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revision 1.1950 by dimitri, Thu Dec 19 01:06:09 2013 UTC revision 1.2105 by jmc, Wed Dec 10 22:26:41 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o useSingleCpuInput separates single-CPU input from single-CPU output  o momentum diagnostics:
8  o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the    - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
9    SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8      mom_vecinv.F to timestep.F (to include Smag-3D contribution).
10    o pkg/seaice/seaice_lsr.F:
11      - fix computation of BU/BV, make sure they are non-zero, only necessary
12        for cubed sphere exchanges and SEAICE_OLx/y>0.
13        This makes calling s/r fill_cs_corner_rl obsolete (removed).
14    o verification/global_ocean.cs32x15/input.seaice
15      - add test for strong implicit coupling and restricted addtive Schwarz
16        methods for LSR
17      - update results/output.seaice.txt
18    o verification/tutorial_global_oce_biogeo:
19      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
20        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
21        update output_adm,_oadm,_tlm.txt
22    o pkg/dic:
23      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
24      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
25        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
26    o verification/tutorial_global_oce_biogeo:
27      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
28        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
29        update output_adm,_oadm,_tlm.txt
30    o eesupp/src:
31      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
32        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
33    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
34      LSR (following Hutchings et al. 2004)
35      - introduce zetaZ as a global variable (requires adjustments in
36        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
37        in seaice_calc_viscosities.F
38      - new flag SEAICEuseStrImpCpl (default off)
39      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
40        momentum equations
41      - JFNK-solver (preconditioner) adjusted to allow using this method
42        (where it does not have any positive effect)
43    o pkg/seaice
44      - add overlap for restrictive additive Schwartz method also to LSR, but
45        turn it off by default (because it only seems to work for non-cubed
46        sphere/llc topologies)
47    o pkg/autodiff
48      - add extra exchanges in addummy_in_steppging also for mnc output
49    o pkg/seaice:
50      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
51        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
52    o pkg/obcs:
53      - add option to specify domain-connected piece Id along OB though files
54        (for now, only used to diagnose PhiVel; default =1 -> global correction)
55      - modify obcs_diag_balance.F to process each connected-part separately;
56        exclude OB where Id = 0 but keep the full divergence there (-> constant
57        Psi along this portion of OB and all inflow derived from grad(Phi))
58      - add example of OB-conect files in verification/so_box_biogeo/input.
59    o pkg/diagnostics:
60      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
61      a) use non zero matrix element across OB and solve for Phi 1 grid point
62         outside OB (i.e, where tracer OBCS are applied).
63      b) global imbalance of inFlow/outFlow across OB: instead of modifying
64         velocity across OB, spread it uniformly along the OB in the RHS.
65    
66    checkpoint65g (2014/11/19)
67    o pkg/diagnostcis:
68      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
69    o pkg/my82,pp81,kl10:
70      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
71        field diffKr as background diffusivity to set minimum diffusivity value.
72    o pkg/seaice:
73      - add new parameter SEAICEuseEVPrev (for revisited EVP by
74        Bouillon et al 2013)
75      - add SEAICE_evpAlpha/Beta to namelist
76      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
77        involve trivial re-ordering of divisions/multiplications that should not
78        have any effects, but ... they do change the results of lab_sea.hb87 so
79        that only 2 digits of agreement remain, in line with the general
80        instability/fragility of the evp-code. For now, I do not care and just
81        update the verification experiment
82    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
83      - remove xx_genarr2d_numsmooth etc
84      - use xx_genarr2d_preproc etc instead
85      - carry out smooth_correl2D at initialization stage rather than during
86        time stepping.
87      - get smoothOpNb from xx_gentim2d_preproc
88    o global_oce_cs32 :
89      - add test of generic ecco capabilities.
90    o pkg/exf/exf_getsurfacefluxes.F :
91      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
92    o pkg/ctrl,ecco :
93      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
94        is defined.
95    o pkg/seaice: add diagnostics for Delta (deformation parameter)
96    o model/src:
97      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
98        diffusivity (background) is specified but ignored.
