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revision 1.1424 by mlosch, Thu May 5 09:24:44 2011 UTC revision 1.1586 by jmc, Tue Jan 31 17:12:24 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o pkg/ctrl:  o pkg/seaice:
8      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
9        of arrays, sign/direction of fluxes; no effect on results.
10      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
11        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
12        note: this should have been done before changing celsius2K default.
13      - to keep results unchanged, add back old value of celsius2K in verification
14        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
15      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
16        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
17        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
18        freezing temp is consistent with value in seaice_growth.F ; this causes
19        differences at machine truncation level: update lab_sea AD output (3/4).
20    o pkg/seaice:
21      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
22        and climsst/sss even when using seaice (to prevent calculation that might
23        use SST on land); does not affect any verification exp.
24      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
25        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
26    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
27      over land (non-legacy code)
28    o vectorize salt_plume package:
29      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
30      - this code computes plumebk everywhere (also over land), thus requires
31        code to avoid divisions by zero and catch the case of kLev=Nr.
32      - efficiency of salt_plume_frac is still sub-optimal
33    o tools (genmake2):
34      - fix makefile NAME specification (option: -makefile NAME) by adding
35        "-f $MAKEFILE" in few places where it was missing including makedepend
36        command (contribution from Paul).
37    
38    checkpoint63i (2012/01/24)
39    o model/src:
40      - add factorized versions of some EOS code to find_rho.F,
41        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
42    o model/src:
43      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
44      - change default celsius2K from 273.16 to 273.15
45      - to keep results unchanged, add back old value of celsius2K in verification
46        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
47         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
48    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
49      to make TAF generate vectorizable code
50    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
51       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
52       have flags that do this more efficiently.
53    o pkg/diagnostics/diagstats_calc.F
54      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
55    o pkg/obcs (with exch2):
56      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
57        and remove code (in obcs_readparms.F) which was based on EXCH of indices
58        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
59    o pkg/exf and seaice exp:
60      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
61        so that switching off area & heff advection flags does not affect results.
62      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
63      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
64        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
65        results of verification experiments: 1D_ocean_ice_column(fwd),
66        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
67        and offline_exf_seaice (all 4).
68    o pkg/seaice:
69      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
70        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
71      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
72        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
73        not multi-dim advection;
74      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
75        SHORTWAVE_HEATING #undef.
76    o optim: make Makefile more robust (?)
77    o pkg/obcs:
78      * fix treatment of obcs_read_pickup for TAF
79    o pkg/shelfice:
80      * add missing initialisation of num_shifwflx
81      * new adjoint verification exp. for isomip
82      * change Prandtl and Schmidt numbers from generic formulations
83        (in terms of model diffus. and visc.) to separate runtime
84        parameters, with Holland and Jenkins (1999) default values.
85    o pkg/exf (interpolation):
86      - extended input field (2 rows) near the N & S poles:
87        * fill in with the symetric value (when even Nb of data in longitude)
88        * add average value at the poles only for scalar quantities ; for vector
89          component interpolation, skip the averaging and keep duplicated values,
90          unless the 2 components have same location (uvInterp=T) in which case
91          interpolate the 2 components together using S/R EXF_INTERP_UV.
92      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
93        together: this allows to account properly for local orientation when
94        averaging at N & S pole.
95      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
96        exf-interpolation near N & S poles. Undef by default.
97      - add debug check/print on 1rst iter if debugLevel >=2.
98    o pkg/exf:
99      - change masking flags definition (no longer "parameter"), put them in
100        common block and set them in S/R EXF_INIT_FIXED.
101      - change recognized masking flag from s,u,v to c,w,s since the mask
102        to use (maskC,W,S) depends on position on model grid and has little to
103        do with scalar/vector difference; fix masking if using P-coordinates.
104      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
105        and update results of exp. global_with_exf (x2).
106      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
107    o pkg/obcs
108      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
109    o pkg/exf (interpolation):
110      - assume periodicity in X only if input field cover full longitude range.
111      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
112        and should vectorise).
113      - fix input lat of the 2 added row (in case we provide N.pole data).
