/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1435 by jmc, Wed May 18 02:21:49 2011 UTC revision 1.1605 by dimitri, Sat Mar 3 16:04:38 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/seaice :
8      - final version of turbulent flux params, as agreed at MIT ice meet:
9           SEAICE_mcPheePiston (default is ~ 0.000875)
10           SEAICE_mcPheeTaper (default is 0.)
11           SEAICE_frazilFrac (defualt is 1.)
12           SEAICE_mcPheeStepFunc (default is false)
13      - changes results at trunction error level
14      - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
15    o added pkg/frazil - see frazil_description.tex for details
16    o pkg/shelfice/shelfice_thermodynamics.F
17      - fix exponents for velocity dependent exchange coefficients: change
18        from 2/3(=0) to 0.66666666666666667
19      - move computation of velocity dependent exchange coefficients into
20        separate loop, so that it applies to both thermodynamics
21      - move some divisions by constants out of loops
22    
23    checkpoint63j (2012/02/16)
24    o pkg/seaice:
25      - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
26      - SItracer:  added run time params, and allow coupling to ocn salinity.
27    o pkg/seaice: remove (almost) all divisions by constants within loops
28      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
29      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
30      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
31      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
32    o pkg/seaice :
33      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
34        = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
35      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
36      - add permanent SItflux diag that corresponds to TFLUX but includes
37        ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
38      - allow activation/testing of a fix for suspected missing term in
39        ocn-ice heat budget (to be confirmed). To test this, you want to
40        undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
41        SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
42      - no change in results, fwd or ad.
43    o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
44      - switch to variable freezing point.
45           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
46      - bug fix : the sublimation term that was missing is now activated.
47           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
48      - bug fix : flooding sign term for SIsal0.NE.0.
49           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
50    o pkg/seaice:
51      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
52        is now the default, and the old default constant freezing point is recovered
53        with SEAICE_tempFrz0    = -1.96,
54             SEAICE_dTempFrz_dS = 0.,
55      - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
56      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
57      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
58        activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
59      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
60        was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
61      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
62        seaice_growth r149 for legacy branch (no results change).
63      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
64        from I. Fenty).
65      - results did not change except for global_ocean.cs32x15, mostly due to the
66        switch to variable freezing point (see above item for detail).
67    o pkg/thsice:
68      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
69        seawater freezing in thsice_calc_thickn (not used).
70    o pkg/seaice: turbulent flux term specification via run time params.
71      - replace CPP switches with run time switches to facilitate testing
72      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
73                       GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
74      - added runtime parameter : SEAICEturbFluxFormula
75      - move Mcphee constants to SEAICE_PARAMS.h
76      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
77                 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
78                 remove seaice_summary call (moved to seaice_init_fixed)
79      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
80        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
81      - seaice_summary.F : add missing report of read turbulent flux term set up
82                           and SITRACER.
83      - seaice_check.F : check range; inform and stop if retired CPPs are used
84                         (incl. SEAICE_AGE).
85      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
86             CPP switch, same computation as before for the different options.
87      - change results at the truncation level.
88    o pkg/seaice:
89      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
90        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
91        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
92      - update verification/*/input*/data.seaice:
93        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
94        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
95        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
96        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
97    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
98      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
99        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
100        difference in results only due to machine truncation.
101      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
102        MaykutPolySatVap; keep MIN_LWDOWN.
103      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
104      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
105        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
106    o pkg/salt_plume:
107      - isolate saltPlumeFlux array exch into a specific S/R called from
108        do_oceanic_phys.F
109      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
110    o verification:
111      - move untested set-up to MITgcm_contrib/verification_other.
112    o pkg/seaice:
113      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
114    o pkg/seaice:
115      - seaice_solve4temp.F (keeping results unchanged):
116        * add 2 future run-time params to select which saturation vapor pressure
117          formula is used and how post-iteration fluxes are set.
118          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
119        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
120          the linearized expression to stay consistent with tsurf finding.
121      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
122        can be < 0.
123    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
124      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
125        conductive heat flux F_c , and add it explicitly when updating tsurf as
126        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
127        so that now F_ia has a consistent meaning through the entire routine.
128        This causes differences at truncation level: update output of fwd exp.
129        global_ocean.cs32x15.seaice.
130    o pkg/seaice:
131      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
132        of arrays, sign/direction of fluxes; no effect on results.
133      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
134        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
135        note: this should have been done before changing celsius2K default.
136      - to keep results unchanged, add back old value of celsius2K in verification
137        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
138      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
139        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
140        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
141        freezing temp is consistent with value in seaice_growth.F ; this causes
142        differences at machine truncation level: update lab_sea AD output (3/4).
143    o pkg/seaice:
144      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
145        and climsst/sss even when using seaice (to prevent calculation that might
146        use SST on land); does not affect any verification exp.
