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revision 1.1498 by jmc, Mon Aug 29 19:46:22 2011 UTC revision 1.1711 by jmc, Thu Aug 9 20:36:11 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf:
8      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
9        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
10    o verification/*/code_ad:
11      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
12      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
13      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
14        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
15    o pkg/seaice :
16      - added possibility to change ice strength/PRESS0 relationship to
17        HEFF, according to the following run time parameters
18        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
19        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
20        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
21    o pkg/ggl90 :
22      - added run time flag mxlSurfFlag to include the code that ensure
23        mixing between first and second level (previously included as a comment)
24    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
25      - add test of newly added dumpAdByRec=T option where
26        we write all records to one file per variable.
27    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
28      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
29        to check that this code is ok with taf and compiles in adjoint.
30    o pkg/autodiff :
31      - added run time param dumpAdByRec : ad dump format switch.
32        If true then write all records to one file per variable.
33        Else write one file per record (remains the default).
34      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
35    o pkg/seaice:
36     - Added SEAICEuseTILT run time switch : if set to
37       false then omit the tilt term in seaice dynamics.
38     - Fix free drift calculation.
39    o pkg/shelfice:
40      When initializing SHELFICEDragQuadratic, set default to be
41      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
42      but retain option to set it independently
43      (inconsistenty spotted by Veronique Dansereau)
44    o eesupp/inc:
45      - in EEPARAMS.h, add real-type constant for some frequently used simple number
46         (0,1,2,1/2), with name explicitly referring to RS/RL type.
47    o model/src:
48      - move balancing of relaxation terms to new S/R balance_relax.F.
49    o pkg/autodiff:
50      re-write active I/O high-level (control) S/R:
51      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
52      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
53      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
54        MDS_READ/WRITE_FIELD); change loops to multi-threads.
55      - update and merge active_file_control_slice.flow into active_file_control.flow
56      - update the calls in lower level S/R (active_file.F, active_file_g.F and
57        active_file_ad.F) keeping the argument list and function unchanged.
58      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
59        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
60      - new low-level active I/O routines, one for each type (RL/RS), for active var
61        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
62        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
63        right type.
64    o autodiff and RS=real*4:
65      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
66        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
67      - change argument type of 3-D mask argument to _RS to match type in the call
68        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
69    o pkg/thsice:
70      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
71      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
72        fresh-water flux: uniform correction or proportional to local precip.
73    o pkg/ctrl:
74      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
75      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
76                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
77      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
78    
79    checkpoint63q (2012/07/30)
80    o pkg/autodiff:
81      note about monitor and snap-shot of ad-variables:
82      a) need to apply ADEXCH before monitor or output of ad-vars to include
83       overlap contributions (was done for adjDump but missing for monitor).
84      b) since ADEXCH implies adding overlap values to interior array, machine
85       truncation error is expected when adding an ADEXCH call in the middle of
86       the time-stepping (although mathematically identical).
87      modifs:
88      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
89        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
90      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
91        apply ADEXCH before monitor or snap-shot of ad-variables:
92           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
93      - implement new method (copy+adexch) for snap-shot and monitor of main model
94        ad-vars (initially not used by default -> output unchanged).
95      - change default (set to 2) to use new method and update few output_adm.txt
96        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
97        and both tutorial_tracer_adjsens tests).
98      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
99        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
100    o pkg/ctrl:
101      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
102      generic control variables via
103      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
104      Only required customization should be S/R ctrl_map_ini_genarr.F
105      (routine in repository contains example)
106    o pkg/exf:
107      - fix and refine checking of surface-relaxation setting when using EXF
108    o verification (adjoint exp):
109      - reduce length of simulation by half for experiment global_ocean.cs32x15
110        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
111    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
112      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
113        of KE that can occur with aggressive optimization
114      + put quadratic bottom drag calculation in separated loops (only done if
115        using bottomDragQuadratic)
116    o model/src: CG2D_NSA
117      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
118         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
119      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
120         change cg2d residual target to be expressed in Wunits (=> do not normalise
121         RHS ; this fix global_max Pb with TAF); update output.
122    o verification/tutorial_tracer_adjsens:
123       improve parameter consistency (and get rid of warnings):
124       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
125       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
126       - use staggerTimeStep (for stability) in som81; use default rotation period.
127    o pkg/exch2:
128      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
129        reset to 0 = 1 long line in X)
130    o pkg/mdsio:
131      - fix reading of dimensions from meta file for large-size domain
132    o model/src:
133      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
134      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
135        Cubed-Sphere Exch with CS-corners inside the domain;
136        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
137        globalArea and to set hasWetCSCorners.
138      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
139        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
140      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
141        useCDscheme and useCubedSphereExchange).
142    o pkg/seaice/seaice_growth.F :
143      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
144        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
145        when the previous code was not correct.
146      - in all cases diagnoze the boundary condition mismatch to SIaaflux
147      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
148        that term to QNET (essentially to set the melt/freeze water to 0degC).
149        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
150    o verification/global_ocean.cs32x15/input.seaice :
151      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
152      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
153      - update results (output.seaice.txt) accordingly.
