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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1589 by gforget, Fri Feb 3 15:21:38 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
9    o pkg/seaice:
10      - seaice_solve4temp.F (keeping results unchanged):
11        * add 2 future run-time params to select which saturation vapor pressure
12          formula is used and how post-iteration fluxes are set.
13          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
14        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
15          the linearized expression to stay consistent with tsurf finding.
16      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
17        can be < 0.
18    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
19      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
20        conductive heat flux F_c , and add it explicitly when updating tsurf as
21        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
22        so that now F_ia has a consistent meaning through the entire routine.
23        This causes differences at truncation level: update output of fwd exp.
24        global_ocean.cs32x15.seaice.
25    o pkg/seaice:
26      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
27        of arrays, sign/direction of fluxes; no effect on results.
28      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
29        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
30        note: this should have been done before changing celsius2K default.
31      - to keep results unchanged, add back old value of celsius2K in verification
32        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
33      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
34        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
35        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
36        freezing temp is consistent with value in seaice_growth.F ; this causes
37        differences at machine truncation level: update lab_sea AD output (3/4).
38    o pkg/seaice:
39      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
40        and climsst/sss even when using seaice (to prevent calculation that might
41        use SST on land); does not affect any verification exp.
42      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
43        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
44    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
45      over land (non-legacy code)
46    o vectorize salt_plume package:
47      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
48      - this code computes plumebk everywhere (also over land), thus requires
49        code to avoid divisions by zero and catch the case of kLev=Nr.
50      - efficiency of salt_plume_frac is still sub-optimal
51    o tools (genmake2):
52      - fix makefile NAME specification (option: -makefile NAME) by adding
53        "-f $MAKEFILE" in few places where it was missing including makedepend
54        command (contribution from Paul).
55    
56    checkpoint63i (2012/01/24)
57    o model/src:
58      - add factorized versions of some EOS code to find_rho.F,
59        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
60    o model/src:
61      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
62      - change default celsius2K from 273.16 to 273.15
63      - to keep results unchanged, add back old value of celsius2K in verification
64        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
65         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
66    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
67      to make TAF generate vectorizable code
68    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
69       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
70       have flags that do this more efficiently.
71    o pkg/diagnostics/diagstats_calc.F
72      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
73    o pkg/obcs (with exch2):
74      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
75        and remove code (in obcs_readparms.F) which was based on EXCH of indices
76        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
77    o pkg/exf and seaice exp:
78      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
79        so that switching off area & heff advection flags does not affect results.
80      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
81      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
82        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
83        results of verification experiments: 1D_ocean_ice_column(fwd),
84        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
85        and offline_exf_seaice (all 4).
86    o pkg/seaice:
87      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
88        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
89      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
90        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
91        not multi-dim advection;
92      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
93        SHORTWAVE_HEATING #undef.
94    o optim: make Makefile more robust (?)
95    o pkg/obcs:
96      * fix treatment of obcs_read_pickup for TAF
97    o pkg/shelfice:
98      * add missing initialisation of num_shifwflx
99      * new adjoint verification exp. for isomip
100      * change Prandtl and Schmidt numbers from generic formulations
101        (in terms of model diffus. and visc.) to separate runtime
102        parameters, with Holland and Jenkins (1999) default values.
103    o pkg/exf (interpolation):
104      - extended input field (2 rows) near the N & S poles:
105        * fill in with the symetric value (when even Nb of data in longitude)
106        * add average value at the poles only for scalar quantities ; for vector
107          component interpolation, skip the averaging and keep duplicated values,
108          unless the 2 components have same location (uvInterp=T) in which case
109          interpolate the 2 components together using S/R EXF_INTERP_UV.
110      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
111        together: this allows to account properly for local orientation when
112        averaging at N & S pole.
113      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
114        exf-interpolation near N & S poles. Undef by default.
115      - add debug check/print on 1rst iter if debugLevel >=2.
116    o pkg/exf:
117      - change masking flags definition (no longer "parameter"), put them in
118        common block and set them in S/R EXF_INIT_FIXED.
119      - change recognized masking flag from s,u,v to c,w,s since the mask
120        to use (maskC,W,S) depends on position on model grid and has little to
121        do with scalar/vector difference; fix masking if using P-coordinates.
122      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
123        and update results of exp. global_with_exf (x2).
124      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
125    o pkg/obcs
126      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
127    o pkg/exf (interpolation):
128      - assume periodicity in X only if input field cover full longitude range.
