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revision 1.1460 by jmc, Tue Jun 21 16:17:31 2011 UTC revision 1.1712 by gforget, Fri Aug 10 14:52:02 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
8      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions jointly.
9       The exclusive ifdefs were removed, to add costs terms (when defined) from both packages.
10      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
11      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
12      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes of
13       "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
14    o pkg/cost : add comments to explain special and/or untested setups.
15    o pkg/exf:
16      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
17        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
18    o verification/*/code_ad:
19      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
20      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
21      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
22        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
23    o pkg/seaice :
24      - added possibility to change ice strength/PRESS0 relationship to
25        HEFF, according to the following run time parameters
26        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
27        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
28        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
29    o pkg/ggl90 :
30      - added run time flag mxlSurfFlag to include the code that ensure
31        mixing between first and second level (previously included as a comment)
32    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
33      - add test of newly added dumpAdByRec=T option where
34        we write all records to one file per variable.
35    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
36      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
37        to check that this code is ok with taf and compiles in adjoint.
38    o pkg/autodiff :
39      - added run time param dumpAdByRec : ad dump format switch.
40        If true then write all records to one file per variable.
41        Else write one file per record (remains the default).
42      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
43    o pkg/seaice:
44     - Added SEAICEuseTILT run time switch : if set to
45       false then omit the tilt term in seaice dynamics.
46     - Fix free drift calculation.
47    o pkg/shelfice:
48      When initializing SHELFICEDragQuadratic, set default to be
49      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
50      but retain option to set it independently
51      (inconsistenty spotted by Veronique Dansereau)
52    o eesupp/inc:
53      - in EEPARAMS.h, add real-type constant for some frequently used simple number
54         (0,1,2,1/2), with name explicitly referring to RS/RL type.
55    o model/src:
56      - move balancing of relaxation terms to new S/R balance_relax.F.
57    o pkg/autodiff:
58      re-write active I/O high-level (control) S/R:
59      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
60      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
61      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
62        MDS_READ/WRITE_FIELD); change loops to multi-threads.
63      - update and merge active_file_control_slice.flow into active_file_control.flow
64      - update the calls in lower level S/R (active_file.F, active_file_g.F and
65        active_file_ad.F) keeping the argument list and function unchanged.
66      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
67        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
68      - new low-level active I/O routines, one for each type (RL/RS), for active var
69        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
70        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
71        right type.
72    o autodiff and RS=real*4:
73      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
74        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
75      - change argument type of 3-D mask argument to _RS to match type in the call
76        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
77    o pkg/thsice:
78      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
79      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
80        fresh-water flux: uniform correction or proportional to local precip.
81    o pkg/ctrl:
82      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
83      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
84                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
85      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
86    
87    checkpoint63q (2012/07/30)
88    o pkg/autodiff:
89      note about monitor and snap-shot of ad-variables:
90      a) need to apply ADEXCH before monitor or output of ad-vars to include
91       overlap contributions (was done for adjDump but missing for monitor).
92      b) since ADEXCH implies adding overlap values to interior array, machine
93       truncation error is expected when adding an ADEXCH call in the middle of
94       the time-stepping (although mathematically identical).
95      modifs:
96      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
97        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
98      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
99        apply ADEXCH before monitor or snap-shot of ad-variables:
100           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
101      - implement new method (copy+adexch) for snap-shot and monitor of main model
102        ad-vars (initially not used by default -> output unchanged).
103      - change default (set to 2) to use new method and update few output_adm.txt
104        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
105        and both tutorial_tracer_adjsens tests).
106      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
107        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
108    o pkg/ctrl:
109      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
110      generic control variables via
111      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
112      Only required customization should be S/R ctrl_map_ini_genarr.F
113      (routine in repository contains example)
114    o pkg/exf:
115      - fix and refine checking of surface-relaxation setting when using EXF
116    o verification (adjoint exp):
117      - reduce length of simulation by half for experiment global_ocean.cs32x15
118        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
119    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
120      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
121        of KE that can occur with aggressive optimization
122      + put quadratic bottom drag calculation in separated loops (only done if
123        using bottomDragQuadratic)
124    o model/src: CG2D_NSA
125      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
126         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
127      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
128         change cg2d residual target to be expressed in Wunits (=> do not normalise
129         RHS ; this fix global_max Pb with TAF); update output.
130    o verification/tutorial_tracer_adjsens:
131       improve parameter consistency (and get rid of warnings):
132       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
133       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
134       - use staggerTimeStep (for stability) in som81; use default rotation period.
135    o pkg/exch2:
136      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
137        reset to 0 = 1 long line in X)
138    o pkg/mdsio:
139      - fix reading of dimensions from meta file for large-size domain
140    o model/src:
141      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
142      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
143        Cubed-Sphere Exch with CS-corners inside the domain;
144        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
145        globalArea and to set hasWetCSCorners.
146      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
147        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
148      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
149        useCDscheme and useCubedSphereExchange).
150    o pkg/seaice/seaice_growth.F :
151      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
152        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
153        when the previous code was not correct.
154      - in all cases diagnoze the boundary condition mismatch to SIaaflux
155      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
156        that term to QNET (essentially to set the melt/freeze water to 0degC).
157        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
158    o verification/global_ocean.cs32x15/input.seaice :
159      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
160      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
161      - update results (output.seaice.txt) accordingly.
162    o verification/lab_sea/input/data.seaice :
163      - remove SEAICEheatConsFix, which is now be tested
164        in global_ocean.cs32x15. The presently coded fix
165        is only consistent with real fresh water + nlfs.
166      - update results (output.txt) accordingly.
167    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
168    o AD_CONFIG.h file:
169      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
170      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
171        add it explicitly in each fortran src file where it is needed.
172        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
173        thus introducing potentially wrong dependency; therefore, better to include
174        it only where it's really needed, and after any other included OPTIONS file
175        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
176        or ALLOW_TANGENTLINEAR_RUN).
