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revision 1.1391 by mlosch, Wed Mar 9 16:18:06 2011 UTC revision 1.1578 by mlosch, Fri Jan 20 15:49:11 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/ctrl/ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.  o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
8      to make TAF generate vectorizable code
9    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
10       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
11       have flags that do this more efficiently.
12    o pkg/diagnostics/diagstats_calc.F
13      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
14    o pkg/obcs (with exch2):
15      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
16        and remove code (in obcs_readparms.F) which was based on EXCH of indices
17        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
18    o pkg/exf and seaice exp:
19      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
20        so that switching off area & heff advection flags does not affect results.
21      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
22      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
23        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
24        results of verification experiments: 1D_ocean_ice_column(fwd),
25        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
26        and offline_exf_seaice (all 4).
27    o pkg/seaice:
28      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
29        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
30      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
31        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
32        not multi-dim advection;
33      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
34        SHORTWAVE_HEATING #undef.
35    o optim: make Makefile more robust (?)
36    o pkg/obcs:
37      * fix treatment of obcs_read_pickup for TAF
38    o pkg/shelfice:
39      * add missing initialisation of num_shifwflx
40      * new adjoint verification exp. for isomip
41      * change Prandtl and Schmidt numbers from generic formulations
42        (in terms of model diffus. and visc.) to separate runtime
43        parameters, with Holland and Jenkins (1999) default values.
44    o pkg/exf (interpolation):
45      - extended input field (2 rows) near the N & S poles:
46        * fill in with the symetric value (when even Nb of data in longitude)
47        * add average value at the poles only for scalar quantities ; for vector
48          component interpolation, skip the averaging and keep duplicated values,
49          unless the 2 components have same location (uvInterp=T) in which case
50          interpolate the 2 components together using S/R EXF_INTERP_UV.
51      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
52        together: this allows to account properly for local orientation when
53        averaging at N & S pole.
54      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
55        exf-interpolation near N & S poles. Undef by default.
56      - add debug check/print on 1rst iter if debugLevel >=2.
57    o pkg/exf:
58      - change masking flags definition (no longer "parameter"), put them in
59        common block and set them in S/R EXF_INIT_FIXED.
60      - change recognized masking flag from s,u,v to c,w,s since the mask
61        to use (maskC,W,S) depends on position on model grid and has little to
62        do with scalar/vector difference; fix masking if using P-coordinates.
63      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
64        and update results of exp. global_with_exf (x2).
65      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
66    o pkg/obcs
67      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
68    o pkg/exf (interpolation):
69      - assume periodicity in X only if input field cover full longitude range.
70      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
71        and should vectorise).
72      - fix input lat of the 2 added row (in case we provide N.pole data).
73    
74    checkpoint63h (2011/12/30)
75    o pkg/seaice:
76      - change declaration of UVM from _RL to _RS in order to get B-grid
77        uIce,vIce monitor when _RS = real*4
78    o pkg/offline:
79      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
80      - compute vertical velocity if not read from file (switch on exactConserv
81        & staggerTimeStep);
82      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
83    o verification:
84      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
85        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
86        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
87      - update output of exp. global_ocean.cs32x15.viscA4 after changing
88        grid-file angles (used here for coriolis-3d);
89      - remove (or gzip) few files not needed to run fizhi-cs experiments.
90    o pkg/exf (vector interpolation):
91      - rotate vector component toward local grid-axis orientation using grid-angles
92        (stored in GRID.h) instead of locally computed rotation angle; keep old code
93        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
94    o pkg/seaice:
95      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
96        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
97    o pkg/PKG_OPTIONS.h files:
98      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
99        outside of the #ifdef ALLOW_THISPKG / #endif block.
100      - update verification/*/code/PKG_OPTIONS.h files.
101    o add a verification experiment (offline_exf_seaice/input.seaice) that test
102      the B-grid LSOR solver
103    o pkg/seaice: sort out emissivity and long wave radiation step 2:
104      - add emissivity for snow and ice as new run-time parameters
105        (unfortunately) that default to the corresponding exf values; this
106        changes results in most verification experiments so that for backward
107        compatibility these parameter have to be set explicitly to inconsistent
108        values (ugly);
109      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
110        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
111        until we agree how to handle this bug properly
112    o pkg/exf (interpolation):
113      - add a set of run-time param ({inputfield}_interpMethod), one for
114        each interpolated input field, to select the interpolation method
115        with a value of zero switching off the interpolation;
116      - print interpolation parameters to standard output;
117      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
118        (to use instead runoff_interpMethod=0 in data.exf).
119      - simplify default setting of interpolation parameters (for all fields,
120        set position to match model grid cell-center position, leading to trivial
121        interpolation in case of regular Lat-Lon grid) and fix for the case of
122        non-uniform delY.
123    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
124       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
125       this factor is absolutely required, because the lw exitance (= out-going
126       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
127       where the reflectivity rho = 1-emissivity for conservation reasons. Once
128       this is established, we can remove the CPP-Flag (if we want to).
