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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1603 by dimitri, Fri Mar 2 01:45:22 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 added pkg/frazil - see frazil_description.tex for details
8    o pkg/shelfice/shelfice_thermodynamics.F
9      - fix exponents for velocity dependent exchange coefficients: change
10        from 2/3(=0) to 0.66666666666666667
11      - move computation of velocity dependent exchange coefficients into
12        separate loop, so that it applies to both thermodynamics
13      - move some divisions by constants out of loops
14    
15    checkpoint63j (2012/02/16)
16    o pkg/seaice:
17      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
18      - SItracer:  added run time params, and allow coupling to ocn salinity.
19    o pkg/seaice: remove (almost) all divisions by constants within loops
20      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
21      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
22      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
23      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
24    o pkg/seaice :
25      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
26        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
27      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
28      - add permanent SItflux diag that corresponds to TFLUX but includes
29        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
30      - allow activation/testing of a fix for suspected missing term in
31        ocn-ice heat budget (to be confirmed). To test this, you want to
32        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
33        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
34      - no change in results, fwd or ad.
35    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
36      - switch to variable freezing point.
37           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
38      - bug fix : the sublimation term that was missing is now activated.
39           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
40      - bug fix : flooding sign term for SIsal0.NE.0.
41           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
42    o pkg/seaice:
43      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
44        is now the default, and the old default constant freezing point is recovered
45        with SEAICE_tempFrz0    = -1.96,
46             SEAICE_dTempFrz_dS = 0.,
47      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
48      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
49      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
50        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
51      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
52        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
53      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
54        seaice_growth r149 for legacy branch (no results change).
55      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
56        from I. Fenty).
57      - results did not change except for global_ocean.cs32x15, mostly due to the
58        switch to variable freezing point (see above item for detail).
59    o pkg/thsice:
60      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
61        seawater freezing in thsice_calc_thickn (not used).
62    o pkg/seaice: turbulent flux term specification via run time params.
63      - replace CPP switches with run time switches to facilitate testing
64      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
65                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
66      - added runtime parameter : SEAICEturbFluxFormula
67      - move Mcphee constants to SEAICE_PARAMS.h
68      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
69                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
70                 remove seaice_summary call (moved to seaice_init_fixed)
71      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
72        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
73      - seaice_summary.F : add missing report of read turbulent flux term set up
74                           and SITRACER.
75      - seaice_check.F : check range; inform and stop if retired CPPs are used
76                         (incl. SEAICE_AGE).
77      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
78             CPP switch, same computation as before for the different options.
79      - change results at the truncation level.
80    o pkg/seaice:
81      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
82        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
83        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
84      - update verification/*/input*/data.seaice:
85        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
86        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
87        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
88        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
89    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
90      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
91        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
92        difference in results only due to machine truncation.
93      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
94        MaykutPolySatVap; keep MIN_LWDOWN.
95      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
96      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
97        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
98    o pkg/salt_plume:
99      - isolate saltPlumeFlux array exch into a specific S/R called from
100        do_oceanic_phys.F
101      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
102    o verification:
103      - move untested set-up to MITgcm_contrib/verification_other.
104    o pkg/seaice:
105      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
106    o pkg/seaice:
107      - seaice_solve4temp.F (keeping results unchanged):
108        * add 2 future run-time params to select which saturation vapor pressure
109          formula is used and how post-iteration fluxes are set.
110          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
111        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
112          the linearized expression to stay consistent with tsurf finding.
113      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
114        can be < 0.
115    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
116      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
117        conductive heat flux F_c , and add it explicitly when updating tsurf as
118        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
119        so that now F_ia has a consistent meaning through the entire routine.
120        This causes differences at truncation level: update output of fwd exp.
121        global_ocean.cs32x15.seaice.
122    o pkg/seaice:
123      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
124        of arrays, sign/direction of fluxes; no effect on results.
125      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
126        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
127        note: this should have been done before changing celsius2K default.
128      - to keep results unchanged, add back old value of celsius2K in verification
129        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
130      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
131        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
132        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
133        freezing temp is consistent with value in seaice_growth.F ; this causes
134        differences at machine truncation level: update lab_sea AD output (3/4).
135    o pkg/seaice:
136      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
137        and climsst/sss even when using seaice (to prevent calculation that might
138        use SST on land); does not affect any verification exp.
139      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
140        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
141    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
142      over land (non-legacy code)
143    o vectorize salt_plume package:
144      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
145      - this code computes plumebk everywhere (also over land), thus requires
146        code to avoid divisions by zero and catch the case of kLev=Nr.
147      - efficiency of salt_plume_frac is still sub-optimal
148    o tools (genmake2):
149      - fix makefile NAME specification (option: -makefile NAME) by adding
150        "-f $MAKEFILE" in few places where it was missing including makedepend
151        command (contribution from Paul).
152    
153    checkpoint63i (2012/01/24)
154    o model/src:
155      - add factorized versions of some EOS code to find_rho.F,
156        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
157    o model/src:
158      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
159      - change default celsius2K from 273.16 to 273.15
160      - to keep results unchanged, add back old value of celsius2K in verification
161        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
162         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
163    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
164      to make TAF generate vectorizable code
165    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
166       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
167       have flags that do this more efficiently.
168    o pkg/diagnostics/diagstats_calc.F
169      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
170    o pkg/obcs (with exch2):
171      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
172        and remove code (in obcs_readparms.F) which was based on EXCH of indices
173        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
174    o pkg/exf and seaice exp:
175      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
176        so that switching off area & heff advection flags does not affect results.
177      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
178      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
179        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
180        results of verification experiments: 1D_ocean_ice_column(fwd),
181        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
182        and offline_exf_seaice (all 4).
183    o pkg/seaice:
184      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
185        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
186      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
187        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
188        not multi-dim advection;
189      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
190        SHORTWAVE_HEATING #undef.
191    o optim: make Makefile more robust (?)
