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revision 1.1520 by mlosch, Tue Oct 25 13:10:24 2011 UTC revision 1.1647 by jmc, Sat Apr 7 20:07:44 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     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
9       (according to useExfYearlyFields).
10    o pkg/cal:
11     - move calendar setting & summary (previously in cal_readparams.F) into new
12       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
13       length of the simulation is set (after SET_PARMS call); This is an attempt
14       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
15     - For safety: keep a record of pkg/cal parameter settings status
16               to allow to STOP if one pkg/cal S/R is called too early.
17     - add a stop in all basic pkg/cal subroutines if called before setting is done.
18     - modify cal_getdate.F: stop when nothing was returned;
19       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
20       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
21    
22    checkpoint63l (2012/04/04)
23    o pkg/bbl:
24      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
25        update global_with_exf output.yearly.txt file.
26    o pkg/cal:
27      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
28      - remove 2 unsused and very short (1 line only) functions ;
29      - remove unsused subroutines from AD-Diff list.
30    o model/src:
31      - start to implement clean wait to stop in initialization S/R (config_check.F,
32         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
33    o folowing PRINT_MESSAGE changes:
34      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
35    o pkg/bbl:
36      - modification so it can work with z*
37      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
38      - global_with_exf/input.yearly verification; changes output.yearly.txt
39    o eesupp/src:
40      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
41        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
42      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
43        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
44      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
45      - when using MPI, always set usingMPI=T ; set default accordingly and stop
46        if not consistent.
47      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
48        argument is zero (in case called within single-thread section).
49    o pkg/fizhi:
50        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
51        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
52    o pkg/exch2:
53      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
54        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
55      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
56        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
57        with bad ones coming from a not-yet-updated halo.
58        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
59    o pkg/frazil:
60        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
61        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
62    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
63    o verification/lab_sea
64      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
65      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
66      * nTimeSteps 3 -> 4
67      * changed reference output accordingly
68    o pkg/ctrl:
69      * fix ctrl_get_gen for xx_sst, xx_sss
70    o pkg/fizhi:
71      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
72        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
73      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
74        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
75        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
76    o pkg/gmredi:
77      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
78    o pkg/fizhi:
79      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
80        (old)aces open64 tuv test.
81    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
82    o pkg/mom_vecinv:
83      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
84        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
85        with non-lin free-surf).
86    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
87      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
88      some compilers (gfortran 4.6.0 on MacOS)
89    o momentum:
90      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
91        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
92        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
93    
94    checkpoint63k (2012/03/17)
95    o model/src:
96       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
97         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
98       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
99         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
100    o model/src: solve_*diagonal.F
101       - replace division with multiplication by inverse (similar to original version)
102         update output of AD exp. global_ocean.90x40x15.
103       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
104         to enable the use of the vectorized & differentiable solve_tridiagonal.F
105       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
106         vertical advection (to get solve_tridiagonal tested in AD mode).
107    o pkg/seaice: ECCO-CLIVAR merge:
108      1. seaice AREA relaxation
109         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
110         * runtime flag: SEAICE_tauAreaObsRelax
111      2. modified global mean cost imbalance code: CPP option
112          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
113    o another iteration on solve_*diagonal.F
114       Make choices independent of AUTODIFF
115       Default will be the adjoinable vectorized version.
116       Alternative choices are:
117       * non-adjoinable original version with low memory footprint:
118         #define SOLVE_DIAGONAL_LOWMEMORY
119       * still adjoinable but does not vectorize (k as inner-most loop):
120         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
121    o testreport
122     - add option to use a home made wrapper around "make"
123     - remove MITGCM_IEEE env. variable (no longer active)
124    o pkg/shelfice
125     - improve computation of friction velocity for velocity dependent
126       exchange coefficients: include velocities into SHELFICEBoundaryLayer
127       block to average velocities vertically
128     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
129    o Modify diagonal solvers, now three versions (upon request):
130      #ifndef SOLVE_DIAGONAL_AUTODIFF
131        1. default version (dating back a while ago)
132      #else /* def SOLVE_DIAGONAL_AUTODIFF */
133      # ifdef SOLVE_DIAGONAL_KINNER
134        2. adjoinable version with k-innermost loop (G. Forget)
135      # else
136        3. adjoinable vectorized version of 2.