177    
178    checkpoint63p (2012/07/06)
179    o pkg/autodiff:
180      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
181      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
182        which are now read from new parameter file "data.autodiff" (inAdExact
183        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
184      - add file "data.autodiff" in all verification/*/input_ad/ directories.
185      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
186        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
187    o verification/tutorial_tracer_adjsens/
188      - add extra sub-verification which uses "SOM" advection scheme
189        (2nd Order-Moment Advection Scheme, Prather Limiter) with
190          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
191        and in data:
192          multiDimAdvection=.TRUE.,
193          tempAdvScheme=81,
194          saltAdvScheme=81,
195    o model/src:
196      - introduce ALLOW_BALANCE_RELAX which allow the removal
197       of the global mean of relaxation terms by setting
198       balanceThetaClimRelax and balanceSaltClimRelax
199      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
200       This case is now treated appropriately in seaice_growth.F
201    o pkg/seaice:
202      - do balanceEmPmR and balanceQnet based on the net fluxes
203        (SItflux) that enter the ocean+ice system rather than QNET
204        and EMPMR. Works best in real fresh water.
205      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
206        out of the diagnotics bloc, and stored in global arrays.
207    
208    checkpoint63o (2012/06/29)
209    o vertical mixing schemes:
210      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
211      - replace computation of density (in Function STATE1, opps_calc.F) by a call
212        to S/R FIND_RHO_SCALAR
213      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
214        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
215        affects output (vermix.ggl90) at truncation level.
216    o testreport:
217      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
218        (nSx,nSy) for the number of threads (from eedata.mth)
219    o model/src:
220      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
221        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
222    o verification/tutorial_tracer_adjsens/
223      - compile with ALLOW_CG2D_NSA
224      - run with nonlinFreeSurf=3
225      - update reference output_adm.txt
226    o tools/genmake2:
227      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
228        refine usePROFILES switching off (only when NetCDF is not available).
229    o verification (atmospheric set-up):
230      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
231    o pkg/profiles : refine profiles and files handling.
232    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
233    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
234      - changes to use model/src/the_main_loop.F rather than the ecco version
235        in ecco type adjoint runs.
236    o model/src:
237      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
238      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
239      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
240    o model/src:
241      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
242        update output of test experiment bottom_ctrl_5x5.
243    o pkg/generic_advdiff:
244      - implement vertical bi-harmonic diffusion (for now, only for T & S and
245        only explicitly).
246    o verification/bottom_ctrl_5x5/
247      update reference output (results changed quite some time ago,
248      not sure when; but new reference results look ok in terms of grdchk)
249    o verification/1D_ocean_ice_column/
250      For verification purposes, the exact adjoint rather than an approx.
251      should be used (e.g., to comare against F.D. or TLM).
252      removed autodiff_inadmode*_ad.F routines in code_ad/
253      Update results/ accordingly.
254    o pkg/cal:
255      - change cal_getdate.F so that output date is function of input time only
256        (less ambiguous, not mixed up with input iteration number).
257      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
258    o pkg/diagnostics:
259      - implement calendarDumps also for stats-diags
260      - implement calendarDumps also for snap-shot output (negative freq)
261      - for now, ignores calendarDumps if non-zero phase-lag.
262    
263    checkpoint63n (2012/06/04)
264    o model/src:
265      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
266        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
267      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
268        similar to calc_r_star.F); update results of experiment internal_wave and
269        tutorial_global_oce_in_p (affected @ truncation level).
270    o pkg/shelfice:
271      - add parameterisation of advective-diffusive flux into the ice shelf
272        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
273      - simply eps3/3a computation
274    o eesupp:
275     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
276       between tiles, just fill-in edges assuming locally periodic subdomain) and
277       add corresponding exchange subroutines (EXCH0);
278     - new CG-solver version (_EX0) for disconnected-tiles special case.
279    o model/src (CG-solvers):
280     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
281       (similar final residual output and max-Iter number as with standard version);
282     - allows to store and use lowest-residual solution (standard & _SR versions);
283     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
284     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
285    o eesup/src:
286     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
287       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
288    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
289    
290    checkpoint63m (2012/04/27)
291    o pkg/shelfice:
292     - account for partical cells in surface level below ice-shelf for hydrostatic
293       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
294    o ad test experiments:
295     - update and rename to "ad_optfile.local" local AD-optfile specific to a
296       particular adjoint verification experiment (in verification/*/code_ad/)
297    o pkg/seaice & pkg/exf:
298     - Part two of ECCO-CLIVAR code merges.
299       Completes merge of seaice area relax. code.
300       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
301       to be set in EXF_OPTIONS.h since this pkg controls its I/O
302       (and avoids second CPP option in SEAICE_OPTIONS.h)
303     - change default value of costIceStart & costIceEnd to a valid date.
304     - add snowPrecip to HSNOW in seaice_growth
305    o pkg/ptracers:
306     - move ptracers summary and setup check into separated S/R ; add a check for
307       valid PTRACERS_Iter0 value (error+stop or just warning).
308    o pkg/cal (+ pkg/ecco):
309     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
310       as input; and for AD, unless both are not differentiable (e.g., k index)).
311    o model/src:
312     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
313       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
314       temporary set to usingZCoords value (to be changed to F when using shelfice).
315     - hydrostatic pressure: implement partial cell near the surface also for
316       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
317       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
318    o pkg/ctrl/ctrl_init.F:
319     - add a formal parameter to s/r ctrl_init_rec to print
320       xx_$(ctrl_valiable)_file for easier debugging
321     - move call of cal_* routines into the if-block where they are really
322       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
323       to specify a startdate
324    o pkg/seaice:
325     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
326       global_ocean.cs32x15/code versions).
327     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
328       verification experiment global_ocean.cs32x15.seaice and update results.
329    o pkg/exf:
330     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
331       (according to useExfYearlyFields).
332    o pkg/cal:
333     - move calendar setting & summary (previously in cal_readparams.F) into new
334       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
335       length of the simulation is set (after SET_PARMS call); This is an attempt
336       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
337     - For safety: keep a record of pkg/cal parameter settings status
338               to allow to STOP if one pkg/cal S/R is called too early.
