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revision 1.1442 by gforget, Wed May 25 23:56:29 2011 UTC revision 1.1623 by jmc, Thu Mar 15 20:42:56 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 model/src: solve_*diagonal.F
8       - replace division with multiplication by inverse (similar to original version)
9         update output of AD exp. global_ocean.90x40x15.
10       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
11         to enable the use of the vectorized & differentiable solve_tridiagonal.F
12       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
13         vertical advection (to get solve_tridiagonal tested in AD mode).
14    o pkg/seaice: ECCO-CLIVAR merge:
15      1. seaice AREA relaxation
16         * CPP option: SEAICE_ALLOW_AREA_RELAXATION
17         * runtime flag: SEAICE_tauAreaObsRelax
18      2. modified global mean cost imbalance code: CPP option
19          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
20    o another iteration on solve_*diagonal.F
21       Make choices independent of AUTODIFF
22       Default will be the adjoinable vectorized version.
23       Alternative choices are:
24       * non-adjoinable original version with low memory footprint:
25         #define SOLVE_DIAGONAL_LOWMEMORY
26       * still adjoinable but does not vectorize (k as inner-most loop):
27         #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
28    o testreport
29     - add option to use a home made wrapper around "make"
30     - remove MITGCM_IEEE env. variable (no longer active)
31    o pkg/shelfice
32     - improve computation of friction velocity for velocity dependent
33       exchange coefficients: include velocities into SHELFICEBoundaryLayer
34       block to average velocities vertically
35     - add TAF store directives for SHI_ALLOW_GAMMAFRICT
36    o Modify diagonal solvers, now three versions (upon request):
37      #ifndef SOLVE_DIAGONAL_AUTODIFF
38        1. default version (dating back a while ago)
39      #else /* def SOLVE_DIAGONAL_AUTODIFF */
40      # ifdef SOLVE_DIAGONAL_KINNER
41        2. adjoinable version with k-innermost loop (G. Forget)
42      # else
43        3. adjoinable vectorized version of 2.
44      # endif
45      #endif /* SOLVE_DIAGONAL_AUTODIFF */
46      All flags are currently set within routines, but could/should be moved to CPP-options.
47      Array bounds for 1. are as before, for 2.,3. cover the entire domain
48      (could be changed for 1. too).
49    o verification/lab_sea (fwd):
50      - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
51        use 7 categories (except hb87), new solve4temp params (except salt_plume),
52        constant salinity (=4) or variable salinity (salt_plume) done through
53        SItracer.
54  o pkg/seaice:  o pkg/seaice:
55   - seaice_growth.F : in EVOLUTION branch, always include    - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
56      - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
57         SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
58        from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
59        SEAICE_freeze got retired) but already better than previously with
60        SEAICE_freeze=123456.7 deg.C;
61      - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
62        (safer multi-threaded setting); always set SEAICEuseEVP;
63      - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
64        SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
65        stop if multiple specifications for the same coeff; make sure default
66        SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
67    o pkg/obcs:
68      - allow to switch to upwind 1rst order advection scheme for the advective
69        flux computation at the open-boundary; disabled for adjoint built.
70    o pkg/ptracers:
71      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
72      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
73      - add parameter to decide when to start a tracer; use internal flag to
74        know which tracer to step-forward; switch this internal flag at the top
75        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
76        for adjoint built.
77    o pkg/seaice:
78      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
79      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
80      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
81    o pkg/ecco:
82      - fix writing of output file DiagnosCost_ClimSalt/Theta
83        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
84    o pkg/seaice:
85      - add missing initialisation of COR_ICE array in dynsolver.F
86      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
87        compiled either way, and is tested in all exps (multidim was only tested
88        in lab_sea ad before).
89      - cosmetic change to prepare for future addition of ITD. no change to results.
90        no defaults change.
91      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
92      - by lack of adequate verification experiments, I further used custom versions
93        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
94        should be correct.
95      - avoid recomputations in ad.
96    o array initialisation in adjoint mode:
97      1) pkg/mom_common/mom_calc_ke.F:
98        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
99        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
100        part this initialisation is gone, resulting in Floating Point Exception
101        (caught by open64 compiler with debug option).
102      2) model/src/convective_weights.F
103        set output convectCount over the full array range (instead of doing
104        an update): this fix a similar issue when called within recomputation (adjoint)
105        which could by-pass the initialisation (normally done in the caller S/R).
106    o pkg/seaice:
107      - final version of turbulent flux params, as agreed at MIT ice meet:
108           SEAICE_mcPheePiston (default is ~ 0.000875)
109           SEAICE_mcPheeTaper (default is 0.)
110           SEAICE_frazilFrac (defualt is 1.)
111           SEAICE_mcPheeStepFunc (default is false)
112      - changes results at trunction error level
113      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
114    o added pkg/frazil:
115      - see frazil_description.tex for details
116      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
117    o pkg/shelfice/shelfice_thermodynamics.F
118      - fix exponents for velocity dependent exchange coefficients: change
119        from 2/3(=0) to 0.66666666666666667
120      - move computation of velocity dependent exchange coefficients into
121        separate loop, so that it applies to both thermodynamics
122      - move some divisions by constants out of loops
123    
124    checkpoint63j (2012/02/16)
125    o pkg/seaice:
126      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
127      - SItracer:  added run time params, and allow coupling to ocn salinity.
