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revision 1.2040 by jmc, Wed Aug 6 23:19:25 2014 UTC revision 1.2119 by mlosch, Wed Jan 28 17:15:12 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/seaice: add the option to prescribe a fixed thickness PDF
8      for thermodynamic calculations
9      - because of divisions of the type 7/7 not exactly equal to 1, this change
10        affects results of some verification experiments by up to 4 digits:
11        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
12        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
13        adjoint: lab_sea, lab_sea.noseaicedyn
14        -> updated
15    
16    checkpoint65i (2015/01/23)
17    o model/src:
18      - change units of frictionHeating field from W to W/m^2
19      - fix bug in frictional heating from stratospheric drag in
20        S/R ATM_PHYS_TENDENCY_APPLY_V
21      - with synchronous time-stepping: move resetting to zero of frictionHeating
22        field from load_fields_driver.F to thermodynamics.F ;
23      - add diagnostics for frictional heating.
24    o model/src & gmredi K3D:
25      - add frictionHeating field to pickup-files (for synchronous time-stepping)
26      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
27      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
28        and name in pickup file).
29      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
30    o model/src:
31      - move (from ini_forcing.F) initialisation of all arrays in header file
32        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
33        (since Nov 2012) with option selectAddFluid=1.
34    o pkg/shelfice:
35      - change units (+ document) of newly added field "shelfIceMassDynTendency"
36      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
37    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
38    o pkg/seaice: two new runtime parameters:
39      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
40        long overdue
41      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
42        parameterization of tensil stress for fast ice (does not do anything yet)
43    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
44        for LSR: move checking overlaps out of JFNK-if-block
45    o pkg/atm_phys:
46      - move copy of grid and dynamical fields out of atm_phys_driver.F into
47        new S/R ATM_PHYS_DYN2PHYS.
48      - fix level height for Linear Free-Surf case (to be consistent with
49        fixed-in-time pressure levels).
50    o pkg/mom_common (bottomdrag):
51      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
52        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
53        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
54    o pkg/shelfice (u/v_drag):
55      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
56      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
57        (now similar to shelfice_u_drag.F)
58      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
59        from mom_vecinv.F (similar to mom_fluxform calls).
60    o pkg/mom_common (bottomdrag):
61      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
62      - add options for alternative discretisation of velocity norm in quadratic
63        bottom drag: averaging of grid-cell-center KE to U.point and V.point
64        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
65        improves when averaging only the other component (e.g. vVel for U bottom
66        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
67      - add options (bottomVisc_pCell) to account for partial-cell in bottom
68        friction (no-slip BC) thus getting the true distance from the bottom;
69        off by default since this also reduces model stability (explicit bottom
70        friction). Changes produce different machine truncation with linear-drag
71        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
72        front_relax (bvp & mxl, 10 & 11 digits).
73    o model/src & mom pkgs:
74      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
75        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
76      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
77        just copy level Nr value to level Nr+1.
78    o doc:
79      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
80    o pkg/streamice:
81      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
82        SHELFICE.h: move array shelficemass to init_varia, initialise
83        from array shelficemassinit, which is set in init_fixed and
84        has option to be set from file; introduce array
85        shelficeMassDynTend array, set thru file in init_fixed
86      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
87        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
88        pkg/streamice
89      - shelfice_thermodynamics.F: call shelfice_step_icemass if
90        SHELFICEMassStepping = .true.
91      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
92    
93    checkpoint65h (2014/12/17)
94    o verification/global_ocean.90x40x15, global_ocean_ebm:
95      - update to generic controls.
96    o pkg/ctrl:
97      - ctrl_map_ini_genarr.F: test for igen>0
98      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
99      - move gentim2d part of ctrl_map_ini_genarr.F to
100        new separate routine : ctrl_map_ini_gentim2d.F
101      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
102        add time variable weights and cyclic controls (time mean,
103        seasonal cycle, etc) capabilities to gentim2d
104    o pkg/ecco:
105      - move reading of error, conversion to weights from
106        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
107    o global_oce_llc90, cs32:
108      - activte sbo.
109      - CTRL_SIZE.h : add maxCtrlProc.
110      - activate the new genctrl capabilities.
111      - update following reorganization of global_oce_input_fields.tar.gz  
112    o pkg/ctrl/ctrl_ad_diff.list:
113      - add missing ctrl_init_rec.f
114    o tools/OAD_support/keepOriginal:
115      - add ctrl_init_rec.F
116    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
117      - avoid recomputations of xx_gentim2d_dummy.