129      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
130        and should vectorise).
131      - fix input lat of the 2 added row (in case we provide N.pole data).
132    
133    checkpoint63h (2011/12/30)
134    o pkg/seaice:
135      - change declaration of UVM from _RL to _RS in order to get B-grid
136        uIce,vIce monitor when _RS = real*4
137    o pkg/offline:
138      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
139      - compute vertical velocity if not read from file (switch on exactConserv
140        & staggerTimeStep);
141      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
142    o verification:
143      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
144        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
145        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
146      - update output of exp. global_ocean.cs32x15.viscA4 after changing
147        grid-file angles (used here for coriolis-3d);
148      - remove (or gzip) few files not needed to run fizhi-cs experiments.
149    o pkg/exf (vector interpolation):
150      - rotate vector component toward local grid-axis orientation using grid-angles
151        (stored in GRID.h) instead of locally computed rotation angle; keep old code
152        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
153    o pkg/seaice:
154      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
155        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
156    o pkg/PKG_OPTIONS.h files:
157      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
158        outside of the #ifdef ALLOW_THISPKG / #endif block.
159      - update verification/*/code/PKG_OPTIONS.h files.
160    o add a verification experiment (offline_exf_seaice/input.seaice) that test
161      the B-grid LSOR solver
162    o pkg/seaice: sort out emissivity and long wave radiation step 2:
163      - add emissivity for snow and ice as new run-time parameters
164        (unfortunately) that default to the corresponding exf values; this
165        changes results in most verification experiments so that for backward
166        compatibility these parameter have to be set explicitly to inconsistent
167        values (ugly);
168      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
169        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
170        until we agree how to handle this bug properly
171    o pkg/exf (interpolation):
172      - add a set of run-time param ({inputfield}_interpMethod), one for
173        each interpolated input field, to select the interpolation method
174        with a value of zero switching off the interpolation;
175      - print interpolation parameters to standard output;
176      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
177        (to use instead runoff_interpMethod=0 in data.exf).
178      - simplify default setting of interpolation parameters (for all fields,
179        set position to match model grid cell-center position, leading to trivial
180        interpolation in case of regular Lat-Lon grid) and fix for the case of
181        non-uniform delY.
182    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
183       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
184       this factor is absolutely required, because the lw exitance (= out-going
185       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
186       where the reflectivity rho = 1-emissivity for conservation reasons. Once
187       this is established, we can remove the CPP-Flag (if we want to).
188    o pkg/seaice:
189      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
190        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
191      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
192        what the name implies (and not emissivity*BoltzmannConstant), this means
193        the old default value of 5.5e-8 now means
194        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
195        S/R exf_readparms
196      - FV-discretization of the B-grid LSOR solver, turn on with
197        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
198        of the calling routine dynsolver, so that B and C-grid code look a
199        little more alike.
200      - fix index bugs in ostres.F (B-grid code)
201    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
202    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
203      default for SEAICE_emissivity, if useEXF; requires setting a wrong
204      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
205      backward compatiblity
206    o model/src: use sigmaR in calc_ivdc
207    
208    checkpoint63g (2011/12/16)
209    o pkg/seaice/seaice_growth.F:
210      fix heat conservation of the coupled ocean-seaice system.
211      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
212      solid vs liquid water treatment is resolved via QNET.
213    o pkg/seaice/seaice_growth.F:
214      add missing term for sublimation in saltFlux, which was breaking conservation.
215    o pkg/seaice/seaice_model.F:
216      Remove this patholigical case treatment in evolution branch,
217      where it is un-necessary and breaks conservation.
218      Update global_ocean.cs32x15/results accordingly for
219      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
220    o model/src:
221      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
222      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
223    o pkg/obcs:
224      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
225      tendency for temperature and salinity that is then applied to update
226      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
227      horizontal advection and diffusion contributions on the boundary (in
228      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
229      removing the mask in S/R timestep_tracer. The advantage of this approach is
230      that the updated tracer values include contributions from the surface
231      forcing and vertical diffusion.
232      This modification changes exp4.stevens because of vertical diffusion.
233    o model/src:
234      change non-curvilinear grid setting to also work with exch2 + blank tiles:
235      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
236        face dimensions.
237      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
238        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
239        and INI_SPHERICAL_POLAR_GRID.
