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revision 1.1391 by mlosch, Wed Mar 9 16:18:06 2011 UTC revision 1.1595 by gforget, Mon Feb 13 16:38:08 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/ctrl/ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.  o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.
8      - switch to variable freezing point.
9           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
10      - bug fix : the sublimation term that was missing is now activated.
11           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
12      - bug fix : flooding sign term for SIsal0.NE.0.
13           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
14    o pkg/seaice:
15      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
16     is now the default, and the old default constant freezing point is recovered with
17     SEAICE_tempFrz0    = -1.96,
18     SEAICE_dTempFrz_dS = 0.,
19      - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.
20      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
21      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
22     activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.
23      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
24     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
25      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
26     seaice_growth r149 for legacy branch (no results change).
27      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).
28      - results did not change except for global_ocean.cs32x15, mostly due to the switch
29      to variable freezing point (see above item for detail).
30    o pkg/thsice:
31      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
32        seawater freezing in thsice_calc_thickn (not used).
33    o pkg/seaice: turbulent flux term specification via run time params.
34      - replace CPP switches with run time switches to facilitate testing
35      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
36      - added runtime parameter : SEAICEturbFluxFormula
37      - move Mcphee constants to SEAICE_PARAMS.h
38      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
39        SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
40        seaice_summary call (moved to seaice_init_fixed)
41      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
42        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
43      - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
44      - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
45      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
46            CPP switch, same computation as before for the different options.
47      - change results at the truncation level.
48    o pkg/seaice:
49      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
50        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
51        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
52      - update verification/*/input*/data.seaice:
53        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
54        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
55        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
56        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
57    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
58      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
59        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
60        difference in results only due to machine truncation.
61      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
62        MaykutPolySatVap; keep MIN_LWDOWN.
63      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
64      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
65        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
66    o pkg/salt_plume:
67      - isolate saltPlumeFlux array exch into a specific S/R called from
68        do_oceanic_phys.F
69      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
70    o verification:
71      - move untested set-up to MITgcm_contrib/verification_other.
72    o pkg/seaice:
73      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
74    o pkg/seaice:
75      - seaice_solve4temp.F (keeping results unchanged):
76        * add 2 future run-time params to select which saturation vapor pressure
77          formula is used and how post-iteration fluxes are set.
78          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
79        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
80          the linearized expression to stay consistent with tsurf finding.
81      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
82        can be < 0.
83    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
84      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
85        conductive heat flux F_c , and add it explicitly when updating tsurf as
86        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
87        so that now F_ia has a consistent meaning through the entire routine.
88        This causes differences at truncation level: update output of fwd exp.
89        global_ocean.cs32x15.seaice.
90    o pkg/seaice:
91      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
92        of arrays, sign/direction of fluxes; no effect on results.
93      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
94        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
95        note: this should have been done before changing celsius2K default.
96      - to keep results unchanged, add back old value of celsius2K in verification
97        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
98      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
99        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
100        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
101        freezing temp is consistent with value in seaice_growth.F ; this causes
102        differences at machine truncation level: update lab_sea AD output (3/4).
103    o pkg/seaice:
104      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
105        and climsst/sss even when using seaice (to prevent calculation that might
106        use SST on land); does not affect any verification exp.
107      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
108        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
109    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
110      over land (non-legacy code)
111    o vectorize salt_plume package:
112      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
113      - this code computes plumebk everywhere (also over land), thus requires
114        code to avoid divisions by zero and catch the case of kLev=Nr.
115      - efficiency of salt_plume_frac is still sub-optimal
116    o tools (genmake2):
117      - fix makefile NAME specification (option: -makefile NAME) by adding
118        "-f $MAKEFILE" in few places where it was missing including makedepend
119        command (contribution from Paul).
120    
121    checkpoint63i (2012/01/24)
122    o model/src:
123      - add factorized versions of some EOS code to find_rho.F,
124        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
125    o model/src:
126      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
127      - change default celsius2K from 273.16 to 273.15
128      - to keep results unchanged, add back old value of celsius2K in verification
129        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
130         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
131    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
132      to make TAF generate vectorizable code
133    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
134       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
135       have flags that do this more efficiently.
136    o pkg/diagnostics/diagstats_calc.F
137      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
138    o pkg/obcs (with exch2):
139      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
140        and remove code (in obcs_readparms.F) which was based on EXCH of indices
141        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
142    o pkg/exf and seaice exp:
143      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
144        so that switching off area & heff advection flags does not affect results.
145      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
146      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
147        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
148        results of verification experiments: 1D_ocean_ice_column(fwd),
149        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
150        and offline_exf_seaice (all 4).
151    o pkg/seaice:
152      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
153        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
154      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
155        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
156        not multi-dim advection;
157      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
158        SHORTWAVE_HEATING #undef.
159    o optim: make Makefile more robust (?)
160    o pkg/obcs:
161      * fix treatment of obcs_read_pickup for TAF
162    o pkg/shelfice:
163      * add missing initialisation of num_shifwflx
164      * new adjoint verification exp. for isomip
165      * change Prandtl and Schmidt numbers from generic formulations
166        (in terms of model diffus. and visc.) to separate runtime
167        parameters, with Holland and Jenkins (1999) default values.
