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revision 1.2008 by jmc, Fri Jun 20 13:13:37 2014 UTC revision 1.2110 by jmc, Sun Jan 4 17:13:26 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 pkg/mom_common (bottomdrag):
8      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
9        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
10        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
11    o pkg/shelfice (u/v_drag):
12      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
13      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
14        (now similar to shelfice_u_drag.F)
15      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
16        from mom_vecinv.F (similar to mom_fluxform calls).
17    o pkg/mom_common (bottomdrag):
18      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
19      - add options for alternative discretisation of velocity norm in quadratic
20        bottom drag: averaging of grid-cell-center KE to U.point and V.point
21        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
22        improves when averaging only the other component (e.g. vVel for U bottom
23        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
24      - add options (bottomVisc_pCell) to account for partial-cell in bottom
25        friction (no-slip BC) thus getting the true distance from the bottom;
26        off by default since this also reduces model stability (explicit bottom
27        friction). Changes produce different machine truncation with linear-drag
28        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
29        front_relax (bvp & mxl, 10 & 11 digits).
30    o model/src & mom pkgs:
31      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
32        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
33      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
34        just copy level Nr value to level Nr+1.
35    o doc:
36      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
37    o pkg/streamice:
38      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
39        SHELFICE.h: move array shelficemass to init_varia, initialise
40        from array shelficemassinit, which is set in init_fixed and
41        has option to be set from file; introduce array
42        shelficeMassDynTend array, set thru file in init_fixed
43      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
44        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
45        pkg/streamice
46      - shelfice_thermodynamics.F: call shelfice_step_icemass if
47        SHELFICEMassStepping = .true.
48      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
49    
50    checkpoint65h (2014/12/17)
51    o verification/global_ocean.90x40x15, global_ocean_ebm:
52      - update to generic controls.
53    o pkg/ctrl:
54      - ctrl_map_ini_genarr.F: test for igen>0
55      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
56      - move gentim2d part of ctrl_map_ini_genarr.F to
57        new separate routine : ctrl_map_ini_gentim2d.F
58      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
59        add time variable weights and cyclic controls (time mean,
60        seasonal cycle, etc) capabilities to gentim2d
61    o pkg/ecco:
62      - move reading of error, conversion to weights from
63        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
64    o global_oce_llc90, cs32:
65      - activte sbo.
66      - CTRL_SIZE.h : add maxCtrlProc.
67      - activate the new genctrl capabilities.
68      - update following reorganization of global_oce_input_fields.tar.gz  
69    o pkg/ctrl/ctrl_ad_diff.list:
70      - add missing ctrl_init_rec.f
71    o tools/OAD_support/keepOriginal:
72      - add ctrl_init_rec.F
73    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
74      - avoid recomputations of xx_gentim2d_dummy.
75    o momentum diagnostics:
76      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
77        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
78    o pkg/seaice/seaice_lsr.F:
79      - fix computation of BU/BV, make sure they are non-zero, only necessary
80        for cubed sphere exchanges and SEAICE_OLx/y>0.
81        This makes calling s/r fill_cs_corner_rl obsolete (removed).
82    o verification/global_ocean.cs32x15/input.seaice
83      - add test for strong implicit coupling and restricted addtive Schwarz
84        methods for LSR
85      - update results/output.seaice.txt
86    o verification/tutorial_global_oce_biogeo:
87      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
88        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
89        update output_adm,_oadm,_tlm.txt
90    o pkg/dic:
91      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
92      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
93        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
94    o verification/tutorial_global_oce_biogeo:
95      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
96        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
97        update output_adm,_oadm,_tlm.txt
98    o eesupp/src:
99      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
100        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
101    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
102      LSR (following Hutchings et al. 2004)
103      - introduce zetaZ as a global variable (requires adjustments in
104        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
105        in seaice_calc_viscosities.F
106      - new flag SEAICEuseStrImpCpl (default off)
107      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
108        momentum equations
109      - JFNK-solver (preconditioner) adjusted to allow using this method
110        (where it does not have any positive effect)
111    o pkg/seaice
112      - add overlap for restrictive additive Schwartz method also to LSR, but
113        turn it off by default (because it only seems to work for non-cubed
114        sphere/llc topologies)
115    o pkg/autodiff
116      - add extra exchanges in addummy_in_steppging also for mnc output
117    o pkg/seaice:
118      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
119        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
120    o pkg/obcs:
121      - add option to specify domain-connected piece Id along OB though files
122        (for now, only used to diagnose PhiVel; default =1 -> global correction)
123      - modify obcs_diag_balance.F to process each connected-part separately;
124        exclude OB where Id = 0 but keep the full divergence there (-> constant
125        Psi along this portion of OB and all inflow derived from grad(Phi))
126      - add example of OB-conect files in verification/so_box_biogeo/input.