154    o verification/lab_sea/input/data.seaice :
155      - remove SEAICEheatConsFix, which is now be tested
156        in global_ocean.cs32x15. The presently coded fix
157        is only consistent with real fresh water + nlfs.
158      - update results (output.txt) accordingly.
159    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
160    o AD_CONFIG.h file:
161      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
162      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
163        add it explicitly in each fortran src file where it is needed.
164        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
165        thus introducing potentially wrong dependency; therefore, better to include
166        it only where it's really needed, and after any other included OPTIONS file
167        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
168        or ALLOW_TANGENTLINEAR_RUN).
169    
170    checkpoint63p (2012/07/06)
171    o pkg/autodiff:
172      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
173      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
174        which are now read from new parameter file "data.autodiff" (inAdExact
175        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
176      - add file "data.autodiff" in all verification/*/input_ad/ directories.
177      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
178        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
179    o verification/tutorial_tracer_adjsens/
180      - add extra sub-verification which uses "SOM" advection scheme
181        (2nd Order-Moment Advection Scheme, Prather Limiter) with
182          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
183        and in data:
184          multiDimAdvection=.TRUE.,
185          tempAdvScheme=81,
186          saltAdvScheme=81,
187    o model/src:
188      - introduce ALLOW_BALANCE_RELAX which allow the removal
189       of the global mean of relaxation terms by setting
190       balanceThetaClimRelax and balanceSaltClimRelax
191      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
192       This case is now treated appropriately in seaice_growth.F
193    o pkg/seaice:
194      - do balanceEmPmR and balanceQnet based on the net fluxes
195        (SItflux) that enter the ocean+ice system rather than QNET
196        and EMPMR. Works best in real fresh water.
197      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
198        out of the diagnotics bloc, and stored in global arrays.
199    
200    checkpoint63o (2012/06/29)
201    o vertical mixing schemes:
202      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
203      - replace computation of density (in Function STATE1, opps_calc.F) by a call
204        to S/R FIND_RHO_SCALAR
205      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
206        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
207        affects output (vermix.ggl90) at truncation level.
208    o testreport:
209      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
210        (nSx,nSy) for the number of threads (from eedata.mth)
211    o model/src:
212      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
213        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
214    o verification/tutorial_tracer_adjsens/
215      - compile with ALLOW_CG2D_NSA
216      - run with nonlinFreeSurf=3
217      - update reference output_adm.txt
218    o tools/genmake2:
219      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
220        refine usePROFILES switching off (only when NetCDF is not available).
221    o verification (atmospheric set-up):
222      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
223    o pkg/profiles : refine profiles and files handling.
224    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
225    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
226      - changes to use model/src/the_main_loop.F rather than the ecco version
227        in ecco type adjoint runs.
228    o model/src:
229      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
230      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
231      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
232    o model/src:
233      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
234        update output of test experiment bottom_ctrl_5x5.
235    o pkg/generic_advdiff:
236      - implement vertical bi-harmonic diffusion (for now, only for T & S and
237        only explicitly).
238    o verification/bottom_ctrl_5x5/
239      update reference output (results changed quite some time ago,
240      not sure when; but new reference results look ok in terms of grdchk)
241    o verification/1D_ocean_ice_column/
242      For verification purposes, the exact adjoint rather than an approx.
243      should be used (e.g., to comare against F.D. or TLM).
244      removed autodiff_inadmode*_ad.F routines in code_ad/
245      Update results/ accordingly.
246    o pkg/cal:
247      - change cal_getdate.F so that output date is function of input time only
248        (less ambiguous, not mixed up with input iteration number).
249      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
250    o pkg/diagnostics:
251      - implement calendarDumps also for stats-diags
252      - implement calendarDumps also for snap-shot output (negative freq)
253      - for now, ignores calendarDumps if non-zero phase-lag.
254    
255    checkpoint63n (2012/06/04)
256    o model/src:
257      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
258        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
259      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
260        similar to calc_r_star.F); update results of experiment internal_wave and
261        tutorial_global_oce_in_p (affected @ truncation level).
262    o pkg/shelfice:
263      - add parameterisation of advective-diffusive flux into the ice shelf
264        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
265      - simply eps3/3a computation
266    o eesupp:
267     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
268       between tiles, just fill-in edges assuming locally periodic subdomain) and
269       add corresponding exchange subroutines (EXCH0);
270     - new CG-solver version (_EX0) for disconnected-tiles special case.
271    o model/src (CG-solvers):
272     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
273       (similar final residual output and max-Iter number as with standard version);
274     - allows to store and use lowest-residual solution (standard & _SR versions);
275     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
276     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
277    o eesup/src:
278     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
279       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
280    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
281    
282    checkpoint63m (2012/04/27)
283    o pkg/shelfice:
284     - account for partical cells in surface level below ice-shelf for hydrostatic
285       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
286    o ad test experiments:
287     - update and rename to "ad_optfile.local" local AD-optfile specific to a
288       particular adjoint verification experiment (in verification/*/code_ad/)
289    o pkg/seaice & pkg/exf:
290     - Part two of ECCO-CLIVAR code merges.
