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revision 1.1461 by jmc, Wed Jun 22 02:31:29 2011 UTC revision 1.1628 by dimitri, Mon Mar 19 21:48:27 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/icefront: fix bug and reorder loop in icefront_init_varia.F
8    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
9      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
10      some compilers (gfortran 4.6.0 on MacOS)
11    o momentum:
12      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
13        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
14        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
15    
16    checkpoint63k (2012/03/17)
17    o model/src:
18       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
19         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
20       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
21         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
22    o model/src: solve_*diagonal.F
23       - replace division with multiplication by inverse (similar to original version)
24         update output of AD exp. global_ocean.90x40x15.
25       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
26         to enable the use of the vectorized & differentiable solve_tridiagonal.F
27       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
28         vertical advection (to get solve_tridiagonal tested in AD mode).
29    o pkg/seaice: ECCO-CLIVAR merge:
30      1. seaice AREA relaxation
31         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
32         * runtime flag: SEAICE_tauAreaObsRelax
33      2. modified global mean cost imbalance code: CPP option
34          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
35    o another iteration on solve_*diagonal.F
36       Make choices independent of AUTODIFF
37       Default will be the adjoinable vectorized version.
38       Alternative choices are:
39       * non-adjoinable original version with low memory footprint:
40         #define SOLVE_DIAGONAL_LOWMEMORY
41       * still adjoinable but does not vectorize (k as inner-most loop):
42         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
43    o testreport
44     - add option to use a home made wrapper around "make"
45     - remove MITGCM_IEEE env. variable (no longer active)
46    o pkg/shelfice
47     - improve computation of friction velocity for velocity dependent
48       exchange coefficients: include velocities into SHELFICEBoundaryLayer
49       block to average velocities vertically
50     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
51    o Modify diagonal solvers, now three versions (upon request):
52      #ifndef SOLVE_DIAGONAL_AUTODIFF
53        1. default version (dating back a while ago)
54      #else /* def SOLVE_DIAGONAL_AUTODIFF */
55      # ifdef SOLVE_DIAGONAL_KINNER
56        2. adjoinable version with k-innermost loop (G. Forget)
57      # else
58        3. adjoinable vectorized version of 2.
59      # endif
60      #endif /* SOLVE_DIAGONAL_AUTODIFF */
61      All flags are currently set within routines, but could/should be moved to CPP-options.
62      Array bounds for 1. are as before, for 2.,3. cover the entire domain
63      (could be changed for 1. too).
64    o verification/lab_sea (fwd):
65      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
66        use 7 categories (except hb87), new solve4temp params (except salt_plume),
67        constant salinity (=4) or variable salinity (salt_plume) done through
68        SItracer.
69    o pkg/seaice:
70      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
71      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
72         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
73        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
74        SEAICE_freeze got retired) but already better than previously with
75        SEAICE_freeze=123456.7 deg.C;
76      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
77        (safer multi-threaded setting); always set SEAICEuseEVP;
78      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
79        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
80        stop if multiple specifications for the same coeff; make sure default
81        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
82    o pkg/obcs:
83      - allow to switch to upwind 1rst order advection scheme for the advective
84        flux computation at the open-boundary; disabled for adjoint built.
85    o pkg/ptracers:
86      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
87      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
88      - add parameter to decide when to start a tracer; use internal flag to
89        know which tracer to step-forward; switch this internal flag at the top
90        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
91        for adjoint built.
92    o pkg/seaice:
93      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
94      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
95      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
96    o pkg/ecco:
97      - fix writing of output file DiagnosCost_ClimSalt/Theta
98        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
99    o pkg/seaice:
100      - add missing initialisation of COR_ICE array in dynsolver.F
101      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
102        compiled either way, and is tested in all exps (multidim was only tested
103        in lab_sea ad before).
104      - cosmetic change to prepare for future addition of ITD. no change to results.
105        no defaults change.
106      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
107      - by lack of adequate verification experiments, I further used custom versions
108        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
109        should be correct.
110      - avoid recomputations in ad.
111    o array initialisation in adjoint mode:
112      1) pkg/mom_common/mom_calc_ke.F:
113        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
114        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
115        part this initialisation is gone, resulting in Floating Point Exception
116        (caught by open64 compiler with debug option).
