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revision 1.1522 by mlosch, Wed Oct 26 09:30:32 2011 UTC revision 1.1609 by gforget, Mon Mar 5 15:34:58 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      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is compiled either
9        way, and is tested in all exps (multidim was only tested in lab_sea ad before).
10      - cosmetic change to prepare for future addition of ITD. no change to results. no defaults change.
11      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
12      - by lack of adequate verification experiments, I further used custom versions of
13        global_ocean.cs32x15 to test multicat or not, with pickup or not. All should be correct.
14      - avoid recomputations in ad.
15    o array initialisation in adjoint mode:
16      1) pkg/mom_common/mom_calc_ke.F:
17        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
18        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
19        part this initialisation is gone, resulting in Floating Point Exception
20        (caught by open64 compiler with debug option).
21      2) model/src/convective_weights.F
22        set output convectCount over the full array range (instead of doing
23        an update): this fix a similar issue when called within recomputation (adjoint)
24        which could by-pass the initialisation (normally done in the caller S/R).
25    o pkg/seaice:
26      - final version of turbulent flux params, as agreed at MIT ice meet:
27           SEAICE_mcPheePiston (default is ~ 0.000875)
28           SEAICE_mcPheeTaper (default is 0.)
29           SEAICE_frazilFrac (defualt is 1.)
30           SEAICE_mcPheeStepFunc (default is false)
31      - changes results at trunction error level
32      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
33    o added pkg/frazil:
34      - see frazil_description.tex for details
35      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
36    o pkg/shelfice/shelfice_thermodynamics.F
37      - fix exponents for velocity dependent exchange coefficients: change
38        from 2/3(=0) to 0.66666666666666667
39      - move computation of velocity dependent exchange coefficients into
40        separate loop, so that it applies to both thermodynamics
41      - move some divisions by constants out of loops
42    
43    checkpoint63j (2012/02/16)
44    o pkg/seaice:
45      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
46      - SItracer:  added run time params, and allow coupling to ocn salinity.
47    o pkg/seaice: remove (almost) all divisions by constants within loops
48      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
49      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
50      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
51      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
52    o pkg/seaice :
53      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
54        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
55      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
56      - add permanent SItflux diag that corresponds to TFLUX but includes
57        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
58      - allow activation/testing of a fix for suspected missing term in
59        ocn-ice heat budget (to be confirmed). To test this, you want to
60        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
61        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
62      - no change in results, fwd or ad.
63    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
64      - switch to variable freezing point.
65           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
66      - bug fix : the sublimation term that was missing is now activated.
67           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
68      - bug fix : flooding sign term for SIsal0.NE.0.
69           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
70    o pkg/seaice:
71      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
72        is now the default, and the old default constant freezing point is recovered
73        with SEAICE_tempFrz0    = -1.96,
74             SEAICE_dTempFrz_dS = 0.,
75      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
76      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
77      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
78        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
79      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
80        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
81      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
82        seaice_growth r149 for legacy branch (no results change).
83      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
84        from I. Fenty).
85      - results did not change except for global_ocean.cs32x15, mostly due to the
86        switch to variable freezing point (see above item for detail).
87    o pkg/thsice:
88      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
89        seawater freezing in thsice_calc_thickn (not used).
90    o pkg/seaice: turbulent flux term specification via run time params.
91      - replace CPP switches with run time switches to facilitate testing
92      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
93                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
94      - added runtime parameter : SEAICEturbFluxFormula
95      - move Mcphee constants to SEAICE_PARAMS.h
96      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
97                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
98                 remove seaice_summary call (moved to seaice_init_fixed)
99      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
100        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
101      - seaice_summary.F : add missing report of read turbulent flux term set up
102                           and SITRACER.
103      - seaice_check.F : check range; inform and stop if retired CPPs are used
104                         (incl. SEAICE_AGE).
105      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
106             CPP switch, same computation as before for the different options.
107      - change results at the truncation level.
