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revision 1.1483 by mlosch, Wed Jul 27 15:00:32 2011 UTC revision 1.1597 by mlosch, Tue Feb 14 14:53:17 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: remove (almost) all divisions by constants within loops
8      in seaice_growth.F and seaice_solve4temp.F
9    o pkg/seaice :
10      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.
11      1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
12      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
13      - add permanent SItflux diag that corresponds to TFLUX but includes
14      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
15      - allow activation/testing of a fix for suspected missing term in
16      ocn-ice heat budget (to be confirmed). To test this, you want to
17      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
18      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
19      - no change in results, fwd or ad.
20    o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.
21      - switch to variable freezing point.
22           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
23      - bug fix : the sublimation term that was missing is now activated.
24           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
25      - bug fix : flooding sign term for SIsal0.NE.0.
26           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
27    o pkg/seaice:
28      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
29     is now the default, and the old default constant freezing point is recovered with
30     SEAICE_tempFrz0    = -1.96,
31     SEAICE_dTempFrz_dS = 0.,
32      - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.
33      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
34      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
35     activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.
36      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
37     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
38      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
39     seaice_growth r149 for legacy branch (no results change).
40      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).
41      - results did not change except for global_ocean.cs32x15, mostly due to the switch
42      to variable freezing point (see above item for detail).
43    o pkg/thsice:
44      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
45        seawater freezing in thsice_calc_thickn (not used).
46    o pkg/seaice: turbulent flux term specification via run time params.
47      - replace CPP switches with run time switches to facilitate testing
48      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
49      - added runtime parameter : SEAICEturbFluxFormula
50      - move Mcphee constants to SEAICE_PARAMS.h
51      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
52        SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
53        seaice_summary call (moved to seaice_init_fixed)
54      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
55        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
56      - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
57      - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
58      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
59            CPP switch, same computation as before for the different options.
60      - change results at the truncation level.
61    o pkg/seaice:
62      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
63        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
64        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
65      - update verification/*/input*/data.seaice:
66        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
67        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
68        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
69        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
70    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
71      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
72        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
73        difference in results only due to machine truncation.
74      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
75        MaykutPolySatVap; keep MIN_LWDOWN.
76      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
77      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
78        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
79    o pkg/salt_plume:
80      - isolate saltPlumeFlux array exch into a specific S/R called from
81        do_oceanic_phys.F
82      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
83    o verification:
84      - move untested set-up to MITgcm_contrib/verification_other.
85    o pkg/seaice:
86      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
87    o pkg/seaice:
88      - seaice_solve4temp.F (keeping results unchanged):
89        * add 2 future run-time params to select which saturation vapor pressure
90          formula is used and how post-iteration fluxes are set.
91          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
92        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
93          the linearized expression to stay consistent with tsurf finding.
94      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
95        can be < 0.
96    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
97      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
98        conductive heat flux F_c , and add it explicitly when updating tsurf as
99        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
100        so that now F_ia has a consistent meaning through the entire routine.
101        This causes differences at truncation level: update output of fwd exp.
102        global_ocean.cs32x15.seaice.
103    o pkg/seaice:
104      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
105        of arrays, sign/direction of fluxes; no effect on results.
106      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
107        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
108        note: this should have been done before changing celsius2K default.
109      - to keep results unchanged, add back old value of celsius2K in verification
110        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
111      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
112        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
113        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
114        freezing temp is consistent with value in seaice_growth.F ; this causes
115        differences at machine truncation level: update lab_sea AD output (3/4).
116    o pkg/seaice:
117      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
118        and climsst/sss even when using seaice (to prevent calculation that might
119        use SST on land); does not affect any verification exp.
120      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
121        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
122    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
123      over land (non-legacy code)
124    o vectorize salt_plume package:
125      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
126      - this code computes plumebk everywhere (also over land), thus requires
127        code to avoid divisions by zero and catch the case of kLev=Nr.
128      - efficiency of salt_plume_frac is still sub-optimal
129    o tools (genmake2):
130      - fix makefile NAME specification (option: -makefile NAME) by adding
131        "-f $MAKEFILE" in few places where it was missing including makedepend
132        command (contribution from Paul).
