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revision 1.2044 by jmc, Mon Aug 11 20:32:15 2014 UTC revision 1.2114 by jmc, Wed Jan 14 20:49:27 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - move (from ini_forcing.F) initialisation of all arrays in header file
9        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
10        (since Nov 2012) with option selectAddFluid=1.
11    o pkg/shelfice:
12      - change units (+ document) of newly added field "shelfIceMassDynTendency"
13      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
14    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
15    o pkg/seaice: two new runtime parameters:
16      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
17        long overdue
18      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
19        parameterization of tensil stress for fast ice (does not do anything yet)
20    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
21        for LSR: move checking overlaps out of JFNK-if-block
22    o pkg/atm_phys:
23      - move copy of grid and dynamical fields out of atm_phys_driver.F into
24        new S/R ATM_PHYS_DYN2PHYS.
25      - fix level height for Linear Free-Surf case (to be consistent with
26        fixed-in-time pressure levels).
27    o pkg/mom_common (bottomdrag):
28      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
29        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
30        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
31    o pkg/shelfice (u/v_drag):
32      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
33      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
34        (now similar to shelfice_u_drag.F)
35      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
36        from mom_vecinv.F (similar to mom_fluxform calls).
37    o pkg/mom_common (bottomdrag):
38      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
39      - add options for alternative discretisation of velocity norm in quadratic
40        bottom drag: averaging of grid-cell-center KE to U.point and V.point
41        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
42        improves when averaging only the other component (e.g. vVel for U bottom
43        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
44      - add options (bottomVisc_pCell) to account for partial-cell in bottom
45        friction (no-slip BC) thus getting the true distance from the bottom;
46        off by default since this also reduces model stability (explicit bottom
47        friction). Changes produce different machine truncation with linear-drag
48        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
49        front_relax (bvp & mxl, 10 & 11 digits).
50    o model/src & mom pkgs:
51      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
52        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
53      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
54        just copy level Nr value to level Nr+1.
55    o doc:
56      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
57    o pkg/streamice:
58      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
59        SHELFICE.h: move array shelficemass to init_varia, initialise
60        from array shelficemassinit, which is set in init_fixed and
61        has option to be set from file; introduce array
62        shelficeMassDynTend array, set thru file in init_fixed
63      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
64        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
65        pkg/streamice
66      - shelfice_thermodynamics.F: call shelfice_step_icemass if
67        SHELFICEMassStepping = .true.
68      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
69    
70    checkpoint65h (2014/12/17)
71    o verification/global_ocean.90x40x15, global_ocean_ebm:
72      - update to generic controls.
73    o pkg/ctrl:
74      - ctrl_map_ini_genarr.F: test for igen>0
75      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
76      - move gentim2d part of ctrl_map_ini_genarr.F to
77        new separate routine : ctrl_map_ini_gentim2d.F
78      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
79        add time variable weights and cyclic controls (time mean,
80        seasonal cycle, etc) capabilities to gentim2d
81    o pkg/ecco:
82      - move reading of error, conversion to weights from
83        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
84    o global_oce_llc90, cs32:
85      - activte sbo.
86      - CTRL_SIZE.h : add maxCtrlProc.
87      - activate the new genctrl capabilities.
88      - update following reorganization of global_oce_input_fields.tar.gz  
89    o pkg/ctrl/ctrl_ad_diff.list:
90      - add missing ctrl_init_rec.f
91    o tools/OAD_support/keepOriginal:
92      - add ctrl_init_rec.F
93    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
94      - avoid recomputations of xx_gentim2d_dummy.
95    o momentum diagnostics:
96      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
97        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
98    o pkg/seaice/seaice_lsr.F:
99      - fix computation of BU/BV, make sure they are non-zero, only necessary
100        for cubed sphere exchanges and SEAICE_OLx/y>0.