240      change test-experiment global_ocean.90x40x15:
241      - split the domain in many more tiles (9x4 tiles of 10x10 each);
242      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
243      - update results of both test (std & dwnslp).
244    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
245       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
246    o model/src:
247      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
248        and fix initialisation when using sigma-coords.
249    o model/src:
250     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
251       to their current value at the beginning of forward_step.F": add a new run-time
252       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
253     - set doResetHFactors=T in the following test exp:
254        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
255        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
256        and tutorial_global_oce_in_p (nonLinFS in p)
257    o pkg/ecco
258      - added IES cost term
259    o verification/advect_xz
260      - scale down the depth by 1/100 (from 200 km to just 2.km)
261      - add secondary test using divergent flow, r-star and implicit vertical advection.
262      - add note (check_conserve_TS.txt) and matlab script to check global
263        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
264    o pkg/rbcs:
265      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
266    o pkg/obcs (Stevens BCs):
267      - fix various problems in the phase speed computations of the Stevens
268        boundary conditions:
269        - sign error for western and southern boundaries,
270        - time tendencies were underestimated by factor of dTracerLev and some just
271          zero (for multidim advection schemes) -> now estimate time tendencies
272          from difference between previous (n) time level and the one before (n-1);
273          this requires storing a field per tracer per boundary, also in the pickup
274          files.
275        - replace deltaTmom in cflMer/Zon computation with dTracerLev
276        - set default phase velocity to cflMer/Zon
277      - update verification experiment exp4.stevens
278    o pkg/generic_advdiff (implicit_r):
279      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
280        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
281      - fix implicit vertical diffusion or advection with NonLin FreeSurf
282        (was using current recip_hFacC instead of future recip_hFacC): set future
283        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
284        solver S/R ;
285      - fill diagnostics of vertical advective fluxes (computed from tendency)
286        when using implicit vert. advection;
287      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
288         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
289         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
290         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
291    o pkg/diagnostics:
292      - add diags for T & S tendency which goes through Adams-Bashforth.
293    
294    checkpoint63f (2011/11/30)
295    o pkg/obcs/obcs_calc_stevens.F:
296      - join some loops to reduce number of if-statements
297      - fix a bug in code for northern and southern boundaries.
298    o pkg/seaice/seaice_init_varia.F
299      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
300        caused zero ice-velocities for the B-grid code
301    o pkg/seaice/seaice_init_fixed.F
302      - fix a bug in the initialisation of the second metric terms
303        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
304      - this affects all seaice configurations with useCurviLinearGrid = .true.
305        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
306        = .true. (default)
307      - the only verification experiment affected is global_ocean.cs32x15:
308        icedyn, seaice, and seaice_dynmix (AD)
309    o pkg/thsice/thsice_diagnostics_state.F
310      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
311        not contain garbage that can lead to surprises in diagstats_calc.F
312    o model/src:
313      - move bi,bj loops inside INTEGR_CONTINUITY ;
314      - call INTEGR_CONTINUITY directly from forward_step.F
315        (previously called from momentum_correction_step.F)
316      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
317        forward_step.F and pkg/ecco/the_main_loop.F
318    o model/src/do_oceanic_phys.F:
319      - reset addMass to zero only if useICEFRONT ;
320      - separated k-loop for rhoInSitu calculation ;
321      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
322        and at constant T,S (= WdRHOdP);
323      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
324        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
325        transport of locally-referenced potential density);
326        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
327    o gluemnc:
328      - replace ncrcat with ncks when adding variables to *.glob.nc
329      - change the way variables without record dimensions are handled so that
330        files that have variables with and without record variables can be glued:
331        add a record dimension with a new unique name to be able to differentiate
332        between variable with and without a-prior record dimensions. Remove
333        this record dimension before adding the variable to the *.glob.nc file.
334        This procedure automatically works also for grid.*.nc files that do not
335        have any record dimension.
336    o verification/cpl_aim+ocn:
337      - generate new reference output on baudelaire (gfortran, mpich2) (previously
338        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
339    o pkg/obcs/obcs_calc_stevens.F:
340      - add code for northern and southern boundaries.
341      - reorder some loops to save some operations and so that drFBar can be scalar
342    o model/src:
343      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
344        truncation) and add diagnostics for Adams-Bashforth tendency increment.
345      - update test-exp. AD output:
346        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
347      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
348        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
349        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
350        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
351        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
352        tutorial_plume_on_slope.