114    
115    checkpoint63h (2011/12/30)
116    o pkg/seaice:
117      - change declaration of UVM from _RL to _RS in order to get B-grid
118        uIce,vIce monitor when _RS = real*4
119    o pkg/offline:
120      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
121      - compute vertical velocity if not read from file (switch on exactConserv
122        & staggerTimeStep);
123      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
124    o verification:
125      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
126        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
127        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
128      - update output of exp. global_ocean.cs32x15.viscA4 after changing
129        grid-file angles (used here for coriolis-3d);
130      - remove (or gzip) few files not needed to run fizhi-cs experiments.
131    o pkg/exf (vector interpolation):
132      - rotate vector component toward local grid-axis orientation using grid-angles
133        (stored in GRID.h) instead of locally computed rotation angle; keep old code
134        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
135    o pkg/seaice:
136      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
137        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
138    o pkg/PKG_OPTIONS.h files:
139      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
140        outside of the #ifdef ALLOW_THISPKG / #endif block.
141      - update verification/*/code/PKG_OPTIONS.h files.
142    o add a verification experiment (offline_exf_seaice/input.seaice) that test
143      the B-grid LSOR solver
144    o pkg/seaice: sort out emissivity and long wave radiation step 2:
145      - add emissivity for snow and ice as new run-time parameters
146        (unfortunately) that default to the corresponding exf values; this
147        changes results in most verification experiments so that for backward
148        compatibility these parameter have to be set explicitly to inconsistent
149        values (ugly);
150      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
151        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
152        until we agree how to handle this bug properly
153    o pkg/exf (interpolation):
154      - add a set of run-time param ({inputfield}_interpMethod), one for
155        each interpolated input field, to select the interpolation method
156        with a value of zero switching off the interpolation;
157      - print interpolation parameters to standard output;
158      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
159        (to use instead runoff_interpMethod=0 in data.exf).
160      - simplify default setting of interpolation parameters (for all fields,
161        set position to match model grid cell-center position, leading to trivial
162        interpolation in case of regular Lat-Lon grid) and fix for the case of
163        non-uniform delY.
164    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
165       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
166       this factor is absolutely required, because the lw exitance (= out-going
167       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
168       where the reflectivity rho = 1-emissivity for conservation reasons. Once
169       this is established, we can remove the CPP-Flag (if we want to).
170    o pkg/seaice:
171      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
172        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
173      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
174        what the name implies (and not emissivity*BoltzmannConstant), this means
175        the old default value of 5.5e-8 now means
176        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
177        S/R exf_readparms
178      - FV-discretization of the B-grid LSOR solver, turn on with
179        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
180        of the calling routine dynsolver, so that B and C-grid code look a
181        little more alike.
182      - fix index bugs in ostres.F (B-grid code)
183    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
184    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
185      default for SEAICE_emissivity, if useEXF; requires setting a wrong
186      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
187      backward compatiblity
188    o model/src: use sigmaR in calc_ivdc
189    
190    checkpoint63g (2011/12/16)
191    o pkg/seaice/seaice_growth.F:
192      fix heat conservation of the coupled ocean-seaice system.
193      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
194      solid vs liquid water treatment is resolved via QNET.
195    o pkg/seaice/seaice_growth.F:
196      add missing term for sublimation in saltFlux, which was breaking conservation.
197    o pkg/seaice/seaice_model.F:
198      Remove this patholigical case treatment in evolution branch,
199      where it is un-necessary and breaks conservation.
200      Update global_ocean.cs32x15/results accordingly for
201      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
202    o model/src:
203      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
204      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
205    o pkg/obcs:
206      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
207      tendency for temperature and salinity that is then applied to update
208      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
209      horizontal advection and diffusion contributions on the boundary (in
210      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
211      removing the mask in S/R timestep_tracer. The advantage of this approach is
212      that the updated tracer values include contributions from the surface
213      forcing and vertical diffusion.
214      This modification changes exp4.stevens because of vertical diffusion.
215    o model/src:
216      change non-curvilinear grid setting to also work with exch2 + blank tiles:
217      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
218        face dimensions.
219      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
220        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
221        and INI_SPHERICAL_POLAR_GRID.
222      change test-experiment global_ocean.90x40x15:
223      - split the domain in many more tiles (9x4 tiles of 10x10 each);
224      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
225      - update results of both test (std & dwnslp).
226    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
227       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
228    o model/src:
229      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
230        and fix initialisation when using sigma-coords.
