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revision 1.1502 by jmc, Wed Sep 21 16:29:49 2011 UTC revision 1.1614 by jmc, Fri Mar 9 20:16:10 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/obcs:
8      - allow to switch to upwind 1rst order advection scheme for the advective
9        flux computation at the open-boundary; disabled for adjoint built.
10    o pkg/ptracers:
11      - rename PTRACERS_RESTART.h -> PTRACERS_START.h
12      - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
13      - add parameter to decide when to start a tracer; use internal flag to
14        know which tracer to step-forward; switch this internal flag at the top
15        of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
16        for adjoint built.
17    o pkg/seaice:
18      - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
19      - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
20      - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
21    o pkg/ecco:
22      - fix writing of output file DiagnosCost_ClimSalt/Theta
23        and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
24    o pkg/seaice:
25      - add missing initialisation of COR_ICE array in dynsolver.F
26      - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
27        compiled either way, and is tested in all exps (multidim was only tested
28        in lab_sea ad before).
29      - cosmetic change to prepare for future addition of ITD. no change to results.
30        no defaults change.
31      - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
32      - by lack of adequate verification experiments, I further used custom versions
33        of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
34        should be correct.
35      - avoid recomputations in ad.
36    o array initialisation in adjoint mode:
37      1) pkg/mom_common/mom_calc_ke.F:
38        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
39        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
40        part this initialisation is gone, resulting in Floating Point Exception
41        (caught by open64 compiler with debug option).
42      2) model/src/convective_weights.F
43        set output convectCount over the full array range (instead of doing
44        an update): this fix a similar issue when called within recomputation (adjoint)
45        which could by-pass the initialisation (normally done in the caller S/R).
46    o pkg/seaice:
47      - final version of turbulent flux params, as agreed at MIT ice meet:
48           SEAICE_mcPheePiston (default is ~ 0.000875)
49           SEAICE_mcPheeTaper (default is 0.)
50           SEAICE_frazilFrac (defualt is 1.)
51           SEAICE_mcPheeStepFunc (default is false)
52      - changes results at trunction error level
53      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
54    o added pkg/frazil:
55      - see frazil_description.tex for details
56      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
57    o pkg/shelfice/shelfice_thermodynamics.F
58      - fix exponents for velocity dependent exchange coefficients: change
59        from 2/3(=0) to 0.66666666666666667
60      - move computation of velocity dependent exchange coefficients into
61        separate loop, so that it applies to both thermodynamics
62      - move some divisions by constants out of loops
63    
64    checkpoint63j (2012/02/16)
65    o pkg/seaice:
66      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
67      - SItracer:  added run time params, and allow coupling to ocn salinity.
68    o pkg/seaice: remove (almost) all divisions by constants within loops
69      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
70      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
71      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
72      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
73    o pkg/seaice :
74      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
75        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
76      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
77      - add permanent SItflux diag that corresponds to TFLUX but includes
78        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
79      - allow activation/testing of a fix for suspected missing term in
80        ocn-ice heat budget (to be confirmed). To test this, you want to
81        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
82        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
83      - no change in results, fwd or ad.
84    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
85      - switch to variable freezing point.
86           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
87      - bug fix : the sublimation term that was missing is now activated.
88           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
89      - bug fix : flooding sign term for SIsal0.NE.0.
90           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
91    o pkg/seaice:
92      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
93        is now the default, and the old default constant freezing point is recovered
94        with SEAICE_tempFrz0    = -1.96,
95             SEAICE_dTempFrz_dS = 0.,
96      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
97      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
98      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
99        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
100      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
101        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
102      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
103        seaice_growth r149 for legacy branch (no results change).
104      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
105        from I. Fenty).
106      - results did not change except for global_ocean.cs32x15, mostly due to the
107        switch to variable freezing point (see above item for detail).
108    o pkg/thsice:
109      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
110        seawater freezing in thsice_calc_thickn (not used).