99    o verification:
100      - in testreport, convert hostname to lower case for default output dir name
101    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
102    o pkg/dic: add modifications from Hajoon:
103      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
104      - light attenuation: add self-shading effect by climatological Chlorophyll
105        (read from file).
106    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
107        compiles when SEAICE_ALLOW_DYNAMICS is undefined
108    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
109        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
110        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
111        approach where CPP_OPTIONS.h includes an omnipotent
112        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
113    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
114        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
115    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
116        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
117        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
118    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
119      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
120      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
121      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
122      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
123    o pkg/ctrl,ecco,exf :
124      - remove variables associated with NON-generic costs,
125        unless ECCO_CTRL_DEPRECATED is defined.
126      - remove NON-generic NON-obcs controls,
127        unless ECCO_CTRL_DEPRECATED is defined.
128    o pkg/ctrl : added ctrl_local_params.h
129    o pkg/ecco : added ecco_local_params.h
130    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
131        experiments, which will progressively be removed once the
132        experiments are revised to use only generic controls/costs.
133    
134    checkpoint65f (2014/10/13)
135    o pkg/ctrl, ecco, seaice : minor changes in headers
136    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
137        cost function and control capabilities added since checkpoint65c.
138    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
139    o pkg/ecco: increase modularity and improve logic
140      - ecco_toolbox.F (new) : basic operations that are often used,
141        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
142        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
143      - cost_gencal.F (new) : determine filnames and records.
144      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
145      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
146        and exploit the above functions leading to more compact code.
147      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
148      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
149        using_ers, using_gfo, using_mdt is now only defined within gencost)
150    o pkg/ecco: extend generic cost capabilities
151      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
152        capabilities via gencost_preproc (+ _c,_i,_r related params),
153        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
154        gencost_outputlevel arguments to cost_generic
155      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
156        and active_read, making room for gencost_preproc to take effect.
157        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
158      - pkg/ecco/cost_generic.F :
159        compute and store misfit maks*(model-data) in localdif that is
160        then used in cost and for output, output misfit if outlev.GT.0
161      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
162        rather gencost_barfile for deciding whether to write barfile
163      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
164      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
165        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
166      - pkg/ecco/ecco_summary.F : report gencost variables
167      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
168    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
169    o pkg/ecco: internal re-organization
170      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
171        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
172        mv relevant variables definition from ecco_cost.h to ecco.h,
173        make sure gencost routines only include ecco.h)
174      - throughout : add missing CCP switches, rm unused variables,
175        and rm un-necessary CPP switches
176      - throughout gencost routines : replace modelstartdate with
177        gencost_startdate when needed
178      - cost_bp_read.F : use arguments, instead of common blocs
179        so that it can be used also by (new) cost_gencost_bpv4.F
180      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
181      - ecco_phys.F : compute etanFull
182      - ecco_readparms.F : rename using_topex as using_tpj, add
183        bpv4-grace to gencost list, initialize added parameters
184      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
185    
186    checkpoint65e (2014/09/28)
187    o pkg/obcs:
188      - replaced the just-added CPP options with run-time variables
189        (see pkg/obcs/OBCS_PARAMS.h for details)
190    o pkg/obcs:
191      - add additional CPP options for sponge boundary layers
192        (see pkg/obcs/OBCS_OPTIONS.h for details)
193    o pkg/atm_phys:
194      - implement simple (obliquity only, assuming circular planet orbit)
195        seasonal cycle for incoming insolation ; used when run-time parameter
196        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
197    o pkg/exf, pkg/ecco, pkg/ctrl:
198      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
199      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
200      - implement gentim2d for xx_tauu, xx_tauv
201    o pkg/ctrl, pkg/ecco :
202      - fix and complement the generic controls implementation
203    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
204        pkg/shelfice/shelfice_thermodynamics.F,
205        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
206        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
207      - add weight in CTRL_GET_GEN calls
208    o pkg/ctrl :
209      - ctrl_get_gen.F : add weight as input parameter, and apply
210        it directly rather than using smooth_correl2Dw (to be retired).
