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revision 1.1595 by gforget, Mon Feb 13 16:38:08 2012 UTC revision 1.1725 by gforget, Tue Aug 28 19:44:16 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 global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.  
8    - switch to variable freezing point.  o pkg/exf : added run time switch useAtmWind to replace ALLOW_ATM_WIND      
9      cpp switch. ALLOW_ATM_WIND now just sets the useAtmWind default (see
10      exf_readparms.F) and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
11    o pkg/exf, autodiff, ctrl, ecco and seaice : remove ALLOW_ATM_WIND
12      brackets, or replace them with useAtmWind ones.
13    o pkg/ctrl, ecco : allow to compile both ALLOW_U/VSTRESS_CONTROL and
14      ALLOW_U/VWIND_CONTROL. Depending on useAtmWind, one is inactive,
15      and the other is active (see exf_getffields.F/exf_getsurfacefluxes.F).
16    o tools/genmake2:
17      - improve error msg when failing in 2nd test of check_for_broken_Ff
18      - fix option '-makefile' short-name (-mf according to genmake2 -help)
19      - source local config file "genmake_local" just after processing the genmake2
20        command arguments (previously done before processing arg).
21    o pkg/grdchk:
22      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
23        to this routine from cost_final has been dropped in g_cost_final)
24      - improve printed information (more explicit msg, no longer using "print *,"
25         fix fcpertminus printed value).
26    o model/src:
27      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
28        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
29        this prevents getting cost-funct reset in adinitialise_varia recomputations.
30    o pkg/dic:
31      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
32        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
33    o pkg/grdchk:
34      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
35      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
36    o pkg/autodiff/ctrl/grdchk :
37      - attempt to sort out what works and what does not,
38        with regard to I/O, and to warn/stop accordingly.
39    o pkg/grdchk:
40      - attempt to fix grdchk in the case of useSingleCpuIO.
41      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
42       statements were moved from grdchk_main.F and into
43       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
44      - a global sum is applied to record numbers icvrec/layer
45       out of grdchk_loc so that they be passed to I/O routines.
46    o pkg/smooth:
47      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
48        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
49    o verification/testreport:
50      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
51      - can also use compressed (gzip) reference output file;
52      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
53        to be easier to collect by testreport.
54      - update existing TLM output (half out-of-date by more than 3 yrs).
55      - report NETCDF & LAPACK settings (from genmake2) in output dir.
56      - report run-time in each individual summary (previously only for AD test);
57        for TLM test, add also TAF version.
58      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
59    
60    checkpoint63r (2012/08/15)
61    o tools/genmake2:
62      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
63    o pkg/ecco/ecco_cost_final.F :
64      - fix fc print statements (to stdout and costfunction0000) so
65        that the printed value is always after the global sum.
66    o pkg/seaice/seaice_dynsolver.F :
67      - fix ice strength assymptote at SEAICE_area_max<1
68        (no change for the standard case of SEAICE_area_max=1)
69    o some cleaning:
70      - pkg source files: ensure that all *.F files from each pkg included the
71        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
72        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
73        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
74        includes;
75      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
76      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
77        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
78        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
79      - update option-file CPP_OPTIONS.h of all AD experiments:
80        * no longer include PACKAGES_CONFIG.h ;
81        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
82        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
83          including ECCO_CPPOPTIONS.h).
84    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
85      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
86        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
87        not necessary accurate).
88      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
89        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
90        deliberately break compilation (a remainder that it needs to be customized)
91      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
92      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
93      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
94    o tools/genamke2:
95      - check for lapack.
96    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
97      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
98        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
99        from both packages.
100      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
101      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
102      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
103        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
104    o pkg/cost : add comments to explain special and/or untested setups.
105    o pkg/exf:
106      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
107        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
108    o verification/*/code_ad:
109      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
110      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
111      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
112        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
113    o pkg/seaice :
114      - added possibility to change ice strength/PRESS0 relationship to
115        HEFF, according to the following run time parameters
116        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
117        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
118        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
119    o pkg/ggl90 :
120      - added run time flag mxlSurfFlag to include the code that ensure
121        mixing between first and second level (previously included as a comment)
122    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
123      - add test of newly added dumpAdByRec=T option where
124        we write all records to one file per variable.
