      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
94      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
95      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
96    
97    checkpoint65d (2014/09/15)
98    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
99      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
100        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
101    o pkg/ctrl/ctrl_map_ini_genarr.F :
102      - remove compilation failure
103      - replace hard coded example
104      - use ctrl_map_ini_gen2D, 3D
105    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
106      - on/off switch based upon xx_genarr2d_weight,3d
107    o src/packages_init_variables.F :
108      - regroup pkg/estimation calls
109      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
110        (moved to ctrl_init_variables)
111    o cost/cost_init_varia.F :
112      - remove ecco_cost_init_varia
113        (moved to ecco_init_varia)
114    o ctrl/ctrl_init_variables.F :
115      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
116      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
117    o ctrl/ctrl_map_ini.F :
118      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
119        (moved to ctrl_init_variables)
120    o ctrl/ctrl_map_ini_ecco.F :
121      - remove ECCO_PHYS (mv to ecco_init_varia)
122      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
123    o ecco/ecco_ad_diff.list :
124      - add ecco_init_varia.f
125    o ecco/ecco_init_varia.F
126      - new routine
127    o pkg/streamice:
128      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
129        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
130      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
131    o pkg/generic_advdiff:
132      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
133    o pkg/exf:
134      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
135         xxg_precip capability
136      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
137    o pkg/ctrl:
138      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
139    o model/src/load_fields_driver.F :
140      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
141        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
142    o OpenAD verification experiments:
143      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
144        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
145        for now, only in pkgs used in OpenAD verification experiments.
146      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
147        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
148        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
149        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
150    o OpenAD verification tests:
151      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
152      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
153        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
154      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
155        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
156    o model/src & generic_advdiff:
157      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
158        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
159        dynamics requires valid tracer forcing only over tile interior but, for
160        some diagnostics, may need to extend it over 1 point in tile halo region.
161      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
162        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
163        setting in temp/salt/ptracer_integrate.F
164    o pkg/dic:
165      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
166        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
167        in gchem_forcing_sep.F
168    o pkg/autodiff & obcs:
169      - add storage of current OB values for U & V (was already done for T & S).
170    
171    checkpoint65c (2014/08/30)
172    o pkg/dic:
173      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
174        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
175        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
176    o verification:
177      - new experiment testing OBCS and DIC pkgs, using params & output from
178        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
179        passage: take OBCS from the last year of a 2 yrs simulation and initial
180        conditions from t=1.yr while keeping the same forcing.
181    o model/src:
182      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
183        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
184    o pkg/diagnostics (Stats-Diags):
185      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
186        a) refine region where stats are computed, excluding where arrhFac=0 ;
187        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
188        c) extend regional stats over the region edges (for U or V pt location).
189    o pkg/gchem:
190      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
191        pkg/dic is currently changing/updating ptracers values beyond the OB).
192    o verification (hs94):
193      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
194        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
195        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
196        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
197    o pkg/ptracers:
198      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
199        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
200      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
201        with AB-2 code (so that it get tested).
202    o model/src:
203      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
204        with AB-2 code (previously only available with AB-3 code).
205        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
206        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
207        there, by calling CYCLE_AB_TRACER).
208    o pkg/generic_advdiff:
209      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
210        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
211        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
212        S/R temp/salt/ptracers_integrate.F
213    o model/src & pkg/ptracers:
214      - remove common block variables gT,gS (in DYNVARS.h), except when
215         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
216      - remove common block variable gPtr.
217    o model/src & pkgs:
218      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
219         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
220         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
221         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
222      + change accordingly all calling S/R.
223      - use local temperature/salinity/ptracer tendency array (without bi,bj)
224        in S/R temp/salt/ptracers_integrate.F
225    o pkg/seaice:
226      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
227        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
228      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
229        in seaice_lsr
230      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
231        in s/r seaice_lsr_calc_coeffs
232    o pkg/mdsio:
233      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
234        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
235        too long (e.g., > MAX_LEN_FNAM/2 )
236    
237    checkpoint65b (2014/08/12)
238    o pkg/matrix:
239      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
240    o model/src:
241      - fix initialisation of geothermalFile; compile geothermal-flux code in
242        natl_box verification experiment.