211      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
212    o pkg/ctrl :
213      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
214        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
215      - re-activate ctrl_summary (call in ctrl_init.F)
216    o pkg/ctrl/ctrl_cost_gen.F :
217      - fix CCP brackets, remove un-necessary myiter, mytime
218    o pkg/ecco, pkg/ctrl :
219      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
220      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
221      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
222      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
223    
224    checkpoint65d (2014/09/15)
225    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
226      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
227        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
228    o pkg/ctrl/ctrl_map_ini_genarr.F :
229      - remove compilation failure
230      - replace hard coded example
231      - use ctrl_map_ini_gen2D, 3D
232    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
233      - on/off switch based upon xx_genarr2d_weight,3d
234    o src/packages_init_variables.F :
235      - regroup pkg/estimation calls
236      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
237        (moved to ctrl_init_variables)
238    o cost/cost_init_varia.F :
239      - remove ecco_cost_init_varia
240        (moved to ecco_init_varia)
241    o ctrl/ctrl_init_variables.F :
242      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
243      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
244    o ctrl/ctrl_map_ini.F :
245      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
246        (moved to ctrl_init_variables)
247    o ctrl/ctrl_map_ini_ecco.F :
248      - remove ECCO_PHYS (mv to ecco_init_varia)
249      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
250    o ecco/ecco_ad_diff.list :
251      - add ecco_init_varia.f
252    o ecco/ecco_init_varia.F
253      - new routine
254    o pkg/streamice:
255      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
256        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
257      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
258    o pkg/generic_advdiff:
259      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
260    o pkg/exf:
261      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
262         xxg_precip capability
263      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
264    o pkg/ctrl:
265      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
266    o model/src/load_fields_driver.F :
267      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
268        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
269    o OpenAD verification experiments:
270      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
271        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
272        for now, only in pkgs used in OpenAD verification experiments.
273      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
274        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
275        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
276        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
277    o OpenAD verification tests:
278      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
279      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
280        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
281      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
282        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
283    o model/src & generic_advdiff:
284      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
285        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
286        dynamics requires valid tracer forcing only over tile interior but, for
287        some diagnostics, may need to extend it over 1 point in tile halo region.
288      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
289        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
290        setting in temp/salt/ptracer_integrate.F
291    o pkg/dic:
292      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
293        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
294        in gchem_forcing_sep.F
295    o pkg/autodiff & obcs:
296      - add storage of current OB values for U & V (was already done for T & S).
297    
298    checkpoint65c (2014/08/30)
299    o pkg/dic:
300      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
301        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
302        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
303    o verification:
304      - new experiment testing OBCS and DIC pkgs, using params & output from
305        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
306        passage: take OBCS from the last year of a 2 yrs simulation and initial
307        conditions from t=1.yr while keeping the same forcing.
308    o model/src:
309      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
310        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
311    o pkg/diagnostics (Stats-Diags):
312      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
313        a) refine region where stats are computed, excluding where arrhFac=0 ;
314        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
315        c) extend regional stats over the region edges (for U or V pt location).
316    o pkg/gchem:
317      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
318        pkg/dic is currently changing/updating ptracers values beyond the OB).
319    o verification (hs94):
320      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
321        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
322        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
323        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
324    o pkg/ptracers:
325      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
326        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
327      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
328        with AB-2 code (so that it get tested).
329    o model/src:
330      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
331        with AB-2 code (previously only available with AB-3 code).
332        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
333        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
334        there, by calling CYCLE_AB_TRACER).
335    o pkg/generic_advdiff:
336      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
337        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
338        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
339        S/R temp/salt/ptracers_integrate.F
340    o model/src & pkg/ptracers:
341      - remove common block variables gT,gS (in DYNVARS.h), except when
342         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
343      - remove common block variable gPtr.
344    o model/src & pkgs:
345      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
346         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
347         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
348         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
349      + change accordingly all calling S/R.
