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revision 1.1915 by jmc, Thu Aug 22 01:20:58 2013 UTC revision 1.2083 by gforget, Thu Oct 16 20:23:21 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,exf :
8      - remove variables associated with NON-generic costs,
9        unless ECCO_CTRL_DEPRECATED is defined.
10      - remove NON-generic NON-obcs controls,
11        unless ECCO_CTRL_DEPRECATED is defined.
12    o pkg/ctrl : added ctrl_local_params.h
13    o pkg/ecco : added ecco_local_params.h
14    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
15      experiments, which will progressively be removed once the
16      experiments are revised to use only generic controls/costs.
17    
18    checkpoint65f (2014/10/13)
19    o pkg/ctrl, ecco, seaice : minor changes in headers
20    o global_oce_llc90 :
21      - ecco_v4 verification experiments now test generic cost
22        function and control capabilities added since checkpoint65c.
23    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
24    o pkg/ecco: increase modularity and improve logic
25      - ecco_toolbox.F (new) : basic operations that are often used,
26        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
27        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
28      - cost_gencal.F (new) : determine filnames and records.
29      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
30      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
31        and exploit the above functions leading to more compact code.
32      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
33      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
34        using_ers, using_gfo, using_mdt is now only defined within gencost)
35    o pkg/ecco: extend generic cost capabilities
36      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
37        capabilities via gencost_preproc (+ _c,_i,_r related params),
38        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
39        gencost_outputlevel arguments to cost_generic
40      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
41        and active_read, making room for gencost_preproc to take effect.
42        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
43      - pkg/ecco/cost_generic.F :
44        compute and store misfit maks*(model-data) in localdif that is
45        then used in cost and for output, output misfit if outlev.GT.0
46      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
47        rather gencost_barfile for deciding whether to write barfile
48      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
49      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
50        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
51      - pkg/ecco/ecco_summary.F : report gencost variables
52      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
53    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
54    o pkg/ecco: internal re-organization
55      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
56        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
57        mv relevant variables definition from ecco_cost.h to ecco.h,
58        make sure gencost routines only include ecco.h)
59      - throughout : add missing CCP switches, rm unused variables,
60        and rm un-necessary CPP switches
61      - throughout gencost routines : replace modelstartdate with
62        gencost_startdate when needed
63      - cost_bp_read.F : use arguments, instead of common blocs
64        so that it can be used also by (new) cost_gencost_bpv4.F
65      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
66      - ecco_phys.F : compute etanFull
67      - ecco_readparms.F : rename using_topex as using_tpj, add
68        bpv4-grace to gencost list, initialize added parameters
69      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
70    
71    checkpoint65e (2014/09/28)
72    o pkg/obcs:
73      - replaced the just-added CPP options with run-time variables
74        (see pkg/obcs/OBCS_PARAMS.h for details)
75    o pkg/obcs:
76      - add additional CPP options for sponge boundary layers
77        (see pkg/obcs/OBCS_OPTIONS.h for details)
78    o pkg/atm_phys:
79      - implement simple (obliquity only, assuming circular planet orbit)
80        seasonal cycle for incoming insolation ; used when run-time parameter
81        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
82    o pkg/exf, pkg/ecco, pkg/ctrl:
83      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
84      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
85      - implement gentim2d for xx_tauu, xx_tauv
86    o pkg/ctrl, pkg/ecco :
87      - fix and complement the generic controls implementation
88    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
89        pkg/shelfice/shelfice_thermodynamics.F,
90        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
91        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
92      - add weight in CTRL_GET_GEN calls
93    o pkg/ctrl :
94      - ctrl_get_gen.F : add weight as input parameter, and apply
95        it directly rather than using smooth_correl2Dw (to be retired).
