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revision 1.1418 by jmc, Thu Apr 28 23:26:39 2011 UTC revision 1.1585 by jmc, Mon Jan 30 18:42:11 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      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
9        and climsst/sss even when using seaice (to prevent calculation that might
10        use SST on land); does not affect any verification exp.
11      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
12        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
13    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
14      over land (non-legacy code)
15    o vectorize salt_plume package:
16      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
17      - this code computes plumebk everywhere (also over land), thus requires
18        code to avoid divisions by zero and catch the case of kLev=Nr.
19      - efficiency of salt_plume_frac is still sub-optimal
20    o tools (genmake2):
21      - fix makefile NAME specification (option: -makefile NAME) by adding
22        "-f $MAKEFILE" in few places where it was missing including makedepend
23        command (contribution from Paul).
24    
25    checkpoint63i (2012/01/24)
26    o model/src:
27      - add factorized versions of some EOS code to find_rho.F,
28        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
29    o model/src:
30      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
31      - change default celsius2K from 273.16 to 273.15
32      - to keep results unchanged, add back old value of celsius2K in verification
33        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
34         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
35    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
36      to make TAF generate vectorizable code
37    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
38       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
39       have flags that do this more efficiently.
40    o pkg/diagnostics/diagstats_calc.F
41      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
42    o pkg/obcs (with exch2):
43      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
44        and remove code (in obcs_readparms.F) which was based on EXCH of indices
45        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
46    o pkg/exf and seaice exp:
47      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
48        so that switching off area & heff advection flags does not affect results.
49      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
50      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
51        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
52        results of verification experiments: 1D_ocean_ice_column(fwd),
53        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
54        and offline_exf_seaice (all 4).
55    o pkg/seaice:
56      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
57        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
58      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
59        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
60        not multi-dim advection;
61      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
62        SHORTWAVE_HEATING #undef.
63    o optim: make Makefile more robust (?)
64    o pkg/obcs:
65      * fix treatment of obcs_read_pickup for TAF
66    o pkg/shelfice:
67      * add missing initialisation of num_shifwflx
68      * new adjoint verification exp. for isomip
69      * change Prandtl and Schmidt numbers from generic formulations
70        (in terms of model diffus. and visc.) to separate runtime
71        parameters, with Holland and Jenkins (1999) default values.
72    o pkg/exf (interpolation):
73      - extended input field (2 rows) near the N & S poles:
74        * fill in with the symetric value (when even Nb of data in longitude)
75        * add average value at the poles only for scalar quantities ; for vector
76          component interpolation, skip the averaging and keep duplicated values,
77          unless the 2 components have same location (uvInterp=T) in which case
78          interpolate the 2 components together using S/R EXF_INTERP_UV.
79      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
80        together: this allows to account properly for local orientation when
81        averaging at N & S pole.
82      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
83        exf-interpolation near N & S poles. Undef by default.
84      - add debug check/print on 1rst iter if debugLevel >=2.
85    o pkg/exf:
86      - change masking flags definition (no longer "parameter"), put them in
87        common block and set them in S/R EXF_INIT_FIXED.
88      - change recognized masking flag from s,u,v to c,w,s since the mask
89        to use (maskC,W,S) depends on position on model grid and has little to
90        do with scalar/vector difference; fix masking if using P-coordinates.
91      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
92        and update results of exp. global_with_exf (x2).
93      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
94    o pkg/obcs
95      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
96    o pkg/exf (interpolation):
97      - assume periodicity in X only if input field cover full longitude range.
98      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
99        and should vectorise).
100      - fix input lat of the 2 added row (in case we provide N.pole data).
101    
102    checkpoint63h (2011/12/30)
103    o pkg/seaice:
104      - change declaration of UVM from _RL to _RS in order to get B-grid
105        uIce,vIce monitor when _RS = real*4
106    o pkg/offline:
107      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
108      - compute vertical velocity if not read from file (switch on exactConserv
109        & staggerTimeStep);
110      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
111    o verification:
112      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
113        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
114        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
115      - update output of exp. global_ocean.cs32x15.viscA4 after changing
116        grid-file angles (used here for coriolis-3d);
117      - remove (or gzip) few files not needed to run fizhi-cs experiments.