128    o pkg/seaice: remove (almost) all divisions by constants within loops
129      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
130      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
131      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
132      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
133    o pkg/seaice :
134      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
135        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
136      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
137      - add permanent SItflux diag that corresponds to TFLUX but includes
138        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
139      - allow activation/testing of a fix for suspected missing term in
140        ocn-ice heat budget (to be confirmed). To test this, you want to
141        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
142        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
143      - no change in results, fwd or ad.
144    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
145      - switch to variable freezing point.
146           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
147      - bug fix : the sublimation term that was missing is now activated.
148           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
149      - bug fix : flooding sign term for SIsal0.NE.0.
150           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
151    o pkg/seaice:
152      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
153        is now the default, and the old default constant freezing point is recovered
154        with SEAICE_tempFrz0    = -1.96,
155             SEAICE_dTempFrz_dS = 0.,
156      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
157      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
158      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
159        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
160      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
161        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
162      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
163        seaice_growth r149 for legacy branch (no results change).
164      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
165        from I. Fenty).
166      - results did not change except for global_ocean.cs32x15, mostly due to the
167        switch to variable freezing point (see above item for detail).
168    o pkg/thsice:
169      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
170        seawater freezing in thsice_calc_thickn (not used).
171    o pkg/seaice: turbulent flux term specification via run time params.
172      - replace CPP switches with run time switches to facilitate testing
173      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
174                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
175      - added runtime parameter : SEAICEturbFluxFormula
176      - move Mcphee constants to SEAICE_PARAMS.h
177      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
178                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
179                 remove seaice_summary call (moved to seaice_init_fixed)
180      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
181        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
182      - seaice_summary.F : add missing report of read turbulent flux term set up
183                           and SITRACER.
184      - seaice_check.F : check range; inform and stop if retired CPPs are used
185                         (incl. SEAICE_AGE).
186      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
187             CPP switch, same computation as before for the different options.
188      - change results at the truncation level.
189    o pkg/seaice:
190      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
191        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
192        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
193      - update verification/*/input*/data.seaice:
194        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
195        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
196        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
197        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
198    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
199      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
200        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
201        difference in results only due to machine truncation.
202      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
203        MaykutPolySatVap; keep MIN_LWDOWN.
204      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
205      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
206        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
207    o pkg/salt_plume:
208      - isolate saltPlumeFlux array exch into a specific S/R called from
209        do_oceanic_phys.F
210      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
211    o verification:
212      - move untested set-up to MITgcm_contrib/verification_other.
213    o pkg/seaice:
214      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
215    o pkg/seaice:
216      - seaice_solve4temp.F (keeping results unchanged):
217        * add 2 future run-time params to select which saturation vapor pressure
218          formula is used and how post-iteration fluxes are set.
219          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
220        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
221          the linearized expression to stay consistent with tsurf finding.
222      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
223        can be < 0.
224    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
225      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
226        conductive heat flux F_c , and add it explicitly when updating tsurf as
227        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
228        so that now F_ia has a consistent meaning through the entire routine.
229        This causes differences at truncation level: update output of fwd exp.
230        global_ocean.cs32x15.seaice.
231    o pkg/seaice:
232      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
233        of arrays, sign/direction of fluxes; no effect on results.
234      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
235        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
236        note: this should have been done before changing celsius2K default.
237      - to keep results unchanged, add back old value of celsius2K in verification
238        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
239      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
240        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
241        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
242        freezing temp is consistent with value in seaice_growth.F ; this causes
243        differences at machine truncation level: update lab_sea AD output (3/4).
244    o pkg/seaice:
245      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
246        and climsst/sss even when using seaice (to prevent calculation that might
247        use SST on land); does not affect any verification exp.
248      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
249        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
250    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
251      over land (non-legacy code)
252    o vectorize salt_plume package:
253      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
254      - this code computes plumebk everywhere (also over land), thus requires
255        code to avoid divisions by zero and catch the case of kLev=Nr.
256      - efficiency of salt_plume_frac is still sub-optimal
257    o tools (genmake2):
258      - fix makefile NAME specification (option: -makefile NAME) by adding
259        "-f $MAKEFILE" in few places where it was missing including makedepend
260        command (contribution from Paul).
261    
262    checkpoint63i (2012/01/24)
263    o model/src:
264      - add factorized versions of some EOS code to find_rho.F,
265        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
266    o model/src:
267      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
268      - change default celsius2K from 273.16 to 273.15
269      - to keep results unchanged, add back old value of celsius2K in verification
270        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
271         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
272    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
273      to make TAF generate vectorizable code
274    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
275       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
276       have flags that do this more efficiently.
