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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1591 by jmc, Sun Feb 5 22:40:31 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
8      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
9        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
10        difference in results only due to machine truncation.
11      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
12        MaykutPolySatVap; keep MIN_LWDOWN.
13      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
14      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
15        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
16    o pkg/salt_plume:
17      - isolate saltPlumeFlux array exch into a specific S/R called from
18        do_oceanic_phys.F
19      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
20    o verification:
21      - move untested set-up to MITgcm_contrib/verification_other.
22  o pkg/seaice:  o pkg/seaice:
23   - seaice_growth.F : in EVOLUTION branch, always include    - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
24    o pkg/seaice:
25      - seaice_solve4temp.F (keeping results unchanged):
26        * add 2 future run-time params to select which saturation vapor pressure
27          formula is used and how post-iteration fluxes are set.
28          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
29        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
30          the linearized expression to stay consistent with tsurf finding.
31      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
32        can be < 0.
33    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
34      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
35        conductive heat flux F_c , and add it explicitly when updating tsurf as
36        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
37        so that now F_ia has a consistent meaning through the entire routine.
38        This causes differences at truncation level: update output of fwd exp.
39        global_ocean.cs32x15.seaice.
40    o pkg/seaice:
41      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
42        of arrays, sign/direction of fluxes; no effect on results.
43      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
44        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
45        note: this should have been done before changing celsius2K default.
46      - to keep results unchanged, add back old value of celsius2K in verification
47        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
48      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
49        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
50        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
51        freezing temp is consistent with value in seaice_growth.F ; this causes
52        differences at machine truncation level: update lab_sea AD output (3/4).
53    o pkg/seaice:
54      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
55        and climsst/sss even when using seaice (to prevent calculation that might
56        use SST on land); does not affect any verification exp.
57      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
58        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
59    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
60      over land (non-legacy code)
61    o vectorize salt_plume package:
62      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
63      - this code computes plumebk everywhere (also over land), thus requires
64        code to avoid divisions by zero and catch the case of kLev=Nr.
65      - efficiency of salt_plume_frac is still sub-optimal
66    o tools (genmake2):
67      - fix makefile NAME specification (option: -makefile NAME) by adding
68        "-f $MAKEFILE" in few places where it was missing including makedepend
69        command (contribution from Paul).
70    
71    checkpoint63i (2012/01/24)
72    o model/src:
73      - add factorized versions of some EOS code to find_rho.F,
74        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
75    o model/src:
76      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
77      - change default celsius2K from 273.16 to 273.15
78      - to keep results unchanged, add back old value of celsius2K in verification
79        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
80         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
81    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
82      to make TAF generate vectorizable code
83    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
84       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
85       have flags that do this more efficiently.
86    o pkg/diagnostics/diagstats_calc.F
87      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
88    o pkg/obcs (with exch2):
89      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
90        and remove code (in obcs_readparms.F) which was based on EXCH of indices
91        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
92    o pkg/exf and seaice exp:
93      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
94        so that switching off area & heff advection flags does not affect results.
95      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
96      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
97        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
98        results of verification experiments: 1D_ocean_ice_column(fwd),
99        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
100        and offline_exf_seaice (all 4).
101    o pkg/seaice:
102      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
103        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
104      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
105        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
106        not multi-dim advection;
107      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
108        SHORTWAVE_HEATING #undef.
109    o optim: make Makefile more robust (?)
110    o pkg/obcs:
111      * fix treatment of obcs_read_pickup for TAF
112    o pkg/shelfice:
113      * add missing initialisation of num_shifwflx
114      * new adjoint verification exp. for isomip
115      * change Prandtl and Schmidt numbers from generic formulations
116        (in terms of model diffus. and visc.) to separate runtime
117        parameters, with Holland and Jenkins (1999) default values.
118    o pkg/exf (interpolation):
119      - extended input field (2 rows) near the N & S poles:
120        * fill in with the symetric value (when even Nb of data in longitude)
121        * add average value at the poles only for scalar quantities ; for vector
122          component interpolation, skip the averaging and keep duplicated values,
123          unless the 2 components have same location (uvInterp=T) in which case
124          interpolate the 2 components together using S/R EXF_INTERP_UV.