118    o pkg/exf (vector interpolation):
119      - rotate vector component toward local grid-axis orientation using grid-angles
120        (stored in GRID.h) instead of locally computed rotation angle; keep old code
121        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
122    o pkg/seaice:
123      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
124        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
125    o pkg/PKG_OPTIONS.h files:
126      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
127        outside of the #ifdef ALLOW_THISPKG / #endif block.
128      - update verification/*/code/PKG_OPTIONS.h files.
129    o add a verification experiment (offline_exf_seaice/input.seaice) that test
130      the B-grid LSOR solver
131    o pkg/seaice: sort out emissivity and long wave radiation step 2:
132      - add emissivity for snow and ice as new run-time parameters
133        (unfortunately) that default to the corresponding exf values; this
134        changes results in most verification experiments so that for backward
135        compatibility these parameter have to be set explicitly to inconsistent
136        values (ugly);
137      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
138        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
139        until we agree how to handle this bug properly
140    o pkg/exf (interpolation):
141      - add a set of run-time param ({inputfield}_interpMethod), one for
142        each interpolated input field, to select the interpolation method
143        with a value of zero switching off the interpolation;
144      - print interpolation parameters to standard output;
145      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
146        (to use instead runoff_interpMethod=0 in data.exf).
147      - simplify default setting of interpolation parameters (for all fields,
148        set position to match model grid cell-center position, leading to trivial
149        interpolation in case of regular Lat-Lon grid) and fix for the case of
150        non-uniform delY.
151    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
152       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
153       this factor is absolutely required, because the lw exitance (= out-going
154       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
155       where the reflectivity rho = 1-emissivity for conservation reasons. Once
156       this is established, we can remove the CPP-Flag (if we want to).
157    o pkg/seaice:
158      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
159        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
160      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
161        what the name implies (and not emissivity*BoltzmannConstant), this means
162        the old default value of 5.5e-8 now means
163        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
164        S/R exf_readparms
165      - FV-discretization of the B-grid LSOR solver, turn on with
166        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
167        of the calling routine dynsolver, so that B and C-grid code look a
168        little more alike.
169      - fix index bugs in ostres.F (B-grid code)
170    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
171    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
172      default for SEAICE_emissivity, if useEXF; requires setting a wrong
173      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
174      backward compatiblity
175    o model/src: use sigmaR in calc_ivdc
176    
177    checkpoint63g (2011/12/16)
178    o pkg/seaice/seaice_growth.F:
179      fix heat conservation of the coupled ocean-seaice system.
180      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
181      solid vs liquid water treatment is resolved via QNET.
182    o pkg/seaice/seaice_growth.F:
183      add missing term for sublimation in saltFlux, which was breaking conservation.
184    o pkg/seaice/seaice_model.F:
185      Remove this patholigical case treatment in evolution branch,
186      where it is un-necessary and breaks conservation.
187      Update global_ocean.cs32x15/results accordingly for
188      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
189    o model/src:
190      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
191      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
192    o pkg/obcs:
193      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
194      tendency for temperature and salinity that is then applied to update
195      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
196      horizontal advection and diffusion contributions on the boundary (in
197      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
198      removing the mask in S/R timestep_tracer. The advantage of this approach is
199      that the updated tracer values include contributions from the surface
200      forcing and vertical diffusion.
201      This modification changes exp4.stevens because of vertical diffusion.
202    o model/src:
203      change non-curvilinear grid setting to also work with exch2 + blank tiles:
204      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
205        face dimensions.
206      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
207        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
208        and INI_SPHERICAL_POLAR_GRID.
209      change test-experiment global_ocean.90x40x15:
210      - split the domain in many more tiles (9x4 tiles of 10x10 each);
211      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
212      - update results of both test (std & dwnslp).
213    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
214       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
215    o model/src:
216      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
217        and fix initialisation when using sigma-coords.
218    o model/src:
219     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
220       to their current value at the beginning of forward_step.F": add a new run-time
221       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
222     - set doResetHFactors=T in the following test exp:
223        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
224        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
225        and tutorial_global_oce_in_p (nonLinFS in p)
226    o pkg/ecco
227      - added IES cost term
228    o verification/advect_xz
229      - scale down the depth by 1/100 (from 200 km to just 2.km)
230      - add secondary test using divergent flow, r-star and implicit vertical advection.