127    o pkg/diagnostics:
128      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
129      a) use non zero matrix element across OB and solve for Phi 1 grid point
130         outside OB (i.e, where tracer OBCS are applied).
131      b) global imbalance of inFlow/outFlow across OB: instead of modifying
132         velocity across OB, spread it uniformly along the OB in the RHS.
133    
134    checkpoint65g (2014/11/19)
135    o pkg/diagnostcis:
136      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
137    o pkg/my82,pp81,kl10:
138      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
139        field diffKr as background diffusivity to set minimum diffusivity value.
140    o pkg/seaice:
141      - add new parameter SEAICEuseEVPrev (for revisited EVP by
142        Bouillon et al 2013)
143      - add SEAICE_evpAlpha/Beta to namelist
144      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
145        involve trivial re-ordering of divisions/multiplications that should not
146        have any effects, but ... they do change the results of lab_sea.hb87 so
147        that only 2 digits of agreement remain, in line with the general
148        instability/fragility of the evp-code. For now, I do not care and just
149        update the verification experiment
150    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
151      - remove xx_genarr2d_numsmooth etc
152      - use xx_genarr2d_preproc etc instead
153      - carry out smooth_correl2D at initialization stage rather than during
154        time stepping.
155      - get smoothOpNb from xx_gentim2d_preproc
156    o global_oce_cs32 :
157      - add test of generic ecco capabilities.
158    o pkg/exf/exf_getsurfacefluxes.F :
159      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
160    o pkg/ctrl,ecco :
161      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
162        is defined.
163    o pkg/seaice: add diagnostics for Delta (deformation parameter)
164    o model/src:
165      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
166        diffusivity (background) is specified but ignored.
167    o verification:
168      - in testreport, convert hostname to lower case for default output dir name
169    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
170    o pkg/dic: add modifications from Hajoon:
171      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
172      - light attenuation: add self-shading effect by climatological Chlorophyll
173        (read from file).
174    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
175        compiles when SEAICE_ALLOW_DYNAMICS is undefined
176    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
177        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
178        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
179        approach where CPP_OPTIONS.h includes an omnipotent
180        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
181    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
182        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
183    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
184        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
185        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
186    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
187      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
188      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
189      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
190      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
191    o pkg/ctrl,ecco,exf :
192      - remove variables associated with NON-generic costs,
193        unless ECCO_CTRL_DEPRECATED is defined.
194      - remove NON-generic NON-obcs controls,
195        unless ECCO_CTRL_DEPRECATED is defined.
196    o pkg/ctrl : added ctrl_local_params.h
197    o pkg/ecco : added ecco_local_params.h
198    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
199        experiments, which will progressively be removed once the
200        experiments are revised to use only generic controls/costs.
201    
202    checkpoint65f (2014/10/13)
203    o pkg/ctrl, ecco, seaice : minor changes in headers
204    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
205        cost function and control capabilities added since checkpoint65c.
206    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
207    o pkg/ecco: increase modularity and improve logic
208      - ecco_toolbox.F (new) : basic operations that are often used,
209        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
210        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
211      - cost_gencal.F (new) : determine filnames and records.
212      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
213      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
214        and exploit the above functions leading to more compact code.