350      - use local temperature/salinity/ptracer tendency array (without bi,bj)
351        in S/R temp/salt/ptracers_integrate.F
352    o pkg/seaice:
353      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
354        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
355      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
356        in seaice_lsr
357      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
358        in s/r seaice_lsr_calc_coeffs
359    o pkg/mdsio:
360      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
361        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
362        too long (e.g., > MAX_LEN_FNAM/2 )
363    
364    checkpoint65b (2014/08/12)
365    o pkg/matrix:
366      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
367    o model/src:
368      - fix initialisation of geothermalFile; compile geothermal-flux code in
369        natl_box verification experiment.
370    o model/src & pkg/down_slope:
371      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
372      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
373        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
374        results at machine truncation level: update output of experiments
375        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
376    o pkg/diagnostics (Stats-Diags):
377      - do not cumulate the full volume when DIAGNOSTICS_FILL is
378        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
379        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
380        times (but Min,Max and StD are still wrong).
381    o model/src:
382      - add geothermal flux forcing: read in ini_forcing.F as time-constant
383        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
384    o model/src:
385      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
386        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
387        arrays are already updated while adjustments (filters, conv.adjustment) are
388        still applied later, in S/R TRACERS_CORRECTION_STEP.
389    o model/src:
390      - store in common bloc array "rhoInSitu" the virtual potential temperature
391        anomaly that is used to compute geopotential: this make the atmos code
392        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
393    o pkg/seaice/seaice_lsr.F
394      - rename integer variable ilcall to ipass (that's what it is called
395        in the residual diagnostics
396      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
397        default) for improved non-linear convergence of the first few steps
398      - adjust a few comments and add new ones to explain some of the store
399        directives
400    o pkg/generic_advdiff (& ptracers):
401      - re-work the code to check for valid advection scheme and for minimum
402        size of overlap (now stored in local common bloc in gad_advscheme.F)
403    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
404      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
405      - add an auxilliary variable "bet" and fix store directives and keys in
406        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
407        less exact gradients in my tests); but there are still
408        recomputation warning (although gradients are sort of OK), when
409        SEAICE_LSR_VECTORIZE is not defined, so this flag and
410        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
411      - update verification experiments lab_sea.
412      - change some comments in S/R seaice_calc_viscosities
413    o model/src:
414      - if staggerTimeStep=T, always apply exchange to velocity field in
415        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
416        (independent of using multi-dim advection or not); no effect on FWD run
417        but affects AD results (at machine truncation level): update output of
418        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
419        and isomip (oad: 12.d).
420    o pkg/generic_advdiff:
421      - stop if doAB_onGtGs is set to FALSE but ignored
422      - refine warning related to stability of tracer time-stepping
423        regarding internal wave dynamics.
424      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
425        on staggerTimeStep & implicitIntGravWave (will now get a warning
426        if potentially unstable).
427    o pkg/kl10:
428      - add new pkg "kl10" for mixing due to internal wave breaking, from
429        http://www.sciencedirect.com/science/article/pii/S1463500310000144
430        (contribution from Jody Klymak), tested in verification experiment
431        verification/internal_wave/input.kl10/
432    o isomip experiment:
433      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
434        (input.htd) and update the output.
435    o cd_code experiments:
436      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
437        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
438        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
439        update the corresponding output.
440    o pkg/seaice:
441      - reduce the number of include files and store directives in
442        S/R seaice_lsr_tridiagu/v
443      - change the order of loops in one case in S/R seaice_lsr_tridiagv
444        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
445        get rid off one store directive (a TAF bug?)
446      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
447        S/R seaice_lsr_tridiagv to change the loop range for consistency
448      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
449      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
450        S/R seaice_lsr_tridiagu/v (requires update of
451        offline_exf_seaice/input.dyn_jfnk)
452    
453    checkpoint65a (2014/07/27)
454    o model/src:
455      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
456        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
457        (topo in p-coords, ice-shelf in z-coords); update output of experiments
458        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
459    o model/src:
460      - collect momentum forcing tendency into local 2-D array (passed as argument
461        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
462        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
463        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
464      - collect T & S forcing tendency into local 2-D array (passed as argument to
465        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
466        affects results at machine truncation level (e.g., ocean: if using
467        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
468        correction due to vertical advection).
469      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
470        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
471        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
472        obcs_ctrl (ad & fwd grd @ 12 & 7).
