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revision 1.1435 by jmc, Wed May 18 02:21:49 2011 UTC revision 1.1610 by jmc, Mon Mar 5 16:23:23 2012 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/seaice :
8      - add missing initialisation of COR_ICE array in dynsolver.F
9      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
10        compiled either way, and is tested in all exps (multidim was only tested
11        in lab_sea ad before).
12      - cosmetic change to prepare for future addition of ITD. no change to results.
13        no defaults change.
14      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
15      - by lack of adequate verification experiments, I further used custom versions
16        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
17        should be correct.
18      - avoid recomputations in ad.
19    o array initialisation in adjoint mode:
20      1) pkg/mom_common/mom_calc_ke.F:
21        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
22        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
23        part this initialisation is gone, resulting in Floating Point Exception
24        (caught by open64 compiler with debug option).
25      2) model/src/convective_weights.F
26        set output convectCount over the full array range (instead of doing
27        an update): this fix a similar issue when called within recomputation (adjoint)
28        which could by-pass the initialisation (normally done in the caller S/R).
29    o pkg/seaice:
30      - final version of turbulent flux params, as agreed at MIT ice meet:
31           SEAICE_mcPheePiston (default is ~ 0.000875)
32           SEAICE_mcPheeTaper (default is 0.)
33           SEAICE_frazilFrac (defualt is 1.)
34           SEAICE_mcPheeStepFunc (default is false)
35      - changes results at trunction error level
36      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
37    o added pkg/frazil:
38      - see frazil_description.tex for details
39      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
40    o pkg/shelfice/shelfice_thermodynamics.F
41      - fix exponents for velocity dependent exchange coefficients: change
42        from 2/3(=0) to 0.66666666666666667
43      - move computation of velocity dependent exchange coefficients into
44        separate loop, so that it applies to both thermodynamics
45      - move some divisions by constants out of loops
46    
47    checkpoint63j (2012/02/16)
48    o pkg/seaice:
49      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
50      - SItracer:  added run time params, and allow coupling to ocn salinity.
51    o pkg/seaice: remove (almost) all divisions by constants within loops
52      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
53      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
54      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
55      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
56    o pkg/seaice :
57      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
58        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
59      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
60      - add permanent SItflux diag that corresponds to TFLUX but includes
61        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
62      - allow activation/testing of a fix for suspected missing term in
63        ocn-ice heat budget (to be confirmed). To test this, you want to
64        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
65        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
66      - no change in results, fwd or ad.
67    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
68      - switch to variable freezing point.
69           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
70      - bug fix : the sublimation term that was missing is now activated.
71           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
72      - bug fix : flooding sign term for SIsal0.NE.0.
73           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
74    o pkg/seaice:
75      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
76        is now the default, and the old default constant freezing point is recovered
77        with SEAICE_tempFrz0    = -1.96,
78             SEAICE_dTempFrz_dS = 0.,
79      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
80      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
81      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
82        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
83      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
84        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
85      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
86        seaice_growth r149 for legacy branch (no results change).
87      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
88        from I. Fenty).
89      - results did not change except for global_ocean.cs32x15, mostly due to the
90        switch to variable freezing point (see above item for detail).
91    o pkg/thsice:
92      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
93        seawater freezing in thsice_calc_thickn (not used).
94    o pkg/seaice: turbulent flux term specification via run time params.
95      - replace CPP switches with run time switches to facilitate testing
96      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
97                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
98      - added runtime parameter : SEAICEturbFluxFormula
99      - move Mcphee constants to SEAICE_PARAMS.h
100      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
101                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
102                 remove seaice_summary call (moved to seaice_init_fixed)
103      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
104        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
105      - seaice_summary.F : add missing report of read turbulent flux term set up
106                           and SITRACER.
107      - seaice_check.F : check range; inform and stop if retired CPPs are used
108                         (incl. SEAICE_AGE).
109      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
110             CPP switch, same computation as before for the different options.
111      - change results at the truncation level.
112    o pkg/seaice:
113      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
114        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
115        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
116      - update verification/*/input*/data.seaice:
117        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
118        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
119        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
120        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
121    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
122      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
123        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
124        difference in results only due to machine truncation.
125      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
126        MaykutPolySatVap; keep MIN_LWDOWN.
127      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
128      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
129        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
130    o pkg/salt_plume:
131      - isolate saltPlumeFlux array exch into a specific S/R called from
132        do_oceanic_phys.F
133      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
134    o verification:
135      - move untested set-up to MITgcm_contrib/verification_other.
136    o pkg/seaice:
137      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
138    o pkg/seaice:
139      - seaice_solve4temp.F (keeping results unchanged):
140        * add 2 future run-time params to select which saturation vapor pressure
141          formula is used and how post-iteration fluxes are set.
142          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
143        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
144          the linearized expression to stay consistent with tsurf finding.
145      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
146        can be < 0.
