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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1574 by jmc, Mon Jan 16 23:53:58 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/exf and seaice exp:
8      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
9        so that switching off area & heff advection flags does not affect results.
10      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
11      - keep seaice_obcs unchanged (using #undef EXF_LWDOWN_WITH_EMISSIVITY)
12        and, using pkg/exf default emissivities, update results of fwd verification
13        experiments: 1D_ocean_ice_column, global_ocean.cs32x15.seaice, lab_sea (x4)
14        and offline_exf_seaice (x3).
15    o pkg/seaice:
16      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
17        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
18      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
19        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
20        not multi-dim advection;
21      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
22        SHORTWAVE_HEATING #undef.
23    o optim: make Makefile more robust (?)
24    o pkg/obcs:
25      * fix treatment of obcs_read_pickup for TAF
26    o pkg/shelfice:
27      * add missing initialisation of num_shifwflx
28      * new adjoint verification exp. for isomip
29      * change Prandtl and Schmidt numbers from generic formulations
30        (in terms of model diffus. and visc.) to separate runtime
31        parameters, with Holland and Jenkins (1999) default values.
32    o pkg/exf (interpolation):
33      - extended input field (2 rows) near the N & S poles:
34        * fill in with the symetric value (when even Nb of data in longitude)
35        * add average value at the poles only for scalar quantities ; for vector
36          component interpolation, skip the averaging and keep duplicated values,
37          unless the 2 components have same location (uvInterp=T) in which case
38          interpolate the 2 components together using S/R EXF_INTERP_UV.
39      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
40        together: this allows to account properly for local orientation when
41        averaging at N & S pole.
42      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
43        exf-interpolation near N & S poles. Undef by default.
44      - add debug check/print on 1rst iter if debugLevel >=2.
45    o pkg/exf:
46      - change masking flags definition (no longer "parameter"), put them in
47        common block and set them in S/R EXF_INIT_FIXED.
48      - change recognized masking flag from s,u,v to c,w,s since the mask
49        to use (maskC,W,S) depends on position on model grid and has little to
50        do with scalar/vector difference; fix masking if using P-coordinates.
51      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
52        and update results of exp. global_with_exf (x2).
53      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
54    o pkg/obcs
55      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
56    o pkg/exf (interpolation):
57      - assume periodicity in X only if input field cover full longitude range.
58      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
59        and should vectorise).
60      - fix input lat of the 2 added row (in case we provide N.pole data).
61    
62    checkpoint63h (2011/12/30)
63    o pkg/seaice:
64      - change declaration of UVM from _RL to _RS in order to get B-grid
65        uIce,vIce monitor when _RS = real*4
66    o pkg/offline:
67      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
68      - compute vertical velocity if not read from file (switch on exactConserv
69        & staggerTimeStep);
70      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
71    o verification:
72      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
73        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
74        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
75      - update output of exp. global_ocean.cs32x15.viscA4 after changing
76        grid-file angles (used here for coriolis-3d);
77      - remove (or gzip) few files not needed to run fizhi-cs experiments.
78    o pkg/exf (vector interpolation):
79      - rotate vector component toward local grid-axis orientation using grid-angles
80        (stored in GRID.h) instead of locally computed rotation angle; keep old code
81        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
82    o pkg/seaice:
83      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
84        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
85    o pkg/PKG_OPTIONS.h files:
86      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
87        outside of the #ifdef ALLOW_THISPKG / #endif block.
88      - update verification/*/code/PKG_OPTIONS.h files.
89    o add a verification experiment (offline_exf_seaice/input.seaice) that test
90      the B-grid LSOR solver
91    o pkg/seaice: sort out emissivity and long wave radiation step 2:
92      - add emissivity for snow and ice as new run-time parameters
93        (unfortunately) that default to the corresponding exf values; this
94        changes results in most verification experiments so that for backward
95        compatibility these parameter have to be set explicitly to inconsistent
96        values (ugly);
97      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
98        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
99        until we agree how to handle this bug properly
100    o pkg/exf (interpolation):
101      - add a set of run-time param ({inputfield}_interpMethod), one for
102        each interpolated input field, to select the interpolation method
103        with a value of zero switching off the interpolation;
104      - print interpolation parameters to standard output;
105      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
106        (to use instead runoff_interpMethod=0 in data.exf).
107      - simplify default setting of interpolation parameters (for all fields,
108        set position to match model grid cell-center position, leading to trivial
109        interpolation in case of regular Lat-Lon grid) and fix for the case of
110        non-uniform delY.
111    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
112       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
113       this factor is absolutely required, because the lw exitance (= out-going
114       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
115       where the reflectivity rho = 1-emissivity for conservation reasons. Once
116       this is established, we can remove the CPP-Flag (if we want to).
117    o pkg/seaice:
118      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
119        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
120      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
121        what the name implies (and not emissivity*BoltzmannConstant), this means
122        the old default value of 5.5e-8 now means
123        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
124        S/R exf_readparms
125      - FV-discretization of the B-grid LSOR solver, turn on with
126        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
127        of the calling routine dynsolver, so that B and C-grid code look a
128        little more alike.