125    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
126      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
127        to check that this code is ok with taf and compiles in adjoint.
128    o pkg/autodiff :
129      - added run time param dumpAdByRec : ad dump format switch.
130        If true then write all records to one file per variable.
131        Else write one file per record (remains the default).
132      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
133    o pkg/seaice:
134     - Added SEAICEuseTILT run time switch : if set to
135       false then omit the tilt term in seaice dynamics.
136     - Fix free drift calculation.
137    o pkg/shelfice:
138      When initializing SHELFICEDragQuadratic, set default to be
139      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
140      but retain option to set it independently
141      (inconsistenty spotted by Veronique Dansereau)
142    o eesupp/inc:
143      - in EEPARAMS.h, add real-type constant for some frequently used simple number
144         (0,1,2,1/2), with name explicitly referring to RS/RL type.
145    o model/src:
146      - move balancing of relaxation terms to new S/R balance_relax.F.
147    o pkg/autodiff:
148      re-write active I/O high-level (control) S/R:
149      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
150      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
151      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
152        MDS_READ/WRITE_FIELD); change loops to multi-threads.
153      - update and merge active_file_control_slice.flow into active_file_control.flow
154      - update the calls in lower level S/R (active_file.F, active_file_g.F and
155        active_file_ad.F) keeping the argument list and function unchanged.
156      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
157        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
158      - new low-level active I/O routines, one for each type (RL/RS), for active var
159        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
160        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
161        right type.
162    o autodiff and RS=real*4:
163      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
164        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
165      - change argument type of 3-D mask argument to _RS to match type in the call
166        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
167    o pkg/thsice:
168      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
169      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
170        fresh-water flux: uniform correction or proportional to local precip.
171    o pkg/ctrl:
172      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
173      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
174                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
175      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
176    
177    checkpoint63q (2012/07/30)
178    o pkg/autodiff:
179      note about monitor and snap-shot of ad-variables:
180      a) need to apply ADEXCH before monitor or output of ad-vars to include
181       overlap contributions (was done for adjDump but missing for monitor).
182      b) since ADEXCH implies adding overlap values to interior array, machine
183       truncation error is expected when adding an ADEXCH call in the middle of
184       the time-stepping (although mathematically identical).
185      modifs:
186      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
187        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
188      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
189        apply ADEXCH before monitor or snap-shot of ad-variables:
190           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
191      - implement new method (copy+adexch) for snap-shot and monitor of main model
192        ad-vars (initially not used by default -> output unchanged).
193      - change default (set to 2) to use new method and update few output_adm.txt
194        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
195        and both tutorial_tracer_adjsens tests).
196      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
197        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
198    o pkg/ctrl:
199      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
200      generic control variables via
201      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
202      Only required customization should be S/R ctrl_map_ini_genarr.F
203      (routine in repository contains example)
204    o pkg/exf:
205      - fix and refine checking of surface-relaxation setting when using EXF
206    o verification (adjoint exp):
207      - reduce length of simulation by half for experiment global_ocean.cs32x15
208        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
209    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
210      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
211        of KE that can occur with aggressive optimization
212      + put quadratic bottom drag calculation in separated loops (only done if
213        using bottomDragQuadratic)
214    o model/src: CG2D_NSA
215      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
216         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
217      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
218         change cg2d residual target to be expressed in Wunits (=> do not normalise
219         RHS ; this fix global_max Pb with TAF); update output.
220    o verification/tutorial_tracer_adjsens:
221       improve parameter consistency (and get rid of warnings):
222       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
223       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
224       - use staggerTimeStep (for stability) in som81; use default rotation period.
225    o pkg/exch2:
226      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
227        reset to 0 = 1 long line in X)
228    o pkg/mdsio:
229      - fix reading of dimensions from meta file for large-size domain
230    o model/src:
231      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
232      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
233        Cubed-Sphere Exch with CS-corners inside the domain;
234        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
235        globalArea and to set hasWetCSCorners.
236      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
237        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
238      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
239        useCDscheme and useCubedSphereExchange).
240    o pkg/seaice/seaice_growth.F :
241      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
242        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
243        when the previous code was not correct.
244      - in all cases diagnoze the boundary condition mismatch to SIaaflux
245      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
246        that term to QNET (essentially to set the melt/freeze water to 0degC).
