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revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2055 by jmc, Sat Aug 30 01:04:15 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/dic:
8      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
9        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
10        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
11    o verification:
12      - new experiment testing OBCS and DIC pkgs, using params & output from
13        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
14        passage: take OBCS from the last year of a 2 yrs simulation and initial
15        conditions from t=1.yr while keeping the same forcing.
16    o model/src:
17      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
18        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
19    o pkg/diagnostics (Stats-Diags):
20      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
21        a) refine region where stats are computed, excluding where arrhFac=0 ;
22        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
23        c) extend regional stats over the region edges (for U or V pt location).
24    o pkg/gchem:
25      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
26        pkg/dic is currently changing/updating ptracers values beyond the OB).
27    o verification (hs94):
28      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
29        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
30        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
31        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
32    o pkg/ptracers:
33      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
34        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
35      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
36        with AB-2 code (so that it get tested).
37    o model/src:
38      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
39        with AB-2 code (previously only available with AB-3 code).
40        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
41        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
42        there, by calling CYCLE_AB_TRACER).
43    o pkg/generic_advdiff:
44      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
45        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
46        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
47        S/R temp/salt/ptracers_integrate.F
48    o model/src & pkg/ptracers:
49      - remove common block variables gT,gS (in DYNVARS.h), except when
50         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
51      - remove common block variable gPtr.
52    o model/src & pkgs:
53      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
54         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
55         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
56         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
57      + change accordingly all calling S/R.
58      - use local temperature/salinity/ptracer tendency array (without bi,bj)
59        in S/R temp/salt/ptracers_integrate.F
60    o pkg/seaice:
61      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
62        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
63      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
64        in seaice_lsr
65      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
66        in s/r seaice_lsr_calc_coeffs
67    o pkg/mdsio:
68      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
69        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
70        too long (e.g., > MAX_LEN_FNAM/2 )
71    
72    checkpoint65b (2014/08/12)
73    o pkg/matrix:
74      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
75    o model/src:
76      - fix initialisation of geothermalFile; compile geothermal-flux code in
77        natl_box verification experiment.
78    o model/src & pkg/down_slope:
79      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
80      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
81        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
82        results at machine truncation level: update output of experiments
83        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
84    o pkg/diagnostics (Stats-Diags):
85      - do not cumulate the full volume when DIAGNOSTICS_FILL is
86        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
87        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
88        times (but Min,Max and StD are still wrong).
89    o model/src:
90      - add geothermal flux forcing: read in ini_forcing.F as time-constant
91        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
92    o model/src:
93      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
94        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
95        arrays are already updated while adjustments (filters, conv.adjustment) are
96        still applied later, in S/R TRACERS_CORRECTION_STEP.
97    o model/src:
98      - store in common bloc array "rhoInSitu" the virtual potential temperature
99        anomaly that is used to compute geopotential: this make the atmos code
100        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
101    o pkg/seaice/seaice_lsr.F
102      - rename integer variable ilcall to ipass (that's what it is called
103        in the residual diagnostics
104      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
105        default) for improved non-linear convergence of the first few steps
106      - adjust a few comments and add new ones to explain some of the store
107        directives
108    o pkg/generic_advdiff (& ptracers):
109      - re-work the code to check for valid advection scheme and for minimum
110        size of overlap (now stored in local common bloc in gad_advscheme.F)
111    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
112      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
113      - add an auxilliary variable "bet" and fix store directives and keys in
114        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
115        less exact gradients in my tests); but there are still
116        recomputation warning (although gradients are sort of OK), when
117        SEAICE_LSR_VECTORIZE is not defined, so this flag and
118        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
119      - update verification experiments lab_sea.
120      - change some comments in S/R seaice_calc_viscosities
121    o model/src:
122      - if staggerTimeStep=T, always apply exchange to velocity field in
123        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
124        (independent of using multi-dim advection or not); no effect on FWD run
125        but affects AD results (at machine truncation level): update output of
126        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
127        and isomip (oad: 12.d).
128    o pkg/generic_advdiff:
129      - stop if doAB_onGtGs is set to FALSE but ignored
130      - refine warning related to stability of tracer time-stepping
131        regarding internal wave dynamics.
132      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
133        on staggerTimeStep & implicitIntGravWave (will now get a warning
134        if potentially unstable).