133    
134    checkpoint63i (2012/01/24)
135    o model/src:
136      - add factorized versions of some EOS code to find_rho.F,
137        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
138    o model/src:
139      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
140      - change default celsius2K from 273.16 to 273.15
141      - to keep results unchanged, add back old value of celsius2K in verification
142        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
143         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
144    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
145      to make TAF generate vectorizable code
146    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
147       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
148       have flags that do this more efficiently.
149    o pkg/diagnostics/diagstats_calc.F
150      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
151    o pkg/obcs (with exch2):
152      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
153        and remove code (in obcs_readparms.F) which was based on EXCH of indices
154        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
155    o pkg/exf and seaice exp:
156      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
157        so that switching off area & heff advection flags does not affect results.
158      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
159      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
160        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
161        results of verification experiments: 1D_ocean_ice_column(fwd),
162        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
163        and offline_exf_seaice (all 4).
164    o pkg/seaice:
165      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
166        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
167      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
168        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
169        not multi-dim advection;
170      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
171        SHORTWAVE_HEATING #undef.
172    o optim: make Makefile more robust (?)
173    o pkg/obcs:
174      * fix treatment of obcs_read_pickup for TAF
175    o pkg/shelfice:
176      * add missing initialisation of num_shifwflx
177      * new adjoint verification exp. for isomip
178      * change Prandtl and Schmidt numbers from generic formulations
179        (in terms of model diffus. and visc.) to separate runtime
180        parameters, with Holland and Jenkins (1999) default values.
181    o pkg/exf (interpolation):
182      - extended input field (2 rows) near the N & S poles:
183        * fill in with the symetric value (when even Nb of data in longitude)
184        * add average value at the poles only for scalar quantities ; for vector
185          component interpolation, skip the averaging and keep duplicated values,
186          unless the 2 components have same location (uvInterp=T) in which case
187          interpolate the 2 components together using S/R EXF_INTERP_UV.
188      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
189        together: this allows to account properly for local orientation when
190        averaging at N & S pole.
191      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
192        exf-interpolation near N & S poles. Undef by default.
193      - add debug check/print on 1rst iter if debugLevel >=2.
194    o pkg/exf:
195      - change masking flags definition (no longer "parameter"), put them in
196        common block and set them in S/R EXF_INIT_FIXED.
197      - change recognized masking flag from s,u,v to c,w,s since the mask
198        to use (maskC,W,S) depends on position on model grid and has little to
199        do with scalar/vector difference; fix masking if using P-coordinates.
200      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
201        and update results of exp. global_with_exf (x2).
202      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
203    o pkg/obcs
204      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
205    o pkg/exf (interpolation):
206      - assume periodicity in X only if input field cover full longitude range.
207      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
208        and should vectorise).
209      - fix input lat of the 2 added row (in case we provide N.pole data).
210    
211    checkpoint63h (2011/12/30)
212    o pkg/seaice:
213      - change declaration of UVM from _RL to _RS in order to get B-grid
214        uIce,vIce monitor when _RS = real*4
215    o pkg/offline:
216      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
217      - compute vertical velocity if not read from file (switch on exactConserv
218        & staggerTimeStep);
219      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
220    o verification:
221      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
222        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
223        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
224      - update output of exp. global_ocean.cs32x15.viscA4 after changing
225        grid-file angles (used here for coriolis-3d);
226      - remove (or gzip) few files not needed to run fizhi-cs experiments.
227    o pkg/exf (vector interpolation):
228      - rotate vector component toward local grid-axis orientation using grid-angles
229        (stored in GRID.h) instead of locally computed rotation angle; keep old code
230        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
231    o pkg/seaice:
232      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
233        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
234    o pkg/PKG_OPTIONS.h files:
235      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
236        outside of the #ifdef ALLOW_THISPKG / #endif block.
237      - update verification/*/code/PKG_OPTIONS.h files.