473    o pkg/ptracers & diagnostics:
474      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
475        title (to avoid some unexpected truncation); sort out ptracers diags units.
476      - collect ptracer forcing tendency into local 2-D array (passed as argument
477        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
478    
479    checkpoint65 (2014/07/18)
480    o pkg/fizhi:
481      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
482        affects results at machine truncation level. Update output of experiments
483        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
484    o pkg/seaice: more clean up
485      - rename TAF common block tapes to be more consistent and remove
486        unnecessary duplicates
487      - add store directives to remove more recomputations, but use smaller
488        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
489        The idea behind this flag is to reduce the memory footprint when the
490        adjoint of the LSR is not required. As of now, defining the flag
491        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
492        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
493        For experiment offline_exf_seaice, this means on a linux box with gfortran
494        nearly a factor of 10 (but keep in mind there is mostly seaice code in
495        this experiment):
496        > size mitgcmuv_ad
497        text    data        bss     dec        hex
498        5100659 1216  220458952  225560827  d71c8fb
499        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
500        but only a moderate increase of 36% for global_ocean.cs32x15:
501        text    data        bss     dec        hex
502        6695027 1648 1014578664 1021275339 3cdf6ccb
503        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
504      - note: there are still recomputations in global_ocean.cs32x15 and
505        offline_exf_seaice and the gradient agreement changes (gets a
506        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
507      - in general, the AD gradients still are wrong
508    o OpenAD
509      - clean up code_oad/ directories somewhat by moving files
510        dontCompile, dontTransform, keepOriginal to OAD_support/
511    o model/src:
512      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
513        (not currently tested): add dissipation terms before NLFS rescaling of
514        tendencies (previously done after).
515    o pkg/diagnostics:
516      - write stats-diags in ascii file with more digits (same as in monitor).
517    o pkg/down_slope:
518      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
519        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
520    o model/src:
521      - new file "apply_forcing.F" containing all the code previously in
522        external_forcing.F, but with new argument list: pass, as new argument,
523        the current level tendency array to update (instead of a direct update
524        of the common bloc array). Change the corresponding calls.
525      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
526        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
527    o pkg/seaice/seaice_lsr, a little bit of clean up
528      - rearrange some code blocks, so that now all calculations for
529        setting up the right-hand-sides done within one single block
530        (I find that easier to read and understand)
531      - rearrange freedrift-code to reduce the number of ifdefs
532      - adjust some indentations and comments
533    
534    checkpoint64z (2014/07/10)
535    o model/src and several pkgs:
536      - change argument list of all S/R called from external_forcing.F and
537        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
538        to pass, as argument, the current level tendency array to update
539        (instead of a direct update of the common bloc array).
540      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
541      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
542    o pkg/seaice/seaice_lsr.F
543      - always initialize local arrays in seaice_lsr_tridiagu/v
544      - add more local tapes to seaice_lsr_tridiagu/v
545      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
546        keep it in bi/bj loop; this seems to be essential
547      - gradients are still wrong but only by 4-7 orders of magnitude
548        instead of 15 orders of magnitude, lab_sea improves a little
549    o pkg/seaice
550      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
551        generates unnecessary code in seaice_lsr_ad
552      - add more store directives in seaice_lsr to avoid unnecessary code
553        in seaice_lsr_ad
554      - exclude some residual computations in seaice_lsr when
555        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
556        in seaice_lsr_ad
557      - add more storing, a new tape (model/src/the_main_loop.F) and
558        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
559        and klockey should be checked by a specialist)
560      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
561        and update lab_sea after previous changes in pkg/seaice below
562    o pkg/autodiff:
563      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
564        viscFacInAd : run time parameters allowing for adjoint switches
565        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
566    o pkg/ecco:
567      - introduce cost_gencost_boxmean.F that computes a box mean
568        temperature (for use in adjoint sensitivity studies).
569    o model/src/set_defaults.F : initialize viscFacAdj to 1.