339     - add a stop in all basic pkg/cal subroutines if called before setting is done.
340     - modify cal_getdate.F: stop when nothing was returned;
341       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
342       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
343    
344    checkpoint63l (2012/04/04)
345    o pkg/bbl:
346      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
347        update global_with_exf output.yearly.txt file.
348    o pkg/cal:
349      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
350      - remove 2 unsused and very short (1 line only) functions ;
351      - remove unsused subroutines from AD-Diff list.
352    o model/src:
353      - start to implement clean wait to stop in initialization S/R (config_check.F,
354         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
355    o folowing PRINT_MESSAGE changes:
356      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
357    o pkg/bbl:
358      - modification so it can work with z*
359      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
360      - global_with_exf/input.yearly verification; changes output.yearly.txt
361    o eesupp/src:
362      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
363        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
364      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
365        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
366      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
367      - when using MPI, always set usingMPI=T ; set default accordingly and stop
368        if not consistent.
369      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
370        argument is zero (in case called within single-thread section).
371    o pkg/fizhi:
372        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
373        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
374    o pkg/exch2:
375      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
376        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
377      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
378        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
379        with bad ones coming from a not-yet-updated halo.
380        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
381    o pkg/frazil:
382        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
383        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
384    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
385    o verification/lab_sea
386      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
387      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
388      * nTimeSteps 3 -> 4
389      * changed reference output accordingly
390    o pkg/ctrl:
391      * fix ctrl_get_gen for xx_sst, xx_sss
392    o pkg/fizhi:
393      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
394        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
395      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
396        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
397        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
398    o pkg/gmredi:
399      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
400    o pkg/fizhi:
401      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
402        (old)aces open64 tuv test.
403    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
404    o pkg/mom_vecinv:
405      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
406        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
407        with non-lin free-surf).
408    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
409      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
410      some compilers (gfortran 4.6.0 on MacOS)
411    o momentum:
412      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
413        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
414        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
415    
416    checkpoint63k (2012/03/17)
417    o model/src:
418       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
419         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
420       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
421         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
422    o model/src: solve_*diagonal.F
423       - replace division with multiplication by inverse (similar to original version)
424         update output of AD exp. global_ocean.90x40x15.
425       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
426         to enable the use of the vectorized & differentiable solve_tridiagonal.F
427       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
428         vertical advection (to get solve_tridiagonal tested in AD mode).
429    o pkg/seaice: ECCO-CLIVAR merge:
430      1. seaice AREA relaxation
431         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
432         * runtime flag: SEAICE_tauAreaObsRelax
433      2. modified global mean cost imbalance code: CPP option
434          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
435    o another iteration on solve_*diagonal.F
436       Make choices independent of AUTODIFF
437       Default will be the adjoinable vectorized version.
438       Alternative choices are:
439       * non-adjoinable original version with low memory footprint:
440         #define SOLVE_DIAGONAL_LOWMEMORY
441       * still adjoinable but does not vectorize (k as inner-most loop):
442         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
443    o testreport
444     - add option to use a home made wrapper around "make"
445     - remove MITGCM_IEEE env. variable (no longer active)
446    o pkg/shelfice
447     - improve computation of friction velocity for velocity dependent
448       exchange coefficients: include velocities into SHELFICEBoundaryLayer
449       block to average velocities vertically
450     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
451    o Modify diagonal solvers, now three versions (upon request):
452      #ifndef SOLVE_DIAGONAL_AUTODIFF
453        1. default version (dating back a while ago)
454      #else /* def SOLVE_DIAGONAL_AUTODIFF */
455      # ifdef SOLVE_DIAGONAL_KINNER
456        2. adjoinable version with k-innermost loop (G. Forget)
457      # else
458        3. adjoinable vectorized version of 2.
459      # endif
460      #endif /* SOLVE_DIAGONAL_AUTODIFF */
461      All flags are currently set within routines, but could/should be moved to CPP-options.
462      Array bounds for 1. are as before, for 2.,3. cover the entire domain
463      (could be changed for 1. too).
464    o verification/lab_sea (fwd):
465      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
466        use 7 categories (except hb87), new solve4temp params (except salt_plume),
467        constant salinity (=4) or variable salinity (salt_plume) done through
468        SItracer.
469    o pkg/seaice:
470      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
471      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
472         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
473        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
474        SEAICE_freeze got retired) but already better than previously with
475        SEAICE_freeze=123456.7 deg.C;
476      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
477        (safer multi-threaded setting); always set SEAICEuseEVP;
478      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
479        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
480        stop if multiple specifications for the same coeff; make sure default
481        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
482    o pkg/obcs:
483      - allow to switch to upwind 1rst order advection scheme for the advective
484        flux computation at the open-boundary; disabled for adjoint built.
485    o pkg/ptracers:
486      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
487      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
488      - add parameter to decide when to start a tracer; use internal flag to
489        know which tracer to step-forward; switch this internal flag at the top
490        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
491        for adjoint built.
492    o pkg/seaice:
493      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
494      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
495      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
496    o pkg/ecco:
497      - fix writing of output file DiagnosCost_ClimSalt/Theta
498        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
499    o pkg/seaice:
500      - add missing initialisation of COR_ICE array in dynsolver.F
501      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
502        compiled either way, and is tested in all exps (multidim was only tested
503        in lab_sea ad before).
504      - cosmetic change to prepare for future addition of ITD. no change to results.
505        no defaults change.
506      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
507      - by lack of adequate verification experiments, I further used custom versions
508        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
509        should be correct.
510      - avoid recomputations in ad.
511    o array initialisation in adjoint mode:
512      1) pkg/mom_common/mom_calc_ke.F:
513        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
514        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
515        part this initialisation is gone, resulting in Floating Point Exception
516        (caught by open64 compiler with debug option).
517      2) model/src/convective_weights.F
518        set output convectCount over the full array range (instead of doing
519        an update): this fix a similar issue when called within recomputation (adjoint)
520        which could by-pass the initialisation (normally done in the caller S/R).
