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revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.2091 by mlosch, Mon Nov 17 09:44:26 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 : add generic pre-processing (xx_genarr2d_preproc etc)
8      - remove xx_genarr2d_numsmooth etc
9      - use xx_genarr2d_preproc etc instead
10      - carry out smooth_correl2D at initialization
11      stage rather than during time stepping.
12      - get smoothOpNb from xx_gentim2d_preproc
13    o global_oce_cs32 :
14      - add test of generic ecco capabilities.
15    o pkg/exf/exf_getsurfacefluxes.F :
16      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
17    o pkg/ctrl,ecco :
18      -  omit un-necessary arguments to ctrl_cost_gen.F
19      unless ECCO_CTRL_DEPRECATED is defined.
20    o pkg/seaice: add diagnostics for Delta (deformation parameter)
21    o model/src:
22      - when ALLOW_3D_DIFFKR is defined, add a STOP if any of the vertical
23        diffusivity (background) is specified but ignored.
24    o verification:
25      - in testreport, convert hostname to lower case for default output dir name
26    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
27    o pkg/dic: add modifications from Hajoon:
28      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
29      - light attenuation: add self-shading effect by climatological Chlorophyll
30        (read from file).
31    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
32        compiles when SEAICE_ALLOW_DYNAMICS is undefined
33    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
34        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
35        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
36        approach where CPP_OPTIONS.h includes an omnipotent
37        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
38    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
39        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
40    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
41        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
42        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
43    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
44      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
45      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
46      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
47      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
48    o pkg/ctrl,ecco,exf :
49      - remove variables associated with NON-generic costs,
50        unless ECCO_CTRL_DEPRECATED is defined.
51      - remove NON-generic NON-obcs controls,
52        unless ECCO_CTRL_DEPRECATED is defined.
53    o pkg/ctrl : added ctrl_local_params.h
54    o pkg/ecco : added ecco_local_params.h
55    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
56        experiments, which will progressively be removed once the
57        experiments are revised to use only generic controls/costs.
58    
59    checkpoint65f (2014/10/13)
60    o pkg/ctrl, ecco, seaice : minor changes in headers
61    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
62        cost function and control capabilities added since checkpoint65c.
63    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
64    o pkg/ecco: increase modularity and improve logic
65      - ecco_toolbox.F (new) : basic operations that are often used,
66        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
67        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
68      - cost_gencal.F (new) : determine filnames and records.
69      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
70      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
71        and exploit the above functions leading to more compact code.
72      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
73      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
74        using_ers, using_gfo, using_mdt is now only defined within gencost)
75    o pkg/ecco: extend generic cost capabilities
76      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
77        capabilities via gencost_preproc (+ _c,_i,_r related params),
78        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
79        gencost_outputlevel arguments to cost_generic
80      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
81        and active_read, making room for gencost_preproc to take effect.
82        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
83      - pkg/ecco/cost_generic.F :
84        compute and store misfit maks*(model-data) in localdif that is
85        then used in cost and for output, output misfit if outlev.GT.0
86      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
87        rather gencost_barfile for deciding whether to write barfile
88      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
89      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
90        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
91      - pkg/ecco/ecco_summary.F : report gencost variables
92      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
93    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
94    o pkg/ecco: internal re-organization
95      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
96        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
97        mv relevant variables definition from ecco_cost.h to ecco.h,
98        make sure gencost routines only include ecco.h)
99      - throughout : add missing CCP switches, rm unused variables,
100        and rm un-necessary CPP switches
101      - throughout gencost routines : replace modelstartdate with
102        gencost_startdate when needed
103      - cost_bp_read.F : use arguments, instead of common blocs
104        so that it can be used also by (new) cost_gencost_bpv4.F
105      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
106      - ecco_phys.F : compute etanFull
107      - ecco_readparms.F : rename using_topex as using_tpj, add
108        bpv4-grace to gencost list, initialize added parameters
109      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
110    
111    checkpoint65e (2014/09/28)
112    o pkg/obcs:
113      - replaced the just-added CPP options with run-time variables
114        (see pkg/obcs/OBCS_PARAMS.h for details)
115    o pkg/obcs:
116      - add additional CPP options for sponge boundary layers
117        (see pkg/obcs/OBCS_OPTIONS.h for details)
118    o pkg/atm_phys:
119      - implement simple (obliquity only, assuming circular planet orbit)
120        seasonal cycle for incoming insolation ; used when run-time parameter
121        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
122    o pkg/exf, pkg/ecco, pkg/ctrl:
123      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
124      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
125      - implement gentim2d for xx_tauu, xx_tauv
126    o pkg/ctrl, pkg/ecco :
127      - fix and complement the generic controls implementation
128    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
129        pkg/shelfice/shelfice_thermodynamics.F,
130        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
131        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
132      - add weight in CTRL_GET_GEN calls
133    o pkg/ctrl :
134      - ctrl_get_gen.F : add weight as input parameter, and apply
135        it directly rather than using smooth_correl2Dw (to be retired).