129    o pkg/seaice:
130      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
131        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
132      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
133        what the name implies (and not emissivity*BoltzmannConstant), this means
134        the old default value of 5.5e-8 now means
135        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
136        S/R exf_readparms
137      - FV-discretization of the B-grid LSOR solver, turn on with
138        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
139        of the calling routine dynsolver, so that B and C-grid code look a
140        little more alike.
141      - fix index bugs in ostres.F (B-grid code)
142    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
143    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
144      default for SEAICE_emissivity, if useEXF; requires setting a wrong
145      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
146      backward compatiblity
147    o model/src: use sigmaR in calc_ivdc
148    
149    checkpoint63g (2011/12/16)
150    o pkg/seaice/seaice_growth.F:
151      fix heat conservation of the coupled ocean-seaice system.
152      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
153      solid vs liquid water treatment is resolved via QNET.
154    o pkg/seaice/seaice_growth.F:
155      add missing term for sublimation in saltFlux, which was breaking conservation.
156    o pkg/seaice/seaice_model.F:
157      Remove this patholigical case treatment in evolution branch,
158      where it is un-necessary and breaks conservation.
159      Update global_ocean.cs32x15/results accordingly for
160      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
161    o model/src:
162      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
163      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
164    o pkg/obcs:
165      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
166      tendency for temperature and salinity that is then applied to update
167      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
168      horizontal advection and diffusion contributions on the boundary (in
169      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
170      removing the mask in S/R timestep_tracer. The advantage of this approach is
171      that the updated tracer values include contributions from the surface
172      forcing and vertical diffusion.
173      This modification changes exp4.stevens because of vertical diffusion.
174    o model/src:
175      change non-curvilinear grid setting to also work with exch2 + blank tiles:
176      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
177        face dimensions.
178      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
179        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
180        and INI_SPHERICAL_POLAR_GRID.
181      change test-experiment global_ocean.90x40x15:
182      - split the domain in many more tiles (9x4 tiles of 10x10 each);
183      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
184      - update results of both test (std & dwnslp).
185    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
186       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
187    o model/src:
188      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
189        and fix initialisation when using sigma-coords.
190    o model/src:
191     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
192       to their current value at the beginning of forward_step.F": add a new run-time
193       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
194     - set doResetHFactors=T in the following test exp:
195        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
196        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
197        and tutorial_global_oce_in_p (nonLinFS in p)
198    o pkg/ecco
199      - added IES cost term
200    o verification/advect_xz
201      - scale down the depth by 1/100 (from 200 km to just 2.km)
202      - add secondary test using divergent flow, r-star and implicit vertical advection.
203      - add note (check_conserve_TS.txt) and matlab script to check global
204        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
205    o pkg/rbcs:
206      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
207    o pkg/obcs (Stevens BCs):
208      - fix various problems in the phase speed computations of the Stevens
209        boundary conditions:
210        - sign error for western and southern boundaries,
211        - time tendencies were underestimated by factor of dTracerLev and some just
212          zero (for multidim advection schemes) -> now estimate time tendencies
213          from difference between previous (n) time level and the one before (n-1);
214          this requires storing a field per tracer per boundary, also in the pickup
215          files.
216        - replace deltaTmom in cflMer/Zon computation with dTracerLev
217        - set default phase velocity to cflMer/Zon
218      - update verification experiment exp4.stevens
219    o pkg/generic_advdiff (implicit_r):
220      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
221        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
222      - fix implicit vertical diffusion or advection with NonLin FreeSurf
223        (was using current recip_hFacC instead of future recip_hFacC): set future
224        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
225        solver S/R ;
226      - fill diagnostics of vertical advective fluxes (computed from tendency)
227        when using implicit vert. advection;
228      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
229         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
230         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
231         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
232    o pkg/diagnostics:
233      - add diags for T & S tendency which goes through Adams-Bashforth.
234    
235    checkpoint63f (2011/11/30)
236    o pkg/obcs/obcs_calc_stevens.F:
237      - join some loops to reduce number of if-statements
238      - fix a bug in code for northern and southern boundaries.
239    o pkg/seaice/seaice_init_varia.F
240      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
241        caused zero ice-velocities for the B-grid code
242    o pkg/seaice/seaice_init_fixed.F
243      - fix a bug in the initialisation of the second metric terms
244        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
245      - this affects all seaice configurations with useCurviLinearGrid = .true.