238    o add a verification experiment (offline_exf_seaice/input.seaice) that test
239      the B-grid LSOR solver
240    o pkg/seaice: sort out emissivity and long wave radiation step 2:
241      - add emissivity for snow and ice as new run-time parameters
242        (unfortunately) that default to the corresponding exf values; this
243        changes results in most verification experiments so that for backward
244        compatibility these parameter have to be set explicitly to inconsistent
245        values (ugly);
246      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
247        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
248        until we agree how to handle this bug properly
249    o pkg/exf (interpolation):
250      - add a set of run-time param ({inputfield}_interpMethod), one for
251        each interpolated input field, to select the interpolation method
252        with a value of zero switching off the interpolation;
253      - print interpolation parameters to standard output;
254      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
255        (to use instead runoff_interpMethod=0 in data.exf).
256      - simplify default setting of interpolation parameters (for all fields,
257        set position to match model grid cell-center position, leading to trivial
258        interpolation in case of regular Lat-Lon grid) and fix for the case of
259        non-uniform delY.
260    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
261       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
262       this factor is absolutely required, because the lw exitance (= out-going
263       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
264       where the reflectivity rho = 1-emissivity for conservation reasons. Once
265       this is established, we can remove the CPP-Flag (if we want to).
266    o pkg/seaice:
267      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
268        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
269      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
270        what the name implies (and not emissivity*BoltzmannConstant), this means
271        the old default value of 5.5e-8 now means
272        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
273        S/R exf_readparms
274      - FV-discretization of the B-grid LSOR solver, turn on with
275        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
276        of the calling routine dynsolver, so that B and C-grid code look a
277        little more alike.
278      - fix index bugs in ostres.F (B-grid code)
279    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
280    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
281      default for SEAICE_emissivity, if useEXF; requires setting a wrong
282      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
283      backward compatiblity
284    o model/src: use sigmaR in calc_ivdc
285    
286    checkpoint63g (2011/12/16)
287    o pkg/seaice/seaice_growth.F:
288      fix heat conservation of the coupled ocean-seaice system.
289      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
290      solid vs liquid water treatment is resolved via QNET.
291    o pkg/seaice/seaice_growth.F:
292      add missing term for sublimation in saltFlux, which was breaking conservation.
293    o pkg/seaice/seaice_model.F:
294      Remove this patholigical case treatment in evolution branch,
295      where it is un-necessary and breaks conservation.
296      Update global_ocean.cs32x15/results accordingly for
297      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
298    o model/src:
299      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
300      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
301    o pkg/obcs:
302      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
303      tendency for temperature and salinity that is then applied to update
304      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
305      horizontal advection and diffusion contributions on the boundary (in
306      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
307      removing the mask in S/R timestep_tracer. The advantage of this approach is
308      that the updated tracer values include contributions from the surface
309      forcing and vertical diffusion.
310      This modification changes exp4.stevens because of vertical diffusion.
311    o model/src:
312      change non-curvilinear grid setting to also work with exch2 + blank tiles:
313      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
314        face dimensions.
315      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
316        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
317        and INI_SPHERICAL_POLAR_GRID.
318      change test-experiment global_ocean.90x40x15:
319      - split the domain in many more tiles (9x4 tiles of 10x10 each);
320      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
321      - update results of both test (std & dwnslp).
322    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
323       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
324    o model/src:
325      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
326        and fix initialisation when using sigma-coords.
327    o model/src:
328     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
329       to their current value at the beginning of forward_step.F": add a new run-time
330       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
331     - set doResetHFactors=T in the following test exp:
332        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
333        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
334        and tutorial_global_oce_in_p (nonLinFS in p)
335    o pkg/ecco
336      - added IES cost term
337    o verification/advect_xz
338      - scale down the depth by 1/100 (from 200 km to just 2.km)
339      - add secondary test using divergent flow, r-star and implicit vertical advection.
340      - add note (check_conserve_TS.txt) and matlab script to check global
341        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
342    o pkg/rbcs:
343      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
344    o pkg/obcs (Stevens BCs):
345      - fix various problems in the phase speed computations of the Stevens
346        boundary conditions:
347        - sign error for western and southern boundaries,
348        - time tendencies were underestimated by factor of dTracerLev and some just
349          zero (for multidim advection schemes) -> now estimate time tendencies
350          from difference between previous (n) time level and the one before (n-1);
351          this requires storing a field per tracer per boundary, also in the pickup
352          files.