136      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
137    o pkg/ctrl :
138      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
139        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
140      - re-activate ctrl_summary (call in ctrl_init.F)
141    o pkg/ctrl/ctrl_cost_gen.F :
142      - fix CCP brackets, remove un-necessary myiter, mytime
143    o pkg/ecco, pkg/ctrl :
144      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
145      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
146      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
147      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
148    
149    checkpoint65d (2014/09/15)
150    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
151      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
152        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
153    o pkg/ctrl/ctrl_map_ini_genarr.F :
154      - remove compilation failure
155      - replace hard coded example
156      - use ctrl_map_ini_gen2D, 3D
157    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
158      - on/off switch based upon xx_genarr2d_weight,3d
159    o src/packages_init_variables.F :
160      - regroup pkg/estimation calls
161      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
162        (moved to ctrl_init_variables)
163    o cost/cost_init_varia.F :
164      - remove ecco_cost_init_varia
165        (moved to ecco_init_varia)
166    o ctrl/ctrl_init_variables.F :
167      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
168      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
169    o ctrl/ctrl_map_ini.F :
170      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
171        (moved to ctrl_init_variables)
172    o ctrl/ctrl_map_ini_ecco.F :
173      - remove ECCO_PHYS (mv to ecco_init_varia)
174      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
175    o ecco/ecco_ad_diff.list :
176      - add ecco_init_varia.f
177    o ecco/ecco_init_varia.F
178      - new routine
179    o pkg/streamice:
180      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
181        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
182      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
183    o pkg/generic_advdiff:
184      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
185    o pkg/exf:
186      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
187         xxg_precip capability
188      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
189    o pkg/ctrl:
190      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
191    o model/src/load_fields_driver.F :
192      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
193        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
194    o OpenAD verification experiments:
195      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
196        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
197        for now, only in pkgs used in OpenAD verification experiments.
198      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
199        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
200        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
201        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
202    o OpenAD verification tests:
203      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
204      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
205        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
206      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
207        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
208    o model/src & generic_advdiff:
209      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
210        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
211        dynamics requires valid tracer forcing only over tile interior but, for
212        some diagnostics, may need to extend it over 1 point in tile halo region.
213      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
214        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
215        setting in temp/salt/ptracer_integrate.F
216    o pkg/dic:
217      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
218        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
219        in gchem_forcing_sep.F
220    o pkg/autodiff & obcs:
221      - add storage of current OB values for U & V (was already done for T & S).
222    
223    checkpoint65c (2014/08/30)
224    o pkg/dic:
225      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
226        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
227        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
228    o verification:
229      - new experiment testing OBCS and DIC pkgs, using params & output from
230        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
231        passage: take OBCS from the last year of a 2 yrs simulation and initial
232        conditions from t=1.yr while keeping the same forcing.
233    o model/src:
234      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
235        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
236    o pkg/diagnostics (Stats-Diags):
237      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
238        a) refine region where stats are computed, excluding where arrhFac=0 ;
239        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
240        c) extend regional stats over the region edges (for U or V pt location).
241    o pkg/gchem:
242      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
243        pkg/dic is currently changing/updating ptracers values beyond the OB).
244    o verification (hs94):
245      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
246        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
247        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
248        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
249    o pkg/ptracers:
250      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
251        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
252      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
253        with AB-2 code (so that it get tested).
254    o model/src:
255      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
256        with AB-2 code (previously only available with AB-3 code).
257        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
258        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
259        there, by calling CYCLE_AB_TRACER).
260    o pkg/generic_advdiff:
261      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
262        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
263        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
264        S/R temp/salt/ptracers_integrate.F
265    o model/src & pkg/ptracers:
266      - remove common block variables gT,gS (in DYNVARS.h), except when
267         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
268      - remove common block variable gPtr.
269    o model/src & pkgs:
270      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
271         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
272         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
273         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
274      + change accordingly all calling S/R.
275      - use local temperature/salinity/ptracer tendency array (without bi,bj)
276        in S/R temp/salt/ptracers_integrate.F
277    o pkg/seaice:
278      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
279        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
280      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
281        in seaice_lsr
282      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
283        in s/r seaice_lsr_calc_coeffs
284    o pkg/mdsio:
285      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
286        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
287        too long (e.g., > MAX_LEN_FNAM/2 )
288    
289    checkpoint65b (2014/08/12)
290    o pkg/matrix:
291      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
292    o model/src:
293      - fix initialisation of geothermalFile; compile geothermal-flux code in
294        natl_box verification experiment.
295    o model/src & pkg/down_slope:
296      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
297      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
298        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
299        results at machine truncation level: update output of experiments
300        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
301    o pkg/diagnostics (Stats-Diags):
302      - do not cumulate the full volume when DIAGNOSTICS_FILL is
303        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
304        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
305        times (but Min,Max and StD are still wrong).
306    o model/src:
307      - add geothermal flux forcing: read in ini_forcing.F as time-constant
308        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
309    o model/src:
310      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
311        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
312        arrays are already updated while adjustments (filters, conv.adjustment) are
313        still applied later, in S/R TRACERS_CORRECTION_STEP.