135    o pkg/kl10:
136      - add new pkg "kl10" for mixing due to internal wave breaking, from
137        http://www.sciencedirect.com/science/article/pii/S1463500310000144
138        (contribution from Jody Klymak), tested in verification experiment
139        verification/internal_wave/input.kl10/
140    o isomip experiment:
141      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
142        (input.htd) and update the output.
143    o cd_code experiments:
144      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
145        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
146        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
147        update the corresponding output.
148    o pkg/seaice:
149      - reduce the number of include files and store directives in
150        S/R seaice_lsr_tridiagu/v
151      - change the order of loops in one case in S/R seaice_lsr_tridiagv
152        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
153        get rid off one store directive (a TAF bug?)
154      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
155        S/R seaice_lsr_tridiagv to change the loop range for consistency
156      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
157      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
158        S/R seaice_lsr_tridiagu/v (requires update of
159        offline_exf_seaice/input.dyn_jfnk)
160    
161    checkpoint65a (2014/07/27)
162    o model/src:
163      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
164        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
165        (topo in p-coords, ice-shelf in z-coords); update output of experiments
166        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
167    o model/src:
168      - collect momentum forcing tendency into local 2-D array (passed as argument
169        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
170        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
171        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
172      - collect T & S forcing tendency into local 2-D array (passed as argument to
173        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
174        affects results at machine truncation level (e.g., ocean: if using
175        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
176        moist correction due to vertical advection).
177      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
178        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
179        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
180        obcs_ctrl (ad & fwd grd @ 12 & 7).
181    o pkg/ptracers & diagnostics:
182      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
183        title (to avoid some unexpected truncation); sort out ptracers diags units.
184      - collect ptracer forcing tendency into local 2-D array (passed as argument
185        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
186    
187    checkpoint65 (2014/07/18)
188    o pkg/fizhi:
189      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
190        affects results at machine truncation level. Update output of experiments
191        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
192    o pkg/seaice: more clean up
193      - rename TAF common block tapes to be more consistent and remove
194        unnecessary duplicates
195      - add store directives to remove more recomputations, but use smaller
196        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
197        The idea behind this flag is to reduce the memory footprint when the
198        adjoint of the LSR is not required. As of now, defining the flag
199        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
200        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
201        For experiment offline_exf_seaice, this means on a linux box with gfortran
202        nearly a factor of 10 (but keep in mind there is mostly seaice code in
203        this experiment):
204        > size mitgcmuv_ad
205        text    data        bss     dec        hex  
206        5100659 1216  220458952  225560827  d71c8fb
207        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
208        but only a moderate increase of 36% for global_ocean.cs32x15:
209        text    data        bss     dec        hex
210        6695027 1648 1014578664 1021275339 3cdf6ccb
211        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
212      - note: there are still recomputations in global_ocean.cs32x15 and
213        offline_exf_seaice and the gradient agreement changes (gets a
214        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
215      - in general, the AD gradients still are wrong
216    o OpenAD
217      - clean up code_oad/ directories somewhat by moving files
218        dontCompile, dontTransform, keepOriginal to OAD_support/
219    o model/src:
220      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
221        (not currently tested): add dissipation terms before NLFS rescaling of
222        tendencies (previously done after).
223    o pkg/diagnostics:
224      - write stats-diags in ascii file with more digits (same as in monitor).
225    o pkg/down_slope:
226      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
227        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
228    o model/src:
229      - new file "apply_forcing.F" containing all the code previously in
230        external_forcing.F, but with new argument list: pass, as new argument,
231        the current level tendency array to update (instead of a direct update
232        of the common bloc array). Change the corresponding calls.
233      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
234        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
235    o pkg/seaice/seaice_lsr, a little bit of clean up
236      - rearrange some code blocks, so that now all calculations for
237        setting up the right-hand-sides done within one single block
238        (I find that easier to read and understand)
239      - rearrange freedrift-code to reduce the number of ifdefs
240      - adjust some indentations and comments
241    
242    checkpoint64z (2014/07/10)
243    o model/src and several pkgs:
244      - change argument list of all S/R called from external_forcing.F and
245        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
246        to pass, as argument, the current level tendency array to update
247        (instead of a direct update of the common bloc array).