96      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
97    o pkg/ctrl :
98      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
99        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
100      - re-activate ctrl_summary (call in ctrl_init.F)
101    o pkg/ctrl/ctrl_cost_gen.F :
102      - fix CCP brackets, remove un-necessary myiter, mytime
103    o pkg/ecco, pkg/ctrl :
104      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
105      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
106      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
107      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
108    
109    checkpoint65d (2014/09/15)
110    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
111      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
112        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
113    o pkg/ctrl/ctrl_map_ini_genarr.F :
114      - remove compilation failure
115      - replace hard coded example
116      - use ctrl_map_ini_gen2D, 3D
117    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
118      - on/off switch based upon xx_genarr2d_weight,3d
119    o src/packages_init_variables.F :
120      - regroup pkg/estimation calls
121      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
122        (moved to ctrl_init_variables)
123    o cost/cost_init_varia.F :
124      - remove ecco_cost_init_varia
125        (moved to ecco_init_varia)
126    o ctrl/ctrl_init_variables.F :
127      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
128      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
129    o ctrl/ctrl_map_ini.F :
130      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
131        (moved to ctrl_init_variables)
132    o ctrl/ctrl_map_ini_ecco.F :
133      - remove ECCO_PHYS (mv to ecco_init_varia)
134      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
135    o ecco/ecco_ad_diff.list :
136      - add ecco_init_varia.f
137    o ecco/ecco_init_varia.F
138      - new routine
139    o pkg/streamice:
140      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
141        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
142      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
143    o pkg/generic_advdiff:
144      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
145    o pkg/exf:
146      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
147         xxg_precip capability
148      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
149    o pkg/ctrl:
150      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
151    o model/src/load_fields_driver.F :
152      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
153        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
154    o OpenAD verification experiments:
155      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
156        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
157        for now, only in pkgs used in OpenAD verification experiments.
158      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
159        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
160        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
161        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
162    o OpenAD verification tests:
163      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
164      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
165        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
166      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
167        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
168    o model/src & generic_advdiff:
169      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
170        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
171        dynamics requires valid tracer forcing only over tile interior but, for
172        some diagnostics, may need to extend it over 1 point in tile halo region.
173      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
174        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
175        setting in temp/salt/ptracer_integrate.F
176    o pkg/dic:
177      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
178        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
179        in gchem_forcing_sep.F
180    o pkg/autodiff & obcs:
181      - add storage of current OB values for U & V (was already done for T & S).
182    
183    checkpoint65c (2014/08/30)
184    o pkg/dic:
185      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
186        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
187        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
188    o verification:
189      - new experiment testing OBCS and DIC pkgs, using params & output from
190        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
191        passage: take OBCS from the last year of a 2 yrs simulation and initial
192        conditions from t=1.yr while keeping the same forcing.
193    o model/src:
194      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
195        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
196    o pkg/diagnostics (Stats-Diags):
197      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
198        a) refine region where stats are computed, excluding where arrhFac=0 ;
199        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
200        c) extend regional stats over the region edges (for U or V pt location).
201    o pkg/gchem:
202      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
203        pkg/dic is currently changing/updating ptracers values beyond the OB).
204    o verification (hs94):
205      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
206        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
207        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
208        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
209    o pkg/ptracers:
210      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
211        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
212      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
213        with AB-2 code (so that it get tested).
214    o model/src:
215      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
216        with AB-2 code (previously only available with AB-3 code).
217        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
218        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
219        there, by calling CYCLE_AB_TRACER).
220    o pkg/generic_advdiff:
221      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
222        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
223        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
224        S/R temp/salt/ptracers_integrate.F
225    o model/src & pkg/ptracers:
226      - remove common block variables gT,gS (in DYNVARS.h), except when
227         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
228      - remove common block variable gPtr.
229    o model/src & pkgs:
230      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
231         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
232         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
233         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
234      + change accordingly all calling S/R.
235      - use local temperature/salinity/ptracer tendency array (without bi,bj)
236        in S/R temp/salt/ptracers_integrate.F
237    o pkg/seaice:
238      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
239        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
240      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
241        in seaice_lsr
242      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
243        in s/r seaice_lsr_calc_coeffs
244    o pkg/mdsio:
245      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
246        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
247        too long (e.g., > MAX_LEN_FNAM/2 )
248    
249    checkpoint65b (2014/08/12)
250    o pkg/matrix:
251      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
252    o model/src:
253      - fix initialisation of geothermalFile; compile geothermal-flux code in
254        natl_box verification experiment.
255    o model/src & pkg/down_slope:
256      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
257      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
258        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
259        results at machine truncation level: update output of experiments
260        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
261    o pkg/diagnostics (Stats-Diags):
262      - do not cumulate the full volume when DIAGNOSTICS_FILL is
263        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
264        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
265        times (but Min,Max and StD are still wrong).
266    o model/src:
267      - add geothermal flux forcing: read in ini_forcing.F as time-constant
268        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
269    o model/src:
270      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
271        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
272        arrays are already updated while adjustments (filters, conv.adjustment) are
273        still applied later, in S/R TRACERS_CORRECTION_STEP.
