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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2029 by jmc, Sat Jul 19 01:26:19 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/ptracers & diagnostics:
8      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
9        title (to avoid some unexpected truncation); sort out ptracers diags units.
10    
11    checkpoint65 (2014/07/18)
12    o pkg/fizhi:
13      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
14        affects results at machine truncation level. Update output of experiments
15        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
16    o pkg/seaice: more clean up
17      - rename TAF common block tapes to be more consistent and remove
18        unnecessary duplicates
19      - add store directives to remove more recomputations, but use smaller
20        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
21        The idea behind this flag is to reduce the memory footprint when the
22        adjoint of the LSR is not required. As of now, defining the flag
23        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
24        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
25        For experiment offline_exf_seaice, this means on a linux box with gfortran
26        nearly a factor of 10 (but keep in mind there is mostly seaice code in
27        this experiment):
28        > size mitgcmuv_ad
29        text    data        bss     dec        hex  
30        5100659 1216  220458952  225560827  d71c8fb
31        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
32        but only a moderate increase of 36% for global_ocean.cs32x15:
33        text    data        bss     dec        hex
34        6695027 1648 1014578664 1021275339 3cdf6ccb
35        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
36      - note: there are still recomputations in global_ocean.cs32x15 and
37        offline_exf_seaice and the gradient agreement changes (gets a
38        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
39      - in general, the AD gradients still are wrong
40    o OpenAD
41      - clean up code_oad/ directories somewhat by moving files
42        dontCompile, dontTransform, keepOriginal to OAD_support/
43    o model/src:
44      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
45        (not currently tested): add dissipation terms before NLFS rescaling of
46        tendencies (previously done after).
47    o pkg/diagnostics:
48      - write stats-diags in ascii file with more digits (same as in monitor).
49    o pkg/down_slope:
50      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
51        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
52    o model/src:
53      - new file "apply_forcing.F" containing all the code previously in
54        external_forcing.F, but with new argument list: pass, as new argument,
55        the current level tendency array to update (instead of a direct update
56        of the common bloc array). Change the corresponding calls.
57      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
58        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
59    o pkg/seaice/seaice_lsr, a little bit of clean up
60      - rearrange some code blocks, so that now all calculations for
61        setting up the right-hand-sides done within one single block
62        (I find that easier to read and understand)
63      - rearrange freedrift-code to reduce the number of ifdefs
64      - adjust some indentations and comments
65    
66    checkpoint64z (2014/07/10)
67    o model/src and several pkgs:
68      - change argument list of all S/R called from external_forcing.F and
69        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
70        to pass, as argument, the current level tendency array to update
71        (instead of a direct update of the common bloc array).
72      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
73      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
74    o pkg/seaice/seaice_lsr.F
75      - always initialize local arrays in seaice_lsr_tridiagu/v
76      - add more local tapes to seaice_lsr_tridiagu/v
77      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
78        keep it in bi/bj loop; this seems to be essential
79      - gradients are still wrong but only by 4-7 orders of magnitude
80        instead of 15 orders of magnitude, lab_sea improves a little
81    o pkg/seaice
82      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
83        generates unnecessary code in seaice_lsr_ad
84      - add more store directives in seaice_lsr to avoid unnecessary code
85        in seaice_lsr_ad
86      - exclude some residual computations in seaice_lsr when
87        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
88        in seaice_lsr_ad
89      - add more storing, a new tape (model/src/the_main_loop.F) and
90        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
91        and klockey should be checked by a specialist)
92      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
93        and update lab_sea after previous changes in pkg/seaice below
94    o pkg/autodiff:
95      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
96        viscFacInAd : run time parameters allowing for adjoint switches
97        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
98    o pkg/ecco:
99      - introduce cost_gencost_boxmean.F that computes a box mean
100        temperature (for use in adjoint sensitivity studies).
101    o model/src/set_defaults.F : initialize viscFacAdj to 1.
102    o pkg/mom_common/mom_calc_visc.F:
103      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
104    o pkg/seaice/seaice_summary.F:
105      - statement for SEAICEadjMODE now in autodiff_readparms.F
106    o pkg/seaice:
107      - remove some store directives and add new ones in an effort to get
108        finally rid off the recomputation warnings. This is successful
109        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
110        defined (i.e. no extensive recomputation warnings left), but there
111        are still too many recomputations on the solver iteration level
112      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
113      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
114        SEAICE_SIZE.h
115      - add a store directive in S/R seaice_calc_viscosities
116    o pkg/seaice (ITD code):
117      - fix definition of Hlimit for multi-threaded case
118      - use double precision arithmetic to compute Hlimit: this affects results;
119        update output of experiment seaice_itd.