248      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
249      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
250    o pkg/seaice/seaice_lsr.F
251      - always initialize local arrays in seaice_lsr_tridiagu/v
252      - add more local tapes to seaice_lsr_tridiagu/v
253      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
254        keep it in bi/bj loop; this seems to be essential
255      - gradients are still wrong but only by 4-7 orders of magnitude
256        instead of 15 orders of magnitude, lab_sea improves a little
257    o pkg/seaice
258      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
259        generates unnecessary code in seaice_lsr_ad
260      - add more store directives in seaice_lsr to avoid unnecessary code
261        in seaice_lsr_ad
262      - exclude some residual computations in seaice_lsr when
263        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
264        in seaice_lsr_ad
265      - add more storing, a new tape (model/src/the_main_loop.F) and
266        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
267        and klockey should be checked by a specialist)
268      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
269        and update lab_sea after previous changes in pkg/seaice below
270    o pkg/autodiff:
271      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
272        viscFacInAd : run time parameters allowing for adjoint switches
273        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
274    o pkg/ecco:
275      - introduce cost_gencost_boxmean.F that computes a box mean
276        temperature (for use in adjoint sensitivity studies).
277    o model/src/set_defaults.F : initialize viscFacAdj to 1.
278    o pkg/mom_common/mom_calc_visc.F:
279      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
280    o pkg/seaice/seaice_summary.F:
281      - statement for SEAICEadjMODE now in autodiff_readparms.F
282    o pkg/seaice:
283      - remove some store directives and add new ones in an effort to get
284        finally rid off the recomputation warnings. This is successful
285        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
286        defined (i.e. no extensive recomputation warnings left), but there
287        are still too many recomputations on the solver iteration level
288      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
289      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
290        SEAICE_SIZE.h
291      - add a store directive in S/R seaice_calc_viscosities
292    o pkg/seaice (ITD code):
293      - fix definition of Hlimit for multi-threaded case
294      - use double precision arithmetic to compute Hlimit: this affects results;
295        update output of experiment seaice_itd.
296    o replace content of verification/seaice_itd
297      - instead of a 1D column use the configuration of offline_exf_seaice
298        to test the ice thickness distribution code with ridging
299      - this is a first shot at this experiment
300      - change of some defaults of ridging parameters SEAICEhStar (from
301        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
302        and lot of new comments.
303    
304    checkpoint64y (2014/06/20)
305    o pkg/seaice/seaice_reg_ridge.F:
306      - modify the regularization of very small volumes of ice; only check
307        total volume HEFF, and do not apply correction to individual ice
308        classes because that leads to funny patterns in the heat and fw-fluxes
309        into the ocean. Adjust seaice_itd/results/output.txt
310      - replace nITD by SEAICE_multDim in loop-ranges
311    o pkg/exf:
312      - add code to process the case field period = -12. with UV interpolation.
313      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
314        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
315    o verification/global_with_exf:
316      - switch all fields period to -12. (was previously untested) in input/data.exf
317        (but keep secondary test ".yearly" unchanged); update the reference output.
318    o pkg/cal:
319      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
320    o pkg/exf:
321      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
322        to replace logical switch "exf_verbose"
323      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
324    o pkg/sbo:
325      - update from Katherine Quinn: evaluate mass directly from density and SSH
326        (budget using Finite Volume method) instead of from bottom pressure.
327      - allow testreport to collect few selected SBO output ; tested in exp.
328        global_ocean.90x40x15 (after updating the results, to include SBO output).
329      - fix some multi-threading issues (in output part).
330    o model/src & most packages:
331      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
332      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
333        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
334        "data.{pkg}" exist ; and leave the S/R (return) just after.
335      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
336        + call LAND_READPARMS from packages_readparms.F
337    o pkg/seaice:
338      - remove code that resets useThSice in S/R seaice_readparms and
339        replace it by a warning in S/R seaice_check
340      - remove parameter MULTDIM, replace with nITD and runtime
341        parameter SEAICE_multDim (still hard-wired to nITD if
342        SEAICE_ITD is defined)
343    
344    checkpoint64x (2014/05/24)
345    o verification/lab_sea:
346      - update adjoint and TLM output following changes to pkg/salt_plume
347      - un-do the update after putting back local recip_Cp in few places.
348    o pkg/salt_plume: modifications by An Nguyen:
349      - add capability to do brine rejection (salt-plume) as function of
350        volume+tracers (instead of only salinity tracer).
351      - conserve volume by exchanging volume from each kLev to above to
352        accommodate in-coming brine volume
353      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
354      - switch KPP surf buoyancy due to brine forcing to 3-d
355        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
356      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
357      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
358        in East/West Arctic.