147      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
148        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
149    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
150      over land (non-legacy code)
151    o vectorize salt_plume package:
152      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
153      - this code computes plumebk everywhere (also over land), thus requires
154        code to avoid divisions by zero and catch the case of kLev=Nr.
155      - efficiency of salt_plume_frac is still sub-optimal
156    o tools (genmake2):
157      - fix makefile NAME specification (option: -makefile NAME) by adding
158        "-f $MAKEFILE" in few places where it was missing including makedepend
159        command (contribution from Paul).
160    
161    checkpoint63i (2012/01/24)
162    o model/src:
163      - add factorized versions of some EOS code to find_rho.F,
164        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
165    o model/src:
166      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
167      - change default celsius2K from 273.16 to 273.15
168      - to keep results unchanged, add back old value of celsius2K in verification
169        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
170         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
171    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
172      to make TAF generate vectorizable code
173    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
174       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
175       have flags that do this more efficiently.
176    o pkg/diagnostics/diagstats_calc.F
177      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
178    o pkg/obcs (with exch2):
179      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
180        and remove code (in obcs_readparms.F) which was based on EXCH of indices
181        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
182    o pkg/exf and seaice exp:
183      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
184        so that switching off area & heff advection flags does not affect results.
185      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
186      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
187        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
188        results of verification experiments: 1D_ocean_ice_column(fwd),
189        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
190        and offline_exf_seaice (all 4).
191    o pkg/seaice:
192      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
193        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
194      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
195        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
196        not multi-dim advection;
197      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
198        SHORTWAVE_HEATING #undef.
199    o optim: make Makefile more robust (?)
200    o pkg/obcs:
201      * fix treatment of obcs_read_pickup for TAF
202    o pkg/shelfice:
203      * add missing initialisation of num_shifwflx
204      * new adjoint verification exp. for isomip
205      * change Prandtl and Schmidt numbers from generic formulations
206        (in terms of model diffus. and visc.) to separate runtime
207        parameters, with Holland and Jenkins (1999) default values.
208    o pkg/exf (interpolation):
209      - extended input field (2 rows) near the N & S poles:
210        * fill in with the symetric value (when even Nb of data in longitude)
211        * add average value at the poles only for scalar quantities ; for vector
212          component interpolation, skip the averaging and keep duplicated values,
213          unless the 2 components have same location (uvInterp=T) in which case
214          interpolate the 2 components together using S/R EXF_INTERP_UV.
215      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
216        together: this allows to account properly for local orientation when
217        averaging at N & S pole.
218      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
219        exf-interpolation near N & S poles. Undef by default.
220      - add debug check/print on 1rst iter if debugLevel >=2.
221    o pkg/exf:
222      - change masking flags definition (no longer "parameter"), put them in
223        common block and set them in S/R EXF_INIT_FIXED.
224      - change recognized masking flag from s,u,v to c,w,s since the mask
225        to use (maskC,W,S) depends on position on model grid and has little to
226        do with scalar/vector difference; fix masking if using P-coordinates.
227      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
228        and update results of exp. global_with_exf (x2).
229      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
230    o pkg/obcs
231      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
232    o pkg/exf (interpolation):
233      - assume periodicity in X only if input field cover full longitude range.
234      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
235        and should vectorise).
236      - fix input lat of the 2 added row (in case we provide N.pole data).
237    
238    checkpoint63h (2011/12/30)
239    o pkg/seaice:
240      - change declaration of UVM from _RL to _RS in order to get B-grid
241        uIce,vIce monitor when _RS = real*4
242    o pkg/offline:
243      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
244      - compute vertical velocity if not read from file (switch on exactConserv
245        & staggerTimeStep);
246      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
247    o verification:
248      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
249        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
250        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
251      - update output of exp. global_ocean.cs32x15.viscA4 after changing
252        grid-file angles (used here for coriolis-3d);
253      - remove (or gzip) few files not needed to run fizhi-cs experiments.
254    o pkg/exf (vector interpolation):
255      - rotate vector component toward local grid-axis orientation using grid-angles
256        (stored in GRID.h) instead of locally computed rotation angle; keep old code
257        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
258    o pkg/seaice:
259      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
260        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
261    o pkg/PKG_OPTIONS.h files:
262      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
263        outside of the #ifdef ALLOW_THISPKG / #endif block.
264      - update verification/*/code/PKG_OPTIONS.h files.