108    o pkg/seaice:
109      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
110        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
111        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
112      - update verification/*/input*/data.seaice:
113        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
114        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
115        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
116        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
117    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
118      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
119        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
120        difference in results only due to machine truncation.
121      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
122        MaykutPolySatVap; keep MIN_LWDOWN.
123      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
124      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
125        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
126    o pkg/salt_plume:
127      - isolate saltPlumeFlux array exch into a specific S/R called from
128        do_oceanic_phys.F
129      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
130    o verification:
131      - move untested set-up to MITgcm_contrib/verification_other.
132    o pkg/seaice:
133      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
134    o pkg/seaice:
135      - seaice_solve4temp.F (keeping results unchanged):
136        * add 2 future run-time params to select which saturation vapor pressure
137          formula is used and how post-iteration fluxes are set.
138          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
139        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
140          the linearized expression to stay consistent with tsurf finding.
141      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
142        can be < 0.
143    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
144      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
145        conductive heat flux F_c , and add it explicitly when updating tsurf as
146        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
147        so that now F_ia has a consistent meaning through the entire routine.
148        This causes differences at truncation level: update output of fwd exp.
149        global_ocean.cs32x15.seaice.
150    o pkg/seaice:
151      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
152        of arrays, sign/direction of fluxes; no effect on results.
153      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
154        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
155        note: this should have been done before changing celsius2K default.
156      - to keep results unchanged, add back old value of celsius2K in verification
157        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
158      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
159        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
160        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
161        freezing temp is consistent with value in seaice_growth.F ; this causes
162        differences at machine truncation level: update lab_sea AD output (3/4).
163    o pkg/seaice:
164      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
165        and climsst/sss even when using seaice (to prevent calculation that might
166        use SST on land); does not affect any verification exp.
167      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
168        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
169    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
170      over land (non-legacy code)
171    o vectorize salt_plume package:
172      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
173      - this code computes plumebk everywhere (also over land), thus requires
174        code to avoid divisions by zero and catch the case of kLev=Nr.
175      - efficiency of salt_plume_frac is still sub-optimal
176    o tools (genmake2):
177      - fix makefile NAME specification (option: -makefile NAME) by adding
178        "-f $MAKEFILE" in few places where it was missing including makedepend
179        command (contribution from Paul).
180    
181    checkpoint63i (2012/01/24)
182    o model/src:
183      - add factorized versions of some EOS code to find_rho.F,
184        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
185    o model/src:
186      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
187      - change default celsius2K from 273.16 to 273.15
188      - to keep results unchanged, add back old value of celsius2K in verification
189        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
190         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
191    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
192      to make TAF generate vectorizable code
193    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
194       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
195       have flags that do this more efficiently.
196    o pkg/diagnostics/diagstats_calc.F
197      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
198    o pkg/obcs (with exch2):
199      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
200        and remove code (in obcs_readparms.F) which was based on EXCH of indices
201        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
202    o pkg/exf and seaice exp:
203      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
204        so that switching off area & heff advection flags does not affect results.
205      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
206      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
207        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
208        results of verification experiments: 1D_ocean_ice_column(fwd),
209        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
210        and offline_exf_seaice (all 4).
211    o pkg/seaice:
212      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
213        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
214      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
215        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
216        not multi-dim advection;
217      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
218        SHORTWAVE_HEATING #undef.
219    o optim: make Makefile more robust (?)
220    o pkg/obcs:
221      * fix treatment of obcs_read_pickup for TAF
222    o pkg/shelfice:
223      * add missing initialisation of num_shifwflx
224      * new adjoint verification exp. for isomip
225      * change Prandtl and Schmidt numbers from generic formulations
226        (in terms of model diffus. and visc.) to separate runtime
227        parameters, with Holland and Jenkins (1999) default values.
228    o pkg/exf (interpolation):
229      - extended input field (2 rows) near the N & S poles:
230        * fill in with the symetric value (when even Nb of data in longitude)
231        * add average value at the poles only for scalar quantities ; for vector
232          component interpolation, skip the averaging and keep duplicated values,
233          unless the 2 components have same location (uvInterp=T) in which case
234          interpolate the 2 components together using S/R EXF_INTERP_UV.
