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revision 1.1484 by jmc, Mon Aug 1 20:47:39 2011 UTC revision 1.1593 by gforget, Tue Feb 7 19:12:06 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: turbulent flux term specification via run time params.
8      - replace CPP switches with run time switches to facilitate testing
9      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
10      - added runtime parameter : SEAICEturbFluxFormula
11      - move Mcphee constants to SEAICE_PARAMS.h
12      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
13       SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
14       seaice_summary call (moved to seaice_init_fixed)
15      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
16       SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
17      - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
18      - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
19      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
20            CPP switch, same computation as before for the different options.
21      - change results at the truncation level.
22    o pkg/seaice:
23      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
24        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
25        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
26      - update verification/*/input*/data.seaice:
27        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
28        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
29        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
30        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
31    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
32      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
33        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
34        difference in results only due to machine truncation.
35      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
36        MaykutPolySatVap; keep MIN_LWDOWN.
37      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
38      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
39        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
40    o pkg/salt_plume:
41      - isolate saltPlumeFlux array exch into a specific S/R called from
42        do_oceanic_phys.F
43      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
44    o verification:
45      - move untested set-up to MITgcm_contrib/verification_other.
46    o pkg/seaice:
47      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
48    o pkg/seaice:
49      - seaice_solve4temp.F (keeping results unchanged):
50        * add 2 future run-time params to select which saturation vapor pressure
51          formula is used and how post-iteration fluxes are set.
52          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
53        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
54          the linearized expression to stay consistent with tsurf finding.
55      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
56        can be < 0.
57    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
58      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
59        conductive heat flux F_c , and add it explicitly when updating tsurf as
60        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
61        so that now F_ia has a consistent meaning through the entire routine.
62        This causes differences at truncation level: update output of fwd exp.
63        global_ocean.cs32x15.seaice.
64    o pkg/seaice:
65      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
66        of arrays, sign/direction of fluxes; no effect on results.
67      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
68        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
69        note: this should have been done before changing celsius2K default.
70      - to keep results unchanged, add back old value of celsius2K in verification
71        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
72      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
73        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
74        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
75        freezing temp is consistent with value in seaice_growth.F ; this causes
76        differences at machine truncation level: update lab_sea AD output (3/4).
77    o pkg/seaice:
78      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
79        and climsst/sss even when using seaice (to prevent calculation that might
80        use SST on land); does not affect any verification exp.
81      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
82        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
83    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
84      over land (non-legacy code)
85    o vectorize salt_plume package:
86      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
87      - this code computes plumebk everywhere (also over land), thus requires
88        code to avoid divisions by zero and catch the case of kLev=Nr.
89      - efficiency of salt_plume_frac is still sub-optimal
90    o tools (genmake2):
91      - fix makefile NAME specification (option: -makefile NAME) by adding
92        "-f $MAKEFILE" in few places where it was missing including makedepend
93        command (contribution from Paul).
94    
95    checkpoint63i (2012/01/24)
96    o model/src:
97      - add factorized versions of some EOS code to find_rho.F,
98        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
99    o model/src:
100      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
101      - change default celsius2K from 273.16 to 273.15
102      - to keep results unchanged, add back old value of celsius2K in verification
103        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
104         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
105    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
106      to make TAF generate vectorizable code
107    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
108       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
109       have flags that do this more efficiently.
110    o pkg/diagnostics/diagstats_calc.F
111      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
112    o pkg/obcs (with exch2):
113      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
114        and remove code (in obcs_readparms.F) which was based on EXCH of indices
115        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
116    o pkg/exf and seaice exp:
117      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
118        so that switching off area & heff advection flags does not affect results.
119      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
120      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
121        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
122        results of verification experiments: 1D_ocean_ice_column(fwd),
123        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
124        and offline_exf_seaice (all 4).
125    o pkg/seaice:
126      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
127        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
128      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
129        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
130        not multi-dim advection;
131      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
132        SHORTWAVE_HEATING #undef.
133    o optim: make Makefile more robust (?)