125      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
126        together: this allows to account properly for local orientation when
127        averaging at N & S pole.
128      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
129        exf-interpolation near N & S poles. Undef by default.
130      - add debug check/print on 1rst iter if debugLevel >=2.
131    o pkg/exf:
132      - change masking flags definition (no longer "parameter"), put them in
133        common block and set them in S/R EXF_INIT_FIXED.
134      - change recognized masking flag from s,u,v to c,w,s since the mask
135        to use (maskC,W,S) depends on position on model grid and has little to
136        do with scalar/vector difference; fix masking if using P-coordinates.
137      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
138        and update results of exp. global_with_exf (x2).
139      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
140    o pkg/obcs
141      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
142    o pkg/exf (interpolation):
143      - assume periodicity in X only if input field cover full longitude range.
144      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
145        and should vectorise).
146      - fix input lat of the 2 added row (in case we provide N.pole data).
147    
148    checkpoint63h (2011/12/30)
149    o pkg/seaice:
150      - change declaration of UVM from _RL to _RS in order to get B-grid
151        uIce,vIce monitor when _RS = real*4
152    o pkg/offline:
153      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
154      - compute vertical velocity if not read from file (switch on exactConserv
155        & staggerTimeStep);
156      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
157    o verification:
158      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
159        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
160        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
161      - update output of exp. global_ocean.cs32x15.viscA4 after changing
162        grid-file angles (used here for coriolis-3d);
163      - remove (or gzip) few files not needed to run fizhi-cs experiments.
164    o pkg/exf (vector interpolation):
165      - rotate vector component toward local grid-axis orientation using grid-angles
166        (stored in GRID.h) instead of locally computed rotation angle; keep old code
167        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
168    o pkg/seaice:
169      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
170        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
171    o pkg/PKG_OPTIONS.h files:
172      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
173        outside of the #ifdef ALLOW_THISPKG / #endif block.
174      - update verification/*/code/PKG_OPTIONS.h files.
175    o add a verification experiment (offline_exf_seaice/input.seaice) that test
176      the B-grid LSOR solver
177    o pkg/seaice: sort out emissivity and long wave radiation step 2:
178      - add emissivity for snow and ice as new run-time parameters
179        (unfortunately) that default to the corresponding exf values; this
180        changes results in most verification experiments so that for backward
181        compatibility these parameter have to be set explicitly to inconsistent
182        values (ugly);
183      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
184        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
185        until we agree how to handle this bug properly
186    o pkg/exf (interpolation):
187      - add a set of run-time param ({inputfield}_interpMethod), one for
188        each interpolated input field, to select the interpolation method
189        with a value of zero switching off the interpolation;
190      - print interpolation parameters to standard output;
191      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
192        (to use instead runoff_interpMethod=0 in data.exf).
193      - simplify default setting of interpolation parameters (for all fields,
194        set position to match model grid cell-center position, leading to trivial
195        interpolation in case of regular Lat-Lon grid) and fix for the case of
196        non-uniform delY.
197    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
198       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
199       this factor is absolutely required, because the lw exitance (= out-going
200       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
201       where the reflectivity rho = 1-emissivity for conservation reasons. Once
202       this is established, we can remove the CPP-Flag (if we want to).
203    o pkg/seaice:
204      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
205        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
206      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
207        what the name implies (and not emissivity*BoltzmannConstant), this means
208        the old default value of 5.5e-8 now means
209        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
210        S/R exf_readparms
211      - FV-discretization of the B-grid LSOR solver, turn on with
212        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
213        of the calling routine dynsolver, so that B and C-grid code look a
214        little more alike.