246        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
247        = .true. (default)
248      - the only verification experiment affected is global_ocean.cs32x15:
249        icedyn, seaice, and seaice_dynmix (AD)
250    o pkg/thsice/thsice_diagnostics_state.F
251      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
252        not contain garbage that can lead to surprises in diagstats_calc.F
253    o model/src:
254      - move bi,bj loops inside INTEGR_CONTINUITY ;
255      - call INTEGR_CONTINUITY directly from forward_step.F
256        (previously called from momentum_correction_step.F)
257      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
258        forward_step.F and pkg/ecco/the_main_loop.F
259    o model/src/do_oceanic_phys.F:
260      - reset addMass to zero only if useICEFRONT ;
261      - separated k-loop for rhoInSitu calculation ;
262      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
263        and at constant T,S (= WdRHOdP);
264      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
265        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
266        transport of locally-referenced potential density);
267        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
268    o gluemnc:
269      - replace ncrcat with ncks when adding variables to *.glob.nc
270      - change the way variables without record dimensions are handled so that
271        files that have variables with and without record variables can be glued:
272        add a record dimension with a new unique name to be able to differentiate
273        between variable with and without a-prior record dimensions. Remove
274        this record dimension before adding the variable to the *.glob.nc file.
275        This procedure automatically works also for grid.*.nc files that do not
276        have any record dimension.
277    o verification/cpl_aim+ocn:
278      - generate new reference output on baudelaire (gfortran, mpich2) (previously
279        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
280    o pkg/obcs/obcs_calc_stevens.F:
281      - add code for northern and southern boundaries.
282      - reorder some loops to save some operations and so that drFBar can be scalar
283    o model/src:
284      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
285        truncation) and add diagnostics for Adams-Bashforth tendency increment.
286      - update test-exp. AD output:
287        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
288      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
289        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
290        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
291        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
292        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
293        tutorial_plume_on_slope.
294    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
295      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
296      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
297      does not even come with an F77 compiler anymore, this should not be
298      a limitation
299    
300    checkpoint63e (2011/11/06)
301    o pkg/seaice adjoint of LSR:
302      - substantially rework STORE dirs.
303      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
304        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
305        and only perform SOLV_MAX_FIXED adjoint iters.
306        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
307        always goes to same record, meaning that the last forward field will be
308        the one used in the adjoint - an approximation.
309      - now produces non-zero LSR-related gradients, and acceptable gradients for
310        An's zonal (x-z) test case (to be checked in)
311      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
312        (but these are screwed up by the thermodynamics in the first place);
313        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
314        output_adm.txt also reflects changes to seaice_lsr
315      - global_ocean.cs32x15:
316        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
317          (output_adm.seaice.txt was updated)
318        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
319          (output_adm.seaice_dynmix.txt)
320    o test-exp. exp4+stevens:
321      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
322    o pkg/seaice (lsr solver):
323      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
324        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
325      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
326      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
327        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
328      - compute (with new S/R) and print initial (+ free-driff sol. if available)
329        and final residual of linearised system.
330    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
331      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
332    o pkg/obcs: Stevens BCs (still only for east and west)
333      - fix Stevens BCs by using intermediate velocities of previous
334        time step as "baroclinic" contribution rather velocity of one grid cell
335        inside the boundaries; more consistent but makes the entire treatment
336        more complicated, requires new pickup files and two new S/Rs:
337        obcs_copy_uv_n and obcs_save_uv_n
338        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
339        (undefined by default)
340      - silently move computation of some grid factors into separate loops to
341        save some recomputations
342      - add a hack for non-linear free surface
343      - add a verification experiment to exp4 that tests this code
344    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
345    
346    checkpoint63d (2011/10/25)
347    o pkg/obcs + seaice-dynamics:
348      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
349        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
350        values (consistent with an implicit method).
351      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
352        return to older implementation (same results as before); note that none of
353        the "experimental" OBCS_SEAICE options are implemented in the new version.
354      - switch test exp. seaice_obcs to use new version (update output).
355    o pkg/seaice:
356      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
357      - add parenthesis in Water-Ice drag calculations (evp & lsr);
358      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
359        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
360      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
361        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
362    o pkg/layers:
363      - Include potential density as new coordinate (Thanks to David Munday)
364    o pkg/dic:
365      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
366        carbonate computation/output to CALC_PCO2_APPROX
367    o pkg/generic_advdiff
368      - make TAF generate code that vectorizes:
369        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
370    o model/src:
371      - improve vectorization also for adjoint code of
372        solve_tridiagonal and solve_pentadiagonal. As this requires up to
373        5 new 3D-fields, this code is only turned on for the combination of
374        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
375        for singular matrix check (only for TARGET_NEC_SX).
376      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
377        ALLOW_AUTODIFF. This flag now needs to be set outside of
378        solve_tri/pentadiagonal.F
379    o pkg/exf:
380      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
381        optional namelist EXF_NML_OBCS).
382      - add many debug-print (to trace down where pkg/cal error msg comes from)
383    o pkg/mom_vecinv/mom_vi_hdissip.F
384      - rearrange loops so that vectorization is improved and in particular
385        the adjoint routine vectorizes. The code is a little longer now, but I
386        think easier to read.
387        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
388    o pkg/seaice:
389      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
390    o pkg/exch2:
391      - alternative code (without tile x tile matrix) for cumulated (global) sum;
392        used as default; keep using matrix version in adjustment.cs-32x32x1.
