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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1590 by jmc, Sat Feb 4 17:25:23 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/salt_plume:
8       - isolate saltPlumeFlux array exch into a specific S/R called from
9         do_oceanic_phys.F
10       - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
11    o verification:
12       - move untested set-up to MITgcm_contrib/verification_other.
13    o pkg/seaice:
14      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
15    o pkg/seaice:
16      - seaice_solve4temp.F (keeping results unchanged):
17        * add 2 future run-time params to select which saturation vapor pressure
18          formula is used and how post-iteration fluxes are set.
19          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
20        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
21          the linearized expression to stay consistent with tsurf finding.
22      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
23        can be < 0.
24    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
25      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
26        conductive heat flux F_c , and add it explicitly when updating tsurf as
27        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
28        so that now F_ia has a consistent meaning through the entire routine.
29        This causes differences at truncation level: update output of fwd exp.
30        global_ocean.cs32x15.seaice.
31    o pkg/seaice:
32      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
33        of arrays, sign/direction of fluxes; no effect on results.
34      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
35        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
36        note: this should have been done before changing celsius2K default.
37      - to keep results unchanged, add back old value of celsius2K in verification
38        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
39      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
40        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
41        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
42        freezing temp is consistent with value in seaice_growth.F ; this causes
43        differences at machine truncation level: update lab_sea AD output (3/4).
44    o pkg/seaice:
45      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
46        and climsst/sss even when using seaice (to prevent calculation that might
47        use SST on land); does not affect any verification exp.
48      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
49        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
50    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
51      over land (non-legacy code)
52    o vectorize salt_plume package:
53      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
54      - this code computes plumebk everywhere (also over land), thus requires
55        code to avoid divisions by zero and catch the case of kLev=Nr.
56      - efficiency of salt_plume_frac is still sub-optimal
57    o tools (genmake2):
58      - fix makefile NAME specification (option: -makefile NAME) by adding
59        "-f $MAKEFILE" in few places where it was missing including makedepend
60        command (contribution from Paul).
61    
62    checkpoint63i (2012/01/24)
63    o model/src:
64      - add factorized versions of some EOS code to find_rho.F,
65        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
66    o model/src:
67      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
68      - change default celsius2K from 273.16 to 273.15
69      - to keep results unchanged, add back old value of celsius2K in verification
70        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
71         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
72    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
73      to make TAF generate vectorizable code
74    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
75       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
76       have flags that do this more efficiently.
77    o pkg/diagnostics/diagstats_calc.F
78      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
79    o pkg/obcs (with exch2):
80      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
81        and remove code (in obcs_readparms.F) which was based on EXCH of indices
82        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
83    o pkg/exf and seaice exp:
84      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
85        so that switching off area & heff advection flags does not affect results.
86      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
87      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
88        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
89        results of verification experiments: 1D_ocean_ice_column(fwd),
90        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
91        and offline_exf_seaice (all 4).
92    o pkg/seaice:
93      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
94        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
95      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
96        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
97        not multi-dim advection;
98      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
99        SHORTWAVE_HEATING #undef.
100    o optim: make Makefile more robust (?)
101    o pkg/obcs:
102      * fix treatment of obcs_read_pickup for TAF
103    o pkg/shelfice:
104      * add missing initialisation of num_shifwflx
105      * new adjoint verification exp. for isomip
106      * change Prandtl and Schmidt numbers from generic formulations
107        (in terms of model diffus. and visc.) to separate runtime
108        parameters, with Holland and Jenkins (1999) default values.
109    o pkg/exf (interpolation):
110      - extended input field (2 rows) near the N & S poles:
111        * fill in with the symetric value (when even Nb of data in longitude)
112        * add average value at the poles only for scalar quantities ; for vector
113          component interpolation, skip the averaging and keep duplicated values,
114          unless the 2 components have same location (uvInterp=T) in which case
115          interpolate the 2 components together using S/R EXF_INTERP_UV.
116      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
117        together: this allows to account properly for local orientation when
118        averaging at N & S pole.
119      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
120        exf-interpolation near N & S poles. Undef by default.
121      - add debug check/print on 1rst iter if debugLevel >=2.
122    o pkg/exf:
123      - change masking flags definition (no longer "parameter"), put them in
124        common block and set them in S/R EXF_INIT_FIXED.
125      - change recognized masking flag from s,u,v to c,w,s since the mask
126        to use (maskC,W,S) depends on position on model grid and has little to
127        do with scalar/vector difference; fix masking if using P-coordinates.