231      - add note (check_conserve_TS.txt) and matlab script to check global
232        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
233    o pkg/rbcs:
234      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
235    o pkg/obcs (Stevens BCs):
236      - fix various problems in the phase speed computations of the Stevens
237        boundary conditions:
238        - sign error for western and southern boundaries,
239        - time tendencies were underestimated by factor of dTracerLev and some just
240          zero (for multidim advection schemes) -> now estimate time tendencies
241          from difference between previous (n) time level and the one before (n-1);
242          this requires storing a field per tracer per boundary, also in the pickup
243          files.
244        - replace deltaTmom in cflMer/Zon computation with dTracerLev
245        - set default phase velocity to cflMer/Zon
246      - update verification experiment exp4.stevens
247    o pkg/generic_advdiff (implicit_r):
248      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
249        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
250      - fix implicit vertical diffusion or advection with NonLin FreeSurf
251        (was using current recip_hFacC instead of future recip_hFacC): set future
252        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
253        solver S/R ;
254      - fill diagnostics of vertical advective fluxes (computed from tendency)
255        when using implicit vert. advection;
256      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
257         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
258         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
259         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
260    o pkg/diagnostics:
261      - add diags for T & S tendency which goes through Adams-Bashforth.
262    
263    checkpoint63f (2011/11/30)
264    o pkg/obcs/obcs_calc_stevens.F:
265      - join some loops to reduce number of if-statements
266      - fix a bug in code for northern and southern boundaries.
267    o pkg/seaice/seaice_init_varia.F
268      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
269        caused zero ice-velocities for the B-grid code
270    o pkg/seaice/seaice_init_fixed.F
271      - fix a bug in the initialisation of the second metric terms
272        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
273      - this affects all seaice configurations with useCurviLinearGrid = .true.
274        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
275        = .true. (default)
276      - the only verification experiment affected is global_ocean.cs32x15:
277        icedyn, seaice, and seaice_dynmix (AD)
278    o pkg/thsice/thsice_diagnostics_state.F
279      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
280        not contain garbage that can lead to surprises in diagstats_calc.F
281    o model/src:
282      - move bi,bj loops inside INTEGR_CONTINUITY ;
283      - call INTEGR_CONTINUITY directly from forward_step.F
284        (previously called from momentum_correction_step.F)
285      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
286        forward_step.F and pkg/ecco/the_main_loop.F
287    o model/src/do_oceanic_phys.F:
288      - reset addMass to zero only if useICEFRONT ;
289      - separated k-loop for rhoInSitu calculation ;
290      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
291        and at constant T,S (= WdRHOdP);
292      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
293        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
294        transport of locally-referenced potential density);
295        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
296    o gluemnc:
297      - replace ncrcat with ncks when adding variables to *.glob.nc
298      - change the way variables without record dimensions are handled so that
299        files that have variables with and without record variables can be glued:
300        add a record dimension with a new unique name to be able to differentiate
301        between variable with and without a-prior record dimensions. Remove
302        this record dimension before adding the variable to the *.glob.nc file.
303        This procedure automatically works also for grid.*.nc files that do not
304        have any record dimension.
305    o verification/cpl_aim+ocn:
306      - generate new reference output on baudelaire (gfortran, mpich2) (previously
307        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
308    o pkg/obcs/obcs_calc_stevens.F:
309      - add code for northern and southern boundaries.
310      - reorder some loops to save some operations and so that drFBar can be scalar
311    o model/src:
312      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
313        truncation) and add diagnostics for Adams-Bashforth tendency increment.
314      - update test-exp. AD output:
315        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
316      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
317        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
318        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
319        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
320        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
321        tutorial_plume_on_slope.
322    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
323      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
324      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
325      does not even come with an F77 compiler anymore, this should not be
326      a limitation
327    
328    checkpoint63e (2011/11/06)
329    o pkg/seaice adjoint of LSR:
330      - substantially rework STORE dirs.
331      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
332        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
333        and only perform SOLV_MAX_FIXED adjoint iters.
334        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
335        always goes to same record, meaning that the last forward field will be
336        the one used in the adjoint - an approximation.
337      - now produces non-zero LSR-related gradients, and acceptable gradients for
338        An's zonal (x-z) test case (to be checked in)
339      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
340        (but these are screwed up by the thermodynamics in the first place);
341        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
342        output_adm.txt also reflects changes to seaice_lsr
343      - global_ocean.cs32x15:
344        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
345          (output_adm.seaice.txt was updated)
346        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
347          (output_adm.seaice_dynmix.txt)
348    o test-exp. exp4+stevens:
349      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
350    o pkg/seaice (lsr solver):
351      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
352        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
353      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
354      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
355        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
356      - compute (with new S/R) and print initial (+ free-driff sol. if available)
357        and final residual of linearised system.