277    o pkg/diagnostics/diagstats_calc.F
278      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
279    o pkg/obcs (with exch2):
280      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
281        and remove code (in obcs_readparms.F) which was based on EXCH of indices
282        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
283    o pkg/exf and seaice exp:
284      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
285        so that switching off area & heff advection flags does not affect results.
286      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
287      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
288        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
289        results of verification experiments: 1D_ocean_ice_column(fwd),
290        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
291        and offline_exf_seaice (all 4).
292    o pkg/seaice:
293      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
294        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
295      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
296        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
297        not multi-dim advection;
298      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
299        SHORTWAVE_HEATING #undef.
300    o optim: make Makefile more robust (?)
301    o pkg/obcs:
302      * fix treatment of obcs_read_pickup for TAF
303    o pkg/shelfice:
304      * add missing initialisation of num_shifwflx
305      * new adjoint verification exp. for isomip
306      * change Prandtl and Schmidt numbers from generic formulations
307        (in terms of model diffus. and visc.) to separate runtime
308        parameters, with Holland and Jenkins (1999) default values.
309    o pkg/exf (interpolation):
310      - extended input field (2 rows) near the N & S poles:
311        * fill in with the symetric value (when even Nb of data in longitude)
312        * add average value at the poles only for scalar quantities ; for vector
313          component interpolation, skip the averaging and keep duplicated values,
314          unless the 2 components have same location (uvInterp=T) in which case
315          interpolate the 2 components together using S/R EXF_INTERP_UV.
316      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
317        together: this allows to account properly for local orientation when
318        averaging at N & S pole.
319      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
320        exf-interpolation near N & S poles. Undef by default.
321      - add debug check/print on 1rst iter if debugLevel >=2.
322    o pkg/exf:
323      - change masking flags definition (no longer "parameter"), put them in
324        common block and set them in S/R EXF_INIT_FIXED.
325      - change recognized masking flag from s,u,v to c,w,s since the mask
326        to use (maskC,W,S) depends on position on model grid and has little to
327        do with scalar/vector difference; fix masking if using P-coordinates.
328      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
329        and update results of exp. global_with_exf (x2).
330      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
331    o pkg/obcs
332      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
333    o pkg/exf (interpolation):
334      - assume periodicity in X only if input field cover full longitude range.
335      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
336        and should vectorise).
337      - fix input lat of the 2 added row (in case we provide N.pole data).
338    
339    checkpoint63h (2011/12/30)
340    o pkg/seaice:
341      - change declaration of UVM from _RL to _RS in order to get B-grid
342        uIce,vIce monitor when _RS = real*4
343    o pkg/offline:
344      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
345      - compute vertical velocity if not read from file (switch on exactConserv
346        & staggerTimeStep);
347      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
348    o verification:
349      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
350        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
351        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
352      - update output of exp. global_ocean.cs32x15.viscA4 after changing
353        grid-file angles (used here for coriolis-3d);
354      - remove (or gzip) few files not needed to run fizhi-cs experiments.
355    o pkg/exf (vector interpolation):
356      - rotate vector component toward local grid-axis orientation using grid-angles
357        (stored in GRID.h) instead of locally computed rotation angle; keep old code
358        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
359    o pkg/seaice:
360      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
361        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
362    o pkg/PKG_OPTIONS.h files:
363      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
364        outside of the #ifdef ALLOW_THISPKG / #endif block.
365      - update verification/*/code/PKG_OPTIONS.h files.
366    o add a verification experiment (offline_exf_seaice/input.seaice) that test
367      the B-grid LSOR solver
368    o pkg/seaice: sort out emissivity and long wave radiation step 2:
369      - add emissivity for snow and ice as new run-time parameters
370        (unfortunately) that default to the corresponding exf values; this
371        changes results in most verification experiments so that for backward
372        compatibility these parameter have to be set explicitly to inconsistent
373        values (ugly);
374      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
375        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
376        until we agree how to handle this bug properly
377    o pkg/exf (interpolation):
378      - add a set of run-time param ({inputfield}_interpMethod), one for
379        each interpolated input field, to select the interpolation method
380        with a value of zero switching off the interpolation;
381      - print interpolation parameters to standard output;
382      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
383        (to use instead runoff_interpMethod=0 in data.exf).
384      - simplify default setting of interpolation parameters (for all fields,
385        set position to match model grid cell-center position, leading to trivial
386        interpolation in case of regular Lat-Lon grid) and fix for the case of
387        non-uniform delY.
388    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
389       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
390       this factor is absolutely required, because the lw exitance (= out-going
391       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
392       where the reflectivity rho = 1-emissivity for conservation reasons. Once
393       this is established, we can remove the CPP-Flag (if we want to).
394    o pkg/seaice:
395      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
396        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
397      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
398        what the name implies (and not emissivity*BoltzmannConstant), this means
399        the old default value of 5.5e-8 now means
400        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
401        S/R exf_readparms
402      - FV-discretization of the B-grid LSOR solver, turn on with
403        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
404        of the calling routine dynsolver, so that B and C-grid code look a
405        little more alike.