247        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
248    o verification/global_ocean.cs32x15/input.seaice :
249      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
250      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
251      - update results (output.seaice.txt) accordingly.
252    o verification/lab_sea/input/data.seaice :
253      - remove SEAICEheatConsFix, which is now be tested
254        in global_ocean.cs32x15. The presently coded fix
255        is only consistent with real fresh water + nlfs.
256      - update results (output.txt) accordingly.
257    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
258    o AD_CONFIG.h file:
259      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
260      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
261        add it explicitly in each fortran src file where it is needed.
262        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
263        thus introducing potentially wrong dependency; therefore, better to include
264        it only where it's really needed, and after any other included OPTIONS file
265        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
266        or ALLOW_TANGENTLINEAR_RUN).
267    
268    checkpoint63p (2012/07/06)
269    o pkg/autodiff:
270      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
271      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
272        which are now read from new parameter file "data.autodiff" (inAdExact
273        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
274      - add file "data.autodiff" in all verification/*/input_ad/ directories.
275      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
276        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
277    o verification/tutorial_tracer_adjsens/
278      - add extra sub-verification which uses "SOM" advection scheme
279        (2nd Order-Moment Advection Scheme, Prather Limiter) with
280          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
281        and in data:
282          multiDimAdvection=.TRUE.,
283          tempAdvScheme=81,
284          saltAdvScheme=81,
285    o model/src:
286      - introduce ALLOW_BALANCE_RELAX which allow the removal
287       of the global mean of relaxation terms by setting
288       balanceThetaClimRelax and balanceSaltClimRelax
289      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
290       This case is now treated appropriately in seaice_growth.F
291    o pkg/seaice:
292      - do balanceEmPmR and balanceQnet based on the net fluxes
293        (SItflux) that enter the ocean+ice system rather than QNET
294        and EMPMR. Works best in real fresh water.
295      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
296        out of the diagnotics bloc, and stored in global arrays.
297    
298    checkpoint63o (2012/06/29)
299    o vertical mixing schemes:
300      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
301      - replace computation of density (in Function STATE1, opps_calc.F) by a call
302        to S/R FIND_RHO_SCALAR
303      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
304        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
305        affects output (vermix.ggl90) at truncation level.
306    o testreport:
307      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
308        (nSx,nSy) for the number of threads (from eedata.mth)
309    o model/src:
310      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
311        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
312    o verification/tutorial_tracer_adjsens/
313      - compile with ALLOW_CG2D_NSA
314      - run with nonlinFreeSurf=3
315      - update reference output_adm.txt
316    o tools/genmake2:
317      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
318        refine usePROFILES switching off (only when NetCDF is not available).
319    o verification (atmospheric set-up):
320      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
321    o pkg/profiles : refine profiles and files handling.
322    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
323    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
324      - changes to use model/src/the_main_loop.F rather than the ecco version
325        in ecco type adjoint runs.
326    o model/src:
327      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
328      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
329      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
330    o model/src:
331      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
332        update output of test experiment bottom_ctrl_5x5.
333    o pkg/generic_advdiff:
334      - implement vertical bi-harmonic diffusion (for now, only for T & S and
335        only explicitly).
336    o verification/bottom_ctrl_5x5/
337      update reference output (results changed quite some time ago,
338      not sure when; but new reference results look ok in terms of grdchk)
339    o verification/1D_ocean_ice_column/
340      For verification purposes, the exact adjoint rather than an approx.
341      should be used (e.g., to comare against F.D. or TLM).
342      removed autodiff_inadmode*_ad.F routines in code_ad/
343      Update results/ accordingly.
344    o pkg/cal:
345      - change cal_getdate.F so that output date is function of input time only
346        (less ambiguous, not mixed up with input iteration number).
347      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
348    o pkg/diagnostics:
349      - implement calendarDumps also for stats-diags
350      - implement calendarDumps also for snap-shot output (negative freq)
351      - for now, ignores calendarDumps if non-zero phase-lag.
352    
353    checkpoint63n (2012/06/04)
354    o model/src:
355      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
356        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
357      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
358        similar to calc_r_star.F); update results of experiment internal_wave and
359        tutorial_global_oce_in_p (affected @ truncation level).
