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revision 1.1393 by jmc, Mon Mar 14 02:12:53 2011 UTC revision 1.1583 by mlosch, Mon Jan 30 11:19:33 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 vectorize salt_plume package:
8      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
9      - this code computes plumebk everywhere (also over land), thus requires
10        code to avoid divisions by zero and catch the case of kLev=Nr.
11      - efficiency of salt_plume_frac is still sub-optimal
12    o tools (genmake2):
13      - fix makefile NAME specification (option: -makefile NAME) by adding
14        "-f $MAKEFILE" in few places where it was missing including makedepend
15        command (contribution from Paul).
16    
17    checkpoint63i (2012/01/24)
18    o model/src:
19      - add factorized versions of some EOS code to find_rho.F,
20        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
21    o model/src:
22      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
23      - change default celsius2K from 273.16 to 273.15
24      - to keep results unchanged, add back old value of celsius2K in verification
25        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
26         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
27    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
28      to make TAF generate vectorizable code
29    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
30       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
31       have flags that do this more efficiently.
32    o pkg/diagnostics/diagstats_calc.F
33      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
34    o pkg/obcs (with exch2):
35      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
36        and remove code (in obcs_readparms.F) which was based on EXCH of indices
37        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
38    o pkg/exf and seaice exp:
39      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
40        so that switching off area & heff advection flags does not affect results.
41      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
42      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
43        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
44        results of verification experiments: 1D_ocean_ice_column(fwd),
45        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
46        and offline_exf_seaice (all 4).
47    o pkg/seaice:
48      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
49        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
50      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
51        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
52        not multi-dim advection;
53      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
54        SHORTWAVE_HEATING #undef.
55    o optim: make Makefile more robust (?)
56    o pkg/obcs:
57      * fix treatment of obcs_read_pickup for TAF
58    o pkg/shelfice:
59      * add missing initialisation of num_shifwflx
60      * new adjoint verification exp. for isomip
61      * change Prandtl and Schmidt numbers from generic formulations
62        (in terms of model diffus. and visc.) to separate runtime
63        parameters, with Holland and Jenkins (1999) default values.
64    o pkg/exf (interpolation):
65      - extended input field (2 rows) near the N & S poles:
66        * fill in with the symetric value (when even Nb of data in longitude)
67        * add average value at the poles only for scalar quantities ; for vector
68          component interpolation, skip the averaging and keep duplicated values,
69          unless the 2 components have same location (uvInterp=T) in which case
70          interpolate the 2 components together using S/R EXF_INTERP_UV.
71      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
72        together: this allows to account properly for local orientation when
73        averaging at N & S pole.
74      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
75        exf-interpolation near N & S poles. Undef by default.
76      - add debug check/print on 1rst iter if debugLevel >=2.
77    o pkg/exf:
78      - change masking flags definition (no longer "parameter"), put them in
79        common block and set them in S/R EXF_INIT_FIXED.
80      - change recognized masking flag from s,u,v to c,w,s since the mask
81        to use (maskC,W,S) depends on position on model grid and has little to
82        do with scalar/vector difference; fix masking if using P-coordinates.
83      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
84        and update results of exp. global_with_exf (x2).
85      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
86    o pkg/obcs
87      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
88    o pkg/exf (interpolation):
89      - assume periodicity in X only if input field cover full longitude range.
90      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
91        and should vectorise).
92      - fix input lat of the 2 added row (in case we provide N.pole data).
93    
94    checkpoint63h (2011/12/30)
95    o pkg/seaice:
96      - change declaration of UVM from _RL to _RS in order to get B-grid
97        uIce,vIce monitor when _RS = real*4
98    o pkg/offline:
99      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
100      - compute vertical velocity if not read from file (switch on exactConserv
101        & staggerTimeStep);
102      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
103    o verification:
104      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
105        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
106        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
107      - update output of exp. global_ocean.cs32x15.viscA4 after changing
108        grid-file angles (used here for coriolis-3d);
109      - remove (or gzip) few files not needed to run fizhi-cs experiments.
110    o pkg/exf (vector interpolation):
111      - rotate vector component toward local grid-axis orientation using grid-angles
112        (stored in GRID.h) instead of locally computed rotation angle; keep old code
113        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
114    o pkg/seaice:
115      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
116        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
117    o pkg/PKG_OPTIONS.h files:
118      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
119        outside of the #ifdef ALLOW_THISPKG / #endif block.
120      - update verification/*/code/PKG_OPTIONS.h files.