406      - fix index bugs in ostres.F (B-grid code)
407    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
408    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
409      default for SEAICE_emissivity, if useEXF; requires setting a wrong
410      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
411      backward compatiblity
412    o model/src: use sigmaR in calc_ivdc
413    
414    checkpoint63g (2011/12/16)
415    o pkg/seaice/seaice_growth.F:
416      fix heat conservation of the coupled ocean-seaice system.
417      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
418      solid vs liquid water treatment is resolved via QNET.
419    o pkg/seaice/seaice_growth.F:
420      add missing term for sublimation in saltFlux, which was breaking conservation.
421    o pkg/seaice/seaice_model.F:
422      Remove this patholigical case treatment in evolution branch,
423      where it is un-necessary and breaks conservation.
424      Update global_ocean.cs32x15/results accordingly for
425      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
426    o model/src:
427      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
428      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
429    o pkg/obcs:
430      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
431      tendency for temperature and salinity that is then applied to update
432      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
433      horizontal advection and diffusion contributions on the boundary (in
434      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
435      removing the mask in S/R timestep_tracer. The advantage of this approach is
436      that the updated tracer values include contributions from the surface
437      forcing and vertical diffusion.
438      This modification changes exp4.stevens because of vertical diffusion.
439    o model/src:
440      change non-curvilinear grid setting to also work with exch2 + blank tiles:
441      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
442        face dimensions.
443      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
444        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
445        and INI_SPHERICAL_POLAR_GRID.
446      change test-experiment global_ocean.90x40x15:
447      - split the domain in many more tiles (9x4 tiles of 10x10 each);
448      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
449      - update results of both test (std & dwnslp).
450    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
451       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
452    o model/src:
453      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
454        and fix initialisation when using sigma-coords.
455    o model/src:
456     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
457       to their current value at the beginning of forward_step.F": add a new run-time
458       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
459     - set doResetHFactors=T in the following test exp:
460        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
461        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
462        and tutorial_global_oce_in_p (nonLinFS in p)
463    o pkg/ecco
464      - added IES cost term
465    o verification/advect_xz
466      - scale down the depth by 1/100 (from 200 km to just 2.km)
467      - add secondary test using divergent flow, r-star and implicit vertical advection.
468      - add note (check_conserve_TS.txt) and matlab script to check global
469        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
470    o pkg/rbcs:
471      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
472    o pkg/obcs (Stevens BCs):
473      - fix various problems in the phase speed computations of the Stevens
474        boundary conditions:
475        - sign error for western and southern boundaries,
476        - time tendencies were underestimated by factor of dTracerLev and some just
477          zero (for multidim advection schemes) -> now estimate time tendencies
478          from difference between previous (n) time level and the one before (n-1);
479          this requires storing a field per tracer per boundary, also in the pickup
480          files.
481        - replace deltaTmom in cflMer/Zon computation with dTracerLev
482        - set default phase velocity to cflMer/Zon
483      - update verification experiment exp4.stevens
484    o pkg/generic_advdiff (implicit_r):
485      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
486        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
487      - fix implicit vertical diffusion or advection with NonLin FreeSurf
488        (was using current recip_hFacC instead of future recip_hFacC): set future
489        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
490        solver S/R ;
491      - fill diagnostics of vertical advective fluxes (computed from tendency)
492        when using implicit vert. advection;
493      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
494         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
495         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
496         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
497    o pkg/diagnostics:
498      - add diags for T & S tendency which goes through Adams-Bashforth.
499    
500    checkpoint63f (2011/11/30)
501    o pkg/obcs/obcs_calc_stevens.F:
502      - join some loops to reduce number of if-statements
503      - fix a bug in code for northern and southern boundaries.
504    o pkg/seaice/seaice_init_varia.F
505      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
506        caused zero ice-velocities for the B-grid code
507    o pkg/seaice/seaice_init_fixed.F
508      - fix a bug in the initialisation of the second metric terms
509        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
510      - this affects all seaice configurations with useCurviLinearGrid = .true.
511        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
512        = .true. (default)
513      - the only verification experiment affected is global_ocean.cs32x15:
514        icedyn, seaice, and seaice_dynmix (AD)
515    o pkg/thsice/thsice_diagnostics_state.F
516      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
517        not contain garbage that can lead to surprises in diagstats_calc.F
518    o model/src:
519      - move bi,bj loops inside INTEGR_CONTINUITY ;
520      - call INTEGR_CONTINUITY directly from forward_step.F
521        (previously called from momentum_correction_step.F)
522      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
523        forward_step.F and pkg/ecco/the_main_loop.F
524    o model/src/do_oceanic_phys.F:
525      - reset addMass to zero only if useICEFRONT ;
526      - separated k-loop for rhoInSitu calculation ;
527      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
528        and at constant T,S (= WdRHOdP);
529      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
530        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
531        transport of locally-referenced potential density);
532        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
533    o gluemnc:
534      - replace ncrcat with ncks when adding variables to *.glob.nc
535      - change the way variables without record dimensions are handled so that
536        files that have variables with and without record variables can be glued:
537        add a record dimension with a new unique name to be able to differentiate
538        between variable with and without a-prior record dimensions. Remove
539        this record dimension before adding the variable to the *.glob.nc file.
