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revision 1.1890 by jmc, Wed Jul 3 21:32:19 2013 UTC revision 1.2094 by jmc, Wed Nov 19 16:49:37 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65g (2014/11/19)
8    o pkg/diagnostcis:
9      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
10    o pkg/my82,pp81,kl10:
11      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
12        field diffKr as background diffusivity to set minimum diffusivity value.
13    o pkg/seaice:
14      - add new parameter SEAICEuseEVPrev (for revisited EVP by
15        Bouillon et al 2013)
16      - add SEAICE_evpAlpha/Beta to namelist
17      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
18        involve trivial re-ordering of divisions/multiplications that should not
19        have any effects, but ... they do change the results of lab_sea.hb87 so
20        that only 2 digits of agreement remain, in line with the general
21        instability/fragility of the evp-code. For now, I do not care and just
22        update the verification experiment
23    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
24      - remove xx_genarr2d_numsmooth etc
25      - use xx_genarr2d_preproc etc instead
26      - carry out smooth_correl2D at initialization stage rather than during
27        time stepping.
28      - get smoothOpNb from xx_gentim2d_preproc
29    o global_oce_cs32 :
30      - add test of generic ecco capabilities.
31    o pkg/exf/exf_getsurfacefluxes.F :
32      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
33    o pkg/ctrl,ecco :
34      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
35        is defined.
36    o pkg/seaice: add diagnostics for Delta (deformation parameter)
37    o model/src:
38      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
39        diffusivity (background) is specified but ignored.
40    o verification:
41      - in testreport, convert hostname to lower case for default output dir name
42    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
43    o pkg/dic: add modifications from Hajoon:
44      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
45      - light attenuation: add self-shading effect by climatological Chlorophyll
46        (read from file).
47    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
48        compiles when SEAICE_ALLOW_DYNAMICS is undefined
49    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
50        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
51        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
52        approach where CPP_OPTIONS.h includes an omnipotent
53        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
54    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
55        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
56    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
57        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
58        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
59    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
60      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
61      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
62      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
63      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
64    o pkg/ctrl,ecco,exf :
65      - remove variables associated with NON-generic costs,
66        unless ECCO_CTRL_DEPRECATED is defined.
67      - remove NON-generic NON-obcs controls,
68        unless ECCO_CTRL_DEPRECATED is defined.
69    o pkg/ctrl : added ctrl_local_params.h
70    o pkg/ecco : added ecco_local_params.h
71    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
72        experiments, which will progressively be removed once the
73        experiments are revised to use only generic controls/costs.
74    
75    checkpoint65f (2014/10/13)
76    o pkg/ctrl, ecco, seaice : minor changes in headers
77    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
78        cost function and control capabilities added since checkpoint65c.
79    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
80    o pkg/ecco: increase modularity and improve logic
81      - ecco_toolbox.F (new) : basic operations that are often used,
82        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
83        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
84      - cost_gencal.F (new) : determine filnames and records.
85      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
86      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
87        and exploit the above functions leading to more compact code.
88      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
89      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
90        using_ers, using_gfo, using_mdt is now only defined within gencost)
91    o pkg/ecco: extend generic cost capabilities
92      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
93        capabilities via gencost_preproc (+ _c,_i,_r related params),
94        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
95        gencost_outputlevel arguments to cost_generic
96      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
97        and active_read, making room for gencost_preproc to take effect.
98        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
99      - pkg/ecco/cost_generic.F :
100        compute and store misfit maks*(model-data) in localdif that is
101        then used in cost and for output, output misfit if outlev.GT.0
102      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
103        rather gencost_barfile for deciding whether to write barfile
104      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
105      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
106        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
107      - pkg/ecco/ecco_summary.F : report gencost variables
108      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
109    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
110    o pkg/ecco: internal re-organization
111      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
112        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
113        mv relevant variables definition from ecco_cost.h to ecco.h,
114        make sure gencost routines only include ecco.h)
115      - throughout : add missing CCP switches, rm unused variables,
116        and rm un-necessary CPP switches
117      - throughout gencost routines : replace modelstartdate with
118        gencost_startdate when needed
119      - cost_bp_read.F : use arguments, instead of common blocs
120        so that it can be used also by (new) cost_gencost_bpv4.F
121      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
122      - ecco_phys.F : compute etanFull
123      - ecco_readparms.F : rename using_topex as using_tpj, add
124        bpv4-grace to gencost list, initialize added parameters
125      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
126    
127    checkpoint65e (2014/09/28)
128    o pkg/obcs:
129      - replaced the just-added CPP options with run-time variables
130        (see pkg/obcs/OBCS_PARAMS.h for details)
131    o pkg/obcs:
132      - add additional CPP options for sponge boundary layers
133        (see pkg/obcs/OBCS_OPTIONS.h for details)
134    o pkg/atm_phys:
135      - implement simple (obliquity only, assuming circular planet orbit)
136        seasonal cycle for incoming insolation ; used when run-time parameter
137        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
138    o pkg/exf, pkg/ecco, pkg/ctrl:
139      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
140      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
141      - implement gentim2d for xx_tauu, xx_tauv
142    o pkg/ctrl, pkg/ecco :
143      - fix and complement the generic controls implementation
144    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
145        pkg/shelfice/shelfice_thermodynamics.F,
146        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
147        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
148      - add weight in CTRL_GET_GEN calls
149    o pkg/ctrl :
150      - ctrl_get_gen.F : add weight as input parameter, and apply
151        it directly rather than using smooth_correl2Dw (to be retired).
