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revision 1.1418 by jmc, Thu Apr 28 23:26:39 2011 UTC revision 1.1619 by jmc, Wed Mar 14 03:51:49 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 testreport
8     - add option to use a home made wrapper around "make"
9     - remove MITGCM_IEEE env. variable (no longer active)
10    o pkg/shelfice
11     - improve computation of friction velocity for velocity dependent
12       exchange coefficients: include velocities into SHELFICEBoundaryLayer
13       block to average velocities vertically
14     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
15    o Modify diagonal solvers, now three versions (upon request):
16      #ifndef SOLVE_DIAGONAL_AUTODIFF
17        1. default version (dating back a while ago)
18      #else /* def SOLVE_DIAGONAL_AUTODIFF */
19      # ifdef SOLVE_DIAGONAL_KINNER
20        2. adjoinable version with k-innermost loop (G. Forget)
21      # else
22        3. adjoinable vectorized version of 2.
23      # endif
24      #endif /* SOLVE_DIAGONAL_AUTODIFF */
25      All flags are currently set within routines, but could/should be moved to CPP-options.
26      Array bounds for 1. are as before, for 2.,3. cover the entire domain
27      (could be changed for 1. too).
28    o verification/lab_sea (fwd):
29      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
30        use 7 categories (except hb87), new solve4temp params (except salt_plume),
31        constant salinity (=4) or variable salinity (salt_plume) done through
32        SItracer.
33    o pkg/seaice:
34      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
35      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
36         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
37        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
38        SEAICE_freeze got retired) but already better than previously with
39        SEAICE_freeze=123456.7 deg.C;
40      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
41        (safer multi-threaded setting); always set SEAICEuseEVP;
42      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
43        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
44        stop if multiple specifications for the same coeff; make sure default
45        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
46    o pkg/obcs:
47      - allow to switch to upwind 1rst order advection scheme for the advective
48        flux computation at the open-boundary; disabled for adjoint built.
49    o pkg/ptracers:
50      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
51      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
52      - add parameter to decide when to start a tracer; use internal flag to
53        know which tracer to step-forward; switch this internal flag at the top
54        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
55        for adjoint built.
56    o pkg/seaice:
57      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
58      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
59      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
60    o pkg/ecco:
61      - fix writing of output file DiagnosCost_ClimSalt/Theta
62        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
63    o pkg/seaice:
64      - add missing initialisation of COR_ICE array in dynsolver.F
65      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
66        compiled either way, and is tested in all exps (multidim was only tested
67        in lab_sea ad before).
68      - cosmetic change to prepare for future addition of ITD. no change to results.
69        no defaults change.
70      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
71      - by lack of adequate verification experiments, I further used custom versions
72        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
73        should be correct.
74      - avoid recomputations in ad.
75    o array initialisation in adjoint mode:
76      1) pkg/mom_common/mom_calc_ke.F:
77        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
78        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
79        part this initialisation is gone, resulting in Floating Point Exception
80        (caught by open64 compiler with debug option).
81      2) model/src/convective_weights.F
82        set output convectCount over the full array range (instead of doing
83        an update): this fix a similar issue when called within recomputation (adjoint)
84        which could by-pass the initialisation (normally done in the caller S/R).
85    o pkg/seaice:
86      - final version of turbulent flux params, as agreed at MIT ice meet:
87           SEAICE_mcPheePiston (default is ~ 0.000875)
88           SEAICE_mcPheeTaper (default is 0.)
89           SEAICE_frazilFrac (defualt is 1.)
90           SEAICE_mcPheeStepFunc (default is false)
91      - changes results at trunction error level
92      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
93    o added pkg/frazil:
94      - see frazil_description.tex for details
95      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
96    o pkg/shelfice/shelfice_thermodynamics.F
97      - fix exponents for velocity dependent exchange coefficients: change
98        from 2/3(=0) to 0.66666666666666667
99      - move computation of velocity dependent exchange coefficients into
100        separate loop, so that it applies to both thermodynamics
101      - move some divisions by constants out of loops
102    
103    checkpoint63j (2012/02/16)
104    o pkg/seaice:
105      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
106      - SItracer:  added run time params, and allow coupling to ocn salinity.
107    o pkg/seaice: remove (almost) all divisions by constants within loops
108      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
109      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
110      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
111      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
112    o pkg/seaice :
113      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
114        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
115      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
116      - add permanent SItflux diag that corresponds to TFLUX but includes
117        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
118      - allow activation/testing of a fix for suspected missing term in
119        ocn-ice heat budget (to be confirmed). To test this, you want to
120        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
121        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
122      - no change in results, fwd or ad.
123    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
124      - switch to variable freezing point.
125           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
126      - bug fix : the sublimation term that was missing is now activated.
127           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
128      - bug fix : flooding sign term for SIsal0.NE.0.
129           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
130    o pkg/seaice:
131      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
132        is now the default, and the old default constant freezing point is recovered
133        with SEAICE_tempFrz0    = -1.96,
134             SEAICE_dTempFrz_dS = 0.,
135      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
136      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
137      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
138        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
139      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
140        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
141      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
142        seaice_growth r149 for legacy branch (no results change).
143      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
144        from I. Fenty).
145      - results did not change except for global_ocean.cs32x15, mostly due to the
146        switch to variable freezing point (see above item for detail).
