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revision 1.1976 by mlosch, Mon Apr 7 14:52:38 2014 UTC revision 1.2082 by jmc, Mon Oct 13 22:24:01 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 pkg/seaice:  checkpoint65f (2014/10/13)
8    - make deltaC a global variable, so that it can be used in ridging code  o pkg/ctrl, ecco, seaice : minor changes in headers
9    o global_oce_llc90 :
10      - ecco_v4 verification experiments now test generic cost
11        function and control capabilities added since checkpoint65c.
12    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
13    o pkg/ecco: increase modularity and improve logic
14      - ecco_toolbox.F (new) : basic operations that are often used,
15        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
16        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
17      - cost_gencal.F (new) : determine filnames and records.
18      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
19      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
20        and exploit the above functions leading to more compact code.
21      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
22      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
23        using_ers, using_gfo, using_mdt is now only defined within gencost)
24    o pkg/ecco: extend generic cost capabilities
25      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
26        capabilities via gencost_preproc (+ _c,_i,_r related params),
27        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
28        gencost_outputlevel arguments to cost_generic
29      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
30        and active_read, making room for gencost_preproc to take effect.
31        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
32      - pkg/ecco/cost_generic.F :
33        compute and store misfit maks*(model-data) in localdif that is
34        then used in cost and for output, output misfit if outlev.GT.0
35      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
36        rather gencost_barfile for deciding whether to write barfile
37      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
38      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
39        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
40      - pkg/ecco/ecco_summary.F : report gencost variables
41      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
42    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
43    o pkg/ecco: internal re-organization
44      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
45        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
46        mv relevant variables definition from ecco_cost.h to ecco.h,
47        make sure gencost routines only include ecco.h)
48      - throughout : add missing CCP switches, rm unused variables,
49        and rm un-necessary CPP switches
50      - throughout gencost routines : replace modelstartdate with
51        gencost_startdate when needed
52      - cost_bp_read.F : use arguments, instead of common blocs
53        so that it can be used also by (new) cost_gencost_bpv4.F
54      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
55      - ecco_phys.F : compute etanFull
56      - ecco_readparms.F : rename using_topex as using_tpj, add
57        bpv4-grace to gencost list, initialize added parameters
58      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
59    
60    checkpoint65e (2014/09/28)
61    o pkg/obcs:
62      - replaced the just-added CPP options with run-time variables
63        (see pkg/obcs/OBCS_PARAMS.h for details)
64    o pkg/obcs:
65      - add additional CPP options for sponge boundary layers
66        (see pkg/obcs/OBCS_OPTIONS.h for details)
67    o pkg/atm_phys:
68      - implement simple (obliquity only, assuming circular planet orbit)
69        seasonal cycle for incoming insolation ; used when run-time parameter
70        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
71    o pkg/exf, pkg/ecco, pkg/ctrl:
72      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
73      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
74      - implement gentim2d for xx_tauu, xx_tauv
75    o pkg/ctrl, pkg/ecco :
76      - fix and complement the generic controls implementation
77    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
78        pkg/shelfice/shelfice_thermodynamics.F,
79        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
80        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
81      - add weight in CTRL_GET_GEN calls
82    o pkg/ctrl :
83      - ctrl_get_gen.F : add weight as input parameter, and apply
84        it directly rather than using smooth_correl2Dw (to be retired).
85      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
86    o pkg/ctrl :
87      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
88        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
89      - re-activate ctrl_summary (call in ctrl_init.F)
90    o pkg/ctrl/ctrl_cost_gen.F :
91      - fix CCP brackets, remove un-necessary myiter, mytime
92    o pkg/ecco, pkg/ctrl :
93      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
94      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
95      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
96      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
97    
98    checkpoint65d (2014/09/15)
99    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
100      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
101        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
102    o pkg/ctrl/ctrl_map_ini_genarr.F :
103      - remove compilation failure
104      - replace hard coded example
105      - use ctrl_map_ini_gen2D, 3D
106    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
107      - on/off switch based upon xx_genarr2d_weight,3d
108    o src/packages_init_variables.F :
109      - regroup pkg/estimation calls
110      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
111        (moved to ctrl_init_variables)
112    o cost/cost_init_varia.F :
113      - remove ecco_cost_init_varia
114        (moved to ecco_init_varia)
115    o ctrl/ctrl_init_variables.F :
116      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
117      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
118    o ctrl/ctrl_map_ini.F :
119      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
120        (moved to ctrl_init_variables)
121    o ctrl/ctrl_map_ini_ecco.F :
122      - remove ECCO_PHYS (mv to ecco_init_varia)
123      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
124    o ecco/ecco_ad_diff.list :
125      - add ecco_init_varia.f
126    o ecco/ecco_init_varia.F
127      - new routine
128    o pkg/streamice:
129      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
130        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
131      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
132    o pkg/generic_advdiff:
133      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
134    o pkg/exf:
135      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
136         xxg_precip capability
137      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
138    o pkg/ctrl:
139      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
140    o model/src/load_fields_driver.F :
141      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
142        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
143    o OpenAD verification experiments:
144      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
145        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
146        for now, only in pkgs used in OpenAD verification experiments.