134    o pkg/obcs:
135      * fix treatment of obcs_read_pickup for TAF
136    o pkg/shelfice:
137      * add missing initialisation of num_shifwflx
138      * new adjoint verification exp. for isomip
139      * change Prandtl and Schmidt numbers from generic formulations
140        (in terms of model diffus. and visc.) to separate runtime
141        parameters, with Holland and Jenkins (1999) default values.
142    o pkg/exf (interpolation):
143      - extended input field (2 rows) near the N & S poles:
144        * fill in with the symetric value (when even Nb of data in longitude)
145        * add average value at the poles only for scalar quantities ; for vector
146          component interpolation, skip the averaging and keep duplicated values,
147          unless the 2 components have same location (uvInterp=T) in which case
148          interpolate the 2 components together using S/R EXF_INTERP_UV.
149      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
150        together: this allows to account properly for local orientation when
151        averaging at N & S pole.
152      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
153        exf-interpolation near N & S poles. Undef by default.
154      - add debug check/print on 1rst iter if debugLevel >=2.
155    o pkg/exf:
156      - change masking flags definition (no longer "parameter"), put them in
157        common block and set them in S/R EXF_INIT_FIXED.
158      - change recognized masking flag from s,u,v to c,w,s since the mask
159        to use (maskC,W,S) depends on position on model grid and has little to
160        do with scalar/vector difference; fix masking if using P-coordinates.
161      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
162        and update results of exp. global_with_exf (x2).
163      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
164    o pkg/obcs
165      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
166    o pkg/exf (interpolation):
167      - assume periodicity in X only if input field cover full longitude range.
168      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
169        and should vectorise).
170      - fix input lat of the 2 added row (in case we provide N.pole data).
171    
172    checkpoint63h (2011/12/30)
173    o pkg/seaice:
174      - change declaration of UVM from _RL to _RS in order to get B-grid
175        uIce,vIce monitor when _RS = real*4
176    o pkg/offline:
177      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
178      - compute vertical velocity if not read from file (switch on exactConserv
179        & staggerTimeStep);
180      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
181    o verification:
182      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
183        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
184        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
185      - update output of exp. global_ocean.cs32x15.viscA4 after changing
186        grid-file angles (used here for coriolis-3d);
187      - remove (or gzip) few files not needed to run fizhi-cs experiments.
188    o pkg/exf (vector interpolation):
189      - rotate vector component toward local grid-axis orientation using grid-angles
190        (stored in GRID.h) instead of locally computed rotation angle; keep old code
191        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
192    o pkg/seaice:
193      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
194        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
195    o pkg/PKG_OPTIONS.h files:
196      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
197        outside of the #ifdef ALLOW_THISPKG / #endif block.
198      - update verification/*/code/PKG_OPTIONS.h files.
199    o add a verification experiment (offline_exf_seaice/input.seaice) that test
200      the B-grid LSOR solver
201    o pkg/seaice: sort out emissivity and long wave radiation step 2:
202      - add emissivity for snow and ice as new run-time parameters
203        (unfortunately) that default to the corresponding exf values; this
204        changes results in most verification experiments so that for backward
205        compatibility these parameter have to be set explicitly to inconsistent
206        values (ugly);
207      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
208        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
209        until we agree how to handle this bug properly
210    o pkg/exf (interpolation):
211      - add a set of run-time param ({inputfield}_interpMethod), one for
212        each interpolated input field, to select the interpolation method
213        with a value of zero switching off the interpolation;
214      - print interpolation parameters to standard output;
215      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
216        (to use instead runoff_interpMethod=0 in data.exf).
217      - simplify default setting of interpolation parameters (for all fields,
218        set position to match model grid cell-center position, leading to trivial
219        interpolation in case of regular Lat-Lon grid) and fix for the case of
220        non-uniform delY.
