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revision 1.2012 by mlosch, Fri Jun 27 14:37:03 2014 UTC revision 1.2107 by jmc, Wed Dec 17 17:58:39 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65h (2014/12/17)
8    o verification/global_ocean.90x40x15, global_ocean_ebm:
9      - update to generic controls.
10    o pkg/ctrl:
11      - ctrl_map_ini_genarr.F: test for igen>0
12      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
13      - move gentim2d part of ctrl_map_ini_genarr.F to
14        new separate routine : ctrl_map_ini_gentim2d.F
15      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
16        add time variable weights and cyclic controls (time mean,
17        seasonal cycle, etc) capabilities to gentim2d
18    o pkg/ecco:
19      - move reading of error, conversion to weights from
20        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
21    o global_oce_llc90, cs32:
22      - activte sbo.
23      - CTRL_SIZE.h : add maxCtrlProc.
24      - activate the new genctrl capabilities.
25      - update following reorganization of global_oce_input_fields.tar.gz  
26    o pkg/ctrl/ctrl_ad_diff.list:
27      - add missing ctrl_init_rec.f
28    o tools/OAD_support/keepOriginal:
29      - add ctrl_init_rec.F
30    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
31      - avoid recomputations of xx_gentim2d_dummy.
32    o momentum diagnostics:
33      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
34        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
35    o pkg/seaice/seaice_lsr.F:
36      - fix computation of BU/BV, make sure they are non-zero, only necessary
37        for cubed sphere exchanges and SEAICE_OLx/y>0.
38        This makes calling s/r fill_cs_corner_rl obsolete (removed).
39    o verification/global_ocean.cs32x15/input.seaice
40      - add test for strong implicit coupling and restricted addtive Schwarz
41        methods for LSR
42      - update results/output.seaice.txt
43    o verification/tutorial_global_oce_biogeo:
44      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
45        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
46        update output_adm,_oadm,_tlm.txt
47    o pkg/dic:
48      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
49      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
50        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
51    o verification/tutorial_global_oce_biogeo:
52      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
53        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
54        update output_adm,_oadm,_tlm.txt
55    o eesupp/src:
56      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
57        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
58    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
59      LSR (following Hutchings et al. 2004)
60      - introduce zetaZ as a global variable (requires adjustments in
61        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
62        in seaice_calc_viscosities.F
63      - new flag SEAICEuseStrImpCpl (default off)
64      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
65        momentum equations
66      - JFNK-solver (preconditioner) adjusted to allow using this method
67        (where it does not have any positive effect)
68  o pkg/seaice  o pkg/seaice
69    - remove unnecessary u/vTmp from subroutine call of    - add overlap for restrictive additive Schwartz method also to LSR, but
70      seaice_lsr_tridiagu/v      turn it off by default (because it only seems to work for non-cubed
71        sphere/llc topologies)
72    o pkg/autodiff
73      - add extra exchanges in addummy_in_steppging also for mnc output
74    o pkg/seaice:
75      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
76        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
77    o pkg/obcs:
78      - add option to specify domain-connected piece Id along OB though files
79        (for now, only used to diagnose PhiVel; default =1 -> global correction)
80      - modify obcs_diag_balance.F to process each connected-part separately;
81        exclude OB where Id = 0 but keep the full divergence there (-> constant
82        Psi along this portion of OB and all inflow derived from grad(Phi))
83      - add example of OB-conect files in verification/so_box_biogeo/input.
84    o pkg/diagnostics:
85      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
86      a) use non zero matrix element across OB and solve for Phi 1 grid point
87         outside OB (i.e, where tracer OBCS are applied).
88      b) global imbalance of inFlow/outFlow across OB: instead of modifying
89         velocity across OB, spread it uniformly along the OB in the RHS.
90    
91    checkpoint65g (2014/11/19)
92    o pkg/diagnostcis:
93      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
94    o pkg/my82,pp81,kl10:
95      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
96        field diffKr as background diffusivity to set minimum diffusivity value.
97    o pkg/seaice:
98      - add new parameter SEAICEuseEVPrev (for revisited EVP by
99        Bouillon et al 2013)
100      - add SEAICE_evpAlpha/Beta to namelist
101      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
102        involve trivial re-ordering of divisions/multiplications that should not
103        have any effects, but ... they do change the results of lab_sea.hb87 so
104        that only 2 digits of agreement remain, in line with the general
105        instability/fragility of the evp-code. For now, I do not care and just
106        update the verification experiment
107    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
108      - remove xx_genarr2d_numsmooth etc
109      - use xx_genarr2d_preproc etc instead
110      - carry out smooth_correl2D at initialization stage rather than during
111        time stepping.