359    o pkg/sbo:
360      - incorporate modifications from Katherine Quinn to enable the use of sbo
361        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
362        output for future testreport verification (unfinished).
363    o pkg/atm_phys:
364      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
365        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
366        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
367    o pkg/seaice
368      seaice_calc_ice_strength.F: modify expression to avoid divisions
369        (affects truncation)
370      seaice_do_ridging.F: clean up the insectarium
371      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
372      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
373      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
374      - add some debugging information and error messages (warnings)
375    o model/src: modifications relatd to atmosphere p*:
376      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
377      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
378        of vertical profile tRef in geopotential background and anomaly.
379      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
380        and pkg/atm_phys.
381      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
382        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
383    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
384    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
385        not used right now, but can be used in BGC packages to fix conservation.
386    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
387        other packages too.
388    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
389        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
390    o model/src:
391      - since we have several heat capacity (even in model/src), define "recip_Cp"
392        as local variable (no longer in common block) to avoid any confusion.
393      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
394    o pkg/exf:
395      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
396        air density as function of air Temp, Humidity and atm pressure.
397    
398    checkpoint64w (2014/05/02)
399    o verification:
400      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
401        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
402        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
403        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
404        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
405    o model/src: for atmosphere in p* coords:
406      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
407      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
408        but not yet activated.
409    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
410      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
411      - this changes the results (but not for any verification experiment, because
412        none tests this), but avoids having an extra field in the restart files
413    o pkg/seaice: remove global variable TICE (not needed)
414      - replace by TICES or local variable where necessary (cost_seaice_test,
415        seaice_diagnostics_state)
416      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
417      - use specific read/write routines for reading and writing individual leves
418        of a multilevel field
419    o pkg/ctrl & model/inc:
420      - move additional anomaly fields of control vars (related to options:
421         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
422        from DYNVARS.h into new header file: CTRL_FIELDS.h
423    o pkg/seaice: some small modifications to the ridging code
424      - make fw2ObyRidge a global variable and add the freshwater flux to
425        seaice_growth
426      - pass actual thickness from seaice_prepare_ridging, so that it is
427        computed only in one place and compute it in the same way as in
428        seaice_growth
429      - initialise more fields in seaice_do_ridging that where cause floating
430        point exceptions over land
431    o pkg/seaice: preparations for ridging code and first real ridging code
432      - move most of "PART 1" of S/R seaice_growth into a new and separate
433        S/R seaice_reg_ridge that will both regularize the state variable after
434        advection call the actual ridging routine;
435      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
436        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
437      - remove ridging code from seaice_advdiff
438      - clean up remaining part 1 of seaice_growth in an attempt to make it
439        more readable (this is probably subjective)
440      - call seaice_itd_redist once in the initialisation phase to have the initial
441        conditions in the correct category
442      - finally: add new ridging routine for ITD code
443    
444    checkpoint64v (2014/04/11)
445    o pkg/ecco:
446      - add runtime parameters mdt[start,end]date[1,2]
447      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
448    o pkg/seaice:
449      - make deltaC a global variable, so that it can be used in ridging code
450      - first step towards ridging: introduce new routines that compute
451        ice strength based on ridging parameters
452      - add diagnostic for HSNOWITD
453      - add opnWtrFrac as a global variable (required for ridging scheme)
454    o pkg/salt_plume + pkg/seaice/seaice_growth.F
455      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
456        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
457    o verification/hs94.1x64x5:
458      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
459      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
460    o autodiff:
461      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
462        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
463        For now, only in pkgs used in verification/hs94.1x64x5.
464      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
465        which are specific to TAF/TAMC).
466      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
467        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
468        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
469      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
470        building mitgcmuv_ad (make adAll).
471    o pkg/ecco:
472      - cost_gencost_seaicev4.F:
473         reformulate proxy cost as function of sst and local param SEAICE_freeze
474         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
475      - add stop statement if old names siv4-[sst,vol] are used
476      - add snapshots + cost reports for atmospheric longwave
477      - remove factor 0.1 in front of wtau[u,v]
478      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
479         ALLOW_TMI_SST_COST_CONTRIBUTION
480    o pkg/atm_phys:
481      - add some diagnostics for Short-wave and for convection S/R.