120    o replace content of verification/seaice_itd
121      - instead of a 1D column use the configuration of offline_exf_seaice
122        to test the ice thickness distribution code with ridging
123      - this is a first shot at this experiment
124      - change of some defaults of ridging parameters SEAICEhStar (from
125        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
126        and lot of new comments.
127    
128    checkpoint64y (2014/06/20)
129    o pkg/seaice/seaice_reg_ridge.F:
130      - modify the regularization of very small volumes of ice; only check
131        total volume HEFF, and do not apply correction to individual ice
132        classes because that leads to funny patterns in the heat and fw-fluxes
133        into the ocean. Adjust seaice_itd/results/output.txt
134      - replace nITD by SEAICE_multDim in loop-ranges
135    o pkg/exf:
136      - add code to process the case field period = -12. with UV interpolation.
137      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
138        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
139    o verification/global_with_exf:
140      - switch all fields period to -12. (was previously untested) in input/data.exf
141        (but keep secondary test ".yearly" unchanged); update the reference output.
142    o pkg/cal:
143      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
144    o pkg/exf:
145      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
146        to replace logical switch "exf_verbose"
147      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
148    o pkg/sbo:
149      - update from Katherine Quinn: evaluate mass directly from density and SSH
150        (budget using Finite Volume method) instead of from bottom pressure.
151      - allow testreport to collect few selected SBO output ; tested in exp.
152        global_ocean.90x40x15 (after updating the results, to include SBO output).
153      - fix some multi-threading issues (in output part).
154    o model/src & most packages:
155      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
156      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
157        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
158        "data.{pkg}" exist ; and leave the S/R (return) just after.
159      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
160        + call LAND_READPARMS from packages_readparms.F
161    o pkg/seaice:
162      - remove code that resets useThSice in S/R seaice_readparms and
163        replace it by a warning in S/R seaice_check
164      - remove parameter MULTDIM, replace with nITD and runtime
165        parameter SEAICE_multDim (still hard-wired to nITD if
166        SEAICE_ITD is defined)
167    
168    checkpoint64x (2014/05/24)
169    o verification/lab_sea:
170      - update adjoint and TLM output following changes to pkg/salt_plume
171      - un-do the update after putting back local recip_Cp in few places.
172    o pkg/salt_plume: modifications by An Nguyen:
173      - add capability to do brine rejection (salt-plume) as function of
174        volume+tracers (instead of only salinity tracer).
175      - conserve volume by exchanging volume from each kLev to above to
176        accommodate in-coming brine volume
177      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
178      - switch KPP surf buoyancy due to brine forcing to 3-d
179        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
180      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
181      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
182        in East/West Arctic.
183    o pkg/sbo:
184      - incorporate modifications from Katherine Quinn to enable the use of sbo
185        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
186        output for future testreport verification (unfinished).
187    o pkg/atm_phys:
188      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
189        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
190        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
191    o pkg/seaice
192      seaice_calc_ice_strength.F: modify expression to avoid divisions
193        (affects truncation)
194      seaice_do_ridging.F: clean up the insectarium
195      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
196      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
197      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
198      - add some debugging information and error messages (warnings)
199    o model/src: modifications relatd to atmosphere p*:
200      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
201      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
202        of vertical profile tRef in geopotential background and anomaly.
203      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
204        and pkg/atm_phys.
205      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
206        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
207    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
208    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
209        not used right now, but can be used in BGC packages to fix conservation.
210    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
211        other packages too.
212    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
213        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
214    o model/src:
215      - since we have several heat capacity (even in model/src), define "recip_Cp"
216        as local variable (no longer in common block) to avoid any confusion.
217      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
218    o pkg/exf:
219      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
220        air density as function of air Temp, Humidity and atm pressure.
221    
222    checkpoint64w (2014/05/02)
223    o verification:
224      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
225        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
226        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
227        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
228        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
229    o model/src: for atmosphere in p* coords:
230      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
231      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
232        but not yet activated.