291       Completes merge of seaice area relax. code.
292       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
293       to be set in EXF_OPTIONS.h since this pkg controls its I/O
294       (and avoids second CPP option in SEAICE_OPTIONS.h)
295     - change default value of costIceStart & costIceEnd to a valid date.
296     - add snowPrecip to HSNOW in seaice_growth
297    o pkg/ptracers:
298     - move ptracers summary and setup check into separated S/R ; add a check for
299       valid PTRACERS_Iter0 value (error+stop or just warning).
300    o pkg/cal (+ pkg/ecco):
301     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
302       as input; and for AD, unless both are not differentiable (e.g., k index)).
303    o model/src:
304     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
305       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
306       temporary set to usingZCoords value (to be changed to F when using shelfice).
307     - hydrostatic pressure: implement partial cell near the surface also for
308       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
309       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
310    o pkg/ctrl/ctrl_init.F:
311     - add a formal parameter to s/r ctrl_init_rec to print
312       xx_$(ctrl_valiable)_file for easier debugging
313     - move call of cal_* routines into the if-block where they are really
314       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
315       to specify a startdate
316    o pkg/seaice:
317     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
318       global_ocean.cs32x15/code versions).
319     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
320       verification experiment global_ocean.cs32x15.seaice and update results.
321    o pkg/exf:
322     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
323       (according to useExfYearlyFields).
324    o pkg/cal:
325     - move calendar setting & summary (previously in cal_readparams.F) into new
326       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
327       length of the simulation is set (after SET_PARMS call); This is an attempt
328       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
329     - For safety: keep a record of pkg/cal parameter settings status
330               to allow to STOP if one pkg/cal S/R is called too early.
331     - add a stop in all basic pkg/cal subroutines if called before setting is done.
332     - modify cal_getdate.F: stop when nothing was returned;
333       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
334       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
335    
336    checkpoint63l (2012/04/04)
337    o pkg/bbl:
338      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
339        update global_with_exf output.yearly.txt file.
340    o pkg/cal:
341      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
342      - remove 2 unsused and very short (1 line only) functions ;
343      - remove unsused subroutines from AD-Diff list.
344    o model/src:
345      - start to implement clean wait to stop in initialization S/R (config_check.F,
346         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
347    o folowing PRINT_MESSAGE changes:
348      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
349    o pkg/bbl:
350      - modification so it can work with z*
351      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
352      - global_with_exf/input.yearly verification; changes output.yearly.txt
353    o eesupp/src:
354      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
355        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
356      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
357        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
358      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
359      - when using MPI, always set usingMPI=T ; set default accordingly and stop
360        if not consistent.
361      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
362        argument is zero (in case called within single-thread section).
363    o pkg/fizhi:
364        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
365        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
366    o pkg/exch2:
367      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
368        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
369      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
370        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
371        with bad ones coming from a not-yet-updated halo.
372        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
373    o pkg/frazil:
374        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
375        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
376    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
377    o verification/lab_sea
378      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
379      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
380      * nTimeSteps 3 -> 4
381      * changed reference output accordingly
382    o pkg/ctrl:
383      * fix ctrl_get_gen for xx_sst, xx_sss
384    o pkg/fizhi:
385      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
386        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
387      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
388        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
389        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
390    o pkg/gmredi:
391      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
392    o pkg/fizhi:
393      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
394        (old)aces open64 tuv test.
395    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
396    o pkg/mom_vecinv:
397      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
398        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
399        with non-lin free-surf).
400    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
401      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
402      some compilers (gfortran 4.6.0 on MacOS)
403    o momentum:
404      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
405        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
406        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
407    
408    checkpoint63k (2012/03/17)
409    o model/src:
410       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
411         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
412       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
413         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
414    o model/src: solve_*diagonal.F
415       - replace division with multiplication by inverse (similar to original version)
416         update output of AD exp. global_ocean.90x40x15.
417       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
418         to enable the use of the vectorized & differentiable solve_tridiagonal.F
419       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
420         vertical advection (to get solve_tridiagonal tested in AD mode).
421    o pkg/seaice: ECCO-CLIVAR merge:
422      1. seaice AREA relaxation
423         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
424         * runtime flag: SEAICE_tauAreaObsRelax
425      2. modified global mean cost imbalance code: CPP option
426          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
427    o another iteration on solve_*diagonal.F
428       Make choices independent of AUTODIFF
429       Default will be the adjoinable vectorized version.
430       Alternative choices are:
431       * non-adjoinable original version with low memory footprint:
432         #define SOLVE_DIAGONAL_LOWMEMORY
433       * still adjoinable but does not vectorize (k as inner-most loop):
434         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
435    o testreport
436     - add option to use a home made wrapper around "make"
437     - remove MITGCM_IEEE env. variable (no longer active)
438    o pkg/shelfice
439     - improve computation of friction velocity for velocity dependent
440       exchange coefficients: include velocities into SHELFICEBoundaryLayer
441       block to average velocities vertically
442     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
443    o Modify diagonal solvers, now three versions (upon request):
444      #ifndef SOLVE_DIAGONAL_AUTODIFF
445        1. default version (dating back a while ago)
446      #else /* def SOLVE_DIAGONAL_AUTODIFF */
447      # ifdef SOLVE_DIAGONAL_KINNER
448        2. adjoinable version with k-innermost loop (G. Forget)
449      # else
450        3. adjoinable vectorized version of 2.