147    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
148      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
149        conductive heat flux F_c , and add it explicitly when updating tsurf as
150        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
151        so that now F_ia has a consistent meaning through the entire routine.
152        This causes differences at truncation level: update output of fwd exp.
153        global_ocean.cs32x15.seaice.
154    o pkg/seaice:
155      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
156        of arrays, sign/direction of fluxes; no effect on results.
157      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
158        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
159        note: this should have been done before changing celsius2K default.
160      - to keep results unchanged, add back old value of celsius2K in verification
161        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
162      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
163        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
164        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
165        freezing temp is consistent with value in seaice_growth.F ; this causes
166        differences at machine truncation level: update lab_sea AD output (3/4).
167    o pkg/seaice:
168      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
169        and climsst/sss even when using seaice (to prevent calculation that might
170        use SST on land); does not affect any verification exp.
171      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
172        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
173    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
174      over land (non-legacy code)
175    o vectorize salt_plume package:
176      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
177      - this code computes plumebk everywhere (also over land), thus requires
178        code to avoid divisions by zero and catch the case of kLev=Nr.
179      - efficiency of salt_plume_frac is still sub-optimal
180    o tools (genmake2):
181      - fix makefile NAME specification (option: -makefile NAME) by adding
182        "-f $MAKEFILE" in few places where it was missing including makedepend
183        command (contribution from Paul).
184    
185    checkpoint63i (2012/01/24)
186    o model/src:
187      - add factorized versions of some EOS code to find_rho.F,
188        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
189    o model/src:
190      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
191      - change default celsius2K from 273.16 to 273.15
192      - to keep results unchanged, add back old value of celsius2K in verification
193        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
194         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
195    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
196      to make TAF generate vectorizable code
197    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
198       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
199       have flags that do this more efficiently.
200    o pkg/diagnostics/diagstats_calc.F
201      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
202    o pkg/obcs (with exch2):
203      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
204        and remove code (in obcs_readparms.F) which was based on EXCH of indices
205        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
206    o pkg/exf and seaice exp:
207      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
208        so that switching off area & heff advection flags does not affect results.
209      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
210      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
211        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
212        results of verification experiments: 1D_ocean_ice_column(fwd),
213        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
214        and offline_exf_seaice (all 4).
215    o pkg/seaice:
216      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
217        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
218      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
219        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
220        not multi-dim advection;
221      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
222        SHORTWAVE_HEATING #undef.
223    o optim: make Makefile more robust (?)
224    o pkg/obcs:
225      * fix treatment of obcs_read_pickup for TAF
226    o pkg/shelfice:
227      * add missing initialisation of num_shifwflx
228      * new adjoint verification exp. for isomip
229      * change Prandtl and Schmidt numbers from generic formulations
230        (in terms of model diffus. and visc.) to separate runtime
231        parameters, with Holland and Jenkins (1999) default values.
232    o pkg/exf (interpolation):
233      - extended input field (2 rows) near the N & S poles:
234        * fill in with the symetric value (when even Nb of data in longitude)
235        * add average value at the poles only for scalar quantities ; for vector
236          component interpolation, skip the averaging and keep duplicated values,
237          unless the 2 components have same location (uvInterp=T) in which case
238          interpolate the 2 components together using S/R EXF_INTERP_UV.
239      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
240        together: this allows to account properly for local orientation when
241        averaging at N & S pole.
242      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
243        exf-interpolation near N & S poles. Undef by default.
244      - add debug check/print on 1rst iter if debugLevel >=2.
245    o pkg/exf:
246      - change masking flags definition (no longer "parameter"), put them in
247        common block and set them in S/R EXF_INIT_FIXED.
248      - change recognized masking flag from s,u,v to c,w,s since the mask
249        to use (maskC,W,S) depends on position on model grid and has little to
250        do with scalar/vector difference; fix masking if using P-coordinates.
251      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
252        and update results of exp. global_with_exf (x2).
253      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
254    o pkg/obcs
255      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
256    o pkg/exf (interpolation):
257      - assume periodicity in X only if input field cover full longitude range.
258      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
259        and should vectorise).
260      - fix input lat of the 2 added row (in case we provide N.pole data).
261    
262    checkpoint63h (2011/12/30)
263    o pkg/seaice:
264      - change declaration of UVM from _RL to _RS in order to get B-grid
265        uIce,vIce monitor when _RS = real*4
266    o pkg/offline:
267      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
268      - compute vertical velocity if not read from file (switch on exactConserv
269        & staggerTimeStep);
270      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
271    o verification:
272      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
273        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
274        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
275      - update output of exp. global_ocean.cs32x15.viscA4 after changing
276        grid-file angles (used here for coriolis-3d);
277      - remove (or gzip) few files not needed to run fizhi-cs experiments.