482    o pkg/seaice/seaice_growth:
483      - fix a bug in the lateral melt parameterization for SEAICE_ITD
484        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
485      - rearrange loop order for better vector code in the same code block
486      - rewrite the floeDiameter formula to have fewer divisions
487      -  (miraculously) none of this changes the results of seaice_itd
488    o pkg/smooth:
489      - move param smooth2Ddiffnbt to pkg/ecco
490    o pkg/salt_plume:
491      - salt_plume_frac.F:
492         clean up local param names
493         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
494    o pkg/rw:
495      - add RS version of S/R READ_MFLDS_LEV.
496    o pkg/streamice:
497      - fix the restart test by writing/reading pickup_streamice files.
498    o pkg/seaice:
499      - refine checks for jfnk-related parameters
500      - comment out if statement with SEAICEuseIMEX parameter as long as there
501        is no IMEX code to avoid confusion and surprises
502    
503    checkpoint64u (2014/03/07)
504    o verification/MLAdjust:
505      - rename secondary test suffix:
506         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
507         0.leithD -> AhFlxF  + switch to flux-form
508         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
509         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
510    o pkg/mom_vecinv:
511      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
512        to be before mom_calc_visc.F)
513      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
514      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
515        this is simpler for the adjoint and for diagnostics.
516    o model/src + pkg/momentum:
517      - add input files for  2-D additional Western and Southern cell-edge wall
518         (e.g., to add "thin-wall" where it is =1).
519      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
520        using 2nd hFacZ that is computed from initial (fix domain) hFac
521      - known limitations of thin wall implementation: not yet coded for sigma
522        coords; not working with CD-scheme neither.
523    o pkg/seaice:
524      - rename recently introduced parameters from (wrong name) AB to
525        BDF (backward difference time discretisation)
526      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
527    o tools/adjoint_options:
528      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
529    
530    checkpoint64t (2014/02/01)
531    o pkg/ecco
532      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
533        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
534      - replace hard-coded record number and period which only work for monthly
535        with read-in runtime param that works for other periods (month,day,year)
536    o pkg/thsice
537      - corrected store directive fixes thsice adjoint gradient checks
538    o genmake2 & testreport:
539      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
540        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
541        Update testreport accordingly. No need to set "export OPENAD=true"
542        in adjoint_options/adjoint_oad anymore (will be removed later).
543    o pkg/shelfice:
544      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
545        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
546        so that surface forcing applies to k=kSurf if using pkg/shelfice.
547    o pkg/ctrl, pkg/grdchk, pkg/ecco:
548      - Changes to make GENARR more modular (i.e. invisible if not used)
549    o model/src/temp_integrate.F and salt_integrate.F
550      - re-include store directives that were removed on Dec 27th.
551    o model/src/external_forcing_surf.F
552      - add storage directives for EmPmR and PmEpR to avoid recomputation of
553        seaice_model in the adjoint that is problematic when seaice_model is
554        turned off in the adjoint. The resolved issue dated back to July when
555        EXTERNAL_FORCING_SURF call was moved.
556        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
557    o pkg/exf/exf_check.F
558      - fix a small bug again (originally found by Wentao Liu, now found again)
559      - streamline error output
560    o pkg/streamice and aim_v23:
561      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
562        Apple's /usr/bin/cpp knows what to do:
563        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
564        Target: x86_64-apple-darwin13.0.0
565    
566    checkpoint64s (2014/01/05)
567    o tools/adjoint_options:
568      - switch to fastopt.net TAF server (instead of default fastopt.de) for
569        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
570    o model/src:
571      - remove some unnecessary TAF storage directives in forward_step.F and
572        in dynamics.F (note: not always removed by TAF, e.g., double storage
573        of kappaRU,kappaRV in former version of dynamics.F).
574    o model/src & pkg/ptracers:
575      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
576        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
577        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
578      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
579      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
580      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
581    o useSingleCpuInput separates single-CPU input from single-CPU output;
582        for now only implemented for in exf_interp_read.F
583    o verification/advect_xy:
584      - fix missing EXCH call in local version of ini_salt.F and update output.
585    o momentum diagnostics:
586      - fix which deltaT is used in Total-Tendency diagnostics.
587      - fix typo in diagnostics for momentum tendency from AB.
