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revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2068 by gforget, Mon Sep 22 14:21:10 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
9      pkg/shelfice/shelfice_thermodynamics.F,
10      verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
11      verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
12     -  add weight in CTRL_GET_GEN calls
13    o pkg/ctrl :
14     - ctrl_get_gen.F : add weight as input parameter, and apply
15       it directly rather than using smooth_correl2Dw (to be retired).
16     - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
17    o pkg/ctrl :
18     - CTRL_GENARR.h : add xx_gentim2d_numsmooth
19     - ctrl_cost_driver.F : bug fix (iarr, not 1)
20     - ctrl_init.F : bug fix (missing iarr)
21     - ctrl_readparms.F : add xx_gentim2d_numsmooth, improve numsmooth defaults
22     - ctrl_summary.F : improved report of controls settings
23    o pkg/ecco/ecco_cost_final.F : add genarr2d, genarr3d cost contributions
24    o pkg/ctrl :
25     - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
26       ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
27     - re-activate ctrl_summary (call in ctrl_init.F)
28    o pkg/ctrl/ctrl_cost_gen.F :
29     - rename ctrl_cost_gen2d input parameters {wmean_gen,wgen,genmask}
30       as {xx_gen_wmean,xx_gen_weight,xx_gen_mask}
31     - add ctrl_cost_gen3d for ARR3D (ctrl_cost_gen2d is for ARR2D,TIM2D)
32    o pkg/ctrl/CTRL_GENARR.h :
33     - add objf_genarr2d,  num_genarr2d, mult_genarr2d
34     - add objf_genarr3d,  num_genarr3d, mult_genarr3d
35     - add wgenarr2d, wgenarr3d
36    o pkg/ctrl/ctrl_readparms.F :
37     - add mult_genarr2d,mult_genarr3d in namelist
38    o pkg/ctrl_map_ini_genarr.F :
39     - bug fixes
40    o pkg/ctrl/ctrl_cost_driver.F :
41     - remove un-necessary cal.h, fix CCP brackets, remove un-necessary
42       myiter, mytime, add return
43    o pkg/ctrl/ctrl_cost_gen.F :
44     - fix CCP brackets, remove un-necessary myiter, mytime
45    o pkg/ecco :
46       - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
47       - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
48       - update cost_forcing_gen calls in cost_forcing.F
49       - update cost_genctrl call in ecco_cost_driver.F
50       - update ecco_ad_diff.list accordingly
51    o pkg/ctrl :
52       - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
53       - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
54       - update ctrl_ad_diff.list accordingly
55    
56    checkpoint65d (2014/09/15)
57    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
58      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
59        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
60    o pkg/ctrl/ctrl_map_ini_genarr.F :
61      - remove compilation failure
62      - replace hard coded example
63      - use ctrl_map_ini_gen2D, 3D
64    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
65      - on/off switch based upon xx_genarr2d_weight,3d
66    o src/packages_init_variables.F :
67      - regroup pkg/estimation calls
68      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
69        (moved to ctrl_init_variables)
70    o cost/cost_init_varia.F :
71      - remove ecco_cost_init_varia
72        (moved to ecco_init_varia)
73    o ctrl/ctrl_init_variables.F :
74      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
75      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
76    o ctrl/ctrl_map_ini.F :
77      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
78        (moved to ctrl_init_variables)
79    o ctrl/ctrl_map_ini_ecco.F :
80      - remove ECCO_PHYS (mv to ecco_init_varia)
81      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
82    o ecco/ecco_ad_diff.list :
83      - add ecco_init_varia.f
84    o ecco/ecco_init_varia.F
85      - new routine
86    o pkg/streamice:
87      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
88        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
89      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
90    o pkg/generic_advdiff:
91      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
92    o pkg/exf:
93      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
94         xxg_precip capability
95      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
96    o pkg/ctrl:
97      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
98    o model/src/load_fields_driver.F :
99      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
100        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
101    o OpenAD verification experiments:
102      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
103        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
104        for now, only in pkgs used in OpenAD verification experiments.
105      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
106        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
107        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
108        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
109    o OpenAD verification tests:
110      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
111      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
112        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
113      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
114        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
115    o model/src & generic_advdiff:
116      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
117        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
118        dynamics requires valid tracer forcing only over tile interior but, for
119        some diagnostics, may need to extend it over 1 point in tile halo region.
120      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
121        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
122        setting in temp/salt/ptracer_integrate.F
123    o pkg/dic:
124      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
125        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
126        in gchem_forcing_sep.F
127    o pkg/autodiff & obcs:
128      - add storage of current OB values for U & V (was already done for T & S).
129    
130    checkpoint65c (2014/08/30)
131    o pkg/dic:
132      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
133        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
134        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
135    o verification:
136      - new experiment testing OBCS and DIC pkgs, using params & output from
137        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
138        passage: take OBCS from the last year of a 2 yrs simulation and initial
139        conditions from t=1.yr while keeping the same forcing.