152      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
153    o pkg/ctrl :
154      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
155        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
156      - re-activate ctrl_summary (call in ctrl_init.F)
157    o pkg/ctrl/ctrl_cost_gen.F :
158      - fix CCP brackets, remove un-necessary myiter, mytime
159    o pkg/ecco, pkg/ctrl :
160      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
161      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
162      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
163      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
164    
165    checkpoint65d (2014/09/15)
166    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
167      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
168        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
169    o pkg/ctrl/ctrl_map_ini_genarr.F :
170      - remove compilation failure
171      - replace hard coded example
172      - use ctrl_map_ini_gen2D, 3D
173    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
174      - on/off switch based upon xx_genarr2d_weight,3d
175    o src/packages_init_variables.F :
176      - regroup pkg/estimation calls
177      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
178        (moved to ctrl_init_variables)
179    o cost/cost_init_varia.F :
180      - remove ecco_cost_init_varia
181        (moved to ecco_init_varia)
182    o ctrl/ctrl_init_variables.F :
183      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
184      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
185    o ctrl/ctrl_map_ini.F :
186      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
187        (moved to ctrl_init_variables)
188    o ctrl/ctrl_map_ini_ecco.F :
189      - remove ECCO_PHYS (mv to ecco_init_varia)
190      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
191    o ecco/ecco_ad_diff.list :
192      - add ecco_init_varia.f
193    o ecco/ecco_init_varia.F
194      - new routine
195    o pkg/streamice:
196      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
197        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
198      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
199    o pkg/generic_advdiff:
200      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
201    o pkg/exf:
202      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
203         xxg_precip capability
204      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
205    o pkg/ctrl:
206      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
207    o model/src/load_fields_driver.F :
208      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
209        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
210    o OpenAD verification experiments:
211      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
212        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
213        for now, only in pkgs used in OpenAD verification experiments.
214      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
215        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
216        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
217        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
218    o OpenAD verification tests:
219      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
220      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
221        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
222      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
223        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
224    o model/src & generic_advdiff:
225      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
226        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
227        dynamics requires valid tracer forcing only over tile interior but, for
228        some diagnostics, may need to extend it over 1 point in tile halo region.
229      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
230        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
231        setting in temp/salt/ptracer_integrate.F
232    o pkg/dic:
233      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
234        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
235        in gchem_forcing_sep.F
236    o pkg/autodiff & obcs:
237      - add storage of current OB values for U & V (was already done for T & S).
238    
239    checkpoint65c (2014/08/30)
240    o pkg/dic:
241      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
242        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
243        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
244    o verification:
245      - new experiment testing OBCS and DIC pkgs, using params & output from
246        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
247        passage: take OBCS from the last year of a 2 yrs simulation and initial
248        conditions from t=1.yr while keeping the same forcing.
249    o model/src:
250      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
251        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
252    o pkg/diagnostics (Stats-Diags):
253      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
254        a) refine region where stats are computed, excluding where arrhFac=0 ;
255        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
256        c) extend regional stats over the region edges (for U or V pt location).
257    o pkg/gchem:
258      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
259        pkg/dic is currently changing/updating ptracers values beyond the OB).
260    o verification (hs94):
261      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
262        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
263        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
264        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
265    o pkg/ptracers:
266      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
267        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
268      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
269        with AB-2 code (so that it get tested).
270    o model/src:
271      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
272        with AB-2 code (previously only available with AB-3 code).
273        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
274        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
275        there, by calling CYCLE_AB_TRACER).
276    o pkg/generic_advdiff:
277      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
278        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
279        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
280        S/R temp/salt/ptracers_integrate.F
281    o model/src & pkg/ptracers:
282      - remove common block variables gT,gS (in DYNVARS.h), except when
283         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
284      - remove common block variable gPtr.
285    o model/src & pkgs:
286      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
287         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
288         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
289         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
290      + change accordingly all calling S/R.
291      - use local temperature/salinity/ptracer tendency array (without bi,bj)
292        in S/R temp/salt/ptracers_integrate.F
293    o pkg/seaice:
294      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
295        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
296      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
297        in seaice_lsr
298      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
299        in s/r seaice_lsr_calc_coeffs
300    o pkg/mdsio:
301      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
302        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
303        too long (e.g., > MAX_LEN_FNAM/2 )
304    
305    checkpoint65b (2014/08/12)
306    o pkg/matrix:
307      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
308    o model/src:
309      - fix initialisation of geothermalFile; compile geothermal-flux code in
310        natl_box verification experiment.
311    o model/src & pkg/down_slope:
312      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
313      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
314        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
315        results at machine truncation level: update output of experiments
316        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
317    o pkg/diagnostics (Stats-Diags):
318      - do not cumulate the full volume when DIAGNOSTICS_FILL is
319        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
320        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
321        times (but Min,Max and StD are still wrong).
322    o model/src:
323      - add geothermal flux forcing: read in ini_forcing.F as time-constant
324        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
325    o model/src:
326      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
327        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
328        arrays are already updated while adjustments (filters, conv.adjustment) are
329        still applied later, in S/R TRACERS_CORRECTION_STEP.