117      2) model/src/convective_weights.F
118        set output convectCount over the full array range (instead of doing
119        an update): this fix a similar issue when called within recomputation (adjoint)
120        which could by-pass the initialisation (normally done in the caller S/R).
121    o pkg/seaice:
122      - final version of turbulent flux params, as agreed at MIT ice meet:
123           SEAICE_mcPheePiston (default is ~ 0.000875)
124           SEAICE_mcPheeTaper (default is 0.)
125           SEAICE_frazilFrac (defualt is 1.)
126           SEAICE_mcPheeStepFunc (default is false)
127      - changes results at trunction error level
128      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
129    o added pkg/frazil:
130      - see frazil_description.tex for details
131      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
132    o pkg/shelfice/shelfice_thermodynamics.F
133      - fix exponents for velocity dependent exchange coefficients: change
134        from 2/3(=0) to 0.66666666666666667
135      - move computation of velocity dependent exchange coefficients into
136        separate loop, so that it applies to both thermodynamics
137      - move some divisions by constants out of loops
138    
139    checkpoint63j (2012/02/16)
140    o pkg/seaice:
141      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
142      - SItracer:  added run time params, and allow coupling to ocn salinity.
143    o pkg/seaice: remove (almost) all divisions by constants within loops
144      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
145      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
146      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
147      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
148    o pkg/seaice :
149      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
150        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
151      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
152      - add permanent SItflux diag that corresponds to TFLUX but includes
153        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
154      - allow activation/testing of a fix for suspected missing term in
155        ocn-ice heat budget (to be confirmed). To test this, you want to
156        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
157        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
158      - no change in results, fwd or ad.
159    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
160      - switch to variable freezing point.
161           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
162      - bug fix : the sublimation term that was missing is now activated.
163           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
164      - bug fix : flooding sign term for SIsal0.NE.0.
165           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
166    o pkg/seaice:
167      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
168        is now the default, and the old default constant freezing point is recovered
169        with SEAICE_tempFrz0    = -1.96,
170             SEAICE_dTempFrz_dS = 0.,
171      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
172      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
173      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
174        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
175      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
176        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
177      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
178        seaice_growth r149 for legacy branch (no results change).
179      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
180        from I. Fenty).
181      - results did not change except for global_ocean.cs32x15, mostly due to the
182        switch to variable freezing point (see above item for detail).
183    o pkg/thsice:
184      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
185        seawater freezing in thsice_calc_thickn (not used).
186    o pkg/seaice: turbulent flux term specification via run time params.
187      - replace CPP switches with run time switches to facilitate testing
188      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
189                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
190      - added runtime parameter : SEAICEturbFluxFormula
191      - move Mcphee constants to SEAICE_PARAMS.h
192      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
193                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
194                 remove seaice_summary call (moved to seaice_init_fixed)
195      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
196        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
197      - seaice_summary.F : add missing report of read turbulent flux term set up
198                           and SITRACER.
199      - seaice_check.F : check range; inform and stop if retired CPPs are used
200                         (incl. SEAICE_AGE).
201      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
202             CPP switch, same computation as before for the different options.
203      - change results at the truncation level.
204    o pkg/seaice:
205      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
206        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
207        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
208      - update verification/*/input*/data.seaice:
209        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
210        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
211        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
212        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
213    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
214      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
215        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
216        difference in results only due to machine truncation.
217      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
218        MaykutPolySatVap; keep MIN_LWDOWN.
219      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
220      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
221        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
222    o pkg/salt_plume:
223      - isolate saltPlumeFlux array exch into a specific S/R called from
224        do_oceanic_phys.F
225      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
226    o verification:
227      - move untested set-up to MITgcm_contrib/verification_other.
228    o pkg/seaice:
229      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
230    o pkg/seaice:
231      - seaice_solve4temp.F (keeping results unchanged):
232        * add 2 future run-time params to select which saturation vapor pressure
233          formula is used and how post-iteration fluxes are set.
234          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
235        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
236          the linearized expression to stay consistent with tsurf finding.
237      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
238        can be < 0.
239    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
240      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
241        conductive heat flux F_c , and add it explicitly when updating tsurf as
242        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
243        so that now F_ia has a consistent meaning through the entire routine.
244        This causes differences at truncation level: update output of fwd exp.
245        global_ocean.cs32x15.seaice.