393    o tools/build_options:
394      - after merging some MPI and/or multi-threads specific optfiles so that
395        the modified default optfile support both built (using genmake2 -mpi
396        for the MPI built, using genmake2 -omp for OpenMP built),
397        move now obsolete optfiles to tools/build_options/unsupported/
398       (add copy of email sent to support list in doc/optfiles_changes.txt)
399    
400    checkpoint63c (2011/09/28)
401    o pkg/ebm:
402      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
403        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
404    o pkg/seaice (SItracer pickup)
405    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
406      To be done:
407      - thorough testing of missing fields in S/R seaice_read_pickup
408      - thorough matching between generic tracers and specific fields used
409        (e.g. volume-weighted age, area-weighted age, salinity, ...)
410    o pkg/grdchk:
411      - all procs calculate and print finite-difference gradient (for testreport)
412      - change description output used by testreport;
413      - AD testing: also compare and report Finite-difference gradient;
414        => update all output_adm*.txt
415    o test exp. global_ocean_ebm:
416      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
417        and turn on exactConserve; update (fwd) output.
418    o pkg/seaice (LSR):
419      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
420      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
421        * identical results with non-CS topology (but save up to half of EXCH calls)
422        * no much changes in cs-32 verification tests since no ice at face edges
423         (differences due to convergence criteria, since nb of iterations changed)
424        * expect some differences on lat-lon-cap grid.
425        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
426    o pkg/exch2:
427      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
428        many tiles); until alternative coding is added, just add a stop.
429    o pkg/kpp:
430      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
431        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
432    o optfiles:
433      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
434        into corresponding standard one, which now support different build:
435        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
436      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
437    o pkg/obcs (seaice):
438      - add missing EXCH for uIce,vIce after applying OBCS;
439      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
440        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
441        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
442      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
443      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
444        and eedata.mth for MPI and mutlti-threaded testing.
445    o pkg/flt:
446      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
447      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
448      - fix pickup and trajectories + profiles output with multi-threads;
449      - add parameter to select group of fields to write along trajectory and
450        profile (default unchanged);
451      - only call PORT_RAND* function when flt_noise <> 0;
452      - add multi-threaded test for verification exp. flt_example.
453    o eesupp/src:
454      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
455      - USE_OMP_THREADING: check that number of threads (from eedata) matches
456        actual number (from env.var. setting).
457    o pkg/ebm:
458      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
459      - add multi-threaded test for verification exp. global_ocean_ebm
460    
461    checkpoint63b (2011/08/29)
462    o pkg/ebm:
463      - fix sign of runoff;
464      - update directly forcing fields (Qnet,EmPmR) to use standard
465        external_forcing_surf.F (remove ebm_forcing_surf.F);
466      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
467      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
468        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
469      - update global_ocean_ebm parameters file data and update output (fwd+ad).
470    o verification/matrix_example:
471      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
472        MPI and mutlti-threaded testing.
473    o pkg/matrix:
474      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
475      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
476      - fix for multi-threaded (remove DATA statement);
477      - use standard DIFFERENT_MULTIPLE function;
478      - add MATRIX_OPTIONS.h
479    o verification/matrix_example:
480       To allow to split the domain in several tiles, change the domain size
481        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
482        Western side) of land points.
483    o (*_)write_pickup:
484      - fix few bugs in mypackage_read/write_pickup.F
485      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
486        array of length 1 (was caught by compiler syntax-check).
487    o pkg/diagnostics (velocity potential solver):
488      - fix initialisation of main diagonal matrix (for overlap values)
489    o tools/build_options:
490      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
491        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
492      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
493        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
494        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
495        and use "-devel" testreport option for standard testing on baudelaire.
496    o pkg/grdchk:
497      - Assume that all gradient-check position are within the same tile
498        corresponding to global indices (iGloTile,jGloTile) and that
499        positions (i,j indices or nbeg) are local to this tile;
500      - set tile local-indices and proc. number according to tile global-indices;
501      - remove grdchkwhichproc from namelist (retired param);
502      - send adjoint gradient to all procs so that all procs print it to STDOUT;
503      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
504    o adding package bbl (Bottom Boundary Layer)
505      description in MITgcm/pkg/bbl/bbl_description.tex
506      example/test experiment in MITgcm_contrib/bbl
507    o adjoint verifications
508      - changed 5 experiments to multi-tiles
509        * global_ocean.90x40x15
510        * obcs_ctrl
511        * offline_exf_seaice
512        * tutorial_dic_adjoffline
513        * tutorial_tracer_adjsens
514        changed reference output for those that crossed tile boundaries
515        (changed choices of gradient check positions)
516      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
517      - temporary bug fix in grdchk_loc.F for obcs
518    o genmake2 & testreport
519      - add target "obj" (just for OBJFILES files) to Makefile;
520      - add option to specify FEXTRAFLAGS on command line.