274    o model/src:
275      - store in common bloc array "rhoInSitu" the virtual potential temperature
276        anomaly that is used to compute geopotential: this make the atmos code
277        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
278    o pkg/seaice/seaice_lsr.F
279      - rename integer variable ilcall to ipass (that's what it is called
280        in the residual diagnostics
281      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
282        default) for improved non-linear convergence of the first few steps
283      - adjust a few comments and add new ones to explain some of the store
284        directives
285    o pkg/generic_advdiff (& ptracers):
286      - re-work the code to check for valid advection scheme and for minimum
287        size of overlap (now stored in local common bloc in gad_advscheme.F)
288    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
289      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
290      - add an auxilliary variable "bet" and fix store directives and keys in
291        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
292        less exact gradients in my tests); but there are still
293        recomputation warning (although gradients are sort of OK), when
294        SEAICE_LSR_VECTORIZE is not defined, so this flag and
295        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
296      - update verification experiments lab_sea.
297      - change some comments in S/R seaice_calc_viscosities
298    o model/src:
299      - if staggerTimeStep=T, always apply exchange to velocity field in
300        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
301        (independent of using multi-dim advection or not); no effect on FWD run
302        but affects AD results (at machine truncation level): update output of
303        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
304        and isomip (oad: 12.d).
305    o pkg/generic_advdiff:
306      - stop if doAB_onGtGs is set to FALSE but ignored
307      - refine warning related to stability of tracer time-stepping
308        regarding internal wave dynamics.
309      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
310        on staggerTimeStep & implicitIntGravWave (will now get a warning
311        if potentially unstable).
312    o pkg/kl10:
313      - add new pkg "kl10" for mixing due to internal wave breaking, from
314        http://www.sciencedirect.com/science/article/pii/S1463500310000144
315        (contribution from Jody Klymak), tested in verification experiment
316        verification/internal_wave/input.kl10/
317    o isomip experiment:
318      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
319        (input.htd) and update the output.
320    o cd_code experiments:
321      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
322        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
323        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
324        update the corresponding output.
325    o pkg/seaice:
326      - reduce the number of include files and store directives in
327        S/R seaice_lsr_tridiagu/v
328      - change the order of loops in one case in S/R seaice_lsr_tridiagv
329        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
330        get rid off one store directive (a TAF bug?)
331      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
332        S/R seaice_lsr_tridiagv to change the loop range for consistency
333      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
334      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
335        S/R seaice_lsr_tridiagu/v (requires update of
336        offline_exf_seaice/input.dyn_jfnk)
337    
338    checkpoint65a (2014/07/27)
339    o model/src:
340      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
341        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
342        (topo in p-coords, ice-shelf in z-coords); update output of experiments
343        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
344    o model/src:
345      - collect momentum forcing tendency into local 2-D array (passed as argument
346        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
347        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
348        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
349      - collect T & S forcing tendency into local 2-D array (passed as argument to
350        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
351        affects results at machine truncation level (e.g., ocean: if using
352        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
353        correction due to vertical advection).
354      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
355        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
356        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
357        obcs_ctrl (ad & fwd grd @ 12 & 7).
358    o pkg/ptracers & diagnostics:
359      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
360        title (to avoid some unexpected truncation); sort out ptracers diags units.
361      - collect ptracer forcing tendency into local 2-D array (passed as argument
362        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
363    
364    checkpoint65 (2014/07/18)
365    o pkg/fizhi:
366      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
367        affects results at machine truncation level. Update output of experiments
368        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
369    o pkg/seaice: more clean up
370      - rename TAF common block tapes to be more consistent and remove
371        unnecessary duplicates
372      - add store directives to remove more recomputations, but use smaller
373        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
374        The idea behind this flag is to reduce the memory footprint when the
375        adjoint of the LSR is not required. As of now, defining the flag
376        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
377        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
378        For experiment offline_exf_seaice, this means on a linux box with gfortran
379        nearly a factor of 10 (but keep in mind there is mostly seaice code in
380        this experiment):
381        > size mitgcmuv_ad
382        text    data        bss     dec        hex  
383        5100659 1216  220458952  225560827  d71c8fb
384        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
385        but only a moderate increase of 36% for global_ocean.cs32x15:
386        text    data        bss     dec        hex
387        6695027 1648 1014578664 1021275339 3cdf6ccb
388        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
389      - note: there are still recomputations in global_ocean.cs32x15 and
390        offline_exf_seaice and the gradient agreement changes (gets a
391        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
392      - in general, the AD gradients still are wrong
393    o OpenAD
394      - clean up code_oad/ directories somewhat by moving files
395        dontCompile, dontTransform, keepOriginal to OAD_support/
396    o model/src:
397      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
398        (not currently tested): add dissipation terms before NLFS rescaling of
399        tendencies (previously done after).