243    o model/src & pkg/down_slope:
244      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
245      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
246        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
247        results at machine truncation level: update output of experiments
248        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
249    o pkg/diagnostics (Stats-Diags):
250      - do not cumulate the full volume when DIAGNOSTICS_FILL is
251        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
252        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
253        times (but Min,Max and StD are still wrong).
254    o model/src:
255      - add geothermal flux forcing: read in ini_forcing.F as time-constant
256        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
257    o model/src:
258      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
259        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
260        arrays are already updated while adjustments (filters, conv.adjustment) are
261        still applied later, in S/R TRACERS_CORRECTION_STEP.
262    o model/src:
263      - store in common bloc array "rhoInSitu" the virtual potential temperature
264        anomaly that is used to compute geopotential: this make the atmos code
265        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
266    o pkg/seaice/seaice_lsr.F
267      - rename integer variable ilcall to ipass (that's what it is called
268        in the residual diagnostics
269      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
270        default) for improved non-linear convergence of the first few steps
271      - adjust a few comments and add new ones to explain some of the store
272        directives
273    o pkg/generic_advdiff (& ptracers):
274      - re-work the code to check for valid advection scheme and for minimum
275        size of overlap (now stored in local common bloc in gad_advscheme.F)
276    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
277      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
278      - add an auxilliary variable "bet" and fix store directives and keys in
279        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
280        less exact gradients in my tests); but there are still
281        recomputation warning (although gradients are sort of OK), when
282        SEAICE_LSR_VECTORIZE is not defined, so this flag and
283        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
284      - update verification experiments lab_sea.
285      - change some comments in S/R seaice_calc_viscosities
286    o model/src:
287      - if staggerTimeStep=T, always apply exchange to velocity field in
288        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
289        (independent of using multi-dim advection or not); no effect on FWD run
290        but affects AD results (at machine truncation level): update output of
291        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
292        and isomip (oad: 12.d).
293    o pkg/generic_advdiff:
294      - stop if doAB_onGtGs is set to FALSE but ignored
295      - refine warning related to stability of tracer time-stepping
296        regarding internal wave dynamics.
297      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
298        on staggerTimeStep & implicitIntGravWave (will now get a warning
299        if potentially unstable).
300    o pkg/kl10:
301      - add new pkg "kl10" for mixing due to internal wave breaking, from
302        http://www.sciencedirect.com/science/article/pii/S1463500310000144
303        (contribution from Jody Klymak), tested in verification experiment
304        verification/internal_wave/input.kl10/
305    o isomip experiment:
306      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
307        (input.htd) and update the output.
308    o cd_code experiments:
309      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
310        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
311        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
312        update the corresponding output.
313    o pkg/seaice:
314      - reduce the number of include files and store directives in
315        S/R seaice_lsr_tridiagu/v
316      - change the order of loops in one case in S/R seaice_lsr_tridiagv
317        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
318        get rid off one store directive (a TAF bug?)
319      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
320        S/R seaice_lsr_tridiagv to change the loop range for consistency
321      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
322      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
323        S/R seaice_lsr_tridiagu/v (requires update of
324        offline_exf_seaice/input.dyn_jfnk)
325    
326    checkpoint65a (2014/07/27)
327    o model/src:
328      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
329        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
330        (topo in p-coords, ice-shelf in z-coords); update output of experiments
331        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
332    o model/src:
333      - collect momentum forcing tendency into local 2-D array (passed as argument
334        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
335        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
336        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
337      - collect T & S forcing tendency into local 2-D array (passed as argument to
338        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
339        affects results at machine truncation level (e.g., ocean: if using
340        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
341        correction due to vertical advection).
342      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
343        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
344        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
345        obcs_ctrl (ad & fwd grd @ 12 & 7).
