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revision 1.1522 by mlosch, Wed Oct 26 09:30:32 2011 UTC revision 1.1706 by jmc, Mon Aug 6 17:24:37 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 eesupp/inc:
8      - in EEPARAMS.h, add real-type constant for some frequently used simple number
9         (0,1,2,1/2), with name explicitly referring to RS/RL type.
10    o model/src:
11      - move balancing of relaxation terms to new S/R balance_relax.F.
12    o pkg/autodiff:
13      re-write active I/O high-level (control) S/R:
14      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
15      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
16      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
17        MDS_READ/WRITE_FIELD); change loops to multi-threads.
18      - update and merge active_file_control_slice.flow into active_file_control.flow
19      - update the calls in lower level S/R (active_file.F, active_file_g.F and
20        active_file_ad.F) keeping the argument list and function unchanged.
21      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
22        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
23      - new low-level active I/O routines, one for each type (RL/RS), for active var
24        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
25        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
26        right type.
27    o autodiff and RS=real*4:
28      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
29        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
30      - change argument type of 3-D mask argument to _RS to match type in the call
31        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
32    o pkg/thsice:
33      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
34      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
35        fresh-water flux: uniform correction or proportional to local precip.
36    o pkg/ctrl:
37      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
38      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
39                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
40      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
41    
42    checkpoint63q (2012/07/30)
43    o pkg/autodiff:
44      note about monitor and snap-shot of ad-variables:
45      a) need to apply ADEXCH before monitor or output of ad-vars to include
46       overlap contributions (was done for adjDump but missing for monitor).
47      b) since ADEXCH implies adding overlap values to interior array, machine
48       truncation error is expected when adding an ADEXCH call in the middle of
49       the time-stepping (although mathematically identical).
50      modifs:
51      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
52        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
53      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
54        apply ADEXCH before monitor or snap-shot of ad-variables:
55           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
56      - implement new method (copy+adexch) for snap-shot and monitor of main model
57        ad-vars (initially not used by default -> output unchanged).
58      - change default (set to 2) to use new method and update few output_adm.txt
59        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
60        and both tutorial_tracer_adjsens tests).
61      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
62        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
63    o pkg/ctrl:
64      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
65      generic control variables via
66      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
67      Only required customization should be S/R ctrl_map_ini_genarr.F
68      (routine in repository contains example)
69    o pkg/exf:
70      - fix and refine checking of surface-relaxation setting when using EXF
71    o verification (adjoint exp):
72      - reduce length of simulation by half for experiment global_ocean.cs32x15
73        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
74    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
75      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
76        of KE that can occur with aggressive optimization
77      + put quadratic bottom drag calculation in separated loops (only done if
78        using bottomDragQuadratic)
79    o model/src: CG2D_NSA
80      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
81         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
82      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
83         change cg2d residual target to be expressed in Wunits (=> do not normalise
84         RHS ; this fix global_max Pb with TAF); update output.
85    o verification/tutorial_tracer_adjsens:
86       improve parameter consistency (and get rid of warnings):
87       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
88       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
89       - use staggerTimeStep (for stability) in som81; use default rotation period.
90    o pkg/exch2:
91      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
92        reset to 0 = 1 long line in X)
93    o pkg/mdsio:
94      - fix reading of dimensions from meta file for large-size domain
95    o model/src:
96      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
97      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
98        Cubed-Sphere Exch with CS-corners inside the domain;
99        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
100        globalArea and to set hasWetCSCorners.
101      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
102        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
103      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
104        useCDscheme and useCubedSphereExchange).
105    o pkg/seaice/seaice_growth.F :
106      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
107        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
108        when the previous code was not correct.
109      - in all cases diagnoze the boundary condition mismatch to SIaaflux
110      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
111        that term to QNET (essentially to set the melt/freeze water to 0degC).
112        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
113    o verification/global_ocean.cs32x15/input.seaice :
114      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
115      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
116      - update results (output.seaice.txt) accordingly.
117    o verification/lab_sea/input/data.seaice :
118      - remove SEAICEheatConsFix, which is now be tested
119        in global_ocean.cs32x15. The presently coded fix
120        is only consistent with real fresh water + nlfs.
121      - update results (output.txt) accordingly.
122    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
123    o AD_CONFIG.h file:
124      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
125      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
126        add it explicitly in each fortran src file where it is needed.
127        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
128        thus introducing potentially wrong dependency; therefore, better to include
129        it only where it's really needed, and after any other included OPTIONS file
130        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
131        or ALLOW_TANGENTLINEAR_RUN).