451      # endif
452      #endif /* SOLVE_DIAGONAL_AUTODIFF */
453      All flags are currently set within routines, but could/should be moved to CPP-options.
454      Array bounds for 1. are as before, for 2.,3. cover the entire domain
455      (could be changed for 1. too).
456    o verification/lab_sea (fwd):
457      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
458        use 7 categories (except hb87), new solve4temp params (except salt_plume),
459        constant salinity (=4) or variable salinity (salt_plume) done through
460        SItracer.
461    o pkg/seaice:
462      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
463      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
464         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
465        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
466        SEAICE_freeze got retired) but already better than previously with
467        SEAICE_freeze=123456.7 deg.C;
468      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
469        (safer multi-threaded setting); always set SEAICEuseEVP;
470      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
471        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
472        stop if multiple specifications for the same coeff; make sure default
473        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
474    o pkg/obcs:
475      - allow to switch to upwind 1rst order advection scheme for the advective
476        flux computation at the open-boundary; disabled for adjoint built.
477    o pkg/ptracers:
478      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
479      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
480      - add parameter to decide when to start a tracer; use internal flag to
481        know which tracer to step-forward; switch this internal flag at the top
482        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
483        for adjoint built.
484    o pkg/seaice:
485      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
486      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
487      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
488    o pkg/ecco:
489      - fix writing of output file DiagnosCost_ClimSalt/Theta
490        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
491    o pkg/seaice:
492      - add missing initialisation of COR_ICE array in dynsolver.F
493      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
494        compiled either way, and is tested in all exps (multidim was only tested
495        in lab_sea ad before).
496      - cosmetic change to prepare for future addition of ITD. no change to results.
497        no defaults change.
498      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
499      - by lack of adequate verification experiments, I further used custom versions
500        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
501        should be correct.
502      - avoid recomputations in ad.
503    o array initialisation in adjoint mode:
504      1) pkg/mom_common/mom_calc_ke.F:
505        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
506        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
507        part this initialisation is gone, resulting in Floating Point Exception
508        (caught by open64 compiler with debug option).
509      2) model/src/convective_weights.F
510        set output convectCount over the full array range (instead of doing
511        an update): this fix a similar issue when called within recomputation (adjoint)
512        which could by-pass the initialisation (normally done in the caller S/R).
513    o pkg/seaice:
514      - final version of turbulent flux params, as agreed at MIT ice meet:
515           SEAICE_mcPheePiston (default is ~ 0.000875)
516           SEAICE_mcPheeTaper (default is 0.)
517           SEAICE_frazilFrac (defualt is 1.)
518           SEAICE_mcPheeStepFunc (default is false)
519      - changes results at trunction error level
520      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
521    o added pkg/frazil:
522      - see frazil_description.tex for details
523      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
524    o pkg/shelfice/shelfice_thermodynamics.F
525      - fix exponents for velocity dependent exchange coefficients: change
526        from 2/3(=0) to 0.66666666666666667
527      - move computation of velocity dependent exchange coefficients into
528        separate loop, so that it applies to both thermodynamics
529      - move some divisions by constants out of loops
530    
531    checkpoint63j (2012/02/16)
532    o pkg/seaice:
533      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
534      - SItracer:  added run time params, and allow coupling to ocn salinity.
535    o pkg/seaice: remove (almost) all divisions by constants within loops
536      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
537      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
538      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
539      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
540    o pkg/seaice :
541      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
542        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
543      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
544      - add permanent SItflux diag that corresponds to TFLUX but includes
545        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
546      - allow activation/testing of a fix for suspected missing term in
547        ocn-ice heat budget (to be confirmed). To test this, you want to
548        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
549        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
550      - no change in results, fwd or ad.
551    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
552      - switch to variable freezing point.
553           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
554      - bug fix : the sublimation term that was missing is now activated.
555           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
556      - bug fix : flooding sign term for SIsal0.NE.0.
557           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
558    o pkg/seaice:
559      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
560        is now the default, and the old default constant freezing point is recovered
561        with SEAICE_tempFrz0    = -1.96,
562             SEAICE_dTempFrz_dS = 0.,
563      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
564      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
565      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
566        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
567      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
568        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
569      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
570        seaice_growth r149 for legacy branch (no results change).
571      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
572        from I. Fenty).
573      - results did not change except for global_ocean.cs32x15, mostly due to the
574        switch to variable freezing point (see above item for detail).
575    o pkg/thsice:
576      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
577        seawater freezing in thsice_calc_thickn (not used).
578    o pkg/seaice: turbulent flux term specification via run time params.
579      - replace CPP switches with run time switches to facilitate testing
580      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
581                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
582      - added runtime parameter : SEAICEturbFluxFormula
583      - move Mcphee constants to SEAICE_PARAMS.h
584      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
585                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
586                 remove seaice_summary call (moved to seaice_init_fixed)
587      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
588        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
589      - seaice_summary.F : add missing report of read turbulent flux term set up
590                           and SITRACER.