221    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
222       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
223       this factor is absolutely required, because the lw exitance (= out-going
224       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
225       where the reflectivity rho = 1-emissivity for conservation reasons. Once
226       this is established, we can remove the CPP-Flag (if we want to).
227    o pkg/seaice:
228      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
229        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
230      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
231        what the name implies (and not emissivity*BoltzmannConstant), this means
232        the old default value of 5.5e-8 now means
233        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
234        S/R exf_readparms
235      - FV-discretization of the B-grid LSOR solver, turn on with
236        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
237        of the calling routine dynsolver, so that B and C-grid code look a
238        little more alike.
239      - fix index bugs in ostres.F (B-grid code)
240    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
241    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
242      default for SEAICE_emissivity, if useEXF; requires setting a wrong
243      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
244      backward compatiblity
245    o model/src: use sigmaR in calc_ivdc
246    
247    checkpoint63g (2011/12/16)
248    o pkg/seaice/seaice_growth.F:
249      fix heat conservation of the coupled ocean-seaice system.
250      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
251      solid vs liquid water treatment is resolved via QNET.
252    o pkg/seaice/seaice_growth.F:
253      add missing term for sublimation in saltFlux, which was breaking conservation.
254    o pkg/seaice/seaice_model.F:
255      Remove this patholigical case treatment in evolution branch,
256      where it is un-necessary and breaks conservation.
257      Update global_ocean.cs32x15/results accordingly for
258      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
259    o model/src:
260      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
261      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
262    o pkg/obcs:
263      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
264      tendency for temperature and salinity that is then applied to update
265      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
266      horizontal advection and diffusion contributions on the boundary (in
267      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
268      removing the mask in S/R timestep_tracer. The advantage of this approach is
269      that the updated tracer values include contributions from the surface
270      forcing and vertical diffusion.
271      This modification changes exp4.stevens because of vertical diffusion.
272    o model/src:
273      change non-curvilinear grid setting to also work with exch2 + blank tiles:
274      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
275        face dimensions.
276      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
277        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
278        and INI_SPHERICAL_POLAR_GRID.
279      change test-experiment global_ocean.90x40x15:
280      - split the domain in many more tiles (9x4 tiles of 10x10 each);
281      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
282      - update results of both test (std & dwnslp).
283    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
284       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
285    o model/src:
286      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
287        and fix initialisation when using sigma-coords.
288    o model/src:
289     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
290       to their current value at the beginning of forward_step.F": add a new run-time
291       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
292     - set doResetHFactors=T in the following test exp:
293        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
294        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
295        and tutorial_global_oce_in_p (nonLinFS in p)
296    o pkg/ecco
297      - added IES cost term
298    o verification/advect_xz
299      - scale down the depth by 1/100 (from 200 km to just 2.km)
300      - add secondary test using divergent flow, r-star and implicit vertical advection.
301      - add note (check_conserve_TS.txt) and matlab script to check global
302        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
303    o pkg/rbcs:
304      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
305    o pkg/obcs (Stevens BCs):
306      - fix various problems in the phase speed computations of the Stevens
307        boundary conditions:
308        - sign error for western and southern boundaries,
309        - time tendencies were underestimated by factor of dTracerLev and some just
310          zero (for multidim advection schemes) -> now estimate time tendencies
311          from difference between previous (n) time level and the one before (n-1);
312          this requires storing a field per tracer per boundary, also in the pickup
313          files.
314        - replace deltaTmom in cflMer/Zon computation with dTracerLev
315        - set default phase velocity to cflMer/Zon
316      - update verification experiment exp4.stevens
317    o pkg/generic_advdiff (implicit_r):
318      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
319        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
320      - fix implicit vertical diffusion or advection with NonLin FreeSurf
321        (was using current recip_hFacC instead of future recip_hFacC): set future
322        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
323        solver S/R ;
324      - fill diagnostics of vertical advective fluxes (computed from tendency)
325        when using implicit vert. advection;
326      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
327         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
328         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
329         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
330    o pkg/diagnostics:
331      - add diags for T & S tendency which goes through Adams-Bashforth.