246    o pkg/seaice:
247      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
248        of arrays, sign/direction of fluxes; no effect on results.
249      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
250        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
251        note: this should have been done before changing celsius2K default.
252      - to keep results unchanged, add back old value of celsius2K in verification
253        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
254      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
255        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
256        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
257        freezing temp is consistent with value in seaice_growth.F ; this causes
258        differences at machine truncation level: update lab_sea AD output (3/4).
259    o pkg/seaice:
260      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
261        and climsst/sss even when using seaice (to prevent calculation that might
262        use SST on land); does not affect any verification exp.
263      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
264        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
265    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
266      over land (non-legacy code)
267    o vectorize salt_plume package:
268      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
269      - this code computes plumebk everywhere (also over land), thus requires
270        code to avoid divisions by zero and catch the case of kLev=Nr.
271      - efficiency of salt_plume_frac is still sub-optimal
272    o tools (genmake2):
273      - fix makefile NAME specification (option: -makefile NAME) by adding
274        "-f $MAKEFILE" in few places where it was missing including makedepend
275        command (contribution from Paul).
276    
277    checkpoint63i (2012/01/24)
278    o model/src:
279      - add factorized versions of some EOS code to find_rho.F,
280        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
281    o model/src:
282      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
283      - change default celsius2K from 273.16 to 273.15
284      - to keep results unchanged, add back old value of celsius2K in verification
285        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
286         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
287    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
288      to make TAF generate vectorizable code
289    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
290       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
291       have flags that do this more efficiently.
292    o pkg/diagnostics/diagstats_calc.F
293      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
294    o pkg/obcs (with exch2):
295      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
296        and remove code (in obcs_readparms.F) which was based on EXCH of indices
297        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
298    o pkg/exf and seaice exp:
299      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
300        so that switching off area & heff advection flags does not affect results.
301      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
302      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
303        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
304        results of verification experiments: 1D_ocean_ice_column(fwd),
305        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
306        and offline_exf_seaice (all 4).
307    o pkg/seaice:
308      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
309        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
310      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
311        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
312        not multi-dim advection;
313      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
314        SHORTWAVE_HEATING #undef.
315    o optim: make Makefile more robust (?)
316    o pkg/obcs:
317      * fix treatment of obcs_read_pickup for TAF
318    o pkg/shelfice:
319      * add missing initialisation of num_shifwflx
320      * new adjoint verification exp. for isomip
321      * change Prandtl and Schmidt numbers from generic formulations
322        (in terms of model diffus. and visc.) to separate runtime
323        parameters, with Holland and Jenkins (1999) default values.
324    o pkg/exf (interpolation):
325      - extended input field (2 rows) near the N & S poles:
326        * fill in with the symetric value (when even Nb of data in longitude)
327        * add average value at the poles only for scalar quantities ; for vector
328          component interpolation, skip the averaging and keep duplicated values,
329          unless the 2 components have same location (uvInterp=T) in which case
330          interpolate the 2 components together using S/R EXF_INTERP_UV.
331      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
332        together: this allows to account properly for local orientation when
333        averaging at N & S pole.
334      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
335        exf-interpolation near N & S poles. Undef by default.
336      - add debug check/print on 1rst iter if debugLevel >=2.
337    o pkg/exf:
338      - change masking flags definition (no longer "parameter"), put them in
339        common block and set them in S/R EXF_INIT_FIXED.
340      - change recognized masking flag from s,u,v to c,w,s since the mask
341        to use (maskC,W,S) depends on position on model grid and has little to
342        do with scalar/vector difference; fix masking if using P-coordinates.
343      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
344        and update results of exp. global_with_exf (x2).
345      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
346    o pkg/obcs
347      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
348    o pkg/exf (interpolation):
349      - assume periodicity in X only if input field cover full longitude range.
350      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
351        and should vectorise).
352      - fix input lat of the 2 added row (in case we provide N.pole data).
353    
354    checkpoint63h (2011/12/30)
355    o pkg/seaice:
356      - change declaration of UVM from _RL to _RS in order to get B-grid
357        uIce,vIce monitor when _RS = real*4
358    o pkg/offline:
359      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
360      - compute vertical velocity if not read from file (switch on exactConserv
361        & staggerTimeStep);
362      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
363    o verification:
364      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
365        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
366        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
367      - update output of exp. global_ocean.cs32x15.viscA4 after changing
368        grid-file angles (used here for coriolis-3d);
369      - remove (or gzip) few files not needed to run fizhi-cs experiments.