215      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
216      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
217        using_ers, using_gfo, using_mdt is now only defined within gencost)
218    o pkg/ecco: extend generic cost capabilities
219      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
220        capabilities via gencost_preproc (+ _c,_i,_r related params),
221        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
222        gencost_outputlevel arguments to cost_generic
223      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
224        and active_read, making room for gencost_preproc to take effect.
225        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
226      - pkg/ecco/cost_generic.F :
227        compute and store misfit maks*(model-data) in localdif that is
228        then used in cost and for output, output misfit if outlev.GT.0
229      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
230        rather gencost_barfile for deciding whether to write barfile
231      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
232      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
233        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
234      - pkg/ecco/ecco_summary.F : report gencost variables
235      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
236    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
237    o pkg/ecco: internal re-organization
238      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
239        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
240        mv relevant variables definition from ecco_cost.h to ecco.h,
241        make sure gencost routines only include ecco.h)
242      - throughout : add missing CCP switches, rm unused variables,
243        and rm un-necessary CPP switches
244      - throughout gencost routines : replace modelstartdate with
245        gencost_startdate when needed
246      - cost_bp_read.F : use arguments, instead of common blocs
247        so that it can be used also by (new) cost_gencost_bpv4.F
248      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
249      - ecco_phys.F : compute etanFull
250      - ecco_readparms.F : rename using_topex as using_tpj, add
251        bpv4-grace to gencost list, initialize added parameters
252      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
253    
254    checkpoint65e (2014/09/28)
255    o pkg/obcs:
256      - replaced the just-added CPP options with run-time variables
257        (see pkg/obcs/OBCS_PARAMS.h for details)
258    o pkg/obcs:
259      - add additional CPP options for sponge boundary layers
260        (see pkg/obcs/OBCS_OPTIONS.h for details)
261    o pkg/atm_phys:
262      - implement simple (obliquity only, assuming circular planet orbit)
263        seasonal cycle for incoming insolation ; used when run-time parameter
264        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
265    o pkg/exf, pkg/ecco, pkg/ctrl:
266      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
267      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
268      - implement gentim2d for xx_tauu, xx_tauv
269    o pkg/ctrl, pkg/ecco :
270      - fix and complement the generic controls implementation
271    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
272        pkg/shelfice/shelfice_thermodynamics.F,
273        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
274        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
275      - add weight in CTRL_GET_GEN calls
276    o pkg/ctrl :
277      - ctrl_get_gen.F : add weight as input parameter, and apply
278        it directly rather than using smooth_correl2Dw (to be retired).
279      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
280    o pkg/ctrl :
281      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
282        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
283      - re-activate ctrl_summary (call in ctrl_init.F)
284    o pkg/ctrl/ctrl_cost_gen.F :
285      - fix CCP brackets, remove un-necessary myiter, mytime
286    o pkg/ecco, pkg/ctrl :
287      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
288      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
289      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
290      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
291    
292    checkpoint65d (2014/09/15)
293    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
294      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
295        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
296    o pkg/ctrl/ctrl_map_ini_genarr.F :
297      - remove compilation failure
298      - replace hard coded example
299      - use ctrl_map_ini_gen2D, 3D
300    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
301      - on/off switch based upon xx_genarr2d_weight,3d
302    o src/packages_init_variables.F :
303      - regroup pkg/estimation calls
304      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
305        (moved to ctrl_init_variables)
306    o cost/cost_init_varia.F :
307      - remove ecco_cost_init_varia
308        (moved to ecco_init_varia)
309    o ctrl/ctrl_init_variables.F :
310      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
311      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
312    o ctrl/ctrl_map_ini.F :
313      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
314        (moved to ctrl_init_variables)
315    o ctrl/ctrl_map_ini_ecco.F :
316      - remove ECCO_PHYS (mv to ecco_init_varia)
317      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
318    o ecco/ecco_ad_diff.list :
319      - add ecco_init_varia.f
320    o ecco/ecco_init_varia.F
321      - new routine
322    o pkg/streamice:
323      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
324        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
325      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
326    o pkg/generic_advdiff:
327      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
328    o pkg/exf:
329      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
330         xxg_precip capability
331      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
332    o pkg/ctrl:
333      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
334    o model/src/load_fields_driver.F :
335      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
336        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
337    o OpenAD verification experiments:
338      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
339        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
340        for now, only in pkgs used in OpenAD verification experiments.