540        This procedure automatically works also for grid.*.nc files that do not
541        have any record dimension.
542    o verification/cpl_aim+ocn:
543      - generate new reference output on baudelaire (gfortran, mpich2) (previously
544        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
545    o pkg/obcs/obcs_calc_stevens.F:
546      - add code for northern and southern boundaries.
547      - reorder some loops to save some operations and so that drFBar can be scalar
548    o model/src:
549      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
550        truncation) and add diagnostics for Adams-Bashforth tendency increment.
551      - update test-exp. AD output:
552        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
553      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
554        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
555        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
556        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
557        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
558        tutorial_plume_on_slope.
559    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
560      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
561      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
562      does not even come with an F77 compiler anymore, this should not be
563      a limitation
564    
565    checkpoint63e (2011/11/06)
566    o pkg/seaice adjoint of LSR:
567      - substantially rework STORE dirs.
568      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
569        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
570        and only perform SOLV_MAX_FIXED adjoint iters.
571        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
572        always goes to same record, meaning that the last forward field will be
573        the one used in the adjoint - an approximation.
574      - now produces non-zero LSR-related gradients, and acceptable gradients for
575        An's zonal (x-z) test case (to be checked in)
576      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
577        (but these are screwed up by the thermodynamics in the first place);
578        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
579        output_adm.txt also reflects changes to seaice_lsr
580      - global_ocean.cs32x15:
581        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
582          (output_adm.seaice.txt was updated)
583        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
584          (output_adm.seaice_dynmix.txt)
585    o test-exp. exp4+stevens:
586      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
587    o pkg/seaice (lsr solver):
588      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
589        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
590      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
591      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
592        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
593      - compute (with new S/R) and print initial (+ free-driff sol. if available)
594        and final residual of linearised system.
595    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
596      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
597    o pkg/obcs: Stevens BCs (still only for east and west)
598      - fix Stevens BCs by using intermediate velocities of previous
599        time step as "baroclinic" contribution rather velocity of one grid cell
600        inside the boundaries; more consistent but makes the entire treatment
601        more complicated, requires new pickup files and two new S/Rs:
602        obcs_copy_uv_n and obcs_save_uv_n
603        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
604        (undefined by default)
605      - silently move computation of some grid factors into separate loops to
606        save some recomputations
607      - add a hack for non-linear free surface
608      - add a verification experiment to exp4 that tests this code
609    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
610    
611    checkpoint63d (2011/10/25)
612    o pkg/obcs + seaice-dynamics:
613      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
614        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
615        values (consistent with an implicit method).
616      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
617        return to older implementation (same results as before); note that none of
618        the "experimental" OBCS_SEAICE options are implemented in the new version.
619      - switch test exp. seaice_obcs to use new version (update output).
620    o pkg/seaice:
621      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
622      - add parenthesis in Water-Ice drag calculations (evp & lsr);
623      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
624        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
625      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
626        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
627    o pkg/layers:
628      - Include potential density as new coordinate (Thanks to David Munday)
629    o pkg/dic:
630      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
631        carbonate computation/output to CALC_PCO2_APPROX
632    o pkg/generic_advdiff
633      - make TAF generate code that vectorizes:
634        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
635    o model/src:
636      - improve vectorization also for adjoint code of
637        solve_tridiagonal and solve_pentadiagonal. As this requires up to
638        5 new 3D-fields, this code is only turned on for the combination of
639        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
640        for singular matrix check (only for TARGET_NEC_SX).
641      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
642        ALLOW_AUTODIFF. This flag now needs to be set outside of
643        solve_tri/pentadiagonal.F
644    o pkg/exf:
645      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
646        optional namelist EXF_NML_OBCS).
647      - add many debug-print (to trace down where pkg/cal error msg comes from)
648    o pkg/mom_vecinv/mom_vi_hdissip.F
649      - rearrange loops so that vectorization is improved and in particular
650        the adjoint routine vectorizes. The code is a little longer now, but I
651        think easier to read.
652        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
653    o pkg/seaice:
654      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
655    o pkg/exch2:
656      - alternative code (without tile x tile matrix) for cumulated (global) sum;
657        used as default; keep using matrix version in adjustment.cs-32x32x1.