140    o model/src:
141      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
142        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
143    o pkg/diagnostics (Stats-Diags):
144      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
145        a) refine region where stats are computed, excluding where arrhFac=0 ;
146        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
147        c) extend regional stats over the region edges (for U or V pt location).
148    o pkg/gchem:
149      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
150        pkg/dic is currently changing/updating ptracers values beyond the OB).
151    o verification (hs94):
152      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
153        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
154        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
155        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
156    o pkg/ptracers:
157      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
158        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
159      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
160        with AB-2 code (so that it get tested).
161    o model/src:
162      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
163        with AB-2 code (previously only available with AB-3 code).
164        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
165        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
166        there, by calling CYCLE_AB_TRACER).
167    o pkg/generic_advdiff:
168      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
169        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
170        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
171        S/R temp/salt/ptracers_integrate.F
172    o model/src & pkg/ptracers:
173      - remove common block variables gT,gS (in DYNVARS.h), except when
174         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
175      - remove common block variable gPtr.
176    o model/src & pkgs:
177      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
178         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
179         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
180         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
181      + change accordingly all calling S/R.
182      - use local temperature/salinity/ptracer tendency array (without bi,bj)
183        in S/R temp/salt/ptracers_integrate.F
184    o pkg/seaice:
185      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
186        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
187      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
188        in seaice_lsr
189      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
190        in s/r seaice_lsr_calc_coeffs
191    o pkg/mdsio:
192      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
193        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
194        too long (e.g., > MAX_LEN_FNAM/2 )
195    
196    checkpoint65b (2014/08/12)
197    o pkg/matrix:
198      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
199    o model/src:
200      - fix initialisation of geothermalFile; compile geothermal-flux code in
201        natl_box verification experiment.
202    o model/src & pkg/down_slope:
203      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
204      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
205        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
206        results at machine truncation level: update output of experiments
207        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
208    o pkg/diagnostics (Stats-Diags):
209      - do not cumulate the full volume when DIAGNOSTICS_FILL is
210        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
211        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
212        times (but Min,Max and StD are still wrong).
213    o model/src:
214      - add geothermal flux forcing: read in ini_forcing.F as time-constant
215        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
216    o model/src:
217      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
218        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
219        arrays are already updated while adjustments (filters, conv.adjustment) are
220        still applied later, in S/R TRACERS_CORRECTION_STEP.
221    o model/src:
222      - store in common bloc array "rhoInSitu" the virtual potential temperature
223        anomaly that is used to compute geopotential: this make the atmos code
224        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
225    o pkg/seaice/seaice_lsr.F
226      - rename integer variable ilcall to ipass (that's what it is called
227        in the residual diagnostics
228      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
229        default) for improved non-linear convergence of the first few steps
230      - adjust a few comments and add new ones to explain some of the store
231        directives
232    o pkg/generic_advdiff (& ptracers):
233      - re-work the code to check for valid advection scheme and for minimum
234        size of overlap (now stored in local common bloc in gad_advscheme.F)
235    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
236      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
237      - add an auxilliary variable "bet" and fix store directives and keys in
238        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
239        less exact gradients in my tests); but there are still
240        recomputation warning (although gradients are sort of OK), when
241        SEAICE_LSR_VECTORIZE is not defined, so this flag and
242        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
243      - update verification experiments lab_sea.
244      - change some comments in S/R seaice_calc_viscosities
245    o model/src:
246      - if staggerTimeStep=T, always apply exchange to velocity field in
247        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
248        (independent of using multi-dim advection or not); no effect on FWD run
249        but affects AD results (at machine truncation level): update output of
250        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
251        and isomip (oad: 12.d).
252    o pkg/generic_advdiff:
253      - stop if doAB_onGtGs is set to FALSE but ignored
254      - refine warning related to stability of tracer time-stepping
255        regarding internal wave dynamics.
256      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
257        on staggerTimeStep & implicitIntGravWave (will now get a warning
258        if potentially unstable).
259    o pkg/kl10:
260      - add new pkg "kl10" for mixing due to internal wave breaking, from
261        http://www.sciencedirect.com/science/article/pii/S1463500310000144
262        (contribution from Jody Klymak), tested in verification experiment
263        verification/internal_wave/input.kl10/
264    o isomip experiment:
265      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
266        (input.htd) and update the output.
267    o cd_code experiments:
268      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
269        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
270        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
271        update the corresponding output.
272    o pkg/seaice:
273      - reduce the number of include files and store directives in
274        S/R seaice_lsr_tridiagu/v
275      - change the order of loops in one case in S/R seaice_lsr_tridiagv
276        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
277        get rid off one store directive (a TAF bug?)
278      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
279        S/R seaice_lsr_tridiagv to change the loop range for consistency
280      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
281      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
282        S/R seaice_lsr_tridiagu/v (requires update of
283        offline_exf_seaice/input.dyn_jfnk)
284    
285    checkpoint65a (2014/07/27)
286    o model/src:
287      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
288        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
289        (topo in p-coords, ice-shelf in z-coords); update output of experiments
290        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
291    o model/src:
292      - collect momentum forcing tendency into local 2-D array (passed as argument
293        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
294        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
295        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
296      - collect T & S forcing tendency into local 2-D array (passed as argument to
297        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
298        affects results at machine truncation level (e.g., ocean: if using
299        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
300        correction due to vertical advection).