231    o model/src:
232     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
233       to their current value at the beginning of forward_step.F": add a new run-time
234       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
235     - set doResetHFactors=T in the following test exp:
236        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
237        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
238        and tutorial_global_oce_in_p (nonLinFS in p)
239    o pkg/ecco
240      - added IES cost term
241    o verification/advect_xz
242      - scale down the depth by 1/100 (from 200 km to just 2.km)
243      - add secondary test using divergent flow, r-star and implicit vertical advection.
244      - add note (check_conserve_TS.txt) and matlab script to check global
245        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
246    o pkg/rbcs:
247      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
248    o pkg/obcs (Stevens BCs):
249      - fix various problems in the phase speed computations of the Stevens
250        boundary conditions:
251        - sign error for western and southern boundaries,
252        - time tendencies were underestimated by factor of dTracerLev and some just
253          zero (for multidim advection schemes) -> now estimate time tendencies
254          from difference between previous (n) time level and the one before (n-1);
255          this requires storing a field per tracer per boundary, also in the pickup
256          files.
257        - replace deltaTmom in cflMer/Zon computation with dTracerLev
258        - set default phase velocity to cflMer/Zon
259      - update verification experiment exp4.stevens
260    o pkg/generic_advdiff (implicit_r):
261      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
262        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
263      - fix implicit vertical diffusion or advection with NonLin FreeSurf
264        (was using current recip_hFacC instead of future recip_hFacC): set future
265        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
266        solver S/R ;
267      - fill diagnostics of vertical advective fluxes (computed from tendency)
268        when using implicit vert. advection;
269      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
270         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
271         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
272         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
273    o pkg/diagnostics:
274      - add diags for T & S tendency which goes through Adams-Bashforth.
275    
276    checkpoint63f (2011/11/30)
277    o pkg/obcs/obcs_calc_stevens.F:
278      - join some loops to reduce number of if-statements
279      - fix a bug in code for northern and southern boundaries.
280    o pkg/seaice/seaice_init_varia.F
281      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
282        caused zero ice-velocities for the B-grid code
283    o pkg/seaice/seaice_init_fixed.F
284      - fix a bug in the initialisation of the second metric terms
285        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
286      - this affects all seaice configurations with useCurviLinearGrid = .true.
287        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
288        = .true. (default)
289      - the only verification experiment affected is global_ocean.cs32x15:
290        icedyn, seaice, and seaice_dynmix (AD)
291    o pkg/thsice/thsice_diagnostics_state.F
292      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
293        not contain garbage that can lead to surprises in diagstats_calc.F
294    o model/src:
295      - move bi,bj loops inside INTEGR_CONTINUITY ;
296      - call INTEGR_CONTINUITY directly from forward_step.F
297        (previously called from momentum_correction_step.F)
298      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
299        forward_step.F and pkg/ecco/the_main_loop.F
300    o model/src/do_oceanic_phys.F:
301      - reset addMass to zero only if useICEFRONT ;
302      - separated k-loop for rhoInSitu calculation ;
303      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
304        and at constant T,S (= WdRHOdP);
305      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
306        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
307        transport of locally-referenced potential density);
308        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
309    o gluemnc:
310      - replace ncrcat with ncks when adding variables to *.glob.nc
311      - change the way variables without record dimensions are handled so that
312        files that have variables with and without record variables can be glued:
313        add a record dimension with a new unique name to be able to differentiate
314        between variable with and without a-prior record dimensions. Remove
315        this record dimension before adding the variable to the *.glob.nc file.
316        This procedure automatically works also for grid.*.nc files that do not
317        have any record dimension.
318    o verification/cpl_aim+ocn:
319      - generate new reference output on baudelaire (gfortran, mpich2) (previously
320        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
321    o pkg/obcs/obcs_calc_stevens.F:
322      - add code for northern and southern boundaries.
323      - reorder some loops to save some operations and so that drFBar can be scalar
324    o model/src:
325      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
326        truncation) and add diagnostics for Adams-Bashforth tendency increment.
327      - update test-exp. AD output:
328        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
329      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
330        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
331        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
332        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
333        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
334        tutorial_plume_on_slope.
335    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
336      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
337      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
338      does not even come with an F77 compiler anymore, this should not be
339      a limitation
340    
341    checkpoint63e (2011/11/06)
342    o pkg/seaice adjoint of LSR:
343      - substantially rework STORE dirs.
344      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
345        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
346        and only perform SOLV_MAX_FIXED adjoint iters.