233    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
234      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
235      - this changes the results (but not for any verification experiment, because
236        none tests this), but avoids having an extra field in the restart files
237    o pkg/seaice: remove global variable TICE (not needed)
238      - replace by TICES or local variable where necessary (cost_seaice_test,
239        seaice_diagnostics_state)
240      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
241      - use specific read/write routines for reading and writing individual leves
242        of a multilevel field
243    o pkg/ctrl & model/inc:
244      - move additional anomaly fields of control vars (related to options:
245         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
246        from DYNVARS.h into new header file: CTRL_FIELDS.h
247    o pkg/seaice: some small modifications to the ridging code
248      - make fw2ObyRidge a global variable and add the freshwater flux to
249        seaice_growth
250      - pass actual thickness from seaice_prepare_ridging, so that it is
251        computed only in one place and compute it in the same way as in
252        seaice_growth
253      - initialise more fields in seaice_do_ridging that where cause floating
254        point exceptions over land
255    o pkg/seaice: preparations for ridging code and first real ridging code
256      - move most of "PART 1" of S/R seaice_growth into a new and separate
257        S/R seaice_reg_ridge that will both regularize the state variable after
258        advection call the actual ridging routine;
259      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
260        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
261      - remove ridging code from seaice_advdiff
262      - clean up remaining part 1 of seaice_growth in an attempt to make it
263        more readable (this is probably subjective)
264      - call seaice_itd_redist once in the initialisation phase to have the initial
265        conditions in the correct category
266      - finally: add new ridging routine for ITD code
267    
268    checkpoint64v (2014/04/11)
269    o pkg/ecco:
270      - add runtime parameters mdt[start,end]date[1,2]
271      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
272    o pkg/seaice:
273      - make deltaC a global variable, so that it can be used in ridging code
274      - first step towards ridging: introduce new routines that compute
275        ice strength based on ridging parameters
276      - add diagnostic for HSNOWITD
277      - add opnWtrFrac as a global variable (required for ridging scheme)
278    o pkg/salt_plume + pkg/seaice/seaice_growth.F
279      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
280        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
281    o verification/hs94.1x64x5:
282      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
283      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
284    o autodiff:
285      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
286        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
287        For now, only in pkgs used in verification/hs94.1x64x5.
288      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
289        which are specific to TAF/TAMC).
290      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
291        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
292        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
293      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
294        building mitgcmuv_ad (make adAll).
295    o pkg/ecco:
296      - cost_gencost_seaicev4.F:
297         reformulate proxy cost as function of sst and local param SEAICE_freeze
298         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
299      - add stop statement if old names siv4-[sst,vol] are used
300      - add snapshots + cost reports for atmospheric longwave
301      - remove factor 0.1 in front of wtau[u,v]
302      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
303         ALLOW_TMI_SST_COST_CONTRIBUTION
304    o pkg/atm_phys:
305      - add some diagnostics for Short-wave and for convection S/R.
306    o pkg/seaice/seaice_growth:
307      - fix a bug in the lateral melt parameterization for SEAICE_ITD
308        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
309      - rearrange loop order for better vector code in the same code block
310      - rewrite the floeDiameter formula to have fewer divisions
311      -  (miraculously) none of this changes the results of seaice_itd
312    o pkg/smooth:
313      - move param smooth2Ddiffnbt to pkg/ecco
314    o pkg/salt_plume:
315      - salt_plume_frac.F:
316         clean up local param names
317         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
318    o pkg/rw:
319      - add RS version of S/R READ_MFLDS_LEV.
320    o pkg/streamice:
321      - fix the restart test by writing/reading pickup_streamice files.
322    o pkg/seaice:
323      - refine checks for jfnk-related parameters
324      - comment out if statement with SEAICEuseIMEX parameter as long as there
325        is no IMEX code to avoid confusion and surprises
326    
327    checkpoint64u (2014/03/07)
328    o verification/MLAdjust:
329      - rename secondary test suffix:
330         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
331         0.leithD -> AhFlxF  + switch to flux-form
332         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
333         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
334    o pkg/mom_vecinv:
335      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
336        to be before mom_calc_visc.F)
337      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
338      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
339        this is simpler for the adjoint and for diagnostics.
340    o model/src + pkg/momentum:
341      - add input files for  2-D additional Western and Southern cell-edge wall
342         (e.g., to add "thin-wall" where it is =1).