132    
133    checkpoint63p (2012/07/06)
134    o pkg/autodiff:
135      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
136      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
137        which are now read from new parameter file "data.autodiff" (inAdExact
138        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
139      - add file "data.autodiff" in all verification/*/input_ad/ directories.
140      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
141        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
142    o verification/tutorial_tracer_adjsens/
143      - add extra sub-verification which uses "SOM" advection scheme
144        (2nd Order-Moment Advection Scheme, Prather Limiter) with
145          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
146        and in data:
147          multiDimAdvection=.TRUE.,
148          tempAdvScheme=81,
149          saltAdvScheme=81,
150    o model/src:
151      - introduce ALLOW_BALANCE_RELAX which allow the removal
152       of the global mean of relaxation terms by setting
153       balanceThetaClimRelax and balanceSaltClimRelax
154      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
155       This case is now treated appropriately in seaice_growth.F
156    o pkg/seaice:
157      - do balanceEmPmR and balanceQnet based on the net fluxes
158        (SItflux) that enter the ocean+ice system rather than QNET
159        and EMPMR. Works best in real fresh water.
160      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
161        out of the diagnotics bloc, and stored in global arrays.
162    
163    checkpoint63o (2012/06/29)
164    o vertical mixing schemes:
165      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
166      - replace computation of density (in Function STATE1, opps_calc.F) by a call
167        to S/R FIND_RHO_SCALAR
168      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
169        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
170        affects output (vermix.ggl90) at truncation level.
171    o testreport:
172      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
173        (nSx,nSy) for the number of threads (from eedata.mth)
174    o model/src:
175      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
176        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
177    o verification/tutorial_tracer_adjsens/
178      - compile with ALLOW_CG2D_NSA
179      - run with nonlinFreeSurf=3
180      - update reference output_adm.txt
181    o tools/genmake2:
182      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
183        refine usePROFILES switching off (only when NetCDF is not available).
184    o verification (atmospheric set-up):
185      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
186    o pkg/profiles : refine profiles and files handling.
187    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
188    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
189      - changes to use model/src/the_main_loop.F rather than the ecco version
190        in ecco type adjoint runs.
191    o model/src:
192      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
193      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
194      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
195    o model/src:
196      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
197        update output of test experiment bottom_ctrl_5x5.
198    o pkg/generic_advdiff:
199      - implement vertical bi-harmonic diffusion (for now, only for T & S and
200        only explicitly).
201    o verification/bottom_ctrl_5x5/
202      update reference output (results changed quite some time ago,
203      not sure when; but new reference results look ok in terms of grdchk)
204    o verification/1D_ocean_ice_column/
205      For verification purposes, the exact adjoint rather than an approx.
206      should be used (e.g., to comare against F.D. or TLM).
207      removed autodiff_inadmode*_ad.F routines in code_ad/
208      Update results/ accordingly.
209    o pkg/cal:
210      - change cal_getdate.F so that output date is function of input time only
211        (less ambiguous, not mixed up with input iteration number).
212      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
213    o pkg/diagnostics:
214      - implement calendarDumps also for stats-diags
215      - implement calendarDumps also for snap-shot output (negative freq)
216      - for now, ignores calendarDumps if non-zero phase-lag.
217    
218    checkpoint63n (2012/06/04)
219    o model/src:
220      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
221        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
222      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
223        similar to calc_r_star.F); update results of experiment internal_wave and
224        tutorial_global_oce_in_p (affected @ truncation level).
225    o pkg/shelfice:
226      - add parameterisation of advective-diffusive flux into the ice shelf
227        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
228      - simply eps3/3a computation
229    o eesupp:
230     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
231       between tiles, just fill-in edges assuming locally periodic subdomain) and
232       add corresponding exchange subroutines (EXCH0);
233     - new CG-solver version (_EX0) for disconnected-tiles special case.
234    o model/src (CG-solvers):
235     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
236       (similar final residual output and max-Iter number as with standard version);
237     - allows to store and use lowest-residual solution (standard & _SR versions);
238     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
239     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
240    o eesup/src:
241     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
242       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
243    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
244    
245    checkpoint63m (2012/04/27)
246    o pkg/shelfice:
247     - account for partical cells in surface level below ice-shelf for hydrostatic
248       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
249    o ad test experiments:
250     - update and rename to "ad_optfile.local" local AD-optfile specific to a
251       particular adjoint verification experiment (in verification/*/code_ad/)
252    o pkg/seaice & pkg/exf:
253     - Part two of ECCO-CLIVAR code merges.