330    o model/src:
331      - store in common bloc array "rhoInSitu" the virtual potential temperature
332        anomaly that is used to compute geopotential: this make the atmos code
333        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
334    o pkg/seaice/seaice_lsr.F
335      - rename integer variable ilcall to ipass (that's what it is called
336        in the residual diagnostics
337      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
338        default) for improved non-linear convergence of the first few steps
339      - adjust a few comments and add new ones to explain some of the store
340        directives
341    o pkg/generic_advdiff (& ptracers):
342      - re-work the code to check for valid advection scheme and for minimum
343        size of overlap (now stored in local common bloc in gad_advscheme.F)
344    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
345      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
346      - add an auxilliary variable "bet" and fix store directives and keys in
347        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
348        less exact gradients in my tests); but there are still
349        recomputation warning (although gradients are sort of OK), when
350        SEAICE_LSR_VECTORIZE is not defined, so this flag and
351        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
352      - update verification experiments lab_sea.
353      - change some comments in S/R seaice_calc_viscosities
354    o model/src:
355      - if staggerTimeStep=T, always apply exchange to velocity field in
356        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
357        (independent of using multi-dim advection or not); no effect on FWD run
358        but affects AD results (at machine truncation level): update output of
359        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
360        and isomip (oad: 12.d).
361    o pkg/generic_advdiff:
362      - stop if doAB_onGtGs is set to FALSE but ignored
363      - refine warning related to stability of tracer time-stepping
364        regarding internal wave dynamics.
365      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
366        on staggerTimeStep & implicitIntGravWave (will now get a warning
367        if potentially unstable).
368    o pkg/kl10:
369      - add new pkg "kl10" for mixing due to internal wave breaking, from
370        http://www.sciencedirect.com/science/article/pii/S1463500310000144
371        (contribution from Jody Klymak), tested in verification experiment
372        verification/internal_wave/input.kl10/
373    o isomip experiment:
374      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
375        (input.htd) and update the output.
376    o cd_code experiments:
377      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
378        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
379        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
380        update the corresponding output.
381    o pkg/seaice:
382      - reduce the number of include files and store directives in
383        S/R seaice_lsr_tridiagu/v
384      - change the order of loops in one case in S/R seaice_lsr_tridiagv
385        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
386        get rid off one store directive (a TAF bug?)
387      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
388        S/R seaice_lsr_tridiagv to change the loop range for consistency
389      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
390      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
391        S/R seaice_lsr_tridiagu/v (requires update of
392        offline_exf_seaice/input.dyn_jfnk)
393    
394    checkpoint65a (2014/07/27)
395    o model/src:
396      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
397        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
398        (topo in p-coords, ice-shelf in z-coords); update output of experiments
399        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
400    o model/src:
401      - collect momentum forcing tendency into local 2-D array (passed as argument
402        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
403        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
404        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
405      - collect T & S forcing tendency into local 2-D array (passed as argument to
406        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
407        affects results at machine truncation level (e.g., ocean: if using
408        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
409        correction due to vertical advection).
410      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
411        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
412        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
413        obcs_ctrl (ad & fwd grd @ 12 & 7).
414    o pkg/ptracers & diagnostics:
415      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
416        title (to avoid some unexpected truncation); sort out ptracers diags units.
417      - collect ptracer forcing tendency into local 2-D array (passed as argument
418        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
419    
420    checkpoint65 (2014/07/18)
421    o pkg/fizhi:
422      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
423        affects results at machine truncation level. Update output of experiments
424        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
425    o pkg/seaice: more clean up
426      - rename TAF common block tapes to be more consistent and remove
427        unnecessary duplicates
428      - add store directives to remove more recomputations, but use smaller
429        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
430        The idea behind this flag is to reduce the memory footprint when the
431        adjoint of the LSR is not required. As of now, defining the flag
432        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
433        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
434        For experiment offline_exf_seaice, this means on a linux box with gfortran
435        nearly a factor of 10 (but keep in mind there is mostly seaice code in
436        this experiment):
437        > size mitgcmuv_ad
438        text    data        bss     dec        hex
439        5100659 1216  220458952  225560827  d71c8fb
440        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
441        but only a moderate increase of 36% for global_ocean.cs32x15:
442        text    data        bss     dec        hex
443        6695027 1648 1014578664 1021275339 3cdf6ccb
444        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
445      - note: there are still recomputations in global_ocean.cs32x15 and
446        offline_exf_seaice and the gradient agreement changes (gets a
447        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
448      - in general, the AD gradients still are wrong
449    o OpenAD
450      - clean up code_oad/ directories somewhat by moving files
451        dontCompile, dontTransform, keepOriginal to OAD_support/
452    o model/src:
453      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
454        (not currently tested): add dissipation terms before NLFS rescaling of
455        tendencies (previously done after).
456    o pkg/diagnostics:
457      - write stats-diags in ascii file with more digits (same as in monitor).
458    o pkg/down_slope:
459      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
460        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
461    o model/src:
462      - new file "apply_forcing.F" containing all the code previously in
463        external_forcing.F, but with new argument list: pass, as new argument,
464        the current level tendency array to update (instead of a direct update
465        of the common bloc array). Change the corresponding calls.
466      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
467        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
468    o pkg/seaice/seaice_lsr, a little bit of clean up
469      - rearrange some code blocks, so that now all calculations for
470        setting up the right-hand-sides done within one single block
471        (I find that easier to read and understand)
472      - rearrange freedrift-code to reduce the number of ifdefs
473      - adjust some indentations and comments
474    
475    checkpoint64z (2014/07/10)
476    o model/src and several pkgs:
477      - change argument list of all S/R called from external_forcing.F and
478        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
479        to pass, as argument, the current level tendency array to update
480        (instead of a direct update of the common bloc array).