265    o add a verification experiment (offline_exf_seaice/input.seaice) that test
266      the B-grid LSOR solver
267    o pkg/seaice: sort out emissivity and long wave radiation step 2:
268      - add emissivity for snow and ice as new run-time parameters
269        (unfortunately) that default to the corresponding exf values; this
270        changes results in most verification experiments so that for backward
271        compatibility these parameter have to be set explicitly to inconsistent
272        values (ugly);
273      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
274        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
275        until we agree how to handle this bug properly
276    o pkg/exf (interpolation):
277      - add a set of run-time param ({inputfield}_interpMethod), one for
278        each interpolated input field, to select the interpolation method
279        with a value of zero switching off the interpolation;
280      - print interpolation parameters to standard output;
281      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
282        (to use instead runoff_interpMethod=0 in data.exf).
283      - simplify default setting of interpolation parameters (for all fields,
284        set position to match model grid cell-center position, leading to trivial
285        interpolation in case of regular Lat-Lon grid) and fix for the case of
286        non-uniform delY.
287    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
288       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
289       this factor is absolutely required, because the lw exitance (= out-going
290       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
291       where the reflectivity rho = 1-emissivity for conservation reasons. Once
292       this is established, we can remove the CPP-Flag (if we want to).
293    o pkg/seaice:
294      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
295        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
296      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
297        what the name implies (and not emissivity*BoltzmannConstant), this means
298        the old default value of 5.5e-8 now means
299        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
300        S/R exf_readparms
301      - FV-discretization of the B-grid LSOR solver, turn on with
302        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
303        of the calling routine dynsolver, so that B and C-grid code look a
304        little more alike.
305      - fix index bugs in ostres.F (B-grid code)
306    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
307    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
308      default for SEAICE_emissivity, if useEXF; requires setting a wrong
309      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
310      backward compatiblity
311    o model/src: use sigmaR in calc_ivdc
312    
313    checkpoint63g (2011/12/16)
314    o pkg/seaice/seaice_growth.F:
315      fix heat conservation of the coupled ocean-seaice system.
316      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
317      solid vs liquid water treatment is resolved via QNET.
318    o pkg/seaice/seaice_growth.F:
319      add missing term for sublimation in saltFlux, which was breaking conservation.
320    o pkg/seaice/seaice_model.F:
321      Remove this patholigical case treatment in evolution branch,
322      where it is un-necessary and breaks conservation.
323      Update global_ocean.cs32x15/results accordingly for
324      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
325    o model/src:
326      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
327      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
328    o pkg/obcs:
329      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
330      tendency for temperature and salinity that is then applied to update
331      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
332      horizontal advection and diffusion contributions on the boundary (in
333      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
334      removing the mask in S/R timestep_tracer. The advantage of this approach is
335      that the updated tracer values include contributions from the surface
336      forcing and vertical diffusion.
337      This modification changes exp4.stevens because of vertical diffusion.
338    o model/src:
339      change non-curvilinear grid setting to also work with exch2 + blank tiles:
340      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
341        face dimensions.
342      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
343        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
344        and INI_SPHERICAL_POLAR_GRID.
345      change test-experiment global_ocean.90x40x15:
346      - split the domain in many more tiles (9x4 tiles of 10x10 each);
347      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
348      - update results of both test (std & dwnslp).
349    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
350       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
351    o model/src:
352      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
353        and fix initialisation when using sigma-coords.
354    o model/src:
355     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
356       to their current value at the beginning of forward_step.F": add a new run-time
357       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
358     - set doResetHFactors=T in the following test exp:
359        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
360        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
361        and tutorial_global_oce_in_p (nonLinFS in p)
362    o pkg/ecco
363      - added IES cost term
364    o verification/advect_xz
365      - scale down the depth by 1/100 (from 200 km to just 2.km)
366      - add secondary test using divergent flow, r-star and implicit vertical advection.
367      - add note (check_conserve_TS.txt) and matlab script to check global
368        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
369    o pkg/rbcs:
370      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
371    o pkg/obcs (Stevens BCs):
372      - fix various problems in the phase speed computations of the Stevens
373        boundary conditions:
374        - sign error for western and southern boundaries,
375        - time tendencies were underestimated by factor of dTracerLev and some just
376          zero (for multidim advection schemes) -> now estimate time tendencies
377          from difference between previous (n) time level and the one before (n-1);
378          this requires storing a field per tracer per boundary, also in the pickup
379          files.
380        - replace deltaTmom in cflMer/Zon computation with dTracerLev
381        - set default phase velocity to cflMer/Zon
382      - update verification experiment exp4.stevens
383    o pkg/generic_advdiff (implicit_r):
384      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
385        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
386      - fix implicit vertical diffusion or advection with NonLin FreeSurf
387        (was using current recip_hFacC instead of future recip_hFacC): set future
388        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
389        solver S/R ;
390      - fill diagnostics of vertical advective fluxes (computed from tendency)
391        when using implicit vert. advection;
392      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
393         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
394         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
395         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
396    o pkg/diagnostics:
397      - add diags for T & S tendency which goes through Adams-Bashforth.