278    o pkg/exf (vector interpolation):
279      - rotate vector component toward local grid-axis orientation using grid-angles
280        (stored in GRID.h) instead of locally computed rotation angle; keep old code
281        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
282    o pkg/seaice:
283      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
284        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
285    o pkg/PKG_OPTIONS.h files:
286      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
287        outside of the #ifdef ALLOW_THISPKG / #endif block.
288      - update verification/*/code/PKG_OPTIONS.h files.
289    o add a verification experiment (offline_exf_seaice/input.seaice) that test
290      the B-grid LSOR solver
291    o pkg/seaice: sort out emissivity and long wave radiation step 2:
292      - add emissivity for snow and ice as new run-time parameters
293        (unfortunately) that default to the corresponding exf values; this
294        changes results in most verification experiments so that for backward
295        compatibility these parameter have to be set explicitly to inconsistent
296        values (ugly);
297      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
298        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
299        until we agree how to handle this bug properly
300    o pkg/exf (interpolation):
301      - add a set of run-time param ({inputfield}_interpMethod), one for
302        each interpolated input field, to select the interpolation method
303        with a value of zero switching off the interpolation;
304      - print interpolation parameters to standard output;
305      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
306        (to use instead runoff_interpMethod=0 in data.exf).
307      - simplify default setting of interpolation parameters (for all fields,
308        set position to match model grid cell-center position, leading to trivial
309        interpolation in case of regular Lat-Lon grid) and fix for the case of
310        non-uniform delY.
311    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
312       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
313       this factor is absolutely required, because the lw exitance (= out-going
314       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
315       where the reflectivity rho = 1-emissivity for conservation reasons. Once
316       this is established, we can remove the CPP-Flag (if we want to).
317    o pkg/seaice:
318      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
319        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
320      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
321        what the name implies (and not emissivity*BoltzmannConstant), this means
322        the old default value of 5.5e-8 now means
323        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
324        S/R exf_readparms
325      - FV-discretization of the B-grid LSOR solver, turn on with
326        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
327        of the calling routine dynsolver, so that B and C-grid code look a
328        little more alike.
329      - fix index bugs in ostres.F (B-grid code)
330    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
331    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
332      default for SEAICE_emissivity, if useEXF; requires setting a wrong
333      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
334      backward compatiblity
335    o model/src: use sigmaR in calc_ivdc
336    
337    checkpoint63g (2011/12/16)
338    o pkg/seaice/seaice_growth.F:
339      fix heat conservation of the coupled ocean-seaice system.
340      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
341      solid vs liquid water treatment is resolved via QNET.
342    o pkg/seaice/seaice_growth.F:
343      add missing term for sublimation in saltFlux, which was breaking conservation.
344    o pkg/seaice/seaice_model.F:
345      Remove this patholigical case treatment in evolution branch,
346      where it is un-necessary and breaks conservation.
347      Update global_ocean.cs32x15/results accordingly for
348      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
349    o model/src:
350      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
351      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
352    o pkg/obcs:
353      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
354      tendency for temperature and salinity that is then applied to update
355      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
356      horizontal advection and diffusion contributions on the boundary (in
357      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
358      removing the mask in S/R timestep_tracer. The advantage of this approach is
359      that the updated tracer values include contributions from the surface
360      forcing and vertical diffusion.
361      This modification changes exp4.stevens because of vertical diffusion.
362    o model/src:
363      change non-curvilinear grid setting to also work with exch2 + blank tiles:
364      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
365        face dimensions.
366      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
367        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
368        and INI_SPHERICAL_POLAR_GRID.
369      change test-experiment global_ocean.90x40x15:
370      - split the domain in many more tiles (9x4 tiles of 10x10 each);
371      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
372      - update results of both test (std & dwnslp).
373    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
374       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
375    o model/src:
376      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
377        and fix initialisation when using sigma-coords.
378    o model/src:
379     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
380       to their current value at the beginning of forward_step.F": add a new run-time
381       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
382     - set doResetHFactors=T in the following test exp:
383        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
384        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
385        and tutorial_global_oce_in_p (nonLinFS in p)
386    o pkg/ecco
387      - added IES cost term
388    o verification/advect_xz
389      - scale down the depth by 1/100 (from 200 km to just 2.km)
390      - add secondary test using divergent flow, r-star and implicit vertical advection.
391      - add note (check_conserve_TS.txt) and matlab script to check global
392        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
393    o pkg/rbcs:
394      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
395    o pkg/obcs (Stevens BCs):
396      - fix various problems in the phase speed computations of the Stevens
397        boundary conditions:
398        - sign error for western and southern boundaries,
399        - time tendencies were underestimated by factor of dTracerLev and some just
400          zero (for multidim advection schemes) -> now estimate time tendencies
401          from difference between previous (n) time level and the one before (n-1);
402          this requires storing a field per tracer per boundary, also in the pickup
403          files.