254       Completes merge of seaice area relax. code.
255       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
256       to be set in EXF_OPTIONS.h since this pkg controls its I/O
257       (and avoids second CPP option in SEAICE_OPTIONS.h)
258     - change default value of costIceStart & costIceEnd to a valid date.
259     - add snowPrecip to HSNOW in seaice_growth
260    o pkg/ptracers:
261     - move ptracers summary and setup check into separated S/R ; add a check for
262       valid PTRACERS_Iter0 value (error+stop or just warning).
263    o pkg/cal (+ pkg/ecco):
264     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
265       as input; and for AD, unless both are not differentiable (e.g., k index)).
266    o model/src:
267     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
268       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
269       temporary set to usingZCoords value (to be changed to F when using shelfice).
270     - hydrostatic pressure: implement partial cell near the surface also for
271       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
272       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
273    o pkg/ctrl/ctrl_init.F:
274     - add a formal parameter to s/r ctrl_init_rec to print
275       xx_$(ctrl_valiable)_file for easier debugging
276     - move call of cal_* routines into the if-block where they are really
277       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
278       to specify a startdate
279    o pkg/seaice:
280     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
281       global_ocean.cs32x15/code versions).
282     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
283       verification experiment global_ocean.cs32x15.seaice and update results.
284    o pkg/exf:
285     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
286       (according to useExfYearlyFields).
287    o pkg/cal:
288     - move calendar setting & summary (previously in cal_readparams.F) into new
289       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
290       length of the simulation is set (after SET_PARMS call); This is an attempt
291       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
292     - For safety: keep a record of pkg/cal parameter settings status
293               to allow to STOP if one pkg/cal S/R is called too early.
294     - add a stop in all basic pkg/cal subroutines if called before setting is done.
295     - modify cal_getdate.F: stop when nothing was returned;
296       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
297       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
298    
299    checkpoint63l (2012/04/04)
300    o pkg/bbl:
301      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
302        update global_with_exf output.yearly.txt file.
303    o pkg/cal:
304      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
305      - remove 2 unsused and very short (1 line only) functions ;
306      - remove unsused subroutines from AD-Diff list.
307    o model/src:
308      - start to implement clean wait to stop in initialization S/R (config_check.F,
309         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
310    o folowing PRINT_MESSAGE changes:
311      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
312    o pkg/bbl:
313      - modification so it can work with z*
314      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
315      - global_with_exf/input.yearly verification; changes output.yearly.txt
316    o eesupp/src:
317      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
318        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
319      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
320        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
321      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
322      - when using MPI, always set usingMPI=T ; set default accordingly and stop
323        if not consistent.
324      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
325        argument is zero (in case called within single-thread section).
326    o pkg/fizhi:
327        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
328        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
329    o pkg/exch2:
330      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
331        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
332      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
333        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
334        with bad ones coming from a not-yet-updated halo.
335        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
336    o pkg/frazil:
337        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
338        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
339    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
340    o verification/lab_sea
341      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
342      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
343      * nTimeSteps 3 -> 4
344      * changed reference output accordingly
345    o pkg/ctrl:
346      * fix ctrl_get_gen for xx_sst, xx_sss
347    o pkg/fizhi:
348      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
349        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
350      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
351        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
352        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
353    o pkg/gmredi:
354      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
355    o pkg/fizhi:
356      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
357        (old)aces open64 tuv test.
358    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
359    o pkg/mom_vecinv:
360      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
361        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
362        with non-lin free-surf).
363    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
364      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
365      some compilers (gfortran 4.6.0 on MacOS)
366    o momentum:
367      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
368        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
369        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
370    
371    checkpoint63k (2012/03/17)
372    o model/src:
373       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
374         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
375       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
376         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
377    o model/src: solve_*diagonal.F
378       - replace division with multiplication by inverse (similar to original version)
379         update output of AD exp. global_ocean.90x40x15.
380       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
381         to enable the use of the vectorized & differentiable solve_tridiagonal.F
382       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
383         vertical advection (to get solve_tridiagonal tested in AD mode).