137      # endif
138      #endif /* SOLVE_DIAGONAL_AUTODIFF */
139      All flags are currently set within routines, but could/should be moved to CPP-options.
140      Array bounds for 1. are as before, for 2.,3. cover the entire domain
141      (could be changed for 1. too).
142    o verification/lab_sea (fwd):
143      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
144        use 7 categories (except hb87), new solve4temp params (except salt_plume),
145        constant salinity (=4) or variable salinity (salt_plume) done through
146        SItracer.
147    o pkg/seaice:
148      - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
149      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
150         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
151        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
152        SEAICE_freeze got retired) but already better than previously with
153        SEAICE_freeze=123456.7 deg.C;
154      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
155        (safer multi-threaded setting); always set SEAICEuseEVP;
156      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
157        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
158        stop if multiple specifications for the same coeff; make sure default
159        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
160    o pkg/obcs:
161      - allow to switch to upwind 1rst order advection scheme for the advective
162        flux computation at the open-boundary; disabled for adjoint built.
163    o pkg/ptracers:
164      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
165      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
166      - add parameter to decide when to start a tracer; use internal flag to
167        know which tracer to step-forward; switch this internal flag at the top
168        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
169        for adjoint built.
170    o pkg/seaice:
171      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
172      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
173      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
174    o pkg/ecco:
175      - fix writing of output file DiagnosCost_ClimSalt/Theta
176        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
177    o pkg/seaice:
178      - add missing initialisation of COR_ICE array in dynsolver.F
179      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
180        compiled either way, and is tested in all exps (multidim was only tested
181        in lab_sea ad before).
182      - cosmetic change to prepare for future addition of ITD. no change to results.
183        no defaults change.
184      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
185      - by lack of adequate verification experiments, I further used custom versions
186        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
187        should be correct.
188      - avoid recomputations in ad.
189    o array initialisation in adjoint mode:
190      1) pkg/mom_common/mom_calc_ke.F:
191        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
192        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
193        part this initialisation is gone, resulting in Floating Point Exception
194        (caught by open64 compiler with debug option).
195      2) model/src/convective_weights.F
196        set output convectCount over the full array range (instead of doing
197        an update): this fix a similar issue when called within recomputation (adjoint)
198        which could by-pass the initialisation (normally done in the caller S/R).
199    o pkg/seaice:
200      - final version of turbulent flux params, as agreed at MIT ice meet:
201           SEAICE_mcPheePiston (default is ~ 0.000875)
202           SEAICE_mcPheeTaper (default is 0.)
203           SEAICE_frazilFrac (defualt is 1.)
204           SEAICE_mcPheeStepFunc (default is false)
205      - changes results at trunction error level
206      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
207    o added pkg/frazil:
208      - see frazil_description.tex for details
209      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
210    o pkg/shelfice/shelfice_thermodynamics.F
211      - fix exponents for velocity dependent exchange coefficients: change
212        from 2/3(=0) to 0.66666666666666667
213      - move computation of velocity dependent exchange coefficients into
214        separate loop, so that it applies to both thermodynamics
215      - move some divisions by constants out of loops
216    
217    checkpoint63j (2012/02/16)
218    o pkg/seaice:
219      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
220      - SItracer:  added run time params, and allow coupling to ocn salinity.
221    o pkg/seaice: remove (almost) all divisions by constants within loops
222      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
223      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
224      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
225      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
226    o pkg/seaice :
227      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
228        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
229      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
230      - add permanent SItflux diag that corresponds to TFLUX but includes
231        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
232      - allow activation/testing of a fix for suspected missing term in
233        ocn-ice heat budget (to be confirmed). To test this, you want to
234        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
235        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
236      - no change in results, fwd or ad.
237    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
238      - switch to variable freezing point.
239           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
240      - bug fix : the sublimation term that was missing is now activated.
241           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
242      - bug fix : flooding sign term for SIsal0.NE.0.
243           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
244    o pkg/seaice:
245      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
246        is now the default, and the old default constant freezing point is recovered
247        with SEAICE_tempFrz0    = -1.96,
248             SEAICE_dTempFrz_dS = 0.,
249      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
250      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
251      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
252        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
253      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
254        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
255      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
256        seaice_growth r149 for legacy branch (no results change).
