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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1634 by heimbach, Fri Mar 23 15:05:31 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 verification/lab_sea
8      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
9      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
10      * nTimeSteps 3 -> 4
11      * changed reference output accordingly
12    o pkg/ctrl:
13      * fix ctrl_get_gen for xx_sst, xx_sss
14    o pkg/fizhi:
15      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
16        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
17      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
18        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
19        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
20    o pkg/gmredi:
21      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
22    o pkg/fizhi:
23      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
24        (old)aces open64 tuv test.
25    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
26    o pkg/mom_vecinv:
27      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
28        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
29        with non-lin free-surf).
30    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
31      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
32      some compilers (gfortran 4.6.0 on MacOS)
33    o momentum:
34      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
35        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
36        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
37    
38    checkpoint63k (2012/03/17)
39    o model/src:
40       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
41         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
42       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
43         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
44    o model/src: solve_*diagonal.F
45       - replace division with multiplication by inverse (similar to original version)
46         update output of AD exp. global_ocean.90x40x15.
47       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
48         to enable the use of the vectorized & differentiable solve_tridiagonal.F
49       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
50         vertical advection (to get solve_tridiagonal tested in AD mode).
51    o pkg/seaice: ECCO-CLIVAR merge:
52      1. seaice AREA relaxation
53         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
54         * runtime flag: SEAICE_tauAreaObsRelax
55      2. modified global mean cost imbalance code: CPP option
56          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
57    o another iteration on solve_*diagonal.F
58       Make choices independent of AUTODIFF
59       Default will be the adjoinable vectorized version.
60       Alternative choices are:
61       * non-adjoinable original version with low memory footprint:
62         #define SOLVE_DIAGONAL_LOWMEMORY
63       * still adjoinable but does not vectorize (k as inner-most loop):
64         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
65    o testreport
66     - add option to use a home made wrapper around "make"
67     - remove MITGCM_IEEE env. variable (no longer active)
68    o pkg/shelfice
69     - improve computation of friction velocity for velocity dependent
70       exchange coefficients: include velocities into SHELFICEBoundaryLayer
71       block to average velocities vertically
72     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
73    o Modify diagonal solvers, now three versions (upon request):
74      #ifndef SOLVE_DIAGONAL_AUTODIFF
75        1. default version (dating back a while ago)
76      #else /* def SOLVE_DIAGONAL_AUTODIFF */
77      # ifdef SOLVE_DIAGONAL_KINNER
78        2. adjoinable version with k-innermost loop (G. Forget)
79      # else
80        3. adjoinable vectorized version of 2.
81      # endif
82      #endif /* SOLVE_DIAGONAL_AUTODIFF */
83      All flags are currently set within routines, but could/should be moved to CPP-options.
84      Array bounds for 1. are as before, for 2.,3. cover the entire domain
85      (could be changed for 1. too).
86    o verification/lab_sea (fwd):
87      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
88        use 7 categories (except hb87), new solve4temp params (except salt_plume),
89        constant salinity (=4) or variable salinity (salt_plume) done through
90        SItracer.
91    o pkg/seaice:
92      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
93      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
94         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
95        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
96        SEAICE_freeze got retired) but already better than previously with
97        SEAICE_freeze=123456.7 deg.C;
98      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
99        (safer multi-threaded setting); always set SEAICEuseEVP;
100      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
101        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
102        stop if multiple specifications for the same coeff; make sure default
103        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
104    o pkg/obcs:
105      - allow to switch to upwind 1rst order advection scheme for the advective
106        flux computation at the open-boundary; disabled for adjoint built.
107    o pkg/ptracers:
108      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
109      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
110      - add parameter to decide when to start a tracer; use internal flag to
111        know which tracer to step-forward; switch this internal flag at the top
112        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
113        for adjoint built.
114    o pkg/seaice:
115      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
116      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
117      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
118    o pkg/ecco:
119      - fix writing of output file DiagnosCost_ClimSalt/Theta
120        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
121    o pkg/seaice:
122      - add missing initialisation of COR_ICE array in dynsolver.F
123      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
124        compiled either way, and is tested in all exps (multidim was only tested
125        in lab_sea ad before).
126      - cosmetic change to prepare for future addition of ITD. no change to results.
127        no defaults change.
128      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
129      - by lack of adequate verification experiments, I further used custom versions
130        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
131        should be correct.
132      - avoid recomputations in ad.
133    o array initialisation in adjoint mode:
134      1) pkg/mom_common/mom_calc_ke.F:
135        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
136        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
137        part this initialisation is gone, resulting in Floating Point Exception
138        (caught by open64 compiler with debug option).
139      2) model/src/convective_weights.F
140        set output convectCount over the full array range (instead of doing
141        an update): this fix a similar issue when called within recomputation (adjoint)
142        which could by-pass the initialisation (normally done in the caller S/R).
