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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1627 by mlosch, Mon Mar 19 14:33:20 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 model/src: move k-loop outside of i/j-loops when (re-)computing R_low
8      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
9      some compilers (gfortran 4.6.0 on MacOS)
10    o momentum:
11      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
12        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
13        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
14    
15    checkpoint63k (2012/03/17)
16    o model/src:
17       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
18         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
19       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
20         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
21    o model/src: solve_*diagonal.F
22       - replace division with multiplication by inverse (similar to original version)
23         update output of AD exp. global_ocean.90x40x15.
24       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
25         to enable the use of the vectorized & differentiable solve_tridiagonal.F
26       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
27         vertical advection (to get solve_tridiagonal tested in AD mode).
28    o pkg/seaice: ECCO-CLIVAR merge:
29      1. seaice AREA relaxation
30         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
31         * runtime flag: SEAICE_tauAreaObsRelax
32      2. modified global mean cost imbalance code: CPP option
33          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
34    o another iteration on solve_*diagonal.F
35       Make choices independent of AUTODIFF
36       Default will be the adjoinable vectorized version.
37       Alternative choices are:
38       * non-adjoinable original version with low memory footprint:
39         #define SOLVE_DIAGONAL_LOWMEMORY
40       * still adjoinable but does not vectorize (k as inner-most loop):
41         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
42    o testreport
43     - add option to use a home made wrapper around "make"
44     - remove MITGCM_IEEE env. variable (no longer active)
45    o pkg/shelfice
46     - improve computation of friction velocity for velocity dependent
47       exchange coefficients: include velocities into SHELFICEBoundaryLayer
48       block to average velocities vertically
49     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
50    o Modify diagonal solvers, now three versions (upon request):
51      #ifndef SOLVE_DIAGONAL_AUTODIFF
52        1. default version (dating back a while ago)
53      #else /* def SOLVE_DIAGONAL_AUTODIFF */
54      # ifdef SOLVE_DIAGONAL_KINNER
55        2. adjoinable version with k-innermost loop (G. Forget)
56      # else
57        3. adjoinable vectorized version of 2.
58      # endif
59      #endif /* SOLVE_DIAGONAL_AUTODIFF */
60      All flags are currently set within routines, but could/should be moved to CPP-options.
61      Array bounds for 1. are as before, for 2.,3. cover the entire domain
62      (could be changed for 1. too).
63    o verification/lab_sea (fwd):
64      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
65        use 7 categories (except hb87), new solve4temp params (except salt_plume),
66        constant salinity (=4) or variable salinity (salt_plume) done through
67        SItracer.
68    o pkg/seaice:
69      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
70      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
71         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
72        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
73        SEAICE_freeze got retired) but already better than previously with
74        SEAICE_freeze=123456.7 deg.C;
75      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
76        (safer multi-threaded setting); always set SEAICEuseEVP;
77      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
78        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
79        stop if multiple specifications for the same coeff; make sure default
80        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
81    o pkg/obcs:
82      - allow to switch to upwind 1rst order advection scheme for the advective
83        flux computation at the open-boundary; disabled for adjoint built.
84    o pkg/ptracers:
85      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
86      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
87      - add parameter to decide when to start a tracer; use internal flag to
88        know which tracer to step-forward; switch this internal flag at the top
89        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
90        for adjoint built.
91    o pkg/seaice:
92      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
93      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
94      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
95    o pkg/ecco:
96      - fix writing of output file DiagnosCost_ClimSalt/Theta
97        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
98    o pkg/seaice:
99      - add missing initialisation of COR_ICE array in dynsolver.F
100      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
101        compiled either way, and is tested in all exps (multidim was only tested
102        in lab_sea ad before).
103      - cosmetic change to prepare for future addition of ITD. no change to results.
104        no defaults change.
105      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
106      - by lack of adequate verification experiments, I further used custom versions
107        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
108        should be correct.
109      - avoid recomputations in ad.
110    o array initialisation in adjoint mode:
111      1) pkg/mom_common/mom_calc_ke.F:
112        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
113        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
114        part this initialisation is gone, resulting in Floating Point Exception
115        (caught by open64 compiler with debug option).