111    o pkg/seaice: turbulent flux term specification via run time params.
112      - replace CPP switches with run time switches to facilitate testing
113      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
114                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
115      - added runtime parameter : SEAICEturbFluxFormula
116      - move Mcphee constants to SEAICE_PARAMS.h
117      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
118                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
119                 remove seaice_summary call (moved to seaice_init_fixed)
120      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
121        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
122      - seaice_summary.F : add missing report of read turbulent flux term set up
123                           and SITRACER.
124      - seaice_check.F : check range; inform and stop if retired CPPs are used
125                         (incl. SEAICE_AGE).
126      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
127             CPP switch, same computation as before for the different options.
128      - change results at the truncation level.
129    o pkg/seaice:
130      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
131        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
132        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
133      - update verification/*/input*/data.seaice:
134        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
135        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
136        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
137        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
138    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
139      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
140        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
141        difference in results only due to machine truncation.
142      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
143        MaykutPolySatVap; keep MIN_LWDOWN.
144      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
145      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
146        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
147    o pkg/salt_plume:
148      - isolate saltPlumeFlux array exch into a specific S/R called from
149        do_oceanic_phys.F
150      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
151    o verification:
152      - move untested set-up to MITgcm_contrib/verification_other.
153    o pkg/seaice:
154      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
155    o pkg/seaice:
156      - seaice_solve4temp.F (keeping results unchanged):
157        * add 2 future run-time params to select which saturation vapor pressure
158          formula is used and how post-iteration fluxes are set.
159          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
160        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
161          the linearized expression to stay consistent with tsurf finding.
162      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
163        can be < 0.
164    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
165      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
166        conductive heat flux F_c , and add it explicitly when updating tsurf as
167        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
168        so that now F_ia has a consistent meaning through the entire routine.
169        This causes differences at truncation level: update output of fwd exp.
170        global_ocean.cs32x15.seaice.
171    o pkg/seaice:
172      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
173        of arrays, sign/direction of fluxes; no effect on results.
174      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
175        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
176        note: this should have been done before changing celsius2K default.
177      - to keep results unchanged, add back old value of celsius2K in verification
178        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
179      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
180        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
181        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
182        freezing temp is consistent with value in seaice_growth.F ; this causes
183        differences at machine truncation level: update lab_sea AD output (3/4).
184    o pkg/seaice:
185      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
186        and climsst/sss even when using seaice (to prevent calculation that might
187        use SST on land); does not affect any verification exp.
188      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
189        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
190    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
191      over land (non-legacy code)
192    o vectorize salt_plume package:
193      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
194      - this code computes plumebk everywhere (also over land), thus requires
195        code to avoid divisions by zero and catch the case of kLev=Nr.
196      - efficiency of salt_plume_frac is still sub-optimal
197    o tools (genmake2):
198      - fix makefile NAME specification (option: -makefile NAME) by adding
199        "-f $MAKEFILE" in few places where it was missing including makedepend
200        command (contribution from Paul).
201    
202    checkpoint63i (2012/01/24)
203    o model/src:
204      - add factorized versions of some EOS code to find_rho.F,
205        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
206    o model/src:
207      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
208      - change default celsius2K from 273.16 to 273.15
209      - to keep results unchanged, add back old value of celsius2K in verification
210        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
211         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
212    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
213      to make TAF generate vectorizable code
214    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
215       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
216       have flags that do this more efficiently.
217    o pkg/diagnostics/diagstats_calc.F
218      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
219    o pkg/obcs (with exch2):
220      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
221        and remove code (in obcs_readparms.F) which was based on EXCH of indices
222        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
223    o pkg/exf and seaice exp:
224      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
225        so that switching off area & heff advection flags does not affect results.
226      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
227      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
228        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
229        results of verification experiments: 1D_ocean_ice_column(fwd),
230        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
231        and offline_exf_seaice (all 4).