129      - fix index bugs in ostres.F (B-grid code)
130    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
131    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
132      default for SEAICE_emissivity, if useEXF; requires setting a wrong
133      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
134      backward compatiblity
135    o model/src: use sigmaR in calc_ivdc
136    
137    checkpoint63g (2011/12/16)
138    o pkg/seaice/seaice_growth.F:
139      fix heat conservation of the coupled ocean-seaice system.
140      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
141      solid vs liquid water treatment is resolved via QNET.
142    o pkg/seaice/seaice_growth.F:
143      add missing term for sublimation in saltFlux, which was breaking conservation.
144    o pkg/seaice/seaice_model.F:
145      Remove this patholigical case treatment in evolution branch,
146      where it is un-necessary and breaks conservation.
147      Update global_ocean.cs32x15/results accordingly for
148      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
149    o model/src:
150      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
151      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
152    o pkg/obcs:
153      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
154      tendency for temperature and salinity that is then applied to update
155      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
156      horizontal advection and diffusion contributions on the boundary (in
157      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
158      removing the mask in S/R timestep_tracer. The advantage of this approach is
159      that the updated tracer values include contributions from the surface
160      forcing and vertical diffusion.
161      This modification changes exp4.stevens because of vertical diffusion.
162    o model/src:
163      change non-curvilinear grid setting to also work with exch2 + blank tiles:
164      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
165        face dimensions.
166      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
167        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
168        and INI_SPHERICAL_POLAR_GRID.
169      change test-experiment global_ocean.90x40x15:
170      - split the domain in many more tiles (9x4 tiles of 10x10 each);
171      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
172      - update results of both test (std & dwnslp).
173    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
174       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
175    o model/src:
176      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
177        and fix initialisation when using sigma-coords.
178    o model/src:
179     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
180       to their current value at the beginning of forward_step.F": add a new run-time
181       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
182     - set doResetHFactors=T in the following test exp:
183        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
184        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
185        and tutorial_global_oce_in_p (nonLinFS in p)
186    o pkg/ecco
187      - added IES cost term
188    o verification/advect_xz
189      - scale down the depth by 1/100 (from 200 km to just 2.km)
190      - add secondary test using divergent flow, r-star and implicit vertical advection.
191      - add note (check_conserve_TS.txt) and matlab script to check global
192        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
193    o pkg/rbcs:
194      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
195    o pkg/obcs (Stevens BCs):
196      - fix various problems in the phase speed computations of the Stevens
197        boundary conditions:
198        - sign error for western and southern boundaries,
199        - time tendencies were underestimated by factor of dTracerLev and some just
200          zero (for multidim advection schemes) -> now estimate time tendencies
201          from difference between previous (n) time level and the one before (n-1);
202          this requires storing a field per tracer per boundary, also in the pickup
203          files.
204        - replace deltaTmom in cflMer/Zon computation with dTracerLev
205        - set default phase velocity to cflMer/Zon
206      - update verification experiment exp4.stevens
207    o pkg/generic_advdiff (implicit_r):
208      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
209        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
210      - fix implicit vertical diffusion or advection with NonLin FreeSurf
211        (was using current recip_hFacC instead of future recip_hFacC): set future
212        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
213        solver S/R ;
214      - fill diagnostics of vertical advective fluxes (computed from tendency)
215        when using implicit vert. advection;
216      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
217         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
218         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
219         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
220    o pkg/diagnostics:
221      - add diags for T & S tendency which goes through Adams-Bashforth.
222    
223    checkpoint63f (2011/11/30)
224    o pkg/obcs/obcs_calc_stevens.F:
225      - join some loops to reduce number of if-statements
226      - fix a bug in code for northern and southern boundaries.
227    o pkg/seaice/seaice_init_varia.F
228      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
229        caused zero ice-velocities for the B-grid code
230    o pkg/seaice/seaice_init_fixed.F
231      - fix a bug in the initialisation of the second metric terms
232        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
233      - this affects all seaice configurations with useCurviLinearGrid = .true.
234        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
235        = .true. (default)
236      - the only verification experiment affected is global_ocean.cs32x15:
237        icedyn, seaice, and seaice_dynmix (AD)
238    o pkg/thsice/thsice_diagnostics_state.F
239      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
240        not contain garbage that can lead to surprises in diagstats_calc.F
241    o model/src:
242      - move bi,bj loops inside INTEGR_CONTINUITY ;
243      - call INTEGR_CONTINUITY directly from forward_step.F
244        (previously called from momentum_correction_step.F)
245      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
246        forward_step.F and pkg/ecco/the_main_loop.F
247    o model/src/do_oceanic_phys.F:
248      - reset addMass to zero only if useICEFRONT ;
249      - separated k-loop for rhoInSitu calculation ;
250      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
251        and at constant T,S (= WdRHOdP);
252      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
253        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
254        transport of locally-referenced potential density);
255        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
256    o gluemnc:
257      - replace ncrcat with ncks when adding variables to *.glob.nc
258      - change the way variables without record dimensions are handled so that
259        files that have variables with and without record variables can be glued:
260        add a record dimension with a new unique name to be able to differentiate
261        between variable with and without a-prior record dimensions. Remove
262        this record dimension before adding the variable to the *.glob.nc file.
263        This procedure automatically works also for grid.*.nc files that do not
264        have any record dimension.
265    o verification/cpl_aim+ocn:
266      - generate new reference output on baudelaire (gfortran, mpich2) (previously
267        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
268    o pkg/obcs/obcs_calc_stevens.F:
269      - add code for northern and southern boundaries.