121    o add a verification experiment (offline_exf_seaice/input.seaice) that test
122      the B-grid LSOR solver
123    o pkg/seaice: sort out emissivity and long wave radiation step 2:
124      - add emissivity for snow and ice as new run-time parameters
125        (unfortunately) that default to the corresponding exf values; this
126        changes results in most verification experiments so that for backward
127        compatibility these parameter have to be set explicitly to inconsistent
128        values (ugly);
129      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
130        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
131        until we agree how to handle this bug properly
132    o pkg/exf (interpolation):
133      - add a set of run-time param ({inputfield}_interpMethod), one for
134        each interpolated input field, to select the interpolation method
135        with a value of zero switching off the interpolation;
136      - print interpolation parameters to standard output;
137      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
138        (to use instead runoff_interpMethod=0 in data.exf).
139      - simplify default setting of interpolation parameters (for all fields,
140        set position to match model grid cell-center position, leading to trivial
141        interpolation in case of regular Lat-Lon grid) and fix for the case of
142        non-uniform delY.
143    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
144       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
145       this factor is absolutely required, because the lw exitance (= out-going
146       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
147       where the reflectivity rho = 1-emissivity for conservation reasons. Once
148       this is established, we can remove the CPP-Flag (if we want to).
149    o pkg/seaice:
150      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
151        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
152      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
153        what the name implies (and not emissivity*BoltzmannConstant), this means
154        the old default value of 5.5e-8 now means
155        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
156        S/R exf_readparms
157      - FV-discretization of the B-grid LSOR solver, turn on with
158        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
159        of the calling routine dynsolver, so that B and C-grid code look a
160        little more alike.
161      - fix index bugs in ostres.F (B-grid code)
162    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
163    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
164      default for SEAICE_emissivity, if useEXF; requires setting a wrong
165      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
166      backward compatiblity
167    o model/src: use sigmaR in calc_ivdc
168    
169    checkpoint63g (2011/12/16)
170    o pkg/seaice/seaice_growth.F:
171      fix heat conservation of the coupled ocean-seaice system.
172      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
173      solid vs liquid water treatment is resolved via QNET.
174    o pkg/seaice/seaice_growth.F:
175      add missing term for sublimation in saltFlux, which was breaking conservation.
176    o pkg/seaice/seaice_model.F:
177      Remove this patholigical case treatment in evolution branch,
178      where it is un-necessary and breaks conservation.
179      Update global_ocean.cs32x15/results accordingly for
180      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
181    o model/src:
182      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
183      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
184    o pkg/obcs:
185      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
186      tendency for temperature and salinity that is then applied to update
187      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
188      horizontal advection and diffusion contributions on the boundary (in
189      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
190      removing the mask in S/R timestep_tracer. The advantage of this approach is
191      that the updated tracer values include contributions from the surface
192      forcing and vertical diffusion.
193      This modification changes exp4.stevens because of vertical diffusion.
194    o model/src:
195      change non-curvilinear grid setting to also work with exch2 + blank tiles:
196      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
197        face dimensions.
198      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
199        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
200        and INI_SPHERICAL_POLAR_GRID.
201      change test-experiment global_ocean.90x40x15:
202      - split the domain in many more tiles (9x4 tiles of 10x10 each);
203      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
204      - update results of both test (std & dwnslp).
205    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
206       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
207    o model/src:
208      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
209        and fix initialisation when using sigma-coords.
210    o model/src:
211     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
212       to their current value at the beginning of forward_step.F": add a new run-time
213       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
214     - set doResetHFactors=T in the following test exp:
215        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
216        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
217        and tutorial_global_oce_in_p (nonLinFS in p)
218    o pkg/ecco
219      - added IES cost term
220    o verification/advect_xz
221      - scale down the depth by 1/100 (from 200 km to just 2.km)
222      - add secondary test using divergent flow, r-star and implicit vertical advection.
223      - add note (check_conserve_TS.txt) and matlab script to check global
224        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
225    o pkg/rbcs:
226      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
227    o pkg/obcs (Stevens BCs):
228      - fix various problems in the phase speed computations of the Stevens
229        boundary conditions:
230        - sign error for western and southern boundaries,
231        - time tendencies were underestimated by factor of dTracerLev and some just
232          zero (for multidim advection schemes) -> now estimate time tendencies
233          from difference between previous (n) time level and the one before (n-1);
234          this requires storing a field per tracer per boundary, also in the pickup
235          files.
236        - replace deltaTmom in cflMer/Zon computation with dTracerLev
237        - set default phase velocity to cflMer/Zon
238      - update verification experiment exp4.stevens
239    o pkg/generic_advdiff (implicit_r):
240      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
241        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
242      - fix implicit vertical diffusion or advection with NonLin FreeSurf
243        (was using current recip_hFacC instead of future recip_hFacC): set future
244        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
245        solver S/R ;
246      - fill diagnostics of vertical advective fluxes (computed from tendency)
247        when using implicit vert. advection;
248      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
249         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
250         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
251         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
252    o pkg/diagnostics:
253      - add diags for T & S tendency which goes through Adams-Bashforth.
254    
255    checkpoint63f (2011/11/30)
256    o pkg/obcs/obcs_calc_stevens.F:
257      - join some loops to reduce number of if-statements
258      - fix a bug in code for northern and southern boundaries.