215      - fix index bugs in ostres.F (B-grid code)
216    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
217    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
218      default for SEAICE_emissivity, if useEXF; requires setting a wrong
219      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
220      backward compatiblity
221    o model/src: use sigmaR in calc_ivdc
222    
223    checkpoint63g (2011/12/16)
224    o pkg/seaice/seaice_growth.F:
225      fix heat conservation of the coupled ocean-seaice system.
226      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
227      solid vs liquid water treatment is resolved via QNET.
228    o pkg/seaice/seaice_growth.F:
229      add missing term for sublimation in saltFlux, which was breaking conservation.
230    o pkg/seaice/seaice_model.F:
231      Remove this patholigical case treatment in evolution branch,
232      where it is un-necessary and breaks conservation.
233      Update global_ocean.cs32x15/results accordingly for
234      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
235    o model/src:
236      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
237      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
238    o pkg/obcs:
239      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
240      tendency for temperature and salinity that is then applied to update
241      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
242      horizontal advection and diffusion contributions on the boundary (in
243      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
244      removing the mask in S/R timestep_tracer. The advantage of this approach is
245      that the updated tracer values include contributions from the surface
246      forcing and vertical diffusion.
247      This modification changes exp4.stevens because of vertical diffusion.
248    o model/src:
249      change non-curvilinear grid setting to also work with exch2 + blank tiles:
250      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
251        face dimensions.
252      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
253        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
254        and INI_SPHERICAL_POLAR_GRID.
255      change test-experiment global_ocean.90x40x15:
256      - split the domain in many more tiles (9x4 tiles of 10x10 each);
257      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
258      - update results of both test (std & dwnslp).
259    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
260       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
261    o model/src:
262      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
263        and fix initialisation when using sigma-coords.
264    o model/src:
265     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
266       to their current value at the beginning of forward_step.F": add a new run-time
267       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
268     - set doResetHFactors=T in the following test exp:
269        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
270        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
271        and tutorial_global_oce_in_p (nonLinFS in p)
272    o pkg/ecco
273      - added IES cost term
274    o verification/advect_xz
275      - scale down the depth by 1/100 (from 200 km to just 2.km)
276      - add secondary test using divergent flow, r-star and implicit vertical advection.
277      - add note (check_conserve_TS.txt) and matlab script to check global
278        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
279    o pkg/rbcs:
280      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
281    o pkg/obcs (Stevens BCs):
282      - fix various problems in the phase speed computations of the Stevens
283        boundary conditions:
284        - sign error for western and southern boundaries,
285        - time tendencies were underestimated by factor of dTracerLev and some just
286          zero (for multidim advection schemes) -> now estimate time tendencies
287          from difference between previous (n) time level and the one before (n-1);
288          this requires storing a field per tracer per boundary, also in the pickup
289          files.
290        - replace deltaTmom in cflMer/Zon computation with dTracerLev
291        - set default phase velocity to cflMer/Zon
292      - update verification experiment exp4.stevens
293    o pkg/generic_advdiff (implicit_r):
294      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
295        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
296      - fix implicit vertical diffusion or advection with NonLin FreeSurf
297        (was using current recip_hFacC instead of future recip_hFacC): set future
298        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
299        solver S/R ;
300      - fill diagnostics of vertical advective fluxes (computed from tendency)
301        when using implicit vert. advection;
302      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
303         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
304         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
305         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
306    o pkg/diagnostics:
307      - add diags for T & S tendency which goes through Adams-Bashforth.
308    
309    checkpoint63f (2011/11/30)
310    o pkg/obcs/obcs_calc_stevens.F:
311      - join some loops to reduce number of if-statements
312      - fix a bug in code for northern and southern boundaries.
313    o pkg/seaice/seaice_init_varia.F
314      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
315        caused zero ice-velocities for the B-grid code
316    o pkg/seaice/seaice_init_fixed.F
317      - fix a bug in the initialisation of the second metric terms
318        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
319      - this affects all seaice configurations with useCurviLinearGrid = .true.