341      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
342        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
343        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
344        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
345    o OpenAD verification tests:
346      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
347      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
348        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
349      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
350        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
351    o model/src & generic_advdiff:
352      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
353        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
354        dynamics requires valid tracer forcing only over tile interior but, for
355        some diagnostics, may need to extend it over 1 point in tile halo region.
356      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
357        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
358        setting in temp/salt/ptracer_integrate.F
359    o pkg/dic:
360      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
361        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
362        in gchem_forcing_sep.F
363    o pkg/autodiff & obcs:
364      - add storage of current OB values for U & V (was already done for T & S).
365    
366    checkpoint65c (2014/08/30)
367    o pkg/dic:
368      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
369        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
370        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
371    o verification:
372      - new experiment testing OBCS and DIC pkgs, using params & output from
373        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
374        passage: take OBCS from the last year of a 2 yrs simulation and initial
375        conditions from t=1.yr while keeping the same forcing.
376    o model/src:
377      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
378        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
379    o pkg/diagnostics (Stats-Diags):
380      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
381        a) refine region where stats are computed, excluding where arrhFac=0 ;
382        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
383        c) extend regional stats over the region edges (for U or V pt location).
384    o pkg/gchem:
385      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
386        pkg/dic is currently changing/updating ptracers values beyond the OB).
387    o verification (hs94):
388      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
389        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
390        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
391        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
392    o pkg/ptracers:
393      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
394        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
395      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
396        with AB-2 code (so that it get tested).
397    o model/src:
398      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
399        with AB-2 code (previously only available with AB-3 code).
400        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
401        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
402        there, by calling CYCLE_AB_TRACER).
403    o pkg/generic_advdiff:
404      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
405        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
406        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
407        S/R temp/salt/ptracers_integrate.F
408    o model/src & pkg/ptracers:
409      - remove common block variables gT,gS (in DYNVARS.h), except when
410         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
411      - remove common block variable gPtr.
412    o model/src & pkgs:
413      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
414         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
415         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
416         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
417      + change accordingly all calling S/R.
418      - use local temperature/salinity/ptracer tendency array (without bi,bj)
419        in S/R temp/salt/ptracers_integrate.F
420    o pkg/seaice:
421      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
422        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
423      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
424        in seaice_lsr
425      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
426        in s/r seaice_lsr_calc_coeffs
427    o pkg/mdsio:
428      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
429        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
430        too long (e.g., > MAX_LEN_FNAM/2 )
431    
432    checkpoint65b (2014/08/12)
433    o pkg/matrix:
434      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
435    o model/src:
436      - fix initialisation of geothermalFile; compile geothermal-flux code in
437        natl_box verification experiment.
438    o model/src & pkg/down_slope:
439      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
440      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
441        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
442        results at machine truncation level: update output of experiments
443        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
444    o pkg/diagnostics (Stats-Diags):
445      - do not cumulate the full volume when DIAGNOSTICS_FILL is
446        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
447        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
448        times (but Min,Max and StD are still wrong).
449    o model/src:
450      - add geothermal flux forcing: read in ini_forcing.F as time-constant
451        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
452    o model/src:
453      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
454        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
455        arrays are already updated while adjustments (filters, conv.adjustment) are
456        still applied later, in S/R TRACERS_CORRECTION_STEP.