384    o pkg/seaice: ECCO-CLIVAR merge:
385      1. seaice AREA relaxation
386         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
387         * runtime flag: SEAICE_tauAreaObsRelax
388      2. modified global mean cost imbalance code: CPP option
389          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
390    o another iteration on solve_*diagonal.F
391       Make choices independent of AUTODIFF
392       Default will be the adjoinable vectorized version.
393       Alternative choices are:
394       * non-adjoinable original version with low memory footprint:
395         #define SOLVE_DIAGONAL_LOWMEMORY
396       * still adjoinable but does not vectorize (k as inner-most loop):
397         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
398    o testreport
399     - add option to use a home made wrapper around "make"
400     - remove MITGCM_IEEE env. variable (no longer active)
401    o pkg/shelfice
402     - improve computation of friction velocity for velocity dependent
403       exchange coefficients: include velocities into SHELFICEBoundaryLayer
404       block to average velocities vertically
405     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
406    o Modify diagonal solvers, now three versions (upon request):
407      #ifndef SOLVE_DIAGONAL_AUTODIFF
408        1. default version (dating back a while ago)
409      #else /* def SOLVE_DIAGONAL_AUTODIFF */
410      # ifdef SOLVE_DIAGONAL_KINNER
411        2. adjoinable version with k-innermost loop (G. Forget)
412      # else
413        3. adjoinable vectorized version of 2.
414      # endif
415      #endif /* SOLVE_DIAGONAL_AUTODIFF */
416      All flags are currently set within routines, but could/should be moved to CPP-options.
417      Array bounds for 1. are as before, for 2.,3. cover the entire domain
418      (could be changed for 1. too).
419    o verification/lab_sea (fwd):
420      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
421        use 7 categories (except hb87), new solve4temp params (except salt_plume),
422        constant salinity (=4) or variable salinity (salt_plume) done through
423        SItracer.
424    o pkg/seaice:
425      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
426      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
427         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
428        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
429        SEAICE_freeze got retired) but already better than previously with
430        SEAICE_freeze=123456.7 deg.C;
431      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
432        (safer multi-threaded setting); always set SEAICEuseEVP;
433      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
434        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
435        stop if multiple specifications for the same coeff; make sure default
436        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
437    o pkg/obcs:
438      - allow to switch to upwind 1rst order advection scheme for the advective
439        flux computation at the open-boundary; disabled for adjoint built.
440    o pkg/ptracers:
441      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
442      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
443      - add parameter to decide when to start a tracer; use internal flag to
444        know which tracer to step-forward; switch this internal flag at the top
445        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
446        for adjoint built.
447    o pkg/seaice:
448      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
449      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
450      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
451    o pkg/ecco:
452      - fix writing of output file DiagnosCost_ClimSalt/Theta
453        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
454    o pkg/seaice:
455      - add missing initialisation of COR_ICE array in dynsolver.F
456      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
457        compiled either way, and is tested in all exps (multidim was only tested
458        in lab_sea ad before).
459      - cosmetic change to prepare for future addition of ITD. no change to results.
460        no defaults change.
461      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
462      - by lack of adequate verification experiments, I further used custom versions
463        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
464        should be correct.
465      - avoid recomputations in ad.
466    o array initialisation in adjoint mode:
467      1) pkg/mom_common/mom_calc_ke.F:
468        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
469        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
470        part this initialisation is gone, resulting in Floating Point Exception
471        (caught by open64 compiler with debug option).
472      2) model/src/convective_weights.F
473        set output convectCount over the full array range (instead of doing
474        an update): this fix a similar issue when called within recomputation (adjoint)
475        which could by-pass the initialisation (normally done in the caller S/R).
476    o pkg/seaice:
477      - final version of turbulent flux params, as agreed at MIT ice meet:
478           SEAICE_mcPheePiston (default is ~ 0.000875)
479           SEAICE_mcPheeTaper (default is 0.)
480           SEAICE_frazilFrac (defualt is 1.)
481           SEAICE_mcPheeStepFunc (default is false)
482      - changes results at trunction error level
483      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
484    o added pkg/frazil:
485      - see frazil_description.tex for details
486      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
487    o pkg/shelfice/shelfice_thermodynamics.F
488      - fix exponents for velocity dependent exchange coefficients: change
489        from 2/3(=0) to 0.66666666666666667
490      - move computation of velocity dependent exchange coefficients into
491        separate loop, so that it applies to both thermodynamics
492      - move some divisions by constants out of loops
493    
494    checkpoint63j (2012/02/16)
495    o pkg/seaice:
496      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
497      - SItracer:  added run time params, and allow coupling to ocn salinity.