521    o pkg/seaice:
522      - final version of turbulent flux params, as agreed at MIT ice meet:
523           SEAICE_mcPheePiston (default is ~ 0.000875)
524           SEAICE_mcPheeTaper (default is 0.)
525           SEAICE_frazilFrac (defualt is 1.)
526           SEAICE_mcPheeStepFunc (default is false)
527      - changes results at trunction error level
528      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
529    o added pkg/frazil:
530      - see frazil_description.tex for details
531      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
532    o pkg/shelfice/shelfice_thermodynamics.F
533      - fix exponents for velocity dependent exchange coefficients: change
534        from 2/3(=0) to 0.66666666666666667
535      - move computation of velocity dependent exchange coefficients into
536        separate loop, so that it applies to both thermodynamics
537      - move some divisions by constants out of loops
538    
539    checkpoint63j (2012/02/16)
540    o pkg/seaice:
541      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
542      - SItracer:  added run time params, and allow coupling to ocn salinity.
543    o pkg/seaice: remove (almost) all divisions by constants within loops
544      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
545      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
546      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
547      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
548    o pkg/seaice :
549      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
550        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
551      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
552      - add permanent SItflux diag that corresponds to TFLUX but includes
553        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
554      - allow activation/testing of a fix for suspected missing term in
555        ocn-ice heat budget (to be confirmed). To test this, you want to
556        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
557        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
558      - no change in results, fwd or ad.
559    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
560      - switch to variable freezing point.
561           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
562      - bug fix : the sublimation term that was missing is now activated.
563           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
564      - bug fix : flooding sign term for SIsal0.NE.0.
565           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
566    o pkg/seaice:
567      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
568        is now the default, and the old default constant freezing point is recovered
569        with SEAICE_tempFrz0    = -1.96,
570             SEAICE_dTempFrz_dS = 0.,
571      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
572      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
573      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
574        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
575      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
576        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
577      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
578        seaice_growth r149 for legacy branch (no results change).
579      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
580        from I. Fenty).
581      - results did not change except for global_ocean.cs32x15, mostly due to the
582        switch to variable freezing point (see above item for detail).
583    o pkg/thsice:
584      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
585        seawater freezing in thsice_calc_thickn (not used).
586    o pkg/seaice: turbulent flux term specification via run time params.
587      - replace CPP switches with run time switches to facilitate testing
588      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
589                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
590      - added runtime parameter : SEAICEturbFluxFormula
591      - move Mcphee constants to SEAICE_PARAMS.h
592      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
593                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
594                 remove seaice_summary call (moved to seaice_init_fixed)
595      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
596        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
597      - seaice_summary.F : add missing report of read turbulent flux term set up
598                           and SITRACER.
599      - seaice_check.F : check range; inform and stop if retired CPPs are used
600                         (incl. SEAICE_AGE).
601      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
602             CPP switch, same computation as before for the different options.
603      - change results at the truncation level.
604    o pkg/seaice:
605      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
606        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
607        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
608      - update verification/*/input*/data.seaice:
609        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
610        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
611        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
612        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
613    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
614      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
615        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
616        difference in results only due to machine truncation.
617      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
618        MaykutPolySatVap; keep MIN_LWDOWN.
619      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
620      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
621        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
622    o pkg/salt_plume:
623      - isolate saltPlumeFlux array exch into a specific S/R called from
624        do_oceanic_phys.F
625      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
626    o verification:
627      - move untested set-up to MITgcm_contrib/verification_other.
628    o pkg/seaice:
629      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
630    o pkg/seaice:
631      - seaice_solve4temp.F (keeping results unchanged):
632        * add 2 future run-time params to select which saturation vapor pressure
633          formula is used and how post-iteration fluxes are set.
634          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
635        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
636          the linearized expression to stay consistent with tsurf finding.
637      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
638        can be < 0.
639    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
640      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
641        conductive heat flux F_c , and add it explicitly when updating tsurf as
642        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
643        so that now F_ia has a consistent meaning through the entire routine.
644        This causes differences at truncation level: update output of fwd exp.
645        global_ocean.cs32x15.seaice.
646    o pkg/seaice:
647      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
648        of arrays, sign/direction of fluxes; no effect on results.
649      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
650        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
651        note: this should have been done before changing celsius2K default.
652      - to keep results unchanged, add back old value of celsius2K in verification
653        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
654      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
655        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
656        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
657        freezing temp is consistent with value in seaice_growth.F ; this causes
658        differences at machine truncation level: update lab_sea AD output (3/4).
659    o pkg/seaice:
660      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
661        and climsst/sss even when using seaice (to prevent calculation that might
662        use SST on land); does not affect any verification exp.
663      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
664        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
665    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
666      over land (non-legacy code)
667    o vectorize salt_plume package:
668      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
669      - this code computes plumebk everywhere (also over land), thus requires
670        code to avoid divisions by zero and catch the case of kLev=Nr.
671      - efficiency of salt_plume_frac is still sub-optimal
672    o tools (genmake2):
673      - fix makefile NAME specification (option: -makefile NAME) by adding
674        "-f $MAKEFILE" in few places where it was missing including makedepend
675        command (contribution from Paul).
676    
677    checkpoint63i (2012/01/24)
678    o model/src:
679      - add factorized versions of some EOS code to find_rho.F,
680        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
681    o model/src:
682      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
683      - change default celsius2K from 273.16 to 273.15
684      - to keep results unchanged, add back old value of celsius2K in verification
685        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
686         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
687    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
688      to make TAF generate vectorizable code
689    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
690       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
691       have flags that do this more efficiently.
692    o pkg/diagnostics/diagstats_calc.F
693      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
694    o pkg/obcs (with exch2):
695      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
696        and remove code (in obcs_readparms.F) which was based on EXCH of indices
697        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
698    o pkg/exf and seaice exp:
699      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
700        so that switching off area & heff advection flags does not affect results.