128      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
129        and update results of exp. global_with_exf (x2).
130      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
131    o pkg/obcs
132      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
133    o pkg/exf (interpolation):
134      - assume periodicity in X only if input field cover full longitude range.
135      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
136        and should vectorise).
137      - fix input lat of the 2 added row (in case we provide N.pole data).
138    
139    checkpoint63h (2011/12/30)
140    o pkg/seaice:
141      - change declaration of UVM from _RL to _RS in order to get B-grid
142        uIce,vIce monitor when _RS = real*4
143    o pkg/offline:
144      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
145      - compute vertical velocity if not read from file (switch on exactConserv
146        & staggerTimeStep);
147      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
148    o verification:
149      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
150        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
151        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
152      - update output of exp. global_ocean.cs32x15.viscA4 after changing
153        grid-file angles (used here for coriolis-3d);
154      - remove (or gzip) few files not needed to run fizhi-cs experiments.
155    o pkg/exf (vector interpolation):
156      - rotate vector component toward local grid-axis orientation using grid-angles
157        (stored in GRID.h) instead of locally computed rotation angle; keep old code
158        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
159    o pkg/seaice:
160      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
161        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
162    o pkg/PKG_OPTIONS.h files:
163      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
164        outside of the #ifdef ALLOW_THISPKG / #endif block.
165      - update verification/*/code/PKG_OPTIONS.h files.
166    o add a verification experiment (offline_exf_seaice/input.seaice) that test
167      the B-grid LSOR solver
168    o pkg/seaice: sort out emissivity and long wave radiation step 2:
169      - add emissivity for snow and ice as new run-time parameters
170        (unfortunately) that default to the corresponding exf values; this
171        changes results in most verification experiments so that for backward
172        compatibility these parameter have to be set explicitly to inconsistent
173        values (ugly);
174      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
175        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
176        until we agree how to handle this bug properly
177    o pkg/exf (interpolation):
178      - add a set of run-time param ({inputfield}_interpMethod), one for
179        each interpolated input field, to select the interpolation method
180        with a value of zero switching off the interpolation;
181      - print interpolation parameters to standard output;
182      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
183        (to use instead runoff_interpMethod=0 in data.exf).
184      - simplify default setting of interpolation parameters (for all fields,
185        set position to match model grid cell-center position, leading to trivial
186        interpolation in case of regular Lat-Lon grid) and fix for the case of
187        non-uniform delY.
188    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
189       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
190       this factor is absolutely required, because the lw exitance (= out-going
191       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
192       where the reflectivity rho = 1-emissivity for conservation reasons. Once
193       this is established, we can remove the CPP-Flag (if we want to).
194    o pkg/seaice:
195      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
196        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
197      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
198        what the name implies (and not emissivity*BoltzmannConstant), this means
199        the old default value of 5.5e-8 now means
200        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
201        S/R exf_readparms
202      - FV-discretization of the B-grid LSOR solver, turn on with
203        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
204        of the calling routine dynsolver, so that B and C-grid code look a
205        little more alike.
206      - fix index bugs in ostres.F (B-grid code)
207    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
208    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
209      default for SEAICE_emissivity, if useEXF; requires setting a wrong
210      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
211      backward compatiblity
212    o model/src: use sigmaR in calc_ivdc
213    
214    checkpoint63g (2011/12/16)
215    o pkg/seaice/seaice_growth.F:
216      fix heat conservation of the coupled ocean-seaice system.
217      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
218      solid vs liquid water treatment is resolved via QNET.
219    o pkg/seaice/seaice_growth.F:
220      add missing term for sublimation in saltFlux, which was breaking conservation.
221    o pkg/seaice/seaice_model.F:
222      Remove this patholigical case treatment in evolution branch,
223      where it is un-necessary and breaks conservation.
224      Update global_ocean.cs32x15/results accordingly for
225      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
226    o model/src:
227      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
228      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
229    o pkg/obcs:
230      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
231      tendency for temperature and salinity that is then applied to update
232      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
233      horizontal advection and diffusion contributions on the boundary (in
234      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
235      removing the mask in S/R timestep_tracer. The advantage of this approach is
236      that the updated tracer values include contributions from the surface
237      forcing and vertical diffusion.
238      This modification changes exp4.stevens because of vertical diffusion.
239    o model/src:
240      change non-curvilinear grid setting to also work with exch2 + blank tiles:
241      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
242        face dimensions.