346    o pkg/ptracers & diagnostics:
347      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
348        title (to avoid some unexpected truncation); sort out ptracers diags units.
349      - collect ptracer forcing tendency into local 2-D array (passed as argument
350        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
351    
352    checkpoint65 (2014/07/18)
353    o pkg/fizhi:
354      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
355        affects results at machine truncation level. Update output of experiments
356        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
357    o pkg/seaice: more clean up
358      - rename TAF common block tapes to be more consistent and remove
359        unnecessary duplicates
360      - add store directives to remove more recomputations, but use smaller
361        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
362        The idea behind this flag is to reduce the memory footprint when the
363        adjoint of the LSR is not required. As of now, defining the flag
364        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
365        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
366        For experiment offline_exf_seaice, this means on a linux box with gfortran
367        nearly a factor of 10 (but keep in mind there is mostly seaice code in
368        this experiment):
369        > size mitgcmuv_ad
370        text    data        bss     dec        hex  
371        5100659 1216  220458952  225560827  d71c8fb
372        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
373        but only a moderate increase of 36% for global_ocean.cs32x15:
374        text    data        bss     dec        hex
375        6695027 1648 1014578664 1021275339 3cdf6ccb
376        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
377      - note: there are still recomputations in global_ocean.cs32x15 and
378        offline_exf_seaice and the gradient agreement changes (gets a
379        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
380      - in general, the AD gradients still are wrong
381    o OpenAD
382      - clean up code_oad/ directories somewhat by moving files
383        dontCompile, dontTransform, keepOriginal to OAD_support/
384    o model/src:
385      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
386        (not currently tested): add dissipation terms before NLFS rescaling of
387        tendencies (previously done after).
388    o pkg/diagnostics:
389      - write stats-diags in ascii file with more digits (same as in monitor).
390    o pkg/down_slope:
391      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
392        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
393    o model/src:
394      - new file "apply_forcing.F" containing all the code previously in
395        external_forcing.F, but with new argument list: pass, as new argument,
396        the current level tendency array to update (instead of a direct update
397        of the common bloc array). Change the corresponding calls.
398      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
399        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
400    o pkg/seaice/seaice_lsr, a little bit of clean up
401      - rearrange some code blocks, so that now all calculations for
402        setting up the right-hand-sides done within one single block
403        (I find that easier to read and understand)
404      - rearrange freedrift-code to reduce the number of ifdefs
405      - adjust some indentations and comments
406    
407    checkpoint64z (2014/07/10)
408    o model/src and several pkgs:
409      - change argument list of all S/R called from external_forcing.F and
410        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
411        to pass, as argument, the current level tendency array to update
412        (instead of a direct update of the common bloc array).
413      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
414      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
415    o pkg/seaice/seaice_lsr.F
416      - always initialize local arrays in seaice_lsr_tridiagu/v
417      - add more local tapes to seaice_lsr_tridiagu/v
418      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
419        keep it in bi/bj loop; this seems to be essential
420      - gradients are still wrong but only by 4-7 orders of magnitude
421        instead of 15 orders of magnitude, lab_sea improves a little
422    o pkg/seaice
423      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
424        generates unnecessary code in seaice_lsr_ad
425      - add more store directives in seaice_lsr to avoid unnecessary code
426        in seaice_lsr_ad
427      - exclude some residual computations in seaice_lsr when
428        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
429        in seaice_lsr_ad
430      - add more storing, a new tape (model/src/the_main_loop.F) and
431        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
432        and klockey should be checked by a specialist)
433      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
434        and update lab_sea after previous changes in pkg/seaice below
435    o pkg/autodiff:
436      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
437        viscFacInAd : run time parameters allowing for adjoint switches
438        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
439    o pkg/ecco:
440      - introduce cost_gencost_boxmean.F that computes a box mean
441        temperature (for use in adjoint sensitivity studies).
442    o model/src/set_defaults.F : initialize viscFacAdj to 1.