147      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
148        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
149        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
150        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
151    o OpenAD verification tests:
152      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
153      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
154        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
155      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
156        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
157    o model/src & generic_advdiff:
158      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
159        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
160        dynamics requires valid tracer forcing only over tile interior but, for
161        some diagnostics, may need to extend it over 1 point in tile halo region.
162      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
163        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
164        setting in temp/salt/ptracer_integrate.F
165    o pkg/dic:
166      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
167        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
168        in gchem_forcing_sep.F
169    o pkg/autodiff & obcs:
170      - add storage of current OB values for U & V (was already done for T & S).
171    
172    checkpoint65c (2014/08/30)
173    o pkg/dic:
174      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
175        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
176        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
177    o verification:
178      - new experiment testing OBCS and DIC pkgs, using params & output from
179        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
180        passage: take OBCS from the last year of a 2 yrs simulation and initial
181        conditions from t=1.yr while keeping the same forcing.
182    o model/src:
183      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
184        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
185    o pkg/diagnostics (Stats-Diags):
186      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
187        a) refine region where stats are computed, excluding where arrhFac=0 ;
188        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
189        c) extend regional stats over the region edges (for U or V pt location).
190    o pkg/gchem:
191      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
192        pkg/dic is currently changing/updating ptracers values beyond the OB).
193    o verification (hs94):
194      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
195        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
196        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
197        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
198    o pkg/ptracers:
199      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
200        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
201      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
202        with AB-2 code (so that it get tested).
203    o model/src:
204      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
205        with AB-2 code (previously only available with AB-3 code).
206        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
207        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
208        there, by calling CYCLE_AB_TRACER).
209    o pkg/generic_advdiff:
210      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
211        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
212        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
213        S/R temp/salt/ptracers_integrate.F
214    o model/src & pkg/ptracers:
215      - remove common block variables gT,gS (in DYNVARS.h), except when
216         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
217      - remove common block variable gPtr.
218    o model/src & pkgs:
219      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
220         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
221         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
222         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
223      + change accordingly all calling S/R.
224      - use local temperature/salinity/ptracer tendency array (without bi,bj)
225        in S/R temp/salt/ptracers_integrate.F
226    o pkg/seaice:
227      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
228        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
229      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
230        in seaice_lsr
231      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
232        in s/r seaice_lsr_calc_coeffs
233    o pkg/mdsio:
234      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
235        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
236        too long (e.g., > MAX_LEN_FNAM/2 )
237    
238    checkpoint65b (2014/08/12)
239    o pkg/matrix:
240      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
241    o model/src:
242      - fix initialisation of geothermalFile; compile geothermal-flux code in
243        natl_box verification experiment.
244    o model/src & pkg/down_slope:
245      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
246      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
247        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
248        results at machine truncation level: update output of experiments
249        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
250    o pkg/diagnostics (Stats-Diags):
251      - do not cumulate the full volume when DIAGNOSTICS_FILL is
252        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
253        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
254        times (but Min,Max and StD are still wrong).
255    o model/src:
256      - add geothermal flux forcing: read in ini_forcing.F as time-constant
257        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
258    o model/src:
259      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
260        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
261        arrays are already updated while adjustments (filters, conv.adjustment) are
262        still applied later, in S/R TRACERS_CORRECTION_STEP.
263    o model/src:
264      - store in common bloc array "rhoInSitu" the virtual potential temperature
265        anomaly that is used to compute geopotential: this make the atmos code
266        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
267    o pkg/seaice/seaice_lsr.F
268      - rename integer variable ilcall to ipass (that's what it is called
269        in the residual diagnostics
270      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
271        default) for improved non-linear convergence of the first few steps
272      - adjust a few comments and add new ones to explain some of the store
273        directives
274    o pkg/generic_advdiff (& ptracers):
275      - re-work the code to check for valid advection scheme and for minimum
276        size of overlap (now stored in local common bloc in gad_advscheme.F)
277    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
278      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
279      - add an auxilliary variable "bet" and fix store directives and keys in
280        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
281        less exact gradients in my tests); but there are still
282        recomputation warning (although gradients are sort of OK), when
283        SEAICE_LSR_VECTORIZE is not defined, so this flag and
284        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
285      - update verification experiments lab_sea.