320        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
321        = .true. (default)
322      - the only verification experiment affected is global_ocean.cs32x15:
323        icedyn, seaice, and seaice_dynmix (AD)
324    o pkg/thsice/thsice_diagnostics_state.F
325      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
326        not contain garbage that can lead to surprises in diagstats_calc.F
327    o model/src:
328      - move bi,bj loops inside INTEGR_CONTINUITY ;
329      - call INTEGR_CONTINUITY directly from forward_step.F
330        (previously called from momentum_correction_step.F)
331      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
332        forward_step.F and pkg/ecco/the_main_loop.F
333    o model/src/do_oceanic_phys.F:
334      - reset addMass to zero only if useICEFRONT ;
335      - separated k-loop for rhoInSitu calculation ;
336      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
337        and at constant T,S (= WdRHOdP);
338      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
339        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
340        transport of locally-referenced potential density);
341        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
342    o gluemnc:
343      - replace ncrcat with ncks when adding variables to *.glob.nc
344      - change the way variables without record dimensions are handled so that
345        files that have variables with and without record variables can be glued:
346        add a record dimension with a new unique name to be able to differentiate
347        between variable with and without a-prior record dimensions. Remove
348        this record dimension before adding the variable to the *.glob.nc file.
349        This procedure automatically works also for grid.*.nc files that do not
350        have any record dimension.
351    o verification/cpl_aim+ocn:
352      - generate new reference output on baudelaire (gfortran, mpich2) (previously
353        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
354    o pkg/obcs/obcs_calc_stevens.F:
355      - add code for northern and southern boundaries.
356      - reorder some loops to save some operations and so that drFBar can be scalar
357    o model/src:
358      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
359        truncation) and add diagnostics for Adams-Bashforth tendency increment.
360      - update test-exp. AD output:
361        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
362      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
363        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
364        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
365        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
366        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
367        tutorial_plume_on_slope.
368    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
369      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
370      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
371      does not even come with an F77 compiler anymore, this should not be
372      a limitation
373    
374    checkpoint63e (2011/11/06)
375    o pkg/seaice adjoint of LSR:
376      - substantially rework STORE dirs.
377      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
378        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
379        and only perform SOLV_MAX_FIXED adjoint iters.
380        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
381        always goes to same record, meaning that the last forward field will be
382        the one used in the adjoint - an approximation.
383      - now produces non-zero LSR-related gradients, and acceptable gradients for
384        An's zonal (x-z) test case (to be checked in)
385      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
386        (but these are screwed up by the thermodynamics in the first place);
387        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
388        output_adm.txt also reflects changes to seaice_lsr
389      - global_ocean.cs32x15:
390        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
391          (output_adm.seaice.txt was updated)
392        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
393          (output_adm.seaice_dynmix.txt)
394    o test-exp. exp4+stevens:
395      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
396    o pkg/seaice (lsr solver):
397      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
398        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
399      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
400      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
401        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
402      - compute (with new S/R) and print initial (+ free-driff sol. if available)
403        and final residual of linearised system.
404    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
405      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
406    o pkg/obcs: Stevens BCs (still only for east and west)
407      - fix Stevens BCs by using intermediate velocities of previous
408        time step as "baroclinic" contribution rather velocity of one grid cell
409        inside the boundaries; more consistent but makes the entire treatment
410        more complicated, requires new pickup files and two new S/Rs:
411        obcs_copy_uv_n and obcs_save_uv_n
412        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
413        (undefined by default)
414      - silently move computation of some grid factors into separate loops to
415        save some recomputations
416      - add a hack for non-linear free surface
417      - add a verification experiment to exp4 that tests this code
418    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
419    
420    checkpoint63d (2011/10/25)
421    o pkg/obcs + seaice-dynamics:
422      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
423        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
424        values (consistent with an implicit method).
425      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
426        return to older implementation (same results as before); note that none of
427        the "experimental" OBCS_SEAICE options are implemented in the new version.
428      - switch test exp. seaice_obcs to use new version (update output).