400    o pkg/diagnostics:
401      - write stats-diags in ascii file with more digits (same as in monitor).
402    o pkg/down_slope:
403      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
404        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
405    o model/src:
406      - new file "apply_forcing.F" containing all the code previously in
407        external_forcing.F, but with new argument list: pass, as new argument,
408        the current level tendency array to update (instead of a direct update
409        of the common bloc array). Change the corresponding calls.
410      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
411        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
412    o pkg/seaice/seaice_lsr, a little bit of clean up
413      - rearrange some code blocks, so that now all calculations for
414        setting up the right-hand-sides done within one single block
415        (I find that easier to read and understand)
416      - rearrange freedrift-code to reduce the number of ifdefs
417      - adjust some indentations and comments
418    
419    checkpoint64z (2014/07/10)
420    o model/src and several pkgs:
421      - change argument list of all S/R called from external_forcing.F and
422        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
423        to pass, as argument, the current level tendency array to update
424        (instead of a direct update of the common bloc array).
425      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
426      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
427    o pkg/seaice/seaice_lsr.F
428      - always initialize local arrays in seaice_lsr_tridiagu/v
429      - add more local tapes to seaice_lsr_tridiagu/v
430      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
431        keep it in bi/bj loop; this seems to be essential
432      - gradients are still wrong but only by 4-7 orders of magnitude
433        instead of 15 orders of magnitude, lab_sea improves a little
434    o pkg/seaice
435      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
436        generates unnecessary code in seaice_lsr_ad
437      - add more store directives in seaice_lsr to avoid unnecessary code
438        in seaice_lsr_ad
439      - exclude some residual computations in seaice_lsr when
440        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
441        in seaice_lsr_ad
442      - add more storing, a new tape (model/src/the_main_loop.F) and
443        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
444        and klockey should be checked by a specialist)
445      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
446        and update lab_sea after previous changes in pkg/seaice below
447    o pkg/autodiff:
448      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
449        viscFacInAd : run time parameters allowing for adjoint switches
450        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
451    o pkg/ecco:
452      - introduce cost_gencost_boxmean.F that computes a box mean
453        temperature (for use in adjoint sensitivity studies).
454    o model/src/set_defaults.F : initialize viscFacAdj to 1.
455    o pkg/mom_common/mom_calc_visc.F:
456      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
457    o pkg/seaice/seaice_summary.F:
458      - statement for SEAICEadjMODE now in autodiff_readparms.F
459    o pkg/seaice:
460      - remove some store directives and add new ones in an effort to get
461        finally rid off the recomputation warnings. This is successful
462        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
463        defined (i.e. no extensive recomputation warnings left), but there
464        are still too many recomputations on the solver iteration level
465      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
466      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
467        SEAICE_SIZE.h
468      - add a store directive in S/R seaice_calc_viscosities
469    o pkg/seaice (ITD code):
470      - fix definition of Hlimit for multi-threaded case
471      - use double precision arithmetic to compute Hlimit: this affects results;
472        update output of experiment seaice_itd.
473    o replace content of verification/seaice_itd
474      - instead of a 1D column use the configuration of offline_exf_seaice
475        to test the ice thickness distribution code with ridging
476      - this is a first shot at this experiment
477      - change of some defaults of ridging parameters SEAICEhStar (from
478        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
479        and lot of new comments.
480    
481    checkpoint64y (2014/06/20)
482    o pkg/seaice/seaice_reg_ridge.F:
483      - modify the regularization of very small volumes of ice; only check
484        total volume HEFF, and do not apply correction to individual ice
485        classes because that leads to funny patterns in the heat and fw-fluxes
486        into the ocean. Adjust seaice_itd/results/output.txt
487      - replace nITD by SEAICE_multDim in loop-ranges
488    o pkg/exf:
489      - add code to process the case field period = -12. with UV interpolation.
490      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
491        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
492    o verification/global_with_exf:
493      - switch all fields period to -12. (was previously untested) in input/data.exf
494        (but keep secondary test ".yearly" unchanged); update the reference output.
495    o pkg/cal:
496      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
497    o pkg/exf:
498      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
499        to replace logical switch "exf_verbose"
500      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
501    o pkg/sbo:
502      - update from Katherine Quinn: evaluate mass directly from density and SSH
503        (budget using Finite Volume method) instead of from bottom pressure.
504      - allow testreport to collect few selected SBO output ; tested in exp.
505        global_ocean.90x40x15 (after updating the results, to include SBO output).