101        This makes calling s/r fill_cs_corner_rl obsolete (removed).
102    o verification/global_ocean.cs32x15/input.seaice
103      - add test for strong implicit coupling and restricted addtive Schwarz
104        methods for LSR
105      - update results/output.seaice.txt
106    o verification/tutorial_global_oce_biogeo:
107      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
108        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
109        update output_adm,_oadm,_tlm.txt
110    o pkg/dic:
111      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
112      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
113        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
114    o verification/tutorial_global_oce_biogeo:
115      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
116        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
117        update output_adm,_oadm,_tlm.txt
118    o eesupp/src:
119      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
120        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
121    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
122      LSR (following Hutchings et al. 2004)
123      - introduce zetaZ as a global variable (requires adjustments in
124        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
125        in seaice_calc_viscosities.F
126      - new flag SEAICEuseStrImpCpl (default off)
127      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
128        momentum equations
129      - JFNK-solver (preconditioner) adjusted to allow using this method
130        (where it does not have any positive effect)
131    o pkg/seaice
132      - add overlap for restrictive additive Schwartz method also to LSR, but
133        turn it off by default (because it only seems to work for non-cubed
134        sphere/llc topologies)
135    o pkg/autodiff
136      - add extra exchanges in addummy_in_steppging also for mnc output
137    o pkg/seaice:
138      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
139        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
140    o pkg/obcs:
141      - add option to specify domain-connected piece Id along OB though files
142        (for now, only used to diagnose PhiVel; default =1 -> global correction)
143      - modify obcs_diag_balance.F to process each connected-part separately;
144        exclude OB where Id = 0 but keep the full divergence there (-> constant
145        Psi along this portion of OB and all inflow derived from grad(Phi))
146      - add example of OB-conect files in verification/so_box_biogeo/input.
147    o pkg/diagnostics:
148      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
149      a) use non zero matrix element across OB and solve for Phi 1 grid point
150         outside OB (i.e, where tracer OBCS are applied).
151      b) global imbalance of inFlow/outFlow across OB: instead of modifying
152         velocity across OB, spread it uniformly along the OB in the RHS.
153    
154    checkpoint65g (2014/11/19)
155    o pkg/diagnostcis:
156      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
157    o pkg/my82,pp81,kl10:
158      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
159        field diffKr as background diffusivity to set minimum diffusivity value.
160    o pkg/seaice:
161      - add new parameter SEAICEuseEVPrev (for revisited EVP by
162        Bouillon et al 2013)
163      - add SEAICE_evpAlpha/Beta to namelist
164      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
165        involve trivial re-ordering of divisions/multiplications that should not
166        have any effects, but ... they do change the results of lab_sea.hb87 so
167        that only 2 digits of agreement remain, in line with the general
168        instability/fragility of the evp-code. For now, I do not care and just
169        update the verification experiment
170    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
171      - remove xx_genarr2d_numsmooth etc
172      - use xx_genarr2d_preproc etc instead
173      - carry out smooth_correl2D at initialization stage rather than during
174        time stepping.
175      - get smoothOpNb from xx_gentim2d_preproc
176    o global_oce_cs32 :
177      - add test of generic ecco capabilities.
178    o pkg/exf/exf_getsurfacefluxes.F :
179      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
180    o pkg/ctrl,ecco :
181      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
182        is defined.
183    o pkg/seaice: add diagnostics for Delta (deformation parameter)
184    o model/src:
185      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
186        diffusivity (background) is specified but ignored.
187    o verification:
188      - in testreport, convert hostname to lower case for default output dir name
189    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
190    o pkg/dic: add modifications from Hajoon:
191      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
192      - light attenuation: add self-shading effect by climatological Chlorophyll
193        (read from file).
194    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
195        compiles when SEAICE_ALLOW_DYNAMICS is undefined
196    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
197        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
198        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
199        approach where CPP_OPTIONS.h includes an omnipotent
200        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
201    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
202        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
203    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
204        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
205        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
206    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
207      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
208      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
209      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
210      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
211    o pkg/ctrl,ecco,exf :
212      - remove variables associated with NON-generic costs,
213        unless ECCO_CTRL_DEPRECATED is defined.
214      - remove NON-generic NON-obcs controls,
215        unless ECCO_CTRL_DEPRECATED is defined.