591      - seaice_check.F : check range; inform and stop if retired CPPs are used
592                         (incl. SEAICE_AGE).
593      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
594             CPP switch, same computation as before for the different options.
595      - change results at the truncation level.
596    o pkg/seaice:
597      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
598        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
599        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
600      - update verification/*/input*/data.seaice:
601        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
602        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
603        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
604        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
605    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
606      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
607        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
608        difference in results only due to machine truncation.
609      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
610        MaykutPolySatVap; keep MIN_LWDOWN.
611      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
612      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
613        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
614    o pkg/salt_plume:
615      - isolate saltPlumeFlux array exch into a specific S/R called from
616        do_oceanic_phys.F
617      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
618    o verification:
619      - move untested set-up to MITgcm_contrib/verification_other.
620    o pkg/seaice:
621      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
622    o pkg/seaice:
623      - seaice_solve4temp.F (keeping results unchanged):
624        * add 2 future run-time params to select which saturation vapor pressure
625          formula is used and how post-iteration fluxes are set.
626          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
627        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
628          the linearized expression to stay consistent with tsurf finding.
629      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
630        can be < 0.
631    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
632      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
633        conductive heat flux F_c , and add it explicitly when updating tsurf as
634        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
635        so that now F_ia has a consistent meaning through the entire routine.
636        This causes differences at truncation level: update output of fwd exp.
637        global_ocean.cs32x15.seaice.
638    o pkg/seaice:
639      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
640        of arrays, sign/direction of fluxes; no effect on results.
641      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
642        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
643        note: this should have been done before changing celsius2K default.
644      - to keep results unchanged, add back old value of celsius2K in verification
645        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
646      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
647        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
648        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
649        freezing temp is consistent with value in seaice_growth.F ; this causes
650        differences at machine truncation level: update lab_sea AD output (3/4).
651    o pkg/seaice:
652      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
653        and climsst/sss even when using seaice (to prevent calculation that might
654        use SST on land); does not affect any verification exp.
655      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
656        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
657    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
658      over land (non-legacy code)
659    o vectorize salt_plume package:
660      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
661      - this code computes plumebk everywhere (also over land), thus requires
662        code to avoid divisions by zero and catch the case of kLev=Nr.
663      - efficiency of salt_plume_frac is still sub-optimal
664    o tools (genmake2):
665      - fix makefile NAME specification (option: -makefile NAME) by adding
666        "-f $MAKEFILE" in few places where it was missing including makedepend
667        command (contribution from Paul).
668    
669    checkpoint63i (2012/01/24)
670    o model/src:
671      - add factorized versions of some EOS code to find_rho.F,
672        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
673    o model/src:
674      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
675      - change default celsius2K from 273.16 to 273.15
676      - to keep results unchanged, add back old value of celsius2K in verification
677        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
678         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
679    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
680      to make TAF generate vectorizable code
681    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
682       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
683       have flags that do this more efficiently.
684    o pkg/diagnostics/diagstats_calc.F
685      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
686    o pkg/obcs (with exch2):
687      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
688        and remove code (in obcs_readparms.F) which was based on EXCH of indices
689        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
690    o pkg/exf and seaice exp:
691      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
692        so that switching off area & heff advection flags does not affect results.
693      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
694      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
695        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
696        results of verification experiments: 1D_ocean_ice_column(fwd),
697        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
698        and offline_exf_seaice (all 4).
699    o pkg/seaice:
700      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
701        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
702      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
703        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
704        not multi-dim advection;
705      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
706        SHORTWAVE_HEATING #undef.
707    o optim: make Makefile more robust (?)
708    o pkg/obcs:
709      * fix treatment of obcs_read_pickup for TAF
710    o pkg/shelfice:
711      * add missing initialisation of num_shifwflx
712      * new adjoint verification exp. for isomip
713      * change Prandtl and Schmidt numbers from generic formulations
714        (in terms of model diffus. and visc.) to separate runtime
715        parameters, with Holland and Jenkins (1999) default values.
716    o pkg/exf (interpolation):
717      - extended input field (2 rows) near the N & S poles:
718        * fill in with the symetric value (when even Nb of data in longitude)
719        * add average value at the poles only for scalar quantities ; for vector
720          component interpolation, skip the averaging and keep duplicated values,
721          unless the 2 components have same location (uvInterp=T) in which case
722          interpolate the 2 components together using S/R EXF_INTERP_UV.
723      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
724        together: this allows to account properly for local orientation when
725        averaging at N & S pole.
726      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
727        exf-interpolation near N & S poles. Undef by default.
728      - add debug check/print on 1rst iter if debugLevel >=2.
729    o pkg/exf:
730      - change masking flags definition (no longer "parameter"), put them in
731        common block and set them in S/R EXF_INIT_FIXED.
732      - change recognized masking flag from s,u,v to c,w,s since the mask
733        to use (maskC,W,S) depends on position on model grid and has little to
734        do with scalar/vector difference; fix masking if using P-coordinates.