270      - reorder some loops to save some operations and so that drFBar can be scalar
271    o model/src:
272      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
273        truncation) and add diagnostics for Adams-Bashforth tendency increment.
274      - update test-exp. AD output:
275        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
276      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
277        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
278        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
279        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
280        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
281        tutorial_plume_on_slope.
282    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
283      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
284      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
285      does not even come with an F77 compiler anymore, this should not be
286      a limitation
287    
288    checkpoint63e (2011/11/06)
289    o pkg/seaice adjoint of LSR:
290      - substantially rework STORE dirs.
291      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
292        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
293        and only perform SOLV_MAX_FIXED adjoint iters.
294        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
295        always goes to same record, meaning that the last forward field will be
296        the one used in the adjoint - an approximation.
297      - now produces non-zero LSR-related gradients, and acceptable gradients for
298        An's zonal (x-z) test case (to be checked in)
299      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
300        (but these are screwed up by the thermodynamics in the first place);
301        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
302        output_adm.txt also reflects changes to seaice_lsr
303      - global_ocean.cs32x15:
304        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
305          (output_adm.seaice.txt was updated)
306        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
307          (output_adm.seaice_dynmix.txt)
308    o test-exp. exp4+stevens:
309      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
310    o pkg/seaice (lsr solver):
311      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
312        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
313      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
314      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
315        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
316      - compute (with new S/R) and print initial (+ free-driff sol. if available)
317        and final residual of linearised system.
318    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
319      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
320    o pkg/obcs: Stevens BCs (still only for east and west)
321      - fix Stevens BCs by using intermediate velocities of previous
322        time step as "baroclinic" contribution rather velocity of one grid cell
323        inside the boundaries; more consistent but makes the entire treatment
324        more complicated, requires new pickup files and two new S/Rs:
325        obcs_copy_uv_n and obcs_save_uv_n
326        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
327        (undefined by default)
328      - silently move computation of some grid factors into separate loops to
329        save some recomputations
330      - add a hack for non-linear free surface
331      - add a verification experiment to exp4 that tests this code
332    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
333    
334    checkpoint63d (2011/10/25)
335    o pkg/obcs + seaice-dynamics:
336      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
337        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
338        values (consistent with an implicit method).
339      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
340        return to older implementation (same results as before); note that none of
341        the "experimental" OBCS_SEAICE options are implemented in the new version.
342      - switch test exp. seaice_obcs to use new version (update output).
343    o pkg/seaice:
344      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
345      - add parenthesis in Water-Ice drag calculations (evp & lsr);
346      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
347        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
348      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
349        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
350    o pkg/layers:
351      - Include potential density as new coordinate (Thanks to David Munday)
352    o pkg/dic:
353      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
354        carbonate computation/output to CALC_PCO2_APPROX
355    o pkg/generic_advdiff
356      - make TAF generate code that vectorizes:
357        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
358    o model/src:
359      - improve vectorization also for adjoint code of
360        solve_tridiagonal and solve_pentadiagonal. As this requires up to
361        5 new 3D-fields, this code is only turned on for the combination of
362        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
363        for singular matrix check (only for TARGET_NEC_SX).
364      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
365        ALLOW_AUTODIFF. This flag now needs to be set outside of
366        solve_tri/pentadiagonal.F
367    o pkg/exf:
368      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
369        optional namelist EXF_NML_OBCS).
370      - add many debug-print (to trace down where pkg/cal error msg comes from)
371    o pkg/mom_vecinv/mom_vi_hdissip.F
372      - rearrange loops so that vectorization is improved and in particular
373        the adjoint routine vectorizes. The code is a little longer now, but I
374        think easier to read.
375        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
376    o pkg/seaice:
377      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
378    o pkg/exch2:
379      - alternative code (without tile x tile matrix) for cumulated (global) sum;
380        used as default; keep using matrix version in adjustment.cs-32x32x1.
381    o tools/build_options:
382      - after merging some MPI and/or multi-threads specific optfiles so that
383        the modified default optfile support both built (using genmake2 -mpi
384        for the MPI built, using genmake2 -omp for OpenMP built),
385        move now obsolete optfiles to tools/build_options/unsupported/
386       (add copy of email sent to support list in doc/optfiles_changes.txt)
387    
388    checkpoint63c (2011/09/28)
389    o pkg/ebm:
390      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
391        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
392    o pkg/seaice (SItracer pickup)
393    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
394      To be done:
395      - thorough testing of missing fields in S/R seaice_read_pickup
396      - thorough matching between generic tracers and specific fields used
397        (e.g. volume-weighted age, area-weighted age, salinity, ...)
398    o pkg/grdchk:
399      - all procs calculate and print finite-difference gradient (for testreport)
400      - change description output used by testreport;
401      - AD testing: also compare and report Finite-difference gradient;
402        => update all output_adm*.txt
403    o test exp. global_ocean_ebm:
404      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
405        and turn on exactConserve; update (fwd) output.
406    o pkg/seaice (LSR):
407      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
408      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
409        * identical results with non-CS topology (but save up to half of EXCH calls)
410        * no much changes in cs-32 verification tests since no ice at face edges
411         (differences due to convergence criteria, since nb of iterations changed)
412        * expect some differences on lat-lon-cap grid.