232    o pkg/seaice:
233      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
234        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
235      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
236        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
237        not multi-dim advection;
238      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
239        SHORTWAVE_HEATING #undef.
240    o optim: make Makefile more robust (?)
241    o pkg/obcs:
242      * fix treatment of obcs_read_pickup for TAF
243    o pkg/shelfice:
244      * add missing initialisation of num_shifwflx
245      * new adjoint verification exp. for isomip
246      * change Prandtl and Schmidt numbers from generic formulations
247        (in terms of model diffus. and visc.) to separate runtime
248        parameters, with Holland and Jenkins (1999) default values.
249    o pkg/exf (interpolation):
250      - extended input field (2 rows) near the N & S poles:
251        * fill in with the symetric value (when even Nb of data in longitude)
252        * add average value at the poles only for scalar quantities ; for vector
253          component interpolation, skip the averaging and keep duplicated values,
254          unless the 2 components have same location (uvInterp=T) in which case
255          interpolate the 2 components together using S/R EXF_INTERP_UV.
256      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
257        together: this allows to account properly for local orientation when
258        averaging at N & S pole.
259      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
260        exf-interpolation near N & S poles. Undef by default.
261      - add debug check/print on 1rst iter if debugLevel >=2.
262    o pkg/exf:
263      - change masking flags definition (no longer "parameter"), put them in
264        common block and set them in S/R EXF_INIT_FIXED.
265      - change recognized masking flag from s,u,v to c,w,s since the mask
266        to use (maskC,W,S) depends on position on model grid and has little to
267        do with scalar/vector difference; fix masking if using P-coordinates.
268      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
269        and update results of exp. global_with_exf (x2).
270      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
271    o pkg/obcs
272      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
273    o pkg/exf (interpolation):
274      - assume periodicity in X only if input field cover full longitude range.
275      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
276        and should vectorise).
277      - fix input lat of the 2 added row (in case we provide N.pole data).
278    
279    checkpoint63h (2011/12/30)
280    o pkg/seaice:
281      - change declaration of UVM from _RL to _RS in order to get B-grid
282        uIce,vIce monitor when _RS = real*4
283    o pkg/offline:
284      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
285      - compute vertical velocity if not read from file (switch on exactConserv
286        & staggerTimeStep);
287      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
288    o verification:
289      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
290        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
291        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
292      - update output of exp. global_ocean.cs32x15.viscA4 after changing
293        grid-file angles (used here for coriolis-3d);
294      - remove (or gzip) few files not needed to run fizhi-cs experiments.
295    o pkg/exf (vector interpolation):
296      - rotate vector component toward local grid-axis orientation using grid-angles
297        (stored in GRID.h) instead of locally computed rotation angle; keep old code
298        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
299    o pkg/seaice:
300      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
301        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
302    o pkg/PKG_OPTIONS.h files:
303      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
304        outside of the #ifdef ALLOW_THISPKG / #endif block.
305      - update verification/*/code/PKG_OPTIONS.h files.
306    o add a verification experiment (offline_exf_seaice/input.seaice) that test
307      the B-grid LSOR solver
308    o pkg/seaice: sort out emissivity and long wave radiation step 2:
309      - add emissivity for snow and ice as new run-time parameters
310        (unfortunately) that default to the corresponding exf values; this
311        changes results in most verification experiments so that for backward
312        compatibility these parameter have to be set explicitly to inconsistent
313        values (ugly);
314      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
315        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
316        until we agree how to handle this bug properly
317    o pkg/exf (interpolation):
318      - add a set of run-time param ({inputfield}_interpMethod), one for
319        each interpolated input field, to select the interpolation method
320        with a value of zero switching off the interpolation;
321      - print interpolation parameters to standard output;
322      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
323        (to use instead runoff_interpMethod=0 in data.exf).
324      - simplify default setting of interpolation parameters (for all fields,
325        set position to match model grid cell-center position, leading to trivial
326        interpolation in case of regular Lat-Lon grid) and fix for the case of
327        non-uniform delY.