570    o pkg/mom_common/mom_calc_visc.F:
571      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
572    o pkg/seaice/seaice_summary.F:
573      - statement for SEAICEadjMODE now in autodiff_readparms.F
574    o pkg/seaice:
575      - remove some store directives and add new ones in an effort to get
576        finally rid off the recomputation warnings. This is successful
577        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
578        defined (i.e. no extensive recomputation warnings left), but there
579        are still too many recomputations on the solver iteration level
580      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
581      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
582        SEAICE_SIZE.h
583      - add a store directive in S/R seaice_calc_viscosities
584    o pkg/seaice (ITD code):
585      - fix definition of Hlimit for multi-threaded case
586      - use double precision arithmetic to compute Hlimit: this affects results;
587        update output of experiment seaice_itd.
588    o replace content of verification/seaice_itd
589      - instead of a 1D column use the configuration of offline_exf_seaice
590        to test the ice thickness distribution code with ridging
591      - this is a first shot at this experiment
592      - change of some defaults of ridging parameters SEAICEhStar (from
593        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
594        and lot of new comments.
595    
596    checkpoint64y (2014/06/20)
597    o pkg/seaice/seaice_reg_ridge.F:
598      - modify the regularization of very small volumes of ice; only check
599        total volume HEFF, and do not apply correction to individual ice
600        classes because that leads to funny patterns in the heat and fw-fluxes
601        into the ocean. Adjust seaice_itd/results/output.txt
602      - replace nITD by SEAICE_multDim in loop-ranges
603    o pkg/exf:
604      - add code to process the case field period = -12. with UV interpolation.
605      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
606        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
607    o verification/global_with_exf:
608      - switch all fields period to -12. (was previously untested) in input/data.exf
609        (but keep secondary test ".yearly" unchanged); update the reference output.
610    o pkg/cal:
611      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
612    o pkg/exf:
613      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
614        to replace logical switch "exf_verbose"
615      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
616    o pkg/sbo:
617      - update from Katherine Quinn: evaluate mass directly from density and SSH
618        (budget using Finite Volume method) instead of from bottom pressure.
619      - allow testreport to collect few selected SBO output ; tested in exp.
620        global_ocean.90x40x15 (after updating the results, to include SBO output).
621      - fix some multi-threading issues (in output part).
622    o model/src & most packages:
623      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
624      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
625        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
626        "data.{pkg}" exist ; and leave the S/R (return) just after.
627      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
628        + call LAND_READPARMS from packages_readparms.F
629    o pkg/seaice:
630      - remove code that resets useThSice in S/R seaice_readparms and
631        replace it by a warning in S/R seaice_check
632      - remove parameter MULTDIM, replace with nITD and runtime
633        parameter SEAICE_multDim (still hard-wired to nITD if
634        SEAICE_ITD is defined)
635    
636    checkpoint64x (2014/05/24)
637    o verification/lab_sea:
638      - update adjoint and TLM output following changes to pkg/salt_plume
639      - un-do the update after putting back local recip_Cp in few places.
640    o pkg/salt_plume: modifications by An Nguyen:
641      - add capability to do brine rejection (salt-plume) as function of
642        volume+tracers (instead of only salinity tracer).
643      - conserve volume by exchanging volume from each kLev to above to
644        accommodate in-coming brine volume
645      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
646      - switch KPP surf buoyancy due to brine forcing to 3-d
647        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
648      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
649      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
650        in East/West Arctic.
651    o pkg/sbo:
652      - incorporate modifications from Katherine Quinn to enable the use of sbo
653        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
654        output for future testreport verification (unfinished).
655    o pkg/atm_phys:
656      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
657        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
658        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
659    o pkg/seaice
660      seaice_calc_ice_strength.F: modify expression to avoid divisions
661        (affects truncation)
662      seaice_do_ridging.F: clean up the insectarium
663      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
664      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
665      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
666      - add some debugging information and error messages (warnings)
667    o model/src: modifications relatd to atmosphere p*:
668      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
669      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
670        of vertical profile tRef in geopotential background and anomaly.
671      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
672        and pkg/atm_phys.
673      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
674        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
675    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
676    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
677        not used right now, but can be used in BGC packages to fix conservation.
678    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
679        other packages too.
