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revision 1.1374 by jmc, Sun Feb 6 00:24:40 2011 UTC revision 1.1611 by jmc, Tue Mar 6 00:08:18 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/ecco:
8      - fix writing of output file DiagnosCost_ClimSalt/Theta
9        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
10    o pkg/seaice :
11      - add missing initialisation of COR_ICE array in dynsolver.F
12      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
13        compiled either way, and is tested in all exps (multidim was only tested
14        in lab_sea ad before).
15      - cosmetic change to prepare for future addition of ITD. no change to results.
16        no defaults change.
17      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
18      - by lack of adequate verification experiments, I further used custom versions
19        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
20        should be correct.
21      - avoid recomputations in ad.
22    o array initialisation in adjoint mode:
23      1) pkg/mom_common/mom_calc_ke.F:
24        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
25        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
26        part this initialisation is gone, resulting in Floating Point Exception
27        (caught by open64 compiler with debug option).
28      2) model/src/convective_weights.F
29        set output convectCount over the full array range (instead of doing
30        an update): this fix a similar issue when called within recomputation (adjoint)
31        which could by-pass the initialisation (normally done in the caller S/R).
32    o pkg/seaice:
33      - final version of turbulent flux params, as agreed at MIT ice meet:
34           SEAICE_mcPheePiston (default is ~ 0.000875)
35           SEAICE_mcPheeTaper (default is 0.)
36           SEAICE_frazilFrac (defualt is 1.)
37           SEAICE_mcPheeStepFunc (default is false)
38      - changes results at trunction error level
39      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
40    o added pkg/frazil:
41      - see frazil_description.tex for details
42      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
43    o pkg/shelfice/shelfice_thermodynamics.F
44      - fix exponents for velocity dependent exchange coefficients: change
45        from 2/3(=0) to 0.66666666666666667
46      - move computation of velocity dependent exchange coefficients into
47        separate loop, so that it applies to both thermodynamics
48      - move some divisions by constants out of loops
49    
50    checkpoint63j (2012/02/16)
51    o pkg/seaice:
52      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
53      - SItracer:  added run time params, and allow coupling to ocn salinity.
54    o pkg/seaice: remove (almost) all divisions by constants within loops
55      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
56      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
57      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
58      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
59    o pkg/seaice :
60      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
61        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
62      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
63      - add permanent SItflux diag that corresponds to TFLUX but includes
64        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
65      - allow activation/testing of a fix for suspected missing term in
66        ocn-ice heat budget (to be confirmed). To test this, you want to
67        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
68        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
69      - no change in results, fwd or ad.
70    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
71      - switch to variable freezing point.
72           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
73      - bug fix : the sublimation term that was missing is now activated.
74           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
75      - bug fix : flooding sign term for SIsal0.NE.0.
76           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
77    o pkg/seaice:
78      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
79        is now the default, and the old default constant freezing point is recovered
80        with SEAICE_tempFrz0    = -1.96,
81             SEAICE_dTempFrz_dS = 0.,
82      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
83      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
84      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
85        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
86      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
87        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
88      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
89        seaice_growth r149 for legacy branch (no results change).
90      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
91        from I. Fenty).
92      - results did not change except for global_ocean.cs32x15, mostly due to the
93        switch to variable freezing point (see above item for detail).
94    o pkg/thsice:
95      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
96        seawater freezing in thsice_calc_thickn (not used).
97    o pkg/seaice: turbulent flux term specification via run time params.
98      - replace CPP switches with run time switches to facilitate testing
99      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
100                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
101      - added runtime parameter : SEAICEturbFluxFormula
102      - move Mcphee constants to SEAICE_PARAMS.h
103      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
104                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
105                 remove seaice_summary call (moved to seaice_init_fixed)
106      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
107        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
108      - seaice_summary.F : add missing report of read turbulent flux term set up
109                           and SITRACER.
110      - seaice_check.F : check range; inform and stop if retired CPPs are used
111                         (incl. SEAICE_AGE).
112      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
113             CPP switch, same computation as before for the different options.
114      - change results at the truncation level.
115    o pkg/seaice:
116      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
117        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
118        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
119      - update verification/*/input*/data.seaice:
120        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
121        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
122        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
123        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
124    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
125      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
126        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
127        difference in results only due to machine truncation.
128      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
129        MaykutPolySatVap; keep MIN_LWDOWN.
130      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
131      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
132        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
133    o pkg/salt_plume:
134      - isolate saltPlumeFlux array exch into a specific S/R called from
135        do_oceanic_phys.F
136      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
137    o verification:
138      - move untested set-up to MITgcm_contrib/verification_other.
139    o pkg/seaice:
140      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
141    o pkg/seaice:
142      - seaice_solve4temp.F (keeping results unchanged):
143        * add 2 future run-time params to select which saturation vapor pressure
144          formula is used and how post-iteration fluxes are set.
145          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
146        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
147          the linearized expression to stay consistent with tsurf finding.
148      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
149        can be < 0.
150    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
151      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
152        conductive heat flux F_c , and add it explicitly when updating tsurf as
153        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
154        so that now F_ia has a consistent meaning through the entire routine.
155        This causes differences at truncation level: update output of fwd exp.
156        global_ocean.cs32x15.seaice.
157    o pkg/seaice:
158      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
159        of arrays, sign/direction of fluxes; no effect on results.
160      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
161        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
162        note: this should have been done before changing celsius2K default.
163      - to keep results unchanged, add back old value of celsius2K in verification
164        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
165      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
166        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
167        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
168        freezing temp is consistent with value in seaice_growth.F ; this causes
169        differences at machine truncation level: update lab_sea AD output (3/4).
170    o pkg/seaice:
171      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
172        and climsst/sss even when using seaice (to prevent calculation that might
173        use SST on land); does not affect any verification exp.
174      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
175        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
176    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
177      over land (non-legacy code)
178    o vectorize salt_plume package:
179      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
180      - this code computes plumebk everywhere (also over land), thus requires
181        code to avoid divisions by zero and catch the case of kLev=Nr.
