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revision 1.1505 by jmc, Mon Sep 26 19:00:49 2011 UTC revision 1.1718 by jmc, Fri Aug 17 21:30:51 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification/testreport:
8      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
9      - can also use compressed (gzip) reference output file;
10      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
11        to be easier to collect by testreport.
12      - update existing TLM output (half out-of-date by more than 3 yrs).
13      - report NETCDF & LAPACK settings (from genmake2) in output dir.
14      - report run-time in each individual summary (previously only for AD test);
15        for TLM test, add also TAF version.
16      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
17    
18    checkpoint63r (2012/08/15)
19    o tools/genmake2:
20      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
21    o pkg/ecco/ecco_cost_final.F :
22      - fix fc print statements (to stdout and costfunction0000) so
23        that the printed value is always after the global sum.
24    o pkg/seaice/seaice_dynsolver.F :
25      - fix ice strength assymptote at SEAICE_area_max<1
26        (no change for the standard case of SEAICE_area_max=1)
27    o some cleaning:
28      - pkg source files: ensure that all *.F files from each pkg included the
29        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
30        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
31        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
32        includes;
33      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
34      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
35        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
36        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
37      - update option-file CPP_OPTIONS.h of all AD experiments:
38        * no longer include PACKAGES_CONFIG.h ;
39        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
40        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
41          including ECCO_CPPOPTIONS.h).
42    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
43      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
44        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
45        not necessary accurate).
46      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
47        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
48        deliberately break compilation (a remainder that it needs to be customized)
49      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
50      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
51      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
52    o tools/genamke2:
53      - check for lapack.
54    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
55      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
56        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
57        from both packages.
58      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
59      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
60      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
61        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
62    o pkg/cost : add comments to explain special and/or untested setups.
63    o pkg/exf:
64      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
65        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
66    o verification/*/code_ad:
67      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
68      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
69      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
70        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
71    o pkg/seaice :
72      - added possibility to change ice strength/PRESS0 relationship to
73        HEFF, according to the following run time parameters
74        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
75        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
76        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
77    o pkg/ggl90 :
78      - added run time flag mxlSurfFlag to include the code that ensure
79        mixing between first and second level (previously included as a comment)
80    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
81      - add test of newly added dumpAdByRec=T option where
82        we write all records to one file per variable.
83    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
84      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
85        to check that this code is ok with taf and compiles in adjoint.
86    o pkg/autodiff :
87      - added run time param dumpAdByRec : ad dump format switch.
88        If true then write all records to one file per variable.
89        Else write one file per record (remains the default).
90      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
91    o pkg/seaice:
92     - Added SEAICEuseTILT run time switch : if set to
93       false then omit the tilt term in seaice dynamics.
94     - Fix free drift calculation.
95    o pkg/shelfice:
96      When initializing SHELFICEDragQuadratic, set default to be
97      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
98      but retain option to set it independently
99      (inconsistenty spotted by Veronique Dansereau)
100    o eesupp/inc:
101      - in EEPARAMS.h, add real-type constant for some frequently used simple number
102         (0,1,2,1/2), with name explicitly referring to RS/RL type.
103    o model/src:
104      - move balancing of relaxation terms to new S/R balance_relax.F.
105    o pkg/autodiff:
106      re-write active I/O high-level (control) S/R:
107      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
108      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
109      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
110        MDS_READ/WRITE_FIELD); change loops to multi-threads.
111      - update and merge active_file_control_slice.flow into active_file_control.flow
112      - update the calls in lower level S/R (active_file.F, active_file_g.F and
113        active_file_ad.F) keeping the argument list and function unchanged.
114      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
115        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
116      - new low-level active I/O routines, one for each type (RL/RS), for active var
117        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
118        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
119        right type.
120    o autodiff and RS=real*4:
121      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
122        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
123      - change argument type of 3-D mask argument to _RS to match type in the call
124        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
125    o pkg/thsice:
126      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
127      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
128        fresh-water flux: uniform correction or proportional to local precip.
129    o pkg/ctrl:
130      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
131      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
132                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
133      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
134    
135    checkpoint63q (2012/07/30)
136    o pkg/autodiff:
137      note about monitor and snap-shot of ad-variables:
138      a) need to apply ADEXCH before monitor or output of ad-vars to include
139       overlap contributions (was done for adjDump but missing for monitor).
140      b) since ADEXCH implies adding overlap values to interior array, machine
141       truncation error is expected when adding an ADEXCH call in the middle of
142       the time-stepping (although mathematically identical).
143      modifs:
144      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
145        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
146      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
147        apply ADEXCH before monitor or snap-shot of ad-variables:
148           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
149      - implement new method (copy+adexch) for snap-shot and monitor of main model
150        ad-vars (initially not used by default -> output unchanged).
151      - change default (set to 2) to use new method and update few output_adm.txt
152        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
153        and both tutorial_tracer_adjsens tests).