301      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
302        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
303        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
304        obcs_ctrl (ad & fwd grd @ 12 & 7).
305    o pkg/ptracers & diagnostics:
306      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
307        title (to avoid some unexpected truncation); sort out ptracers diags units.
308      - collect ptracer forcing tendency into local 2-D array (passed as argument
309        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
310    
311    checkpoint65 (2014/07/18)
312    o pkg/fizhi:
313      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
314        affects results at machine truncation level. Update output of experiments
315        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
316    o pkg/seaice: more clean up
317      - rename TAF common block tapes to be more consistent and remove
318        unnecessary duplicates
319      - add store directives to remove more recomputations, but use smaller
320        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
321        The idea behind this flag is to reduce the memory footprint when the
322        adjoint of the LSR is not required. As of now, defining the flag
323        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
324        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
325        For experiment offline_exf_seaice, this means on a linux box with gfortran
326        nearly a factor of 10 (but keep in mind there is mostly seaice code in
327        this experiment):
328        > size mitgcmuv_ad
329        text    data        bss     dec        hex  
330        5100659 1216  220458952  225560827  d71c8fb
331        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
332        but only a moderate increase of 36% for global_ocean.cs32x15:
333        text    data        bss     dec        hex
334        6695027 1648 1014578664 1021275339 3cdf6ccb
335        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
336      - note: there are still recomputations in global_ocean.cs32x15 and
337        offline_exf_seaice and the gradient agreement changes (gets a
338        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
339      - in general, the AD gradients still are wrong
340    o OpenAD
341      - clean up code_oad/ directories somewhat by moving files
342        dontCompile, dontTransform, keepOriginal to OAD_support/
343    o model/src:
344      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
345        (not currently tested): add dissipation terms before NLFS rescaling of
346        tendencies (previously done after).
347    o pkg/diagnostics:
348      - write stats-diags in ascii file with more digits (same as in monitor).
349    o pkg/down_slope:
350      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
351        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
352    o model/src:
353      - new file "apply_forcing.F" containing all the code previously in
354        external_forcing.F, but with new argument list: pass, as new argument,
355        the current level tendency array to update (instead of a direct update
356        of the common bloc array). Change the corresponding calls.
357      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
358        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
359    o pkg/seaice/seaice_lsr, a little bit of clean up
360      - rearrange some code blocks, so that now all calculations for
361        setting up the right-hand-sides done within one single block
362        (I find that easier to read and understand)
363      - rearrange freedrift-code to reduce the number of ifdefs
364      - adjust some indentations and comments
365    
366    checkpoint64z (2014/07/10)
367    o model/src and several pkgs:
368      - change argument list of all S/R called from external_forcing.F and
369        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
370        to pass, as argument, the current level tendency array to update
371        (instead of a direct update of the common bloc array).
372      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
373      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
374    o pkg/seaice/seaice_lsr.F
375      - always initialize local arrays in seaice_lsr_tridiagu/v
376      - add more local tapes to seaice_lsr_tridiagu/v
377      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
378        keep it in bi/bj loop; this seems to be essential
379      - gradients are still wrong but only by 4-7 orders of magnitude
380        instead of 15 orders of magnitude, lab_sea improves a little
381    o pkg/seaice
382      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
383        generates unnecessary code in seaice_lsr_ad
384      - add more store directives in seaice_lsr to avoid unnecessary code
385        in seaice_lsr_ad
386      - exclude some residual computations in seaice_lsr when
387        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
388        in seaice_lsr_ad
389      - add more storing, a new tape (model/src/the_main_loop.F) and
390        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
391        and klockey should be checked by a specialist)
392      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
393        and update lab_sea after previous changes in pkg/seaice below
394    o pkg/autodiff:
395      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
396        viscFacInAd : run time parameters allowing for adjoint switches
397        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
398    o pkg/ecco:
399      - introduce cost_gencost_boxmean.F that computes a box mean
400        temperature (for use in adjoint sensitivity studies).
401    o model/src/set_defaults.F : initialize viscFacAdj to 1.
402    o pkg/mom_common/mom_calc_visc.F:
403      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
404    o pkg/seaice/seaice_summary.F:
405      - statement for SEAICEadjMODE now in autodiff_readparms.F
406    o pkg/seaice:
407      - remove some store directives and add new ones in an effort to get
408        finally rid off the recomputation warnings. This is successful
409        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
410        defined (i.e. no extensive recomputation warnings left), but there
411        are still too many recomputations on the solver iteration level
412      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
413      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
414        SEAICE_SIZE.h
415      - add a store directive in S/R seaice_calc_viscosities
416    o pkg/seaice (ITD code):
417      - fix definition of Hlimit for multi-threaded case
418      - use double precision arithmetic to compute Hlimit: this affects results;
419        update output of experiment seaice_itd.