257      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
258        from I. Fenty).
259      - results did not change except for global_ocean.cs32x15, mostly due to the
260        switch to variable freezing point (see above item for detail).
261    o pkg/thsice:
262      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
263        seawater freezing in thsice_calc_thickn (not used).
264    o pkg/seaice: turbulent flux term specification via run time params.
265      - replace CPP switches with run time switches to facilitate testing
266      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
267                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
268      - added runtime parameter : SEAICEturbFluxFormula
269      - move Mcphee constants to SEAICE_PARAMS.h
270      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
271                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
272                 remove seaice_summary call (moved to seaice_init_fixed)
273      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
274        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
275      - seaice_summary.F : add missing report of read turbulent flux term set up
276                           and SITRACER.
277      - seaice_check.F : check range; inform and stop if retired CPPs are used
278                         (incl. SEAICE_AGE).
279      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
280             CPP switch, same computation as before for the different options.
281      - change results at the truncation level.
282    o pkg/seaice:
283      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
284        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
285        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
286      - update verification/*/input*/data.seaice:
287        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
288        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
289        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
290        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
291    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
292      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
293        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
294        difference in results only due to machine truncation.
295      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
296        MaykutPolySatVap; keep MIN_LWDOWN.
297      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
298      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
299        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
300    o pkg/salt_plume:
301      - isolate saltPlumeFlux array exch into a specific S/R called from
302        do_oceanic_phys.F
303      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
304    o verification:
305      - move untested set-up to MITgcm_contrib/verification_other.
306    o pkg/seaice:
307      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
308    o pkg/seaice:
309      - seaice_solve4temp.F (keeping results unchanged):
310        * add 2 future run-time params to select which saturation vapor pressure
311          formula is used and how post-iteration fluxes are set.
312          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
313        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
314          the linearized expression to stay consistent with tsurf finding.
315      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
316        can be < 0.
317    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
318      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
319        conductive heat flux F_c , and add it explicitly when updating tsurf as
320        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
321        so that now F_ia has a consistent meaning through the entire routine.
322        This causes differences at truncation level: update output of fwd exp.
323        global_ocean.cs32x15.seaice.
324    o pkg/seaice:
325      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
326        of arrays, sign/direction of fluxes; no effect on results.
327      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
328        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
329        note: this should have been done before changing celsius2K default.
330      - to keep results unchanged, add back old value of celsius2K in verification
331        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
332      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
333        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
334        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
335        freezing temp is consistent with value in seaice_growth.F ; this causes
336        differences at machine truncation level: update lab_sea AD output (3/4).
337    o pkg/seaice:
338      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
339        and climsst/sss even when using seaice (to prevent calculation that might
340        use SST on land); does not affect any verification exp.
341      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
342        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
343    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
344      over land (non-legacy code)
345    o vectorize salt_plume package:
346      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
347      - this code computes plumebk everywhere (also over land), thus requires
348        code to avoid divisions by zero and catch the case of kLev=Nr.
349      - efficiency of salt_plume_frac is still sub-optimal
350    o tools (genmake2):
351      - fix makefile NAME specification (option: -makefile NAME) by adding
352        "-f $MAKEFILE" in few places where it was missing including makedepend
353        command (contribution from Paul).
354    
355    checkpoint63i (2012/01/24)
356    o model/src:
357      - add factorized versions of some EOS code to find_rho.F,
358        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
359    o model/src:
360      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
361      - change default celsius2K from 273.16 to 273.15
362      - to keep results unchanged, add back old value of celsius2K in verification
363        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
364         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
365    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
366      to make TAF generate vectorizable code
367    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
368       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
369       have flags that do this more efficiently.
370    o pkg/diagnostics/diagstats_calc.F
371      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
372    o pkg/obcs (with exch2):
373      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
374        and remove code (in obcs_readparms.F) which was based on EXCH of indices
375        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
376    o pkg/exf and seaice exp:
377      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
378        so that switching off area & heff advection flags does not affect results.