259    o pkg/seaice/seaice_init_varia.F
260      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
261        caused zero ice-velocities for the B-grid code
262    o pkg/seaice/seaice_init_fixed.F
263      - fix a bug in the initialisation of the second metric terms
264        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
265      - this affects all seaice configurations with useCurviLinearGrid = .true.
266        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
267        = .true. (default)
268      - the only verification experiment affected is global_ocean.cs32x15:
269        icedyn, seaice, and seaice_dynmix (AD)
270    o pkg/thsice/thsice_diagnostics_state.F
271      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
272        not contain garbage that can lead to surprises in diagstats_calc.F
273    o model/src:
274      - move bi,bj loops inside INTEGR_CONTINUITY ;
275      - call INTEGR_CONTINUITY directly from forward_step.F
276        (previously called from momentum_correction_step.F)
277      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
278        forward_step.F and pkg/ecco/the_main_loop.F
279    o model/src/do_oceanic_phys.F:
280      - reset addMass to zero only if useICEFRONT ;
281      - separated k-loop for rhoInSitu calculation ;
282      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
283        and at constant T,S (= WdRHOdP);
284      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
285        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
286        transport of locally-referenced potential density);
287        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
288    o gluemnc:
289      - replace ncrcat with ncks when adding variables to *.glob.nc
290      - change the way variables without record dimensions are handled so that
291        files that have variables with and without record variables can be glued:
292        add a record dimension with a new unique name to be able to differentiate
293        between variable with and without a-prior record dimensions. Remove
294        this record dimension before adding the variable to the *.glob.nc file.
295        This procedure automatically works also for grid.*.nc files that do not
296        have any record dimension.
297    o verification/cpl_aim+ocn:
298      - generate new reference output on baudelaire (gfortran, mpich2) (previously
299        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
300    o pkg/obcs/obcs_calc_stevens.F:
301      - add code for northern and southern boundaries.
302      - reorder some loops to save some operations and so that drFBar can be scalar
303    o model/src:
304      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
305        truncation) and add diagnostics for Adams-Bashforth tendency increment.
306      - update test-exp. AD output:
307        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
308      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
309        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
310        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
311        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
312        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
313        tutorial_plume_on_slope.
314    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
315      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
316      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
317      does not even come with an F77 compiler anymore, this should not be
318      a limitation
319    
320    checkpoint63e (2011/11/06)
321    o pkg/seaice adjoint of LSR:
322      - substantially rework STORE dirs.
323      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
324        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
325        and only perform SOLV_MAX_FIXED adjoint iters.
326        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
327        always goes to same record, meaning that the last forward field will be
328        the one used in the adjoint - an approximation.
329      - now produces non-zero LSR-related gradients, and acceptable gradients for
330        An's zonal (x-z) test case (to be checked in)
331      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
332        (but these are screwed up by the thermodynamics in the first place);
333        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
334        output_adm.txt also reflects changes to seaice_lsr
335      - global_ocean.cs32x15:
336        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
337          (output_adm.seaice.txt was updated)
338        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
339          (output_adm.seaice_dynmix.txt)
340    o test-exp. exp4+stevens:
341      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
342    o pkg/seaice (lsr solver):
343      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
344        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
345      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
346      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
347        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
348      - compute (with new S/R) and print initial (+ free-driff sol. if available)
349        and final residual of linearised system.
350    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
351      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
352    o pkg/obcs: Stevens BCs (still only for east and west)
353      - fix Stevens BCs by using intermediate velocities of previous
354        time step as "baroclinic" contribution rather velocity of one grid cell
355        inside the boundaries; more consistent but makes the entire treatment
356        more complicated, requires new pickup files and two new S/Rs:
357        obcs_copy_uv_n and obcs_save_uv_n
358        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
359        (undefined by default)
360      - silently move computation of some grid factors into separate loops to
361        save some recomputations
362      - add a hack for non-linear free surface
363      - add a verification experiment to exp4 that tests this code
364    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
365    
366    checkpoint63d (2011/10/25)
367    o pkg/obcs + seaice-dynamics:
368      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
369        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
370        values (consistent with an implicit method).
371      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
372        return to older implementation (same results as before); note that none of
373        the "experimental" OBCS_SEAICE options are implemented in the new version.
374      - switch test exp. seaice_obcs to use new version (update output).
375    o pkg/seaice:
376      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
377      - add parenthesis in Water-Ice drag calculations (evp & lsr);
378      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
379        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
380      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
381        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
382    o pkg/layers:
383      - Include potential density as new coordinate (Thanks to David Munday)
384    o pkg/dic:
385      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
386        carbonate computation/output to CALC_PCO2_APPROX
387    o pkg/generic_advdiff
388      - make TAF generate code that vectorizes:
389        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
390    o model/src:
391      - improve vectorization also for adjoint code of
392        solve_tridiagonal and solve_pentadiagonal. As this requires up to
393        5 new 3D-fields, this code is only turned on for the combination of
394        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
395        for singular matrix check (only for TARGET_NEC_SX).