420    o replace content of verification/seaice_itd
421      - instead of a 1D column use the configuration of offline_exf_seaice
422        to test the ice thickness distribution code with ridging
423      - this is a first shot at this experiment
424      - change of some defaults of ridging parameters SEAICEhStar (from
425        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
426        and lot of new comments.
427    
428    checkpoint64y (2014/06/20)
429    o pkg/seaice/seaice_reg_ridge.F:
430      - modify the regularization of very small volumes of ice; only check
431        total volume HEFF, and do not apply correction to individual ice
432        classes because that leads to funny patterns in the heat and fw-fluxes
433        into the ocean. Adjust seaice_itd/results/output.txt
434      - replace nITD by SEAICE_multDim in loop-ranges
435    o pkg/exf:
436      - add code to process the case field period = -12. with UV interpolation.
437      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
438        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
439    o verification/global_with_exf:
440      - switch all fields period to -12. (was previously untested) in input/data.exf
441        (but keep secondary test ".yearly" unchanged); update the reference output.
442    o pkg/cal:
443      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
444    o pkg/exf:
445      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
446        to replace logical switch "exf_verbose"
447      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
448    o pkg/sbo:
449      - update from Katherine Quinn: evaluate mass directly from density and SSH
450        (budget using Finite Volume method) instead of from bottom pressure.
451      - allow testreport to collect few selected SBO output ; tested in exp.
452        global_ocean.90x40x15 (after updating the results, to include SBO output).
453      - fix some multi-threading issues (in output part).
454    o model/src & most packages:
455      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
456      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
457        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
458        "data.{pkg}" exist ; and leave the S/R (return) just after.
459      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
460        + call LAND_READPARMS from packages_readparms.F
461    o pkg/seaice:
462      - remove code that resets useThSice in S/R seaice_readparms and
463        replace it by a warning in S/R seaice_check
464      - remove parameter MULTDIM, replace with nITD and runtime
465        parameter SEAICE_multDim (still hard-wired to nITD if
466        SEAICE_ITD is defined)
467    
468    checkpoint64x (2014/05/24)
469    o verification/lab_sea:
470      - update adjoint and TLM output following changes to pkg/salt_plume
471      - un-do the update after putting back local recip_Cp in few places.
472    o pkg/salt_plume: modifications by An Nguyen:
473      - add capability to do brine rejection (salt-plume) as function of
474        volume+tracers (instead of only salinity tracer).
475      - conserve volume by exchanging volume from each kLev to above to
476        accommodate in-coming brine volume
477      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
478      - switch KPP surf buoyancy due to brine forcing to 3-d
479        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
480      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
481      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
482        in East/West Arctic.
483    o pkg/sbo:
484      - incorporate modifications from Katherine Quinn to enable the use of sbo
485        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
486        output for future testreport verification (unfinished).
487    o pkg/atm_phys:
488      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
489        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
490        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
491    o pkg/seaice
492      seaice_calc_ice_strength.F: modify expression to avoid divisions
493        (affects truncation)
494      seaice_do_ridging.F: clean up the insectarium
495      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
496      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
497      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
498      - add some debugging information and error messages (warnings)
499    o model/src: modifications relatd to atmosphere p*:
500      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
501      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
502        of vertical profile tRef in geopotential background and anomaly.
503      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
504        and pkg/atm_phys.
505      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
506        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
507    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
508    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
509        not used right now, but can be used in BGC packages to fix conservation.
510    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
511        other packages too.
512    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
513        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
514    o model/src:
515      - since we have several heat capacity (even in model/src), define "recip_Cp"
516        as local variable (no longer in common block) to avoid any confusion.
517      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
518    o pkg/exf:
519      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
520        air density as function of air Temp, Humidity and atm pressure.
521    
522    checkpoint64w (2014/05/02)
523    o verification:
524      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
525        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
526        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
527        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
528        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
529    o model/src: for atmosphere in p* coords:
530      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
531      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
532        but not yet activated.