147    o pkg/thsice:
148      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
149        seawater freezing in thsice_calc_thickn (not used).
150    o pkg/seaice: turbulent flux term specification via run time params.
151      - replace CPP switches with run time switches to facilitate testing
152      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
153                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
154      - added runtime parameter : SEAICEturbFluxFormula
155      - move Mcphee constants to SEAICE_PARAMS.h
156      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
157                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
158                 remove seaice_summary call (moved to seaice_init_fixed)
159      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
160        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
161      - seaice_summary.F : add missing report of read turbulent flux term set up
162                           and SITRACER.
163      - seaice_check.F : check range; inform and stop if retired CPPs are used
164                         (incl. SEAICE_AGE).
165      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
166             CPP switch, same computation as before for the different options.
167      - change results at the truncation level.
168    o pkg/seaice:
169      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
170        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
171        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
172      - update verification/*/input*/data.seaice:
173        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
174        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
175        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
176        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
177    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
178      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
179        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
180        difference in results only due to machine truncation.
181      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
182        MaykutPolySatVap; keep MIN_LWDOWN.
183      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
184      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
185        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
186    o pkg/salt_plume:
187      - isolate saltPlumeFlux array exch into a specific S/R called from
188        do_oceanic_phys.F
189      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
190    o verification:
191      - move untested set-up to MITgcm_contrib/verification_other.
192    o pkg/seaice:
193      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
194    o pkg/seaice:
195      - seaice_solve4temp.F (keeping results unchanged):
196        * add 2 future run-time params to select which saturation vapor pressure
197          formula is used and how post-iteration fluxes are set.
198          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
199        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
200          the linearized expression to stay consistent with tsurf finding.
201      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
202        can be < 0.
203    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
204      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
205        conductive heat flux F_c , and add it explicitly when updating tsurf as
206        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
207        so that now F_ia has a consistent meaning through the entire routine.
208        This causes differences at truncation level: update output of fwd exp.
209        global_ocean.cs32x15.seaice.
210    o pkg/seaice:
211      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
212        of arrays, sign/direction of fluxes; no effect on results.
213      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
214        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
215        note: this should have been done before changing celsius2K default.
216      - to keep results unchanged, add back old value of celsius2K in verification
217        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
218      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
219        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
220        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
221        freezing temp is consistent with value in seaice_growth.F ; this causes
222        differences at machine truncation level: update lab_sea AD output (3/4).
223    o pkg/seaice:
224      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
225        and climsst/sss even when using seaice (to prevent calculation that might
226        use SST on land); does not affect any verification exp.
227      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
228        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
229    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
230      over land (non-legacy code)
231    o vectorize salt_plume package:
232      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
233      - this code computes plumebk everywhere (also over land), thus requires
234        code to avoid divisions by zero and catch the case of kLev=Nr.
235      - efficiency of salt_plume_frac is still sub-optimal
236    o tools (genmake2):
237      - fix makefile NAME specification (option: -makefile NAME) by adding
238        "-f $MAKEFILE" in few places where it was missing including makedepend
239        command (contribution from Paul).
240    
241    checkpoint63i (2012/01/24)
242    o model/src:
243      - add factorized versions of some EOS code to find_rho.F,
244        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
245    o model/src:
246      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
247      - change default celsius2K from 273.16 to 273.15
248      - to keep results unchanged, add back old value of celsius2K in verification
249        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
250         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
251    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
252      to make TAF generate vectorizable code
253    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
254       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
255       have flags that do this more efficiently.
256    o pkg/diagnostics/diagstats_calc.F
257      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
258    o pkg/obcs (with exch2):
259      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
260        and remove code (in obcs_readparms.F) which was based on EXCH of indices
261        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
262    o pkg/exf and seaice exp:
263      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
264        so that switching off area & heff advection flags does not affect results.
265      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
266      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
267        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
268        results of verification experiments: 1D_ocean_ice_column(fwd),
269        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
270        and offline_exf_seaice (all 4).
271    o pkg/seaice:
272      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
273        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
274      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
275        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
276        not multi-dim advection;
277      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
278        SHORTWAVE_HEATING #undef.
279    o optim: make Makefile more robust (?)
280    o pkg/obcs:
281      * fix treatment of obcs_read_pickup for TAF
282    o pkg/shelfice:
283      * add missing initialisation of num_shifwflx
284      * new adjoint verification exp. for isomip
285      * change Prandtl and Schmidt numbers from generic formulations
286        (in terms of model diffus. and visc.) to separate runtime
287        parameters, with Holland and Jenkins (1999) default values.
288    o pkg/exf (interpolation):
289      - extended input field (2 rows) near the N & S poles:
290        * fill in with the symetric value (when even Nb of data in longitude)
291        * add average value at the poles only for scalar quantities ; for vector
292          component interpolation, skip the averaging and keep duplicated values,
293          unless the 2 components have same location (uvInterp=T) in which case
294          interpolate the 2 components together using S/R EXF_INTERP_UV.
295      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
296        together: this allows to account properly for local orientation when
297        averaging at N & S pole.
298      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
299        exf-interpolation near N & S poles. Undef by default.
300      - add debug check/print on 1rst iter if debugLevel >=2.
301    o pkg/exf:
302      - change masking flags definition (no longer "parameter"), put them in
303        common block and set them in S/R EXF_INIT_FIXED.