112      - get smoothOpNb from xx_gentim2d_preproc
113    o global_oce_cs32 :
114      - add test of generic ecco capabilities.
115    o pkg/exf/exf_getsurfacefluxes.F :
116      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
117    o pkg/ctrl,ecco :
118      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
119        is defined.
120    o pkg/seaice: add diagnostics for Delta (deformation parameter)
121    o model/src:
122      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
123        diffusivity (background) is specified but ignored.
124    o verification:
125      - in testreport, convert hostname to lower case for default output dir name
126    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
127    o pkg/dic: add modifications from Hajoon:
128      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
129      - light attenuation: add self-shading effect by climatological Chlorophyll
130        (read from file).
131    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
132        compiles when SEAICE_ALLOW_DYNAMICS is undefined
133    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
134        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
135        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
136        approach where CPP_OPTIONS.h includes an omnipotent
137        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
138    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
139        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
140    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
141        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
142        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
143    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
144      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
145      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
146      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
147      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
148    o pkg/ctrl,ecco,exf :
149      - remove variables associated with NON-generic costs,
150        unless ECCO_CTRL_DEPRECATED is defined.
151      - remove NON-generic NON-obcs controls,
152        unless ECCO_CTRL_DEPRECATED is defined.
153    o pkg/ctrl : added ctrl_local_params.h
154    o pkg/ecco : added ecco_local_params.h
155    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
156        experiments, which will progressively be removed once the
157        experiments are revised to use only generic controls/costs.
158    
159    checkpoint65f (2014/10/13)
160    o pkg/ctrl, ecco, seaice : minor changes in headers
161    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
162        cost function and control capabilities added since checkpoint65c.
163    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
164    o pkg/ecco: increase modularity and improve logic
165      - ecco_toolbox.F (new) : basic operations that are often used,
166        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
167        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
168      - cost_gencal.F (new) : determine filnames and records.
169      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
170      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
171        and exploit the above functions leading to more compact code.
172      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
173      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
174        using_ers, using_gfo, using_mdt is now only defined within gencost)
175    o pkg/ecco: extend generic cost capabilities
176      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
177        capabilities via gencost_preproc (+ _c,_i,_r related params),
178        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
179        gencost_outputlevel arguments to cost_generic
180      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
181        and active_read, making room for gencost_preproc to take effect.
182        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
183      - pkg/ecco/cost_generic.F :
184        compute and store misfit maks*(model-data) in localdif that is
185        then used in cost and for output, output misfit if outlev.GT.0
186      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
187        rather gencost_barfile for deciding whether to write barfile
188      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
189      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
190        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
191      - pkg/ecco/ecco_summary.F : report gencost variables
192      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
193    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
194    o pkg/ecco: internal re-organization
195      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
196        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
197        mv relevant variables definition from ecco_cost.h to ecco.h,
198        make sure gencost routines only include ecco.h)
199      - throughout : add missing CCP switches, rm unused variables,
200        and rm un-necessary CPP switches
201      - throughout gencost routines : replace modelstartdate with
202        gencost_startdate when needed
203      - cost_bp_read.F : use arguments, instead of common blocs
204        so that it can be used also by (new) cost_gencost_bpv4.F
205      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
206      - ecco_phys.F : compute etanFull
207      - ecco_readparms.F : rename using_topex as using_tpj, add
208        bpv4-grace to gencost list, initialize added parameters
209      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
210    
211    checkpoint65e (2014/09/28)
212    o pkg/obcs:
213      - replaced the just-added CPP options with run-time variables
214        (see pkg/obcs/OBCS_PARAMS.h for details)
215    o pkg/obcs:
216      - add additional CPP options for sponge boundary layers
217        (see pkg/obcs/OBCS_OPTIONS.h for details)
218    o pkg/atm_phys:
219      - implement simple (obliquity only, assuming circular planet orbit)
220        seasonal cycle for incoming insolation ; used when run-time parameter
221        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
222    o pkg/exf, pkg/ecco, pkg/ctrl:
223      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
224      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
225      - implement gentim2d for xx_tauu, xx_tauv
226    o pkg/ctrl, pkg/ecco :
227      - fix and complement the generic controls implementation
228    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
229        pkg/shelfice/shelfice_thermodynamics.F,
230        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
231        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
232      - add weight in CTRL_GET_GEN calls
233    o pkg/ctrl :
234      - ctrl_get_gen.F : add weight as input parameter, and apply
235        it directly rather than using smooth_correl2Dw (to be retired).