168    o pkg/exf (interpolation):
169      - extended input field (2 rows) near the N & S poles:
170        * fill in with the symetric value (when even Nb of data in longitude)
171        * add average value at the poles only for scalar quantities ; for vector
172          component interpolation, skip the averaging and keep duplicated values,
173          unless the 2 components have same location (uvInterp=T) in which case
174          interpolate the 2 components together using S/R EXF_INTERP_UV.
175      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
176        together: this allows to account properly for local orientation when
177        averaging at N & S pole.
178      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
179        exf-interpolation near N & S poles. Undef by default.
180      - add debug check/print on 1rst iter if debugLevel >=2.
181    o pkg/exf:
182      - change masking flags definition (no longer "parameter"), put them in
183        common block and set them in S/R EXF_INIT_FIXED.
184      - change recognized masking flag from s,u,v to c,w,s since the mask
185        to use (maskC,W,S) depends on position on model grid and has little to
186        do with scalar/vector difference; fix masking if using P-coordinates.
187      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
188        and update results of exp. global_with_exf (x2).
189      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
190    o pkg/obcs
191      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
192    o pkg/exf (interpolation):
193      - assume periodicity in X only if input field cover full longitude range.
194      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
195        and should vectorise).
196      - fix input lat of the 2 added row (in case we provide N.pole data).
197    
198    checkpoint63h (2011/12/30)
199    o pkg/seaice:
200      - change declaration of UVM from _RL to _RS in order to get B-grid
201        uIce,vIce monitor when _RS = real*4
202    o pkg/offline:
203      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
204      - compute vertical velocity if not read from file (switch on exactConserv
205        & staggerTimeStep);
206      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
207    o verification:
208      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
209        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
210        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
211      - update output of exp. global_ocean.cs32x15.viscA4 after changing
212        grid-file angles (used here for coriolis-3d);
213      - remove (or gzip) few files not needed to run fizhi-cs experiments.
214    o pkg/exf (vector interpolation):
215      - rotate vector component toward local grid-axis orientation using grid-angles
216        (stored in GRID.h) instead of locally computed rotation angle; keep old code
217        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
218    o pkg/seaice:
219      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
220        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
221    o pkg/PKG_OPTIONS.h files:
222      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
223        outside of the #ifdef ALLOW_THISPKG / #endif block.
224      - update verification/*/code/PKG_OPTIONS.h files.
225    o add a verification experiment (offline_exf_seaice/input.seaice) that test
226      the B-grid LSOR solver
227    o pkg/seaice: sort out emissivity and long wave radiation step 2:
228      - add emissivity for snow and ice as new run-time parameters
229        (unfortunately) that default to the corresponding exf values; this
230        changes results in most verification experiments so that for backward
231        compatibility these parameter have to be set explicitly to inconsistent
232        values (ugly);
233      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
234        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
235        until we agree how to handle this bug properly
236    o pkg/exf (interpolation):
237      - add a set of run-time param ({inputfield}_interpMethod), one for
238        each interpolated input field, to select the interpolation method
239        with a value of zero switching off the interpolation;
240      - print interpolation parameters to standard output;
241      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
242        (to use instead runoff_interpMethod=0 in data.exf).
243      - simplify default setting of interpolation parameters (for all fields,
244        set position to match model grid cell-center position, leading to trivial
245        interpolation in case of regular Lat-Lon grid) and fix for the case of
246        non-uniform delY.
247    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
248       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
249       this factor is absolutely required, because the lw exitance (= out-going
250       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
251       where the reflectivity rho = 1-emissivity for conservation reasons. Once
252       this is established, we can remove the CPP-Flag (if we want to).
253    o pkg/seaice:
254      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
255        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
256      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
257        what the name implies (and not emissivity*BoltzmannConstant), this means
258        the old default value of 5.5e-8 now means
259        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
260        S/R exf_readparms
261      - FV-discretization of the B-grid LSOR solver, turn on with
262        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
263        of the calling routine dynsolver, so that B and C-grid code look a
264        little more alike.
265      - fix index bugs in ostres.F (B-grid code)
266    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
267    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
268      default for SEAICE_emissivity, if useEXF; requires setting a wrong
269      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
270      backward compatiblity
271    o model/src: use sigmaR in calc_ivdc
272    
273    checkpoint63g (2011/12/16)
274    o pkg/seaice/seaice_growth.F:
275      fix heat conservation of the coupled ocean-seaice system.
276      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
277      solid vs liquid water treatment is resolved via QNET.
278    o pkg/seaice/seaice_growth.F:
279      add missing term for sublimation in saltFlux, which was breaking conservation.
280    o pkg/seaice/seaice_model.F:
281      Remove this patholigical case treatment in evolution branch,
282      where it is un-necessary and breaks conservation.
283      Update global_ocean.cs32x15/results accordingly for
284      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
285    o model/src:
286      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
287      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
288    o pkg/obcs:
289      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
290      tendency for temperature and salinity that is then applied to update
291      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
292      horizontal advection and diffusion contributions on the boundary (in
293      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
294      removing the mask in S/R timestep_tracer. The advantage of this approach is
295      that the updated tracer values include contributions from the surface
296      forcing and vertical diffusion.
297      This modification changes exp4.stevens because of vertical diffusion.
298    o model/src:
299      change non-curvilinear grid setting to also work with exch2 + blank tiles:
300      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
301        face dimensions.
302      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
303        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
304        and INI_SPHERICAL_POLAR_GRID.
305      change test-experiment global_ocean.90x40x15:
306      - split the domain in many more tiles (9x4 tiles of 10x10 each);
307      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
308      - update results of both test (std & dwnslp).