398    
399    checkpoint63f (2011/11/30)
400    o pkg/obcs/obcs_calc_stevens.F:
401      - join some loops to reduce number of if-statements
402      - fix a bug in code for northern and southern boundaries.
403    o pkg/seaice/seaice_init_varia.F
404      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
405        caused zero ice-velocities for the B-grid code
406    o pkg/seaice/seaice_init_fixed.F
407      - fix a bug in the initialisation of the second metric terms
408        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
409      - this affects all seaice configurations with useCurviLinearGrid = .true.
410        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
411        = .true. (default)
412      - the only verification experiment affected is global_ocean.cs32x15:
413        icedyn, seaice, and seaice_dynmix (AD)
414    o pkg/thsice/thsice_diagnostics_state.F
415      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
416        not contain garbage that can lead to surprises in diagstats_calc.F
417    o model/src:
418      - move bi,bj loops inside INTEGR_CONTINUITY ;
419      - call INTEGR_CONTINUITY directly from forward_step.F
420        (previously called from momentum_correction_step.F)
421      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
422        forward_step.F and pkg/ecco/the_main_loop.F
423    o model/src/do_oceanic_phys.F:
424      - reset addMass to zero only if useICEFRONT ;
425      - separated k-loop for rhoInSitu calculation ;
426      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
427        and at constant T,S (= WdRHOdP);
428      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
429        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
430        transport of locally-referenced potential density);
431        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
432    o gluemnc:
433      - replace ncrcat with ncks when adding variables to *.glob.nc
434      - change the way variables without record dimensions are handled so that
435        files that have variables with and without record variables can be glued:
436        add a record dimension with a new unique name to be able to differentiate
437        between variable with and without a-prior record dimensions. Remove
438        this record dimension before adding the variable to the *.glob.nc file.
439        This procedure automatically works also for grid.*.nc files that do not
440        have any record dimension.
441    o verification/cpl_aim+ocn:
442      - generate new reference output on baudelaire (gfortran, mpich2) (previously
443        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
444    o pkg/obcs/obcs_calc_stevens.F:
445      - add code for northern and southern boundaries.
446      - reorder some loops to save some operations and so that drFBar can be scalar
447    o model/src:
448      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
449        truncation) and add diagnostics for Adams-Bashforth tendency increment.
450      - update test-exp. AD output:
451        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
452      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
453        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
454        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
455        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
456        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
457        tutorial_plume_on_slope.
458    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
459      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
460      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
461      does not even come with an F77 compiler anymore, this should not be
462      a limitation
463    
464    checkpoint63e (2011/11/06)
465    o pkg/seaice adjoint of LSR:
466      - substantially rework STORE dirs.
467      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
468        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
469        and only perform SOLV_MAX_FIXED adjoint iters.
470        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
471        always goes to same record, meaning that the last forward field will be
472        the one used in the adjoint - an approximation.
473      - now produces non-zero LSR-related gradients, and acceptable gradients for
474        An's zonal (x-z) test case (to be checked in)
475      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
476        (but these are screwed up by the thermodynamics in the first place);
477        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
478        output_adm.txt also reflects changes to seaice_lsr
479      - global_ocean.cs32x15:
480        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
481          (output_adm.seaice.txt was updated)
482        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
483          (output_adm.seaice_dynmix.txt)
484    o test-exp. exp4+stevens:
485      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
486    o pkg/seaice (lsr solver):
487      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
488        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
489      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
490      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
491        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
492      - compute (with new S/R) and print initial (+ free-driff sol. if available)
493        and final residual of linearised system.
494    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
495      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
496    o pkg/obcs: Stevens BCs (still only for east and west)
497      - fix Stevens BCs by using intermediate velocities of previous
498        time step as "baroclinic" contribution rather velocity of one grid cell
499        inside the boundaries; more consistent but makes the entire treatment
500        more complicated, requires new pickup files and two new S/Rs:
501        obcs_copy_uv_n and obcs_save_uv_n
502        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
503        (undefined by default)
504      - silently move computation of some grid factors into separate loops to
505        save some recomputations
506      - add a hack for non-linear free surface
507      - add a verification experiment to exp4 that tests this code
508    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
509    
510    checkpoint63d (2011/10/25)
511    o pkg/obcs + seaice-dynamics:
512      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
513        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
514        values (consistent with an implicit method).
515      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
516        return to older implementation (same results as before); note that none of
517        the "experimental" OBCS_SEAICE options are implemented in the new version.
518      - switch test exp. seaice_obcs to use new version (update output).