182      - efficiency of salt_plume_frac is still sub-optimal
183    o tools (genmake2):
184      - fix makefile NAME specification (option: -makefile NAME) by adding
185        "-f $MAKEFILE" in few places where it was missing including makedepend
186        command (contribution from Paul).
187    
188    checkpoint63i (2012/01/24)
189    o model/src:
190      - add factorized versions of some EOS code to find_rho.F,
191        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
192    o model/src:
193      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
194      - change default celsius2K from 273.16 to 273.15
195      - to keep results unchanged, add back old value of celsius2K in verification
196        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
197         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
198    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
199      to make TAF generate vectorizable code
200    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
201       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
202       have flags that do this more efficiently.
203    o pkg/diagnostics/diagstats_calc.F
204      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
205    o pkg/obcs (with exch2):
206      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
207        and remove code (in obcs_readparms.F) which was based on EXCH of indices
208        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
209    o pkg/exf and seaice exp:
210      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
211        so that switching off area & heff advection flags does not affect results.
212      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
213      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
214        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
215        results of verification experiments: 1D_ocean_ice_column(fwd),
216        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
217        and offline_exf_seaice (all 4).
218    o pkg/seaice:
219      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
220        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
221      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
222        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
223        not multi-dim advection;
224      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
225        SHORTWAVE_HEATING #undef.
226    o optim: make Makefile more robust (?)
227    o pkg/obcs:
228      * fix treatment of obcs_read_pickup for TAF
229    o pkg/shelfice:
230      * add missing initialisation of num_shifwflx
231      * new adjoint verification exp. for isomip
232      * change Prandtl and Schmidt numbers from generic formulations
233        (in terms of model diffus. and visc.) to separate runtime
234        parameters, with Holland and Jenkins (1999) default values.
235    o pkg/exf (interpolation):
236      - extended input field (2 rows) near the N & S poles:
237        * fill in with the symetric value (when even Nb of data in longitude)
238        * add average value at the poles only for scalar quantities ; for vector
239          component interpolation, skip the averaging and keep duplicated values,
240          unless the 2 components have same location (uvInterp=T) in which case
241          interpolate the 2 components together using S/R EXF_INTERP_UV.
242      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
243        together: this allows to account properly for local orientation when
244        averaging at N & S pole.
245      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
246        exf-interpolation near N & S poles. Undef by default.
247      - add debug check/print on 1rst iter if debugLevel >=2.
248    o pkg/exf:
249      - change masking flags definition (no longer "parameter"), put them in
250        common block and set them in S/R EXF_INIT_FIXED.
251      - change recognized masking flag from s,u,v to c,w,s since the mask
252        to use (maskC,W,S) depends on position on model grid and has little to
253        do with scalar/vector difference; fix masking if using P-coordinates.
254      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
255        and update results of exp. global_with_exf (x2).
256      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
257    o pkg/obcs
258      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
259    o pkg/exf (interpolation):
260      - assume periodicity in X only if input field cover full longitude range.
261      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
262        and should vectorise).
263      - fix input lat of the 2 added row (in case we provide N.pole data).
264    
265    checkpoint63h (2011/12/30)
266    o pkg/seaice:
267      - change declaration of UVM from _RL to _RS in order to get B-grid
268        uIce,vIce monitor when _RS = real*4
269    o pkg/offline:
270      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
271      - compute vertical velocity if not read from file (switch on exactConserv
272        & staggerTimeStep);
273      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
274    o verification:
275      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
276        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
277        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
278      - update output of exp. global_ocean.cs32x15.viscA4 after changing
279        grid-file angles (used here for coriolis-3d);
280      - remove (or gzip) few files not needed to run fizhi-cs experiments.
281    o pkg/exf (vector interpolation):
282      - rotate vector component toward local grid-axis orientation using grid-angles
283        (stored in GRID.h) instead of locally computed rotation angle; keep old code
284        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
285    o pkg/seaice:
286      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
287        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
288    o pkg/PKG_OPTIONS.h files:
289      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
290        outside of the #ifdef ALLOW_THISPKG / #endif block.
291      - update verification/*/code/PKG_OPTIONS.h files.
292    o add a verification experiment (offline_exf_seaice/input.seaice) that test
293      the B-grid LSOR solver
294    o pkg/seaice: sort out emissivity and long wave radiation step 2:
295      - add emissivity for snow and ice as new run-time parameters
296        (unfortunately) that default to the corresponding exf values; this
297        changes results in most verification experiments so that for backward
298        compatibility these parameter have to be set explicitly to inconsistent
299        values (ugly);
300      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
301        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
302        until we agree how to handle this bug properly
303    o pkg/exf (interpolation):
304      - add a set of run-time param ({inputfield}_interpMethod), one for
305        each interpolated input field, to select the interpolation method
306        with a value of zero switching off the interpolation;
307      - print interpolation parameters to standard output;
308      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
309        (to use instead runoff_interpMethod=0 in data.exf).
310      - simplify default setting of interpolation parameters (for all fields,
311        set position to match model grid cell-center position, leading to trivial
312        interpolation in case of regular Lat-Lon grid) and fix for the case of
313        non-uniform delY.
314    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
315       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
316       this factor is absolutely required, because the lw exitance (= out-going
317       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
318       where the reflectivity rho = 1-emissivity for conservation reasons. Once
319       this is established, we can remove the CPP-Flag (if we want to).
320    o pkg/seaice:
321      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
322        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
323      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
324        what the name implies (and not emissivity*BoltzmannConstant), this means
325        the old default value of 5.5e-8 now means
326        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
327        S/R exf_readparms
328      - FV-discretization of the B-grid LSOR solver, turn on with
329        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
330        of the calling routine dynsolver, so that B and C-grid code look a
331        little more alike.