118    o momentum diagnostics:
119      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
120        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
121    o pkg/seaice/seaice_lsr.F:
122      - fix computation of BU/BV, make sure they are non-zero, only necessary
123        for cubed sphere exchanges and SEAICE_OLx/y>0.
124        This makes calling s/r fill_cs_corner_rl obsolete (removed).
125    o verification/global_ocean.cs32x15/input.seaice
126      - add test for strong implicit coupling and restricted addtive Schwarz
127        methods for LSR
128      - update results/output.seaice.txt
129    o verification/tutorial_global_oce_biogeo:
130      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
131        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
132        update output_adm,_oadm,_tlm.txt
133    o pkg/dic:
134      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
135      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
136        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
137    o verification/tutorial_global_oce_biogeo:
138      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
139        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
140        update output_adm,_oadm,_tlm.txt
141    o eesupp/src:
142      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
143        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
144    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
145      LSR (following Hutchings et al. 2004)
146      - introduce zetaZ as a global variable (requires adjustments in
147        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
148        in seaice_calc_viscosities.F
149      - new flag SEAICEuseStrImpCpl (default off)
150      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
151        momentum equations
152      - JFNK-solver (preconditioner) adjusted to allow using this method
153        (where it does not have any positive effect)
154    o pkg/seaice
155      - add overlap for restrictive additive Schwartz method also to LSR, but
156        turn it off by default (because it only seems to work for non-cubed
157        sphere/llc topologies)
158    o pkg/autodiff
159      - add extra exchanges in addummy_in_steppging also for mnc output
160    o pkg/seaice:
161      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
162        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
163    o pkg/obcs:
164      - add option to specify domain-connected piece Id along OB though files
165        (for now, only used to diagnose PhiVel; default =1 -> global correction)
166      - modify obcs_diag_balance.F to process each connected-part separately;
167        exclude OB where Id = 0 but keep the full divergence there (-> constant
168        Psi along this portion of OB and all inflow derived from grad(Phi))
169      - add example of OB-conect files in verification/so_box_biogeo/input.
170    o pkg/diagnostics:
171      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
172      a) use non zero matrix element across OB and solve for Phi 1 grid point
173         outside OB (i.e, where tracer OBCS are applied).
174      b) global imbalance of inFlow/outFlow across OB: instead of modifying
175         velocity across OB, spread it uniformly along the OB in the RHS.
176    
177    checkpoint65g (2014/11/19)
178    o pkg/diagnostcis:
179      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
180    o pkg/my82,pp81,kl10:
181      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
182        field diffKr as background diffusivity to set minimum diffusivity value.
183    o pkg/seaice:
184      - add new parameter SEAICEuseEVPrev (for revisited EVP by
185        Bouillon et al 2013)
186      - add SEAICE_evpAlpha/Beta to namelist
187      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
188        involve trivial re-ordering of divisions/multiplications that should not
189        have any effects, but ... they do change the results of lab_sea.hb87 so
190        that only 2 digits of agreement remain, in line with the general
191        instability/fragility of the evp-code. For now, I do not care and just
192        update the verification experiment
193    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
194      - remove xx_genarr2d_numsmooth etc
195      - use xx_genarr2d_preproc etc instead
196      - carry out smooth_correl2D at initialization stage rather than during
197        time stepping.
198      - get smoothOpNb from xx_gentim2d_preproc
199    o global_oce_cs32 :
200      - add test of generic ecco capabilities.
201    o pkg/exf/exf_getsurfacefluxes.F :
202      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
203    o pkg/ctrl,ecco :
204      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
205        is defined.
206    o pkg/seaice: add diagnostics for Delta (deformation parameter)
207    o model/src:
208      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
209        diffusivity (background) is specified but ignored.
210    o verification:
211      - in testreport, convert hostname to lower case for default output dir name
212    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
213    o pkg/dic: add modifications from Hajoon:
214      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
215      - light attenuation: add self-shading effect by climatological Chlorophyll
216        (read from file).
217    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
218        compiles when SEAICE_ALLOW_DYNAMICS is undefined
219    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
220        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
221        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
222        approach where CPP_OPTIONS.h includes an omnipotent
223        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
224    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
225        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
226    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
227        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
228        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
229    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
230      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
231      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
232      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
233      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
234    o pkg/ctrl,ecco,exf :
235      - remove variables associated with NON-generic costs,
236        unless ECCO_CTRL_DEPRECATED is defined.
237      - remove NON-generic NON-obcs controls,
238        unless ECCO_CTRL_DEPRECATED is defined.