413        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
414    o pkg/exch2:
415      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
416        many tiles); until alternative coding is added, just add a stop.
417    o pkg/kpp:
418      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
419        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
420    o optfiles:
421      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
422        into corresponding standard one, which now support different build:
423        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
424      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
425    o pkg/obcs (seaice):
426      - add missing EXCH for uIce,vIce after applying OBCS;
427      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
428        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
429        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
430      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
431      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
432        and eedata.mth for MPI and mutlti-threaded testing.
433    o pkg/flt:
434      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
435      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
436      - fix pickup and trajectories + profiles output with multi-threads;
437      - add parameter to select group of fields to write along trajectory and
438        profile (default unchanged);
439      - only call PORT_RAND* function when flt_noise <> 0;
440      - add multi-threaded test for verification exp. flt_example.
441    o eesupp/src:
442      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
443      - USE_OMP_THREADING: check that number of threads (from eedata) matches
444        actual number (from env.var. setting).
445    o pkg/ebm:
446      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
447      - add multi-threaded test for verification exp. global_ocean_ebm
448    
449    checkpoint63b (2011/08/29)
450    o pkg/ebm:
451      - fix sign of runoff;
452      - update directly forcing fields (Qnet,EmPmR) to use standard
453        external_forcing_surf.F (remove ebm_forcing_surf.F);
454      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
455      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
456        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
457      - update global_ocean_ebm parameters file data and update output (fwd+ad).
458    o verification/matrix_example:
459      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
460        MPI and mutlti-threaded testing.
461    o pkg/matrix:
462      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
463      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
464      - fix for multi-threaded (remove DATA statement);
465      - use standard DIFFERENT_MULTIPLE function;
466      - add MATRIX_OPTIONS.h
467    o verification/matrix_example:
468       To allow to split the domain in several tiles, change the domain size
469        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
470        Western side) of land points.
471    o (*_)write_pickup:
472      - fix few bugs in mypackage_read/write_pickup.F
473      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
474        array of length 1 (was caught by compiler syntax-check).
475    o pkg/diagnostics (velocity potential solver):
476      - fix initialisation of main diagonal matrix (for overlap values)
477    o tools/build_options:
478      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
479        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
480      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
481        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
482        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
483        and use "-devel" testreport option for standard testing on baudelaire.
484    o pkg/grdchk:
485      - Assume that all gradient-check position are within the same tile
486        corresponding to global indices (iGloTile,jGloTile) and that
487        positions (i,j indices or nbeg) are local to this tile;
488      - set tile local-indices and proc. number according to tile global-indices;
489      - remove grdchkwhichproc from namelist (retired param);
490      - send adjoint gradient to all procs so that all procs print it to STDOUT;
491      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
492    o adding package bbl (Bottom Boundary Layer)
493      description in MITgcm/pkg/bbl/bbl_description.tex
494      example/test experiment in MITgcm_contrib/bbl
495    o adjoint verifications
496      - changed 5 experiments to multi-tiles
497        * global_ocean.90x40x15
498        * obcs_ctrl
499        * offline_exf_seaice
500        * tutorial_dic_adjoffline
501        * tutorial_tracer_adjsens
502        changed reference output for those that crossed tile boundaries
503        (changed choices of gradient check positions)
504      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
505      - temporary bug fix in grdchk_loc.F for obcs
506    o genmake2 & testreport
507      - add target "obj" (just for OBJFILES files) to Makefile;
508      - add option to specify FEXTRAFLAGS on command line.
509    o pkg/mypackage:
510      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
511    
512    checkpoint63a (2011/08/02)
513    o pkg/diagnostics (velocity potential):
514      - fix velocity-potential calculation when using OBCS: balance net inflow
515        at each level (new S/R OBCS_DIAG_BALANCE).
516      - fix some of the problems with OBCS in stream-function calculation.
517    o pkg/exf/exf_readparms.F
518      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
519        EXF_NML_OBCS) more consistent, so that you need not have these lists
520        in data.exf when they are not used.
521    o optim/optim_readdata.F:
522      - add some output about obcs variables that might help debugging
523      - add a check about nvarlength
524    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
525    o pkg/diagnostics (velocity potential):
526      - fix mask for OBCS (still problems in stream-function with OBCS);
527      - add specific parameter (default = main code CG2D params) for solver;
528      - in case of poor convergence, use solution corresponding to lowest residual.
529    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
530      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
531      and should be avoided where possible.
532    o model/src (rStar):
533      - include r* effect on reference-state (PhiRef) in totPhiHyd
534        (so that it's really the potential anomaly at the cell center);
535        affect solution only if z* with full pressure in EOS.
536      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
537        update output (because of z* in totPhiHyd and viscA4 changes);
538      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
539        @ constant r) until interpolation at constant r is implemented.
540    o pkg/diagnostics
541      - fix RCENTER diagnostics in case cell center is not at interface middle
542    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
543      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
544      that THETA and SALT are "conservative temperature" and "absolute
545      salinity"
546    o pkg/ctrl
547      - fix computation of endrec in s/r ctrl_init_rec
548      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
549    o pkg/seaice/seaice_growth.F
550      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
551        remove then obsolete STORE directives
552      - fix STORE directives for tice and tices, so that only the
553        appropriate part of the fields are stored (and not the entire
554        field); update global_ocean.cs32x15.seaice AD output.