243      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
244        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
245        and INI_SPHERICAL_POLAR_GRID.
246      change test-experiment global_ocean.90x40x15:
247      - split the domain in many more tiles (9x4 tiles of 10x10 each);
248      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
249      - update results of both test (std & dwnslp).
250    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
251       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
252    o model/src:
253      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
254        and fix initialisation when using sigma-coords.
255    o model/src:
256     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
257       to their current value at the beginning of forward_step.F": add a new run-time
258       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
259     - set doResetHFactors=T in the following test exp:
260        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
261        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
262        and tutorial_global_oce_in_p (nonLinFS in p)
263    o pkg/ecco
264      - added IES cost term
265    o verification/advect_xz
266      - scale down the depth by 1/100 (from 200 km to just 2.km)
267      - add secondary test using divergent flow, r-star and implicit vertical advection.
268      - add note (check_conserve_TS.txt) and matlab script to check global
269        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
270    o pkg/rbcs:
271      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
272    o pkg/obcs (Stevens BCs):
273      - fix various problems in the phase speed computations of the Stevens
274        boundary conditions:
275        - sign error for western and southern boundaries,
276        - time tendencies were underestimated by factor of dTracerLev and some just
277          zero (for multidim advection schemes) -> now estimate time tendencies
278          from difference between previous (n) time level and the one before (n-1);
279          this requires storing a field per tracer per boundary, also in the pickup
280          files.
281        - replace deltaTmom in cflMer/Zon computation with dTracerLev
282        - set default phase velocity to cflMer/Zon
283      - update verification experiment exp4.stevens
284    o pkg/generic_advdiff (implicit_r):
285      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
286        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
287      - fix implicit vertical diffusion or advection with NonLin FreeSurf
288        (was using current recip_hFacC instead of future recip_hFacC): set future
289        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
290        solver S/R ;
291      - fill diagnostics of vertical advective fluxes (computed from tendency)
292        when using implicit vert. advection;
293      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
294         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
295         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
296         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
297    o pkg/diagnostics:
298      - add diags for T & S tendency which goes through Adams-Bashforth.
299    
300    checkpoint63f (2011/11/30)
301    o pkg/obcs/obcs_calc_stevens.F:
302      - join some loops to reduce number of if-statements
303      - fix a bug in code for northern and southern boundaries.
304    o pkg/seaice/seaice_init_varia.F
305      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
306        caused zero ice-velocities for the B-grid code
307    o pkg/seaice/seaice_init_fixed.F
308      - fix a bug in the initialisation of the second metric terms
309        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
310      - this affects all seaice configurations with useCurviLinearGrid = .true.
311        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
312        = .true. (default)
313      - the only verification experiment affected is global_ocean.cs32x15:
314        icedyn, seaice, and seaice_dynmix (AD)
315    o pkg/thsice/thsice_diagnostics_state.F
316      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
317        not contain garbage that can lead to surprises in diagstats_calc.F
318    o model/src:
319      - move bi,bj loops inside INTEGR_CONTINUITY ;
320      - call INTEGR_CONTINUITY directly from forward_step.F
321        (previously called from momentum_correction_step.F)
322      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
323        forward_step.F and pkg/ecco/the_main_loop.F
324    o model/src/do_oceanic_phys.F:
325      - reset addMass to zero only if useICEFRONT ;
326      - separated k-loop for rhoInSitu calculation ;
327      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
328        and at constant T,S (= WdRHOdP);
329      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
330        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
331        transport of locally-referenced potential density);
332        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
333    o gluemnc:
334      - replace ncrcat with ncks when adding variables to *.glob.nc
335      - change the way variables without record dimensions are handled so that
336        files that have variables with and without record variables can be glued:
337        add a record dimension with a new unique name to be able to differentiate
338        between variable with and without a-prior record dimensions. Remove
339        this record dimension before adding the variable to the *.glob.nc file.
340        This procedure automatically works also for grid.*.nc files that do not
341        have any record dimension.
342    o verification/cpl_aim+ocn:
343      - generate new reference output on baudelaire (gfortran, mpich2) (previously
344        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
345    o pkg/obcs/obcs_calc_stevens.F:
346      - add code for northern and southern boundaries.
347      - reorder some loops to save some operations and so that drFBar can be scalar
348    o model/src:
349      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
350        truncation) and add diagnostics for Adams-Bashforth tendency increment.