370    o pkg/exf (vector interpolation):
371      - rotate vector component toward local grid-axis orientation using grid-angles
372        (stored in GRID.h) instead of locally computed rotation angle; keep old code
373        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
374    o pkg/seaice:
375      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
376        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
377    o pkg/PKG_OPTIONS.h files:
378      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
379        outside of the #ifdef ALLOW_THISPKG / #endif block.
380      - update verification/*/code/PKG_OPTIONS.h files.
381    o add a verification experiment (offline_exf_seaice/input.seaice) that test
382      the B-grid LSOR solver
383    o pkg/seaice: sort out emissivity and long wave radiation step 2:
384      - add emissivity for snow and ice as new run-time parameters
385        (unfortunately) that default to the corresponding exf values; this
386        changes results in most verification experiments so that for backward
387        compatibility these parameter have to be set explicitly to inconsistent
388        values (ugly);
389      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
390        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
391        until we agree how to handle this bug properly
392    o pkg/exf (interpolation):
393      - add a set of run-time param ({inputfield}_interpMethod), one for
394        each interpolated input field, to select the interpolation method
395        with a value of zero switching off the interpolation;
396      - print interpolation parameters to standard output;
397      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
398        (to use instead runoff_interpMethod=0 in data.exf).
399      - simplify default setting of interpolation parameters (for all fields,
400        set position to match model grid cell-center position, leading to trivial
401        interpolation in case of regular Lat-Lon grid) and fix for the case of
402        non-uniform delY.
403    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
404       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
405       this factor is absolutely required, because the lw exitance (= out-going
406       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
407       where the reflectivity rho = 1-emissivity for conservation reasons. Once
408       this is established, we can remove the CPP-Flag (if we want to).
409    o pkg/seaice:
410      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
411        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
412      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
413        what the name implies (and not emissivity*BoltzmannConstant), this means
414        the old default value of 5.5e-8 now means
415        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
416        S/R exf_readparms
417      - FV-discretization of the B-grid LSOR solver, turn on with
418        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
419        of the calling routine dynsolver, so that B and C-grid code look a
420        little more alike.
421      - fix index bugs in ostres.F (B-grid code)
422    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
423    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
424      default for SEAICE_emissivity, if useEXF; requires setting a wrong
425      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
426      backward compatiblity
427    o model/src: use sigmaR in calc_ivdc
428    
429    checkpoint63g (2011/12/16)
430    o pkg/seaice/seaice_growth.F:
431      fix heat conservation of the coupled ocean-seaice system.
432      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
433      solid vs liquid water treatment is resolved via QNET.
434    o pkg/seaice/seaice_growth.F:
435      add missing term for sublimation in saltFlux, which was breaking conservation.
436    o pkg/seaice/seaice_model.F:
437      Remove this patholigical case treatment in evolution branch,
438      where it is un-necessary and breaks conservation.
439      Update global_ocean.cs32x15/results accordingly for
440      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
441    o model/src:
442      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
443      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
444    o pkg/obcs:
445      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
446      tendency for temperature and salinity that is then applied to update
447      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
448      horizontal advection and diffusion contributions on the boundary (in
449      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
450      removing the mask in S/R timestep_tracer. The advantage of this approach is
451      that the updated tracer values include contributions from the surface
452      forcing and vertical diffusion.
453      This modification changes exp4.stevens because of vertical diffusion.
454    o model/src:
455      change non-curvilinear grid setting to also work with exch2 + blank tiles:
456      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
457        face dimensions.
458      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
459        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
460        and INI_SPHERICAL_POLAR_GRID.
461      change test-experiment global_ocean.90x40x15:
462      - split the domain in many more tiles (9x4 tiles of 10x10 each);
463      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
464      - update results of both test (std & dwnslp).
465    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
466       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
467    o model/src:
468      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
469        and fix initialisation when using sigma-coords.