343      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
344        using 2nd hFacZ that is computed from initial (fix domain) hFac
345      - known limitations of thin wall implementation: not yet coded for sigma
346        coords; not working with CD-scheme neither.
347    o pkg/seaice:
348      - rename recently introduced parameters from (wrong name) AB to
349        BDF (backward difference time discretisation)
350      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
351    o tools/adjoint_options:
352      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
353    
354    checkpoint64t (2014/02/01)
355    o pkg/ecco
356      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
357        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
358      - replace hard-coded record number and period which only work for monthly
359        with read-in runtime param that works for other periods (month,day,year)
360    o pkg/thsice
361      - corrected store directive fixes thsice adjoint gradient checks
362    o genmake2 & testreport:
363      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
364        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
365        Update testreport accordingly. No need to set "export OPENAD=true"
366        in adjoint_options/adjoint_oad anymore (will be removed later).
367    o pkg/shelfice:
368      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
369        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
370        so that surface forcing applies to k=kSurf if using pkg/shelfice.
371    o pkg/ctrl, pkg/grdchk, pkg/ecco:
372      - Changes to make GENARR more modular (i.e. invisible if not used)
373    o model/src/temp_integrate.F and salt_integrate.F
374      - re-include store directives that were removed on Dec 27th.
375    o model/src/external_forcing_surf.F
376      - add storage directives for EmPmR and PmEpR to avoid recomputation of
377        seaice_model in the adjoint that is problematic when seaice_model is
378        turned off in the adjoint. The resolved issue dated back to July when
379        EXTERNAL_FORCING_SURF call was moved.
380        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
381    o pkg/exf/exf_check.F
382      - fix a small bug again (originally found by Wentao Liu, now found again)
383      - streamline error output
384    o pkg/streamice and aim_v23:
385      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
386        Apple's /usr/bin/cpp knows what to do:
387        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
388        Target: x86_64-apple-darwin13.0.0
389    
390    checkpoint64s (2014/01/05)
391    o tools/adjoint_options:
392      - switch to fastopt.net TAF server (instead of default fastopt.de) for
393        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
394    o model/src:
395      - remove some unnecessary TAF storage directives in forward_step.F and
396        in dynamics.F (note: not always removed by TAF, e.g., double storage
397        of kappaRU,kappaRV in former version of dynamics.F).
398    o model/src & pkg/ptracers:
399      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
400        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
401        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
402      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
403      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
404      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
405    o useSingleCpuInput separates single-CPU input from single-CPU output;
406        for now only implemented for in exf_interp_read.F
407    o verification/advect_xy:
408      - fix missing EXCH call in local version of ini_salt.F and update output.
409    o momentum diagnostics:
410      - fix which deltaT is used in Total-Tendency diagnostics.
411      - fix typo in diagnostics for momentum tendency from AB.
412    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
413        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
414    
415    checkpoint64r (2013/12/08)
416    o verification/*/results:
417      - Update reference output of experiments that were passing with just 13 digits
418         (make it easier to detect future changes in results)
419    o model/src & pkg/ptracers:
420      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
421        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
422        to inside ptracers_integrate.F ; remove ptracers_advection.F
423    o coupling interface pkgs:
424        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
425      - change the config check to test the agreement of Ocean Depth
426        with ATM land/sea mask (instead of ATM orography);
427      - send to coupler the number of coupler time-steps to do for this run:
428        this allows to check for consistency and don't need anymore to be
429        specified in parameter file "data";
430      in coupler:
431      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
432      - improve report to log-file of config setting (pass log-file unit to few S/R)
433    o pkg/compon_communic:
434      - add coupling send/receive for non-tiled integer vector;
435      - add S/R to check and stop if any proc has an error (similar to
436        eesupp/src/stop_if_error.F but single thread and across Comm_World).
437    o pkg/exch2:
438      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
439        through list of all tiles my proc owns.
440    o model/src:
441      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
442        from rTrans) to simplify dependencies (no need to store rTrans anymore in
443        calling S/R); this affects AD results at machine truncation level:
444        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
445        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
446    o tools/build_options:
447      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
448    o coupling interface pkgs:
449        [compon_communic, atm_compon_interf & ocn_compon_interf]
450      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
451        to each S/R that needs it; remove un-used variables.
