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revision 1.1498 by jmc, Mon Aug 29 19:46:22 2011 UTC revision 1.1608 by jmc, Mon Mar 5 02:14:27 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 array initialisation in adjoint mode:
8      1) pkg/mom_common/mom_calc_ke.F:
9        add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
10        The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
11        part this initialisation is gone, resulting in Floating Point Exception
12        (caught by open64 compiler with debug option).
13      2) model/src/convective_weights.F
14        set output convectCount over the full array range (instead of doing
15        an update): this fix a similar issue when called within recomputation (adjoint)
16        which could by-pass the initialisation (normally done in the caller S/R).
17    o pkg/seaice:
18      - final version of turbulent flux params, as agreed at MIT ice meet:
19           SEAICE_mcPheePiston (default is ~ 0.000875)
20           SEAICE_mcPheeTaper (default is 0.)
21           SEAICE_frazilFrac (defualt is 1.)
22           SEAICE_mcPheeStepFunc (default is false)
23      - changes results at trunction error level
24      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
25    o added pkg/frazil:
26      - see frazil_description.tex for details
27      - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
28    o pkg/shelfice/shelfice_thermodynamics.F
29      - fix exponents for velocity dependent exchange coefficients: change
30        from 2/3(=0) to 0.66666666666666667
31      - move computation of velocity dependent exchange coefficients into
32        separate loop, so that it applies to both thermodynamics
33      - move some divisions by constants out of loops
34    
35    checkpoint63j (2012/02/16)
36    o pkg/seaice:
37      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
38      - SItracer:  added run time params, and allow coupling to ocn salinity.
39    o pkg/seaice: remove (almost) all divisions by constants within loops
40      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
41      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
42      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
43      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
44    o pkg/seaice :
45      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
46        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
47      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
48      - add permanent SItflux diag that corresponds to TFLUX but includes
49        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
50      - allow activation/testing of a fix for suspected missing term in
51        ocn-ice heat budget (to be confirmed). To test this, you want to
52        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
53        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
54      - no change in results, fwd or ad.
55    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
56      - switch to variable freezing point.
57           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
58      - bug fix : the sublimation term that was missing is now activated.
59           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
60      - bug fix : flooding sign term for SIsal0.NE.0.
61           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
62    o pkg/seaice:
63      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
64        is now the default, and the old default constant freezing point is recovered
65        with SEAICE_tempFrz0    = -1.96,
66             SEAICE_dTempFrz_dS = 0.,
67      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
68      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
69      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
70        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
71      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
72        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
73      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
74        seaice_growth r149 for legacy branch (no results change).
75      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
76        from I. Fenty).
77      - results did not change except for global_ocean.cs32x15, mostly due to the
78        switch to variable freezing point (see above item for detail).
79    o pkg/thsice:
80      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
81        seawater freezing in thsice_calc_thickn (not used).
82    o pkg/seaice: turbulent flux term specification via run time params.
83      - replace CPP switches with run time switches to facilitate testing
84      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
85                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
86      - added runtime parameter : SEAICEturbFluxFormula
87      - move Mcphee constants to SEAICE_PARAMS.h
88      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
89                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
90                 remove seaice_summary call (moved to seaice_init_fixed)
91      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
92        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
93      - seaice_summary.F : add missing report of read turbulent flux term set up
94                           and SITRACER.
95      - seaice_check.F : check range; inform and stop if retired CPPs are used
96                         (incl. SEAICE_AGE).
97      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
98             CPP switch, same computation as before for the different options.
99      - change results at the truncation level.
100    o pkg/seaice:
101      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
102        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
103        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
104      - update verification/*/input*/data.seaice:
105        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
106        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
107        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
108        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
109    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
110      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
111        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
112        difference in results only due to machine truncation.