519    o pkg/seaice:
520      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
521      - add parenthesis in Water-Ice drag calculations (evp & lsr);
522      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
523        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
524      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
525        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
526    o pkg/layers:
527      - Include potential density as new coordinate (Thanks to David Munday)
528    o pkg/dic:
529      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
530        carbonate computation/output to CALC_PCO2_APPROX
531    o pkg/generic_advdiff
532      - make TAF generate code that vectorizes:
533        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
534    o model/src:
535      - improve vectorization also for adjoint code of
536        solve_tridiagonal and solve_pentadiagonal. As this requires up to
537        5 new 3D-fields, this code is only turned on for the combination of
538        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
539        for singular matrix check (only for TARGET_NEC_SX).
540      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
541        ALLOW_AUTODIFF. This flag now needs to be set outside of
542        solve_tri/pentadiagonal.F
543    o pkg/exf:
544      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
545        optional namelist EXF_NML_OBCS).
546      - add many debug-print (to trace down where pkg/cal error msg comes from)
547    o pkg/mom_vecinv/mom_vi_hdissip.F
548      - rearrange loops so that vectorization is improved and in particular
549        the adjoint routine vectorizes. The code is a little longer now, but I
550        think easier to read.
551        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
552    o pkg/seaice:
553      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
554    o pkg/exch2:
555      - alternative code (without tile x tile matrix) for cumulated (global) sum;
556        used as default; keep using matrix version in adjustment.cs-32x32x1.
557    o tools/build_options:
558      - after merging some MPI and/or multi-threads specific optfiles so that
559        the modified default optfile support both built (using genmake2 -mpi
560        for the MPI built, using genmake2 -omp for OpenMP built),
561        move now obsolete optfiles to tools/build_options/unsupported/
562       (add copy of email sent to support list in doc/optfiles_changes.txt)
563    
564    checkpoint63c (2011/09/28)
565    o pkg/ebm:
566      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
567        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
568    o pkg/seaice (SItracer pickup)
569    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
570      To be done:
571      - thorough testing of missing fields in S/R seaice_read_pickup
572      - thorough matching between generic tracers and specific fields used
573        (e.g. volume-weighted age, area-weighted age, salinity, ...)
574    o pkg/grdchk:
575      - all procs calculate and print finite-difference gradient (for testreport)
576      - change description output used by testreport;
577      - AD testing: also compare and report Finite-difference gradient;
578        => update all output_adm*.txt
579    o test exp. global_ocean_ebm:
580      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
581        and turn on exactConserve; update (fwd) output.
582    o pkg/seaice (LSR):
583      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
584      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
585        * identical results with non-CS topology (but save up to half of EXCH calls)
586        * no much changes in cs-32 verification tests since no ice at face edges
587         (differences due to convergence criteria, since nb of iterations changed)
588        * expect some differences on lat-lon-cap grid.
589        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
590    o pkg/exch2:
591      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
592        many tiles); until alternative coding is added, just add a stop.
593    o pkg/kpp:
594      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
595        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
596    o optfiles:
597      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
598        into corresponding standard one, which now support different build:
599        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
600      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
601    o pkg/obcs (seaice):
602      - add missing EXCH for uIce,vIce after applying OBCS;
603      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
604        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
605        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
606      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
607      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
608        and eedata.mth for MPI and mutlti-threaded testing.
609    o pkg/flt:
610      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
611      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
612      - fix pickup and trajectories + profiles output with multi-threads;
613      - add parameter to select group of fields to write along trajectory and
614        profile (default unchanged);
615      - only call PORT_RAND* function when flt_noise <> 0;
616      - add multi-threaded test for verification exp. flt_example.
617    o eesupp/src:
618      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
619      - USE_OMP_THREADING: check that number of threads (from eedata) matches
620        actual number (from env.var. setting).
621    o pkg/ebm:
622      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
623      - add multi-threaded test for verification exp. global_ocean_ebm
624    
625    checkpoint63b (2011/08/29)
626    o pkg/ebm:
627      - fix sign of runoff;
628      - update directly forcing fields (Qnet,EmPmR) to use standard
629        external_forcing_surf.F (remove ebm_forcing_surf.F);
630      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
631      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
632        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
633      - update global_ocean_ebm parameters file data and update output (fwd+ad).
634    o verification/matrix_example:
635      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
636        MPI and mutlti-threaded testing.
637    o pkg/matrix:
638      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
639      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
640      - fix for multi-threaded (remove DATA statement);
641      - use standard DIFFERENT_MULTIPLE function;
642      - add MATRIX_OPTIONS.h
643    o verification/matrix_example:
644       To allow to split the domain in several tiles, change the domain size
645        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
646        Western side) of land points.
647    o (*_)write_pickup:
648      - fix few bugs in mypackage_read/write_pickup.F
649      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
650        array of length 1 (was caught by compiler syntax-check).
651    o pkg/diagnostics (velocity potential solver):
652      - fix initialisation of main diagonal matrix (for overlap values)
653    o tools/build_options:
654      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
655        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
656      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
657        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
658        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
659        and use "-devel" testreport option for standard testing on baudelaire.