239    o pkg/ctrl : added ctrl_local_params.h
240    o pkg/ecco : added ecco_local_params.h
241    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
242        experiments, which will progressively be removed once the
243        experiments are revised to use only generic controls/costs.
244    
245    checkpoint65f (2014/10/13)
246    o pkg/ctrl, ecco, seaice : minor changes in headers
247    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
248        cost function and control capabilities added since checkpoint65c.
249    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
250    o pkg/ecco: increase modularity and improve logic
251      - ecco_toolbox.F (new) : basic operations that are often used,
252        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
253        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
254      - cost_gencal.F (new) : determine filnames and records.
255      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
256      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
257        and exploit the above functions leading to more compact code.
258      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
259      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
260        using_ers, using_gfo, using_mdt is now only defined within gencost)
261    o pkg/ecco: extend generic cost capabilities
262      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
263        capabilities via gencost_preproc (+ _c,_i,_r related params),
264        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
265        gencost_outputlevel arguments to cost_generic
266      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
267        and active_read, making room for gencost_preproc to take effect.
268        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
269      - pkg/ecco/cost_generic.F :
270        compute and store misfit maks*(model-data) in localdif that is
271        then used in cost and for output, output misfit if outlev.GT.0
272      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
273        rather gencost_barfile for deciding whether to write barfile
274      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
275      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
276        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
277      - pkg/ecco/ecco_summary.F : report gencost variables
278      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
279    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
280    o pkg/ecco: internal re-organization
281      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
282        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
283        mv relevant variables definition from ecco_cost.h to ecco.h,
284        make sure gencost routines only include ecco.h)
285      - throughout : add missing CCP switches, rm unused variables,
286        and rm un-necessary CPP switches
287      - throughout gencost routines : replace modelstartdate with
288        gencost_startdate when needed
289      - cost_bp_read.F : use arguments, instead of common blocs
290        so that it can be used also by (new) cost_gencost_bpv4.F
291      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
292      - ecco_phys.F : compute etanFull
293      - ecco_readparms.F : rename using_topex as using_tpj, add
294        bpv4-grace to gencost list, initialize added parameters
295      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
296    
297    checkpoint65e (2014/09/28)
298    o pkg/obcs:
299      - replaced the just-added CPP options with run-time variables
300        (see pkg/obcs/OBCS_PARAMS.h for details)
301    o pkg/obcs:
302      - add additional CPP options for sponge boundary layers
303        (see pkg/obcs/OBCS_OPTIONS.h for details)
304    o pkg/atm_phys:
305      - implement simple (obliquity only, assuming circular planet orbit)
306        seasonal cycle for incoming insolation ; used when run-time parameter
307        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
308    o pkg/exf, pkg/ecco, pkg/ctrl:
309      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
310      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
311      - implement gentim2d for xx_tauu, xx_tauv
312    o pkg/ctrl, pkg/ecco :
313      - fix and complement the generic controls implementation
314    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
315        pkg/shelfice/shelfice_thermodynamics.F,
316        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
317        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
318      - add weight in CTRL_GET_GEN calls
319    o pkg/ctrl :
320      - ctrl_get_gen.F : add weight as input parameter, and apply
321        it directly rather than using smooth_correl2Dw (to be retired).
322      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
323    o pkg/ctrl :
324      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
325        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
326      - re-activate ctrl_summary (call in ctrl_init.F)
327    o pkg/ctrl/ctrl_cost_gen.F :
328      - fix CCP brackets, remove un-necessary myiter, mytime
329    o pkg/ecco, pkg/ctrl :
330      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
331      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
332      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
333      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
334    
335    checkpoint65d (2014/09/15)
336    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
337      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
338        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
339    o pkg/ctrl/ctrl_map_ini_genarr.F :
340      - remove compilation failure
341      - replace hard coded example
342      - use ctrl_map_ini_gen2D, 3D
343    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
344      - on/off switch based upon xx_genarr2d_weight,3d
345    o src/packages_init_variables.F :
346      - regroup pkg/estimation calls
347      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
348        (moved to ctrl_init_variables)
349    o cost/cost_init_varia.F :
350      - remove ecco_cost_init_varia
351        (moved to ecco_init_varia)
352    o ctrl/ctrl_init_variables.F :
353      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
354      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
355    o ctrl/ctrl_map_ini.F :
356      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
357        (moved to ctrl_init_variables)
358    o ctrl/ctrl_map_ini_ecco.F :
359      - remove ECCO_PHYS (mv to ecco_init_varia)
360      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
361    o ecco/ecco_ad_diff.list :
362      - add ecco_init_varia.f
363    o ecco/ecco_init_varia.F
364      - new routine
365    o pkg/streamice:
366      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
367        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
368      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
369    o pkg/generic_advdiff:
370      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
371    o pkg/exf:
372      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
373         xxg_precip capability
374      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
375    o pkg/ctrl:
376      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
377    o model/src/load_fields_driver.F :
378      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
379        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
380    o OpenAD verification experiments:
381      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
382        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
383        for now, only in pkgs used in OpenAD verification experiments.