236      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
237    o pkg/ctrl :
238      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
239        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
240      - re-activate ctrl_summary (call in ctrl_init.F)
241    o pkg/ctrl/ctrl_cost_gen.F :
242      - fix CCP brackets, remove un-necessary myiter, mytime
243    o pkg/ecco, pkg/ctrl :
244      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
245      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
246      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
247      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
248    
249    checkpoint65d (2014/09/15)
250    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
251      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
252        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
253    o pkg/ctrl/ctrl_map_ini_genarr.F :
254      - remove compilation failure
255      - replace hard coded example
256      - use ctrl_map_ini_gen2D, 3D
257    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
258      - on/off switch based upon xx_genarr2d_weight,3d
259    o src/packages_init_variables.F :
260      - regroup pkg/estimation calls
261      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
262        (moved to ctrl_init_variables)
263    o cost/cost_init_varia.F :
264      - remove ecco_cost_init_varia
265        (moved to ecco_init_varia)
266    o ctrl/ctrl_init_variables.F :
267      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
268      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
269    o ctrl/ctrl_map_ini.F :
270      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
271        (moved to ctrl_init_variables)
272    o ctrl/ctrl_map_ini_ecco.F :
273      - remove ECCO_PHYS (mv to ecco_init_varia)
274      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
275    o ecco/ecco_ad_diff.list :
276      - add ecco_init_varia.f
277    o ecco/ecco_init_varia.F
278      - new routine
279    o pkg/streamice:
280      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
281        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
282      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
283    o pkg/generic_advdiff:
284      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
285    o pkg/exf:
286      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
287         xxg_precip capability
288      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
289    o pkg/ctrl:
290      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
291    o model/src/load_fields_driver.F :
292      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
293        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
294    o OpenAD verification experiments:
295      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
296        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
297        for now, only in pkgs used in OpenAD verification experiments.
298      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
299        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
300        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
301        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
302    o OpenAD verification tests:
303      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
304      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
305        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
306      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
307        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
308    o model/src & generic_advdiff:
309      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
310        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
311        dynamics requires valid tracer forcing only over tile interior but, for
312        some diagnostics, may need to extend it over 1 point in tile halo region.
313      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
314        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
315        setting in temp/salt/ptracer_integrate.F
316    o pkg/dic:
317      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
318        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
319        in gchem_forcing_sep.F
320    o pkg/autodiff & obcs:
321      - add storage of current OB values for U & V (was already done for T & S).
322    
323    checkpoint65c (2014/08/30)
324    o pkg/dic:
325      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
326        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
327        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
328    o verification:
329      - new experiment testing OBCS and DIC pkgs, using params & output from
330        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
331        passage: take OBCS from the last year of a 2 yrs simulation and initial
332        conditions from t=1.yr while keeping the same forcing.
333    o model/src:
334      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
335        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
336    o pkg/diagnostics (Stats-Diags):
337      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
338        a) refine region where stats are computed, excluding where arrhFac=0 ;
339        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
340        c) extend regional stats over the region edges (for U or V pt location).
341    o pkg/gchem:
342      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
343        pkg/dic is currently changing/updating ptracers values beyond the OB).
344    o verification (hs94):
345      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
346        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
347        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
348        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
349    o pkg/ptracers:
350      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
351        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
352      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
353        with AB-2 code (so that it get tested).
354    o model/src:
355      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
356        with AB-2 code (previously only available with AB-3 code).
357        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
358        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
359        there, by calling CYCLE_AB_TRACER).
360    o pkg/generic_advdiff:
361      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
362        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
363        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
364        S/R temp/salt/ptracers_integrate.F
365    o model/src & pkg/ptracers:
366      - remove common block variables gT,gS (in DYNVARS.h), except when
367         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
368      - remove common block variable gPtr.
369    o model/src & pkgs:
370      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
371         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
372         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
373         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
374      + change accordingly all calling S/R.
375      - use local temperature/salinity/ptracer tendency array (without bi,bj)
376        in S/R temp/salt/ptracers_integrate.F
377    o pkg/seaice:
378      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
379        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
380      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
381        in seaice_lsr
382      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
383        in s/r seaice_lsr_calc_coeffs
384    o pkg/mdsio:
385      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
386        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
387        too long (e.g., > MAX_LEN_FNAM/2 )
388    
389    checkpoint65b (2014/08/12)
390    o pkg/matrix:
391      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
392    o model/src:
393      - fix initialisation of geothermalFile; compile geothermal-flux code in
394        natl_box verification experiment.