452      - change component tile registration (cpl_register.F in both compon_interf
453        and mitcomponent_tile_register.F) to pass the full list of tiles
454        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
455      - with pkg/exch2: adopt the same convention used for I/O to define mapping
456        towards coupler global array (unless W2_useE2ioLayOut=F):
457         a) can now use different tiling between atm & ocn comp.
458         b) no needs to modify the run-Off map when changing tiling (was needed
459            even if using the same tiling between atm & ocn).
460         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
461            full land tiles); not yet tested.
462      - check for valid mapping from comp. tile to coupler global array
463      - improve report of tile registration results to log file.
464    o pkg/exch2:
465      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
466        tile-registration (CPL_REGISTER);
467      - activate (un-comment) definition and setting of "W2_tileIndex" list to
468        store the local bi,bj indices of each tile;
469      - also print bi,bj in local report to log file;
470      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
471        Jun 2009 modif of pkg/exch2).
472    o testing on baudelaire:
473      - run 2 tests at a time: no significant slow down (since enough cpu) and
474        get the full set of test done earlier
475      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
476    o model/src/thermodynamics.F and routines called from it:
477      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
478        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
479        velocity (outp) by adding bolus velocity.
480      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
481        mass transport from velocity + lateral grid cell area
482      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
483      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
484     in thermodynamics.F
485      - remove k from thermodynamics.F and move it to temp_integrate.F
486        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
487        loop).
488      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
489        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
490        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
491        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
492      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
493        global_ocean.90x40x15, tutorial_global_oce_biogeo and
494        tutorial_tracer_adjsens (+ TLM output).
495    o tools/OAD_support and (verification/*/) code_oad:
496      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
497        module conversion ; remove unneeded CPP_EEOPTIONS.h.
498      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
499        version (closer to model/inc/CPP_OPTIONS.h).
500    o model/src:
501      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
502        retired list of parameters (routine FREEZE has been replace by surface
503        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
504    o pkg/gmredi:
505      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
506        velocity (same scheme but affects machine truncation) for GM_AdvForm.
507      - update output of FWD experiments: front_relax.bvp,
508        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
509    
510    checkpoint64q (2013/11/17)
511    o verification:
512      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
513        tutorial_global_oce_biogeo and global_ocean.90x40x15.
514      - generate new output (growth & melt) for seaice_itd experiment after
515        updating the input pickup_seaice files (previously wrong).
516    o pkg/cost:
517      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
518        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
519        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
520          cannot be applied to var in common block).
521        o allows to get results independent of tile-per-proc setting (if using
522          slower GLOBAL_SUM_SEND_RECV option).
523      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
524        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
525        forward gradients: update output).
526      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
527        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
528    o pkg/mom_common:
529      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
530        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
531        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
532        ensure that all field value that are used are set.
533    o tutorial_deep_convection (smag3d):
534      - add missing scaling in mom_calc_smag_3d.F;
535      - set smag3D_coeff in input.smag3d such that results do not change.
536    o pkg/dic:
537      - change dic_cost.F to compute cost on each tile first and then apply
538        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
539        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
540      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
541    o eesupp/src & pkg/mdsio:
542      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
543        (from pkg/mdsio) since they are no longer used for tape IO.
544      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
545        (+ keep a copy in pkg/atm_ocn_coupler).
546    o verification/isomip:
547      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
548    o tools/build_options:
549      - optfile linux_amd64_ifort11, fast (no ieee) case:
550        to get a working restart for all experiments, add "-fp-model source"
551        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
552    
553    checkpoint64p (2013/10/20)
554    o pkg/autodiff:
555      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
556        criteria, return to simple (default) tape IO format.
557    o pkg/mdsio (+ eesupp/src):
558      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
559        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
560      - fix globalFile and singleCpuIO options using simpler global mapping.
561      - new pairs of scatter/gather vector S/R (one for each type, generated from
562        template) corresponding to simpler global mapping.
563      - adread_write.F: switch to new S/R (but leave old calls commented) and write
564        to globalFile when parameter globalFiles is set to True.
565      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
566    o pkg/autodiff:
567      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
568        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
569        missing, just add a STOP if array type do not match.
570    o pkg/exf:
571      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
572         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
573         and rename array obsSIce to exf_iceFraction.
574    o tutorial_deep_convection:
575      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
576        for now all in this exp. code dir.