332      - fix index bugs in ostres.F (B-grid code)
333    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
334    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
335      default for SEAICE_emissivity, if useEXF; requires setting a wrong
336      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
337      backward compatiblity
338    o model/src: use sigmaR in calc_ivdc
339    
340    checkpoint63g (2011/12/16)
341    o pkg/seaice/seaice_growth.F:
342      fix heat conservation of the coupled ocean-seaice system.
343      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
344      solid vs liquid water treatment is resolved via QNET.
345    o pkg/seaice/seaice_growth.F:
346      add missing term for sublimation in saltFlux, which was breaking conservation.
347    o pkg/seaice/seaice_model.F:
348      Remove this patholigical case treatment in evolution branch,
349      where it is un-necessary and breaks conservation.
350      Update global_ocean.cs32x15/results accordingly for
351      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
352    o model/src:
353      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
354      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
355    o pkg/obcs:
356      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
357      tendency for temperature and salinity that is then applied to update
358      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
359      horizontal advection and diffusion contributions on the boundary (in
360      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
361      removing the mask in S/R timestep_tracer. The advantage of this approach is
362      that the updated tracer values include contributions from the surface
363      forcing and vertical diffusion.
364      This modification changes exp4.stevens because of vertical diffusion.
365    o model/src:
366      change non-curvilinear grid setting to also work with exch2 + blank tiles:
367      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
368        face dimensions.
369      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
370        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
371        and INI_SPHERICAL_POLAR_GRID.
372      change test-experiment global_ocean.90x40x15:
373      - split the domain in many more tiles (9x4 tiles of 10x10 each);
374      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
375      - update results of both test (std & dwnslp).
376    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
377       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
378    o model/src:
379      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
380        and fix initialisation when using sigma-coords.
381    o model/src:
382     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
383       to their current value at the beginning of forward_step.F": add a new run-time
384       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
385     - set doResetHFactors=T in the following test exp:
386        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
387        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
388        and tutorial_global_oce_in_p (nonLinFS in p)
389    o pkg/ecco
390      - added IES cost term
391    o verification/advect_xz
392      - scale down the depth by 1/100 (from 200 km to just 2.km)
393      - add secondary test using divergent flow, r-star and implicit vertical advection.
394      - add note (check_conserve_TS.txt) and matlab script to check global
395        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
396    o pkg/rbcs:
397      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
398    o pkg/obcs (Stevens BCs):
399      - fix various problems in the phase speed computations of the Stevens
400        boundary conditions:
401        - sign error for western and southern boundaries,
402        - time tendencies were underestimated by factor of dTracerLev and some just
403          zero (for multidim advection schemes) -> now estimate time tendencies
404          from difference between previous (n) time level and the one before (n-1);
405          this requires storing a field per tracer per boundary, also in the pickup
406          files.
407        - replace deltaTmom in cflMer/Zon computation with dTracerLev
408        - set default phase velocity to cflMer/Zon
409      - update verification experiment exp4.stevens
410    o pkg/generic_advdiff (implicit_r):
411      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
412        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
413      - fix implicit vertical diffusion or advection with NonLin FreeSurf
414        (was using current recip_hFacC instead of future recip_hFacC): set future
415        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
416        solver S/R ;
417      - fill diagnostics of vertical advective fluxes (computed from tendency)
418        when using implicit vert. advection;
419      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
420         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
421         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
422         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
423    o pkg/diagnostics:
424      - add diags for T & S tendency which goes through Adams-Bashforth.
425    
426    checkpoint63f (2011/11/30)
427    o pkg/obcs/obcs_calc_stevens.F:
428      - join some loops to reduce number of if-statements
429      - fix a bug in code for northern and southern boundaries.
430    o pkg/seaice/seaice_init_varia.F
431      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
432        caused zero ice-velocities for the B-grid code
433    o pkg/seaice/seaice_init_fixed.F
434      - fix a bug in the initialisation of the second metric terms
435        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
436      - this affects all seaice configurations with useCurviLinearGrid = .true.
437        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
438        = .true. (default)
439      - the only verification experiment affected is global_ocean.cs32x15:
440        icedyn, seaice, and seaice_dynmix (AD)
441    o pkg/thsice/thsice_diagnostics_state.F
442      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
443        not contain garbage that can lead to surprises in diagstats_calc.F
444    o model/src:
445      - move bi,bj loops inside INTEGR_CONTINUITY ;
446      - call INTEGR_CONTINUITY directly from forward_step.F
447        (previously called from momentum_correction_step.F)
448      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
449        forward_step.F and pkg/ecco/the_main_loop.F
450    o model/src/do_oceanic_phys.F:
451      - reset addMass to zero only if useICEFRONT ;
452      - separated k-loop for rhoInSitu calculation ;
453      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
454        and at constant T,S (= WdRHOdP);
455      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
456        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
457        transport of locally-referenced potential density);
458        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
459    o gluemnc:
460      - replace ncrcat with ncks when adding variables to *.glob.nc
461      - change the way variables without record dimensions are handled so that
462        files that have variables with and without record variables can be glued:
463        add a record dimension with a new unique name to be able to differentiate
464        between variable with and without a-prior record dimensions. Remove
465        this record dimension before adding the variable to the *.glob.nc file.
466        This procedure automatically works also for grid.*.nc files that do not
467        have any record dimension.
468    o verification/cpl_aim+ocn:
469      - generate new reference output on baudelaire (gfortran, mpich2) (previously
470        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
471    o pkg/obcs/obcs_calc_stevens.F:
472      - add code for northern and southern boundaries.
473      - reorder some loops to save some operations and so that drFBar can be scalar
474    o model/src:
475      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
476        truncation) and add diagnostics for Adams-Bashforth tendency increment.
477      - update test-exp. AD output:
478        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
479      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
480        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
481        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
482        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
483        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
484        tutorial_plume_on_slope.
485    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
486      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
487      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
488      does not even come with an F77 compiler anymore, this should not be
489      a limitation
490    
491    checkpoint63e (2011/11/06)
492    o pkg/seaice adjoint of LSR:
493      - substantially rework STORE dirs.
494      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
495        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
496        and only perform SOLV_MAX_FIXED adjoint iters.