396      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
397        ALLOW_AUTODIFF. This flag now needs to be set outside of
398        solve_tri/pentadiagonal.F
399    o pkg/exf:
400      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
401        optional namelist EXF_NML_OBCS).
402      - add many debug-print (to trace down where pkg/cal error msg comes from)
403    o pkg/mom_vecinv/mom_vi_hdissip.F
404      - rearrange loops so that vectorization is improved and in particular
405        the adjoint routine vectorizes. The code is a little longer now, but I
406        think easier to read.
407        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
408    o pkg/seaice:
409      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
410    o pkg/exch2:
411      - alternative code (without tile x tile matrix) for cumulated (global) sum;
412        used as default; keep using matrix version in adjustment.cs-32x32x1.
413    o tools/build_options:
414      - after merging some MPI and/or multi-threads specific optfiles so that
415        the modified default optfile support both built (using genmake2 -mpi
416        for the MPI built, using genmake2 -omp for OpenMP built),
417        move now obsolete optfiles to tools/build_options/unsupported/
418       (add copy of email sent to support list in doc/optfiles_changes.txt)
419    
420    checkpoint63c (2011/09/28)
421    o pkg/ebm:
422      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
423        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
424    o pkg/seaice (SItracer pickup)
425    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
426      To be done:
427      - thorough testing of missing fields in S/R seaice_read_pickup
428      - thorough matching between generic tracers and specific fields used
429        (e.g. volume-weighted age, area-weighted age, salinity, ...)
430    o pkg/grdchk:
431      - all procs calculate and print finite-difference gradient (for testreport)
432      - change description output used by testreport;
433      - AD testing: also compare and report Finite-difference gradient;
434        => update all output_adm*.txt
435    o test exp. global_ocean_ebm:
436      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
437        and turn on exactConserve; update (fwd) output.
438    o pkg/seaice (LSR):
439      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
440      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
441        * identical results with non-CS topology (but save up to half of EXCH calls)
442        * no much changes in cs-32 verification tests since no ice at face edges
443         (differences due to convergence criteria, since nb of iterations changed)
444        * expect some differences on lat-lon-cap grid.
445        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
446    o pkg/exch2:
447      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
448        many tiles); until alternative coding is added, just add a stop.
449    o pkg/kpp:
450      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
451        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
452    o optfiles:
453      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
454        into corresponding standard one, which now support different build:
455        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
456      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
457    o pkg/obcs (seaice):
458      - add missing EXCH for uIce,vIce after applying OBCS;
459      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
460        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
461        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
462      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
463      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
464        and eedata.mth for MPI and mutlti-threaded testing.
465    o pkg/flt:
466      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
467      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
468      - fix pickup and trajectories + profiles output with multi-threads;
469      - add parameter to select group of fields to write along trajectory and
470        profile (default unchanged);
471      - only call PORT_RAND* function when flt_noise <> 0;
472      - add multi-threaded test for verification exp. flt_example.
473    o eesupp/src:
474      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
475      - USE_OMP_THREADING: check that number of threads (from eedata) matches
476        actual number (from env.var. setting).
477    o pkg/ebm:
478      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
479      - add multi-threaded test for verification exp. global_ocean_ebm
480    
481    checkpoint63b (2011/08/29)
482    o pkg/ebm:
483      - fix sign of runoff;
484      - update directly forcing fields (Qnet,EmPmR) to use standard
485        external_forcing_surf.F (remove ebm_forcing_surf.F);
486      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
487      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
488        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
489      - update global_ocean_ebm parameters file data and update output (fwd+ad).
490    o verification/matrix_example:
491      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
492        MPI and mutlti-threaded testing.
493    o pkg/matrix:
494      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
495      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
496      - fix for multi-threaded (remove DATA statement);
497      - use standard DIFFERENT_MULTIPLE function;
498      - add MATRIX_OPTIONS.h
499    o verification/matrix_example:
500       To allow to split the domain in several tiles, change the domain size
501        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
502        Western side) of land points.
503    o (*_)write_pickup:
504      - fix few bugs in mypackage_read/write_pickup.F
505      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
506        array of length 1 (was caught by compiler syntax-check).
507    o pkg/diagnostics (velocity potential solver):
508      - fix initialisation of main diagonal matrix (for overlap values)
509    o tools/build_options:
510      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
511        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
512      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
513        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
514        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
515        and use "-devel" testreport option for standard testing on baudelaire.