116      2) model/src/convective_weights.F
117        set output convectCount over the full array range (instead of doing
118        an update): this fix a similar issue when called within recomputation (adjoint)
119        which could by-pass the initialisation (normally done in the caller S/R).
120    o pkg/seaice:
121      - final version of turbulent flux params, as agreed at MIT ice meet:
122           SEAICE_mcPheePiston (default is ~ 0.000875)
123           SEAICE_mcPheeTaper (default is 0.)
124           SEAICE_frazilFrac (defualt is 1.)
125           SEAICE_mcPheeStepFunc (default is false)
126      - changes results at trunction error level
127      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
128    o added pkg/frazil:
129      - see frazil_description.tex for details
130      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
131    o pkg/shelfice/shelfice_thermodynamics.F
132      - fix exponents for velocity dependent exchange coefficients: change
133        from 2/3(=0) to 0.66666666666666667
134      - move computation of velocity dependent exchange coefficients into
135        separate loop, so that it applies to both thermodynamics
136      - move some divisions by constants out of loops
137    
138    checkpoint63j (2012/02/16)
139    o pkg/seaice:
140      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
141      - SItracer:  added run time params, and allow coupling to ocn salinity.
142    o pkg/seaice: remove (almost) all divisions by constants within loops
143      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
144      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
145      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
146      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
147    o pkg/seaice :
148      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
149        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
150      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
151      - add permanent SItflux diag that corresponds to TFLUX but includes
152        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
153      - allow activation/testing of a fix for suspected missing term in
154        ocn-ice heat budget (to be confirmed). To test this, you want to
155        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
156        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
157      - no change in results, fwd or ad.
158    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
159      - switch to variable freezing point.
160           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
161      - bug fix : the sublimation term that was missing is now activated.
162           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
163      - bug fix : flooding sign term for SIsal0.NE.0.
164           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
165    o pkg/seaice:
166      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
167        is now the default, and the old default constant freezing point is recovered
168        with SEAICE_tempFrz0    = -1.96,
169             SEAICE_dTempFrz_dS = 0.,
170      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
171      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
172      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
173        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
174      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
175        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
176      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
177        seaice_growth r149 for legacy branch (no results change).
178      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
179        from I. Fenty).
180      - results did not change except for global_ocean.cs32x15, mostly due to the
181        switch to variable freezing point (see above item for detail).
182    o pkg/thsice:
183      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
184        seawater freezing in thsice_calc_thickn (not used).
185    o pkg/seaice: turbulent flux term specification via run time params.
186      - replace CPP switches with run time switches to facilitate testing
187      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
188                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
189      - added runtime parameter : SEAICEturbFluxFormula
190      - move Mcphee constants to SEAICE_PARAMS.h
191      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
192                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
193                 remove seaice_summary call (moved to seaice_init_fixed)
194      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
195        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
196      - seaice_summary.F : add missing report of read turbulent flux term set up
197                           and SITRACER.
198      - seaice_check.F : check range; inform and stop if retired CPPs are used
199                         (incl. SEAICE_AGE).
200      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
201             CPP switch, same computation as before for the different options.
202      - change results at the truncation level.
203    o pkg/seaice:
204      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
205        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
206        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
207      - update verification/*/input*/data.seaice:
208        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
209        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
210        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
211        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
212    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
213      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
214        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
215        difference in results only due to machine truncation.
216      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
217        MaykutPolySatVap; keep MIN_LWDOWN.
218      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
219      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
220        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
221    o pkg/salt_plume:
222      - isolate saltPlumeFlux array exch into a specific S/R called from
223        do_oceanic_phys.F
224      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
225    o verification:
226      - move untested set-up to MITgcm_contrib/verification_other.
227    o pkg/seaice:
228      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
229    o pkg/seaice:
230      - seaice_solve4temp.F (keeping results unchanged):
231        * add 2 future run-time params to select which saturation vapor pressure
232          formula is used and how post-iteration fluxes are set.
233          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
234        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
235          the linearized expression to stay consistent with tsurf finding.
236      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
237        can be < 0.
238    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
239      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
240        conductive heat flux F_c , and add it explicitly when updating tsurf as
241        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
242        so that now F_ia has a consistent meaning through the entire routine.
243        This causes differences at truncation level: update output of fwd exp.
244        global_ocean.cs32x15.seaice.
