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revision 1.1418 by jmc, Thu Apr 28 23:26:39 2011 UTC revision 1.1600 by gforget, Thu Feb 16 01:40:04 2012 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    o pkg/seaice: overhaul of seaice_summary.F after jan 2012 clean-up of seaice_growth.F etc.
7    o pkg/seaice SItracer :  added run time params, and allow coupling to ocn salinity.
8    o pkg/seaice: remove (almost) all divisions by constants within loops
9      in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
10      results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
11      those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
12      output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
13    o pkg/seaice :
14      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.
15      1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
16      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
17      - add permanent SItflux diag that corresponds to TFLUX but includes
18      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
19      - allow activation/testing of a fix for suspected missing term in
20      ocn-ice heat budget (to be confirmed). To test this, you want to
21      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
22      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
23      - no change in results, fwd or ad.
24    o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.
25      - switch to variable freezing point.
26           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
27      - bug fix : the sublimation term that was missing is now activated.
28           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
29      - bug fix : flooding sign term for SIsal0.NE.0.
30           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
31    o pkg/seaice:
32      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
33     is now the default, and the old default constant freezing point is recovered with
34     SEAICE_tempFrz0    = -1.96,
35     SEAICE_dTempFrz_dS = 0.,
36      - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.
37      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
38      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
39     activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.
40      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
41     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
42      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
43     seaice_growth r149 for legacy branch (no results change).
44      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).
45      - results did not change except for global_ocean.cs32x15, mostly due to the switch
46      to variable freezing point (see above item for detail).
47    o pkg/thsice:
48      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
49        seawater freezing in thsice_calc_thickn (not used).
50    o pkg/seaice: turbulent flux term specification via run time params.
51      - replace CPP switches with run time switches to facilitate testing
52      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
53      - added runtime parameter : SEAICEturbFluxFormula
54      - move Mcphee constants to SEAICE_PARAMS.h
55      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
56        SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
57        seaice_summary call (moved to seaice_init_fixed)
58      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
59        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
60      - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
61      - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
62      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
63            CPP switch, same computation as before for the different options.
64      - change results at the truncation level.
65    o pkg/seaice:
66      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
67        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
68        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
69      - update verification/*/input*/data.seaice:
70        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
71        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
72        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
73        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
74    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
75      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
76        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
77        difference in results only due to machine truncation.
78      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
79        MaykutPolySatVap; keep MIN_LWDOWN.
80      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
81      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
82        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
83    o pkg/salt_plume:
84      - isolate saltPlumeFlux array exch into a specific S/R called from
85        do_oceanic_phys.F
86      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
87    o verification:
88      - move untested set-up to MITgcm_contrib/verification_other.
89    o pkg/seaice:
90      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
91    o pkg/seaice:
92      - seaice_solve4temp.F (keeping results unchanged):
93        * add 2 future run-time params to select which saturation vapor pressure
94          formula is used and how post-iteration fluxes are set.
95          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
96        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
97          the linearized expression to stay consistent with tsurf finding.
98      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
99        can be < 0.
100    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
101      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
102        conductive heat flux F_c , and add it explicitly when updating tsurf as
103        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
104        so that now F_ia has a consistent meaning through the entire routine.
105        This causes differences at truncation level: update output of fwd exp.
106        global_ocean.cs32x15.seaice.
107    o pkg/seaice:
108      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
109        of arrays, sign/direction of fluxes; no effect on results.
110      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
111        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
112        note: this should have been done before changing celsius2K default.
113      - to keep results unchanged, add back old value of celsius2K in verification
114        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
115      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
116        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
117        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
118        freezing temp is consistent with value in seaice_growth.F ; this causes
119        differences at machine truncation level: update lab_sea AD output (3/4).
120    o pkg/seaice:
121      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
122        and climsst/sss even when using seaice (to prevent calculation that might
123        use SST on land); does not affect any verification exp.
124      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
125        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
126    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
127      over land (non-legacy code)
128    o vectorize salt_plume package:
129      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
130      - this code computes plumebk everywhere (also over land), thus requires
131        code to avoid divisions by zero and catch the case of kLev=Nr.
132      - efficiency of salt_plume_frac is still sub-optimal
133    o tools (genmake2):
134      - fix makefile NAME specification (option: -makefile NAME) by adding
135        "-f $MAKEFILE" in few places where it was missing including makedepend
136        command (contribution from Paul).
137    
138    checkpoint63i (2012/01/24)
139    o model/src:
140      - add factorized versions of some EOS code to find_rho.F,
141        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
142    o model/src:
143      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
144      - change default celsius2K from 273.16 to 273.15
145      - to keep results unchanged, add back old value of celsius2K in verification
146        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
147         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
148    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
149      to make TAF generate vectorizable code
150    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
151       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
152       have flags that do this more efficiently.