113      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
114        MaykutPolySatVap; keep MIN_LWDOWN.
115      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
116      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
117        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
118    o pkg/salt_plume:
119      - isolate saltPlumeFlux array exch into a specific S/R called from
120        do_oceanic_phys.F
121      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
122    o verification:
123      - move untested set-up to MITgcm_contrib/verification_other.
124    o pkg/seaice:
125      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
126    o pkg/seaice:
127      - seaice_solve4temp.F (keeping results unchanged):
128        * add 2 future run-time params to select which saturation vapor pressure
129          formula is used and how post-iteration fluxes are set.
130          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
131        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
132          the linearized expression to stay consistent with tsurf finding.
133      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
134        can be < 0.
135    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
136      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
137        conductive heat flux F_c , and add it explicitly when updating tsurf as
138        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
139        so that now F_ia has a consistent meaning through the entire routine.
140        This causes differences at truncation level: update output of fwd exp.
141        global_ocean.cs32x15.seaice.
142    o pkg/seaice:
143      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
144        of arrays, sign/direction of fluxes; no effect on results.
145      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
146        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
147        note: this should have been done before changing celsius2K default.
148      - to keep results unchanged, add back old value of celsius2K in verification
149        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
150      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
151        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
152        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
153        freezing temp is consistent with value in seaice_growth.F ; this causes
154        differences at machine truncation level: update lab_sea AD output (3/4).
155    o pkg/seaice:
156      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
157        and climsst/sss even when using seaice (to prevent calculation that might
158        use SST on land); does not affect any verification exp.
159      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
160        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
161    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
162      over land (non-legacy code)
163    o vectorize salt_plume package:
164      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
165      - this code computes plumebk everywhere (also over land), thus requires
166        code to avoid divisions by zero and catch the case of kLev=Nr.
167      - efficiency of salt_plume_frac is still sub-optimal
168    o tools (genmake2):
169      - fix makefile NAME specification (option: -makefile NAME) by adding
170        "-f $MAKEFILE" in few places where it was missing including makedepend
171        command (contribution from Paul).
172    
173    checkpoint63i (2012/01/24)
174    o model/src:
175      - add factorized versions of some EOS code to find_rho.F,
176        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
177    o model/src:
178      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
179      - change default celsius2K from 273.16 to 273.15
180      - to keep results unchanged, add back old value of celsius2K in verification
181        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
182         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
183    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
184      to make TAF generate vectorizable code
185    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
186       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
187       have flags that do this more efficiently.
188    o pkg/diagnostics/diagstats_calc.F
189      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
190    o pkg/obcs (with exch2):
191      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
192        and remove code (in obcs_readparms.F) which was based on EXCH of indices
193        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
194    o pkg/exf and seaice exp:
195      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
196        so that switching off area & heff advection flags does not affect results.
197      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
198      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
199        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
200        results of verification experiments: 1D_ocean_ice_column(fwd),
201        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
202        and offline_exf_seaice (all 4).
203    o pkg/seaice:
204      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
205        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
206      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
207        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
208        not multi-dim advection;
209      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
210        SHORTWAVE_HEATING #undef.
211    o optim: make Makefile more robust (?)
212    o pkg/obcs:
213      * fix treatment of obcs_read_pickup for TAF
214    o pkg/shelfice:
215      * add missing initialisation of num_shifwflx
216      * new adjoint verification exp. for isomip
217      * change Prandtl and Schmidt numbers from generic formulations
218        (in terms of model diffus. and visc.) to separate runtime
219        parameters, with Holland and Jenkins (1999) default values.
220    o pkg/exf (interpolation):
221      - extended input field (2 rows) near the N & S poles:
222        * fill in with the symetric value (when even Nb of data in longitude)
223        * add average value at the poles only for scalar quantities ; for vector
224          component interpolation, skip the averaging and keep duplicated values,
225          unless the 2 components have same location (uvInterp=T) in which case
226          interpolate the 2 components together using S/R EXF_INTERP_UV.
227      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
228        together: this allows to account properly for local orientation when
229        averaging at N & S pole.