143    o pkg/seaice:
144      - final version of turbulent flux params, as agreed at MIT ice meet:
145           SEAICE_mcPheePiston (default is ~ 0.000875)
146           SEAICE_mcPheeTaper (default is 0.)
147           SEAICE_frazilFrac (defualt is 1.)
148           SEAICE_mcPheeStepFunc (default is false)
149      - changes results at trunction error level
150      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
151    o added pkg/frazil:
152      - see frazil_description.tex for details
153      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
154    o pkg/shelfice/shelfice_thermodynamics.F
155      - fix exponents for velocity dependent exchange coefficients: change
156        from 2/3(=0) to 0.66666666666666667
157      - move computation of velocity dependent exchange coefficients into
158        separate loop, so that it applies to both thermodynamics
159      - move some divisions by constants out of loops
160    
161    checkpoint63j (2012/02/16)
162    o pkg/seaice:
163      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
164      - SItracer:  added run time params, and allow coupling to ocn salinity.
165    o pkg/seaice: remove (almost) all divisions by constants within loops
166      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
167      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
168      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
169      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
170    o pkg/seaice :
171      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
172        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
173      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
174      - add permanent SItflux diag that corresponds to TFLUX but includes
175        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
176      - allow activation/testing of a fix for suspected missing term in
177        ocn-ice heat budget (to be confirmed). To test this, you want to
178        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
179        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
180      - no change in results, fwd or ad.
181    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
182      - switch to variable freezing point.
183           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
184      - bug fix : the sublimation term that was missing is now activated.
185           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
186      - bug fix : flooding sign term for SIsal0.NE.0.
187           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
188    o pkg/seaice:
189      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
190        is now the default, and the old default constant freezing point is recovered
191        with SEAICE_tempFrz0    = -1.96,
192             SEAICE_dTempFrz_dS = 0.,
193      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
194      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
195      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
196        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
197      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
198        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
199      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
200        seaice_growth r149 for legacy branch (no results change).
201      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
202        from I. Fenty).
203      - results did not change except for global_ocean.cs32x15, mostly due to the
204        switch to variable freezing point (see above item for detail).
205    o pkg/thsice:
206      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
207        seawater freezing in thsice_calc_thickn (not used).
208    o pkg/seaice: turbulent flux term specification via run time params.
209      - replace CPP switches with run time switches to facilitate testing
210      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
211                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
212      - added runtime parameter : SEAICEturbFluxFormula
213      - move Mcphee constants to SEAICE_PARAMS.h
214      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
215                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
216                 remove seaice_summary call (moved to seaice_init_fixed)
217      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
218        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
219      - seaice_summary.F : add missing report of read turbulent flux term set up
220                           and SITRACER.
221      - seaice_check.F : check range; inform and stop if retired CPPs are used
222                         (incl. SEAICE_AGE).
223      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
224             CPP switch, same computation as before for the different options.
225      - change results at the truncation level.
226    o pkg/seaice:
227      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
228        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
229        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
230      - update verification/*/input*/data.seaice:
231        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
232        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
233        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
234        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
235    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
236      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
237        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
238        difference in results only due to machine truncation.
239      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
240        MaykutPolySatVap; keep MIN_LWDOWN.
241      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
242      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
243        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
244    o pkg/salt_plume:
245      - isolate saltPlumeFlux array exch into a specific S/R called from
246        do_oceanic_phys.F
247      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
248    o verification:
249      - move untested set-up to MITgcm_contrib/verification_other.
250    o pkg/seaice:
251      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
252    o pkg/seaice:
253      - seaice_solve4temp.F (keeping results unchanged):
254        * add 2 future run-time params to select which saturation vapor pressure
255          formula is used and how post-iteration fluxes are set.
256          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
257        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
258          the linearized expression to stay consistent with tsurf finding.
259      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
260        can be < 0.
261    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
262      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
263        conductive heat flux F_c , and add it explicitly when updating tsurf as
264        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
265        so that now F_ia has a consistent meaning through the entire routine.
266        This causes differences at truncation level: update output of fwd exp.
267        global_ocean.cs32x15.seaice.
268    o pkg/seaice:
269      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
270        of arrays, sign/direction of fluxes; no effect on results.
271      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
272        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
273        note: this should have been done before changing celsius2K default.
274      - to keep results unchanged, add back old value of celsius2K in verification
275        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
276      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
277        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
278        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
279        freezing temp is consistent with value in seaice_growth.F ; this causes
280        differences at machine truncation level: update lab_sea AD output (3/4).
281    o pkg/seaice:
282      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
283        and climsst/sss even when using seaice (to prevent calculation that might
284        use SST on land); does not affect any verification exp.
285      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
286        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
287    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
288      over land (non-legacy code)
289    o vectorize salt_plume package:
290      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
291      - this code computes plumebk everywhere (also over land), thus requires
292        code to avoid divisions by zero and catch the case of kLev=Nr.
293      - efficiency of salt_plume_frac is still sub-optimal
294    o tools (genmake2):
295      - fix makefile NAME specification (option: -makefile NAME) by adding
296        "-f $MAKEFILE" in few places where it was missing including makedepend
297        command (contribution from Paul).