735      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
736        and update results of exp. global_with_exf (x2).
737      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
738    o pkg/obcs
739      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
740    o pkg/exf (interpolation):
741      - assume periodicity in X only if input field cover full longitude range.
742      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
743        and should vectorise).
744      - fix input lat of the 2 added row (in case we provide N.pole data).
745    
746    checkpoint63h (2011/12/30)
747    o pkg/seaice:
748      - change declaration of UVM from _RL to _RS in order to get B-grid
749        uIce,vIce monitor when _RS = real*4
750    o pkg/offline:
751      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
752      - compute vertical velocity if not read from file (switch on exactConserv
753        & staggerTimeStep);
754      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
755    o verification:
756      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
757        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
758        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
759      - update output of exp. global_ocean.cs32x15.viscA4 after changing
760        grid-file angles (used here for coriolis-3d);
761      - remove (or gzip) few files not needed to run fizhi-cs experiments.
762    o pkg/exf (vector interpolation):
763      - rotate vector component toward local grid-axis orientation using grid-angles
764        (stored in GRID.h) instead of locally computed rotation angle; keep old code
765        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
766    o pkg/seaice:
767      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
768        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
769    o pkg/PKG_OPTIONS.h files:
770      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
771        outside of the #ifdef ALLOW_THISPKG / #endif block.
772      - update verification/*/code/PKG_OPTIONS.h files.
773    o add a verification experiment (offline_exf_seaice/input.seaice) that test
774      the B-grid LSOR solver
775    o pkg/seaice: sort out emissivity and long wave radiation step 2:
776      - add emissivity for snow and ice as new run-time parameters
777        (unfortunately) that default to the corresponding exf values; this
778        changes results in most verification experiments so that for backward
779        compatibility these parameter have to be set explicitly to inconsistent
780        values (ugly);
781      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
782        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
783        until we agree how to handle this bug properly
784    o pkg/exf (interpolation):
785      - add a set of run-time param ({inputfield}_interpMethod), one for
786        each interpolated input field, to select the interpolation method
787        with a value of zero switching off the interpolation;
788      - print interpolation parameters to standard output;
789      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
790        (to use instead runoff_interpMethod=0 in data.exf).
791      - simplify default setting of interpolation parameters (for all fields,
792        set position to match model grid cell-center position, leading to trivial
793        interpolation in case of regular Lat-Lon grid) and fix for the case of
794        non-uniform delY.
795    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
796       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
797       this factor is absolutely required, because the lw exitance (= out-going
798       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
799       where the reflectivity rho = 1-emissivity for conservation reasons. Once
800       this is established, we can remove the CPP-Flag (if we want to).
801    o pkg/seaice:
802      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
803        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
804      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
805        what the name implies (and not emissivity*BoltzmannConstant), this means
806        the old default value of 5.5e-8 now means
807        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
808        S/R exf_readparms
809      - FV-discretization of the B-grid LSOR solver, turn on with
810        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
811        of the calling routine dynsolver, so that B and C-grid code look a
812        little more alike.
813      - fix index bugs in ostres.F (B-grid code)
814    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
815    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
816      default for SEAICE_emissivity, if useEXF; requires setting a wrong
817      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
818      backward compatiblity
819    o model/src: use sigmaR in calc_ivdc
820    
821    checkpoint63g (2011/12/16)
822    o pkg/seaice/seaice_growth.F:
823      fix heat conservation of the coupled ocean-seaice system.
824      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
825      solid vs liquid water treatment is resolved via QNET.
826    o pkg/seaice/seaice_growth.F:
827      add missing term for sublimation in saltFlux, which was breaking conservation.
828    o pkg/seaice/seaice_model.F:
829      Remove this patholigical case treatment in evolution branch,
830      where it is un-necessary and breaks conservation.
831      Update global_ocean.cs32x15/results accordingly for
832      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
833    o model/src:
834      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
835      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
836    o pkg/obcs:
837      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
838      tendency for temperature and salinity that is then applied to update
839      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
840      horizontal advection and diffusion contributions on the boundary (in
841      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
842      removing the mask in S/R timestep_tracer. The advantage of this approach is
843      that the updated tracer values include contributions from the surface
844      forcing and vertical diffusion.
845      This modification changes exp4.stevens because of vertical diffusion.
846    o model/src:
847      change non-curvilinear grid setting to also work with exch2 + blank tiles:
848      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
849        face dimensions.
850      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
851        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
852        and INI_SPHERICAL_POLAR_GRID.
853      change test-experiment global_ocean.90x40x15:
854      - split the domain in many more tiles (9x4 tiles of 10x10 each);
855      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
856      - update results of both test (std & dwnslp).
857    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
858       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
859    o model/src:
860      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
861        and fix initialisation when using sigma-coords.
862    o model/src:
863     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
864       to their current value at the beginning of forward_step.F": add a new run-time
865       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
866     - set doResetHFactors=T in the following test exp:
867        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
868        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
869        and tutorial_global_oce_in_p (nonLinFS in p)
870    o pkg/ecco
871      - added IES cost term
872    o verification/advect_xz
873      - scale down the depth by 1/100 (from 200 km to just 2.km)
874      - add secondary test using divergent flow, r-star and implicit vertical advection.