314    o model/src:
315      - store in common bloc array "rhoInSitu" the virtual potential temperature
316        anomaly that is used to compute geopotential: this make the atmos code
317        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
318    o pkg/seaice/seaice_lsr.F
319      - rename integer variable ilcall to ipass (that's what it is called
320        in the residual diagnostics
321      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
322        default) for improved non-linear convergence of the first few steps
323      - adjust a few comments and add new ones to explain some of the store
324        directives
325    o pkg/generic_advdiff (& ptracers):
326      - re-work the code to check for valid advection scheme and for minimum
327        size of overlap (now stored in local common bloc in gad_advscheme.F)
328    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
329      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
330      - add an auxilliary variable "bet" and fix store directives and keys in
331        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
332        less exact gradients in my tests); but there are still
333        recomputation warning (although gradients are sort of OK), when
334        SEAICE_LSR_VECTORIZE is not defined, so this flag and
335        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
336      - update verification experiments lab_sea.
337      - change some comments in S/R seaice_calc_viscosities
338    o model/src:
339      - if staggerTimeStep=T, always apply exchange to velocity field in
340        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
341        (independent of using multi-dim advection or not); no effect on FWD run
342        but affects AD results (at machine truncation level): update output of
343        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
344        and isomip (oad: 12.d).
345    o pkg/generic_advdiff:
346      - stop if doAB_onGtGs is set to FALSE but ignored
347      - refine warning related to stability of tracer time-stepping
348        regarding internal wave dynamics.
349      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
350        on staggerTimeStep & implicitIntGravWave (will now get a warning
351        if potentially unstable).
352    o pkg/kl10:
353      - add new pkg "kl10" for mixing due to internal wave breaking, from
354        http://www.sciencedirect.com/science/article/pii/S1463500310000144
355        (contribution from Jody Klymak), tested in verification experiment
356        verification/internal_wave/input.kl10/
357    o isomip experiment:
358      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
359        (input.htd) and update the output.
360    o cd_code experiments:
361      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
362        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
363        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
364        update the corresponding output.
365    o pkg/seaice:
366      - reduce the number of include files and store directives in
367        S/R seaice_lsr_tridiagu/v
368      - change the order of loops in one case in S/R seaice_lsr_tridiagv
369        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
370        get rid off one store directive (a TAF bug?)
371      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
372        S/R seaice_lsr_tridiagv to change the loop range for consistency
373      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
374      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
375        S/R seaice_lsr_tridiagu/v (requires update of
376        offline_exf_seaice/input.dyn_jfnk)
377    
378    checkpoint65a (2014/07/27)
379    o model/src:
380      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
381        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
382        (topo in p-coords, ice-shelf in z-coords); update output of experiments
383        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
384    o model/src:
385      - collect momentum forcing tendency into local 2-D array (passed as argument
386        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
387        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
388        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
389      - collect T & S forcing tendency into local 2-D array (passed as argument to
390        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
391        affects results at machine truncation level (e.g., ocean: if using
392        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
393        correction due to vertical advection).
394      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
395        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
396        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
397        obcs_ctrl (ad & fwd grd @ 12 & 7).
398    o pkg/ptracers & diagnostics:
399      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
400        title (to avoid some unexpected truncation); sort out ptracers diags units.
401      - collect ptracer forcing tendency into local 2-D array (passed as argument
402        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
403    
404    checkpoint65 (2014/07/18)
405    o pkg/fizhi:
406      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
407        affects results at machine truncation level. Update output of experiments
408        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
409    o pkg/seaice: more clean up
410      - rename TAF common block tapes to be more consistent and remove
411        unnecessary duplicates
412      - add store directives to remove more recomputations, but use smaller
413        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
414        The idea behind this flag is to reduce the memory footprint when the
415        adjoint of the LSR is not required. As of now, defining the flag
416        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
417        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
418        For experiment offline_exf_seaice, this means on a linux box with gfortran
419        nearly a factor of 10 (but keep in mind there is mostly seaice code in
420        this experiment):
421        > size mitgcmuv_ad
422        text    data        bss     dec        hex  
423        5100659 1216  220458952  225560827  d71c8fb
424        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
425        but only a moderate increase of 36% for global_ocean.cs32x15:
426        text    data        bss     dec        hex
427        6695027 1648 1014578664 1021275339 3cdf6ccb
428        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
429      - note: there are still recomputations in global_ocean.cs32x15 and
430        offline_exf_seaice and the gradient agreement changes (gets a
431        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
432      - in general, the AD gradients still are wrong
433    o OpenAD
434      - clean up code_oad/ directories somewhat by moving files
435        dontCompile, dontTransform, keepOriginal to OAD_support/
436    o model/src:
437      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
438        (not currently tested): add dissipation terms before NLFS rescaling of
439        tendencies (previously done after).
440    o pkg/diagnostics:
441      - write stats-diags in ascii file with more digits (same as in monitor).