481      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
482      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
483    o pkg/seaice/seaice_lsr.F
484      - always initialize local arrays in seaice_lsr_tridiagu/v
485      - add more local tapes to seaice_lsr_tridiagu/v
486      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
487        keep it in bi/bj loop; this seems to be essential
488      - gradients are still wrong but only by 4-7 orders of magnitude
489        instead of 15 orders of magnitude, lab_sea improves a little
490    o pkg/seaice
491      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
492        generates unnecessary code in seaice_lsr_ad
493      - add more store directives in seaice_lsr to avoid unnecessary code
494        in seaice_lsr_ad
495      - exclude some residual computations in seaice_lsr when
496        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
497        in seaice_lsr_ad
498      - add more storing, a new tape (model/src/the_main_loop.F) and
499        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
500        and klockey should be checked by a specialist)
501      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
502        and update lab_sea after previous changes in pkg/seaice below
503    o pkg/autodiff:
504      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
505        viscFacInAd : run time parameters allowing for adjoint switches
506        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
507    o pkg/ecco:
508      - introduce cost_gencost_boxmean.F that computes a box mean
509        temperature (for use in adjoint sensitivity studies).
510    o model/src/set_defaults.F : initialize viscFacAdj to 1.
511    o pkg/mom_common/mom_calc_visc.F:
512      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
513    o pkg/seaice/seaice_summary.F:
514      - statement for SEAICEadjMODE now in autodiff_readparms.F
515    o pkg/seaice:
516      - remove some store directives and add new ones in an effort to get
517        finally rid off the recomputation warnings. This is successful
518        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
519        defined (i.e. no extensive recomputation warnings left), but there
520        are still too many recomputations on the solver iteration level
521      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
522      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
523        SEAICE_SIZE.h
524      - add a store directive in S/R seaice_calc_viscosities
525    o pkg/seaice (ITD code):
526      - fix definition of Hlimit for multi-threaded case
527      - use double precision arithmetic to compute Hlimit: this affects results;
528        update output of experiment seaice_itd.
529    o replace content of verification/seaice_itd
530      - instead of a 1D column use the configuration of offline_exf_seaice
531        to test the ice thickness distribution code with ridging
532      - this is a first shot at this experiment
533      - change of some defaults of ridging parameters SEAICEhStar (from
534        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
535        and lot of new comments.
536    
537    checkpoint64y (2014/06/20)
538    o pkg/seaice/seaice_reg_ridge.F:
539      - modify the regularization of very small volumes of ice; only check
540        total volume HEFF, and do not apply correction to individual ice
541        classes because that leads to funny patterns in the heat and fw-fluxes
542        into the ocean. Adjust seaice_itd/results/output.txt
543      - replace nITD by SEAICE_multDim in loop-ranges
544    o pkg/exf:
545      - add code to process the case field period = -12. with UV interpolation.
546      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
547        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
548    o verification/global_with_exf:
549      - switch all fields period to -12. (was previously untested) in input/data.exf
550        (but keep secondary test ".yearly" unchanged); update the reference output.
551    o pkg/cal:
552      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
553    o pkg/exf:
554      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
555        to replace logical switch "exf_verbose"
556      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
557    o pkg/sbo:
558      - update from Katherine Quinn: evaluate mass directly from density and SSH
559        (budget using Finite Volume method) instead of from bottom pressure.
560      - allow testreport to collect few selected SBO output ; tested in exp.
561        global_ocean.90x40x15 (after updating the results, to include SBO output).
562      - fix some multi-threading issues (in output part).
563    o model/src & most packages:
564      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
565      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
566        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
567        "data.{pkg}" exist ; and leave the S/R (return) just after.
568      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
569        + call LAND_READPARMS from packages_readparms.F
570    o pkg/seaice:
571      - remove code that resets useThSice in S/R seaice_readparms and
572        replace it by a warning in S/R seaice_check
573      - remove parameter MULTDIM, replace with nITD and runtime
574        parameter SEAICE_multDim (still hard-wired to nITD if
575        SEAICE_ITD is defined)
576    
577    checkpoint64x (2014/05/24)
578    o verification/lab_sea:
579      - update adjoint and TLM output following changes to pkg/salt_plume
580      - un-do the update after putting back local recip_Cp in few places.
581    o pkg/salt_plume: modifications by An Nguyen:
582      - add capability to do brine rejection (salt-plume) as function of
583        volume+tracers (instead of only salinity tracer).
584      - conserve volume by exchanging volume from each kLev to above to
585        accommodate in-coming brine volume
586      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
587      - switch KPP surf buoyancy due to brine forcing to 3-d
588        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
589      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
590      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
591        in East/West Arctic.
592    o pkg/sbo:
593      - incorporate modifications from Katherine Quinn to enable the use of sbo
594        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
595        output for future testreport verification (unfinished).
596    o pkg/atm_phys:
597      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
598        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
599        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
600    o pkg/seaice
601      seaice_calc_ice_strength.F: modify expression to avoid divisions
602        (affects truncation)
603      seaice_do_ridging.F: clean up the insectarium
604      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
605      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
606      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
607      - add some debugging information and error messages (warnings)
608    o model/src: modifications relatd to atmosphere p*:
609      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
610      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
611        of vertical profile tRef in geopotential background and anomaly.
