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revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2103 by mlosch, Tue Dec 9 14:17:23 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification/global_ocean.cs32x15/input.seaice
8      - add test for strong implicit coupling and restricted addtive Schwarz
9        methods for LSR
10      - update results/output.seaice.txt
11    o verification/tutorial_global_oce_biogeo:
12      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
13        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
14        update output_adm,_oadm,_tlm.txt
15    o pkg/dic:
16      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
17      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
18        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
19    o verification/tutorial_global_oce_biogeo:
20      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
21        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
22        update output_adm,_oadm,_tlm.txt
23    o eesupp/src:
24      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
25        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
26    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
27      LSR (following Hutchings et al. 2004)
28      - introduce zetaZ as a global variable (requires adjustments in
29        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
30        in seaice_calc_viscosities.F
31      - new flag SEAICEuseStrImpCpl (default off)
32      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
33        momentum equations
34      - JFNK-solver (preconditioner) adjusted to allow using this method
35        (where it does not have any positive effect)
36    o pkg/seaice
37      - add overlap for restrictive additive Schwartz method also to LSR, but
38        turn it off by default (because it only seems to work for non-cubed
39        sphere/llc topologies)
40    o pkg/autodiff
41      - add extra exchanges in addummy_in_steppging also for mnc output
42    o pkg/seaice:
43      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
44        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
45    o pkg/obcs:
46      - add option to specify domain-connected piece Id along OB though files
47        (for now, only used to diagnose PhiVel; default =1 -> global correction)
48      - modify obcs_diag_balance.F to process each connected-part separately;
49        exclude OB where Id = 0 but keep the full divergence there (-> constant
50        Psi along this portion of OB and all inflow derived from grad(Phi))
51      - add example of OB-conect files in verification/so_box_biogeo/input.
52    o pkg/diagnostics:
53      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
54      a) use non zero matrix element across OB and solve for Phi 1 grid point
55         outside OB (i.e, where tracer OBCS are applied).
56      b) global imbalance of inFlow/outFlow across OB: instead of modifying
57         velocity across OB, spread it uniformly along the OB in the RHS.
58    
59    checkpoint65g (2014/11/19)
60    o pkg/diagnostcis:
61      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
62    o pkg/my82,pp81,kl10:
63      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
64        field diffKr as background diffusivity to set minimum diffusivity value.
65    o pkg/seaice:
66      - add new parameter SEAICEuseEVPrev (for revisited EVP by
67        Bouillon et al 2013)
68      - add SEAICE_evpAlpha/Beta to namelist
69      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
70        involve trivial re-ordering of divisions/multiplications that should not
71        have any effects, but ... they do change the results of lab_sea.hb87 so
72        that only 2 digits of agreement remain, in line with the general
73        instability/fragility of the evp-code. For now, I do not care and just
74        update the verification experiment
75    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
76      - remove xx_genarr2d_numsmooth etc
77      - use xx_genarr2d_preproc etc instead
78      - carry out smooth_correl2D at initialization stage rather than during
79        time stepping.
80      - get smoothOpNb from xx_gentim2d_preproc
81    o global_oce_cs32 :
82      - add test of generic ecco capabilities.
83    o pkg/exf/exf_getsurfacefluxes.F :
84      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
85    o pkg/ctrl,ecco :
86      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
87        is defined.
88    o pkg/seaice: add diagnostics for Delta (deformation parameter)
89    o model/src:
90      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
91        diffusivity (background) is specified but ignored.
92    o verification:
93      - in testreport, convert hostname to lower case for default output dir name
94    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
95    o pkg/dic: add modifications from Hajoon:
96      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
97      - light attenuation: add self-shading effect by climatological Chlorophyll
98        (read from file).
99    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
100        compiles when SEAICE_ALLOW_DYNAMICS is undefined
101    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
102        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
103        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
104        approach where CPP_OPTIONS.h includes an omnipotent
105        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
106    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
107        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
108    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
109        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
110        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
111    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
112      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
113      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
114      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
115      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
116    o pkg/ctrl,ecco,exf :
117      - remove variables associated with NON-generic costs,
118        unless ECCO_CTRL_DEPRECATED is defined.
119      - remove NON-generic NON-obcs controls,
120        unless ECCO_CTRL_DEPRECATED is defined.
121    o pkg/ctrl : added ctrl_local_params.h
122    o pkg/ecco : added ecco_local_params.h
123    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
124        experiments, which will progressively be removed once the
125        experiments are revised to use only generic controls/costs.
126    
127    checkpoint65f (2014/10/13)
128    o pkg/ctrl, ecco, seaice : minor changes in headers
129    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
130        cost function and control capabilities added since checkpoint65c.
131    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
132    o pkg/ecco: increase modularity and improve logic
133      - ecco_toolbox.F (new) : basic operations that are often used,
134        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
135        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
136      - cost_gencal.F (new) : determine filnames and records.
137      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
138      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
139        and exploit the above functions leading to more compact code.
140      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
141      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
142        using_ers, using_gfo, using_mdt is now only defined within gencost)
143    o pkg/ecco: extend generic cost capabilities
144      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
145        capabilities via gencost_preproc (+ _c,_i,_r related params),
146        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
147        gencost_outputlevel arguments to cost_generic
148      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
149        and active_read, making room for gencost_preproc to take effect.