506      - fix some multi-threading issues (in output part).
507    o model/src & most packages:
508      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
509      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
510        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
511        "data.{pkg}" exist ; and leave the S/R (return) just after.
512      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
513        + call LAND_READPARMS from packages_readparms.F
514    o pkg/seaice:
515      - remove code that resets useThSice in S/R seaice_readparms and
516        replace it by a warning in S/R seaice_check
517      - remove parameter MULTDIM, replace with nITD and runtime
518        parameter SEAICE_multDim (still hard-wired to nITD if
519        SEAICE_ITD is defined)
520    
521    checkpoint64x (2014/05/24)
522    o verification/lab_sea:
523      - update adjoint and TLM output following changes to pkg/salt_plume
524      - un-do the update after putting back local recip_Cp in few places.
525    o pkg/salt_plume: modifications by An Nguyen:
526      - add capability to do brine rejection (salt-plume) as function of
527        volume+tracers (instead of only salinity tracer).
528      - conserve volume by exchanging volume from each kLev to above to
529        accommodate in-coming brine volume
530      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
531      - switch KPP surf buoyancy due to brine forcing to 3-d
532        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
533      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
534      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
535        in East/West Arctic.
536    o pkg/sbo:
537      - incorporate modifications from Katherine Quinn to enable the use of sbo
538        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
539        output for future testreport verification (unfinished).
540    o pkg/atm_phys:
541      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
542        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
543        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
544    o pkg/seaice
545      seaice_calc_ice_strength.F: modify expression to avoid divisions
546        (affects truncation)
547      seaice_do_ridging.F: clean up the insectarium
548      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
549      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
550      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
551      - add some debugging information and error messages (warnings)
552    o model/src: modifications relatd to atmosphere p*:
553      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
554      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
555        of vertical profile tRef in geopotential background and anomaly.
556      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
557        and pkg/atm_phys.
558      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
559        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
560    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
561    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
562        not used right now, but can be used in BGC packages to fix conservation.
563    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
564        other packages too.
565    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
566        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
567    o model/src:
568      - since we have several heat capacity (even in model/src), define "recip_Cp"
569        as local variable (no longer in common block) to avoid any confusion.
570      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
571    o pkg/exf:
572      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
573        air density as function of air Temp, Humidity and atm pressure.
574    
575    checkpoint64w (2014/05/02)
576    o verification:
577      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
578        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
579        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
580        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
581        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
582    o model/src: for atmosphere in p* coords:
583      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
584      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
585        but not yet activated.
586    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
587      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
588      - this changes the results (but not for any verification experiment, because
589        none tests this), but avoids having an extra field in the restart files
590    o pkg/seaice: remove global variable TICE (not needed)
591      - replace by TICES or local variable where necessary (cost_seaice_test,
592        seaice_diagnostics_state)
593      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
594      - use specific read/write routines for reading and writing individual leves
595        of a multilevel field
596    o pkg/ctrl & model/inc:
597      - move additional anomaly fields of control vars (related to options:
598         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
599        from DYNVARS.h into new header file: CTRL_FIELDS.h
600    o pkg/seaice: some small modifications to the ridging code
601      - make fw2ObyRidge a global variable and add the freshwater flux to
602        seaice_growth
603      - pass actual thickness from seaice_prepare_ridging, so that it is
604        computed only in one place and compute it in the same way as in
605        seaice_growth
606      - initialise more fields in seaice_do_ridging that where cause floating
607        point exceptions over land
608    o pkg/seaice: preparations for ridging code and first real ridging code
609      - move most of "PART 1" of S/R seaice_growth into a new and separate
610        S/R seaice_reg_ridge that will both regularize the state variable after
611        advection call the actual ridging routine;
612      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
613        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
614      - remove ridging code from seaice_advdiff
615      - clean up remaining part 1 of seaice_growth in an attempt to make it
616        more readable (this is probably subjective)
617      - call seaice_itd_redist once in the initialisation phase to have the initial
618        conditions in the correct category
619      - finally: add new ridging routine for ITD code
620    
621    checkpoint64v (2014/04/11)
622    o pkg/ecco:
623      - add runtime parameters mdt[start,end]date[1,2]
624      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
625    o pkg/seaice:
626      - make deltaC a global variable, so that it can be used in ridging code
627      - first step towards ridging: introduce new routines that compute
628        ice strength based on ridging parameters
629      - add diagnostic for HSNOWITD
630      - add opnWtrFrac as a global variable (required for ridging scheme)
631    o pkg/salt_plume + pkg/seaice/seaice_growth.F
632      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
633        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
634    o verification/hs94.1x64x5:
635      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
636      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
637    o autodiff:
638      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
639        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
640        For now, only in pkgs used in verification/hs94.1x64x5.
641      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
642        which are specific to TAF/TAMC).