351      - update test-exp. AD output:
352        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
353      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
354        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
355        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
356        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
357        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
358        tutorial_plume_on_slope.
359    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
360      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
361      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
362      does not even come with an F77 compiler anymore, this should not be
363      a limitation
364    
365    checkpoint63e (2011/11/06)
366    o pkg/seaice adjoint of LSR:
367      - substantially rework STORE dirs.
368      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
369        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
370        and only perform SOLV_MAX_FIXED adjoint iters.
371        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
372        always goes to same record, meaning that the last forward field will be
373        the one used in the adjoint - an approximation.
374      - now produces non-zero LSR-related gradients, and acceptable gradients for
375        An's zonal (x-z) test case (to be checked in)
376      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
377        (but these are screwed up by the thermodynamics in the first place);
378        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
379        output_adm.txt also reflects changes to seaice_lsr
380      - global_ocean.cs32x15:
381        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
382          (output_adm.seaice.txt was updated)
383        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
384          (output_adm.seaice_dynmix.txt)
385    o test-exp. exp4+stevens:
386      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
387    o pkg/seaice (lsr solver):
388      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
389        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
390      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
391      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
392        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
393      - compute (with new S/R) and print initial (+ free-driff sol. if available)
394        and final residual of linearised system.
395    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
396      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
397    o pkg/obcs: Stevens BCs (still only for east and west)
398      - fix Stevens BCs by using intermediate velocities of previous
399        time step as "baroclinic" contribution rather velocity of one grid cell
400        inside the boundaries; more consistent but makes the entire treatment
401        more complicated, requires new pickup files and two new S/Rs:
402        obcs_copy_uv_n and obcs_save_uv_n
403        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
404        (undefined by default)
405      - silently move computation of some grid factors into separate loops to
406        save some recomputations
407      - add a hack for non-linear free surface
408      - add a verification experiment to exp4 that tests this code
409    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
410    
411    checkpoint63d (2011/10/25)
412    o pkg/obcs + seaice-dynamics:
413      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
414        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
415        values (consistent with an implicit method).
416      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
417        return to older implementation (same results as before); note that none of
418        the "experimental" OBCS_SEAICE options are implemented in the new version.
419      - switch test exp. seaice_obcs to use new version (update output).
420    o pkg/seaice:
421      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
422      - add parenthesis in Water-Ice drag calculations (evp & lsr);
423      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
424        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
425      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
426        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
427    o pkg/layers:
428      - Include potential density as new coordinate (Thanks to David Munday)
429    o pkg/dic:
430      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
431        carbonate computation/output to CALC_PCO2_APPROX
432    o pkg/generic_advdiff
433      - make TAF generate code that vectorizes:
434        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
435    o model/src:
436      - improve vectorization also for adjoint code of
437        solve_tridiagonal and solve_pentadiagonal. As this requires up to
438        5 new 3D-fields, this code is only turned on for the combination of
439        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
440        for singular matrix check (only for TARGET_NEC_SX).
441      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
442        ALLOW_AUTODIFF. This flag now needs to be set outside of
443        solve_tri/pentadiagonal.F
444    o pkg/exf:
445      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
446        optional namelist EXF_NML_OBCS).
447      - add many debug-print (to trace down where pkg/cal error msg comes from)
448    o pkg/mom_vecinv/mom_vi_hdissip.F
449      - rearrange loops so that vectorization is improved and in particular
450        the adjoint routine vectorizes. The code is a little longer now, but I
451        think easier to read.
452        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
453    o pkg/seaice:
454      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
455    o pkg/exch2:
456      - alternative code (without tile x tile matrix) for cumulated (global) sum;
457        used as default; keep using matrix version in adjustment.cs-32x32x1.
458    o tools/build_options:
459      - after merging some MPI and/or multi-threads specific optfiles so that
460        the modified default optfile support both built (using genmake2 -mpi
461        for the MPI built, using genmake2 -omp for OpenMP built),
462        move now obsolete optfiles to tools/build_options/unsupported/
463       (add copy of email sent to support list in doc/optfiles_changes.txt)
464    
465    checkpoint63c (2011/09/28)
466    o pkg/ebm:
467      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
468        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
469    o pkg/seaice (SItracer pickup)
470    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
471      To be done:
472      - thorough testing of missing fields in S/R seaice_read_pickup
473      - thorough matching between generic tracers and specific fields used
474        (e.g. volume-weighted age, area-weighted age, salinity, ...)