192    o pkg/obcs:
193      * fix treatment of obcs_read_pickup for TAF
194    o pkg/shelfice:
195      * add missing initialisation of num_shifwflx
196      * new adjoint verification exp. for isomip
197      * change Prandtl and Schmidt numbers from generic formulations
198        (in terms of model diffus. and visc.) to separate runtime
199        parameters, with Holland and Jenkins (1999) default values.
200    o pkg/exf (interpolation):
201      - extended input field (2 rows) near the N & S poles:
202        * fill in with the symetric value (when even Nb of data in longitude)
203        * add average value at the poles only for scalar quantities ; for vector
204          component interpolation, skip the averaging and keep duplicated values,
205          unless the 2 components have same location (uvInterp=T) in which case
206          interpolate the 2 components together using S/R EXF_INTERP_UV.
207      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
208        together: this allows to account properly for local orientation when
209        averaging at N & S pole.
210      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
211        exf-interpolation near N & S poles. Undef by default.
212      - add debug check/print on 1rst iter if debugLevel >=2.
213    o pkg/exf:
214      - change masking flags definition (no longer "parameter"), put them in
215        common block and set them in S/R EXF_INIT_FIXED.
216      - change recognized masking flag from s,u,v to c,w,s since the mask
217        to use (maskC,W,S) depends on position on model grid and has little to
218        do with scalar/vector difference; fix masking if using P-coordinates.
219      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
220        and update results of exp. global_with_exf (x2).
221      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
222    o pkg/obcs
223      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
224    o pkg/exf (interpolation):
225      - assume periodicity in X only if input field cover full longitude range.
226      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
227        and should vectorise).
228      - fix input lat of the 2 added row (in case we provide N.pole data).
229    
230    checkpoint63h (2011/12/30)
231    o pkg/seaice:
232      - change declaration of UVM from _RL to _RS in order to get B-grid
233        uIce,vIce monitor when _RS = real*4
234    o pkg/offline:
235      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
236      - compute vertical velocity if not read from file (switch on exactConserv
237        & staggerTimeStep);
238      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
239    o verification:
240      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
241        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
242        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
243      - update output of exp. global_ocean.cs32x15.viscA4 after changing
244        grid-file angles (used here for coriolis-3d);
245      - remove (or gzip) few files not needed to run fizhi-cs experiments.
246    o pkg/exf (vector interpolation):
247      - rotate vector component toward local grid-axis orientation using grid-angles
248        (stored in GRID.h) instead of locally computed rotation angle; keep old code
249        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
250    o pkg/seaice:
251      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
252        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
253    o pkg/PKG_OPTIONS.h files:
254      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
255        outside of the #ifdef ALLOW_THISPKG / #endif block.
256      - update verification/*/code/PKG_OPTIONS.h files.
257    o add a verification experiment (offline_exf_seaice/input.seaice) that test
258      the B-grid LSOR solver
259    o pkg/seaice: sort out emissivity and long wave radiation step 2:
260      - add emissivity for snow and ice as new run-time parameters
261        (unfortunately) that default to the corresponding exf values; this
262        changes results in most verification experiments so that for backward
263        compatibility these parameter have to be set explicitly to inconsistent
264        values (ugly);
265      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
266        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
267        until we agree how to handle this bug properly
268    o pkg/exf (interpolation):
269      - add a set of run-time param ({inputfield}_interpMethod), one for
270        each interpolated input field, to select the interpolation method
271        with a value of zero switching off the interpolation;
272      - print interpolation parameters to standard output;
273      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
274        (to use instead runoff_interpMethod=0 in data.exf).
275      - simplify default setting of interpolation parameters (for all fields,
276        set position to match model grid cell-center position, leading to trivial
277        interpolation in case of regular Lat-Lon grid) and fix for the case of
278        non-uniform delY.
279    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
280       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
281       this factor is absolutely required, because the lw exitance (= out-going
282       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
283       where the reflectivity rho = 1-emissivity for conservation reasons. Once
284       this is established, we can remove the CPP-Flag (if we want to).
285    o pkg/seaice:
286      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
287        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
288      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
289        what the name implies (and not emissivity*BoltzmannConstant), this means
290        the old default value of 5.5e-8 now means
291        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
292        S/R exf_readparms
293      - FV-discretization of the B-grid LSOR solver, turn on with
294        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
295        of the calling routine dynsolver, so that B and C-grid code look a
296        little more alike.
297      - fix index bugs in ostres.F (B-grid code)
298    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
299    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
300      default for SEAICE_emissivity, if useEXF; requires setting a wrong
301      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
302      backward compatiblity
303    o model/src: use sigmaR in calc_ivdc
304    
305    checkpoint63g (2011/12/16)
306    o pkg/seaice/seaice_growth.F:
307      fix heat conservation of the coupled ocean-seaice system.
308      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
309      solid vs liquid water treatment is resolved via QNET.
310    o pkg/seaice/seaice_growth.F:
311      add missing term for sublimation in saltFlux, which was breaking conservation.
312    o pkg/seaice/seaice_model.F:
313      Remove this patholigical case treatment in evolution branch,
314      where it is un-necessary and breaks conservation.
315      Update global_ocean.cs32x15/results accordingly for
316      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
317    o model/src:
318      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
319      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
320    o pkg/obcs:
321      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
322      tendency for temperature and salinity that is then applied to update
323      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
324      horizontal advection and diffusion contributions on the boundary (in
325      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
326      removing the mask in S/R timestep_tracer. The advantage of this approach is
327      that the updated tracer values include contributions from the surface
328      forcing and vertical diffusion.
329      This modification changes exp4.stevens because of vertical diffusion.
330    o model/src:
331      change non-curvilinear grid setting to also work with exch2 + blank tiles:
332      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
333        face dimensions.
334      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
335        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
336        and INI_SPHERICAL_POLAR_GRID.
337      change test-experiment global_ocean.90x40x15:
338      - split the domain in many more tiles (9x4 tiles of 10x10 each);
339      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
340      - update results of both test (std & dwnslp).