442    o pkg/down_slope:
443      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
444        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
445    o model/src:
446      - new file "apply_forcing.F" containing all the code previously in
447        external_forcing.F, but with new argument list: pass, as new argument,
448        the current level tendency array to update (instead of a direct update
449        of the common bloc array). Change the corresponding calls.
450      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
451        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
452    o pkg/seaice/seaice_lsr, a little bit of clean up
453      - rearrange some code blocks, so that now all calculations for
454        setting up the right-hand-sides done within one single block
455        (I find that easier to read and understand)
456      - rearrange freedrift-code to reduce the number of ifdefs
457      - adjust some indentations and comments
458    
459    checkpoint64z (2014/07/10)
460    o model/src and several pkgs:
461      - change argument list of all S/R called from external_forcing.F and
462        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
463        to pass, as argument, the current level tendency array to update
464        (instead of a direct update of the common bloc array).
465      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
466      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
467    o pkg/seaice/seaice_lsr.F
468      - always initialize local arrays in seaice_lsr_tridiagu/v
469      - add more local tapes to seaice_lsr_tridiagu/v
470      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
471        keep it in bi/bj loop; this seems to be essential
472      - gradients are still wrong but only by 4-7 orders of magnitude
473        instead of 15 orders of magnitude, lab_sea improves a little
474    o pkg/seaice
475      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
476        generates unnecessary code in seaice_lsr_ad
477      - add more store directives in seaice_lsr to avoid unnecessary code
478        in seaice_lsr_ad
479      - exclude some residual computations in seaice_lsr when
480        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
481        in seaice_lsr_ad
482      - add more storing, a new tape (model/src/the_main_loop.F) and
483        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
484        and klockey should be checked by a specialist)
485      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
486        and update lab_sea after previous changes in pkg/seaice below
487    o pkg/autodiff:
488      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
489        viscFacInAd : run time parameters allowing for adjoint switches
490        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
491    o pkg/ecco:
492      - introduce cost_gencost_boxmean.F that computes a box mean
493        temperature (for use in adjoint sensitivity studies).
494    o model/src/set_defaults.F : initialize viscFacAdj to 1.
495    o pkg/mom_common/mom_calc_visc.F:
496      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
497    o pkg/seaice/seaice_summary.F:
498      - statement for SEAICEadjMODE now in autodiff_readparms.F
499    o pkg/seaice:
500      - remove some store directives and add new ones in an effort to get
501        finally rid off the recomputation warnings. This is successful
502        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
503        defined (i.e. no extensive recomputation warnings left), but there
504        are still too many recomputations on the solver iteration level
505      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
506      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
507        SEAICE_SIZE.h
508      - add a store directive in S/R seaice_calc_viscosities
509    o pkg/seaice (ITD code):
510      - fix definition of Hlimit for multi-threaded case
511      - use double precision arithmetic to compute Hlimit: this affects results;
512        update output of experiment seaice_itd.
513    o replace content of verification/seaice_itd
514      - instead of a 1D column use the configuration of offline_exf_seaice
515        to test the ice thickness distribution code with ridging
516      - this is a first shot at this experiment
517      - change of some defaults of ridging parameters SEAICEhStar (from
518        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
519        and lot of new comments.
520    
521    checkpoint64y (2014/06/20)
522    o pkg/seaice/seaice_reg_ridge.F:
523      - modify the regularization of very small volumes of ice; only check
524        total volume HEFF, and do not apply correction to individual ice
525        classes because that leads to funny patterns in the heat and fw-fluxes
526        into the ocean. Adjust seaice_itd/results/output.txt
527      - replace nITD by SEAICE_multDim in loop-ranges
528    o pkg/exf:
529      - add code to process the case field period = -12. with UV interpolation.
530      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
531        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
532    o verification/global_with_exf:
533      - switch all fields period to -12. (was previously untested) in input/data.exf
534        (but keep secondary test ".yearly" unchanged); update the reference output.
535    o pkg/cal:
536      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
537    o pkg/exf:
538      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
539        to replace logical switch "exf_verbose"
540      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
541    o pkg/sbo:
542      - update from Katherine Quinn: evaluate mass directly from density and SSH
543        (budget using Finite Volume method) instead of from bottom pressure.
544      - allow testreport to collect few selected SBO output ; tested in exp.
545        global_ocean.90x40x15 (after updating the results, to include SBO output).
546      - fix some multi-threading issues (in output part).
547    o model/src & most packages:
548      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
549      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
550        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
551        "data.{pkg}" exist ; and leave the S/R (return) just after.
552      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
553        + call LAND_READPARMS from packages_readparms.F
554    o pkg/seaice:
555      - remove code that resets useThSice in S/R seaice_readparms and
556        replace it by a warning in S/R seaice_check
557      - remove parameter MULTDIM, replace with nITD and runtime
558        parameter SEAICE_multDim (still hard-wired to nITD if
559        SEAICE_ITD is defined)
560    
561    checkpoint64x (2014/05/24)
562    o verification/lab_sea:
563      - update adjoint and TLM output following changes to pkg/salt_plume
564      - un-do the update after putting back local recip_Cp in few places.