353        - replace deltaTmom in cflMer/Zon computation with dTracerLev
354        - set default phase velocity to cflMer/Zon
355      - update verification experiment exp4.stevens
356    o pkg/generic_advdiff (implicit_r):
357      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
358        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
359      - fix implicit vertical diffusion or advection with NonLin FreeSurf
360        (was using current recip_hFacC instead of future recip_hFacC): set future
361        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
362        solver S/R ;
363      - fill diagnostics of vertical advective fluxes (computed from tendency)
364        when using implicit vert. advection;
365      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
366         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
367         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
368         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
369    o pkg/diagnostics:
370      - add diags for T & S tendency which goes through Adams-Bashforth.
371    
372    checkpoint63f (2011/11/30)
373    o pkg/obcs/obcs_calc_stevens.F:
374      - join some loops to reduce number of if-statements
375      - fix a bug in code for northern and southern boundaries.
376    o pkg/seaice/seaice_init_varia.F
377      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
378        caused zero ice-velocities for the B-grid code
379    o pkg/seaice/seaice_init_fixed.F
380      - fix a bug in the initialisation of the second metric terms
381        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
382      - this affects all seaice configurations with useCurviLinearGrid = .true.
383        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
384        = .true. (default)
385      - the only verification experiment affected is global_ocean.cs32x15:
386        icedyn, seaice, and seaice_dynmix (AD)
387    o pkg/thsice/thsice_diagnostics_state.F
388      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
389        not contain garbage that can lead to surprises in diagstats_calc.F
390    o model/src:
391      - move bi,bj loops inside INTEGR_CONTINUITY ;
392      - call INTEGR_CONTINUITY directly from forward_step.F
393        (previously called from momentum_correction_step.F)
394      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
395        forward_step.F and pkg/ecco/the_main_loop.F
396    o model/src/do_oceanic_phys.F:
397      - reset addMass to zero only if useICEFRONT ;
398      - separated k-loop for rhoInSitu calculation ;
399      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
400        and at constant T,S (= WdRHOdP);
401      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
402        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
403        transport of locally-referenced potential density);
404        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
405    o gluemnc:
406      - replace ncrcat with ncks when adding variables to *.glob.nc
407      - change the way variables without record dimensions are handled so that
408        files that have variables with and without record variables can be glued:
409        add a record dimension with a new unique name to be able to differentiate
410        between variable with and without a-prior record dimensions. Remove
411        this record dimension before adding the variable to the *.glob.nc file.
412        This procedure automatically works also for grid.*.nc files that do not
413        have any record dimension.
414    o verification/cpl_aim+ocn:
415      - generate new reference output on baudelaire (gfortran, mpich2) (previously
416        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
417    o pkg/obcs/obcs_calc_stevens.F:
418      - add code for northern and southern boundaries.
419      - reorder some loops to save some operations and so that drFBar can be scalar
420    o model/src:
421      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
422        truncation) and add diagnostics for Adams-Bashforth tendency increment.
423      - update test-exp. AD output:
424        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
425      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
426        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
427        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
428        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
429        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
430        tutorial_plume_on_slope.
431    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
432      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
433      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
434      does not even come with an F77 compiler anymore, this should not be
435      a limitation
436    
437    checkpoint63e (2011/11/06)
438    o pkg/seaice adjoint of LSR:
439      - substantially rework STORE dirs.
440      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
441        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
442        and only perform SOLV_MAX_FIXED adjoint iters.
443        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
444        always goes to same record, meaning that the last forward field will be
445        the one used in the adjoint - an approximation.
446      - now produces non-zero LSR-related gradients, and acceptable gradients for
447        An's zonal (x-z) test case (to be checked in)
448      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
449        (but these are screwed up by the thermodynamics in the first place);
450        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
451        output_adm.txt also reflects changes to seaice_lsr
452      - global_ocean.cs32x15:
453        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
454          (output_adm.seaice.txt was updated)
455        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
456          (output_adm.seaice_dynmix.txt)
457    o test-exp. exp4+stevens:
458      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
459    o pkg/seaice (lsr solver):
460      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
461        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
462      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
463      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
464        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
465      - compute (with new S/R) and print initial (+ free-driff sol. if available)
466        and final residual of linearised system.