498    o pkg/seaice: remove (almost) all divisions by constants within loops
499      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
500      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
501      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
502      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
503    o pkg/seaice :
504      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
505        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
506      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
507      - add permanent SItflux diag that corresponds to TFLUX but includes
508        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
509      - allow activation/testing of a fix for suspected missing term in
510        ocn-ice heat budget (to be confirmed). To test this, you want to
511        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
512        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
513      - no change in results, fwd or ad.
514    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
515      - switch to variable freezing point.
516           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
517      - bug fix : the sublimation term that was missing is now activated.
518           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
519      - bug fix : flooding sign term for SIsal0.NE.0.
520           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
521    o pkg/seaice:
522      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
523        is now the default, and the old default constant freezing point is recovered
524        with SEAICE_tempFrz0    = -1.96,
525             SEAICE_dTempFrz_dS = 0.,
526      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
527      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
528      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
529        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
530      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
531        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
532      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
533        seaice_growth r149 for legacy branch (no results change).
534      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
535        from I. Fenty).
536      - results did not change except for global_ocean.cs32x15, mostly due to the
537        switch to variable freezing point (see above item for detail).
538    o pkg/thsice:
539      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
540        seawater freezing in thsice_calc_thickn (not used).
541    o pkg/seaice: turbulent flux term specification via run time params.
542      - replace CPP switches with run time switches to facilitate testing
543      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
544                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
545      - added runtime parameter : SEAICEturbFluxFormula
546      - move Mcphee constants to SEAICE_PARAMS.h
547      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
548                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
549                 remove seaice_summary call (moved to seaice_init_fixed)
550      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
551        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
552      - seaice_summary.F : add missing report of read turbulent flux term set up
553                           and SITRACER.
554      - seaice_check.F : check range; inform and stop if retired CPPs are used
555                         (incl. SEAICE_AGE).
556      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
557             CPP switch, same computation as before for the different options.
558      - change results at the truncation level.
559    o pkg/seaice:
560      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
561        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
562        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
563      - update verification/*/input*/data.seaice:
564        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
565        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
566        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
567        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
568    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
569      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
570        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
571        difference in results only due to machine truncation.
572      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
573        MaykutPolySatVap; keep MIN_LWDOWN.
574      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
575      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
576        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
577    o pkg/salt_plume:
578      - isolate saltPlumeFlux array exch into a specific S/R called from
579        do_oceanic_phys.F
580      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
581    o verification:
582      - move untested set-up to MITgcm_contrib/verification_other.
583    o pkg/seaice:
584      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
585    o pkg/seaice:
586      - seaice_solve4temp.F (keeping results unchanged):
587        * add 2 future run-time params to select which saturation vapor pressure
588          formula is used and how post-iteration fluxes are set.
589          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
590        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
591          the linearized expression to stay consistent with tsurf finding.
592      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
593        can be < 0.
594    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
595      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
596        conductive heat flux F_c , and add it explicitly when updating tsurf as
597        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
598        so that now F_ia has a consistent meaning through the entire routine.
599        This causes differences at truncation level: update output of fwd exp.
600        global_ocean.cs32x15.seaice.
601    o pkg/seaice:
602      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
603        of arrays, sign/direction of fluxes; no effect on results.
604      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
605        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
606        note: this should have been done before changing celsius2K default.
607      - to keep results unchanged, add back old value of celsius2K in verification
608        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
609      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
610        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
611        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
612        freezing temp is consistent with value in seaice_growth.F ; this causes
613        differences at machine truncation level: update lab_sea AD output (3/4).
614    o pkg/seaice:
615      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
616        and climsst/sss even when using seaice (to prevent calculation that might
617        use SST on land); does not affect any verification exp.
618      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
619        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
620    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
621      over land (non-legacy code)
622    o vectorize salt_plume package:
623      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
624      - this code computes plumebk everywhere (also over land), thus requires
625        code to avoid divisions by zero and catch the case of kLev=Nr.
626      - efficiency of salt_plume_frac is still sub-optimal
627    o tools (genmake2):
628      - fix makefile NAME specification (option: -makefile NAME) by adding
629        "-f $MAKEFILE" in few places where it was missing including makedepend
630        command (contribution from Paul).
631    
632    checkpoint63i (2012/01/24)
633    o model/src:
634      - add factorized versions of some EOS code to find_rho.F,
635        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
636    o model/src:
637      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
638      - change default celsius2K from 273.16 to 273.15
639      - to keep results unchanged, add back old value of celsius2K in verification
640        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
641         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
642    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
643      to make TAF generate vectorizable code
644    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
645       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
646       have flags that do this more efficiently.