216    o pkg/ctrl : added ctrl_local_params.h
217    o pkg/ecco : added ecco_local_params.h
218    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
219        experiments, which will progressively be removed once the
220        experiments are revised to use only generic controls/costs.
221    
222    checkpoint65f (2014/10/13)
223    o pkg/ctrl, ecco, seaice : minor changes in headers
224    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
225        cost function and control capabilities added since checkpoint65c.
226    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
227    o pkg/ecco: increase modularity and improve logic
228      - ecco_toolbox.F (new) : basic operations that are often used,
229        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
230        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
231      - cost_gencal.F (new) : determine filnames and records.
232      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
233      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
234        and exploit the above functions leading to more compact code.
235      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
236      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
237        using_ers, using_gfo, using_mdt is now only defined within gencost)
238    o pkg/ecco: extend generic cost capabilities
239      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
240        capabilities via gencost_preproc (+ _c,_i,_r related params),
241        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
242        gencost_outputlevel arguments to cost_generic
243      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
244        and active_read, making room for gencost_preproc to take effect.
245        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
246      - pkg/ecco/cost_generic.F :
247        compute and store misfit maks*(model-data) in localdif that is
248        then used in cost and for output, output misfit if outlev.GT.0
249      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
250        rather gencost_barfile for deciding whether to write barfile
251      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
252      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
253        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
254      - pkg/ecco/ecco_summary.F : report gencost variables
255      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
256    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
257    o pkg/ecco: internal re-organization
258      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
259        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
260        mv relevant variables definition from ecco_cost.h to ecco.h,
261        make sure gencost routines only include ecco.h)
262      - throughout : add missing CCP switches, rm unused variables,
263        and rm un-necessary CPP switches
264      - throughout gencost routines : replace modelstartdate with
265        gencost_startdate when needed
266      - cost_bp_read.F : use arguments, instead of common blocs
267        so that it can be used also by (new) cost_gencost_bpv4.F
268      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
269      - ecco_phys.F : compute etanFull
270      - ecco_readparms.F : rename using_topex as using_tpj, add
271        bpv4-grace to gencost list, initialize added parameters
272      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
273    
274    checkpoint65e (2014/09/28)
275    o pkg/obcs:
276      - replaced the just-added CPP options with run-time variables
277        (see pkg/obcs/OBCS_PARAMS.h for details)
278    o pkg/obcs:
279      - add additional CPP options for sponge boundary layers
280        (see pkg/obcs/OBCS_OPTIONS.h for details)
281    o pkg/atm_phys:
282      - implement simple (obliquity only, assuming circular planet orbit)
283        seasonal cycle for incoming insolation ; used when run-time parameter
284        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
285    o pkg/exf, pkg/ecco, pkg/ctrl:
286      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
287      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
288      - implement gentim2d for xx_tauu, xx_tauv
289    o pkg/ctrl, pkg/ecco :
290      - fix and complement the generic controls implementation
291    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
292        pkg/shelfice/shelfice_thermodynamics.F,
293        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
294        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
295      - add weight in CTRL_GET_GEN calls
296    o pkg/ctrl :
297      - ctrl_get_gen.F : add weight as input parameter, and apply
298        it directly rather than using smooth_correl2Dw (to be retired).
299      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
300    o pkg/ctrl :
301      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
302        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
303      - re-activate ctrl_summary (call in ctrl_init.F)
304    o pkg/ctrl/ctrl_cost_gen.F :
305      - fix CCP brackets, remove un-necessary myiter, mytime
306    o pkg/ecco, pkg/ctrl :
307      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
308      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
309      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
310      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
311    
312    checkpoint65d (2014/09/15)
313    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
314      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
315        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
316    o pkg/ctrl/ctrl_map_ini_genarr.F :
317      - remove compilation failure
318      - replace hard coded example
319      - use ctrl_map_ini_gen2D, 3D
320    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
321      - on/off switch based upon xx_genarr2d_weight,3d
322    o src/packages_init_variables.F :
323      - regroup pkg/estimation calls
324      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
325        (moved to ctrl_init_variables)
326    o cost/cost_init_varia.F :
327      - remove ecco_cost_init_varia
328        (moved to ecco_init_varia)
329    o ctrl/ctrl_init_variables.F :
330      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
331      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
332    o ctrl/ctrl_map_ini.F :
333      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
334        (moved to ctrl_init_variables)
335    o ctrl/ctrl_map_ini_ecco.F :
336      - remove ECCO_PHYS (mv to ecco_init_varia)
337      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
338    o ecco/ecco_ad_diff.list :
339      - add ecco_init_varia.f
340    o ecco/ecco_init_varia.F
341      - new routine
342    o pkg/streamice:
343      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
344        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
345      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
346    o pkg/generic_advdiff:
347      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
348    o pkg/exf:
349      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
350         xxg_precip capability
351      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
352    o pkg/ctrl:
353      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
354    o model/src/load_fields_driver.F :
355      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
356        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
357    o OpenAD verification experiments:
358      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
359        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
360        for now, only in pkgs used in OpenAD verification experiments.