153    o pkg/diagnostics/diagstats_calc.F
154      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
155    o pkg/obcs (with exch2):
156      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
157        and remove code (in obcs_readparms.F) which was based on EXCH of indices
158        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
159    o pkg/exf and seaice exp:
160      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
161        so that switching off area & heff advection flags does not affect results.
162      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
163      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
164        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
165        results of verification experiments: 1D_ocean_ice_column(fwd),
166        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
167        and offline_exf_seaice (all 4).
168    o pkg/seaice:
169      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
170        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
171      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
172        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
173        not multi-dim advection;
174      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
175        SHORTWAVE_HEATING #undef.
176    o optim: make Makefile more robust (?)
177    o pkg/obcs:
178      * fix treatment of obcs_read_pickup for TAF
179    o pkg/shelfice:
180      * add missing initialisation of num_shifwflx
181      * new adjoint verification exp. for isomip
182      * change Prandtl and Schmidt numbers from generic formulations
183        (in terms of model diffus. and visc.) to separate runtime
184        parameters, with Holland and Jenkins (1999) default values.
185    o pkg/exf (interpolation):
186      - extended input field (2 rows) near the N & S poles:
187        * fill in with the symetric value (when even Nb of data in longitude)
188        * add average value at the poles only for scalar quantities ; for vector
189          component interpolation, skip the averaging and keep duplicated values,
190          unless the 2 components have same location (uvInterp=T) in which case
191          interpolate the 2 components together using S/R EXF_INTERP_UV.
192      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
193        together: this allows to account properly for local orientation when
194        averaging at N & S pole.
195      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
196        exf-interpolation near N & S poles. Undef by default.
197      - add debug check/print on 1rst iter if debugLevel >=2.
198    o pkg/exf:
199      - change masking flags definition (no longer "parameter"), put them in
200        common block and set them in S/R EXF_INIT_FIXED.
201      - change recognized masking flag from s,u,v to c,w,s since the mask
202        to use (maskC,W,S) depends on position on model grid and has little to
203        do with scalar/vector difference; fix masking if using P-coordinates.
204      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
205        and update results of exp. global_with_exf (x2).
206      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
207    o pkg/obcs
208      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
209    o pkg/exf (interpolation):
210      - assume periodicity in X only if input field cover full longitude range.
211      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
212        and should vectorise).
213      - fix input lat of the 2 added row (in case we provide N.pole data).
214    
215    checkpoint63h (2011/12/30)
216    o pkg/seaice:
217      - change declaration of UVM from _RL to _RS in order to get B-grid
218        uIce,vIce monitor when _RS = real*4
219    o pkg/offline:
220      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
221      - compute vertical velocity if not read from file (switch on exactConserv
222        & staggerTimeStep);
223      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
224    o verification:
225      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
226        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
227        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
228      - update output of exp. global_ocean.cs32x15.viscA4 after changing
229        grid-file angles (used here for coriolis-3d);
230      - remove (or gzip) few files not needed to run fizhi-cs experiments.
231    o pkg/exf (vector interpolation):
232      - rotate vector component toward local grid-axis orientation using grid-angles
233        (stored in GRID.h) instead of locally computed rotation angle; keep old code
234        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
235    o pkg/seaice:
236      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
237        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
238    o pkg/PKG_OPTIONS.h files:
239      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
240        outside of the #ifdef ALLOW_THISPKG / #endif block.
241      - update verification/*/code/PKG_OPTIONS.h files.
242    o add a verification experiment (offline_exf_seaice/input.seaice) that test
243      the B-grid LSOR solver
244    o pkg/seaice: sort out emissivity and long wave radiation step 2:
245      - add emissivity for snow and ice as new run-time parameters
246        (unfortunately) that default to the corresponding exf values; this
247        changes results in most verification experiments so that for backward
248        compatibility these parameter have to be set explicitly to inconsistent
249        values (ugly);
250      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
251        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
252        until we agree how to handle this bug properly
253    o pkg/exf (interpolation):
254      - add a set of run-time param ({inputfield}_interpMethod), one for
255        each interpolated input field, to select the interpolation method
256        with a value of zero switching off the interpolation;
257      - print interpolation parameters to standard output;
258      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
259        (to use instead runoff_interpMethod=0 in data.exf).
260      - simplify default setting of interpolation parameters (for all fields,
261        set position to match model grid cell-center position, leading to trivial
262        interpolation in case of regular Lat-Lon grid) and fix for the case of
263        non-uniform delY.
264    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
265       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
266       this factor is absolutely required, because the lw exitance (= out-going
267       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
268       where the reflectivity rho = 1-emissivity for conservation reasons. Once
269       this is established, we can remove the CPP-Flag (if we want to).