443    o pkg/mom_common/mom_calc_visc.F:
444      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
445    o pkg/seaice/seaice_summary.F:
446      - statement for SEAICEadjMODE now in autodiff_readparms.F
447    o pkg/seaice:
448      - remove some store directives and add new ones in an effort to get
449        finally rid off the recomputation warnings. This is successful
450        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
451        defined (i.e. no extensive recomputation warnings left), but there
452        are still too many recomputations on the solver iteration level
453      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
454      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
455        SEAICE_SIZE.h
456      - add a store directive in S/R seaice_calc_viscosities
457    o pkg/seaice (ITD code):
458      - fix definition of Hlimit for multi-threaded case
459      - use double precision arithmetic to compute Hlimit: this affects results;
460        update output of experiment seaice_itd.
461    o replace content of verification/seaice_itd
462      - instead of a 1D column use the configuration of offline_exf_seaice
463        to test the ice thickness distribution code with ridging
464      - this is a first shot at this experiment
465      - change of some defaults of ridging parameters SEAICEhStar (from
466        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
467        and lot of new comments.
468    
469    checkpoint64y (2014/06/20)
470    o pkg/seaice/seaice_reg_ridge.F:
471      - modify the regularization of very small volumes of ice; only check
472        total volume HEFF, and do not apply correction to individual ice
473        classes because that leads to funny patterns in the heat and fw-fluxes
474        into the ocean. Adjust seaice_itd/results/output.txt
475      - replace nITD by SEAICE_multDim in loop-ranges
476    o pkg/exf:
477      - add code to process the case field period = -12. with UV interpolation.
478      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
479        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
480    o verification/global_with_exf:
481      - switch all fields period to -12. (was previously untested) in input/data.exf
482        (but keep secondary test ".yearly" unchanged); update the reference output.
483    o pkg/cal:
484      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
485    o pkg/exf:
486      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
487        to replace logical switch "exf_verbose"
488      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
489    o pkg/sbo:
490      - update from Katherine Quinn: evaluate mass directly from density and SSH
491        (budget using Finite Volume method) instead of from bottom pressure.
492      - allow testreport to collect few selected SBO output ; tested in exp.
493        global_ocean.90x40x15 (after updating the results, to include SBO output).
494      - fix some multi-threading issues (in output part).
495    o model/src & most packages:
496      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
497      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
498        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
499        "data.{pkg}" exist ; and leave the S/R (return) just after.
500      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
501        + call LAND_READPARMS from packages_readparms.F
502    o pkg/seaice:
503      - remove code that resets useThSice in S/R seaice_readparms and
504        replace it by a warning in S/R seaice_check
505      - remove parameter MULTDIM, replace with nITD and runtime
506        parameter SEAICE_multDim (still hard-wired to nITD if
507        SEAICE_ITD is defined)
508    
509    checkpoint64x (2014/05/24)
510    o verification/lab_sea:
511      - update adjoint and TLM output following changes to pkg/salt_plume
512      - un-do the update after putting back local recip_Cp in few places.
513    o pkg/salt_plume: modifications by An Nguyen:
514      - add capability to do brine rejection (salt-plume) as function of
515        volume+tracers (instead of only salinity tracer).
516      - conserve volume by exchanging volume from each kLev to above to
517        accommodate in-coming brine volume
518      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
519      - switch KPP surf buoyancy due to brine forcing to 3-d
520        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
521      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
522      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
523        in East/West Arctic.
524    o pkg/sbo:
525      - incorporate modifications from Katherine Quinn to enable the use of sbo
526        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
527        output for future testreport verification (unfinished).
528    o pkg/atm_phys:
529      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
530        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
531        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
532    o pkg/seaice
533      seaice_calc_ice_strength.F: modify expression to avoid divisions
534        (affects truncation)
535      seaice_do_ridging.F: clean up the insectarium
536      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
537      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
538      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
539      - add some debugging information and error messages (warnings)
540    o model/src: modifications relatd to atmosphere p*:
541      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
542      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
543        of vertical profile tRef in geopotential background and anomaly.
544      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
545        and pkg/atm_phys.