533    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
534      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
535      - this changes the results (but not for any verification experiment, because
536        none tests this), but avoids having an extra field in the restart files
537    o pkg/seaice: remove global variable TICE (not needed)
538      - replace by TICES or local variable where necessary (cost_seaice_test,
539        seaice_diagnostics_state)
540      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
541      - use specific read/write routines for reading and writing individual leves
542        of a multilevel field
543    o pkg/ctrl & model/inc:
544      - move additional anomaly fields of control vars (related to options:
545         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
546        from DYNVARS.h into new header file: CTRL_FIELDS.h
547    o pkg/seaice: some small modifications to the ridging code
548      - make fw2ObyRidge a global variable and add the freshwater flux to
549        seaice_growth
550      - pass actual thickness from seaice_prepare_ridging, so that it is
551        computed only in one place and compute it in the same way as in
552        seaice_growth
553      - initialise more fields in seaice_do_ridging that where cause floating
554        point exceptions over land
555    o pkg/seaice: preparations for ridging code and first real ridging code
556      - move most of "PART 1" of S/R seaice_growth into a new and separate
557        S/R seaice_reg_ridge that will both regularize the state variable after
558        advection call the actual ridging routine;
559      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
560        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
561      - remove ridging code from seaice_advdiff
562      - clean up remaining part 1 of seaice_growth in an attempt to make it
563        more readable (this is probably subjective)
564      - call seaice_itd_redist once in the initialisation phase to have the initial
565        conditions in the correct category
566      - finally: add new ridging routine for ITD code
567    
568    checkpoint64v (2014/04/11)
569    o pkg/ecco:
570      - add runtime parameters mdt[start,end]date[1,2]
571      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
572    o pkg/seaice:
573      - make deltaC a global variable, so that it can be used in ridging code
574      - first step towards ridging: introduce new routines that compute
575        ice strength based on ridging parameters
576      - add diagnostic for HSNOWITD
577      - add opnWtrFrac as a global variable (required for ridging scheme)
578    o pkg/salt_plume + pkg/seaice/seaice_growth.F
579      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
580        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
581    o verification/hs94.1x64x5:
582      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
583      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
584    o autodiff:
585      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
586        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
587        For now, only in pkgs used in verification/hs94.1x64x5.
588      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
589        which are specific to TAF/TAMC).
590      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
591        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
592        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
593      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
594        building mitgcmuv_ad (make adAll).
595    o pkg/ecco:
596      - cost_gencost_seaicev4.F:
597         reformulate proxy cost as function of sst and local param SEAICE_freeze
598         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
599      - add stop statement if old names siv4-[sst,vol] are used
600      - add snapshots + cost reports for atmospheric longwave
601      - remove factor 0.1 in front of wtau[u,v]
602      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
603         ALLOW_TMI_SST_COST_CONTRIBUTION
604    o pkg/atm_phys:
605      - add some diagnostics for Short-wave and for convection S/R.
606    o pkg/seaice/seaice_growth:
607      - fix a bug in the lateral melt parameterization for SEAICE_ITD
608        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
609      - rearrange loop order for better vector code in the same code block
610      - rewrite the floeDiameter formula to have fewer divisions
611      -  (miraculously) none of this changes the results of seaice_itd
612    o pkg/smooth:
613      - move param smooth2Ddiffnbt to pkg/ecco
614    o pkg/salt_plume:
615      - salt_plume_frac.F:
616         clean up local param names
617         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
618    o pkg/rw:
619      - add RS version of S/R READ_MFLDS_LEV.
620    o pkg/streamice:
621      - fix the restart test by writing/reading pickup_streamice files.
622    o pkg/seaice:
623      - refine checks for jfnk-related parameters
624      - comment out if statement with SEAICEuseIMEX parameter as long as there
625        is no IMEX code to avoid confusion and surprises
626    
627    checkpoint64u (2014/03/07)
628    o verification/MLAdjust:
629      - rename secondary test suffix:
630         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
631         0.leithD -> AhFlxF  + switch to flux-form
632         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
633         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
634    o pkg/mom_vecinv:
635      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
636        to be before mom_calc_visc.F)
637      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
638      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
639        this is simpler for the adjoint and for diagnostics.
640    o model/src + pkg/momentum:
641      - add input files for  2-D additional Western and Southern cell-edge wall
642         (e.g., to add "thin-wall" where it is =1).
643      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
644        using 2nd hFacZ that is computed from initial (fix domain) hFac
645      - known limitations of thin wall implementation: not yet coded for sigma
646        coords; not working with CD-scheme neither.
647    o pkg/seaice:
648      - rename recently introduced parameters from (wrong name) AB to
649        BDF (backward difference time discretisation)
650      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
651    o tools/adjoint_options:
652      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
653    
654    checkpoint64t (2014/02/01)
655    o pkg/ecco
656      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
657        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
658      - replace hard-coded record number and period which only work for monthly
659        with read-in runtime param that works for other periods (month,day,year)
660    o pkg/thsice
661      - corrected store directive fixes thsice adjoint gradient checks
662    o genmake2 & testreport:
663      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
664        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
665        Update testreport accordingly. No need to set "export OPENAD=true"
666        in adjoint_options/adjoint_oad anymore (will be removed later).
667    o pkg/shelfice:
668      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
669        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
670        so that surface forcing applies to k=kSurf if using pkg/shelfice.
671    o pkg/ctrl, pkg/grdchk, pkg/ecco:
672      - Changes to make GENARR more modular (i.e. invisible if not used)
673    o model/src/temp_integrate.F and salt_integrate.F
674      - re-include store directives that were removed on Dec 27th.