588    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
589        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
590    
591    checkpoint64r (2013/12/08)
592    o verification/*/results:
593      - Update reference output of experiments that were passing with just 13 digits
594         (make it easier to detect future changes in results)
595    o model/src & pkg/ptracers:
596      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
597        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
598        to inside ptracers_integrate.F ; remove ptracers_advection.F
599    o coupling interface pkgs:
600        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
601      - change the config check to test the agreement of Ocean Depth
602        with ATM land/sea mask (instead of ATM orography);
603      - send to coupler the number of coupler time-steps to do for this run:
604        this allows to check for consistency and don't need anymore to be
605        specified in parameter file "data";
606      in coupler:
607      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
608      - improve report to log-file of config setting (pass log-file unit to few S/R)
609    o pkg/compon_communic:
610      - add coupling send/receive for non-tiled integer vector;
611      - add S/R to check and stop if any proc has an error (similar to
612        eesupp/src/stop_if_error.F but single thread and across Comm_World).
613    o pkg/exch2:
614      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
615        through list of all tiles my proc owns.
616    o model/src:
617      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
618        from rTrans) to simplify dependencies (no need to store rTrans anymore in
619        calling S/R); this affects AD results at machine truncation level:
620        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
621        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
622    o tools/build_options:
623      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
624    o coupling interface pkgs:
625        [compon_communic, atm_compon_interf & ocn_compon_interf]
626      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
627        to each S/R that needs it; remove un-used variables.
628      - change component tile registration (cpl_register.F in both compon_interf
629        and mitcomponent_tile_register.F) to pass the full list of tiles
630        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
631      - with pkg/exch2: adopt the same convention used for I/O to define mapping
632        towards coupler global array (unless W2_useE2ioLayOut=F):
633         a) can now use different tiling between atm & ocn comp.
634         b) no needs to modify the run-Off map when changing tiling (was needed
635            even if using the same tiling between atm & ocn).
636         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
637            full land tiles); not yet tested.
638      - check for valid mapping from comp. tile to coupler global array
639      - improve report of tile registration results to log file.
640    o pkg/exch2:
641      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
642        tile-registration (CPL_REGISTER);
643      - activate (un-comment) definition and setting of "W2_tileIndex" list to
644        store the local bi,bj indices of each tile;
645      - also print bi,bj in local report to log file;
646      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
647        Jun 2009 modif of pkg/exch2).
648    o testing on baudelaire:
649      - run 2 tests at a time: no significant slow down (since enough cpu) and
650        get the full set of test done earlier
651      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
652    o model/src/thermodynamics.F and routines called from it:
653      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
654        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
655        velocity (outp) by adding bolus velocity.
656      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
657        mass transport from velocity + lateral grid cell area
658      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
659      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
660     in thermodynamics.F
661      - remove k from thermodynamics.F and move it to temp_integrate.F
662        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
663        loop).
664      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
665        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
666        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
667        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
668      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
669        global_ocean.90x40x15, tutorial_global_oce_biogeo and
670        tutorial_tracer_adjsens (+ TLM output).
671    o tools/OAD_support and (verification/*/) code_oad:
672      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
673        module conversion ; remove unneeded CPP_EEOPTIONS.h.
674      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
675        version (closer to model/inc/CPP_OPTIONS.h).
676    o model/src:
677      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
678        retired list of parameters (routine FREEZE has been replace by surface
679        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
680    o pkg/gmredi:
681      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
682        velocity (same scheme but affects machine truncation) for GM_AdvForm.
683      - update output of FWD experiments: front_relax.bvp,
684        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
685    
686    checkpoint64q (2013/11/17)
687    o verification:
688      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
689        tutorial_global_oce_biogeo and global_ocean.90x40x15.
690      - generate new output (growth & melt) for seaice_itd experiment after
691        updating the input pickup_seaice files (previously wrong).
692    o pkg/cost:
693      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
694        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
695        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
696          cannot be applied to var in common block).
697        o allows to get results independent of tile-per-proc setting (if using
698          slower GLOBAL_SUM_SEND_RECV option).
699      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
700        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
701        forward gradients: update output).
702      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
703        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
704    o pkg/mom_common:
705      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
706        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
707        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
708        ensure that all field value that are used are set.
709    o tutorial_deep_convection (smag3d):
710      - add missing scaling in mom_calc_smag_3d.F;
711      - set smag3D_coeff in input.smag3d such that results do not change.
712    o pkg/dic:
713      - change dic_cost.F to compute cost on each tile first and then apply
714        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
715        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
716      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
717    o eesupp/src & pkg/mdsio:
718      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
719        (from pkg/mdsio) since they are no longer used for tape IO.