701      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
702      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
703        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
704        results of verification experiments: 1D_ocean_ice_column(fwd),
705        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
706        and offline_exf_seaice (all 4).
707    o pkg/seaice:
708      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
709        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
710      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
711        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
712        not multi-dim advection;
713      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
714        SHORTWAVE_HEATING #undef.
715    o optim: make Makefile more robust (?)
716    o pkg/obcs:
717      * fix treatment of obcs_read_pickup for TAF
718    o pkg/shelfice:
719      * add missing initialisation of num_shifwflx
720      * new adjoint verification exp. for isomip
721      * change Prandtl and Schmidt numbers from generic formulations
722        (in terms of model diffus. and visc.) to separate runtime
723        parameters, with Holland and Jenkins (1999) default values.
724    o pkg/exf (interpolation):
725      - extended input field (2 rows) near the N & S poles:
726        * fill in with the symetric value (when even Nb of data in longitude)
727        * add average value at the poles only for scalar quantities ; for vector
728          component interpolation, skip the averaging and keep duplicated values,
729          unless the 2 components have same location (uvInterp=T) in which case
730          interpolate the 2 components together using S/R EXF_INTERP_UV.
731      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
732        together: this allows to account properly for local orientation when
733        averaging at N & S pole.
734      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
735        exf-interpolation near N & S poles. Undef by default.
736      - add debug check/print on 1rst iter if debugLevel >=2.
737    o pkg/exf:
738      - change masking flags definition (no longer "parameter"), put them in
739        common block and set them in S/R EXF_INIT_FIXED.
740      - change recognized masking flag from s,u,v to c,w,s since the mask
741        to use (maskC,W,S) depends on position on model grid and has little to
742        do with scalar/vector difference; fix masking if using P-coordinates.
743      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
744        and update results of exp. global_with_exf (x2).
745      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
746    o pkg/obcs
747      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
748    o pkg/exf (interpolation):
749      - assume periodicity in X only if input field cover full longitude range.
750      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
751        and should vectorise).
752      - fix input lat of the 2 added row (in case we provide N.pole data).
753    
754    checkpoint63h (2011/12/30)
755    o pkg/seaice:
756      - change declaration of UVM from _RL to _RS in order to get B-grid
757        uIce,vIce monitor when _RS = real*4
758    o pkg/offline:
759      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
760      - compute vertical velocity if not read from file (switch on exactConserv
761        & staggerTimeStep);
762      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
763    o verification:
764      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
765        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
766        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
767      - update output of exp. global_ocean.cs32x15.viscA4 after changing
768        grid-file angles (used here for coriolis-3d);
769      - remove (or gzip) few files not needed to run fizhi-cs experiments.
770    o pkg/exf (vector interpolation):
771      - rotate vector component toward local grid-axis orientation using grid-angles
772        (stored in GRID.h) instead of locally computed rotation angle; keep old code
773        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
774    o pkg/seaice:
775      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
776        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
777    o pkg/PKG_OPTIONS.h files:
778      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
779        outside of the #ifdef ALLOW_THISPKG / #endif block.
780      - update verification/*/code/PKG_OPTIONS.h files.
781    o add a verification experiment (offline_exf_seaice/input.seaice) that test
782      the B-grid LSOR solver
783    o pkg/seaice: sort out emissivity and long wave radiation step 2:
784      - add emissivity for snow and ice as new run-time parameters
785        (unfortunately) that default to the corresponding exf values; this
786        changes results in most verification experiments so that for backward
787        compatibility these parameter have to be set explicitly to inconsistent
788        values (ugly);
789      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
790        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
791        until we agree how to handle this bug properly
792    o pkg/exf (interpolation):
793      - add a set of run-time param ({inputfield}_interpMethod), one for
794        each interpolated input field, to select the interpolation method
795        with a value of zero switching off the interpolation;
796      - print interpolation parameters to standard output;
797      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
798        (to use instead runoff_interpMethod=0 in data.exf).
799      - simplify default setting of interpolation parameters (for all fields,
800        set position to match model grid cell-center position, leading to trivial
801        interpolation in case of regular Lat-Lon grid) and fix for the case of
802        non-uniform delY.
803    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
804       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
805       this factor is absolutely required, because the lw exitance (= out-going
806       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
807       where the reflectivity rho = 1-emissivity for conservation reasons. Once
808       this is established, we can remove the CPP-Flag (if we want to).
809    o pkg/seaice:
810      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
811        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
812      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
813        what the name implies (and not emissivity*BoltzmannConstant), this means
814        the old default value of 5.5e-8 now means
815        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
816        S/R exf_readparms
817      - FV-discretization of the B-grid LSOR solver, turn on with
818        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
819        of the calling routine dynsolver, so that B and C-grid code look a
820        little more alike.
821      - fix index bugs in ostres.F (B-grid code)
822    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
823    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
824      default for SEAICE_emissivity, if useEXF; requires setting a wrong
825      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
826      backward compatiblity
827    o model/src: use sigmaR in calc_ivdc
828    
829    checkpoint63g (2011/12/16)
830    o pkg/seaice/seaice_growth.F:
831      fix heat conservation of the coupled ocean-seaice system.
832      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
833      solid vs liquid water treatment is resolved via QNET.
834    o pkg/seaice/seaice_growth.F:
835      add missing term for sublimation in saltFlux, which was breaking conservation.
836    o pkg/seaice/seaice_model.F:
837      Remove this patholigical case treatment in evolution branch,
838      where it is un-necessary and breaks conservation.
839      Update global_ocean.cs32x15/results accordingly for
840      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
841    o model/src:
842      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
843      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
844    o pkg/obcs:
845      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
846      tendency for temperature and salinity that is then applied to update
847      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
848      horizontal advection and diffusion contributions on the boundary (in
849      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
850      removing the mask in S/R timestep_tracer. The advantage of this approach is
851      that the updated tracer values include contributions from the surface
852      forcing and vertical diffusion.
853      This modification changes exp4.stevens because of vertical diffusion.
854    o model/src:
855      change non-curvilinear grid setting to also work with exch2 + blank tiles:
856      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
857        face dimensions.