270    o pkg/seaice:
271      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
272        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
273      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
274        what the name implies (and not emissivity*BoltzmannConstant), this means
275        the old default value of 5.5e-8 now means
276        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
277        S/R exf_readparms
278      - FV-discretization of the B-grid LSOR solver, turn on with
279        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
280        of the calling routine dynsolver, so that B and C-grid code look a
281        little more alike.
282      - fix index bugs in ostres.F (B-grid code)
283    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
284    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
285      default for SEAICE_emissivity, if useEXF; requires setting a wrong
286      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
287      backward compatiblity
288    o model/src: use sigmaR in calc_ivdc
289    
290    checkpoint63g (2011/12/16)
291    o pkg/seaice/seaice_growth.F:
292      fix heat conservation of the coupled ocean-seaice system.
293      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
294      solid vs liquid water treatment is resolved via QNET.
295    o pkg/seaice/seaice_growth.F:
296      add missing term for sublimation in saltFlux, which was breaking conservation.
297    o pkg/seaice/seaice_model.F:
298      Remove this patholigical case treatment in evolution branch,
299      where it is un-necessary and breaks conservation.
300      Update global_ocean.cs32x15/results accordingly for
301      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
302    o model/src:
303      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
304      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
305    o pkg/obcs:
306      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
307      tendency for temperature and salinity that is then applied to update
308      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
309      horizontal advection and diffusion contributions on the boundary (in
310      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
311      removing the mask in S/R timestep_tracer. The advantage of this approach is
312      that the updated tracer values include contributions from the surface
313      forcing and vertical diffusion.
314      This modification changes exp4.stevens because of vertical diffusion.
315    o model/src:
316      change non-curvilinear grid setting to also work with exch2 + blank tiles:
317      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
318        face dimensions.
319      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
320        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
321        and INI_SPHERICAL_POLAR_GRID.
322      change test-experiment global_ocean.90x40x15:
323      - split the domain in many more tiles (9x4 tiles of 10x10 each);
324      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
325      - update results of both test (std & dwnslp).
326    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
327       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
328    o model/src:
329      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
330        and fix initialisation when using sigma-coords.
331    o model/src:
332     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
333       to their current value at the beginning of forward_step.F": add a new run-time
334       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
335     - set doResetHFactors=T in the following test exp:
336        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
337        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
338        and tutorial_global_oce_in_p (nonLinFS in p)
339    o pkg/ecco
340      - added IES cost term
341    o verification/advect_xz
342      - scale down the depth by 1/100 (from 200 km to just 2.km)
343      - add secondary test using divergent flow, r-star and implicit vertical advection.
344      - add note (check_conserve_TS.txt) and matlab script to check global
345        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
346    o pkg/rbcs:
347      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
348    o pkg/obcs (Stevens BCs):
349      - fix various problems in the phase speed computations of the Stevens
350        boundary conditions:
351        - sign error for western and southern boundaries,
352        - time tendencies were underestimated by factor of dTracerLev and some just
353          zero (for multidim advection schemes) -> now estimate time tendencies
354          from difference between previous (n) time level and the one before (n-1);
355          this requires storing a field per tracer per boundary, also in the pickup
356          files.
357        - replace deltaTmom in cflMer/Zon computation with dTracerLev
358        - set default phase velocity to cflMer/Zon
359      - update verification experiment exp4.stevens
360    o pkg/generic_advdiff (implicit_r):
361      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
362        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
363      - fix implicit vertical diffusion or advection with NonLin FreeSurf
364        (was using current recip_hFacC instead of future recip_hFacC): set future
365        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
366        solver S/R ;
367      - fill diagnostics of vertical advective fluxes (computed from tendency)
368        when using implicit vert. advection;
369      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
370         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
371         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
372         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
373    o pkg/diagnostics:
374      - add diags for T & S tendency which goes through Adams-Bashforth.
375    
376    checkpoint63f (2011/11/30)
377    o pkg/obcs/obcs_calc_stevens.F:
378      - join some loops to reduce number of if-statements
379      - fix a bug in code for northern and southern boundaries.
380    o pkg/seaice/seaice_init_varia.F
381      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
382        caused zero ice-velocities for the B-grid code
383    o pkg/seaice/seaice_init_fixed.F
384      - fix a bug in the initialisation of the second metric terms
385        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
386      - this affects all seaice configurations with useCurviLinearGrid = .true.