358    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
359      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
360    o pkg/obcs: Stevens BCs (still only for east and west)
361      - fix Stevens BCs by using intermediate velocities of previous
362        time step as "baroclinic" contribution rather velocity of one grid cell
363        inside the boundaries; more consistent but makes the entire treatment
364        more complicated, requires new pickup files and two new S/Rs:
365        obcs_copy_uv_n and obcs_save_uv_n
366        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
367        (undefined by default)
368      - silently move computation of some grid factors into separate loops to
369        save some recomputations
370      - add a hack for non-linear free surface
371      - add a verification experiment to exp4 that tests this code
372    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
373    
374    checkpoint63d (2011/10/25)
375    o pkg/obcs + seaice-dynamics:
376      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
377        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
378        values (consistent with an implicit method).
379      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
380        return to older implementation (same results as before); note that none of
381        the "experimental" OBCS_SEAICE options are implemented in the new version.
382      - switch test exp. seaice_obcs to use new version (update output).
383    o pkg/seaice:
384      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
385      - add parenthesis in Water-Ice drag calculations (evp & lsr);
386      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
387        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
388      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
389        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
390    o pkg/layers:
391      - Include potential density as new coordinate (Thanks to David Munday)
392    o pkg/dic:
393      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
394        carbonate computation/output to CALC_PCO2_APPROX
395    o pkg/generic_advdiff
396      - make TAF generate code that vectorizes:
397        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
398    o model/src:
399      - improve vectorization also for adjoint code of
400        solve_tridiagonal and solve_pentadiagonal. As this requires up to
401        5 new 3D-fields, this code is only turned on for the combination of
402        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
403        for singular matrix check (only for TARGET_NEC_SX).
404      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
405        ALLOW_AUTODIFF. This flag now needs to be set outside of
406        solve_tri/pentadiagonal.F
407    o pkg/exf:
408      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
409        optional namelist EXF_NML_OBCS).
410      - add many debug-print (to trace down where pkg/cal error msg comes from)
411    o pkg/mom_vecinv/mom_vi_hdissip.F
412      - rearrange loops so that vectorization is improved and in particular
413        the adjoint routine vectorizes. The code is a little longer now, but I
414        think easier to read.
415        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
416    o pkg/seaice:
417      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
418    o pkg/exch2:
419      - alternative code (without tile x tile matrix) for cumulated (global) sum;
420        used as default; keep using matrix version in adjustment.cs-32x32x1.
421    o tools/build_options:
422      - after merging some MPI and/or multi-threads specific optfiles so that
423        the modified default optfile support both built (using genmake2 -mpi
424        for the MPI built, using genmake2 -omp for OpenMP built),
425        move now obsolete optfiles to tools/build_options/unsupported/
426       (add copy of email sent to support list in doc/optfiles_changes.txt)
427    
428    checkpoint63c (2011/09/28)
429    o pkg/ebm:
430      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
431        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
432    o pkg/seaice (SItracer pickup)
433    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
434      To be done:
435      - thorough testing of missing fields in S/R seaice_read_pickup
436      - thorough matching between generic tracers and specific fields used
437        (e.g. volume-weighted age, area-weighted age, salinity, ...)
438    o pkg/grdchk:
439      - all procs calculate and print finite-difference gradient (for testreport)
440      - change description output used by testreport;
441      - AD testing: also compare and report Finite-difference gradient;
442        => update all output_adm*.txt
443    o test exp. global_ocean_ebm:
444      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
445        and turn on exactConserve; update (fwd) output.
446    o pkg/seaice (LSR):
447      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
448      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
449        * identical results with non-CS topology (but save up to half of EXCH calls)
450        * no much changes in cs-32 verification tests since no ice at face edges
451         (differences due to convergence criteria, since nb of iterations changed)
452        * expect some differences on lat-lon-cap grid.
453        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
454    o pkg/exch2:
455      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
456        many tiles); until alternative coding is added, just add a stop.
457    o pkg/kpp:
458      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
459        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
460    o optfiles:
461      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
462        into corresponding standard one, which now support different build:
463        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
464      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
465    o pkg/obcs (seaice):
466      - add missing EXCH for uIce,vIce after applying OBCS;
467      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
468        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
469        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
470      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
471      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
472        and eedata.mth for MPI and mutlti-threaded testing.