429    o pkg/seaice:
430      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
431      - add parenthesis in Water-Ice drag calculations (evp & lsr);
432      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
433        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
434      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
435        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
436    o pkg/layers:
437      - Include potential density as new coordinate (Thanks to David Munday)
438    o pkg/dic:
439      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
440        carbonate computation/output to CALC_PCO2_APPROX
441    o pkg/generic_advdiff
442      - make TAF generate code that vectorizes:
443        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
444    o model/src:
445      - improve vectorization also for adjoint code of
446        solve_tridiagonal and solve_pentadiagonal. As this requires up to
447        5 new 3D-fields, this code is only turned on for the combination of
448        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
449        for singular matrix check (only for TARGET_NEC_SX).
450      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
451        ALLOW_AUTODIFF. This flag now needs to be set outside of
452        solve_tri/pentadiagonal.F
453    o pkg/exf:
454      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
455        optional namelist EXF_NML_OBCS).
456      - add many debug-print (to trace down where pkg/cal error msg comes from)
457    o pkg/mom_vecinv/mom_vi_hdissip.F
458      - rearrange loops so that vectorization is improved and in particular
459        the adjoint routine vectorizes. The code is a little longer now, but I
460        think easier to read.
461        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
462    o pkg/seaice:
463      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
464    o pkg/exch2:
465      - alternative code (without tile x tile matrix) for cumulated (global) sum;
466        used as default; keep using matrix version in adjustment.cs-32x32x1.
467    o tools/build_options:
468      - after merging some MPI and/or multi-threads specific optfiles so that
469        the modified default optfile support both built (using genmake2 -mpi
470        for the MPI built, using genmake2 -omp for OpenMP built),
471        move now obsolete optfiles to tools/build_options/unsupported/
472       (add copy of email sent to support list in doc/optfiles_changes.txt)
473    
474    checkpoint63c (2011/09/28)
475    o pkg/ebm:
476      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
477        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
478    o pkg/seaice (SItracer pickup)
479    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
480      To be done:
481      - thorough testing of missing fields in S/R seaice_read_pickup
482      - thorough matching between generic tracers and specific fields used
483        (e.g. volume-weighted age, area-weighted age, salinity, ...)
484    o pkg/grdchk:
485      - all procs calculate and print finite-difference gradient (for testreport)
486      - change description output used by testreport;
487      - AD testing: also compare and report Finite-difference gradient;
488        => update all output_adm*.txt
489    o test exp. global_ocean_ebm:
490      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
491        and turn on exactConserve; update (fwd) output.
492    o pkg/seaice (LSR):
493      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
494      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
495        * identical results with non-CS topology (but save up to half of EXCH calls)
496        * no much changes in cs-32 verification tests since no ice at face edges
497         (differences due to convergence criteria, since nb of iterations changed)
498        * expect some differences on lat-lon-cap grid.
499        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
500    o pkg/exch2:
501      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
502        many tiles); until alternative coding is added, just add a stop.
503    o pkg/kpp:
504      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
505        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
506    o optfiles:
507      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
508        into corresponding standard one, which now support different build:
509        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
510      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
511    o pkg/obcs (seaice):
512      - add missing EXCH for uIce,vIce after applying OBCS;
513      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
514        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
515        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
516      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
517      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
518        and eedata.mth for MPI and mutlti-threaded testing.
519    o pkg/flt:
520      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
521      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
522      - fix pickup and trajectories + profiles output with multi-threads;
523      - add parameter to select group of fields to write along trajectory and
524        profile (default unchanged);
525      - only call PORT_RAND* function when flt_noise <> 0;
526      - add multi-threaded test for verification exp. flt_example.
527    o eesupp/src:
528      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
529      - USE_OMP_THREADING: check that number of threads (from eedata) matches
530        actual number (from env.var. setting).
531    o pkg/ebm:
532      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
533      - add multi-threaded test for verification exp. global_ocean_ebm
534    
535    checkpoint63b (2011/08/29)
536    o pkg/ebm:
537      - fix sign of runoff;
538      - update directly forcing fields (Qnet,EmPmR) to use standard
539        external_forcing_surf.F (remove ebm_forcing_surf.F);
540      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
541      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
542        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
543      - update global_ocean_ebm parameters file data and update output (fwd+ad).