286      - change some comments in S/R seaice_calc_viscosities
287    o model/src:
288      - if staggerTimeStep=T, always apply exchange to velocity field in
289        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
290        (independent of using multi-dim advection or not); no effect on FWD run
291        but affects AD results (at machine truncation level): update output of
292        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
293        and isomip (oad: 12.d).
294    o pkg/generic_advdiff:
295      - stop if doAB_onGtGs is set to FALSE but ignored
296      - refine warning related to stability of tracer time-stepping
297        regarding internal wave dynamics.
298      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
299        on staggerTimeStep & implicitIntGravWave (will now get a warning
300        if potentially unstable).
301    o pkg/kl10:
302      - add new pkg "kl10" for mixing due to internal wave breaking, from
303        http://www.sciencedirect.com/science/article/pii/S1463500310000144
304        (contribution from Jody Klymak), tested in verification experiment
305        verification/internal_wave/input.kl10/
306    o isomip experiment:
307      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
308        (input.htd) and update the output.
309    o cd_code experiments:
310      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
311        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
312        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
313        update the corresponding output.
314    o pkg/seaice:
315      - reduce the number of include files and store directives in
316        S/R seaice_lsr_tridiagu/v
317      - change the order of loops in one case in S/R seaice_lsr_tridiagv
318        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
319        get rid off one store directive (a TAF bug?)
320      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
321        S/R seaice_lsr_tridiagv to change the loop range for consistency
322      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
323      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
324        S/R seaice_lsr_tridiagu/v (requires update of
325        offline_exf_seaice/input.dyn_jfnk)
326    
327    checkpoint65a (2014/07/27)
328    o model/src:
329      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
330        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
331        (topo in p-coords, ice-shelf in z-coords); update output of experiments
332        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
333    o model/src:
334      - collect momentum forcing tendency into local 2-D array (passed as argument
335        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
336        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
337        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
338      - collect T & S forcing tendency into local 2-D array (passed as argument to
339        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
340        affects results at machine truncation level (e.g., ocean: if using
341        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
342        correction due to vertical advection).
343      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
344        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
345        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
346        obcs_ctrl (ad & fwd grd @ 12 & 7).
347    o pkg/ptracers & diagnostics:
348      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
349        title (to avoid some unexpected truncation); sort out ptracers diags units.
350      - collect ptracer forcing tendency into local 2-D array (passed as argument
351        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
352    
353    checkpoint65 (2014/07/18)
354    o pkg/fizhi:
355      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
356        affects results at machine truncation level. Update output of experiments
357        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
358    o pkg/seaice: more clean up
359      - rename TAF common block tapes to be more consistent and remove
360        unnecessary duplicates
361      - add store directives to remove more recomputations, but use smaller
362        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
363        The idea behind this flag is to reduce the memory footprint when the
364        adjoint of the LSR is not required. As of now, defining the flag
365        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
366        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
367        For experiment offline_exf_seaice, this means on a linux box with gfortran
368        nearly a factor of 10 (but keep in mind there is mostly seaice code in
369        this experiment):
370        > size mitgcmuv_ad
371        text    data        bss     dec        hex  
372        5100659 1216  220458952  225560827  d71c8fb
373        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
374        but only a moderate increase of 36% for global_ocean.cs32x15:
375        text    data        bss     dec        hex
376        6695027 1648 1014578664 1021275339 3cdf6ccb
377        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
378      - note: there are still recomputations in global_ocean.cs32x15 and
379        offline_exf_seaice and the gradient agreement changes (gets a
380        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
381      - in general, the AD gradients still are wrong
382    o OpenAD
383      - clean up code_oad/ directories somewhat by moving files
384        dontCompile, dontTransform, keepOriginal to OAD_support/
385    o model/src:
386      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
387        (not currently tested): add dissipation terms before NLFS rescaling of
388        tendencies (previously done after).
389    o pkg/diagnostics:
390      - write stats-diags in ascii file with more digits (same as in monitor).