858      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
859        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
860        and INI_SPHERICAL_POLAR_GRID.
861      change test-experiment global_ocean.90x40x15:
862      - split the domain in many more tiles (9x4 tiles of 10x10 each);
863      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
864      - update results of both test (std & dwnslp).
865    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
866       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
867    o model/src:
868      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
869        and fix initialisation when using sigma-coords.
870    o model/src:
871     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
872       to their current value at the beginning of forward_step.F": add a new run-time
873       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
874     - set doResetHFactors=T in the following test exp:
875        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
876        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
877        and tutorial_global_oce_in_p (nonLinFS in p)
878    o pkg/ecco
879      - added IES cost term
880    o verification/advect_xz
881      - scale down the depth by 1/100 (from 200 km to just 2.km)
882      - add secondary test using divergent flow, r-star and implicit vertical advection.
883      - add note (check_conserve_TS.txt) and matlab script to check global
884        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
885    o pkg/rbcs:
886      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
887    o pkg/obcs (Stevens BCs):
888      - fix various problems in the phase speed computations of the Stevens
889        boundary conditions:
890        - sign error for western and southern boundaries,
891        - time tendencies were underestimated by factor of dTracerLev and some just
892          zero (for multidim advection schemes) -> now estimate time tendencies
893          from difference between previous (n) time level and the one before (n-1);
894          this requires storing a field per tracer per boundary, also in the pickup
895          files.
896        - replace deltaTmom in cflMer/Zon computation with dTracerLev
897        - set default phase velocity to cflMer/Zon
898      - update verification experiment exp4.stevens
899    o pkg/generic_advdiff (implicit_r):
900      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
901        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
902      - fix implicit vertical diffusion or advection with NonLin FreeSurf
903        (was using current recip_hFacC instead of future recip_hFacC): set future
904        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
905        solver S/R ;
906      - fill diagnostics of vertical advective fluxes (computed from tendency)
907        when using implicit vert. advection;
908      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
909         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
910         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
911         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
912    o pkg/diagnostics:
913      - add diags for T & S tendency which goes through Adams-Bashforth.
914    
915    checkpoint63f (2011/11/30)
916    o pkg/obcs/obcs_calc_stevens.F:
917      - join some loops to reduce number of if-statements
918      - fix a bug in code for northern and southern boundaries.
919    o pkg/seaice/seaice_init_varia.F
920      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
921        caused zero ice-velocities for the B-grid code
922    o pkg/seaice/seaice_init_fixed.F
923      - fix a bug in the initialisation of the second metric terms
924        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
925      - this affects all seaice configurations with useCurviLinearGrid = .true.
926        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
927        = .true. (default)
928      - the only verification experiment affected is global_ocean.cs32x15:
929        icedyn, seaice, and seaice_dynmix (AD)
930    o pkg/thsice/thsice_diagnostics_state.F
931      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
932        not contain garbage that can lead to surprises in diagstats_calc.F
933    o model/src:
934      - move bi,bj loops inside INTEGR_CONTINUITY ;
935      - call INTEGR_CONTINUITY directly from forward_step.F
936        (previously called from momentum_correction_step.F)
937      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
938        forward_step.F and pkg/ecco/the_main_loop.F
939    o model/src/do_oceanic_phys.F:
940      - reset addMass to zero only if useICEFRONT ;
941      - separated k-loop for rhoInSitu calculation ;
942      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
943        and at constant T,S (= WdRHOdP);
944      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
945        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
946        transport of locally-referenced potential density);
947        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
948    o gluemnc:
949      - replace ncrcat with ncks when adding variables to *.glob.nc
950      - change the way variables without record dimensions are handled so that
951        files that have variables with and without record variables can be glued:
952        add a record dimension with a new unique name to be able to differentiate
953        between variable with and without a-prior record dimensions. Remove
954        this record dimension before adding the variable to the *.glob.nc file.
955        This procedure automatically works also for grid.*.nc files that do not
956        have any record dimension.
957    o verification/cpl_aim+ocn:
958      - generate new reference output on baudelaire (gfortran, mpich2) (previously
959        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
960    o pkg/obcs/obcs_calc_stevens.F:
961      - add code for northern and southern boundaries.
962      - reorder some loops to save some operations and so that drFBar can be scalar
963    o model/src:
964      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
965        truncation) and add diagnostics for Adams-Bashforth tendency increment.
966      - update test-exp. AD output:
967        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
968      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
969        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
970        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
971        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
972        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
973        tutorial_plume_on_slope.
974    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
975      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
976      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
977      does not even come with an F77 compiler anymore, this should not be
978      a limitation
979    
980    checkpoint63e (2011/11/06)
981    o pkg/seaice adjoint of LSR:
982      - substantially rework STORE dirs.
983      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
984        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
985        and only perform SOLV_MAX_FIXED adjoint iters.
986        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
987        always goes to same record, meaning that the last forward field will be
988        the one used in the adjoint - an approximation.
989      - now produces non-zero LSR-related gradients, and acceptable gradients for
990        An's zonal (x-z) test case (to be checked in)
991      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
992        (but these are screwed up by the thermodynamics in the first place);
993        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
994        output_adm.txt also reflects changes to seaice_lsr
995      - global_ocean.cs32x15:
996        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
997          (output_adm.seaice.txt was updated)
998        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
999          (output_adm.seaice_dynmix.txt)
1000    o test-exp. exp4+stevens:
1001      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1002    o pkg/seaice (lsr solver):
1003      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1004        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1005      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1006      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1007        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1008      - compute (with new S/R) and print initial (+ free-driff sol. if available)
1009        and final residual of linearised system.