473    o pkg/flt:
474      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
475      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
476      - fix pickup and trajectories + profiles output with multi-threads;
477      - add parameter to select group of fields to write along trajectory and
478        profile (default unchanged);
479      - only call PORT_RAND* function when flt_noise <> 0;
480      - add multi-threaded test for verification exp. flt_example.
481    o eesupp/src:
482      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
483      - USE_OMP_THREADING: check that number of threads (from eedata) matches
484        actual number (from env.var. setting).
485    o pkg/ebm:
486      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
487      - add multi-threaded test for verification exp. global_ocean_ebm
488    
489    checkpoint63b (2011/08/29)
490    o pkg/ebm:
491      - fix sign of runoff;
492      - update directly forcing fields (Qnet,EmPmR) to use standard
493        external_forcing_surf.F (remove ebm_forcing_surf.F);
494      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
495      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
496        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
497      - update global_ocean_ebm parameters file data and update output (fwd+ad).
498    o verification/matrix_example:
499      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
500        MPI and mutlti-threaded testing.
501    o pkg/matrix:
502      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
503      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
504      - fix for multi-threaded (remove DATA statement);
505      - use standard DIFFERENT_MULTIPLE function;
506      - add MATRIX_OPTIONS.h
507    o verification/matrix_example:
508       To allow to split the domain in several tiles, change the domain size
509        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
510        Western side) of land points.
511    o (*_)write_pickup:
512      - fix few bugs in mypackage_read/write_pickup.F
513      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
514        array of length 1 (was caught by compiler syntax-check).
515    o pkg/diagnostics (velocity potential solver):
516      - fix initialisation of main diagonal matrix (for overlap values)
517    o tools/build_options:
518      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
519        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
520      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
521        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
522        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
523        and use "-devel" testreport option for standard testing on baudelaire.
524    o pkg/grdchk:
525      - Assume that all gradient-check position are within the same tile
526        corresponding to global indices (iGloTile,jGloTile) and that
527        positions (i,j indices or nbeg) are local to this tile;
528      - set tile local-indices and proc. number according to tile global-indices;
529      - remove grdchkwhichproc from namelist (retired param);
530      - send adjoint gradient to all procs so that all procs print it to STDOUT;
531      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
532    o adding package bbl (Bottom Boundary Layer)
533      description in MITgcm/pkg/bbl/bbl_description.tex
534      example/test experiment in MITgcm_contrib/bbl
535    o adjoint verifications
536      - changed 5 experiments to multi-tiles
537        * global_ocean.90x40x15
538        * obcs_ctrl
539        * offline_exf_seaice
540        * tutorial_dic_adjoffline
541        * tutorial_tracer_adjsens
542        changed reference output for those that crossed tile boundaries
543        (changed choices of gradient check positions)
544      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
545      - temporary bug fix in grdchk_loc.F for obcs
546    o genmake2 & testreport
547      - add target "obj" (just for OBJFILES files) to Makefile;
548      - add option to specify FEXTRAFLAGS on command line.
549    o pkg/mypackage:
550      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
551    
552    checkpoint63a (2011/08/02)
553    o pkg/diagnostics (velocity potential):
554      - fix velocity-potential calculation when using OBCS: balance net inflow
555        at each level (new S/R OBCS_DIAG_BALANCE).
556      - fix some of the problems with OBCS in stream-function calculation.
557    o pkg/exf/exf_readparms.F
558      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
559        EXF_NML_OBCS) more consistent, so that you need not have these lists
560        in data.exf when they are not used.
561    o optim/optim_readdata.F:
562      - add some output about obcs variables that might help debugging
563      - add a check about nvarlength
564    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
565    o pkg/diagnostics (velocity potential):
566      - fix mask for OBCS (still problems in stream-function with OBCS);
567      - add specific parameter (default = main code CG2D params) for solver;
568      - in case of poor convergence, use solution corresponding to lowest residual.
569    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
570      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
571      and should be avoided where possible.
572    o model/src (rStar):
573      - include r* effect on reference-state (PhiRef) in totPhiHyd
574        (so that it's really the potential anomaly at the cell center);
575        affect solution only if z* with full pressure in EOS.