395    o model/src & pkg/down_slope:
396      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
397      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
398        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
399        results at machine truncation level: update output of experiments
400        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
401    o pkg/diagnostics (Stats-Diags):
402      - do not cumulate the full volume when DIAGNOSTICS_FILL is
403        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
404        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
405        times (but Min,Max and StD are still wrong).
406    o model/src:
407      - add geothermal flux forcing: read in ini_forcing.F as time-constant
408        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
409    o model/src:
410      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
411        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
412        arrays are already updated while adjustments (filters, conv.adjustment) are
413        still applied later, in S/R TRACERS_CORRECTION_STEP.
414    o model/src:
415      - store in common bloc array "rhoInSitu" the virtual potential temperature
416        anomaly that is used to compute geopotential: this make the atmos code
417        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
418    o pkg/seaice/seaice_lsr.F
419      - rename integer variable ilcall to ipass (that's what it is called
420        in the residual diagnostics
421      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
422        default) for improved non-linear convergence of the first few steps
423      - adjust a few comments and add new ones to explain some of the store
424        directives
425    o pkg/generic_advdiff (& ptracers):
426      - re-work the code to check for valid advection scheme and for minimum
427        size of overlap (now stored in local common bloc in gad_advscheme.F)
428    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
429      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
430      - add an auxilliary variable "bet" and fix store directives and keys in
431        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
432        less exact gradients in my tests); but there are still
433        recomputation warning (although gradients are sort of OK), when
434        SEAICE_LSR_VECTORIZE is not defined, so this flag and
435        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
436      - update verification experiments lab_sea.
437      - change some comments in S/R seaice_calc_viscosities
438    o model/src:
439      - if staggerTimeStep=T, always apply exchange to velocity field in
440        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
441        (independent of using multi-dim advection or not); no effect on FWD run
442        but affects AD results (at machine truncation level): update output of
443        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
444        and isomip (oad: 12.d).
445    o pkg/generic_advdiff:
446      - stop if doAB_onGtGs is set to FALSE but ignored
447      - refine warning related to stability of tracer time-stepping
448        regarding internal wave dynamics.
449      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
450        on staggerTimeStep & implicitIntGravWave (will now get a warning
451        if potentially unstable).
452    o pkg/kl10:
453      - add new pkg "kl10" for mixing due to internal wave breaking, from
454        http://www.sciencedirect.com/science/article/pii/S1463500310000144
455        (contribution from Jody Klymak), tested in verification experiment
456        verification/internal_wave/input.kl10/
457    o isomip experiment:
458      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
459        (input.htd) and update the output.
460    o cd_code experiments:
461      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
462        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
463        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
464        update the corresponding output.
465    o pkg/seaice:
466      - reduce the number of include files and store directives in
467        S/R seaice_lsr_tridiagu/v
468      - change the order of loops in one case in S/R seaice_lsr_tridiagv
469        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
470        get rid off one store directive (a TAF bug?)
471      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
472        S/R seaice_lsr_tridiagv to change the loop range for consistency
473      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
474      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
475        S/R seaice_lsr_tridiagu/v (requires update of
476        offline_exf_seaice/input.dyn_jfnk)
477    
478    checkpoint65a (2014/07/27)
479    o model/src:
480      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
481        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
482        (topo in p-coords, ice-shelf in z-coords); update output of experiments
483        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
484    o model/src:
485      - collect momentum forcing tendency into local 2-D array (passed as argument
486        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
487        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
488        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
489      - collect T & S forcing tendency into local 2-D array (passed as argument to
490        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
491        affects results at machine truncation level (e.g., ocean: if using
492        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
493        correction due to vertical advection).
494      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
495        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
496        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
497        obcs_ctrl (ad & fwd grd @ 12 & 7).
498    o pkg/ptracers & diagnostics:
499      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
500        title (to avoid some unexpected truncation); sort out ptracers diags units.
