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revision 1.1950 by dimitri, Thu Dec 19 01:06:09 2013 UTC revision 1.2071 by gforget, Wed Sep 24 20:54:02 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 pkg/atm_phys:
8  o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the    - implement simple (obliquity only, assuming circular planet orbit)
9    SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8      seasonal cycle for incoming insolation ; used when run-time parameter
10        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
11    o pkg/exf, pkg/ecco, pkg/ctrl:
12        - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
13        - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
14        - implement gentim2d for xx_tauu, xx_tauv
15    o pkg/ctrl, pkg/ecco :
16        - fix and complement the generic controls implementation
17    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
18        pkg/shelfice/shelfice_thermodynamics.F,
19        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
20        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
21      - add weight in CTRL_GET_GEN calls
22    o pkg/ctrl :
23      - ctrl_get_gen.F : add weight as input parameter, and apply
24        it directly rather than using smooth_correl2Dw (to be retired).
25      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
26    o pkg/ctrl :
27      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
28        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
29      - re-activate ctrl_summary (call in ctrl_init.F)
30    o pkg/ctrl/ctrl_cost_gen.F :
31      - fix CCP brackets, remove un-necessary myiter, mytime
32    o pkg/ecco, pkg/ctrl :
33      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
34      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
35      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
36      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
37    
38    checkpoint65d (2014/09/15)
39    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
40      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
41        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
42    o pkg/ctrl/ctrl_map_ini_genarr.F :
43      - remove compilation failure
44      - replace hard coded example
45      - use ctrl_map_ini_gen2D, 3D
46    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
47      - on/off switch based upon xx_genarr2d_weight,3d
48    o src/packages_init_variables.F :
49      - regroup pkg/estimation calls
50      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
51        (moved to ctrl_init_variables)
52    o cost/cost_init_varia.F :
53      - remove ecco_cost_init_varia
54        (moved to ecco_init_varia)
55    o ctrl/ctrl_init_variables.F :
56      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
57      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
58    o ctrl/ctrl_map_ini.F :
59      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
60        (moved to ctrl_init_variables)
61    o ctrl/ctrl_map_ini_ecco.F :
62      - remove ECCO_PHYS (mv to ecco_init_varia)
63      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
64    o ecco/ecco_ad_diff.list :
65      - add ecco_init_varia.f
66    o ecco/ecco_init_varia.F
67      - new routine
68    o pkg/streamice:
69      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
70        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
71      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
72    o pkg/generic_advdiff:
73      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
74    o pkg/exf:
75      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
76         xxg_precip capability
77      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
78    o pkg/ctrl:
79      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
80    o model/src/load_fields_driver.F :
81      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
82        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
83    o OpenAD verification experiments:
84      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
85        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
86        for now, only in pkgs used in OpenAD verification experiments.
87      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
88        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
89        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
90        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
91    o OpenAD verification tests:
92      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
93      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
94        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
95      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
96        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
97    o model/src & generic_advdiff:
98      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
99        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
100        dynamics requires valid tracer forcing only over tile interior but, for
101        some diagnostics, may need to extend it over 1 point in tile halo region.
102      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
103        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
104        setting in temp/salt/ptracer_integrate.F
105    o pkg/dic:
106      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
107        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
108        in gchem_forcing_sep.F
109    o pkg/autodiff & obcs:
110      - add storage of current OB values for U & V (was already done for T & S).
111    
112    checkpoint65c (2014/08/30)
113    o pkg/dic:
114      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
115        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
116        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
117    o verification:
118      - new experiment testing OBCS and DIC pkgs, using params & output from
119        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
120        passage: take OBCS from the last year of a 2 yrs simulation and initial
121        conditions from t=1.yr while keeping the same forcing.
122    o model/src:
123      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
124        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
125    o pkg/diagnostics (Stats-Diags):
126      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
127        a) refine region where stats are computed, excluding where arrhFac=0 ;
128        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
129        c) extend regional stats over the region edges (for U or V pt location).
130    o pkg/gchem:
131      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
132        pkg/dic is currently changing/updating ptracers values beyond the OB).
133    o verification (hs94):
134      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
135        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
136        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
137        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
138    o pkg/ptracers:
139      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
140        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
141      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
142        with AB-2 code (so that it get tested).