309    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
310       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
311    o model/src:
312      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
313        and fix initialisation when using sigma-coords.
314    o model/src:
315     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
316       to their current value at the beginning of forward_step.F": add a new run-time
317       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
318     - set doResetHFactors=T in the following test exp:
319        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
320        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
321        and tutorial_global_oce_in_p (nonLinFS in p)
322    o pkg/ecco
323      - added IES cost term
324    o verification/advect_xz
325      - scale down the depth by 1/100 (from 200 km to just 2.km)
326      - add secondary test using divergent flow, r-star and implicit vertical advection.
327      - add note (check_conserve_TS.txt) and matlab script to check global
328        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
329    o pkg/rbcs:
330      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
331    o pkg/obcs (Stevens BCs):
332      - fix various problems in the phase speed computations of the Stevens
333        boundary conditions:
334        - sign error for western and southern boundaries,
335        - time tendencies were underestimated by factor of dTracerLev and some just
336          zero (for multidim advection schemes) -> now estimate time tendencies
337          from difference between previous (n) time level and the one before (n-1);
338          this requires storing a field per tracer per boundary, also in the pickup
339          files.
340        - replace deltaTmom in cflMer/Zon computation with dTracerLev
341        - set default phase velocity to cflMer/Zon
342      - update verification experiment exp4.stevens
343    o pkg/generic_advdiff (implicit_r):
344      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
345        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
346      - fix implicit vertical diffusion or advection with NonLin FreeSurf
347        (was using current recip_hFacC instead of future recip_hFacC): set future
348        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
349        solver S/R ;
350      - fill diagnostics of vertical advective fluxes (computed from tendency)
351        when using implicit vert. advection;
352      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
353         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
354         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
355         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
356    o pkg/diagnostics:
357      - add diags for T & S tendency which goes through Adams-Bashforth.
358    
359    checkpoint63f (2011/11/30)
360    o pkg/obcs/obcs_calc_stevens.F:
361      - join some loops to reduce number of if-statements
362      - fix a bug in code for northern and southern boundaries.
363    o pkg/seaice/seaice_init_varia.F
364      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
365        caused zero ice-velocities for the B-grid code
366    o pkg/seaice/seaice_init_fixed.F
367      - fix a bug in the initialisation of the second metric terms
368        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
369      - this affects all seaice configurations with useCurviLinearGrid = .true.
370        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
371        = .true. (default)
372      - the only verification experiment affected is global_ocean.cs32x15:
373        icedyn, seaice, and seaice_dynmix (AD)
374    o pkg/thsice/thsice_diagnostics_state.F
375      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
376        not contain garbage that can lead to surprises in diagstats_calc.F
377    o model/src:
378      - move bi,bj loops inside INTEGR_CONTINUITY ;
379      - call INTEGR_CONTINUITY directly from forward_step.F
380        (previously called from momentum_correction_step.F)
381      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
382        forward_step.F and pkg/ecco/the_main_loop.F
383    o model/src/do_oceanic_phys.F:
384      - reset addMass to zero only if useICEFRONT ;
385      - separated k-loop for rhoInSitu calculation ;
386      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
387        and at constant T,S (= WdRHOdP);
388      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
389        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
390        transport of locally-referenced potential density);
391        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
392    o gluemnc:
393      - replace ncrcat with ncks when adding variables to *.glob.nc
394      - change the way variables without record dimensions are handled so that
395        files that have variables with and without record variables can be glued:
396        add a record dimension with a new unique name to be able to differentiate
397        between variable with and without a-prior record dimensions. Remove
398        this record dimension before adding the variable to the *.glob.nc file.
399        This procedure automatically works also for grid.*.nc files that do not
400        have any record dimension.
401    o verification/cpl_aim+ocn:
402      - generate new reference output on baudelaire (gfortran, mpich2) (previously
403        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
404    o pkg/obcs/obcs_calc_stevens.F:
405      - add code for northern and southern boundaries.
406      - reorder some loops to save some operations and so that drFBar can be scalar
407    o model/src:
408      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
409        truncation) and add diagnostics for Adams-Bashforth tendency increment.
410      - update test-exp. AD output:
411        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
412      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
413        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
414        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
415        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
416        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
417        tutorial_plume_on_slope.
418    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
419      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
420      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
421      does not even come with an F77 compiler anymore, this should not be
422      a limitation
423    
424    checkpoint63e (2011/11/06)
425    o pkg/seaice adjoint of LSR:
426      - substantially rework STORE dirs.
427      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
428        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
429        and only perform SOLV_MAX_FIXED adjoint iters.
430        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
431        always goes to same record, meaning that the last forward field will be
432        the one used in the adjoint - an approximation.
433      - now produces non-zero LSR-related gradients, and acceptable gradients for
434        An's zonal (x-z) test case (to be checked in)
435      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
436        (but these are screwed up by the thermodynamics in the first place);
437        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
438        output_adm.txt also reflects changes to seaice_lsr
439      - global_ocean.cs32x15:
440        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
441          (output_adm.seaice.txt was updated)
442        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
443          (output_adm.seaice_dynmix.txt)
444    o test-exp. exp4+stevens:
445      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
446    o pkg/seaice (lsr solver):
447      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
448        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
449      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
450      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
451        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
452      - compute (with new S/R) and print initial (+ free-driff sol. if available)
453        and final residual of linearised system.