576      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
577        update output (because of z* in totPhiHyd and viscA4 changes);
578      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
579        @ constant r) until interpolation at constant r is implemented.
580    o pkg/diagnostics
581      - fix RCENTER diagnostics in case cell center is not at interface middle
582    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
583      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
584      that THETA and SALT are "conservative temperature" and "absolute
585      salinity"
586    o pkg/ctrl
587      - fix computation of endrec in s/r ctrl_init_rec
588      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
589    o pkg/seaice/seaice_growth.F
590      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
591        remove then obsolete STORE directives
592      - fix STORE directives for tice and tices, so that only the
593        appropriate part of the fields are stored (and not the entire
594        field); update global_ocean.cs32x15.seaice AD output.
595      - cosmetic changes: adjust CPP flags and indentation for better
596        legibilty
597    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
598      Chris Wilson)
599    o pkg/gmredi:
600       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
601       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
602    
603    checkpoint63  (2011/07/11)
604    o pkg/exch2:
605     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
606     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
607       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
608       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
609    o pkg/diagnostics:
610     - deal with pairs of post-processed diags which are computed together; in
611       particular, re-order list of diags within 1 file to save 2nd computation.
612     - add S/R to compute velocity stream-function (called after velocity-potential
613       calculation) from divergence free transport -> new diagnostics "PsiVEL".
614     - add parameter to select grid-point location where PsiVEL == 0.
615    o eesupp/src:
616       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
617       (specific S/R needed with exch2 topology - for now, just print an error msg)
618    o pkg/shelfice
619     - Implement friction velocity-dependent transfer coefficients following
620       Holland and Jenkins, JPO, 1999
621       Original code by M. Losch with small modifs.
622       Enable with CPP option SHI_ALLOW_GAMMAFRICT
623       and runtime flag SHELFICEuseGammaFrict
624    o verification lab_sea & global_ocean.cs32x15:
625     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
626       does not miss some dependencies (but is slower) and also works with many files
627       (default makedepend limitation for AD built).
628     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
629    o pkg/diagnostics:
630     - add run-time parameter "useMissingValue" (def=False) to fill land-point
631        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
632       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
633     - Extend the use of "missing_value" setting from data.diagnostics for the case
634       of counter-diagnostics (where fraction-weight is zero). This applies both to
635       MNC and MDS output files.
636    o pkg/seaice/seaice_growth.F:
637      - add 'a priori' cap of latent heat flux based on actual mass considerations
638        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
639        non-legacy seaice_solve4temp.
640      - add diagnostic of the residual sublimation freshwater flux (the freshwater
641        flux taken from the ocean if the total actual latent heat fluxes exceed
642        the maximum)
643      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
644       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
645      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
646       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
647      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
648      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
649    o verification 1D_ocean_ice_column:
650       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
651       update results
652    o pkg/diagnostics:
653     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
654       which are not filled-up but computed from other diags ; In this case, the mate
655       diag points to the primary (filled-up) diag to used for post processing.
656     - Update Velocity-potential computation using post-processed diag framework.
657     ==> Change the ordering of fields and time-periods in MDS output file
658       when using periodic averaging: now writes one time record with the full set
659       of fields for this time period, then the next time reccord (it used to be
660       one field with the full set of time records then the next field).
661         Note: this is now similar to NetCDF (MNC) output file. <==
662    
663    checkpoint62z (2011/06/21)
664    o adjoint monitor:
665     - Add adjoint monitor output for packages exf, seaice
666       and update relevant testreport output
667    o pkg/seaice:
668     - re-order diags inits so that they appear in order in available_diagnostics.log
669     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
670       area/heff/hsnow preceeding thermodynamic growth/melt.
671     - modified diag: SIdA; output actual effect, as the description states.
672     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
673     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
674       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
675        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
676     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
677     - added diagnostics for seaice generic tracers (SItr*).
678     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
679     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
680     I. Fenty: 18-Jun-2011:
681     Minor changes to seaice package:
682     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
683        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
684       - Differentiated "regularization variables" from "floor variables"
685        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
686        * hiceMin became SEAICE_hice_reg (old hiceMin)
687          (with _reg meaning regularization variable)
688       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
689        so as to ensure energy conservation when going between phases
690      - A22 was not used anywhere
691     2) Changed regularization procedure for heffActual and hsnowActual to ensure
692        well-boundedness and smooth adjoint in seaice_growth.F
693     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
694        because the old regularization always set heffActual >= 0.05 cm
695     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
696        on AREA when HEFF > 0.