647    o pkg/diagnostics/diagstats_calc.F
648      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
649    o pkg/obcs (with exch2):
650      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
651        and remove code (in obcs_readparms.F) which was based on EXCH of indices
652        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
653    o pkg/exf and seaice exp:
654      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
655        so that switching off area & heff advection flags does not affect results.
656      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
657      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
658        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
659        results of verification experiments: 1D_ocean_ice_column(fwd),
660        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
661        and offline_exf_seaice (all 4).
662    o pkg/seaice:
663      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
664        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
665      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
666        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
667        not multi-dim advection;
668      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
669        SHORTWAVE_HEATING #undef.
670    o optim: make Makefile more robust (?)
671    o pkg/obcs:
672      * fix treatment of obcs_read_pickup for TAF
673    o pkg/shelfice:
674      * add missing initialisation of num_shifwflx
675      * new adjoint verification exp. for isomip
676      * change Prandtl and Schmidt numbers from generic formulations
677        (in terms of model diffus. and visc.) to separate runtime
678        parameters, with Holland and Jenkins (1999) default values.
679    o pkg/exf (interpolation):
680      - extended input field (2 rows) near the N & S poles:
681        * fill in with the symetric value (when even Nb of data in longitude)
682        * add average value at the poles only for scalar quantities ; for vector
683          component interpolation, skip the averaging and keep duplicated values,
684          unless the 2 components have same location (uvInterp=T) in which case
685          interpolate the 2 components together using S/R EXF_INTERP_UV.
686      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
687        together: this allows to account properly for local orientation when
688        averaging at N & S pole.
689      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
690        exf-interpolation near N & S poles. Undef by default.
691      - add debug check/print on 1rst iter if debugLevel >=2.
692    o pkg/exf:
693      - change masking flags definition (no longer "parameter"), put them in
694        common block and set them in S/R EXF_INIT_FIXED.
695      - change recognized masking flag from s,u,v to c,w,s since the mask
696        to use (maskC,W,S) depends on position on model grid and has little to
697        do with scalar/vector difference; fix masking if using P-coordinates.
698      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
699        and update results of exp. global_with_exf (x2).
700      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
701    o pkg/obcs
702      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
703    o pkg/exf (interpolation):
704      - assume periodicity in X only if input field cover full longitude range.
705      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
706        and should vectorise).
707      - fix input lat of the 2 added row (in case we provide N.pole data).
708    
709    checkpoint63h (2011/12/30)
710    o pkg/seaice:
711      - change declaration of UVM from _RL to _RS in order to get B-grid
712        uIce,vIce monitor when _RS = real*4
713    o pkg/offline:
714      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
715      - compute vertical velocity if not read from file (switch on exactConserv
716        & staggerTimeStep);
717      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
718    o verification:
719      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
720        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
721        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
722      - update output of exp. global_ocean.cs32x15.viscA4 after changing
723        grid-file angles (used here for coriolis-3d);
724      - remove (or gzip) few files not needed to run fizhi-cs experiments.
725    o pkg/exf (vector interpolation):
726      - rotate vector component toward local grid-axis orientation using grid-angles
727        (stored in GRID.h) instead of locally computed rotation angle; keep old code
728        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
729    o pkg/seaice:
730      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
731        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
732    o pkg/PKG_OPTIONS.h files:
733      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
734        outside of the #ifdef ALLOW_THISPKG / #endif block.
735      - update verification/*/code/PKG_OPTIONS.h files.
736    o add a verification experiment (offline_exf_seaice/input.seaice) that test
737      the B-grid LSOR solver
738    o pkg/seaice: sort out emissivity and long wave radiation step 2:
739      - add emissivity for snow and ice as new run-time parameters
740        (unfortunately) that default to the corresponding exf values; this
741        changes results in most verification experiments so that for backward
742        compatibility these parameter have to be set explicitly to inconsistent
743        values (ugly);
744      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
745        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
746        until we agree how to handle this bug properly
747    o pkg/exf (interpolation):
748      - add a set of run-time param ({inputfield}_interpMethod), one for
749        each interpolated input field, to select the interpolation method
750        with a value of zero switching off the interpolation;
751      - print interpolation parameters to standard output;
752      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
753        (to use instead runoff_interpMethod=0 in data.exf).