457    o model/src:
458      - store in common bloc array "rhoInSitu" the virtual potential temperature
459        anomaly that is used to compute geopotential: this make the atmos code
460        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
461    o pkg/seaice/seaice_lsr.F
462      - rename integer variable ilcall to ipass (that's what it is called
463        in the residual diagnostics
464      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
465        default) for improved non-linear convergence of the first few steps
466      - adjust a few comments and add new ones to explain some of the store
467        directives
468    o pkg/generic_advdiff (& ptracers):
469      - re-work the code to check for valid advection scheme and for minimum
470        size of overlap (now stored in local common bloc in gad_advscheme.F)
471    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
472      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
473      - add an auxilliary variable "bet" and fix store directives and keys in
474        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
475        less exact gradients in my tests); but there are still
476        recomputation warning (although gradients are sort of OK), when
477        SEAICE_LSR_VECTORIZE is not defined, so this flag and
478        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
479      - update verification experiments lab_sea.
480      - change some comments in S/R seaice_calc_viscosities
481    o model/src:
482      - if staggerTimeStep=T, always apply exchange to velocity field in
483        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
484        (independent of using multi-dim advection or not); no effect on FWD run
485        but affects AD results (at machine truncation level): update output of
486        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
487        and isomip (oad: 12.d).
488    o pkg/generic_advdiff:
489      - stop if doAB_onGtGs is set to FALSE but ignored
490      - refine warning related to stability of tracer time-stepping
491        regarding internal wave dynamics.
492      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
493        on staggerTimeStep & implicitIntGravWave (will now get a warning
494        if potentially unstable).
495    o pkg/kl10:
496      - add new pkg "kl10" for mixing due to internal wave breaking, from
497        http://www.sciencedirect.com/science/article/pii/S1463500310000144
498        (contribution from Jody Klymak), tested in verification experiment
499        verification/internal_wave/input.kl10/
500    o isomip experiment:
501      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
502        (input.htd) and update the output.
503    o cd_code experiments:
504      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
505        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
506        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
507        update the corresponding output.
508    o pkg/seaice:
509      - reduce the number of include files and store directives in
510        S/R seaice_lsr_tridiagu/v
511      - change the order of loops in one case in S/R seaice_lsr_tridiagv
512        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
513        get rid off one store directive (a TAF bug?)
514      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
515        S/R seaice_lsr_tridiagv to change the loop range for consistency
516      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
517      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
518        S/R seaice_lsr_tridiagu/v (requires update of
519        offline_exf_seaice/input.dyn_jfnk)
520    
521    checkpoint65a (2014/07/27)
522    o model/src:
523      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
524        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
525        (topo in p-coords, ice-shelf in z-coords); update output of experiments
526        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
527    o model/src:
528      - collect momentum forcing tendency into local 2-D array (passed as argument
529        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
530        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
531        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
532      - collect T & S forcing tendency into local 2-D array (passed as argument to
533        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
534        affects results at machine truncation level (e.g., ocean: if using
535        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
536        correction due to vertical advection).
537      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
538        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
539        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
540        obcs_ctrl (ad & fwd grd @ 12 & 7).
541    o pkg/ptracers & diagnostics:
542      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
543        title (to avoid some unexpected truncation); sort out ptracers diags units.
544      - collect ptracer forcing tendency into local 2-D array (passed as argument
545        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
546    
547    checkpoint65 (2014/07/18)
548    o pkg/fizhi:
549      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
550        affects results at machine truncation level. Update output of experiments
551        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
552    o pkg/seaice: more clean up
553      - rename TAF common block tapes to be more consistent and remove
554        unnecessary duplicates
555      - add store directives to remove more recomputations, but use smaller
556        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
557        The idea behind this flag is to reduce the memory footprint when the
558        adjoint of the LSR is not required. As of now, defining the flag
559        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
560        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
561        For experiment offline_exf_seaice, this means on a linux box with gfortran
562        nearly a factor of 10 (but keep in mind there is mostly seaice code in
563        this experiment):
564        > size mitgcmuv_ad
565        text    data        bss     dec        hex
566        5100659 1216  220458952  225560827  d71c8fb
567        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
568        but only a moderate increase of 36% for global_ocean.cs32x15:
569        text    data        bss     dec        hex
570        6695027 1648 1014578664 1021275339 3cdf6ccb
571        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
572      - note: there are still recomputations in global_ocean.cs32x15 and
573        offline_exf_seaice and the gradient agreement changes (gets a
574        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
575      - in general, the AD gradients still are wrong
576    o OpenAD
577      - clean up code_oad/ directories somewhat by moving files
578        dontCompile, dontTransform, keepOriginal to OAD_support/
579    o model/src:
580      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
581        (not currently tested): add dissipation terms before NLFS rescaling of
582        tendencies (previously done after).