475    o pkg/grdchk:
476      - all procs calculate and print finite-difference gradient (for testreport)
477      - change description output used by testreport;
478      - AD testing: also compare and report Finite-difference gradient;
479        => update all output_adm*.txt
480    o test exp. global_ocean_ebm:
481      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
482        and turn on exactConserve; update (fwd) output.
483    o pkg/seaice (LSR):
484      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
485      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
486        * identical results with non-CS topology (but save up to half of EXCH calls)
487        * no much changes in cs-32 verification tests since no ice at face edges
488         (differences due to convergence criteria, since nb of iterations changed)
489        * expect some differences on lat-lon-cap grid.
490        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
491    o pkg/exch2:
492      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
493        many tiles); until alternative coding is added, just add a stop.
494    o pkg/kpp:
495      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
496        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
497    o optfiles:
498      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
499        into corresponding standard one, which now support different build:
500        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
501      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
502    o pkg/obcs (seaice):
503      - add missing EXCH for uIce,vIce after applying OBCS;
504      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
505        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
506        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
507      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
508      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
509        and eedata.mth for MPI and mutlti-threaded testing.
510    o pkg/flt:
511      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
512      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
513      - fix pickup and trajectories + profiles output with multi-threads;
514      - add parameter to select group of fields to write along trajectory and
515        profile (default unchanged);
516      - only call PORT_RAND* function when flt_noise <> 0;
517      - add multi-threaded test for verification exp. flt_example.
518    o eesupp/src:
519      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
520      - USE_OMP_THREADING: check that number of threads (from eedata) matches
521        actual number (from env.var. setting).
522    o pkg/ebm:
523      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
524      - add multi-threaded test for verification exp. global_ocean_ebm
525    
526    checkpoint63b (2011/08/29)
527    o pkg/ebm:
528      - fix sign of runoff;
529      - update directly forcing fields (Qnet,EmPmR) to use standard
530        external_forcing_surf.F (remove ebm_forcing_surf.F);
531      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
532      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
533        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
534      - update global_ocean_ebm parameters file data and update output (fwd+ad).
535    o verification/matrix_example:
536      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
537        MPI and mutlti-threaded testing.
538    o pkg/matrix:
539      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
540      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
541      - fix for multi-threaded (remove DATA statement);
542      - use standard DIFFERENT_MULTIPLE function;
543      - add MATRIX_OPTIONS.h
544    o verification/matrix_example:
545       To allow to split the domain in several tiles, change the domain size
546        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
547        Western side) of land points.
548    o (*_)write_pickup:
549      - fix few bugs in mypackage_read/write_pickup.F
550      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
551        array of length 1 (was caught by compiler syntax-check).
552    o pkg/diagnostics (velocity potential solver):
553      - fix initialisation of main diagonal matrix (for overlap values)
554    o tools/build_options:
555      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
556        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
557      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
558        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
559        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
560        and use "-devel" testreport option for standard testing on baudelaire.
561    o pkg/grdchk:
562      - Assume that all gradient-check position are within the same tile
563        corresponding to global indices (iGloTile,jGloTile) and that
564        positions (i,j indices or nbeg) are local to this tile;
565      - set tile local-indices and proc. number according to tile global-indices;
566      - remove grdchkwhichproc from namelist (retired param);
567      - send adjoint gradient to all procs so that all procs print it to STDOUT;
568      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
569    o adding package bbl (Bottom Boundary Layer)
570      description in MITgcm/pkg/bbl/bbl_description.tex
571      example/test experiment in MITgcm_contrib/bbl
572    o adjoint verifications
573      - changed 5 experiments to multi-tiles
574        * global_ocean.90x40x15
575        * obcs_ctrl
576        * offline_exf_seaice
577        * tutorial_dic_adjoffline
578        * tutorial_tracer_adjsens
579        changed reference output for those that crossed tile boundaries
580        (changed choices of gradient check positions)
581      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
582      - temporary bug fix in grdchk_loc.F for obcs
583    o genmake2 & testreport
584      - add target "obj" (just for OBJFILES files) to Makefile;
585      - add option to specify FEXTRAFLAGS on command line.
586    o pkg/mypackage:
587      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
588    
589    checkpoint63a (2011/08/02)
590    o pkg/diagnostics (velocity potential):
591      - fix velocity-potential calculation when using OBCS: balance net inflow
592        at each level (new S/R OBCS_DIAG_BALANCE).