341    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
342       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
343    o model/src:
344      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
345        and fix initialisation when using sigma-coords.
346    o model/src:
347     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
348       to their current value at the beginning of forward_step.F": add a new run-time
349       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
350     - set doResetHFactors=T in the following test exp:
351        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
352        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
353        and tutorial_global_oce_in_p (nonLinFS in p)
354    o pkg/ecco
355      - added IES cost term
356    o verification/advect_xz
357      - scale down the depth by 1/100 (from 200 km to just 2.km)
358      - add secondary test using divergent flow, r-star and implicit vertical advection.
359      - add note (check_conserve_TS.txt) and matlab script to check global
360        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
361    o pkg/rbcs:
362      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
363    o pkg/obcs (Stevens BCs):
364      - fix various problems in the phase speed computations of the Stevens
365        boundary conditions:
366        - sign error for western and southern boundaries,
367        - time tendencies were underestimated by factor of dTracerLev and some just
368          zero (for multidim advection schemes) -> now estimate time tendencies
369          from difference between previous (n) time level and the one before (n-1);
370          this requires storing a field per tracer per boundary, also in the pickup
371          files.
372        - replace deltaTmom in cflMer/Zon computation with dTracerLev
373        - set default phase velocity to cflMer/Zon
374      - update verification experiment exp4.stevens
375    o pkg/generic_advdiff (implicit_r):
376      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
377        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
378      - fix implicit vertical diffusion or advection with NonLin FreeSurf
379        (was using current recip_hFacC instead of future recip_hFacC): set future
380        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
381        solver S/R ;
382      - fill diagnostics of vertical advective fluxes (computed from tendency)
383        when using implicit vert. advection;
384      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
385         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
386         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
387         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
388    o pkg/diagnostics:
389      - add diags for T & S tendency which goes through Adams-Bashforth.
390    
391    checkpoint63f (2011/11/30)
392    o pkg/obcs/obcs_calc_stevens.F:
393      - join some loops to reduce number of if-statements
394      - fix a bug in code for northern and southern boundaries.
395    o pkg/seaice/seaice_init_varia.F
396      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
397        caused zero ice-velocities for the B-grid code
398    o pkg/seaice/seaice_init_fixed.F
399      - fix a bug in the initialisation of the second metric terms
400        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
401      - this affects all seaice configurations with useCurviLinearGrid = .true.
402        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
403        = .true. (default)
404      - the only verification experiment affected is global_ocean.cs32x15:
405        icedyn, seaice, and seaice_dynmix (AD)
406    o pkg/thsice/thsice_diagnostics_state.F
407      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
408        not contain garbage that can lead to surprises in diagstats_calc.F
409    o model/src:
410      - move bi,bj loops inside INTEGR_CONTINUITY ;
411      - call INTEGR_CONTINUITY directly from forward_step.F
412        (previously called from momentum_correction_step.F)
413      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
414        forward_step.F and pkg/ecco/the_main_loop.F
415    o model/src/do_oceanic_phys.F:
416      - reset addMass to zero only if useICEFRONT ;
417      - separated k-loop for rhoInSitu calculation ;
418      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
419        and at constant T,S (= WdRHOdP);
420      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
421        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
422        transport of locally-referenced potential density);
423        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
424    o gluemnc:
425      - replace ncrcat with ncks when adding variables to *.glob.nc
426      - change the way variables without record dimensions are handled so that
427        files that have variables with and without record variables can be glued:
428        add a record dimension with a new unique name to be able to differentiate
429        between variable with and without a-prior record dimensions. Remove
430        this record dimension before adding the variable to the *.glob.nc file.
431        This procedure automatically works also for grid.*.nc files that do not
432        have any record dimension.
433    o verification/cpl_aim+ocn:
434      - generate new reference output on baudelaire (gfortran, mpich2) (previously
435        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
436    o pkg/obcs/obcs_calc_stevens.F:
437      - add code for northern and southern boundaries.
438      - reorder some loops to save some operations and so that drFBar can be scalar
439    o model/src:
440      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
441        truncation) and add diagnostics for Adams-Bashforth tendency increment.
442      - update test-exp. AD output:
443        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
444      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
445        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
446        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
447        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
448        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
449        tutorial_plume_on_slope.
450    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
451      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
452      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
453      does not even come with an F77 compiler anymore, this should not be
454      a limitation
455    
456    checkpoint63e (2011/11/06)
457    o pkg/seaice adjoint of LSR:
458      - substantially rework STORE dirs.
459      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
460        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
461        and only perform SOLV_MAX_FIXED adjoint iters.
462        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
463        always goes to same record, meaning that the last forward field will be
464        the one used in the adjoint - an approximation.
465      - now produces non-zero LSR-related gradients, and acceptable gradients for
466        An's zonal (x-z) test case (to be checked in)
467      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
468        (but these are screwed up by the thermodynamics in the first place);
469        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
470        output_adm.txt also reflects changes to seaice_lsr
471      - global_ocean.cs32x15:
472        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
473          (output_adm.seaice.txt was updated)
474        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
475          (output_adm.seaice_dynmix.txt)
476    o test-exp. exp4+stevens:
477      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
478    o pkg/seaice (lsr solver):
479      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
480        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
481      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
482      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
483        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
484      - compute (with new S/R) and print initial (+ free-driff sol. if available)
485        and final residual of linearised system.
486    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
487      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
488    o pkg/obcs: Stevens BCs (still only for east and west)
489      - fix Stevens BCs by using intermediate velocities of previous
490        time step as "baroclinic" contribution rather velocity of one grid cell
491        inside the boundaries; more consistent but makes the entire treatment
492        more complicated, requires new pickup files and two new S/Rs:
493        obcs_copy_uv_n and obcs_save_uv_n
494        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
495        (undefined by default)
496      - silently move computation of some grid factors into separate loops to
497        save some recomputations
498      - add a hack for non-linear free surface
499      - add a verification experiment to exp4 that tests this code
500    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
501    
502    checkpoint63d (2011/10/25)
503    o pkg/obcs + seaice-dynamics:
504      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
505        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
506        values (consistent with an implicit method).