754      - simplify default setting of interpolation parameters (for all fields,
755        set position to match model grid cell-center position, leading to trivial
756        interpolation in case of regular Lat-Lon grid) and fix for the case of
757        non-uniform delY.
758    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
759       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
760       this factor is absolutely required, because the lw exitance (= out-going
761       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
762       where the reflectivity rho = 1-emissivity for conservation reasons. Once
763       this is established, we can remove the CPP-Flag (if we want to).
764    o pkg/seaice:
765      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
766        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
767      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
768        what the name implies (and not emissivity*BoltzmannConstant), this means
769        the old default value of 5.5e-8 now means
770        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
771        S/R exf_readparms
772      - FV-discretization of the B-grid LSOR solver, turn on with
773        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
774        of the calling routine dynsolver, so that B and C-grid code look a
775        little more alike.
776      - fix index bugs in ostres.F (B-grid code)
777    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
778    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
779      default for SEAICE_emissivity, if useEXF; requires setting a wrong
780      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
781      backward compatiblity
782    o model/src: use sigmaR in calc_ivdc
783    
784    checkpoint63g (2011/12/16)
785    o pkg/seaice/seaice_growth.F:
786      fix heat conservation of the coupled ocean-seaice system.
787      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
788      solid vs liquid water treatment is resolved via QNET.
789    o pkg/seaice/seaice_growth.F:
790      add missing term for sublimation in saltFlux, which was breaking conservation.
791    o pkg/seaice/seaice_model.F:
792      Remove this patholigical case treatment in evolution branch,
793      where it is un-necessary and breaks conservation.
794      Update global_ocean.cs32x15/results accordingly for
795      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
796    o model/src:
797      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
798      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
799    o pkg/obcs:
800      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
801      tendency for temperature and salinity that is then applied to update
802      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
803      horizontal advection and diffusion contributions on the boundary (in
804      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
805      removing the mask in S/R timestep_tracer. The advantage of this approach is
806      that the updated tracer values include contributions from the surface
807      forcing and vertical diffusion.
808      This modification changes exp4.stevens because of vertical diffusion.
809    o model/src:
810      change non-curvilinear grid setting to also work with exch2 + blank tiles:
811      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
812        face dimensions.
813      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
814        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
815        and INI_SPHERICAL_POLAR_GRID.
816      change test-experiment global_ocean.90x40x15:
817      - split the domain in many more tiles (9x4 tiles of 10x10 each);
818      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
819      - update results of both test (std & dwnslp).
820    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
821       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
822    o model/src:
823      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
824        and fix initialisation when using sigma-coords.
825    o model/src:
826     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
827       to their current value at the beginning of forward_step.F": add a new run-time
828       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
829     - set doResetHFactors=T in the following test exp:
830        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
831        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
832        and tutorial_global_oce_in_p (nonLinFS in p)
833    o pkg/ecco
834      - added IES cost term
835    o verification/advect_xz
836      - scale down the depth by 1/100 (from 200 km to just 2.km)
837      - add secondary test using divergent flow, r-star and implicit vertical advection.
838      - add note (check_conserve_TS.txt) and matlab script to check global
839        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
840    o pkg/rbcs:
841      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
842    o pkg/obcs (Stevens BCs):
843      - fix various problems in the phase speed computations of the Stevens
844        boundary conditions:
845        - sign error for western and southern boundaries,
846        - time tendencies were underestimated by factor of dTracerLev and some just
847          zero (for multidim advection schemes) -> now estimate time tendencies
848          from difference between previous (n) time level and the one before (n-1);
849          this requires storing a field per tracer per boundary, also in the pickup
850          files.
851        - replace deltaTmom in cflMer/Zon computation with dTracerLev
852        - set default phase velocity to cflMer/Zon
853      - update verification experiment exp4.stevens
854    o pkg/generic_advdiff (implicit_r):
855      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
856        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
857      - fix implicit vertical diffusion or advection with NonLin FreeSurf
858        (was using current recip_hFacC instead of future recip_hFacC): set future
859        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
860        solver S/R ;
861      - fill diagnostics of vertical advective fluxes (computed from tendency)
862        when using implicit vert. advection;
863      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
864         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
865         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
866         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
867    o pkg/diagnostics:
868      - add diags for T & S tendency which goes through Adams-Bashforth.
869    
870    checkpoint63f (2011/11/30)
871    o pkg/obcs/obcs_calc_stevens.F:
872      - join some loops to reduce number of if-statements
873      - fix a bug in code for northern and southern boundaries.