565    o pkg/salt_plume: modifications by An Nguyen:
566      - add capability to do brine rejection (salt-plume) as function of
567        volume+tracers (instead of only salinity tracer).
568      - conserve volume by exchanging volume from each kLev to above to
569        accommodate in-coming brine volume
570      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
571      - switch KPP surf buoyancy due to brine forcing to 3-d
572        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
573      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
574      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
575        in East/West Arctic.
576    o pkg/sbo:
577      - incorporate modifications from Katherine Quinn to enable the use of sbo
578        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
579        output for future testreport verification (unfinished).
580    o pkg/atm_phys:
581      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
582        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
583        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
584    o pkg/seaice
585      seaice_calc_ice_strength.F: modify expression to avoid divisions
586        (affects truncation)
587      seaice_do_ridging.F: clean up the insectarium
588      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
589      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
590      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
591      - add some debugging information and error messages (warnings)
592    o model/src: modifications relatd to atmosphere p*:
593      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
594      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
595        of vertical profile tRef in geopotential background and anomaly.
596      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
597        and pkg/atm_phys.
598      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
599        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
600    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
601    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
602        not used right now, but can be used in BGC packages to fix conservation.
603    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
604        other packages too.
605    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
606        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
607    o model/src:
608      - since we have several heat capacity (even in model/src), define "recip_Cp"
609        as local variable (no longer in common block) to avoid any confusion.
610      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
611    o pkg/exf:
612      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
613        air density as function of air Temp, Humidity and atm pressure.
614    
615    checkpoint64w (2014/05/02)
616    o verification:
617      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
618        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
619        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
620        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
621        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
622    o model/src: for atmosphere in p* coords:
623      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
624      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
625        but not yet activated.
626    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
627      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
628      - this changes the results (but not for any verification experiment, because
629        none tests this), but avoids having an extra field in the restart files
630    o pkg/seaice: remove global variable TICE (not needed)
631      - replace by TICES or local variable where necessary (cost_seaice_test,
632        seaice_diagnostics_state)
633      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
634      - use specific read/write routines for reading and writing individual leves
635        of a multilevel field
636    o pkg/ctrl & model/inc:
637      - move additional anomaly fields of control vars (related to options:
638         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
639        from DYNVARS.h into new header file: CTRL_FIELDS.h
640    o pkg/seaice: some small modifications to the ridging code
641      - make fw2ObyRidge a global variable and add the freshwater flux to
642        seaice_growth
643      - pass actual thickness from seaice_prepare_ridging, so that it is
644        computed only in one place and compute it in the same way as in
645        seaice_growth
646      - initialise more fields in seaice_do_ridging that where cause floating
647        point exceptions over land
648    o pkg/seaice: preparations for ridging code and first real ridging code
649      - move most of "PART 1" of S/R seaice_growth into a new and separate
650        S/R seaice_reg_ridge that will both regularize the state variable after
651        advection call the actual ridging routine;
652      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
653        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
654      - remove ridging code from seaice_advdiff
655      - clean up remaining part 1 of seaice_growth in an attempt to make it
656        more readable (this is probably subjective)
657      - call seaice_itd_redist once in the initialisation phase to have the initial
658        conditions in the correct category
659      - finally: add new ridging routine for ITD code
660    
661    checkpoint64v (2014/04/11)
662    o pkg/ecco:
663      - add runtime parameters mdt[start,end]date[1,2]
664      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
665    o pkg/seaice:
666      - make deltaC a global variable, so that it can be used in ridging code
667      - first step towards ridging: introduce new routines that compute
668        ice strength based on ridging parameters
669      - add diagnostic for HSNOWITD
670      - add opnWtrFrac as a global variable (required for ridging scheme)
671    o pkg/salt_plume + pkg/seaice/seaice_growth.F
672      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
673        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
674    o verification/hs94.1x64x5:
675      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
676      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
677    o autodiff:
678      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
679        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
680        For now, only in pkgs used in verification/hs94.1x64x5.
681      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
682        which are specific to TAF/TAMC).
683      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
684        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
685        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
686      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
687        building mitgcmuv_ad (make adAll).
688    o pkg/ecco:
689      - cost_gencost_seaicev4.F:
690         reformulate proxy cost as function of sst and local param SEAICE_freeze
691         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
692      - add stop statement if old names siv4-[sst,vol] are used
693      - add snapshots + cost reports for atmospheric longwave
694      - remove factor 0.1 in front of wtau[u,v]
695      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
696         ALLOW_TMI_SST_COST_CONTRIBUTION
697    o pkg/atm_phys:
698      - add some diagnostics for Short-wave and for convection S/R.
699    o pkg/seaice/seaice_growth:
700      - fix a bug in the lateral melt parameterization for SEAICE_ITD
701        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
702      - rearrange loop order for better vector code in the same code block
703      - rewrite the floeDiameter formula to have fewer divisions
704      -  (miraculously) none of this changes the results of seaice_itd
705    o pkg/smooth:
706      - move param smooth2Ddiffnbt to pkg/ecco
707    o pkg/salt_plume:
708      - salt_plume_frac.F:
709         clean up local param names
710         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
711    o pkg/rw:
712      - add RS version of S/R READ_MFLDS_LEV.