697      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
698        requiring that DISABLE_AREA_FLOOR *not* be defined
699     Affected verifications:
700      - 1D_ocean_ice_column (output.txt output_adm.txt)
701      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
702    o pkg/diagnostics:
703      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
704      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
705        (was _RL, now integer) with option = 0 to retrieve all levels.
706      - add pieces of code to compute velocity potential at each level (new diagnostics
707        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
708        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
709      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
710        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
711        and in diagnostics_fract_fill.F (do not need a valid pointer for the
712        diagnostics counter-mate); check that definition of counter-diagnostic
713        includes a valid counter-mate (in diagnostics_set_levels.F).
714    o model/src (rStar):
715      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
716        affect solution only if z* with full pressure in EOS;
717        update output of test-exp global_ocean.90x40x15.
718    o pkg/seaice:
719      - introduce siEps=1e-5 parameter
720      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
721      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
722      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
723        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
724        as well as ice cover age and ridging index (attached to AREA).
725        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
726        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
727        Up to SItrMaxNum=3 tracers can be used simultaneously.
728    o pkg/salt_plume:
729      -introduce SPsalFRAC run time parameter that sets the fraction of the
730       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
731       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
732    o model debug options:
733      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
734        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
735      - Refine debug-msg printing selection (3 new levels):
736        debugMode  : controls printing of debug messages (sequence of S/R calls).
737        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
738         debLevZero =  0 ; /* level of disabled aux. msg printing */
739         debLevA =  1 ; /* level of minimum  aux. msg printing */
740         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
741         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
742         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
743         debLevE =  5 ; /* level of extensive debug printing */
744        New debugLevel default: with default debugMode value (=F),
745          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
746          and if debugMode=T, default debugLevel = 4 (debLevD).
747        Relation with previous settings:
748         debLevB (=2) corresponds to former debLevA (=1)
749         debLevD (=4) corresponds to former debLevB (=2)
750        Note:
751         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
752         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
753            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
754      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
755        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
756    o pkg/obcs:
757      - change OBCSfixTopo default from True to False (should not change the results);
758        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
759    o pkg/thsice:
760      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
761        2nd layer seaice sublimation (unlikely to happen)
762      - use Interior mask for OBCS in thsice_advection.F (similar to what is
763        done in gad_advection & seaice_advection).
764    o adjoint:
765      bug fix spotted by Gael Forget:
766      seaice_advection and thsice_advection still had
767      legacy CPP options to avoid CS corner updates for adjoint
768    o pkg/seaice:
769      => Change some of the defaults (2011/05/29):
770         - change SEAICEuseFluxForm default (from False to True)
771         - change DIFF1 default (from 0.004 m/s to 0. m/s)
772         And print warnings if DIFF1 is not set in data.seaice and centered
773          avection scheme is used without any diffusion.
774      also:
775      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
776      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
777      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
778        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
779        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
780      update results of test exp.:
781         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
782             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
783             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
784         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
785         seaice_obcs: output (SEAICEuseFluxForm=T)
786      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
787          for standard fwd & AD lab_sea tests (to keep the same output).
788    o pkg/seaice/seaice_growth.F:
789      - use Ian Fenty's capping formulas for actual ice
790      thickness thoughout EVOLUTION branch.
791      - put treatment pathological case #2) in CPP brackets
792      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
793      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
794    o pkg/seaice:
795      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
796      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
797      also pass fac as a param, which can be 1. (to update the tendency
798      field) or the time step (to update the field itself).
799      - seaice_advdiff.F: for multidim, call seaice_diffusion with
800      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
801      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
802      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
803      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
804    o pkg/seaice:
805      diffusion with centered advection scheme (diffus.F & advect.F):
806      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
807        to just compute the laplacian of input-field.
808      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
809      - fix flux-form version in diffus.F to conserve tracer.
810      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
811       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
812    
813    checkpoint62y (2011/05/26)
814    o pkg/seaice:
815     - seaice_growth.F : in EVOLUTION branch, always include
816       a_QSWbyATM_cover in qnet (as it should be).
817     - verification/global_ocean.cs32x15 : update results accordingly
818       (output.seaice.txt output_adm.seaice.txt).
819    o pkg/seaice + obcs:
820     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
821       equivalent of assuming no tracer gradient outside the OB region.