150        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
151      - pkg/ecco/cost_generic.F :
152        compute and store misfit maks*(model-data) in localdif that is
153        then used in cost and for output, output misfit if outlev.GT.0
154      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
155        rather gencost_barfile for deciding whether to write barfile
156      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
157      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
158        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
159      - pkg/ecco/ecco_summary.F : report gencost variables
160      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
161    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
162    o pkg/ecco: internal re-organization
163      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
164        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
165        mv relevant variables definition from ecco_cost.h to ecco.h,
166        make sure gencost routines only include ecco.h)
167      - throughout : add missing CCP switches, rm unused variables,
168        and rm un-necessary CPP switches
169      - throughout gencost routines : replace modelstartdate with
170        gencost_startdate when needed
171      - cost_bp_read.F : use arguments, instead of common blocs
172        so that it can be used also by (new) cost_gencost_bpv4.F
173      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
174      - ecco_phys.F : compute etanFull
175      - ecco_readparms.F : rename using_topex as using_tpj, add
176        bpv4-grace to gencost list, initialize added parameters
177      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
178    
179    checkpoint65e (2014/09/28)
180    o pkg/obcs:
181      - replaced the just-added CPP options with run-time variables
182        (see pkg/obcs/OBCS_PARAMS.h for details)
183    o pkg/obcs:
184      - add additional CPP options for sponge boundary layers
185        (see pkg/obcs/OBCS_OPTIONS.h for details)
186    o pkg/atm_phys:
187      - implement simple (obliquity only, assuming circular planet orbit)
188        seasonal cycle for incoming insolation ; used when run-time parameter
189        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
190    o pkg/exf, pkg/ecco, pkg/ctrl:
191      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
192      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
193      - implement gentim2d for xx_tauu, xx_tauv
194    o pkg/ctrl, pkg/ecco :
195      - fix and complement the generic controls implementation
196    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
197        pkg/shelfice/shelfice_thermodynamics.F,
198        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
199        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
200      - add weight in CTRL_GET_GEN calls
201    o pkg/ctrl :
202      - ctrl_get_gen.F : add weight as input parameter, and apply
203        it directly rather than using smooth_correl2Dw (to be retired).
204      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
205    o pkg/ctrl :
206      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
207        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
208      - re-activate ctrl_summary (call in ctrl_init.F)
209    o pkg/ctrl/ctrl_cost_gen.F :
210      - fix CCP brackets, remove un-necessary myiter, mytime
211    o pkg/ecco, pkg/ctrl :
212      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
213      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
214      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
215      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
216    
217    checkpoint65d (2014/09/15)
218    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
219      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
220        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
221    o pkg/ctrl/ctrl_map_ini_genarr.F :
222      - remove compilation failure
223      - replace hard coded example
224      - use ctrl_map_ini_gen2D, 3D
225    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
226      - on/off switch based upon xx_genarr2d_weight,3d
227    o src/packages_init_variables.F :
228      - regroup pkg/estimation calls
229      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
230        (moved to ctrl_init_variables)
231    o cost/cost_init_varia.F :
232      - remove ecco_cost_init_varia
233        (moved to ecco_init_varia)
234    o ctrl/ctrl_init_variables.F :
235      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
236      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
237    o ctrl/ctrl_map_ini.F :
238      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
239        (moved to ctrl_init_variables)
240    o ctrl/ctrl_map_ini_ecco.F :
241      - remove ECCO_PHYS (mv to ecco_init_varia)
242      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
243    o ecco/ecco_ad_diff.list :
244      - add ecco_init_varia.f
245    o ecco/ecco_init_varia.F
246      - new routine
247    o pkg/streamice:
248      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
249        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
250      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
251    o pkg/generic_advdiff:
252      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
253    o pkg/exf:
254      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
255         xxg_precip capability
256      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
257    o pkg/ctrl:
258      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
259    o model/src/load_fields_driver.F :
260      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
261        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
262    o OpenAD verification experiments:
263      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
264        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
265        for now, only in pkgs used in OpenAD verification experiments.
266      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
267        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
268        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
269        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
270    o OpenAD verification tests:
271      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
272      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
273        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
274      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
275        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
276    o model/src & generic_advdiff:
277      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
278        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
279        dynamics requires valid tracer forcing only over tile interior but, for
280        some diagnostics, may need to extend it over 1 point in tile halo region.
281      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
282        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
283        setting in temp/salt/ptracer_integrate.F
284    o pkg/dic:
285      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
286        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
287        in gchem_forcing_sep.F
288    o pkg/autodiff & obcs:
289      - add storage of current OB values for U & V (was already done for T & S).
290    
291    checkpoint65c (2014/08/30)
292    o pkg/dic:
293      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
294        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
295        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
296    o verification:
297      - new experiment testing OBCS and DIC pkgs, using params & output from
298        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
299        passage: take OBCS from the last year of a 2 yrs simulation and initial
300        conditions from t=1.yr while keeping the same forcing.
301    o model/src:
302      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
303        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
304    o pkg/diagnostics (Stats-Diags):
305      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
306        a) refine region where stats are computed, excluding where arrhFac=0 ;
307        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
308        c) extend regional stats over the region edges (for U or V pt location).
309    o pkg/gchem:
310      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
311        pkg/dic is currently changing/updating ptracers values beyond the OB).
312    o verification (hs94):
313      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
314        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
315        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
316        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
317    o pkg/ptracers:
318      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
319        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
320      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
321        with AB-2 code (so that it get tested).
322    o model/src:
323      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
324        with AB-2 code (previously only available with AB-3 code).
325        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
326        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
327        there, by calling CYCLE_AB_TRACER).
328    o pkg/generic_advdiff:
329      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
330        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
331        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
332        S/R temp/salt/ptracers_integrate.F
333    o model/src & pkg/ptracers:
334      - remove common block variables gT,gS (in DYNVARS.h), except when
335         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
336      - remove common block variable gPtr.
337    o model/src & pkgs:
338      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
339         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
340         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
341         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
342      + change accordingly all calling S/R.