304      - change recognized masking flag from s,u,v to c,w,s since the mask
305        to use (maskC,W,S) depends on position on model grid and has little to
306        do with scalar/vector difference; fix masking if using P-coordinates.
307      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
308        and update results of exp. global_with_exf (x2).
309      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
310    o pkg/obcs
311      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
312    o pkg/exf (interpolation):
313      - assume periodicity in X only if input field cover full longitude range.
314      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
315        and should vectorise).
316      - fix input lat of the 2 added row (in case we provide N.pole data).
317    
318    checkpoint63h (2011/12/30)
319    o pkg/seaice:
320      - change declaration of UVM from _RL to _RS in order to get B-grid
321        uIce,vIce monitor when _RS = real*4
322    o pkg/offline:
323      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
324      - compute vertical velocity if not read from file (switch on exactConserv
325        & staggerTimeStep);
326      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
327    o verification:
328      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
329        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
330        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
331      - update output of exp. global_ocean.cs32x15.viscA4 after changing
332        grid-file angles (used here for coriolis-3d);
333      - remove (or gzip) few files not needed to run fizhi-cs experiments.
334    o pkg/exf (vector interpolation):
335      - rotate vector component toward local grid-axis orientation using grid-angles
336        (stored in GRID.h) instead of locally computed rotation angle; keep old code
337        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
338    o pkg/seaice:
339      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
340        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
341    o pkg/PKG_OPTIONS.h files:
342      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
343        outside of the #ifdef ALLOW_THISPKG / #endif block.
344      - update verification/*/code/PKG_OPTIONS.h files.
345    o add a verification experiment (offline_exf_seaice/input.seaice) that test
346      the B-grid LSOR solver
347    o pkg/seaice: sort out emissivity and long wave radiation step 2:
348      - add emissivity for snow and ice as new run-time parameters
349        (unfortunately) that default to the corresponding exf values; this
350        changes results in most verification experiments so that for backward
351        compatibility these parameter have to be set explicitly to inconsistent
352        values (ugly);
353      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
354        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
355        until we agree how to handle this bug properly
356    o pkg/exf (interpolation):
357      - add a set of run-time param ({inputfield}_interpMethod), one for
358        each interpolated input field, to select the interpolation method
359        with a value of zero switching off the interpolation;
360      - print interpolation parameters to standard output;
361      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
362        (to use instead runoff_interpMethod=0 in data.exf).
363      - simplify default setting of interpolation parameters (for all fields,
364        set position to match model grid cell-center position, leading to trivial
365        interpolation in case of regular Lat-Lon grid) and fix for the case of
366        non-uniform delY.
367    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
368       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
369       this factor is absolutely required, because the lw exitance (= out-going
370       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
371       where the reflectivity rho = 1-emissivity for conservation reasons. Once
372       this is established, we can remove the CPP-Flag (if we want to).
373    o pkg/seaice:
374      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
375        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
376      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
377        what the name implies (and not emissivity*BoltzmannConstant), this means
378        the old default value of 5.5e-8 now means
379        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
380        S/R exf_readparms
381      - FV-discretization of the B-grid LSOR solver, turn on with
382        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
383        of the calling routine dynsolver, so that B and C-grid code look a
384        little more alike.
385      - fix index bugs in ostres.F (B-grid code)
386    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
387    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
388      default for SEAICE_emissivity, if useEXF; requires setting a wrong
389      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
390      backward compatiblity
391    o model/src: use sigmaR in calc_ivdc
392    
393    checkpoint63g (2011/12/16)
394    o pkg/seaice/seaice_growth.F:
395      fix heat conservation of the coupled ocean-seaice system.
396      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
397      solid vs liquid water treatment is resolved via QNET.
398    o pkg/seaice/seaice_growth.F:
399      add missing term for sublimation in saltFlux, which was breaking conservation.
400    o pkg/seaice/seaice_model.F:
401      Remove this patholigical case treatment in evolution branch,
402      where it is un-necessary and breaks conservation.
403      Update global_ocean.cs32x15/results accordingly for
404      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
405    o model/src:
406      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
407      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
408    o pkg/obcs:
409      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
410      tendency for temperature and salinity that is then applied to update
411      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
412      horizontal advection and diffusion contributions on the boundary (in
413      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
414      removing the mask in S/R timestep_tracer. The advantage of this approach is
415      that the updated tracer values include contributions from the surface
416      forcing and vertical diffusion.
417      This modification changes exp4.stevens because of vertical diffusion.
418    o model/src:
419      change non-curvilinear grid setting to also work with exch2 + blank tiles:
420      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
421        face dimensions.
422      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
423        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
424        and INI_SPHERICAL_POLAR_GRID.
425      change test-experiment global_ocean.90x40x15:
426      - split the domain in many more tiles (9x4 tiles of 10x10 each);
427      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
428      - update results of both test (std & dwnslp).
429    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
430       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
431    o model/src:
432      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
433        and fix initialisation when using sigma-coords.
434    o model/src:
435     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
436       to their current value at the beginning of forward_step.F": add a new run-time
437       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
438     - set doResetHFactors=T in the following test exp:
439        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
440        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
441        and tutorial_global_oce_in_p (nonLinFS in p)
442    o pkg/ecco
443      - added IES cost term
444    o verification/advect_xz
445      - scale down the depth by 1/100 (from 200 km to just 2.km)
446      - add secondary test using divergent flow, r-star and implicit vertical advection.