154      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
155        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
156    o pkg/ctrl:
157      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
158      generic control variables via
159      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
160      Only required customization should be S/R ctrl_map_ini_genarr.F
161      (routine in repository contains example)
162    o pkg/exf:
163      - fix and refine checking of surface-relaxation setting when using EXF
164    o verification (adjoint exp):
165      - reduce length of simulation by half for experiment global_ocean.cs32x15
166        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
167    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
168      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
169        of KE that can occur with aggressive optimization
170      + put quadratic bottom drag calculation in separated loops (only done if
171        using bottomDragQuadratic)
172    o model/src: CG2D_NSA
173      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
174         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
175      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
176         change cg2d residual target to be expressed in Wunits (=> do not normalise
177         RHS ; this fix global_max Pb with TAF); update output.
178    o verification/tutorial_tracer_adjsens:
179       improve parameter consistency (and get rid of warnings):
180       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
181       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
182       - use staggerTimeStep (for stability) in som81; use default rotation period.
183    o pkg/exch2:
184      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
185        reset to 0 = 1 long line in X)
186    o pkg/mdsio:
187      - fix reading of dimensions from meta file for large-size domain
188    o model/src:
189      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
190      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
191        Cubed-Sphere Exch with CS-corners inside the domain;
192        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
193        globalArea and to set hasWetCSCorners.
194      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
195        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
196      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
197        useCDscheme and useCubedSphereExchange).
198    o pkg/seaice/seaice_growth.F :
199      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
200        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
201        when the previous code was not correct.
202      - in all cases diagnoze the boundary condition mismatch to SIaaflux
203      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
204        that term to QNET (essentially to set the melt/freeze water to 0degC).
205        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
206    o verification/global_ocean.cs32x15/input.seaice :
207      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
208      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
209      - update results (output.seaice.txt) accordingly.
210    o verification/lab_sea/input/data.seaice :
211      - remove SEAICEheatConsFix, which is now be tested
212        in global_ocean.cs32x15. The presently coded fix
213        is only consistent with real fresh water + nlfs.
214      - update results (output.txt) accordingly.
215    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
216    o AD_CONFIG.h file:
217      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
218      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
219        add it explicitly in each fortran src file where it is needed.
220        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
221        thus introducing potentially wrong dependency; therefore, better to include
222        it only where it's really needed, and after any other included OPTIONS file
223        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
224        or ALLOW_TANGENTLINEAR_RUN).
225    
226    checkpoint63p (2012/07/06)
227    o pkg/autodiff:
228      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
229      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
230        which are now read from new parameter file "data.autodiff" (inAdExact
231        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
232      - add file "data.autodiff" in all verification/*/input_ad/ directories.
233      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
234        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
235    o verification/tutorial_tracer_adjsens/
236      - add extra sub-verification which uses "SOM" advection scheme
237        (2nd Order-Moment Advection Scheme, Prather Limiter) with
238          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
239        and in data:
240          multiDimAdvection=.TRUE.,
241          tempAdvScheme=81,
242          saltAdvScheme=81,
243    o model/src:
244      - introduce ALLOW_BALANCE_RELAX which allow the removal
245       of the global mean of relaxation terms by setting
246       balanceThetaClimRelax and balanceSaltClimRelax
247      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
248       This case is now treated appropriately in seaice_growth.F
249    o pkg/seaice:
250      - do balanceEmPmR and balanceQnet based on the net fluxes
251        (SItflux) that enter the ocean+ice system rather than QNET
252        and EMPMR. Works best in real fresh water.
253      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
254        out of the diagnotics bloc, and stored in global arrays.
255    
256    checkpoint63o (2012/06/29)
257    o vertical mixing schemes:
258      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
259      - replace computation of density (in Function STATE1, opps_calc.F) by a call
260        to S/R FIND_RHO_SCALAR
261      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
262        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
263        affects output (vermix.ggl90) at truncation level.
264    o testreport:
265      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
266        (nSx,nSy) for the number of threads (from eedata.mth)
267    o model/src:
268      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
269        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
270    o verification/tutorial_tracer_adjsens/
271      - compile with ALLOW_CG2D_NSA
272      - run with nonlinFreeSurf=3
273      - update reference output_adm.txt
274    o tools/genmake2:
275      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
276        refine usePROFILES switching off (only when NetCDF is not available).
277    o verification (atmospheric set-up):
278      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
279    o pkg/profiles : refine profiles and files handling.
280    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
281    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
282      - changes to use model/src/the_main_loop.F rather than the ecco version
283        in ecco type adjoint runs.
284    o model/src:
285      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
286      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
287      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
288    o model/src:
289      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
290        update output of test experiment bottom_ctrl_5x5.
291    o pkg/generic_advdiff:
292      - implement vertical bi-harmonic diffusion (for now, only for T & S and
293        only explicitly).
294    o verification/bottom_ctrl_5x5/
295      update reference output (results changed quite some time ago,
296      not sure when; but new reference results look ok in terms of grdchk)
297    o verification/1D_ocean_ice_column/
298      For verification purposes, the exact adjoint rather than an approx.
299      should be used (e.g., to comare against F.D. or TLM).