360    o pkg/shelfice:
361      - add parameterisation of advective-diffusive flux into the ice shelf
362        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
363      - simply eps3/3a computation
364    o eesupp:
365     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
366       between tiles, just fill-in edges assuming locally periodic subdomain) and
367       add corresponding exchange subroutines (EXCH0);
368     - new CG-solver version (_EX0) for disconnected-tiles special case.
369    o model/src (CG-solvers):
370     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
371       (similar final residual output and max-Iter number as with standard version);
372     - allows to store and use lowest-residual solution (standard & _SR versions);
373     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
374     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
375    o eesup/src:
376     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
377       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
378    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
379    
380    checkpoint63m (2012/04/27)
381    o pkg/shelfice:
382     - account for partical cells in surface level below ice-shelf for hydrostatic
383       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
384    o ad test experiments:
385     - update and rename to "ad_optfile.local" local AD-optfile specific to a
386       particular adjoint verification experiment (in verification/*/code_ad/)
387    o pkg/seaice & pkg/exf:
388     - Part two of ECCO-CLIVAR code merges.
389       Completes merge of seaice area relax. code.
390       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
391       to be set in EXF_OPTIONS.h since this pkg controls its I/O
392       (and avoids second CPP option in SEAICE_OPTIONS.h)
393     - change default value of costIceStart & costIceEnd to a valid date.
394     - add snowPrecip to HSNOW in seaice_growth
395    o pkg/ptracers:
396     - move ptracers summary and setup check into separated S/R ; add a check for
397       valid PTRACERS_Iter0 value (error+stop or just warning).
398    o pkg/cal (+ pkg/ecco):
399     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
400       as input; and for AD, unless both are not differentiable (e.g., k index)).
401    o model/src:
402     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
403       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
404       temporary set to usingZCoords value (to be changed to F when using shelfice).
405     - hydrostatic pressure: implement partial cell near the surface also for
406       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
407       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
408    o pkg/ctrl/ctrl_init.F:
409     - add a formal parameter to s/r ctrl_init_rec to print
410       xx_$(ctrl_valiable)_file for easier debugging
411     - move call of cal_* routines into the if-block where they are really
412       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
413       to specify a startdate
414    o pkg/seaice:
415     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
416       global_ocean.cs32x15/code versions).
417     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
418       verification experiment global_ocean.cs32x15.seaice and update results.
419    o pkg/exf:
420     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
421       (according to useExfYearlyFields).
422    o pkg/cal:
423     - move calendar setting & summary (previously in cal_readparams.F) into new
424       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
425       length of the simulation is set (after SET_PARMS call); This is an attempt
426       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
427     - For safety: keep a record of pkg/cal parameter settings status
428               to allow to STOP if one pkg/cal S/R is called too early.
429     - add a stop in all basic pkg/cal subroutines if called before setting is done.
430     - modify cal_getdate.F: stop when nothing was returned;
431       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
432       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
433    
434    checkpoint63l (2012/04/04)
435    o pkg/bbl:
436      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
437        update global_with_exf output.yearly.txt file.
438    o pkg/cal:
439      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
440      - remove 2 unsused and very short (1 line only) functions ;
441      - remove unsused subroutines from AD-Diff list.
442    o model/src:
443      - start to implement clean wait to stop in initialization S/R (config_check.F,
444         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
445    o folowing PRINT_MESSAGE changes:
446      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
447    o pkg/bbl:
448      - modification so it can work with z*
449      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
450      - global_with_exf/input.yearly verification; changes output.yearly.txt
451    o eesupp/src:
452      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
453        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
454      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
455        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
456      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
457      - when using MPI, always set usingMPI=T ; set default accordingly and stop
458        if not consistent.
459      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
460        argument is zero (in case called within single-thread section).
461    o pkg/fizhi:
462        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
463        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
464    o pkg/exch2:
465      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
466        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
467      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
468        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
469        with bad ones coming from a not-yet-updated halo.
470        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
471    o pkg/frazil:
472        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
473        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
474    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
475    o verification/lab_sea
476      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
477      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
478      * nTimeSteps 3 -> 4
479      * changed reference output accordingly
480    o pkg/ctrl:
481      * fix ctrl_get_gen for xx_sst, xx_sss
482    o pkg/fizhi:
483      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
484        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
485      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
486        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
487        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
488    o pkg/gmredi:
489      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
490    o pkg/fizhi:
491      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
492        (old)aces open64 tuv test.