660    o pkg/grdchk:
661      - Assume that all gradient-check position are within the same tile
662        corresponding to global indices (iGloTile,jGloTile) and that
663        positions (i,j indices or nbeg) are local to this tile;
664      - set tile local-indices and proc. number according to tile global-indices;
665      - remove grdchkwhichproc from namelist (retired param);
666      - send adjoint gradient to all procs so that all procs print it to STDOUT;
667      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
668    o adding package bbl (Bottom Boundary Layer)
669      description in MITgcm/pkg/bbl/bbl_description.tex
670      example/test experiment in MITgcm_contrib/bbl
671    o adjoint verifications
672      - changed 5 experiments to multi-tiles
673        * global_ocean.90x40x15
674        * obcs_ctrl
675        * offline_exf_seaice
676        * tutorial_dic_adjoffline
677        * tutorial_tracer_adjsens
678        changed reference output for those that crossed tile boundaries
679        (changed choices of gradient check positions)
680      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
681      - temporary bug fix in grdchk_loc.F for obcs
682    o genmake2 & testreport
683      - add target "obj" (just for OBJFILES files) to Makefile;
684      - add option to specify FEXTRAFLAGS on command line.
685    o pkg/mypackage:
686      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
687    
688    checkpoint63a (2011/08/02)
689    o pkg/diagnostics (velocity potential):
690      - fix velocity-potential calculation when using OBCS: balance net inflow
691        at each level (new S/R OBCS_DIAG_BALANCE).
692      - fix some of the problems with OBCS in stream-function calculation.
693    o pkg/exf/exf_readparms.F
694      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
695        EXF_NML_OBCS) more consistent, so that you need not have these lists
696        in data.exf when they are not used.
697    o optim/optim_readdata.F:
698      - add some output about obcs variables that might help debugging
699      - add a check about nvarlength
700    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
701    o pkg/diagnostics (velocity potential):
702      - fix mask for OBCS (still problems in stream-function with OBCS);
703      - add specific parameter (default = main code CG2D params) for solver;
704      - in case of poor convergence, use solution corresponding to lowest residual.
705    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
706      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
707      and should be avoided where possible.
708    o model/src (rStar):
709      - include r* effect on reference-state (PhiRef) in totPhiHyd
710        (so that it's really the potential anomaly at the cell center);
711        affect solution only if z* with full pressure in EOS.
712      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
713        update output (because of z* in totPhiHyd and viscA4 changes);
714      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
715        @ constant r) until interpolation at constant r is implemented.
716    o pkg/diagnostics
717      - fix RCENTER diagnostics in case cell center is not at interface middle
718    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
719      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
720      that THETA and SALT are "conservative temperature" and "absolute
721      salinity"
722    o pkg/ctrl
723      - fix computation of endrec in s/r ctrl_init_rec
724      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
725    o pkg/seaice/seaice_growth.F
726      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
727        remove then obsolete STORE directives
728      - fix STORE directives for tice and tices, so that only the
729        appropriate part of the fields are stored (and not the entire
730        field); update global_ocean.cs32x15.seaice AD output.
731      - cosmetic changes: adjust CPP flags and indentation for better
732        legibilty
733    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
734      Chris Wilson)
735    o pkg/gmredi:
736       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
737       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
738    
739    checkpoint63  (2011/07/11)
740    o pkg/exch2:
741     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
742     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
743       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
744       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
745    o pkg/diagnostics:
746     - deal with pairs of post-processed diags which are computed together; in
747       particular, re-order list of diags within 1 file to save 2nd computation.
748     - add S/R to compute velocity stream-function (called after velocity-potential
749       calculation) from divergence free transport -> new diagnostics "PsiVEL".
750     - add parameter to select grid-point location where PsiVEL == 0.
751    o eesupp/src:
752       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
753       (specific S/R needed with exch2 topology - for now, just print an error msg)
754    o pkg/shelfice
755     - Implement friction velocity-dependent transfer coefficients following
756       Holland and Jenkins, JPO, 1999
757       Original code by M. Losch with small modifs.
758       Enable with CPP option SHI_ALLOW_GAMMAFRICT
759       and runtime flag SHELFICEuseGammaFrict
760    o verification lab_sea & global_ocean.cs32x15:
761     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
762       does not miss some dependencies (but is slower) and also works with many files
763       (default makedepend limitation for AD built).
764     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
765    o pkg/diagnostics:
766     - add run-time parameter "useMissingValue" (def=False) to fill land-point
767        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
768       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
769     - Extend the use of "missing_value" setting from data.diagnostics for the case
770       of counter-diagnostics (where fraction-weight is zero). This applies both to
771       MNC and MDS output files.
772    o pkg/seaice/seaice_growth.F:
773      - add 'a priori' cap of latent heat flux based on actual mass considerations
774        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
775        non-legacy seaice_solve4temp.