404        - replace deltaTmom in cflMer/Zon computation with dTracerLev
405        - set default phase velocity to cflMer/Zon
406      - update verification experiment exp4.stevens
407    o pkg/generic_advdiff (implicit_r):
408      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
409        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
410      - fix implicit vertical diffusion or advection with NonLin FreeSurf
411        (was using current recip_hFacC instead of future recip_hFacC): set future
412        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
413        solver S/R ;
414      - fill diagnostics of vertical advective fluxes (computed from tendency)
415        when using implicit vert. advection;
416      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
417         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
418         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
419         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
420    o pkg/diagnostics:
421      - add diags for T & S tendency which goes through Adams-Bashforth.
422    
423    checkpoint63f (2011/11/30)
424    o pkg/obcs/obcs_calc_stevens.F:
425      - join some loops to reduce number of if-statements
426      - fix a bug in code for northern and southern boundaries.
427    o pkg/seaice/seaice_init_varia.F
428      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
429        caused zero ice-velocities for the B-grid code
430    o pkg/seaice/seaice_init_fixed.F
431      - fix a bug in the initialisation of the second metric terms
432        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
433      - this affects all seaice configurations with useCurviLinearGrid = .true.
434        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
435        = .true. (default)
436      - the only verification experiment affected is global_ocean.cs32x15:
437        icedyn, seaice, and seaice_dynmix (AD)
438    o pkg/thsice/thsice_diagnostics_state.F
439      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
440        not contain garbage that can lead to surprises in diagstats_calc.F
441    o model/src:
442      - move bi,bj loops inside INTEGR_CONTINUITY ;
443      - call INTEGR_CONTINUITY directly from forward_step.F
444        (previously called from momentum_correction_step.F)
445      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
446        forward_step.F and pkg/ecco/the_main_loop.F
447    o model/src/do_oceanic_phys.F:
448      - reset addMass to zero only if useICEFRONT ;
449      - separated k-loop for rhoInSitu calculation ;
450      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
451        and at constant T,S (= WdRHOdP);
452      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
453        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
454        transport of locally-referenced potential density);
455        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
456    o gluemnc:
457      - replace ncrcat with ncks when adding variables to *.glob.nc
458      - change the way variables without record dimensions are handled so that
459        files that have variables with and without record variables can be glued:
460        add a record dimension with a new unique name to be able to differentiate
461        between variable with and without a-prior record dimensions. Remove
462        this record dimension before adding the variable to the *.glob.nc file.
463        This procedure automatically works also for grid.*.nc files that do not
464        have any record dimension.
465    o verification/cpl_aim+ocn:
466      - generate new reference output on baudelaire (gfortran, mpich2) (previously
467        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
468    o pkg/obcs/obcs_calc_stevens.F:
469      - add code for northern and southern boundaries.
470      - reorder some loops to save some operations and so that drFBar can be scalar
471    o model/src:
472      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
473        truncation) and add diagnostics for Adams-Bashforth tendency increment.
474      - update test-exp. AD output:
475        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
476      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
477        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
478        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
479        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
480        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
481        tutorial_plume_on_slope.
482    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
483      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
484      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
485      does not even come with an F77 compiler anymore, this should not be
486      a limitation
487    
488    checkpoint63e (2011/11/06)
489    o pkg/seaice adjoint of LSR:
490      - substantially rework STORE dirs.
491      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
492        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
493        and only perform SOLV_MAX_FIXED adjoint iters.
494        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
495        always goes to same record, meaning that the last forward field will be
496        the one used in the adjoint - an approximation.
497      - now produces non-zero LSR-related gradients, and acceptable gradients for
498        An's zonal (x-z) test case (to be checked in)
499      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
500        (but these are screwed up by the thermodynamics in the first place);
501        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
502        output_adm.txt also reflects changes to seaice_lsr
503      - global_ocean.cs32x15:
504        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
505          (output_adm.seaice.txt was updated)
506        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
507          (output_adm.seaice_dynmix.txt)
508    o test-exp. exp4+stevens:
509      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
510    o pkg/seaice (lsr solver):
511      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
512        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
513      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
514      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
515        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
516      - compute (with new S/R) and print initial (+ free-driff sol. if available)
517        and final residual of linearised system.
518    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
519      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
520    o pkg/obcs: Stevens BCs (still only for east and west)
521      - fix Stevens BCs by using intermediate velocities of previous
522        time step as "baroclinic" contribution rather velocity of one grid cell
523        inside the boundaries; more consistent but makes the entire treatment
524        more complicated, requires new pickup files and two new S/Rs:
525        obcs_copy_uv_n and obcs_save_uv_n
526        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
527        (undefined by default)
528      - silently move computation of some grid factors into separate loops to
529        save some recomputations
530      - add a hack for non-linear free surface
531      - add a verification experiment to exp4 that tests this code
532    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
533    
534    checkpoint63d (2011/10/25)
535    o pkg/obcs + seaice-dynamics:
536      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
537        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
538        values (consistent with an implicit method).