1010    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1011      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1012    o pkg/obcs: Stevens BCs (still only for east and west)
1013      - fix Stevens BCs by using intermediate velocities of previous
1014        time step as "baroclinic" contribution rather velocity of one grid cell
1015        inside the boundaries; more consistent but makes the entire treatment
1016        more complicated, requires new pickup files and two new S/Rs:
1017        obcs_copy_uv_n and obcs_save_uv_n
1018        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1019        (undefined by default)
1020      - silently move computation of some grid factors into separate loops to
1021        save some recomputations
1022      - add a hack for non-linear free surface
1023      - add a verification experiment to exp4 that tests this code
1024    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1025    
1026    checkpoint63d (2011/10/25)
1027    o pkg/obcs + seaice-dynamics:
1028      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1029        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1030        values (consistent with an implicit method).
1031      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1032        return to older implementation (same results as before); note that none of
1033        the "experimental" OBCS_SEAICE options are implemented in the new version.
1034      - switch test exp. seaice_obcs to use new version (update output).
1035    o pkg/seaice:
1036      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1037      - add parenthesis in Water-Ice drag calculations (evp & lsr);
1038      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1039        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1040      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1041        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1042    o pkg/layers:
1043      - Include potential density as new coordinate (Thanks to David Munday)
1044    o pkg/dic:
1045      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1046        carbonate computation/output to CALC_PCO2_APPROX
1047    o pkg/generic_advdiff
1048      - make TAF generate code that vectorizes:
1049        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1050    o model/src:
1051      - improve vectorization also for adjoint code of
1052        solve_tridiagonal and solve_pentadiagonal. As this requires up to
1053        5 new 3D-fields, this code is only turned on for the combination of
1054        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1055        for singular matrix check (only for TARGET_NEC_SX).
1056      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1057        ALLOW_AUTODIFF. This flag now needs to be set outside of
1058        solve_tri/pentadiagonal.F
1059    o pkg/exf:
1060      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1061        optional namelist EXF_NML_OBCS).
1062      - add many debug-print (to trace down where pkg/cal error msg comes from)
1063    o pkg/mom_vecinv/mom_vi_hdissip.F
1064      - rearrange loops so that vectorization is improved and in particular
1065        the adjoint routine vectorizes. The code is a little longer now, but I
1066        think easier to read.
1067        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1068    o pkg/seaice:
1069      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1070    o pkg/exch2:
1071      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1072        used as default; keep using matrix version in adjustment.cs-32x32x1.
1073    o tools/build_options:
1074      - after merging some MPI and/or multi-threads specific optfiles so that
1075        the modified default optfile support both built (using genmake2 -mpi
1076        for the MPI built, using genmake2 -omp for OpenMP built),
1077        move now obsolete optfiles to tools/build_options/unsupported/
1078       (add copy of email sent to support list in doc/optfiles_changes.txt)
1079    
1080    checkpoint63c (2011/09/28)
1081    o pkg/ebm:
1082      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1083        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1084    o pkg/seaice (SItracer pickup)
1085    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1086      To be done:
1087      - thorough testing of missing fields in S/R seaice_read_pickup
1088      - thorough matching between generic tracers and specific fields used
1089        (e.g. volume-weighted age, area-weighted age, salinity, ...)
1090    o pkg/grdchk:
1091      - all procs calculate and print finite-difference gradient (for testreport)
1092      - change description output used by testreport;
1093      - AD testing: also compare and report Finite-difference gradient;
1094        => update all output_adm*.txt
1095    o test exp. global_ocean_ebm:
1096      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1097        and turn on exactConserve; update (fwd) output.
1098    o pkg/seaice (LSR):
1099      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1100      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1101        * identical results with non-CS topology (but save up to half of EXCH calls)
1102        * no much changes in cs-32 verification tests since no ice at face edges
1103         (differences due to convergence criteria, since nb of iterations changed)
1104        * expect some differences on lat-lon-cap grid.
1105        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1106    o pkg/exch2:
1107      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1108        many tiles); until alternative coding is added, just add a stop.
1109    o pkg/kpp:
1110      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1111        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1112    o optfiles:
1113      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1114        into corresponding standard one, which now support different build:
1115        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1116      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1117    o pkg/obcs (seaice):
1118      - add missing EXCH for uIce,vIce after applying OBCS;
1119      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1120        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1121        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1122      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1123      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1124        and eedata.mth for MPI and mutlti-threaded testing.
1125    o pkg/flt:
1126      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1127      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1128      - fix pickup and trajectories + profiles output with multi-threads;
1129      - add parameter to select group of fields to write along trajectory and
1130        profile (default unchanged);
1131      - only call PORT_RAND* function when flt_noise <> 0;
1132      - add multi-threaded test for verification exp. flt_example.
1133    o eesupp/src:
1134      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1135      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1136        actual number (from env.var. setting).
1137    o pkg/ebm:
1138      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1139      - add multi-threaded test for verification exp. global_ocean_ebm
1140    
1141    checkpoint63b (2011/08/29)
1142    o pkg/ebm:
1143      - fix sign of runoff;
1144      - update directly forcing fields (Qnet,EmPmR) to use standard
1145        external_forcing_surf.F (remove ebm_forcing_surf.F);
1146      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1147      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1148        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1149      - update global_ocean_ebm parameters file data and update output (fwd+ad).
1150    o verification/matrix_example:
1151      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1152        MPI and mutlti-threaded testing.
1153    o pkg/matrix:
1154      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1155      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1156      - fix for multi-threaded (remove DATA statement);
1157      - use standard DIFFERENT_MULTIPLE function;
1158      - add MATRIX_OPTIONS.h
1159    o verification/matrix_example:
1160       To allow to split the domain in several tiles, change the domain size
1161        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1162        Western side) of land points.
1163    o (*_)write_pickup:
1164      - fix few bugs in mypackage_read/write_pickup.F
1165      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1166        array of length 1 (was caught by compiler syntax-check).
1167    o pkg/diagnostics (velocity potential solver):
1168      - fix initialisation of main diagonal matrix (for overlap values)
1169    o tools/build_options:
1170      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1171        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1172      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1173        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1174        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1175        and use "-devel" testreport option for standard testing on baudelaire.