347        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
348        always goes to same record, meaning that the last forward field will be
349        the one used in the adjoint - an approximation.
350      - now produces non-zero LSR-related gradients, and acceptable gradients for
351        An's zonal (x-z) test case (to be checked in)
352      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
353        (but these are screwed up by the thermodynamics in the first place);
354        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
355        output_adm.txt also reflects changes to seaice_lsr
356      - global_ocean.cs32x15:
357        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
358          (output_adm.seaice.txt was updated)
359        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
360          (output_adm.seaice_dynmix.txt)
361    o test-exp. exp4+stevens:
362      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
363    o pkg/seaice (lsr solver):
364      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
365        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
366      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
367      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
368        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
369      - compute (with new S/R) and print initial (+ free-driff sol. if available)
370        and final residual of linearised system.
371    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
372      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
373    o pkg/obcs: Stevens BCs (still only for east and west)
374      - fix Stevens BCs by using intermediate velocities of previous
375        time step as "baroclinic" contribution rather velocity of one grid cell
376        inside the boundaries; more consistent but makes the entire treatment
377        more complicated, requires new pickup files and two new S/Rs:
378        obcs_copy_uv_n and obcs_save_uv_n
379        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
380        (undefined by default)
381      - silently move computation of some grid factors into separate loops to
382        save some recomputations
383      - add a hack for non-linear free surface
384      - add a verification experiment to exp4 that tests this code
385    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
386    
387    checkpoint63d (2011/10/25)
388    o pkg/obcs + seaice-dynamics:
389      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
390        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
391        values (consistent with an implicit method).
392      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
393        return to older implementation (same results as before); note that none of
394        the "experimental" OBCS_SEAICE options are implemented in the new version.
395      - switch test exp. seaice_obcs to use new version (update output).
396    o pkg/seaice:
397      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
398      - add parenthesis in Water-Ice drag calculations (evp & lsr);
399      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
400        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
401      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
402        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
403    o pkg/layers:
404      - Include potential density as new coordinate (Thanks to David Munday)
405    o pkg/dic:
406      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
407        carbonate computation/output to CALC_PCO2_APPROX
408    o pkg/generic_advdiff
409      - make TAF generate code that vectorizes:
410        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
411    o model/src:
412      - improve vectorization also for adjoint code of
413        solve_tridiagonal and solve_pentadiagonal. As this requires up to
414        5 new 3D-fields, this code is only turned on for the combination of
415        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
416        for singular matrix check (only for TARGET_NEC_SX).
417      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
418        ALLOW_AUTODIFF. This flag now needs to be set outside of
419        solve_tri/pentadiagonal.F
420    o pkg/exf:
421      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
422        optional namelist EXF_NML_OBCS).
423      - add many debug-print (to trace down where pkg/cal error msg comes from)
424    o pkg/mom_vecinv/mom_vi_hdissip.F
425      - rearrange loops so that vectorization is improved and in particular
426        the adjoint routine vectorizes. The code is a little longer now, but I
427        think easier to read.
428        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
429    o pkg/seaice:
430      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
431    o pkg/exch2:
432      - alternative code (without tile x tile matrix) for cumulated (global) sum;
433        used as default; keep using matrix version in adjustment.cs-32x32x1.
434    o tools/build_options:
435      - after merging some MPI and/or multi-threads specific optfiles so that
436        the modified default optfile support both built (using genmake2 -mpi
437        for the MPI built, using genmake2 -omp for OpenMP built),
438        move now obsolete optfiles to tools/build_options/unsupported/
439       (add copy of email sent to support list in doc/optfiles_changes.txt)
440    
441    checkpoint63c (2011/09/28)
442    o pkg/ebm:
443      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
444        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
445    o pkg/seaice (SItracer pickup)
446    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
447      To be done:
448      - thorough testing of missing fields in S/R seaice_read_pickup
449      - thorough matching between generic tracers and specific fields used
450        (e.g. volume-weighted age, area-weighted age, salinity, ...)
451    o pkg/grdchk:
452      - all procs calculate and print finite-difference gradient (for testreport)
453      - change description output used by testreport;
454      - AD testing: also compare and report Finite-difference gradient;
455        => update all output_adm*.txt
456    o test exp. global_ocean_ebm:
457      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
458        and turn on exactConserve; update (fwd) output.