379      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
380      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
381        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
382        results of verification experiments: 1D_ocean_ice_column(fwd),
383        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
384        and offline_exf_seaice (all 4).
385    o pkg/seaice:
386      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
387        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
388      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
389        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
390        not multi-dim advection;
391      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
392        SHORTWAVE_HEATING #undef.
393    o optim: make Makefile more robust (?)
394    o pkg/obcs:
395      * fix treatment of obcs_read_pickup for TAF
396    o pkg/shelfice:
397      * add missing initialisation of num_shifwflx
398      * new adjoint verification exp. for isomip
399      * change Prandtl and Schmidt numbers from generic formulations
400        (in terms of model diffus. and visc.) to separate runtime
401        parameters, with Holland and Jenkins (1999) default values.
402    o pkg/exf (interpolation):
403      - extended input field (2 rows) near the N & S poles:
404        * fill in with the symetric value (when even Nb of data in longitude)
405        * add average value at the poles only for scalar quantities ; for vector
406          component interpolation, skip the averaging and keep duplicated values,
407          unless the 2 components have same location (uvInterp=T) in which case
408          interpolate the 2 components together using S/R EXF_INTERP_UV.
409      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
410        together: this allows to account properly for local orientation when
411        averaging at N & S pole.
412      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
413        exf-interpolation near N & S poles. Undef by default.
414      - add debug check/print on 1rst iter if debugLevel >=2.
415    o pkg/exf:
416      - change masking flags definition (no longer "parameter"), put them in
417        common block and set them in S/R EXF_INIT_FIXED.
418      - change recognized masking flag from s,u,v to c,w,s since the mask
419        to use (maskC,W,S) depends on position on model grid and has little to
420        do with scalar/vector difference; fix masking if using P-coordinates.
421      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
422        and update results of exp. global_with_exf (x2).
423      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
424    o pkg/obcs
425      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
426    o pkg/exf (interpolation):
427      - assume periodicity in X only if input field cover full longitude range.
428      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
429        and should vectorise).
430      - fix input lat of the 2 added row (in case we provide N.pole data).
431    
432    checkpoint63h (2011/12/30)
433    o pkg/seaice:
434      - change declaration of UVM from _RL to _RS in order to get B-grid
435        uIce,vIce monitor when _RS = real*4
436    o pkg/offline:
437      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
438      - compute vertical velocity if not read from file (switch on exactConserv
439        & staggerTimeStep);
440      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
441    o verification:
442      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
443        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
444        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
445      - update output of exp. global_ocean.cs32x15.viscA4 after changing
446        grid-file angles (used here for coriolis-3d);
447      - remove (or gzip) few files not needed to run fizhi-cs experiments.
448    o pkg/exf (vector interpolation):
449      - rotate vector component toward local grid-axis orientation using grid-angles
450        (stored in GRID.h) instead of locally computed rotation angle; keep old code
451        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
452    o pkg/seaice:
453      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
454        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
455    o pkg/PKG_OPTIONS.h files:
456      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
457        outside of the #ifdef ALLOW_THISPKG / #endif block.
458      - update verification/*/code/PKG_OPTIONS.h files.
459    o add a verification experiment (offline_exf_seaice/input.seaice) that test
460      the B-grid LSOR solver
461    o pkg/seaice: sort out emissivity and long wave radiation step 2:
462      - add emissivity for snow and ice as new run-time parameters
463        (unfortunately) that default to the corresponding exf values; this
464        changes results in most verification experiments so that for backward
465        compatibility these parameter have to be set explicitly to inconsistent
466        values (ugly);
467      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
468        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
469        until we agree how to handle this bug properly
470    o pkg/exf (interpolation):
471      - add a set of run-time param ({inputfield}_interpMethod), one for
472        each interpolated input field, to select the interpolation method
473        with a value of zero switching off the interpolation;
474      - print interpolation parameters to standard output;
475      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
476        (to use instead runoff_interpMethod=0 in data.exf).
477      - simplify default setting of interpolation parameters (for all fields,
478        set position to match model grid cell-center position, leading to trivial
479        interpolation in case of regular Lat-Lon grid) and fix for the case of
480        non-uniform delY.