387        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
388        = .true. (default)
389      - the only verification experiment affected is global_ocean.cs32x15:
390        icedyn, seaice, and seaice_dynmix (AD)
391    o pkg/thsice/thsice_diagnostics_state.F
392      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
393        not contain garbage that can lead to surprises in diagstats_calc.F
394    o model/src:
395      - move bi,bj loops inside INTEGR_CONTINUITY ;
396      - call INTEGR_CONTINUITY directly from forward_step.F
397        (previously called from momentum_correction_step.F)
398      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
399        forward_step.F and pkg/ecco/the_main_loop.F
400    o model/src/do_oceanic_phys.F:
401      - reset addMass to zero only if useICEFRONT ;
402      - separated k-loop for rhoInSitu calculation ;
403      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
404        and at constant T,S (= WdRHOdP);
405      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
406        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
407        transport of locally-referenced potential density);
408        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
409    o gluemnc:
410      - replace ncrcat with ncks when adding variables to *.glob.nc
411      - change the way variables without record dimensions are handled so that
412        files that have variables with and without record variables can be glued:
413        add a record dimension with a new unique name to be able to differentiate
414        between variable with and without a-prior record dimensions. Remove
415        this record dimension before adding the variable to the *.glob.nc file.
416        This procedure automatically works also for grid.*.nc files that do not
417        have any record dimension.
418    o verification/cpl_aim+ocn:
419      - generate new reference output on baudelaire (gfortran, mpich2) (previously
420        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
421    o pkg/obcs/obcs_calc_stevens.F:
422      - add code for northern and southern boundaries.
423      - reorder some loops to save some operations and so that drFBar can be scalar
424    o model/src:
425      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
426        truncation) and add diagnostics for Adams-Bashforth tendency increment.
427      - update test-exp. AD output:
428        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
429      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
430        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
431        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
432        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
433        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
434        tutorial_plume_on_slope.
435    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
436      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
437      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
438      does not even come with an F77 compiler anymore, this should not be
439      a limitation
440    
441    checkpoint63e (2011/11/06)
442    o pkg/seaice adjoint of LSR:
443      - substantially rework STORE dirs.
444      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
445        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
446        and only perform SOLV_MAX_FIXED adjoint iters.
447        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
448        always goes to same record, meaning that the last forward field will be
449        the one used in the adjoint - an approximation.
450      - now produces non-zero LSR-related gradients, and acceptable gradients for
451        An's zonal (x-z) test case (to be checked in)
452      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
453        (but these are screwed up by the thermodynamics in the first place);
454        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
455        output_adm.txt also reflects changes to seaice_lsr
456      - global_ocean.cs32x15:
457        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
458          (output_adm.seaice.txt was updated)
459        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
460          (output_adm.seaice_dynmix.txt)
461    o test-exp. exp4+stevens:
462      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
463    o pkg/seaice (lsr solver):
464      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
465        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
466      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
467      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
468        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
469      - compute (with new S/R) and print initial (+ free-driff sol. if available)
470        and final residual of linearised system.
471    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
472      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
473    o pkg/obcs: Stevens BCs (still only for east and west)
474      - fix Stevens BCs by using intermediate velocities of previous
475        time step as "baroclinic" contribution rather velocity of one grid cell
476        inside the boundaries; more consistent but makes the entire treatment
477        more complicated, requires new pickup files and two new S/Rs:
478        obcs_copy_uv_n and obcs_save_uv_n
479        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
480        (undefined by default)
481      - silently move computation of some grid factors into separate loops to
482        save some recomputations
483      - add a hack for non-linear free surface
484      - add a verification experiment to exp4 that tests this code
485    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
486    
487    checkpoint63d (2011/10/25)
488    o pkg/obcs + seaice-dynamics:
489      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
490        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
491        values (consistent with an implicit method).
492      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
493        return to older implementation (same results as before); note that none of
494        the "experimental" OBCS_SEAICE options are implemented in the new version.
495      - switch test exp. seaice_obcs to use new version (update output).
496    o pkg/seaice:
497      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
498      - add parenthesis in Water-Ice drag calculations (evp & lsr);
499      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
500        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
501      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
502        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
503    o pkg/layers:
504      - Include potential density as new coordinate (Thanks to David Munday)
505    o pkg/dic:
506      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
507        carbonate computation/output to CALC_PCO2_APPROX
508    o pkg/generic_advdiff
509      - make TAF generate code that vectorizes:
510        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
511    o model/src:
512      - improve vectorization also for adjoint code of
513        solve_tridiagonal and solve_pentadiagonal. As this requires up to
514        5 new 3D-fields, this code is only turned on for the combination of
515        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
516        for singular matrix check (only for TARGET_NEC_SX).
517      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
518        ALLOW_AUTODIFF. This flag now needs to be set outside of
519        solve_tri/pentadiagonal.F
520    o pkg/exf:
521      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
522        optional namelist EXF_NML_OBCS).
523      - add many debug-print (to trace down where pkg/cal error msg comes from)
524    o pkg/mom_vecinv/mom_vi_hdissip.F
525      - rearrange loops so that vectorization is improved and in particular
526        the adjoint routine vectorizes. The code is a little longer now, but I
527        think easier to read.
528        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
529    o pkg/seaice:
530      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
531    o pkg/exch2:
532      - alternative code (without tile x tile matrix) for cumulated (global) sum;
533        used as default; keep using matrix version in adjustment.cs-32x32x1.