343      - use local temperature/salinity/ptracer tendency array (without bi,bj)
344        in S/R temp/salt/ptracers_integrate.F
345    o pkg/seaice:
346      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
347        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
348      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
349        in seaice_lsr
350      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
351        in s/r seaice_lsr_calc_coeffs
352    o pkg/mdsio:
353      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
354        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
355        too long (e.g., > MAX_LEN_FNAM/2 )
356    
357    checkpoint65b (2014/08/12)
358    o pkg/matrix:
359      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
360    o model/src:
361      - fix initialisation of geothermalFile; compile geothermal-flux code in
362        natl_box verification experiment.
363    o model/src & pkg/down_slope:
364      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
365      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
366        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
367        results at machine truncation level: update output of experiments
368        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
369    o pkg/diagnostics (Stats-Diags):
370      - do not cumulate the full volume when DIAGNOSTICS_FILL is
371        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
372        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
373        times (but Min,Max and StD are still wrong).
374    o model/src:
375      - add geothermal flux forcing: read in ini_forcing.F as time-constant
376        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
377    o model/src:
378      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
379        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
380        arrays are already updated while adjustments (filters, conv.adjustment) are
381        still applied later, in S/R TRACERS_CORRECTION_STEP.
382    o model/src:
383      - store in common bloc array "rhoInSitu" the virtual potential temperature
384        anomaly that is used to compute geopotential: this make the atmos code
385        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
386    o pkg/seaice/seaice_lsr.F
387      - rename integer variable ilcall to ipass (that's what it is called
388        in the residual diagnostics
389      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
390        default) for improved non-linear convergence of the first few steps
391      - adjust a few comments and add new ones to explain some of the store
392        directives
393    o pkg/generic_advdiff (& ptracers):
394      - re-work the code to check for valid advection scheme and for minimum
395        size of overlap (now stored in local common bloc in gad_advscheme.F)
396    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
397      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
398      - add an auxilliary variable "bet" and fix store directives and keys in
399        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
400        less exact gradients in my tests); but there are still
401        recomputation warning (although gradients are sort of OK), when
402        SEAICE_LSR_VECTORIZE is not defined, so this flag and
403        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
404      - update verification experiments lab_sea.
405      - change some comments in S/R seaice_calc_viscosities
406    o model/src:
407      - if staggerTimeStep=T, always apply exchange to velocity field in
408        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
409        (independent of using multi-dim advection or not); no effect on FWD run
410        but affects AD results (at machine truncation level): update output of
411        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
412        and isomip (oad: 12.d).
413    o pkg/generic_advdiff:
414      - stop if doAB_onGtGs is set to FALSE but ignored
415      - refine warning related to stability of tracer time-stepping
416        regarding internal wave dynamics.
417      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
418        on staggerTimeStep & implicitIntGravWave (will now get a warning
419        if potentially unstable).
420    o pkg/kl10:
421      - add new pkg "kl10" for mixing due to internal wave breaking, from
422        http://www.sciencedirect.com/science/article/pii/S1463500310000144
423        (contribution from Jody Klymak), tested in verification experiment
424        verification/internal_wave/input.kl10/
425    o isomip experiment:
426      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
427        (input.htd) and update the output.
428    o cd_code experiments:
429      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
430        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
431        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
432        update the corresponding output.
433    o pkg/seaice:
434      - reduce the number of include files and store directives in
435        S/R seaice_lsr_tridiagu/v
436      - change the order of loops in one case in S/R seaice_lsr_tridiagv
437        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
438        get rid off one store directive (a TAF bug?)
439      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
440        S/R seaice_lsr_tridiagv to change the loop range for consistency
441      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
442      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
443        S/R seaice_lsr_tridiagu/v (requires update of
444        offline_exf_seaice/input.dyn_jfnk)
445    
446    checkpoint65a (2014/07/27)
447    o model/src:
448      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
449        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
450        (topo in p-coords, ice-shelf in z-coords); update output of experiments
451        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
452    o model/src:
453      - collect momentum forcing tendency into local 2-D array (passed as argument
454        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
455        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
456        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
457      - collect T & S forcing tendency into local 2-D array (passed as argument to
458        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
459        affects results at machine truncation level (e.g., ocean: if using
460        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
461        correction due to vertical advection).
462      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
463        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
464        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
465        obcs_ctrl (ad & fwd grd @ 12 & 7).
466    o pkg/ptracers & diagnostics:
467      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
468        title (to avoid some unexpected truncation); sort out ptracers diags units.
469      - collect ptracer forcing tendency into local 2-D array (passed as argument
470        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
471    
472    checkpoint65 (2014/07/18)
473    o pkg/fizhi:
474      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
475        affects results at machine truncation level. Update output of experiments
476        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
477    o pkg/seaice: more clean up
478      - rename TAF common block tapes to be more consistent and remove
479        unnecessary duplicates
480      - add store directives to remove more recomputations, but use smaller
481        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
482        The idea behind this flag is to reduce the memory footprint when the
483        adjoint of the LSR is not required. As of now, defining the flag
484        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
485        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
486        For experiment offline_exf_seaice, this means on a linux box with gfortran
487        nearly a factor of 10 (but keep in mind there is mostly seaice code in
488        this experiment):
489        > size mitgcmuv_ad
490        text    data        bss     dec        hex
491        5100659 1216  220458952  225560827  d71c8fb
492        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
493        but only a moderate increase of 36% for global_ocean.cs32x15:
494        text    data        bss     dec        hex
495        6695027 1648 1014578664 1021275339 3cdf6ccb
496        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
497      - note: there are still recomputations in global_ocean.cs32x15 and
498        offline_exf_seaice and the gradient agreement changes (gets a
499        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
500      - in general, the AD gradients still are wrong
501    o OpenAD
502      - clean up code_oad/ directories somewhat by moving files
503        dontCompile, dontTransform, keepOriginal to OAD_support/
504    o model/src:
505      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
506        (not currently tested): add dissipation terms before NLFS rescaling of
507        tendencies (previously done after).