245    o pkg/seaice:
246      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
247        of arrays, sign/direction of fluxes; no effect on results.
248      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
249        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
250        note: this should have been done before changing celsius2K default.
251      - to keep results unchanged, add back old value of celsius2K in verification
252        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
253      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
254        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
255        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
256        freezing temp is consistent with value in seaice_growth.F ; this causes
257        differences at machine truncation level: update lab_sea AD output (3/4).
258    o pkg/seaice:
259      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
260        and climsst/sss even when using seaice (to prevent calculation that might
261        use SST on land); does not affect any verification exp.
262      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
263        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
264    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
265      over land (non-legacy code)
266    o vectorize salt_plume package:
267      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
268      - this code computes plumebk everywhere (also over land), thus requires
269        code to avoid divisions by zero and catch the case of kLev=Nr.
270      - efficiency of salt_plume_frac is still sub-optimal
271    o tools (genmake2):
272      - fix makefile NAME specification (option: -makefile NAME) by adding
273        "-f $MAKEFILE" in few places where it was missing including makedepend
274        command (contribution from Paul).
275    
276    checkpoint63i (2012/01/24)
277    o model/src:
278      - add factorized versions of some EOS code to find_rho.F,
279        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
280    o model/src:
281      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
282      - change default celsius2K from 273.16 to 273.15
283      - to keep results unchanged, add back old value of celsius2K in verification
284        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
285         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
286    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
287      to make TAF generate vectorizable code
288    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
289       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
290       have flags that do this more efficiently.
291    o pkg/diagnostics/diagstats_calc.F
292      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
293    o pkg/obcs (with exch2):
294      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
295        and remove code (in obcs_readparms.F) which was based on EXCH of indices
296        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
297    o pkg/exf and seaice exp:
298      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
299        so that switching off area & heff advection flags does not affect results.
300      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
301      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
302        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
303        results of verification experiments: 1D_ocean_ice_column(fwd),
304        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
305        and offline_exf_seaice (all 4).
306    o pkg/seaice:
307      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
308        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
309      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
310        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
311        not multi-dim advection;
312      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
313        SHORTWAVE_HEATING #undef.
314    o optim: make Makefile more robust (?)
315    o pkg/obcs:
316      * fix treatment of obcs_read_pickup for TAF
317    o pkg/shelfice:
318      * add missing initialisation of num_shifwflx
319      * new adjoint verification exp. for isomip
320      * change Prandtl and Schmidt numbers from generic formulations
321        (in terms of model diffus. and visc.) to separate runtime
322        parameters, with Holland and Jenkins (1999) default values.
323    o pkg/exf (interpolation):
324      - extended input field (2 rows) near the N & S poles:
325        * fill in with the symetric value (when even Nb of data in longitude)
326        * add average value at the poles only for scalar quantities ; for vector
327          component interpolation, skip the averaging and keep duplicated values,
328          unless the 2 components have same location (uvInterp=T) in which case
329          interpolate the 2 components together using S/R EXF_INTERP_UV.
330      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
331        together: this allows to account properly for local orientation when
332        averaging at N & S pole.
333      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
334        exf-interpolation near N & S poles. Undef by default.
335      - add debug check/print on 1rst iter if debugLevel >=2.
336    o pkg/exf:
337      - change masking flags definition (no longer "parameter"), put them in
338        common block and set them in S/R EXF_INIT_FIXED.
339      - change recognized masking flag from s,u,v to c,w,s since the mask
340        to use (maskC,W,S) depends on position on model grid and has little to
341        do with scalar/vector difference; fix masking if using P-coordinates.
342      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
343        and update results of exp. global_with_exf (x2).
344      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
345    o pkg/obcs
346      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
347    o pkg/exf (interpolation):
348      - assume periodicity in X only if input field cover full longitude range.
349      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
350        and should vectorise).
351      - fix input lat of the 2 added row (in case we provide N.pole data).
352    
353    checkpoint63h (2011/12/30)
354    o pkg/seaice:
355      - change declaration of UVM from _RL to _RS in order to get B-grid
356        uIce,vIce monitor when _RS = real*4
357    o pkg/offline:
358      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
359      - compute vertical velocity if not read from file (switch on exactConserv
360        & staggerTimeStep);
361      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
362    o verification:
363      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
364        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
365        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
366      - update output of exp. global_ocean.cs32x15.viscA4 after changing
367        grid-file angles (used here for coriolis-3d);
368      - remove (or gzip) few files not needed to run fizhi-cs experiments.