534    o tools/build_options:
535      - after merging some MPI and/or multi-threads specific optfiles so that
536        the modified default optfile support both built (using genmake2 -mpi
537        for the MPI built, using genmake2 -omp for OpenMP built),
538        move now obsolete optfiles to tools/build_options/unsupported/
539       (add copy of email sent to support list in doc/optfiles_changes.txt)
540    
541    checkpoint63c (2011/09/28)
542    o pkg/ebm:
543      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
544        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
545    o pkg/seaice (SItracer pickup)
546    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
547      To be done:
548      - thorough testing of missing fields in S/R seaice_read_pickup
549      - thorough matching between generic tracers and specific fields used
550        (e.g. volume-weighted age, area-weighted age, salinity, ...)
551    o pkg/grdchk:
552      - all procs calculate and print finite-difference gradient (for testreport)
553      - change description output used by testreport;
554      - AD testing: also compare and report Finite-difference gradient;
555        => update all output_adm*.txt
556    o test exp. global_ocean_ebm:
557      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
558        and turn on exactConserve; update (fwd) output.
559    o pkg/seaice (LSR):
560      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
561      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
562        * identical results with non-CS topology (but save up to half of EXCH calls)
563        * no much changes in cs-32 verification tests since no ice at face edges
564         (differences due to convergence criteria, since nb of iterations changed)
565        * expect some differences on lat-lon-cap grid.
566        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
567    o pkg/exch2:
568      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
569        many tiles); until alternative coding is added, just add a stop.
570    o pkg/kpp:
571      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
572        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
573    o optfiles:
574      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
575        into corresponding standard one, which now support different build:
576        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
577      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
578    o pkg/obcs (seaice):
579      - add missing EXCH for uIce,vIce after applying OBCS;
580      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
581        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
582        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
583      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
584      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
585        and eedata.mth for MPI and mutlti-threaded testing.
586    o pkg/flt:
587      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
588      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
589      - fix pickup and trajectories + profiles output with multi-threads;
590      - add parameter to select group of fields to write along trajectory and
591        profile (default unchanged);
592      - only call PORT_RAND* function when flt_noise <> 0;
593      - add multi-threaded test for verification exp. flt_example.
594    o eesupp/src:
595      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
596      - USE_OMP_THREADING: check that number of threads (from eedata) matches
597        actual number (from env.var. setting).
598    o pkg/ebm:
599      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
600      - add multi-threaded test for verification exp. global_ocean_ebm
601    
602    checkpoint63b (2011/08/29)
603    o pkg/ebm:
604      - fix sign of runoff;
605      - update directly forcing fields (Qnet,EmPmR) to use standard
606        external_forcing_surf.F (remove ebm_forcing_surf.F);
607      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
608      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
609        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
610      - update global_ocean_ebm parameters file data and update output (fwd+ad).
611    o verification/matrix_example:
612      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
613        MPI and mutlti-threaded testing.
614    o pkg/matrix:
615      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
616      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
617      - fix for multi-threaded (remove DATA statement);
618      - use standard DIFFERENT_MULTIPLE function;
619      - add MATRIX_OPTIONS.h
620    o verification/matrix_example:
621       To allow to split the domain in several tiles, change the domain size
622        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
623        Western side) of land points.
624    o (*_)write_pickup:
625      - fix few bugs in mypackage_read/write_pickup.F
626      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
627        array of length 1 (was caught by compiler syntax-check).
628    o pkg/diagnostics (velocity potential solver):
629      - fix initialisation of main diagonal matrix (for overlap values)
630    o tools/build_options:
631      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
632        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
633      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
634        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
635        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
636        and use "-devel" testreport option for standard testing on baudelaire.
637    o pkg/grdchk:
638      - Assume that all gradient-check position are within the same tile
639        corresponding to global indices (iGloTile,jGloTile) and that
640        positions (i,j indices or nbeg) are local to this tile;
641      - set tile local-indices and proc. number according to tile global-indices;
642      - remove grdchkwhichproc from namelist (retired param);
643      - send adjoint gradient to all procs so that all procs print it to STDOUT;
644      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
645    o adding package bbl (Bottom Boundary Layer)
646      description in MITgcm/pkg/bbl/bbl_description.tex
647      example/test experiment in MITgcm_contrib/bbl
648    o adjoint verifications
649      - changed 5 experiments to multi-tiles
650        * global_ocean.90x40x15
651        * obcs_ctrl
652        * offline_exf_seaice
653        * tutorial_dic_adjoffline
654        * tutorial_tracer_adjsens
655        changed reference output for those that crossed tile boundaries
656        (changed choices of gradient check positions)
657      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
658      - temporary bug fix in grdchk_loc.F for obcs
659    o genmake2 & testreport
660      - add target "obj" (just for OBJFILES files) to Makefile;
661      - add option to specify FEXTRAFLAGS on command line.