300      removed autodiff_inadmode*_ad.F routines in code_ad/
301      Update results/ accordingly.
302    o pkg/cal:
303      - change cal_getdate.F so that output date is function of input time only
304        (less ambiguous, not mixed up with input iteration number).
305      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
306    o pkg/diagnostics:
307      - implement calendarDumps also for stats-diags
308      - implement calendarDumps also for snap-shot output (negative freq)
309      - for now, ignores calendarDumps if non-zero phase-lag.
310    
311    checkpoint63n (2012/06/04)
312    o model/src:
313      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
314        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
315      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
316        similar to calc_r_star.F); update results of experiment internal_wave and
317        tutorial_global_oce_in_p (affected @ truncation level).
318    o pkg/shelfice:
319      - add parameterisation of advective-diffusive flux into the ice shelf
320        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
321      - simply eps3/3a computation
322    o eesupp:
323     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
324       between tiles, just fill-in edges assuming locally periodic subdomain) and
325       add corresponding exchange subroutines (EXCH0);
326     - new CG-solver version (_EX0) for disconnected-tiles special case.
327    o model/src (CG-solvers):
328     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
329       (similar final residual output and max-Iter number as with standard version);
330     - allows to store and use lowest-residual solution (standard & _SR versions);
331     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
332     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
333    o eesup/src:
334     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
335       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
336    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
337    
338    checkpoint63m (2012/04/27)
339    o pkg/shelfice:
340     - account for partical cells in surface level below ice-shelf for hydrostatic
341       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
342    o ad test experiments:
343     - update and rename to "ad_optfile.local" local AD-optfile specific to a
344       particular adjoint verification experiment (in verification/*/code_ad/)
345    o pkg/seaice & pkg/exf:
346     - Part two of ECCO-CLIVAR code merges.
347       Completes merge of seaice area relax. code.
348       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
349       to be set in EXF_OPTIONS.h since this pkg controls its I/O
350       (and avoids second CPP option in SEAICE_OPTIONS.h)
351     - change default value of costIceStart & costIceEnd to a valid date.
352     - add snowPrecip to HSNOW in seaice_growth
353    o pkg/ptracers:
354     - move ptracers summary and setup check into separated S/R ; add a check for
355       valid PTRACERS_Iter0 value (error+stop or just warning).
356    o pkg/cal (+ pkg/ecco):
357     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
358       as input; and for AD, unless both are not differentiable (e.g., k index)).
359    o model/src:
360     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
361       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
362       temporary set to usingZCoords value (to be changed to F when using shelfice).
363     - hydrostatic pressure: implement partial cell near the surface also for
364       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
365       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
366    o pkg/ctrl/ctrl_init.F:
367     - add a formal parameter to s/r ctrl_init_rec to print
368       xx_$(ctrl_valiable)_file for easier debugging
369     - move call of cal_* routines into the if-block where they are really
370       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
371       to specify a startdate
372    o pkg/seaice:
373     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
374       global_ocean.cs32x15/code versions).
375     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
376       verification experiment global_ocean.cs32x15.seaice and update results.
377    o pkg/exf:
378     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
379       (according to useExfYearlyFields).
380    o pkg/cal:
381     - move calendar setting & summary (previously in cal_readparams.F) into new
382       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
383       length of the simulation is set (after SET_PARMS call); This is an attempt
384       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
385     - For safety: keep a record of pkg/cal parameter settings status
386               to allow to STOP if one pkg/cal S/R is called too early.
387     - add a stop in all basic pkg/cal subroutines if called before setting is done.
388     - modify cal_getdate.F: stop when nothing was returned;
389       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
390       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
391    
392    checkpoint63l (2012/04/04)
393    o pkg/bbl:
394      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
395        update global_with_exf output.yearly.txt file.
396    o pkg/cal:
397      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
398      - remove 2 unsused and very short (1 line only) functions ;
399      - remove unsused subroutines from AD-Diff list.
400    o model/src:
401      - start to implement clean wait to stop in initialization S/R (config_check.F,
402         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
403    o folowing PRINT_MESSAGE changes:
404      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
405    o pkg/bbl:
406      - modification so it can work with z*
407      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
408      - global_with_exf/input.yearly verification; changes output.yearly.txt
409    o eesupp/src:
410      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
411        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
412      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
413        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
414      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
415      - when using MPI, always set usingMPI=T ; set default accordingly and stop
416        if not consistent.
417      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
418        argument is zero (in case called within single-thread section).
419    o pkg/fizhi:
420        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
421        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
422    o pkg/exch2:
423      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
424        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
425      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
426        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
427        with bad ones coming from a not-yet-updated halo.
428        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
429    o pkg/frazil:
430        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
431        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
432    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
433    o verification/lab_sea
434      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
435      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
436      * nTimeSteps 3 -> 4
437      * changed reference output accordingly
438    o pkg/ctrl:
439      * fix ctrl_get_gen for xx_sst, xx_sss
440    o pkg/fizhi:
441      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
442        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
443      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
444        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
445        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
446    o pkg/gmredi:
447      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
448    o pkg/fizhi:
449      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
450        (old)aces open64 tuv test.