369    o pkg/exf (vector interpolation):
370      - rotate vector component toward local grid-axis orientation using grid-angles
371        (stored in GRID.h) instead of locally computed rotation angle; keep old code
372        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
373    o pkg/seaice:
374      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
375        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
376    o pkg/PKG_OPTIONS.h files:
377      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
378        outside of the #ifdef ALLOW_THISPKG / #endif block.
379      - update verification/*/code/PKG_OPTIONS.h files.
380    o add a verification experiment (offline_exf_seaice/input.seaice) that test
381      the B-grid LSOR solver
382    o pkg/seaice: sort out emissivity and long wave radiation step 2:
383      - add emissivity for snow and ice as new run-time parameters
384        (unfortunately) that default to the corresponding exf values; this
385        changes results in most verification experiments so that for backward
386        compatibility these parameter have to be set explicitly to inconsistent
387        values (ugly);
388      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
389        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
390        until we agree how to handle this bug properly
391    o pkg/exf (interpolation):
392      - add a set of run-time param ({inputfield}_interpMethod), one for
393        each interpolated input field, to select the interpolation method
394        with a value of zero switching off the interpolation;
395      - print interpolation parameters to standard output;
396      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
397        (to use instead runoff_interpMethod=0 in data.exf).
398      - simplify default setting of interpolation parameters (for all fields,
399        set position to match model grid cell-center position, leading to trivial
400        interpolation in case of regular Lat-Lon grid) and fix for the case of
401        non-uniform delY.
402    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
403       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
404       this factor is absolutely required, because the lw exitance (= out-going
405       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
406       where the reflectivity rho = 1-emissivity for conservation reasons. Once
407       this is established, we can remove the CPP-Flag (if we want to).
408    o pkg/seaice:
409      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
410        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
411      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
412        what the name implies (and not emissivity*BoltzmannConstant), this means
413        the old default value of 5.5e-8 now means
414        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
415        S/R exf_readparms
416      - FV-discretization of the B-grid LSOR solver, turn on with
417        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
418        of the calling routine dynsolver, so that B and C-grid code look a
419        little more alike.
420      - fix index bugs in ostres.F (B-grid code)
421    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
422    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
423      default for SEAICE_emissivity, if useEXF; requires setting a wrong
424      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
425      backward compatiblity
426    o model/src: use sigmaR in calc_ivdc
427    
428    checkpoint63g (2011/12/16)
429    o pkg/seaice/seaice_growth.F:
430      fix heat conservation of the coupled ocean-seaice system.
431      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
432      solid vs liquid water treatment is resolved via QNET.
433    o pkg/seaice/seaice_growth.F:
434      add missing term for sublimation in saltFlux, which was breaking conservation.
435    o pkg/seaice/seaice_model.F:
436      Remove this patholigical case treatment in evolution branch,
437      where it is un-necessary and breaks conservation.
438      Update global_ocean.cs32x15/results accordingly for
439      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
440    o model/src:
441      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
442      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
443    o pkg/obcs:
444      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
445      tendency for temperature and salinity that is then applied to update
446      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
447      horizontal advection and diffusion contributions on the boundary (in
448      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
449      removing the mask in S/R timestep_tracer. The advantage of this approach is
450      that the updated tracer values include contributions from the surface
451      forcing and vertical diffusion.
452      This modification changes exp4.stevens because of vertical diffusion.
453    o model/src:
454      change non-curvilinear grid setting to also work with exch2 + blank tiles:
455      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
456        face dimensions.
457      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
458        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
459        and INI_SPHERICAL_POLAR_GRID.
460      change test-experiment global_ocean.90x40x15:
461      - split the domain in many more tiles (9x4 tiles of 10x10 each);
462      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
463      - update results of both test (std & dwnslp).
464    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
465       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
466    o model/src:
467      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
468        and fix initialisation when using sigma-coords.