459    o pkg/seaice (LSR):
460      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
461      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
462        * identical results with non-CS topology (but save up to half of EXCH calls)
463        * no much changes in cs-32 verification tests since no ice at face edges
464         (differences due to convergence criteria, since nb of iterations changed)
465        * expect some differences on lat-lon-cap grid.
466        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
467    o pkg/exch2:
468      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
469        many tiles); until alternative coding is added, just add a stop.
470    o pkg/kpp:
471      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
472        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
473    o optfiles:
474      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
475        into corresponding standard one, which now support different build:
476        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
477      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
478    o pkg/obcs (seaice):
479      - add missing EXCH for uIce,vIce after applying OBCS;
480      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
481        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
482        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
483      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
484      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
485        and eedata.mth for MPI and mutlti-threaded testing.
486    o pkg/flt:
487      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
488      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
489      - fix pickup and trajectories + profiles output with multi-threads;
490      - add parameter to select group of fields to write along trajectory and
491        profile (default unchanged);
492      - only call PORT_RAND* function when flt_noise <> 0;
493      - add multi-threaded test for verification exp. flt_example.
494    o eesupp/src:
495      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
496      - USE_OMP_THREADING: check that number of threads (from eedata) matches
497        actual number (from env.var. setting).
498    o pkg/ebm:
499      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
500      - add multi-threaded test for verification exp. global_ocean_ebm
501    
502    checkpoint63b (2011/08/29)
503    o pkg/ebm:
504      - fix sign of runoff;
505      - update directly forcing fields (Qnet,EmPmR) to use standard
506        external_forcing_surf.F (remove ebm_forcing_surf.F);
507      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
508      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
509        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
510      - update global_ocean_ebm parameters file data and update output (fwd+ad).
511    o verification/matrix_example:
512      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
513        MPI and mutlti-threaded testing.
514    o pkg/matrix:
515      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
516      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
517      - fix for multi-threaded (remove DATA statement);
518      - use standard DIFFERENT_MULTIPLE function;
519      - add MATRIX_OPTIONS.h
520    o verification/matrix_example:
521       To allow to split the domain in several tiles, change the domain size
522        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
523        Western side) of land points.
524    o (*_)write_pickup:
525      - fix few bugs in mypackage_read/write_pickup.F
526      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
527        array of length 1 (was caught by compiler syntax-check).
528    o pkg/diagnostics (velocity potential solver):
529      - fix initialisation of main diagonal matrix (for overlap values)
530    o tools/build_options:
531      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
532        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
533      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
534        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
535        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
536        and use "-devel" testreport option for standard testing on baudelaire.
537    o pkg/grdchk:
538      - Assume that all gradient-check position are within the same tile
539        corresponding to global indices (iGloTile,jGloTile) and that
540        positions (i,j indices or nbeg) are local to this tile;
541      - set tile local-indices and proc. number according to tile global-indices;
542      - remove grdchkwhichproc from namelist (retired param);
543      - send adjoint gradient to all procs so that all procs print it to STDOUT;
544      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
545    o adding package bbl (Bottom Boundary Layer)
546      description in MITgcm/pkg/bbl/bbl_description.tex
547      example/test experiment in MITgcm_contrib/bbl
548    o adjoint verifications
549      - changed 5 experiments to multi-tiles
550        * global_ocean.90x40x15
551        * obcs_ctrl
552        * offline_exf_seaice
553        * tutorial_dic_adjoffline
554        * tutorial_tracer_adjsens
555        changed reference output for those that crossed tile boundaries
556        (changed choices of gradient check positions)
557      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
558      - temporary bug fix in grdchk_loc.F for obcs
559    o genmake2 & testreport
560      - add target "obj" (just for OBJFILES files) to Makefile;
561      - add option to specify FEXTRAFLAGS on command line.
562    o pkg/mypackage:
563      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
564    
565    checkpoint63a (2011/08/02)
566    o pkg/diagnostics (velocity potential):
567      - fix velocity-potential calculation when using OBCS: balance net inflow
568        at each level (new S/R OBCS_DIAG_BALANCE).
569      - fix some of the problems with OBCS in stream-function calculation.
570    o pkg/exf/exf_readparms.F
571      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
572        EXF_NML_OBCS) more consistent, so that you need not have these lists
573        in data.exf when they are not used.