328    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
329       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
330       this factor is absolutely required, because the lw exitance (= out-going
331       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
332       where the reflectivity rho = 1-emissivity for conservation reasons. Once
333       this is established, we can remove the CPP-Flag (if we want to).
334    o pkg/seaice:
335      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
336        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
337      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
338        what the name implies (and not emissivity*BoltzmannConstant), this means
339        the old default value of 5.5e-8 now means
340        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
341        S/R exf_readparms
342      - FV-discretization of the B-grid LSOR solver, turn on with
343        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
344        of the calling routine dynsolver, so that B and C-grid code look a
345        little more alike.
346      - fix index bugs in ostres.F (B-grid code)
347    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
348    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
349      default for SEAICE_emissivity, if useEXF; requires setting a wrong
350      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
351      backward compatiblity
352    o model/src: use sigmaR in calc_ivdc
353    
354    checkpoint63g (2011/12/16)
355    o pkg/seaice/seaice_growth.F:
356      fix heat conservation of the coupled ocean-seaice system.
357      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
358      solid vs liquid water treatment is resolved via QNET.
359    o pkg/seaice/seaice_growth.F:
360      add missing term for sublimation in saltFlux, which was breaking conservation.
361    o pkg/seaice/seaice_model.F:
362      Remove this patholigical case treatment in evolution branch,
363      where it is un-necessary and breaks conservation.
364      Update global_ocean.cs32x15/results accordingly for
365      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
366    o model/src:
367      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
368      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
369    o pkg/obcs:
370      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
371      tendency for temperature and salinity that is then applied to update
372      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
373      horizontal advection and diffusion contributions on the boundary (in
374      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
375      removing the mask in S/R timestep_tracer. The advantage of this approach is
376      that the updated tracer values include contributions from the surface
377      forcing and vertical diffusion.
378      This modification changes exp4.stevens because of vertical diffusion.
379    o model/src:
380      change non-curvilinear grid setting to also work with exch2 + blank tiles:
381      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
382        face dimensions.
383      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
384        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
385        and INI_SPHERICAL_POLAR_GRID.
386      change test-experiment global_ocean.90x40x15:
387      - split the domain in many more tiles (9x4 tiles of 10x10 each);
388      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
389      - update results of both test (std & dwnslp).
390    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
391       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
392    o model/src:
393      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
394        and fix initialisation when using sigma-coords.
395    o model/src:
396     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
397       to their current value at the beginning of forward_step.F": add a new run-time
398       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
399     - set doResetHFactors=T in the following test exp:
400        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
401        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
402        and tutorial_global_oce_in_p (nonLinFS in p)
403    o pkg/ecco
404      - added IES cost term
405    o verification/advect_xz
406      - scale down the depth by 1/100 (from 200 km to just 2.km)
407      - add secondary test using divergent flow, r-star and implicit vertical advection.
408      - add note (check_conserve_TS.txt) and matlab script to check global
409        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
410    o pkg/rbcs:
411      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
412    o pkg/obcs (Stevens BCs):
413      - fix various problems in the phase speed computations of the Stevens
414        boundary conditions:
415        - sign error for western and southern boundaries,
416        - time tendencies were underestimated by factor of dTracerLev and some just
417          zero (for multidim advection schemes) -> now estimate time tendencies
418          from difference between previous (n) time level and the one before (n-1);
419          this requires storing a field per tracer per boundary, also in the pickup
420          files.
421        - replace deltaTmom in cflMer/Zon computation with dTracerLev
422        - set default phase velocity to cflMer/Zon
423      - update verification experiment exp4.stevens
424    o pkg/generic_advdiff (implicit_r):
425      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
426        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
427      - fix implicit vertical diffusion or advection with NonLin FreeSurf
428        (was using current recip_hFacC instead of future recip_hFacC): set future
429        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
430        solver S/R ;
431      - fill diagnostics of vertical advective fluxes (computed from tendency)
432        when using implicit vert. advection;
433      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
434         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
435         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
436         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
437    o pkg/diagnostics:
438      - add diags for T & S tendency which goes through Adams-Bashforth.