469    o model/src:
470     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
471       to their current value at the beginning of forward_step.F": add a new run-time
472       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
473     - set doResetHFactors=T in the following test exp:
474        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
475        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
476        and tutorial_global_oce_in_p (nonLinFS in p)
477    o pkg/ecco
478      - added IES cost term
479    o verification/advect_xz
480      - scale down the depth by 1/100 (from 200 km to just 2.km)
481      - add secondary test using divergent flow, r-star and implicit vertical advection.
482      - add note (check_conserve_TS.txt) and matlab script to check global
483        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
484    o pkg/rbcs:
485      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
486    o pkg/obcs (Stevens BCs):
487      - fix various problems in the phase speed computations of the Stevens
488        boundary conditions:
489        - sign error for western and southern boundaries,
490        - time tendencies were underestimated by factor of dTracerLev and some just
491          zero (for multidim advection schemes) -> now estimate time tendencies
492          from difference between previous (n) time level and the one before (n-1);
493          this requires storing a field per tracer per boundary, also in the pickup
494          files.
495        - replace deltaTmom in cflMer/Zon computation with dTracerLev
496        - set default phase velocity to cflMer/Zon
497      - update verification experiment exp4.stevens
498    o pkg/generic_advdiff (implicit_r):
499      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
500        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
501      - fix implicit vertical diffusion or advection with NonLin FreeSurf
502        (was using current recip_hFacC instead of future recip_hFacC): set future
503        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
504        solver S/R ;
505      - fill diagnostics of vertical advective fluxes (computed from tendency)
506        when using implicit vert. advection;
507      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
508         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
509         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
510         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
511    o pkg/diagnostics:
512      - add diags for T & S tendency which goes through Adams-Bashforth.
513    
514    checkpoint63f (2011/11/30)
515    o pkg/obcs/obcs_calc_stevens.F:
516      - join some loops to reduce number of if-statements
517      - fix a bug in code for northern and southern boundaries.
518    o pkg/seaice/seaice_init_varia.F
519      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
520        caused zero ice-velocities for the B-grid code
521    o pkg/seaice/seaice_init_fixed.F
522      - fix a bug in the initialisation of the second metric terms
523        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
524      - this affects all seaice configurations with useCurviLinearGrid = .true.
525        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
526        = .true. (default)
527      - the only verification experiment affected is global_ocean.cs32x15:
528        icedyn, seaice, and seaice_dynmix (AD)
529    o pkg/thsice/thsice_diagnostics_state.F
530      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
531        not contain garbage that can lead to surprises in diagstats_calc.F
532    o model/src:
533      - move bi,bj loops inside INTEGR_CONTINUITY ;
534      - call INTEGR_CONTINUITY directly from forward_step.F
535        (previously called from momentum_correction_step.F)
536      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
537        forward_step.F and pkg/ecco/the_main_loop.F
538    o model/src/do_oceanic_phys.F:
539      - reset addMass to zero only if useICEFRONT ;
540      - separated k-loop for rhoInSitu calculation ;
541      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
542        and at constant T,S (= WdRHOdP);
543      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
544        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
545        transport of locally-referenced potential density);
546        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
547    o gluemnc:
548      - replace ncrcat with ncks when adding variables to *.glob.nc
549      - change the way variables without record dimensions are handled so that
550        files that have variables with and without record variables can be glued:
551        add a record dimension with a new unique name to be able to differentiate
552        between variable with and without a-prior record dimensions. Remove
553        this record dimension before adding the variable to the *.glob.nc file.
554        This procedure automatically works also for grid.*.nc files that do not
555        have any record dimension.
556    o verification/cpl_aim+ocn:
557      - generate new reference output on baudelaire (gfortran, mpich2) (previously
558        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
559    o pkg/obcs/obcs_calc_stevens.F:
560      - add code for northern and southern boundaries.
561      - reorder some loops to save some operations and so that drFBar can be scalar
562    o model/src:
563      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
564        truncation) and add diagnostics for Adams-Bashforth tendency increment.
565      - update test-exp. AD output:
566        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
567      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
568        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
569        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
570        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
571        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
572        tutorial_plume_on_slope.
573    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
574      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
575      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
576      does not even come with an F77 compiler anymore, this should not be
577      a limitation
578    
579    checkpoint63e (2011/11/06)
580    o pkg/seaice adjoint of LSR:
581      - substantially rework STORE dirs.