298    
299    checkpoint63i (2012/01/24)
300    o model/src:
301      - add factorized versions of some EOS code to find_rho.F,
302        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
303    o model/src:
304      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
305      - change default celsius2K from 273.16 to 273.15
306      - to keep results unchanged, add back old value of celsius2K in verification
307        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
308         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
309    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
310      to make TAF generate vectorizable code
311    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
312       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
313       have flags that do this more efficiently.
314    o pkg/diagnostics/diagstats_calc.F
315      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
316    o pkg/obcs (with exch2):
317      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
318        and remove code (in obcs_readparms.F) which was based on EXCH of indices
319        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
320    o pkg/exf and seaice exp:
321      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
322        so that switching off area & heff advection flags does not affect results.
323      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
324      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
325        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
326        results of verification experiments: 1D_ocean_ice_column(fwd),
327        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
328        and offline_exf_seaice (all 4).
329    o pkg/seaice:
330      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
331        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
332      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
333        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
334        not multi-dim advection;
335      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
336        SHORTWAVE_HEATING #undef.
337    o optim: make Makefile more robust (?)
338    o pkg/obcs:
339      * fix treatment of obcs_read_pickup for TAF
340    o pkg/shelfice:
341      * add missing initialisation of num_shifwflx
342      * new adjoint verification exp. for isomip
343      * change Prandtl and Schmidt numbers from generic formulations
344        (in terms of model diffus. and visc.) to separate runtime
345        parameters, with Holland and Jenkins (1999) default values.
346    o pkg/exf (interpolation):
347      - extended input field (2 rows) near the N & S poles:
348        * fill in with the symetric value (when even Nb of data in longitude)
349        * add average value at the poles only for scalar quantities ; for vector
350          component interpolation, skip the averaging and keep duplicated values,
351          unless the 2 components have same location (uvInterp=T) in which case
352          interpolate the 2 components together using S/R EXF_INTERP_UV.
353      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
354        together: this allows to account properly for local orientation when
355        averaging at N & S pole.
356      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
357        exf-interpolation near N & S poles. Undef by default.
358      - add debug check/print on 1rst iter if debugLevel >=2.
359    o pkg/exf:
360      - change masking flags definition (no longer "parameter"), put them in
361        common block and set them in S/R EXF_INIT_FIXED.
362      - change recognized masking flag from s,u,v to c,w,s since the mask
363        to use (maskC,W,S) depends on position on model grid and has little to
364        do with scalar/vector difference; fix masking if using P-coordinates.
365      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
366        and update results of exp. global_with_exf (x2).
367      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
368    o pkg/obcs
369      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
370    o pkg/exf (interpolation):
371      - assume periodicity in X only if input field cover full longitude range.
372      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
373        and should vectorise).
374      - fix input lat of the 2 added row (in case we provide N.pole data).
375    
376    checkpoint63h (2011/12/30)
377    o pkg/seaice:
378      - change declaration of UVM from _RL to _RS in order to get B-grid
379        uIce,vIce monitor when _RS = real*4
380    o pkg/offline:
381      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
382      - compute vertical velocity if not read from file (switch on exactConserv
383        & staggerTimeStep);
384      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
385    o verification:
386      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
387        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
388        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
389      - update output of exp. global_ocean.cs32x15.viscA4 after changing
390        grid-file angles (used here for coriolis-3d);
391      - remove (or gzip) few files not needed to run fizhi-cs experiments.
392    o pkg/exf (vector interpolation):
393      - rotate vector component toward local grid-axis orientation using grid-angles
394        (stored in GRID.h) instead of locally computed rotation angle; keep old code
395        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
396    o pkg/seaice:
397      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
398        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
399    o pkg/PKG_OPTIONS.h files:
400      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
401        outside of the #ifdef ALLOW_THISPKG / #endif block.
402      - update verification/*/code/PKG_OPTIONS.h files.
403    o add a verification experiment (offline_exf_seaice/input.seaice) that test
404      the B-grid LSOR solver
405    o pkg/seaice: sort out emissivity and long wave radiation step 2:
406      - add emissivity for snow and ice as new run-time parameters
407        (unfortunately) that default to the corresponding exf values; this
408        changes results in most verification experiments so that for backward
409        compatibility these parameter have to be set explicitly to inconsistent
410        values (ugly);
411      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
412        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
413        until we agree how to handle this bug properly
414    o pkg/exf (interpolation):
415      - add a set of run-time param ({inputfield}_interpMethod), one for
416        each interpolated input field, to select the interpolation method
417        with a value of zero switching off the interpolation;
418      - print interpolation parameters to standard output;
419      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
420        (to use instead runoff_interpMethod=0 in data.exf).
421      - simplify default setting of interpolation parameters (for all fields,
422        set position to match model grid cell-center position, leading to trivial
423        interpolation in case of regular Lat-Lon grid) and fix for the case of
424        non-uniform delY.