230      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
231        exf-interpolation near N & S poles. Undef by default.
232      - add debug check/print on 1rst iter if debugLevel >=2.
233    o pkg/exf:
234      - change masking flags definition (no longer "parameter"), put them in
235        common block and set them in S/R EXF_INIT_FIXED.
236      - change recognized masking flag from s,u,v to c,w,s since the mask
237        to use (maskC,W,S) depends on position on model grid and has little to
238        do with scalar/vector difference; fix masking if using P-coordinates.
239      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
240        and update results of exp. global_with_exf (x2).
241      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
242    o pkg/obcs
243      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
244    o pkg/exf (interpolation):
245      - assume periodicity in X only if input field cover full longitude range.
246      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
247        and should vectorise).
248      - fix input lat of the 2 added row (in case we provide N.pole data).
249    
250    checkpoint63h (2011/12/30)
251    o pkg/seaice:
252      - change declaration of UVM from _RL to _RS in order to get B-grid
253        uIce,vIce monitor when _RS = real*4
254    o pkg/offline:
255      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
256      - compute vertical velocity if not read from file (switch on exactConserv
257        & staggerTimeStep);
258      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
259    o verification:
260      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
261        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
262        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
263      - update output of exp. global_ocean.cs32x15.viscA4 after changing
264        grid-file angles (used here for coriolis-3d);
265      - remove (or gzip) few files not needed to run fizhi-cs experiments.
266    o pkg/exf (vector interpolation):
267      - rotate vector component toward local grid-axis orientation using grid-angles
268        (stored in GRID.h) instead of locally computed rotation angle; keep old code
269        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
270    o pkg/seaice:
271      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
272        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
273    o pkg/PKG_OPTIONS.h files:
274      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
275        outside of the #ifdef ALLOW_THISPKG / #endif block.
276      - update verification/*/code/PKG_OPTIONS.h files.
277    o add a verification experiment (offline_exf_seaice/input.seaice) that test
278      the B-grid LSOR solver
279    o pkg/seaice: sort out emissivity and long wave radiation step 2:
280      - add emissivity for snow and ice as new run-time parameters
281        (unfortunately) that default to the corresponding exf values; this
282        changes results in most verification experiments so that for backward
283        compatibility these parameter have to be set explicitly to inconsistent
284        values (ugly);
285      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
286        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
287        until we agree how to handle this bug properly
288    o pkg/exf (interpolation):
289      - add a set of run-time param ({inputfield}_interpMethod), one for
290        each interpolated input field, to select the interpolation method
291        with a value of zero switching off the interpolation;
292      - print interpolation parameters to standard output;
293      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
294        (to use instead runoff_interpMethod=0 in data.exf).
295      - simplify default setting of interpolation parameters (for all fields,
296        set position to match model grid cell-center position, leading to trivial
297        interpolation in case of regular Lat-Lon grid) and fix for the case of
298        non-uniform delY.
299    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
300       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
301       this factor is absolutely required, because the lw exitance (= out-going
302       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
303       where the reflectivity rho = 1-emissivity for conservation reasons. Once
304       this is established, we can remove the CPP-Flag (if we want to).
305    o pkg/seaice:
306      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
307        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
308      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
309        what the name implies (and not emissivity*BoltzmannConstant), this means
310        the old default value of 5.5e-8 now means
311        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
312        S/R exf_readparms
313      - FV-discretization of the B-grid LSOR solver, turn on with
314        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
315        of the calling routine dynsolver, so that B and C-grid code look a
316        little more alike.
317      - fix index bugs in ostres.F (B-grid code)
318    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
319    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
320      default for SEAICE_emissivity, if useEXF; requires setting a wrong
321      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
322      backward compatiblity
323    o model/src: use sigmaR in calc_ivdc
324    
325    checkpoint63g (2011/12/16)
326    o pkg/seaice/seaice_growth.F:
327      fix heat conservation of the coupled ocean-seaice system.