447      - add note (check_conserve_TS.txt) and matlab script to check global
448        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
449    o pkg/rbcs:
450      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
451    o pkg/obcs (Stevens BCs):
452      - fix various problems in the phase speed computations of the Stevens
453        boundary conditions:
454        - sign error for western and southern boundaries,
455        - time tendencies were underestimated by factor of dTracerLev and some just
456          zero (for multidim advection schemes) -> now estimate time tendencies
457          from difference between previous (n) time level and the one before (n-1);
458          this requires storing a field per tracer per boundary, also in the pickup
459          files.
460        - replace deltaTmom in cflMer/Zon computation with dTracerLev
461        - set default phase velocity to cflMer/Zon
462      - update verification experiment exp4.stevens
463    o pkg/generic_advdiff (implicit_r):
464      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
465        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
466      - fix implicit vertical diffusion or advection with NonLin FreeSurf
467        (was using current recip_hFacC instead of future recip_hFacC): set future
468        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
469        solver S/R ;
470      - fill diagnostics of vertical advective fluxes (computed from tendency)
471        when using implicit vert. advection;
472      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
473         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
474         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
475         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
476    o pkg/diagnostics:
477      - add diags for T & S tendency which goes through Adams-Bashforth.
478    
479    checkpoint63f (2011/11/30)
480    o pkg/obcs/obcs_calc_stevens.F:
481      - join some loops to reduce number of if-statements
482      - fix a bug in code for northern and southern boundaries.
483    o pkg/seaice/seaice_init_varia.F
484      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
485        caused zero ice-velocities for the B-grid code
486    o pkg/seaice/seaice_init_fixed.F
487      - fix a bug in the initialisation of the second metric terms
488        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
489      - this affects all seaice configurations with useCurviLinearGrid = .true.
490        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
491        = .true. (default)
492      - the only verification experiment affected is global_ocean.cs32x15:
493        icedyn, seaice, and seaice_dynmix (AD)
494    o pkg/thsice/thsice_diagnostics_state.F
495      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
496        not contain garbage that can lead to surprises in diagstats_calc.F
497    o model/src:
498      - move bi,bj loops inside INTEGR_CONTINUITY ;
499      - call INTEGR_CONTINUITY directly from forward_step.F
500        (previously called from momentum_correction_step.F)
501      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
502        forward_step.F and pkg/ecco/the_main_loop.F
503    o model/src/do_oceanic_phys.F:
504      - reset addMass to zero only if useICEFRONT ;
505      - separated k-loop for rhoInSitu calculation ;
506      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
507        and at constant T,S (= WdRHOdP);
508      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
509        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
510        transport of locally-referenced potential density);
511        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
512    o gluemnc:
513      - replace ncrcat with ncks when adding variables to *.glob.nc
514      - change the way variables without record dimensions are handled so that
515        files that have variables with and without record variables can be glued:
516        add a record dimension with a new unique name to be able to differentiate
517        between variable with and without a-prior record dimensions. Remove
518        this record dimension before adding the variable to the *.glob.nc file.
519        This procedure automatically works also for grid.*.nc files that do not
520        have any record dimension.
521    o verification/cpl_aim+ocn:
522      - generate new reference output on baudelaire (gfortran, mpich2) (previously
523        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
524    o pkg/obcs/obcs_calc_stevens.F:
525      - add code for northern and southern boundaries.
526      - reorder some loops to save some operations and so that drFBar can be scalar
527    o model/src:
528      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
529        truncation) and add diagnostics for Adams-Bashforth tendency increment.
530      - update test-exp. AD output:
531        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
532      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
533        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
534        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
535        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
536        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
537        tutorial_plume_on_slope.
538    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
539      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
540      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
541      does not even come with an F77 compiler anymore, this should not be
542      a limitation
543    
544    checkpoint63e (2011/11/06)
545    o pkg/seaice adjoint of LSR:
546      - substantially rework STORE dirs.
547      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
548        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
549        and only perform SOLV_MAX_FIXED adjoint iters.
550        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
551        always goes to same record, meaning that the last forward field will be
552        the one used in the adjoint - an approximation.
553      - now produces non-zero LSR-related gradients, and acceptable gradients for
554        An's zonal (x-z) test case (to be checked in)
555      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
556        (but these are screwed up by the thermodynamics in the first place);
557        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
558        output_adm.txt also reflects changes to seaice_lsr
559      - global_ocean.cs32x15:
560        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
561          (output_adm.seaice.txt was updated)
562        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
563          (output_adm.seaice_dynmix.txt)
564    o test-exp. exp4+stevens:
565      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
566    o pkg/seaice (lsr solver):
567      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
568        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
569      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
570      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
571        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
572      - compute (with new S/R) and print initial (+ free-driff sol. if available)
573        and final residual of linearised system.
574    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
575      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
576    o pkg/obcs: Stevens BCs (still only for east and west)
577      - fix Stevens BCs by using intermediate velocities of previous
578        time step as "baroclinic" contribution rather velocity of one grid cell
579        inside the boundaries; more consistent but makes the entire treatment
580        more complicated, requires new pickup files and two new S/Rs:
581        obcs_copy_uv_n and obcs_save_uv_n
582        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
583        (undefined by default)
584      - silently move computation of some grid factors into separate loops to
585        save some recomputations
586      - add a hack for non-linear free surface
587      - add a verification experiment to exp4 that tests this code
588    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
589    
590    checkpoint63d (2011/10/25)
591    o pkg/obcs + seaice-dynamics:
592      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
593        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
594        values (consistent with an implicit method).