501      - collect ptracer forcing tendency into local 2-D array (passed as argument
502        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
503    
504    checkpoint65 (2014/07/18)
505    o pkg/fizhi:
506      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
507        affects results at machine truncation level. Update output of experiments
508        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
509    o pkg/seaice: more clean up
510      - rename TAF common block tapes to be more consistent and remove
511        unnecessary duplicates
512      - add store directives to remove more recomputations, but use smaller
513        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
514        The idea behind this flag is to reduce the memory footprint when the
515        adjoint of the LSR is not required. As of now, defining the flag
516        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
517        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
518        For experiment offline_exf_seaice, this means on a linux box with gfortran
519        nearly a factor of 10 (but keep in mind there is mostly seaice code in
520        this experiment):
521        > size mitgcmuv_ad
522        text    data        bss     dec        hex
523        5100659 1216  220458952  225560827  d71c8fb
524        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
525        but only a moderate increase of 36% for global_ocean.cs32x15:
526        text    data        bss     dec        hex
527        6695027 1648 1014578664 1021275339 3cdf6ccb
528        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
529      - note: there are still recomputations in global_ocean.cs32x15 and
530        offline_exf_seaice and the gradient agreement changes (gets a
531        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
532      - in general, the AD gradients still are wrong
533    o OpenAD
534      - clean up code_oad/ directories somewhat by moving files
535        dontCompile, dontTransform, keepOriginal to OAD_support/
536    o model/src:
537      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
538        (not currently tested): add dissipation terms before NLFS rescaling of
539        tendencies (previously done after).
540    o pkg/diagnostics:
541      - write stats-diags in ascii file with more digits (same as in monitor).
542    o pkg/down_slope:
543      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
544        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
545    o model/src:
546      - new file "apply_forcing.F" containing all the code previously in
547        external_forcing.F, but with new argument list: pass, as new argument,
548        the current level tendency array to update (instead of a direct update
549        of the common bloc array). Change the corresponding calls.
550      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
551        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
552    o pkg/seaice/seaice_lsr, a little bit of clean up
553      - rearrange some code blocks, so that now all calculations for
554        setting up the right-hand-sides done within one single block
555        (I find that easier to read and understand)
556      - rearrange freedrift-code to reduce the number of ifdefs
557      - adjust some indentations and comments
558    
559    checkpoint64z (2014/07/10)
560    o model/src and several pkgs:
561      - change argument list of all S/R called from external_forcing.F and
562        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
563        to pass, as argument, the current level tendency array to update
564        (instead of a direct update of the common bloc array).
565      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
566      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
567    o pkg/seaice/seaice_lsr.F
568      - always initialize local arrays in seaice_lsr_tridiagu/v
569      - add more local tapes to seaice_lsr_tridiagu/v
570      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
571        keep it in bi/bj loop; this seems to be essential
572      - gradients are still wrong but only by 4-7 orders of magnitude
573        instead of 15 orders of magnitude, lab_sea improves a little
574    o pkg/seaice
575      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
576        generates unnecessary code in seaice_lsr_ad
577      - add more store directives in seaice_lsr to avoid unnecessary code
578        in seaice_lsr_ad
579      - exclude some residual computations in seaice_lsr when
580        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
581        in seaice_lsr_ad
582      - add more storing, a new tape (model/src/the_main_loop.F) and
583        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
584        and klockey should be checked by a specialist)
585      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
586        and update lab_sea after previous changes in pkg/seaice below
587    o pkg/autodiff:
588      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
589        viscFacInAd : run time parameters allowing for adjoint switches
590        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
591    o pkg/ecco:
592      - introduce cost_gencost_boxmean.F that computes a box mean
593        temperature (for use in adjoint sensitivity studies).
594    o model/src/set_defaults.F : initialize viscFacAdj to 1.
595    o pkg/mom_common/mom_calc_visc.F:
596      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
597    o pkg/seaice/seaice_summary.F:
598      - statement for SEAICEadjMODE now in autodiff_readparms.F
599    o pkg/seaice:
600    - remove some store directives and add new ones in an effort to get    - remove some store directives and add new ones in an effort to get
601      finally rid off the recomputation warnings. This is successful      finally rid off the recomputation warnings. This is successful
602      for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation      when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
603      warnings left), but there are still too many recomputations on the      defined (i.e. no extensive recomputation warnings left), but there
604      solver iteration level      are still too many recomputations on the solver iteration level
605      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
606    - move definition of MPSEUDOTIMESTEPS into TAMC-block in    - move definition of MPSEUDOTIMESTEPS into TAMC-block in
607      SEAICE_SIZE.h      SEAICE_SIZE.h
608    - add a store directive in S/R seaice_calc_viscosities    - add a store directive in S/R seaice_calc_viscosities
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