544    o verification/matrix_example:
545      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
546        MPI and mutlti-threaded testing.
547    o pkg/matrix:
548      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
549      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
550      - fix for multi-threaded (remove DATA statement);
551      - use standard DIFFERENT_MULTIPLE function;
552      - add MATRIX_OPTIONS.h
553    o verification/matrix_example:
554       To allow to split the domain in several tiles, change the domain size
555        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
556        Western side) of land points.
557    o (*_)write_pickup:
558      - fix few bugs in mypackage_read/write_pickup.F
559      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
560        array of length 1 (was caught by compiler syntax-check).
561    o pkg/diagnostics (velocity potential solver):
562      - fix initialisation of main diagonal matrix (for overlap values)
563    o tools/build_options:
564      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
565        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
566      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
567        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
568        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
569        and use "-devel" testreport option for standard testing on baudelaire.
570    o pkg/grdchk:
571      - Assume that all gradient-check position are within the same tile
572        corresponding to global indices (iGloTile,jGloTile) and that
573        positions (i,j indices or nbeg) are local to this tile;
574      - set tile local-indices and proc. number according to tile global-indices;
575      - remove grdchkwhichproc from namelist (retired param);
576      - send adjoint gradient to all procs so that all procs print it to STDOUT;
577      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
578    o adding package bbl (Bottom Boundary Layer)
579      description in MITgcm/pkg/bbl/bbl_description.tex
580      example/test experiment in MITgcm_contrib/bbl
581    o adjoint verifications
582      - changed 5 experiments to multi-tiles
583        * global_ocean.90x40x15
584        * obcs_ctrl
585        * offline_exf_seaice
586        * tutorial_dic_adjoffline
587        * tutorial_tracer_adjsens
588        changed reference output for those that crossed tile boundaries
589        (changed choices of gradient check positions)
590      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
591      - temporary bug fix in grdchk_loc.F for obcs
592    o genmake2 & testreport
593      - add target "obj" (just for OBJFILES files) to Makefile;
594      - add option to specify FEXTRAFLAGS on command line.
595    o pkg/mypackage:
596      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
597    
598    checkpoint63a (2011/08/02)
599    o pkg/diagnostics (velocity potential):
600      - fix velocity-potential calculation when using OBCS: balance net inflow
601        at each level (new S/R OBCS_DIAG_BALANCE).
602      - fix some of the problems with OBCS in stream-function calculation.
603    o pkg/exf/exf_readparms.F
604      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
605        EXF_NML_OBCS) more consistent, so that you need not have these lists
606        in data.exf when they are not used.
607    o optim/optim_readdata.F:
608      - add some output about obcs variables that might help debugging
609      - add a check about nvarlength
610    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
611    o pkg/diagnostics (velocity potential):
612      - fix mask for OBCS (still problems in stream-function with OBCS);
613      - add specific parameter (default = main code CG2D params) for solver;
614      - in case of poor convergence, use solution corresponding to lowest residual.
615    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
616      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
617      and should be avoided where possible.
618    o model/src (rStar):
619      - include r* effect on reference-state (PhiRef) in totPhiHyd
620        (so that it's really the potential anomaly at the cell center);
621        affect solution only if z* with full pressure in EOS.
622      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
623        update output (because of z* in totPhiHyd and viscA4 changes);
624      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
625        @ constant r) until interpolation at constant r is implemented.
626    o pkg/diagnostics
627      - fix RCENTER diagnostics in case cell center is not at interface middle
628    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
629      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
630      that THETA and SALT are "conservative temperature" and "absolute
631      salinity"
632    o pkg/ctrl
633      - fix computation of endrec in s/r ctrl_init_rec
634      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
635    o pkg/seaice/seaice_growth.F
636      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
637        remove then obsolete STORE directives
638      - fix STORE directives for tice and tices, so that only the
639        appropriate part of the fields are stored (and not the entire
640        field); update global_ocean.cs32x15.seaice AD output.