497        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
498        always goes to same record, meaning that the last forward field will be
499        the one used in the adjoint - an approximation.
500      - now produces non-zero LSR-related gradients, and acceptable gradients for
501        An's zonal (x-z) test case (to be checked in)
502      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
503        (but these are screwed up by the thermodynamics in the first place);
504        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
505        output_adm.txt also reflects changes to seaice_lsr
506      - global_ocean.cs32x15:
507        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
508          (output_adm.seaice.txt was updated)
509        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
510          (output_adm.seaice_dynmix.txt)
511    o test-exp. exp4+stevens:
512      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
513    o pkg/seaice (lsr solver):
514      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
515        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
516      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
517      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
518        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
519      - compute (with new S/R) and print initial (+ free-driff sol. if available)
520        and final residual of linearised system.
521    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
522      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
523    o pkg/obcs: Stevens BCs (still only for east and west)
524      - fix Stevens BCs by using intermediate velocities of previous
525        time step as "baroclinic" contribution rather velocity of one grid cell
526        inside the boundaries; more consistent but makes the entire treatment
527        more complicated, requires new pickup files and two new S/Rs:
528        obcs_copy_uv_n and obcs_save_uv_n
529        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
530        (undefined by default)
531      - silently move computation of some grid factors into separate loops to
532        save some recomputations
533      - add a hack for non-linear free surface
534      - add a verification experiment to exp4 that tests this code
535    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
536    
537    checkpoint63d (2011/10/25)
538    o pkg/obcs + seaice-dynamics:
539      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
540        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
541        values (consistent with an implicit method).
542      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
543        return to older implementation (same results as before); note that none of
544        the "experimental" OBCS_SEAICE options are implemented in the new version.
545      - switch test exp. seaice_obcs to use new version (update output).
546    o pkg/seaice:
547      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
548      - add parenthesis in Water-Ice drag calculations (evp & lsr);
549      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
550        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
551      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
552        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
553    o pkg/layers:
554      - Include potential density as new coordinate (Thanks to David Munday)
555    o pkg/dic:
556      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
557        carbonate computation/output to CALC_PCO2_APPROX
558    o pkg/generic_advdiff
559      - make TAF generate code that vectorizes:
560        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
561    o model/src:
562      - improve vectorization also for adjoint code of
563        solve_tridiagonal and solve_pentadiagonal. As this requires up to
564        5 new 3D-fields, this code is only turned on for the combination of
565        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
566        for singular matrix check (only for TARGET_NEC_SX).
567      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
568        ALLOW_AUTODIFF. This flag now needs to be set outside of
569        solve_tri/pentadiagonal.F
570    o pkg/exf:
571      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
572        optional namelist EXF_NML_OBCS).
573      - add many debug-print (to trace down where pkg/cal error msg comes from)
574    o pkg/mom_vecinv/mom_vi_hdissip.F
575      - rearrange loops so that vectorization is improved and in particular
576        the adjoint routine vectorizes. The code is a little longer now, but I
577        think easier to read.
578        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
579    o pkg/seaice:
580      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
581    o pkg/exch2:
582      - alternative code (without tile x tile matrix) for cumulated (global) sum;
583        used as default; keep using matrix version in adjustment.cs-32x32x1.
584    o tools/build_options:
585      - after merging some MPI and/or multi-threads specific optfiles so that
586        the modified default optfile support both built (using genmake2 -mpi
587        for the MPI built, using genmake2 -omp for OpenMP built),
588        move now obsolete optfiles to tools/build_options/unsupported/
589       (add copy of email sent to support list in doc/optfiles_changes.txt)
590    
591    checkpoint63c (2011/09/28)
592    o pkg/ebm:
593      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
594        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
595    o pkg/seaice (SItracer pickup)
596    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
597      To be done:
598      - thorough testing of missing fields in S/R seaice_read_pickup
599      - thorough matching between generic tracers and specific fields used
600        (e.g. volume-weighted age, area-weighted age, salinity, ...)
601    o pkg/grdchk:
602      - all procs calculate and print finite-difference gradient (for testreport)
603      - change description output used by testreport;
604      - AD testing: also compare and report Finite-difference gradient;
605        => update all output_adm*.txt
606    o test exp. global_ocean_ebm:
607      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
608        and turn on exactConserve; update (fwd) output.
609    o pkg/seaice (LSR):
610      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
611      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
612        * identical results with non-CS topology (but save up to half of EXCH calls)
613        * no much changes in cs-32 verification tests since no ice at face edges
614         (differences due to convergence criteria, since nb of iterations changed)
615        * expect some differences on lat-lon-cap grid.
616        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
617    o pkg/exch2:
618      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
619        many tiles); until alternative coding is added, just add a stop.
620    o pkg/kpp:
621      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
622        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
623    o optfiles:
624      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
625        into corresponding standard one, which now support different build:
626        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
627      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
628    o pkg/obcs (seaice):
629      - add missing EXCH for uIce,vIce after applying OBCS;
630      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
631        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
632        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
633      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
634      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
635        and eedata.mth for MPI and mutlti-threaded testing.
636    o pkg/flt:
637      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
638      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
639      - fix pickup and trajectories + profiles output with multi-threads;
640      - add parameter to select group of fields to write along trajectory and
641        profile (default unchanged);
642      - only call PORT_RAND* function when flt_noise <> 0;
643      - add multi-threaded test for verification exp. flt_example.
644    o eesupp/src:
645      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
646      - USE_OMP_THREADING: check that number of threads (from eedata) matches
647        actual number (from env.var. setting).
648    o pkg/ebm:
649      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
650      - add multi-threaded test for verification exp. global_ocean_ebm
651    
652    checkpoint63b (2011/08/29)
653    o pkg/ebm:
654      - fix sign of runoff;
655      - update directly forcing fields (Qnet,EmPmR) to use standard
656        external_forcing_surf.F (remove ebm_forcing_surf.F);
657      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
658      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
659        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
660      - update global_ocean_ebm parameters file data and update output (fwd+ad).