353    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
354      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
355      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
356      does not even come with an F77 compiler anymore, this should not be
357      a limitation
358    
359    checkpoint63e (2011/11/06)
360    o pkg/seaice adjoint of LSR:
361      - substantially rework STORE dirs.
362      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
363        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
364        and only perform SOLV_MAX_FIXED adjoint iters.
365        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
366        always goes to same record, meaning that the last forward field will be
367        the one used in the adjoint - an approximation.
368      - now produces non-zero LSR-related gradients, and acceptable gradients for
369        An's zonal (x-z) test case (to be checked in)
370      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
371        (but these are screwed up by the thermodynamics in the first place);
372        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
373        output_adm.txt also reflects changes to seaice_lsr
374      - global_ocean.cs32x15:
375        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
376          (output_adm.seaice.txt was updated)
377        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
378          (output_adm.seaice_dynmix.txt)
379    o test-exp. exp4+stevens:
380      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
381    o pkg/seaice (lsr solver):
382      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
383        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
384      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
385      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
386        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
387      - compute (with new S/R) and print initial (+ free-driff sol. if available)
388        and final residual of linearised system.
389    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
390      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
391    o pkg/obcs: Stevens BCs (still only for east and west)
392      - fix Stevens BCs by using intermediate velocities of previous
393        time step as "baroclinic" contribution rather velocity of one grid cell
394        inside the boundaries; more consistent but makes the entire treatment
395        more complicated, requires new pickup files and two new S/Rs:
396        obcs_copy_uv_n and obcs_save_uv_n
397        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
398        (undefined by default)
399      - silently move computation of some grid factors into separate loops to
400        save some recomputations
401      - add a hack for non-linear free surface
402      - add a verification experiment to exp4 that tests this code
403    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
404    
405    checkpoint63d (2011/10/25)
406    o pkg/obcs + seaice-dynamics:
407      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
408        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
409        values (consistent with an implicit method).
410      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
411        return to older implementation (same results as before); note that none of
412        the "experimental" OBCS_SEAICE options are implemented in the new version.
413      - switch test exp. seaice_obcs to use new version (update output).
414    o pkg/seaice:
415      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
416      - add parenthesis in Water-Ice drag calculations (evp & lsr);
417      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
418        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
419      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
420        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
421    o pkg/layers:
422      - Include potential density as new coordinate (Thanks to David Munday)
423    o pkg/dic:
424      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
425        carbonate computation/output to CALC_PCO2_APPROX
426    o pkg/generic_advdiff
427      - make TAF generate code that vectorizes:
428        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
429    o model/src:
430      - improve vectorization also for adjoint code of
431        solve_tridiagonal and solve_pentadiagonal. As this requires up to
432        5 new 3D-fields, this code is only turned on for the combination of
433        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
434        for singular matrix check (only for TARGET_NEC_SX).
435      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
436        ALLOW_AUTODIFF. This flag now needs to be set outside of
437        solve_tri/pentadiagonal.F
438    o pkg/exf:
439      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
440        optional namelist EXF_NML_OBCS).
441      - add many debug-print (to trace down where pkg/cal error msg comes from)
442    o pkg/mom_vecinv/mom_vi_hdissip.F
443      - rearrange loops so that vectorization is improved and in particular
444        the adjoint routine vectorizes. The code is a little longer now, but I
445        think easier to read.
446        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
447    o pkg/seaice:
448      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
449    o pkg/exch2:
450      - alternative code (without tile x tile matrix) for cumulated (global) sum;
451        used as default; keep using matrix version in adjustment.cs-32x32x1.
452    o tools/build_options:
453      - after merging some MPI and/or multi-threads specific optfiles so that
454        the modified default optfile support both built (using genmake2 -mpi
455        for the MPI built, using genmake2 -omp for OpenMP built),
456        move now obsolete optfiles to tools/build_options/unsupported/
457       (add copy of email sent to support list in doc/optfiles_changes.txt)
458    
459    checkpoint63c (2011/09/28)
460    o pkg/ebm:
461      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
462        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
463    o pkg/seaice (SItracer pickup)
464    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
465      To be done:
466      - thorough testing of missing fields in S/R seaice_read_pickup
467      - thorough matching between generic tracers and specific fields used
468        (e.g. volume-weighted age, area-weighted age, salinity, ...)