143    o model/src:
144      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
145        with AB-2 code (previously only available with AB-3 code).
146        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
147        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
148        there, by calling CYCLE_AB_TRACER).
149    o pkg/generic_advdiff:
150      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
151        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
152        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
153        S/R temp/salt/ptracers_integrate.F
154    o model/src & pkg/ptracers:
155      - remove common block variables gT,gS (in DYNVARS.h), except when
156         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
157      - remove common block variable gPtr.
158    o model/src & pkgs:
159      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
160         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
161         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
162         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
163      + change accordingly all calling S/R.
164      - use local temperature/salinity/ptracer tendency array (without bi,bj)
165        in S/R temp/salt/ptracers_integrate.F
166    o pkg/seaice:
167      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
168        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
169      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
170        in seaice_lsr
171      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
172        in s/r seaice_lsr_calc_coeffs
173    o pkg/mdsio:
174      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
175        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
176        too long (e.g., > MAX_LEN_FNAM/2 )
177    
178    checkpoint65b (2014/08/12)
179    o pkg/matrix:
180      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
181    o model/src:
182      - fix initialisation of geothermalFile; compile geothermal-flux code in
183        natl_box verification experiment.
184    o model/src & pkg/down_slope:
185      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
186      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
187        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
188        results at machine truncation level: update output of experiments
189        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
190    o pkg/diagnostics (Stats-Diags):
191      - do not cumulate the full volume when DIAGNOSTICS_FILL is
192        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
193        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
194        times (but Min,Max and StD are still wrong).
195    o model/src:
196      - add geothermal flux forcing: read in ini_forcing.F as time-constant
197        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
198    o model/src:
199      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
200        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
201        arrays are already updated while adjustments (filters, conv.adjustment) are
202        still applied later, in S/R TRACERS_CORRECTION_STEP.
203    o model/src:
204      - store in common bloc array "rhoInSitu" the virtual potential temperature
205        anomaly that is used to compute geopotential: this make the atmos code
206        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
207    o pkg/seaice/seaice_lsr.F
208      - rename integer variable ilcall to ipass (that's what it is called
209        in the residual diagnostics
210      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
211        default) for improved non-linear convergence of the first few steps
212      - adjust a few comments and add new ones to explain some of the store
213        directives
214    o pkg/generic_advdiff (& ptracers):
215      - re-work the code to check for valid advection scheme and for minimum
216        size of overlap (now stored in local common bloc in gad_advscheme.F)
217    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
218      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
219      - add an auxilliary variable "bet" and fix store directives and keys in
220        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
221        less exact gradients in my tests); but there are still
222        recomputation warning (although gradients are sort of OK), when
223        SEAICE_LSR_VECTORIZE is not defined, so this flag and
224        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
225      - update verification experiments lab_sea.
226      - change some comments in S/R seaice_calc_viscosities
227    o model/src:
228      - if staggerTimeStep=T, always apply exchange to velocity field in
229        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
230        (independent of using multi-dim advection or not); no effect on FWD run
231        but affects AD results (at machine truncation level): update output of
232        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
233        and isomip (oad: 12.d).
234    o pkg/generic_advdiff:
235      - stop if doAB_onGtGs is set to FALSE but ignored
236      - refine warning related to stability of tracer time-stepping
237        regarding internal wave dynamics.
238      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
239        on staggerTimeStep & implicitIntGravWave (will now get a warning
240        if potentially unstable).
241    o pkg/kl10:
242      - add new pkg "kl10" for mixing due to internal wave breaking, from
243        http://www.sciencedirect.com/science/article/pii/S1463500310000144
244        (contribution from Jody Klymak), tested in verification experiment
245        verification/internal_wave/input.kl10/
246    o isomip experiment:
247      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
248        (input.htd) and update the output.
249    o cd_code experiments:
250      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
251        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
252        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
253        update the corresponding output.
254    o pkg/seaice:
255      - reduce the number of include files and store directives in
256        S/R seaice_lsr_tridiagu/v
257      - change the order of loops in one case in S/R seaice_lsr_tridiagv
258        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
259        get rid off one store directive (a TAF bug?)