822       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
823     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
824       after changes above);
825     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
826       only at OB location (instead of over a band of OLx width).
827    o pkg/seaice:
828     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
829       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
830    o pkg/obcs:
831      - split header file "OBCS.h" into 4 separated files:
832        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
833       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
834         (contain no conditional statement which depends on OBCS options).
835      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
836        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
837    o ctrl, cost, grdchk & autodiff pkgs:
838      - make options file more standard (like other {PKG}_OPTIONS.h file but
839        with AD_CONFIG.h); clean-up some of the included header files.
840    o pkg/obcs:
841      - do not mask tracer when applying OB (tracer == 0 could generate problems)
842      - apply tracer OB values to tracer field only at OB location (instead of
843        over a band of OLx width)
844      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
845      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
846        obcs_apply_tloc.F & obcs_apply_sloc.F
847    o obcs in model/src:
848      - call OBCS_APPLY_W only if NonHydrostatic.
849      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
850      - reset dEtaHdt and wVel to zero outside OB interior region ;
851      - leave tracer unchanged outside OB interior region: This has no effect
852        on the solution but just to prevent unrealistic tracer value outside OB.
853      - zero out velocity outside OB interior region: This has no effect on
854        the solution but just to prevent unrealistic velocity outside OB.
855    o obcs and non-lin free-surf:
856       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
857       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
858       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
859       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
860       update results of test-exp. exp4(nlfs).
861    o exp4 (nlfs) test-exp:
862       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
863       with NonLin-FreeSurf); update output.nlfs.txt
864    o obcs and 2d/3d solver norm:
865       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
866       and outside OB interior region (will allow to place OB further inside the
867       domain). Depending on the domain, can affects cg2d-Norm (previous
868       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
869       and cg3d-Norm (previous Norm was computed before canceling OB terms),
870       e.g. in tutorial_plume_on_slope.
871      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
872    o pkg rbcs:
873      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
874      - add capability to apply relaxation to horizontal velocity uVel & vVel.
875    o pkg/grdchk: add gradient check for control variable xx_shifwflx
876    o pkg/shelfice/shelfice_init_fixed.F
877      fix CPP-flag combinations
878    o pkg/seaice: Merge iceage code of Pierre Rampal
879      * update/change/correct ice age calculations
880      * add age updates for pathological cases
881      Probably needs more testing...
882    
883    checkpoint62x (2011/05/13)
884    o pkg/mom_vecinv:
885       high-order vorticity scheme: use interior masks (maskInW & S)
886       to zero-out (outside OB) gradient of vorticity.
887    o verification exp.:
888       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
889       hs94.128x64x5 and seaice_obcs ; update results.
890    o pkg/obcs:
891      fix bug in OBeta for YZ sections in obcs_exf_load.F
892    o pkg/ctrl, pkg/shelfice, and optim:
893      - add new control variable xx_shifwflx (fresh water flux underneath ice
894        shelves). This is almost as tedious as obcs-ctrl, because the
895        variables needs its own mask.
896      - add a cost function term that penalizes the deviation of xx_shifwflx
897        from the first guess (zero) in analogy to other control variables
898    o pkg/shelfice:
899      - start basic adjoint
900    o pkg/ctrl:
901      - remove extra 2D field "for good measure" when initializing in
902        ctrl_set_globfld_[xy/xz/yz].F
903      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
904      - improve error messages in ctrl_set_unpack_*
905    o OBC implementation in momentum:
906       use interior masks (maskInC,W & S) in momentum S/R:
907       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
908       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
909       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
910       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
911       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
912        (and also with Leith/Smagorinsky harmonic-viscosity).
913       Update output of experiment dome and exp4 (+nlfs).
914    o exp4 test-exp:
915      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
916        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
917        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
918        time-varying OB at Western-side for wVel (NonHyd); update output.
919      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
920        and biharmonic-viscosity ; also use prescribed time varying OB.
921    o pkg/obcs:
922      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
923    o model/src:
924      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
925      - initialise startTime & nIter0 with unlikely values: allows to set one
926        from the other without ambiguity.
927    o seaice_obcs test-exp.:
928      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
929  o pkg/obcs:  o pkg/obcs:
930    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
931      no longer needed with maskInC,W,S in pkg/generic_advdiff.      no longer needed with maskInC,W,S in pkg/generic_advdiff.
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