391    o pkg/down_slope:
392      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
393        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
394    o model/src:
395      - new file "apply_forcing.F" containing all the code previously in
396        external_forcing.F, but with new argument list: pass, as new argument,
397        the current level tendency array to update (instead of a direct update
398        of the common bloc array). Change the corresponding calls.
399      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
400        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
401    o pkg/seaice/seaice_lsr, a little bit of clean up
402      - rearrange some code blocks, so that now all calculations for
403        setting up the right-hand-sides done within one single block
404        (I find that easier to read and understand)
405      - rearrange freedrift-code to reduce the number of ifdefs
406      - adjust some indentations and comments
407    
408    checkpoint64z (2014/07/10)
409    o model/src and several pkgs:
410      - change argument list of all S/R called from external_forcing.F and
411        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
412        to pass, as argument, the current level tendency array to update
413        (instead of a direct update of the common bloc array).
414      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
415      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
416    o pkg/seaice/seaice_lsr.F
417      - always initialize local arrays in seaice_lsr_tridiagu/v
418      - add more local tapes to seaice_lsr_tridiagu/v
419      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
420        keep it in bi/bj loop; this seems to be essential
421      - gradients are still wrong but only by 4-7 orders of magnitude
422        instead of 15 orders of magnitude, lab_sea improves a little
423    o pkg/seaice
424      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
425        generates unnecessary code in seaice_lsr_ad
426      - add more store directives in seaice_lsr to avoid unnecessary code
427        in seaice_lsr_ad
428      - exclude some residual computations in seaice_lsr when
429        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
430        in seaice_lsr_ad
431      - add more storing, a new tape (model/src/the_main_loop.F) and
432        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
433        and klockey should be checked by a specialist)
434      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
435        and update lab_sea after previous changes in pkg/seaice below
436    o pkg/autodiff:
437      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
438        viscFacInAd : run time parameters allowing for adjoint switches
439        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
440    o pkg/ecco:
441      - introduce cost_gencost_boxmean.F that computes a box mean
442        temperature (for use in adjoint sensitivity studies).
443    o model/src/set_defaults.F : initialize viscFacAdj to 1.
444    o pkg/mom_common/mom_calc_visc.F:
445      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
446    o pkg/seaice/seaice_summary.F:
447      - statement for SEAICEadjMODE now in autodiff_readparms.F
448    o pkg/seaice:
449      - remove some store directives and add new ones in an effort to get
450        finally rid off the recomputation warnings. This is successful
451        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
452        defined (i.e. no extensive recomputation warnings left), but there
453        are still too many recomputations on the solver iteration level
454      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
455      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
456        SEAICE_SIZE.h
457      - add a store directive in S/R seaice_calc_viscosities
458    o pkg/seaice (ITD code):
459      - fix definition of Hlimit for multi-threaded case
460      - use double precision arithmetic to compute Hlimit: this affects results;
461        update output of experiment seaice_itd.
462    o replace content of verification/seaice_itd
463      - instead of a 1D column use the configuration of offline_exf_seaice
464        to test the ice thickness distribution code with ridging
465      - this is a first shot at this experiment
466      - change of some defaults of ridging parameters SEAICEhStar (from
467        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
468        and lot of new comments.
469    
470    checkpoint64y (2014/06/20)
471    o pkg/seaice/seaice_reg_ridge.F:
472      - modify the regularization of very small volumes of ice; only check
473        total volume HEFF, and do not apply correction to individual ice
474        classes because that leads to funny patterns in the heat and fw-fluxes
475        into the ocean. Adjust seaice_itd/results/output.txt
476      - replace nITD by SEAICE_multDim in loop-ranges
477    o pkg/exf:
478      - add code to process the case field period = -12. with UV interpolation.
479      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
480        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
481    o verification/global_with_exf:
482      - switch all fields period to -12. (was previously untested) in input/data.exf
483        (but keep secondary test ".yearly" unchanged); update the reference output.
484    o pkg/cal:
485      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
486    o pkg/exf:
487      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
488        to replace logical switch "exf_verbose"
489      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
490    o pkg/sbo:
491      - update from Katherine Quinn: evaluate mass directly from density and SSH
492        (budget using Finite Volume method) instead of from bottom pressure.
493      - allow testreport to collect few selected SBO output ; tested in exp.
494        global_ocean.90x40x15 (after updating the results, to include SBO output).
495      - fix some multi-threading issues (in output part).
496    o model/src & most packages:
497      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
498      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
499        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
500        "data.{pkg}" exist ; and leave the S/R (return) just after.