612      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
613        and pkg/atm_phys.
614      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
615        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
616    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
617    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
618        not used right now, but can be used in BGC packages to fix conservation.
619    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
620        other packages too.
621    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
622        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
623    o model/src:
624      - since we have several heat capacity (even in model/src), define "recip_Cp"
625        as local variable (no longer in common block) to avoid any confusion.
626      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
627    o pkg/exf:
628      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
629        air density as function of air Temp, Humidity and atm pressure.
630    
631    checkpoint64w (2014/05/02)
632    o verification:
633      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
634        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
635        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
636        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
637        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
638    o model/src: for atmosphere in p* coords:
639      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
640      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
641        but not yet activated.
642    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
643      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
644      - this changes the results (but not for any verification experiment, because
645        none tests this), but avoids having an extra field in the restart files
646    o pkg/seaice: remove global variable TICE (not needed)
647      - replace by TICES or local variable where necessary (cost_seaice_test,
648        seaice_diagnostics_state)
649      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
650      - use specific read/write routines for reading and writing individual leves
651        of a multilevel field
652    o pkg/ctrl & model/inc:
653      - move additional anomaly fields of control vars (related to options:
654         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
655        from DYNVARS.h into new header file: CTRL_FIELDS.h
656    o pkg/seaice: some small modifications to the ridging code
657      - make fw2ObyRidge a global variable and add the freshwater flux to
658        seaice_growth
659      - pass actual thickness from seaice_prepare_ridging, so that it is
660        computed only in one place and compute it in the same way as in
661        seaice_growth
662      - initialise more fields in seaice_do_ridging that where cause floating
663        point exceptions over land
664    o pkg/seaice: preparations for ridging code and first real ridging code
665      - move most of "PART 1" of S/R seaice_growth into a new and separate
666        S/R seaice_reg_ridge that will both regularize the state variable after
667        advection call the actual ridging routine;
668      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
669        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
670      - remove ridging code from seaice_advdiff
671      - clean up remaining part 1 of seaice_growth in an attempt to make it
672        more readable (this is probably subjective)
673      - call seaice_itd_redist once in the initialisation phase to have the initial
674        conditions in the correct category
675      - finally: add new ridging routine for ITD code
676    
677    checkpoint64v (2014/04/11)
678    o pkg/ecco:
679      - add runtime parameters mdt[start,end]date[1,2]
680      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
681    o pkg/seaice:
682      - make deltaC a global variable, so that it can be used in ridging code
683      - first step towards ridging: introduce new routines that compute
684        ice strength based on ridging parameters
685      - add diagnostic for HSNOWITD
686      - add opnWtrFrac as a global variable (required for ridging scheme)
687    o pkg/salt_plume + pkg/seaice/seaice_growth.F
688      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
689        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
690    o verification/hs94.1x64x5:
691      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
692      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
693    o autodiff:
694      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
695        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
696        For now, only in pkgs used in verification/hs94.1x64x5.
697      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
698        which are specific to TAF/TAMC).
699      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
700        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
701        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
702      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
703        building mitgcmuv_ad (make adAll).
704    o pkg/ecco:
705      - cost_gencost_seaicev4.F:
706         reformulate proxy cost as function of sst and local param SEAICE_freeze
707         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
708      - add stop statement if old names siv4-[sst,vol] are used
709      - add snapshots + cost reports for atmospheric longwave
710      - remove factor 0.1 in front of wtau[u,v]
711      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
712         ALLOW_TMI_SST_COST_CONTRIBUTION
713    o pkg/atm_phys:
714      - add some diagnostics for Short-wave and for convection S/R.
715    o pkg/seaice/seaice_growth:
716      - fix a bug in the lateral melt parameterization for SEAICE_ITD
717        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
718      - rearrange loop order for better vector code in the same code block
719      - rewrite the floeDiameter formula to have fewer divisions
720      -  (miraculously) none of this changes the results of seaice_itd
721    o pkg/smooth:
722      - move param smooth2Ddiffnbt to pkg/ecco
723    o pkg/salt_plume:
724      - salt_plume_frac.F:
725         clean up local param names
726         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
727    o pkg/rw:
728      - add RS version of S/R READ_MFLDS_LEV.
729    o pkg/streamice:
730      - fix the restart test by writing/reading pickup_streamice files.
731    o pkg/seaice:
732      - refine checks for jfnk-related parameters
733      - comment out if statement with SEAICEuseIMEX parameter as long as there
734        is no IMEX code to avoid confusion and surprises
735    
736    checkpoint64u (2014/03/07)
737    o verification/MLAdjust:
738      - rename secondary test suffix:
739         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
740         0.leithD -> AhFlxF  + switch to flux-form
741         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
742         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
743    o pkg/mom_vecinv:
744      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
745        to be before mom_calc_visc.F)
746      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
747      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
748        this is simpler for the adjoint and for diagnostics.
749    o model/src + pkg/momentum:
750      - add input files for  2-D additional Western and Southern cell-edge wall
751         (e.g., to add "thin-wall" where it is =1).
752      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
753        using 2nd hFacZ that is computed from initial (fix domain) hFac
754      - known limitations of thin wall implementation: not yet coded for sigma
755        coords; not working with CD-scheme neither.