643      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
644        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
645        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
646      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
647        building mitgcmuv_ad (make adAll).
648    o pkg/ecco:
649      - cost_gencost_seaicev4.F:
650         reformulate proxy cost as function of sst and local param SEAICE_freeze
651         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
652      - add stop statement if old names siv4-[sst,vol] are used
653      - add snapshots + cost reports for atmospheric longwave
654      - remove factor 0.1 in front of wtau[u,v]
655      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
656         ALLOW_TMI_SST_COST_CONTRIBUTION
657    o pkg/atm_phys:
658      - add some diagnostics for Short-wave and for convection S/R.
659    o pkg/seaice/seaice_growth:
660      - fix a bug in the lateral melt parameterization for SEAICE_ITD
661        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
662      - rearrange loop order for better vector code in the same code block
663      - rewrite the floeDiameter formula to have fewer divisions
664      -  (miraculously) none of this changes the results of seaice_itd
665    o pkg/smooth:
666      - move param smooth2Ddiffnbt to pkg/ecco
667    o pkg/salt_plume:
668      - salt_plume_frac.F:
669         clean up local param names
670         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
671    o pkg/rw:
672      - add RS version of S/R READ_MFLDS_LEV.
673    o pkg/streamice:
674      - fix the restart test by writing/reading pickup_streamice files.
675    o pkg/seaice:
676      - refine checks for jfnk-related parameters
677      - comment out if statement with SEAICEuseIMEX parameter as long as there
678        is no IMEX code to avoid confusion and surprises
679    
680    checkpoint64u (2014/03/07)
681    o verification/MLAdjust:
682      - rename secondary test suffix:
683         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
684         0.leithD -> AhFlxF  + switch to flux-form
685         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
686         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
687    o pkg/mom_vecinv:
688      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
689        to be before mom_calc_visc.F)
690      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
691      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
692        this is simpler for the adjoint and for diagnostics.
693    o model/src + pkg/momentum:
694      - add input files for  2-D additional Western and Southern cell-edge wall
695         (e.g., to add "thin-wall" where it is =1).
696      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
697        using 2nd hFacZ that is computed from initial (fix domain) hFac
698      - known limitations of thin wall implementation: not yet coded for sigma
699        coords; not working with CD-scheme neither.
700    o pkg/seaice:
701      - rename recently introduced parameters from (wrong name) AB to
702        BDF (backward difference time discretisation)
703      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
704    o tools/adjoint_options:
705      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
706    
707    checkpoint64t (2014/02/01)
708    o pkg/ecco
709      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
710        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
711      - replace hard-coded record number and period which only work for monthly
712        with read-in runtime param that works for other periods (month,day,year)
713    o pkg/thsice
714      - corrected store directive fixes thsice adjoint gradient checks
715    o genmake2 & testreport:
716      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
717        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
718        Update testreport accordingly. No need to set "export OPENAD=true"
719        in adjoint_options/adjoint_oad anymore (will be removed later).
720    o pkg/shelfice:
721      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
722        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
723        so that surface forcing applies to k=kSurf if using pkg/shelfice.
724    o pkg/ctrl, pkg/grdchk, pkg/ecco:
725      - Changes to make GENARR more modular (i.e. invisible if not used)
726    o model/src/temp_integrate.F and salt_integrate.F
727      - re-include store directives that were removed on Dec 27th.
728    o model/src/external_forcing_surf.F
729      - add storage directives for EmPmR and PmEpR to avoid recomputation of
730        seaice_model in the adjoint that is problematic when seaice_model is
731        turned off in the adjoint. The resolved issue dated back to July when
732        EXTERNAL_FORCING_SURF call was moved.
733        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
734    o pkg/exf/exf_check.F
735      - fix a small bug again (originally found by Wentao Liu, now found again)
736      - streamline error output
737    o pkg/streamice and aim_v23:
738      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
739        Apple's /usr/bin/cpp knows what to do:
740        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
741        Target: x86_64-apple-darwin13.0.0
742    
743    checkpoint64s (2014/01/05)
744    o tools/adjoint_options:
745      - switch to fastopt.net TAF server (instead of default fastopt.de) for
746        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
747    o model/src:
748      - remove some unnecessary TAF storage directives in forward_step.F and
749        in dynamics.F (note: not always removed by TAF, e.g., double storage
750        of kappaRU,kappaRV in former version of dynamics.F).