661    o verification/matrix_example:
662      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
663        MPI and mutlti-threaded testing.
664    o pkg/matrix:
665      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
666      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
667      - fix for multi-threaded (remove DATA statement);
668      - use standard DIFFERENT_MULTIPLE function;
669      - add MATRIX_OPTIONS.h
670    o verification/matrix_example:
671       To allow to split the domain in several tiles, change the domain size
672        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
673        Western side) of land points.
674    o (*_)write_pickup:
675      - fix few bugs in mypackage_read/write_pickup.F
676      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
677        array of length 1 (was caught by compiler syntax-check).
678    o pkg/diagnostics (velocity potential solver):
679      - fix initialisation of main diagonal matrix (for overlap values)
680    o tools/build_options:
681      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
682        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
683      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
684        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
685        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
686        and use "-devel" testreport option for standard testing on baudelaire.
687    o pkg/grdchk:
688      - Assume that all gradient-check position are within the same tile
689        corresponding to global indices (iGloTile,jGloTile) and that
690        positions (i,j indices or nbeg) are local to this tile;
691      - set tile local-indices and proc. number according to tile global-indices;
692      - remove grdchkwhichproc from namelist (retired param);
693      - send adjoint gradient to all procs so that all procs print it to STDOUT;
694      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
695    o adding package bbl (Bottom Boundary Layer)
696      description in MITgcm/pkg/bbl/bbl_description.tex
697      example/test experiment in MITgcm_contrib/bbl
698    o adjoint verifications
699      - changed 5 experiments to multi-tiles
700        * global_ocean.90x40x15
701        * obcs_ctrl
702        * offline_exf_seaice
703        * tutorial_dic_adjoffline
704        * tutorial_tracer_adjsens
705        changed reference output for those that crossed tile boundaries
706        (changed choices of gradient check positions)
707      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
708      - temporary bug fix in grdchk_loc.F for obcs
709    o genmake2 & testreport
710      - add target "obj" (just for OBJFILES files) to Makefile;
711      - add option to specify FEXTRAFLAGS on command line.
712    o pkg/mypackage:
713      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
714    
715    checkpoint63a (2011/08/02)
716    o pkg/diagnostics (velocity potential):
717      - fix velocity-potential calculation when using OBCS: balance net inflow
718        at each level (new S/R OBCS_DIAG_BALANCE).
719      - fix some of the problems with OBCS in stream-function calculation.
720    o pkg/exf/exf_readparms.F
721      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
722        EXF_NML_OBCS) more consistent, so that you need not have these lists
723        in data.exf when they are not used.
724    o optim/optim_readdata.F:
725      - add some output about obcs variables that might help debugging
726      - add a check about nvarlength
727    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
728    o pkg/diagnostics (velocity potential):
729      - fix mask for OBCS (still problems in stream-function with OBCS);
730      - add specific parameter (default = main code CG2D params) for solver;
731      - in case of poor convergence, use solution corresponding to lowest residual.
732    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
733      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
734      and should be avoided where possible.
735    o model/src (rStar):
736      - include r* effect on reference-state (PhiRef) in totPhiHyd
737        (so that it's really the potential anomaly at the cell center);
738        affect solution only if z* with full pressure in EOS.
739      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
740        update output (because of z* in totPhiHyd and viscA4 changes);
741      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
742        @ constant r) until interpolation at constant r is implemented.
743    o pkg/diagnostics
744      - fix RCENTER diagnostics in case cell center is not at interface middle
745    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
746      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
747      that THETA and SALT are "conservative temperature" and "absolute
748      salinity"
749    o pkg/ctrl
750      - fix computation of endrec in s/r ctrl_init_rec
751      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
752    o pkg/seaice/seaice_growth.F
753      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
754        remove then obsolete STORE directives
755      - fix STORE directives for tice and tices, so that only the
756        appropriate part of the fields are stored (and not the entire
757        field); update global_ocean.cs32x15.seaice AD output.
758      - cosmetic changes: adjust CPP flags and indentation for better
759        legibilty
760    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
761      Chris Wilson)
762    o pkg/gmredi:
763       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
764       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
765    
766    checkpoint63  (2011/07/11)
767    o pkg/exch2:
768     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
769     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
770       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
771       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
772    o pkg/diagnostics:
773     - deal with pairs of post-processed diags which are computed together; in
774       particular, re-order list of diags within 1 file to save 2nd computation.
775     - add S/R to compute velocity stream-function (called after velocity-potential
776       calculation) from divergence free transport -> new diagnostics "PsiVEL".
777     - add parameter to select grid-point location where PsiVEL == 0.
778    o eesupp/src:
779       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
780       (specific S/R needed with exch2 topology - for now, just print an error msg)
781    o pkg/shelfice
782     - Implement friction velocity-dependent transfer coefficients following
783       Holland and Jenkins, JPO, 1999
784       Original code by M. Losch with small modifs.
785       Enable with CPP option SHI_ALLOW_GAMMAFRICT
786       and runtime flag SHELFICEuseGammaFrict
787    o verification lab_sea & global_ocean.cs32x15:
788     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
789       does not miss some dependencies (but is slower) and also works with many files
790       (default makedepend limitation for AD built).
791     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
792    o pkg/diagnostics:
793     - add run-time parameter "useMissingValue" (def=False) to fill land-point
794        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
795       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
796     - Extend the use of "missing_value" setting from data.diagnostics for the case
797       of counter-diagnostics (where fraction-weight is zero). This applies both to
798       MNC and MDS output files.
799    o pkg/seaice/seaice_growth.F:
800      - add 'a priori' cap of latent heat flux based on actual mass considerations
801        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
802        non-legacy seaice_solve4temp.
803      - add diagnostic of the residual sublimation freshwater flux (the freshwater
804        flux taken from the ocean if the total actual latent heat fluxes exceed
805        the maximum)
806      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
807       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
808      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
809       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
810      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
811      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
812    o verification 1D_ocean_ice_column:
813       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
814       update results
815    o pkg/diagnostics:
816     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
817       which are not filled-up but computed from other diags ; In this case, the mate
818       diag points to the primary (filled-up) diag to used for post processing.