555      - cosmetic changes: adjust CPP flags and indentation for better
556        legibilty
557    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
558      Chris Wilson)
559    o pkg/gmredi:
560       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
561       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
562    
563    checkpoint63  (2011/07/11)
564    o pkg/exch2:
565     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
566     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
567       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
568       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
569    o pkg/diagnostics:
570     - deal with pairs of post-processed diags which are computed together; in
571       particular, re-order list of diags within 1 file to save 2nd computation.
572     - add S/R to compute velocity stream-function (called after velocity-potential
573       calculation) from divergence free transport -> new diagnostics "PsiVEL".
574     - add parameter to select grid-point location where PsiVEL == 0.
575    o eesupp/src:
576       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
577       (specific S/R needed with exch2 topology - for now, just print an error msg)
578    o pkg/shelfice
579     - Implement friction velocity-dependent transfer coefficients following
580       Holland and Jenkins, JPO, 1999
581       Original code by M. Losch with small modifs.
582       Enable with CPP option SHI_ALLOW_GAMMAFRICT
583       and runtime flag SHELFICEuseGammaFrict
584    o verification lab_sea & global_ocean.cs32x15:
585     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
586       does not miss some dependencies (but is slower) and also works with many files
587       (default makedepend limitation for AD built).
588     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
589    o pkg/diagnostics:
590     - add run-time parameter "useMissingValue" (def=False) to fill land-point
591        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
592       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
593     - Extend the use of "missing_value" setting from data.diagnostics for the case
594       of counter-diagnostics (where fraction-weight is zero). This applies both to
595       MNC and MDS output files.
596    o pkg/seaice/seaice_growth.F:
597      - add 'a priori' cap of latent heat flux based on actual mass considerations
598        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
599        non-legacy seaice_solve4temp.
600      - add diagnostic of the residual sublimation freshwater flux (the freshwater
601        flux taken from the ocean if the total actual latent heat fluxes exceed
602        the maximum)
603      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
604       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
605      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
606       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
607      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
608      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
609    o verification 1D_ocean_ice_column:
610       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
611       update results
612    o pkg/diagnostics:
613     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
614       which are not filled-up but computed from other diags ; In this case, the mate
615       diag points to the primary (filled-up) diag to used for post processing.
616     - Update Velocity-potential computation using post-processed diag framework.
617     ==> Change the ordering of fields and time-periods in MDS output file
618       when using periodic averaging: now writes one time record with the full set
619       of fields for this time period, then the next time reccord (it used to be
620       one field with the full set of time records then the next field).
621         Note: this is now similar to NetCDF (MNC) output file. <==
622    
623    checkpoint62z (2011/06/21)
624    o adjoint monitor:
625     - Add adjoint monitor output for packages exf, seaice
626       and update relevant testreport output
627    o pkg/seaice:
628     - re-order diags inits so that they appear in order in available_diagnostics.log
629     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
630       area/heff/hsnow preceeding thermodynamic growth/melt.
631     - modified diag: SIdA; output actual effect, as the description states.
632     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
633     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
634       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
635        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
636     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
637     - added diagnostics for seaice generic tracers (SItr*).
638     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
639     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
640     I. Fenty: 18-Jun-2011:
641     Minor changes to seaice package:
642     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
643        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
644       - Differentiated "regularization variables" from "floor variables"
645        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
646        * hiceMin became SEAICE_hice_reg (old hiceMin)
647          (with _reg meaning regularization variable)
648       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
649        so as to ensure energy conservation when going between phases
650      - A22 was not used anywhere
651     2) Changed regularization procedure for heffActual and hsnowActual to ensure
652        well-boundedness and smooth adjoint in seaice_growth.F
653     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
654        because the old regularization always set heffActual >= 0.05 cm
655     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
656        on AREA when HEFF > 0.
657      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
658        requiring that DISABLE_AREA_FLOOR *not* be defined
659     Affected verifications:
660      - 1D_ocean_ice_column (output.txt output_adm.txt)
661      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
662    o pkg/diagnostics:
663      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
664      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
665        (was _RL, now integer) with option = 0 to retrieve all levels.
666      - add pieces of code to compute velocity potential at each level (new diagnostics
667        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
668        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
669      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
670        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
671        and in diagnostics_fract_fill.F (do not need a valid pointer for the
672        diagnostics counter-mate); check that definition of counter-diagnostic
673        includes a valid counter-mate (in diagnostics_set_levels.F).
674    o model/src (rStar):
675      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
676        affect solution only if z* with full pressure in EOS;
677        update output of test-exp global_ocean.90x40x15.
678    o pkg/seaice:
679      - introduce siEps=1e-5 parameter
680      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
681      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
682      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
683        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
684        as well as ice cover age and ridging index (attached to AREA).
685        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
686        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
687        Up to SItrMaxNum=3 tracers can be used simultaneously.
688    o pkg/salt_plume:
689      -introduce SPsalFRAC run time parameter that sets the fraction of the
690       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
691       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
692    o model debug options:
693      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
694        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
695      - Refine debug-msg printing selection (3 new levels):
696        debugMode  : controls printing of debug messages (sequence of S/R calls).