451    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
452    o pkg/mom_vecinv:
453      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
454        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
455        with non-lin free-surf).
456    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
457      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
458      some compilers (gfortran 4.6.0 on MacOS)
459    o momentum:
460      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
461        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
462        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
463    
464    checkpoint63k (2012/03/17)
465    o model/src:
466       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
467         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
468       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
469         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
470    o model/src: solve_*diagonal.F
471       - replace division with multiplication by inverse (similar to original version)
472         update output of AD exp. global_ocean.90x40x15.
473       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
474         to enable the use of the vectorized & differentiable solve_tridiagonal.F
475       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
476         vertical advection (to get solve_tridiagonal tested in AD mode).
477    o pkg/seaice: ECCO-CLIVAR merge:
478      1. seaice AREA relaxation
479         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
480         * runtime flag: SEAICE_tauAreaObsRelax
481      2. modified global mean cost imbalance code: CPP option
482          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
483    o another iteration on solve_*diagonal.F
484       Make choices independent of AUTODIFF
485       Default will be the adjoinable vectorized version.
486       Alternative choices are:
487       * non-adjoinable original version with low memory footprint:
488         #define SOLVE_DIAGONAL_LOWMEMORY
489       * still adjoinable but does not vectorize (k as inner-most loop):
490         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
491    o testreport
492     - add option to use a home made wrapper around "make"
493     - remove MITGCM_IEEE env. variable (no longer active)
494    o pkg/shelfice
495     - improve computation of friction velocity for velocity dependent
496       exchange coefficients: include velocities into SHELFICEBoundaryLayer
497       block to average velocities vertically
498     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
499    o Modify diagonal solvers, now three versions (upon request):
500      #ifndef SOLVE_DIAGONAL_AUTODIFF
501        1. default version (dating back a while ago)
502      #else /* def SOLVE_DIAGONAL_AUTODIFF */
503      # ifdef SOLVE_DIAGONAL_KINNER
504        2. adjoinable version with k-innermost loop (G. Forget)
505      # else
506        3. adjoinable vectorized version of 2.
507      # endif
508      #endif /* SOLVE_DIAGONAL_AUTODIFF */
509      All flags are currently set within routines, but could/should be moved to CPP-options.
510      Array bounds for 1. are as before, for 2.,3. cover the entire domain
511      (could be changed for 1. too).
512    o verification/lab_sea (fwd):
513      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
514        use 7 categories (except hb87), new solve4temp params (except salt_plume),
515        constant salinity (=4) or variable salinity (salt_plume) done through
516        SItracer.
517    o pkg/seaice:
518      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
519      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
520         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
521        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
522        SEAICE_freeze got retired) but already better than previously with
523        SEAICE_freeze=123456.7 deg.C;
524      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
525        (safer multi-threaded setting); always set SEAICEuseEVP;
526      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
527        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
528        stop if multiple specifications for the same coeff; make sure default
529        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
530    o pkg/obcs:
531      - allow to switch to upwind 1rst order advection scheme for the advective
532        flux computation at the open-boundary; disabled for adjoint built.
533    o pkg/ptracers:
534      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
535      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
536      - add parameter to decide when to start a tracer; use internal flag to
537        know which tracer to step-forward; switch this internal flag at the top
538        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
539        for adjoint built.
540    o pkg/seaice:
541      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
542      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
543      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
544    o pkg/ecco:
545      - fix writing of output file DiagnosCost_ClimSalt/Theta
546        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
547    o pkg/seaice:
548      - add missing initialisation of COR_ICE array in dynsolver.F
549      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
550        compiled either way, and is tested in all exps (multidim was only tested
551        in lab_sea ad before).
552      - cosmetic change to prepare for future addition of ITD. no change to results.
553        no defaults change.
554      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
555      - by lack of adequate verification experiments, I further used custom versions
556        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
557        should be correct.
558      - avoid recomputations in ad.
559    o array initialisation in adjoint mode:
560      1) pkg/mom_common/mom_calc_ke.F:
561        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
562        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
563        part this initialisation is gone, resulting in Floating Point Exception
564        (caught by open64 compiler with debug option).
565      2) model/src/convective_weights.F
566        set output convectCount over the full array range (instead of doing
567        an update): this fix a similar issue when called within recomputation (adjoint)
568        which could by-pass the initialisation (normally done in the caller S/R).
569    o pkg/seaice:
570      - final version of turbulent flux params, as agreed at MIT ice meet:
571           SEAICE_mcPheePiston (default is ~ 0.000875)
572           SEAICE_mcPheeTaper (default is 0.)
573           SEAICE_frazilFrac (defualt is 1.)
574           SEAICE_mcPheeStepFunc (default is false)
575      - changes results at trunction error level
576      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
577    o added pkg/frazil:
578      - see frazil_description.tex for details
579      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
580    o pkg/shelfice/shelfice_thermodynamics.F
581      - fix exponents for velocity dependent exchange coefficients: change
582        from 2/3(=0) to 0.66666666666666667
583      - move computation of velocity dependent exchange coefficients into
584        separate loop, so that it applies to both thermodynamics
585      - move some divisions by constants out of loops
586    
587    checkpoint63j (2012/02/16)
588    o pkg/seaice:
589      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
590      - SItracer:  added run time params, and allow coupling to ocn salinity.