819     - Update Velocity-potential computation using post-processed diag framework.
820     ==> Change the ordering of fields and time-periods in MDS output file
821       when using periodic averaging: now writes one time record with the full set
822       of fields for this time period, then the next time reccord (it used to be
823       one field with the full set of time records then the next field).
824         Note: this is now similar to NetCDF (MNC) output file. <==
825    
826    checkpoint62z (2011/06/21)
827    o adjoint monitor:
828     - Add adjoint monitor output for packages exf, seaice
829       and update relevant testreport output
830    o pkg/seaice:
831     - re-order diags inits so that they appear in order in available_diagnostics.log
832     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
833       area/heff/hsnow preceeding thermodynamic growth/melt.
834     - modified diag: SIdA; output actual effect, as the description states.
835     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
836     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
837       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
838        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
839     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
840     - added diagnostics for seaice generic tracers (SItr*).
841     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
842     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
843     I. Fenty: 18-Jun-2011:
844     Minor changes to seaice package:
845     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
846        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
847       - Differentiated "regularization variables" from "floor variables"
848        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
849        * hiceMin became SEAICE_hice_reg (old hiceMin)
850          (with _reg meaning regularization variable)
851       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
852        so as to ensure energy conservation when going between phases
853      - A22 was not used anywhere
854     2) Changed regularization procedure for heffActual and hsnowActual to ensure
855        well-boundedness and smooth adjoint in seaice_growth.F
856     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
857        because the old regularization always set heffActual >= 0.05 cm
858     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
859        on AREA when HEFF > 0.
860      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
861        requiring that DISABLE_AREA_FLOOR *not* be defined
862     Affected verifications:
863      - 1D_ocean_ice_column (output.txt output_adm.txt)
864      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
865    o pkg/diagnostics:
866      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
867      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
868        (was _RL, now integer) with option = 0 to retrieve all levels.
869      - add pieces of code to compute velocity potential at each level (new diagnostics
870        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
871        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
872      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
873        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
874        and in diagnostics_fract_fill.F (do not need a valid pointer for the
875        diagnostics counter-mate); check that definition of counter-diagnostic
876        includes a valid counter-mate (in diagnostics_set_levels.F).
877    o model/src (rStar):
878      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
879        affect solution only if z* with full pressure in EOS;
880        update output of test-exp global_ocean.90x40x15.
881    o pkg/seaice:
882      - introduce siEps=1e-5 parameter
883      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
884      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
885      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
886        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
887        as well as ice cover age and ridging index (attached to AREA).
888        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
889        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
890        Up to SItrMaxNum=3 tracers can be used simultaneously.
891    o pkg/salt_plume:
892      -introduce SPsalFRAC run time parameter that sets the fraction of the
893       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
894       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
895    o model debug options:
896      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
897        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
898      - Refine debug-msg printing selection (3 new levels):
899        debugMode  : controls printing of debug messages (sequence of S/R calls).
900        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
901         debLevZero =  0 ; /* level of disabled aux. msg printing */
902         debLevA =  1 ; /* level of minimum  aux. msg printing */
903         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
904         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
905         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
906         debLevE =  5 ; /* level of extensive debug printing */
907        New debugLevel default: with default debugMode value (=F),
908          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
909          and if debugMode=T, default debugLevel = 4 (debLevD).
910        Relation with previous settings:
911         debLevB (=2) corresponds to former debLevA (=1)
912         debLevD (=4) corresponds to former debLevB (=2)
913        Note:
914         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
915         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
916            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
917      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
918        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
919    o pkg/obcs:
920      - change OBCSfixTopo default from True to False (should not change the results);
921        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
922    o pkg/thsice:
923      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
924        2nd layer seaice sublimation (unlikely to happen)
925      - use Interior mask for OBCS in thsice_advection.F (similar to what is
926        done in gad_advection & seaice_advection).
927    o adjoint:
928      bug fix spotted by Gael Forget:
929      seaice_advection and thsice_advection still had
930      legacy CPP options to avoid CS corner updates for adjoint
931    o pkg/seaice:
932      => Change some of the defaults (2011/05/29):
933         - change SEAICEuseFluxForm default (from False to True)
934         - change DIFF1 default (from 0.004 m/s to 0. m/s)
935         And print warnings if DIFF1 is not set in data.seaice and centered
936          avection scheme is used without any diffusion.
937      also:
938      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
939      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
940      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
941        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
942        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
943      update results of test exp.:
944         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
945             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
946             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
947         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
948         seaice_obcs: output (SEAICEuseFluxForm=T)
949      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
950          for standard fwd & AD lab_sea tests (to keep the same output).
951    o pkg/seaice/seaice_growth.F:
952      - use Ian Fenty's capping formulas for actual ice
953      thickness thoughout EVOLUTION branch.
954      - put treatment pathological case #2) in CPP brackets
955      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
956      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
957    o pkg/seaice:
958      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
959      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
960      also pass fac as a param, which can be 1. (to update the tendency
961      field) or the time step (to update the field itself).
962      - seaice_advdiff.F: for multidim, call seaice_diffusion with
963      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
964      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
965      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
966      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
967    o pkg/seaice:
968      diffusion with centered advection scheme (diffus.F & advect.F):
969      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
970        to just compute the laplacian of input-field.
971      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
972      - fix flux-form version in diffus.F to conserve tracer.
973      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
974       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
975    
976    checkpoint62y (2011/05/26)
977    o pkg/seaice:
978     - seaice_growth.F : in EVOLUTION branch, always include
979       a_QSWbyATM_cover in qnet (as it should be).
980     - verification/global_ocean.cs32x15 : update results accordingly
981       (output.seaice.txt output_adm.seaice.txt).
982    o pkg/seaice + obcs:
983     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
984       equivalent of assuming no tracer gradient outside the OB region.