697        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
698         debLevZero =  0 ; /* level of disabled aux. msg printing */
699         debLevA =  1 ; /* level of minimum  aux. msg printing */
700         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
701         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
702         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
703         debLevE =  5 ; /* level of extensive debug printing */
704        New debugLevel default: with default debugMode value (=F),
705          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
706          and if debugMode=T, default debugLevel = 4 (debLevD).
707        Relation with previous settings:
708         debLevB (=2) corresponds to former debLevA (=1)
709         debLevD (=4) corresponds to former debLevB (=2)
710        Note:
711         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
712         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
713            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
714      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
715        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
716    o pkg/obcs:
717      - change OBCSfixTopo default from True to False (should not change the results);
718        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
719    o pkg/thsice:
720      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
721        2nd layer seaice sublimation (unlikely to happen)
722      - use Interior mask for OBCS in thsice_advection.F (similar to what is
723        done in gad_advection & seaice_advection).
724    o adjoint:
725      bug fix spotted by Gael Forget:
726      seaice_advection and thsice_advection still had
727      legacy CPP options to avoid CS corner updates for adjoint
728    o pkg/seaice:
729      => Change some of the defaults (2011/05/29):
730         - change SEAICEuseFluxForm default (from False to True)
731         - change DIFF1 default (from 0.004 m/s to 0. m/s)
732         And print warnings if DIFF1 is not set in data.seaice and centered
733          avection scheme is used without any diffusion.
734      also:
735      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
736      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
737      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
738        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
739        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
740      update results of test exp.:
741         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
742             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
743             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
744         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
745         seaice_obcs: output (SEAICEuseFluxForm=T)
746      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
747          for standard fwd & AD lab_sea tests (to keep the same output).
748    o pkg/seaice/seaice_growth.F:
749      - use Ian Fenty's capping formulas for actual ice
750      thickness thoughout EVOLUTION branch.
751      - put treatment pathological case #2) in CPP brackets
752      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
753      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
754    o pkg/seaice:
755      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
756      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
757      also pass fac as a param, which can be 1. (to update the tendency
758      field) or the time step (to update the field itself).
759      - seaice_advdiff.F: for multidim, call seaice_diffusion with
760      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
761      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
762      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
763      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
764    o pkg/seaice:
765      diffusion with centered advection scheme (diffus.F & advect.F):
766      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
767        to just compute the laplacian of input-field.
768      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
769      - fix flux-form version in diffus.F to conserve tracer.
770      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
771       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
772    
773    checkpoint62y (2011/05/26)
774    o pkg/seaice:
775     - seaice_growth.F : in EVOLUTION branch, always include
776       a_QSWbyATM_cover in qnet (as it should be).
777     - verification/global_ocean.cs32x15 : update results accordingly
778       (output.seaice.txt output_adm.seaice.txt).
779    o pkg/seaice + obcs:
780     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
781       equivalent of assuming no tracer gradient outside the OB region.
782       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
783     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
784       after changes above);
785     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
786       only at OB location (instead of over a band of OLx width).
787    o pkg/seaice:
788     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
789       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
790    o pkg/obcs:
791      - split header file "OBCS.h" into 4 separated files:
792        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
793       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
794         (contain no conditional statement which depends on OBCS options).
795      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
796        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
797    o ctrl, cost, grdchk & autodiff pkgs:
798      - make options file more standard (like other {PKG}_OPTIONS.h file but
799        with AD_CONFIG.h); clean-up some of the included header files.
800    o pkg/obcs:
801      - do not mask tracer when applying OB (tracer == 0 could generate problems)
802      - apply tracer OB values to tracer field only at OB location (instead of
803        over a band of OLx width)
804      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
805      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
806        obcs_apply_tloc.F & obcs_apply_sloc.F
807    o obcs in model/src:
808      - call OBCS_APPLY_W only if NonHydrostatic.
809      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
810      - reset dEtaHdt and wVel to zero outside OB interior region ;
811      - leave tracer unchanged outside OB interior region: This has no effect
812        on the solution but just to prevent unrealistic tracer value outside OB.
813      - zero out velocity outside OB interior region: This has no effect on
814        the solution but just to prevent unrealistic velocity outside OB.
815    o obcs and non-lin free-surf:
816       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
817       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
818       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
819       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
820       update results of test-exp. exp4(nlfs).
821    o exp4 (nlfs) test-exp:
822       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
823       with NonLin-FreeSurf); update output.nlfs.txt
824    o obcs and 2d/3d solver norm:
825       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
826       and outside OB interior region (will allow to place OB further inside the
827       domain). Depending on the domain, can affects cg2d-Norm (previous
828       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
829       and cg3d-Norm (previous Norm was computed before canceling OB terms),
830       e.g. in tutorial_plume_on_slope.
831      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
832    o pkg rbcs:
833      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
834      - add capability to apply relaxation to horizontal velocity uVel & vVel.
835    o pkg/grdchk: add gradient check for control variable xx_shifwflx
836    o pkg/shelfice/shelfice_init_fixed.F
837      fix CPP-flag combinations
838    o pkg/seaice: Merge iceage code of Pierre Rampal
839      * update/change/correct ice age calculations
840      * add age updates for pathological cases
841      Probably needs more testing...
842    
843    checkpoint62x (2011/05/13)
844    o pkg/mom_vecinv:
845       high-order vorticity scheme: use interior masks (maskInW & S)
846       to zero-out (outside OB) gradient of vorticity.