260      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
261        S/R seaice_lsr_tridiagv to change the loop range for consistency
262      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
263      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
264        S/R seaice_lsr_tridiagu/v (requires update of
265        offline_exf_seaice/input.dyn_jfnk)
266    
267    checkpoint65a (2014/07/27)
268    o model/src:
269      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
270        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
271        (topo in p-coords, ice-shelf in z-coords); update output of experiments
272        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
273    o model/src:
274      - collect momentum forcing tendency into local 2-D array (passed as argument
275        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
276        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
277        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
278      - collect T & S forcing tendency into local 2-D array (passed as argument to
279        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
280        affects results at machine truncation level (e.g., ocean: if using
281        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
282        correction due to vertical advection).
283      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
284        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
285        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
286        obcs_ctrl (ad & fwd grd @ 12 & 7).
287    o pkg/ptracers & diagnostics:
288      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
289        title (to avoid some unexpected truncation); sort out ptracers diags units.
290      - collect ptracer forcing tendency into local 2-D array (passed as argument
291        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
292    
293    checkpoint65 (2014/07/18)
294    o pkg/fizhi:
295      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
296        affects results at machine truncation level. Update output of experiments
297        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
298    o pkg/seaice: more clean up
299      - rename TAF common block tapes to be more consistent and remove
300        unnecessary duplicates
301      - add store directives to remove more recomputations, but use smaller
302        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
303        The idea behind this flag is to reduce the memory footprint when the
304        adjoint of the LSR is not required. As of now, defining the flag
305        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
306        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
307        For experiment offline_exf_seaice, this means on a linux box with gfortran
308        nearly a factor of 10 (but keep in mind there is mostly seaice code in
309        this experiment):
310        > size mitgcmuv_ad
311        text    data        bss     dec        hex  
312        5100659 1216  220458952  225560827  d71c8fb
313        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
314        but only a moderate increase of 36% for global_ocean.cs32x15:
315        text    data        bss     dec        hex
316        6695027 1648 1014578664 1021275339 3cdf6ccb
317        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
318      - note: there are still recomputations in global_ocean.cs32x15 and
319        offline_exf_seaice and the gradient agreement changes (gets a
320        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
321      - in general, the AD gradients still are wrong
322    o OpenAD
323      - clean up code_oad/ directories somewhat by moving files
324        dontCompile, dontTransform, keepOriginal to OAD_support/
325    o model/src:
326      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
327        (not currently tested): add dissipation terms before NLFS rescaling of
328        tendencies (previously done after).
329    o pkg/diagnostics:
330      - write stats-diags in ascii file with more digits (same as in monitor).
331    o pkg/down_slope:
332      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
333        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
334    o model/src:
335      - new file "apply_forcing.F" containing all the code previously in
336        external_forcing.F, but with new argument list: pass, as new argument,
337        the current level tendency array to update (instead of a direct update
338        of the common bloc array). Change the corresponding calls.
339      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
340        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
341    o pkg/seaice/seaice_lsr, a little bit of clean up
342      - rearrange some code blocks, so that now all calculations for
343        setting up the right-hand-sides done within one single block
344        (I find that easier to read and understand)
345      - rearrange freedrift-code to reduce the number of ifdefs
346      - adjust some indentations and comments
347    
348    checkpoint64z (2014/07/10)
349    o model/src and several pkgs:
350      - change argument list of all S/R called from external_forcing.F and
351        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
352        to pass, as argument, the current level tendency array to update
353        (instead of a direct update of the common bloc array).
354      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
355      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
356    o pkg/seaice/seaice_lsr.F
357      - always initialize local arrays in seaice_lsr_tridiagu/v
358      - add more local tapes to seaice_lsr_tridiagu/v
359      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
360        keep it in bi/bj loop; this seems to be essential
361      - gradients are still wrong but only by 4-7 orders of magnitude
362        instead of 15 orders of magnitude, lab_sea improves a little
363    o pkg/seaice
364      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
365        generates unnecessary code in seaice_lsr_ad
366      - add more store directives in seaice_lsr to avoid unnecessary code
367        in seaice_lsr_ad
368      - exclude some residual computations in seaice_lsr when
369        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
370        in seaice_lsr_ad
371      - add more storing, a new tape (model/src/the_main_loop.F) and
372        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
373        and klockey should be checked by a specialist)
374      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
375        and update lab_sea after previous changes in pkg/seaice below
376    o pkg/autodiff:
377      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
378        viscFacInAd : run time parameters allowing for adjoint switches
379        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
380    o pkg/ecco:
381      - introduce cost_gencost_boxmean.F that computes a box mean
382        temperature (for use in adjoint sensitivity studies).