328      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
329      solid vs liquid water treatment is resolved via QNET.
330    o pkg/seaice/seaice_growth.F:
331      add missing term for sublimation in saltFlux, which was breaking conservation.
332    o pkg/seaice/seaice_model.F:
333      Remove this patholigical case treatment in evolution branch,
334      where it is un-necessary and breaks conservation.
335      Update global_ocean.cs32x15/results accordingly for
336      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
337    o model/src:
338      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
339      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
340    o pkg/obcs:
341      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
342      tendency for temperature and salinity that is then applied to update
343      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
344      horizontal advection and diffusion contributions on the boundary (in
345      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
346      removing the mask in S/R timestep_tracer. The advantage of this approach is
347      that the updated tracer values include contributions from the surface
348      forcing and vertical diffusion.
349      This modification changes exp4.stevens because of vertical diffusion.
350    o model/src:
351      change non-curvilinear grid setting to also work with exch2 + blank tiles:
352      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
353        face dimensions.
354      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
355        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
356        and INI_SPHERICAL_POLAR_GRID.
357      change test-experiment global_ocean.90x40x15:
358      - split the domain in many more tiles (9x4 tiles of 10x10 each);
359      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
360      - update results of both test (std & dwnslp).
361    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
362       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
363    o model/src:
364      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
365        and fix initialisation when using sigma-coords.
366    o model/src:
367     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
368       to their current value at the beginning of forward_step.F": add a new run-time
369       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
370     - set doResetHFactors=T in the following test exp:
371        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
372        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
373        and tutorial_global_oce_in_p (nonLinFS in p)
374    o pkg/ecco
375      - added IES cost term
376    o verification/advect_xz
377      - scale down the depth by 1/100 (from 200 km to just 2.km)
378      - add secondary test using divergent flow, r-star and implicit vertical advection.
379      - add note (check_conserve_TS.txt) and matlab script to check global
380        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
381    o pkg/rbcs:
382      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
383    o pkg/obcs (Stevens BCs):
384      - fix various problems in the phase speed computations of the Stevens
385        boundary conditions:
386        - sign error for western and southern boundaries,
387        - time tendencies were underestimated by factor of dTracerLev and some just
388          zero (for multidim advection schemes) -> now estimate time tendencies
389          from difference between previous (n) time level and the one before (n-1);
390          this requires storing a field per tracer per boundary, also in the pickup
391          files.
392        - replace deltaTmom in cflMer/Zon computation with dTracerLev
393        - set default phase velocity to cflMer/Zon
394      - update verification experiment exp4.stevens
395    o pkg/generic_advdiff (implicit_r):
396      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
397        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
398      - fix implicit vertical diffusion or advection with NonLin FreeSurf
399        (was using current recip_hFacC instead of future recip_hFacC): set future
400        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
401        solver S/R ;
402      - fill diagnostics of vertical advective fluxes (computed from tendency)
403        when using implicit vert. advection;
404      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
405         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
406         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
407         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
408    o pkg/diagnostics:
409      - add diags for T & S tendency which goes through Adams-Bashforth.
410    
411    checkpoint63f (2011/11/30)
412    o pkg/obcs/obcs_calc_stevens.F:
413      - join some loops to reduce number of if-statements
414      - fix a bug in code for northern and southern boundaries.
415    o pkg/seaice/seaice_init_varia.F
416      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
417        caused zero ice-velocities for the B-grid code
418    o pkg/seaice/seaice_init_fixed.F
419      - fix a bug in the initialisation of the second metric terms
420        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
421      - this affects all seaice configurations with useCurviLinearGrid = .true.