235      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
236        together: this allows to account properly for local orientation when
237        averaging at N & S pole.
238      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
239        exf-interpolation near N & S poles. Undef by default.
240      - add debug check/print on 1rst iter if debugLevel >=2.
241    o pkg/exf:
242      - change masking flags definition (no longer "parameter"), put them in
243        common block and set them in S/R EXF_INIT_FIXED.
244      - change recognized masking flag from s,u,v to c,w,s since the mask
245        to use (maskC,W,S) depends on position on model grid and has little to
246        do with scalar/vector difference; fix masking if using P-coordinates.
247      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
248        and update results of exp. global_with_exf (x2).
249      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
250    o pkg/obcs
251      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
252    o pkg/exf (interpolation):
253      - assume periodicity in X only if input field cover full longitude range.
254      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
255        and should vectorise).
256      - fix input lat of the 2 added row (in case we provide N.pole data).
257    
258    checkpoint63h (2011/12/30)
259    o pkg/seaice:
260      - change declaration of UVM from _RL to _RS in order to get B-grid
261        uIce,vIce monitor when _RS = real*4
262    o pkg/offline:
263      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
264      - compute vertical velocity if not read from file (switch on exactConserv
265        & staggerTimeStep);
266      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
267    o verification:
268      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
269        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
270        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
271      - update output of exp. global_ocean.cs32x15.viscA4 after changing
272        grid-file angles (used here for coriolis-3d);
273      - remove (or gzip) few files not needed to run fizhi-cs experiments.
274    o pkg/exf (vector interpolation):
275      - rotate vector component toward local grid-axis orientation using grid-angles
276        (stored in GRID.h) instead of locally computed rotation angle; keep old code
277        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
278    o pkg/seaice:
279      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
280        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
281    o pkg/PKG_OPTIONS.h files:
282      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
283        outside of the #ifdef ALLOW_THISPKG / #endif block.
284      - update verification/*/code/PKG_OPTIONS.h files.
285    o add a verification experiment (offline_exf_seaice/input.seaice) that test
286      the B-grid LSOR solver
287    o pkg/seaice: sort out emissivity and long wave radiation step 2:
288      - add emissivity for snow and ice as new run-time parameters
289        (unfortunately) that default to the corresponding exf values; this
290        changes results in most verification experiments so that for backward
291        compatibility these parameter have to be set explicitly to inconsistent
292        values (ugly);
293      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
294        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
295        until we agree how to handle this bug properly
296    o pkg/exf (interpolation):
297      - add a set of run-time param ({inputfield}_interpMethod), one for
298        each interpolated input field, to select the interpolation method
299        with a value of zero switching off the interpolation;
300      - print interpolation parameters to standard output;
301      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
302        (to use instead runoff_interpMethod=0 in data.exf).
303      - simplify default setting of interpolation parameters (for all fields,
304        set position to match model grid cell-center position, leading to trivial
305        interpolation in case of regular Lat-Lon grid) and fix for the case of
306        non-uniform delY.
307    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
308       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
309       this factor is absolutely required, because the lw exitance (= out-going
310       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
311       where the reflectivity rho = 1-emissivity for conservation reasons. Once
312       this is established, we can remove the CPP-Flag (if we want to).
313    o pkg/seaice:
314      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
315        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
316      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
317        what the name implies (and not emissivity*BoltzmannConstant), this means
318        the old default value of 5.5e-8 now means
319        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
320        S/R exf_readparms
321      - FV-discretization of the B-grid LSOR solver, turn on with
322        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
323        of the calling routine dynsolver, so that B and C-grid code look a
324        little more alike.
325      - fix index bugs in ostres.F (B-grid code)
326    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
327    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
328      default for SEAICE_emissivity, if useEXF; requires setting a wrong
329      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
330      backward compatiblity
331    o model/src: use sigmaR in calc_ivdc
332    
333    checkpoint63g (2011/12/16)
334    o pkg/seaice/seaice_growth.F:
335      fix heat conservation of the coupled ocean-seaice system.