425    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
426       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
427       this factor is absolutely required, because the lw exitance (= out-going
428       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
429       where the reflectivity rho = 1-emissivity for conservation reasons. Once
430       this is established, we can remove the CPP-Flag (if we want to).
431    o pkg/seaice:
432      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
433        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
434      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
435        what the name implies (and not emissivity*BoltzmannConstant), this means
436        the old default value of 5.5e-8 now means
437        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
438        S/R exf_readparms
439      - FV-discretization of the B-grid LSOR solver, turn on with
440        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
441        of the calling routine dynsolver, so that B and C-grid code look a
442        little more alike.
443      - fix index bugs in ostres.F (B-grid code)
444    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
445    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
446      default for SEAICE_emissivity, if useEXF; requires setting a wrong
447      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
448      backward compatiblity
449    o model/src: use sigmaR in calc_ivdc
450    
451    checkpoint63g (2011/12/16)
452    o pkg/seaice/seaice_growth.F:
453      fix heat conservation of the coupled ocean-seaice system.
454      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
455      solid vs liquid water treatment is resolved via QNET.
456    o pkg/seaice/seaice_growth.F:
457      add missing term for sublimation in saltFlux, which was breaking conservation.
458    o pkg/seaice/seaice_model.F:
459      Remove this patholigical case treatment in evolution branch,
460      where it is un-necessary and breaks conservation.
461      Update global_ocean.cs32x15/results accordingly for
462      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
463    o model/src:
464      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
465      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
466    o pkg/obcs:
467      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
468      tendency for temperature and salinity that is then applied to update
469      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
470      horizontal advection and diffusion contributions on the boundary (in
471      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
472      removing the mask in S/R timestep_tracer. The advantage of this approach is
473      that the updated tracer values include contributions from the surface
474      forcing and vertical diffusion.
475      This modification changes exp4.stevens because of vertical diffusion.
476    o model/src:
477      change non-curvilinear grid setting to also work with exch2 + blank tiles:
478      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
479        face dimensions.
480      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
481        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
482        and INI_SPHERICAL_POLAR_GRID.
483      change test-experiment global_ocean.90x40x15:
484      - split the domain in many more tiles (9x4 tiles of 10x10 each);
485      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
486      - update results of both test (std & dwnslp).
487    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
488       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
489    o model/src:
490      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
491        and fix initialisation when using sigma-coords.
492    o model/src:
493     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
494       to their current value at the beginning of forward_step.F": add a new run-time
495       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
496     - set doResetHFactors=T in the following test exp:
497        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
498        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
499        and tutorial_global_oce_in_p (nonLinFS in p)
500    o pkg/ecco
501      - added IES cost term
502    o verification/advect_xz
503      - scale down the depth by 1/100 (from 200 km to just 2.km)
504      - add secondary test using divergent flow, r-star and implicit vertical advection.
505      - add note (check_conserve_TS.txt) and matlab script to check global
506        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
507    o pkg/rbcs:
508      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
509    o pkg/obcs (Stevens BCs):
510      - fix various problems in the phase speed computations of the Stevens
511        boundary conditions:
512        - sign error for western and southern boundaries,
513        - time tendencies were underestimated by factor of dTracerLev and some just
514          zero (for multidim advection schemes) -> now estimate time tendencies
515          from difference between previous (n) time level and the one before (n-1);
516          this requires storing a field per tracer per boundary, also in the pickup
517          files.
518        - replace deltaTmom in cflMer/Zon computation with dTracerLev
519        - set default phase velocity to cflMer/Zon
520      - update verification experiment exp4.stevens
521    o pkg/generic_advdiff (implicit_r):
522      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
523        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
524      - fix implicit vertical diffusion or advection with NonLin FreeSurf
525        (was using current recip_hFacC instead of future recip_hFacC): set future
526        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
527        solver S/R ;
528      - fill diagnostics of vertical advective fluxes (computed from tendency)
529        when using implicit vert. advection;
530      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
531         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
532         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
533         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
534    o pkg/diagnostics:
535      - add diags for T & S tendency which goes through Adams-Bashforth.
536    
537    checkpoint63f (2011/11/30)
538    o pkg/obcs/obcs_calc_stevens.F:
539      - join some loops to reduce number of if-statements
540      - fix a bug in code for northern and southern boundaries.
541    o pkg/seaice/seaice_init_varia.F
542      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
543        caused zero ice-velocities for the B-grid code
544    o pkg/seaice/seaice_init_fixed.F
545      - fix a bug in the initialisation of the second metric terms
546        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
547      - this affects all seaice configurations with useCurviLinearGrid = .true.