454    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
455      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
456    o pkg/obcs: Stevens BCs (still only for east and west)
457      - fix Stevens BCs by using intermediate velocities of previous
458        time step as "baroclinic" contribution rather velocity of one grid cell
459        inside the boundaries; more consistent but makes the entire treatment
460        more complicated, requires new pickup files and two new S/Rs:
461        obcs_copy_uv_n and obcs_save_uv_n
462        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
463        (undefined by default)
464      - silently move computation of some grid factors into separate loops to
465        save some recomputations
466      - add a hack for non-linear free surface
467      - add a verification experiment to exp4 that tests this code
468    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
469    
470    checkpoint63d (2011/10/25)
471    o pkg/obcs + seaice-dynamics:
472      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
473        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
474        values (consistent with an implicit method).
475      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
476        return to older implementation (same results as before); note that none of
477        the "experimental" OBCS_SEAICE options are implemented in the new version.
478      - switch test exp. seaice_obcs to use new version (update output).
479    o pkg/seaice:
480      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
481      - add parenthesis in Water-Ice drag calculations (evp & lsr);
482      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
483        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
484      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
485        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
486    o pkg/layers:
487      - Include potential density as new coordinate (Thanks to David Munday)
488    o pkg/dic:
489      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
490        carbonate computation/output to CALC_PCO2_APPROX
491    o pkg/generic_advdiff
492      - make TAF generate code that vectorizes:
493        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
494    o model/src:
495      - improve vectorization also for adjoint code of
496        solve_tridiagonal and solve_pentadiagonal. As this requires up to
497        5 new 3D-fields, this code is only turned on for the combination of
498        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
499        for singular matrix check (only for TARGET_NEC_SX).
500      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
501        ALLOW_AUTODIFF. This flag now needs to be set outside of
502        solve_tri/pentadiagonal.F
503    o pkg/exf:
504      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
505        optional namelist EXF_NML_OBCS).
506      - add many debug-print (to trace down where pkg/cal error msg comes from)
507    o pkg/mom_vecinv/mom_vi_hdissip.F
508      - rearrange loops so that vectorization is improved and in particular
509        the adjoint routine vectorizes. The code is a little longer now, but I
510        think easier to read.
511        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
512    o pkg/seaice:
513      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
514    o pkg/exch2:
515      - alternative code (without tile x tile matrix) for cumulated (global) sum;
516        used as default; keep using matrix version in adjustment.cs-32x32x1.
517    o tools/build_options:
518      - after merging some MPI and/or multi-threads specific optfiles so that
519        the modified default optfile support both built (using genmake2 -mpi
520        for the MPI built, using genmake2 -omp for OpenMP built),
521        move now obsolete optfiles to tools/build_options/unsupported/
522       (add copy of email sent to support list in doc/optfiles_changes.txt)
523    
524    checkpoint63c (2011/09/28)
525    o pkg/ebm:
526      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
527        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
528    o pkg/seaice (SItracer pickup)
529    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
530      To be done:
531      - thorough testing of missing fields in S/R seaice_read_pickup
532      - thorough matching between generic tracers and specific fields used
533        (e.g. volume-weighted age, area-weighted age, salinity, ...)
534    o pkg/grdchk:
535      - all procs calculate and print finite-difference gradient (for testreport)
536      - change description output used by testreport;
537      - AD testing: also compare and report Finite-difference gradient;
538        => update all output_adm*.txt
539    o test exp. global_ocean_ebm:
540      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
541        and turn on exactConserve; update (fwd) output.
542    o pkg/seaice (LSR):
543      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
544      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
545        * identical results with non-CS topology (but save up to half of EXCH calls)
546        * no much changes in cs-32 verification tests since no ice at face edges
547         (differences due to convergence criteria, since nb of iterations changed)
548        * expect some differences on lat-lon-cap grid.
549        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
550    o pkg/exch2:
551      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
552        many tiles); until alternative coding is added, just add a stop.
553    o pkg/kpp:
554      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
555        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
556    o optfiles:
557      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
558        into corresponding standard one, which now support different build:
559        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
560      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
561    o pkg/obcs (seaice):
562      - add missing EXCH for uIce,vIce after applying OBCS;
563      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
564        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
565        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
566      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
567      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
568        and eedata.mth for MPI and mutlti-threaded testing.
569    o pkg/flt:
570      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
571      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
572      - fix pickup and trajectories + profiles output with multi-threads;
573      - add parameter to select group of fields to write along trajectory and
574        profile (default unchanged);
575      - only call PORT_RAND* function when flt_noise <> 0;
576      - add multi-threaded test for verification exp. flt_example.
577    o eesupp/src:
578      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
579      - USE_OMP_THREADING: check that number of threads (from eedata) matches
580        actual number (from env.var. setting).
581    o pkg/ebm:
582      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
583      - add multi-threaded test for verification exp. global_ocean_ebm
584    
585    checkpoint63b (2011/08/29)
586    o pkg/ebm:
587      - fix sign of runoff;
588      - update directly forcing fields (Qnet,EmPmR) to use standard
589        external_forcing_surf.F (remove ebm_forcing_surf.F);
590      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
591      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
592        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
593      - update global_ocean_ebm parameters file data and update output (fwd+ad).