332    
333    checkpoint63f (2011/11/30)
334    o pkg/obcs/obcs_calc_stevens.F:
335      - join some loops to reduce number of if-statements
336      - fix a bug in code for northern and southern boundaries.
337    o pkg/seaice/seaice_init_varia.F
338      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
339        caused zero ice-velocities for the B-grid code
340    o pkg/seaice/seaice_init_fixed.F
341      - fix a bug in the initialisation of the second metric terms
342        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
343      - this affects all seaice configurations with useCurviLinearGrid = .true.
344        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
345        = .true. (default)
346      - the only verification experiment affected is global_ocean.cs32x15:
347        icedyn, seaice, and seaice_dynmix (AD)
348    o pkg/thsice/thsice_diagnostics_state.F
349      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
350        not contain garbage that can lead to surprises in diagstats_calc.F
351    o model/src:
352      - move bi,bj loops inside INTEGR_CONTINUITY ;
353      - call INTEGR_CONTINUITY directly from forward_step.F
354        (previously called from momentum_correction_step.F)
355      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
356        forward_step.F and pkg/ecco/the_main_loop.F
357    o model/src/do_oceanic_phys.F:
358      - reset addMass to zero only if useICEFRONT ;
359      - separated k-loop for rhoInSitu calculation ;
360      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
361        and at constant T,S (= WdRHOdP);
362      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
363        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
364        transport of locally-referenced potential density);
365        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
366    o gluemnc:
367      - replace ncrcat with ncks when adding variables to *.glob.nc
368      - change the way variables without record dimensions are handled so that
369        files that have variables with and without record variables can be glued:
370        add a record dimension with a new unique name to be able to differentiate
371        between variable with and without a-prior record dimensions. Remove
372        this record dimension before adding the variable to the *.glob.nc file.
373        This procedure automatically works also for grid.*.nc files that do not
374        have any record dimension.
375    o verification/cpl_aim+ocn:
376      - generate new reference output on baudelaire (gfortran, mpich2) (previously
377        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
378    o pkg/obcs/obcs_calc_stevens.F:
379      - add code for northern and southern boundaries.
380      - reorder some loops to save some operations and so that drFBar can be scalar
381    o model/src:
382      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
383        truncation) and add diagnostics for Adams-Bashforth tendency increment.
384      - update test-exp. AD output:
385        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
386      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
387        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
388        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
389        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
390        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
391        tutorial_plume_on_slope.
392    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
393      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
394      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
395      does not even come with an F77 compiler anymore, this should not be
396      a limitation
397    
398    checkpoint63e (2011/11/06)
399    o pkg/seaice adjoint of LSR:
400      - substantially rework STORE dirs.
401      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
402        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
403        and only perform SOLV_MAX_FIXED adjoint iters.
404        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
405        always goes to same record, meaning that the last forward field will be
406        the one used in the adjoint - an approximation.
407      - now produces non-zero LSR-related gradients, and acceptable gradients for
408        An's zonal (x-z) test case (to be checked in)
409      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
410        (but these are screwed up by the thermodynamics in the first place);
411        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
412        output_adm.txt also reflects changes to seaice_lsr
413      - global_ocean.cs32x15:
414        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
415          (output_adm.seaice.txt was updated)
416        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
417          (output_adm.seaice_dynmix.txt)
418    o test-exp. exp4+stevens:
419      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
420    o pkg/seaice (lsr solver):
421      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
422        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
423      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
424      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
425        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
426      - compute (with new S/R) and print initial (+ free-driff sol. if available)
427        and final residual of linearised system.