470    o model/src:
471     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
472       to their current value at the beginning of forward_step.F": add a new run-time
473       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
474     - set doResetHFactors=T in the following test exp:
475        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
476        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
477        and tutorial_global_oce_in_p (nonLinFS in p)
478    o pkg/ecco
479      - added IES cost term
480    o verification/advect_xz
481      - scale down the depth by 1/100 (from 200 km to just 2.km)
482      - add secondary test using divergent flow, r-star and implicit vertical advection.
483      - add note (check_conserve_TS.txt) and matlab script to check global
484        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
485    o pkg/rbcs:
486      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
487    o pkg/obcs (Stevens BCs):
488      - fix various problems in the phase speed computations of the Stevens
489        boundary conditions:
490        - sign error for western and southern boundaries,
491        - time tendencies were underestimated by factor of dTracerLev and some just
492          zero (for multidim advection schemes) -> now estimate time tendencies
493          from difference between previous (n) time level and the one before (n-1);
494          this requires storing a field per tracer per boundary, also in the pickup
495          files.
496        - replace deltaTmom in cflMer/Zon computation with dTracerLev
497        - set default phase velocity to cflMer/Zon
498      - update verification experiment exp4.stevens
499    o pkg/generic_advdiff (implicit_r):
500      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
501        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
502      - fix implicit vertical diffusion or advection with NonLin FreeSurf
503        (was using current recip_hFacC instead of future recip_hFacC): set future
504        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
505        solver S/R ;
506      - fill diagnostics of vertical advective fluxes (computed from tendency)
507        when using implicit vert. advection;
508      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
509         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
510         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
511         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
512    o pkg/diagnostics:
513      - add diags for T & S tendency which goes through Adams-Bashforth.
514    
515    checkpoint63f (2011/11/30)
516    o pkg/obcs/obcs_calc_stevens.F:
517      - join some loops to reduce number of if-statements
518      - fix a bug in code for northern and southern boundaries.
519    o pkg/seaice/seaice_init_varia.F
520      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
521        caused zero ice-velocities for the B-grid code
522    o pkg/seaice/seaice_init_fixed.F
523      - fix a bug in the initialisation of the second metric terms
524        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
525      - this affects all seaice configurations with useCurviLinearGrid = .true.
526        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
527        = .true. (default)
528      - the only verification experiment affected is global_ocean.cs32x15:
529        icedyn, seaice, and seaice_dynmix (AD)
530    o pkg/thsice/thsice_diagnostics_state.F
531      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
532        not contain garbage that can lead to surprises in diagstats_calc.F
533    o model/src:
534      - move bi,bj loops inside INTEGR_CONTINUITY ;
535      - call INTEGR_CONTINUITY directly from forward_step.F
536        (previously called from momentum_correction_step.F)
537      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
538        forward_step.F and pkg/ecco/the_main_loop.F
539    o model/src/do_oceanic_phys.F:
540      - reset addMass to zero only if useICEFRONT ;
541      - separated k-loop for rhoInSitu calculation ;
542      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
543        and at constant T,S (= WdRHOdP);
544      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
545        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
546        transport of locally-referenced potential density);
547        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
548    o gluemnc:
549      - replace ncrcat with ncks when adding variables to *.glob.nc
550      - change the way variables without record dimensions are handled so that
551        files that have variables with and without record variables can be glued:
552        add a record dimension with a new unique name to be able to differentiate
553        between variable with and without a-prior record dimensions. Remove
554        this record dimension before adding the variable to the *.glob.nc file.
555        This procedure automatically works also for grid.*.nc files that do not
556        have any record dimension.
557    o verification/cpl_aim+ocn:
558      - generate new reference output on baudelaire (gfortran, mpich2) (previously
559        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
560    o pkg/obcs/obcs_calc_stevens.F:
561      - add code for northern and southern boundaries.
562      - reorder some loops to save some operations and so that drFBar can be scalar
563    o model/src:
564      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
565        truncation) and add diagnostics for Adams-Bashforth tendency increment.
566      - update test-exp. AD output:
567        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
568      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
569        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
570        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
571        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
572        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
573        tutorial_plume_on_slope.
574    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
575      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
576      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
577      does not even come with an F77 compiler anymore, this should not be
578      a limitation
579    
580    checkpoint63e (2011/11/06)
581    o pkg/seaice adjoint of LSR:
582      - substantially rework STORE dirs.