875      - add note (check_conserve_TS.txt) and matlab script to check global
876        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
877    o pkg/rbcs:
878      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
879    o pkg/obcs (Stevens BCs):
880      - fix various problems in the phase speed computations of the Stevens
881        boundary conditions:
882        - sign error for western and southern boundaries,
883        - time tendencies were underestimated by factor of dTracerLev and some just
884          zero (for multidim advection schemes) -> now estimate time tendencies
885          from difference between previous (n) time level and the one before (n-1);
886          this requires storing a field per tracer per boundary, also in the pickup
887          files.
888        - replace deltaTmom in cflMer/Zon computation with dTracerLev
889        - set default phase velocity to cflMer/Zon
890      - update verification experiment exp4.stevens
891    o pkg/generic_advdiff (implicit_r):
892      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
893        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
894      - fix implicit vertical diffusion or advection with NonLin FreeSurf
895        (was using current recip_hFacC instead of future recip_hFacC): set future
896        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
897        solver S/R ;
898      - fill diagnostics of vertical advective fluxes (computed from tendency)
899        when using implicit vert. advection;
900      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
901         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
902         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
903         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
904    o pkg/diagnostics:
905      - add diags for T & S tendency which goes through Adams-Bashforth.
906    
907    checkpoint63f (2011/11/30)
908    o pkg/obcs/obcs_calc_stevens.F:
909      - join some loops to reduce number of if-statements
910      - fix a bug in code for northern and southern boundaries.
911    o pkg/seaice/seaice_init_varia.F
912      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
913        caused zero ice-velocities for the B-grid code
914    o pkg/seaice/seaice_init_fixed.F
915      - fix a bug in the initialisation of the second metric terms
916        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
917      - this affects all seaice configurations with useCurviLinearGrid = .true.
918        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
919        = .true. (default)
920      - the only verification experiment affected is global_ocean.cs32x15:
921        icedyn, seaice, and seaice_dynmix (AD)
922    o pkg/thsice/thsice_diagnostics_state.F
923      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
924        not contain garbage that can lead to surprises in diagstats_calc.F
925    o model/src:
926      - move bi,bj loops inside INTEGR_CONTINUITY ;
927      - call INTEGR_CONTINUITY directly from forward_step.F
928        (previously called from momentum_correction_step.F)
929      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
930        forward_step.F and pkg/ecco/the_main_loop.F
931    o model/src/do_oceanic_phys.F:
932      - reset addMass to zero only if useICEFRONT ;
933      - separated k-loop for rhoInSitu calculation ;
934      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
935        and at constant T,S (= WdRHOdP);
936      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
937        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
938        transport of locally-referenced potential density);
939        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
940    o gluemnc:
941      - replace ncrcat with ncks when adding variables to *.glob.nc
942      - change the way variables without record dimensions are handled so that
943        files that have variables with and without record variables can be glued:
944        add a record dimension with a new unique name to be able to differentiate
945        between variable with and without a-prior record dimensions. Remove
946        this record dimension before adding the variable to the *.glob.nc file.
947        This procedure automatically works also for grid.*.nc files that do not
948        have any record dimension.
949    o verification/cpl_aim+ocn:
950      - generate new reference output on baudelaire (gfortran, mpich2) (previously
951        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
952    o pkg/obcs/obcs_calc_stevens.F:
953      - add code for northern and southern boundaries.
954      - reorder some loops to save some operations and so that drFBar can be scalar
955    o model/src:
956      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
957        truncation) and add diagnostics for Adams-Bashforth tendency increment.
958      - update test-exp. AD output:
959        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
960      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
961        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
962        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
963        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
964        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
965        tutorial_plume_on_slope.
966    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
967      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
968      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
969      does not even come with an F77 compiler anymore, this should not be
970      a limitation
971    
972    checkpoint63e (2011/11/06)
973    o pkg/seaice adjoint of LSR:
974      - substantially rework STORE dirs.
975      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
976        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
977        and only perform SOLV_MAX_FIXED adjoint iters.
978        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
979        always goes to same record, meaning that the last forward field will be
980        the one used in the adjoint - an approximation.
981      - now produces non-zero LSR-related gradients, and acceptable gradients for
982        An's zonal (x-z) test case (to be checked in)
983      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
984        (but these are screwed up by the thermodynamics in the first place);
985        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
986        output_adm.txt also reflects changes to seaice_lsr
987      - global_ocean.cs32x15:
988        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
989          (output_adm.seaice.txt was updated)
990        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
991          (output_adm.seaice_dynmix.txt)
992    o test-exp. exp4+stevens:
993      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
994    o pkg/seaice (lsr solver):
995      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
996        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
997      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
998      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
999        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1000      - compute (with new S/R) and print initial (+ free-driff sol. if available)
1001        and final residual of linearised system.