713    o pkg/streamice:
714      - fix the restart test by writing/reading pickup_streamice files.
715    o pkg/seaice:
716      - refine checks for jfnk-related parameters
717      - comment out if statement with SEAICEuseIMEX parameter as long as there
718        is no IMEX code to avoid confusion and surprises
719    
720    checkpoint64u (2014/03/07)
721    o verification/MLAdjust:
722      - rename secondary test suffix:
723         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
724         0.leithD -> AhFlxF  + switch to flux-form
725         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
726         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
727    o pkg/mom_vecinv:
728      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
729        to be before mom_calc_visc.F)
730      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
731      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
732        this is simpler for the adjoint and for diagnostics.
733    o model/src + pkg/momentum:
734      - add input files for  2-D additional Western and Southern cell-edge wall
735         (e.g., to add "thin-wall" where it is =1).
736      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
737        using 2nd hFacZ that is computed from initial (fix domain) hFac
738      - known limitations of thin wall implementation: not yet coded for sigma
739        coords; not working with CD-scheme neither.
740    o pkg/seaice:
741      - rename recently introduced parameters from (wrong name) AB to
742        BDF (backward difference time discretisation)
743      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
744    o tools/adjoint_options:
745      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
746    
747    checkpoint64t (2014/02/01)
748    o pkg/ecco
749      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
750        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
751      - replace hard-coded record number and period which only work for monthly
752        with read-in runtime param that works for other periods (month,day,year)
753    o pkg/thsice
754      - corrected store directive fixes thsice adjoint gradient checks
755    o genmake2 & testreport:
756      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
757        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
758        Update testreport accordingly. No need to set "export OPENAD=true"
759        in adjoint_options/adjoint_oad anymore (will be removed later).
760    o pkg/shelfice:
761      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
762        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
763        so that surface forcing applies to k=kSurf if using pkg/shelfice.
764    o pkg/ctrl, pkg/grdchk, pkg/ecco:
765      - Changes to make GENARR more modular (i.e. invisible if not used)
766    o model/src/temp_integrate.F and salt_integrate.F
767      - re-include store directives that were removed on Dec 27th.
768    o model/src/external_forcing_surf.F
769      - add storage directives for EmPmR and PmEpR to avoid recomputation of
770        seaice_model in the adjoint that is problematic when seaice_model is
771        turned off in the adjoint. The resolved issue dated back to July when
772        EXTERNAL_FORCING_SURF call was moved.
773        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
774    o pkg/exf/exf_check.F
775      - fix a small bug again (originally found by Wentao Liu, now found again)
776      - streamline error output
777    o pkg/streamice and aim_v23:
778      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
779        Apple's /usr/bin/cpp knows what to do:
780        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
781        Target: x86_64-apple-darwin13.0.0
782    
783    checkpoint64s (2014/01/05)
784    o tools/adjoint_options:
785      - switch to fastopt.net TAF server (instead of default fastopt.de) for
786        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
787    o model/src:
788      - remove some unnecessary TAF storage directives in forward_step.F and
789        in dynamics.F (note: not always removed by TAF, e.g., double storage
790        of kappaRU,kappaRV in former version of dynamics.F).
791    o model/src & pkg/ptracers:
792      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
793        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
794        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
795      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
796      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
797      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
798    o useSingleCpuInput separates single-CPU input from single-CPU output;
799        for now only implemented for in exf_interp_read.F
800    o verification/advect_xy:
801      - fix missing EXCH call in local version of ini_salt.F and update output.
802    o momentum diagnostics:
803      - fix which deltaT is used in Total-Tendency diagnostics.
804      - fix typo in diagnostics for momentum tendency from AB.
805    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
806        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
807    
808    checkpoint64r (2013/12/08)
809    o verification/*/results:
810      - Update reference output of experiments that were passing with just 13 digits
811         (make it easier to detect future changes in results)
812    o model/src & pkg/ptracers:
813      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
814        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
815        to inside ptracers_integrate.F ; remove ptracers_advection.F
816    o coupling interface pkgs:
817        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
818      - change the config check to test the agreement of Ocean Depth
819        with ATM land/sea mask (instead of ATM orography);
820      - send to coupler the number of coupler time-steps to do for this run:
821        this allows to check for consistency and don't need anymore to be
822        specified in parameter file "data";
823      in coupler:
824      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
825      - improve report to log-file of config setting (pass log-file unit to few S/R)
826    o pkg/compon_communic:
827      - add coupling send/receive for non-tiled integer vector;
828      - add S/R to check and stop if any proc has an error (similar to
829        eesupp/src/stop_if_error.F but single thread and across Comm_World).
830    o pkg/exch2:
831      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
832        through list of all tiles my proc owns.