582      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
583        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
584        and only perform SOLV_MAX_FIXED adjoint iters.
585        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
586        always goes to same record, meaning that the last forward field will be
587        the one used in the adjoint - an approximation.
588      - now produces non-zero LSR-related gradients, and acceptable gradients for
589        An's zonal (x-z) test case (to be checked in)
590      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
591        (but these are screwed up by the thermodynamics in the first place);
592        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
593        output_adm.txt also reflects changes to seaice_lsr
594      - global_ocean.cs32x15:
595        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
596          (output_adm.seaice.txt was updated)
597        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
598          (output_adm.seaice_dynmix.txt)
599    o test-exp. exp4+stevens:
600      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
601    o pkg/seaice (lsr solver):
602      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
603        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
604      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
605      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
606        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
607      - compute (with new S/R) and print initial (+ free-driff sol. if available)
608        and final residual of linearised system.
609    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
610      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
611    o pkg/obcs: Stevens BCs (still only for east and west)
612      - fix Stevens BCs by using intermediate velocities of previous
613        time step as "baroclinic" contribution rather velocity of one grid cell
614        inside the boundaries; more consistent but makes the entire treatment
615        more complicated, requires new pickup files and two new S/Rs:
616        obcs_copy_uv_n and obcs_save_uv_n
617        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
618        (undefined by default)
619      - silently move computation of some grid factors into separate loops to
620        save some recomputations
621      - add a hack for non-linear free surface
622      - add a verification experiment to exp4 that tests this code
623    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
624    
625    checkpoint63d (2011/10/25)
626    o pkg/obcs + seaice-dynamics:
627      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
628        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
629        values (consistent with an implicit method).
630      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
631        return to older implementation (same results as before); note that none of
632        the "experimental" OBCS_SEAICE options are implemented in the new version.
633      - switch test exp. seaice_obcs to use new version (update output).
634    o pkg/seaice:
635      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
636      - add parenthesis in Water-Ice drag calculations (evp & lsr);
637      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
638        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
639      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
640        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
641    o pkg/layers:
642      - Include potential density as new coordinate (Thanks to David Munday)
643    o pkg/dic:
644      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
645        carbonate computation/output to CALC_PCO2_APPROX
646    o pkg/generic_advdiff
647      - make TAF generate code that vectorizes:
648        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
649    o model/src:
650      - improve vectorization also for adjoint code of
651        solve_tridiagonal and solve_pentadiagonal. As this requires up to
652        5 new 3D-fields, this code is only turned on for the combination of
653        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
654        for singular matrix check (only for TARGET_NEC_SX).
655      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
656        ALLOW_AUTODIFF. This flag now needs to be set outside of
657        solve_tri/pentadiagonal.F
658    o pkg/exf:
659      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
660        optional namelist EXF_NML_OBCS).
661      - add many debug-print (to trace down where pkg/cal error msg comes from)
662    o pkg/mom_vecinv/mom_vi_hdissip.F
663      - rearrange loops so that vectorization is improved and in particular
664        the adjoint routine vectorizes. The code is a little longer now, but I
665        think easier to read.
666        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
667    o pkg/seaice:
668      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
669    o pkg/exch2:
670      - alternative code (without tile x tile matrix) for cumulated (global) sum;
671        used as default; keep using matrix version in adjustment.cs-32x32x1.
672    o tools/build_options:
673      - after merging some MPI and/or multi-threads specific optfiles so that
674        the modified default optfile support both built (using genmake2 -mpi
675        for the MPI built, using genmake2 -omp for OpenMP built),
676        move now obsolete optfiles to tools/build_options/unsupported/
677       (add copy of email sent to support list in doc/optfiles_changes.txt)
678    
679    checkpoint63c (2011/09/28)
680    o pkg/ebm:
681      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
682        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
683    o pkg/seaice (SItracer pickup)
684    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
685      To be done:
686      - thorough testing of missing fields in S/R seaice_read_pickup
687      - thorough matching between generic tracers and specific fields used
688        (e.g. volume-weighted age, area-weighted age, salinity, ...)