595      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
596        return to older implementation (same results as before); note that none of
597        the "experimental" OBCS_SEAICE options are implemented in the new version.
598      - switch test exp. seaice_obcs to use new version (update output).
599    o pkg/seaice:
600      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
601      - add parenthesis in Water-Ice drag calculations (evp & lsr);
602      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
603        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
604      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
605        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
606    o pkg/layers:
607      - Include potential density as new coordinate (Thanks to David Munday)
608    o pkg/dic:
609      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
610        carbonate computation/output to CALC_PCO2_APPROX
611    o pkg/generic_advdiff
612      - make TAF generate code that vectorizes:
613        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
614    o model/src:
615      - improve vectorization also for adjoint code of
616        solve_tridiagonal and solve_pentadiagonal. As this requires up to
617        5 new 3D-fields, this code is only turned on for the combination of
618        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
619        for singular matrix check (only for TARGET_NEC_SX).
620      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
621        ALLOW_AUTODIFF. This flag now needs to be set outside of
622        solve_tri/pentadiagonal.F
623    o pkg/exf:
624      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
625        optional namelist EXF_NML_OBCS).
626      - add many debug-print (to trace down where pkg/cal error msg comes from)
627    o pkg/mom_vecinv/mom_vi_hdissip.F
628      - rearrange loops so that vectorization is improved and in particular
629        the adjoint routine vectorizes. The code is a little longer now, but I
630        think easier to read.
631        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
632    o pkg/seaice:
633      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
634    o pkg/exch2:
635      - alternative code (without tile x tile matrix) for cumulated (global) sum;
636        used as default; keep using matrix version in adjustment.cs-32x32x1.
637    o tools/build_options:
638      - after merging some MPI and/or multi-threads specific optfiles so that
639        the modified default optfile support both built (using genmake2 -mpi
640        for the MPI built, using genmake2 -omp for OpenMP built),
641        move now obsolete optfiles to tools/build_options/unsupported/
642       (add copy of email sent to support list in doc/optfiles_changes.txt)
643    
644    checkpoint63c (2011/09/28)
645    o pkg/ebm:
646      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
647        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
648    o pkg/seaice (SItracer pickup)
649    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
650      To be done:
651      - thorough testing of missing fields in S/R seaice_read_pickup
652      - thorough matching between generic tracers and specific fields used
653        (e.g. volume-weighted age, area-weighted age, salinity, ...)
654    o pkg/grdchk:
655      - all procs calculate and print finite-difference gradient (for testreport)
656      - change description output used by testreport;
657      - AD testing: also compare and report Finite-difference gradient;
658        => update all output_adm*.txt
659    o test exp. global_ocean_ebm:
660      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
661        and turn on exactConserve; update (fwd) output.
662    o pkg/seaice (LSR):
663      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
664      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
665        * identical results with non-CS topology (but save up to half of EXCH calls)
666        * no much changes in cs-32 verification tests since no ice at face edges
667         (differences due to convergence criteria, since nb of iterations changed)
668        * expect some differences on lat-lon-cap grid.
669        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
670    o pkg/exch2:
671      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
672        many tiles); until alternative coding is added, just add a stop.
673    o pkg/kpp:
674      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
675        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
676    o optfiles:
677      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
678        into corresponding standard one, which now support different build:
679        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
680      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
681    o pkg/obcs (seaice):
682      - add missing EXCH for uIce,vIce after applying OBCS;
683      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
684        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
685        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
686      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
687      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
688        and eedata.mth for MPI and mutlti-threaded testing.
689    o pkg/flt:
690      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
691      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
692      - fix pickup and trajectories + profiles output with multi-threads;
693      - add parameter to select group of fields to write along trajectory and
694        profile (default unchanged);
695      - only call PORT_RAND* function when flt_noise <> 0;
696      - add multi-threaded test for verification exp. flt_example.
697    o eesupp/src:
698      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
699      - USE_OMP_THREADING: check that number of threads (from eedata) matches
700        actual number (from env.var. setting).
701    o pkg/ebm:
702      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
703      - add multi-threaded test for verification exp. global_ocean_ebm
704    
705    checkpoint63b (2011/08/29)
706    o pkg/ebm:
707      - fix sign of runoff;
708      - update directly forcing fields (Qnet,EmPmR) to use standard
709        external_forcing_surf.F (remove ebm_forcing_surf.F);
710      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
711      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
712        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
713      - update global_ocean_ebm parameters file data and update output (fwd+ad).
714    o verification/matrix_example:
715      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
716        MPI and mutlti-threaded testing.
717    o pkg/matrix:
718      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
719      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
720      - fix for multi-threaded (remove DATA statement);
721      - use standard DIFFERENT_MULTIPLE function;
722      - add MATRIX_OPTIONS.h
723    o verification/matrix_example:
724       To allow to split the domain in several tiles, change the domain size
725        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
726        Western side) of land points.
727    o (*_)write_pickup:
728      - fix few bugs in mypackage_read/write_pickup.F
729      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
730        array of length 1 (was caught by compiler syntax-check).