467    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
468      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
469    o pkg/obcs: Stevens BCs (still only for east and west)
470      - fix Stevens BCs by using intermediate velocities of previous
471        time step as "baroclinic" contribution rather velocity of one grid cell
472        inside the boundaries; more consistent but makes the entire treatment
473        more complicated, requires new pickup files and two new S/Rs:
474        obcs_copy_uv_n and obcs_save_uv_n
475        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
476        (undefined by default)
477      - silently move computation of some grid factors into separate loops to
478        save some recomputations
479      - add a hack for non-linear free surface
480      - add a verification experiment to exp4 that tests this code
481    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
482    
483    checkpoint63d (2011/10/25)
484    o pkg/obcs + seaice-dynamics:
485      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
486        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
487        values (consistent with an implicit method).
488      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
489        return to older implementation (same results as before); note that none of
490        the "experimental" OBCS_SEAICE options are implemented in the new version.
491      - switch test exp. seaice_obcs to use new version (update output).
492    o pkg/seaice:
493      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
494      - add parenthesis in Water-Ice drag calculations (evp & lsr);
495      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
496        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
497      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
498        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
499    o pkg/layers:
500      - Include potential density as new coordinate (Thanks to David Munday)
501    o pkg/dic:
502      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
503        carbonate computation/output to CALC_PCO2_APPROX
504    o pkg/generic_advdiff
505      - make TAF generate code that vectorizes:
506        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
507    o model/src:
508      - improve vectorization also for adjoint code of
509        solve_tridiagonal and solve_pentadiagonal. As this requires up to
510        5 new 3D-fields, this code is only turned on for the combination of
511        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
512        for singular matrix check (only for TARGET_NEC_SX).
513      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
514        ALLOW_AUTODIFF. This flag now needs to be set outside of
515        solve_tri/pentadiagonal.F
516    o pkg/exf:
517      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
518        optional namelist EXF_NML_OBCS).
519      - add many debug-print (to trace down where pkg/cal error msg comes from)
520    o pkg/mom_vecinv/mom_vi_hdissip.F
521      - rearrange loops so that vectorization is improved and in particular
522        the adjoint routine vectorizes. The code is a little longer now, but I
523        think easier to read.
524        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
525    o pkg/seaice:
526      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
527    o pkg/exch2:
528      - alternative code (without tile x tile matrix) for cumulated (global) sum;
529        used as default; keep using matrix version in adjustment.cs-32x32x1.
530    o tools/build_options:
531      - after merging some MPI and/or multi-threads specific optfiles so that
532        the modified default optfile support both built (using genmake2 -mpi
533        for the MPI built, using genmake2 -omp for OpenMP built),
534        move now obsolete optfiles to tools/build_options/unsupported/
535       (add copy of email sent to support list in doc/optfiles_changes.txt)
536    
537    checkpoint63c (2011/09/28)
538    o pkg/ebm:
539      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
540        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
541    o pkg/seaice (SItracer pickup)
542    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
543      To be done:
544      - thorough testing of missing fields in S/R seaice_read_pickup
545      - thorough matching between generic tracers and specific fields used
546        (e.g. volume-weighted age, area-weighted age, salinity, ...)
547    o pkg/grdchk:
548      - all procs calculate and print finite-difference gradient (for testreport)
549      - change description output used by testreport;
550      - AD testing: also compare and report Finite-difference gradient;
551        => update all output_adm*.txt
552    o test exp. global_ocean_ebm:
553      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
554        and turn on exactConserve; update (fwd) output.
555    o pkg/seaice (LSR):
556      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
557      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
558        * identical results with non-CS topology (but save up to half of EXCH calls)
559        * no much changes in cs-32 verification tests since no ice at face edges
560         (differences due to convergence criteria, since nb of iterations changed)
561        * expect some differences on lat-lon-cap grid.
562        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
563    o pkg/exch2:
564      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
565        many tiles); until alternative coding is added, just add a stop.