756    o pkg/seaice:
757      - rename recently introduced parameters from (wrong name) AB to
758        BDF (backward difference time discretisation)
759      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
760    o tools/adjoint_options:
761      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
762    
763    checkpoint64t (2014/02/01)
764    o pkg/ecco
765      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
766        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
767      - replace hard-coded record number and period which only work for monthly
768        with read-in runtime param that works for other periods (month,day,year)
769    o pkg/thsice
770      - corrected store directive fixes thsice adjoint gradient checks
771    o genmake2 & testreport:
772      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
773        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
774        Update testreport accordingly. No need to set "export OPENAD=true"
775        in adjoint_options/adjoint_oad anymore (will be removed later).
776    o pkg/shelfice:
777      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
778        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
779        so that surface forcing applies to k=kSurf if using pkg/shelfice.
780    o pkg/ctrl, pkg/grdchk, pkg/ecco:
781      - Changes to make GENARR more modular (i.e. invisible if not used)
782    o model/src/temp_integrate.F and salt_integrate.F
783      - re-include store directives that were removed on Dec 27th.
784    o model/src/external_forcing_surf.F
785      - add storage directives for EmPmR and PmEpR to avoid recomputation of
786        seaice_model in the adjoint that is problematic when seaice_model is
787        turned off in the adjoint. The resolved issue dated back to July when
788        EXTERNAL_FORCING_SURF call was moved.
789        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
790    o pkg/exf/exf_check.F
791      - fix a small bug again (originally found by Wentao Liu, now found again)
792      - streamline error output
793    o pkg/streamice and aim_v23:
794      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
795        Apple's /usr/bin/cpp knows what to do:
796        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
797        Target: x86_64-apple-darwin13.0.0
798    
799    checkpoint64s (2014/01/05)
800    o tools/adjoint_options:
801      - switch to fastopt.net TAF server (instead of default fastopt.de) for
802        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
803    o model/src:
804      - remove some unnecessary TAF storage directives in forward_step.F and
805        in dynamics.F (note: not always removed by TAF, e.g., double storage
806        of kappaRU,kappaRV in former version of dynamics.F).
807    o model/src & pkg/ptracers:
808      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
809        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
810        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
811      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
812      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
813      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
814    o useSingleCpuInput separates single-CPU input from single-CPU output;
815        for now only implemented for in exf_interp_read.F
816    o verification/advect_xy:
817      - fix missing EXCH call in local version of ini_salt.F and update output.
818    o momentum diagnostics:
819      - fix which deltaT is used in Total-Tendency diagnostics.
820      - fix typo in diagnostics for momentum tendency from AB.
821    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
822        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
823    
824    checkpoint64r (2013/12/08)
825    o verification/*/results:
826      - Update reference output of experiments that were passing with just 13 digits
827         (make it easier to detect future changes in results)
828    o model/src & pkg/ptracers:
829      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
830        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
831        to inside ptracers_integrate.F ; remove ptracers_advection.F
832    o coupling interface pkgs:
833        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
834      - change the config check to test the agreement of Ocean Depth
835        with ATM land/sea mask (instead of ATM orography);
836      - send to coupler the number of coupler time-steps to do for this run:
837        this allows to check for consistency and don't need anymore to be
838        specified in parameter file "data";
839      in coupler:
840      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
841      - improve report to log-file of config setting (pass log-file unit to few S/R)
842    o pkg/compon_communic:
843      - add coupling send/receive for non-tiled integer vector;
844      - add S/R to check and stop if any proc has an error (similar to
845        eesupp/src/stop_if_error.F but single thread and across Comm_World).
846    o pkg/exch2:
847      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
848        through list of all tiles my proc owns.
849    o model/src:
850      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
851        from rTrans) to simplify dependencies (no need to store rTrans anymore in
852        calling S/R); this affects AD results at machine truncation level:
853        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
854        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
855    o tools/build_options:
856      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
857    o coupling interface pkgs:
858        [compon_communic, atm_compon_interf & ocn_compon_interf]
859      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
860        to each S/R that needs it; remove un-used variables.
861      - change component tile registration (cpl_register.F in both compon_interf
862        and mitcomponent_tile_register.F) to pass the full list of tiles
863        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
864      - with pkg/exch2: adopt the same convention used for I/O to define mapping
865        towards coupler global array (unless W2_useE2ioLayOut=F):
866         a) can now use different tiling between atm & ocn comp.
867         b) no needs to modify the run-Off map when changing tiling (was needed
868            even if using the same tiling between atm & ocn).
869         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
870            full land tiles); not yet tested.
871      - check for valid mapping from comp. tile to coupler global array
872      - improve report of tile registration results to log file.
873    o pkg/exch2:
874      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
875        tile-registration (CPL_REGISTER);
876      - activate (un-comment) definition and setting of "W2_tileIndex" list to
877        store the local bi,bj indices of each tile;
878      - also print bi,bj in local report to log file;
879      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
880        Jun 2009 modif of pkg/exch2).
881    o testing on baudelaire:
882      - run 2 tests at a time: no significant slow down (since enough cpu) and
883        get the full set of test done earlier
884      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
885    o model/src/thermodynamics.F and routines called from it:
886      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
887        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
888        velocity (outp) by adding bolus velocity.
889      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
890        mass transport from velocity + lateral grid cell area
891      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
892      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
893     in thermodynamics.F
894      - remove k from thermodynamics.F and move it to temp_integrate.F
895        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
896        loop).
897      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
898        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
899        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
900        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
901      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
902        global_ocean.90x40x15, tutorial_global_oce_biogeo and
903        tutorial_tracer_adjsens (+ TLM output).