1002    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1003      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1004    o pkg/obcs: Stevens BCs (still only for east and west)
1005      - fix Stevens BCs by using intermediate velocities of previous
1006        time step as "baroclinic" contribution rather velocity of one grid cell
1007        inside the boundaries; more consistent but makes the entire treatment
1008        more complicated, requires new pickup files and two new S/Rs:
1009        obcs_copy_uv_n and obcs_save_uv_n
1010        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1011        (undefined by default)
1012      - silently move computation of some grid factors into separate loops to
1013        save some recomputations
1014      - add a hack for non-linear free surface
1015      - add a verification experiment to exp4 that tests this code
1016    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1017    
1018    checkpoint63d (2011/10/25)
1019    o pkg/obcs + seaice-dynamics:
1020      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1021        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1022        values (consistent with an implicit method).
1023      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1024        return to older implementation (same results as before); note that none of
1025        the "experimental" OBCS_SEAICE options are implemented in the new version.
1026      - switch test exp. seaice_obcs to use new version (update output).
1027    o pkg/seaice:
1028      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1029      - add parenthesis in Water-Ice drag calculations (evp & lsr);
1030      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1031        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1032      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1033        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1034    o pkg/layers:
1035      - Include potential density as new coordinate (Thanks to David Munday)
1036    o pkg/dic:
1037      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1038        carbonate computation/output to CALC_PCO2_APPROX
1039    o pkg/generic_advdiff
1040      - make TAF generate code that vectorizes:
1041        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1042    o model/src:
1043      - improve vectorization also for adjoint code of
1044        solve_tridiagonal and solve_pentadiagonal. As this requires up to
1045        5 new 3D-fields, this code is only turned on for the combination of
1046        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1047        for singular matrix check (only for TARGET_NEC_SX).
1048      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1049        ALLOW_AUTODIFF. This flag now needs to be set outside of
1050        solve_tri/pentadiagonal.F
1051    o pkg/exf:
1052      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1053        optional namelist EXF_NML_OBCS).
1054      - add many debug-print (to trace down where pkg/cal error msg comes from)
1055    o pkg/mom_vecinv/mom_vi_hdissip.F
1056      - rearrange loops so that vectorization is improved and in particular
1057        the adjoint routine vectorizes. The code is a little longer now, but I
1058        think easier to read.
1059        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1060    o pkg/seaice:
1061      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1062    o pkg/exch2:
1063      - alternative code (without tile x tile matrix) for cumulated (global) sum;
1064        used as default; keep using matrix version in adjustment.cs-32x32x1.
1065    o tools/build_options:
1066      - after merging some MPI and/or multi-threads specific optfiles so that
1067        the modified default optfile support both built (using genmake2 -mpi
1068        for the MPI built, using genmake2 -omp for OpenMP built),
1069        move now obsolete optfiles to tools/build_options/unsupported/
1070       (add copy of email sent to support list in doc/optfiles_changes.txt)
1071    
1072    checkpoint63c (2011/09/28)
1073    o pkg/ebm:
1074      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1075        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1076    o pkg/seaice (SItracer pickup)
1077    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1078      To be done:
1079      - thorough testing of missing fields in S/R seaice_read_pickup
1080      - thorough matching between generic tracers and specific fields used
1081        (e.g. volume-weighted age, area-weighted age, salinity, ...)
1082    o pkg/grdchk:
1083      - all procs calculate and print finite-difference gradient (for testreport)
1084      - change description output used by testreport;
1085      - AD testing: also compare and report Finite-difference gradient;
1086        => update all output_adm*.txt
1087    o test exp. global_ocean_ebm:
1088      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1089        and turn on exactConserve; update (fwd) output.
1090    o pkg/seaice (LSR):
1091      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1092      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1093        * identical results with non-CS topology (but save up to half of EXCH calls)
1094        * no much changes in cs-32 verification tests since no ice at face edges
1095         (differences due to convergence criteria, since nb of iterations changed)
1096        * expect some differences on lat-lon-cap grid.
1097        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1098    o pkg/exch2:
1099      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1100        many tiles); until alternative coding is added, just add a stop.
1101    o pkg/kpp:
1102      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1103        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1104    o optfiles:
1105      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1106        into corresponding standard one, which now support different build:
1107        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1108      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1109    o pkg/obcs (seaice):
1110      - add missing EXCH for uIce,vIce after applying OBCS;
1111      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1112        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1113        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1114      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1115      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1116        and eedata.mth for MPI and mutlti-threaded testing.
1117    o pkg/flt:
1118      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1119      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1120      - fix pickup and trajectories + profiles output with multi-threads;
1121      - add parameter to select group of fields to write along trajectory and
1122        profile (default unchanged);
1123      - only call PORT_RAND* function when flt_noise <> 0;
1124      - add multi-threaded test for verification exp. flt_example.
1125    o eesupp/src:
1126      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1127      - USE_OMP_THREADING: check that number of threads (from eedata) matches
1128        actual number (from env.var. setting).
1129  o pkg/ebm:  o pkg/ebm:
1130    - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.    - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1131    - add multi-threaded test for verification exp. global_ocean_ebm    - add multi-threaded test for verification exp. global_ocean_ebm
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