383    o model/src/set_defaults.F : initialize viscFacAdj to 1.
384    o pkg/mom_common/mom_calc_visc.F:
385      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
386    o pkg/seaice/seaice_summary.F:
387      - statement for SEAICEadjMODE now in autodiff_readparms.F
388    o pkg/seaice:
389      - remove some store directives and add new ones in an effort to get
390        finally rid off the recomputation warnings. This is successful
391        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
392        defined (i.e. no extensive recomputation warnings left), but there
393        are still too many recomputations on the solver iteration level
394      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
395      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
396        SEAICE_SIZE.h
397      - add a store directive in S/R seaice_calc_viscosities
398    o pkg/seaice (ITD code):
399      - fix definition of Hlimit for multi-threaded case
400      - use double precision arithmetic to compute Hlimit: this affects results;
401        update output of experiment seaice_itd.
402    o replace content of verification/seaice_itd
403      - instead of a 1D column use the configuration of offline_exf_seaice
404        to test the ice thickness distribution code with ridging
405      - this is a first shot at this experiment
406      - change of some defaults of ridging parameters SEAICEhStar (from
407        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
408        and lot of new comments.
409    
410    checkpoint64y (2014/06/20)
411    o pkg/seaice/seaice_reg_ridge.F:
412      - modify the regularization of very small volumes of ice; only check
413        total volume HEFF, and do not apply correction to individual ice
414        classes because that leads to funny patterns in the heat and fw-fluxes
415        into the ocean. Adjust seaice_itd/results/output.txt
416      - replace nITD by SEAICE_multDim in loop-ranges
417    o pkg/exf:
418      - add code to process the case field period = -12. with UV interpolation.
419      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
420        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
421    o verification/global_with_exf:
422      - switch all fields period to -12. (was previously untested) in input/data.exf
423        (but keep secondary test ".yearly" unchanged); update the reference output.
424    o pkg/cal:
425      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
426    o pkg/exf:
427      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
428        to replace logical switch "exf_verbose"
429      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
430    o pkg/sbo:
431      - update from Katherine Quinn: evaluate mass directly from density and SSH
432        (budget using Finite Volume method) instead of from bottom pressure.
433      - allow testreport to collect few selected SBO output ; tested in exp.
434        global_ocean.90x40x15 (after updating the results, to include SBO output).
435      - fix some multi-threading issues (in output part).
436    o model/src & most packages:
437      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
438      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
439        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
440        "data.{pkg}" exist ; and leave the S/R (return) just after.
441      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
442        + call LAND_READPARMS from packages_readparms.F
443    o pkg/seaice:
444      - remove code that resets useThSice in S/R seaice_readparms and
445        replace it by a warning in S/R seaice_check
446      - remove parameter MULTDIM, replace with nITD and runtime
447        parameter SEAICE_multDim (still hard-wired to nITD if
448        SEAICE_ITD is defined)
449    
450    checkpoint64x (2014/05/24)
451    o verification/lab_sea:
452      - update adjoint and TLM output following changes to pkg/salt_plume
453      - un-do the update after putting back local recip_Cp in few places.
454    o pkg/salt_plume: modifications by An Nguyen:
455      - add capability to do brine rejection (salt-plume) as function of
456        volume+tracers (instead of only salinity tracer).
457      - conserve volume by exchanging volume from each kLev to above to
458        accommodate in-coming brine volume
459      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
460      - switch KPP surf buoyancy due to brine forcing to 3-d
461        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
462      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
463      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
464        in East/West Arctic.
465    o pkg/sbo:
466      - incorporate modifications from Katherine Quinn to enable the use of sbo
467        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
468        output for future testreport verification (unfinished).
469    o pkg/atm_phys:
470      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
471        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
472        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
473    o pkg/seaice
474      seaice_calc_ice_strength.F: modify expression to avoid divisions
475        (affects truncation)
476      seaice_do_ridging.F: clean up the insectarium
477      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
478      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
479      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
480      - add some debugging information and error messages (warnings)
481    o model/src: modifications relatd to atmosphere p*:
482      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
483      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
484        of vertical profile tRef in geopotential background and anomaly.