516    o pkg/grdchk:
517      - Assume that all gradient-check position are within the same tile
518        corresponding to global indices (iGloTile,jGloTile) and that
519        positions (i,j indices or nbeg) are local to this tile;
520      - set tile local-indices and proc. number according to tile global-indices;
521      - remove grdchkwhichproc from namelist (retired param);
522      - send adjoint gradient to all procs so that all procs print it to STDOUT;
523      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
524    o adding package bbl (Bottom Boundary Layer)
525      description in MITgcm/pkg/bbl/bbl_description.tex
526      example/test experiment in MITgcm_contrib/bbl
527    o adjoint verifications
528      - changed 5 experiments to multi-tiles
529        * global_ocean.90x40x15
530        * obcs_ctrl
531        * offline_exf_seaice
532        * tutorial_dic_adjoffline
533        * tutorial_tracer_adjsens
534        changed reference output for those that crossed tile boundaries
535        (changed choices of gradient check positions)
536      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
537      - temporary bug fix in grdchk_loc.F for obcs
538    o genmake2 & testreport
539      - add target "obj" (just for OBJFILES files) to Makefile;
540      - add option to specify FEXTRAFLAGS on command line.
541    o pkg/mypackage:
542      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
543    
544    checkpoint63a (2011/08/02)
545    o pkg/diagnostics (velocity potential):
546      - fix velocity-potential calculation when using OBCS: balance net inflow
547        at each level (new S/R OBCS_DIAG_BALANCE).
548      - fix some of the problems with OBCS in stream-function calculation.
549    o pkg/exf/exf_readparms.F
550      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
551        EXF_NML_OBCS) more consistent, so that you need not have these lists
552        in data.exf when they are not used.
553    o optim/optim_readdata.F:
554      - add some output about obcs variables that might help debugging
555      - add a check about nvarlength
556    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
557    o pkg/diagnostics (velocity potential):
558      - fix mask for OBCS (still problems in stream-function with OBCS);
559      - add specific parameter (default = main code CG2D params) for solver;
560      - in case of poor convergence, use solution corresponding to lowest residual.
561    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
562      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
563      and should be avoided where possible.
564    o model/src (rStar):
565      - include r* effect on reference-state (PhiRef) in totPhiHyd
566        (so that it's really the potential anomaly at the cell center);
567        affect solution only if z* with full pressure in EOS.
568      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
569        update output (because of z* in totPhiHyd and viscA4 changes);
570      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
571        @ constant r) until interpolation at constant r is implemented.
572    o pkg/diagnostics
573      - fix RCENTER diagnostics in case cell center is not at interface middle
574    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
575      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
576      that THETA and SALT are "conservative temperature" and "absolute
577      salinity"
578    o pkg/ctrl
579      - fix computation of endrec in s/r ctrl_init_rec
580      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
581    o pkg/seaice/seaice_growth.F
582      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
583        remove then obsolete STORE directives
584      - fix STORE directives for tice and tices, so that only the
585        appropriate part of the fields are stored (and not the entire
586        field); update global_ocean.cs32x15.seaice AD output.
587      - cosmetic changes: adjust CPP flags and indentation for better
588        legibilty
589    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
590      Chris Wilson)
591    o pkg/gmredi:
592       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
593       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
594    
595    checkpoint63  (2011/07/11)
596    o pkg/exch2:
597     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
598     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
599       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
600       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
601    o pkg/diagnostics:
602     - deal with pairs of post-processed diags which are computed together; in
603       particular, re-order list of diags within 1 file to save 2nd computation.
604     - add S/R to compute velocity stream-function (called after velocity-potential
605       calculation) from divergence free transport -> new diagnostics "PsiVEL".
606     - add parameter to select grid-point location where PsiVEL == 0.
607    o eesupp/src:
608       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
609       (specific S/R needed with exch2 topology - for now, just print an error msg)
610    o pkg/shelfice
611     - Implement friction velocity-dependent transfer coefficients following
612       Holland and Jenkins, JPO, 1999
613       Original code by M. Losch with small modifs.
614       Enable with CPP option SHI_ALLOW_GAMMAFRICT
615       and runtime flag SHELFICEuseGammaFrict
616    o verification lab_sea & global_ocean.cs32x15:
617     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
618       does not miss some dependencies (but is slower) and also works with many files
619       (default makedepend limitation for AD built).
620     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
621    o pkg/diagnostics:
622     - add run-time parameter "useMissingValue" (def=False) to fill land-point
623        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
624       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
625     - Extend the use of "missing_value" setting from data.diagnostics for the case
626       of counter-diagnostics (where fraction-weight is zero). This applies both to
627       MNC and MDS output files.
628    o pkg/seaice/seaice_growth.F:
629      - add 'a priori' cap of latent heat flux based on actual mass considerations
630        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
631        non-legacy seaice_solve4temp.
632      - add diagnostic of the residual sublimation freshwater flux (the freshwater
633        flux taken from the ocean if the total actual latent heat fluxes exceed
634        the maximum)
635      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
636       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
637      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
638       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
639      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
640      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
641    o verification 1D_ocean_ice_column:
642       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
643       update results
644    o pkg/diagnostics:
645     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
646       which are not filled-up but computed from other diags ; In this case, the mate
647       diag points to the primary (filled-up) diag to used for post processing.