776      - add diagnostic of the residual sublimation freshwater flux (the freshwater
777        flux taken from the ocean if the total actual latent heat fluxes exceed
778        the maximum)
779      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
780       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
781      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
782       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
783      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
784      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
785    o verification 1D_ocean_ice_column:
786       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
787       update results
788    o pkg/diagnostics:
789     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
790       which are not filled-up but computed from other diags ; In this case, the mate
791       diag points to the primary (filled-up) diag to used for post processing.
792     - Update Velocity-potential computation using post-processed diag framework.
793     ==> Change the ordering of fields and time-periods in MDS output file
794       when using periodic averaging: now writes one time record with the full set
795       of fields for this time period, then the next time reccord (it used to be
796       one field with the full set of time records then the next field).
797         Note: this is now similar to NetCDF (MNC) output file. <==
798    
799    checkpoint62z (2011/06/21)
800    o adjoint monitor:
801     - Add adjoint monitor output for packages exf, seaice
802       and update relevant testreport output
803    o pkg/seaice:
804     - re-order diags inits so that they appear in order in available_diagnostics.log
805     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
806       area/heff/hsnow preceeding thermodynamic growth/melt.
807     - modified diag: SIdA; output actual effect, as the description states.
808     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
809     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
810       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
811        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
812     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
813     - added diagnostics for seaice generic tracers (SItr*).
814     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
815     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
816     I. Fenty: 18-Jun-2011:
817     Minor changes to seaice package:
818     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
819        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
820       - Differentiated "regularization variables" from "floor variables"
821        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
822        * hiceMin became SEAICE_hice_reg (old hiceMin)
823          (with _reg meaning regularization variable)
824       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
825        so as to ensure energy conservation when going between phases
826      - A22 was not used anywhere
827     2) Changed regularization procedure for heffActual and hsnowActual to ensure
828        well-boundedness and smooth adjoint in seaice_growth.F
829     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
830        because the old regularization always set heffActual >= 0.05 cm
831     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
832        on AREA when HEFF > 0.
833      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
834        requiring that DISABLE_AREA_FLOOR *not* be defined
835     Affected verifications:
836      - 1D_ocean_ice_column (output.txt output_adm.txt)
837      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
838    o pkg/diagnostics:
839      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
840      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
841        (was _RL, now integer) with option = 0 to retrieve all levels.
842      - add pieces of code to compute velocity potential at each level (new diagnostics
843        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
844        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
845      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
846        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
847        and in diagnostics_fract_fill.F (do not need a valid pointer for the
848        diagnostics counter-mate); check that definition of counter-diagnostic
849        includes a valid counter-mate (in diagnostics_set_levels.F).
850    o model/src (rStar):
851      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
852        affect solution only if z* with full pressure in EOS;
853        update output of test-exp global_ocean.90x40x15.
854    o pkg/seaice:
855      - introduce siEps=1e-5 parameter
856      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
857      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
858      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
859        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
860        as well as ice cover age and ridging index (attached to AREA).
861        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
862        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
863        Up to SItrMaxNum=3 tracers can be used simultaneously.
864    o pkg/salt_plume:
865      -introduce SPsalFRAC run time parameter that sets the fraction of the
866       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
867       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
868    o model debug options:
869      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
870        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
871      - Refine debug-msg printing selection (3 new levels):
872        debugMode  : controls printing of debug messages (sequence of S/R calls).
873        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
874         debLevZero =  0 ; /* level of disabled aux. msg printing */
875         debLevA =  1 ; /* level of minimum  aux. msg printing */
876         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
877         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
878         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
879         debLevE =  5 ; /* level of extensive debug printing */
880        New debugLevel default: with default debugMode value (=F),
881          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
882          and if debugMode=T, default debugLevel = 4 (debLevD).
883        Relation with previous settings:
884         debLevB (=2) corresponds to former debLevA (=1)
885         debLevD (=4) corresponds to former debLevB (=2)
886        Note:
887         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
888         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
889            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
890      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
891        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
892    o pkg/obcs:
893      - change OBCSfixTopo default from True to False (should not change the results);
894        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
895    o pkg/thsice:
896      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
897        2nd layer seaice sublimation (unlikely to happen)
898      - use Interior mask for OBCS in thsice_advection.F (similar to what is
899        done in gad_advection & seaice_advection).
900    o adjoint:
901      bug fix spotted by Gael Forget:
902      seaice_advection and thsice_advection still had
903      legacy CPP options to avoid CS corner updates for adjoint
904    o pkg/seaice:
905      => Change some of the defaults (2011/05/29):
906         - change SEAICEuseFluxForm default (from False to True)
907         - change DIFF1 default (from 0.004 m/s to 0. m/s)
908         And print warnings if DIFF1 is not set in data.seaice and centered
909          avection scheme is used without any diffusion.