485      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
486        and pkg/atm_phys.
487      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
488        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
489    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
490    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
491        not used right now, but can be used in BGC packages to fix conservation.
492    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
493        other packages too.
494    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
495        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
496    o model/src:
497      - since we have several heat capacity (even in model/src), define "recip_Cp"
498        as local variable (no longer in common block) to avoid any confusion.
499      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
500    o pkg/exf:
501      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
502        air density as function of air Temp, Humidity and atm pressure.
503    
504    checkpoint64w (2014/05/02)
505    o verification:
506      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
507        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
508        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
509        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
510        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
511    o model/src: for atmosphere in p* coords:
512      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
513      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
514        but not yet activated.
515    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
516      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
517      - this changes the results (but not for any verification experiment, because
518        none tests this), but avoids having an extra field in the restart files
519    o pkg/seaice: remove global variable TICE (not needed)
520      - replace by TICES or local variable where necessary (cost_seaice_test,
521        seaice_diagnostics_state)
522      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
523      - use specific read/write routines for reading and writing individual leves
524        of a multilevel field
525    o pkg/ctrl & model/inc:
526      - move additional anomaly fields of control vars (related to options:
527         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
528        from DYNVARS.h into new header file: CTRL_FIELDS.h
529    o pkg/seaice: some small modifications to the ridging code
530      - make fw2ObyRidge a global variable and add the freshwater flux to
531        seaice_growth
532      - pass actual thickness from seaice_prepare_ridging, so that it is
533        computed only in one place and compute it in the same way as in
534        seaice_growth
535      - initialise more fields in seaice_do_ridging that where cause floating
536        point exceptions over land
537    o pkg/seaice: preparations for ridging code and first real ridging code
538      - move most of "PART 1" of S/R seaice_growth into a new and separate
539        S/R seaice_reg_ridge that will both regularize the state variable after
540        advection call the actual ridging routine;
541      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
542        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
543      - remove ridging code from seaice_advdiff
544      - clean up remaining part 1 of seaice_growth in an attempt to make it
545        more readable (this is probably subjective)
546      - call seaice_itd_redist once in the initialisation phase to have the initial
547        conditions in the correct category
548      - finally: add new ridging routine for ITD code
549    
550    checkpoint64v (2014/04/11)
551    o pkg/ecco:
552      - add runtime parameters mdt[start,end]date[1,2]
553      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
554    o pkg/seaice:
555      - make deltaC a global variable, so that it can be used in ridging code
556      - first step towards ridging: introduce new routines that compute
557        ice strength based on ridging parameters
558      - add diagnostic for HSNOWITD
559      - add opnWtrFrac as a global variable (required for ridging scheme)
560    o pkg/salt_plume + pkg/seaice/seaice_growth.F
561      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
562        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
563    o verification/hs94.1x64x5:
564      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
565      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
566    o autodiff:
567      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
568        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
569        For now, only in pkgs used in verification/hs94.1x64x5.
570      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
571        which are specific to TAF/TAMC).
572      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
573        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
574        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
575      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
576        building mitgcmuv_ad (make adAll).
577    o pkg/ecco:
578      - cost_gencost_seaicev4.F:
579         reformulate proxy cost as function of sst and local param SEAICE_freeze
580         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
581      - add stop statement if old names siv4-[sst,vol] are used
582      - add snapshots + cost reports for atmospheric longwave
583      - remove factor 0.1 in front of wtau[u,v]
584      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
585         ALLOW_TMI_SST_COST_CONTRIBUTION
586    o pkg/atm_phys:
587      - add some diagnostics for Short-wave and for convection S/R.
588    o pkg/seaice/seaice_growth:
589      - fix a bug in the lateral melt parameterization for SEAICE_ITD
590        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
591      - rearrange loop order for better vector code in the same code block
592      - rewrite the floeDiameter formula to have fewer divisions
593      -  (miraculously) none of this changes the results of seaice_itd
594    o pkg/smooth:
595      - move param smooth2Ddiffnbt to pkg/ecco
596    o pkg/salt_plume:
597      - salt_plume_frac.F:
598         clean up local param names
599         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
600    o pkg/rw:
601      - add RS version of S/R READ_MFLDS_LEV.