731    o pkg/diagnostics (velocity potential solver):
732      - fix initialisation of main diagonal matrix (for overlap values)
733    o tools/build_options:
734      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
735        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
736      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
737        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
738        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
739        and use "-devel" testreport option for standard testing on baudelaire.
740    o pkg/grdchk:
741      - Assume that all gradient-check position are within the same tile
742        corresponding to global indices (iGloTile,jGloTile) and that
743        positions (i,j indices or nbeg) are local to this tile;
744      - set tile local-indices and proc. number according to tile global-indices;
745      - remove grdchkwhichproc from namelist (retired param);
746      - send adjoint gradient to all procs so that all procs print it to STDOUT;
747      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
748    o adding package bbl (Bottom Boundary Layer)
749      description in MITgcm/pkg/bbl/bbl_description.tex
750      example/test experiment in MITgcm_contrib/bbl
751    o adjoint verifications
752      - changed 5 experiments to multi-tiles
753        * global_ocean.90x40x15
754        * obcs_ctrl
755        * offline_exf_seaice
756        * tutorial_dic_adjoffline
757        * tutorial_tracer_adjsens
758        changed reference output for those that crossed tile boundaries
759        (changed choices of gradient check positions)
760      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
761      - temporary bug fix in grdchk_loc.F for obcs
762    o genmake2 & testreport
763      - add target "obj" (just for OBJFILES files) to Makefile;
764      - add option to specify FEXTRAFLAGS on command line.
765    o pkg/mypackage:
766      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
767    
768    checkpoint63a (2011/08/02)
769    o pkg/diagnostics (velocity potential):
770      - fix velocity-potential calculation when using OBCS: balance net inflow
771        at each level (new S/R OBCS_DIAG_BALANCE).
772      - fix some of the problems with OBCS in stream-function calculation.
773    o pkg/exf/exf_readparms.F
774      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
775        EXF_NML_OBCS) more consistent, so that you need not have these lists
776        in data.exf when they are not used.
777    o optim/optim_readdata.F:
778      - add some output about obcs variables that might help debugging
779      - add a check about nvarlength
780    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
781    o pkg/diagnostics (velocity potential):
782      - fix mask for OBCS (still problems in stream-function with OBCS);
783      - add specific parameter (default = main code CG2D params) for solver;
784      - in case of poor convergence, use solution corresponding to lowest residual.
785    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
786      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
787      and should be avoided where possible.
788    o model/src (rStar):
789      - include r* effect on reference-state (PhiRef) in totPhiHyd
790        (so that it's really the potential anomaly at the cell center);
791        affect solution only if z* with full pressure in EOS.
792      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
793        update output (because of z* in totPhiHyd and viscA4 changes);
794      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
795        @ constant r) until interpolation at constant r is implemented.
796    o pkg/diagnostics
797      - fix RCENTER diagnostics in case cell center is not at interface middle
798    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
799      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
800      that THETA and SALT are "conservative temperature" and "absolute
801      salinity"
802    o pkg/ctrl
803      - fix computation of endrec in s/r ctrl_init_rec
804      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
805    o pkg/seaice/seaice_growth.F
806      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
807        remove then obsolete STORE directives
808      - fix STORE directives for tice and tices, so that only the
809        appropriate part of the fields are stored (and not the entire
810        field); update global_ocean.cs32x15.seaice AD output.
811      - cosmetic changes: adjust CPP flags and indentation for better
812        legibilty
813    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
814      Chris Wilson)
815    o pkg/gmredi:
816       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
817       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
818    
819    checkpoint63  (2011/07/11)
820    o pkg/exch2:
821     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
822     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
823       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
824       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
825    o pkg/diagnostics:
826     - deal with pairs of post-processed diags which are computed together; in
827       particular, re-order list of diags within 1 file to save 2nd computation.
828     - add S/R to compute velocity stream-function (called after velocity-potential
829       calculation) from divergence free transport -> new diagnostics "PsiVEL".
830     - add parameter to select grid-point location where PsiVEL == 0.
831    o eesupp/src:
832       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
833       (specific S/R needed with exch2 topology - for now, just print an error msg)
834    o pkg/shelfice
835     - Implement friction velocity-dependent transfer coefficients following
836       Holland and Jenkins, JPO, 1999
837       Original code by M. Losch with small modifs.
838       Enable with CPP option SHI_ALLOW_GAMMAFRICT
839       and runtime flag SHELFICEuseGammaFrict
840    o verification lab_sea & global_ocean.cs32x15:
841     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
842       does not miss some dependencies (but is slower) and also works with many files
843       (default makedepend limitation for AD built).
844     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
845    o pkg/diagnostics:
846     - add run-time parameter "useMissingValue" (def=False) to fill land-point
847        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
848       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
849     - Extend the use of "missing_value" setting from data.diagnostics for the case
850       of counter-diagnostics (where fraction-weight is zero). This applies both to
851       MNC and MDS output files.
852    o pkg/seaice/seaice_growth.F:
853      - add 'a priori' cap of latent heat flux based on actual mass considerations
854        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
855        non-legacy seaice_solve4temp.