521    o pkg/mypackage:
522      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
523    
524    checkpoint63a (2011/08/02)
525    o pkg/diagnostics (velocity potential):
526      - fix velocity-potential calculation when using OBCS: balance net inflow
527        at each level (new S/R OBCS_DIAG_BALANCE).
528      - fix some of the problems with OBCS in stream-function calculation.
529    o pkg/exf/exf_readparms.F
530      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
531        EXF_NML_OBCS) more consistent, so that you need not have these lists
532        in data.exf when they are not used.
533    o optim/optim_readdata.F:
534      - add some output about obcs variables that might help debugging
535      - add a check about nvarlength
536    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
537    o pkg/diagnostics (velocity potential):
538      - fix mask for OBCS (still problems in stream-function with OBCS);
539      - add specific parameter (default = main code CG2D params) for solver;
540      - in case of poor convergence, use solution corresponding to lowest residual.
541    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
542      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
543      and should be avoided where possible.
544    o model/src (rStar):
545      - include r* effect on reference-state (PhiRef) in totPhiHyd
546        (so that it's really the potential anomaly at the cell center);
547        affect solution only if z* with full pressure in EOS.
548      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
549        update output (because of z* in totPhiHyd and viscA4 changes);
550      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
551        @ constant r) until interpolation at constant r is implemented.
552    o pkg/diagnostics
553      - fix RCENTER diagnostics in case cell center is not at interface middle
554    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
555      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
556      that THETA and SALT are "conservative temperature" and "absolute
557      salinity"
558    o pkg/ctrl
559      - fix computation of endrec in s/r ctrl_init_rec
560      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
561    o pkg/seaice/seaice_growth.F
562      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
563        remove then obsolete STORE directives
564      - fix STORE directives for tice and tices, so that only the
565        appropriate part of the fields are stored (and not the entire
566        field); update global_ocean.cs32x15.seaice AD output.
567      - cosmetic changes: adjust CPP flags and indentation for better
568        legibilty
569    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
570      Chris Wilson)
571    o pkg/gmredi:
572       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
573       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
574    
575    checkpoint63  (2011/07/11)
576    o pkg/exch2:
577     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
578     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
579       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
580       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
581    o pkg/diagnostics:
582     - deal with pairs of post-processed diags which are computed together; in
583       particular, re-order list of diags within 1 file to save 2nd computation.
584     - add S/R to compute velocity stream-function (called after velocity-potential
585       calculation) from divergence free transport -> new diagnostics "PsiVEL".
586     - add parameter to select grid-point location where PsiVEL == 0.
587    o eesupp/src:
588       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
589       (specific S/R needed with exch2 topology - for now, just print an error msg)
590    o pkg/shelfice
591     - Implement friction velocity-dependent transfer coefficients following
592       Holland and Jenkins, JPO, 1999
593       Original code by M. Losch with small modifs.
594       Enable with CPP option SHI_ALLOW_GAMMAFRICT
595       and runtime flag SHELFICEuseGammaFrict
596    o verification lab_sea & global_ocean.cs32x15:
597     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
598       does not miss some dependencies (but is slower) and also works with many files
599       (default makedepend limitation for AD built).
600     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
601    o pkg/diagnostics:
602     - add run-time parameter "useMissingValue" (def=False) to fill land-point
603        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
604       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
605     - Extend the use of "missing_value" setting from data.diagnostics for the case
606       of counter-diagnostics (where fraction-weight is zero). This applies both to
607       MNC and MDS output files.
608    o pkg/seaice/seaice_growth.F:
609      - add 'a priori' cap of latent heat flux based on actual mass considerations
610        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
611        non-legacy seaice_solve4temp.
612      - add diagnostic of the residual sublimation freshwater flux (the freshwater
613        flux taken from the ocean if the total actual latent heat fluxes exceed
614        the maximum)
615      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
616       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
617      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
618       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
619      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
620      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
621    o verification 1D_ocean_ice_column:
622       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
623       update results
624    o pkg/diagnostics:
625     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
626       which are not filled-up but computed from other diags ; In this case, the mate
627       diag points to the primary (filled-up) diag to used for post processing.
628     - Update Velocity-potential computation using post-processed diag framework.
629     ==> Change the ordering of fields and time-periods in MDS output file
630       when using periodic averaging: now writes one time record with the full set
631       of fields for this time period, then the next time reccord (it used to be
632       one field with the full set of time records then the next field).
633         Note: this is now similar to NetCDF (MNC) output file. <==
634    
635    checkpoint62z (2011/06/21)
636    o adjoint monitor:
637     - Add adjoint monitor output for packages exf, seaice
638       and update relevant testreport output
639    o pkg/seaice:
640     - re-order diags inits so that they appear in order in available_diagnostics.log
641     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
642       area/heff/hsnow preceeding thermodynamic growth/melt.
643     - modified diag: SIdA; output actual effect, as the description states.