508    o pkg/diagnostics:
509      - write stats-diags in ascii file with more digits (same as in monitor).
510    o pkg/down_slope:
511      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
512        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
513    o model/src:
514      - new file "apply_forcing.F" containing all the code previously in
515        external_forcing.F, but with new argument list: pass, as new argument,
516        the current level tendency array to update (instead of a direct update
517        of the common bloc array). Change the corresponding calls.
518      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
519        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
520    o pkg/seaice/seaice_lsr, a little bit of clean up
521      - rearrange some code blocks, so that now all calculations for
522        setting up the right-hand-sides done within one single block
523        (I find that easier to read and understand)
524      - rearrange freedrift-code to reduce the number of ifdefs
525      - adjust some indentations and comments
526    
527    checkpoint64z (2014/07/10)
528    o model/src and several pkgs:
529      - change argument list of all S/R called from external_forcing.F and
530        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
531        to pass, as argument, the current level tendency array to update
532        (instead of a direct update of the common bloc array).
533      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
534      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
535    o pkg/seaice/seaice_lsr.F
536      - always initialize local arrays in seaice_lsr_tridiagu/v
537      - add more local tapes to seaice_lsr_tridiagu/v
538      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
539        keep it in bi/bj loop; this seems to be essential
540      - gradients are still wrong but only by 4-7 orders of magnitude
541        instead of 15 orders of magnitude, lab_sea improves a little
542    o pkg/seaice
543      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
544        generates unnecessary code in seaice_lsr_ad
545      - add more store directives in seaice_lsr to avoid unnecessary code
546        in seaice_lsr_ad
547      - exclude some residual computations in seaice_lsr when
548        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
549        in seaice_lsr_ad
550      - add more storing, a new tape (model/src/the_main_loop.F) and
551        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
552        and klockey should be checked by a specialist)
553      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
554        and update lab_sea after previous changes in pkg/seaice below
555    o pkg/autodiff:
556      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
557        viscFacInAd : run time parameters allowing for adjoint switches
558        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
559    o pkg/ecco:
560      - introduce cost_gencost_boxmean.F that computes a box mean
561        temperature (for use in adjoint sensitivity studies).
562    o model/src/set_defaults.F : initialize viscFacAdj to 1.
563    o pkg/mom_common/mom_calc_visc.F:
564      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
565    o pkg/seaice/seaice_summary.F:
566      - statement for SEAICEadjMODE now in autodiff_readparms.F
567    o pkg/seaice:
568      - remove some store directives and add new ones in an effort to get
569        finally rid off the recomputation warnings. This is successful
570        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
571        defined (i.e. no extensive recomputation warnings left), but there
572        are still too many recomputations on the solver iteration level
573      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
574      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
575        SEAICE_SIZE.h
576      - add a store directive in S/R seaice_calc_viscosities
577    o pkg/seaice (ITD code):
578      - fix definition of Hlimit for multi-threaded case
579      - use double precision arithmetic to compute Hlimit: this affects results;
580        update output of experiment seaice_itd.
581    o replace content of verification/seaice_itd
582      - instead of a 1D column use the configuration of offline_exf_seaice
583        to test the ice thickness distribution code with ridging
584      - this is a first shot at this experiment
585      - change of some defaults of ridging parameters SEAICEhStar (from
586        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
587        and lot of new comments.
588    
589    checkpoint64y (2014/06/20)
590    o pkg/seaice/seaice_reg_ridge.F:
591      - modify the regularization of very small volumes of ice; only check
592        total volume HEFF, and do not apply correction to individual ice
593        classes because that leads to funny patterns in the heat and fw-fluxes
594        into the ocean. Adjust seaice_itd/results/output.txt
595      - replace nITD by SEAICE_multDim in loop-ranges
596    o pkg/exf:
597      - add code to process the case field period = -12. with UV interpolation.
598      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
599        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
600    o verification/global_with_exf:
601      - switch all fields period to -12. (was previously untested) in input/data.exf
602        (but keep secondary test ".yearly" unchanged); update the reference output.
603    o pkg/cal:
604      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
605    o pkg/exf:
606      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
607        to replace logical switch "exf_verbose"
608      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
609    o pkg/sbo:
610      - update from Katherine Quinn: evaluate mass directly from density and SSH
611        (budget using Finite Volume method) instead of from bottom pressure.
612      - allow testreport to collect few selected SBO output ; tested in exp.
613        global_ocean.90x40x15 (after updating the results, to include SBO output).
614      - fix some multi-threading issues (in output part).
615    o model/src & most packages:
616      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
617      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
618        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
619        "data.{pkg}" exist ; and leave the S/R (return) just after.
620      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
621        + call LAND_READPARMS from packages_readparms.F
622    o pkg/seaice:
623      - remove code that resets useThSice in S/R seaice_readparms and
624        replace it by a warning in S/R seaice_check
625      - remove parameter MULTDIM, replace with nITD and runtime
626        parameter SEAICE_multDim (still hard-wired to nITD if
627        SEAICE_ITD is defined)
628    
629    checkpoint64x (2014/05/24)
630    o verification/lab_sea:
631      - update adjoint and TLM output following changes to pkg/salt_plume
632      - un-do the update after putting back local recip_Cp in few places.