856      - add diagnostic of the residual sublimation freshwater flux (the freshwater
857        flux taken from the ocean if the total actual latent heat fluxes exceed
858        the maximum)
859      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
860       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
861      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
862       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
863      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
864      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
865    o verification 1D_ocean_ice_column:
866       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
867       update results
868    o pkg/diagnostics:
869     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
870       which are not filled-up but computed from other diags ; In this case, the mate
871       diag points to the primary (filled-up) diag to used for post processing.
872     - Update Velocity-potential computation using post-processed diag framework.
873     ==> Change the ordering of fields and time-periods in MDS output file
874       when using periodic averaging: now writes one time record with the full set
875       of fields for this time period, then the next time reccord (it used to be
876       one field with the full set of time records then the next field).
877         Note: this is now similar to NetCDF (MNC) output file. <==
878    
879    checkpoint62z (2011/06/21)
880    o adjoint monitor:
881     - Add adjoint monitor output for packages exf, seaice
882       and update relevant testreport output
883    o pkg/seaice:
884     - re-order diags inits so that they appear in order in available_diagnostics.log
885     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
886       area/heff/hsnow preceeding thermodynamic growth/melt.
887     - modified diag: SIdA; output actual effect, as the description states.
888     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
889     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
890       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
891        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
892     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
893     - added diagnostics for seaice generic tracers (SItr*).
894     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
895     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
896     I. Fenty: 18-Jun-2011:
897     Minor changes to seaice package:
898     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
899        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
900       - Differentiated "regularization variables" from "floor variables"
901        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
902        * hiceMin became SEAICE_hice_reg (old hiceMin)
903          (with _reg meaning regularization variable)
904       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
905        so as to ensure energy conservation when going between phases
906      - A22 was not used anywhere
907     2) Changed regularization procedure for heffActual and hsnowActual to ensure
908        well-boundedness and smooth adjoint in seaice_growth.F
909     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
910        because the old regularization always set heffActual >= 0.05 cm
911     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
912        on AREA when HEFF > 0.
913      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
914        requiring that DISABLE_AREA_FLOOR *not* be defined
915     Affected verifications:
916      - 1D_ocean_ice_column (output.txt output_adm.txt)
917      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
918    o pkg/diagnostics:
919      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
920      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
921        (was _RL, now integer) with option = 0 to retrieve all levels.
922      - add pieces of code to compute velocity potential at each level (new diagnostics
923        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
924        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
925      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
926        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
927        and in diagnostics_fract_fill.F (do not need a valid pointer for the
928        diagnostics counter-mate); check that definition of counter-diagnostic
929        includes a valid counter-mate (in diagnostics_set_levels.F).
930    o model/src (rStar):
931      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
932        affect solution only if z* with full pressure in EOS;
933        update output of test-exp global_ocean.90x40x15.
934    o pkg/seaice:
935      - introduce siEps=1e-5 parameter
936      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
937      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
938      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
939        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
940        as well as ice cover age and ridging index (attached to AREA).
941        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
942        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
943        Up to SItrMaxNum=3 tracers can be used simultaneously.
944    o pkg/salt_plume:
945      -introduce SPsalFRAC run time parameter that sets the fraction of the
946       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
947       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
948    o model debug options:
949      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
950        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
951      - Refine debug-msg printing selection (3 new levels):
952        debugMode  : controls printing of debug messages (sequence of S/R calls).
953        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
954         debLevZero =  0 ; /* level of disabled aux. msg printing */
955         debLevA =  1 ; /* level of minimum  aux. msg printing */
956         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
957         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
958         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
959         debLevE =  5 ; /* level of extensive debug printing */
960        New debugLevel default: with default debugMode value (=F),
961          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
962          and if debugMode=T, default debugLevel = 4 (debLevD).
963        Relation with previous settings:
964         debLevB (=2) corresponds to former debLevA (=1)
965         debLevD (=4) corresponds to former debLevB (=2)
966        Note:
967         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
968         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
969            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
970      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
971        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
972    o pkg/obcs:
973      - change OBCSfixTopo default from True to False (should not change the results);
974        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
975    o pkg/thsice:
976      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
977        2nd layer seaice sublimation (unlikely to happen)
978      - use Interior mask for OBCS in thsice_advection.F (similar to what is
979        done in gad_advection & seaice_advection).
980    o adjoint:
981      bug fix spotted by Gael Forget:
982      seaice_advection and thsice_advection still had
983      legacy CPP options to avoid CS corner updates for adjoint
984    o pkg/seaice:
985      => Change some of the defaults (2011/05/29):
986         - change SEAICEuseFluxForm default (from False to True)
987         - change DIFF1 default (from 0.004 m/s to 0. m/s)
988         And print warnings if DIFF1 is not set in data.seaice and centered
989          avection scheme is used without any diffusion.
990      also:
991      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
992      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
993      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
994        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
995        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
996      update results of test exp.:
997         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
998             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
999             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1000         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1001         seaice_obcs: output (SEAICEuseFluxForm=T)
1002      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1003          for standard fwd & AD lab_sea tests (to keep the same output).
1004    o pkg/seaice/seaice_growth.F:
1005      - use Ian Fenty's capping formulas for actual ice
1006      thickness thoughout EVOLUTION branch.
1007      - put treatment pathological case #2) in CPP brackets
1008      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1009      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1010    o pkg/seaice:
1011      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1012      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1013      also pass fac as a param, which can be 1. (to update the tendency
1014      field) or the time step (to update the field itself).