904    o tools/OAD_support and (verification/*/) code_oad:
905      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
906        module conversion ; remove unneeded CPP_EEOPTIONS.h.
907      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
908        version (closer to model/inc/CPP_OPTIONS.h).
909    o model/src:
910      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
911        retired list of parameters (routine FREEZE has been replace by surface
912        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
913    o pkg/gmredi:
914      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
915        velocity (same scheme but affects machine truncation) for GM_AdvForm.
916      - update output of FWD experiments: front_relax.bvp,
917        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
918    
919    checkpoint64q (2013/11/17)
920    o verification:
921      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
922        tutorial_global_oce_biogeo and global_ocean.90x40x15.
923      - generate new output (growth & melt) for seaice_itd experiment after
924        updating the input pickup_seaice files (previously wrong).
925    o pkg/cost:
926      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
927        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
928        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
929          cannot be applied to var in common block).
930        o allows to get results independent of tile-per-proc setting (if using
931          slower GLOBAL_SUM_SEND_RECV option).
932      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
933        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
934        forward gradients: update output).
935      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
936        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
937    o pkg/mom_common:
938      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
939        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
940        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
941        ensure that all field value that are used are set.
942    o tutorial_deep_convection (smag3d):
943      - add missing scaling in mom_calc_smag_3d.F;
944      - set smag3D_coeff in input.smag3d such that results do not change.
945    o pkg/dic:
946      - change dic_cost.F to compute cost on each tile first and then apply
947        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
948        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
949      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
950    o eesupp/src & pkg/mdsio:
951      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
952        (from pkg/mdsio) since they are no longer used for tape IO.
953      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
954        (+ keep a copy in pkg/atm_ocn_coupler).
955    o verification/isomip:
956      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
957    o tools/build_options:
958      - optfile linux_amd64_ifort11, fast (no ieee) case:
959        to get a working restart for all experiments, add "-fp-model source"
960        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
961    
962    checkpoint64p (2013/10/20)
963    o pkg/autodiff:
964      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
965        criteria, return to simple (default) tape IO format.
966    o pkg/mdsio (+ eesupp/src):
967      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
968        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
969      - fix globalFile and singleCpuIO options using simpler global mapping.
970      - new pairs of scatter/gather vector S/R (one for each type, generated from
971        template) corresponding to simpler global mapping.
972      - adread_write.F: switch to new S/R (but leave old calls commented) and write
973        to globalFile when parameter globalFiles is set to True.
974      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
975    o pkg/autodiff:
976      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
977        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
978        missing, just add a STOP if array type do not match.
979    o pkg/exf:
980      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
981         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
982         and rename array obsSIce to exf_iceFraction.
983    o tutorial_deep_convection:
984      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
985        for now all in this exp. code dir.
986      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
987        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
988    o eesupp/src:
989      - added SINGLE_DISK_IO option because reading of parameter files on
990        very large number of processors did not work with existing set-up
991    
992    checkpoint64o (2013/09/25)
993    o pkg/atm_phys & atm_compon_interf:
994      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
995    o tools/build_options:
996      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
997        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
998        remove CPP setting (was identical to genmake2 default).
999    o pkg/gmredi & model/src: Some updating and work done on the residual model.
1000      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
1001      - fixed up the calculation of the eddy stress and how it is added to the
1002        external forcing via taueddy_external_forcing.F
1003      - at the moment, it is very experimental and only works with the variable eddy
1004        diffusivity calculated in gmredi_k3d.F
1005    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
1006        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
1007    o testreport (& tools/do_tst_2+2):
1008      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
1009    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
1010      - remove CPP='cpp -traditional -P' (this is genmake2 default)
1011      - add switch (for big setups) to use 'medium' memory-model (but leave it
1012        commented out for now). Note: needed with FC 19 to compile big setups.
1013    o pkg/atm_compon_interf:
1014      - regroup per field origin (model & pkgs) the coupling storage routines
1015         (which accumalate in time each coupling field)
1016      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
1017        update accordingly + simplify aim_do_physics.F
1018    
1019    checkpoint64n (2013/08/26)
1020    o pkg/bbl:
1021      - update formulation to reduce dispersion of tracer properties in bbl
1022      - replaced horizontal and vertical transport parameters with velocities
1023      - changes results for verification/global_with_exf.yearly
1024    o verification/halfpipe_streamice:
1025      - change to matrix construction; update both Fwd & AD output.
1026    o verification/tutorial_tracer_adjsens:
1027      - OpenAD test: switch to vector-invariant momentum since fluxform with
1028        rStar causes problems with OpenAD; update output.
1029    o tools:
1030      - genmake2: define a common prefix for all temp-file names ; move them
1031        to local /tmp disk (but would be easy to move them back);
1032      - xmakedepend: apply the same switch for temp-files.
1033    o pkg/offline:
1034      - changes for use with rStar (NLFS): assume that we continue to provide
1035        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
1036        output files) and apply r* scaling at each time-step (function of the time
1037        varying Eta field); use normal pickup files (needed for restart with NLFS).
1038    o adjoint with OpenAD:
1039      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
1040        package openad.  This package has to be compiled for all runs with OpenAD
1041        instead of specifying code_oad_all as a modification directory.
1042      - link the fortran templates from tools/OAD_support to the build directory
1043        for preprocessing to avoid conflicts between different setups compiled
1044        simultaneously and simplify cleanup.