548        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
549        = .true. (default)
550      - the only verification experiment affected is global_ocean.cs32x15:
551        icedyn, seaice, and seaice_dynmix (AD)
552    o pkg/thsice/thsice_diagnostics_state.F
553      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
554        not contain garbage that can lead to surprises in diagstats_calc.F
555    o model/src:
556      - move bi,bj loops inside INTEGR_CONTINUITY ;
557      - call INTEGR_CONTINUITY directly from forward_step.F
558        (previously called from momentum_correction_step.F)
559      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
560        forward_step.F and pkg/ecco/the_main_loop.F
561    o model/src/do_oceanic_phys.F:
562      - reset addMass to zero only if useICEFRONT ;
563      - separated k-loop for rhoInSitu calculation ;
564      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
565        and at constant T,S (= WdRHOdP);
566      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
567        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
568        transport of locally-referenced potential density);
569        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
570    o gluemnc:
571      - replace ncrcat with ncks when adding variables to *.glob.nc
572      - change the way variables without record dimensions are handled so that
573        files that have variables with and without record variables can be glued:
574        add a record dimension with a new unique name to be able to differentiate
575        between variable with and without a-prior record dimensions. Remove
576        this record dimension before adding the variable to the *.glob.nc file.
577        This procedure automatically works also for grid.*.nc files that do not
578        have any record dimension.
579    o verification/cpl_aim+ocn:
580      - generate new reference output on baudelaire (gfortran, mpich2) (previously
581        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
582    o pkg/obcs/obcs_calc_stevens.F:
583      - add code for northern and southern boundaries.
584      - reorder some loops to save some operations and so that drFBar can be scalar
585    o model/src:
586      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
587        truncation) and add diagnostics for Adams-Bashforth tendency increment.
588      - update test-exp. AD output:
589        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
590      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
591        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
592        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
593        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
594        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
595        tutorial_plume_on_slope.
596    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
597      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
598      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
599      does not even come with an F77 compiler anymore, this should not be
600      a limitation
601    
602    checkpoint63e (2011/11/06)
603    o pkg/seaice adjoint of LSR:
604      - substantially rework STORE dirs.
605      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
606        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
607        and only perform SOLV_MAX_FIXED adjoint iters.
608        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
609        always goes to same record, meaning that the last forward field will be
610        the one used in the adjoint - an approximation.
611      - now produces non-zero LSR-related gradients, and acceptable gradients for
612        An's zonal (x-z) test case (to be checked in)
613      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
614        (but these are screwed up by the thermodynamics in the first place);
615        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
616        output_adm.txt also reflects changes to seaice_lsr
617      - global_ocean.cs32x15:
618        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
619          (output_adm.seaice.txt was updated)
620        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
621          (output_adm.seaice_dynmix.txt)
622    o test-exp. exp4+stevens:
623      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
624    o pkg/seaice (lsr solver):
625      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
626        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
627      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
628      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
629        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
630      - compute (with new S/R) and print initial (+ free-driff sol. if available)
631        and final residual of linearised system.
632    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
633      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
634    o pkg/obcs: Stevens BCs (still only for east and west)
635      - fix Stevens BCs by using intermediate velocities of previous
636        time step as "baroclinic" contribution rather velocity of one grid cell
637        inside the boundaries; more consistent but makes the entire treatment
638        more complicated, requires new pickup files and two new S/Rs:
639        obcs_copy_uv_n and obcs_save_uv_n
640        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
641        (undefined by default)
642      - silently move computation of some grid factors into separate loops to
643        save some recomputations
644      - add a hack for non-linear free surface
645      - add a verification experiment to exp4 that tests this code
646    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
647    
648    checkpoint63d (2011/10/25)
649    o pkg/obcs + seaice-dynamics:
650      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
651        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
652        values (consistent with an implicit method).
653      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
654        return to older implementation (same results as before); note that none of
655        the "experimental" OBCS_SEAICE options are implemented in the new version.
656      - switch test exp. seaice_obcs to use new version (update output).
657    o pkg/seaice:
658      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
659      - add parenthesis in Water-Ice drag calculations (evp & lsr);
660      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
661        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
662      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
663        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
664    o pkg/layers:
665      - Include potential density as new coordinate (Thanks to David Munday)
666    o pkg/dic:
667      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
668        carbonate computation/output to CALC_PCO2_APPROX
669    o pkg/generic_advdiff
670      - make TAF generate code that vectorizes:
671        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
672    o model/src:
673      - improve vectorization also for adjoint code of
674        solve_tridiagonal and solve_pentadiagonal. As this requires up to
675        5 new 3D-fields, this code is only turned on for the combination of
676        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
677        for singular matrix check (only for TARGET_NEC_SX).
678      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
679        ALLOW_AUTODIFF. This flag now needs to be set outside of
680        solve_tri/pentadiagonal.F
681    o pkg/exf:
682      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
683        optional namelist EXF_NML_OBCS).
684      - add many debug-print (to trace down where pkg/cal error msg comes from)
685    o pkg/mom_vecinv/mom_vi_hdissip.F
686      - rearrange loops so that vectorization is improved and in particular
687        the adjoint routine vectorizes. The code is a little longer now, but I
688        think easier to read.