591    o pkg/seaice: remove (almost) all divisions by constants within loops
592      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
593      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
594      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
595      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
596    o pkg/seaice :
597      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
598        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
599      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
600      - add permanent SItflux diag that corresponds to TFLUX but includes
601        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
602      - allow activation/testing of a fix for suspected missing term in
603        ocn-ice heat budget (to be confirmed). To test this, you want to
604        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
605        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
606      - no change in results, fwd or ad.
607    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
608      - switch to variable freezing point.
609           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
610      - bug fix : the sublimation term that was missing is now activated.
611           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
612      - bug fix : flooding sign term for SIsal0.NE.0.
613           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
614    o pkg/seaice:
615      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
616        is now the default, and the old default constant freezing point is recovered
617        with SEAICE_tempFrz0    = -1.96,
618             SEAICE_dTempFrz_dS = 0.,
619      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
620      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
621      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
622        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
623      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
624        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
625      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
626        seaice_growth r149 for legacy branch (no results change).
627      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
628        from I. Fenty).
629      - results did not change except for global_ocean.cs32x15, mostly due to the
630        switch to variable freezing point (see above item for detail).
631    o pkg/thsice:
632      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
633        seawater freezing in thsice_calc_thickn (not used).
634    o pkg/seaice: turbulent flux term specification via run time params.
635      - replace CPP switches with run time switches to facilitate testing
636      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
637                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
638      - added runtime parameter : SEAICEturbFluxFormula
639      - move Mcphee constants to SEAICE_PARAMS.h
640      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
641                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
642                 remove seaice_summary call (moved to seaice_init_fixed)
643      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
644        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
645      - seaice_summary.F : add missing report of read turbulent flux term set up
646                           and SITRACER.
647      - seaice_check.F : check range; inform and stop if retired CPPs are used
648                         (incl. SEAICE_AGE).
649      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
650             CPP switch, same computation as before for the different options.
651      - change results at the truncation level.
652    o pkg/seaice:
653      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
654        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
655        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
656      - update verification/*/input*/data.seaice:
657        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
658        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
659        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
660        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
661    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
662      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
663        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
664        difference in results only due to machine truncation.
665      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
666        MaykutPolySatVap; keep MIN_LWDOWN.
667      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
668      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
669        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
670    o pkg/salt_plume:
671      - isolate saltPlumeFlux array exch into a specific S/R called from
672        do_oceanic_phys.F
673      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
674    o verification:
675      - move untested set-up to MITgcm_contrib/verification_other.
676    o pkg/seaice:
677      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
678    o pkg/seaice:
679      - seaice_solve4temp.F (keeping results unchanged):
680        * add 2 future run-time params to select which saturation vapor pressure
681          formula is used and how post-iteration fluxes are set.
682          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
683        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
684          the linearized expression to stay consistent with tsurf finding.
685      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
686        can be < 0.
687    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
688      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
689        conductive heat flux F_c , and add it explicitly when updating tsurf as
690        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
691        so that now F_ia has a consistent meaning through the entire routine.
692        This causes differences at truncation level: update output of fwd exp.
693        global_ocean.cs32x15.seaice.
694    o pkg/seaice:
695      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
696        of arrays, sign/direction of fluxes; no effect on results.
697      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
698        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
699        note: this should have been done before changing celsius2K default.
700      - to keep results unchanged, add back old value of celsius2K in verification
701        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
702      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
703        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
704        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
705        freezing temp is consistent with value in seaice_growth.F ; this causes
706        differences at machine truncation level: update lab_sea AD output (3/4).
707    o pkg/seaice:
708      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
709        and climsst/sss even when using seaice (to prevent calculation that might
710        use SST on land); does not affect any verification exp.
711      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
712        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
713    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
714      over land (non-legacy code)
715    o vectorize salt_plume package:
716      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
717      - this code computes plumebk everywhere (also over land), thus requires
718        code to avoid divisions by zero and catch the case of kLev=Nr.
719      - efficiency of salt_plume_frac is still sub-optimal
720    o tools (genmake2):
721      - fix makefile NAME specification (option: -makefile NAME) by adding
722        "-f $MAKEFILE" in few places where it was missing including makedepend
723        command (contribution from Paul).
724    
725    checkpoint63i (2012/01/24)
726    o model/src:
727      - add factorized versions of some EOS code to find_rho.F,
728        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
729    o model/src:
730      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
731      - change default celsius2K from 273.16 to 273.15
732      - to keep results unchanged, add back old value of celsius2K in verification
733        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
734         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
735    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
736      to make TAF generate vectorizable code
737    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
738       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
739       have flags that do this more efficiently.