507      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
508        return to older implementation (same results as before); note that none of
509        the "experimental" OBCS_SEAICE options are implemented in the new version.
510      - switch test exp. seaice_obcs to use new version (update output).
511    o pkg/seaice:
512      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
513      - add parenthesis in Water-Ice drag calculations (evp & lsr);
514      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
515        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
516      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
517        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
518    o pkg/layers:
519      - Include potential density as new coordinate (Thanks to David Munday)
520    o pkg/dic:
521      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
522        carbonate computation/output to CALC_PCO2_APPROX
523    o pkg/generic_advdiff
524      - make TAF generate code that vectorizes:
525        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
526    o model/src:
527      - improve vectorization also for adjoint code of
528        solve_tridiagonal and solve_pentadiagonal. As this requires up to
529        5 new 3D-fields, this code is only turned on for the combination of
530        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
531        for singular matrix check (only for TARGET_NEC_SX).
532      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
533        ALLOW_AUTODIFF. This flag now needs to be set outside of
534        solve_tri/pentadiagonal.F
535    o pkg/exf:
536      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
537        optional namelist EXF_NML_OBCS).
538      - add many debug-print (to trace down where pkg/cal error msg comes from)
539    o pkg/mom_vecinv/mom_vi_hdissip.F
540      - rearrange loops so that vectorization is improved and in particular
541        the adjoint routine vectorizes. The code is a little longer now, but I
542        think easier to read.
543        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
544    o pkg/seaice:
545      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
546    o pkg/exch2:
547      - alternative code (without tile x tile matrix) for cumulated (global) sum;
548        used as default; keep using matrix version in adjustment.cs-32x32x1.
549    o tools/build_options:
550      - after merging some MPI and/or multi-threads specific optfiles so that
551        the modified default optfile support both built (using genmake2 -mpi
552        for the MPI built, using genmake2 -omp for OpenMP built),
553        move now obsolete optfiles to tools/build_options/unsupported/
554       (add copy of email sent to support list in doc/optfiles_changes.txt)
555    
556    checkpoint63c (2011/09/28)
557    o pkg/ebm:
558      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
559        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
560    o pkg/seaice (SItracer pickup)
561    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
562      To be done:
563      - thorough testing of missing fields in S/R seaice_read_pickup
564      - thorough matching between generic tracers and specific fields used
565        (e.g. volume-weighted age, area-weighted age, salinity, ...)
566    o pkg/grdchk:
567      - all procs calculate and print finite-difference gradient (for testreport)
568      - change description output used by testreport;
569      - AD testing: also compare and report Finite-difference gradient;
570        => update all output_adm*.txt
571    o test exp. global_ocean_ebm:
572      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
573        and turn on exactConserve; update (fwd) output.
574    o pkg/seaice (LSR):
575      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
576      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
577        * identical results with non-CS topology (but save up to half of EXCH calls)
578        * no much changes in cs-32 verification tests since no ice at face edges
579         (differences due to convergence criteria, since nb of iterations changed)
580        * expect some differences on lat-lon-cap grid.
581        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
582    o pkg/exch2:
583      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
584        many tiles); until alternative coding is added, just add a stop.
585    o pkg/kpp:
586      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
587        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
588    o optfiles:
589      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
590        into corresponding standard one, which now support different build:
591        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
592      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
593    o pkg/obcs (seaice):
594      - add missing EXCH for uIce,vIce after applying OBCS;
595      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
596        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
597        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
598      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
599      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
600        and eedata.mth for MPI and mutlti-threaded testing.
601    o pkg/flt:
602      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
603      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
604      - fix pickup and trajectories + profiles output with multi-threads;
605      - add parameter to select group of fields to write along trajectory and
606        profile (default unchanged);
607      - only call PORT_RAND* function when flt_noise <> 0;
608      - add multi-threaded test for verification exp. flt_example.
609    o eesupp/src:
610      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
611      - USE_OMP_THREADING: check that number of threads (from eedata) matches
612        actual number (from env.var. setting).
613    o pkg/ebm:
614      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
615      - add multi-threaded test for verification exp. global_ocean_ebm
616    
617    checkpoint63b (2011/08/29)
618    o pkg/ebm:
619      - fix sign of runoff;
620      - update directly forcing fields (Qnet,EmPmR) to use standard
621        external_forcing_surf.F (remove ebm_forcing_surf.F);
622      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
623      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
624        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
625      - update global_ocean_ebm parameters file data and update output (fwd+ad).
626    o verification/matrix_example:
627      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
628        MPI and mutlti-threaded testing.
629    o pkg/matrix:
630      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
631      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
632      - fix for multi-threaded (remove DATA statement);
633      - use standard DIFFERENT_MULTIPLE function;
634      - add MATRIX_OPTIONS.h
635    o verification/matrix_example:
636       To allow to split the domain in several tiles, change the domain size
637        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
638        Western side) of land points.
639    o (*_)write_pickup:
640      - fix few bugs in mypackage_read/write_pickup.F
641      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
642        array of length 1 (was caught by compiler syntax-check).
643    o pkg/diagnostics (velocity potential solver):
644      - fix initialisation of main diagonal matrix (for overlap values)
645    o tools/build_options:
646      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
647        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
648      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
649        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
650        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
651        and use "-devel" testreport option for standard testing on baudelaire.