644     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
645     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
646       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
647        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
648     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
649     - added diagnostics for seaice generic tracers (SItr*).
650     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
651     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
652     I. Fenty: 18-Jun-2011:
653     Minor changes to seaice package:
654     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
655        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
656       - Differentiated "regularization variables" from "floor variables"
657        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
658        * hiceMin became SEAICE_hice_reg (old hiceMin)
659          (with _reg meaning regularization variable)
660       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
661        so as to ensure energy conservation when going between phases
662      - A22 was not used anywhere
663     2) Changed regularization procedure for heffActual and hsnowActual to ensure
664        well-boundedness and smooth adjoint in seaice_growth.F
665     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
666        because the old regularization always set heffActual >= 0.05 cm
667     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
668        on AREA when HEFF > 0.
669      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
670        requiring that DISABLE_AREA_FLOOR *not* be defined
671     Affected verifications:
672      - 1D_ocean_ice_column (output.txt output_adm.txt)
673      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
674    o pkg/diagnostics:
675      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
676      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
677        (was _RL, now integer) with option = 0 to retrieve all levels.
678      - add pieces of code to compute velocity potential at each level (new diagnostics
679        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
680        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
681      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
682        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
683        and in diagnostics_fract_fill.F (do not need a valid pointer for the
684        diagnostics counter-mate); check that definition of counter-diagnostic
685        includes a valid counter-mate (in diagnostics_set_levels.F).
686    o model/src (rStar):
687      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
688        affect solution only if z* with full pressure in EOS;
689        update output of test-exp global_ocean.90x40x15.
690    o pkg/seaice:
691      - introduce siEps=1e-5 parameter
692      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
693      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
694      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
695        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
696        as well as ice cover age and ridging index (attached to AREA).
697        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
698        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
699        Up to SItrMaxNum=3 tracers can be used simultaneously.
700    o pkg/salt_plume:
701      -introduce SPsalFRAC run time parameter that sets the fraction of the
702       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
703       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
704    o model debug options:
705      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
706        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
707      - Refine debug-msg printing selection (3 new levels):
708        debugMode  : controls printing of debug messages (sequence of S/R calls).
709        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
710         debLevZero =  0 ; /* level of disabled aux. msg printing */
711         debLevA =  1 ; /* level of minimum  aux. msg printing */
712         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
713         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
714         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
715         debLevE =  5 ; /* level of extensive debug printing */
716        New debugLevel default: with default debugMode value (=F),
717          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
718          and if debugMode=T, default debugLevel = 4 (debLevD).
719        Relation with previous settings:
720         debLevB (=2) corresponds to former debLevA (=1)
721         debLevD (=4) corresponds to former debLevB (=2)
722        Note:
723         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
724         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
725            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
726      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
727        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
728    o pkg/obcs:
729      - change OBCSfixTopo default from True to False (should not change the results);
730        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
731    o pkg/thsice:
732      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
733        2nd layer seaice sublimation (unlikely to happen)
734      - use Interior mask for OBCS in thsice_advection.F (similar to what is
735        done in gad_advection & seaice_advection).
736    o adjoint:
737      bug fix spotted by Gael Forget:
738      seaice_advection and thsice_advection still had
739      legacy CPP options to avoid CS corner updates for adjoint
740    o pkg/seaice:
741      => Change some of the defaults (2011/05/29):
742         - change SEAICEuseFluxForm default (from False to True)
743         - change DIFF1 default (from 0.004 m/s to 0. m/s)
744         And print warnings if DIFF1 is not set in data.seaice and centered
745          avection scheme is used without any diffusion.
746      also:
747      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
748      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
749      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
750        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
751        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
752      update results of test exp.:
753         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
754             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
755             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
756         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
757         seaice_obcs: output (SEAICEuseFluxForm=T)
758      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
759          for standard fwd & AD lab_sea tests (to keep the same output).
760    o pkg/seaice/seaice_growth.F:
761      - use Ian Fenty's capping formulas for actual ice
762      thickness thoughout EVOLUTION branch.
763      - put treatment pathological case #2) in CPP brackets
764      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
765      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
766    o pkg/seaice:
767      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
768      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
769      also pass fac as a param, which can be 1. (to update the tendency
770      field) or the time step (to update the field itself).
771      - seaice_advdiff.F: for multidim, call seaice_diffusion with
772      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
773      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
774      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
775      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
776    o pkg/seaice:
777      diffusion with centered advection scheme (diffus.F & advect.F):
778      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
779        to just compute the laplacian of input-field.
780      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
781      - fix flux-form version in diffus.F to conserve tracer.
782      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
783       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
784    
785    checkpoint62y (2011/05/26)
786    o pkg/seaice:
787     - seaice_growth.F : in EVOLUTION branch, always include
788       a_QSWbyATM_cover in qnet (as it should be).
789     - verification/global_ocean.cs32x15 : update results accordingly
790       (output.seaice.txt output_adm.seaice.txt).