501      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
502        + call LAND_READPARMS from packages_readparms.F
503    o pkg/seaice:
504      - remove code that resets useThSice in S/R seaice_readparms and
505        replace it by a warning in S/R seaice_check
506      - remove parameter MULTDIM, replace with nITD and runtime
507        parameter SEAICE_multDim (still hard-wired to nITD if
508        SEAICE_ITD is defined)
509    
510    checkpoint64x (2014/05/24)
511    o verification/lab_sea:
512      - update adjoint and TLM output following changes to pkg/salt_plume
513      - un-do the update after putting back local recip_Cp in few places.
514    o pkg/salt_plume: modifications by An Nguyen:
515      - add capability to do brine rejection (salt-plume) as function of
516        volume+tracers (instead of only salinity tracer).
517      - conserve volume by exchanging volume from each kLev to above to
518        accommodate in-coming brine volume
519      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
520      - switch KPP surf buoyancy due to brine forcing to 3-d
521        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
522      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
523      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
524        in East/West Arctic.
525    o pkg/sbo:
526      - incorporate modifications from Katherine Quinn to enable the use of sbo
527        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
528        output for future testreport verification (unfinished).
529    o pkg/atm_phys:
530      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
531        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
532        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
533    o pkg/seaice
534      seaice_calc_ice_strength.F: modify expression to avoid divisions
535        (affects truncation)
536      seaice_do_ridging.F: clean up the insectarium
537      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
538      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
539      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
540      - add some debugging information and error messages (warnings)
541    o model/src: modifications relatd to atmosphere p*:
542      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
543      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
544        of vertical profile tRef in geopotential background and anomaly.
545      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
546        and pkg/atm_phys.
547      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
548        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
549    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
550    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
551        not used right now, but can be used in BGC packages to fix conservation.
552    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
553        other packages too.
554    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
555        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
556    o model/src:
557      - since we have several heat capacity (even in model/src), define "recip_Cp"
558        as local variable (no longer in common block) to avoid any confusion.
559      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
560    o pkg/exf:
561      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
562        air density as function of air Temp, Humidity and atm pressure.
563    
564    checkpoint64w (2014/05/02)
565    o verification:
566      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
567        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
568        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
569        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
570        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
571    o model/src: for atmosphere in p* coords:
572      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
573      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
574        but not yet activated.
575    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
576      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
577      - this changes the results (but not for any verification experiment, because
578        none tests this), but avoids having an extra field in the restart files
579    o pkg/seaice: remove global variable TICE (not needed)
580      - replace by TICES or local variable where necessary (cost_seaice_test,
581        seaice_diagnostics_state)
582      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
583      - use specific read/write routines for reading and writing individual leves
584        of a multilevel field
585    o pkg/ctrl & model/inc:
586      - move additional anomaly fields of control vars (related to options:
587         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
588        from DYNVARS.h into new header file: CTRL_FIELDS.h
589    o pkg/seaice: some small modifications to the ridging code
590      - make fw2ObyRidge a global variable and add the freshwater flux to
591        seaice_growth
592      - pass actual thickness from seaice_prepare_ridging, so that it is
593        computed only in one place and compute it in the same way as in
594        seaice_growth
595      - initialise more fields in seaice_do_ridging that where cause floating
596        point exceptions over land
597    o pkg/seaice: preparations for ridging code and first real ridging code
598      - move most of "PART 1" of S/R seaice_growth into a new and separate
599        S/R seaice_reg_ridge that will both regularize the state variable after
600        advection call the actual ridging routine;
601      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
602        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
603      - remove ridging code from seaice_advdiff
604      - clean up remaining part 1 of seaice_growth in an attempt to make it
605        more readable (this is probably subjective)
606      - call seaice_itd_redist once in the initialisation phase to have the initial
607        conditions in the correct category
608      - finally: add new ridging routine for ITD code
609    
610    checkpoint64v (2014/04/11)
611    o pkg/ecco:
612      - add runtime parameters mdt[start,end]date[1,2]
613      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
614    o pkg/seaice:
615      - make deltaC a global variable, so that it can be used in ridging code
616    - first step towards ridging: introduce new routines that compute    - first step towards ridging: introduce new routines that compute
617      ice strength based on ridging parameters      ice strength based on ridging parameters
618      - add diagnostic for HSNOWITD
619      - add opnWtrFrac as a global variable (required for ridging scheme)
620    o pkg/salt_plume + pkg/seaice/seaice_growth.F
621      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
622        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
623  o verification/hs94.1x64x5:  o verification/hs94.1x64x5:
624    - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h    - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
625    - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.    - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
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