689        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
690    o pkg/seaice:
691      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
692    o pkg/exch2:
693      - alternative code (without tile x tile matrix) for cumulated (global) sum;
694        used as default; keep using matrix version in adjustment.cs-32x32x1.
695    o tools/build_options:
696      - after merging some MPI and/or multi-threads specific optfiles so that
697        the modified default optfile support both built (using genmake2 -mpi
698        for the MPI built, using genmake2 -omp for OpenMP built),
699        move now obsolete optfiles to tools/build_options/unsupported/
700       (add copy of email sent to support list in doc/optfiles_changes.txt)
701    
702    checkpoint63c (2011/09/28)
703    o pkg/ebm:
704      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
705        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
706    o pkg/seaice (SItracer pickup)
707    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
708      To be done:
709      - thorough testing of missing fields in S/R seaice_read_pickup
710      - thorough matching between generic tracers and specific fields used
711        (e.g. volume-weighted age, area-weighted age, salinity, ...)
712    o pkg/grdchk:
713      - all procs calculate and print finite-difference gradient (for testreport)
714      - change description output used by testreport;
715      - AD testing: also compare and report Finite-difference gradient;
716        => update all output_adm*.txt
717    o test exp. global_ocean_ebm:
718      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
719        and turn on exactConserve; update (fwd) output.
720    o pkg/seaice (LSR):
721      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
722      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
723        * identical results with non-CS topology (but save up to half of EXCH calls)
724        * no much changes in cs-32 verification tests since no ice at face edges
725         (differences due to convergence criteria, since nb of iterations changed)
726        * expect some differences on lat-lon-cap grid.
727        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
728    o pkg/exch2:
729      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
730        many tiles); until alternative coding is added, just add a stop.
731    o pkg/kpp:
732      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
733        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
734    o optfiles:
735      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
736        into corresponding standard one, which now support different build:
737        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
738      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
739    o pkg/obcs (seaice):
740      - add missing EXCH for uIce,vIce after applying OBCS;
741      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
742        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
743        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
744      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
745      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
746        and eedata.mth for MPI and mutlti-threaded testing.
747    o pkg/flt:
748      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
749      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
750      - fix pickup and trajectories + profiles output with multi-threads;
751      - add parameter to select group of fields to write along trajectory and
752        profile (default unchanged);
753      - only call PORT_RAND* function when flt_noise <> 0;
754      - add multi-threaded test for verification exp. flt_example.
755    o eesupp/src:
756      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
757      - USE_OMP_THREADING: check that number of threads (from eedata) matches
758        actual number (from env.var. setting).
759    o pkg/ebm:
760      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
761      - add multi-threaded test for verification exp. global_ocean_ebm
762    
763    checkpoint63b (2011/08/29)
764    o pkg/ebm:
765      - fix sign of runoff;
766      - update directly forcing fields (Qnet,EmPmR) to use standard
767        external_forcing_surf.F (remove ebm_forcing_surf.F);
768      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
769      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
770        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
771      - update global_ocean_ebm parameters file data and update output (fwd+ad).
772    o verification/matrix_example:
773      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
774        MPI and mutlti-threaded testing.
775    o pkg/matrix:
776      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
777      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
778      - fix for multi-threaded (remove DATA statement);
779      - use standard DIFFERENT_MULTIPLE function;
780      - add MATRIX_OPTIONS.h
781    o verification/matrix_example:
782       To allow to split the domain in several tiles, change the domain size
783        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
784        Western side) of land points.
785    o (*_)write_pickup:
786      - fix few bugs in mypackage_read/write_pickup.F
787      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
788        array of length 1 (was caught by compiler syntax-check).
789    o pkg/diagnostics (velocity potential solver):
790      - fix initialisation of main diagonal matrix (for overlap values)
791    o tools/build_options:
792      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
793        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
794      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
795        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
796        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
797        and use "-devel" testreport option for standard testing on baudelaire.
798    o pkg/grdchk:
799      - Assume that all gradient-check position are within the same tile
800        corresponding to global indices (iGloTile,jGloTile) and that
801        positions (i,j indices or nbeg) are local to this tile;
802      - set tile local-indices and proc. number according to tile global-indices;
803      - remove grdchkwhichproc from namelist (retired param);
804      - send adjoint gradient to all procs so that all procs print it to STDOUT;
805      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
806    o adding package bbl (Bottom Boundary Layer)
807      description in MITgcm/pkg/bbl/bbl_description.tex
808      example/test experiment in MITgcm_contrib/bbl
809    o adjoint verifications
810      - changed 5 experiments to multi-tiles
811        * global_ocean.90x40x15
812        * obcs_ctrl
813        * offline_exf_seaice
814        * tutorial_dic_adjoffline
815        * tutorial_tracer_adjsens
816        changed reference output for those that crossed tile boundaries
817        (changed choices of gradient check positions)
818      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
819      - temporary bug fix in grdchk_loc.F for obcs
820    o genmake2 & testreport
821      - add target "obj" (just for OBJFILES files) to Makefile;
822      - add option to specify FEXTRAFLAGS on command line.