428    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
429      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
430    o pkg/obcs: Stevens BCs (still only for east and west)
431      - fix Stevens BCs by using intermediate velocities of previous
432        time step as "baroclinic" contribution rather velocity of one grid cell
433        inside the boundaries; more consistent but makes the entire treatment
434        more complicated, requires new pickup files and two new S/Rs:
435        obcs_copy_uv_n and obcs_save_uv_n
436        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
437        (undefined by default)
438      - silently move computation of some grid factors into separate loops to
439        save some recomputations
440      - add a hack for non-linear free surface
441      - add a verification experiment to exp4 that tests this code
442    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
443    
444    checkpoint63d (2011/10/25)
445    o pkg/obcs + seaice-dynamics:
446      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
447        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
448        values (consistent with an implicit method).
449      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
450        return to older implementation (same results as before); note that none of
451        the "experimental" OBCS_SEAICE options are implemented in the new version.
452      - switch test exp. seaice_obcs to use new version (update output).
453    o pkg/seaice:
454      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
455      - add parenthesis in Water-Ice drag calculations (evp & lsr);
456      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
457        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
458      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
459        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
460    o pkg/layers:
461      - Include potential density as new coordinate (Thanks to David Munday)
462    o pkg/dic:
463      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
464        carbonate computation/output to CALC_PCO2_APPROX
465    o pkg/generic_advdiff
466      - make TAF generate code that vectorizes:
467        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
468    o model/src:
469      - improve vectorization also for adjoint code of
470        solve_tridiagonal and solve_pentadiagonal. As this requires up to
471        5 new 3D-fields, this code is only turned on for the combination of
472        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
473        for singular matrix check (only for TARGET_NEC_SX).
474      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
475        ALLOW_AUTODIFF. This flag now needs to be set outside of
476        solve_tri/pentadiagonal.F
477    o pkg/exf:
478      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
479        optional namelist EXF_NML_OBCS).
480      - add many debug-print (to trace down where pkg/cal error msg comes from)
481    o pkg/mom_vecinv/mom_vi_hdissip.F
482      - rearrange loops so that vectorization is improved and in particular
483        the adjoint routine vectorizes. The code is a little longer now, but I
484        think easier to read.
485        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
486    o pkg/seaice:
487      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
488    o pkg/exch2:
489      - alternative code (without tile x tile matrix) for cumulated (global) sum;
490        used as default; keep using matrix version in adjustment.cs-32x32x1.
491    o tools/build_options:
492      - after merging some MPI and/or multi-threads specific optfiles so that
493        the modified default optfile support both built (using genmake2 -mpi
494        for the MPI built, using genmake2 -omp for OpenMP built),
495        move now obsolete optfiles to tools/build_options/unsupported/
496       (add copy of email sent to support list in doc/optfiles_changes.txt)
497    
498    checkpoint63c (2011/09/28)
499    o pkg/ebm:
500      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
501        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
502    o pkg/seaice (SItracer pickup)
503    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
504      To be done:
505      - thorough testing of missing fields in S/R seaice_read_pickup
506      - thorough matching between generic tracers and specific fields used
507        (e.g. volume-weighted age, area-weighted age, salinity, ...)
508    o pkg/grdchk:
509      - all procs calculate and print finite-difference gradient (for testreport)
510      - change description output used by testreport;
511      - AD testing: also compare and report Finite-difference gradient;
512        => update all output_adm*.txt
513    o test exp. global_ocean_ebm:
514      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
515        and turn on exactConserve; update (fwd) output.
516    o pkg/seaice (LSR):
517      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
518      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
519        * identical results with non-CS topology (but save up to half of EXCH calls)
520        * no much changes in cs-32 verification tests since no ice at face edges
521         (differences due to convergence criteria, since nb of iterations changed)
522        * expect some differences on lat-lon-cap grid.
523        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
524    o pkg/exch2:
525      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
526        many tiles); until alternative coding is added, just add a stop.