422        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
423        = .true. (default)
424      - the only verification experiment affected is global_ocean.cs32x15:
425        icedyn, seaice, and seaice_dynmix (AD)
426    o pkg/thsice/thsice_diagnostics_state.F
427      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
428        not contain garbage that can lead to surprises in diagstats_calc.F
429    o model/src:
430      - move bi,bj loops inside INTEGR_CONTINUITY ;
431      - call INTEGR_CONTINUITY directly from forward_step.F
432        (previously called from momentum_correction_step.F)
433      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
434        forward_step.F and pkg/ecco/the_main_loop.F
435    o model/src/do_oceanic_phys.F:
436      - reset addMass to zero only if useICEFRONT ;
437      - separated k-loop for rhoInSitu calculation ;
438      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
439        and at constant T,S (= WdRHOdP);
440      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
441        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
442        transport of locally-referenced potential density);
443        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
444    o gluemnc:
445      - replace ncrcat with ncks when adding variables to *.glob.nc
446      - change the way variables without record dimensions are handled so that
447        files that have variables with and without record variables can be glued:
448        add a record dimension with a new unique name to be able to differentiate
449        between variable with and without a-prior record dimensions. Remove
450        this record dimension before adding the variable to the *.glob.nc file.
451        This procedure automatically works also for grid.*.nc files that do not
452        have any record dimension.
453    o verification/cpl_aim+ocn:
454      - generate new reference output on baudelaire (gfortran, mpich2) (previously
455        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
456    o pkg/obcs/obcs_calc_stevens.F:
457      - add code for northern and southern boundaries.
458      - reorder some loops to save some operations and so that drFBar can be scalar
459    o model/src:
460      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
461        truncation) and add diagnostics for Adams-Bashforth tendency increment.
462      - update test-exp. AD output:
463        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
464      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
465        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
466        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
467        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
468        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
469        tutorial_plume_on_slope.
470    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
471      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
472      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
473      does not even come with an F77 compiler anymore, this should not be
474      a limitation
475    
476    checkpoint63e (2011/11/06)
477    o pkg/seaice adjoint of LSR:
478      - substantially rework STORE dirs.
479      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
480        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
481        and only perform SOLV_MAX_FIXED adjoint iters.
482        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
483        always goes to same record, meaning that the last forward field will be
484        the one used in the adjoint - an approximation.
485      - now produces non-zero LSR-related gradients, and acceptable gradients for
486        An's zonal (x-z) test case (to be checked in)
487      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
488        (but these are screwed up by the thermodynamics in the first place);
489        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
490        output_adm.txt also reflects changes to seaice_lsr
491      - global_ocean.cs32x15:
492        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
493          (output_adm.seaice.txt was updated)
494        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
495          (output_adm.seaice_dynmix.txt)
496    o test-exp. exp4+stevens:
497      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
498    o pkg/seaice (lsr solver):
499      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
500        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
501      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
502      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
503        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
504      - compute (with new S/R) and print initial (+ free-driff sol. if available)
505        and final residual of linearised system.
506    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
507      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
508    o pkg/obcs: Stevens BCs (still only for east and west)
509      - fix Stevens BCs by using intermediate velocities of previous
510        time step as "baroclinic" contribution rather velocity of one grid cell
511        inside the boundaries; more consistent but makes the entire treatment
512        more complicated, requires new pickup files and two new S/Rs:
513        obcs_copy_uv_n and obcs_save_uv_n
514        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
515        (undefined by default)
516      - silently move computation of some grid factors into separate loops to
517        save some recomputations
518      - add a hack for non-linear free surface
519      - add a verification experiment to exp4 that tests this code
520    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
521    
522    checkpoint63d (2011/10/25)
523    o pkg/obcs + seaice-dynamics:
524      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
525        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
526        values (consistent with an implicit method).
527      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
528        return to older implementation (same results as before); note that none of
529        the "experimental" OBCS_SEAICE options are implemented in the new version.
530      - switch test exp. seaice_obcs to use new version (update output).