336      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
337      solid vs liquid water treatment is resolved via QNET.
338    o pkg/seaice/seaice_growth.F:
339      add missing term for sublimation in saltFlux, which was breaking conservation.
340    o pkg/seaice/seaice_model.F:
341      Remove this patholigical case treatment in evolution branch,
342      where it is un-necessary and breaks conservation.
343      Update global_ocean.cs32x15/results accordingly for
344      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
345    o model/src:
346      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
347      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
348    o pkg/obcs:
349      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
350      tendency for temperature and salinity that is then applied to update
351      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
352      horizontal advection and diffusion contributions on the boundary (in
353      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
354      removing the mask in S/R timestep_tracer. The advantage of this approach is
355      that the updated tracer values include contributions from the surface
356      forcing and vertical diffusion.
357      This modification changes exp4.stevens because of vertical diffusion.
358    o model/src:
359      change non-curvilinear grid setting to also work with exch2 + blank tiles:
360      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
361        face dimensions.
362      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
363        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
364        and INI_SPHERICAL_POLAR_GRID.
365      change test-experiment global_ocean.90x40x15:
366      - split the domain in many more tiles (9x4 tiles of 10x10 each);
367      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
368      - update results of both test (std & dwnslp).
369    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
370       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
371    o model/src:
372      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
373        and fix initialisation when using sigma-coords.
374    o model/src:
375     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
376       to their current value at the beginning of forward_step.F": add a new run-time
377       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
378     - set doResetHFactors=T in the following test exp:
379        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
380        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
381        and tutorial_global_oce_in_p (nonLinFS in p)
382    o pkg/ecco
383      - added IES cost term
384    o verification/advect_xz
385      - scale down the depth by 1/100 (from 200 km to just 2.km)
386      - add secondary test using divergent flow, r-star and implicit vertical advection.
387      - add note (check_conserve_TS.txt) and matlab script to check global
388        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
389    o pkg/rbcs:
390      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
391    o pkg/obcs (Stevens BCs):
392      - fix various problems in the phase speed computations of the Stevens
393        boundary conditions:
394        - sign error for western and southern boundaries,
395        - time tendencies were underestimated by factor of dTracerLev and some just
396          zero (for multidim advection schemes) -> now estimate time tendencies
397          from difference between previous (n) time level and the one before (n-1);
398          this requires storing a field per tracer per boundary, also in the pickup
399          files.
400        - replace deltaTmom in cflMer/Zon computation with dTracerLev
401        - set default phase velocity to cflMer/Zon
402      - update verification experiment exp4.stevens
403    o pkg/generic_advdiff (implicit_r):
404      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
405        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
406      - fix implicit vertical diffusion or advection with NonLin FreeSurf
407        (was using current recip_hFacC instead of future recip_hFacC): set future
408        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
409        solver S/R ;
410      - fill diagnostics of vertical advective fluxes (computed from tendency)
411        when using implicit vert. advection;
412      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
413         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
414         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
415         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
416    o pkg/diagnostics:
417      - add diags for T & S tendency which goes through Adams-Bashforth.
418    
419    checkpoint63f (2011/11/30)
420    o pkg/obcs/obcs_calc_stevens.F:
421      - join some loops to reduce number of if-statements
422      - fix a bug in code for northern and southern boundaries.
423    o pkg/seaice/seaice_init_varia.F
424      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
425        caused zero ice-velocities for the B-grid code
426    o pkg/seaice/seaice_init_fixed.F
427      - fix a bug in the initialisation of the second metric terms
428        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
429      - this affects all seaice configurations with useCurviLinearGrid = .true.
