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revision 1.2040 by jmc, Wed Aug 6 23:19:25 2014 UTC revision 1.2118 by jmc, Fri Jan 23 14:51:49 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65i (2015/01/23)
8    o model/src:
9      - change units of frictionHeating field from W to W/m^2
10      - fix bug in frictional heating from stratospheric drag in
11        S/R ATM_PHYS_TENDENCY_APPLY_V
12      - with synchronous time-stepping: move resetting to zero of frictionHeating
13        field from load_fields_driver.F to thermodynamics.F ;
14      - add diagnostics for frictional heating.
15    o model/src & gmredi K3D:
16      - add frictionHeating field to pickup-files (for synchronous time-stepping)
17      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
18      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
19        and name in pickup file).
20      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
21    o model/src:
22      - move (from ini_forcing.F) initialisation of all arrays in header file
23        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
24        (since Nov 2012) with option selectAddFluid=1.
25    o pkg/shelfice:
26      - change units (+ document) of newly added field "shelfIceMassDynTendency"
27      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
28    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
29    o pkg/seaice: two new runtime parameters:
30      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
31        long overdue
32      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
33        parameterization of tensil stress for fast ice (does not do anything yet)
34    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
35        for LSR: move checking overlaps out of JFNK-if-block
36    o pkg/atm_phys:
37      - move copy of grid and dynamical fields out of atm_phys_driver.F into
38        new S/R ATM_PHYS_DYN2PHYS.
39      - fix level height for Linear Free-Surf case (to be consistent with
40        fixed-in-time pressure levels).
41    o pkg/mom_common (bottomdrag):
42      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
43        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
44        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
45    o pkg/shelfice (u/v_drag):
46      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
47      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
48        (now similar to shelfice_u_drag.F)
49      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
50        from mom_vecinv.F (similar to mom_fluxform calls).
51    o pkg/mom_common (bottomdrag):
52      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
53      - add options for alternative discretisation of velocity norm in quadratic
54        bottom drag: averaging of grid-cell-center KE to U.point and V.point
55        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
56        improves when averaging only the other component (e.g. vVel for U bottom
57        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
58      - add options (bottomVisc_pCell) to account for partial-cell in bottom
59        friction (no-slip BC) thus getting the true distance from the bottom;
60        off by default since this also reduces model stability (explicit bottom
61        friction). Changes produce different machine truncation with linear-drag
62        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
63        front_relax (bvp & mxl, 10 & 11 digits).
64    o model/src & mom pkgs:
65      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
66        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
67      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
68        just copy level Nr value to level Nr+1.
69    o doc:
70      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
71    o pkg/streamice:
72      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
73        SHELFICE.h: move array shelficemass to init_varia, initialise
74        from array shelficemassinit, which is set in init_fixed and
75        has option to be set from file; introduce array
76        shelficeMassDynTend array, set thru file in init_fixed
77      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
78        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
79        pkg/streamice
80      - shelfice_thermodynamics.F: call shelfice_step_icemass if
81        SHELFICEMassStepping = .true.
82      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
83    
84    checkpoint65h (2014/12/17)
85    o verification/global_ocean.90x40x15, global_ocean_ebm:
86      - update to generic controls.
87    o pkg/ctrl:
88      - ctrl_map_ini_genarr.F: test for igen>0
89      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
90      - move gentim2d part of ctrl_map_ini_genarr.F to
91        new separate routine : ctrl_map_ini_gentim2d.F
92      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
93        add time variable weights and cyclic controls (time mean,
94        seasonal cycle, etc) capabilities to gentim2d
95    o pkg/ecco:
96      - move reading of error, conversion to weights from
97        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
98    o global_oce_llc90, cs32:
99      - activte sbo.
100      - CTRL_SIZE.h : add maxCtrlProc.
101      - activate the new genctrl capabilities.
102      - update following reorganization of global_oce_input_fields.tar.gz  
103    o pkg/ctrl/ctrl_ad_diff.list:
104      - add missing ctrl_init_rec.f
105    o tools/OAD_support/keepOriginal:
106      - add ctrl_init_rec.F
107    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
108      - avoid recomputations of xx_gentim2d_dummy.
109    o momentum diagnostics:
110      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
111        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
112    o pkg/seaice/seaice_lsr.F:
113      - fix computation of BU/BV, make sure they are non-zero, only necessary
114        for cubed sphere exchanges and SEAICE_OLx/y>0.