469    o pkg/grdchk:
470      - all procs calculate and print finite-difference gradient (for testreport)
471      - change description output used by testreport;
472      - AD testing: also compare and report Finite-difference gradient;
473        => update all output_adm*.txt
474    o test exp. global_ocean_ebm:
475      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
476        and turn on exactConserve; update (fwd) output.
477    o pkg/seaice (LSR):
478      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
479      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
480        * identical results with non-CS topology (but save up to half of EXCH calls)
481        * no much changes in cs-32 verification tests since no ice at face edges
482         (differences due to convergence criteria, since nb of iterations changed)
483        * expect some differences on lat-lon-cap grid.
484        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
485    o pkg/exch2:
486      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
487        many tiles); until alternative coding is added, just add a stop.
488    o pkg/kpp:
489      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
490        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
491    o optfiles:
492      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
493        into corresponding standard one, which now support different build:
494        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
495      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
496    o pkg/obcs (seaice):
497      - add missing EXCH for uIce,vIce after applying OBCS;
498      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
499        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
500        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
501      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
502      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
503        and eedata.mth for MPI and mutlti-threaded testing.
504    o pkg/flt:
505      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
506      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
507      - fix pickup and trajectories + profiles output with multi-threads;
508      - add parameter to select group of fields to write along trajectory and
509        profile (default unchanged);
510      - only call PORT_RAND* function when flt_noise <> 0;
511      - add multi-threaded test for verification exp. flt_example.
512    o eesupp/src:
513      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
514      - USE_OMP_THREADING: check that number of threads (from eedata) matches
515        actual number (from env.var. setting).
516    o pkg/ebm:
517      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
518      - add multi-threaded test for verification exp. global_ocean_ebm
519    
520    checkpoint63b (2011/08/29)
521    o pkg/ebm:
522      - fix sign of runoff;
523      - update directly forcing fields (Qnet,EmPmR) to use standard
524        external_forcing_surf.F (remove ebm_forcing_surf.F);
525      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
526      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
527        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
528      - update global_ocean_ebm parameters file data and update output (fwd+ad).
529    o verification/matrix_example:
530      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
531        MPI and mutlti-threaded testing.
532    o pkg/matrix:
533      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
534      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
535      - fix for multi-threaded (remove DATA statement);
536      - use standard DIFFERENT_MULTIPLE function;
537      - add MATRIX_OPTIONS.h
538    o verification/matrix_example:
539       To allow to split the domain in several tiles, change the domain size
540        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
541        Western side) of land points.
542    o (*_)write_pickup:
543      - fix few bugs in mypackage_read/write_pickup.F
544      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
545        array of length 1 (was caught by compiler syntax-check).
546    o pkg/diagnostics (velocity potential solver):
547      - fix initialisation of main diagonal matrix (for overlap values)
548    o tools/build_options:
549      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
550        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
551      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
552        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
553        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
554        and use "-devel" testreport option for standard testing on baudelaire.
555    o pkg/grdchk:
556      - Assume that all gradient-check position are within the same tile
557        corresponding to global indices (iGloTile,jGloTile) and that
558        positions (i,j indices or nbeg) are local to this tile;
559      - set tile local-indices and proc. number according to tile global-indices;
560      - remove grdchkwhichproc from namelist (retired param);
561      - send adjoint gradient to all procs so that all procs print it to STDOUT;
562      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
563    o adding package bbl (Bottom Boundary Layer)
564      description in MITgcm/pkg/bbl/bbl_description.tex
565      example/test experiment in MITgcm_contrib/bbl
566    o adjoint verifications
567      - changed 5 experiments to multi-tiles
568        * global_ocean.90x40x15
569        * obcs_ctrl
570        * offline_exf_seaice
571        * tutorial_dic_adjoffline
572        * tutorial_tracer_adjsens
573        changed reference output for those that crossed tile boundaries
574        (changed choices of gradient check positions)
575      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
576      - temporary bug fix in grdchk_loc.F for obcs
577    o genmake2 & testreport
578      - add target "obj" (just for OBJFILES files) to Makefile;
579      - add option to specify FEXTRAFLAGS on command line.
580    o pkg/mypackage:
581      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
582    
583    checkpoint63a (2011/08/02)
584    o pkg/diagnostics (velocity potential):
585      - fix velocity-potential calculation when using OBCS: balance net inflow
586        at each level (new S/R OBCS_DIAG_BALANCE).
587      - fix some of the problems with OBCS in stream-function calculation.