539      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
540        return to older implementation (same results as before); note that none of
541        the "experimental" OBCS_SEAICE options are implemented in the new version.
542      - switch test exp. seaice_obcs to use new version (update output).
543    o pkg/seaice:
544      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
545      - add parenthesis in Water-Ice drag calculations (evp & lsr);
546      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
547        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
548      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
549        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
550    o pkg/layers:
551      - Include potential density as new coordinate (Thanks to David Munday)
552    o pkg/dic:
553      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
554        carbonate computation/output to CALC_PCO2_APPROX
555    o pkg/generic_advdiff
556      - make TAF generate code that vectorizes:
557        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
558    o model/src:
559      - improve vectorization also for adjoint code of
560        solve_tridiagonal and solve_pentadiagonal. As this requires up to
561        5 new 3D-fields, this code is only turned on for the combination of
562        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
563        for singular matrix check (only for TARGET_NEC_SX).
564      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
565        ALLOW_AUTODIFF. This flag now needs to be set outside of
566        solve_tri/pentadiagonal.F
567    o pkg/exf:
568      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
569        optional namelist EXF_NML_OBCS).
570      - add many debug-print (to trace down where pkg/cal error msg comes from)
571    o pkg/mom_vecinv/mom_vi_hdissip.F
572      - rearrange loops so that vectorization is improved and in particular
573        the adjoint routine vectorizes. The code is a little longer now, but I
574        think easier to read.
575        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
576    o pkg/seaice:
577      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
578    o pkg/exch2:
579      - alternative code (without tile x tile matrix) for cumulated (global) sum;
580        used as default; keep using matrix version in adjustment.cs-32x32x1.
581    o tools/build_options:
582      - after merging some MPI and/or multi-threads specific optfiles so that
583        the modified default optfile support both built (using genmake2 -mpi
584        for the MPI built, using genmake2 -omp for OpenMP built),
585        move now obsolete optfiles to tools/build_options/unsupported/
586       (add copy of email sent to support list in doc/optfiles_changes.txt)
587    
588    checkpoint63c (2011/09/28)
589    o pkg/ebm:
590      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
591        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
592    o pkg/seaice (SItracer pickup)
593    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
594      To be done:
595      - thorough testing of missing fields in S/R seaice_read_pickup
596      - thorough matching between generic tracers and specific fields used
597        (e.g. volume-weighted age, area-weighted age, salinity, ...)
598    o pkg/grdchk:
599      - all procs calculate and print finite-difference gradient (for testreport)
600      - change description output used by testreport;
601      - AD testing: also compare and report Finite-difference gradient;
602        => update all output_adm*.txt
603    o test exp. global_ocean_ebm:
604      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
605        and turn on exactConserve; update (fwd) output.
606    o pkg/seaice (LSR):
607      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
608      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
609        * identical results with non-CS topology (but save up to half of EXCH calls)
610        * no much changes in cs-32 verification tests since no ice at face edges
611         (differences due to convergence criteria, since nb of iterations changed)
612        * expect some differences on lat-lon-cap grid.
613        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
614    o pkg/exch2:
615      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
616        many tiles); until alternative coding is added, just add a stop.
617    o pkg/kpp:
618      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
619        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
620    o optfiles:
621      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
622        into corresponding standard one, which now support different build:
623        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
624      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
625    o pkg/obcs (seaice):
626      - add missing EXCH for uIce,vIce after applying OBCS;
627      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
628        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
629        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
630      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
631      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
632        and eedata.mth for MPI and mutlti-threaded testing.
633    o pkg/flt:
634      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
635      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
636      - fix pickup and trajectories + profiles output with multi-threads;
637      - add parameter to select group of fields to write along trajectory and
638        profile (default unchanged);
639      - only call PORT_RAND* function when flt_noise <> 0;
640      - add multi-threaded test for verification exp. flt_example.
641    o eesupp/src:
642      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
643      - USE_OMP_THREADING: check that number of threads (from eedata) matches
644        actual number (from env.var. setting).
645    o pkg/ebm:
646      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
647      - add multi-threaded test for verification exp. global_ocean_ebm
648    
649    checkpoint63b (2011/08/29)
650    o pkg/ebm:
651      - fix sign of runoff;
652      - update directly forcing fields (Qnet,EmPmR) to use standard
653        external_forcing_surf.F (remove ebm_forcing_surf.F);
654      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
655      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
656        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
657      - update global_ocean_ebm parameters file data and update output (fwd+ad).
658    o verification/matrix_example:
659      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
660        MPI and mutlti-threaded testing.
661    o pkg/matrix:
662      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
663      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
664      - fix for multi-threaded (remove DATA statement);
665      - use standard DIFFERENT_MULTIPLE function;
666      - add MATRIX_OPTIONS.h
667    o verification/matrix_example:
668       To allow to split the domain in several tiles, change the domain size
669        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
670        Western side) of land points.
671    o (*_)write_pickup:
672      - fix few bugs in mypackage_read/write_pickup.F
673      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
674        array of length 1 (was caught by compiler syntax-check).