493    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
494    o pkg/mom_vecinv:
495      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
496        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
497        with non-lin free-surf).
498    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
499      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
500      some compilers (gfortran 4.6.0 on MacOS)
501    o momentum:
502      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
503        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
504        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
505    
506    checkpoint63k (2012/03/17)
507    o model/src:
508       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
509         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
510       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
511         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
512    o model/src: solve_*diagonal.F
513       - replace division with multiplication by inverse (similar to original version)
514         update output of AD exp. global_ocean.90x40x15.
515       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
516         to enable the use of the vectorized & differentiable solve_tridiagonal.F
517       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
518         vertical advection (to get solve_tridiagonal tested in AD mode).
519    o pkg/seaice: ECCO-CLIVAR merge:
520      1. seaice AREA relaxation
521         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
522         * runtime flag: SEAICE_tauAreaObsRelax
523      2. modified global mean cost imbalance code: CPP option
524          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
525    o another iteration on solve_*diagonal.F
526       Make choices independent of AUTODIFF
527       Default will be the adjoinable vectorized version.
528       Alternative choices are:
529       * non-adjoinable original version with low memory footprint:
530         #define SOLVE_DIAGONAL_LOWMEMORY
531       * still adjoinable but does not vectorize (k as inner-most loop):
532         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
533    o testreport
534     - add option to use a home made wrapper around "make"
535     - remove MITGCM_IEEE env. variable (no longer active)
536    o pkg/shelfice
537     - improve computation of friction velocity for velocity dependent
538       exchange coefficients: include velocities into SHELFICEBoundaryLayer
539       block to average velocities vertically
540     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
541    o Modify diagonal solvers, now three versions (upon request):
542      #ifndef SOLVE_DIAGONAL_AUTODIFF
543        1. default version (dating back a while ago)
544      #else /* def SOLVE_DIAGONAL_AUTODIFF */
545      # ifdef SOLVE_DIAGONAL_KINNER
546        2. adjoinable version with k-innermost loop (G. Forget)
547      # else
548        3. adjoinable vectorized version of 2.
549      # endif
550      #endif /* SOLVE_DIAGONAL_AUTODIFF */
551      All flags are currently set within routines, but could/should be moved to CPP-options.
552      Array bounds for 1. are as before, for 2.,3. cover the entire domain
553      (could be changed for 1. too).
554    o verification/lab_sea (fwd):
555      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
556        use 7 categories (except hb87), new solve4temp params (except salt_plume),
557        constant salinity (=4) or variable salinity (salt_plume) done through
558        SItracer.
559    o pkg/seaice:
560      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
561      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
562         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
563        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
564        SEAICE_freeze got retired) but already better than previously with
565        SEAICE_freeze=123456.7 deg.C;
566      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
567        (safer multi-threaded setting); always set SEAICEuseEVP;
568      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
569        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
570        stop if multiple specifications for the same coeff; make sure default
571        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
572    o pkg/obcs:
573      - allow to switch to upwind 1rst order advection scheme for the advective
574        flux computation at the open-boundary; disabled for adjoint built.
575    o pkg/ptracers:
576      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
577      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
578      - add parameter to decide when to start a tracer; use internal flag to
579        know which tracer to step-forward; switch this internal flag at the top
580        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
581        for adjoint built.
582    o pkg/seaice:
583      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
584      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
585      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
586    o pkg/ecco:
587      - fix writing of output file DiagnosCost_ClimSalt/Theta
588        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
589    o pkg/seaice:
590      - add missing initialisation of COR_ICE array in dynsolver.F
591      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
592        compiled either way, and is tested in all exps (multidim was only tested
593        in lab_sea ad before).
594      - cosmetic change to prepare for future addition of ITD. no change to results.
595        no defaults change.
596      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
597      - by lack of adequate verification experiments, I further used custom versions
598        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
599        should be correct.
600      - avoid recomputations in ad.
601    o array initialisation in adjoint mode:
602      1) pkg/mom_common/mom_calc_ke.F:
603        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
604        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
605        part this initialisation is gone, resulting in Floating Point Exception
606        (caught by open64 compiler with debug option).