574    o optim/optim_readdata.F:
575      - add some output about obcs variables that might help debugging
576      - add a check about nvarlength
577    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
578    o pkg/diagnostics (velocity potential):
579      - fix mask for OBCS (still problems in stream-function with OBCS);
580      - add specific parameter (default = main code CG2D params) for solver;
581      - in case of poor convergence, use solution corresponding to lowest residual.
582    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
583      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
584      and should be avoided where possible.
585    o model/src (rStar):
586      - include r* effect on reference-state (PhiRef) in totPhiHyd
587        (so that it's really the potential anomaly at the cell center);
588        affect solution only if z* with full pressure in EOS.
589      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
590        update output (because of z* in totPhiHyd and viscA4 changes);
591      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
592        @ constant r) until interpolation at constant r is implemented.
593    o pkg/diagnostics
594      - fix RCENTER diagnostics in case cell center is not at interface middle
595    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
596      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
597      that THETA and SALT are "conservative temperature" and "absolute
598      salinity"
599    o pkg/ctrl
600      - fix computation of endrec in s/r ctrl_init_rec
601      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
602    o pkg/seaice/seaice_growth.F
603      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
604        remove then obsolete STORE directives
605      - fix STORE directives for tice and tices, so that only the
606        appropriate part of the fields are stored (and not the entire
607        field); update global_ocean.cs32x15.seaice AD output.
608      - cosmetic changes: adjust CPP flags and indentation for better
609        legibilty
610    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
611      Chris Wilson)
612    o pkg/gmredi:
613       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
614       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
615    
616    checkpoint63  (2011/07/11)
617    o pkg/exch2:
618     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
619     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
620       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
621       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
622    o pkg/diagnostics:
623     - deal with pairs of post-processed diags which are computed together; in
624       particular, re-order list of diags within 1 file to save 2nd computation.
625     - add S/R to compute velocity stream-function (called after velocity-potential
626       calculation) from divergence free transport -> new diagnostics "PsiVEL".
627     - add parameter to select grid-point location where PsiVEL == 0.
628    o eesupp/src:
629       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
630       (specific S/R needed with exch2 topology - for now, just print an error msg)
631    o pkg/shelfice
632     - Implement friction velocity-dependent transfer coefficients following
633       Holland and Jenkins, JPO, 1999
634       Original code by M. Losch with small modifs.
635       Enable with CPP option SHI_ALLOW_GAMMAFRICT
636       and runtime flag SHELFICEuseGammaFrict
637    o verification lab_sea & global_ocean.cs32x15:
638     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
639       does not miss some dependencies (but is slower) and also works with many files
640       (default makedepend limitation for AD built).
641     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
642    o pkg/diagnostics:
643     - add run-time parameter "useMissingValue" (def=False) to fill land-point
644        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
645       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
646     - Extend the use of "missing_value" setting from data.diagnostics for the case
647       of counter-diagnostics (where fraction-weight is zero). This applies both to
648       MNC and MDS output files.
649    o pkg/seaice/seaice_growth.F:
650      - add 'a priori' cap of latent heat flux based on actual mass considerations
651        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
652        non-legacy seaice_solve4temp.
653      - add diagnostic of the residual sublimation freshwater flux (the freshwater
654        flux taken from the ocean if the total actual latent heat fluxes exceed
655        the maximum)
656      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
657       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
658      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
659       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
660      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
661      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
662    o verification 1D_ocean_ice_column:
663       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
664       update results
665    o pkg/diagnostics:
666     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
667       which are not filled-up but computed from other diags ; In this case, the mate
668       diag points to the primary (filled-up) diag to used for post processing.
669     - Update Velocity-potential computation using post-processed diag framework.
670     ==> Change the ordering of fields and time-periods in MDS output file
671       when using periodic averaging: now writes one time record with the full set
672       of fields for this time period, then the next time reccord (it used to be
673       one field with the full set of time records then the next field).
674         Note: this is now similar to NetCDF (MNC) output file. <==
675    
676    checkpoint62z (2011/06/21)
677    o adjoint monitor:
678     - Add adjoint monitor output for packages exf, seaice
679       and update relevant testreport output
680    o pkg/seaice:
681     - re-order diags inits so that they appear in order in available_diagnostics.log
682     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
683       area/heff/hsnow preceeding thermodynamic growth/melt.