740    o pkg/diagnostics/diagstats_calc.F
741      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
742    o pkg/obcs (with exch2):
743      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
744        and remove code (in obcs_readparms.F) which was based on EXCH of indices
745        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
746    o pkg/exf and seaice exp:
747      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
748        so that switching off area & heff advection flags does not affect results.
749      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
750      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
751        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
752        results of verification experiments: 1D_ocean_ice_column(fwd),
753        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
754        and offline_exf_seaice (all 4).
755    o pkg/seaice:
756      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
757        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
758      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
759        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
760        not multi-dim advection;
761      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
762        SHORTWAVE_HEATING #undef.
763    o optim: make Makefile more robust (?)
764    o pkg/obcs:
765      * fix treatment of obcs_read_pickup for TAF
766    o pkg/shelfice:
767      * add missing initialisation of num_shifwflx
768      * new adjoint verification exp. for isomip
769      * change Prandtl and Schmidt numbers from generic formulations
770        (in terms of model diffus. and visc.) to separate runtime
771        parameters, with Holland and Jenkins (1999) default values.
772    o pkg/exf (interpolation):
773      - extended input field (2 rows) near the N & S poles:
774        * fill in with the symetric value (when even Nb of data in longitude)
775        * add average value at the poles only for scalar quantities ; for vector
776          component interpolation, skip the averaging and keep duplicated values,
777          unless the 2 components have same location (uvInterp=T) in which case
778          interpolate the 2 components together using S/R EXF_INTERP_UV.
779      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
780        together: this allows to account properly for local orientation when
781        averaging at N & S pole.
782      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
783        exf-interpolation near N & S poles. Undef by default.
784      - add debug check/print on 1rst iter if debugLevel >=2.
785    o pkg/exf:
786      - change masking flags definition (no longer "parameter"), put them in
787        common block and set them in S/R EXF_INIT_FIXED.
788      - change recognized masking flag from s,u,v to c,w,s since the mask
789        to use (maskC,W,S) depends on position on model grid and has little to
790        do with scalar/vector difference; fix masking if using P-coordinates.
791      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
792        and update results of exp. global_with_exf (x2).
793      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
794    o pkg/obcs
795      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
796    o pkg/exf (interpolation):
797      - assume periodicity in X only if input field cover full longitude range.
798      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
799        and should vectorise).
800      - fix input lat of the 2 added row (in case we provide N.pole data).
801    
802    checkpoint63h (2011/12/30)
803    o pkg/seaice:
804      - change declaration of UVM from _RL to _RS in order to get B-grid
805        uIce,vIce monitor when _RS = real*4
806    o pkg/offline:
807      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
808      - compute vertical velocity if not read from file (switch on exactConserv
809        & staggerTimeStep);
810      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
811    o verification:
812      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
813        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
814        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
815      - update output of exp. global_ocean.cs32x15.viscA4 after changing
816        grid-file angles (used here for coriolis-3d);
817      - remove (or gzip) few files not needed to run fizhi-cs experiments.
818    o pkg/exf (vector interpolation):
819      - rotate vector component toward local grid-axis orientation using grid-angles
820        (stored in GRID.h) instead of locally computed rotation angle; keep old code
821        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
822    o pkg/seaice:
823      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
824        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
825    o pkg/PKG_OPTIONS.h files:
826      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
827        outside of the #ifdef ALLOW_THISPKG / #endif block.
828      - update verification/*/code/PKG_OPTIONS.h files.
829    o add a verification experiment (offline_exf_seaice/input.seaice) that test
830      the B-grid LSOR solver
831    o pkg/seaice: sort out emissivity and long wave radiation step 2:
832      - add emissivity for snow and ice as new run-time parameters
833        (unfortunately) that default to the corresponding exf values; this
834        changes results in most verification experiments so that for backward
835        compatibility these parameter have to be set explicitly to inconsistent
836        values (ugly);
837      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
838        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
839        until we agree how to handle this bug properly
840    o pkg/exf (interpolation):
841      - add a set of run-time param ({inputfield}_interpMethod), one for
842        each interpolated input field, to select the interpolation method
843        with a value of zero switching off the interpolation;
844      - print interpolation parameters to standard output;
845      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
846        (to use instead runoff_interpMethod=0 in data.exf).
847      - simplify default setting of interpolation parameters (for all fields,
848        set position to match model grid cell-center position, leading to trivial
849        interpolation in case of regular Lat-Lon grid) and fix for the case of
850        non-uniform delY.
851    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
852       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
853       this factor is absolutely required, because the lw exitance (= out-going
854       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
855       where the reflectivity rho = 1-emissivity for conservation reasons. Once
856       this is established, we can remove the CPP-Flag (if we want to).
857    o pkg/seaice:
858      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
859        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
860      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
861        what the name implies (and not emissivity*BoltzmannConstant), this means
862        the old default value of 5.5e-8 now means
863        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
864        S/R exf_readparms
865      - FV-discretization of the B-grid LSOR solver, turn on with
866        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
867        of the calling routine dynsolver, so that B and C-grid code look a
868        little more alike.