847    o verification exp.:
848       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
849       hs94.128x64x5 and seaice_obcs ; update results.
850    o pkg/obcs:
851      fix bug in OBeta for YZ sections in obcs_exf_load.F
852    o pkg/ctrl, pkg/shelfice, and optim:
853      - add new control variable xx_shifwflx (fresh water flux underneath ice
854        shelves). This is almost as tedious as obcs-ctrl, because the
855        variables needs its own mask.
856      - add a cost function term that penalizes the deviation of xx_shifwflx
857        from the first guess (zero) in analogy to other control variables
858    o pkg/shelfice:
859      - start basic adjoint
860    o pkg/ctrl:
861      - remove extra 2D field "for good measure" when initializing in
862        ctrl_set_globfld_[xy/xz/yz].F
863      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
864      - improve error messages in ctrl_set_unpack_*
865    o OBC implementation in momentum:
866       use interior masks (maskInC,W & S) in momentum S/R:
867       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
868       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
869       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
870       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
871       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
872        (and also with Leith/Smagorinsky harmonic-viscosity).
873       Update output of experiment dome and exp4 (+nlfs).
874    o exp4 test-exp:
875      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
876        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
877        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
878        time-varying OB at Western-side for wVel (NonHyd); update output.
879      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
880        and biharmonic-viscosity ; also use prescribed time varying OB.
881    o pkg/obcs:
882      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
883    o model/src:
884      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
885      - initialise startTime & nIter0 with unlikely values: allows to set one
886        from the other without ambiguity.
887    o seaice_obcs test-exp.:
888      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
889    o pkg/obcs:
890      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
891        no longer needed with maskInC,W,S in pkg/generic_advdiff.
892    o pkg/seaice:
893      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
894        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
895      - fixed bug in the initialization of sea ice salinity variable HSALT
896        in seaice_init_varia.F  (removed dependence on ICE2WATR)
897    o fizhi-cs test exp.:
898       switch reference output convention for these 2 non-standard test-exp,
899        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
900          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
901       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
902    o model/inc:
903      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
904        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
905    o pkg/seaice:
906      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
907    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
908      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
909        and initial HSALT
910    
911    checkpoint62w (2011/04/26)
912    o pkg/mom_fluxform:
913      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
914      - use parameter "sideDragFactor" in no-slip BC side-drag part.
915      - update output of exp. global_ocean.90x40x15
916    o pkg/mom_vecinv:
917      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
918    o update seaice exp.:
919      use more consistent parameter values (remove "backward compatability only":
920       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
921      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
922       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
923    o update test-exp global_ocean.90x40x15:
924      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
925      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
926      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
927      o turn on zStar & viscA4 in standard set-up (dir input/)
928        and update output files: output.txt & output.dwnslp.txt
929    o new AD-test experiment: obcs_ctrl
930      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
931    o pkg/dic:
932      fix two bugs in handling water vapour pressure in carbonate chemistry
933      and air-sea fluxes. Found by Val Bennington and Galen McKinley
934      (add DIC Option = WATERVAP_BUG to recover old results)
935      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
936    o adding allowInteriorFreezing option to check for water below freezing point
937      at depth and bring the negative heat anomaly to the surface level
938    o pkgs _fields_load:
939      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
940      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
941        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
942        rbcs to get interpolation weights and time reccord number.
943      - fix multi-threading in aim_fields_load.F
944      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
945    o external_fields_load:
946      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
947       interpolation weights) to use in a periodic time-series ; do not divide by
948       time-step to convert to integer:
949       - this fixes case where externForcingPeriod is not multiple of time-step
950          (Thanks to Christopher L. Wolfe)
951       - this fixes case where externForcingPeriod is an odd multiple of time-step
952         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
953      store index of time-record which is currently loaded:
954       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
955       - needed for the adjoint but not yet used because of extensive recomputations;
956         (to be fixed soon)
957    
958    checkpoint62v (2011/04/02)
959    o verification/1D_ocean_ice_column added to test Ian Fenty's
960      pkg/seaice_growth.F modifications for improving sea ice code differentiability
961    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
962      (new velocity statistics after changing maskInW & maskInS definition)
963    o pkg/generic_advdiff with OBCS:
964      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
965      equivalent to assumption of no tracer gradient outside the OB region.
966      This will affect the results if using obcs+biharmonic diffusion.
967      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
968    o pkg/obcs:
969      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
970      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
971      in Interior region. No impact on solution but affects Velocity monitor stats.
972    o pkg/ptracers (adjoint)
973      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
974      tape file for each tracer
975    o model/inc/src and pkg/autodiff: add parameters that allow to turn
976      of parts of the adjoint code at run time. For now, there are only
977      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
978      parameters are set in data.pkg.
979      This is the lazy coward's version of doing this, but still useful for
980      debugging. In order to do it right, everything needs to be moved to
981      pkg/autodiff.
982    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
983      the end; this fixes the adjoint balancing code for open boundaries.