577      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
578        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
579    o eesupp/src:
580      - added SINGLE_DISK_IO option because reading of parameter files on
581        very large number of processors did not work with existing set-up
582    
583    checkpoint64o (2013/09/25)
584    o pkg/atm_phys & atm_compon_interf:
585      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
586    o tools/build_options:
587      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
588        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
589        remove CPP setting (was identical to genmake2 default).
590    o pkg/gmredi & model/src: Some updating and work done on the residual model.
591      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
592      - fixed up the calculation of the eddy stress and how it is added to the
593        external forcing via taueddy_external_forcing.F
594      - at the moment, it is very experimental and only works with the variable eddy
595        diffusivity calculated in gmredi_k3d.F
596    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
597        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
598    o testreport (& tools/do_tst_2+2):
599      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
600    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
601      - remove CPP='cpp -traditional -P' (this is genmake2 default)
602      - add switch (for big setups) to use 'medium' memory-model (but leave it
603        commented out for now). Note: needed with FC 19 to compile big setups.
604    o pkg/atm_compon_interf:
605      - regroup per field origin (model & pkgs) the coupling storage routines
606         (which accumalate in time each coupling field)
607      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
608        update accordingly + simplify aim_do_physics.F
609    
610    checkpoint64n (2013/08/26)
611    o pkg/bbl:
612      - update formulation to reduce dispersion of tracer properties in bbl
613      - replaced horizontal and vertical transport parameters with velocities
614      - changes results for verification/global_with_exf.yearly
615    o verification/halfpipe_streamice:
616      - change to matrix construction; update both Fwd & AD output.
617    o verification/tutorial_tracer_adjsens:
618      - OpenAD test: switch to vector-invariant momentum since fluxform with
619        rStar causes problems with OpenAD; update output.
620    o tools:
621      - genmake2: define a common prefix for all temp-file names ; move them
622        to local /tmp disk (but would be easy to move them back);
623      - xmakedepend: apply the same switch for temp-files.
624    o pkg/offline:
625      - changes for use with rStar (NLFS): assume that we continue to provide
626        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
627        output files) and apply r* scaling at each time-step (function of the time
628        varying Eta field); use normal pickup files (needed for restart with NLFS).
629    o adjoint with OpenAD:
630      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
631        package openad.  This package has to be compiled for all runs with OpenAD
632        instead of specifying code_oad_all as a modification directory.
633      - link the fortran templates from tools/OAD_support to the build directory
634        for preprocessing to avoid conflicts between different setups compiled
635        simultaneously and simplify cleanup.
636    o pkg/exf:
637      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
638        main model or other pkgs are exchanged in EXF_MAPFIELDS).
639    o model/src:
640      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
641        (similar to do_fields_blocking_exchanges.F).
642    o tools/genmake2:
643      - remove TAF output src code just before calling staf (when not doing a fresh
644        built, will stop if things go wrong with staf).
645      - fix target "adobj" (left from TAF version-2 transition)
646    o pkg/diagnostics:
647      - add a parameter to track the status of pkg/diagnostics activation;
648        this replace/extend the use of logical param "settingDiags" (to check
649        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
650        New S/R to print error message and stop when pkgStatus is not right.
651      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
652    
653    checkpoint64m (2013/08/13)
654    o model/inc:
655      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
656        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
657    o pkg/kpp & aim_v23:
658      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
659    o pkg/seaice:
660      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
661        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
662      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
663    o eesupp/src:
664      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
665        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
666    o switch to TAF version-2:
667      - add flow directives to "freeze" naming convention for ad-routines that
668        are used in I/O routines of adjoint state and associated common blocks
669        that are used in adcommon.h (backward compatible with version-1)
670      - update all ad-optfiles (in tools/adjoint_options + few local to some
671        verification exp) to switch to latest TAF version (currently 2.5.5);
672        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
673        out except for diva).
674      - the major change with TAF version-2 is that both the differentiated
675        routines and the forward routines (new) are returned as part of the TAF
676        output source code. Update genmake2 accordingly.
677      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
678        with version-2 when compared to TLM or FWD gradient); other experiments
679        output show minor changes (machine truncation level); update the few AD &
680        TLM output with 12 matching digits only (some prior to version-2 switch).
681    
682    checkpoint64l (2013/08/05)
683    o model/src:
684      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
685      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
686        when using TAF but only if using OpenAD.
687    o pkg/mom_common+fluxform+vecinv:
688      - always set horiz. viscosity arrays to background value before calling
689        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
690        only when using variable horiz. viscosity (useVariableVisc=T);
691      - simplify mom_vecinv.F (only 1 block for momViscosity).