869      - fix index bugs in ostres.F (B-grid code)
870    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
871    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
872      default for SEAICE_emissivity, if useEXF; requires setting a wrong
873      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
874      backward compatiblity
875    o model/src: use sigmaR in calc_ivdc
876    
877    checkpoint63g (2011/12/16)
878    o pkg/seaice/seaice_growth.F:
879      fix heat conservation of the coupled ocean-seaice system.
880      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
881      solid vs liquid water treatment is resolved via QNET.
882    o pkg/seaice/seaice_growth.F:
883      add missing term for sublimation in saltFlux, which was breaking conservation.
884    o pkg/seaice/seaice_model.F:
885      Remove this patholigical case treatment in evolution branch,
886      where it is un-necessary and breaks conservation.
887      Update global_ocean.cs32x15/results accordingly for
888      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
889    o model/src:
890      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
891      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
892    o pkg/obcs:
893      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
894      tendency for temperature and salinity that is then applied to update
895      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
896      horizontal advection and diffusion contributions on the boundary (in
897      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
898      removing the mask in S/R timestep_tracer. The advantage of this approach is
899      that the updated tracer values include contributions from the surface
900      forcing and vertical diffusion.
901      This modification changes exp4.stevens because of vertical diffusion.
902    o model/src:
903      change non-curvilinear grid setting to also work with exch2 + blank tiles:
904      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
905        face dimensions.
906      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
907        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
908        and INI_SPHERICAL_POLAR_GRID.
909      change test-experiment global_ocean.90x40x15:
910      - split the domain in many more tiles (9x4 tiles of 10x10 each);
911      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
912      - update results of both test (std & dwnslp).
913    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
914       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
915    o model/src:
916      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
917        and fix initialisation when using sigma-coords.
918    o model/src:
919     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
920       to their current value at the beginning of forward_step.F": add a new run-time
921       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
922     - set doResetHFactors=T in the following test exp:
923        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
924        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
925        and tutorial_global_oce_in_p (nonLinFS in p)
926    o pkg/ecco
927      - added IES cost term
928    o verification/advect_xz
929      - scale down the depth by 1/100 (from 200 km to just 2.km)
930      - add secondary test using divergent flow, r-star and implicit vertical advection.
931      - add note (check_conserve_TS.txt) and matlab script to check global
932        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
933    o pkg/rbcs:
934      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
935    o pkg/obcs (Stevens BCs):
936      - fix various problems in the phase speed computations of the Stevens
937        boundary conditions:
938        - sign error for western and southern boundaries,
939        - time tendencies were underestimated by factor of dTracerLev and some just
940          zero (for multidim advection schemes) -> now estimate time tendencies
941          from difference between previous (n) time level and the one before (n-1);
942          this requires storing a field per tracer per boundary, also in the pickup
943          files.
944        - replace deltaTmom in cflMer/Zon computation with dTracerLev
945        - set default phase velocity to cflMer/Zon
946      - update verification experiment exp4.stevens
947    o pkg/generic_advdiff (implicit_r):
948      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
949        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
950      - fix implicit vertical diffusion or advection with NonLin FreeSurf
951        (was using current recip_hFacC instead of future recip_hFacC): set future
952        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
953        solver S/R ;
954      - fill diagnostics of vertical advective fluxes (computed from tendency)
955        when using implicit vert. advection;
956      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
957         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
958         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
959         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
960    o pkg/diagnostics:
961      - add diags for T & S tendency which goes through Adams-Bashforth.
962    
963    checkpoint63f (2011/11/30)
964    o pkg/obcs/obcs_calc_stevens.F:
965      - join some loops to reduce number of if-statements
966      - fix a bug in code for northern and southern boundaries.
967    o pkg/seaice/seaice_init_varia.F
968      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
969        caused zero ice-velocities for the B-grid code
970    o pkg/seaice/seaice_init_fixed.F
971      - fix a bug in the initialisation of the second metric terms
972        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
973      - this affects all seaice configurations with useCurviLinearGrid = .true.
974        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
975        = .true. (default)
976      - the only verification experiment affected is global_ocean.cs32x15:
977        icedyn, seaice, and seaice_dynmix (AD)
978    o pkg/thsice/thsice_diagnostics_state.F
979      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
980        not contain garbage that can lead to surprises in diagstats_calc.F
981    o model/src:
982      - move bi,bj loops inside INTEGR_CONTINUITY ;
983      - call INTEGR_CONTINUITY directly from forward_step.F
984        (previously called from momentum_correction_step.F)
985      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
986        forward_step.F and pkg/ecco/the_main_loop.F
987    o model/src/do_oceanic_phys.F:
988      - reset addMass to zero only if useICEFRONT ;
989      - separated k-loop for rhoInSitu calculation ;
990      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
991        and at constant T,S (= WdRHOdP);
992      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
993        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
994        transport of locally-referenced potential density);
995        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
996    o gluemnc:
997      - replace ncrcat with ncks when adding variables to *.glob.nc
998      - change the way variables without record dimensions are handled so that
999        files that have variables with and without record variables can be glued:
1000        add a record dimension with a new unique name to be able to differentiate
1001        between variable with and without a-prior record dimensions. Remove
1002        this record dimension before adding the variable to the *.glob.nc file.