648     - Update Velocity-potential computation using post-processed diag framework.
649     ==> Change the ordering of fields and time-periods in MDS output file
650       when using periodic averaging: now writes one time record with the full set
651       of fields for this time period, then the next time reccord (it used to be
652       one field with the full set of time records then the next field).
653         Note: this is now similar to NetCDF (MNC) output file. <==
654    
655    checkpoint62z (2011/06/21)
656    o adjoint monitor:
657     - Add adjoint monitor output for packages exf, seaice
658       and update relevant testreport output
659    o pkg/seaice:
660     - re-order diags inits so that they appear in order in available_diagnostics.log
661     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
662       area/heff/hsnow preceeding thermodynamic growth/melt.
663     - modified diag: SIdA; output actual effect, as the description states.
664     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
665     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
666       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
667        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
668     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
669     - added diagnostics for seaice generic tracers (SItr*).
670     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
671     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
672     I. Fenty: 18-Jun-2011:
673     Minor changes to seaice package:
674     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
675        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
676       - Differentiated "regularization variables" from "floor variables"
677        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
678        * hiceMin became SEAICE_hice_reg (old hiceMin)
679          (with _reg meaning regularization variable)
680       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
681        so as to ensure energy conservation when going between phases
682      - A22 was not used anywhere
683     2) Changed regularization procedure for heffActual and hsnowActual to ensure
684        well-boundedness and smooth adjoint in seaice_growth.F
685     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
686        because the old regularization always set heffActual >= 0.05 cm
687     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
688        on AREA when HEFF > 0.
689      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
690        requiring that DISABLE_AREA_FLOOR *not* be defined
691     Affected verifications:
692      - 1D_ocean_ice_column (output.txt output_adm.txt)
693      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
694    o pkg/diagnostics:
695      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
696      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
697        (was _RL, now integer) with option = 0 to retrieve all levels.
698      - add pieces of code to compute velocity potential at each level (new diagnostics
699        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
700        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
701      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
702        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
703        and in diagnostics_fract_fill.F (do not need a valid pointer for the
704        diagnostics counter-mate); check that definition of counter-diagnostic
705        includes a valid counter-mate (in diagnostics_set_levels.F).
706    o model/src (rStar):
707      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
708        affect solution only if z* with full pressure in EOS;
709        update output of test-exp global_ocean.90x40x15.
710    o pkg/seaice:
711      - introduce siEps=1e-5 parameter
712      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
713      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
714      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
715        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
716        as well as ice cover age and ridging index (attached to AREA).
717        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
718        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
719        Up to SItrMaxNum=3 tracers can be used simultaneously.
720    o pkg/salt_plume:
721      -introduce SPsalFRAC run time parameter that sets the fraction of the
722       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
723       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
724    o model debug options:
725      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
726        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
727      - Refine debug-msg printing selection (3 new levels):
728        debugMode  : controls printing of debug messages (sequence of S/R calls).
729        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
730         debLevZero =  0 ; /* level of disabled aux. msg printing */
731         debLevA =  1 ; /* level of minimum  aux. msg printing */
732         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
733         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
734         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
735         debLevE =  5 ; /* level of extensive debug printing */
736        New debugLevel default: with default debugMode value (=F),
737          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
738          and if debugMode=T, default debugLevel = 4 (debLevD).
739        Relation with previous settings:
740         debLevB (=2) corresponds to former debLevA (=1)
741         debLevD (=4) corresponds to former debLevB (=2)
742        Note:
743         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
744         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
745            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
746      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
747        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
748    o pkg/obcs:
749      - change OBCSfixTopo default from True to False (should not change the results);
750        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
751    o pkg/thsice:
752      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
753        2nd layer seaice sublimation (unlikely to happen)
754      - use Interior mask for OBCS in thsice_advection.F (similar to what is
755        done in gad_advection & seaice_advection).
756    o adjoint:
757      bug fix spotted by Gael Forget:
758      seaice_advection and thsice_advection still had
759      legacy CPP options to avoid CS corner updates for adjoint
760    o pkg/seaice:
761      => Change some of the defaults (2011/05/29):
762         - change SEAICEuseFluxForm default (from False to True)
763         - change DIFF1 default (from 0.004 m/s to 0. m/s)
764         And print warnings if DIFF1 is not set in data.seaice and centered
765          avection scheme is used without any diffusion.
766      also:
767      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
768      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
769      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
770        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
771        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
772      update results of test exp.:
773         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
774             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
775             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
776         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
777         seaice_obcs: output (SEAICEuseFluxForm=T)
778      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
779          for standard fwd & AD lab_sea tests (to keep the same output).
780    o pkg/seaice/seaice_growth.F:
781      - use Ian Fenty's capping formulas for actual ice
782      thickness thoughout EVOLUTION branch.