115        This makes calling s/r fill_cs_corner_rl obsolete (removed).
116    o verification/global_ocean.cs32x15/input.seaice
117      - add test for strong implicit coupling and restricted addtive Schwarz
118        methods for LSR
119      - update results/output.seaice.txt
120    o verification/tutorial_global_oce_biogeo:
121      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
122        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
123        update output_adm,_oadm,_tlm.txt
124    o pkg/dic:
125      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
126      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
127        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
128    o verification/tutorial_global_oce_biogeo:
129      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
130        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
131        update output_adm,_oadm,_tlm.txt
132    o eesupp/src:
133      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
134        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
135    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
136      LSR (following Hutchings et al. 2004)
137      - introduce zetaZ as a global variable (requires adjustments in
138        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
139        in seaice_calc_viscosities.F
140      - new flag SEAICEuseStrImpCpl (default off)
141      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
142        momentum equations
143      - JFNK-solver (preconditioner) adjusted to allow using this method
144        (where it does not have any positive effect)
145    o pkg/seaice
146      - add overlap for restrictive additive Schwartz method also to LSR, but
147        turn it off by default (because it only seems to work for non-cubed
148        sphere/llc topologies)
149    o pkg/autodiff
150      - add extra exchanges in addummy_in_steppging also for mnc output
151    o pkg/seaice:
152      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
153        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
154    o pkg/obcs:
155      - add option to specify domain-connected piece Id along OB though files
156        (for now, only used to diagnose PhiVel; default =1 -> global correction)
157      - modify obcs_diag_balance.F to process each connected-part separately;
158        exclude OB where Id = 0 but keep the full divergence there (-> constant
159        Psi along this portion of OB and all inflow derived from grad(Phi))
160      - add example of OB-conect files in verification/so_box_biogeo/input.
161    o pkg/diagnostics:
162      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
163      a) use non zero matrix element across OB and solve for Phi 1 grid point
164         outside OB (i.e, where tracer OBCS are applied).
165      b) global imbalance of inFlow/outFlow across OB: instead of modifying
166         velocity across OB, spread it uniformly along the OB in the RHS.
167    
168    checkpoint65g (2014/11/19)
169    o pkg/diagnostcis:
170      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
171    o pkg/my82,pp81,kl10:
172      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
173        field diffKr as background diffusivity to set minimum diffusivity value.
174    o pkg/seaice:
175      - add new parameter SEAICEuseEVPrev (for revisited EVP by
176        Bouillon et al 2013)
177      - add SEAICE_evpAlpha/Beta to namelist
178      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
179        involve trivial re-ordering of divisions/multiplications that should not
180        have any effects, but ... they do change the results of lab_sea.hb87 so
181        that only 2 digits of agreement remain, in line with the general
182        instability/fragility of the evp-code. For now, I do not care and just
183        update the verification experiment
184    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
185      - remove xx_genarr2d_numsmooth etc
186      - use xx_genarr2d_preproc etc instead
187      - carry out smooth_correl2D at initialization stage rather than during
188        time stepping.
189      - get smoothOpNb from xx_gentim2d_preproc
190    o global_oce_cs32 :
191      - add test of generic ecco capabilities.
192    o pkg/exf/exf_getsurfacefluxes.F :
193      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
194    o pkg/ctrl,ecco :
195      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
196        is defined.
197    o pkg/seaice: add diagnostics for Delta (deformation parameter)
198    o model/src:
199      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
200        diffusivity (background) is specified but ignored.
201    o verification:
202      - in testreport, convert hostname to lower case for default output dir name
203    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
204    o pkg/dic: add modifications from Hajoon:
205      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
206      - light attenuation: add self-shading effect by climatological Chlorophyll
207        (read from file).
208    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
209        compiles when SEAICE_ALLOW_DYNAMICS is undefined
210    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
211        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
212        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
213        approach where CPP_OPTIONS.h includes an omnipotent
214        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
215    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
216        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
217    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
218        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
219        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
220    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
221      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
222      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
223      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
224      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
225    o pkg/ctrl,ecco,exf :
226      - remove variables associated with NON-generic costs,
227        unless ECCO_CTRL_DEPRECATED is defined.
228      - remove NON-generic NON-obcs controls,
229        unless ECCO_CTRL_DEPRECATED is defined.
230    o pkg/ctrl : added ctrl_local_params.h
231    o pkg/ecco : added ecco_local_params.h
232    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
233        experiments, which will progressively be removed once the
234        experiments are revised to use only generic controls/costs.