751    o model/src & pkg/ptracers:
752      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
753        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
754        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
755      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
756      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
757      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
758    o useSingleCpuInput separates single-CPU input from single-CPU output;
759        for now only implemented for in exf_interp_read.F
760    o verification/advect_xy:
761      - fix missing EXCH call in local version of ini_salt.F and update output.
762    o momentum diagnostics:
763      - fix which deltaT is used in Total-Tendency diagnostics.
764      - fix typo in diagnostics for momentum tendency from AB.
765    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
766        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
767    
768    checkpoint64r (2013/12/08)
769    o verification/*/results:
770      - Update reference output of experiments that were passing with just 13 digits
771         (make it easier to detect future changes in results)
772    o model/src & pkg/ptracers:
773      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
774        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
775        to inside ptracers_integrate.F ; remove ptracers_advection.F
776    o coupling interface pkgs:
777        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
778      - change the config check to test the agreement of Ocean Depth
779        with ATM land/sea mask (instead of ATM orography);
780      - send to coupler the number of coupler time-steps to do for this run:
781        this allows to check for consistency and don't need anymore to be
782        specified in parameter file "data";
783      in coupler:
784      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
785      - improve report to log-file of config setting (pass log-file unit to few S/R)
786    o pkg/compon_communic:
787      - add coupling send/receive for non-tiled integer vector;
788      - add S/R to check and stop if any proc has an error (similar to
789        eesupp/src/stop_if_error.F but single thread and across Comm_World).
790    o pkg/exch2:
791      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
792        through list of all tiles my proc owns.
793    o model/src:
794      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
795        from rTrans) to simplify dependencies (no need to store rTrans anymore in
796        calling S/R); this affects AD results at machine truncation level:
797        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
798        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
799    o tools/build_options:
800      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
801    o coupling interface pkgs:
802        [compon_communic, atm_compon_interf & ocn_compon_interf]
803      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
804        to each S/R that needs it; remove un-used variables.
805      - change component tile registration (cpl_register.F in both compon_interf
806        and mitcomponent_tile_register.F) to pass the full list of tiles
807        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
808      - with pkg/exch2: adopt the same convention used for I/O to define mapping
809        towards coupler global array (unless W2_useE2ioLayOut=F):
810         a) can now use different tiling between atm & ocn comp.
811         b) no needs to modify the run-Off map when changing tiling (was needed
812            even if using the same tiling between atm & ocn).
813         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
814            full land tiles); not yet tested.
815      - check for valid mapping from comp. tile to coupler global array
816      - improve report of tile registration results to log file.
817    o pkg/exch2:
818      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
819        tile-registration (CPL_REGISTER);
820      - activate (un-comment) definition and setting of "W2_tileIndex" list to
821        store the local bi,bj indices of each tile;
822      - also print bi,bj in local report to log file;
823      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
824        Jun 2009 modif of pkg/exch2).
825    o testing on baudelaire:
826      - run 2 tests at a time: no significant slow down (since enough cpu) and
827        get the full set of test done earlier
828      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
829    o model/src/thermodynamics.F and routines called from it:
830      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
831        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
832        velocity (outp) by adding bolus velocity.
833      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
834        mass transport from velocity + lateral grid cell area
835      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
836      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
837     in thermodynamics.F
838      - remove k from thermodynamics.F and move it to temp_integrate.F
839        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
840        loop).
841      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
842        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
843        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
844        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
845      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
846        global_ocean.90x40x15, tutorial_global_oce_biogeo and
847        tutorial_tracer_adjsens (+ TLM output).
848    o tools/OAD_support and (verification/*/) code_oad:
849      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
850        module conversion ; remove unneeded CPP_EEOPTIONS.h.
851      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
852        version (closer to model/inc/CPP_OPTIONS.h).
853    o model/src:
854      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
855        retired list of parameters (routine FREEZE has been replace by surface
856        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
857    o pkg/gmredi:
858      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
859        velocity (same scheme but affects machine truncation) for GM_AdvForm.
860      - update output of FWD experiments: front_relax.bvp,
861        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
862    
863    checkpoint64q (2013/11/17)
864    o verification:
865      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
866        tutorial_global_oce_biogeo and global_ocean.90x40x15.
867      - generate new output (growth & melt) for seaice_itd experiment after
868        updating the input pickup_seaice files (previously wrong).