833    o model/src:
834      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
835        from rTrans) to simplify dependencies (no need to store rTrans anymore in
836        calling S/R); this affects AD results at machine truncation level:
837        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
838        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
839    o tools/build_options:
840      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
841    o coupling interface pkgs:
842        [compon_communic, atm_compon_interf & ocn_compon_interf]
843      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
844        to each S/R that needs it; remove un-used variables.
845      - change component tile registration (cpl_register.F in both compon_interf
846        and mitcomponent_tile_register.F) to pass the full list of tiles
847        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
848      - with pkg/exch2: adopt the same convention used for I/O to define mapping
849        towards coupler global array (unless W2_useE2ioLayOut=F):
850         a) can now use different tiling between atm & ocn comp.
851         b) no needs to modify the run-Off map when changing tiling (was needed
852            even if using the same tiling between atm & ocn).
853         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
854            full land tiles); not yet tested.
855      - check for valid mapping from comp. tile to coupler global array
856      - improve report of tile registration results to log file.
857    o pkg/exch2:
858      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
859        tile-registration (CPL_REGISTER);
860      - activate (un-comment) definition and setting of "W2_tileIndex" list to
861        store the local bi,bj indices of each tile;
862      - also print bi,bj in local report to log file;
863      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
864        Jun 2009 modif of pkg/exch2).
865    o testing on baudelaire:
866      - run 2 tests at a time: no significant slow down (since enough cpu) and
867        get the full set of test done earlier
868      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
869    o model/src/thermodynamics.F and routines called from it:
870      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
871        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
872        velocity (outp) by adding bolus velocity.
873      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
874        mass transport from velocity + lateral grid cell area
875      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
876      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
877     in thermodynamics.F
878      - remove k from thermodynamics.F and move it to temp_integrate.F
879        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
880        loop).
881      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
882        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
883        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
884        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
885      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
886        global_ocean.90x40x15, tutorial_global_oce_biogeo and
887        tutorial_tracer_adjsens (+ TLM output).
888    o tools/OAD_support and (verification/*/) code_oad:
889      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
890        module conversion ; remove unneeded CPP_EEOPTIONS.h.
891      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
892        version (closer to model/inc/CPP_OPTIONS.h).
893    o model/src:
894      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
895        retired list of parameters (routine FREEZE has been replace by surface
896        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
897    o pkg/gmredi:
898      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
899        velocity (same scheme but affects machine truncation) for GM_AdvForm.
900      - update output of FWD experiments: front_relax.bvp,
901        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
902    
903    checkpoint64q (2013/11/17)
904    o verification:
905      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
906        tutorial_global_oce_biogeo and global_ocean.90x40x15.
907      - generate new output (growth & melt) for seaice_itd experiment after
908        updating the input pickup_seaice files (previously wrong).
909    o pkg/cost:
910      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
911        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
912        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
913          cannot be applied to var in common block).
914        o allows to get results independent of tile-per-proc setting (if using
915          slower GLOBAL_SUM_SEND_RECV option).
916      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
917        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
918        forward gradients: update output).
919      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
920        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
921    o pkg/mom_common:
922      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
923        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
924        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
925        ensure that all field value that are used are set.
926    o tutorial_deep_convection (smag3d):
927      - add missing scaling in mom_calc_smag_3d.F;
928      - set smag3D_coeff in input.smag3d such that results do not change.
929    o pkg/dic:
930      - change dic_cost.F to compute cost on each tile first and then apply
931        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
932        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
933      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
934    o eesupp/src & pkg/mdsio:
935      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
936        (from pkg/mdsio) since they are no longer used for tape IO.
937      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
938        (+ keep a copy in pkg/atm_ocn_coupler).
939    o verification/isomip:
940      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
941    o tools/build_options:
942      - optfile linux_amd64_ifort11, fast (no ieee) case:
943        to get a working restart for all experiments, add "-fp-model source"
944        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
945    
946    checkpoint64p (2013/10/20)
947    o pkg/autodiff:
948      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
949        criteria, return to simple (default) tape IO format.
950    o pkg/mdsio (+ eesupp/src):
951      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
952        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
953      - fix globalFile and singleCpuIO options using simpler global mapping.
954      - new pairs of scatter/gather vector S/R (one for each type, generated from
955        template) corresponding to simpler global mapping.
956      - adread_write.F: switch to new S/R (but leave old calls commented) and write
957        to globalFile when parameter globalFiles is set to True.
958      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
959    o pkg/autodiff:
960      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
961        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
962        missing, just add a STOP if array type do not match.
963    o pkg/exf:
964      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
965         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
966         and rename array obsSIce to exf_iceFraction.
967    o tutorial_deep_convection:
968      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
969        for now all in this exp. code dir.
970      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
971        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
972    o eesupp/src:
973      - added SINGLE_DISK_IO option because reading of parameter files on
974        very large number of processors did not work with existing set-up
975    
976    checkpoint64o (2013/09/25)
977    o pkg/atm_phys & atm_compon_interf:
978      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
979    o tools/build_options:
980      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
981        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
982        remove CPP setting (was identical to genmake2 default).
983    o pkg/gmredi & model/src: Some updating and work done on the residual model.