594    o verification/matrix_example:
595      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
596        MPI and mutlti-threaded testing.
597    o pkg/matrix:
598      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
599      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
600      - fix for multi-threaded (remove DATA statement);
601      - use standard DIFFERENT_MULTIPLE function;
602      - add MATRIX_OPTIONS.h
603    o verification/matrix_example:
604       To allow to split the domain in several tiles, change the domain size
605        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
606        Western side) of land points.
607    o (*_)write_pickup:
608      - fix few bugs in mypackage_read/write_pickup.F
609      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
610        array of length 1 (was caught by compiler syntax-check).
611    o pkg/diagnostics (velocity potential solver):
612      - fix initialisation of main diagonal matrix (for overlap values)
613    o tools/build_options:
614      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
615        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
616      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
617        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
618        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
619        and use "-devel" testreport option for standard testing on baudelaire.
620    o pkg/grdchk:
621      - Assume that all gradient-check position are within the same tile
622        corresponding to global indices (iGloTile,jGloTile) and that
623        positions (i,j indices or nbeg) are local to this tile;
624      - set tile local-indices and proc. number according to tile global-indices;
625      - remove grdchkwhichproc from namelist (retired param);
626      - send adjoint gradient to all procs so that all procs print it to STDOUT;
627      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
628    o adding package bbl (Bottom Boundary Layer)
629      description in MITgcm/pkg/bbl/bbl_description.tex
630      example/test experiment in MITgcm_contrib/bbl
631    o adjoint verifications
632      - changed 5 experiments to multi-tiles
633        * global_ocean.90x40x15
634        * obcs_ctrl
635        * offline_exf_seaice
636        * tutorial_dic_adjoffline
637        * tutorial_tracer_adjsens
638        changed reference output for those that crossed tile boundaries
639        (changed choices of gradient check positions)
640      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
641      - temporary bug fix in grdchk_loc.F for obcs
642    o genmake2 & testreport
643      - add target "obj" (just for OBJFILES files) to Makefile;
644      - add option to specify FEXTRAFLAGS on command line.
645    o pkg/mypackage:
646      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
647    
648    checkpoint63a (2011/08/02)
649    o pkg/diagnostics (velocity potential):
650      - fix velocity-potential calculation when using OBCS: balance net inflow
651        at each level (new S/R OBCS_DIAG_BALANCE).
652      - fix some of the problems with OBCS in stream-function calculation.
653    o pkg/exf/exf_readparms.F
654      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
655        EXF_NML_OBCS) more consistent, so that you need not have these lists
656        in data.exf when they are not used.
657    o optim/optim_readdata.F:
658      - add some output about obcs variables that might help debugging
659      - add a check about nvarlength
660    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
661    o pkg/diagnostics (velocity potential):
662      - fix mask for OBCS (still problems in stream-function with OBCS);
663      - add specific parameter (default = main code CG2D params) for solver;
664      - in case of poor convergence, use solution corresponding to lowest residual.
665    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
666      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
667      and should be avoided where possible.
668    o model/src (rStar):
669      - include r* effect on reference-state (PhiRef) in totPhiHyd
670        (so that it's really the potential anomaly at the cell center);
671        affect solution only if z* with full pressure in EOS.
672      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
673        update output (because of z* in totPhiHyd and viscA4 changes);
674      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
675        @ constant r) until interpolation at constant r is implemented.
676    o pkg/diagnostics
677      - fix RCENTER diagnostics in case cell center is not at interface middle
678    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
679      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
680      that THETA and SALT are "conservative temperature" and "absolute
681      salinity"
682    o pkg/ctrl
683      - fix computation of endrec in s/r ctrl_init_rec
684      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
685    o pkg/seaice/seaice_growth.F
686      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
687        remove then obsolete STORE directives
688      - fix STORE directives for tice and tices, so that only the
689        appropriate part of the fields are stored (and not the entire
690        field); update global_ocean.cs32x15.seaice AD output.
691      - cosmetic changes: adjust CPP flags and indentation for better
692        legibilty
693    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
694      Chris Wilson)
695    o pkg/gmredi:
696       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
697       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
698    
699    checkpoint63  (2011/07/11)
700    o pkg/exch2:
701     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
702     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
703       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
704       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
705    o pkg/diagnostics:
706     - deal with pairs of post-processed diags which are computed together; in
707       particular, re-order list of diags within 1 file to save 2nd computation.
708     - add S/R to compute velocity stream-function (called after velocity-potential
709       calculation) from divergence free transport -> new diagnostics "PsiVEL".
710     - add parameter to select grid-point location where PsiVEL == 0.
711    o eesupp/src:
712       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
713       (specific S/R needed with exch2 topology - for now, just print an error msg)
714    o pkg/shelfice
715     - Implement friction velocity-dependent transfer coefficients following
716       Holland and Jenkins, JPO, 1999
717       Original code by M. Losch with small modifs.
718       Enable with CPP option SHI_ALLOW_GAMMAFRICT
719       and runtime flag SHELFICEuseGammaFrict
720    o verification lab_sea & global_ocean.cs32x15:
721     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
722       does not miss some dependencies (but is slower) and also works with many files
723       (default makedepend limitation for AD built).
724     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
725    o pkg/diagnostics:
726     - add run-time parameter "useMissingValue" (def=False) to fill land-point
727        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
728       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
729     - Extend the use of "missing_value" setting from data.diagnostics for the case
730       of counter-diagnostics (where fraction-weight is zero). This applies both to
731       MNC and MDS output files.
732    o pkg/seaice/seaice_growth.F:
733      - add 'a priori' cap of latent heat flux based on actual mass considerations
734        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
735        non-legacy seaice_solve4temp.