662    o pkg/mypackage:
663      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
664    
665    checkpoint63a (2011/08/02)
666    o pkg/diagnostics (velocity potential):
667      - fix velocity-potential calculation when using OBCS: balance net inflow
668        at each level (new S/R OBCS_DIAG_BALANCE).
669      - fix some of the problems with OBCS in stream-function calculation.
670    o pkg/exf/exf_readparms.F
671      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
672        EXF_NML_OBCS) more consistent, so that you need not have these lists
673        in data.exf when they are not used.
674    o optim/optim_readdata.F:
675      - add some output about obcs variables that might help debugging
676      - add a check about nvarlength
677    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
678    o pkg/diagnostics (velocity potential):
679      - fix mask for OBCS (still problems in stream-function with OBCS);
680      - add specific parameter (default = main code CG2D params) for solver;
681      - in case of poor convergence, use solution corresponding to lowest residual.
682    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
683      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
684      and should be avoided where possible.
685    o model/src (rStar):
686      - include r* effect on reference-state (PhiRef) in totPhiHyd
687        (so that it's really the potential anomaly at the cell center);
688        affect solution only if z* with full pressure in EOS.
689      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
690        update output (because of z* in totPhiHyd and viscA4 changes);
691      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
692        @ constant r) until interpolation at constant r is implemented.
693    o pkg/diagnostics
694      - fix RCENTER diagnostics in case cell center is not at interface middle
695    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
696      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
697      that THETA and SALT are "conservative temperature" and "absolute
698      salinity"
699    o pkg/ctrl
700      - fix computation of endrec in s/r ctrl_init_rec
701      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
702    o pkg/seaice/seaice_growth.F
703      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
704        remove then obsolete STORE directives
705      - fix STORE directives for tice and tices, so that only the
706        appropriate part of the fields are stored (and not the entire
707        field); update global_ocean.cs32x15.seaice AD output.
708      - cosmetic changes: adjust CPP flags and indentation for better
709        legibilty
710    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
711      Chris Wilson)
712    o pkg/gmredi:
713       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
714       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
715    
716    checkpoint63  (2011/07/11)
717    o pkg/exch2:
718     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
719     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
720       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
721       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
722    o pkg/diagnostics:
723     - deal with pairs of post-processed diags which are computed together; in
724       particular, re-order list of diags within 1 file to save 2nd computation.
725     - add S/R to compute velocity stream-function (called after velocity-potential
726       calculation) from divergence free transport -> new diagnostics "PsiVEL".
727     - add parameter to select grid-point location where PsiVEL == 0.
728    o eesupp/src:
729       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
730       (specific S/R needed with exch2 topology - for now, just print an error msg)
731    o pkg/shelfice
732     - Implement friction velocity-dependent transfer coefficients following
733       Holland and Jenkins, JPO, 1999
734       Original code by M. Losch with small modifs.
735       Enable with CPP option SHI_ALLOW_GAMMAFRICT
736       and runtime flag SHELFICEuseGammaFrict
737    o verification lab_sea & global_ocean.cs32x15:
738     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
739       does not miss some dependencies (but is slower) and also works with many files
740       (default makedepend limitation for AD built).
741     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
742    o pkg/diagnostics:
743     - add run-time parameter "useMissingValue" (def=False) to fill land-point
744        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
745       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
746     - Extend the use of "missing_value" setting from data.diagnostics for the case
747       of counter-diagnostics (where fraction-weight is zero). This applies both to
748       MNC and MDS output files.
749    o pkg/seaice/seaice_growth.F:
750      - add 'a priori' cap of latent heat flux based on actual mass considerations
751        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
752        non-legacy seaice_solve4temp.
753      - add diagnostic of the residual sublimation freshwater flux (the freshwater
754        flux taken from the ocean if the total actual latent heat fluxes exceed
755        the maximum)
756      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
757       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
758      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
759       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
760      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
761      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
762    o verification 1D_ocean_ice_column:
763       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
764       update results
765    o pkg/diagnostics:
766     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
767       which are not filled-up but computed from other diags ; In this case, the mate
768       diag points to the primary (filled-up) diag to used for post processing.
769     - Update Velocity-potential computation using post-processed diag framework.
770     ==> Change the ordering of fields and time-periods in MDS output file
771       when using periodic averaging: now writes one time record with the full set
772       of fields for this time period, then the next time reccord (it used to be
773       one field with the full set of time records then the next field).
774         Note: this is now similar to NetCDF (MNC) output file. <==
775    
776    checkpoint62z (2011/06/21)
777    o adjoint monitor:
778     - Add adjoint monitor output for packages exf, seaice
779       and update relevant testreport output
780    o pkg/seaice:
781     - re-order diags inits so that they appear in order in available_diagnostics.log
782     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
783       area/heff/hsnow preceeding thermodynamic growth/melt.