984      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
985      - fixed up the calculation of the eddy stress and how it is added to the
986        external forcing via taueddy_external_forcing.F
987      - at the moment, it is very experimental and only works with the variable eddy
988        diffusivity calculated in gmredi_k3d.F
989    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
990        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
991    o testreport (& tools/do_tst_2+2):
992      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
993    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
994      - remove CPP='cpp -traditional -P' (this is genmake2 default)
995      - add switch (for big setups) to use 'medium' memory-model (but leave it
996        commented out for now). Note: needed with FC 19 to compile big setups.
997    o pkg/atm_compon_interf:
998      - regroup per field origin (model & pkgs) the coupling storage routines
999         (which accumalate in time each coupling field)
1000      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
1001        update accordingly + simplify aim_do_physics.F
1002    
1003    checkpoint64n (2013/08/26)
1004    o pkg/bbl:
1005      - update formulation to reduce dispersion of tracer properties in bbl
1006      - replaced horizontal and vertical transport parameters with velocities
1007      - changes results for verification/global_with_exf.yearly
1008    o verification/halfpipe_streamice:
1009      - change to matrix construction; update both Fwd & AD output.
1010    o verification/tutorial_tracer_adjsens:
1011      - OpenAD test: switch to vector-invariant momentum since fluxform with
1012        rStar causes problems with OpenAD; update output.
1013    o tools:
1014      - genmake2: define a common prefix for all temp-file names ; move them
1015        to local /tmp disk (but would be easy to move them back);
1016      - xmakedepend: apply the same switch for temp-files.
1017    o pkg/offline:
1018      - changes for use with rStar (NLFS): assume that we continue to provide
1019        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
1020        output files) and apply r* scaling at each time-step (function of the time
1021        varying Eta field); use normal pickup files (needed for restart with NLFS).
1022    o adjoint with OpenAD:
1023      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
1024        package openad.  This package has to be compiled for all runs with OpenAD
1025        instead of specifying code_oad_all as a modification directory.
1026      - link the fortran templates from tools/OAD_support to the build directory
1027        for preprocessing to avoid conflicts between different setups compiled
1028        simultaneously and simplify cleanup.
1029    o pkg/exf:
1030      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
1031        main model or other pkgs are exchanged in EXF_MAPFIELDS).
1032    o model/src:
1033      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
1034        (similar to do_fields_blocking_exchanges.F).
1035    o tools/genmake2:
1036      - remove TAF output src code just before calling staf (when not doing a fresh
1037        built, will stop if things go wrong with staf).
1038      - fix target "adobj" (left from TAF version-2 transition)
1039    o pkg/diagnostics:
1040      - add a parameter to track the status of pkg/diagnostics activation;
1041        this replace/extend the use of logical param "settingDiags" (to check
1042        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
1043        New S/R to print error message and stop when pkgStatus is not right.
1044      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
1045    
1046    checkpoint64m (2013/08/13)
1047    o model/inc:
1048      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
1049        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
1050    o pkg/kpp & aim_v23:
1051      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1052    o pkg/seaice:
1053      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
1054        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
1055      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1056    o eesupp/src:
1057      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
1058        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1059    o switch to TAF version-2:
1060      - add flow directives to "freeze" naming convention for ad-routines that
1061        are used in I/O routines of adjoint state and associated common blocks
1062        that are used in adcommon.h (backward compatible with version-1)
1063      - update all ad-optfiles (in tools/adjoint_options + few local to some
1064        verification exp) to switch to latest TAF version (currently 2.5.5);
1065        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1066        out except for diva).
1067      - the major change with TAF version-2 is that both the differentiated
1068        routines and the forward routines (new) are returned as part of the TAF
1069        output source code. Update genmake2 accordingly.
1070      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1071        with version-2 when compared to TLM or FWD gradient); other experiments
1072        output show minor changes (machine truncation level); update the few AD &
1073        TLM output with 12 matching digits only (some prior to version-2 switch).
1074    
1075    checkpoint64l (2013/08/05)
1076    o model/src:
1077      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1078      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1079        when using TAF but only if using OpenAD.
1080    o pkg/mom_common+fluxform+vecinv:
1081      - always set horiz. viscosity arrays to background value before calling
1082        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1083        only when using variable horiz. viscosity (useVariableVisc=T);
1084      - simplify mom_vecinv.F (only 1 block for momViscosity).
1085    o pkg/mom_common: variable horiz. viscosity in NH code
1086      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1087        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1088      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1089        useBiharmonicVisc & useVariableVisc.
1090      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1091        in calc_gw.F, version 1.27, 2006/06/20):
1092        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1093        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1094      - change background horiz viscosity in vertical momentum (gW) to always be
1095        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1096        any type of variable viscosity, e.g., viscAh/4Grid)
1097      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1098        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1099        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1100        default viscAh,viscA4 is zero).
1101    o model/src:
1102      - extend length of drC & recip_drC from Nr to Nr+1.
1103  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
1104    - genmake2: do not create local ./mpi_headers dir when no file to copy into.    - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1105    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
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