985       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
986     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
987       after changes above);
988     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
989       only at OB location (instead of over a band of OLx width).
990    o pkg/seaice:
991     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
992       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
993    o pkg/obcs:
994      - split header file "OBCS.h" into 4 separated files:
995        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
996       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
997         (contain no conditional statement which depends on OBCS options).
998      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
999        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1000    o ctrl, cost, grdchk & autodiff pkgs:
1001      - make options file more standard (like other {PKG}_OPTIONS.h file but
1002        with AD_CONFIG.h); clean-up some of the included header files.
1003    o pkg/obcs:
1004      - do not mask tracer when applying OB (tracer == 0 could generate problems)
1005      - apply tracer OB values to tracer field only at OB location (instead of
1006        over a band of OLx width)
1007      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1008      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1009        obcs_apply_tloc.F & obcs_apply_sloc.F
1010    o obcs in model/src:
1011      - call OBCS_APPLY_W only if NonHydrostatic.
1012      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1013      - reset dEtaHdt and wVel to zero outside OB interior region ;
1014      - leave tracer unchanged outside OB interior region: This has no effect
1015        on the solution but just to prevent unrealistic tracer value outside OB.
1016      - zero out velocity outside OB interior region: This has no effect on
1017        the solution but just to prevent unrealistic velocity outside OB.
1018    o obcs and non-lin free-surf:
1019       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1020       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1021       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1022       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1023       update results of test-exp. exp4(nlfs).
1024    o exp4 (nlfs) test-exp:
1025       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1026       with NonLin-FreeSurf); update output.nlfs.txt
1027    o obcs and 2d/3d solver norm:
1028       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1029       and outside OB interior region (will allow to place OB further inside the
1030       domain). Depending on the domain, can affects cg2d-Norm (previous
1031       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1032       and cg3d-Norm (previous Norm was computed before canceling OB terms),
1033       e.g. in tutorial_plume_on_slope.
1034      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1035    o pkg rbcs:
1036      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1037      - add capability to apply relaxation to horizontal velocity uVel & vVel.
1038    o pkg/grdchk: add gradient check for control variable xx_shifwflx
1039    o pkg/shelfice/shelfice_init_fixed.F
1040      fix CPP-flag combinations
1041    o pkg/seaice: Merge iceage code of Pierre Rampal
1042      * update/change/correct ice age calculations
1043      * add age updates for pathological cases
1044      Probably needs more testing...
1045    
1046    checkpoint62x (2011/05/13)
1047    o pkg/mom_vecinv:
1048       high-order vorticity scheme: use interior masks (maskInW & S)
1049       to zero-out (outside OB) gradient of vorticity.
1050    o verification exp.:
1051       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1052       hs94.128x64x5 and seaice_obcs ; update results.
1053    o pkg/obcs:
1054      fix bug in OBeta for YZ sections in obcs_exf_load.F
1055    o pkg/ctrl, pkg/shelfice, and optim:
1056      - add new control variable xx_shifwflx (fresh water flux underneath ice
1057        shelves). This is almost as tedious as obcs-ctrl, because the
1058        variables needs its own mask.
1059      - add a cost function term that penalizes the deviation of xx_shifwflx
1060        from the first guess (zero) in analogy to other control variables
1061    o pkg/shelfice:
1062      - start basic adjoint
1063    o pkg/ctrl:
1064      - remove extra 2D field "for good measure" when initializing in
1065        ctrl_set_globfld_[xy/xz/yz].F
1066      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1067      - improve error messages in ctrl_set_unpack_*
1068    o OBC implementation in momentum:
1069       use interior masks (maskInC,W & S) in momentum S/R:
1070       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1071       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1072       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1073       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1074       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1075        (and also with Leith/Smagorinsky harmonic-viscosity).
1076       Update output of experiment dome and exp4 (+nlfs).
1077    o exp4 test-exp:
1078      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1079        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1080        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1081        time-varying OB at Western-side for wVel (NonHyd); update output.
1082      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1083        and biharmonic-viscosity ; also use prescribed time varying OB.
1084    o pkg/obcs:
1085      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1086    o model/src:
1087      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1088      - initialise startTime & nIter0 with unlikely values: allows to set one
1089        from the other without ambiguity.
1090    o seaice_obcs test-exp.:
1091      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1092    o pkg/obcs:
1093      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1094        no longer needed with maskInC,W,S in pkg/generic_advdiff.
1095    o pkg/seaice:
1096      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1097        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1098      - fixed bug in the initialization of sea ice salinity variable HSALT
1099        in seaice_init_varia.F  (removed dependence on ICE2WATR)
1100    o fizhi-cs test exp.:
1101       switch reference output convention for these 2 non-standard test-exp,
1102        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1103          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1104       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1105    o model/inc:
1106      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1107        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1108    o pkg/seaice:
1109      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1110    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1111      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1112        and initial HSALT
1113    
1114    checkpoint62w (2011/04/26)
1115    o pkg/mom_fluxform:
1116      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1117      - use parameter "sideDragFactor" in no-slip BC side-drag part.
1118      - update output of exp. global_ocean.90x40x15
1119    o pkg/mom_vecinv:
1120      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1121    o update seaice exp.:
1122      use more consistent parameter values (remove "backward compatability only":
1123       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1124      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1125       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1126    o update test-exp global_ocean.90x40x15:
1127      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1128      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1129      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1130      o turn on zStar & viscA4 in standard set-up (dir input/)
1131        and update output files: output.txt & output.dwnslp.txt
1132    o new AD-test experiment: obcs_ctrl
1133      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1134    o pkg/dic:
1135      fix two bugs in handling water vapour pressure in carbonate chemistry
1136      and air-sea fluxes. Found by Val Bennington and Galen McKinley
1137      (add DIC Option = WATERVAP_BUG to recover old results)
1138      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1139    o adding allowInteriorFreezing option to check for water below freezing point
1140      at depth and bring the negative heat anomaly to the surface level
1141    o pkgs _fields_load:
1142      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1143      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1144        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1145        rbcs to get interpolation weights and time reccord number.