675    o model/src/external_forcing_surf.F
676      - add storage directives for EmPmR and PmEpR to avoid recomputation of
677        seaice_model in the adjoint that is problematic when seaice_model is
678        turned off in the adjoint. The resolved issue dated back to July when
679        EXTERNAL_FORCING_SURF call was moved.
680        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
681    o pkg/exf/exf_check.F
682      - fix a small bug again (originally found by Wentao Liu, now found again)
683      - streamline error output
684    o pkg/streamice and aim_v23:
685      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
686        Apple's /usr/bin/cpp knows what to do:
687        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
688        Target: x86_64-apple-darwin13.0.0
689    
690    checkpoint64s (2014/01/05)
691    o tools/adjoint_options:
692      - switch to fastopt.net TAF server (instead of default fastopt.de) for
693        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
694    o model/src:
695      - remove some unnecessary TAF storage directives in forward_step.F and
696        in dynamics.F (note: not always removed by TAF, e.g., double storage
697        of kappaRU,kappaRV in former version of dynamics.F).
698    o model/src & pkg/ptracers:
699      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
700        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
701        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
702      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
703      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
704      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
705    o useSingleCpuInput separates single-CPU input from single-CPU output;
706        for now only implemented for in exf_interp_read.F
707    o verification/advect_xy:
708      - fix missing EXCH call in local version of ini_salt.F and update output.
709    o momentum diagnostics:
710      - fix which deltaT is used in Total-Tendency diagnostics.
711      - fix typo in diagnostics for momentum tendency from AB.
712    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
713        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
714    
715    checkpoint64r (2013/12/08)
716    o verification/*/results:
717      - Update reference output of experiments that were passing with just 13 digits
718         (make it easier to detect future changes in results)
719    o model/src & pkg/ptracers:
720      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
721        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
722        to inside ptracers_integrate.F ; remove ptracers_advection.F
723    o coupling interface pkgs:
724        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
725      - change the config check to test the agreement of Ocean Depth
726        with ATM land/sea mask (instead of ATM orography);
727      - send to coupler the number of coupler time-steps to do for this run:
728        this allows to check for consistency and don't need anymore to be
729        specified in parameter file "data";
730      in coupler:
731      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
732      - improve report to log-file of config setting (pass log-file unit to few S/R)
733    o pkg/compon_communic:
734      - add coupling send/receive for non-tiled integer vector;
735      - add S/R to check and stop if any proc has an error (similar to
736        eesupp/src/stop_if_error.F but single thread and across Comm_World).
737    o pkg/exch2:
738      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
739        through list of all tiles my proc owns.
740    o model/src:
741      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
742        from rTrans) to simplify dependencies (no need to store rTrans anymore in
743        calling S/R); this affects AD results at machine truncation level:
744        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
745        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
746    o tools/build_options:
747      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
748    o coupling interface pkgs:
749        [compon_communic, atm_compon_interf & ocn_compon_interf]
750      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
751        to each S/R that needs it; remove un-used variables.
752      - change component tile registration (cpl_register.F in both compon_interf
753        and mitcomponent_tile_register.F) to pass the full list of tiles
754        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
755      - with pkg/exch2: adopt the same convention used for I/O to define mapping
756        towards coupler global array (unless W2_useE2ioLayOut=F):
757         a) can now use different tiling between atm & ocn comp.
758         b) no needs to modify the run-Off map when changing tiling (was needed
759            even if using the same tiling between atm & ocn).
760         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
761            full land tiles); not yet tested.
762      - check for valid mapping from comp. tile to coupler global array
763      - improve report of tile registration results to log file.
764    o pkg/exch2:
765      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
766        tile-registration (CPL_REGISTER);
767      - activate (un-comment) definition and setting of "W2_tileIndex" list to
768        store the local bi,bj indices of each tile;
769      - also print bi,bj in local report to log file;
770      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
771        Jun 2009 modif of pkg/exch2).
772    o testing on baudelaire:
773      - run 2 tests at a time: no significant slow down (since enough cpu) and
774        get the full set of test done earlier
775      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
776    o model/src/thermodynamics.F and routines called from it:
777      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
778        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
779        velocity (outp) by adding bolus velocity.
780      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
781        mass transport from velocity + lateral grid cell area
782      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
783      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
784     in thermodynamics.F
785      - remove k from thermodynamics.F and move it to temp_integrate.F
786        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
787        loop).
788      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
789        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
790        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
791        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
792      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
793        global_ocean.90x40x15, tutorial_global_oce_biogeo and
794        tutorial_tracer_adjsens (+ TLM output).
795    o tools/OAD_support and (verification/*/) code_oad:
796      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
797        module conversion ; remove unneeded CPP_EEOPTIONS.h.
798      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
799        version (closer to model/inc/CPP_OPTIONS.h).
800    o model/src:
801      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
802        retired list of parameters (routine FREEZE has been replace by surface
803        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
804    o pkg/gmredi:
805      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
806        velocity (same scheme but affects machine truncation) for GM_AdvForm.
807      - update output of FWD experiments: front_relax.bvp,
808        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
809    
810    checkpoint64q (2013/11/17)
811    o verification:
812      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
813        tutorial_global_oce_biogeo and global_ocean.90x40x15.