791    o pkg/seaice + obcs:
792     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
793       equivalent of assuming no tracer gradient outside the OB region.
794       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
795     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
796       after changes above);
797     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
798       only at OB location (instead of over a band of OLx width).
799    o pkg/seaice:
800     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
801       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
802    o pkg/obcs:
803      - split header file "OBCS.h" into 4 separated files:
804        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
805       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
806         (contain no conditional statement which depends on OBCS options).
807      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
808        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
809    o ctrl, cost, grdchk & autodiff pkgs:
810      - make options file more standard (like other {PKG}_OPTIONS.h file but
811        with AD_CONFIG.h); clean-up some of the included header files.
812    o pkg/obcs:
813      - do not mask tracer when applying OB (tracer == 0 could generate problems)
814      - apply tracer OB values to tracer field only at OB location (instead of
815        over a band of OLx width)
816      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
817      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
818        obcs_apply_tloc.F & obcs_apply_sloc.F
819    o obcs in model/src:
820      - call OBCS_APPLY_W only if NonHydrostatic.
821      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
822      - reset dEtaHdt and wVel to zero outside OB interior region ;
823      - leave tracer unchanged outside OB interior region: This has no effect
824        on the solution but just to prevent unrealistic tracer value outside OB.
825      - zero out velocity outside OB interior region: This has no effect on
826        the solution but just to prevent unrealistic velocity outside OB.
827    o obcs and non-lin free-surf:
828       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
829       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
830       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
831       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
832       update results of test-exp. exp4(nlfs).
833    o exp4 (nlfs) test-exp:
834       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
835       with NonLin-FreeSurf); update output.nlfs.txt
836    o obcs and 2d/3d solver norm:
837       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
838       and outside OB interior region (will allow to place OB further inside the
839       domain). Depending on the domain, can affects cg2d-Norm (previous
840       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
841       and cg3d-Norm (previous Norm was computed before canceling OB terms),
842       e.g. in tutorial_plume_on_slope.
843      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
844    o pkg rbcs:
845      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
846      - add capability to apply relaxation to horizontal velocity uVel & vVel.
847    o pkg/grdchk: add gradient check for control variable xx_shifwflx
848    o pkg/shelfice/shelfice_init_fixed.F
849      fix CPP-flag combinations
850    o pkg/seaice: Merge iceage code of Pierre Rampal
851      * update/change/correct ice age calculations
852      * add age updates for pathological cases
853      Probably needs more testing...
854    
855    checkpoint62x (2011/05/13)
856    o pkg/mom_vecinv:
857       high-order vorticity scheme: use interior masks (maskInW & S)
858       to zero-out (outside OB) gradient of vorticity.
859    o verification exp.:
860       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
861       hs94.128x64x5 and seaice_obcs ; update results.
862    o pkg/obcs:
863      fix bug in OBeta for YZ sections in obcs_exf_load.F
864    o pkg/ctrl, pkg/shelfice, and optim:
865      - add new control variable xx_shifwflx (fresh water flux underneath ice
866        shelves). This is almost as tedious as obcs-ctrl, because the
867        variables needs its own mask.
868      - add a cost function term that penalizes the deviation of xx_shifwflx
869        from the first guess (zero) in analogy to other control variables
870    o pkg/shelfice:
871      - start basic adjoint
872    o pkg/ctrl:
873      - remove extra 2D field "for good measure" when initializing in
874        ctrl_set_globfld_[xy/xz/yz].F
875      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
876      - improve error messages in ctrl_set_unpack_*
877    o OBC implementation in momentum:
878       use interior masks (maskInC,W & S) in momentum S/R:
879       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
880       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
881       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
882       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
883       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
884        (and also with Leith/Smagorinsky harmonic-viscosity).
885       Update output of experiment dome and exp4 (+nlfs).
886    o exp4 test-exp:
887      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
888        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
889        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
890        time-varying OB at Western-side for wVel (NonHyd); update output.
891      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
892        and biharmonic-viscosity ; also use prescribed time varying OB.
893    o pkg/obcs:
894      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
895    o model/src:
896      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
897      - initialise startTime & nIter0 with unlikely values: allows to set one
898        from the other without ambiguity.
899    o seaice_obcs test-exp.:
900      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
901    o pkg/obcs:
902      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
903        no longer needed with maskInC,W,S in pkg/generic_advdiff.
904    o pkg/seaice:
905      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
906        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
907      - fixed bug in the initialization of sea ice salinity variable HSALT
908        in seaice_init_varia.F  (removed dependence on ICE2WATR)
909    o fizhi-cs test exp.:
910       switch reference output convention for these 2 non-standard test-exp,
911        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
912          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
913       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
914    o model/inc:
915      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
916        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
917    o pkg/seaice:
918      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
919    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
920      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
921        and initial HSALT
922    
923    checkpoint62w (2011/04/26)
924    o pkg/mom_fluxform:
925      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
926      - use parameter "sideDragFactor" in no-slip BC side-drag part.