689    o pkg/grdchk:
690      - all procs calculate and print finite-difference gradient (for testreport)
691      - change description output used by testreport;
692      - AD testing: also compare and report Finite-difference gradient;
693        => update all output_adm*.txt
694    o test exp. global_ocean_ebm:
695      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
696        and turn on exactConserve; update (fwd) output.
697    o pkg/seaice (LSR):
698      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
699      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
700        * identical results with non-CS topology (but save up to half of EXCH calls)
701        * no much changes in cs-32 verification tests since no ice at face edges
702         (differences due to convergence criteria, since nb of iterations changed)
703        * expect some differences on lat-lon-cap grid.
704        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
705    o pkg/exch2:
706      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
707        many tiles); until alternative coding is added, just add a stop.
708    o pkg/kpp:
709      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
710        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
711    o optfiles:
712      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
713        into corresponding standard one, which now support different build:
714        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
715      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
716    o pkg/obcs (seaice):
717      - add missing EXCH for uIce,vIce after applying OBCS;
718      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
719        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
720        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
721      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
722      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
723        and eedata.mth for MPI and mutlti-threaded testing.
724    o pkg/flt:
725      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
726      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
727      - fix pickup and trajectories + profiles output with multi-threads;
728      - add parameter to select group of fields to write along trajectory and
729        profile (default unchanged);
730      - only call PORT_RAND* function when flt_noise <> 0;
731      - add multi-threaded test for verification exp. flt_example.
732    o eesupp/src:
733      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
734      - USE_OMP_THREADING: check that number of threads (from eedata) matches
735        actual number (from env.var. setting).
736    o pkg/ebm:
737      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
738      - add multi-threaded test for verification exp. global_ocean_ebm
739    
740    checkpoint63b (2011/08/29)
741    o pkg/ebm:
742      - fix sign of runoff;
743      - update directly forcing fields (Qnet,EmPmR) to use standard
744        external_forcing_surf.F (remove ebm_forcing_surf.F);
745      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
746      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
747        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
748      - update global_ocean_ebm parameters file data and update output (fwd+ad).
749    o verification/matrix_example:
750      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
751        MPI and mutlti-threaded testing.
752    o pkg/matrix:
753      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
754      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
755      - fix for multi-threaded (remove DATA statement);
756      - use standard DIFFERENT_MULTIPLE function;
757      - add MATRIX_OPTIONS.h
758    o verification/matrix_example:
759       To allow to split the domain in several tiles, change the domain size
760        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
761        Western side) of land points.
762    o (*_)write_pickup:
763      - fix few bugs in mypackage_read/write_pickup.F
764      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
765        array of length 1 (was caught by compiler syntax-check).
766    o pkg/diagnostics (velocity potential solver):
767      - fix initialisation of main diagonal matrix (for overlap values)
768    o tools/build_options:
769      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
770        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
771      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
772        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
773        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
774        and use "-devel" testreport option for standard testing on baudelaire.
775    o pkg/grdchk:
776      - Assume that all gradient-check position are within the same tile
777        corresponding to global indices (iGloTile,jGloTile) and that
778        positions (i,j indices or nbeg) are local to this tile;
779      - set tile local-indices and proc. number according to tile global-indices;
780      - remove grdchkwhichproc from namelist (retired param);
781      - send adjoint gradient to all procs so that all procs print it to STDOUT;
782      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
783    o adding package bbl (Bottom Boundary Layer)
784      description in MITgcm/pkg/bbl/bbl_description.tex
785      example/test experiment in MITgcm_contrib/bbl
786    o adjoint verifications
787      - changed 5 experiments to multi-tiles
788        * global_ocean.90x40x15
789        * obcs_ctrl
790        * offline_exf_seaice
791        * tutorial_dic_adjoffline
792        * tutorial_tracer_adjsens
793        changed reference output for those that crossed tile boundaries
794        (changed choices of gradient check positions)
795      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
796      - temporary bug fix in grdchk_loc.F for obcs
797    o genmake2 & testreport
798      - add target "obj" (just for OBJFILES files) to Makefile;
799      - add option to specify FEXTRAFLAGS on command line.
800    o pkg/mypackage:
801      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
802    
803    checkpoint63a (2011/08/02)
804    o pkg/diagnostics (velocity potential):
805      - fix velocity-potential calculation when using OBCS: balance net inflow
806        at each level (new S/R OBCS_DIAG_BALANCE).