658    o tools/build_options:
659      - after merging some MPI and/or multi-threads specific optfiles so that
660        the modified default optfile support both built (using genmake2 -mpi
661        for the MPI built, using genmake2 -omp for OpenMP built),
662        move now obsolete optfiles to tools/build_options/unsupported/
663       (add copy of email sent to support list in doc/optfiles_changes.txt)
664    
665    checkpoint63c (2011/09/28)
666    o pkg/ebm:
667      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
668        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
669    o pkg/seaice (SItracer pickup)
670    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
671      To be done:
672      - thorough testing of missing fields in S/R seaice_read_pickup
673      - thorough matching between generic tracers and specific fields used
674        (e.g. volume-weighted age, area-weighted age, salinity, ...)
675    o pkg/grdchk:
676      - all procs calculate and print finite-difference gradient (for testreport)
677      - change description output used by testreport;
678      - AD testing: also compare and report Finite-difference gradient;
679        => update all output_adm*.txt
680    o test exp. global_ocean_ebm:
681      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
682        and turn on exactConserve; update (fwd) output.
683    o pkg/seaice (LSR):
684      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
685      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
686        * identical results with non-CS topology (but save up to half of EXCH calls)
687        * no much changes in cs-32 verification tests since no ice at face edges
688         (differences due to convergence criteria, since nb of iterations changed)
689        * expect some differences on lat-lon-cap grid.
690        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
691    o pkg/exch2:
692      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
693        many tiles); until alternative coding is added, just add a stop.
694    o pkg/kpp:
695      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
696        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
697    o optfiles:
698      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
699        into corresponding standard one, which now support different build:
700        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
701      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
702    o pkg/obcs (seaice):
703      - add missing EXCH for uIce,vIce after applying OBCS;
704      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
705        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
706        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
707      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
708      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
709        and eedata.mth for MPI and mutlti-threaded testing.
710    o pkg/flt:
711      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
712      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
713      - fix pickup and trajectories + profiles output with multi-threads;
714      - add parameter to select group of fields to write along trajectory and
715        profile (default unchanged);
716      - only call PORT_RAND* function when flt_noise <> 0;
717      - add multi-threaded test for verification exp. flt_example.
718    o eesupp/src:
719      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
720      - USE_OMP_THREADING: check that number of threads (from eedata) matches
721        actual number (from env.var. setting).
722    o pkg/ebm:
723      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
724      - add multi-threaded test for verification exp. global_ocean_ebm
725    
726    checkpoint63b (2011/08/29)
727    o pkg/ebm:
728      - fix sign of runoff;
729      - update directly forcing fields (Qnet,EmPmR) to use standard
730        external_forcing_surf.F (remove ebm_forcing_surf.F);
731      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
732      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
733        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
734      - update global_ocean_ebm parameters file data and update output (fwd+ad).
735    o verification/matrix_example:
736      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
737        MPI and mutlti-threaded testing.
738    o pkg/matrix:
739      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
740      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
741      - fix for multi-threaded (remove DATA statement);
742      - use standard DIFFERENT_MULTIPLE function;
743      - add MATRIX_OPTIONS.h
744    o verification/matrix_example:
745       To allow to split the domain in several tiles, change the domain size
746        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
747        Western side) of land points.
748    o (*_)write_pickup:
749      - fix few bugs in mypackage_read/write_pickup.F
750      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
751        array of length 1 (was caught by compiler syntax-check).
752    o pkg/diagnostics (velocity potential solver):
753      - fix initialisation of main diagonal matrix (for overlap values)
754    o tools/build_options:
755      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
756        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
757      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
758        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
759        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
760        and use "-devel" testreport option for standard testing on baudelaire.
761    o pkg/grdchk:
762      - Assume that all gradient-check position are within the same tile
763        corresponding to global indices (iGloTile,jGloTile) and that
764        positions (i,j indices or nbeg) are local to this tile;
765      - set tile local-indices and proc. number according to tile global-indices;
766      - remove grdchkwhichproc from namelist (retired param);
767      - send adjoint gradient to all procs so that all procs print it to STDOUT;
768      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
769    o adding package bbl (Bottom Boundary Layer)
770      description in MITgcm/pkg/bbl/bbl_description.tex
771      example/test experiment in MITgcm_contrib/bbl
772    o adjoint verifications
773      - changed 5 experiments to multi-tiles
774        * global_ocean.90x40x15
775        * obcs_ctrl
776        * offline_exf_seaice
777        * tutorial_dic_adjoffline
778        * tutorial_tracer_adjsens
779        changed reference output for those that crossed tile boundaries
780        (changed choices of gradient check positions)
781      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
782      - temporary bug fix in grdchk_loc.F for obcs
783    o genmake2 & testreport
784      - add target "obj" (just for OBJFILES files) to Makefile;
785      - add option to specify FEXTRAFLAGS on command line.
786    o pkg/mypackage:
787      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
788    
789    checkpoint63a (2011/08/02)
790    o pkg/diagnostics (velocity potential):
791      - fix velocity-potential calculation when using OBCS: balance net inflow
792        at each level (new S/R OBCS_DIAG_BALANCE).
793      - fix some of the problems with OBCS in stream-function calculation.