583      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
584        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
585        and only perform SOLV_MAX_FIXED adjoint iters.
586        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
587        always goes to same record, meaning that the last forward field will be
588        the one used in the adjoint - an approximation.
589      - now produces non-zero LSR-related gradients, and acceptable gradients for
590        An's zonal (x-z) test case (to be checked in)
591      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
592        (but these are screwed up by the thermodynamics in the first place);
593        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
594        output_adm.txt also reflects changes to seaice_lsr
595      - global_ocean.cs32x15:
596        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
597          (output_adm.seaice.txt was updated)
598        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
599          (output_adm.seaice_dynmix.txt)
600    o test-exp. exp4+stevens:
601      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
602    o pkg/seaice (lsr solver):
603      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
604        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
605      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
606      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
607        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
608      - compute (with new S/R) and print initial (+ free-driff sol. if available)
609        and final residual of linearised system.
610    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
611      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
612    o pkg/obcs: Stevens BCs (still only for east and west)
613      - fix Stevens BCs by using intermediate velocities of previous
614        time step as "baroclinic" contribution rather velocity of one grid cell
615        inside the boundaries; more consistent but makes the entire treatment
616        more complicated, requires new pickup files and two new S/Rs:
617        obcs_copy_uv_n and obcs_save_uv_n
618        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
619        (undefined by default)
620      - silently move computation of some grid factors into separate loops to
621        save some recomputations
622      - add a hack for non-linear free surface
623      - add a verification experiment to exp4 that tests this code
624    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
625    
626    checkpoint63d (2011/10/25)
627    o pkg/obcs + seaice-dynamics:
628      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
629        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
630        values (consistent with an implicit method).
631      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
632        return to older implementation (same results as before); note that none of
633        the "experimental" OBCS_SEAICE options are implemented in the new version.
634      - switch test exp. seaice_obcs to use new version (update output).
635    o pkg/seaice:
636      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
637      - add parenthesis in Water-Ice drag calculations (evp & lsr);
638      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
639        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
640      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
641        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
642    o pkg/layers:
643      - Include potential density as new coordinate (Thanks to David Munday)
644    o pkg/dic:
645      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
646        carbonate computation/output to CALC_PCO2_APPROX
647    o pkg/generic_advdiff
648      - make TAF generate code that vectorizes:
649        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
650    o model/src:
651      - improve vectorization also for adjoint code of
652        solve_tridiagonal and solve_pentadiagonal. As this requires up to
653        5 new 3D-fields, this code is only turned on for the combination of
654        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
655        for singular matrix check (only for TARGET_NEC_SX).
656      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
657        ALLOW_AUTODIFF. This flag now needs to be set outside of
658        solve_tri/pentadiagonal.F
659    o pkg/exf:
660      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
661        optional namelist EXF_NML_OBCS).
662      - add many debug-print (to trace down where pkg/cal error msg comes from)
663    o pkg/mom_vecinv/mom_vi_hdissip.F
664      - rearrange loops so that vectorization is improved and in particular
665        the adjoint routine vectorizes. The code is a little longer now, but I
666        think easier to read.
667        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
668    o pkg/seaice:
669      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
670    o pkg/exch2:
671      - alternative code (without tile x tile matrix) for cumulated (global) sum;
672        used as default; keep using matrix version in adjustment.cs-32x32x1.
673    o tools/build_options:
674      - after merging some MPI and/or multi-threads specific optfiles so that
675        the modified default optfile support both built (using genmake2 -mpi
676        for the MPI built, using genmake2 -omp for OpenMP built),
677        move now obsolete optfiles to tools/build_options/unsupported/
678       (add copy of email sent to support list in doc/optfiles_changes.txt)
679    
680    checkpoint63c (2011/09/28)
681    o pkg/ebm:
682      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
683        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
684    o pkg/seaice (SItracer pickup)
685    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
686      To be done:
687      - thorough testing of missing fields in S/R seaice_read_pickup
688      - thorough matching between generic tracers and specific fields used
689        (e.g. volume-weighted age, area-weighted age, salinity, ...)
690    o pkg/grdchk:
691      - all procs calculate and print finite-difference gradient (for testreport)
692      - change description output used by testreport;
693      - AD testing: also compare and report Finite-difference gradient;
694        => update all output_adm*.txt
695    o test exp. global_ocean_ebm:
696      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
697        and turn on exactConserve; update (fwd) output.