684     - modified diag: SIdA; output actual effect, as the description states.
685     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
686     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
687       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
688        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
689     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
690     - added diagnostics for seaice generic tracers (SItr*).
691     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
692     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
693     I. Fenty: 18-Jun-2011:
694     Minor changes to seaice package:
695     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
696        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
697       - Differentiated "regularization variables" from "floor variables"
698        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
699        * hiceMin became SEAICE_hice_reg (old hiceMin)
700          (with _reg meaning regularization variable)
701       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
702        so as to ensure energy conservation when going between phases
703      - A22 was not used anywhere
704     2) Changed regularization procedure for heffActual and hsnowActual to ensure
705        well-boundedness and smooth adjoint in seaice_growth.F
706     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
707        because the old regularization always set heffActual >= 0.05 cm
708     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
709        on AREA when HEFF > 0.
710      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
711        requiring that DISABLE_AREA_FLOOR *not* be defined
712     Affected verifications:
713      - 1D_ocean_ice_column (output.txt output_adm.txt)
714      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
715    o pkg/diagnostics:
716      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
717      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
718        (was _RL, now integer) with option = 0 to retrieve all levels.
719      - add pieces of code to compute velocity potential at each level (new diagnostics
720        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
721        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
722      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
723        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
724        and in diagnostics_fract_fill.F (do not need a valid pointer for the
725        diagnostics counter-mate); check that definition of counter-diagnostic
726        includes a valid counter-mate (in diagnostics_set_levels.F).
727    o model/src (rStar):
728      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
729        affect solution only if z* with full pressure in EOS;
730        update output of test-exp global_ocean.90x40x15.
731    o pkg/seaice:
732      - introduce siEps=1e-5 parameter
733      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
734      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
735      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
736        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
737        as well as ice cover age and ridging index (attached to AREA).
738        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
739        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
740        Up to SItrMaxNum=3 tracers can be used simultaneously.
741    o pkg/salt_plume:
742      -introduce SPsalFRAC run time parameter that sets the fraction of the
743       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
744       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
745    o model debug options:
746      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
747        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
748      - Refine debug-msg printing selection (3 new levels):
749        debugMode  : controls printing of debug messages (sequence of S/R calls).
750        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
751         debLevZero =  0 ; /* level of disabled aux. msg printing */
752         debLevA =  1 ; /* level of minimum  aux. msg printing */
753         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
754         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
755         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
756         debLevE =  5 ; /* level of extensive debug printing */
757        New debugLevel default: with default debugMode value (=F),
758          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
759          and if debugMode=T, default debugLevel = 4 (debLevD).
760        Relation with previous settings:
761         debLevB (=2) corresponds to former debLevA (=1)
762         debLevD (=4) corresponds to former debLevB (=2)
763        Note:
764         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
765         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
766            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
767      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
768        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
769    o pkg/obcs:
770      - change OBCSfixTopo default from True to False (should not change the results);
771        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
772    o pkg/thsice:
773      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
774        2nd layer seaice sublimation (unlikely to happen)
775      - use Interior mask for OBCS in thsice_advection.F (similar to what is
776        done in gad_advection & seaice_advection).
777    o adjoint:
778      bug fix spotted by Gael Forget:
779      seaice_advection and thsice_advection still had
780      legacy CPP options to avoid CS corner updates for adjoint
781    o pkg/seaice:
782      => Change some of the defaults (2011/05/29):
783         - change SEAICEuseFluxForm default (from False to True)
784         - change DIFF1 default (from 0.004 m/s to 0. m/s)
785         And print warnings if DIFF1 is not set in data.seaice and centered
786          avection scheme is used without any diffusion.
787      also:
788      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
789      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
790      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
791        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
792        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
793      update results of test exp.:
794         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
795             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
796             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
797         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
798         seaice_obcs: output (SEAICEuseFluxForm=T)
799      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
800          for standard fwd & AD lab_sea tests (to keep the same output).
801    o pkg/seaice/seaice_growth.F:
802      - use Ian Fenty's capping formulas for actual ice
803      thickness thoughout EVOLUTION branch.
804      - put treatment pathological case #2) in CPP brackets
805      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
806      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
807    o pkg/seaice:
808      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
809      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
810      also pass fac as a param, which can be 1. (to update the tendency
811      field) or the time step (to update the field itself).