807      - fix some of the problems with OBCS in stream-function calculation.
808    o pkg/exf/exf_readparms.F
809      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
810        EXF_NML_OBCS) more consistent, so that you need not have these lists
811        in data.exf when they are not used.
812    o optim/optim_readdata.F:
813      - add some output about obcs variables that might help debugging
814      - add a check about nvarlength
815    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
816    o pkg/diagnostics (velocity potential):
817      - fix mask for OBCS (still problems in stream-function with OBCS);
818      - add specific parameter (default = main code CG2D params) for solver;
819      - in case of poor convergence, use solution corresponding to lowest residual.
820    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
821      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
822      and should be avoided where possible.
823    o model/src (rStar):
824      - include r* effect on reference-state (PhiRef) in totPhiHyd
825        (so that it's really the potential anomaly at the cell center);
826        affect solution only if z* with full pressure in EOS.
827      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
828        update output (because of z* in totPhiHyd and viscA4 changes);
829      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
830        @ constant r) until interpolation at constant r is implemented.
831    o pkg/diagnostics
832      - fix RCENTER diagnostics in case cell center is not at interface middle
833    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
834      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
835      that THETA and SALT are "conservative temperature" and "absolute
836      salinity"
837    o pkg/ctrl
838      - fix computation of endrec in s/r ctrl_init_rec
839      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
840    o pkg/seaice/seaice_growth.F
841      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
842        remove then obsolete STORE directives
843      - fix STORE directives for tice and tices, so that only the
844        appropriate part of the fields are stored (and not the entire
845        field); update global_ocean.cs32x15.seaice AD output.
846      - cosmetic changes: adjust CPP flags and indentation for better
847        legibilty
848    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
849      Chris Wilson)
850    o pkg/gmredi:
851       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
852       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
853    
854    checkpoint63  (2011/07/11)
855    o pkg/exch2:
856     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
857     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
858       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
859       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
860    o pkg/diagnostics:
861     - deal with pairs of post-processed diags which are computed together; in
862       particular, re-order list of diags within 1 file to save 2nd computation.
863     - add S/R to compute velocity stream-function (called after velocity-potential
864       calculation) from divergence free transport -> new diagnostics "PsiVEL".
865     - add parameter to select grid-point location where PsiVEL == 0.
866    o eesupp/src:
867       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
868       (specific S/R needed with exch2 topology - for now, just print an error msg)
869    o pkg/shelfice
870     - Implement friction velocity-dependent transfer coefficients following
871       Holland and Jenkins, JPO, 1999
872       Original code by M. Losch with small modifs.
873       Enable with CPP option SHI_ALLOW_GAMMAFRICT
874       and runtime flag SHELFICEuseGammaFrict
875    o verification lab_sea & global_ocean.cs32x15:
876     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
877       does not miss some dependencies (but is slower) and also works with many files
878       (default makedepend limitation for AD built).
879     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
880    o pkg/diagnostics:
881     - add run-time parameter "useMissingValue" (def=False) to fill land-point
882        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
883       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
884     - Extend the use of "missing_value" setting from data.diagnostics for the case
885       of counter-diagnostics (where fraction-weight is zero). This applies both to
886       MNC and MDS output files.
887    o pkg/seaice/seaice_growth.F:
888      - add 'a priori' cap of latent heat flux based on actual mass considerations
889        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
890        non-legacy seaice_solve4temp.
891      - add diagnostic of the residual sublimation freshwater flux (the freshwater
892        flux taken from the ocean if the total actual latent heat fluxes exceed
893        the maximum)
894      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
895       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
896      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
897       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
898      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
899      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
900    o verification 1D_ocean_ice_column:
901       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
902       update results
903  o pkg/diagnostics:  o pkg/diagnostics:
904   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
905     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
906     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.
907   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
908   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
909     when using periodic averaging: now writes one time record with the full set     when using periodic averaging: now writes one time record with the full set
910     of fields for this time period, then the next time reccord (it used to be     of fields for this time period, then the next time reccord (it used to be
911     one field with the full set of time records then the next field).     one field with the full set of time records then the next field).
912     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
913    
914  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
915  o adjoint monitor:  o adjoint monitor:
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