593      - fix some of the problems with OBCS in stream-function calculation.
594    o pkg/exf/exf_readparms.F
595      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
596        EXF_NML_OBCS) more consistent, so that you need not have these lists
597        in data.exf when they are not used.
598    o optim/optim_readdata.F:
599      - add some output about obcs variables that might help debugging
600      - add a check about nvarlength
601    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
602    o pkg/diagnostics (velocity potential):
603      - fix mask for OBCS (still problems in stream-function with OBCS);
604      - add specific parameter (default = main code CG2D params) for solver;
605      - in case of poor convergence, use solution corresponding to lowest residual.
606    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
607      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
608      and should be avoided where possible.
609    o model/src (rStar):
610      - include r* effect on reference-state (PhiRef) in totPhiHyd
611        (so that it's really the potential anomaly at the cell center);
612        affect solution only if z* with full pressure in EOS.
613      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
614        update output (because of z* in totPhiHyd and viscA4 changes);
615      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
616        @ constant r) until interpolation at constant r is implemented.
617    o pkg/diagnostics
618      - fix RCENTER diagnostics in case cell center is not at interface middle
619    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
620      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
621      that THETA and SALT are "conservative temperature" and "absolute
622      salinity"
623    o pkg/ctrl
624      - fix computation of endrec in s/r ctrl_init_rec
625      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
626    o pkg/seaice/seaice_growth.F
627      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
628        remove then obsolete STORE directives
629      - fix STORE directives for tice and tices, so that only the
630        appropriate part of the fields are stored (and not the entire
631        field); update global_ocean.cs32x15.seaice AD output.
632      - cosmetic changes: adjust CPP flags and indentation for better
633        legibilty
634    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
635      Chris Wilson)
636    o pkg/gmredi:
637       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
638       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
639    
640    checkpoint63  (2011/07/11)
641    o pkg/exch2:
642     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
643     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
644       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
645       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
646    o pkg/diagnostics:
647     - deal with pairs of post-processed diags which are computed together; in
648       particular, re-order list of diags within 1 file to save 2nd computation.
649     - add S/R to compute velocity stream-function (called after velocity-potential
650       calculation) from divergence free transport -> new diagnostics "PsiVEL".
651     - add parameter to select grid-point location where PsiVEL == 0.
652    o eesupp/src:
653       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
654       (specific S/R needed with exch2 topology - for now, just print an error msg)
655    o pkg/shelfice
656     - Implement friction velocity-dependent transfer coefficients following
657       Holland and Jenkins, JPO, 1999
658       Original code by M. Losch with small modifs.
659       Enable with CPP option SHI_ALLOW_GAMMAFRICT
660       and runtime flag SHELFICEuseGammaFrict
661    o verification lab_sea & global_ocean.cs32x15:
662     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
663       does not miss some dependencies (but is slower) and also works with many files
664       (default makedepend limitation for AD built).
665     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
666    o pkg/diagnostics:
667     - add run-time parameter "useMissingValue" (def=False) to fill land-point
668        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
669       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
670     - Extend the use of "missing_value" setting from data.diagnostics for the case
671       of counter-diagnostics (where fraction-weight is zero). This applies both to
672       MNC and MDS output files.
673    o pkg/seaice/seaice_growth.F:
674      - add 'a priori' cap of latent heat flux based on actual mass considerations
675        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
676        non-legacy seaice_solve4temp.
677      - add diagnostic of the residual sublimation freshwater flux (the freshwater
678        flux taken from the ocean if the total actual latent heat fluxes exceed
679        the maximum)
680      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
681       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
682      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
683       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
684      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
685      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
686    o verification 1D_ocean_ice_column:
687       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
688       update results
689    o pkg/diagnostics:
690     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
691       which are not filled-up but computed from other diags ; In this case, the mate
692       diag points to the primary (filled-up) diag to used for post processing.
693     - Update Velocity-potential computation using post-processed diag framework.
694     ==> Change the ordering of fields and time-periods in MDS output file
695       when using periodic averaging: now writes one time record with the full set
696       of fields for this time period, then the next time reccord (it used to be
697       one field with the full set of time records then the next field).
698         Note: this is now similar to NetCDF (MNC) output file. <==
699    
700    checkpoint62z (2011/06/21)
701    o adjoint monitor:
702     - Add adjoint monitor output for packages exf, seaice
703       and update relevant testreport output
704    o pkg/seaice:
705     - re-order diags inits so that they appear in order in available_diagnostics.log
706     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
707       area/heff/hsnow preceeding thermodynamic growth/melt.