588    o pkg/exf/exf_readparms.F
589      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
590        EXF_NML_OBCS) more consistent, so that you need not have these lists
591        in data.exf when they are not used.
592    o optim/optim_readdata.F:
593      - add some output about obcs variables that might help debugging
594      - add a check about nvarlength
595    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
596    o pkg/diagnostics (velocity potential):
597      - fix mask for OBCS (still problems in stream-function with OBCS);
598      - add specific parameter (default = main code CG2D params) for solver;
599      - in case of poor convergence, use solution corresponding to lowest residual.
600    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
601      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
602      and should be avoided where possible.
603    o model/src (rStar):
604      - include r* effect on reference-state (PhiRef) in totPhiHyd
605        (so that it's really the potential anomaly at the cell center);
606        affect solution only if z* with full pressure in EOS.
607      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
608        update output (because of z* in totPhiHyd and viscA4 changes);
609      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
610        @ constant r) until interpolation at constant r is implemented.
611    o pkg/diagnostics
612      - fix RCENTER diagnostics in case cell center is not at interface middle
613    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
614      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
615      that THETA and SALT are "conservative temperature" and "absolute
616      salinity"
617    o pkg/ctrl
618      - fix computation of endrec in s/r ctrl_init_rec
619      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
620    o pkg/seaice/seaice_growth.F
621      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
622        remove then obsolete STORE directives
623      - fix STORE directives for tice and tices, so that only the
624        appropriate part of the fields are stored (and not the entire
625        field); update global_ocean.cs32x15.seaice AD output.
626      - cosmetic changes: adjust CPP flags and indentation for better
627        legibilty
628    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
629      Chris Wilson)
630    o pkg/gmredi:
631       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
632       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
633    
634    checkpoint63  (2011/07/11)
635    o pkg/exch2:
636     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
637     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
638       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
639       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
640    o pkg/diagnostics:
641     - deal with pairs of post-processed diags which are computed together; in
642       particular, re-order list of diags within 1 file to save 2nd computation.
643     - add S/R to compute velocity stream-function (called after velocity-potential
644       calculation) from divergence free transport -> new diagnostics "PsiVEL".
645     - add parameter to select grid-point location where PsiVEL == 0.
646    o eesupp/src:
647       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
648       (specific S/R needed with exch2 topology - for now, just print an error msg)
649    o pkg/shelfice
650     - Implement friction velocity-dependent transfer coefficients following
651       Holland and Jenkins, JPO, 1999
652       Original code by M. Losch with small modifs.
653       Enable with CPP option SHI_ALLOW_GAMMAFRICT
654       and runtime flag SHELFICEuseGammaFrict
655    o verification lab_sea & global_ocean.cs32x15:
656     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
657       does not miss some dependencies (but is slower) and also works with many files
658       (default makedepend limitation for AD built).
659     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
660    o pkg/diagnostics:
661     - add run-time parameter "useMissingValue" (def=False) to fill land-point
662        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
663       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
664     - Extend the use of "missing_value" setting from data.diagnostics for the case
665       of counter-diagnostics (where fraction-weight is zero). This applies both to
666       MNC and MDS output files.
667    o pkg/seaice/seaice_growth.F:
668      - add 'a priori' cap of latent heat flux based on actual mass considerations
669        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
670        non-legacy seaice_solve4temp.
671      - add diagnostic of the residual sublimation freshwater flux (the freshwater
672        flux taken from the ocean if the total actual latent heat fluxes exceed
673        the maximum)
674      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
675       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
676      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
677       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
678      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
679      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
680    o verification 1D_ocean_ice_column:
681       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
682       update results
683    o pkg/diagnostics:
684     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
685       which are not filled-up but computed from other diags ; In this case, the mate
686       diag points to the primary (filled-up) diag to used for post processing.
687     - Update Velocity-potential computation using post-processed diag framework.
688     ==> Change the ordering of fields and time-periods in MDS output file
689       when using periodic averaging: now writes one time record with the full set
690       of fields for this time period, then the next time reccord (it used to be
691       one field with the full set of time records then the next field).
692         Note: this is now similar to NetCDF (MNC) output file. <==
693    
694    checkpoint62z (2011/06/21)
695    o adjoint monitor:
696     - Add adjoint monitor output for packages exf, seaice
697       and update relevant testreport output
698    o pkg/seaice:
699     - re-order diags inits so that they appear in order in available_diagnostics.log
700     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
701       area/heff/hsnow preceeding thermodynamic growth/melt.