698    o pkg/seaice (LSR):
699      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
700      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
701        * identical results with non-CS topology (but save up to half of EXCH calls)
702        * no much changes in cs-32 verification tests since no ice at face edges
703         (differences due to convergence criteria, since nb of iterations changed)
704        * expect some differences on lat-lon-cap grid.
705        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
706    o pkg/exch2:
707      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
708        many tiles); until alternative coding is added, just add a stop.
709    o pkg/kpp:
710      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
711        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
712    o optfiles:
713      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
714        into corresponding standard one, which now support different build:
715        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
716      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
717    o pkg/obcs (seaice):
718      - add missing EXCH for uIce,vIce after applying OBCS;
719      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
720        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
721        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
722      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
723      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
724        and eedata.mth for MPI and mutlti-threaded testing.
725    o pkg/flt:
726      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
727      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
728      - fix pickup and trajectories + profiles output with multi-threads;
729      - add parameter to select group of fields to write along trajectory and
730        profile (default unchanged);
731      - only call PORT_RAND* function when flt_noise <> 0;
732      - add multi-threaded test for verification exp. flt_example.
733    o eesupp/src:
734      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
735      - USE_OMP_THREADING: check that number of threads (from eedata) matches
736        actual number (from env.var. setting).
737    o pkg/ebm:
738      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
739      - add multi-threaded test for verification exp. global_ocean_ebm
740    
741    checkpoint63b (2011/08/29)
742    o pkg/ebm:
743      - fix sign of runoff;
744      - update directly forcing fields (Qnet,EmPmR) to use standard
745        external_forcing_surf.F (remove ebm_forcing_surf.F);
746      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
747      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
748        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
749      - update global_ocean_ebm parameters file data and update output (fwd+ad).
750    o verification/matrix_example:
751      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
752        MPI and mutlti-threaded testing.
753    o pkg/matrix:
754      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
755      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
756      - fix for multi-threaded (remove DATA statement);
757      - use standard DIFFERENT_MULTIPLE function;
758      - add MATRIX_OPTIONS.h
759    o verification/matrix_example:
760       To allow to split the domain in several tiles, change the domain size
761        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
762        Western side) of land points.
763    o (*_)write_pickup:
764      - fix few bugs in mypackage_read/write_pickup.F
765      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
766        array of length 1 (was caught by compiler syntax-check).
767    o pkg/diagnostics (velocity potential solver):
768      - fix initialisation of main diagonal matrix (for overlap values)
769    o tools/build_options:
770      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
771        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
772      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
773        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
774        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
775        and use "-devel" testreport option for standard testing on baudelaire.
776    o pkg/grdchk:
777      - Assume that all gradient-check position are within the same tile
778        corresponding to global indices (iGloTile,jGloTile) and that
779        positions (i,j indices or nbeg) are local to this tile;
780      - set tile local-indices and proc. number according to tile global-indices;
781      - remove grdchkwhichproc from namelist (retired param);
782      - send adjoint gradient to all procs so that all procs print it to STDOUT;
783      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
784    o adding package bbl (Bottom Boundary Layer)
785      description in MITgcm/pkg/bbl/bbl_description.tex
786      example/test experiment in MITgcm_contrib/bbl
787    o adjoint verifications
788      - changed 5 experiments to multi-tiles
789        * global_ocean.90x40x15
790        * obcs_ctrl
791        * offline_exf_seaice
792        * tutorial_dic_adjoffline
793        * tutorial_tracer_adjsens
794        changed reference output for those that crossed tile boundaries
795        (changed choices of gradient check positions)
796      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
797      - temporary bug fix in grdchk_loc.F for obcs
798    o genmake2 & testreport
799      - add target "obj" (just for OBJFILES files) to Makefile;
800      - add option to specify FEXTRAFLAGS on command line.
801    o pkg/mypackage:
802      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
803    
804    checkpoint63a (2011/08/02)
805    o pkg/diagnostics (velocity potential):
806      - fix velocity-potential calculation when using OBCS: balance net inflow
807        at each level (new S/R OBCS_DIAG_BALANCE).
808      - fix some of the problems with OBCS in stream-function calculation.