546      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
547        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
548    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
549    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
550        not used right now, but can be used in BGC packages to fix conservation.
551    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
552        other packages too.
553    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
554        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
555    o model/src:
556      - since we have several heat capacity (even in model/src), define "recip_Cp"
557        as local variable (no longer in common block) to avoid any confusion.
558      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
559    o pkg/exf:
560      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
561        air density as function of air Temp, Humidity and atm pressure.
562    
563    checkpoint64w (2014/05/02)
564    o verification:
565      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
566        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
567        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
568        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
569        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
570    o model/src: for atmosphere in p* coords:
571      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
572      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
573        but not yet activated.
574    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
575      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
576      - this changes the results (but not for any verification experiment, because
577        none tests this), but avoids having an extra field in the restart files
578    o pkg/seaice: remove global variable TICE (not needed)
579      - replace by TICES or local variable where necessary (cost_seaice_test,
580        seaice_diagnostics_state)
581      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
582      - use specific read/write routines for reading and writing individual leves
583        of a multilevel field
584    o pkg/ctrl & model/inc:
585      - move additional anomaly fields of control vars (related to options:
586         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
587        from DYNVARS.h into new header file: CTRL_FIELDS.h
588    o pkg/seaice: some small modifications to the ridging code
589      - make fw2ObyRidge a global variable and add the freshwater flux to
590        seaice_growth
591      - pass actual thickness from seaice_prepare_ridging, so that it is
592        computed only in one place and compute it in the same way as in
593        seaice_growth
594      - initialise more fields in seaice_do_ridging that where cause floating
595        point exceptions over land
596    o pkg/seaice: preparations for ridging code and first real ridging code
597      - move most of "PART 1" of S/R seaice_growth into a new and separate
598        S/R seaice_reg_ridge that will both regularize the state variable after
599        advection call the actual ridging routine;
600      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
601        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
602      - remove ridging code from seaice_advdiff
603      - clean up remaining part 1 of seaice_growth in an attempt to make it
604        more readable (this is probably subjective)
605      - call seaice_itd_redist once in the initialisation phase to have the initial
606        conditions in the correct category
607      - finally: add new ridging routine for ITD code
608    
609    checkpoint64v (2014/04/11)
610    o pkg/ecco:
611      - add runtime parameters mdt[start,end]date[1,2]
612      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
613    o pkg/seaice:
614      - make deltaC a global variable, so that it can be used in ridging code
615      - first step towards ridging: introduce new routines that compute
616        ice strength based on ridging parameters
617      - add diagnostic for HSNOWITD
618      - add opnWtrFrac as a global variable (required for ridging scheme)
619    o pkg/salt_plume + pkg/seaice/seaice_growth.F
620      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
621        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
622    o verification/hs94.1x64x5:
623      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
624      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
625    o autodiff:
626      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
627        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
628        For now, only in pkgs used in verification/hs94.1x64x5.
629      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
630        which are specific to TAF/TAMC).
631      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
632        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
633        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
634      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
635        building mitgcmuv_ad (make adAll).
636    o pkg/ecco:
637      - cost_gencost_seaicev4.F:
638         reformulate proxy cost as function of sst and local param SEAICE_freeze
639         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
640      - add stop statement if old names siv4-[sst,vol] are used
641      - add snapshots + cost reports for atmospheric longwave
642      - remove factor 0.1 in front of wtau[u,v]
643      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
644         ALLOW_TMI_SST_COST_CONTRIBUTION
645    o pkg/atm_phys:
646      - add some diagnostics for Short-wave and for convection S/R.
647    o pkg/seaice/seaice_growth:
648      - fix a bug in the lateral melt parameterization for SEAICE_ITD
649        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
650      - rearrange loop order for better vector code in the same code block
651      - rewrite the floeDiameter formula to have fewer divisions
652      -  (miraculously) none of this changes the results of seaice_itd
653    o pkg/smooth:
654      - move param smooth2Ddiffnbt to pkg/ecco
655    o pkg/salt_plume:
656      - salt_plume_frac.F:
657         clean up local param names
658         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
659    o pkg/rw:
660      - add RS version of S/R READ_MFLDS_LEV.