720      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
721        (+ keep a copy in pkg/atm_ocn_coupler).
722    o verification/isomip:
723      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
724    o tools/build_options:
725      - optfile linux_amd64_ifort11, fast (no ieee) case:
726        to get a working restart for all experiments, add "-fp-model source"
727        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
728    
729    checkpoint64p (2013/10/20)
730    o pkg/autodiff:
731      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
732        criteria, return to simple (default) tape IO format.
733    o pkg/mdsio (+ eesupp/src):
734      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
735        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
736      - fix globalFile and singleCpuIO options using simpler global mapping.
737      - new pairs of scatter/gather vector S/R (one for each type, generated from
738        template) corresponding to simpler global mapping.
739      - adread_write.F: switch to new S/R (but leave old calls commented) and write
740        to globalFile when parameter globalFiles is set to True.
741      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
742    o pkg/autodiff:
743      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
744        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
745        missing, just add a STOP if array type do not match.
746    o pkg/exf:
747      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
748         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
749         and rename array obsSIce to exf_iceFraction.
750    o tutorial_deep_convection:
751      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
752        for now all in this exp. code dir.
753      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
754        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
755    o eesupp/src:
756      - added SINGLE_DISK_IO option because reading of parameter files on
757        very large number of processors did not work with existing set-up
758    
759    checkpoint64o (2013/09/25)
760    o pkg/atm_phys & atm_compon_interf:
761      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
762    o tools/build_options:
763      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
764        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
765        remove CPP setting (was identical to genmake2 default).
766    o pkg/gmredi & model/src: Some updating and work done on the residual model.
767      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
768      - fixed up the calculation of the eddy stress and how it is added to the
769        external forcing via taueddy_external_forcing.F
770      - at the moment, it is very experimental and only works with the variable eddy
771        diffusivity calculated in gmredi_k3d.F
772    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
773        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
774    o testreport (& tools/do_tst_2+2):
775      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
776    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
777      - remove CPP='cpp -traditional -P' (this is genmake2 default)
778      - add switch (for big setups) to use 'medium' memory-model (but leave it
779        commented out for now). Note: needed with FC 19 to compile big setups.
780    o pkg/atm_compon_interf:
781      - regroup per field origin (model & pkgs) the coupling storage routines
782         (which accumalate in time each coupling field)
783      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
784        update accordingly + simplify aim_do_physics.F
785    
786    checkpoint64n (2013/08/26)
787    o pkg/bbl:
788      - update formulation to reduce dispersion of tracer properties in bbl
789      - replaced horizontal and vertical transport parameters with velocities
790      - changes results for verification/global_with_exf.yearly
791    o verification/halfpipe_streamice:
792      - change to matrix construction; update both Fwd & AD output.
793    o verification/tutorial_tracer_adjsens:
794      - OpenAD test: switch to vector-invariant momentum since fluxform with
795        rStar causes problems with OpenAD; update output.
796    o tools:
797      - genmake2: define a common prefix for all temp-file names ; move them
798        to local /tmp disk (but would be easy to move them back);
799      - xmakedepend: apply the same switch for temp-files.
800    o pkg/offline:
801      - changes for use with rStar (NLFS): assume that we continue to provide
802        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
803        output files) and apply r* scaling at each time-step (function of the time
804        varying Eta field); use normal pickup files (needed for restart with NLFS).
805    o adjoint with OpenAD:
806      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
807        package openad.  This package has to be compiled for all runs with OpenAD
808        instead of specifying code_oad_all as a modification directory.
809      - link the fortran templates from tools/OAD_support to the build directory
810        for preprocessing to avoid conflicts between different setups compiled
811        simultaneously and simplify cleanup.
812    o pkg/exf:
813      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
814        main model or other pkgs are exchanged in EXF_MAPFIELDS).
815    o model/src:
816      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
817        (similar to do_fields_blocking_exchanges.F).
818    o tools/genmake2:
819      - remove TAF output src code just before calling staf (when not doing a fresh
820        built, will stop if things go wrong with staf).