607      2) model/src/convective_weights.F
608        set output convectCount over the full array range (instead of doing
609        an update): this fix a similar issue when called within recomputation (adjoint)
610        which could by-pass the initialisation (normally done in the caller S/R).
611    o pkg/seaice:
612      - final version of turbulent flux params, as agreed at MIT ice meet:
613           SEAICE_mcPheePiston (default is ~ 0.000875)
614           SEAICE_mcPheeTaper (default is 0.)
615           SEAICE_frazilFrac (defualt is 1.)
616           SEAICE_mcPheeStepFunc (default is false)
617      - changes results at trunction error level
618      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
619    o added pkg/frazil:
620      - see frazil_description.tex for details
621      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
622    o pkg/shelfice/shelfice_thermodynamics.F
623      - fix exponents for velocity dependent exchange coefficients: change
624        from 2/3(=0) to 0.66666666666666667
625      - move computation of velocity dependent exchange coefficients into
626        separate loop, so that it applies to both thermodynamics
627      - move some divisions by constants out of loops
628    
629    checkpoint63j (2012/02/16)
630    o pkg/seaice:
631      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
632      - SItracer:  added run time params, and allow coupling to ocn salinity.
633    o pkg/seaice: remove (almost) all divisions by constants within loops
634      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
635      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
636      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
637      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
638    o pkg/seaice :
639      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
640        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
641      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
642      - add permanent SItflux diag that corresponds to TFLUX but includes
643        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
644      - allow activation/testing of a fix for suspected missing term in
645        ocn-ice heat budget (to be confirmed). To test this, you want to
646        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
647        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
648      - no change in results, fwd or ad.
649    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
650      - switch to variable freezing point.
651         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.         Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
652    - bug fix : the sublimation term that was missing is now activated.    - bug fix : the sublimation term that was missing is now activated.
653         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.         Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
654    - bug fix : flooding sign term for SIsal0.NE.0.    - bug fix : flooding sign term for SIsal0.NE.0.
655         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.         Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
656  o pkg/seaice:  o pkg/seaice:
657    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT    - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
658   is now the default, and the old default constant freezing point is recovered with      is now the default, and the old default constant freezing point is recovered
659   SEAICE_tempFrz0    = -1.96,      with SEAICE_tempFrz0    = -1.96,
660   SEAICE_dTempFrz_dS = 0.,           SEAICE_dTempFrz_dS = 0.,
661    - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.    - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
662    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.    - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
663    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now    - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
664   activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.      activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
665    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)    - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
666   was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).      was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
667    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in    - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
668   seaice_growth r149 for legacy branch (no results change).      seaice_growth r149 for legacy branch (no results change).
669    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).    - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
670    - results did not change except for global_ocean.cs32x15, mostly due to the switch      from I. Fenty).
671    to variable freezing point (see above item for detail).    - results did not change except for global_ocean.cs32x15, mostly due to the
672        switch to variable freezing point (see above item for detail).
673  o pkg/thsice:  o pkg/thsice:
674    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of    - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
675      seawater freezing in thsice_calc_thickn (not used).      seawater freezing in thsice_calc_thickn (not used).
676  o pkg/seaice: turbulent flux term specification via run time params.  o pkg/seaice: turbulent flux term specification via run time params.
677    - replace CPP switches with run time switches to facilitate testing    - replace CPP switches with run time switches to facilitate testing
678    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR    - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
679                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
680    - added runtime parameter : SEAICEturbFluxFormula    - added runtime parameter : SEAICEturbFluxFormula
681    - move Mcphee constants to SEAICE_PARAMS.h    - move Mcphee constants to SEAICE_PARAMS.h
682    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;    - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
683      SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove               SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
684      seaice_summary call (moved to seaice_init_fixed)               remove seaice_summary call (moved to seaice_init_fixed)
685    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on    - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
686      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)      SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
687    - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).    - seaice_summary.F : add missing report of read turbulent flux term set up
688    - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).                         and SITRACER.
689      - seaice_check.F : check range; inform and stop if retired CPPs are used
690                         (incl. SEAICE_AGE).
691    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without    - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
692          CPP switch, same computation as before for the different options.           CPP switch, same computation as before for the different options.
693    - change results at the truncation level.    - change results at the truncation level.
694  o pkg/seaice:  o pkg/seaice:
695    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:    - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
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