652    o pkg/grdchk:
653      - Assume that all gradient-check position are within the same tile
654        corresponding to global indices (iGloTile,jGloTile) and that
655        positions (i,j indices or nbeg) are local to this tile;
656      - set tile local-indices and proc. number according to tile global-indices;
657      - remove grdchkwhichproc from namelist (retired param);
658      - send adjoint gradient to all procs so that all procs print it to STDOUT;
659      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
660    o adding package bbl (Bottom Boundary Layer)
661      description in MITgcm/pkg/bbl/bbl_description.tex
662      example/test experiment in MITgcm_contrib/bbl
663    o adjoint verifications
664      - changed 5 experiments to multi-tiles
665        * global_ocean.90x40x15
666        * obcs_ctrl
667        * offline_exf_seaice
668        * tutorial_dic_adjoffline
669        * tutorial_tracer_adjsens
670        changed reference output for those that crossed tile boundaries
671        (changed choices of gradient check positions)
672      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
673      - temporary bug fix in grdchk_loc.F for obcs
674    o genmake2 & testreport
675      - add target "obj" (just for OBJFILES files) to Makefile;
676      - add option to specify FEXTRAFLAGS on command line.
677    o pkg/mypackage:
678      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
679    
680    checkpoint63a (2011/08/02)
681    o pkg/diagnostics (velocity potential):
682      - fix velocity-potential calculation when using OBCS: balance net inflow
683        at each level (new S/R OBCS_DIAG_BALANCE).
684      - fix some of the problems with OBCS in stream-function calculation.
685    o pkg/exf/exf_readparms.F
686      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
687        EXF_NML_OBCS) more consistent, so that you need not have these lists
688        in data.exf when they are not used.
689    o optim/optim_readdata.F:
690      - add some output about obcs variables that might help debugging
691      - add a check about nvarlength
692    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
693    o pkg/diagnostics (velocity potential):
694      - fix mask for OBCS (still problems in stream-function with OBCS);
695      - add specific parameter (default = main code CG2D params) for solver;
696      - in case of poor convergence, use solution corresponding to lowest residual.
697    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
698      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
699      and should be avoided where possible.
700    o model/src (rStar):
701      - include r* effect on reference-state (PhiRef) in totPhiHyd
702        (so that it's really the potential anomaly at the cell center);
703        affect solution only if z* with full pressure in EOS.
704      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
705        update output (because of z* in totPhiHyd and viscA4 changes);
706      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
707        @ constant r) until interpolation at constant r is implemented.
708    o pkg/diagnostics
709      - fix RCENTER diagnostics in case cell center is not at interface middle
710    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
711      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
712      that THETA and SALT are "conservative temperature" and "absolute
713      salinity"
714    o pkg/ctrl
715      - fix computation of endrec in s/r ctrl_init_rec
716      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
717    o pkg/seaice/seaice_growth.F
718      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
719        remove then obsolete STORE directives
720      - fix STORE directives for tice and tices, so that only the
721        appropriate part of the fields are stored (and not the entire
722        field); update global_ocean.cs32x15.seaice AD output.
723      - cosmetic changes: adjust CPP flags and indentation for better
724        legibilty
725    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
726      Chris Wilson)
727    o pkg/gmredi:
728       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
729       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
730    
731    checkpoint63  (2011/07/11)
732    o pkg/exch2:
733     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
734     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
735       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
736       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
737    o pkg/diagnostics:
738     - deal with pairs of post-processed diags which are computed together; in
739       particular, re-order list of diags within 1 file to save 2nd computation.
740     - add S/R to compute velocity stream-function (called after velocity-potential
741       calculation) from divergence free transport -> new diagnostics "PsiVEL".
742     - add parameter to select grid-point location where PsiVEL == 0.
743    o eesupp/src:
744       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
745       (specific S/R needed with exch2 topology - for now, just print an error msg)
746    o pkg/shelfice
747     - Implement friction velocity-dependent transfer coefficients following
748       Holland and Jenkins, JPO, 1999
749       Original code by M. Losch with small modifs.
750       Enable with CPP option SHI_ALLOW_GAMMAFRICT
751       and runtime flag SHELFICEuseGammaFrict
752    o verification lab_sea & global_ocean.cs32x15:
753     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
754       does not miss some dependencies (but is slower) and also works with many files
755       (default makedepend limitation for AD built).
756     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
757    o pkg/diagnostics:
758     - add run-time parameter "useMissingValue" (def=False) to fill land-point
759        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
760       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
761     - Extend the use of "missing_value" setting from data.diagnostics for the case
762       of counter-diagnostics (where fraction-weight is zero). This applies both to
763       MNC and MDS output files.
764    o pkg/seaice/seaice_growth.F:
765      - add 'a priori' cap of latent heat flux based on actual mass considerations
766        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
767        non-legacy seaice_solve4temp.
768      - add diagnostic of the residual sublimation freshwater flux (the freshwater
769        flux taken from the ocean if the total actual latent heat fluxes exceed
770        the maximum)
771      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
772       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
773      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
774       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
775      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
776      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
777    o verification 1D_ocean_ice_column:
778       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
779       update results
780    o pkg/diagnostics:
781     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
782       which are not filled-up but computed from other diags ; In this case, the mate
783       diag points to the primary (filled-up) diag to used for post processing.
784     - Update Velocity-potential computation using post-processed diag framework.
785     ==> Change the ordering of fields and time-periods in MDS output file
786       when using periodic averaging: now writes one time record with the full set
787       of fields for this time period, then the next time reccord (it used to be
788       one field with the full set of time records then the next field).
789         Note: this is now similar to NetCDF (MNC) output file. <==
790    
791    checkpoint62z (2011/06/21)
792    o adjoint monitor:
793     - Add adjoint monitor output for packages exf, seaice
794       and update relevant testreport output
795    o pkg/seaice:
796     - re-order diags inits so that they appear in order in available_diagnostics.log
797     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
798       area/heff/hsnow preceeding thermodynamic growth/melt.
799     - modified diag: SIdA; output actual effect, as the description states.
800     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
801     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
802       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
803        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
804     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
805     - added diagnostics for seaice generic tracers (SItr*).