527    o pkg/kpp:
528      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
529        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
530    o optfiles:
531      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
532        into corresponding standard one, which now support different build:
533        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
534      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
535    o pkg/obcs (seaice):
536      - add missing EXCH for uIce,vIce after applying OBCS;
537      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
538        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
539        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
540      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
541      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
542        and eedata.mth for MPI and mutlti-threaded testing.
543    o pkg/flt:
544      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
545      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
546      - fix pickup and trajectories + profiles output with multi-threads;
547      - add parameter to select group of fields to write along trajectory and
548        profile (default unchanged);
549      - only call PORT_RAND* function when flt_noise <> 0;
550      - add multi-threaded test for verification exp. flt_example.
551    o eesupp/src:
552      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
553      - USE_OMP_THREADING: check that number of threads (from eedata) matches
554        actual number (from env.var. setting).
555    o pkg/ebm:
556      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
557      - add multi-threaded test for verification exp. global_ocean_ebm
558    
559    checkpoint63b (2011/08/29)
560    o pkg/ebm:
561      - fix sign of runoff;
562      - update directly forcing fields (Qnet,EmPmR) to use standard
563        external_forcing_surf.F (remove ebm_forcing_surf.F);
564      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
565      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
566        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
567      - update global_ocean_ebm parameters file data and update output (fwd+ad).
568    o verification/matrix_example:
569      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
570        MPI and mutlti-threaded testing.
571    o pkg/matrix:
572      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
573      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
574      - fix for multi-threaded (remove DATA statement);
575      - use standard DIFFERENT_MULTIPLE function;
576      - add MATRIX_OPTIONS.h
577    o verification/matrix_example:
578       To allow to split the domain in several tiles, change the domain size
579        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
580        Western side) of land points.
581    o (*_)write_pickup:
582      - fix few bugs in mypackage_read/write_pickup.F
583      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
584        array of length 1 (was caught by compiler syntax-check).
585    o pkg/diagnostics (velocity potential solver):
586      - fix initialisation of main diagonal matrix (for overlap values)
587    o tools/build_options:
588      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
589        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
590      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
591        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
592        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
593        and use "-devel" testreport option for standard testing on baudelaire.
594    o pkg/grdchk:
595      - Assume that all gradient-check position are within the same tile
596        corresponding to global indices (iGloTile,jGloTile) and that
597        positions (i,j indices or nbeg) are local to this tile;
598      - set tile local-indices and proc. number according to tile global-indices;
599      - remove grdchkwhichproc from namelist (retired param);
600      - send adjoint gradient to all procs so that all procs print it to STDOUT;
601      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
602    o adding package bbl (Bottom Boundary Layer)
603      description in MITgcm/pkg/bbl/bbl_description.tex
604      example/test experiment in MITgcm_contrib/bbl
605    o adjoint verifications
606      - changed 5 experiments to multi-tiles
607        * global_ocean.90x40x15
608        * obcs_ctrl
609        * offline_exf_seaice
610        * tutorial_dic_adjoffline
611        * tutorial_tracer_adjsens
612        changed reference output for those that crossed tile boundaries
613        (changed choices of gradient check positions)
614      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
615      - temporary bug fix in grdchk_loc.F for obcs
616    o genmake2 & testreport
617      - add target "obj" (just for OBJFILES files) to Makefile;
618      - add option to specify FEXTRAFLAGS on command line.
619    o pkg/mypackage:
620      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
621    
622    checkpoint63a (2011/08/02)
623  o pkg/diagnostics (velocity potential):  o pkg/diagnostics (velocity potential):
624    - fix velocity-potential calculation when using OBCS: balance net inflow    - fix velocity-potential calculation when using OBCS: balance net inflow
625      at each level (new S/R OBCS_DIAG_BALANCE).      at each level (new S/R OBCS_DIAG_BALANCE).
# Line 54  o pkg/gmredi: Line 670  o pkg/gmredi:
670     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
671     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)
672    
673  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
674  o pkg/exch2:  o pkg/exch2:
675   - 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
676   - 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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