633    o pkg/salt_plume: modifications by An Nguyen:
634      - add capability to do brine rejection (salt-plume) as function of
635        volume+tracers (instead of only salinity tracer).
636      - conserve volume by exchanging volume from each kLev to above to
637        accommodate in-coming brine volume
638      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
639      - switch KPP surf buoyancy due to brine forcing to 3-d
640        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
641      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
642      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
643        in East/West Arctic.
644    o pkg/sbo:
645      - incorporate modifications from Katherine Quinn to enable the use of sbo
646        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
647        output for future testreport verification (unfinished).
648    o pkg/atm_phys:
649      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
650        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
651        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
652    o pkg/seaice
653      seaice_calc_ice_strength.F: modify expression to avoid divisions
654        (affects truncation)
655      seaice_do_ridging.F: clean up the insectarium
656      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
657      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
658      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
659      - add some debugging information and error messages (warnings)
660    o model/src: modifications relatd to atmosphere p*:
661      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
662      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
663        of vertical profile tRef in geopotential background and anomaly.
664      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
665        and pkg/atm_phys.
666      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
667        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
668    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
669    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
670        not used right now, but can be used in BGC packages to fix conservation.
671    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
672        other packages too.
673    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
674        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
675    o model/src:
676      - since we have several heat capacity (even in model/src), define "recip_Cp"
677        as local variable (no longer in common block) to avoid any confusion.
678      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
679    o pkg/exf:
680      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
681        air density as function of air Temp, Humidity and atm pressure.
682    
683    checkpoint64w (2014/05/02)
684    o verification:
685      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
686        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
687        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
688        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
689        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
690    o model/src: for atmosphere in p* coords:
691      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
692      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
693        but not yet activated.
694    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
695      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
696      - this changes the results (but not for any verification experiment, because
697        none tests this), but avoids having an extra field in the restart files
698    o pkg/seaice: remove global variable TICE (not needed)
699      - replace by TICES or local variable where necessary (cost_seaice_test,
700        seaice_diagnostics_state)
701      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
702      - use specific read/write routines for reading and writing individual leves
703        of a multilevel field
704    o pkg/ctrl & model/inc:
705      - move additional anomaly fields of control vars (related to options:
706         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
707        from DYNVARS.h into new header file: CTRL_FIELDS.h
708    o pkg/seaice: some small modifications to the ridging code
709      - make fw2ObyRidge a global variable and add the freshwater flux to
710        seaice_growth
711      - pass actual thickness from seaice_prepare_ridging, so that it is
712        computed only in one place and compute it in the same way as in
713        seaice_growth
714      - initialise more fields in seaice_do_ridging that where cause floating
715        point exceptions over land
716    o pkg/seaice: preparations for ridging code and first real ridging code
717      - move most of "PART 1" of S/R seaice_growth into a new and separate
718        S/R seaice_reg_ridge that will both regularize the state variable after
719        advection call the actual ridging routine;
720      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
721        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
722      - remove ridging code from seaice_advdiff
723      - clean up remaining part 1 of seaice_growth in an attempt to make it
724        more readable (this is probably subjective)
725      - call seaice_itd_redist once in the initialisation phase to have the initial
726        conditions in the correct category
727      - finally: add new ridging routine for ITD code
728    
729    checkpoint64v (2014/04/11)
730    o pkg/ecco:
731      - add runtime parameters mdt[start,end]date[1,2]
732      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
733    o pkg/seaice:
734      - make deltaC a global variable, so that it can be used in ridging code
735      - first step towards ridging: introduce new routines that compute
736        ice strength based on ridging parameters
737      - add diagnostic for HSNOWITD
738      - add opnWtrFrac as a global variable (required for ridging scheme)
739    o pkg/salt_plume + pkg/seaice/seaice_growth.F
740      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
741        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
742    o verification/hs94.1x64x5:
743      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
744      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
745    o autodiff:
746      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
747        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
748        For now, only in pkgs used in verification/hs94.1x64x5.
749      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
750        which are specific to TAF/TAMC).
751      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
752        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
753        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
754      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
755        building mitgcmuv_ad (make adAll).
756    o pkg/ecco:
757      - cost_gencost_seaicev4.F:
758         reformulate proxy cost as function of sst and local param SEAICE_freeze
759         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
760      - add stop statement if old names siv4-[sst,vol] are used
761      - add snapshots + cost reports for atmospheric longwave
762      - remove factor 0.1 in front of wtau[u,v]
763      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
764         ALLOW_TMI_SST_COST_CONTRIBUTION
765    o pkg/atm_phys:
766      - add some diagnostics for Short-wave and for convection S/R.
767    o pkg/seaice/seaice_growth:
768      - fix a bug in the lateral melt parameterization for SEAICE_ITD
769        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
770      - rearrange loop order for better vector code in the same code block
771      - rewrite the floeDiameter formula to have fewer divisions
772      -  (miraculously) none of this changes the results of seaice_itd
773    o pkg/smooth:
774      - move param smooth2Ddiffnbt to pkg/ecco
775    o pkg/salt_plume:
776      - salt_plume_frac.F:
777         clean up local param names
778         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
779    o pkg/rw:
780      - add RS version of S/R READ_MFLDS_LEV.
781    o pkg/streamice:
782      - fix the restart test by writing/reading pickup_streamice files.
783    o pkg/seaice:
784      - refine checks for jfnk-related parameters
785      - comment out if statement with SEAICEuseIMEX parameter as long as there
786        is no IMEX code to avoid confusion and surprises
787    
788    checkpoint64u (2014/03/07)
789    o verification/MLAdjust:
790      - rename secondary test suffix:
791         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
792         0.leithD -> AhFlxF  + switch to flux-form
793         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
794         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
795    o pkg/mom_vecinv:
796      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
797        to be before mom_calc_visc.F)
798      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
799      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
800        this is simpler for the adjoint and for diagnostics.