806     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
807     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
808     I. Fenty: 18-Jun-2011:
809     Minor changes to seaice package:
810     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
811        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
812       - Differentiated "regularization variables" from "floor variables"
813        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
814        * hiceMin became SEAICE_hice_reg (old hiceMin)
815          (with _reg meaning regularization variable)
816       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
817        so as to ensure energy conservation when going between phases
818      - A22 was not used anywhere
819     2) Changed regularization procedure for heffActual and hsnowActual to ensure
820        well-boundedness and smooth adjoint in seaice_growth.F
821     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
822        because the old regularization always set heffActual >= 0.05 cm
823     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
824        on AREA when HEFF > 0.
825      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
826        requiring that DISABLE_AREA_FLOOR *not* be defined
827     Affected verifications:
828      - 1D_ocean_ice_column (output.txt output_adm.txt)
829      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
830    o pkg/diagnostics:
831      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
832      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
833        (was _RL, now integer) with option = 0 to retrieve all levels.
834      - add pieces of code to compute velocity potential at each level (new diagnostics
835        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
836        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
837      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
838        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
839        and in diagnostics_fract_fill.F (do not need a valid pointer for the
840        diagnostics counter-mate); check that definition of counter-diagnostic
841        includes a valid counter-mate (in diagnostics_set_levels.F).
842    o model/src (rStar):
843      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
844        affect solution only if z* with full pressure in EOS;
845        update output of test-exp global_ocean.90x40x15.
846    o pkg/seaice:
847      - introduce siEps=1e-5 parameter
848      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
849      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
850      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
851        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
852        as well as ice cover age and ridging index (attached to AREA).
853        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
854        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
855        Up to SItrMaxNum=3 tracers can be used simultaneously.
856    o pkg/salt_plume:
857      -introduce SPsalFRAC run time parameter that sets the fraction of the
858       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
859       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
860    o model debug options:
861      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
862        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
863      - Refine debug-msg printing selection (3 new levels):
864        debugMode  : controls printing of debug messages (sequence of S/R calls).
865        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
866         debLevZero =  0 ; /* level of disabled aux. msg printing */
867         debLevA =  1 ; /* level of minimum  aux. msg printing */
868         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
869         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
870         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
871         debLevE =  5 ; /* level of extensive debug printing */
872        New debugLevel default: with default debugMode value (=F),
873          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
874          and if debugMode=T, default debugLevel = 4 (debLevD).
875        Relation with previous settings:
876         debLevB (=2) corresponds to former debLevA (=1)
877         debLevD (=4) corresponds to former debLevB (=2)
878        Note:
879         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
880         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
881            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
882      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
883        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
884    o pkg/obcs:
885      - change OBCSfixTopo default from True to False (should not change the results);
886        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
887    o pkg/thsice:
888      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
889        2nd layer seaice sublimation (unlikely to happen)
890      - use Interior mask for OBCS in thsice_advection.F (similar to what is
891        done in gad_advection & seaice_advection).
892    o adjoint:
893      bug fix spotted by Gael Forget:
894      seaice_advection and thsice_advection still had
895      legacy CPP options to avoid CS corner updates for adjoint
896    o pkg/seaice:
897      => Change some of the defaults (2011/05/29):
898         - change SEAICEuseFluxForm default (from False to True)
899         - change DIFF1 default (from 0.004 m/s to 0. m/s)
900         And print warnings if DIFF1 is not set in data.seaice and centered
901          avection scheme is used without any diffusion.
902      also:
903      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
904      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
905      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
906        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
907        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
908      update results of test exp.:
909         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
910             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
911             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
912         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
913         seaice_obcs: output (SEAICEuseFluxForm=T)
914      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
915          for standard fwd & AD lab_sea tests (to keep the same output).
916    o pkg/seaice/seaice_growth.F:
917      - use Ian Fenty's capping formulas for actual ice
918      thickness thoughout EVOLUTION branch.
919      - put treatment pathological case #2) in CPP brackets
920      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
921      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
922    o pkg/seaice:
923      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
924      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
925      also pass fac as a param, which can be 1. (to update the tendency
926      field) or the time step (to update the field itself).
927      - seaice_advdiff.F: for multidim, call seaice_diffusion with
928      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
929      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
930      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
931      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
932    o pkg/seaice:
933      diffusion with centered advection scheme (diffus.F & advect.F):
934      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
935        to just compute the laplacian of input-field.
936      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
937      - fix flux-form version in diffus.F to conserve tracer.
938      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
939       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
940    
941    checkpoint62y (2011/05/26)
942    o pkg/seaice:
943     - seaice_growth.F : in EVOLUTION branch, always include
944       a_QSWbyATM_cover in qnet (as it should be).
945     - verification/global_ocean.cs32x15 : update results accordingly
946       (output.seaice.txt output_adm.seaice.txt).
947    o pkg/seaice + obcs:
948     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
949       equivalent of assuming no tracer gradient outside the OB region.
950       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
951     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
952       after changes above);
953     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
954       only at OB location (instead of over a band of OLx width).
955    o pkg/seaice:
956     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
957       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
958    o pkg/obcs:
959      - split header file "OBCS.h" into 4 separated files:
960        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
961       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
962         (contain no conditional statement which depends on OBCS options).
963      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
964        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
965    o ctrl, cost, grdchk & autodiff pkgs:
966      - make options file more standard (like other {PKG}_OPTIONS.h file but
967        with AD_CONFIG.h); clean-up some of the included header files.
968    o pkg/obcs:
969      - do not mask tracer when applying OB (tracer == 0 could generate problems)
970      - apply tracer OB values to tracer field only at OB location (instead of
971        over a band of OLx width)
972      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
973      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
974        obcs_apply_tloc.F & obcs_apply_sloc.F
975    o obcs in model/src:
976      - call OBCS_APPLY_W only if NonHydrostatic.
977      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
978      - reset dEtaHdt and wVel to zero outside OB interior region ;
979      - leave tracer unchanged outside OB interior region: This has no effect
980        on the solution but just to prevent unrealistic tracer value outside OB.