439    
440    checkpoint63f (2011/11/30)
441    o pkg/obcs/obcs_calc_stevens.F:
442      - join some loops to reduce number of if-statements
443      - fix a bug in code for northern and southern boundaries.
444    o pkg/seaice/seaice_init_varia.F
445      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
446        caused zero ice-velocities for the B-grid code
447    o pkg/seaice/seaice_init_fixed.F
448      - fix a bug in the initialisation of the second metric terms
449        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
450      - this affects all seaice configurations with useCurviLinearGrid = .true.
451        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
452        = .true. (default)
453      - the only verification experiment affected is global_ocean.cs32x15:
454        icedyn, seaice, and seaice_dynmix (AD)
455    o pkg/thsice/thsice_diagnostics_state.F
456      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
457        not contain garbage that can lead to surprises in diagstats_calc.F
458    o model/src:
459      - move bi,bj loops inside INTEGR_CONTINUITY ;
460      - call INTEGR_CONTINUITY directly from forward_step.F
461        (previously called from momentum_correction_step.F)
462      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
463        forward_step.F and pkg/ecco/the_main_loop.F
464    o model/src/do_oceanic_phys.F:
465      - reset addMass to zero only if useICEFRONT ;
466      - separated k-loop for rhoInSitu calculation ;
467      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
468        and at constant T,S (= WdRHOdP);
469      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
470        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
471        transport of locally-referenced potential density);
472        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
473    o gluemnc:
474      - replace ncrcat with ncks when adding variables to *.glob.nc
475      - change the way variables without record dimensions are handled so that
476        files that have variables with and without record variables can be glued:
477        add a record dimension with a new unique name to be able to differentiate
478        between variable with and without a-prior record dimensions. Remove
479        this record dimension before adding the variable to the *.glob.nc file.
480        This procedure automatically works also for grid.*.nc files that do not
481        have any record dimension.
482    o verification/cpl_aim+ocn:
483      - generate new reference output on baudelaire (gfortran, mpich2) (previously
484        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
485    o pkg/obcs/obcs_calc_stevens.F:
486      - add code for northern and southern boundaries.
487      - reorder some loops to save some operations and so that drFBar can be scalar
488    o model/src:
489      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
490        truncation) and add diagnostics for Adams-Bashforth tendency increment.
491      - update test-exp. AD output:
492        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
493      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
494        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
495        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
496        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
497        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
498        tutorial_plume_on_slope.
499    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
500      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
501      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
502      does not even come with an F77 compiler anymore, this should not be
503      a limitation
504    
505    checkpoint63e (2011/11/06)
506    o pkg/seaice adjoint of LSR:
507      - substantially rework STORE dirs.
508      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
509        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
510        and only perform SOLV_MAX_FIXED adjoint iters.
511        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
512        always goes to same record, meaning that the last forward field will be
513        the one used in the adjoint - an approximation.
514      - now produces non-zero LSR-related gradients, and acceptable gradients for
515        An's zonal (x-z) test case (to be checked in)
516      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
517        (but these are screwed up by the thermodynamics in the first place);
518        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
519        output_adm.txt also reflects changes to seaice_lsr
520      - global_ocean.cs32x15:
521        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
522          (output_adm.seaice.txt was updated)
523        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
524          (output_adm.seaice_dynmix.txt)
525    o test-exp. exp4+stevens:
526      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
527    o pkg/seaice (lsr solver):
528      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
529        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
530      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
531      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
532        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
533      - compute (with new S/R) and print initial (+ free-driff sol. if available)
534        and final residual of linearised system.