481    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
482       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
483       this factor is absolutely required, because the lw exitance (= out-going
484       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
485       where the reflectivity rho = 1-emissivity for conservation reasons. Once
486       this is established, we can remove the CPP-Flag (if we want to).
487    o pkg/seaice:
488      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
489        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
490      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
491        what the name implies (and not emissivity*BoltzmannConstant), this means
492        the old default value of 5.5e-8 now means
493        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
494        S/R exf_readparms
495      - FV-discretization of the B-grid LSOR solver, turn on with
496        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
497        of the calling routine dynsolver, so that B and C-grid code look a
498        little more alike.
499      - fix index bugs in ostres.F (B-grid code)
500    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
501    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
502      default for SEAICE_emissivity, if useEXF; requires setting a wrong
503      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
504      backward compatiblity
505    o model/src: use sigmaR in calc_ivdc
506    
507    checkpoint63g (2011/12/16)
508    o pkg/seaice/seaice_growth.F:
509      fix heat conservation of the coupled ocean-seaice system.
510      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
511      solid vs liquid water treatment is resolved via QNET.
512    o pkg/seaice/seaice_growth.F:
513      add missing term for sublimation in saltFlux, which was breaking conservation.
514    o pkg/seaice/seaice_model.F:
515      Remove this patholigical case treatment in evolution branch,
516      where it is un-necessary and breaks conservation.
517      Update global_ocean.cs32x15/results accordingly for
518      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
519    o model/src:
520      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
521      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
522    o pkg/obcs:
523      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
524      tendency for temperature and salinity that is then applied to update
525      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
526      horizontal advection and diffusion contributions on the boundary (in
527      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
528      removing the mask in S/R timestep_tracer. The advantage of this approach is
529      that the updated tracer values include contributions from the surface
530      forcing and vertical diffusion.
531      This modification changes exp4.stevens because of vertical diffusion.
532    o model/src:
533      change non-curvilinear grid setting to also work with exch2 + blank tiles:
534      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
535        face dimensions.
536      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
537        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
538        and INI_SPHERICAL_POLAR_GRID.
539      change test-experiment global_ocean.90x40x15:
540      - split the domain in many more tiles (9x4 tiles of 10x10 each);
541      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
542      - update results of both test (std & dwnslp).
543    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
544       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
545    o model/src:
546      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
547        and fix initialisation when using sigma-coords.
548    o model/src:
549     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
550       to their current value at the beginning of forward_step.F": add a new run-time
551       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
552     - set doResetHFactors=T in the following test exp:
553        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
554        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
555        and tutorial_global_oce_in_p (nonLinFS in p)
556    o pkg/ecco
557      - added IES cost term
558    o verification/advect_xz
559      - scale down the depth by 1/100 (from 200 km to just 2.km)
560      - add secondary test using divergent flow, r-star and implicit vertical advection.
561      - add note (check_conserve_TS.txt) and matlab script to check global
562        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
563    o pkg/rbcs:
564      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
565    o pkg/obcs (Stevens BCs):
566      - fix various problems in the phase speed computations of the Stevens
567        boundary conditions:
568        - sign error for western and southern boundaries,
569        - time tendencies were underestimated by factor of dTracerLev and some just
570          zero (for multidim advection schemes) -> now estimate time tendencies
571          from difference between previous (n) time level and the one before (n-1);
572          this requires storing a field per tracer per boundary, also in the pickup
573          files.
574        - replace deltaTmom in cflMer/Zon computation with dTracerLev
575        - set default phase velocity to cflMer/Zon
576      - update verification experiment exp4.stevens
577    o pkg/generic_advdiff (implicit_r):
578      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
579        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
580      - fix implicit vertical diffusion or advection with NonLin FreeSurf
581        (was using current recip_hFacC instead of future recip_hFacC): set future
582        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
583        solver S/R ;
584      - fill diagnostics of vertical advective fluxes (computed from tendency)
585        when using implicit vert. advection;
586      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
587         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
588         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
589         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
590    o pkg/diagnostics:
591      - add diags for T & S tendency which goes through Adams-Bashforth.
592    
593    checkpoint63f (2011/11/30)
594    o pkg/obcs/obcs_calc_stevens.F:
595      - join some loops to reduce number of if-statements
596      - fix a bug in code for northern and southern boundaries.