910      also:
911      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
912      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
913      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
914        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
915        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
916      update results of test exp.:
917         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
918             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
919             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
920         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
921         seaice_obcs: output (SEAICEuseFluxForm=T)
922      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
923          for standard fwd & AD lab_sea tests (to keep the same output).
924    o pkg/seaice/seaice_growth.F:
925      - use Ian Fenty's capping formulas for actual ice
926      thickness thoughout EVOLUTION branch.
927      - put treatment pathological case #2) in CPP brackets
928      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
929      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
930    o pkg/seaice:
931      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
932      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
933      also pass fac as a param, which can be 1. (to update the tendency
934      field) or the time step (to update the field itself).
935      - seaice_advdiff.F: for multidim, call seaice_diffusion with
936      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
937      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
938      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
939      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
940    o pkg/seaice:
941      diffusion with centered advection scheme (diffus.F & advect.F):
942      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
943        to just compute the laplacian of input-field.
944      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
945      - fix flux-form version in diffus.F to conserve tracer.
946      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
947       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
948    
949    checkpoint62y (2011/05/26)
950    o pkg/seaice:
951     - seaice_growth.F : in EVOLUTION branch, always include
952       a_QSWbyATM_cover in qnet (as it should be).
953     - verification/global_ocean.cs32x15 : update results accordingly
954       (output.seaice.txt output_adm.seaice.txt).
955    o pkg/seaice + obcs:
956     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
957       equivalent of assuming no tracer gradient outside the OB region.
958       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
959     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
960       after changes above);
961     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
962       only at OB location (instead of over a band of OLx width).
963    o pkg/seaice:
964     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
965       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
966    o pkg/obcs:
967      - split header file "OBCS.h" into 4 separated files:
968        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
969       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
970         (contain no conditional statement which depends on OBCS options).
971      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
972        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
973    o ctrl, cost, grdchk & autodiff pkgs:
974      - make options file more standard (like other {PKG}_OPTIONS.h file but
975        with AD_CONFIG.h); clean-up some of the included header files.
976    o pkg/obcs:
977      - do not mask tracer when applying OB (tracer == 0 could generate problems)
978      - apply tracer OB values to tracer field only at OB location (instead of
979        over a band of OLx width)
980      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
981      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
982        obcs_apply_tloc.F & obcs_apply_sloc.F
983    o obcs in model/src:
984      - call OBCS_APPLY_W only if NonHydrostatic.
985      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
986      - reset dEtaHdt and wVel to zero outside OB interior region ;
987      - leave tracer unchanged outside OB interior region: This has no effect
988        on the solution but just to prevent unrealistic tracer value outside OB.
989      - zero out velocity outside OB interior region: This has no effect on
990        the solution but just to prevent unrealistic velocity outside OB.
991    o obcs and non-lin free-surf:
992       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
993       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
994       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
995       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
996       update results of test-exp. exp4(nlfs).
997    o exp4 (nlfs) test-exp:
998       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
999       with NonLin-FreeSurf); update output.nlfs.txt
1000  o obcs and 2d/3d solver norm:  o obcs and 2d/3d solver norm:
1001     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1002     and outside OB interior region (will allow to place OB further inside the     and outside OB interior region (will allow to place OB further inside the
1003     domain). Depending on the domain, can affects cg2d-Norm (previous     domain). Depending on the domain, can affects cg2d-Norm (previous
1004     cancelation outside OB was only partial), e.g. in exp4 & obcs_ctrl,     cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1005     and cg3d-Norm (previous Norm was computed before canceling OB terms),     and cg3d-Norm (previous Norm was computed before canceling OB terms),
1006     e.g. in tutorial_plume_on_slope.     e.g. in tutorial_plume_on_slope.
1007    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
# Line 20  o pkg/shelfice/shelfice_init_fixed.F Line 1013  o pkg/shelfice/shelfice_init_fixed.F
1013    fix CPP-flag combinations    fix CPP-flag combinations
1014  o pkg/seaice: Merge iceage code of Pierre Rampal  o pkg/seaice: Merge iceage code of Pierre Rampal
1015    * update/change/correct ice age calculations    * update/change/correct ice age calculations
1016    * add age updates for pathological cases    * add age updates for pathological cases
1017    Probably needs more testing...    Probably needs more testing...
1018    
1019  checkpoint62x (2011/05/13)  checkpoint62x (2011/05/13)
Legend:
Removed from v.1.1435  
changed lines
  Added in v.1.1605
  ViewVC Help
Powered by ViewVC 1.1.22