661    o pkg/streamice:
662      - fix the restart test by writing/reading pickup_streamice files.
663    o pkg/seaice:
664      - refine checks for jfnk-related parameters
665      - comment out if statement with SEAICEuseIMEX parameter as long as there
666        is no IMEX code to avoid confusion and surprises
667    
668    checkpoint64u (2014/03/07)
669    o verification/MLAdjust:
670      - rename secondary test suffix:
671         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
672         0.leithD -> AhFlxF  + switch to flux-form
673         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
674         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
675    o pkg/mom_vecinv:
676      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
677        to be before mom_calc_visc.F)
678      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
679      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
680        this is simpler for the adjoint and for diagnostics.
681    o model/src + pkg/momentum:
682      - add input files for  2-D additional Western and Southern cell-edge wall
683         (e.g., to add "thin-wall" where it is =1).
684      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
685        using 2nd hFacZ that is computed from initial (fix domain) hFac
686      - known limitations of thin wall implementation: not yet coded for sigma
687        coords; not working with CD-scheme neither.
688    o pkg/seaice:
689      - rename recently introduced parameters from (wrong name) AB to
690        BDF (backward difference time discretisation)
691      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
692    o tools/adjoint_options:
693      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
694    
695    checkpoint64t (2014/02/01)
696    o pkg/ecco
697      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
698        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
699      - replace hard-coded record number and period which only work for monthly
700        with read-in runtime param that works for other periods (month,day,year)
701    o pkg/thsice
702      - corrected store directive fixes thsice adjoint gradient checks
703    o genmake2 & testreport:
704      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
705        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
706        Update testreport accordingly. No need to set "export OPENAD=true"
707        in adjoint_options/adjoint_oad anymore (will be removed later).
708    o pkg/shelfice:
709      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
710        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
711        so that surface forcing applies to k=kSurf if using pkg/shelfice.
712    o pkg/ctrl, pkg/grdchk, pkg/ecco:
713      - Changes to make GENARR more modular (i.e. invisible if not used)
714    o model/src/temp_integrate.F and salt_integrate.F
715      - re-include store directives that were removed on Dec 27th.
716    o model/src/external_forcing_surf.F
717      - add storage directives for EmPmR and PmEpR to avoid recomputation of
718        seaice_model in the adjoint that is problematic when seaice_model is
719        turned off in the adjoint. The resolved issue dated back to July when
720        EXTERNAL_FORCING_SURF call was moved.
721        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
722    o pkg/exf/exf_check.F
723      - fix a small bug again (originally found by Wentao Liu, now found again)
724      - streamline error output
725    o pkg/streamice and aim_v23:
726      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
727        Apple's /usr/bin/cpp knows what to do:
728        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
729        Target: x86_64-apple-darwin13.0.0
730    
731    checkpoint64s (2014/01/05)
732    o tools/adjoint_options:
733      - switch to fastopt.net TAF server (instead of default fastopt.de) for
734        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
735    o model/src:
736      - remove some unnecessary TAF storage directives in forward_step.F and
737        in dynamics.F (note: not always removed by TAF, e.g., double storage
738        of kappaRU,kappaRV in former version of dynamics.F).
739    o model/src & pkg/ptracers:
740      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
741        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
742        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
743      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
744      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
745      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
746    o useSingleCpuInput separates single-CPU input from single-CPU output;
747        for now only implemented for in exf_interp_read.F
748    o verification/advect_xy:
749      - fix missing EXCH call in local version of ini_salt.F and update output.
750    o momentum diagnostics:
751      - fix which deltaT is used in Total-Tendency diagnostics.
752      - fix typo in diagnostics for momentum tendency from AB.