583    o pkg/diagnostics:
584      - write stats-diags in ascii file with more digits (same as in monitor).
585    o pkg/down_slope:
586      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
587        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
588    o model/src:
589      - new file "apply_forcing.F" containing all the code previously in
590        external_forcing.F, but with new argument list: pass, as new argument,
591        the current level tendency array to update (instead of a direct update
592        of the common bloc array). Change the corresponding calls.
593      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
594        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
595    o pkg/seaice/seaice_lsr, a little bit of clean up
596      - rearrange some code blocks, so that now all calculations for
597        setting up the right-hand-sides done within one single block
598        (I find that easier to read and understand)
599      - rearrange freedrift-code to reduce the number of ifdefs
600      - adjust some indentations and comments
601    
602    checkpoint64z (2014/07/10)
603    o model/src and several pkgs:
604      - change argument list of all S/R called from external_forcing.F and
605        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
606        to pass, as argument, the current level tendency array to update
607        (instead of a direct update of the common bloc array).
608      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
609      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
610    o pkg/seaice/seaice_lsr.F
611      - always initialize local arrays in seaice_lsr_tridiagu/v
612      - add more local tapes to seaice_lsr_tridiagu/v
613      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
614        keep it in bi/bj loop; this seems to be essential
615      - gradients are still wrong but only by 4-7 orders of magnitude
616        instead of 15 orders of magnitude, lab_sea improves a little
617    o pkg/seaice
618      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
619        generates unnecessary code in seaice_lsr_ad
620      - add more store directives in seaice_lsr to avoid unnecessary code
621        in seaice_lsr_ad
622      - exclude some residual computations in seaice_lsr when
623        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
624        in seaice_lsr_ad
625      - add more storing, a new tape (model/src/the_main_loop.F) and
626        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
627        and klockey should be checked by a specialist)
628      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
629        and update lab_sea after previous changes in pkg/seaice below
630    o pkg/autodiff:
631      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
632        viscFacInAd : run time parameters allowing for adjoint switches
633        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
634    o pkg/ecco:
635      - introduce cost_gencost_boxmean.F that computes a box mean
636        temperature (for use in adjoint sensitivity studies).
637    o model/src/set_defaults.F : initialize viscFacAdj to 1.
638    o pkg/mom_common/mom_calc_visc.F:
639      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
640    o pkg/seaice/seaice_summary.F:
641      - statement for SEAICEadjMODE now in autodiff_readparms.F
642    o pkg/seaice:
643      - remove some store directives and add new ones in an effort to get
644        finally rid off the recomputation warnings. This is successful
645        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
646        defined (i.e. no extensive recomputation warnings left), but there
647        are still too many recomputations on the solver iteration level
648      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
649      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
650        SEAICE_SIZE.h
651      - add a store directive in S/R seaice_calc_viscosities
652    o pkg/seaice (ITD code):
653      - fix definition of Hlimit for multi-threaded case
654      - use double precision arithmetic to compute Hlimit: this affects results;
655        update output of experiment seaice_itd.
656    o replace content of verification/seaice_itd
657      - instead of a 1D column use the configuration of offline_exf_seaice
658        to test the ice thickness distribution code with ridging
659      - this is a first shot at this experiment
660      - change of some defaults of ridging parameters SEAICEhStar (from
661        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
662        and lot of new comments.
663    
664  checkpoint64y (2014/06/20)  checkpoint64y (2014/06/20)
665  o pkg/seaice/seaice_reg_ridge.F:  o pkg/seaice/seaice_reg_ridge.F:
666    - modify the regularization of very small volumes of ice; only check    - modify the regularization of very small volumes of ice; only check
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