821      - fix target "adobj" (left from TAF version-2 transition)
822    o pkg/diagnostics:
823      - add a parameter to track the status of pkg/diagnostics activation;
824        this replace/extend the use of logical param "settingDiags" (to check
825        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
826        New S/R to print error message and stop when pkgStatus is not right.
827      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
828    
829    checkpoint64m (2013/08/13)
830    o model/inc:
831      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
832        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
833    o pkg/kpp & aim_v23:
834      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
835    o pkg/seaice:
836      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
837        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
838      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
839    o eesupp/src:
840      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
841        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
842    o switch to TAF version-2:
843      - add flow directives to "freeze" naming convention for ad-routines that
844        are used in I/O routines of adjoint state and associated common blocks
845        that are used in adcommon.h (backward compatible with version-1)
846      - update all ad-optfiles (in tools/adjoint_options + few local to some
847        verification exp) to switch to latest TAF version (currently 2.5.5);
848        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
849        out except for diva).
850      - the major change with TAF version-2 is that both the differentiated
851        routines and the forward routines (new) are returned as part of the TAF
852        output source code. Update genmake2 accordingly.
853      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
854        with version-2 when compared to TLM or FWD gradient); other experiments
855        output show minor changes (machine truncation level); update the few AD &
856        TLM output with 12 matching digits only (some prior to version-2 switch).
857    
858    checkpoint64l (2013/08/05)
859    o model/src:
860      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
861      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
862        when using TAF but only if using OpenAD.
863    o pkg/mom_common+fluxform+vecinv:
864      - always set horiz. viscosity arrays to background value before calling
865        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
866        only when using variable horiz. viscosity (useVariableVisc=T);
867      - simplify mom_vecinv.F (only 1 block for momViscosity).
868    o pkg/mom_common: variable horiz. viscosity in NH code
869      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
870        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
871      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
872        useBiharmonicVisc & useVariableVisc.
873      - fix old bug (already in 1rst implementation of variable horizontal viscosity
874        in calc_gw.F, version 1.27, 2006/06/20):
875        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
876        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
877      - change background horiz viscosity in vertical momentum (gW) to always be
878        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
879        any type of variable viscosity, e.g., viscAh/4Grid)
880      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
881        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
882        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
883        default viscAh,viscA4 is zero).
884    o model/src:
885      - extend length of drC & recip_drC from Nr to Nr+1.
886    o Divided Adjoint (DIVA) with MPI:
887      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
888      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
889        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
890    
891    checkpoint64k (2013/07/23)
892    o tools/OAD_support:
893      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
894        and remove it from genmake2.
895    o tools/build_options:
896      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
897        MPI_HEADER_FILES list (let genmake2 find the missing headers)
898    o verification/halfpipe_streamice:
899      - change to driving stress formulation; update both Fwd & AD output.
900    o tools/genmake2 and Divided Adjoint with MPI:
901      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
902      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
903      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
904        Makefile, which is set by genmake2, and check which mpi-headers are needed.
905        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
906      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
907    o testreport:
908      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
909        perform additional runs (number of additional runs is "add_DIVA_runs" taken
910        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
911    o verification/lab_sea (AD test):
912      - change to test Divided Adjoint Run in this set-up (both standard AD test
913        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
914    o pkg atm_ & ocn_compon_interf:
915      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
916        staggerTimeStep implementation) and disable (retired) corresponding
917        parameter.
918    o pkg/offline:
919      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
920      - add S/R OFFLINE_CHECK to print offline parameter summary
921        and stop if loading a file that is not used;
922      - enable to calculate GMRedi tensor, KPP mixing and convective index
923        when the corresponding file(s) is/are not specified (but pkg is used).
924      - comment out resetting of monitorFreq (to endTime) since it still useful
925        for monitoring CFL numbers and checking offline fields.
926    o OpenAD:
927      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
928        smaller standard output) and generate new (smaller) output (on baudelaire
929        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
930    o model/src:
931      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
932        (where external_forcing_adjust was called) and change list of arguments;
933      - merge external_forcing_adjust.F into external_forcing_surf.F
934      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
935        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
936        previously in file "balance_relax.F", now removed); remove corresponding
937        arrays in FFIELDS.h.
938      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
939        a hack for getting back surfaceForcingS (loaded from file) when using
940        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
941      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
942        (was getting only 11 digits for AD-grad, due to different truncation
943         error in AD code).
944    
945    checkpoint64j (2013/07/04)
946    o pkg/offline:
947      - to enable the use of other features with pkg offline (e.g., obcs),
948        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
949      - comment out "allowFreezing" (now active) in 2 offline testing exp.
950  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
951    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
952    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
953    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
954  o pkg/atm_phys:  o pkg/atm_phys:
955    - 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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