869    o pkg/cost:
870      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
871        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
872        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
873          cannot be applied to var in common block).
874        o allows to get results independent of tile-per-proc setting (if using
875          slower GLOBAL_SUM_SEND_RECV option).
876      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
877        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
878        forward gradients: update output).
879      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
880        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
881    o pkg/mom_common:
882      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
883        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
884        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
885        ensure that all field value that are used are set.
886    o tutorial_deep_convection (smag3d):
887      - add missing scaling in mom_calc_smag_3d.F;
888      - set smag3D_coeff in input.smag3d such that results do not change.
889    o pkg/dic:
890      - change dic_cost.F to compute cost on each tile first and then apply
891        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
892        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
893      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
894    o eesupp/src & pkg/mdsio:
895      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
896        (from pkg/mdsio) since they are no longer used for tape IO.
897      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
898        (+ keep a copy in pkg/atm_ocn_coupler).
899    o verification/isomip:
900      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
901    o tools/build_options:
902      - optfile linux_amd64_ifort11, fast (no ieee) case:
903        to get a working restart for all experiments, add "-fp-model source"
904        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
905    
906    checkpoint64p (2013/10/20)
907    o pkg/autodiff:
908      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
909        criteria, return to simple (default) tape IO format.
910    o pkg/mdsio (+ eesupp/src):
911      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
912        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
913      - fix globalFile and singleCpuIO options using simpler global mapping.
914      - new pairs of scatter/gather vector S/R (one for each type, generated from
915        template) corresponding to simpler global mapping.
916      - adread_write.F: switch to new S/R (but leave old calls commented) and write
917        to globalFile when parameter globalFiles is set to True.
918      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
919    o pkg/autodiff:
920      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
921        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
922        missing, just add a STOP if array type do not match.
923    o pkg/exf:
924      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
925         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
926         and rename array obsSIce to exf_iceFraction.
927    o tutorial_deep_convection:
928      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
929        for now all in this exp. code dir.
930      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
931        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
932    o eesupp/src:
933      - added SINGLE_DISK_IO option because reading of parameter files on
934        very large number of processors did not work with existing set-up
935    
936    checkpoint64o (2013/09/25)
937    o pkg/atm_phys & atm_compon_interf:
938      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
939    o tools/build_options:
940      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
941        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
942        remove CPP setting (was identical to genmake2 default).
943    o pkg/gmredi & model/src: Some updating and work done on the residual model.
944      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
945      - fixed up the calculation of the eddy stress and how it is added to the
946        external forcing via taueddy_external_forcing.F
947      - at the moment, it is very experimental and only works with the variable eddy
948        diffusivity calculated in gmredi_k3d.F
949    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
950        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
951    o testreport (& tools/do_tst_2+2):
952      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
953    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
954      - remove CPP='cpp -traditional -P' (this is genmake2 default)
955      - add switch (for big setups) to use 'medium' memory-model (but leave it
956        commented out for now). Note: needed with FC 19 to compile big setups.
957    o pkg/atm_compon_interf:
958      - regroup per field origin (model & pkgs) the coupling storage routines
959         (which accumalate in time each coupling field)
960      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
961        update accordingly + simplify aim_do_physics.F
962    
963    checkpoint64n (2013/08/26)
964    o pkg/bbl:
965      - update formulation to reduce dispersion of tracer properties in bbl
966      - replaced horizontal and vertical transport parameters with velocities
967      - changes results for verification/global_with_exf.yearly
968    o verification/halfpipe_streamice:
969      - change to matrix construction; update both Fwd & AD output.
970    o verification/tutorial_tracer_adjsens:
971      - OpenAD test: switch to vector-invariant momentum since fluxform with
972        rStar causes problems with OpenAD; update output.
973  o tools:  o tools:
974    - genmake2: define a common prefix for all temp-file names ; allow to move    - genmake2: define a common prefix for all temp-file names ; move them
975      them to local /tmp disc (but commented out for now);      to local /tmp disk (but would be easy to move them back);
976    - xmakedepend: add the same switch for temp-files (but commented out).    - xmakedepend: apply the same switch for temp-files.
977  o pkg/offline:  o pkg/offline:
978    - changes for usewith rStar (NLFS): assume that we continue to provide    - changes for use with rStar (NLFS): assume that we continue to provide
979      UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid      UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
980      output files) and apply r* scaling at each time-step (function of the time      output files) and apply r* scaling at each time-step (function of the time
981      varying Eta field); use normal pickup files (needed for restart with NLFS).      varying Eta field); use normal pickup files (needed for restart with NLFS).
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