1003        This procedure automatically works also for grid.*.nc files that do not
1004        have any record dimension.
1005    o verification/cpl_aim+ocn:
1006      - generate new reference output on baudelaire (gfortran, mpich2) (previously
1007        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1008    o pkg/obcs/obcs_calc_stevens.F:
1009      - add code for northern and southern boundaries.
1010      - reorder some loops to save some operations and so that drFBar can be scalar
1011    o model/src:
1012      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1013        truncation) and add diagnostics for Adams-Bashforth tendency increment.
1014      - update test-exp. AD output:
1015        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1016      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1017        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1018        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1019        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1020        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1021        tutorial_plume_on_slope.
1022    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1023      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1024      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1025      does not even come with an F77 compiler anymore, this should not be
1026      a limitation
1027    
1028    checkpoint63e (2011/11/06)
1029    o pkg/seaice adjoint of LSR:
1030      - substantially rework STORE dirs.
1031      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1032        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1033        and only perform SOLV_MAX_FIXED adjoint iters.
1034        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1035        always goes to same record, meaning that the last forward field will be
1036        the one used in the adjoint - an approximation.
1037      - now produces non-zero LSR-related gradients, and acceptable gradients for
1038        An's zonal (x-z) test case (to be checked in)
1039      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1040        (but these are screwed up by the thermodynamics in the first place);
1041        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1042        output_adm.txt also reflects changes to seaice_lsr
1043      - global_ocean.cs32x15:
1044        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1045          (output_adm.seaice.txt was updated)
1046        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1047          (output_adm.seaice_dynmix.txt)
1048    o test-exp. exp4+stevens:
1049      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1050    o pkg/seaice (lsr solver):
1051      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1052        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1053      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1054      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1055        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1056      - compute (with new S/R) and print initial (+ free-driff sol. if available)
1057        and final residual of linearised system.
1058    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1059      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1060    o pkg/obcs: Stevens BCs (still only for east and west)
1061      - fix Stevens BCs by using intermediate velocities of previous
1062        time step as "baroclinic" contribution rather velocity of one grid cell
1063        inside the boundaries; more consistent but makes the entire treatment
1064        more complicated, requires new pickup files and two new S/Rs:
1065        obcs_copy_uv_n and obcs_save_uv_n
1066        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1067        (undefined by default)
1068      - silently move computation of some grid factors into separate loops to
1069        save some recomputations
1070      - add a hack for non-linear free surface
1071      - add a verification experiment to exp4 that tests this code
1072    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1073    
1074    checkpoint63d (2011/10/25)
1075    o pkg/obcs + seaice-dynamics:
1076      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1077        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1078        values (consistent with an implicit method).
1079      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1080        return to older implementation (same results as before); note that none of
1081        the "experimental" OBCS_SEAICE options are implemented in the new version.
1082      - switch test exp. seaice_obcs to use new version (update output).
1083    o pkg/seaice:
1084      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1085      - add parenthesis in Water-Ice drag calculations (evp & lsr);
1086      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1087        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1088      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1089        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1090    o pkg/layers:
1091      - Include potential density as new coordinate (Thanks to David Munday)
1092    o pkg/dic:
1093      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1094        carbonate computation/output to CALC_PCO2_APPROX
1095    o pkg/generic_advdiff
1096      - make TAF generate code that vectorizes:
1097        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1098    o model/src:
1099      - improve vectorization also for adjoint code of
1100        solve_tridiagonal and solve_pentadiagonal. As this requires up to
1101        5 new 3D-fields, this code is only turned on for the combination of
1102        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1103        for singular matrix check (only for TARGET_NEC_SX).
1104      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1105        ALLOW_AUTODIFF. This flag now needs to be set outside of
1106        solve_tri/pentadiagonal.F
1107    o pkg/exf:
1108      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1109        optional namelist EXF_NML_OBCS).
1110      - add many debug-print (to trace down where pkg/cal error msg comes from)
1111    o pkg/mom_vecinv/mom_vi_hdissip.F
1112      - rearrange loops so that vectorization is improved and in particular
1113        the adjoint routine vectorizes. The code is a little longer now, but I
1114        think easier to read.
1115        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1116    o pkg/seaice:
1117      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1118    o pkg/exch2:
1119      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1120        used as default; keep using matrix version in adjustment.cs-32x32x1.
1121    o tools/build_options:
1122      - after merging some MPI and/or multi-threads specific optfiles so that
1123        the modified default optfile support both built (using genmake2 -mpi
1124        for the MPI built, using genmake2 -omp for OpenMP built),
1125        move now obsolete optfiles to tools/build_options/unsupported/
1126       (add copy of email sent to support list in doc/optfiles_changes.txt)
1127    
1128    checkpoint63c (2011/09/28)
1129    o pkg/ebm:
1130      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1131        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1132  o pkg/seaice (SItracer pickup)  o pkg/seaice (SItracer pickup)
1133  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1134    To be done:    To be done:
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