361      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
362        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
363        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
364        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
365    o OpenAD verification tests:
366      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
367      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
368        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
369      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
370        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
371    o model/src & generic_advdiff:
372      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
373        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
374        dynamics requires valid tracer forcing only over tile interior but, for
375        some diagnostics, may need to extend it over 1 point in tile halo region.
376      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
377        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
378        setting in temp/salt/ptracer_integrate.F
379    o pkg/dic:
380      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
381        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
382        in gchem_forcing_sep.F
383    o pkg/autodiff & obcs:
384      - add storage of current OB values for U & V (was already done for T & S).
385    
386    checkpoint65c (2014/08/30)
387    o pkg/dic:
388      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
389        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
390        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
391    o verification:
392      - new experiment testing OBCS and DIC pkgs, using params & output from
393        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
394        passage: take OBCS from the last year of a 2 yrs simulation and initial
395        conditions from t=1.yr while keeping the same forcing.
396    o model/src:
397      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
398        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
399    o pkg/diagnostics (Stats-Diags):
400      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
401        a) refine region where stats are computed, excluding where arrhFac=0 ;
402        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
403        c) extend regional stats over the region edges (for U or V pt location).
404    o pkg/gchem:
405      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
406        pkg/dic is currently changing/updating ptracers values beyond the OB).
407    o verification (hs94):
408      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
409        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
410        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
411        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
412    o pkg/ptracers:
413      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
414        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
415      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
416        with AB-2 code (so that it get tested).
417    o model/src:
418      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
419        with AB-2 code (previously only available with AB-3 code).
420        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
421        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
422        there, by calling CYCLE_AB_TRACER).
423    o pkg/generic_advdiff:
424      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
425        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
426        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
427        S/R temp/salt/ptracers_integrate.F
428    o model/src & pkg/ptracers:
429      - remove common block variables gT,gS (in DYNVARS.h), except when
430         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
431      - remove common block variable gPtr.
432    o model/src & pkgs:
433      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
434         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
435         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
436         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
437      + change accordingly all calling S/R.
438      - use local temperature/salinity/ptracer tendency array (without bi,bj)
439        in S/R temp/salt/ptracers_integrate.F
440    o pkg/seaice:
441      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
442        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
443      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
444        in seaice_lsr
445      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
446        in s/r seaice_lsr_calc_coeffs
447    o pkg/mdsio:
448      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
449        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
450        too long (e.g., > MAX_LEN_FNAM/2 )
451    
452    checkpoint65b (2014/08/12)
453  o pkg/matrix:  o pkg/matrix:
454    - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP    - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
455  o model/src:  o model/src:
# Line 106  o model/src: Line 552  o model/src:
552    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
553      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
554      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
555      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
556      moist correction due to vertical advection).      correction due to vertical advection).
557    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
558      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
559      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 136  o pkg/seaice: more clean up Line 582  o pkg/seaice: more clean up
582      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
583      this experiment):      this experiment):
584      > size mitgcmuv_ad      > size mitgcmuv_ad
585      text    data        bss     dec        hex        text    data        bss     dec        hex
586      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
587      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
588      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
589      text    data        bss     dec        hex      text    data        bss     dec        hex
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