692    o pkg/mom_common: variable horiz. viscosity in NH code
693      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
694        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
695      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
696        useBiharmonicVisc & useVariableVisc.
697      - fix old bug (already in 1rst implementation of variable horizontal viscosity
698        in calc_gw.F, version 1.27, 2006/06/20):
699        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
700        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
701      - change background horiz viscosity in vertical momentum (gW) to always be
702        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
703        any type of variable viscosity, e.g., viscAh/4Grid)
704      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
705        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
706        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
707        default viscAh,viscA4 is zero).
708    o model/src:
709      - extend length of drC & recip_drC from Nr to Nr+1.
710    o Divided Adjoint (DIVA) with MPI:
711      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
712      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
713        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
714    
715    checkpoint64k (2013/07/23)
716    o tools/OAD_support:
717      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
718        and remove it from genmake2.
719    o tools/build_options:
720      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
721        MPI_HEADER_FILES list (let genmake2 find the missing headers)
722    o verification/halfpipe_streamice:
723      - change to driving stress formulation; update both Fwd & AD output.
724    o tools/genmake2 and Divided Adjoint with MPI:
725      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
726      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
727      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
728        Makefile, which is set by genmake2, and check which mpi-headers are needed.
729        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
730      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
731    o testreport:
732      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
733        perform additional runs (number of additional runs is "add_DIVA_runs" taken
734        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
735    o verification/lab_sea (AD test):
736      - change to test Divided Adjoint Run in this set-up (both standard AD test
737        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
738    o pkg atm_ & ocn_compon_interf:
739      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
740        staggerTimeStep implementation) and disable (retired) corresponding
741        parameter.
742    o pkg/offline:
743      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
744      - add S/R OFFLINE_CHECK to print offline parameter summary
745        and stop if loading a file that is not used;
746      - enable to calculate GMRedi tensor, KPP mixing and convective index
747        when the corresponding file(s) is/are not specified (but pkg is used).
748      - comment out resetting of monitorFreq (to endTime) since it still useful
749        for monitoring CFL numbers and checking offline fields.
750    o OpenAD:
751      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
752        smaller standard output) and generate new (smaller) output (on baudelaire
753        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
754    o model/src:
755      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
756        (where external_forcing_adjust was called) and change list of arguments;
757      - merge external_forcing_adjust.F into external_forcing_surf.F
758      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
759        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
760        previously in file "balance_relax.F", now removed); remove corresponding
761        arrays in FFIELDS.h.
762      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
763        a hack for getting back surfaceForcingS (loaded from file) when using
764        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
765      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
766        (was getting only 11 digits for AD-grad, due to different truncation
767         error in AD code).
768    
769    checkpoint64j (2013/07/04)
770    o pkg/offline:
771      - to enable the use of other features with pkg offline (e.g., obcs),
772        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
773      - comment out "allowFreezing" (now active) in 2 offline testing exp.
774    o pkg/exf ALLOW_RUNOFTEMP
775      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
776      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
777      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
778    o pkg/atm_phys:
779      - allows to add some damping on uVel,vVel (strength only function of k).
780    o verification, ad-tests:
781      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
782        global_ocean_ebm and offline_exf_seaice.thsice.
783    o verification/halfpipe_streamice:
784      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
785        flux input boundary conditions to be ignored; a fix for this bug changed
786        verification results for forward test.
787      - add adjoint test.
788    o pkg/ptracers:
789      - allow to restart without SOM pickup (resetting SOM to zero).
790    o pkg/gmredi:
791      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
792      - It uses mixing length theory and suppression by steering level effects to
793        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
794        to JPO, for more details).
795      - It also uses the diffusivity to calculate an eddy induced streamfunction
796        based on a PV closure (rather than a buoyancy closure as in GM).
797      - New files added to pkg/gmredi:
798        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
799          induced overturning streamfunction (called from gmredi_calc_tensor)
800        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
801          for use in gmredi_k3d
802        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
803          the eddy diffusivity
804    
805  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
806  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 837  o pkg/cfc:
837      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
838    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
839    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
840    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
841      similar to thsice_advdiff.
842      Note that for the B-grid case the routine parameters uc/vc are overwritten.
843  o pkg/cfc:  o pkg/cfc:
844    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
845      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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