235    
236    checkpoint65f (2014/10/13)
237    o pkg/ctrl, ecco, seaice : minor changes in headers
238    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
239        cost function and control capabilities added since checkpoint65c.
240    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
241    o pkg/ecco: increase modularity and improve logic
242      - ecco_toolbox.F (new) : basic operations that are often used,
243        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
244        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
245      - cost_gencal.F (new) : determine filnames and records.
246      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
247      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
248        and exploit the above functions leading to more compact code.
249      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
250      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
251        using_ers, using_gfo, using_mdt is now only defined within gencost)
252    o pkg/ecco: extend generic cost capabilities
253      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
254        capabilities via gencost_preproc (+ _c,_i,_r related params),
255        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
256        gencost_outputlevel arguments to cost_generic
257      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
258        and active_read, making room for gencost_preproc to take effect.
259        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
260      - pkg/ecco/cost_generic.F :
261        compute and store misfit maks*(model-data) in localdif that is
262        then used in cost and for output, output misfit if outlev.GT.0
263      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
264        rather gencost_barfile for deciding whether to write barfile
265      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
266      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
267        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
268      - pkg/ecco/ecco_summary.F : report gencost variables
269      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
270    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
271    o pkg/ecco: internal re-organization
272      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
273        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
274        mv relevant variables definition from ecco_cost.h to ecco.h,
275        make sure gencost routines only include ecco.h)
276      - throughout : add missing CCP switches, rm unused variables,
277        and rm un-necessary CPP switches
278      - throughout gencost routines : replace modelstartdate with
279        gencost_startdate when needed
280      - cost_bp_read.F : use arguments, instead of common blocs
281        so that it can be used also by (new) cost_gencost_bpv4.F
282      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
283      - ecco_phys.F : compute etanFull
284      - ecco_readparms.F : rename using_topex as using_tpj, add
285        bpv4-grace to gencost list, initialize added parameters
286      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
287    
288    checkpoint65e (2014/09/28)
289    o pkg/obcs:
290      - replaced the just-added CPP options with run-time variables
291        (see pkg/obcs/OBCS_PARAMS.h for details)
292    o pkg/obcs:
293      - add additional CPP options for sponge boundary layers
294        (see pkg/obcs/OBCS_OPTIONS.h for details)
295    o pkg/atm_phys:
296      - implement simple (obliquity only, assuming circular planet orbit)
297        seasonal cycle for incoming insolation ; used when run-time parameter
298        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
299    o pkg/exf, pkg/ecco, pkg/ctrl:
300      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
301      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
302      - implement gentim2d for xx_tauu, xx_tauv
303    o pkg/ctrl, pkg/ecco :
304      - fix and complement the generic controls implementation
305    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
306        pkg/shelfice/shelfice_thermodynamics.F,
307        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
308        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
309      - add weight in CTRL_GET_GEN calls
310    o pkg/ctrl :
311      - ctrl_get_gen.F : add weight as input parameter, and apply
312        it directly rather than using smooth_correl2Dw (to be retired).
313      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
314    o pkg/ctrl :
315      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
316        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
317      - re-activate ctrl_summary (call in ctrl_init.F)
318    o pkg/ctrl/ctrl_cost_gen.F :
319      - fix CCP brackets, remove un-necessary myiter, mytime
320    o pkg/ecco, pkg/ctrl :
321      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
322      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
323      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
324      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
325    
326    checkpoint65d (2014/09/15)
327    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
328      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
329        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
330    o pkg/ctrl/ctrl_map_ini_genarr.F :
331      - remove compilation failure
332      - replace hard coded example
333      - use ctrl_map_ini_gen2D, 3D
334    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
335      - on/off switch based upon xx_genarr2d_weight,3d
336    o src/packages_init_variables.F :
337      - regroup pkg/estimation calls
338      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
339        (moved to ctrl_init_variables)
340    o cost/cost_init_varia.F :
341      - remove ecco_cost_init_varia
342        (moved to ecco_init_varia)
343    o ctrl/ctrl_init_variables.F :
344      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
345      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
346    o ctrl/ctrl_map_ini.F :
347      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
348        (moved to ctrl_init_variables)
349    o ctrl/ctrl_map_ini_ecco.F :
350      - remove ECCO_PHYS (mv to ecco_init_varia)
351      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
352    o ecco/ecco_ad_diff.list :
353      - add ecco_init_varia.f
354    o ecco/ecco_init_varia.F
355      - new routine
356    o pkg/streamice:
357      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
358        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
359      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
360    o pkg/generic_advdiff:
361      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
362    o pkg/exf:
363      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
364         xxg_precip capability
365      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
366    o pkg/ctrl:
367      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
368    o model/src/load_fields_driver.F :
369      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
370        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
371    o OpenAD verification experiments:
372      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
373        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
374        for now, only in pkgs used in OpenAD verification experiments.