784     - modified diag: SIdA; output actual effect, as the description states.
785     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
786     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
787       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
788        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
789     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
790     - added diagnostics for seaice generic tracers (SItr*).
791     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
792     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
793     I. Fenty: 18-Jun-2011:
794     Minor changes to seaice package:
795     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
796        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
797       - Differentiated "regularization variables" from "floor variables"
798        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
799        * hiceMin became SEAICE_hice_reg (old hiceMin)
800          (with _reg meaning regularization variable)
801       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
802        so as to ensure energy conservation when going between phases
803      - A22 was not used anywhere
804     2) Changed regularization procedure for heffActual and hsnowActual to ensure
805        well-boundedness and smooth adjoint in seaice_growth.F
806     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
807        because the old regularization always set heffActual >= 0.05 cm
808     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
809        on AREA when HEFF > 0.
810      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
811        requiring that DISABLE_AREA_FLOOR *not* be defined
812     Affected verifications:
813      - 1D_ocean_ice_column (output.txt output_adm.txt)
814      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
815    o pkg/diagnostics:
816      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
817      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
818        (was _RL, now integer) with option = 0 to retrieve all levels.
819      - add pieces of code to compute velocity potential at each level (new diagnostics
820        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
821        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
822      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
823        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
824        and in diagnostics_fract_fill.F (do not need a valid pointer for the
825        diagnostics counter-mate); check that definition of counter-diagnostic
826        includes a valid counter-mate (in diagnostics_set_levels.F).
827    o model/src (rStar):
828      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
829        affect solution only if z* with full pressure in EOS;
830        update output of test-exp global_ocean.90x40x15.
831    o pkg/seaice:
832      - introduce siEps=1e-5 parameter
833      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
834      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
835      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
836        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
837        as well as ice cover age and ridging index (attached to AREA).
838        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
839        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
840        Up to SItrMaxNum=3 tracers can be used simultaneously.
841    o pkg/salt_plume:
842      -introduce SPsalFRAC run time parameter that sets the fraction of the
843       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
844       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
845    o model debug options:
846      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
847        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
848      - Refine debug-msg printing selection (3 new levels):
849        debugMode  : controls printing of debug messages (sequence of S/R calls).
850        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
851         debLevZero =  0 ; /* level of disabled aux. msg printing */
852         debLevA =  1 ; /* level of minimum  aux. msg printing */
853         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
854         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
855         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
856         debLevE =  5 ; /* level of extensive debug printing */
857        New debugLevel default: with default debugMode value (=F),
858          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
859          and if debugMode=T, default debugLevel = 4 (debLevD).
860        Relation with previous settings:
861         debLevB (=2) corresponds to former debLevA (=1)
862         debLevD (=4) corresponds to former debLevB (=2)
863        Note:
864         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
865         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
866            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
867      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
868        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
869    o pkg/obcs:
870      - change OBCSfixTopo default from True to False (should not change the results);
871        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
872    o pkg/thsice:
873      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
874        2nd layer seaice sublimation (unlikely to happen)
875      - use Interior mask for OBCS in thsice_advection.F (similar to what is
876        done in gad_advection & seaice_advection).
877    o adjoint:
878      bug fix spotted by Gael Forget:
879      seaice_advection and thsice_advection still had
880      legacy CPP options to avoid CS corner updates for adjoint
881    o pkg/seaice:
882      => Change some of the defaults (2011/05/29):
883         - change SEAICEuseFluxForm default (from False to True)
884         - change DIFF1 default (from 0.004 m/s to 0. m/s)
885         And print warnings if DIFF1 is not set in data.seaice and centered
886          avection scheme is used without any diffusion.
887      also:
888      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
889      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
890      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
891        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
892        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
893      update results of test exp.:
894         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
895             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
896             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
897         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
898         seaice_obcs: output (SEAICEuseFluxForm=T)
899      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
900          for standard fwd & AD lab_sea tests (to keep the same output).
901    o pkg/seaice/seaice_growth.F:
902      - use Ian Fenty's capping formulas for actual ice
903      thickness thoughout EVOLUTION branch.
904      - put treatment pathological case #2) in CPP brackets
905      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
906      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
907    o pkg/seaice:
908      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
909      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
910      also pass fac as a param, which can be 1. (to update the tendency
911      field) or the time step (to update the field itself).
912      - seaice_advdiff.F: for multidim, call seaice_diffusion with
913      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
914      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
915      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
916      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
917    o pkg/seaice:
918      diffusion with centered advection scheme (diffus.F & advect.F):
919      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
920        to just compute the laplacian of input-field.
921      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
922      - fix flux-form version in diffus.F to conserve tracer.