602    o pkg/streamice:
603      - fix the restart test by writing/reading pickup_streamice files.
604    o pkg/seaice:
605      - refine checks for jfnk-related parameters
606      - comment out if statement with SEAICEuseIMEX parameter as long as there
607        is no IMEX code to avoid confusion and surprises
608    
609    checkpoint64u (2014/03/07)
610    o verification/MLAdjust:
611      - rename secondary test suffix:
612         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
613         0.leithD -> AhFlxF  + switch to flux-form
614         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
615         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
616    o pkg/mom_vecinv:
617      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
618        to be before mom_calc_visc.F)
619      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
620      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
621        this is simpler for the adjoint and for diagnostics.
622    o model/src + pkg/momentum:
623      - add input files for  2-D additional Western and Southern cell-edge wall
624         (e.g., to add "thin-wall" where it is =1).
625      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
626        using 2nd hFacZ that is computed from initial (fix domain) hFac
627      - known limitations of thin wall implementation: not yet coded for sigma
628        coords; not working with CD-scheme neither.
629    o pkg/seaice:
630      - rename recently introduced parameters from (wrong name) AB to
631        BDF (backward difference time discretisation)
632      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
633    o tools/adjoint_options:
634      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
635    
636    checkpoint64t (2014/02/01)
637    o pkg/ecco
638      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
639        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
640      - replace hard-coded record number and period which only work for monthly
641        with read-in runtime param that works for other periods (month,day,year)
642    o pkg/thsice
643      - corrected store directive fixes thsice adjoint gradient checks
644    o genmake2 & testreport:
645      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
646        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
647        Update testreport accordingly. No need to set "export OPENAD=true"
648        in adjoint_options/adjoint_oad anymore (will be removed later).
649    o pkg/shelfice:
650      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
651        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
652        so that surface forcing applies to k=kSurf if using pkg/shelfice.
653    o pkg/ctrl, pkg/grdchk, pkg/ecco:
654      - Changes to make GENARR more modular (i.e. invisible if not used)
655    o model/src/temp_integrate.F and salt_integrate.F
656      - re-include store directives that were removed on Dec 27th.
657    o model/src/external_forcing_surf.F
658      - add storage directives for EmPmR and PmEpR to avoid recomputation of
659        seaice_model in the adjoint that is problematic when seaice_model is
660        turned off in the adjoint. The resolved issue dated back to July when
661        EXTERNAL_FORCING_SURF call was moved.
662        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
663    o pkg/exf/exf_check.F
664      - fix a small bug again (originally found by Wentao Liu, now found again)
665      - streamline error output
666    o pkg/streamice and aim_v23:
667      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
668        Apple's /usr/bin/cpp knows what to do:
669        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
670        Target: x86_64-apple-darwin13.0.0
671    
672    checkpoint64s (2014/01/05)
673    o tools/adjoint_options:
674      - switch to fastopt.net TAF server (instead of default fastopt.de) for
675        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
676    o model/src:
677      - remove some unnecessary TAF storage directives in forward_step.F and
678        in dynamics.F (note: not always removed by TAF, e.g., double storage
679        of kappaRU,kappaRV in former version of dynamics.F).
680    o model/src & pkg/ptracers:
681      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
682        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
683        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
684      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
685      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
686      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
687    o useSingleCpuInput separates single-CPU input from single-CPU output;
688        for now only implemented for in exf_interp_read.F
689    o verification/advect_xy:
690      - fix missing EXCH call in local version of ini_salt.F and update output.
691    o momentum diagnostics:
692      - fix which deltaT is used in Total-Tendency diagnostics.
693      - fix typo in diagnostics for momentum tendency from AB.
694    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
695        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
696    
697  checkpoint64r (2013/12/08)  checkpoint64r (2013/12/08)
698  o verification/*/results:  o verification/*/results:
# Line 112  o verification: Line 798  o verification:
798  o pkg/cost:  o pkg/cost:
799    - 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
800      (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:
801      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
802        cannot be applied to var in common block).        cannot be applied to var in common block).
803      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
804        slower GLOBAL_SUM_SEND_RECV option).        slower GLOBAL_SUM_SEND_RECV option).
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