801    o model/src + pkg/momentum:
802      - add input files for  2-D additional Western and Southern cell-edge wall
803         (e.g., to add "thin-wall" where it is =1).
804      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
805        using 2nd hFacZ that is computed from initial (fix domain) hFac
806      - known limitations of thin wall implementation: not yet coded for sigma
807        coords; not working with CD-scheme neither.
808    o pkg/seaice:
809      - rename recently introduced parameters from (wrong name) AB to
810        BDF (backward difference time discretisation)
811      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
812    o tools/adjoint_options:
813      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
814    
815    checkpoint64t (2014/02/01)
816    o pkg/ecco
817      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
818        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
819      - replace hard-coded record number and period which only work for monthly
820        with read-in runtime param that works for other periods (month,day,year)
821    o pkg/thsice
822      - corrected store directive fixes thsice adjoint gradient checks
823    o genmake2 & testreport:
824      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
825        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
826        Update testreport accordingly. No need to set "export OPENAD=true"
827        in adjoint_options/adjoint_oad anymore (will be removed later).
828    o pkg/shelfice:
829      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
830        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
831        so that surface forcing applies to k=kSurf if using pkg/shelfice.
832    o pkg/ctrl, pkg/grdchk, pkg/ecco:
833      - Changes to make GENARR more modular (i.e. invisible if not used)
834    o model/src/temp_integrate.F and salt_integrate.F
835      - re-include store directives that were removed on Dec 27th.
836    o model/src/external_forcing_surf.F
837      - add storage directives for EmPmR and PmEpR to avoid recomputation of
838        seaice_model in the adjoint that is problematic when seaice_model is
839        turned off in the adjoint. The resolved issue dated back to July when
840        EXTERNAL_FORCING_SURF call was moved.
841        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
842    o pkg/exf/exf_check.F
843      - fix a small bug again (originally found by Wentao Liu, now found again)
844      - streamline error output
845    o pkg/streamice and aim_v23:
846      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
847        Apple's /usr/bin/cpp knows what to do:
848        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
849        Target: x86_64-apple-darwin13.0.0
850    
851    checkpoint64s (2014/01/05)
852    o tools/adjoint_options:
853      - switch to fastopt.net TAF server (instead of default fastopt.de) for
854        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
855    o model/src:
856      - remove some unnecessary TAF storage directives in forward_step.F and
857        in dynamics.F (note: not always removed by TAF, e.g., double storage
858        of kappaRU,kappaRV in former version of dynamics.F).
859    o model/src & pkg/ptracers:
860      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
861        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
862        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
863      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
864      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
865      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
866    o useSingleCpuInput separates single-CPU input from single-CPU output;
867        for now only implemented for in exf_interp_read.F
868    o verification/advect_xy:
869      - fix missing EXCH call in local version of ini_salt.F and update output.
870    o momentum diagnostics:
871      - fix which deltaT is used in Total-Tendency diagnostics.
872      - fix typo in diagnostics for momentum tendency from AB.
873    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
874        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
875    
876    checkpoint64r (2013/12/08)
877    o verification/*/results:
878      - Update reference output of experiments that were passing with just 13 digits
879         (make it easier to detect future changes in results)
880    o model/src & pkg/ptracers:
881      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
882        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
883        to inside ptracers_integrate.F ; remove ptracers_advection.F
884    o coupling interface pkgs:
885        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
886      - change the config check to test the agreement of Ocean Depth
887        with ATM land/sea mask (instead of ATM orography);
888      - send to coupler the number of coupler time-steps to do for this run:
889        this allows to check for consistency and don't need anymore to be
890        specified in parameter file "data";
891      in coupler:
892      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
893      - improve report to log-file of config setting (pass log-file unit to few S/R)
894    o pkg/compon_communic:
895      - add coupling send/receive for non-tiled integer vector;
896      - add S/R to check and stop if any proc has an error (similar to
897        eesupp/src/stop_if_error.F but single thread and across Comm_World).
898    o pkg/exch2:
899      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
900        through list of all tiles my proc owns.
901    o model/src:
902      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
903        from rTrans) to simplify dependencies (no need to store rTrans anymore in
904        calling S/R); this affects AD results at machine truncation level:
905        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
906        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
907    o tools/build_options:
908      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
909    o coupling interface pkgs:
910        [compon_communic, atm_compon_interf & ocn_compon_interf]
911      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
912        to each S/R that needs it; remove un-used variables.
913      - change component tile registration (cpl_register.F in both compon_interf
914        and mitcomponent_tile_register.F) to pass the full list of tiles
915        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
916      - with pkg/exch2: adopt the same convention used for I/O to define mapping
917        towards coupler global array (unless W2_useE2ioLayOut=F):
918         a) can now use different tiling between atm & ocn comp.
919         b) no needs to modify the run-Off map when changing tiling (was needed
920            even if using the same tiling between atm & ocn).
921         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
922            full land tiles); not yet tested.
923      - check for valid mapping from comp. tile to coupler global array
924      - improve report of tile registration results to log file.
925    o pkg/exch2:
926      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
927        tile-registration (CPL_REGISTER);
928      - activate (un-comment) definition and setting of "W2_tileIndex" list to
929        store the local bi,bj indices of each tile;
930      - also print bi,bj in local report to log file;
931      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
932        Jun 2009 modif of pkg/exch2).
933    o testing on baudelaire:
934      - run 2 tests at a time: no significant slow down (since enough cpu) and
935        get the full set of test done earlier
936      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
937    o model/src/thermodynamics.F and routines called from it:
938      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
939        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
940        velocity (outp) by adding bolus velocity.