814      - generate new output (growth & melt) for seaice_itd experiment after
815        updating the input pickup_seaice files (previously wrong).
816    o pkg/cost:
817      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
818        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
819        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
820          cannot be applied to var in common block).
821        o allows to get results independent of tile-per-proc setting (if using
822          slower GLOBAL_SUM_SEND_RECV option).
823      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
824        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
825        forward gradients: update output).
826      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
827        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
828    o pkg/mom_common:
829      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
830        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
831        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
832        ensure that all field value that are used are set.
833    o tutorial_deep_convection (smag3d):
834      - add missing scaling in mom_calc_smag_3d.F;
835      - set smag3D_coeff in input.smag3d such that results do not change.
836    o pkg/dic:
837      - change dic_cost.F to compute cost on each tile first and then apply
838        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
839        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
840      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
841    o eesupp/src & pkg/mdsio:
842      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
843        (from pkg/mdsio) since they are no longer used for tape IO.
844      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
845        (+ keep a copy in pkg/atm_ocn_coupler).
846    o verification/isomip:
847      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
848    o tools/build_options:
849      - optfile linux_amd64_ifort11, fast (no ieee) case:
850        to get a working restart for all experiments, add "-fp-model source"
851        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
852    
853    checkpoint64p (2013/10/20)
854    o pkg/autodiff:
855      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
856        criteria, return to simple (default) tape IO format.
857    o pkg/mdsio (+ eesupp/src):
858      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
859        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
860      - fix globalFile and singleCpuIO options using simpler global mapping.
861      - new pairs of scatter/gather vector S/R (one for each type, generated from
862        template) corresponding to simpler global mapping.
863      - adread_write.F: switch to new S/R (but leave old calls commented) and write
864        to globalFile when parameter globalFiles is set to True.
865      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
866    o pkg/autodiff:
867      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
868        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
869        missing, just add a STOP if array type do not match.
870    o pkg/exf:
871      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
872         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
873         and rename array obsSIce to exf_iceFraction.
874    o tutorial_deep_convection:
875      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
876        for now all in this exp. code dir.
877      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
878        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
879    o eesupp/src:
880      - added SINGLE_DISK_IO option because reading of parameter files on
881        very large number of processors did not work with existing set-up
882    
883    checkpoint64o (2013/09/25)
884    o pkg/atm_phys & atm_compon_interf:
885      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
886    o tools/build_options:
887      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
888        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
889        remove CPP setting (was identical to genmake2 default).
890    o pkg/gmredi & model/src: Some updating and work done on the residual model.
891      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
892      - fixed up the calculation of the eddy stress and how it is added to the
893        external forcing via taueddy_external_forcing.F
894      - at the moment, it is very experimental and only works with the variable eddy
895        diffusivity calculated in gmredi_k3d.F
896    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
897        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
898    o testreport (& tools/do_tst_2+2):
899      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
900    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
901      - remove CPP='cpp -traditional -P' (this is genmake2 default)
902      - add switch (for big setups) to use 'medium' memory-model (but leave it
903        commented out for now). Note: needed with FC 19 to compile big setups.
904    o pkg/atm_compon_interf:
905      - regroup per field origin (model & pkgs) the coupling storage routines
906         (which accumalate in time each coupling field)
907      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
908        update accordingly + simplify aim_do_physics.F
909    
910    checkpoint64n (2013/08/26)
911    o pkg/bbl:
912      - update formulation to reduce dispersion of tracer properties in bbl
913      - replaced horizontal and vertical transport parameters with velocities
914      - changes results for verification/global_with_exf.yearly
915    o verification/halfpipe_streamice:
916      - change to matrix construction; update both Fwd & AD output.
917    o verification/tutorial_tracer_adjsens:
918      - OpenAD test: switch to vector-invariant momentum since fluxform with
919        rStar causes problems with OpenAD; update output.
920    o tools:
921      - genmake2: define a common prefix for all temp-file names ; move them
922        to local /tmp disk (but would be easy to move them back);
923      - xmakedepend: apply the same switch for temp-files.
924    o pkg/offline:
925      - changes for use with rStar (NLFS): assume that we continue to provide
926        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
927        output files) and apply r* scaling at each time-step (function of the time
928        varying Eta field); use normal pickup files (needed for restart with NLFS).
929    o adjoint with OpenAD:
930      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
931        package openad.  This package has to be compiled for all runs with OpenAD
932        instead of specifying code_oad_all as a modification directory.
933      - link the fortran templates from tools/OAD_support to the build directory
934        for preprocessing to avoid conflicts between different setups compiled
935        simultaneously and simplify cleanup.
936    o pkg/exf:
937      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
938        main model or other pkgs are exchanged in EXF_MAPFIELDS).
939    o model/src:
940      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
941        (similar to do_fields_blocking_exchanges.F).
942    o tools/genmake2:
943      - remove TAF output src code just before calling staf (when not doing a fresh
944        built, will stop if things go wrong with staf).