1176    o pkg/grdchk:
1177      - Assume that all gradient-check position are within the same tile
1178        corresponding to global indices (iGloTile,jGloTile) and that
1179        positions (i,j indices or nbeg) are local to this tile;
1180      - set tile local-indices and proc. number according to tile global-indices;
1181      - remove grdchkwhichproc from namelist (retired param);
1182      - send adjoint gradient to all procs so that all procs print it to STDOUT;
1183      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1184    o adding package bbl (Bottom Boundary Layer)
1185      description in MITgcm/pkg/bbl/bbl_description.tex
1186      example/test experiment in MITgcm_contrib/bbl
1187    o adjoint verifications
1188      - changed 5 experiments to multi-tiles
1189        * global_ocean.90x40x15
1190        * obcs_ctrl
1191        * offline_exf_seaice
1192        * tutorial_dic_adjoffline
1193        * tutorial_tracer_adjsens
1194        changed reference output for those that crossed tile boundaries
1195        (changed choices of gradient check positions)
1196      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1197      - temporary bug fix in grdchk_loc.F for obcs
1198    o genmake2 & testreport
1199      - add target "obj" (just for OBJFILES files) to Makefile;
1200      - add option to specify FEXTRAFLAGS on command line.
1201    o pkg/mypackage:
1202      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1203    
1204    checkpoint63a (2011/08/02)
1205    o pkg/diagnostics (velocity potential):
1206      - fix velocity-potential calculation when using OBCS: balance net inflow
1207        at each level (new S/R OBCS_DIAG_BALANCE).
1208      - fix some of the problems with OBCS in stream-function calculation.
1209    o pkg/exf/exf_readparms.F
1210      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1211        EXF_NML_OBCS) more consistent, so that you need not have these lists
1212        in data.exf when they are not used.
1213    o optim/optim_readdata.F:
1214      - add some output about obcs variables that might help debugging
1215      - add a check about nvarlength
1216    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1217    o pkg/diagnostics (velocity potential):
1218      - fix mask for OBCS (still problems in stream-function with OBCS);
1219      - add specific parameter (default = main code CG2D params) for solver;
1220      - in case of poor convergence, use solution corresponding to lowest residual.
1221    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1222      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1223      and should be avoided where possible.
1224    o model/src (rStar):
1225      - include r* effect on reference-state (PhiRef) in totPhiHyd
1226        (so that it's really the potential anomaly at the cell center);
1227        affect solution only if z* with full pressure in EOS.
1228      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1229        update output (because of z* in totPhiHyd and viscA4 changes);
1230      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1231        @ constant r) until interpolation at constant r is implemented.
1232    o pkg/diagnostics
1233      - fix RCENTER diagnostics in case cell center is not at interface middle
1234    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1235      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1236      that THETA and SALT are "conservative temperature" and "absolute
1237      salinity"
1238    o pkg/ctrl
1239      - fix computation of endrec in s/r ctrl_init_rec
1240      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1241    o pkg/seaice/seaice_growth.F
1242      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1243        remove then obsolete STORE directives
1244      - fix STORE directives for tice and tices, so that only the
1245        appropriate part of the fields are stored (and not the entire
1246        field); update global_ocean.cs32x15.seaice AD output.
1247      - cosmetic changes: adjust CPP flags and indentation for better
1248        legibilty
1249    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1250      Chris Wilson)
1251    o pkg/gmredi:
1252       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1253       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1254    
1255    checkpoint63  (2011/07/11)
1256    o pkg/exch2:
1257     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1258     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1259       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1260       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1261    o pkg/diagnostics:
1262     - deal with pairs of post-processed diags which are computed together; in
1263       particular, re-order list of diags within 1 file to save 2nd computation.
1264     - add S/R to compute velocity stream-function (called after velocity-potential
1265       calculation) from divergence free transport -> new diagnostics "PsiVEL".
1266     - add parameter to select grid-point location where PsiVEL == 0.
1267    o eesupp/src:
1268       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1269       (specific S/R needed with exch2 topology - for now, just print an error msg)
1270    o pkg/shelfice
1271     - Implement friction velocity-dependent transfer coefficients following
1272       Holland and Jenkins, JPO, 1999
1273       Original code by M. Losch with small modifs.
1274       Enable with CPP option SHI_ALLOW_GAMMAFRICT
1275       and runtime flag SHELFICEuseGammaFrict
1276    o verification lab_sea & global_ocean.cs32x15:
1277     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1278       does not miss some dependencies (but is slower) and also works with many files
1279       (default makedepend limitation for AD built).
1280     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1281    o pkg/diagnostics:
1282     - add run-time parameter "useMissingValue" (def=False) to fill land-point
1283        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1284       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1285     - Extend the use of "missing_value" setting from data.diagnostics for the case
1286       of counter-diagnostics (where fraction-weight is zero). This applies both to
1287       MNC and MDS output files.
1288    o pkg/seaice/seaice_growth.F:
1289      - add 'a priori' cap of latent heat flux based on actual mass considerations
1290        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1291        non-legacy seaice_solve4temp.
1292      - add diagnostic of the residual sublimation freshwater flux (the freshwater
1293        flux taken from the ocean if the total actual latent heat fluxes exceed
1294        the maximum)
1295      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1296       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1297      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1298       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1299      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1300      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1301    o verification 1D_ocean_ice_column:
1302       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1303       update results
1304    o pkg/diagnostics:
1305     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1306       which are not filled-up but computed from other diags ; In this case, the mate
1307       diag points to the primary (filled-up) diag to used for post processing.
1308     - Update Velocity-potential computation using post-processed diag framework.
1309     ==> Change the ordering of fields and time-periods in MDS output file
1310       when using periodic averaging: now writes one time record with the full set
1311       of fields for this time period, then the next time reccord (it used to be
1312       one field with the full set of time records then the next field).
1313         Note: this is now similar to NetCDF (MNC) output file. <==
1314    
1315  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
1316  o adjoint monitor:  o adjoint monitor:
1317   - Add adjoint monitor output for packages exf, seaice   - Add adjoint monitor output for packages exf, seaice
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