708     - modified diag: SIdA; output actual effect, as the description states.
709     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
710     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
711       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
712        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
713     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
714     - added diagnostics for seaice generic tracers (SItr*).
715     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
716     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
717     I. Fenty: 18-Jun-2011:
718     Minor changes to seaice package:
719     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
720        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
721       - Differentiated "regularization variables" from "floor variables"
722        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
723        * hiceMin became SEAICE_hice_reg (old hiceMin)
724          (with _reg meaning regularization variable)
725       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
726        so as to ensure energy conservation when going between phases
727      - A22 was not used anywhere
728     2) Changed regularization procedure for heffActual and hsnowActual to ensure
729        well-boundedness and smooth adjoint in seaice_growth.F
730     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
731        because the old regularization always set heffActual >= 0.05 cm
732     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
733        on AREA when HEFF > 0.
734      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
735        requiring that DISABLE_AREA_FLOOR *not* be defined
736     Affected verifications:
737      - 1D_ocean_ice_column (output.txt output_adm.txt)
738      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
739    o pkg/diagnostics:
740      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
741      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
742        (was _RL, now integer) with option = 0 to retrieve all levels.
743      - add pieces of code to compute velocity potential at each level (new diagnostics
744        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
745        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
746      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
747        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
748        and in diagnostics_fract_fill.F (do not need a valid pointer for the
749        diagnostics counter-mate); check that definition of counter-diagnostic
750        includes a valid counter-mate (in diagnostics_set_levels.F).
751    o model/src (rStar):
752      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
753        affect solution only if z* with full pressure in EOS;
754        update output of test-exp global_ocean.90x40x15.
755    o pkg/seaice:
756      - introduce siEps=1e-5 parameter
757      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
758      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
759      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
760        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
761        as well as ice cover age and ridging index (attached to AREA).
762        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
763        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
764        Up to SItrMaxNum=3 tracers can be used simultaneously.
765    o pkg/salt_plume:
766      -introduce SPsalFRAC run time parameter that sets the fraction of the
767       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
768       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
769    o model debug options:
770      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
771        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
772      - Refine debug-msg printing selection (3 new levels):
773        debugMode  : controls printing of debug messages (sequence of S/R calls).
774        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
775         debLevZero =  0 ; /* level of disabled aux. msg printing */
776         debLevA =  1 ; /* level of minimum  aux. msg printing */
777         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
778         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
779         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
780         debLevE =  5 ; /* level of extensive debug printing */
781        New debugLevel default: with default debugMode value (=F),
782          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
783          and if debugMode=T, default debugLevel = 4 (debLevD).
784        Relation with previous settings:
785         debLevB (=2) corresponds to former debLevA (=1)
786         debLevD (=4) corresponds to former debLevB (=2)
787        Note:
788         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
789         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
790            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
791      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
792        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
793    o pkg/obcs:
794      - change OBCSfixTopo default from True to False (should not change the results);
795        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
796    o pkg/thsice:
797      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
798        2nd layer seaice sublimation (unlikely to happen)
799      - use Interior mask for OBCS in thsice_advection.F (similar to what is
800        done in gad_advection & seaice_advection).
801    o adjoint:
802      bug fix spotted by Gael Forget:
803      seaice_advection and thsice_advection still had
804      legacy CPP options to avoid CS corner updates for adjoint
805    o pkg/seaice:
806      => Change some of the defaults (2011/05/29):
807         - change SEAICEuseFluxForm default (from False to True)
808         - change DIFF1 default (from 0.004 m/s to 0. m/s)
809         And print warnings if DIFF1 is not set in data.seaice and centered
810          avection scheme is used without any diffusion.
811      also:
812      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
813      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
814      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
815        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
816        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
817      update results of test exp.:
818         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
819             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
820             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
821         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
822         seaice_obcs: output (SEAICEuseFluxForm=T)
823      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
824          for standard fwd & AD lab_sea tests (to keep the same output).
825  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
826    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
827    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
828    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
829    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
830    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
831  o pkg/seaice:  o pkg/seaice:
832    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
833    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
834    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
835    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
836    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
837    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
838    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
839    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
840    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.  
841  o pkg/seaice:  o pkg/seaice:
842    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
843    - 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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