783      - put treatment pathological case #2) in CPP brackets
784      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
785      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
786    o pkg/seaice:
787      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
788      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
789      also pass fac as a param, which can be 1. (to update the tendency
790      field) or the time step (to update the field itself).
791      - seaice_advdiff.F: for multidim, call seaice_diffusion with
792      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
793      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
794      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
795      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
796    o pkg/seaice:
797      diffusion with centered advection scheme (diffus.F & advect.F):
798      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
799        to just compute the laplacian of input-field.
800      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
801      - fix flux-form version in diffus.F to conserve tracer.
802      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
803       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
804    
805    checkpoint62y (2011/05/26)
806    o pkg/seaice:
807     - seaice_growth.F : in EVOLUTION branch, always include
808       a_QSWbyATM_cover in qnet (as it should be).
809     - verification/global_ocean.cs32x15 : update results accordingly
810       (output.seaice.txt output_adm.seaice.txt).
811    o pkg/seaice + obcs:
812     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
813       equivalent of assuming no tracer gradient outside the OB region.
814       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
815     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
816       after changes above);
817     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
818       only at OB location (instead of over a band of OLx width).
819    o pkg/seaice:
820     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
821       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
822    o pkg/obcs:
823      - split header file "OBCS.h" into 4 separated files:
824        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
825       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
826         (contain no conditional statement which depends on OBCS options).
827      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
828        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
829    o ctrl, cost, grdchk & autodiff pkgs:
830      - make options file more standard (like other {PKG}_OPTIONS.h file but
831        with AD_CONFIG.h); clean-up some of the included header files.
832    o pkg/obcs:
833      - do not mask tracer when applying OB (tracer == 0 could generate problems)
834      - apply tracer OB values to tracer field only at OB location (instead of
835        over a band of OLx width)
836      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
837      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
838        obcs_apply_tloc.F & obcs_apply_sloc.F
839    o obcs in model/src:
840      - call OBCS_APPLY_W only if NonHydrostatic.
841      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
842      - reset dEtaHdt and wVel to zero outside OB interior region ;
843      - leave tracer unchanged outside OB interior region: This has no effect
844        on the solution but just to prevent unrealistic tracer value outside OB.
845      - zero out velocity outside OB interior region: This has no effect on
846        the solution but just to prevent unrealistic velocity outside OB.
847    o obcs and non-lin free-surf:
848       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
849       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
850       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
851       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
852       update results of test-exp. exp4(nlfs).
853    o exp4 (nlfs) test-exp:
854       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
855       with NonLin-FreeSurf); update output.nlfs.txt
856    o obcs and 2d/3d solver norm:
857       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
858       and outside OB interior region (will allow to place OB further inside the
859       domain). Depending on the domain, can affects cg2d-Norm (previous
860       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
861       and cg3d-Norm (previous Norm was computed before canceling OB terms),
862       e.g. in tutorial_plume_on_slope.
863      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
864    o pkg rbcs:
865      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
866      - add capability to apply relaxation to horizontal velocity uVel & vVel.
867    o pkg/grdchk: add gradient check for control variable xx_shifwflx
868    o pkg/shelfice/shelfice_init_fixed.F
869      fix CPP-flag combinations
870    o pkg/seaice: Merge iceage code of Pierre Rampal
871      * update/change/correct ice age calculations
872      * add age updates for pathological cases
873      Probably needs more testing...
874    
875    checkpoint62x (2011/05/13)
876    o pkg/mom_vecinv:
877       high-order vorticity scheme: use interior masks (maskInW & S)
878       to zero-out (outside OB) gradient of vorticity.
879    o verification exp.:
880       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
881       hs94.128x64x5 and seaice_obcs ; update results.
882    o pkg/obcs:
883      fix bug in OBeta for YZ sections in obcs_exf_load.F
884    o pkg/ctrl, pkg/shelfice, and optim:
885      - add new control variable xx_shifwflx (fresh water flux underneath ice
886        shelves). This is almost as tedious as obcs-ctrl, because the
887        variables needs its own mask.
888      - add a cost function term that penalizes the deviation of xx_shifwflx
889        from the first guess (zero) in analogy to other control variables
890    o pkg/shelfice:
891      - start basic adjoint
892    o pkg/ctrl:
893      - remove extra 2D field "for good measure" when initializing in
894        ctrl_set_globfld_[xy/xz/yz].F
895      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
896      - improve error messages in ctrl_set_unpack_*
897    o OBC implementation in momentum:
898       use interior masks (maskInC,W & S) in momentum S/R:
899       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
900       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
901       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
902       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
903       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
904        (and also with Leith/Smagorinsky harmonic-viscosity).
905       Update output of experiment dome and exp4 (+nlfs).
906    o exp4 test-exp:
907      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
908        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
909        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
910        time-varying OB at Western-side for wVel (NonHyd); update output.