1146      - fix multi-threading in aim_fields_load.F
1147      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1148    o external_fields_load:
1149      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1150       interpolation weights) to use in a periodic time-series ; do not divide by
1151       time-step to convert to integer:
1152       - this fixes case where externForcingPeriod is not multiple of time-step
1153          (Thanks to Christopher L. Wolfe)
1154       - this fixes case where externForcingPeriod is an odd multiple of time-step
1155         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1156      store index of time-record which is currently loaded:
1157       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1158       - needed for the adjoint but not yet used because of extensive recomputations;
1159         (to be fixed soon)
1160    
1161    checkpoint62v (2011/04/02)
1162    o verification/1D_ocean_ice_column added to test Ian Fenty's
1163      pkg/seaice_growth.F modifications for improving sea ice code differentiability
1164    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1165      (new velocity statistics after changing maskInW & maskInS definition)
1166    o pkg/generic_advdiff with OBCS:
1167      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1168      equivalent to assumption of no tracer gradient outside the OB region.
1169      This will affect the results if using obcs+biharmonic diffusion.
1170      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1171    o pkg/obcs:
1172      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1173      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1174      in Interior region. No impact on solution but affects Velocity monitor stats.
1175    o pkg/ptracers (adjoint)
1176      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1177      tape file for each tracer
1178    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1179      of parts of the adjoint code at run time. For now, there are only
1180      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1181      parameters are set in data.pkg.
1182      This is the lazy coward's version of doing this, but still useful for
1183      debugging. In order to do it right, everything needs to be moved to
1184      pkg/autodiff.
1185    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1186      the end; this fixes the adjoint balancing code for open boundaries.
1187    o pkg/ctrl:
1188      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1189        xx_${varname}period =   0.,  means time-independent control part
1190        xx_${varname}period = -12., means one-year-periodic monthly control part
1191      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1192        clean up ctrl_init a little, remove unused variables
1193      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1194      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1195    
1196    checkpoint62u (2011/03/15)
1197    o model/src:
1198      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1199        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1200      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1201        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1202    o pkg/ctrl/obcs/ecco:
1203      - remove obsolete, unused, and partially broken code:
1204        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1205        ALLOW_CTRL_OBCS_BALANCE
1206      - put a stop statement into ecco/cost_obcsvol.F, but also add
1207        cost_obcsvol to ecco_ad_diff.list
1208    o pkg/ecco: fix counting cost function contributions for obcs (code
1209      by Matt M.) and diffkr for diagnostics
1210    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1211      add cost penalty terms for initial uvel, vvel, eta controls
1212      and I/O for prior error files
1213    o pkg/mdsio:
1214       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1215       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1216       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1217    o pkg/ctrl:
1218     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1219       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1220       unused and superfluous variables
1221     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1222    o pkg/ecco
1223     - enable adjoint of Stevens OB
1224    o pkg/ctrl/ecco/grdchk:
1225      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1226        Fortunately, we do not have any tests for the numerous cpp-flagged
1227        option of "obcs as control parameters" so we will never know
1228        if this is an improvement (but at least now things compile).
1229      - remove an obsolete initialization from ecco_cost_init_barfiles.F
1230      - fix some problems within never used ifdefs to make the code compile
1231    o pkg/obcs:
1232     - Refine Interior mask definition to work with more complex OB (e.g.
1233       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1234       read in Interior mask from file. Check if Interior mask is consistent
1235       with OB list of indices.
1236    o pkg/seaice
1237     - beginning code for a seaice tracer package,
1238       but currently only used for seaice age: SEAICE_AGE
1239       SEAICE_num = 4
1240       iTracer = 1: area-weighted ice age
1241               = 2: volume-weighted ice age
1242               = 3, 4: template for one-year vs. multi-year ice
1243       data.seaice has new namelist SEAICE_PARM03 for arrays related to
1244       SEAICE_num
1245    
1246    checkpoint62t (2011/03/05)
1247    o pkg/obcs:
1248     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1249       then normal component. This ensures that the normal component is set
1250       correctly even when it conficts with tangential setting from an other OB.
1251       Affects results of test-experiment seaice_obcs: update the output.txt
1252    o pkg/obcs:
1253     - add code to monitor statistics of dynamical fields at OB.
1254     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1255       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1256       - change default: balance the Net inflow through all OB (instead of balancing
1257         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1258     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1259       to match Nortern OB inflow (OBCS_balanceFacN=0).
1260    o pkg/seaice:
1261     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1262    o pkg/seaice (seaice_growth v 1.113):
1263     - reverting seaice_growth to v 1.111 in order to have code with exact bit
1264       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1265       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1266       runtime flag SEAICEareaFormula is kept but is inactive
1267    o model/src:
1268     - add new param to scale curvilinear grid distance and area when using
1269       a different sphere radius from the grid-files.
1270     - test/check multi-threads EXCH applied to local variable (cg2d_x)
1271    o adjoint:
1272     - enable adjoint of Stevens OB
1273     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1274       (a bit delicate because of potentially modified adj. common block structure;
1275       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1276    
1277    checkpoint62s (2011/02/15)
1278    o pkg/seaice (seaice_growth v 1.112):
1279     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1280       computing the ice cover tendency from effective thickness tendencies. Include
1281       Ian Fenty's formula.
1282     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1283       SEAICEareaFormula.
1284     - simplify notations for the various d_HEFF/d_AREA terms.
1285    o pkg/gmredi:
1286     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1287       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1288       add a verification test-run (front_relax.bvp) to test GM_useBVP.
1289    o pkg/seaice (seaice_growth v 1.111):
1290     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1291     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1292       also melt ice.
1293    o pkg/seaice:
1294     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1295     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1296  o pkg/cheapaml:  o pkg/cheapaml:
1297   - from Nico Wienders: New version of this package.   - from Nico Wienders: New version of this package.
1298  o pkg/flt:  o pkg/flt:
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