812      - seaice_advdiff.F: for multidim, call seaice_diffusion with
813      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
814      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
815      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
816      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
817    o pkg/seaice:
818      diffusion with centered advection scheme (diffus.F & advect.F):
819      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
820        to just compute the laplacian of input-field.
821      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
822      - fix flux-form version in diffus.F to conserve tracer.
823      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
824       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
825    
826    checkpoint62y (2011/05/26)
827    o pkg/seaice:
828     - seaice_growth.F : in EVOLUTION branch, always include
829       a_QSWbyATM_cover in qnet (as it should be).
830     - verification/global_ocean.cs32x15 : update results accordingly
831       (output.seaice.txt output_adm.seaice.txt).
832    o pkg/seaice + obcs:
833     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
834       equivalent of assuming no tracer gradient outside the OB region.
835       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
836     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
837       after changes above);
838     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
839       only at OB location (instead of over a band of OLx width).
840    o pkg/seaice:
841     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
842       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
843    o pkg/obcs:
844      - split header file "OBCS.h" into 4 separated files:
845        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
846       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
847         (contain no conditional statement which depends on OBCS options).
848      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
849        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
850    o ctrl, cost, grdchk & autodiff pkgs:
851      - make options file more standard (like other {PKG}_OPTIONS.h file but
852        with AD_CONFIG.h); clean-up some of the included header files.
853    o pkg/obcs:
854      - do not mask tracer when applying OB (tracer == 0 could generate problems)
855      - apply tracer OB values to tracer field only at OB location (instead of
856        over a band of OLx width)
857      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
858      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
859        obcs_apply_tloc.F & obcs_apply_sloc.F
860    o obcs in model/src:
861      - call OBCS_APPLY_W only if NonHydrostatic.
862      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
863      - reset dEtaHdt and wVel to zero outside OB interior region ;
864      - leave tracer unchanged outside OB interior region: This has no effect
865        on the solution but just to prevent unrealistic tracer value outside OB.
866      - zero out velocity outside OB interior region: This has no effect on
867        the solution but just to prevent unrealistic velocity outside OB.
868    o obcs and non-lin free-surf:
869       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
870       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
871       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
872       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
873       update results of test-exp. exp4(nlfs).
874    o exp4 (nlfs) test-exp:
875       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
876       with NonLin-FreeSurf); update output.nlfs.txt
877    o obcs and 2d/3d solver norm:
878       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
879       and outside OB interior region (will allow to place OB further inside the
880       domain). Depending on the domain, can affects cg2d-Norm (previous
881       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
882       and cg3d-Norm (previous Norm was computed before canceling OB terms),
883       e.g. in tutorial_plume_on_slope.
884      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
885    o pkg rbcs:
886      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
887      - add capability to apply relaxation to horizontal velocity uVel & vVel.
888    o pkg/grdchk: add gradient check for control variable xx_shifwflx
889    o pkg/shelfice/shelfice_init_fixed.F
890      fix CPP-flag combinations
891    o pkg/seaice: Merge iceage code of Pierre Rampal
892      * update/change/correct ice age calculations
893      * add age updates for pathological cases
894      Probably needs more testing...
895    
896    checkpoint62x (2011/05/13)
897    o pkg/mom_vecinv:
898       high-order vorticity scheme: use interior masks (maskInW & S)
899       to zero-out (outside OB) gradient of vorticity.
900    o verification exp.:
901       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
902       hs94.128x64x5 and seaice_obcs ; update results.
903    o pkg/obcs:
904      fix bug in OBeta for YZ sections in obcs_exf_load.F
905    o pkg/ctrl, pkg/shelfice, and optim:
906      - add new control variable xx_shifwflx (fresh water flux underneath ice
907        shelves). This is almost as tedious as obcs-ctrl, because the
908        variables needs its own mask.
909      - add a cost function term that penalizes the deviation of xx_shifwflx
910        from the first guess (zero) in analogy to other control variables
911    o pkg/shelfice:
912      - start basic adjoint
913    o pkg/ctrl:
914      - remove extra 2D field "for good measure" when initializing in
915        ctrl_set_globfld_[xy/xz/yz].F
916    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
917    - improve error messages in ctrl_set_unpack_*    - improve error messages in ctrl_set_unpack_*
918  o OBC implementation in momentum:  o OBC implementation in momentum:
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