680    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
681        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
682    o model/src:
683      - since we have several heat capacity (even in model/src), define "recip_Cp"
684        as local variable (no longer in common block) to avoid any confusion.
685      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
686    o pkg/exf:
687      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
688        air density as function of air Temp, Humidity and atm pressure.
689    
690    checkpoint64w (2014/05/02)
691    o verification:
692      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
693        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
694        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
695        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
696        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
697    o model/src: for atmosphere in p* coords:
698      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
699      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
700        but not yet activated.
701    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
702      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
703      - this changes the results (but not for any verification experiment, because
704        none tests this), but avoids having an extra field in the restart files
705    o pkg/seaice: remove global variable TICE (not needed)
706      - replace by TICES or local variable where necessary (cost_seaice_test,
707        seaice_diagnostics_state)
708      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
709      - use specific read/write routines for reading and writing individual leves
710        of a multilevel field
711    o pkg/ctrl & model/inc:
712      - move additional anomaly fields of control vars (related to options:
713         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
714        from DYNVARS.h into new header file: CTRL_FIELDS.h
715    o pkg/seaice: some small modifications to the ridging code
716      - make fw2ObyRidge a global variable and add the freshwater flux to
717        seaice_growth
718      - pass actual thickness from seaice_prepare_ridging, so that it is
719        computed only in one place and compute it in the same way as in
720        seaice_growth
721      - initialise more fields in seaice_do_ridging that where cause floating
722        point exceptions over land
723    o pkg/seaice: preparations for ridging code and first real ridging code
724      - move most of "PART 1" of S/R seaice_growth into a new and separate
725        S/R seaice_reg_ridge that will both regularize the state variable after
726        advection call the actual ridging routine;
727      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
728        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
729      - remove ridging code from seaice_advdiff
730      - clean up remaining part 1 of seaice_growth in an attempt to make it
731        more readable (this is probably subjective)
732      - call seaice_itd_redist once in the initialisation phase to have the initial
733        conditions in the correct category
734      - finally: add new ridging routine for ITD code
735    
736    checkpoint64v (2014/04/11)
737    o pkg/ecco:
738      - add runtime parameters mdt[start,end]date[1,2]
739      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
740    o pkg/seaice:
741      - make deltaC a global variable, so that it can be used in ridging code
742      - first step towards ridging: introduce new routines that compute
743        ice strength based on ridging parameters
744      - add diagnostic for HSNOWITD
745      - add opnWtrFrac as a global variable (required for ridging scheme)
746    o pkg/salt_plume + pkg/seaice/seaice_growth.F
747      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
748        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
749    o verification/hs94.1x64x5:
750      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
751      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
752    o autodiff:
753      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
754        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
755        For now, only in pkgs used in verification/hs94.1x64x5.
756      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
757        which are specific to TAF/TAMC).
758      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
759        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
760        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
761      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
762        building mitgcmuv_ad (make adAll).
763    o pkg/ecco:
764      - cost_gencost_seaicev4.F:
765         reformulate proxy cost as function of sst and local param SEAICE_freeze
766         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
767      - add stop statement if old names siv4-[sst,vol] are used
768      - add snapshots + cost reports for atmospheric longwave
769      - remove factor 0.1 in front of wtau[u,v]
770      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
771         ALLOW_TMI_SST_COST_CONTRIBUTION
772    o pkg/atm_phys:
773      - add some diagnostics for Short-wave and for convection S/R.
774    o pkg/seaice/seaice_growth:
775      - fix a bug in the lateral melt parameterization for SEAICE_ITD
776        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
777      - rearrange loop order for better vector code in the same code block
778      - rewrite the floeDiameter formula to have fewer divisions
779      -  (miraculously) none of this changes the results of seaice_itd
780    o pkg/smooth:
781      - move param smooth2Ddiffnbt to pkg/ecco
782    o pkg/salt_plume:
783      - salt_plume_frac.F:
784         clean up local param names
785         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
786    o pkg/rw:
787      - add RS version of S/R READ_MFLDS_LEV.
788    o pkg/streamice:
789      - fix the restart test by writing/reading pickup_streamice files.