702     - modified diag: SIdA; output actual effect, as the description states.
703     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
704     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
705       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
706        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
707     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
708     - added diagnostics for seaice generic tracers (SItr*).
709     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
710     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
711     I. Fenty: 18-Jun-2011:
712     Minor changes to seaice package:
713     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
714        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
715       - Differentiated "regularization variables" from "floor variables"
716        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
717        * hiceMin became SEAICE_hice_reg (old hiceMin)
718          (with _reg meaning regularization variable)
719       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
720        so as to ensure energy conservation when going between phases
721      - A22 was not used anywhere
722     2) Changed regularization procedure for heffActual and hsnowActual to ensure
723        well-boundedness and smooth adjoint in seaice_growth.F
724     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
725        because the old regularization always set heffActual >= 0.05 cm
726     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
727        on AREA when HEFF > 0.
728      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
729        requiring that DISABLE_AREA_FLOOR *not* be defined
730     Affected verifications:
731      - 1D_ocean_ice_column (output.txt output_adm.txt)
732      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
733    o pkg/diagnostics:
734      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
735      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
736        (was _RL, now integer) with option = 0 to retrieve all levels.
737      - add pieces of code to compute velocity potential at each level (new diagnostics
738        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
739        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
740      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
741        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
742        and in diagnostics_fract_fill.F (do not need a valid pointer for the
743        diagnostics counter-mate); check that definition of counter-diagnostic
744        includes a valid counter-mate (in diagnostics_set_levels.F).
745    o model/src (rStar):
746      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
747        affect solution only if z* with full pressure in EOS;
748        update output of test-exp global_ocean.90x40x15.
749    o pkg/seaice:
750      - introduce siEps=1e-5 parameter
751      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
752      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
753      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
754        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
755        as well as ice cover age and ridging index (attached to AREA).
756        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
757        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
758        Up to SItrMaxNum=3 tracers can be used simultaneously.
759    o pkg/salt_plume:
760      -introduce SPsalFRAC run time parameter that sets the fraction of the
761       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
762       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
763    o model debug options:
764      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
765        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
766      - Refine debug-msg printing selection (3 new levels):
767        debugMode  : controls printing of debug messages (sequence of S/R calls).
768        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
769         debLevZero =  0 ; /* level of disabled aux. msg printing */
770         debLevA =  1 ; /* level of minimum  aux. msg printing */
771         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
772         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
773         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
774         debLevE =  5 ; /* level of extensive debug printing */
775        New debugLevel default: with default debugMode value (=F),
776          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
777          and if debugMode=T, default debugLevel = 4 (debLevD).
778        Relation with previous settings:
779         debLevB (=2) corresponds to former debLevA (=1)
780         debLevD (=4) corresponds to former debLevB (=2)
781        Note:
782         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
783         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
784            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
785      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
786        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
787    o pkg/obcs:
788      - change OBCSfixTopo default from True to False (should not change the results);
789        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
790    o pkg/thsice:
791      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
792        2nd layer seaice sublimation (unlikely to happen)
793      - use Interior mask for OBCS in thsice_advection.F (similar to what is
794        done in gad_advection & seaice_advection).
795    o adjoint:
796      bug fix spotted by Gael Forget:
797      seaice_advection and thsice_advection still had
798      legacy CPP options to avoid CS corner updates for adjoint
799    o pkg/seaice:
800      => Change some of the defaults (2011/05/29):
801         - change SEAICEuseFluxForm default (from False to True)
802         - change DIFF1 default (from 0.004 m/s to 0. m/s)
803         And print warnings if DIFF1 is not set in data.seaice and centered
804          avection scheme is used without any diffusion.
805      also:
806      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
807      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
808      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
809        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
810        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
811      update results of test exp.:
812         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
813             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
814             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
815         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
816         seaice_obcs: output (SEAICEuseFluxForm=T)
817      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
818          for standard fwd & AD lab_sea tests (to keep the same output).
819  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
820    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
821    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
822    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
823    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
824    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
825  o pkg/seaice:  o pkg/seaice:
826    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
827    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
828    also pass fac as a param, which can be 1. (to update the tendency    also pass fac as a param, which can be 1. (to update the tendency
829    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
830    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
831    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
832    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
833    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
834    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.  
   is specified to be >0, then DIFF1 is set to 0.  
835  o pkg/seaice:  o pkg/seaice:
836    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
837    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
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