531    o pkg/seaice:
532      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
533      - add parenthesis in Water-Ice drag calculations (evp & lsr);
534      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
535        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
536      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
537        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
538    o pkg/layers:
539      - Include potential density as new coordinate (Thanks to David Munday)
540    o pkg/dic:
541      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
542        carbonate computation/output to CALC_PCO2_APPROX
543    o pkg/generic_advdiff
544      - make TAF generate code that vectorizes:
545        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
546    o model/src:
547      - improve vectorization also for adjoint code of
548        solve_tridiagonal and solve_pentadiagonal. As this requires up to
549        5 new 3D-fields, this code is only turned on for the combination of
550        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
551        for singular matrix check (only for TARGET_NEC_SX).
552      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
553        ALLOW_AUTODIFF. This flag now needs to be set outside of
554        solve_tri/pentadiagonal.F
555    o pkg/exf:
556      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
557        optional namelist EXF_NML_OBCS).
558      - add many debug-print (to trace down where pkg/cal error msg comes from)
559    o pkg/mom_vecinv/mom_vi_hdissip.F
560      - rearrange loops so that vectorization is improved and in particular
561        the adjoint routine vectorizes. The code is a little longer now, but I
562        think easier to read.
563        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
564    o pkg/seaice:
565      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
566    o pkg/exch2:
567      - alternative code (without tile x tile matrix) for cumulated (global) sum;
568        used as default; keep using matrix version in adjustment.cs-32x32x1.
569    o tools/build_options:
570      - after merging some MPI and/or multi-threads specific optfiles so that
571        the modified default optfile support both built (using genmake2 -mpi
572        for the MPI built, using genmake2 -omp for OpenMP built),
573        move now obsolete optfiles to tools/build_options/unsupported/
574       (add copy of email sent to support list in doc/optfiles_changes.txt)
575    
576    checkpoint63c (2011/09/28)
577    o pkg/ebm:
578      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
579        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
580    o pkg/seaice (SItracer pickup)
581    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
582      To be done:
583      - thorough testing of missing fields in S/R seaice_read_pickup
584      - thorough matching between generic tracers and specific fields used
585        (e.g. volume-weighted age, area-weighted age, salinity, ...)
586    o pkg/grdchk:
587      - all procs calculate and print finite-difference gradient (for testreport)
588      - change description output used by testreport;
589      - AD testing: also compare and report Finite-difference gradient;
590        => update all output_adm*.txt
591    o test exp. global_ocean_ebm:
592      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
593        and turn on exactConserve; update (fwd) output.
594    o pkg/seaice (LSR):
595      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
596      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
597        * identical results with non-CS topology (but save up to half of EXCH calls)
598        * no much changes in cs-32 verification tests since no ice at face edges
599         (differences due to convergence criteria, since nb of iterations changed)
600        * expect some differences on lat-lon-cap grid.
601        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
602    o pkg/exch2:
603      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
604        many tiles); until alternative coding is added, just add a stop.
605    o pkg/kpp:
606      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
607        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
608    o optfiles:
609      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
610        into corresponding standard one, which now support different build:
611        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
612      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
613    o pkg/obcs (seaice):
614      - add missing EXCH for uIce,vIce after applying OBCS;
615      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
616        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
617        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
618      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
619      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
620        and eedata.mth for MPI and mutlti-threaded testing.
621    o pkg/flt:
622      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
623      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
624      - fix pickup and trajectories + profiles output with multi-threads;
625      - add parameter to select group of fields to write along trajectory and
626        profile (default unchanged);
627      - only call PORT_RAND* function when flt_noise <> 0;
628      - add multi-threaded test for verification exp. flt_example.
629    o eesupp/src:
630      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
631      - USE_OMP_THREADING: check that number of threads (from eedata) matches
632        actual number (from env.var. setting).
633  o pkg/ebm:  o pkg/ebm:
634    - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.    - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
635    - add multi-threaded test for verification exp. global_ocean_ebm    - add multi-threaded test for verification exp. global_ocean_ebm

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