675    o pkg/diagnostics (velocity potential solver):
676      - fix initialisation of main diagonal matrix (for overlap values)
677    o tools/build_options:
678      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
679        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
680      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
681        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
682        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
683        and use "-devel" testreport option for standard testing on baudelaire.
684    o pkg/grdchk:
685      - Assume that all gradient-check position are within the same tile
686        corresponding to global indices (iGloTile,jGloTile) and that
687        positions (i,j indices or nbeg) are local to this tile;
688      - set tile local-indices and proc. number according to tile global-indices;
689      - remove grdchkwhichproc from namelist (retired param);
690      - send adjoint gradient to all procs so that all procs print it to STDOUT;
691      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
692    o adding package bbl (Bottom Boundary Layer)
693      description in MITgcm/pkg/bbl/bbl_description.tex
694      example/test experiment in MITgcm_contrib/bbl
695    o adjoint verifications
696      - changed 5 experiments to multi-tiles
697        * global_ocean.90x40x15
698        * obcs_ctrl
699        * offline_exf_seaice
700        * tutorial_dic_adjoffline
701        * tutorial_tracer_adjsens
702        changed reference output for those that crossed tile boundaries
703        (changed choices of gradient check positions)
704      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
705      - temporary bug fix in grdchk_loc.F for obcs
706    o genmake2 & testreport
707      - add target "obj" (just for OBJFILES files) to Makefile;
708      - add option to specify FEXTRAFLAGS on command line.
709    o pkg/mypackage:
710      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
711    
712    checkpoint63a (2011/08/02)
713    o pkg/diagnostics (velocity potential):
714      - fix velocity-potential calculation when using OBCS: balance net inflow
715        at each level (new S/R OBCS_DIAG_BALANCE).
716      - fix some of the problems with OBCS in stream-function calculation.
717    o pkg/exf/exf_readparms.F
718      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
719        EXF_NML_OBCS) more consistent, so that you need not have these lists
720        in data.exf when they are not used.
721    o optim/optim_readdata.F:
722      - add some output about obcs variables that might help debugging
723      - add a check about nvarlength
724    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
725    o pkg/diagnostics (velocity potential):
726      - fix mask for OBCS (still problems in stream-function with OBCS);
727      - add specific parameter (default = main code CG2D params) for solver;
728      - in case of poor convergence, use solution corresponding to lowest residual.
729    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
730      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
731      and should be avoided where possible.
732    o model/src (rStar):
733      - include r* effect on reference-state (PhiRef) in totPhiHyd
734        (so that it's really the potential anomaly at the cell center);
735        affect solution only if z* with full pressure in EOS.
736      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
737        update output (because of z* in totPhiHyd and viscA4 changes);
738      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
739        @ constant r) until interpolation at constant r is implemented.
740    o pkg/diagnostics
741      - fix RCENTER diagnostics in case cell center is not at interface middle
742    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
743      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
744      that THETA and SALT are "conservative temperature" and "absolute
745      salinity"
746    o pkg/ctrl
747      - fix computation of endrec in s/r ctrl_init_rec
748      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
749    o pkg/seaice/seaice_growth.F
750      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
751        remove then obsolete STORE directives
752      - fix STORE directives for tice and tices, so that only the
753        appropriate part of the fields are stored (and not the entire
754        field); update global_ocean.cs32x15.seaice AD output.
755      - cosmetic changes: adjust CPP flags and indentation for better
756        legibilty
757    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
758      Chris Wilson)
759    o pkg/gmredi:
760       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
761       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
762    
763    checkpoint63  (2011/07/11)
764    o pkg/exch2:
765     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
766     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
767       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
768       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
769    o pkg/diagnostics:
770     - deal with pairs of post-processed diags which are computed together; in
771       particular, re-order list of diags within 1 file to save 2nd computation.
772     - add S/R to compute velocity stream-function (called after velocity-potential
773       calculation) from divergence free transport -> new diagnostics "PsiVEL".
774     - add parameter to select grid-point location where PsiVEL == 0.
775    o eesupp/src:
776       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
777       (specific S/R needed with exch2 topology - for now, just print an error msg)
778    o pkg/shelfice
779     - Implement friction velocity-dependent transfer coefficients following
780       Holland and Jenkins, JPO, 1999
781       Original code by M. Losch with small modifs.
782       Enable with CPP option SHI_ALLOW_GAMMAFRICT
783       and runtime flag SHELFICEuseGammaFrict
784    o verification lab_sea & global_ocean.cs32x15:
785     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
786       does not miss some dependencies (but is slower) and also works with many files
787       (default makedepend limitation for AD built).