911      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
912        and biharmonic-viscosity ; also use prescribed time varying OB.
913    o pkg/obcs:
914      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
915    o model/src:
916      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
917      - initialise startTime & nIter0 with unlikely values: allows to set one
918        from the other without ambiguity.
919    o seaice_obcs test-exp.:
920      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
921    o pkg/obcs:
922      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
923        no longer needed with maskInC,W,S in pkg/generic_advdiff.
924    o pkg/seaice:
925      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
926        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
927      - fixed bug in the initialization of sea ice salinity variable HSALT
928        in seaice_init_varia.F  (removed dependence on ICE2WATR)
929    o fizhi-cs test exp.:
930       switch reference output convention for these 2 non-standard test-exp,
931        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
932          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
933       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
934    o model/inc:
935      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
936        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
937    o pkg/seaice:
938      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
939    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
940      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
941        and initial HSALT
942    
943    checkpoint62w (2011/04/26)
944    o pkg/mom_fluxform:
945      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
946      - use parameter "sideDragFactor" in no-slip BC side-drag part.
947      - update output of exp. global_ocean.90x40x15
948    o pkg/mom_vecinv:
949      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
950    o update seaice exp.:
951      use more consistent parameter values (remove "backward compatability only":
952       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
953      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
954       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
955    o update test-exp global_ocean.90x40x15:
956      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
957      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
958      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
959      o turn on zStar & viscA4 in standard set-up (dir input/)
960        and update output files: output.txt & output.dwnslp.txt
961    o new AD-test experiment: obcs_ctrl
962      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
963    o pkg/dic:
964      fix two bugs in handling water vapour pressure in carbonate chemistry
965      and air-sea fluxes. Found by Val Bennington and Galen McKinley
966      (add DIC Option = WATERVAP_BUG to recover old results)
967      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
968    o adding allowInteriorFreezing option to check for water below freezing point
969      at depth and bring the negative heat anomaly to the surface level
970    o pkgs _fields_load:
971      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
972      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
973        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
974        rbcs to get interpolation weights and time reccord number.
975      - fix multi-threading in aim_fields_load.F
976      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
977    o external_fields_load:
978      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
979       interpolation weights) to use in a periodic time-series ; do not divide by
980       time-step to convert to integer:
981       - this fixes case where externForcingPeriod is not multiple of time-step
982          (Thanks to Christopher L. Wolfe)
983       - this fixes case where externForcingPeriod is an odd multiple of time-step
984         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
985      store index of time-record which is currently loaded:
986       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
987       - needed for the adjoint but not yet used because of extensive recomputations;
988         (to be fixed soon)
989    
990    checkpoint62v (2011/04/02)
991    o verification/1D_ocean_ice_column added to test Ian Fenty's
992      pkg/seaice_growth.F modifications for improving sea ice code differentiability
993    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
994      (new velocity statistics after changing maskInW & maskInS definition)
995    o pkg/generic_advdiff with OBCS:
996      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
997      equivalent to assumption of no tracer gradient outside the OB region.
998      This will affect the results if using obcs+biharmonic diffusion.
999      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1000    o pkg/obcs:
1001      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1002      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1003      in Interior region. No impact on solution but affects Velocity monitor stats.
1004    o pkg/ptracers (adjoint)
1005      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1006      tape file for each tracer
1007    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1008      of parts of the adjoint code at run time. For now, there are only
1009      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1010      parameters are set in data.pkg.
1011      This is the lazy coward's version of doing this, but still useful for
1012      debugging. In order to do it right, everything needs to be moved to
1013      pkg/autodiff.
1014    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1015      the end; this fixes the adjoint balancing code for open boundaries.
1016    o pkg/ctrl:
1017      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1018        xx_${varname}period =   0.,  means time-independent control part
1019        xx_${varname}period = -12., means one-year-periodic monthly control part
1020      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1021        clean up ctrl_init a little, remove unused variables
1022      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1023      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1024    
1025    checkpoint62u (2011/03/15)
1026    o model/src:
1027      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1028        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1029      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1030        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1031    o pkg/ctrl/obcs/ecco:
1032      - remove obsolete, unused, and partially broken code:
1033        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1034        ALLOW_CTRL_OBCS_BALANCE
1035      - put a stop statement into ecco/cost_obcsvol.F, but also add
1036        cost_obcsvol to ecco_ad_diff.list
1037    o pkg/ecco: fix counting cost function contributions for obcs (code
1038      by Matt M.) and diffkr for diagnostics
1039    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1040      add cost penalty terms for initial uvel, vvel, eta controls
1041      and I/O for prior error files
1042  o pkg/mdsio:  o pkg/mdsio:
1043     move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option     move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1044     (new argument) to check for tiled file in mdsioLocalDir : this fix the     (new argument) to check for tiled file in mdsioLocalDir : this fix the
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