566    o pkg/kpp:
567      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
568        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
569    o optfiles:
570      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
571        into corresponding standard one, which now support different build:
572        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
573      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
574    o pkg/obcs (seaice):
575      - add missing EXCH for uIce,vIce after applying OBCS;
576      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
577        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
578        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
579      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
580      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
581        and eedata.mth for MPI and mutlti-threaded testing.
582    o pkg/flt:
583      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
584      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
585      - fix pickup and trajectories + profiles output with multi-threads;
586      - add parameter to select group of fields to write along trajectory and
587        profile (default unchanged);
588      - only call PORT_RAND* function when flt_noise <> 0;
589      - add multi-threaded test for verification exp. flt_example.
590    o eesupp/src:
591      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
592      - USE_OMP_THREADING: check that number of threads (from eedata) matches
593        actual number (from env.var. setting).
594    o pkg/ebm:
595      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
596      - add multi-threaded test for verification exp. global_ocean_ebm
597    
598    checkpoint63b (2011/08/29)
599    o pkg/ebm:
600      - fix sign of runoff;
601      - update directly forcing fields (Qnet,EmPmR) to use standard
602        external_forcing_surf.F (remove ebm_forcing_surf.F);
603      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
604      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
605        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
606      - update global_ocean_ebm parameters file data and update output (fwd+ad).
607    o verification/matrix_example:
608      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
609        MPI and mutlti-threaded testing.
610    o pkg/matrix:
611      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
612      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
613      - fix for multi-threaded (remove DATA statement);
614      - use standard DIFFERENT_MULTIPLE function;
615      - add MATRIX_OPTIONS.h
616    o verification/matrix_example:
617       To allow to split the domain in several tiles, change the domain size
618        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
619        Western side) of land points.
620    o (*_)write_pickup:
621      - fix few bugs in mypackage_read/write_pickup.F
622      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
623        array of length 1 (was caught by compiler syntax-check).
624    o pkg/diagnostics (velocity potential solver):
625      - fix initialisation of main diagonal matrix (for overlap values)
626    o tools/build_options:
627      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
628        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
629      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
630        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
631        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
632        and use "-devel" testreport option for standard testing on baudelaire.
633    o pkg/grdchk:
634      - Assume that all gradient-check position are within the same tile
635        corresponding to global indices (iGloTile,jGloTile) and that
636        positions (i,j indices or nbeg) are local to this tile;
637      - set tile local-indices and proc. number according to tile global-indices;
638      - remove grdchkwhichproc from namelist (retired param);
639      - send adjoint gradient to all procs so that all procs print it to STDOUT;
640      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
641    o adding package bbl (Bottom Boundary Layer)
642      description in MITgcm/pkg/bbl/bbl_description.tex
643      example/test experiment in MITgcm_contrib/bbl
644    o adjoint verifications
645      - changed 5 experiments to multi-tiles
646        * global_ocean.90x40x15
647        * obcs_ctrl
648        * offline_exf_seaice
649        * tutorial_dic_adjoffline
650        * tutorial_tracer_adjsens
651        changed reference output for those that crossed tile boundaries
652        (changed choices of gradient check positions)
653      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
654      - temporary bug fix in grdchk_loc.F for obcs
655    o genmake2 & testreport
656      - add target "obj" (just for OBJFILES files) to Makefile;
657      - add option to specify FEXTRAFLAGS on command line.
658    o pkg/mypackage:
659      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
660    
661    checkpoint63a (2011/08/02)
662    o pkg/diagnostics (velocity potential):
663      - fix velocity-potential calculation when using OBCS: balance net inflow
664        at each level (new S/R OBCS_DIAG_BALANCE).
665      - fix some of the problems with OBCS in stream-function calculation.
666  o pkg/exf/exf_readparms.F  o pkg/exf/exf_readparms.F
667    - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,    - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
668      EXF_NML_OBCS) more consistent, so that you need not have these lists      EXF_NML_OBCS) more consistent, so that you need not have these lists
669      in data.exf when they are not used.      in data.exf when they are not used.
670  o optim/optim_readdata.F:  o optim/optim_readdata.F:
# Line 50  o pkg/gmredi: Line 709  o pkg/gmredi:
709     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
710     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
711    
712  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
713  o pkg/exch2:  o pkg/exch2:
714   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
715   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
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