641      - cosmetic changes: adjust CPP flags and indentation for better
642        legibilty
643    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
644      Chris Wilson)
645    o pkg/gmredi:
646       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
647       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
648    
649    checkpoint63  (2011/07/11)
650    o pkg/exch2:
651     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
652     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
653       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
654       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
655    o pkg/diagnostics:
656     - deal with pairs of post-processed diags which are computed together; in
657       particular, re-order list of diags within 1 file to save 2nd computation.
658     - add S/R to compute velocity stream-function (called after velocity-potential
659       calculation) from divergence free transport -> new diagnostics "PsiVEL".
660     - add parameter to select grid-point location where PsiVEL == 0.
661    o eesupp/src:
662       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
663       (specific S/R needed with exch2 topology - for now, just print an error msg)
664    o pkg/shelfice
665     - Implement friction velocity-dependent transfer coefficients following
666       Holland and Jenkins, JPO, 1999
667       Original code by M. Losch with small modifs.
668       Enable with CPP option SHI_ALLOW_GAMMAFRICT
669       and runtime flag SHELFICEuseGammaFrict
670    o verification lab_sea & global_ocean.cs32x15:
671     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
672       does not miss some dependencies (but is slower) and also works with many files
673       (default makedepend limitation for AD built).
674     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
675    o pkg/diagnostics:
676     - add run-time parameter "useMissingValue" (def=False) to fill land-point
677        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
678       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
679     - Extend the use of "missing_value" setting from data.diagnostics for the case
680       of counter-diagnostics (where fraction-weight is zero). This applies both to
681       MNC and MDS output files.
682    o pkg/seaice/seaice_growth.F:
683      - add 'a priori' cap of latent heat flux based on actual mass considerations
684        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
685        non-legacy seaice_solve4temp.
686      - add diagnostic of the residual sublimation freshwater flux (the freshwater
687        flux taken from the ocean if the total actual latent heat fluxes exceed
688        the maximum)
689      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
690       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
691      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
692       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
693      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
694      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
695    o verification 1D_ocean_ice_column:
696       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
697       update results
698    o pkg/diagnostics:
699     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
700       which are not filled-up but computed from other diags ; In this case, the mate
701       diag points to the primary (filled-up) diag to used for post processing.
702     - Update Velocity-potential computation using post-processed diag framework.
703     ==> Change the ordering of fields and time-periods in MDS output file
704       when using periodic averaging: now writes one time record with the full set
705       of fields for this time period, then the next time reccord (it used to be
706       one field with the full set of time records then the next field).
707         Note: this is now similar to NetCDF (MNC) output file. <==
708    
709    checkpoint62z (2011/06/21)
710    o adjoint monitor:
711     - Add adjoint monitor output for packages exf, seaice
712       and update relevant testreport output
713    o pkg/seaice:
714     - re-order diags inits so that they appear in order in available_diagnostics.log
715     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
716       area/heff/hsnow preceeding thermodynamic growth/melt.
717     - modified diag: SIdA; output actual effect, as the description states.
718     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
719     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
720       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
721        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
722     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
723     - added diagnostics for seaice generic tracers (SItr*).
724     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
725     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
726     I. Fenty: 18-Jun-2011:
727     Minor changes to seaice package:
728     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
729        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
730       - Differentiated "regularization variables" from "floor variables"
731        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
732        * hiceMin became SEAICE_hice_reg (old hiceMin)
733          (with _reg meaning regularization variable)
734       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
735        so as to ensure energy conservation when going between phases
736      - A22 was not used anywhere
737     2) Changed regularization procedure for heffActual and hsnowActual to ensure
738        well-boundedness and smooth adjoint in seaice_growth.F
739     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
740        because the old regularization always set heffActual >= 0.05 cm
741     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
742        on AREA when HEFF > 0.