823    o pkg/mypackage:
824      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
825    
826    checkpoint63a (2011/08/02)
827    o pkg/diagnostics (velocity potential):
828      - fix velocity-potential calculation when using OBCS: balance net inflow
829        at each level (new S/R OBCS_DIAG_BALANCE).
830      - fix some of the problems with OBCS in stream-function calculation.
831    o pkg/exf/exf_readparms.F
832      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
833        EXF_NML_OBCS) more consistent, so that you need not have these lists
834        in data.exf when they are not used.
835    o optim/optim_readdata.F:
836      - add some output about obcs variables that might help debugging
837      - add a check about nvarlength
838    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
839    o pkg/diagnostics (velocity potential):
840      - fix mask for OBCS (still problems in stream-function with OBCS);
841      - add specific parameter (default = main code CG2D params) for solver;
842      - in case of poor convergence, use solution corresponding to lowest residual.
843    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
844      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
845      and should be avoided where possible.
846    o model/src (rStar):
847      - include r* effect on reference-state (PhiRef) in totPhiHyd
848        (so that it's really the potential anomaly at the cell center);
849        affect solution only if z* with full pressure in EOS.
850      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
851        update output (because of z* in totPhiHyd and viscA4 changes);
852      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
853        @ constant r) until interpolation at constant r is implemented.
854    o pkg/diagnostics
855      - fix RCENTER diagnostics in case cell center is not at interface middle
856    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
857      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
858      that THETA and SALT are "conservative temperature" and "absolute
859      salinity"
860    o pkg/ctrl
861      - fix computation of endrec in s/r ctrl_init_rec
862      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
863    o pkg/seaice/seaice_growth.F
864      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
865        remove then obsolete STORE directives
866      - fix STORE directives for tice and tices, so that only the
867        appropriate part of the fields are stored (and not the entire
868        field); update global_ocean.cs32x15.seaice AD output.
869      - cosmetic changes: adjust CPP flags and indentation for better
870        legibilty
871    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
872      Chris Wilson)
873    o pkg/gmredi:
874       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
875       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
876    
877    checkpoint63  (2011/07/11)
878    o pkg/exch2:
879     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
880     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
881       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
882       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
883    o pkg/diagnostics:
884     - deal with pairs of post-processed diags which are computed together; in
885       particular, re-order list of diags within 1 file to save 2nd computation.
886     - add S/R to compute velocity stream-function (called after velocity-potential
887       calculation) from divergence free transport -> new diagnostics "PsiVEL".
888     - add parameter to select grid-point location where PsiVEL == 0.
889    o eesupp/src:
890       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
891       (specific S/R needed with exch2 topology - for now, just print an error msg)
892    o pkg/shelfice
893     - Implement friction velocity-dependent transfer coefficients following
894       Holland and Jenkins, JPO, 1999
895       Original code by M. Losch with small modifs.
896       Enable with CPP option SHI_ALLOW_GAMMAFRICT
897       and runtime flag SHELFICEuseGammaFrict
898    o verification lab_sea & global_ocean.cs32x15:
899     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
900       does not miss some dependencies (but is slower) and also works with many files
901       (default makedepend limitation for AD built).
902     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
903    o pkg/diagnostics:
904     - add run-time parameter "useMissingValue" (def=False) to fill land-point
905        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
906       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
907     - Extend the use of "missing_value" setting from data.diagnostics for the case
908       of counter-diagnostics (where fraction-weight is zero). This applies both to
909       MNC and MDS output files.
910    o pkg/seaice/seaice_growth.F:
911      - add 'a priori' cap of latent heat flux based on actual mass considerations
912        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
913        non-legacy seaice_solve4temp.
914      - add diagnostic of the residual sublimation freshwater flux (the freshwater
915        flux taken from the ocean if the total actual latent heat fluxes exceed
916        the maximum)
917      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
918       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
919      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
920       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
921      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
922      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
923    o verification 1D_ocean_ice_column:
924       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
925       update results
926    o pkg/diagnostics:
927     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
928       which are not filled-up but computed from other diags ; In this case, the mate
929       diag points to the primary (filled-up) diag to used for post processing.
930     - Update Velocity-potential computation using post-processed diag framework.
931     ==> Change the ordering of fields and time-periods in MDS output file
932       when using periodic averaging: now writes one time record with the full set
933       of fields for this time period, then the next time reccord (it used to be
934       one field with the full set of time records then the next field).
935         Note: this is now similar to NetCDF (MNC) output file. <==
936    
937    checkpoint62z (2011/06/21)
938    o adjoint monitor:
939     - Add adjoint monitor output for packages exf, seaice
940       and update relevant testreport output
941    o pkg/seaice:
942     - re-order diags inits so that they appear in order in available_diagnostics.log
943     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
944       area/heff/hsnow preceeding thermodynamic growth/melt.