927      - update output of exp. global_ocean.90x40x15
928    o pkg/mom_vecinv:
929      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
930    o update seaice exp.:
931      use more consistent parameter values (remove "backward compatability only":
932       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
933      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
934       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
935    o update test-exp global_ocean.90x40x15:
936      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
937      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
938      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
939      o turn on zStar & viscA4 in standard set-up (dir input/)
940        and update output files: output.txt & output.dwnslp.txt
941    o new AD-test experiment: obcs_ctrl
942      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
943    o pkg/dic:
944      fix two bugs in handling water vapour pressure in carbonate chemistry
945      and air-sea fluxes. Found by Val Bennington and Galen McKinley
946      (add DIC Option = WATERVAP_BUG to recover old results)
947      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
948    o adding allowInteriorFreezing option to check for water below freezing point
949      at depth and bring the negative heat anomaly to the surface level
950    o pkgs _fields_load:
951      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
952      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
953        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
954        rbcs to get interpolation weights and time reccord number.
955      - fix multi-threading in aim_fields_load.F
956      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
957    o external_fields_load:
958      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
959       interpolation weights) to use in a periodic time-series ; do not divide by
960       time-step to convert to integer:
961       - this fixes case where externForcingPeriod is not multiple of time-step
962          (Thanks to Christopher L. Wolfe)
963       - this fixes case where externForcingPeriod is an odd multiple of time-step
964         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
965      store index of time-record which is currently loaded:
966       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
967       - needed for the adjoint but not yet used because of extensive recomputations;
968         (to be fixed soon)
969    
970    checkpoint62v (2011/04/02)
971    o verification/1D_ocean_ice_column added to test Ian Fenty's
972      pkg/seaice_growth.F modifications for improving sea ice code differentiability
973    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
974      (new velocity statistics after changing maskInW & maskInS definition)
975    o pkg/generic_advdiff with OBCS:
976      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
977      equivalent to assumption of no tracer gradient outside the OB region.
978      This will affect the results if using obcs+biharmonic diffusion.
979      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
980    o pkg/obcs:
981      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
982      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
983      in Interior region. No impact on solution but affects Velocity monitor stats.
984    o pkg/ptracers (adjoint)
985      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
986      tape file for each tracer
987    o model/inc/src and pkg/autodiff: add parameters that allow to turn
988      of parts of the adjoint code at run time. For now, there are only
989      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
990      parameters are set in data.pkg.
991      This is the lazy coward's version of doing this, but still useful for
992      debugging. In order to do it right, everything needs to be moved to
993      pkg/autodiff.
994    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
995      the end; this fixes the adjoint balancing code for open boundaries.
996    o pkg/ctrl:
997      - change behavior of xx_${varname}period to be analogous to exf-conventions:
998        xx_${varname}period =   0.,  means time-independent control part
999        xx_${varname}period = -12., means one-year-periodic monthly control part
1000      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1001        clean up ctrl_init a little, remove unused variables
1002      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1003      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1004    
1005    checkpoint62u (2011/03/15)
1006    o model/src:
1007      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1008        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1009      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1010        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1011    o pkg/ctrl/obcs/ecco:
1012      - remove obsolete, unused, and partially broken code:
1013        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1014        ALLOW_CTRL_OBCS_BALANCE
1015      - put a stop statement into ecco/cost_obcsvol.F, but also add
1016        cost_obcsvol to ecco_ad_diff.list
1017    o pkg/ecco: fix counting cost function contributions for obcs (code
1018      by Matt M.) and diffkr for diagnostics
1019    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1020      add cost penalty terms for initial uvel, vvel, eta controls
1021      and I/O for prior error files
1022    o pkg/mdsio:
1023       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1024       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1025       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1026    o pkg/ctrl:
1027     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1028       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1029       unused and superfluous variables
1030     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1031  o pkg/ecco  o pkg/ecco
1032   - enable adjoint of Stevens OB   - enable adjoint of Stevens OB
1033  o pkg/ctrl/ecco/grdchk:  o pkg/ctrl/ecco/grdchk:
1034    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.    - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1035      Fortunately, we do not have any tests for the numerous cpp-flagged      Fortunately, we do not have any tests for the numerous cpp-flagged
1036      option of "obcs as control parameters" so we will never know      option of "obcs as control parameters" so we will never know
1037      if this is an improvement (but at least now things compile).      if this is an improvement (but at least now things compile).
1038    - remove an obsolete initialization from ecco_cost_init_barfiles.F    - remove an obsolete initialization from ecco_cost_init_barfiles.F
1039    - fix some problems within never used ifdefs to make the code compile    - fix some problems within never used ifdefs to make the code compile
1040  o pkg/obcs:  o pkg/obcs:
1041   - Refine Interior mask definition to work with more complex OB (e.g.   - Refine Interior mask definition to work with more complex OB (e.g.
1042     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
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