794    o pkg/exf/exf_readparms.F
795      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
796        EXF_NML_OBCS) more consistent, so that you need not have these lists
797        in data.exf when they are not used.
798    o optim/optim_readdata.F:
799      - add some output about obcs variables that might help debugging
800      - add a check about nvarlength
801    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
802    o pkg/diagnostics (velocity potential):
803      - fix mask for OBCS (still problems in stream-function with OBCS);
804      - add specific parameter (default = main code CG2D params) for solver;
805      - in case of poor convergence, use solution corresponding to lowest residual.
806    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
807      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
808      and should be avoided where possible.
809    o model/src (rStar):
810      - include r* effect on reference-state (PhiRef) in totPhiHyd
811        (so that it's really the potential anomaly at the cell center);
812        affect solution only if z* with full pressure in EOS.
813      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
814        update output (because of z* in totPhiHyd and viscA4 changes);
815      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
816        @ constant r) until interpolation at constant r is implemented.
817    o pkg/diagnostics
818      - fix RCENTER diagnostics in case cell center is not at interface middle
819    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
820      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
821      that THETA and SALT are "conservative temperature" and "absolute
822      salinity"
823    o pkg/ctrl
824      - fix computation of endrec in s/r ctrl_init_rec
825      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
826    o pkg/seaice/seaice_growth.F
827      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
828        remove then obsolete STORE directives
829      - fix STORE directives for tice and tices, so that only the
830        appropriate part of the fields are stored (and not the entire
831        field); update global_ocean.cs32x15.seaice AD output.
832      - cosmetic changes: adjust CPP flags and indentation for better
833        legibilty
834    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
835      Chris Wilson)
836    o pkg/gmredi:
837       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
838       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
839    
840    checkpoint63  (2011/07/11)
841    o pkg/exch2:
842     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
843     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
844       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
845       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
846    o pkg/diagnostics:
847     - deal with pairs of post-processed diags which are computed together; in
848       particular, re-order list of diags within 1 file to save 2nd computation.
849     - add S/R to compute velocity stream-function (called after velocity-potential
850       calculation) from divergence free transport -> new diagnostics "PsiVEL".
851     - add parameter to select grid-point location where PsiVEL == 0.
852    o eesupp/src:
853       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
854       (specific S/R needed with exch2 topology - for now, just print an error msg)
855    o pkg/shelfice
856     - Implement friction velocity-dependent transfer coefficients following
857       Holland and Jenkins, JPO, 1999
858       Original code by M. Losch with small modifs.
859       Enable with CPP option SHI_ALLOW_GAMMAFRICT
860       and runtime flag SHELFICEuseGammaFrict
861    o verification lab_sea & global_ocean.cs32x15:
862     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
863       does not miss some dependencies (but is slower) and also works with many files
864       (default makedepend limitation for AD built).
865     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
866    o pkg/diagnostics:
867     - add run-time parameter "useMissingValue" (def=False) to fill land-point
868        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
869       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
870     - Extend the use of "missing_value" setting from data.diagnostics for the case
871       of counter-diagnostics (where fraction-weight is zero). This applies both to
872       MNC and MDS output files.
873    o pkg/seaice/seaice_growth.F:
874      - add 'a priori' cap of latent heat flux based on actual mass considerations
875        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
876        non-legacy seaice_solve4temp.
877      - add diagnostic of the residual sublimation freshwater flux (the freshwater
878        flux taken from the ocean if the total actual latent heat fluxes exceed
879        the maximum)
880      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
881       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
882      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
883       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
884      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
885      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
886    o verification 1D_ocean_ice_column:
887       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
888       update results
889    o pkg/diagnostics:
890     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
891       which are not filled-up but computed from other diags ; In this case, the mate
892       diag points to the primary (filled-up) diag to used for post processing.
893     - Update Velocity-potential computation using post-processed diag framework.
894     ==> Change the ordering of fields and time-periods in MDS output file
895       when using periodic averaging: now writes one time record with the full set
896       of fields for this time period, then the next time reccord (it used to be
897       one field with the full set of time records then the next field).
898         Note: this is now similar to NetCDF (MNC) output file. <==
899    
900    checkpoint62z (2011/06/21)
901    o adjoint monitor:
902     - Add adjoint monitor output for packages exf, seaice
903       and update relevant testreport output
904    o pkg/seaice:
905     - re-order diags inits so that they appear in order in available_diagnostics.log
906     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
907       area/heff/hsnow preceeding thermodynamic growth/melt.
908     - modified diag: SIdA; output actual effect, as the description states.
909     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
910     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
911       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
912        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
913     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
914     - added diagnostics for seaice generic tracers (SItr*).
915     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
916     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
917     I. Fenty: 18-Jun-2011:
918     Minor changes to seaice package:
919     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
920        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
921       - Differentiated "regularization variables" from "floor variables"
922        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
923        * hiceMin became SEAICE_hice_reg (old hiceMin)
924          (with _reg meaning regularization variable)
925       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
926        so as to ensure energy conservation when going between phases
927      - A22 was not used anywhere
928     2) Changed regularization procedure for heffActual and hsnowActual to ensure
929        well-boundedness and smooth adjoint in seaice_growth.F
930     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
931        because the old regularization always set heffActual >= 0.05 cm
932     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
933        on AREA when HEFF > 0.