535    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
536      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
537    o pkg/obcs: Stevens BCs (still only for east and west)
538      - fix Stevens BCs by using intermediate velocities of previous
539        time step as "baroclinic" contribution rather velocity of one grid cell
540        inside the boundaries; more consistent but makes the entire treatment
541        more complicated, requires new pickup files and two new S/Rs:
542        obcs_copy_uv_n and obcs_save_uv_n
543        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
544        (undefined by default)
545      - silently move computation of some grid factors into separate loops to
546        save some recomputations
547      - add a hack for non-linear free surface
548      - add a verification experiment to exp4 that tests this code
549    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
550    
551    checkpoint63d (2011/10/25)
552    o pkg/obcs + seaice-dynamics:
553      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
554        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
555        values (consistent with an implicit method).
556      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
557        return to older implementation (same results as before); note that none of
558        the "experimental" OBCS_SEAICE options are implemented in the new version.
559      - switch test exp. seaice_obcs to use new version (update output).
560    o pkg/seaice:
561      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
562      - add parenthesis in Water-Ice drag calculations (evp & lsr);
563      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
564        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
565      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
566        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
567    o pkg/layers:
568      - Include potential density as new coordinate (Thanks to David Munday)
569    o pkg/dic:
570      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
571        carbonate computation/output to CALC_PCO2_APPROX
572    o pkg/generic_advdiff
573      - make TAF generate code that vectorizes:
574        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
575    o model/src:
576      - improve vectorization also for adjoint code of
577        solve_tridiagonal and solve_pentadiagonal. As this requires up to
578        5 new 3D-fields, this code is only turned on for the combination of
579        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
580        for singular matrix check (only for TARGET_NEC_SX).
581      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
582        ALLOW_AUTODIFF. This flag now needs to be set outside of
583        solve_tri/pentadiagonal.F
584    o pkg/exf:
585      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
586        optional namelist EXF_NML_OBCS).
587      - add many debug-print (to trace down where pkg/cal error msg comes from)
588    o pkg/mom_vecinv/mom_vi_hdissip.F
589      - rearrange loops so that vectorization is improved and in particular
590        the adjoint routine vectorizes. The code is a little longer now, but I
591        think easier to read.
592        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
593    o pkg/seaice:
594      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
595    o pkg/exch2:
596      - alternative code (without tile x tile matrix) for cumulated (global) sum;
597        used as default; keep using matrix version in adjustment.cs-32x32x1.
598    o tools/build_options:
599      - after merging some MPI and/or multi-threads specific optfiles so that
600        the modified default optfile support both built (using genmake2 -mpi
601        for the MPI built, using genmake2 -omp for OpenMP built),
602        move now obsolete optfiles to tools/build_options/unsupported/
603       (add copy of email sent to support list in doc/optfiles_changes.txt)
604    
605    checkpoint63c (2011/09/28)
606    o pkg/ebm:
607      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
608        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
609    o pkg/seaice (SItracer pickup)
610    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
611      To be done:
612      - thorough testing of missing fields in S/R seaice_read_pickup
613      - thorough matching between generic tracers and specific fields used
614        (e.g. volume-weighted age, area-weighted age, salinity, ...)
615    o pkg/grdchk:
616      - all procs calculate and print finite-difference gradient (for testreport)
617      - change description output used by testreport;
618      - AD testing: also compare and report Finite-difference gradient;
619        => update all output_adm*.txt
620    o test exp. global_ocean_ebm:
621      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
622        and turn on exactConserve; update (fwd) output.
623    o pkg/seaice (LSR):
624      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
625      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
626        * identical results with non-CS topology (but save up to half of EXCH calls)
627        * no much changes in cs-32 verification tests since no ice at face edges
628         (differences due to convergence criteria, since nb of iterations changed)
629        * expect some differences on lat-lon-cap grid.
630        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
631  o pkg/exch2:  o pkg/exch2:
632    - add new CPP option to disable Cumul-Sum matrix (to save storage when using    - add new CPP option to disable Cumul-Sum matrix (to save storage when using
633      many tiles); until alternative coding is added, just add a stop.      many tiles); until alternative coding is added, just add a stop.

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