981      - zero out velocity outside OB interior region: This has no effect on
982        the solution but just to prevent unrealistic velocity outside OB.
983    o obcs and non-lin free-surf:
984       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
985       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
986       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
987       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
988       update results of test-exp. exp4(nlfs).
989    o exp4 (nlfs) test-exp:
990       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
991       with NonLin-FreeSurf); update output.nlfs.txt
992    o obcs and 2d/3d solver norm:
993       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
994       and outside OB interior region (will allow to place OB further inside the
995       domain). Depending on the domain, can affects cg2d-Norm (previous
996       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
997       and cg3d-Norm (previous Norm was computed before canceling OB terms),
998       e.g. in tutorial_plume_on_slope.
999      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1000    o pkg rbcs:
1001      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1002      - add capability to apply relaxation to horizontal velocity uVel & vVel.
1003    o pkg/grdchk: add gradient check for control variable xx_shifwflx
1004    o pkg/shelfice/shelfice_init_fixed.F
1005      fix CPP-flag combinations
1006    o pkg/seaice: Merge iceage code of Pierre Rampal
1007      * update/change/correct ice age calculations
1008      * add age updates for pathological cases
1009      Probably needs more testing...
1010    
1011    checkpoint62x (2011/05/13)
1012    o pkg/mom_vecinv:
1013       high-order vorticity scheme: use interior masks (maskInW & S)
1014       to zero-out (outside OB) gradient of vorticity.
1015    o verification exp.:
1016       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1017       hs94.128x64x5 and seaice_obcs ; update results.
1018    o pkg/obcs:
1019      fix bug in OBeta for YZ sections in obcs_exf_load.F
1020    o pkg/ctrl, pkg/shelfice, and optim:
1021      - add new control variable xx_shifwflx (fresh water flux underneath ice
1022        shelves). This is almost as tedious as obcs-ctrl, because the
1023        variables needs its own mask.
1024      - add a cost function term that penalizes the deviation of xx_shifwflx
1025        from the first guess (zero) in analogy to other control variables
1026    o pkg/shelfice:
1027      - start basic adjoint
1028    o pkg/ctrl:
1029      - remove extra 2D field "for good measure" when initializing in
1030        ctrl_set_globfld_[xy/xz/yz].F
1031      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1032      - improve error messages in ctrl_set_unpack_*
1033    o OBC implementation in momentum:
1034       use interior masks (maskInC,W & S) in momentum S/R:
1035       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1036       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1037       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1038       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1039       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1040        (and also with Leith/Smagorinsky harmonic-viscosity).
1041       Update output of experiment dome and exp4 (+nlfs).
1042    o exp4 test-exp:
1043      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1044        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1045        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1046        time-varying OB at Western-side for wVel (NonHyd); update output.
1047      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1048        and biharmonic-viscosity ; also use prescribed time varying OB.
1049    o pkg/obcs:
1050      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1051    o model/src:
1052      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1053      - initialise startTime & nIter0 with unlikely values: allows to set one
1054        from the other without ambiguity.
1055    o seaice_obcs test-exp.:
1056      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1057    o pkg/obcs:
1058      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1059        no longer needed with maskInC,W,S in pkg/generic_advdiff.
1060    o pkg/seaice:
1061      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1062        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1063      - fixed bug in the initialization of sea ice salinity variable HSALT
1064        in seaice_init_varia.F  (removed dependence on ICE2WATR)
1065    o fizhi-cs test exp.:
1066       switch reference output convention for these 2 non-standard test-exp,
1067        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1068          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1069       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1070    o model/inc:
1071      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1072        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1073    o pkg/seaice:
1074      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1075    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1076      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1077        and initial HSALT
1078    
1079    checkpoint62w (2011/04/26)
1080    o pkg/mom_fluxform:
1081      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1082      - use parameter "sideDragFactor" in no-slip BC side-drag part.
1083      - update output of exp. global_ocean.90x40x15
1084    o pkg/mom_vecinv:
1085      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1086    o update seaice exp.:
1087      use more consistent parameter values (remove "backward compatability only":
1088       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1089      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1090       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1091    o update test-exp global_ocean.90x40x15:
1092      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1093      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1094      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1095      o turn on zStar & viscA4 in standard set-up (dir input/)
1096        and update output files: output.txt & output.dwnslp.txt
1097    o new AD-test experiment: obcs_ctrl
1098      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1099    o pkg/dic:
1100      fix two bugs in handling water vapour pressure in carbonate chemistry
1101      and air-sea fluxes. Found by Val Bennington and Galen McKinley
1102      (add DIC Option = WATERVAP_BUG to recover old results)
1103      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1104    o adding allowInteriorFreezing option to check for water below freezing point
1105      at depth and bring the negative heat anomaly to the surface level
1106    o pkgs _fields_load:
1107      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1108      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1109        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1110        rbcs to get interpolation weights and time reccord number.
1111      - fix multi-threading in aim_fields_load.F
1112      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1113    o external_fields_load:
1114      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1115       interpolation weights) to use in a periodic time-series ; do not divide by
1116       time-step to convert to integer:
1117       - this fixes case where externForcingPeriod is not multiple of time-step
1118          (Thanks to Christopher L. Wolfe)
1119       - this fixes case where externForcingPeriod is an odd multiple of time-step
1120         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1121      store index of time-record which is currently loaded:
1122       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1123       - needed for the adjoint but not yet used because of extensive recomputations;
1124         (to be fixed soon)
1125    
1126    checkpoint62v (2011/04/02)
1127    o verification/1D_ocean_ice_column added to test Ian Fenty's
1128      pkg/seaice_growth.F modifications for improving sea ice code differentiability
1129    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1130      (new velocity statistics after changing maskInW & maskInS definition)
1131    o pkg/generic_advdiff with OBCS:
1132      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1133      equivalent to assumption of no tracer gradient outside the OB region.