809    o pkg/exf/exf_readparms.F
810      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
811        EXF_NML_OBCS) more consistent, so that you need not have these lists
812        in data.exf when they are not used.
813    o optim/optim_readdata.F:
814      - add some output about obcs variables that might help debugging
815      - add a check about nvarlength
816    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
817    o pkg/diagnostics (velocity potential):
818      - fix mask for OBCS (still problems in stream-function with OBCS);
819      - add specific parameter (default = main code CG2D params) for solver;
820      - in case of poor convergence, use solution corresponding to lowest residual.
821    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
822      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
823      and should be avoided where possible.
824    o model/src (rStar):
825      - include r* effect on reference-state (PhiRef) in totPhiHyd
826        (so that it's really the potential anomaly at the cell center);
827        affect solution only if z* with full pressure in EOS.
828      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
829        update output (because of z* in totPhiHyd and viscA4 changes);
830      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
831        @ constant r) until interpolation at constant r is implemented.
832    o pkg/diagnostics
833      - fix RCENTER diagnostics in case cell center is not at interface middle
834    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
835      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
836      that THETA and SALT are "conservative temperature" and "absolute
837      salinity"
838    o pkg/ctrl
839      - fix computation of endrec in s/r ctrl_init_rec
840      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
841    o pkg/seaice/seaice_growth.F
842      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
843        remove then obsolete STORE directives
844      - fix STORE directives for tice and tices, so that only the
845        appropriate part of the fields are stored (and not the entire
846        field); update global_ocean.cs32x15.seaice AD output.
847      - cosmetic changes: adjust CPP flags and indentation for better
848        legibilty
849    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
850      Chris Wilson)
851    o pkg/gmredi:
852       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
853       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
854    
855    checkpoint63  (2011/07/11)
856    o pkg/exch2:
857     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
858     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
859       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
860       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
861    o pkg/diagnostics:
862     - deal with pairs of post-processed diags which are computed together; in
863       particular, re-order list of diags within 1 file to save 2nd computation.
864     - add S/R to compute velocity stream-function (called after velocity-potential
865       calculation) from divergence free transport -> new diagnostics "PsiVEL".
866     - add parameter to select grid-point location where PsiVEL == 0.
867    o eesupp/src:
868       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
869       (specific S/R needed with exch2 topology - for now, just print an error msg)
870    o pkg/shelfice
871     - Implement friction velocity-dependent transfer coefficients following
872       Holland and Jenkins, JPO, 1999
873       Original code by M. Losch with small modifs.
874       Enable with CPP option SHI_ALLOW_GAMMAFRICT
875       and runtime flag SHELFICEuseGammaFrict
876    o verification lab_sea & global_ocean.cs32x15:
877     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
878       does not miss some dependencies (but is slower) and also works with many files
879       (default makedepend limitation for AD built).
880     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
881    o pkg/diagnostics:
882     - add run-time parameter "useMissingValue" (def=False) to fill land-point
883        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
884       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
885     - Extend the use of "missing_value" setting from data.diagnostics for the case
886       of counter-diagnostics (where fraction-weight is zero). This applies both to
887       MNC and MDS output files.
888    o pkg/seaice/seaice_growth.F:
889      - add 'a priori' cap of latent heat flux based on actual mass considerations
890        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
891        non-legacy seaice_solve4temp.
892      - add diagnostic of the residual sublimation freshwater flux (the freshwater
893        flux taken from the ocean if the total actual latent heat fluxes exceed
894        the maximum)
895      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
896       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
897      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
898       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
899      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
900      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
901    o verification 1D_ocean_ice_column:
902       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
903       update results
904  o pkg/diagnostics:  o pkg/diagnostics:
905   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
906     which are not filled-up but computed from other diags ; In this case, the mate     which are not filled-up but computed from other diags ; In this case, the mate
907     diag points to the primary (filled-up) diag to used for post processing.     diag points to the primary (filled-up) diag to used for post processing.
908   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
909     ==> Change the ordering of fields and time-periods in MDS output file
910       when using periodic averaging: now writes one time record with the full set
911       of fields for this time period, then the next time reccord (it used to be
912       one field with the full set of time records then the next field).
913         Note: this is now similar to NetCDF (MNC) output file. <==
914    
915  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
916  o adjoint monitor:  o adjoint monitor:
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