874    o pkg/seaice/seaice_init_varia.F
875      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
876        caused zero ice-velocities for the B-grid code
877    o pkg/seaice/seaice_init_fixed.F
878      - fix a bug in the initialisation of the second metric terms
879        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
880      - this affects all seaice configurations with useCurviLinearGrid = .true.
881        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
882        = .true. (default)
883      - the only verification experiment affected is global_ocean.cs32x15:
884        icedyn, seaice, and seaice_dynmix (AD)
885    o pkg/thsice/thsice_diagnostics_state.F
886      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
887        not contain garbage that can lead to surprises in diagstats_calc.F
888    o model/src:
889      - move bi,bj loops inside INTEGR_CONTINUITY ;
890      - call INTEGR_CONTINUITY directly from forward_step.F
891        (previously called from momentum_correction_step.F)
892      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
893        forward_step.F and pkg/ecco/the_main_loop.F
894    o model/src/do_oceanic_phys.F:
895      - reset addMass to zero only if useICEFRONT ;
896      - separated k-loop for rhoInSitu calculation ;
897      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
898        and at constant T,S (= WdRHOdP);
899      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
900        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
901        transport of locally-referenced potential density);
902        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
903    o gluemnc:
904      - replace ncrcat with ncks when adding variables to *.glob.nc
905      - change the way variables without record dimensions are handled so that
906        files that have variables with and without record variables can be glued:
907        add a record dimension with a new unique name to be able to differentiate
908        between variable with and without a-prior record dimensions. Remove
909        this record dimension before adding the variable to the *.glob.nc file.
910        This procedure automatically works also for grid.*.nc files that do not
911        have any record dimension.
912    o verification/cpl_aim+ocn:
913      - generate new reference output on baudelaire (gfortran, mpich2) (previously
914        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
915    o pkg/obcs/obcs_calc_stevens.F:
916      - add code for northern and southern boundaries.
917      - reorder some loops to save some operations and so that drFBar can be scalar
918    o model/src:
919      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
920        truncation) and add diagnostics for Adams-Bashforth tendency increment.
921      - update test-exp. AD output:
922        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
923      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
924        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
925        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
926        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
927        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
928        tutorial_plume_on_slope.
929    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
930      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
931      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
932      does not even come with an F77 compiler anymore, this should not be
933      a limitation
934    
935    checkpoint63e (2011/11/06)
936    o pkg/seaice adjoint of LSR:
937      - substantially rework STORE dirs.
938      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
939        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
940        and only perform SOLV_MAX_FIXED adjoint iters.
941        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
942        always goes to same record, meaning that the last forward field will be
943        the one used in the adjoint - an approximation.
944      - now produces non-zero LSR-related gradients, and acceptable gradients for
945        An's zonal (x-z) test case (to be checked in)
946      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
947        (but these are screwed up by the thermodynamics in the first place);
948        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
949        output_adm.txt also reflects changes to seaice_lsr
950      - global_ocean.cs32x15:
951        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
952          (output_adm.seaice.txt was updated)
953        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
954          (output_adm.seaice_dynmix.txt)
955    o test-exp. exp4+stevens:
956      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
957    o pkg/seaice (lsr solver):
958      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
959        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
960      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
961      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
962        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
963      - compute (with new S/R) and print initial (+ free-driff sol. if available)
964        and final residual of linearised system.
965  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
966    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
967  o pkg/obcs: Stevens BCs (still only for east and west)  o pkg/obcs: Stevens BCs (still only for east and west)
968    - fix Stevens BCs by using intermediate velocities of previous    - fix Stevens BCs by using intermediate velocities of previous
969      time step as "baroclinic" contribution rather velocity of one grid cell      time step as "baroclinic" contribution rather velocity of one grid cell
970      inside the boundaries; more consistent but makes the entire treatment      inside the boundaries; more consistent but makes the entire treatment
971      more complicated, requires new pickup files and two new S/Rs:      more complicated, requires new pickup files and two new S/Rs:
972      obcs_copy_uv_n and obcs_save_uv_n      obcs_copy_uv_n and obcs_save_uv_n
973      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
974      (undefined by default)      (undefined by default)
975    - silently move computation of some grid factors into separate loops to    - silently move computation of some grid factors into separate loops to
976      save some recomputations      save some recomputations
977    - add a hack for non-linear free surface    - add a hack for non-linear free surface
978    - add a verification experiment to exp4 that tests this code    - add a verification experiment to exp4 that tests this code
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