1134      This will affect the results if using obcs+biharmonic diffusion.
1135      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1136    o pkg/obcs:
1137      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1138      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1139      in Interior region. No impact on solution but affects Velocity monitor stats.
1140    o pkg/ptracers (adjoint)
1141      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1142      tape file for each tracer
1143    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1144      of parts of the adjoint code at run time. For now, there are only
1145      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1146      parameters are set in data.pkg.
1147      This is the lazy coward's version of doing this, but still useful for
1148      debugging. In order to do it right, everything needs to be moved to
1149      pkg/autodiff.
1150    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1151      the end; this fixes the adjoint balancing code for open boundaries.
1152    o pkg/ctrl:
1153      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1154        xx_${varname}period =   0.,  means time-independent control part
1155        xx_${varname}period = -12., means one-year-periodic monthly control part
1156      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1157        clean up ctrl_init a little, remove unused variables
1158      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1159      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1160    
1161    checkpoint62u (2011/03/15)
1162    o model/src:
1163      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1164        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1165      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1166        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1167    o pkg/ctrl/obcs/ecco:
1168      - remove obsolete, unused, and partially broken code:
1169        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1170        ALLOW_CTRL_OBCS_BALANCE
1171      - put a stop statement into ecco/cost_obcsvol.F, but also add
1172        cost_obcsvol to ecco_ad_diff.list
1173    o pkg/ecco: fix counting cost function contributions for obcs (code
1174      by Matt M.) and diffkr for diagnostics
1175    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1176      add cost penalty terms for initial uvel, vvel, eta controls
1177      and I/O for prior error files
1178    o pkg/mdsio:
1179       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1180       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1181       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1182    o pkg/ctrl:
1183     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1184       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1185       unused and superfluous variables
1186     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1187    o pkg/ecco
1188     - enable adjoint of Stevens OB
1189    o pkg/ctrl/ecco/grdchk:
1190      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1191        Fortunately, we do not have any tests for the numerous cpp-flagged
1192        option of "obcs as control parameters" so we will never know
1193        if this is an improvement (but at least now things compile).
1194      - remove an obsolete initialization from ecco_cost_init_barfiles.F
1195      - fix some problems within never used ifdefs to make the code compile
1196    o pkg/obcs:
1197     - Refine Interior mask definition to work with more complex OB (e.g.
1198       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1199       read in Interior mask from file. Check if Interior mask is consistent
1200       with OB list of indices.
1201    o pkg/seaice
1202     - beginning code for a seaice tracer package,
1203       but currently only used for seaice age: SEAICE_AGE
1204       SEAICE_num = 4
1205       iTracer = 1: area-weighted ice age
1206               = 2: volume-weighted ice age
1207               = 3, 4: template for one-year vs. multi-year ice
1208       data.seaice has new namelist SEAICE_PARM03 for arrays related to
1209       SEAICE_num
1210    
1211    checkpoint62t (2011/03/05)
1212    o pkg/obcs:
1213     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1214       then normal component. This ensures that the normal component is set
1215       correctly even when it conficts with tangential setting from an other OB.
1216       Affects results of test-experiment seaice_obcs: update the output.txt
1217    o pkg/obcs:
1218     - add code to monitor statistics of dynamical fields at OB.
1219     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1220       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1221       - change default: balance the Net inflow through all OB (instead of balancing
1222         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1223     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1224       to match Nortern OB inflow (OBCS_balanceFacN=0).
1225    o pkg/seaice:
1226     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1227    o pkg/seaice (seaice_growth v 1.113):
1228     - reverting seaice_growth to v 1.111 in order to have code with exact bit
1229       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1230       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1231       runtime flag SEAICEareaFormula is kept but is inactive
1232    o model/src:
1233     - add new param to scale curvilinear grid distance and area when using
1234       a different sphere radius from the grid-files.
1235     - test/check multi-threads EXCH applied to local variable (cg2d_x)
1236    o adjoint:
1237     - enable adjoint of Stevens OB
1238     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1239       (a bit delicate because of potentially modified adj. common block structure;
1240       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1241    
1242    checkpoint62s (2011/02/15)
1243    o pkg/seaice (seaice_growth v 1.112):
1244     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1245       computing the ice cover tendency from effective thickness tendencies. Include
1246       Ian Fenty's formula.
1247     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1248       SEAICEareaFormula.
1249     - simplify notations for the various d_HEFF/d_AREA terms.
1250    o pkg/gmredi:
1251     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1252       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1253       add a verification test-run (front_relax.bvp) to test GM_useBVP.
1254    o pkg/seaice (seaice_growth v 1.111):
1255     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1256     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1257       also melt ice.
1258    o pkg/seaice:
1259     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1260     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1261    o pkg/cheapaml:
1262     - from Nico Wienders: New version of this package.
1263    o pkg/flt:
1264     - add CPP options to prevent floats to re-enter the opposite side of
1265       a periodic domain (default: keep periodicity)
1266    o pkg/gmredi:
1267     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1268       (needed for multi-dim advection).
1269     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1270    o model/src:
1271     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1272    o tutorial_tracer_adjsens
1273     - extend to NLFS and replace maskC by hFacC
1274       (change reference output accordingly)
1275    
1276    checkpoint62r (2011/01/24)
1277    o testreport:
1278     - add option -deloutp (-do) to remove output file after successful run
1279     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1280       extract exact list of procs from this file ; adjust COMMAND by
1281       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1282  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
1283    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
1284  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1285    exf/cal    exf/cal
1286    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1287      and handle case of obcs?period == 0      and handle case of obcs?period == 0
1288      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
1289      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
1290      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
1291    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
1292      ALLOW_CAL is not defined      ALLOW_CAL is not defined
1293    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
1294                     S/R exf_swapfields                     S/R exf_swapfields
1295  o testreport:  o testreport:
1296     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 1299  o testreport:
1299  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1300    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
1301    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
1302    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
1303    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
1304  o pkg/seaice  o pkg/seaice
1305    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
1306    timestepping loop    timestepping loop
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