788     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
789    o pkg/diagnostics:
790     - add run-time parameter "useMissingValue" (def=False) to fill land-point
791        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
792       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
793     - Extend the use of "missing_value" setting from data.diagnostics for the case
794       of counter-diagnostics (where fraction-weight is zero). This applies both to
795       MNC and MDS output files.
796    o pkg/seaice/seaice_growth.F:
797      - add 'a priori' cap of latent heat flux based on actual mass considerations
798        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
799        non-legacy seaice_solve4temp.
800      - add diagnostic of the residual sublimation freshwater flux (the freshwater
801        flux taken from the ocean if the total actual latent heat fluxes exceed
802        the maximum)
803      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
804       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
805      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
806       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
807      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
808      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
809    o verification 1D_ocean_ice_column:
810       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
811       update results
812    o pkg/diagnostics:
813     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
814       which are not filled-up but computed from other diags ; In this case, the mate
815       diag points to the primary (filled-up) diag to used for post processing.
816     - Update Velocity-potential computation using post-processed diag framework.
817     ==> Change the ordering of fields and time-periods in MDS output file
818       when using periodic averaging: now writes one time record with the full set
819       of fields for this time period, then the next time reccord (it used to be
820       one field with the full set of time records then the next field).
821         Note: this is now similar to NetCDF (MNC) output file. <==
822    
823    checkpoint62z (2011/06/21)
824    o adjoint monitor:
825     - Add adjoint monitor output for packages exf, seaice
826       and update relevant testreport output
827    o pkg/seaice:
828     - re-order diags inits so that they appear in order in available_diagnostics.log
829     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
830       area/heff/hsnow preceeding thermodynamic growth/melt.
831     - modified diag: SIdA; output actual effect, as the description states.
832     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
833     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
834       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
835        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
836     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
837     - added diagnostics for seaice generic tracers (SItr*).
838     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
839     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
840     I. Fenty: 18-Jun-2011:
841     Minor changes to seaice package:
842     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
843        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
844       - Differentiated "regularization variables" from "floor variables"
845        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
846        * hiceMin became SEAICE_hice_reg (old hiceMin)
847          (with _reg meaning regularization variable)
848       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
849        so as to ensure energy conservation when going between phases
850      - A22 was not used anywhere
851     2) Changed regularization procedure for heffActual and hsnowActual to ensure
852        well-boundedness and smooth adjoint in seaice_growth.F
853     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
854        because the old regularization always set heffActual >= 0.05 cm
855     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
856        on AREA when HEFF > 0.
857      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
858        requiring that DISABLE_AREA_FLOOR *not* be defined
859     Affected verifications:
860      - 1D_ocean_ice_column (output.txt output_adm.txt)
861      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
862    o pkg/diagnostics:
863      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
864      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
865        (was _RL, now integer) with option = 0 to retrieve all levels.
866      - add pieces of code to compute velocity potential at each level (new diagnostics
867        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
868        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
869      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
870        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
871        and in diagnostics_fract_fill.F (do not need a valid pointer for the
872        diagnostics counter-mate); check that definition of counter-diagnostic
873        includes a valid counter-mate (in diagnostics_set_levels.F).
874    o model/src (rStar):
875      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
876        affect solution only if z* with full pressure in EOS;
877        update output of test-exp global_ocean.90x40x15.
878    o pkg/seaice:
879      - introduce siEps=1e-5 parameter
880      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
881      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
882      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
883        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
884        as well as ice cover age and ridging index (attached to AREA).
885        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
886        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
887        Up to SItrMaxNum=3 tracers can be used simultaneously.
888    o pkg/salt_plume:
889      -introduce SPsalFRAC run time parameter that sets the fraction of the
890       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
891       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
892    o model debug options:
893      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
894        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
895      - Refine debug-msg printing selection (3 new levels):
896        debugMode  : controls printing of debug messages (sequence of S/R calls).
897        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
898         debLevZero =  0 ; /* level of disabled aux. msg printing */
899         debLevA =  1 ; /* level of minimum  aux. msg printing */
900         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
901         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
902         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
903         debLevE =  5 ; /* level of extensive debug printing */
904        New debugLevel default: with default debugMode value (=F),
905          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
906          and if debugMode=T, default debugLevel = 4 (debLevD).
907        Relation with previous settings:
908         debLevB (=2) corresponds to former debLevA (=1)
909         debLevD (=4) corresponds to former debLevB (=2)
910        Note:
911         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
912         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
913            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
914      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
915        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
916    o pkg/obcs:
917      - change OBCSfixTopo default from True to False (should not change the results);
918        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
919    o pkg/thsice:
920      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
921        2nd layer seaice sublimation (unlikely to happen)
922      - use Interior mask for OBCS in thsice_advection.F (similar to what is
923        done in gad_advection & seaice_advection).