384      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
385        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
386        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
387        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
388    o OpenAD verification tests:
389      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
390      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
391        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
392      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
393        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
394    o model/src & generic_advdiff:
395      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
396        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
397        dynamics requires valid tracer forcing only over tile interior but, for
398        some diagnostics, may need to extend it over 1 point in tile halo region.
399      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
400        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
401        setting in temp/salt/ptracer_integrate.F
402    o pkg/dic:
403      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
404        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
405        in gchem_forcing_sep.F
406    o pkg/autodiff & obcs:
407      - add storage of current OB values for U & V (was already done for T & S).
408    
409    checkpoint65c (2014/08/30)
410    o pkg/dic:
411      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
412        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
413        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
414    o verification:
415      - new experiment testing OBCS and DIC pkgs, using params & output from
416        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
417        passage: take OBCS from the last year of a 2 yrs simulation and initial
418        conditions from t=1.yr while keeping the same forcing.
419    o model/src:
420      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
421        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
422    o pkg/diagnostics (Stats-Diags):
423      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
424        a) refine region where stats are computed, excluding where arrhFac=0 ;
425        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
426        c) extend regional stats over the region edges (for U or V pt location).
427    o pkg/gchem:
428      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
429        pkg/dic is currently changing/updating ptracers values beyond the OB).
430    o verification (hs94):
431      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
432        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
433        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
434        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
435    o pkg/ptracers:
436      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
437        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
438      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
439        with AB-2 code (so that it get tested).
440    o model/src:
441      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
442        with AB-2 code (previously only available with AB-3 code).
443        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
444        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
445        there, by calling CYCLE_AB_TRACER).
446    o pkg/generic_advdiff:
447      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
448        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
449        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
450        S/R temp/salt/ptracers_integrate.F
451    o model/src & pkg/ptracers:
452      - remove common block variables gT,gS (in DYNVARS.h), except when
453         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
454      - remove common block variable gPtr.
455    o model/src & pkgs:
456      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
457         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
458         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
459         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
460      + change accordingly all calling S/R.
461      - use local temperature/salinity/ptracer tendency array (without bi,bj)
462        in S/R temp/salt/ptracers_integrate.F
463    o pkg/seaice:
464      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
465        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
466      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
467        in seaice_lsr
468      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
469        in s/r seaice_lsr_calc_coeffs
470    o pkg/mdsio:
471      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
472        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
473        too long (e.g., > MAX_LEN_FNAM/2 )
474    
475    checkpoint65b (2014/08/12)
476    o pkg/matrix:
477      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
478    o model/src:
479      - fix initialisation of geothermalFile; compile geothermal-flux code in
480        natl_box verification experiment.
481    o model/src & pkg/down_slope:
482      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
483      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
484        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
485        results at machine truncation level: update output of experiments
486        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
487    o pkg/diagnostics (Stats-Diags):
488      - do not cumulate the full volume when DIAGNOSTICS_FILL is
489        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
490        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
491        times (but Min,Max and StD are still wrong).
492    o model/src:
493      - add geothermal flux forcing: read in ini_forcing.F as time-constant
494        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
495    o model/src:
496      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
497        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
498        arrays are already updated while adjustments (filters, conv.adjustment) are
499        still applied later, in S/R TRACERS_CORRECTION_STEP.
500  o model/src:  o model/src:
501    - store in common bloc array "rhoInSitu" the virtual potential temperature    - store in common bloc array "rhoInSitu" the virtual potential temperature
502      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 575  o model/src:
575    - 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
576      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.
577      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
578      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
579      moist correction due to vertical advection).      correction due to vertical advection).
580    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
581      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
582      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 605  o pkg/seaice: more clean up
605      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
606      this experiment):      this experiment):
607      > size mitgcmuv_ad      > size mitgcmuv_ad
608      text    data        bss     dec        hex        text    data        bss     dec        hex
609      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
610      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
611      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
612      text    data        bss     dec        hex      text    data        bss     dec        hex
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