736      - add diagnostic of the residual sublimation freshwater flux (the freshwater
737        flux taken from the ocean if the total actual latent heat fluxes exceed
738        the maximum)
739      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
740       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
741      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
742       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
743      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
744      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
745    o verification 1D_ocean_ice_column:
746       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
747       update results
748    o pkg/diagnostics:
749     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
750       which are not filled-up but computed from other diags ; In this case, the mate
751       diag points to the primary (filled-up) diag to used for post processing.
752     - Update Velocity-potential computation using post-processed diag framework.
753     ==> Change the ordering of fields and time-periods in MDS output file
754       when using periodic averaging: now writes one time record with the full set
755       of fields for this time period, then the next time reccord (it used to be
756       one field with the full set of time records then the next field).
757         Note: this is now similar to NetCDF (MNC) output file. <==
758    
759    checkpoint62z (2011/06/21)
760    o adjoint monitor:
761     - Add adjoint monitor output for packages exf, seaice
762       and update relevant testreport output
763    o pkg/seaice:
764     - re-order diags inits so that they appear in order in available_diagnostics.log
765     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
766       area/heff/hsnow preceeding thermodynamic growth/melt.
767     - modified diag: SIdA; output actual effect, as the description states.
768     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
769     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
770       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
771        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
772     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
773     - added diagnostics for seaice generic tracers (SItr*).
774     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
775     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
776     I. Fenty: 18-Jun-2011:
777     Minor changes to seaice package:
778     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
779        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
780       - Differentiated "regularization variables" from "floor variables"
781        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
782        * hiceMin became SEAICE_hice_reg (old hiceMin)
783          (with _reg meaning regularization variable)
784       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
785        so as to ensure energy conservation when going between phases
786      - A22 was not used anywhere
787     2) Changed regularization procedure for heffActual and hsnowActual to ensure
788        well-boundedness and smooth adjoint in seaice_growth.F
789     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
790        because the old regularization always set heffActual >= 0.05 cm
791     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
792        on AREA when HEFF > 0.
793      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
794        requiring that DISABLE_AREA_FLOOR *not* be defined
795     Affected verifications:
796      - 1D_ocean_ice_column (output.txt output_adm.txt)
797      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
798    o pkg/diagnostics:
799      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
800      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
801        (was _RL, now integer) with option = 0 to retrieve all levels.
802      - add pieces of code to compute velocity potential at each level (new diagnostics
803        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
804        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
805      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
806        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
807        and in diagnostics_fract_fill.F (do not need a valid pointer for the
808        diagnostics counter-mate); check that definition of counter-diagnostic
809        includes a valid counter-mate (in diagnostics_set_levels.F).
810    o model/src (rStar):
811      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
812        affect solution only if z* with full pressure in EOS;
813        update output of test-exp global_ocean.90x40x15.
814    o pkg/seaice:
815      - introduce siEps=1e-5 parameter
816      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
817      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
818      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
819        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
820        as well as ice cover age and ridging index (attached to AREA).
821        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
822        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
823        Up to SItrMaxNum=3 tracers can be used simultaneously.
824    o pkg/salt_plume:
825      -introduce SPsalFRAC run time parameter that sets the fraction of the
826       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
827       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
828    o model debug options:
829      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
830        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
831      - Refine debug-msg printing selection (3 new levels):
832        debugMode  : controls printing of debug messages (sequence of S/R calls).
833        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
834         debLevZero =  0 ; /* level of disabled aux. msg printing */
835         debLevA =  1 ; /* level of minimum  aux. msg printing */
836         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
837         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
838         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
839         debLevE =  5 ; /* level of extensive debug printing */
840        New debugLevel default: with default debugMode value (=F),
841          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
842          and if debugMode=T, default debugLevel = 4 (debLevD).
843        Relation with previous settings:
844         debLevB (=2) corresponds to former debLevA (=1)
845         debLevD (=4) corresponds to former debLevB (=2)
846        Note:
847         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
848         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
849            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
850      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
851        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
852    o pkg/obcs:
853      - change OBCSfixTopo default from True to False (should not change the results);
854        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
855    o pkg/thsice:
856      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
857        2nd layer seaice sublimation (unlikely to happen)
858      - use Interior mask for OBCS in thsice_advection.F (similar to what is
859        done in gad_advection & seaice_advection).
860    o adjoint:
861      bug fix spotted by Gael Forget:
862      seaice_advection and thsice_advection still had
863      legacy CPP options to avoid CS corner updates for adjoint
864    o pkg/seaice:
865      => Change some of the defaults (2011/05/29):
866         - change SEAICEuseFluxForm default (from False to True)
867         - change DIFF1 default (from 0.004 m/s to 0. m/s)
868         And print warnings if DIFF1 is not set in data.seaice and centered
869          avection scheme is used without any diffusion.
870      also:
871      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
872      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
873      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
874        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
875        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
876      update results of test exp.:
877         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
878             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
879             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
880         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
881         seaice_obcs: output (SEAICEuseFluxForm=T)
882      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
883          for standard fwd & AD lab_sea tests (to keep the same output).
884    o pkg/seaice/seaice_growth.F:
885      - use Ian Fenty's capping formulas for actual ice
886      thickness thoughout EVOLUTION branch.