984    o pkg/ctrl:
985      - change behavior of xx_${varname}period to be analogous to exf-conventions:
986        xx_${varname}period =   0.,  means time-independent control part
987        xx_${varname}period = -12., means one-year-periodic monthly control part
988      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
989        clean up ctrl_init a little, remove unused variables
990      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
991      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
992    
993    checkpoint62u (2011/03/15)
994    o model/src:
995      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
996        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
997      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
998        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
999    o pkg/ctrl/obcs/ecco:
1000      - remove obsolete, unused, and partially broken code:
1001        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1002        ALLOW_CTRL_OBCS_BALANCE
1003      - put a stop statement into ecco/cost_obcsvol.F, but also add
1004        cost_obcsvol to ecco_ad_diff.list
1005    o pkg/ecco: fix counting cost function contributions for obcs (code
1006      by Matt M.) and diffkr for diagnostics
1007    o pkg/ecco, pkg/ctrl, pkg/grdchk:
1008      add cost penalty terms for initial uvel, vvel, eta controls
1009      and I/O for prior error files
1010    o pkg/mdsio:
1011       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1012       (new argument) to check for tiled file in mdsioLocalDir : this fix the
1013       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1014    o pkg/ctrl:
1015     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1016       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1017       unused and superfluous variables
1018     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1019    o pkg/ecco
1020     - enable adjoint of Stevens OB
1021    o pkg/ctrl/ecco/grdchk:
1022      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1023        Fortunately, we do not have any tests for the numerous cpp-flagged
1024        option of "obcs as control parameters" so we will never know
1025        if this is an improvement (but at least now things compile).
1026      - remove an obsolete initialization from ecco_cost_init_barfiles.F
1027      - fix some problems within never used ifdefs to make the code compile
1028    o pkg/obcs:
1029     - Refine Interior mask definition to work with more complex OB (e.g.
1030       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1031       read in Interior mask from file. Check if Interior mask is consistent
1032       with OB list of indices.
1033    o pkg/seaice
1034     - beginning code for a seaice tracer package,
1035       but currently only used for seaice age: SEAICE_AGE
1036       SEAICE_num = 4
1037       iTracer = 1: area-weighted ice age
1038               = 2: volume-weighted ice age
1039               = 3, 4: template for one-year vs. multi-year ice
1040       data.seaice has new namelist SEAICE_PARM03 for arrays related to
1041       SEAICE_num
1042    
1043    checkpoint62t (2011/03/05)
1044    o pkg/obcs:
1045     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1046       then normal component. This ensures that the normal component is set
1047       correctly even when it conficts with tangential setting from an other OB.
1048       Affects results of test-experiment seaice_obcs: update the output.txt
1049    o pkg/obcs:
1050     - add code to monitor statistics of dynamical fields at OB.
1051     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1052       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1053       - change default: balance the Net inflow through all OB (instead of balancing
1054         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1055     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1056       to match Nortern OB inflow (OBCS_balanceFacN=0).
1057    o pkg/seaice:
1058     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1059    o pkg/seaice (seaice_growth v 1.113):
1060     - reverting seaice_growth to v 1.111 in order to have code with exact bit
1061       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1062       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1063       runtime flag SEAICEareaFormula is kept but is inactive
1064    o model/src:
1065     - add new param to scale curvilinear grid distance and area when using
1066       a different sphere radius from the grid-files.
1067     - test/check multi-threads EXCH applied to local variable (cg2d_x)
1068    o adjoint:
1069     - enable adjoint of Stevens OB
1070     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1071       (a bit delicate because of potentially modified adj. common block structure;
1072       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1073    
1074    checkpoint62s (2011/02/15)
1075    o pkg/seaice (seaice_growth v 1.112):
1076     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1077       computing the ice cover tendency from effective thickness tendencies. Include
1078       Ian Fenty's formula.
1079     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1080       SEAICEareaFormula.
1081     - simplify notations for the various d_HEFF/d_AREA terms.
1082    o pkg/gmredi:
1083     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1084       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1085       add a verification test-run (front_relax.bvp) to test GM_useBVP.
1086    o pkg/seaice (seaice_growth v 1.111):
1087     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1088     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1089       also melt ice.
1090    o pkg/seaice:
1091     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1092     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1093    o pkg/cheapaml:
1094     - from Nico Wienders: New version of this package.
1095    o pkg/flt:
1096     - add CPP options to prevent floats to re-enter the opposite side of
1097       a periodic domain (default: keep periodicity)
1098    o pkg/gmredi:
1099     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1100       (needed for multi-dim advection).
1101     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1102    o model/src:
1103     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1104    o tutorial_tracer_adjsens
1105     - extend to NLFS and replace maskC by hFacC
1106       (change reference output accordingly)
1107    
1108    checkpoint62r (2011/01/24)
1109    o testreport:
1110     - add option -deloutp (-do) to remove output file after successful run
1111     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1112       extract exact list of procs from this file ; adjust COMMAND by
1113       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1114  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
1115    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
1116  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1117    exf/cal    exf/cal
1118    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1119      and handle case of obcs?period == 0      and handle case of obcs?period == 0
1120      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
1121      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
1122      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
1123    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
1124      ALLOW_CAL is not defined      ALLOW_CAL is not defined
1125    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
1126                     S/R exf_swapfields                     S/R exf_swapfields
1127  o testreport:  o testreport:
1128     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 1131  o testreport:
1131  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1132    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
1133    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
1134    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
1135    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
1136  o pkg/seaice  o pkg/seaice
1137    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
1138    timestepping loop    timestepping loop
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