945     - modified diag: SIdA; output actual effect, as the description states.
946     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
947     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
948       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
949        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
950     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
951     - added diagnostics for seaice generic tracers (SItr*).
952     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
953     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
954     I. Fenty: 18-Jun-2011:
955     Minor changes to seaice package:
956     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
957        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
958       - Differentiated "regularization variables" from "floor variables"
959        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
960        * hiceMin became SEAICE_hice_reg (old hiceMin)
961          (with _reg meaning regularization variable)
962       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
963        so as to ensure energy conservation when going between phases
964      - A22 was not used anywhere
965     2) Changed regularization procedure for heffActual and hsnowActual to ensure
966        well-boundedness and smooth adjoint in seaice_growth.F
967     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
968        because the old regularization always set heffActual >= 0.05 cm
969     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
970        on AREA when HEFF > 0.
971      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
972        requiring that DISABLE_AREA_FLOOR *not* be defined
973     Affected verifications:
974      - 1D_ocean_ice_column (output.txt output_adm.txt)
975      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
976    o pkg/diagnostics:
977      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
978      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
979        (was _RL, now integer) with option = 0 to retrieve all levels.
980      - add pieces of code to compute velocity potential at each level (new diagnostics
981        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
982        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
983      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
984        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
985        and in diagnostics_fract_fill.F (do not need a valid pointer for the
986        diagnostics counter-mate); check that definition of counter-diagnostic
987        includes a valid counter-mate (in diagnostics_set_levels.F).
988    o model/src (rStar):
989      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
990        affect solution only if z* with full pressure in EOS;
991        update output of test-exp global_ocean.90x40x15.
992    o pkg/seaice:
993      - introduce siEps=1e-5 parameter
994      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
995      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
996      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
997        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
998        as well as ice cover age and ridging index (attached to AREA).
999        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1000        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1001        Up to SItrMaxNum=3 tracers can be used simultaneously.
1002    o pkg/salt_plume:
1003      -introduce SPsalFRAC run time parameter that sets the fraction of the
1004       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1005       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1006    o model debug options:
1007      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1008        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1009      - Refine debug-msg printing selection (3 new levels):
1010        debugMode  : controls printing of debug messages (sequence of S/R calls).
1011        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1012         debLevZero =  0 ; /* level of disabled aux. msg printing */
1013         debLevA =  1 ; /* level of minimum  aux. msg printing */
1014         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
1015         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
1016         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1017         debLevE =  5 ; /* level of extensive debug printing */
1018        New debugLevel default: with default debugMode value (=F),
1019          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1020          and if debugMode=T, default debugLevel = 4 (debLevD).
1021        Relation with previous settings:
1022         debLevB (=2) corresponds to former debLevA (=1)
1023         debLevD (=4) corresponds to former debLevB (=2)
1024        Note:
1025         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1026         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1027            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1028      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1029        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1030    o pkg/obcs:
1031      - change OBCSfixTopo default from True to False (should not change the results);
1032        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1033    o pkg/thsice:
1034      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1035        2nd layer seaice sublimation (unlikely to happen)
1036      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1037        done in gad_advection & seaice_advection).
1038    o adjoint:
1039      bug fix spotted by Gael Forget:
1040      seaice_advection and thsice_advection still had
1041      legacy CPP options to avoid CS corner updates for adjoint
1042    o pkg/seaice:
1043      => Change some of the defaults (2011/05/29):
1044         - change SEAICEuseFluxForm default (from False to True)
1045         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1046         And print warnings if DIFF1 is not set in data.seaice and centered
1047          avection scheme is used without any diffusion.
1048      also:
1049      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1050      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1051      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1052        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1053        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1054      update results of test exp.:
1055         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1056             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1057             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1058         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1059         seaice_obcs: output (SEAICEuseFluxForm=T)
1060      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1061          for standard fwd & AD lab_sea tests (to keep the same output).
1062    o pkg/seaice/seaice_growth.F:
1063      - use Ian Fenty's capping formulas for actual ice
1064      thickness thoughout EVOLUTION branch.
1065      - put treatment pathological case #2) in CPP brackets
1066      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1067      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1068    o pkg/seaice:
1069      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1070      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1071      also pass fac as a param, which can be 1. (to update the tendency
1072      field) or the time step (to update the field itself).
1073      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1074      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1075      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1076      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1077      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1078    o pkg/seaice:
1079      diffusion with centered advection scheme (diffus.F & advect.F):
1080      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1081        to just compute the laplacian of input-field.
1082      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1083      - fix flux-form version in diffus.F to conserve tracer.
1084      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1085       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1086    
1087    checkpoint62y (2011/05/26)
1088  o pkg/seaice:  o pkg/seaice:
1089   - seaice_growth.F : in EVOLUTION branch, always include   - seaice_growth.F : in EVOLUTION branch, always include
1090     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
1091   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
1092     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
1093  o pkg/seaice + obcs:  o pkg/seaice + obcs:
1094   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1095     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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