1015      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1016      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1017      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1018      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1019      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1020    o pkg/seaice:
1021      diffusion with centered advection scheme (diffus.F & advect.F):
1022      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1023        to just compute the laplacian of input-field.
1024      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1025      - fix flux-form version in diffus.F to conserve tracer.
1026      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1027       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1028    
1029    checkpoint62y (2011/05/26)
1030    o pkg/seaice:
1031     - seaice_growth.F : in EVOLUTION branch, always include
1032       a_QSWbyATM_cover in qnet (as it should be).
1033     - verification/global_ocean.cs32x15 : update results accordingly
1034       (output.seaice.txt output_adm.seaice.txt).
1035    o pkg/seaice + obcs:
1036     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1037       equivalent of assuming no tracer gradient outside the OB region.
1038       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
1039     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
1040       after changes above);
1041     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
1042       only at OB location (instead of over a band of OLx width).
1043    o pkg/seaice:
1044     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
1045       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
1046    o pkg/obcs:
1047      - split header file "OBCS.h" into 4 separated files:
1048        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
1049       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
1050         (contain no conditional statement which depends on OBCS options).
1051      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
1052        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1053    o ctrl, cost, grdchk & autodiff pkgs:
1054      - make options file more standard (like other {PKG}_OPTIONS.h file but
1055        with AD_CONFIG.h); clean-up some of the included header files.
1056    o pkg/obcs:
1057      - do not mask tracer when applying OB (tracer == 0 could generate problems)
1058      - apply tracer OB values to tracer field only at OB location (instead of
1059        over a band of OLx width)
1060      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1061      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1062        obcs_apply_tloc.F & obcs_apply_sloc.F
1063    o obcs in model/src:
1064      - call OBCS_APPLY_W only if NonHydrostatic.
1065      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1066      - reset dEtaHdt and wVel to zero outside OB interior region ;
1067      - leave tracer unchanged outside OB interior region: This has no effect
1068        on the solution but just to prevent unrealistic tracer value outside OB.
1069      - zero out velocity outside OB interior region: This has no effect on
1070        the solution but just to prevent unrealistic velocity outside OB.
1071    o obcs and non-lin free-surf:
1072       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1073       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1074       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1075       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1076       update results of test-exp. exp4(nlfs).
1077    o exp4 (nlfs) test-exp:
1078       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1079       with NonLin-FreeSurf); update output.nlfs.txt
1080    o obcs and 2d/3d solver norm:
1081       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1082       and outside OB interior region (will allow to place OB further inside the
1083       domain). Depending on the domain, can affects cg2d-Norm (previous
1084       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1085       and cg3d-Norm (previous Norm was computed before canceling OB terms),
1086       e.g. in tutorial_plume_on_slope.
1087      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1088    o pkg rbcs:
1089      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1090      - add capability to apply relaxation to horizontal velocity uVel & vVel.
1091    o pkg/grdchk: add gradient check for control variable xx_shifwflx
1092    o pkg/shelfice/shelfice_init_fixed.F
1093      fix CPP-flag combinations
1094    o pkg/seaice: Merge iceage code of Pierre Rampal
1095      * update/change/correct ice age calculations
1096      * add age updates for pathological cases
1097      Probably needs more testing...
1098    
1099    checkpoint62x (2011/05/13)
1100    o pkg/mom_vecinv:
1101       high-order vorticity scheme: use interior masks (maskInW & S)
1102       to zero-out (outside OB) gradient of vorticity.
1103    o verification exp.:
1104       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1105       hs94.128x64x5 and seaice_obcs ; update results.
1106    o pkg/obcs:
1107      fix bug in OBeta for YZ sections in obcs_exf_load.F
1108    o pkg/ctrl, pkg/shelfice, and optim:
1109      - add new control variable xx_shifwflx (fresh water flux underneath ice
1110        shelves). This is almost as tedious as obcs-ctrl, because the
1111        variables needs its own mask.
1112      - add a cost function term that penalizes the deviation of xx_shifwflx
1113        from the first guess (zero) in analogy to other control variables
1114    o pkg/shelfice:
1115      - start basic adjoint
1116    o pkg/ctrl:
1117      - remove extra 2D field "for good measure" when initializing in
1118        ctrl_set_globfld_[xy/xz/yz].F
1119      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1120      - improve error messages in ctrl_set_unpack_*
1121    o OBC implementation in momentum:
1122       use interior masks (maskInC,W & S) in momentum S/R:
1123       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1124       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1125       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1126       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1127       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1128        (and also with Leith/Smagorinsky harmonic-viscosity).
1129       Update output of experiment dome and exp4 (+nlfs).
1130    o exp4 test-exp:
1131      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1132        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1133        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1134        time-varying OB at Western-side for wVel (NonHyd); update output.
1135      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1136        and biharmonic-viscosity ; also use prescribed time varying OB.
1137    o pkg/obcs:
1138      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1139    o model/src:
1140      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1141      - initialise startTime & nIter0 with unlikely values: allows to set one
1142        from the other without ambiguity.
1143    o seaice_obcs test-exp.:
1144      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1145  o pkg/obcs:  o pkg/obcs:
1146    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1147      no longer needed with maskInC,W,S in pkg/generic_advdiff.      no longer needed with maskInC,W,S in pkg/generic_advdiff.
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