375      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
376        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
377        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
378        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
379    o OpenAD verification tests:
380      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
381      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
382        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
383      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
384        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
385    o model/src & generic_advdiff:
386      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
387        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
388        dynamics requires valid tracer forcing only over tile interior but, for
389        some diagnostics, may need to extend it over 1 point in tile halo region.
390      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
391        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
392        setting in temp/salt/ptracer_integrate.F
393    o pkg/dic:
394      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
395        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
396        in gchem_forcing_sep.F
397    o pkg/autodiff & obcs:
398      - add storage of current OB values for U & V (was already done for T & S).
399    
400    checkpoint65c (2014/08/30)
401    o pkg/dic:
402      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
403        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
404        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
405    o verification:
406      - new experiment testing OBCS and DIC pkgs, using params & output from
407        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
408        passage: take OBCS from the last year of a 2 yrs simulation and initial
409        conditions from t=1.yr while keeping the same forcing.
410    o model/src:
411      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
412        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
413    o pkg/diagnostics (Stats-Diags):
414      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
415        a) refine region where stats are computed, excluding where arrhFac=0 ;
416        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
417        c) extend regional stats over the region edges (for U or V pt location).
418    o pkg/gchem:
419      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
420        pkg/dic is currently changing/updating ptracers values beyond the OB).
421    o verification (hs94):
422      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
423        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
424        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
425        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
426    o pkg/ptracers:
427      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
428        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
429      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
430        with AB-2 code (so that it get tested).
431    o model/src:
432      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
433        with AB-2 code (previously only available with AB-3 code).
434        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
435        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
436        there, by calling CYCLE_AB_TRACER).
437    o pkg/generic_advdiff:
438      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
439        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
440        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
441        S/R temp/salt/ptracers_integrate.F
442    o model/src & pkg/ptracers:
443      - remove common block variables gT,gS (in DYNVARS.h), except when
444         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
445      - remove common block variable gPtr.
446    o model/src & pkgs:
447      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
448         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
449         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
450         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
451      + change accordingly all calling S/R.
452      - use local temperature/salinity/ptracer tendency array (without bi,bj)
453        in S/R temp/salt/ptracers_integrate.F
454    o pkg/seaice:
455      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
456        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
457      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
458        in seaice_lsr
459      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
460        in s/r seaice_lsr_calc_coeffs
461    o pkg/mdsio:
462      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
463        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
464        too long (e.g., > MAX_LEN_FNAM/2 )
465    
466    checkpoint65b (2014/08/12)
467    o pkg/matrix:
468      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
469    o model/src:
470      - fix initialisation of geothermalFile; compile geothermal-flux code in
471        natl_box verification experiment.
472    o model/src & pkg/down_slope:
473      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
474      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
475        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
476        results at machine truncation level: update output of experiments
477        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
478    o pkg/diagnostics (Stats-Diags):
479      - do not cumulate the full volume when DIAGNOSTICS_FILL is
480        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
481        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
482        times (but Min,Max and StD are still wrong).
483    o model/src:
484      - add geothermal flux forcing: read in ini_forcing.F as time-constant
485        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
486    o model/src:
487      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
488        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
489        arrays are already updated while adjustments (filters, conv.adjustment) are
490        still applied later, in S/R TRACERS_CORRECTION_STEP.
491  o model/src:  o model/src:
492    - store in common bloc array "rhoInSitu" the virtual potential temperature    - store in common bloc array "rhoInSitu" the virtual potential temperature
493      anomaly that is used to compute geopotential: this make the atmos code      anomaly that is used to compute geopotential: this make the atmos code
# Line 82  o model/src: Line 566  o model/src:
566    - 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
567      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.
568      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
569      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
570      moist correction due to vertical advection).      correction due to vertical advection).
571    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
572      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
573      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 112  o pkg/seaice: more clean up Line 596  o pkg/seaice: more clean up
596      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
597      this experiment):      this experiment):
598      > size mitgcmuv_ad      > size mitgcmuv_ad
599      text    data        bss     dec        hex        text    data        bss     dec        hex
600      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
601      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
602      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
603      text    data        bss     dec        hex      text    data        bss     dec        hex
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