924    o adjoint:
925      bug fix spotted by Gael Forget:
926      seaice_advection and thsice_advection still had
927      legacy CPP options to avoid CS corner updates for adjoint
928    o pkg/seaice:
929      => Change some of the defaults (2011/05/29):
930         - change SEAICEuseFluxForm default (from False to True)
931         - change DIFF1 default (from 0.004 m/s to 0. m/s)
932         And print warnings if DIFF1 is not set in data.seaice and centered
933          avection scheme is used without any diffusion.
934      also:
935      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
936      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
937      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
938        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
939        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
940      update results of test exp.:
941         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
942             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
943             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
944         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
945         seaice_obcs: output (SEAICEuseFluxForm=T)
946      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
947          for standard fwd & AD lab_sea tests (to keep the same output).
948    o pkg/seaice/seaice_growth.F:
949      - use Ian Fenty's capping formulas for actual ice
950      thickness thoughout EVOLUTION branch.
951      - put treatment pathological case #2) in CPP brackets
952      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
953      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
954    o pkg/seaice:
955      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
956      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
957      also pass fac as a param, which can be 1. (to update the tendency
958      field) or the time step (to update the field itself).
959      - seaice_advdiff.F: for multidim, call seaice_diffusion with
960      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
961      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
962      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
963      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
964    o pkg/seaice:
965      diffusion with centered advection scheme (diffus.F & advect.F):
966      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
967        to just compute the laplacian of input-field.
968      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
969      - fix flux-form version in diffus.F to conserve tracer.
970      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
971       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
972    
973    checkpoint62y (2011/05/26)
974    o pkg/seaice:
975     - seaice_growth.F : in EVOLUTION branch, always include
976       a_QSWbyATM_cover in qnet (as it should be).
977     - verification/global_ocean.cs32x15 : update results accordingly
978       (output.seaice.txt output_adm.seaice.txt).
979    o pkg/seaice + obcs:
980     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
981       equivalent of assuming no tracer gradient outside the OB region.
982       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
983     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
984       after changes above);
985     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
986       only at OB location (instead of over a band of OLx width).
987    o pkg/seaice:
988     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
989       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
990    o pkg/obcs:
991      - split header file "OBCS.h" into 4 separated files:
992        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
993       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
994         (contain no conditional statement which depends on OBCS options).
995      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
996        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
997    o ctrl, cost, grdchk & autodiff pkgs:
998      - make options file more standard (like other {PKG}_OPTIONS.h file but
999        with AD_CONFIG.h); clean-up some of the included header files.
1000    o pkg/obcs:
1001      - do not mask tracer when applying OB (tracer == 0 could generate problems)
1002      - apply tracer OB values to tracer field only at OB location (instead of
1003        over a band of OLx width)
1004      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1005      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1006        obcs_apply_tloc.F & obcs_apply_sloc.F
1007    o obcs in model/src:
1008      - call OBCS_APPLY_W only if NonHydrostatic.
1009      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1010      - reset dEtaHdt and wVel to zero outside OB interior region ;
1011      - leave tracer unchanged outside OB interior region: This has no effect
1012        on the solution but just to prevent unrealistic tracer value outside OB.
1013      - zero out velocity outside OB interior region: This has no effect on
1014        the solution but just to prevent unrealistic velocity outside OB.
1015    o obcs and non-lin free-surf:
1016       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1017       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1018       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1019       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1020       update results of test-exp. exp4(nlfs).
1021    o exp4 (nlfs) test-exp:
1022       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1023       with NonLin-FreeSurf); update output.nlfs.txt
1024  o obcs and 2d/3d solver norm:  o obcs and 2d/3d solver norm:
1025     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1026     and outside OB interior region (will allow to place OB further inside the     and outside OB interior region (will allow to place OB further inside the
1027     domain). Depending on the domain, can affects cg2d-Norm (previous     domain). Depending on the domain, can affects cg2d-Norm (previous
1028     cancelation outside OB was only partial), e.g. in exp4 & obcs_ctrl,     cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1029     and cg3d-Norm (previous Norm was computed before canceling OB terms),     and cg3d-Norm (previous Norm was computed before canceling OB terms),
1030     e.g. in tutorial_plume_on_slope.     e.g. in tutorial_plume_on_slope.
1031    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
# Line 20  o pkg/shelfice/shelfice_init_fixed.F Line 1037  o pkg/shelfice/shelfice_init_fixed.F
1037    fix CPP-flag combinations    fix CPP-flag combinations
1038  o pkg/seaice: Merge iceage code of Pierre Rampal  o pkg/seaice: Merge iceage code of Pierre Rampal
1039    * update/change/correct ice age calculations    * update/change/correct ice age calculations
1040    * add age updates for pathological cases    * add age updates for pathological cases
1041    Probably needs more testing...    Probably needs more testing...
1042    
1043  checkpoint62x (2011/05/13)  checkpoint62x (2011/05/13)
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