887      - put treatment pathological case #2) in CPP brackets
888      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
889      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
890    o pkg/seaice:
891      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
892      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
893      also pass fac as a param, which can be 1. (to update the tendency
894      field) or the time step (to update the field itself).
895      - seaice_advdiff.F: for multidim, call seaice_diffusion with
896      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
897      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
898      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
899      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
900    o pkg/seaice:
901      diffusion with centered advection scheme (diffus.F & advect.F):
902      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
903        to just compute the laplacian of input-field.
904      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
905      - fix flux-form version in diffus.F to conserve tracer.
906      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
907       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
908    
909    checkpoint62y (2011/05/26)
910    o pkg/seaice:
911     - seaice_growth.F : in EVOLUTION branch, always include
912       a_QSWbyATM_cover in qnet (as it should be).
913     - verification/global_ocean.cs32x15 : update results accordingly
914       (output.seaice.txt output_adm.seaice.txt).
915    o pkg/seaice + obcs:
916     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
917       equivalent of assuming no tracer gradient outside the OB region.
918       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
919     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
920       after changes above);
921     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
922       only at OB location (instead of over a band of OLx width).
923    o pkg/seaice:
924     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
925       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
926    o pkg/obcs:
927      - split header file "OBCS.h" into 4 separated files:
928        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
929       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
930         (contain no conditional statement which depends on OBCS options).
931      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
932        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
933    o ctrl, cost, grdchk & autodiff pkgs:
934      - make options file more standard (like other {PKG}_OPTIONS.h file but
935        with AD_CONFIG.h); clean-up some of the included header files.
936    o pkg/obcs:
937      - do not mask tracer when applying OB (tracer == 0 could generate problems)
938      - apply tracer OB values to tracer field only at OB location (instead of
939        over a band of OLx width)
940      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
941      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
942        obcs_apply_tloc.F & obcs_apply_sloc.F
943    o obcs in model/src:
944      - call OBCS_APPLY_W only if NonHydrostatic.
945      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
946      - reset dEtaHdt and wVel to zero outside OB interior region ;
947      - leave tracer unchanged outside OB interior region: This has no effect
948        on the solution but just to prevent unrealistic tracer value outside OB.
949      - zero out velocity outside OB interior region: This has no effect on
950        the solution but just to prevent unrealistic velocity outside OB.
951    o obcs and non-lin free-surf:
952       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
953       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
954       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
955       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
956       update results of test-exp. exp4(nlfs).
957    o exp4 (nlfs) test-exp:
958       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
959       with NonLin-FreeSurf); update output.nlfs.txt
960    o obcs and 2d/3d solver norm:
961       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
962       and outside OB interior region (will allow to place OB further inside the
963       domain). Depending on the domain, can affects cg2d-Norm (previous
964       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
965       and cg3d-Norm (previous Norm was computed before canceling OB terms),
966       e.g. in tutorial_plume_on_slope.
967      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
968    o pkg rbcs:
969      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
970      - add capability to apply relaxation to horizontal velocity uVel & vVel.
971    o pkg/grdchk: add gradient check for control variable xx_shifwflx
972    o pkg/shelfice/shelfice_init_fixed.F
973      fix CPP-flag combinations
974    o pkg/seaice: Merge iceage code of Pierre Rampal
975      * update/change/correct ice age calculations
976      * add age updates for pathological cases
977      Probably needs more testing...
978    
979    checkpoint62x (2011/05/13)
980    o pkg/mom_vecinv:
981       high-order vorticity scheme: use interior masks (maskInW & S)
982       to zero-out (outside OB) gradient of vorticity.
983    o verification exp.:
984       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
985       hs94.128x64x5 and seaice_obcs ; update results.
986    o pkg/obcs:
987      fix bug in OBeta for YZ sections in obcs_exf_load.F
988    o pkg/ctrl, pkg/shelfice, and optim:
989      - add new control variable xx_shifwflx (fresh water flux underneath ice
990        shelves). This is almost as tedious as obcs-ctrl, because the
991        variables needs its own mask.
992      - add a cost function term that penalizes the deviation of xx_shifwflx
993        from the first guess (zero) in analogy to other control variables
994    o pkg/shelfice:
995      - start basic adjoint
996    o pkg/ctrl:
997      - remove extra 2D field "for good measure" when initializing in
998        ctrl_set_globfld_[xy/xz/yz].F
999      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1000      - improve error messages in ctrl_set_unpack_*
1001    o OBC implementation in momentum:
1002       use interior masks (maskInC,W & S) in momentum S/R:
1003       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1004       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1005       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1006       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1007       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1008        (and also with Leith/Smagorinsky harmonic-viscosity).
1009       Update output of experiment dome and exp4 (+nlfs).
1010    o exp4 test-exp:
1011      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1012        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1013        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1014        time-varying OB at Western-side for wVel (NonHyd); update output.
1015      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1016        and biharmonic-viscosity ; also use prescribed time varying OB.
1017    o pkg/obcs:
1018      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1019    o model/src:
1020      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1021      - initialise startTime & nIter0 with unlikely values: allows to set one
1022        from the other without ambiguity.
1023    o seaice_obcs test-exp.:
1024      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1025    o pkg/obcs:
1026      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1027        no longer needed with maskInC,W,S in pkg/generic_advdiff.