430        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
431        = .true. (default)
432      - the only verification experiment affected is global_ocean.cs32x15:
433        icedyn, seaice, and seaice_dynmix (AD)
434    o pkg/thsice/thsice_diagnostics_state.F
435      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
436        not contain garbage that can lead to surprises in diagstats_calc.F
437    o model/src:
438      - move bi,bj loops inside INTEGR_CONTINUITY ;
439      - call INTEGR_CONTINUITY directly from forward_step.F
440        (previously called from momentum_correction_step.F)
441      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
442        forward_step.F and pkg/ecco/the_main_loop.F
443    o model/src/do_oceanic_phys.F:
444      - reset addMass to zero only if useICEFRONT ;
445      - separated k-loop for rhoInSitu calculation ;
446      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
447        and at constant T,S (= WdRHOdP);
448      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
449        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
450        transport of locally-referenced potential density);
451        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
452    o gluemnc:
453      - replace ncrcat with ncks when adding variables to *.glob.nc
454      - change the way variables without record dimensions are handled so that
455        files that have variables with and without record variables can be glued:
456        add a record dimension with a new unique name to be able to differentiate
457        between variable with and without a-prior record dimensions. Remove
458        this record dimension before adding the variable to the *.glob.nc file.
459        This procedure automatically works also for grid.*.nc files that do not
460        have any record dimension.
461    o verification/cpl_aim+ocn:
462      - generate new reference output on baudelaire (gfortran, mpich2) (previously
463        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
464    o pkg/obcs/obcs_calc_stevens.F:
465      - add code for northern and southern boundaries.
466      - reorder some loops to save some operations and so that drFBar can be scalar
467    o model/src:
468      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
469        truncation) and add diagnostics for Adams-Bashforth tendency increment.
470      - update test-exp. AD output:
471        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
472      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
473        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
474        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
475        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
476        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
477        tutorial_plume_on_slope.
478    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
479      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
480      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
481      does not even come with an F77 compiler anymore, this should not be
482      a limitation
483    
484    checkpoint63e (2011/11/06)
485    o pkg/seaice adjoint of LSR:
486      - substantially rework STORE dirs.
487      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
488        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
489        and only perform SOLV_MAX_FIXED adjoint iters.
490        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
491        always goes to same record, meaning that the last forward field will be
492        the one used in the adjoint - an approximation.
493      - now produces non-zero LSR-related gradients, and acceptable gradients for
494        An's zonal (x-z) test case (to be checked in)
495      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
496        (but these are screwed up by the thermodynamics in the first place);
497        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
498        output_adm.txt also reflects changes to seaice_lsr
499      - global_ocean.cs32x15:
500        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
501          (output_adm.seaice.txt was updated)
502        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
503          (output_adm.seaice_dynmix.txt)
504    o test-exp. exp4+stevens:
505      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
506    o pkg/seaice (lsr solver):
507      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
508        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
509      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
510      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
511        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
512      - compute (with new S/R) and print initial (+ free-driff sol. if available)
513        and final residual of linearised system.
514  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
515    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
516  o pkg/obcs: Stevens BCs (still only for east and west)  o pkg/obcs: Stevens BCs (still only for east and west)
517    - fix Stevens BCs by using intermediate velocities of previous    - fix Stevens BCs by using intermediate velocities of previous
518      time step as "baroclinic" contribution rather velocity of one grid cell      time step as "baroclinic" contribution rather velocity of one grid cell
519      inside the boundaries; more consistent but makes the entire treatment      inside the boundaries; more consistent but makes the entire treatment
520      more complicated, requires new pickup files and two new S/Rs:      more complicated, requires new pickup files and two new S/Rs:
521      obcs_copy_uv_n and obcs_save_uv_n      obcs_copy_uv_n and obcs_save_uv_n
522      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
523      (undefined by default)      (undefined by default)
524    - silently move computation of some grid factors into separate loops to    - silently move computation of some grid factors into separate loops to
525      save some recomputations      save some recomputations
526    - add a hack for non-linear free surface    - add a hack for non-linear free surface
527    - add a verification experiment to exp4 that tests this code    - add a verification experiment to exp4 that tests this code
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