753    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
754        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
755    
756    checkpoint64r (2013/12/08)
757    o verification/*/results:
758      - Update reference output of experiments that were passing with just 13 digits
759         (make it easier to detect future changes in results)
760    o model/src & pkg/ptracers:
761      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
762        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
763        to inside ptracers_integrate.F ; remove ptracers_advection.F
764    o coupling interface pkgs:
765        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
766      - change the config check to test the agreement of Ocean Depth
767        with ATM land/sea mask (instead of ATM orography);
768      - send to coupler the number of coupler time-steps to do for this run:
769        this allows to check for consistency and don't need anymore to be
770        specified in parameter file "data";
771      in coupler:
772      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
773      - improve report to log-file of config setting (pass log-file unit to few S/R)
774    o pkg/compon_communic:
775      - add coupling send/receive for non-tiled integer vector;
776      - add S/R to check and stop if any proc has an error (similar to
777        eesupp/src/stop_if_error.F but single thread and across Comm_World).
778    o pkg/exch2:
779      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
780        through list of all tiles my proc owns.
781    o model/src:
782      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
783        from rTrans) to simplify dependencies (no need to store rTrans anymore in
784        calling S/R); this affects AD results at machine truncation level:
785        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
786        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
787    o tools/build_options:
788      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
789    o coupling interface pkgs:
790        [compon_communic, atm_compon_interf & ocn_compon_interf]
791      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
792        to each S/R that needs it; remove un-used variables.
793      - change component tile registration (cpl_register.F in both compon_interf
794        and mitcomponent_tile_register.F) to pass the full list of tiles
795        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
796      - with pkg/exch2: adopt the same convention used for I/O to define mapping
797        towards coupler global array (unless W2_useE2ioLayOut=F):
798         a) can now use different tiling between atm & ocn comp.
799         b) no needs to modify the run-Off map when changing tiling (was needed
800            even if using the same tiling between atm & ocn).
801         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
802            full land tiles); not yet tested.
803      - check for valid mapping from comp. tile to coupler global array
804      - improve report of tile registration results to log file.
805    o pkg/exch2:
806      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
807        tile-registration (CPL_REGISTER);
808      - activate (un-comment) definition and setting of "W2_tileIndex" list to
809        store the local bi,bj indices of each tile;
810      - also print bi,bj in local report to log file;
811      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
812        Jun 2009 modif of pkg/exch2).
813    o testing on baudelaire:
814      - run 2 tests at a time: no significant slow down (since enough cpu) and
815        get the full set of test done earlier
816      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
817  o model/src/thermodynamics.F and routines called from it:  o model/src/thermodynamics.F and routines called from it:
818    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &    - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
819      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual      gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
# Line 23  o model/src/thermodynamics.F and routine Line 833  o model/src/thermodynamics.F and routine
833    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,    - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
834      global_ocean.90x40x15, tutorial_global_oce_biogeo and      global_ocean.90x40x15, tutorial_global_oce_biogeo and
835      tutorial_tracer_adjsens (+ TLM output).      tutorial_tracer_adjsens (+ TLM output).
836  o toolm/OAD_support and (verification/*/) code_oad:  o tools/OAD_support and (verification/*/) code_oad:
837    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to    - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
838      module conversion ; remove unneeded CPP_EEOPTIONS.h.      module conversion ; remove unneeded CPP_EEOPTIONS.h.
839    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard    - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
840      version (closer to model/incCPP_OPTIONS.h).      version (closer to model/inc/CPP_OPTIONS.h).
841  o model/src:  o model/src:
842    - remove parameter "useOldFreezing" from PARAMS.h and push it to the    - remove parameter "useOldFreezing" from PARAMS.h and push it to the
843      retired list of parameters (routine FREEZE has been replace by surface      retired list of parameters (routine FREEZE has been replace by surface
# Line 47  o verification: Line 857  o verification:
857  o pkg/cost:  o pkg/cost:
858    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
859      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
860      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
861        cannot be applied to var in common block).        cannot be applied to var in common block).
862      o allows to get results independent of tile-per-proc setting (if using      o allows to get results independent of tile-per-proc setting (if using
863        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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