1028    o pkg/seaice:
1029      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1030        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1031      - fixed bug in the initialization of sea ice salinity variable HSALT
1032        in seaice_init_varia.F  (removed dependence on ICE2WATR)
1033    o fizhi-cs test exp.:
1034       switch reference output convention for these 2 non-standard test-exp,
1035        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1036          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1037       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1038    o model/inc:
1039      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1040        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1041    o pkg/seaice:
1042      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1043    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1044      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1045        and initial HSALT
1046    
1047    checkpoint62w (2011/04/26)
1048    o pkg/mom_fluxform:
1049      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1050      - use parameter "sideDragFactor" in no-slip BC side-drag part.
1051      - update output of exp. global_ocean.90x40x15
1052    o pkg/mom_vecinv:
1053      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1054    o update seaice exp.:
1055      use more consistent parameter values (remove "backward compatability only":
1056       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1057      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1058       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1059    o update test-exp global_ocean.90x40x15:
1060      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1061      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1062      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1063      o turn on zStar & viscA4 in standard set-up (dir input/)
1064        and update output files: output.txt & output.dwnslp.txt
1065    o new AD-test experiment: obcs_ctrl
1066      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1067    o pkg/dic:
1068      fix two bugs in handling water vapour pressure in carbonate chemistry
1069      and air-sea fluxes. Found by Val Bennington and Galen McKinley
1070      (add DIC Option = WATERVAP_BUG to recover old results)
1071      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1072    o adding allowInteriorFreezing option to check for water below freezing point
1073      at depth and bring the negative heat anomaly to the surface level
1074    o pkgs _fields_load:
1075      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1076      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1077        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1078        rbcs to get interpolation weights and time reccord number.
1079      - fix multi-threading in aim_fields_load.F
1080      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1081    o external_fields_load:
1082      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1083       interpolation weights) to use in a periodic time-series ; do not divide by
1084       time-step to convert to integer:
1085       - this fixes case where externForcingPeriod is not multiple of time-step
1086          (Thanks to Christopher L. Wolfe)
1087       - this fixes case where externForcingPeriod is an odd multiple of time-step
1088         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1089      store index of time-record which is currently loaded:
1090       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1091       - needed for the adjoint but not yet used because of extensive recomputations;
1092         (to be fixed soon)
1093    
1094    checkpoint62v (2011/04/02)
1095    o verification/1D_ocean_ice_column added to test Ian Fenty's
1096      pkg/seaice_growth.F modifications for improving sea ice code differentiability
1097    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1098      (new velocity statistics after changing maskInW & maskInS definition)
1099    o pkg/generic_advdiff with OBCS:
1100      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1101      equivalent to assumption of no tracer gradient outside the OB region.
1102      This will affect the results if using obcs+biharmonic diffusion.
1103      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1104    o pkg/obcs:
1105      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1106      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1107      in Interior region. No impact on solution but affects Velocity monitor stats.
1108    o pkg/ptracers (adjoint)
1109      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1110      tape file for each tracer
1111    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1112      of parts of the adjoint code at run time. For now, there are only
1113      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1114      parameters are set in data.pkg.
1115      This is the lazy coward's version of doing this, but still useful for
1116      debugging. In order to do it right, everything needs to be moved to
1117      pkg/autodiff.
1118    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1119      the end; this fixes the adjoint balancing code for open boundaries.
1120    o pkg/ctrl:
1121      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1122        xx_${varname}period =   0.,  means time-independent control part
1123        xx_${varname}period = -12., means one-year-periodic monthly control part
1124      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1125        clean up ctrl_init a little, remove unused variables
1126      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1127      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1128    
1129    checkpoint62u (2011/03/15)
1130    o model/src:
1131      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1132        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1133      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1134        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1135    o pkg/ctrl/obcs/ecco:
1136      - remove obsolete, unused, and partially broken code:
1137        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1138        ALLOW_CTRL_OBCS_BALANCE
1139      - put a stop statement into ecco/cost_obcsvol.F, but also add
1140        cost_obcsvol to ecco_ad_diff.list
1141    o pkg/ecco: fix counting cost function contributions for obcs (code
1142      by Matt M.) and diffkr for diagnostics
1143    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1144      add cost penalty terms for initial uvel, vvel, eta controls
1145      and I/O for prior error files
1146    o pkg/mdsio:
1147       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1148       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1149       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1150    o pkg/ctrl:
1151     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1152       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1153       unused and superfluous variables
1154     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1155  o pkg/ecco  o pkg/ecco
1156   - enable adjoint of Stevens OB   - enable adjoint of Stevens OB
1157  o pkg/ctrl/ecco/grdchk:  o pkg/ctrl/ecco/grdchk:
1158    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1159      Fortunately, we do not have any tests for the numerous cpp-flagged      Fortunately, we do not have any tests for the numerous cpp-flagged
1160      option of "obcs as control parameters" so we will never know      option of "obcs as control parameters" so we will never know
1161      if this is an improvement (but at least now things compile).      if this is an improvement (but at least now things compile).
1162    - remove an obsolete initialization from ecco_cost_init_barfiles.F    - remove an obsolete initialization from ecco_cost_init_barfiles.F
1163    - fix some problems within never used ifdefs to make the code compile    - fix some problems within never used ifdefs to make the code compile
1164  o pkg/obcs:  o pkg/obcs:
1165   - Refine Interior mask definition to work with more complex OB (e.g.   - Refine Interior mask definition to work with more complex OB (e.g.
1166     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
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