941      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
942        mass transport from velocity + lateral grid cell area
943      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
944      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
945     in thermodynamics.F
946      - remove k from thermodynamics.F and move it to temp_integrate.F
947        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
948        loop).
949      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
950        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
951        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
952        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
953      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
954        global_ocean.90x40x15, tutorial_global_oce_biogeo and
955        tutorial_tracer_adjsens (+ TLM output).
956    o tools/OAD_support and (verification/*/) code_oad:
957      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
958        module conversion ; remove unneeded CPP_EEOPTIONS.h.
959      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
960        version (closer to model/inc/CPP_OPTIONS.h).
961    o model/src:
962      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
963        retired list of parameters (routine FREEZE has been replace by surface
964        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
965    o pkg/gmredi:
966      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
967        velocity (same scheme but affects machine truncation) for GM_AdvForm.
968      - update output of FWD experiments: front_relax.bvp,
969        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
970    
971    checkpoint64q (2013/11/17)
972    o verification:
973      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
974        tutorial_global_oce_biogeo and global_ocean.90x40x15.
975      - generate new output (growth & melt) for seaice_itd experiment after
976        updating the input pickup_seaice files (previously wrong).
977    o pkg/cost:
978      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
979        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
980        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
981          cannot be applied to var in common block).
982        o allows to get results independent of tile-per-proc setting (if using
983          slower GLOBAL_SUM_SEND_RECV option).
984      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
985        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
986        forward gradients: update output).
987      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
988        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
989    o pkg/mom_common:
990      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
991        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
992        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
993        ensure that all field value that are used are set.
994    o tutorial_deep_convection (smag3d):
995      - add missing scaling in mom_calc_smag_3d.F;
996      - set smag3D_coeff in input.smag3d such that results do not change.
997    o pkg/dic:
998      - change dic_cost.F to compute cost on each tile first and then apply
999        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
1000        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
1001      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
1002    o eesupp/src & pkg/mdsio:
1003      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
1004        (from pkg/mdsio) since they are no longer used for tape IO.
1005      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
1006        (+ keep a copy in pkg/atm_ocn_coupler).
1007    o verification/isomip:
1008      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
1009    o tools/build_options:
1010      - optfile linux_amd64_ifort11, fast (no ieee) case:
1011        to get a working restart for all experiments, add "-fp-model source"
1012        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
1013    
1014    checkpoint64p (2013/10/20)
1015    o pkg/autodiff:
1016      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
1017        criteria, return to simple (default) tape IO format.
1018    o pkg/mdsio (+ eesupp/src):
1019      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
1020        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
1021      - fix globalFile and singleCpuIO options using simpler global mapping.
1022      - new pairs of scatter/gather vector S/R (one for each type, generated from
1023        template) corresponding to simpler global mapping.
1024      - adread_write.F: switch to new S/R (but leave old calls commented) and write
1025        to globalFile when parameter globalFiles is set to True.
1026      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
1027    o pkg/autodiff:
1028      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
1029        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
1030        missing, just add a STOP if array type do not match.
1031    o pkg/exf:
1032      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
1033         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
1034         and rename array obsSIce to exf_iceFraction.
1035    o tutorial_deep_convection:
1036      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
1037        for now all in this exp. code dir.
1038      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
1039        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
1040    o eesupp/src:
1041      - added SINGLE_DISK_IO option because reading of parameter files on
1042        very large number of processors did not work with existing set-up
1043    
1044    checkpoint64o (2013/09/25)
1045    o pkg/atm_phys & atm_compon_interf:
1046      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
1047    o tools/build_options:
1048      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
1049        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
1050        remove CPP setting (was identical to genmake2 default).
1051    o pkg/gmredi & model/src: Some updating and work done on the residual model.
1052      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
1053      - fixed up the calculation of the eddy stress and how it is added to the
1054        external forcing via taueddy_external_forcing.F
1055      - at the moment, it is very experimental and only works with the variable eddy
1056        diffusivity calculated in gmredi_k3d.F
1057    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
1058        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
1059    o testreport (& tools/do_tst_2+2):
1060      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
1061    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
1062      - remove CPP='cpp -traditional -P' (this is genmake2 default)
1063      - add switch (for big setups) to use 'medium' memory-model (but leave it
1064        commented out for now). Note: needed with FC 19 to compile big setups.
1065    o pkg/atm_compon_interf:
1066      - regroup per field origin (model & pkgs) the coupling storage routines
1067         (which accumalate in time each coupling field)
1068      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
1069        update accordingly + simplify aim_do_physics.F
1070    
1071    checkpoint64n (2013/08/26)
1072    o pkg/bbl:
1073      - update formulation to reduce dispersion of tracer properties in bbl
1074      - replaced horizontal and vertical transport parameters with velocities
1075      - changes results for verification/global_with_exf.yearly
1076    o verification/halfpipe_streamice:
1077      - change to matrix construction; update both Fwd & AD output.
1078    o verification/tutorial_tracer_adjsens:
1079      - OpenAD test: switch to vector-invariant momentum since fluxform with
1080        rStar causes problems with OpenAD; update output.
1081    o tools:
1082      - genmake2: define a common prefix for all temp-file names ; move them
1083        to local /tmp disk (but would be easy to move them back);
1084      - xmakedepend: apply the same switch for temp-files.
1085    o pkg/offline:
1086      - changes for use with rStar (NLFS): assume that we continue to provide
1087        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
1088        output files) and apply r* scaling at each time-step (function of the time
1089        varying Eta field); use normal pickup files (needed for restart with NLFS).