934      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
935        requiring that DISABLE_AREA_FLOOR *not* be defined
936     Affected verifications:
937      - 1D_ocean_ice_column (output.txt output_adm.txt)
938      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
939    o pkg/diagnostics:
940      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
941      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
942        (was _RL, now integer) with option = 0 to retrieve all levels.
943      - add pieces of code to compute velocity potential at each level (new diagnostics
944        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
945        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
946      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
947        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
948        and in diagnostics_fract_fill.F (do not need a valid pointer for the
949        diagnostics counter-mate); check that definition of counter-diagnostic
950        includes a valid counter-mate (in diagnostics_set_levels.F).
951    o model/src (rStar):
952      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
953        affect solution only if z* with full pressure in EOS;
954        update output of test-exp global_ocean.90x40x15.
955    o pkg/seaice:
956      - introduce siEps=1e-5 parameter
957      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
958      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
959      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
960        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
961        as well as ice cover age and ridging index (attached to AREA).
962        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
963        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
964        Up to SItrMaxNum=3 tracers can be used simultaneously.
965    o pkg/salt_plume:
966      -introduce SPsalFRAC run time parameter that sets the fraction of the
967       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
968       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
969    o model debug options:
970      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
971        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
972      - Refine debug-msg printing selection (3 new levels):
973        debugMode  : controls printing of debug messages (sequence of S/R calls).
974        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
975         debLevZero =  0 ; /* level of disabled aux. msg printing */
976         debLevA =  1 ; /* level of minimum  aux. msg printing */
977         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
978         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
979         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
980         debLevE =  5 ; /* level of extensive debug printing */
981        New debugLevel default: with default debugMode value (=F),
982          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
983          and if debugMode=T, default debugLevel = 4 (debLevD).
984        Relation with previous settings:
985         debLevB (=2) corresponds to former debLevA (=1)
986         debLevD (=4) corresponds to former debLevB (=2)
987        Note:
988         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
989         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
990            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
991      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
992        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
993    o pkg/obcs:
994      - change OBCSfixTopo default from True to False (should not change the results);
995        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
996    o pkg/thsice:
997      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
998        2nd layer seaice sublimation (unlikely to happen)
999      - use Interior mask for OBCS in thsice_advection.F (similar to what is
1000        done in gad_advection & seaice_advection).
1001    o adjoint:
1002      bug fix spotted by Gael Forget:
1003      seaice_advection and thsice_advection still had
1004      legacy CPP options to avoid CS corner updates for adjoint
1005    o pkg/seaice:
1006      => Change some of the defaults (2011/05/29):
1007         - change SEAICEuseFluxForm default (from False to True)
1008         - change DIFF1 default (from 0.004 m/s to 0. m/s)
1009         And print warnings if DIFF1 is not set in data.seaice and centered
1010          avection scheme is used without any diffusion.
1011      also:
1012      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1013      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1014      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1015        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1016        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1017      update results of test exp.:
1018         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1019             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1020             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1021         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1022         seaice_obcs: output (SEAICEuseFluxForm=T)
1023      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1024          for standard fwd & AD lab_sea tests (to keep the same output).
1025    o pkg/seaice/seaice_growth.F:
1026      - use Ian Fenty's capping formulas for actual ice
1027      thickness thoughout EVOLUTION branch.
1028      - put treatment pathological case #2) in CPP brackets
1029      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1030      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1031    o pkg/seaice:
1032      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1033      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1034      also pass fac as a param, which can be 1. (to update the tendency
1035      field) or the time step (to update the field itself).
1036      - seaice_advdiff.F: for multidim, call seaice_diffusion with
1037      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1038      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1039      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1040      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1041    o pkg/seaice:
1042      diffusion with centered advection scheme (diffus.F & advect.F):
1043      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1044        to just compute the laplacian of input-field.
1045      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1046      - fix flux-form version in diffus.F to conserve tracer.
1047      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1048       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1049    
1050    checkpoint62y (2011/05/26)
1051    o pkg/seaice:
1052     - seaice_growth.F : in EVOLUTION branch, always include
1053     a_QSWbyATM_cover in qnet (as it should be).     a_QSWbyATM_cover in qnet (as it should be).
1054   - verification/global_ocean.cs32x15 : update results accordingly   - verification/global_ocean.cs32x15 : update results accordingly
1055     (output.seaice.txt output_adm.seaice.txt).     (output.seaice.txt output_adm.seaice.txt).
1056  o pkg/seaice + obcs:  o pkg/seaice + obcs:
1057   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:   - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1058     equivalent of assuming no tracer gradient outside the OB region.     equivalent of assuming no tracer gradient outside the OB region.
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