923      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
924       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
925    
926    checkpoint62y (2011/05/26)
927    o pkg/seaice:
928     - seaice_growth.F : in EVOLUTION branch, always include
929       a_QSWbyATM_cover in qnet (as it should be).
930     - verification/global_ocean.cs32x15 : update results accordingly
931       (output.seaice.txt output_adm.seaice.txt).
932    o pkg/seaice + obcs:
933     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
934       equivalent of assuming no tracer gradient outside the OB region.
935       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
936     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
937       after changes above);
938     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
939       only at OB location (instead of over a band of OLx width).
940    o pkg/seaice:
941     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
942       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
943    o pkg/obcs:
944      - split header file "OBCS.h" into 4 separated files:
945        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
946       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
947         (contain no conditional statement which depends on OBCS options).
948      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
949        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
950    o ctrl, cost, grdchk & autodiff pkgs:
951      - make options file more standard (like other {PKG}_OPTIONS.h file but
952        with AD_CONFIG.h); clean-up some of the included header files.
953    o pkg/obcs:
954      - do not mask tracer when applying OB (tracer == 0 could generate problems)
955      - apply tracer OB values to tracer field only at OB location (instead of
956        over a band of OLx width)
957      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
958      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
959        obcs_apply_tloc.F & obcs_apply_sloc.F
960    o obcs in model/src:
961      - call OBCS_APPLY_W only if NonHydrostatic.
962      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
963      - reset dEtaHdt and wVel to zero outside OB interior region ;
964      - leave tracer unchanged outside OB interior region: This has no effect
965        on the solution but just to prevent unrealistic tracer value outside OB.
966      - zero out velocity outside OB interior region: This has no effect on
967        the solution but just to prevent unrealistic velocity outside OB.
968    o obcs and non-lin free-surf:
969       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
970       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
971       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
972       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
973       update results of test-exp. exp4(nlfs).
974    o exp4 (nlfs) test-exp:
975       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
976       with NonLin-FreeSurf); update output.nlfs.txt
977    o obcs and 2d/3d solver norm:
978       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
979       and outside OB interior region (will allow to place OB further inside the
980       domain). Depending on the domain, can affects cg2d-Norm (previous
981       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
982       and cg3d-Norm (previous Norm was computed before canceling OB terms),
983       e.g. in tutorial_plume_on_slope.
984      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
985    o pkg rbcs:
986      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
987      - add capability to apply relaxation to horizontal velocity uVel & vVel.
988    o pkg/grdchk: add gradient check for control variable xx_shifwflx
989    o pkg/shelfice/shelfice_init_fixed.F
990      fix CPP-flag combinations
991    o pkg/seaice: Merge iceage code of Pierre Rampal
992      * update/change/correct ice age calculations
993      * add age updates for pathological cases
994      Probably needs more testing...
995    
996    checkpoint62x (2011/05/13)
997    o pkg/mom_vecinv:
998       high-order vorticity scheme: use interior masks (maskInW & S)
999       to zero-out (outside OB) gradient of vorticity.
1000    o verification exp.:
1001       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1002       hs94.128x64x5 and seaice_obcs ; update results.
1003    o pkg/obcs:
1004      fix bug in OBeta for YZ sections in obcs_exf_load.F
1005    o pkg/ctrl, pkg/shelfice, and optim:
1006      - add new control variable xx_shifwflx (fresh water flux underneath ice
1007        shelves). This is almost as tedious as obcs-ctrl, because the
1008        variables needs its own mask.
1009      - add a cost function term that penalizes the deviation of xx_shifwflx
1010        from the first guess (zero) in analogy to other control variables
1011    o pkg/shelfice:
1012      - start basic adjoint
1013    o pkg/ctrl:
1014      - remove extra 2D field "for good measure" when initializing in
1015        ctrl_set_globfld_[xy/xz/yz].F
1016      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1017      - improve error messages in ctrl_set_unpack_*
1018    o OBC implementation in momentum:
1019       use interior masks (maskInC,W & S) in momentum S/R:
1020       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1021       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1022       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1023       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1024       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1025        (and also with Leith/Smagorinsky harmonic-viscosity).
1026       Update output of experiment dome and exp4 (+nlfs).
1027    o exp4 test-exp:
1028      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1029        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1030        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1031        time-varying OB at Western-side for wVel (NonHyd); update output.
1032      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1033        and biharmonic-viscosity ; also use prescribed time varying OB.
1034    o pkg/obcs:
1035      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1036    o model/src:
1037      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1038      - initialise startTime & nIter0 with unlikely values: allows to set one
1039        from the other without ambiguity.
1040    o seaice_obcs test-exp.:
1041      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1042  o pkg/obcs:  o pkg/obcs:
1043    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:    - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1044      no longer needed with maskInC,W,S in pkg/generic_advdiff.      no longer needed with maskInC,W,S in pkg/generic_advdiff.
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