1090    o adjoint with OpenAD:
1091      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
1092        package openad.  This package has to be compiled for all runs with OpenAD
1093        instead of specifying code_oad_all as a modification directory.
1094      - link the fortran templates from tools/OAD_support to the build directory
1095        for preprocessing to avoid conflicts between different setups compiled
1096        simultaneously and simplify cleanup.
1097    o pkg/exf:
1098      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
1099        main model or other pkgs are exchanged in EXF_MAPFIELDS).
1100    o model/src:
1101      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
1102        (similar to do_fields_blocking_exchanges.F).
1103    o tools/genmake2:
1104      - remove TAF output src code just before calling staf (when not doing a fresh
1105        built, will stop if things go wrong with staf).
1106      - fix target "adobj" (left from TAF version-2 transition)
1107    o pkg/diagnostics:
1108      - add a parameter to track the status of pkg/diagnostics activation;
1109        this replace/extend the use of logical param "settingDiags" (to check
1110        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
1111        New S/R to print error message and stop when pkgStatus is not right.
1112      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
1113    
1114    checkpoint64m (2013/08/13)
1115    o model/inc:
1116      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
1117        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
1118    o pkg/kpp & aim_v23:
1119      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1120    o pkg/seaice:
1121      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
1122        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
1123      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1124    o eesupp/src:
1125      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
1126        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1127    o switch to TAF version-2:
1128      - add flow directives to "freeze" naming convention for ad-routines that
1129        are used in I/O routines of adjoint state and associated common blocks
1130        that are used in adcommon.h (backward compatible with version-1)
1131      - update all ad-optfiles (in tools/adjoint_options + few local to some
1132        verification exp) to switch to latest TAF version (currently 2.5.5);
1133        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1134        out except for diva).
1135      - the major change with TAF version-2 is that both the differentiated
1136        routines and the forward routines (new) are returned as part of the TAF
1137        output source code. Update genmake2 accordingly.
1138      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1139        with version-2 when compared to TLM or FWD gradient); other experiments
1140        output show minor changes (machine truncation level); update the few AD &
1141        TLM output with 12 matching digits only (some prior to version-2 switch).
1142    
1143    checkpoint64l (2013/08/05)
1144    o model/src:
1145      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1146      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1147        when using TAF but only if using OpenAD.
1148    o pkg/mom_common+fluxform+vecinv:
1149      - always set horiz. viscosity arrays to background value before calling
1150        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1151        only when using variable horiz. viscosity (useVariableVisc=T);
1152      - simplify mom_vecinv.F (only 1 block for momViscosity).
1153    o pkg/mom_common: variable horiz. viscosity in NH code
1154      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1155        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1156      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1157        useBiharmonicVisc & useVariableVisc.
1158      - fix old bug (already in 1rst implementation of variable horizontal viscosity
1159        in calc_gw.F, version 1.27, 2006/06/20):
1160        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1161        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1162      - change background horiz viscosity in vertical momentum (gW) to always be
1163        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1164        any type of variable viscosity, e.g., viscAh/4Grid)
1165      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1166        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
1167        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1168        default viscAh,viscA4 is zero).
1169    o model/src:
1170      - extend length of drC & recip_drC from Nr to Nr+1.
1171    o Divided Adjoint (DIVA) with MPI:
1172      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1173      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1174        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1175    
1176    checkpoint64k (2013/07/23)
1177    o tools/OAD_support:
1178      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1179        and remove it from genmake2.
1180    o tools/build_options:
1181      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1182        MPI_HEADER_FILES list (let genmake2 find the missing headers)
1183    o verification/halfpipe_streamice:
1184      - change to driving stress formulation; update both Fwd & AD output.
1185    o tools/genmake2 and Divided Adjoint with MPI:
1186      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1187      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1188      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1189        Makefile, which is set by genmake2, and check which mpi-headers are needed.
1190        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1191      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1192    o testreport:
1193      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1194        perform additional runs (number of additional runs is "add_DIVA_runs" taken
1195        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1196    o verification/lab_sea (AD test):
1197      - change to test Divided Adjoint Run in this set-up (both standard AD test
1198        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1199    o pkg atm_ & ocn_compon_interf:
1200      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1201        staggerTimeStep implementation) and disable (retired) corresponding
1202        parameter.
1203    o pkg/offline:
1204      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1205      - add S/R OFFLINE_CHECK to print offline parameter summary
1206        and stop if loading a file that is not used;
1207      - enable to calculate GMRedi tensor, KPP mixing and convective index
1208        when the corresponding file(s) is/are not specified (but pkg is used).
1209      - comment out resetting of monitorFreq (to endTime) since it still useful
1210        for monitoring CFL numbers and checking offline fields.
1211    o OpenAD:
1212      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1213        smaller standard output) and generate new (smaller) output (on baudelaire
1214        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1215    o model/src:
1216      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1217        (where external_forcing_adjust was called) and change list of arguments;
1218      - merge external_forcing_adjust.F into external_forcing_surf.F
1219      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1220        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1221        previously in file "balance_relax.F", now removed); remove corresponding
1222        arrays in FFIELDS.h.
1223      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1224        a hack for getting back surfaceForcingS (loaded from file) when using
1225        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1226      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1227        (was getting only 11 digits for AD-grad, due to different truncation
1228         error in AD code).
1229    
1230    checkpoint64j (2013/07/04)
1231    o pkg/offline:
1232      - to enable the use of other features with pkg offline (e.g., obcs),
1233        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1234      - comment out "allowFreezing" (now active) in 2 offline testing exp.
1235  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
1236    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1237    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1238    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1239  o pkg/atm_phys:  o pkg/atm_phys:
1240    - 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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