1045    o pkg/exf:
1046      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
1047        main model or other pkgs are exchanged in EXF_MAPFIELDS).
1048    o model/src:
1049      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
1050        (similar to do_fields_blocking_exchanges.F).
1051    o tools/genmake2:
1052      - remove TAF output src code just before calling staf (when not doing a fresh
1053        built, will stop if things go wrong with staf).
1054      - fix target "adobj" (left from TAF version-2 transition)
1055    o pkg/diagnostics:
1056      - add a parameter to track the status of pkg/diagnostics activation;
1057        this replace/extend the use of logical param "settingDiags" (to check
1058        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
1059        New S/R to print error message and stop when pkgStatus is not right.
1060      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
1061    
1062    checkpoint64m (2013/08/13)
1063    o model/inc:
1064      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
1065        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
1066    o pkg/kpp & aim_v23:
1067      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1068    o pkg/seaice:
1069      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
1070        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
1071      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1072    o eesupp/src:
1073      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
1074        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1075    o switch to TAF version-2:
1076      - add flow directives to "freeze" naming convention for ad-routines that
1077        are used in I/O routines of adjoint state and associated common blocks
1078        that are used in adcommon.h (backward compatible with version-1)
1079      - update all ad-optfiles (in tools/adjoint_options + few local to some
1080        verification exp) to switch to latest TAF version (currently 2.5.5);
1081        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1082        out except for diva).
1083      - the major change with TAF version-2 is that both the differentiated
1084        routines and the forward routines (new) are returned as part of the TAF
1085        output source code. Update genmake2 accordingly.
1086      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1087        with version-2 when compared to TLM or FWD gradient); other experiments
1088        output show minor changes (machine truncation level); update the few AD &
1089        TLM output with 12 matching digits only (some prior to version-2 switch).
1090    
1091    checkpoint64l (2013/08/05)
1092    o model/src:
1093      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1094      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1095        when using TAF but only if using OpenAD.
1096    o pkg/mom_common+fluxform+vecinv:
1097      - always set horiz. viscosity arrays to background value before calling
1098        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1099        only when using variable horiz. viscosity (useVariableVisc=T);
1100      - simplify mom_vecinv.F (only 1 block for momViscosity).
1101    o pkg/mom_common: variable horiz. viscosity in NH code
1102      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1103        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1104      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1105        useBiharmonicVisc & useVariableVisc.
1106      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1107        in calc_gw.F, version 1.27, 2006/06/20):
1108        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1109        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1110      - change background horiz viscosity in vertical momentum (gW) to always be
1111        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1112        any type of variable viscosity, e.g., viscAh/4Grid)
1113      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1114        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1115        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1116        default viscAh,viscA4 is zero).
1117    o model/src:
1118      - extend length of drC & recip_drC from Nr to Nr+1.
1119    o Divided Adjoint (DIVA) with MPI:
1120      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1121      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1122        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1123    
1124    checkpoint64k (2013/07/23)
1125    o tools/OAD_support:
1126      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1127        and remove it from genmake2.
1128    o tools/build_options:
1129      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1130        MPI_HEADER_FILES list (let genmake2 find the missing headers)
1131    o verification/halfpipe_streamice:
1132      - change to driving stress formulation; update both Fwd & AD output.
1133    o tools/genmake2 and Divided Adjoint with MPI:
1134      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1135      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1136      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1137        Makefile, which is set by genmake2, and check which mpi-headers are needed.
1138        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1139      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1140    o testreport:
1141      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1142        perform additional runs (number of additional runs is "add_DIVA_runs" taken
1143        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1144    o verification/lab_sea (AD test):
1145      - change to test Divided Adjoint Run in this set-up (both standard AD test
1146        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1147    o pkg atm_ & ocn_compon_interf:
1148      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1149        staggerTimeStep implementation) and disable (retired) corresponding
1150        parameter.
1151    o pkg/offline:
1152      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1153      - add S/R OFFLINE_CHECK to print offline parameter summary
1154        and stop if loading a file that is not used;
1155      - enable to calculate GMRedi tensor, KPP mixing and convective index
1156        when the corresponding file(s) is/are not specified (but pkg is used).
1157      - comment out resetting of monitorFreq (to endTime) since it still useful
1158        for monitoring CFL numbers and checking offline fields.
1159    o OpenAD:
1160      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1161        smaller standard output) and generate new (smaller) output (on baudelaire
1162        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1163    o model/src:
1164      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1165        (where external_forcing_adjust was called) and change list of arguments;
1166      - merge external_forcing_adjust.F into external_forcing_surf.F
1167      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1168        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1169        previously in file "balance_relax.F", now removed); remove corresponding
1170        arrays in FFIELDS.h.
1171      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1172        a hack for getting back surfaceForcingS (loaded from file) when using
1173        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1174      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1175        (was getting only 11 digits for AD-grad, due to different truncation
1176         error in AD code).
1177    
1178    checkpoint64j (2013/07/04)
1179  o pkg/offline:  o pkg/offline:
1180    - to enable the use of other features with pkg offline (e.g., obcs),    - to enable the use of other features with pkg offline (e.g., obcs),
1181      also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.      also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1182    - comment out "allowFreezing" (now active) in 2 offline testing exp.    - comment out "allowFreezing" (now active) in 2 offline testing exp.
1183  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
1184    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1185    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1186    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1187  o pkg/atm_phys:  o pkg/atm_phys:
1188    - 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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