597    o pkg/seaice/seaice_init_varia.F
598      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
599        caused zero ice-velocities for the B-grid code
600    o pkg/seaice/seaice_init_fixed.F
601      - fix a bug in the initialisation of the second metric terms
602        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
603      - this affects all seaice configurations with useCurviLinearGrid = .true.
604        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
605        = .true. (default)
606      - the only verification experiment affected is global_ocean.cs32x15:
607        icedyn, seaice, and seaice_dynmix (AD)
608    o pkg/thsice/thsice_diagnostics_state.F
609      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
610        not contain garbage that can lead to surprises in diagstats_calc.F
611    o model/src:
612      - move bi,bj loops inside INTEGR_CONTINUITY ;
613      - call INTEGR_CONTINUITY directly from forward_step.F
614        (previously called from momentum_correction_step.F)
615      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
616        forward_step.F and pkg/ecco/the_main_loop.F
617    o model/src/do_oceanic_phys.F:
618      - reset addMass to zero only if useICEFRONT ;
619      - separated k-loop for rhoInSitu calculation ;
620      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
621        and at constant T,S (= WdRHOdP);
622      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
623        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
624        transport of locally-referenced potential density);
625        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
626    o gluemnc:
627      - replace ncrcat with ncks when adding variables to *.glob.nc
628      - change the way variables without record dimensions are handled so that
629        files that have variables with and without record variables can be glued:
630        add a record dimension with a new unique name to be able to differentiate
631        between variable with and without a-prior record dimensions. Remove
632        this record dimension before adding the variable to the *.glob.nc file.
633        This procedure automatically works also for grid.*.nc files that do not
634        have any record dimension.
635    o verification/cpl_aim+ocn:
636      - generate new reference output on baudelaire (gfortran, mpich2) (previously
637        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
638    o pkg/obcs/obcs_calc_stevens.F:
639      - add code for northern and southern boundaries.
640      - reorder some loops to save some operations and so that drFBar can be scalar
641    o model/src:
642      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
643        truncation) and add diagnostics for Adams-Bashforth tendency increment.
644      - update test-exp. AD output:
645        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
646      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
647        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
648        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
649        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
650        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
651        tutorial_plume_on_slope.
652    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
653      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
654      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
655      does not even come with an F77 compiler anymore, this should not be
656      a limitation
657    
658    checkpoint63e (2011/11/06)
659    o pkg/seaice adjoint of LSR:
660      - substantially rework STORE dirs.
661      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
662        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
663        and only perform SOLV_MAX_FIXED adjoint iters.
664        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
665        always goes to same record, meaning that the last forward field will be
666        the one used in the adjoint - an approximation.
667      - now produces non-zero LSR-related gradients, and acceptable gradients for
668        An's zonal (x-z) test case (to be checked in)
669      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
670        (but these are screwed up by the thermodynamics in the first place);
671        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
672        output_adm.txt also reflects changes to seaice_lsr
673      - global_ocean.cs32x15:
674        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
675          (output_adm.seaice.txt was updated)
676        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
677          (output_adm.seaice_dynmix.txt)
678    o test-exp. exp4+stevens:
679      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
680    o pkg/seaice (lsr solver):
681      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
682        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
683      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
684      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
685        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
686      - compute (with new S/R) and print initial (+ free-driff sol. if available)
687        and final residual of linearised system.
688    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
689      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
690    o pkg/obcs: Stevens BCs (still only for east and west)
691      - fix Stevens BCs by using intermediate velocities of previous
692        time step as "baroclinic" contribution rather velocity of one grid cell
693        inside the boundaries; more consistent but makes the entire treatment
694        more complicated, requires new pickup files and two new S/Rs:
695        obcs_copy_uv_n and obcs_save_uv_n
696        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
697        (undefined by default)
698      - silently move computation of some grid factors into separate loops to
699        save some recomputations
700      - add a hack for non-linear free surface
701      - add a verification experiment to exp4 that tests this code
702  o make gluemnc/xplodemnc work with (moron) non-GNU shell tools  o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
703    
704  checkpoint63d (2011/10/25)  checkpoint63d (2011/10/25)
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