945      - fix target "adobj" (left from TAF version-2 transition)
946    o pkg/diagnostics:
947      - add a parameter to track the status of pkg/diagnostics activation;
948        this replace/extend the use of logical param "settingDiags" (to check
949        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
950        New S/R to print error message and stop when pkgStatus is not right.
951      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
952    
953    checkpoint64m (2013/08/13)
954    o model/inc:
955      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
956        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
957    o pkg/kpp & aim_v23:
958      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
959    o pkg/seaice:
960      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
961        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
962      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
963    o eesupp/src:
964      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
965        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
966    o switch to TAF version-2:
967      - add flow directives to "freeze" naming convention for ad-routines that
968        are used in I/O routines of adjoint state and associated common blocks
969        that are used in adcommon.h (backward compatible with version-1)
970      - update all ad-optfiles (in tools/adjoint_options + few local to some
971        verification exp) to switch to latest TAF version (currently 2.5.5);
972        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
973        out except for diva).
974      - the major change with TAF version-2 is that both the differentiated
975        routines and the forward routines (new) are returned as part of the TAF
976        output source code. Update genmake2 accordingly.
977      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
978        with version-2 when compared to TLM or FWD gradient); other experiments
979        output show minor changes (machine truncation level); update the few AD &
980        TLM output with 12 matching digits only (some prior to version-2 switch).
981    
982    checkpoint64l (2013/08/05)
983    o model/src:
984      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
985      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
986        when using TAF but only if using OpenAD.
987    o pkg/mom_common+fluxform+vecinv:
988      - always set horiz. viscosity arrays to background value before calling
989        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
990        only when using variable horiz. viscosity (useVariableVisc=T);
991      - simplify mom_vecinv.F (only 1 block for momViscosity).
992    o pkg/mom_common: variable horiz. viscosity in NH code
993      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
994        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
995      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
996        useBiharmonicVisc & useVariableVisc.
997      - fix old bug (already in 1rst implementation of variable horizontal viscosity
998        in calc_gw.F, version 1.27, 2006/06/20):
999        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1000        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1001      - change background horiz viscosity in vertical momentum (gW) to always be
1002        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1003        any type of variable viscosity, e.g., viscAh/4Grid)
1004      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1005        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1006        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1007        default viscAh,viscA4 is zero).
1008    o model/src:
1009      - extend length of drC & recip_drC from Nr to Nr+1.
1010    o Divided Adjoint (DIVA) with MPI:
1011      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1012      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1013        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1014    
1015    checkpoint64k (2013/07/23)
1016    o tools/OAD_support:
1017      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1018        and remove it from genmake2.
1019    o tools/build_options:
1020      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1021        MPI_HEADER_FILES list (let genmake2 find the missing headers)
1022    o verification/halfpipe_streamice:
1023      - change to driving stress formulation; update both Fwd & AD output.
1024    o tools/genmake2 and Divided Adjoint with MPI:
1025      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1026      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1027      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1028        Makefile, which is set by genmake2, and check which mpi-headers are needed.
1029        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1030      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1031    o testreport:
1032      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1033        perform additional runs (number of additional runs is "add_DIVA_runs" taken
1034        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1035    o verification/lab_sea (AD test):
1036      - change to test Divided Adjoint Run in this set-up (both standard AD test
1037        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1038    o pkg atm_ & ocn_compon_interf:
1039      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1040        staggerTimeStep implementation) and disable (retired) corresponding
1041        parameter.
1042    o pkg/offline:
1043      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1044      - add S/R OFFLINE_CHECK to print offline parameter summary
1045        and stop if loading a file that is not used;
1046      - enable to calculate GMRedi tensor, KPP mixing and convective index
1047        when the corresponding file(s) is/are not specified (but pkg is used).
1048      - comment out resetting of monitorFreq (to endTime) since it still useful
1049        for monitoring CFL numbers and checking offline fields.
1050    o OpenAD:
1051      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1052        smaller standard output) and generate new (smaller) output (on baudelaire
1053        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1054    o model/src:
1055      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1056        (where external_forcing_adjust was called) and change list of arguments;
1057      - merge external_forcing_adjust.F into external_forcing_surf.F
1058      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1059        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1060        previously in file "balance_relax.F", now removed); remove corresponding
1061        arrays in FFIELDS.h.
1062      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1063        a hack for getting back surfaceForcingS (loaded from file) when using
1064        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1065      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1066        (was getting only 11 digits for AD-grad, due to different truncation
1067         error in AD code).
1068    
1069    checkpoint64j (2013/07/04)
1070    o pkg/offline:
1071      - to enable the use of other features with pkg offline (e.g., obcs),
1072        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1073      - comment out "allowFreezing" (now active) in 2 offline testing exp.
1074  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
1075    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1076    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1077    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1078  o pkg/atm_phys:  o pkg/atm_phys:
1079    - allows to add some damping on uVel,vVel (strength only function of k).    - allows to add some damping on uVel,vVel (strength only function of k).
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