790    o pkg/seaice:
791      - refine checks for jfnk-related parameters
792      - comment out if statement with SEAICEuseIMEX parameter as long as there
793        is no IMEX code to avoid confusion and surprises
794    
795    checkpoint64u (2014/03/07)
796    o verification/MLAdjust:
797      - rename secondary test suffix:
798         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
799         0.leithD -> AhFlxF  + switch to flux-form
800         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
801         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
802    o pkg/mom_vecinv:
803      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
804        to be before mom_calc_visc.F)
805      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
806      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
807        this is simpler for the adjoint and for diagnostics.
808    o model/src + pkg/momentum:
809      - add input files for  2-D additional Western and Southern cell-edge wall
810         (e.g., to add "thin-wall" where it is =1).
811      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
812        using 2nd hFacZ that is computed from initial (fix domain) hFac
813      - known limitations of thin wall implementation: not yet coded for sigma
814        coords; not working with CD-scheme neither.
815    o pkg/seaice:
816      - rename recently introduced parameters from (wrong name) AB to
817        BDF (backward difference time discretisation)
818      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
819    o tools/adjoint_options:
820      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
821    
822    checkpoint64t (2014/02/01)
823    o pkg/ecco
824      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
825        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
826      - replace hard-coded record number and period which only work for monthly
827        with read-in runtime param that works for other periods (month,day,year)
828    o pkg/thsice
829      - corrected store directive fixes thsice adjoint gradient checks
830    o genmake2 & testreport:
831      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
832        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
833        Update testreport accordingly. No need to set "export OPENAD=true"
834        in adjoint_options/adjoint_oad anymore (will be removed later).
835    o pkg/shelfice:
836      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
837        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
838        so that surface forcing applies to k=kSurf if using pkg/shelfice.
839    o pkg/ctrl, pkg/grdchk, pkg/ecco:
840      - Changes to make GENARR more modular (i.e. invisible if not used)
841    o model/src/temp_integrate.F and salt_integrate.F
842      - re-include store directives that were removed on Dec 27th.
843    o model/src/external_forcing_surf.F
844      - add storage directives for EmPmR and PmEpR to avoid recomputation of
845        seaice_model in the adjoint that is problematic when seaice_model is
846        turned off in the adjoint. The resolved issue dated back to July when
847        EXTERNAL_FORCING_SURF call was moved.
848        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
849    o pkg/exf/exf_check.F
850      - fix a small bug again (originally found by Wentao Liu, now found again)
851      - streamline error output
852    o pkg/streamice and aim_v23:
853      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
854        Apple's /usr/bin/cpp knows what to do:
855        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
856        Target: x86_64-apple-darwin13.0.0
857    
858    checkpoint64s (2014/01/05)
859    o tools/adjoint_options:
860      - switch to fastopt.net TAF server (instead of default fastopt.de) for
861        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
862    o model/src:
863      - remove some unnecessary TAF storage directives in forward_step.F and
864        in dynamics.F (note: not always removed by TAF, e.g., double storage
865        of kappaRU,kappaRV in former version of dynamics.F).
866    o model/src & pkg/ptracers:
867      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
868        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
869        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
870      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
871      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
872      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
873    o useSingleCpuInput separates single-CPU input from single-CPU output;
874        for now only implemented for in exf_interp_read.F
875    o verification/advect_xy:
876      - fix missing EXCH call in local version of ini_salt.F and update output.
877    o momentum diagnostics:
878      - fix which deltaT is used in Total-Tendency diagnostics.
879      - fix typo in diagnostics for momentum tendency from AB.
880    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
881        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
882    
883  checkpoint64r (2013/12/08)  checkpoint64r (2013/12/08)
884  o verification/*/results:  o verification/*/results:
# Line 112  o verification: Line 984  o verification:
984  o pkg/cost:  o pkg/cost:
985    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL    - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
986      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:      (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
987      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL      o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
988        cannot be applied to var in common block).        cannot be applied to var in common block).
989      o allows to get results independent of tile-per-proc setting (if using      o allows to get results independent of tile-per-proc setting (if using
990        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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