743      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
744        requiring that DISABLE_AREA_FLOOR *not* be defined
745     Affected verifications:
746      - 1D_ocean_ice_column (output.txt output_adm.txt)
747      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
748    o pkg/diagnostics:
749      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
750      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
751        (was _RL, now integer) with option = 0 to retrieve all levels.
752      - add pieces of code to compute velocity potential at each level (new diagnostics
753        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
754        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
755      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
756        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
757        and in diagnostics_fract_fill.F (do not need a valid pointer for the
758        diagnostics counter-mate); check that definition of counter-diagnostic
759        includes a valid counter-mate (in diagnostics_set_levels.F).
760    o model/src (rStar):
761      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
762        affect solution only if z* with full pressure in EOS;
763        update output of test-exp global_ocean.90x40x15.
764    o pkg/seaice:
765      - introduce siEps=1e-5 parameter
766      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
767      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
768      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
769        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
770        as well as ice cover age and ridging index (attached to AREA).
771        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
772        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
773        Up to SItrMaxNum=3 tracers can be used simultaneously.
774    o pkg/salt_plume:
775      -introduce SPsalFRAC run time parameter that sets the fraction of the
776       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
777       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
778    o model debug options:
779      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
780        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
781      - Refine debug-msg printing selection (3 new levels):
782        debugMode  : controls printing of debug messages (sequence of S/R calls).
783        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
784         debLevZero =  0 ; /* level of disabled aux. msg printing */
785         debLevA =  1 ; /* level of minimum  aux. msg printing */
786         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
787         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
788         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
789         debLevE =  5 ; /* level of extensive debug printing */
790        New debugLevel default: with default debugMode value (=F),
791          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
792          and if debugMode=T, default debugLevel = 4 (debLevD).
793        Relation with previous settings:
794         debLevB (=2) corresponds to former debLevA (=1)
795         debLevD (=4) corresponds to former debLevB (=2)
796        Note:
797         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
798         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
799            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
800      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
801        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
802    o pkg/obcs:
803      - change OBCSfixTopo default from True to False (should not change the results);
804        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
805    o pkg/thsice:
806      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
807        2nd layer seaice sublimation (unlikely to happen)
808      - use Interior mask for OBCS in thsice_advection.F (similar to what is
809        done in gad_advection & seaice_advection).
810    o adjoint:
811      bug fix spotted by Gael Forget:
812      seaice_advection and thsice_advection still had
813      legacy CPP options to avoid CS corner updates for adjoint
814    o pkg/seaice:
815      => Change some of the defaults (2011/05/29):
816         - change SEAICEuseFluxForm default (from False to True)
817         - change DIFF1 default (from 0.004 m/s to 0. m/s)
818         And print warnings if DIFF1 is not set in data.seaice and centered
819          avection scheme is used without any diffusion.
820      also:
821      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
822      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
823      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
824        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
825        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
826      update results of test exp.:
827         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
828             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
829             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
830         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
831         seaice_obcs: output (SEAICEuseFluxForm=T)
832      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
833          for standard fwd & AD lab_sea tests (to keep the same output).
834    o pkg/seaice/seaice_growth.F:
835      - use Ian Fenty's capping formulas for actual ice
836      thickness thoughout EVOLUTION branch.
837      - put treatment pathological case #2) in CPP brackets
838      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
839      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
840    o pkg/seaice:
841      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
842      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
843      also pass fac as a param, which can be 1. (to update the tendency
844      field) or the time step (to update the field itself).
845      - seaice_advdiff.F: for multidim, call seaice_diffusion with
846      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
847      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
848      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
849      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
850    o pkg/seaice:
851      diffusion with centered advection scheme (diffus.F & advect.F):
852      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
853        to just compute the laplacian of input-field.
854      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
855      - fix flux-form version in diffus.F to conserve tracer.
856      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
857       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
858    
859    checkpoint62y (2011/05/26)
860    o pkg/seaice:
861     - seaice_growth.F : in EVOLUTION branch, always include
862     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
863   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
864     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
865  o pkg/seaice + obcs:  o pkg/seaice + obcs:
866   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
867     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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